检索结果-内蒙古大学图书馆

A Holistic 4D Approach to Optimize Intrinsic and Extrinsic Factors Contributing to Variability in microarray Biosensing in Glycomics

引用

SENSORS 2023年第12期23卷 5362页

作者： Kundalia, Paras H. Pazitna, Lucia Kianickova, Kristina Jane, Eduard Lorencova, Lenka Katrlik, Jaroslav Slovak Acad Sci Inst Chem Dept Glycobiotechnol SK-84538 Bratislava Slovakia

Protein-carbohydrate interactions happen to be a crucial facet of biology, discharging a myriad of functions. microarrays have become a premier choice to discern the selectivity, sensitivity and breadth of these interactions in a high-throughput manner. The precise recognition of target glycan ligands among the plethora of others is central for any glycan-targeting probe being tested by microarray analyses. Ever since the introduction of the microarray as an elemental tool for high-throughput glycoprofiling, numerous distinct array platforms possessing different customizations and assemblies have been developed. Accompanying these customizations are various factors ushering variances across array platforms. In this primer, we investigate the influence of various extrinsic factors, namely printing parameters, incubation procedures, analyses and array storage conditions on the protein-carbohydrate interactions and evaluate these factors for the optimal performance of microarray glycomics analysis. We hereby propose a 4D approach (Design-Dispense-Detect-Deduce) to minimize the effect of these extrinsic factors on glycomics microarray analyses and thereby streamline cross-platform analyses and comparisons. This work will aid in optimizing microarray analyses for glycomics, minimize cross-platform disparities and bolster the further development of this technology.

关键词： microarray biosensor affinity-based methods high-throughput glycoprofiling glycan lectin non-contact spotting piezo-electric dispensing

来源：评论

学校读者我要写书评

暂无评论

SVM-ABC based cancer microarray (gene expression) hybrid method for data classification

引用

COMPUTATIONAL INTELLIGENCE 2023年第6期39卷 1054-1072页

作者： Gulande, Punam Awale, R. N. VJTI Dept Elect Mumbai Maharashtra India

microarray technology presents a challenge due to the large dimensionality of the data, which can be difficult to interpret. To address this challenge, the article proposes a feature extraction-based cancer classification technique coupled with artificial bee colony optimization (ABC) algorithm. The ABC-support vector machine (SVM) method is used to classify the lung cancer datasets and compared them with existing techniques in terms of precision, recall, F-measure, and accuracy. The proposed ABC-SVM has the advantage of dealing with complex nonlinear data, providing good flexibility. Simulation analysis was conducted with 30% of the data reserved for testing the proposed method. The results indicate that the proposed attribute classification technique, which uses fewer genes, performs better than other modalities. The classifiers, such as naive Bayes, multi-class SVM, and linear discriminant analysis, were also compared and the proposed method outperformed these classifiers and state-of-the-art techniques. Overall, this study demonstrates the potential of using intelligent algorithms and feature extraction techniques to improve the accuracy of cancer diagnosis using microarray gene expression data.

关键词： ABC genes expression lung cancer microarray NB SVM

来源：评论

学校读者我要写书评

暂无评论

microarray-guided evaluation of the frequency, B-cell origins, and selectivity of human glycan-binding antibodies reveals new insights and novel antibodies

引用

JOURNAL OF BIOLOGICAL CHEMISTRY 2022年第10期298卷 102468页

作者： Temme, J. Sebastian Crainic, Jennifer A. Walker, Laura M. Yang, Weizhun Tan, Zibin Huang, Xuefei Gildersleeve, Jeffrey C. NCI Chem Biol Lab Ctr Canc Res Frederick MD 21702 USA Adimab LLC Lebanon NH USA Adagio Therapeut Inc Waltham MA USA Michigan State Univ Dept Chem E Lansing MI USA Michigan State Univ Inst Quantitat Hlth Sci & Engn E Lansing MI USA Michigan State Univ Dept Biomed Engn E Lansing MI USA

