Heyam H. Al-Baity^*, Nourah Al-Mutlaq

CMC-Computers, Materials & Continua, Vol.67, No.3, pp. 3089-3106, 2021, DOI:10.32604/cmc.2021.015291 - 01 March 2021

Abstract 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… More >

XIAOYU WANG^1,2,#,*, TAKESHI YAMAMOTO^2,#, MAKOTO KADOWAKI², YIFU YANG¹

BIOCELL, Vol.45, No.2, pp. 395-415, 2021, DOI:10.32604/biocell.2021.012280 - 19 February 2021

Abstract Mast cells are the main effector cells in IgE-associated allergic disorders, and we have reported that mucosal mast cells (MMCs) play a more important role in the development of food allergy (FA). IgE with antigen or calcium ionophore stimulation can lead to the activation of MMCs via a calcium-dependent pathway. The purpose of the present study was to identify gene signatures with IgE/antigen (dinitrophenyl-bovine serum albumin, DNP-BSA) or calcium ionophore (A23187) on the activation of MMCs. Differentially expressed genes between the two types of samples were identified with microarray analysis. Gene ontology functional and pathway… More >

Hans Christian Correa-Aguado^1,3, Gloria Viviana Cerrillo-Rojas¹, Alejandro Rocha-Uribe², Ruth Elena Soria-Guerra², José Francisco Morales-Domínguez^1,*

Phyton-International Journal of Experimental Botany, Vol.90, No.2, pp. 515-531, 2021, DOI:10.32604/phyton.2021.013619 - 07 February 2021

Abstract The need for renewable energy sources makes microalgae an essential feedstock for biofuels production. The molecular aspects and the response to nitrogen (N)-limited conditions with a phytohormone stimulus in microalgae have been slightly explored. In this work, Scenedesmus obliquus was used as a study model to analyze the effect of benzyl amino purine (BAP) and gibberellic acid (GA) coupled to nitrogen limitation on cell growth, biomass and fatty acids. The selected 10^-5 M BAP increased the biomass by 1.44-fold, and 10^-6 M GA by 1.35-fold. The total lipids also increased by 2.8 and 1.11-fold, respectively. The 10^-5 M… More >

YONG LIU^1,2,#, ZHIHUA JU^1,#, QIANG JIANG¹, WENHAO LIU¹, CHUNHONG YANG¹, YARAN ZHANG¹, XIUGE WANG¹, YAPING GAO¹, XIAOCHAO WEI¹, YAN SUN¹, JINPENG WANG¹, MINGHAI HOU¹, LING YANG², JINMING HUANG^1,*

BIOCELL, Vol.45, No.1, pp. 79-87, 2021, DOI:10.32604/biocell.2021.013583 - 26 January 2021

Abstract F-box and WD-40 domain protein 11 (FBXW11) is an important component of the E3 ubiquitin-ligase enzyme that plays a key role in the ubiquitin-dependent regulation of spermatogenesis. In our previous research, the mRNA expression of FBXW11 in bull sperm with high motility is significantly higher than that with low motility. In the present study, the protein expression levels of FBXW11 in bull testicular tissues with low-performance sperm quality groups were significantly higher than those in normal performance groups. The immunohistochemistry result demonstrated that FBXW11 protein was located in the periphery of Leydig cells and seminiferous… More >

Annemarie E. M. Post^*†, Johan Bussink^*, Fred C. G. J. Sweep^†, Paul N. Span^*

Oncology Research, Vol.28, No.1, pp. 33-40, 2020, DOI:10.3727/096504019X15555794826018

Abstract Tamoxifen-induced radioresistance, reported in vitro, might pose a problem for patients who receive neoadjuvant tamoxifen treatment and subsequently receive radiotherapy after surgery. Previous studies suggested that DNA damage repair or cell cycle genes are involved, and could therefore be targeted to preclude the occurrence of cross-resistance. We aimed to characterize the observed cross-resistance by investigating gene expression of DNA damage repair genes and cell cycle genes in estrogen receptor-positive MCF-7 breast cancer cells that were cultured to tamoxifen resistance. RNA sequencing was performed, and expression of genes characteristic for several DNA damage repair pathways was… More >

