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981.
Bordewich M Semple C 《IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM》2008,5(2):275-280
The Nature Reserve Selection Problem is a problem that arises in the context of studying biodiversity conservation. Subject to budgetary constraints, the problem is to select a set of regions to conserve so that the phylogenetic diversity of the set of species contained within those regions is maximized. Recently, it was shown in a paper by Moulton et al. that this problem is NP-hard. In this paper, we establish a tight polynomial-time approximation algorithm for the Nature Reserve Section Problem. Furthermore, we resolve a question on the computational complexity of a related problem left open in Moulton et al. 相似文献
982.
983.
Fujimoto R Kinoshita Y Kawabe A Kinoshita T Takashima K Nordborg M Nasrallah ME Shimizu KK Kudoh H Kakutani T 《PLoS genetics》2008,4(4):e1000048
A central question in genomic imprinting is how a specific sequence is recognized as the target for epigenetic marking. In both mammals and plants, imprinted genes are often associated with tandem repeats and transposon-related sequences, but the role of these elements in epigenetic gene silencing remains elusive. FWA is an imprinted gene in Arabidopsis thaliana expressed specifically in the female gametophyte and endosperm. Tissue-specific and imprinted expression of FWA depends on DNA methylation in the FWA promoter, which is comprised of two direct repeats containing a sequence related to a SINE retroelement. Methylation of this element causes epigenetic silencing, but it is not known whether the methylation is targeted to the SINE-related sequence itself or the direct repeat structure is also necessary. Here we show that the repeat structure in the FWA promoter is highly diverse in species within the genus Arabidopsis. Four independent tandem repeat formation events were found in three closely related species. Another related species, A. halleri, did not have a tandem repeat in the FWA promoter. Unexpectedly, even in this species, FWA expression was imprinted and the FWA promoter was methylated. In addition, our expression analysis of FWA gene in vegetative tissues revealed high frequency of intra-specific variation in the expression level. In conclusion, we show that the tandem repeat structure is dispensable for the epigenetic silencing of the FWA gene. Rather, SINE-related sequence is sufficient for imprinting, vegetative silencing, and targeting of DNA methylation. Frequent independent tandem repeat formation events in the FWA promoter led us to propose that they may be a consequence, rather than cause, of the epigenetic control. The possible significance of epigenetic variation in reproductive strategies during evolution is also discussed. 相似文献
984.
985.
Harikrishnan LS Kamau MG Herpin TF Morton GC Liu Y Cooper CB Salvati ME Qiao JX Wang TC Adam LP Taylor DS Chen AY Yin X Seethala R Peterson TL Nirschl DS Miller AV Weigelt CA Appiah KK O'Connell JC Michael Lawrence R 《Bioorganic & medicinal chemistry letters》2008,18(8):2640-2644
2-Arylbenzoxazole 5 was identified as a hit from a fluorescence-based high-throughput screen for CETP inhibitors. The synthesis and SAR investigation employing array synthesis of the A- and B-rings are described. 相似文献
986.
The pine-oak woodlands of the Mexican highlands harbour significant biological diversity, yet little is known about the evolutionary history of organisms inhabiting this region. We assessed genetic and phenotypic differentiation in 482 individuals representing 27 populations of the Mexican jay ( Aphelocoma ultramarina ) — a widespread bird species of the Mexican highlands — to test whether populations in the central and northern Mexican sierras display discrete breaks between groups, which would be consistent with a role for the different mountain chains in divergence and speciation. We found abrupt breaks in mitochondrial DNA (mtDNA; ND2 and control region) delineating four major genetic groups found in the Sierra Madre Occidental, Sierra Madre Oriental, southern Central Plateau (Bajio), and Transvolcanic Belt. These mtDNA groups were largely corroborated by data from nuclear microsatellites and phenotypic data, except that clades from the Central Plateau and Sierra Madre Oriental showed clinal change in these data sets. Uncertainty about the mutation rate for our mitochondrial markers warrants considerable caution with regard to estimating divergence times, but the major genetic groups appear to have split before the most extreme period of glacial cycling that marked the last 0.7 million years and after Mexico's period of major mountain formation. The fact that some genetic breaks do not coincide with well-known geographic barriers suggests a role for ecology in divergence and speciation, and we discuss implications for taxonomy and conservation. 相似文献
987.
