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1.
摘要:目的 通过应用全基因组测序(whole genome sequencing, WGS)技术分析某三级医疗机构耐碳青霉烯类抗生素鲍曼不 动杆菌(carbapenem-resistant Acinetobacter baumannii, CRAB)的耐药基因、毒力因子及同源性。方法 收集该院2020年1月至3月 重症监护病房(Intensive care unit, ICU)、神经外科分离的11株医院感染CRAB菌株,通过二代测序平台进行全基因组测序, 应用 基因组流行病学中心(Center for genomic epidemiology, CGE)ResFinder 4. 0软件分析其耐药基因型,并应用MORPHEUS在线制作 热图,应用毒力因子数据库(virulence factors of pathogenic bacteria, VFDB)VFanalyzer软件筛选毒力因子,应用MLST软件检测菌 株的ST型,应用Kaptive软件检测荚膜型,应用CSI Phylogeny 1. 4软件及FigTree v1. 4. 4软件构建最大似然树(maximum likelihood tree, MLT)以分析其同源性。结果 11株CRAB对亚胺培南、美罗培南、头孢菌素、环丙沙星均呈现耐药,而对阿米卡星、左氧 氟沙星耐药的菌株株数较少。11株CRAB共检测出18种耐药基因,11株同时携带碳青霉烯酶耐药基因blaOXA-23和blaOXA-66,β-内酰 胺酶耐药基因以blaTEM-1D和blaADC-25为主,大部分菌株携带多种外排泵相关耐药基因及抗菌药物修饰酶耐药基因。11株CRAB均携 带多种毒力因子,包括外膜孔蛋白、脂多糖、生物膜、外排泵、磷脂酶和效应蛋白等,如OmpA、Lps、Csu、Pga、Ade、Plc、 Bas、Bau、Ent、Hem、Aba、Bfm、Pbp和Kat等。11株CRAB均为ST2-K22型,同源性分析结果显示C组内同源性关系相近,存 在院内传播的可能。结论 该院CRAB的耐药性、毒力特征复杂多样,同源性分析显示该院存在1种优势克隆株,该克隆株有医 院内传播的风险。  相似文献   
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《Journal of endodontics》2022,48(4):479-486
IntroductionAsepsis in endodontics aims to control all potential sources of infection. Inadvertent introduction of bacteria into the root canal system may occur when the aseptic chain is breached during treatment. Therefore, measures are taken to prevent such microbial access and establish an aseptic environment. This study aimed to assess potential bacterial contamination and the potential risk of iatrogenic introduction from 7 sites comprising surfaces, instruments, and files acquired during the treatment of 30 vital, pulpitic teeth.MethodsBacterial samples were collected from access burs, files, endodontic rulers, rubber dam surfaces, gloves, and instruments. Genomic DNA was extracted and quantified by quantitative polymerase chain reaction. Bacterial types were determined using next-generation sequencing.ResultsHigh frequencies of contamination and microbial numbers were encountered in all sample types examined.Thirty-eight percent of the initial files introduced into the root canal had significant levels of bacteria at the point of obturation, including endodontic pathogens. Around half of the rubber dam surfaces were contaminated with substantial bacterial loads at the time of obturation, and bacteria were also detected in 20%–30% of gloves, instruments, and rulers before obturation. Next-generation sequencing revealed the predominant oral or endodontic origin of these contaminants, with the following genera identified: Streptococcus, Rothia, Granulicatella, Cutibacterium, Corynebacterium, Peptostreptococcus, and Fusobacterium. Together, these findings highlight the potential risk of reintroducing endodontically relevant bacteria during treatment.ConclusionsGloves, rubber dams, instruments, and files acquire bacterial contamination during treatment at high frequencies and loads. This highlights the potential risk of iatrogenic contamination at the clinically vulnerable point of canal obturation. Measures to address these may improve clinical outcomes.  相似文献   
3.
目的 研究凉血通瘀方对高血压大鼠急性脑出血模型脑组织miRNA表达的影响,对差异表达的miRNA靶基因进行分析,探索凉血通瘀方可能的药效机制。方法 将自发性高血压大鼠随机分成对照组(B)和实验组(C)。适应性饲养一周后,C组灌胃凉血通瘀方,B组灌胃等体积生理盐水,连续5天,每天1次。构建脑出血模型后收集脑组织,借助全转录组测序技术获得miRNA表达量,与miRBase数据库比对获取已知miRNA,使用miRDeep2预测新miRNA。差异分析软件为DESeq2,筛选阈值为|log2FC| ≥1 并且P <0.05。对显著差异表达的miRNA进行靶基因预测,对靶基因进行GO功能、KEGG通路富集和PPI网络分析。结果 实验组和对照组对比,共发现21个显著差异表达的miRNA,上调有9个,下调有12个,共预测得到1243个有统计学意义的靶基因。GO富集分析发现,生物过程中突触囊泡分泌的调节、神经递质分泌的调节和神经递质运输的调节占前三位,神经元投射终点、全膜、质膜区域和细胞投射则是主要的细胞成分。分子功能分别为小GTPase绑定、底物特异性跨膜转运蛋白活性和离子跨膜转运体活性。通路分析结果显示,靶基因在癌证通路、pI3K-Akt信号通路、人类乳头瘤病毒感染、神经活性配体-受体相互作用和MAPK通路等分布广泛。采用STRING网站和Cytoscape软件,根据MCC算法筛选出ADRA2C、CASR、CCL28、CCR1、DRD2、GNAT3、GRM2、DYNC1LI1、GABBR1、GNAI1等核心靶基因。结论 凉血通瘀方对脑出血急性期鼠脑组织内miRNA的表达有重要影响;显著差异表达miRNAs可能通过靶向核心基因调控凉血通瘀方干预急性脑出血的病理过程及预后。  相似文献   
