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121.
Olivier Gascuel 《Journal of Classification》2000,17(1):67-99
O (n
4), where n is the number of objects. We describe the application of the MVR method to two data models: the weighted least-squares (WLS)
model (V is diagonal), where the MVR method can be reduced to an O(n
3) time complexity; a model arising from the study of biological sequences, which involves a complex non-diagonal V matrix
that is estimated from the dissimilarity matrix Δ. For both models, we provide simulation results that show a significant
error reduction in the reconstruction of T, relative to classical agglomerative algorithms. 相似文献
122.
Pierron G Tirode F Lucchesi C Reynaud S Ballet S Cohen-Gogo S Perrin V Coindre JM Delattre O 《Nature genetics》2012,44(4):461-466
The identification of subtype-specific translocations has revolutionized the diagnostics of sarcoma and has provided new insight into oncogenesis. We used RNA-seq to investigate samples from individuals diagnosed with small round cell tumors of bone, possibly Ewing sarcoma, but which lacked the canonical EWSR1-ETS translocation. A new fusion was observed between BCOR (encoding the BCL6 co-repressor) and CCNB3 (encoding the testis-specific cyclin B3) on the X chromosome. RNA-seq results were confirmed by RT-PCR and through cloning of the tumor-specific genomic translocation breakpoints. In total, 24 BCOR-CCNB3-positive tumors were identified among a series of 594 sarcoma cases. Gene profiling experiments indicated that BCOR-CCNB3-positive cases are biologically distinct from other sarcomas, particularly Ewing sarcoma. Finally, we show that CCNB3 immunohistochemistry is a powerful diagnostic marker for this subgroup of sarcoma and that overexpression of BCOR-CCNB3 or of truncated CCNB3 activates S phase in NIH3T3 cells. Thus, the intrachromosomal X-chromosome fusion described here represents a new subtype of bone sarcoma caused by a newly identified gene fusion mechanism. 相似文献
123.
The genome of Theobroma cacao 总被引:2,自引:0,他引:2
Argout X Salse J Aury JM Guiltinan MJ Droc G Gouzy J Allegre M Chaparro C Legavre T Maximova SN Abrouk M Murat F Fouet O Poulain J Ruiz M Roguet Y Rodier-Goud M Barbosa-Neto JF Sabot F Kudrna D Ammiraju JS Schuster SC Carlson JE Sallet E Schiex T Dievart A Kramer M Gelley L Shi Z Bérard A Viot C Boccara M Risterucci AM Guignon V Sabau X Axtell MJ Ma Z Zhang Y Brown S Bourge M Golser W Song X Clement D Rivallan R Tahi M Akaza JM Pitollat B Gramacho K D'Hont A Brunel D Infante D Kebe I Costet P 《Nature genetics》2011,43(2):101-108
We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions. 相似文献
124.
Intra- and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways 总被引:2,自引:0,他引:2
In RNA interference (RNAi), double-stranded RNA (dsRNA) is processed into short interfering RNA (siRNA) to mediate sequence-specific gene knockdown. The genetics of plant RNAi is not understood, nor are the bases for its spreading between cells. Here, we unravel the requirements for biogenesis and action of siRNAs directing RNAi in Arabidopsis thaliana and show how alternative routes redundantly mediate this process under extreme dsRNA dosages. We found that SMD1 and SMD2, required for intercellular but not intracellular RNAi, are allelic to RDR2 and NRPD1a, respectively, previously implicated in siRNA-directed heterochromatin formation through the action of DCL3 and AGO4. However, neither DCL3 nor AGO4 is required for non-cell autonomous RNAi, uncovering a new pathway for RNAi spreading or detection in recipient cells. Finally, we show that the genetics of RNAi is distinct from that of antiviral silencing and propose that this experimental silencing pathway has a direct endogenous plant counterpart. 相似文献
125.
