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101.
Resource limitation represents an important constraint on ecological communities, which restricts the total abundance, biomass, and community energy flux a given community can support. However, the exact relationship among these three measures of biological activity remains unclear. Here we use a simple framework that links abundance and biomass with an energetic constraint. Under constant energetic availability, it is expected that changes in abundance and biomass can result from shifts in the distribution of individual masses. We test these predictions using long-term data from a desert rodent community. Total energy use for the community has not changed directionally for 25 years, but species composition has. As a result, the average body size has decreased by almost 50%, and average abundance has doubled. These results lend support to the idea of resource limitation on desert rodent communities and demonstrate that systems are able to maintain community energy flux in the face of environmental change, through changes in composition and structure. 相似文献
102.
Callister SJ Barry RC Adkins JN Johnson ET Qian WJ Webb-Robertson BJ Smith RD Lipton MS 《Journal of proteome research》2006,5(2):277-286
Central tendency, linear regression, locally weighted regression, and quantile techniques were investigated for normalization of peptide abundance measurements obtained from high-throughput liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR MS). Arbitrary abundances of peptides were obtained from three sample sets, including a standard protein sample, two Deinococcus radiodurans samples taken from different growth phases, and two mouse striatum samples from control and methamphetamine-stressed mice (strain C57BL/6). The selected normalization techniques were evaluated in both the absence and presence of biological variability by estimating extraneous variability prior to and following normalization. Prior to normalization, replicate runs from each sample set were observed to be statistically different, while following normalization replicate runs were no longer statistically different. Although all techniques reduced systematic bias to some degree, assigned ranks among the techniques revealed that for most LC-FTICR-MS analyses linear regression normalization ranked either first or second. However, the lack of a definitive trend among the techniques suggested the need for additional investigation into adapting normalization approaches for label-free proteomics. Nevertheless, this study serves as an important step for evaluating approaches that address systematic biases related to relative quantification and label-free proteomics. 相似文献
103.
Threshold-dependent BMP-mediated repression: a model for a conserved mechanism that patterns the neuroectoderm 总被引:1,自引:0,他引:1
Subdivision of the neuroectoderm into three rows of cells along the dorsal-ventral axis by neural identity genes is a highly conserved developmental process. While neural identity genes are expressed in remarkably similar patterns in vertebrates and invertebrates, previous work suggests that these patterns may be regulated by distinct upstream genetic pathways. Here we ask whether a potential conserved source of positional information provided by the BMP signaling contributes to patterning the neuroectoderm. We have addressed this question in two ways: First, we asked whether BMPs can act as bona fide morphogens to pattern the Drosophila neuroectoderm in a dose-dependent fashion, and second, we examined whether BMPs might act in a similar fashion in patterning the vertebrate neuroectoderm. In this study, we show that graded BMP signaling participates in organizing the neural axis in Drosophila by repressing expression of neural identity genes in a threshold-dependent fashion. We also provide evidence for a similar organizing activity of BMP signaling in chick neural plate explants, which may operate by the same double negative mechanism that acts earlier during neural induction. We propose that BMPs played an ancestral role in patterning the metazoan neuroectoderm by threshold-dependent repression of neural identity genes. 相似文献
104.
Genome-wide association (GWA) studies are a powerful approach for identifying novel genetic risk factors associated with human
disease. A GWA study typically requires the inclusion of thousands of samples to have sufficient statistical power to detect
single nucleotide polymorphisms that are associated with only modest increases in risk of disease given the heavy burden of
a multiple test correction that is necessary to maintain valid statistical tests. Low statistical power and the high financial
cost of performing a GWA study remains prohibitive for many scientific investigators anxious to perform such a study using
their own samples. A number of remedies have been suggested to increase statistical power and decrease cost, including the
utilization of free publicly available genotype data and multi-stage genotyping designs. Herein, we compare the statistical
power and relative costs of alternative association study designs that use cases and screened controls to study designs that
are based only on, or additionally include, free public control genotype data. We describe a novel replication-based two-stage
study design, which uses free public control genotype data in the first stage and follow-up genotype data on case-matched
controls in the second stage that preserves many of the advantages inherent when using only an epidemiologically matched set
of controls. Specifically, we show that our proposed two-stage design can substantially increase statistical power and decrease
cost of performing a GWA study while controlling the type-I error rate that can be inflated when using public controls due
to differences in ancestry and batch genotype effects. 相似文献
105.
106.