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ObjectivesWe investigated whether nanopore 16S amplicon sequencing is capable of bacterial identification in patients with knee prosthetic joint infection (PJI), and we compared its efficacy with conventional culture studies.MethodsIn total, 36 patients who had clinical manifestation suspected of PJI were enrolled in this study. To begin, synovial fluids were aspirated from the affected knee using aseptic technique and tissues specimens were obtained during the surgery. Next, DNA was extracted from the synovial fluid or tissues, and 16S rDNA PCR was performed. In PCR positive cases, nanopore amplicon sequencing was then performed for up to 3 h. The results of amplicon sequencing were compared to those of conventional culture studies.ResultsOf the 36 patients enrolled, 22 were classified as true infections according to the MSIS criteria whereas 14 were considered uninfected. Among the 22 PJI cases, 19 cases were culture positive (CP-PJI) while three cases were culture negative (CN-PJI). In 14 of 19 (73.7 %) CP- PJI cases, 16S sequencing identified concordant bacteria with conventional culture studies with a significantly shorter turnaround time. In some cases, nanopore 16S sequencing was superior to culture studies in the species-level identification of pathogen and detection of polymicrobial infections. Altogether, in the majority of PJI candidate patients (32 of 36, 88.9 %), 16S sequencing achieved identical results to cultures studies with a significantly reduced turnaround time (100.9 ± 32.5 h vs. 10.8 ± 7.7 h, p < 0.001).ConclusionsNanopore 16S sequencing was found to be particularly useful for pathogen identification in knee PJI. Although the sensitivity was not superior to culture studies, the nanopore 16S sequencing was much faster, and species-level identification and detection of polymicrobial infections were superior to culture studies.  相似文献   
6.
PurposeTo estimate the cost-effectiveness of genome sequencing (GS) for diagnosing critically ill infants and noncritically ill pediatric patients (children) with suspected rare genetic diseases from a United States health sector perspective.MethodsA decision-analytic model was developed to simulate the diagnostic trajectory of patients. Parameter estimates were derived from a targeted literature review and meta-analysis. The model simulated clinical and economic outcomes associated with 3 diagnostic pathways: (1) standard diagnostic care, (2) GS, and (3) standard diagnostic care followed by GS.ResultsFor children, costs of GS ($7284) were similar to that of standard care ($7355) and lower than that of standard care followed by GS pathways ($12,030). In critically ill infants, when cost estimates were based on the length of stay in the neonatal intensive care unit, the lowest cost pathway was GS ($209,472). When only diagnostic test costs were included, the cost per diagnosis was $17,940 for standard, $17,019 for GS, and $20,255 for standard care followed by GS.ConclusionThe results of this economic model suggest that GS may be cost neutral or possibly cost saving as a first line diagnostic tool for children and critically ill infants.  相似文献   
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 目的 探讨分析鹦鹉热衣原体肺炎患者的临床表现及辅助检查结果特征,以提高对该病的认识。方法 回顾性分析某医院2019年6月- 2021年8月经宏基因组二代测序(mNGS)诊断鹦鹉热衣原体肺炎的9例患者临床资料。结果 9例患者中男性7例,女性2 例,包含1例妊娠36+2周孕妇;年龄25~70岁,中位年龄63岁;临床主要表现为高热(9例)、咳嗽(9例)、咳痰(7例)。白细胞计数正常8例,淋巴细胞计数降低9例,CRP升高9例,ESR升高9例,PCT正常4例,门冬氨酸氨基转移酶和丙氨酸氨基转移酶升高6例。9例患者胸部 CT均表现为斑片或斑片实变影。经血及肺泡灌洗液mNGS确诊后使用多西环素、莫西沙星、左氧氟沙星、阿奇霉素单药治疗方案,疗程14~21 d,均好转出院。结论 鹦鹉热衣原体肺炎临床表现多样、诊断困难,mNGS检测可以快速明确病原学诊断,有助于及时启动特异性抗感染治疗,可减少抗菌药物的使用,改善预后。  相似文献   
10.
Background: Familial adenomatous polyposis (FAP) is a hereditary disorder primarily caused by germline mutations in the APC gene. The most common type of mutation in the APC gene is point mutation, while deletion mutation is much less frequent. The current study was conducted to investigate the mutation spectrum of the APC gene in Vietnamese FAP patients. Methods: Patients with the clinical diagnosis of FAP on colorectal endoscopy were screened for mutations in the APC gene using Sanger sequencing. Those who exhibited no point mutation subsequently underwent MLPA assay to detect deletion and duplication mutations. Besides, the relatives of patients with mutated APC genes were recruited for detecting carrier status. Results: Sixty-three patients with clinical colorectal polyposis were recruited. Mutations in the APC gene were detected in 26/63 patients (41.3%). Genetic analysis of 105 asymptomatic relatives of these 26 patients found mutations in the APC gene in 55 individuals (52.4%). Conclusion: We successfully established the APC gene mutation spectrum in Vietnamese FAP patients for the first time. Of importance, we discovered two novel point mutations in the APC gene. The high prevalence of carrier status in asymptomatic family members of patients with mutation emphasizes the crucial role of appropriate genetic screening for early diagnosis, surveillance, and preventive measurements.  相似文献   
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