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941.
942.
RNAmmer: consistent and rapid annotation of ribosomal RNA genes 总被引:7,自引:0,他引:7
Lagesen K Hallin P Rødland EA Staerfeldt HH Rognes T Ussery DW 《Nucleic acids research》2007,35(9):3100-3108
The publication of a complete genome sequence is usually accompanied by annotations of its genes. In contrast to protein coding genes, genes for ribosomal RNA (rRNA) are often poorly or inconsistently annotated. This makes comparative studies based on rRNA genes difficult. We have therefore created computational predictors for the major rRNA species from all kingdoms of life and compiled them into a program called RNAmmer. The program uses hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project. A pre-screening step makes the method fast with little loss of sensitivity, enabling the analysis of a complete bacterial genome in less than a minute. Results from running RNAmmer on a large set of genomes indicate that the location of rRNAs can be predicted with a very high level of accuracy. Novel, unannotated rRNAs are also predicted in many genomes. The software as well as the genome analysis results are available at the CBS web server. 相似文献
943.
944.
Gilbert MT Djurhuus D Melchior L Lynnerup N Worobey M Wilson AS Andreasen C Dissing J 《American journal of physical anthropology》2007,133(2):847-853
The 15th century Inuit mummies excavated at Qilakitsoq in Greenland in 1978 were exceptionally well preserved and represent the largest find of naturally mummified specimens from the Arctic. The estimated ages of the individuals, their distribution between two adjacent graves, the results of tissue typing, and incomplete STR results led researchers to conclude that the eight mummies formed two distinct family groups: A grandmother (I/5), two daughters (I/3, I/4), and their two children (I/1, I/2) in one grave, and two sisters (II/6, II/8) and a daughter (II/7) of one of them in the other. Using mtDNA from hair and nail, we have reanalyzed the mummies. The results allowed the unambiguous assignment of each of the mummies to one of three mtDNA haplogroups: A2b (I/5); A2a (I/2, I/3, II/6, II/8); A2a-311 (I/1, I/4, II/7), excluded some of the previous relations, and pointed to new ones. I/5 is not the grandmother/mother of the individuals in Grave I, and she is not maternally related to any of the seven other mummies; I/3 and I/4 are not sisters and II/7 is neither the daughter of II/6 nor of II/8. However, I/1 may be the child of either I/4 or II/7 and these two may be sisters. I/2 may be the son of I/3, who may be the daughter of either II/6 or II/8, and these two may be sisters. The observation of haplogroups A2a and A2b amongst the 550-year-old Inuit puts a lower limit on the age of the two lineages in Greenland. 相似文献
945.
946.
A Wetland Change Model has been developed to identify the vulnerability of coastal wetlands at broad spatial (regional to
global (mean spatial resolution of 85 km)) and temporal scales (modelling period of 100 years). The model provides a dynamic
and integrated assessment of wetland loss, and a means of estimating the transitions between different vegetated wetland types
and open water under a range of scenarios of sea-level rise and changes in accommodation space from human intervention. This
paper is an overview of key issues raised in the process of quantifying broad-scale vulnerabilities of coastal wetlands to
forcing from sea-level rise discussing controlling factors of tidal range, sediment availability and accommodation space,
identification of response lags and defining the threshold for wetland loss and transition. 相似文献
947.
The intentional introduction of red king crab, Paralithodes camtschatica (Tilesius, 1815) in the Barents Sea represent one of a few successful cases and one that now supports a commercial fishery.
Introductions of alien species into new environments are often associated with genetic bottlenecks, which cause a reduction
in the genetic variation, and this could be important for the spreading potential of the species in the Atlantic Ocean. Red
king crab samples collected in the Varangerfjord located on the Barents Sea (northern Norway) were compared with reference
crab samples collected from the Bering Sea and Kamchatka regions in the Pacific Ocean. All samples were screened for eleven
microsatellite loci, based on the development of species-specific primers. The observed number of alleles per locus was similar,
and no reduction in genetic variation, including gene diversity and allelic richness, was detected between the Varangerfjord
sample and the reference sample from Okhotsk Sea near Kamchatka, indicating no genetic bottlenecking at least for the microsatellite
loci investigated. The same results were found in comparison with the sample from Bering Sea. The level of genetic differentiation
among the samples, measured as overall F
ST
across all loci, was relatively low (0.0238) with a range of 0.0035–0.1000 for the various loci investigated. The largest
pairwise F
ST
values were found between the Bering Sea and Varangerfjord/Barents Sea samples, with a value of 0.0194 across all loci tested.
The lowest value (0.0101) was found between the Varangerfjord and Kamchatka samples. Genetic differentiation based on exact
tests on allele frequencies revealed highly significant differences between all pairwise comparisons. The high level of genetic
variation found in the Varangerfjord/Barents Sea sample could be of significance with respect to further spreading of the
species to other regions in the North Atlantic Ocean. 相似文献
948.
