检索结果-南通市图书馆

Machine Learning in Lung Cancer Radiomics

Machine Intelligence Research 2023年第6期20卷 753-782页

作者： Jiaqi Li Zhuofeng Li Lei Wei Xuegong Zhang Bioinformatics division Beijing National Research Center for Information Science and Technology(BNRIST)and Ministry of Education Key Laboratory of BioinformaticsDepartment of AutomationTsinghua UniversityBeijing100084China School of medicine Tsinghua UniversityBeijing100084China

Lung cancer is the leading cause of cancer-related deaths *** imaging technologies such as computed tomography(CT)and positron emission tomography(PET)are routinely used for non-invasive lung cancer *** clinical practice,physicians investigate the characteristics of tumors such as the size,shape and location from CT and PET images to make ***,scientists have proposed various computational image features that can capture more information than that directly perceivable by human eyes,which promotes the rise of *** is a research field on the conversion of medical images into high-dimensional features with data-driven methods to help subsequent data mining for better clinical decision *** analysis has four major steps:image preprocessing,tumor segmentation,feature extraction and clinical *** learning,including the high-profile deep learning,facilitates the development and application of radiomic *** radiomic methods have been proposed recently,such as the construction of radiomic signatures,tumor habitat analysis,cluster pattern characterization and end-to-end prediction of tumor *** methods have been applied in many studies aiming at lung cancer diagnosis,treatment and monitoring,shedding light on future non-invasive evaluations of the nodule malignancy,histological subtypes,genomic properties and treatment *** this review,we summarized and categorized the studies on the general workflow,methods for clinical prediction and clinical applications of machine learning in lung cancer radiomic studies,introduced some commonly-used software tools,and discussed the limitations of current methods and possible future directions.

关键词： Machine learning lung cancer radiomics medical image clinical application

来源：

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Vaccine therapy for dysbiosis-related diseases

引用

World Journal of Gastroenterology 2020年第21期26卷 2758-2767页

作者： Kosuke Fujimoto Satoshi Uematsu Department of Immunology and genomics Osaka City University Graduate School of MedicineOsaka 545-8585Japan division of Innate Immune Regulation International Research and Development Center for Mucosal VaccinesThe Institute of Medical ScienceThe University of TokyoTokyo 113-8654Japan division of Metagenome medicine Human Genome CenterThe Institute of Medical ScienceThe University of TokyoTokyo 113-8654Japan Collaborative Research Institute for Innovative Microbiology The University of TokyoTokyo 113-8654Japan

Progress in genomic analysis has resulted in the proposal that the intestinal microbiota is a crucial environmental factor in the development of multifactorial diseases,such as obesity,diabetes,rheumatoid arthritis,and inflammatory bowel diseases represented by Crohn’s disease and ulcerative *** gut microbiome contributes to the pathogenesis of such disorders;however,there are few effective treatments for controlling only disease-mediating ***,we review current knowledge about the intestinal microbiome in health and disease,and discuss a regulatory strategy using a parenteral vaccine with emulsified curdlan and CpG oligodeoxynucleotides,which we have recently *** other conventional injectable immunizations,our vaccine contributes to the induction of antigen-specific systemic and mucosal *** vaccine strategy can prevent infectious diseases such as Streptococcus pneumoniae infection,and control metabolic symptoms mediated by intestinal bacteria(*** ramosum)by induction of high titers of antigen-specific IgA at target mucosal *** the future,our vaccination approach could be an effective therapy for common infectious diseases and dysbiosis-related disorders that have been difficult to control so far.

关键词： Dysbiosis IgA Microbiome Mucosal immunity Pathobiont Vaccine

来源：

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Landscape of BRIP1 molecular lesions in gastrointestinal cancers from published genomic studies

引用

World Journal of Gastroenterology 2020年第11期26卷 1197-1207页

作者： Ioannis A Voutsadakis Algoma District Cancer Program Sault Area HospitalSault Ste MarieON P6B 0A8Canada Section of Internal medicine Division of Clinical SciencesNorthern Ontario School of MedicineSudburyON P0M 2Z0Canada