The immune system produces a diverse collection of anti-glycan antibodies that are critical for host defense. At present, however, we know very little about the binding properties, origins, and sequences of these antibodies because of a lack of access to a variety of defined individual antibodies. To address this challenge, we used a glycan microarray with over 800 different components to screen a panel of 516 human mono-clonal antibodies that had been randomly cloned from different B-cell subsets originating from healthy human sub-jects. We obtained 26 antiglycan antibodies, most of which bound microbial carbohydrates. The majority of the antiglycan antibodies identified in the screen displayed selective binding for specific glycan motifs on our array and lacked poly-reactivity. We found that antiglycan antibodies were about twice as likely than expected to originate from IgG+ memory B cells, whereas none were isolated from naive, early emigrant, or immature B cells. Therefore, our results indicate that certain B-cell subsets in our panel are enriched in antiglycan antibodies, and IgG+ memory B cells may be a promising source of such antibodies. Furthermore, some of the newly identified anti-bodies bound glycans for which there are no reported mono-clonal antibodies available, and these may be useful as research tools, diagnostics, or therapeutic agents. Overall, the results provide insight into the types and properties of antiglycan antibodies produced by the human immune system and a framework for the identification of novel antiglycan antibodies in the future.

关键词： antibody antigen carbohydrate carbohydrate-binding protein glycobiology microarray monoclonal antibody

来源：评论

学校读者我要写书评

暂无评论

Insights into 8-manno-oligosaccharide uptake and metabolism in Bifidobacterium adolescentis DSMZ 20083 from whole-genome microarray analysis

引用

MICROBIOLOGICAL RESEARCH 2023年第0期266卷 000-000页

作者： Mary, Priyanka Rose Monica, P. Kapoor, Mukesh CSIR Cent Food Technol Res Inst Dept Microbiol & Fermentat Technol Mysuru 570020 India Acad Sci & Innovat Res AcSIR Ghaziabad 201002 Uttar Pradesh India

Metabolism of non-digestible dietary glycans directly influences the structure and composition of human gut microbiota and, in turn, the host health. 8-Mannans form an integral component of the modern diet as naturally occurring dietary fibre or additives in processed foods. In the present study, in vitro fermentation and TLC studies were used to determine the ability of adult-associated Bifidobacterium adolescentis DSMZ 20083 to utilise 8-manno-oligosaccharides from guar gum, locust bean gum, konjac root, and copra meal generated using GH26 endo-8-mannanase (ManB-1601). Further, to gain insights into the underlying molecular mechanism, a whole-genome microarray analysis, RT-qPCR, and molecular docking studies were employed to reconstruct the copra meal 8-manno-oligosaccharides (CM-8-MOS) utilisation pathway in B. adolescentis DSMZ 20083. B. adolescentis DSMZ 20083 grew appreciably (O.D600 nm up to 0.8) on all tested 8-manno-oligosaccharides but maximally on CM-8-MOS. CM-8-MOS having DP2-3 were found to deplete from the fermentation media. Whole-genome transcriptome analysis, RT-qPCR, and molecular docking studies suggested that in B. adolescentis DSMZ 20083, ABC & MFS transporters are possibly involved in the uptake of DP >= 2 and DP >= 3 linear CM-8-MOS, respectively, while GH1 8-glucosidase, and GH32 8-fructofuranosidase possibly cleave linear CM-8-MOS into monosaccharides. Sugar absorption and utilisation pathways;Bifid shunt, ABC transport system, pyruvate metabolism, glycolysis/gluconeogenesis, pentose, and glucouronate inter-conversions were also found up -regulated following the growth on CM-8-MOS. This is the first study reporting on possible molecular de-terminants used by B. adolescentis DSMZ 20083 to utilise 8-manno-oligosaccharides. Our studies can prove resourceful to food and nutraceutical industries, aiming at precision microbiome modulation using 8-manno-oligosaccharides.