Truhlar SM Cervantes CF Torpey JW Kjaergaard M Komives EA 《Protein science : a publication of the Protein Society》2008,17(9):1636-1639
Advances in NMR spectroscopy have enabled the study of larger proteins that typically have significant overlap in their spectra. Specific (15)N-amino acid incorporation is a powerful tool for reducing spectral overlap and attaining reliable sequential assignments. However, scrambling of the label during protein expression is a common problem. We describe a rapid method to evaluate the fidelity of specific (15)N-amino acid incorporation. The selectively labeled protein is proteolyzed, and the resulting peptides are analyzed using MALDI mass spectrometry. The (15)N incorporation is determined by analyzing the isotopic abundance of the peptides in the mass spectra using the program DEX. This analysis determined that expression with a 10-fold excess of unlabeled amino acids relative to the (15)N-amino acid prevents the scrambling of the (15)N label that is observed when equimolar amounts are used. MALDI TOF-TOF MS/MS data provide additional information that shows where the "extra" (15)N labels are incorporated, which can be useful in confirming ambiguous assignments. The described procedure provides a rapid technique to monitor the fidelity of selective labeling that does not require a lot of protein. These advantages make it an ideal way of determining optimal expression conditions for selectively labeled NMR samples. 相似文献
988.
Peterson KJ Cotton JA Gehling JG Pisani D 《Philosophical transactions of the Royal Society of London. Series B, Biological sciences》2008,363(1496):1435-1443
Unravelling the timing of the metazoan radiation is crucial for elucidating the macroevolutionary processes associated with the Cambrian explosion. Because estimates of metazoan divergence times derived from molecular clocks range from quite shallow (Ediacaran) to very deep (Mesoproterozoic), it has been difficult to ascertain whether there is concordance or quite dramatic discordance between the genetic and geological fossil records. Here, we show using a range of molecular clock methods that the major pulse of metazoan divergence times was during the Ediacaran, which is consistent with a synoptic reading of the Ediacaran macrobiota. These estimates are robust to changes in priors, and are returned with or without the inclusion of a palaeontologically derived maximal calibration point. Therefore, the two historical records of life both suggest that although the cradle of Metazoa lies in the Cryogenian, and despite the explosion of ecology that occurs in the Cambrian, it is the emergence of bilaterian taxa in the Ediacaran that sets the tempo and mode of macroevolution for the remainder of geological time. 相似文献
989.
In this study the distance, at which polar bears detected and actively responded to approaching snowmobiles was measured and
the behavioural response was recorded. The study was performed on Svalbard, an arctic island where human traffic has increased
substantially in recent years. Fieldwork was conduced in April and/or May during the years 2003–2005. Polar bears were observed
on ice with telescopes and binoculars. Undisturbed polar bears were observed continuously and their behaviours recorded, during
the time when two snowmobiles moved toward the bear(s). Distances between the bear, the observer, and the approaching snowmobiles
were measured using GPS positions taken on the track towards the bear. Data on the behavioural response of 20 encounters with
bears were collected. On average, bears were alerted to the snowmobiles at 1,164 m. Mean distance at which the locomotive
response occurred was 843 m, and there was a statistical significant difference in distance between sex and age classes [326 m
(95% CI = 138–496 m) for adult males; 1,534 m (95% CI = 508–2,768 m) for adult females with cubs; 164 m (95% CI = 49–543 m)
for two adult females without cubs; and 1,160 m (95% CI = 375–1,353 m) for single medium sized bears]. The responses of the
polar bears to the snowmobiles were categorized according to intensity and persistence of reactions. Females with cubs and
single medium sized bears tended to show more intense responses than adult males and lone adult females. Wind direction affects
sound and odour transmission, and although an effect on response distance was not found, the response intensity was affected
by wind direction. We conclude that female polar bears with small cubs in particular may have a greater risk to be disturbed,
since they react at greater distances with amplified reactions; thus, users of snowmobiles should take particular care in
areas where females with cubs are present. 相似文献
990.
Until recently, studies on polar bear (Ursus maritimus) movements and space use have used data collected by satellite telemetry collars that provided positions infrequently (typically
weekly) and with low precision (by Doppler Shift method). A new generation of transmitters incorporated into collars use the
Global Positioning System (GPS) to provide highly accurate positions, and have the ability to provide many positions per day.
We used data from two GPS collars fitted to female polar bears, that attempted to collect six positions per day (4-h apart)
for 546 days (from April 2000 to September 2001) and 413 days (from April 2000 to May 2001) to estimate how estimated speed
of movement and home range size increase with increasing number of data points. Using all the positions, we estimated that
the bears moved a minimum of 14.3 and 15.8 km per day on average. The fractal dimension (D) of the movement pathways for the two bears were D = 1.28 and 1.31, respectively, indicating low tortousity of the movements. Their minimum estimated annual home range areas
were 20,794 and 112,183 km2. Simulations showed that a commonly used sampling regime of one location every 6th day would have significantly underestimated
the movement rates and the home range sizes compared to our estimates. We also used the high accuracy of GPS positions to
look at distances moved within 4-h periods. Maximum movement rate during a 4-h period for the two bears was 4.21 and 4.58 km/h,
respectively. Variation in median values by month was significant (0.01 km/h in November for N23476 to 1.48 km/h in December
for N7955). Diurnal variation was observed to differ between defined periods. 相似文献