BACKGROUND BRIP1 is a helicase that partners with BRCA1 in the homologous recombination(HR) step in the repair of DNA inter-strand cross-link lesions. It is a rare cause of hereditary ovarian cancer in patients with no mutations of BRCA1 or BRCA2. The role of the protein in other cancers such as gastrointestinal(GI) carcinomas is less well characterized but given its role in DNA repair it could be a candidate tumor suppressor similarly to the two BRCA *** To analyze the role of helicase BRIP1(FANCJ) in GI cancers *** Publicly available data from genomic studies of esophageal, gastric, pancreatic,cholangiocarcinomas and colorectal cancers were interrogated to unveil the role of BRIP1 in these carcinomas and to discover associations of lesions in BRIP1 with other more common molecular defects in these *** Molecular lesions in BRIP1 were rare(3.6% of all samples) in GI cancers and consisted almost exclusively of mutations and amplifications. Among mutations,40% were possibly pathogenic according to the Onco KB database. A majority of BRIP1 mutated GI cancers were hyper-mutated due to concomitant mutations in mismatch repair or polymerase ε and δ1 genes. No associations were discovered between amplifications of BRIP1 and any mutated genes. In gastroesophageal cancers BRIP1 amplification commonly co-occurs with ERBB2 *** Overall BRIP1 molecular defects do not seem to play a major role in GI cancers whereas mutations frequently occur in hypermutated carcinomas and co-occur with other HR genes mutations. Despite their rarity, BRIP1 defects may present an opportunity for therapeutic interventions similar to other HR defects.

关键词： BRIP1 FANCJ BACH1 Gastrointestinal cancers Mutations Copy number alterations

来源：

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Antenatal use of bosentan and/or sildenafil attenuates pulmonary features in rats with congenital diaphragmatic hernia

引用

World Journal of Pediatrics 2014年第4期10卷 354-359页

作者： María de Lourdes Lemus-Varela Amed Soliz Belinda Claudia Gómez-Meda Ana Lourdes Zamora-Perez José Manuel Ornelas-Aguirre Valery Melnikov Blanca Miriam Torres-Mendoza Guillermo Moisés Zúñiga-González division of Neonatology High Specialty Medical UnitPediatric HospitalWestern National Medical CenterMexican Social Security InstituteGuadalajaraJaliscoMéxico Neonatal Intensive Care Unit Division of NeonatologyMiami Children's HospitalMiami FLDUSA Molecular Biology in medicine Institute Molecular Biology and Genomic DepartmentHealth Sciences University CenterUniversity of GuadalajaraGuadalajaraJaliscoMéxico Odontology Research Institute Integrated Odontology Clinic DepartmentHealth Sciences University CenterUniversity of GuadalajaraGuadalajaraJaliscoMéxico Pathology Department High Specialty Medical UnitNorth-western National Medical CenterMexican Social Security InstituteCiudad ObregónSonoraMéxico School of medicine University of ColimaColimaMéxico division of Neurosciences Western Biomedical Research CenterMexican Social Security Institute and Department of ClinicsHealth Sciences University CenterUniversity of GuadalajaraGuadalajaraJaliscoMéxico Mutagenesis Laboratory Western Biomedical Research CenterMexican Social Security InstituteGuadalajaraJaliscoMéxico

Background:Lung hypoplasia,pulmonary persistent hypertension of the newborn and its morphological changes are the main features in congenital diaphragmatic hernia(CDH).This study was undertaken to investigate if antenatal use of sildenafil and/or bosentan attenuates vascular remodeling,promotes branching,and improves alveolarization in experimental nitrofeninduced ***:Nitrofen(100 mg)was gavage-fed to pregnant rats at post conception day(PCD)9 to induce *** rats were randomized to 5 groups:1)control;2)nitrofen;3)nitrofen+sildenafil 100 mg/kg per day at PCD 16-20;4)nitrofen+bosentan 30 mg/kg per day,at PCD 16-20,and 5)nitrofen+bosentan+sildenafil,same doses and administration *** cesarean delivery,the offsprings were sacrifi *** diaphragmatic defect and pulmonary hypoplasia were identified,and the lungs were *** wall thickness,bronchiolar density and alveolarization were ***:The offsprings with CDH were characterized by severe pulmonary hypoplasia(lung weight-to-body weight ratio:0.0263[95%confidence interval(CI)0.0242-0.0278)]in the nitrofen group versus 0.0385(95%CI 0.0355-0.0424)in the control group(P=0.0001).Pulmonary arterial wall thickness was decreased to 3.0(95%CI 2.8-3.7)μm in the nitrofen+sildenafil group versus 5.0(95%CI 4.1-4.9)μm in the nitrofen group(P=0.02).Terminal bronchioles increased to 13.7(95%CI 10.7-15.2)μm in the nitrofen+bosentan group in contrast to 8.7(95%CI 7.2-9.4)μm in the nitrofen group(P=0.002).More significant differences(P=0.0001)were seen in terminal bronchioles in the nitrofen+sildenafil+bosentan group than in the nitrofen group[14.0(95%CI 12.5-15.4)μm versus 8.5(95%CI 7.1-9.3)μm].Pulmonary arterial wall thickness was also decreased in the former ***:In this rat model,antenatal treatment with sildenafil attenuates vascular *** promotes the development of terminal bronchioles in nitrofen-induced CDH.