Knut E. Jørstad P. A. Prodohl A.-L. Agnalt M. Hughes E. Farestveit A. F. Ferguson 《Hydrobiologia》2007,590(1):103-114
American lobsters (Homarus americanus H. Milne Edwards, 1837) are imported live to Europe and should according regulations be kept in land-based tanks until sold. In spite of the strict regulations aimed specifically at preventing the introduction of this species into the NE Atlantic, several specimens of H. americanus have been captured in the wild, especially in Oslofjord, Norway since 1999. One of the great concerns is interbreeding between the introduced American species and the local European lobster, H. gammarus (Linnaeus, 1758). For this reason an awareness campaign was launched in 2000 focusing on morphologically “unusual” lobsters caught in local waters. Morphological characters have been based on colour and sub-ventral spines on the rostrum. Two samples of H. americanus were used for comparisons, as well as samples of European lobster from Oslofjord collected in 1992. Previous genetic analyses (allozymes, mtDNA and microsatellite DNA) have demonstrated that the American lobster is distinct from its European counterpart, with several additional alleles at many loci in addition to different allelic frequency distribution of alleles of “shared” alleles. During the present study, thirteen microsatellite loci were tested in the initial screening, and the three most discriminating loci (Hgam98, Hgam197b and Hgam47b) were used in a detailed comparison between the two species. A total of 45 unusual lobsters were reported captured from Ålesund (west) to Oslofjord (southeast) from 2001 to 2005 and these were analysed for the three microsatellite loci. Nine specimens were identified as American lobsters. Comparisons between morphological and genetic characteristics revealed that morphological differences are not reliable in discrimination the two species, or to identify hybrids. Further, some loci display almost no overlapping in allele frequency distribution for the reference samples analysed, thus providing a reliable tool to identify hybrids. 相似文献
949.
The pollen grains of Ambrosia spp. are considered to be important aeroallergens in parts of southern and central Europe. Back-trajectories have been analysed
with the aim of finding the likely sources of Ambrosia pollen grains that arrived at Poznań (Poland). Temporal variations in Ambrosia pollen at Poznań from 1995–2005 were examined in order to identify Ambrosia pollen episodes suitable for further investigation using back-trajectory analysis. The trajectories were calculated using
the transport model within the Lagrangian air pollution model, ACDEP (Atmospheric Chemistry and Deposition). Analysis identified
two separate populations in Ambrosia pollen episodes, those that peaked in the early morning between 4 a.m. and 8 a.m., and those that peaked in the afternoon
between 2 p.m. and 6 p.m.. Six Ambrosia pollen episodes between 2001 and 2005 were examined using back-trajectory analysis. The results showed that Ambrosia pollen episodes that peaked in the early morning usually arrived at Poznań from a southerly direction after passing over
southern Poland, the Czech Republic, Slovakia and Hungary, whereas air masses that brought Ambrosia pollen to Poznań during the afternoon arrived from a more easterly direction and predominantly stayed within the borders
of Poland. Back-trajectory analysis has shown that there is a possibility that long-range transport brings Ambrosia pollen to Poznań from southern Poland, the Czech Republic, Slovakia and Hungary. There is also a likelihood that Ambrosia is present in Poland, as shown by the arrival of pollen during the afternoon that originated primarily from within the country. 相似文献
950.
The extended Moran effect and large-scale synchronous fluctuations in the size of great tit and blue tit populations 总被引:1,自引:0,他引:1
Saether BE Engen S Grøtan V Fiedler W Matthysen E Visser ME Wright J Møller AP Adriaensen F van Balen H Balmer D Mainwaring MC McCleery RH Pampus M Winkel W 《The Journal of animal ecology》2007,76(2):315-325
1. Synchronous fluctuations of geographically separated populations are in general explained by the Moran effect, i.e. a common influence on the local population dynamics of environmental variables that are correlated in space. Empirical support for such a Moran effect has been difficult to provide, mainly due to problems separating out effects of local population dynamics, demographic stochasticity and dispersal that also influence the spatial scaling of population processes. Here we generalize the Moran effect by decomposing the spatial autocorrelation function for fluctuations in the size of great tit Parus major and blue tit Cyanistes caeruleus populations into components due to spatial correlations in the environmental noise, local differences in the strength of density regulation and the effects of demographic stochasticity. 2. Differences between localities in the strength of density dependence and nonlinearity in the density regulation had a small effect on population synchrony, whereas demographic stochasticity reduced the effects of the spatial correlation in environmental noise on the spatial correlations in population size by 21.7% and 23.3% in the great tit and blue tit, respectively. 3. Different environmental variables, such as beech mast and climate, induce a common environmental forcing on the dynamics of central European great and blue tit populations. This generates synchronous fluctuations in the size of populations located several hundred kilometres apart. 4. Although these environmental variables were autocorrelated over large areas, their contribution to the spatial synchrony in the population fluctuations differed, dependent on the spatial scaling of their effects on the local population dynamics. We also demonstrate that this effect can lead to the paradoxical result that a common environmental variable can induce spatial desynchronization of the population fluctuations. 5. This demonstrates that a proper understanding of the ecological consequences of environmental changes, especially those that occur simultaneously over large areas, will require information about the spatial scaling of their effects on local population dynamics. 相似文献