关键词： 8-Manno-oligosaccharides B adolescentis DSMZ 20083 microarray Utilisation

来源：评论

学校读者我要写书评

暂无评论

Improved multi-layer binary firefly algorithm for optimizing feature selection and classification of microarray data

引用

BIOMEDICAL SIGNAL PROCESSING AND CONTROL 2023年第Part1期79卷 000-000页

作者： Xie, Weidong Wang, Linjie Yu, Kun Shi, Tengfei Li, Wei Northeastern Univ Sch Comp Sci & Engn Shenyang Peoples R China Northeastern Univ Biomed & Informat Engn Sch Shenyang Peoples R China Northeastern Univ Key Lab Intelligent Comp Med Image MIIC Minist Educ Shenyang Peoples R China

Gene microarray technology can detect many gene expressions simultaneously, which is essential for disease diagnosis. However, microarray data are usually characterized by small samples and high dimensionality, which requires obtaining the most matching genes to the disease before building a classification model. In this paper, we propose an improved multilayer binary firefly-based method that is divided into two phases. The first stage reduces the dimensionality space by improved Max-Relevance and Min-Redundancy (mRMR). The second stage refines the feature space from coarse-grained level to fine-grained level by improved multilayer binary firefly algorithm (MBFA) at each recursive step. We built a stacking classifier model based on attention mechanism in publicly available gene microarray data and evaluated them compared to advanced hybrid feature selection methods. The experimental results show that compared with the classical chi square test, variance, logistic regression and decision tree methods, the proposed method can achieve higher classification accuracy with fewer features. In addition, the proposed method also shows excellent results in comparison with different published hybrid feature selection methods.

关键词： microarray Feature selection Biofeature Firefly algorithm

来源：评论

学校读者我要写书评

暂无评论

microarray expression results of VEGF, YAP1 and PTEN immunostains in preeclampsia cases

引用

Journal of Immunoassay and Immunochemistry 2023年第2期44卷 204-212页

作者： Atigan, Ayhan Karakaya, Yeliz Arman Kiliç, Derya Guler, Omer Tolga Department of Obstetrics and Gynecology Faculty of Medicine Karabuk University Karabuk Turkey Department of Pathology Faculty of Medicine Pamukkale University Denizli Turkey Department of Obstetrics and Gynecology Faculty of Medicine Pamukkale University Denizli Turkey

We aimed to evaluate the expression of YAP1, PTEN, VEGF in the placentas of patients with preeclampsia and placentas of healthy pregnant women for trophoblast invasion, which is similar to cancer etiopathogenesis. The placentas of 70 women who gave birth, including 30 preeclampsia and 40 healthy controls, were evaluated. YAP1, PTEN and VEGF immunohistochemical staining were performed using the microarray method on placental tissue. The mean ± standard deviation for YAP1, PTEN and VEGF intensity were;1.57 ± 0.71,2.59 ± 0.80, 1.61 ± 0.59, respectively. PTEN intensity was statistically significantly lower in the preeclampsia group than in the control group (2.37 ± 0.99 vs 2.75 ± 0.58, p = .049). There was no difference between the groups in terms of YAP1 and VEGF staining (p > .05). The etiopathogenesis of preeclampsia is still unclear. However, since trophoblast invasion and endothelial repair have similar aspects with cancer mechanisms, both preeclampsia and cancer studies are progressing by supporting each other. Our study is a prototype study showing that large-participation studies can be carried out easily by using the microarray method as an economic model. © 2023 Taylor & Francis.

关键词： immunohistochemistry microarray preeclampsia PTEN VEGF YAP1

来源：评论

学校读者我要写书评

暂无评论

Orientation Error Modeling and Analysis of microarray Polarized Light Compass

Orientation Error Modeling and Analysis of Microarray Polari...

引用

2024 International Conference on Guidance, Navigation and Control

作者： Mei, Chunrui He, Xiaofeng Fan, Chen Natl Univ Def Technol Coll Intelligence Sci & Technol Changsha 410073 Peoples R China Xichang Satellite Launch Ctr Wenchang 571300 Peoples R China