Yeager M Orr N Hayes RB Jacobs KB Kraft P Wacholder S Minichiello MJ Fearnhead P Yu K Chatterjee N Wang Z Welch R Staats BJ Calle EE Feigelson HS Thun MJ Rodriguez C Albanes D Virtamo J Weinstein S Schumacher FR Giovannucci E Willett WC Cancel-Tassin G Cussenot O Valeri A Andriole GL Gelmann EP Tucker M Gerhard DS Fraumeni JF Hoover R Hunter DJ Chanock SJ Thomas G 《Nature genetics》2007,39(5):645-649
Recently, common variants on human chromosome 8q24 were found to be associated with prostate cancer risk. While conducting a genome-wide association study in the Cancer Genetic Markers of Susceptibility project with 550,000 SNPs in a nested case-control study (1,172 cases and 1,157 controls of European origin), we identified a new association at 8q24 with an independent effect on prostate cancer susceptibility. The most significant signal is 70 kb centromeric to the previously reported SNP, rs1447295, but shows little evidence of linkage disequilibrium with it. A combined analysis with four additional studies (total: 4,296 cases and 4,299 controls) confirms association with prostate cancer for rs6983267 in the centromeric locus (P = 9.42 x 10(-13); heterozygote odds ratio (OR): 1.26, 95% confidence interval (c.i.): 1.13-1.41; homozygote OR: 1.58, 95% c.i.: 1.40-1.78). Each SNP remained significant in a joint analysis after adjusting for the other (rs1447295 P = 1.41 x 10(-11); rs6983267 P = 6.62 x 10(-10)). These observations, combined with compelling evidence for a recombination hotspot between the two markers, indicate the presence of at least two independent loci within 8q24 that contribute to prostate cancer in men of European ancestry. We estimate that the population attributable risk of the new locus, marked by rs6983267, is higher than the locus marked by rs1447295 (21% versus 9%). 相似文献
126.
Michel M. Dacorogna Cindy L. Gauvreau Ulrich A. Müller Richard B. Olsen Olivier V. Pictet 《Journal of forecasting》1996,15(3):203-227
A forecasting model based on high-frequency market makers quotes of financial instruments is presented. The statistical behaviour of these time series leads to discussion of the appropriate time scale for forecasting. We introduce variable time scales in a general way and define the new concept of intrinsic time. The latter reflects better the actual trading activity. Changing time scale means forecasting in two steps, first an intrinsic time forecast against physical time, then a price forecast against intrinsic time. The forecasting model consists, for both steps, of a linear combination of non-linear price-based indicators. The indicator weights are continuously re-optimized through a modified linear regression on a moving sample of past prices. The out-of-sample performance of this algorithm is reported on a set of important FX rates and interest rates over many years. It is remarkably consistent. Results for short horizons as well as techniques to measure this performance are discussed. 相似文献
127.
One primary goal for metaphysical theories of natural kinds is to account for their epistemic fruitfulness. According to cluster theories of natural kinds, this epistemic fruitfulness is grounded in the regular and stable co-occurrence of a broad set of properties. In this paper, I defend the view that such a cluster theory is insufficient to adequately account for the epistemic fruitfulness of kinds. I argue that cluster theories can indeed account for the projectibility of natural kinds, but not for several other epistemic operations that natural kinds support. Natural kinds also play a role in scientific explanations and categorizations. A theory of natural kinds can only account for these additional kind-based epistemic practices if it also analyzes their causal structure. 相似文献
128.
There are three kinds of sources available to reconstruct the reflections that led Einstein to special relativity: a few contemporary letters and documents, his impersonal accounts of the genesis of this theory, and recollections of his own path. At first glance, contradictions within and between these sources hamper the reliability of Einstein’s accounts. Yet, a closer analysis reveals much more consistency than foreseen and helps eliminate the dubious, contradictory elements. It then becomes possible to combine the three kinds of sources to produce a minimally speculative and yet fairly coherent account of the genesis of special relativity. 相似文献
129.
Thomas G Jacobs KB Yeager M Kraft P Wacholder S Orr N Yu K Chatterjee N Welch R Hutchinson A Crenshaw A Cancel-Tassin G Staats BJ Wang Z Gonzalez-Bosquet J Fang J Deng X Berndt SI Calle EE Feigelson HS Thun MJ Rodriguez C Albanes D Virtamo J Weinstein S Schumacher FR Giovannucci E Willett WC Cussenot O Valeri A Andriole GL Crawford ED Tucker M Gerhard DS Fraumeni JF Hoover R Hayes RB Hunter DJ Chanock SJ 《Nature genetics》2008,40(3):310-315
130.
Olivier GALLAY~ Max-Olivier HONGLER~ ~STI-IPR-LPM Station BM . Ecole Polytechnique Fédérale de Lausanne 《系统科学与系统工程学报(英文版)》2008,17(2):241-254
We consider queueing networks (QN's) with feedback loops roamed by "intelligent" agents, able to select their routing on the basis of their measured waiting times at the QN nodes. This is an idealized model to discuss the dynamics of customers who stay loyal to a service supplier, provided their service time remains below a critical threshold. For these QN's, we show that the traffic flows may exhibit collective patterns typically encountered in multi-agent systems. In simple network topologies, the emergent cooperative behaviors manifest themselves via stable macroscopic temporal oscillations, synchronization of the queue contents and stabilization by noise phenomena. For a wide range of control parameters, the underlying presence of the law of large numbers enables us to use deterministic evolution laws to analytically characterize the cooperative evolution of our multi-agent systems. In particular, we study the case where the servers are sporadically subject, to failures altering their ordinary behavior. 相似文献