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81.
82.
Recycling of the asialoglycoprotein receptor in isolated rat hepatocytes. ATP depletion blocks receptor recycling but not a single round of endocytosis 总被引:14,自引:0,他引:14
Continuous endocytosis of 125I-asialo-orosomucoid (ASOR) mediated by the galactosyl receptor in rat hepatocytes is a cyclic process. 125I-ASOR-receptor complexes are internalized, processed, and the ligand is degraded while the receptor is returned to the cell surface for reutilization. Since a true cycle has a thermodynamic requirement for the input of external energy, we examined the effects of changes in intracellular ATP levels on the function of the receptor cycle. Hepatocytes were depleted of ATP to various extents prior to endocytosis by incubating cells at 15 degrees C in the presence of 2 mM NaF and 0-20 mM NaN3. A luciferase-luciferin bioluminescence assay was used to quantitate the amount of cellular ATP. ATP-depleted cells were allowed to bind 125I-ASOR at 0 degrees C, washed through discontinuous Percoll gradients, and only viable cells were isolated and incubated at 37 degrees C to initiate a synchronous single round of endocytosis. The extent of internalization of this surface-bound 125I-ASOR was unaffected by an ATP depletion to less than 1% of the control level. The rate of internalization of surface-bound ligand was unaffected until the ATP levels decreased to 30% or less; at greater than 98% ATP depletion the initial rate decreased by a maximum of 55% and the kinetics became biphasic. In contrast, continuous endocytosis in the presence of excess ASOR was inhibited by only a 25% decline in cellular ATP content and demonstrated a very sharp threshold response to changing ATP levels. Continuous endocytosis, which requires receptor recycling, was completely inhibited when the total cellular ATP level decreased by only 40%. We conclude that the internalization phase of endocytosis is not dependent on ATP but that the processing and/or externalization phases of the complete receptor cycle are either directly or indirectly dependent on ATP and very sensitive to changes in cellular ATP content. 相似文献
83.
Specific recognition of altered polypeptides by widely distributed methyltransferases 总被引:6,自引:0,他引:6
Protein carboxyl methyltransferase activity has been detected in extracts prepared from bacterial cells (Salmonella typhimurium), amphibian (Xenopus laevis) oocytes, and transformed mammalian cell lines. This activity appears to specifically recognize altered aspartyl residues based on the observation that the synthetic peptide L-Val-L-Tyr-L-Pro-L-isoAsp-Gly-L-Ala is a good methyl-accepting substrate for the methyltransferase activity, but that the corresponding peptide containing a normal L-aspartyl residue is not. These activities are similar to those of the previously described human erythrocyte and bovine brain enzymes which catalyze the formation of polypeptide D-aspartyl beta-methyl esters and L-isoaspartyl alpha-methyl esters. The wide distribution of these enzymatic activites suggest that the methylation of atypical proteins is an essential function in cells. 相似文献
84.
Dale G. Nimmo Sarah Avitabile Sam C. Banks Rebecca Bliege Bird Kate Callister Michael F. Clarke Chris R. Dickman Tim S. Doherty Don A. Driscoll Aaron C. Greenville Angie Haslem Luke T. Kelly Sally A. Kenny Jos J. Lahoz‐Monfort Connie Lee Steven Leonard Harry Moore Thomas M. Newsome Catherine L. Parr Euan G. Ritchie Kathryn Schneider James M. Turner Simon Watson Martin Westbrooke Mike Wouters Matthew White Andrew F. Bennett 《Biological reviews of the Cambridge Philosophical Society》2019,94(3):981-998
Movement is a trait of fundamental importance in ecosystems subject to frequent disturbances, such as fire‐prone ecosystems. Despite this, the role of movement in facilitating responses to fire has received little attention. Herein, we consider how animal movement interacts with fire history to shape species distributions. We consider how fire affects movement between habitat patches of differing fire histories that occur across a range of spatial and temporal scales, from daily foraging bouts to infrequent dispersal events, and annual migrations. We review animal movements in response to the immediate and abrupt impacts of fire, and the longer‐term successional changes that fires set in train. We discuss how the novel threats of altered fire regimes, landscape fragmentation, and invasive species result in suboptimal movements that drive populations downwards. We then outline the types of data needed to study animal movements in relation to fire and novel threats, to hasten the integration of movement ecology and fire ecology. We conclude by outlining a research agenda for the integration of movement ecology and fire ecology by identifying key research questions that emerge from our synthesis of animal movements in fire‐prone ecosystems. 相似文献
85.