ISBN: (纸本)9789819622504;9789819622481;9789819622474

Polarized light orientation is a new navigation method based on atmospheric polarized light field, which has the advantages of anti-interference and no accumulation of errors, can provide a technical way for the autonomous orientation of micro-unmanned platforms under the condition of satellite rejection. Under complex weather conditions, the orientation accuracy of polarized light decreases, and the existing orientation error analysis and research are not systematic enough. In this paper, the orientation error model of polarized light is constructed based on Rayleigh atmosphere model. Secondly, the model is modeled for solar position error, horizontal attitude angles error, incident light polarization angle error, light intensity error, time error and position error, and the simulation quantitative analysis is carried out. The results show that: when the solar height angle is close to 90 degrees, the solar height angle error is the main error source affecting the orientation. When solar altitude is small, the horizontal attitude angles error, the incident light polarization angle error and the light intensity error are the main influencing factors of orientation accuracy, of which horizontal attitude angles error is the most important. In position error, longitude error is the main error source relative to latitude error. Under the positioning accuracy of 0.2 degrees and UTC timing, orientation error caused by position error and time error is less than 0.1 degrees. In addition, a feasible way to reduce the orientation error caused by the light intensity error is found through error analysis. When the noise amplitude reaches half of the light intensity amplitude, the simulation results show that the orientation error is reduced from 0.85 degrees to 0.23 degrees. This discovery lays a foundation for further improving the environmental applicability and availability of the microarray polarized light compass.

关键词： Polarized light orientation Rayleigh scattering model Error modeling microarray Simulation analysis

来源：评论

学校读者我要写书评

暂无评论

microarray analysis of breast cancer gene expression profiling in response to 2-deoxyglucose, metformin, and glucose starvation

引用

CANCER CELL INTERNATIONAL 2022年第1期22卷 123-123页

作者： Aoun, Rita El Hadi, Christopher Tahtouh, Roula El Habre, Rita Hilal, George St Joseph Univ Fac Med Canc & Metab Lab Beirut Lebanon St Joseph Univ Fac Med Beirut Lebanon

Background Breast cancer (BC) is the most frequently diagnosed cancer in women. Altering glucose metabolism and its effects on cancer progression and treatment resistance is an emerging interest in BC research. For instance, combining chemotherapy with glucose-lowering drugs (2-deoxyglucose (2-DG), metformin (MET)) or glucose starvation (GS) has shown better outcomes than with chemotherapy alone. However, the genes and molecular mechanisms that govern the action of these glucose deprivation conditions have not been fully elucidated. Here, we investigated the differentially expressed genes in MCF-7 and MDA-MB-231 BC cell lines upon treatment with glucose-lowering drugs (2-DG, MET) and GS using microarray analysis to study the difference in biological functions between the glucose challenges and their effect on the vulnerability of BC cells. Methods MDA-MB-231 and MCF-7 cells were treated with 20 mM MET or 4 mM 2-DG for 48 h. GS was performed by gradually decreasing the glucose concentration in the culture medium to 0 g/L, in which the cells remained with fetal bovine serum for one week. Expression profiling was carried out using Affymetrix Human Clariom S microarrays. Differentially expressed genes were obtained from the Transcriptome Analysis Console and enriched using DAVID and R packages. Results Our results showed that MDA-MB-231 cells were more responsive to glucose deprivation than MCF-7 cells. Endoplasmic reticulum stress response and cell cycle inhibition were detected after all three glucose deprivations in MDA-MB-231 cells and only under the metformin and GS conditions in MCF-7 cells. Induction of apoptosis and inhibition of DNA replication were observed with all three treatments in MDA-MB-231 cells and metformin-treated MCF-7 cells. Upregulation of cellular response to reactive oxygen species and inhibition of DNA repair mechanisms resulted after metformin and GS administration in MDA-MB-231 cell lines and metformin-treated MCF-7 cells. Autophagy was induc

关键词： Breast cancer Triple-negative breast cancer Hormone receptor-positive subtype 2-deoxyglucose Metformin Glucose starvation microarray

来源：评论

学校读者我要写书评

暂无评论

Screening and validating circular RNAs that estimate disease risk and treatment response of pediatric acute myeloid leukemia: a microarray-based analyses and RT-qPCR validation

引用

JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY 2023年第13期149卷 11233-11245页

作者： Ye, Fanghua Fan, Chenying Peng, Min Liu, Siqin Dong, Jiajia Yang, Liangchun Zhang, Hui Cent South Univ Xiangya Hosp Dept Pediat 87 Xiangya Rd Changsha 410008 Peoples R China