关键词： antenatal treatment bosentan congenital diaphragmatic hernia pulmonary hypoplasia sildenafil

来源：

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Quantifying E2F1 protein dynamics in single cells

引用

Quantitative Biology 2020年第1期8卷 20-30页

作者： Bernard Mathey-Prevot Bao-Tran Parker Carolyn Im Cierra Hong Peng Dong Guang Yao Lingchong You Department of Pharmacology and Cancer Biology Duke University School of MedicineDurhamNC 27710USA Duke University School of medicine DurhamNC 27710USA Molecular and Cellular Biology University of ArizonaTucsonAZ 85721USA Department of Biomedical Engineering Duke UniversityDurhamNC 27705USA Center for genomic and Computational Biology Duke UniversityDurhamNC 27705USA Department of Molecular Genetics and Microbiology Duke University School of MedicineDurhamNC 27708USA Department of Pediatrics Duke University School of MedicineDurhamNC 27708USA University of North Carolina School of medicine Chapel HillNC 27516USA Janelia Research Campus Howard Hughes Medical InstituteAshburnVA 20147USA

Background:E2F1 protein,a major effector of the Rb/E2F pathway plays a central role in regulating cell-fate decisions involved in proliferation,apoptosis,and *** expression is highly dynamic and tightly modulated through a combination of transcriptional,translational and posttranslational ***,the mechanisms by which its expression and activity can promote different cellular outcomes remain to be fully *** better document E2F1 expression in live cells,we have engineered a series of fluorescent E2F1 protein reporters that quantitatively capture E2F1 protein ***:Reporter constructs,under the control of the mouse or human E2F1 proximal promoter,were designed to express an E2F1-Venus fusion protein incapable of binding *** addition,constructs either included or excluded the y untranslated region(3fUTR)of the E2F1 *** constructs were introduced into fibroblasts and epithelial cells,and expression of the fusion reporter protein was validated and quantified in single cells using live ***:In all cases,expression of the reporter protein effectively recapitulated the behavior of E2F1 under various conditions,including cell cycle progression and genotoxic *** or little fluorescent signal of the reporter was detected in G〇,but as the cycle progressed,expression of the reporter protein steadily increased in the nucleus,peaking a few hours before cell division,but declining to baseline 2-3 h prior to the onset of *** absence of the E2F13 fUTR in the constructs led to considerably higher steady-state levels of the fusion protein,which although normally regulated,exhibited a slightly less complex dynamic profile during the cell cycle or genotoxic ***,the presence or absence of Rb failed to impact the overall detection and levels of the reporter ***:Our validated E2F1 protein reporters complement nicely other reporters of the Rb/E2F pathway and provide a unique tool to f

关键词： protein E2F1 reporter cell cycle

来源：

维普期刊数据库

同方期刊数据库评论

在线全文

学校读者我要写书评

暂无评论

Understanding Spatial Genome Organization:Methods and Insights

引用

genomics, Proteomics & Bioinformatics 2016年第1期14卷 7-20页

作者： Vijay Ramani Jay Shendure Zhijun Duan Department of Genome Sciences University of WashingtonSeattleWA 98195USA Institute for Stem Cell and Regenerative medicine University of WashingtonSeattleWA 98109USA division of Hematology University of WashingtonSeattleWA 98195USA Department of medicine University of WashingtonSeattleWA 98195USA Howard Hughes Medical Institute SeattleWA 98195USA

The manner by which eukaryotic genomes are packaged into nuclei while maintaining crucial nuclear functions remains one of the fundamental mysteries in biology. Over the last ten years, we have witnessed rapid advances in both microscopic and nucleic acid-based approaches to map genome architecture, and the application of these approaches to the dissection of higher- order chromosomal structures has yielded much new information. It is becoming increasingly clear, for example, that interphase chromosomes form stable, multilevel hierarchical structures. Among them, self-associating domains like so-called topologically associating domains （TADs） appear to be building blocks for large-scale genomic organization. This review describes features of these broadly-defined hierarchical structures, insights into the mechanisms underlying their formation, our current understanding of how interactions in the nuclear space are linked to gene regulation, and important future directions for the field.