Andrea Lapucci^*†1, Gabriele Perrone^*†1, Antonello Di Paolo^‡§, Cristina Napoli^*†, Ida Landini^*†, Giandomenico Roviello^*†, Laura Calosi^¶, Antonio Giuseppe Naccarato^#, Alfredo Falcone^#, Daniele Bani^¶, Enrico Mini^*†§2, Stefania Nobili^*†§2,3

Oncology Research, Vol.28, No.6, pp. 631-644, 2020, DOI:10.3727/096504020X16056983169118

Abstract The benefit of adjuvant chemotherapy in the early stages of colorectal cancer (CRC) is still disappointing and the prediction of treatment outcome quite difficult. Recently, through a transcriptomic approach, we evidenced a role of PNN and KCNQ1OT1 gene expression in predicting response to fluoropyrimidine-based adjuvant chemotherapy in stage III CRC patients. Thus, the aim of this study was to validate in an independent cohort of stages II–III CRC patients our previous findings. PNN and KCNQ1OT1 mRNA expression levels were evaluated in 74 formalin-fixed paraffin-embedded tumor and matched normal mucosa samples obtained by stages II–III CRC patients treated… More >

Bo Ling, Zuliang Huang, Suoyi Huang, Li Qian, Genliang Li, Qianli Tang

Oncology Research, Vol.28, No.6, pp. 561-578, 2020, DOI:10.3727/096504020X15907428281601

Abstract There is growing evidence on the clinical significance of tumor microenvironment (TME) cells in predicting prognosis and therapeutic effects. However, cell interactions in tumor microenvironments have not been thoroughly studied or systematically analyzed so far. In this study, 22 immune cell components in the lung adenocarcinoma (LUAD) TME were analyzed using gene expression profile from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The TME-based molecular subtypes of LUAD were defined to evaluate further the relationship between molecular subtypes, prognosis, and clinical characteristics. A TME risk score model was constructed by using the More >

BICHUN ZHAO¹, XUEQING WU^2,*, YITONG YUAN¹, YUANTAO GAO¹, XIAO LI², RUOCHEN DU¹, SUMING XU², RUXIN ZHANG¹, CHUNFANG WANG^1,*

BIOCELL, Vol.44, No.4, pp. 487-499, 2020, DOI:10.32604/biocell.2020.011638 - 24 December 2020

Abstract In vitro maturation (IVM), a promising assisted reproductive technology (ART), has been evolving in clinical trials and applications. There is a huge potential demand for IVM in clinical practice because it reduces the stimulation of gonadotropins to patients and provides evidence for the safety of neonatal birth. Unfortunately, the maturation rate of oocytes in vivo is not as high as it is in vivo due to a different microenvironment. Moreover, there are still controversies in predicting the developmental capability of oocytes in IVM. The granulosa cells (GCs) and cumulus cells (CCs), closely surrounding the oocytes, play a critical… More >

REN FANG^#, WEIXIONG HUANG^#, JINYAN YAO, XING LONG, JI ZHANG, SHUANGYUN ZHOU, BIAO DENG, WENZHONG TANG, ZHENYU AN^*

BIOCELL, Vol.44, No.4, pp. 737-750, 2020, DOI:10.32604/biocell.2020.012933 - 24 December 2020

Abstract Annona squamosa is a multipurpose fruit tree employed in nutritional, medicinal, and industrial fields. Its fruit is significantly enriched in sugars, making it an excellent species to study sugar accumulation in fruit. However, the scarcity of genomic resources hinders genetic studies in this species. This study aimed at generating large-scale genomic resources in A. squamosa and deciphering the molecular basis of its high sugar content. Herein, we sequenced and characterized the full-length transcriptome of A. squamosa fruit using PacBio Iso-seq. In addition, we analyzed the changes in sugar content over five fruit growth and ripening stages, and we… More >

Swathypriyadharsini P^1,∗, K.Premalatha^2,†

Computer Systems Science and Engineering, Vol.35, No.1, pp. 39-50, 2020, DOI:10.32604/csse.2020.35.039

Abstract Microarrays have reformed biotechnological research in the past decade. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks with larger volume of genes also increases the challenges of comprehending and interpretation of the resulting mass of data. Clustering addresses these challenges, which is essential in the data mining process to reveal natural structures and identify interesting patterns in the underlying data. The clustering of gene expression data has been proven to be useful in making known the natural structure inherent… More >