Badr Benjelloun Frdric Boyer Ian Streeter Wahid Zamani Stefan Engelen Adriana Alberti Florian J. Alberto Mohamed BenBati Mustapha Ibnelbachyr Mouad Chentouf Abdelmajid Bechchari Hamid R. Rezaei Saeid Naderi Alessandra Stella Abdelkader Chikhi Laura Clarke James Kijas Paul Flicek Pierre Taberlet Franois Pompanon 《Molecular ecology resources》2019,19(6):1497-1515
Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low‐coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high‐density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low‐density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes. 相似文献
86.
Heena Dhiman Matthias P. Gerstl David Ruckerbauer Michael Hanscho Heinz Himmelbauer Colin Clarke Niall Barron Jürgen Zanghellini Nicole Borth 《Biotechnology journal》2019,14(7)
The increasingdemandfor biopharmaceutical products drives the search for efficient cell factories that are able to sustainably support rapid growth, high productivity, and product quality. As these depend on energy generation, here the genomic variation in nuclear genes associated with mitochondria and energy metabolism and the mitochondrial genome of 14 cell lines is investigated. The variants called enable reliable tracing of lineages. Unique sequence variations are observed in cell lines adapted to grow in protein‐free media, enriched in signaling pathways or mitogen‐activated protein kinase 3. High‐producing cell lines bear unique mutations in nicotinamide adenine dinucleotide (NADH) dehydrogenase (ND2 and ND4) and in peroxisomal acyl‐CoA synthetase (ACSL4), involved in lipid metabolism. As phenotypes are determined not only by functional mutations, but also by the exquisite regulation of expression patterns, it is not surprising that ≈50% of the genes investigated here are found to be differentially methylated and thus epigenetically controlled, enabling a clear distinction of high producers, and cells adapted to a minimal, glutamine (Gln)‐free medium. Similar pathways are enriched as those identified by genome variation. This strengthens the hypothesis that these phenomena act together to define cell behavior. 相似文献
87.
Diana A. Robledo-Ruiz Alexandra Pavlova Rohan H. Clarke Michael J. L. Magrath Bruce Quin Katherine A. Harrisson Han Ming Gan Gabriel W. Low Paul Sunnucks 《Molecular ecology resources》2022,22(1):239-253
Conservation breeding management aims to reduce inbreeding and maximize the retention of genetic diversity in endangered populations. However, breeding management of wild populations is still rare, and there is a need for approaches that provide data-driven evidence of the likelihood of success of alternative in situ strategies. Here, we provide an analytical framework that uses in silico simulations to evaluate, for real wild populations, (i) the degree of population-level inbreeding avoidance, (ii) the genetic quality of mating pairs, and (iii) the potential genetic benefits of implementing two breeding management strategies. The proposed strategies aim to improve the genetic quality of breeding pairs by splitting detrimental pairs and allowing the members to re-pair in different ways. We apply the framework to the wild population of the Critically Endangered helmeted honeyeater by combining genomic data and field observations to estimate the inbreeding (i.e., pair-kinship) and genetic quality (i.e., Mate Suitability Index) of all mating pairs for seven consecutive breeding seasons. We found no evidence of population-level inbreeding avoidance and that ~91.6% of breeding pairs were detrimental to the genetic health of the population. Furthermore, the framework revealed that neither proposed management strategy would significantly improve the genetic quality or reduce inbreeding of the mating pairs in this population. Our results demonstrate the usefulness of our analytical framework for testing the efficacy of different in situ breeding management strategies and for making evidence-based management decisions. 相似文献
88.