关键词： Chromatin ChromosomeEpigenomics 4D nucleomeHi-C

来源：

维普期刊数据库

同方期刊数据库评论

在线全文

学校读者我要写书评

暂无评论

Comprehensive molecular analysis to predict the efficacy ofchemotherapy containing bevacizumab in patients with metastaticcolorectal cancer

引用

Oncology Research 2023年第6期31卷 855-866页

作者： SUNG HEE LIM HEE JIN CHO KYOUNG-MEE KIM HO YEONG LIM WON KI KANG JEEYUN LEE YOUNG SUK PARK HEE CHEOL KIM SEUNG TAE KIM division of Hematology/Oncology Department of MedicineSamsung Medical CenterSungkyunkwan University School of MedicineGangnam-guSeoul06351Korea Precision medicine Research Institute Samsung Medical CenterGangnam-guSeoul06351Korea Department of Biomedical Convergence Science and Technology Kyungpook National UniversityDaegu41566Korea Department of Pathology and Translational genomics Samsung Medical CenterSungkyunkwan University School of MedicineSeoul06351Korea Department of Surgery Samsung Medical CenterSungkyunkwan University School of MedicineGangnam-guSeoul06351Korea

Background:Although bevacizumab is an important treatment for metastatic colorectal cancer(CRC),not allpatients with CRC benefit from it;in unselected patient populations,only modest survival benefits have been ***:We evaluated clinical outcomes in 110 patients using comprehensive molecular characterization to identifybiomarkers for a response to bevacizumab-containing *** molecular analysis comprised whole-exomesequencing,ribonucleic acid sequencing,and a methylation array on patient ***:genomic and molecularcharacterization was successfully conducted in 103 *** of 103 CRC samples were hypermutated,and none ofthe non-hypermutant tumors were microsatellite *** those 103 patients,89 had adenocarcinoma(ADC),15 were diagnosed with mucinous ADC,and six had signet-ring cell carcinoma(SRCC).Consensus molecular subtype(CMS)2 was unique to *** the four SRCCs,two were CMS1,one was CMS4,and the other was *** status was a significantly enriched factor in responders to bevacizumab *** growth factorreceptor(FGFR)1/2 signaling was upregulated in non-responders,whereas cell cycle,transfer ribonucleic acidprocessing,nucleotide excision repair,and oxidative phosphorylation pathways were enriched in ***,IGF1 was differentially expressed in non-responders(log2 fold change=−1.43,p=4.11×10^(−5),falsediscovery rate=0.098),and FLT1 was highly methylated in non-responders(p=7.55×10^(−3)).When the molecularpathways were reanalyzed separately according to the backbone chemotherapy(FOLFOX ***),thesignificance of the molecular pathways varied according to the backbone ***:This studysought a subset of CRC patients with a distinct clinical response to chemotherapy containing *** need to be validated in a large group of homogenous patient cohort and examined according to the differentchemotherapy backbones to create personalized therapeutic oppor

关键词： Bevacizumab Whole-exome sequencing Ribonucleic acid sequencing Methylation array Colorectal cancer

来源：

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Genetic polymorphisms predict response to anti-tumor necrosis factor treatment in Crohn's disease

引用

World Journal of Gastroenterology 2017年第27期23卷 4958-4967页

作者： Uri Netz Jane Victoria Carter Maurice Robert Eichenberger Gerald Wayne Dryden Jianmin Pan Shesh Nath Rai Susan Galandiuk Price Institute of Surgical Research the Hiram C.Polk Jr.MD Department of SurgeryUniversity of Louisville School of Medicine Department of Surgery A Soroka University Medical Center Faculty of Health Sciences Ben-Gurion University of the Negev Department of medicine Division of GastroenterologyHepatology and Nutrition University of Louisville School of Medicine Louisville Department of Bioinformatics and Biostatistics University of Louisville School of Public Health and Information Sciences

To investigate genetic factors that might help define which Crohn’s disease (CD) patients are likely to benefit from anti-tumor necrosis factor (TNF) therapy. METHODSThis was a prospective cohort study. Patients were recruited from a university digestive disease practice database. We included CD patients who received anti-TNF therapy, had available medical records (with information on treatment duration and efficacy) and who consented to participation. Patients with allergic reactions were excluded. Patients were grouped as ever-responders or non-responders. genomic DNA was extracted from peripheral blood, and 7 single nucleotide polymorphisms (SNPs) were assessed. The main outcome measure (following exposure to the drug) was response to therapy. The patient genotypes were assessed as the predictors of outcome. Possible confounders and effect modifiers included age, gender, race, and socioeconomic status disease, as well as disease characteristics (such as Montreal criteria). RESULTS121 patients were included. Twenty-one were non-responders, and 100 were ever-responders. Fas ligand SNP (rs763110) genotype frequencies, TNF gene -308 SNP (rs1800629) genotype frequencies, and their combination, were significantly different between groups on multivariable analysis controlling for Montreal disease behavior and perianal disease. The odds of a patient with a Fas ligand CC genotype being a non-responder were four-fold higher as compared to a TC or TT genotype (P = 0.009, OR = 4.30, 95%CI: 1.45-12.80). The presence of the A (minor) TNF gene -308 allele correlated with three-fold higher odds of being a non-responder (P = 0.049, OR = 2.88, 95%CI: 1.01-8.22). Patients with the combination of the Fas ligand CC genotype and the TNF -308 A allele had nearly five-fold higher odds of being a non-responder (P = 0.015, OR = 4.76, 95%CI: 1.35-16.77). No difference was seen for the remaining SNPs. CONCLUSIONThe Fas-ligand SNP and TNF gene -308 SNP are associated with anti-TNF treatment