Ethan A. Merritt Tracy L. Arakaki J. Robert Gillespie Eric T. Larson Angela Kelley Natascha Mueller Alberto J. Napuli Jessica Kim Li Zhang Christophe L.M.J. Verlinde Erkang Fan Frank Zucker Frederick S. Buckner Wesley C. Van Voorhis Wim G.J. Hol 《Journal of molecular biology》2010,397(2):481-494
Crystal structures of histidyl-tRNA synthetase (HisRS) from the eukaryotic parasites Trypanosoma brucei and Trypanosoma cruzi provide a first structural view of a eukaryotic form of this enzyme and reveal differences from bacterial homologs. HisRSs in general contain an extra domain inserted between conserved motifs 2 and 3 of the Class II aminoacyl-tRNA synthetase catalytic core. The current structures show that the three-dimensional topology of this domain is very different in bacterial and archaeal/eukaryotic forms of the enzyme. Comparison of apo and histidine-bound trypanosomal structures indicates substantial active-site rearrangement upon histidine binding but relatively little subsequent rearrangement after reaction of histidine with ATP to form the enzyme's first reaction product, histidyladenylate. The specific residues involved in forming the binding pocket for the adenine moiety differ substantially both from the previously characterized binding site in bacterial structures and from the homologous residues in human HisRSs. The essentiality of the single HisRS gene in T. brucei is shown by a severe depression of parasite growth rate that results from even partial suppression of expression by RNA interference. 相似文献
107.
Ozören N Masumoto J Franchi L Kanneganti TD Body-Malapel M Ertürk I Jagirdar R Zhu L Inohara N Bertin J Coyle A Grant EP Núñez G 《Journal of immunology (Baltimore, Md. : 1950)》2006,176(7):4337-4342
Apoptosis-associated speck-like protein containing a C-terminal caspase recruitment domain (ASC) is an adaptor molecule that has recently been implicated in the activation of caspase-1. We have studied the role of ASC in the host defense against the intracellular pathogen Listeria monocytogenes. ASC was found to be essential for the secretion of IL-1beta/IL-18, but dispensable for IL-6, TNF-alpha, and IFN-beta production, in macrophages infected with Listeria. Activation of caspase-1 was abolished in ASC-deficient macrophages, whereas activation of NF-kappaB and p38 was unaffected. In contrast, secretion of IL-1beta, IL-6, and TNF-alpha was reduced in TLR2-deficient macrophages infected with Listeria; this was associated with impaired activation of NF-kappaB and p38, but normal caspase-1 processing. Analysis of Listeria mutants revealed that cytosolic invasion was required for ASC-dependent IL-1beta secretion, consistent with a critical role for cytosolic signaling in the activation of caspase-1. Secretion of IL-1beta in response to lipopeptide, a TLR2 agonist, was greatly reduced in ASC-null macrophages and was abolished in TLR2-deficient macrophages. These results demonstrate that TLR2 and ASC regulate the secretion of IL-1beta via distinct mechanisms in response to Listeria. ASC, but not TLR2, is required for caspase-1 activation independent of NF-kappaB in Listeria-infected macrophages. 相似文献
108.
McGrath FD Brouwer MC Arlaud GJ Daha MR Hack CE Roos A 《Journal of immunology (Baltimore, Md. : 1950)》2006,176(5):2950-2957
C1q acts as the recognition unit of the first complement component, C1, and binds to immunoglobulins IgG and IgM, as well as to non-Ig ligands, such as C-reactive protein (CRP). IgG and IgM are recognized via the globular head regions of C1q (C1qGR), whereas CRP has been postulated to interact with the collagen-like region (C1qCLR). In the present study, we used a series of nine mAbs to C1q, five directed against C1qGR and four against C1qCLR, to inhibit the interaction of C1q with CRP. The F(ab')(2) of each of the five mAbs directed against C1qGR inhibited binding of C1q to polymerized IgG. These five mAbs also successfully inhibited the interaction of C1q with CRP. Moreover, these five mAbs inhibited C1 activation by CRP as well as by polymerized IgG in vitro. In contrast, none of the four mAbs against C1qCLR inhibited C1q interaction with CRP or IgG, or could reduce activation of complement by CRP or polymerized IgG. These results provide the first evidence that the interaction of C1q with CRP or IgG involves sites located in the C1qGR, whereas sites in the CLR do not seem to be involved in the physiological interaction of C1q with CRP. 相似文献
109.
Ischemia induces nuclear NOX2 expression in cardiomyocytes and subsequently activates apoptosis 总被引:1,自引:1,他引:0