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ITMSQ: A software tool for N‐ and C‐terminal fragment ion pairs based isobaric tandem mass spectrometry quantification 下载免费PDF全文
Li‐Qi Xie Lei Zhang Ai‐Ying Nie Guo‐Quan Yan Jun Yao Yang Zhang Peng‐Yuan Yang Hao‐Jie Lu 《Proteomics》2015,15(22):3755-3764
Tandem MS (MS2) quantification using the series of N‐ and C‐terminal fragment ion pairs generated from isobaric‐labelled peptides was recently considered an accurate strategy in quantitative proteomics. However, the presence of multiplexed terminal fragment ion in MS2 spectra may reduce the efficiency of peptide identification, resulting in lower identification scores or even incorrect assignments. To address this issue, we developed a quantitative software tool, denoted isobaric tandem MS quantification (ITMSQ), to improve N‐ and C‐terminal fragment ion pairs based isobaric MS2 quantification. A spectrum splitting module was designed to separate the MS2 spectra from different samples, increasing the accuracy of both identification and quantification. ITMSQ offers a convenient interface through which parameters can be changed along with the labelling method, and the result files and all of the intermediate files can be exported. We performed an analysis of in vivo terminal amino acid labelling labelled HeLa samples and found that the numbers of quantified proteins and peptides increased by 13.64 and 27.52% after spectrum splitting, respectively. In conclusion, ITMSQ provides an accurate and reliable quantitative solutionfor N‐ and C‐terminal fragment ion pairs based isobaric MS2 quantitative methods. 相似文献
73.
基于微滴式数字聚合酶链式反应(Droplet digital polymerase chain reaction,dd PCR)设计一种检测肠癌游离循环DNA(Circulating cell free DNA,cf DNA)中KRAS(V-Ki-ras2 Kirsten ratsarcoma viral oncogene homolog)基因突变的新方法并评估其灵敏度和准确性。根据肠癌病人KRAS基因的突变类型设计并合成,采用dd PCR扩增并评估其灵敏度和准确性;根据AMRS-PCR引物设计原理设计KRAS基因的实时定量PCR扩增引物并评估其准确性,进而比较dd PCR和q PCR二者之间的优缺点;最后针对52例肠癌病人的cf DNA采用dd PCR进行检测,研究dd PCR在cf DNA KRAS基因突变检测的应用。成功使用dd PCR和q PCR两种方法对KRAS野生型及7种突变型建立检测方法,使用质粒标准品及实际样品验证该两种方法可行并对其假阳性率、线性范围及检测下限等性能进行了评价,最后成功对52例临床患者和20例正常人的血浆cf DNA样本进行检测,临床灵敏度为97.64%,临床特异性为81.43%。dd PCR的检测性能优于q PCR,LOD达到个位数DNA拷贝,最低可确认突变浓度达到0.01%–0.04%。样本提取效率在方法学建立中也十分重要,直接影响到灵敏度和Cut Off值的判定。临床患者检测结果显示其KRAS突变率接近报道水平。 相似文献
74.
The monocyte locomotion inhibitory factor (MLIF) is an anti-inflammatory oligopeptide produced by Entamoeba histolytica. Among its different effects, it inhibits locomotion of human monocytes, hence its original name. The carboxyl-terminal end group Cys-Asn-Ser is the pharmacophore of anti-inflammatory peptide Met-Gln-Cys-Asn-Ser. In this study, the N-terminal of Cys-Asn-Ser was modified. With the aim to enhance the antioxidant ability and penetrability of Cys-Asn-Ser, we designed and synthesized two tetrapeptides Tyr-Cys-Asn-Ser and His-Cys-Asn-Ser. The neuroprotective effects of Tyr-Cys-Asn-Ser and His-Cys-Asn-Ser on focal ischemia reperfusion were investigated, and their pharmacological activities compared with Cys-Asn-Ser were studied. In order to study the mechanism of neuroprotective effect of these peptides, the level of oxidative stress markers malondialdehyde (MDA) and superoxide dismutase (SOD) and pro-inflammatory factors interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), and myeloperoxidase (MPO) were detected in brain tissue homogenate. 相似文献
75.
Yao Shi Juan Yuan Vilma Rraklli Eva Maxymovitz Miriam Cipullo Mingzhi Liu Shuijie Li Isabelle Westerlund Oscar C Bedoya-Reina Petra Bullova Joanna Rorbach C Christofer Juhlin Adam Stenman Catharina Larsson Per Kogner Maureen J OSullivan Susanne Schlisio Johan Holmberg 《Nucleic acids research》2021,49(5):2509
76.
Thomas M Davis Melanie E Shields Qian Zhang Denise Tombolato-Terzić Jeffrey L Bennetzen Ana C Pontaroli Hao Wang Qin Yao Phillip SanMiguel Kevin M Folta 《BMC plant biology》2010,10(1):81
Background
Strawberry (Fragaria spp.) is the familiar name of a group of economically important crop plants and wild relatives that also represent an emerging system for the study of gene and genome evolution. Its small stature, rapid seed-to-seed cycle, transformability and miniscule basic genome make strawberry an attractive system to study processes related to plant physiology, development and crop production; yet it lacks substantial genomics-level resources. This report addresses this deficiency by characterizing 0.71 Mbp of gene space from a diploid species (F. vesca). The twenty large genomic tracks (30-52 kb) captured as fosmid inserts comprise gene regions with roles in flowering, disease resistance, and metabolism. 相似文献77.
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79.
Li Y Schwabe RF DeVries-Seimon T Yao PM Gerbod-Giannone MC Tall AR Davis RJ Flavell R Brenner DA Tabas I 《The Journal of biological chemistry》2005,280(23):21763-21772
Two key features of atherosclerotic plaques that precipitate acute atherothrombotic vascular occlusion ("vulnerable plaques") are abundant inflammatory mediators and macrophages with excess unesterified, or "free," cholesterol (FC). Herein we show that FC accumulation in macrophages leads to the induction and secretion of two inflammatory cytokines, tumor necrosis factor-alpha (TNF-alpha) and interleukin-6 (IL-6). The increases in TNF-alpha and IL-6 mRNA and protein were mediated by FC-induced activation of the IkappaB kinase/NF-kappaB pathway as well as activation of MKK3/p38, Erk1/2, and JNK1/2 mitogen-activated protein kinases (MAPK). Activation of IkappaB kinase and JNK1/2 was needed for the induction of both cytokines. However, MKK3/p38 signaling was specifically involved in TNF-alpha induction, and Erk1/2 signaling was required for IL-6. Most interestingly, activation of all of the signaling pathways and induction of both cytokines required cholesterol trafficking to the endoplasmic reticulum (ER). The CHOP branch of the unfolded protein response, an ER stress pathway, was required for Erk1/2 activation and IL-6 induction. In contrast, one or more other ER-related pathways were responsible for activation of p38, JNK1/2, and IkappaB kinase/NF-kappaB and for the induction of TNF-alpha. These data suggest a novel scenario in which cytokines are induced in macrophages by endogenous cellular events triggered by excess ER cholesterol rather than by exogenous immune cell mediators. Moreover, this model may help explain the relationship between FC accumulation and inflammation in vulnerable plaques. 相似文献
80.