关键词： Anti-tumor necrosis factor Fas ligand Antibody Response Crohn’s disease Single nucleotide polymorphisms Genotype Tumor necrosis factor gene

来源：

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

On-chip detection of a single nucleotide polymorphism without polymerase amplification

引用

Nano Research 2014年第9期7卷 1302-1310页

作者： Jinhee Han Matthew Tan Lakshmana Sudheendra Robert H. Weiss Ian M. Kennedy Department of Mechanical and Aerospace Engineering University of California Davis California 95616 USA division of Nephrology Department of Internal Medicine University of California Davis California 95616 USA Medical Service Sacramento VA Medical Center Sacramento California 95655 USA

A nanoparticle-assembled photonic crystal （PC） array was used to detect single nucleotide polymorphism （SNP）. The assay platform with PC nanostructure enhanced the fluorescent signal from nanoparticle-hybridized DNA complexes due to phase matching of excitation and emission. Nanoparticles coupled with probe DNA were trapped into nanowells in an array by using an electrophoretic particle entrapment system. The PC/DNA assay platform was able to identify a 1 base pair （bp） difference in synthesized nucleotide sequences that mimicked the mutation seen in a feline model of human autosomal dominant polycystic kidney disease （PKD） with a sensitivity of 0.9 fg/mL （50 aM）-sensitivity, which corresponds to 30 oligos/array. The reliability of the PC/DNA assay platform to detect SNP in a real sample was demonstrated by using genomic DNA （gDNA） extracted from the urine and blood of two PKD-wild type and three PKD positive cats. The standard curves for PKD positive （PKD＋） and negative （PKD-） DNA were created using two feline-urine samples. An additional three urine samples were analyzed in a similar fashion and showed satisfactory agreement with the standard curve, confirming the presence of the mutation in affected urine. The limit of detection （LOD） was 0.005 ng/mL which corresponds to 6 fg per array for gDNA in urine and blood. The PC system demonstrated the ability to detect a number of genome equivalents for the PKD SNP that was very similar to the results reported with real time polymerase chain reaction （PCR）. The favorable comparison with quantitative PCR suggests that the PC technology may find application well beyond the detection of the PKD SNP, into areas where a simple, cheap and portable nucleic acid analvsis is desirable.

关键词： photonic crystal array single nucleotidepolymorphisms DNA polycystic kidney disease real time polymerasechain reaction (PCR)

来源：

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Neutrophil-sourced TNF in cancer:deciphering an intricate orchestrator of immunosuppressive communication in the tumor microenvironment

引用

Signal Transduction and Targeted Therapy 2023年第8期8卷 3558-3560页

作者： Xinyuan Zhao Ye Lu Li Cui Stomatological Hospital School of StomatologySouthern Medical UniversityGuangzhou 510280 GuangdongChina division of Oral Biology and medicine School of DentistryUniversity of CaliforniaLos AngelesLos Angeles 90095 CAUSA

In a recent Cancer Discovery publication,Bianchi et *** a crucial mechanism driving therapeutic resistance in pancreatic ductal adenocarcinoma(PDAC),orchestrated by cell-autonomous Cxcl1 and TNF from polymorphonuclear myeloid-derived suppressor cells(PMN-MDSCs).This insight provides fresh perspectives for surmounting such resistance in PDAC.1 PDAC represents a highly aggressive malignancy exhibiting substantial therapeutic resistance,attributable to factors such as intractable genomic aberrations,immunosuppression mediated by myeloid cells,and pro-inflammatory activation of cancerassociated fibroblasts.

关键词： cancer Cancer

来源：

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

欢迎您,

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

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

请选择保存的检索档案：

请选择收藏分类：

通借通还

欢迎您,

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

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

在线全文

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：