PurposeCircular RNA (circRNA) is a type of novel non-coding RNA with close involvement in the tumorigenesis and treatment response of leukemias. This study aimed to screen and validate candidate circRNAs that estimate disease risk and response to induction therapy of pediatric acute myeloid leukemia (AML).MethodsBone marrow samples were obtained from 4 complete response (CR) pediatric AML patients, 4 non-CR pediatric AML patients, and 4 controls to screen differentially expressed circRNAs (DECs) through microarray analyses. Ten candidate circRNAs were selected and validated in 40 pediatric AML patients and 10 controls through reverse transcription-quantitative polymerase chain *** assay discovered 378 upregulated DECs and 688 downregulated DECs in pediatric AML patients vs. controls;832 upregulated DECs and 950 downregulated DECs in CR AML patients vs. non-CR AML patients. Then cross-analysis identified 441 DECs that both related to pediatric AML risk and CR achievement. Further validation of ten candidate circRNAs in larger sample-sized populations showed that circ_0032891, circ_0076995, circ_0014352, circ_0047663, circ_0007444, circ_0001684, circ_0000544, and circ_0005354 were related to pediatric AML risk;circ_0032891, circ_0076995, circ_0014352, circ_0047663, circ_0007444, circ_0001684, and circ_0000544 were related to CR achievement in pediatric AML patients. Regarding the correlation of candidate circRNAs with survival profile, only circ_0032891, circ_0076995, and circ_0000544 forecasted event-free survival;circ_0076995 and circ_0001684 estimated overall survival in pediatric AML *** profile is intensively implicated in the disease risk and treatment response of pediatric AML, especially that circ_0032891, circ_0000544, circ_0076995, and circ_0001684 are related to pediatric AML risk, CR achievement, and survival.

关键词： Pediatric acute myeloid leukemia microarray Circular RNA profile RT-qPCR validation Treatment response

来源：评论

学校读者我要写书评

暂无评论

microarray and in silico analysis of DNA repair genes between human testis of patients with nonobstructive azoospermia and normal cells

引用

CELL BIOCHEMISTRY AND FUNCTION 2022年第8期40卷 865-879页

作者： Karoii, Danial Hashemi Azizi, Hossein Skutella, Thomas Amol Univ Special Modern Technol Fac Biotechnol Amol Iran Heidelberg Univ Med Fac Inst Anat & Cell Biol Heidelberg Germany

DNA repair processes are critical to maintaining genomic integrity. As a result, dysregulation of repair genes is likely to be linked with health implications, such as an increased prevalence of infertility and an accelerated rate of aging. We evaluated all the DNA repair genes (322 genes) by microarray. This study has provided insight into the connection between DNA repair genes, including RAD23B, OBFC2A, PMS1, UBE2V1, ERCC5, SMUG1, RFC4, PMS2L5, MMS19, SHFM1, INO80, PMS2L1, CHEK2, TRIP13, and POLD4. The microarray analysis of six human cases with different nonobstructive azoospermia revealed that RAD23B, OBFC2A, PMS1, UBE2V1, ERCC5, SMUG1, RFC4, PMS2L5, MMS19, SHFM1, and INO80 were upregulated, and expression of PMS2L1, CHEK2, TRIP13, and POLD4 was downregulated versus the normal case. For this purpose, Enrich Shiny GO, STRING, and Cytoscape online evaluation was applied to predict proteins' functional and molecular interactions and then performed to recognize the master pathways. Functional enrichment analysis revealed that the biological process (BP) terms "base-excision repair, AP site formation," "nucleotide-excision repair, DNA gap filling," and "nucleotide-excision repair, preincision complex assembly" was significantly overexpressed in upregulated differentially expressed genes (DEGs). BP analysis of downregulated DEGs highlighted "histone phosphorylation," "DNA damage response, detection DNA response," "mitotic cell cycle checkpoint signaling," and "double-strand break repair." Overrepresented molecular function (MF) terms in upregulated DEGs included "Oxidized base lesion DNA N-glycosylase activity," "uracil DNA N-glycosylase activity," "bubble DNA binding" and "DNA clamp loader activity." Interestingly, MF investigation of downregulated DEGs showed overexpression in "heterotrimeric G-protein complex," "5 '-deoxyribose-5-phosphate lyase activity," "minor groove of adenine-thymine-rich DNA binding," and "histone kinase activity." Our findings suggest that

关键词： DNA repair gene expression in-silico microarray nonobstructive azoospermia

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：