Swan L. S. Sow Mark V. Brown Laurence J. Clarke Andrew Bissett Jodie van de Kamp Thomas W. Trull Eric J. Raes Justin R. Seymour Anna R. Bramucci Martin Ostrowski Philip W. Boyd Bruce E. Deagle Paula C. Pardo Bernadette M. Sloyan Levente Bodrossy 《Environmental microbiology》2022,24(5):2449-2466
We investigated the Southern Ocean (SO) prokaryote community structure via zero-radius operational taxonomic unit (zOTU) libraries generated from 16S rRNA gene sequencing of 223 full water column profiles. Samples reveal the prokaryote diversity trend between discrete water masses across multiple depths and latitudes in Indian (71–99°E, summer) and Pacific (170–174°W, autumn-winter) sectors of the SO. At higher taxonomic levels (phylum-family) we observed water masses to harbour distinct communities across both sectors, but observed sectorial variations at lower taxonomic levels (genus-zOTU) and relative abundance shifts for key taxa such as Flavobacteria, SAR324/Marinimicrobia, Nitrosopumilus and Nitrosopelagicus at both epi- and bathy-abyssopelagic water masses. Common surface bacteria were abundant in several deep-water masses and vice-versa suggesting connectivity between surface and deep-water microbial assemblages. Bacteria from same-sector Antarctic Bottom Water samples showed patchy, high beta-diversity which did not correlate well with measured environmental parameters or geographical distance. Unconventional depth distribution patterns were observed for key archaeal groups: Crenarchaeota was found across all depths in the water column and persistent high relative abundances of common epipelagic archaeon Nitrosopelagicus was observed in deep-water masses. Our findings reveal substantial regional variability of SO prokaryote assemblages that we argue should be considered in wide-scale SO ecosystem microbial modelling. 相似文献
89.
Colin Clarke Clair Gallagher Ronan M. Kelly Michael Henry Paula Meleady Christopher C. Frye Matthew D. Osborne Ciaran P Brady Niall Barron Martin Clynes 《Biotechnology and bioengineering》2019,116(6):1556-1562
In this study, we report an investigation of a panel of clonally-derived Chinese hamster ovary (CHO) cell lines exhibiting variability in the proportion of full-length IgG4 Fc-fusion protein produced. The recombinant protein was found to be degraded during cell culture into four shorter “clipped” species (three of the four cleavage sites occurred at arginine residues) and preliminary analyses suggested that a host cell enzyme was responsible for proteolysis. To identify the specific enzyme responsible, RNA sequencing was used to identify gene expression differences between the cell lines with a “high” and “low” clipping phenotype. From this analysis, six protease-encoding genes were found to be significantly upregulated in those cell lines yielding the lowest proportion of full-length IgG4 Fc-fusion protein. Four of these protease candidates were deprioritized after examination of their cleavage site specificity. The remaining enzymes, Adam19 and Furin, were found to be capable of cleavage at arginine residues, and inhibitors for both proteases were added to cell-free media to determine if the product degradation could be reduced. While the Adam19 inhibitor had no impact, Furin inhibitor I (specific for the proprotein convertase family of enzymes) was found to result in a 33–39% increase in complete IgG4 Fc-fusion protein when compared with untreated samples. 相似文献
90.
Tom?Ashmore Lee?D.?Roberts Andrea?J.?Morash Aleksandra?O.?Kotwica John?Finnerty James?A.?West Steven?A.?Murfitt Bernadette?O.?Fernandez Cristina?Branco Andrew?S.?Cowburn Kieran?Clarke Randall?S.?Johnson Martin?Feelisch Julian?L.?Griffin Andrew?J.?MurrayEmail author 《BMC biology》2015,13(1):110