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71.
Deciphering the genomic architecture of the stickleback brain with a novel multilocus gene‐mapping approach
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Zitong Li Baocheng Guo Jing Yang Gábor Herczeg Abigél Gonda Gergely Balázs Takahito Shikano Federico C. F. Calboli Juha Merilä 《Molecular ecology》2017,26(6):1557-1575
Quantitative traits important to organismal function and fitness, such as brain size, are presumably controlled by many small‐effect loci. Deciphering the genetic architecture of such traits with traditional quantitative trait locus (QTL) mapping methods is challenging. Here, we investigated the genetic architecture of brain size (and the size of five different brain parts) in nine‐spined sticklebacks (Pungitius pungitius) with the aid of novel multilocus QTL‐mapping approaches based on a de‐biased LASSO method. Apart from having more statistical power to detect QTL and reduced rate of false positives than conventional QTL‐mapping approaches, the developed methods can handle large marker panels and provide estimates of genomic heritability. Single‐locus analyses of an F2 interpopulation cross with 239 individuals and 15 198, fully informative single nucleotide polymorphisms (SNPs) uncovered 79 QTL associated with variation in stickleback brain size traits. Many of these loci were in strong linkage disequilibrium (LD) with each other, and consequently, a multilocus mapping of individual SNPs, accounting for LD structure in the data, recovered only four significant QTL. However, a multilocus mapping of SNPs grouped by linkage group (LG) identified 14 LGs (1–6 depending on the trait) that influence variation in brain traits. For instance, 17.6% of the variation in relative brain size was explainable by cumulative effects of SNPs distributed over six LGs, whereas 42% of the variation was accounted for by all 21 LGs. Hence, the results suggest that variation in stickleback brain traits is influenced by many small‐effect loci. Apart from suggesting moderately heritable (h2 ≈ 0.15–0.42) multifactorial genetic architecture of brain traits, the results highlight the challenges in identifying the loci contributing to variation in quantitative traits. Nevertheless, the results demonstrate that the novel QTL‐mapping approach developed here has distinctive advantages over the traditional QTL‐mapping methods in analyses of dense marker panels. 相似文献
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Tatsuya Uezu Sae Kakutani Akino Nakajima Yoshiomi Takagi 《Journal of theoretical biology》2009,258(2):281-288
The clone of the ciliated protozoan Paramecium caudatum has the immaturity period of about 60 fissions and the lifespan of about 600 fissions. These life cycle figures have been depicted through laboratory experiments that allow continuous cell divisions for hundreds, which never occur in nature. We here constructed the nature-mimicking model culture that alternated the log- and stationary phases to allow conjugation, and computer-simulated the age structure modifying parameters such as cell distributions to start the culture, fission rates, death rates, immaturity periods, probabilities of conjugation, proportions of transplantation and so on. The average and maximum ages in the culture after thousands of alternations were converged to 43±2 and 140±5 fissions, respectively, when parameters for the immaturity period and the maximum clonal lifespan were set at 60 and 600 fissions. This result explains why cells collected in nature are usually young and vigorous. The average and maximum ages proportionally prolonged as the immaturity period was prolonged, as reported true for species of the ciliate. These results indicate the validity of our simulation. The average and maximum ages remained unchanged when the initial condition for starting the culture was changed from two complementary mating-type cells to a population with a quadratic-function distribution, and when the fission rate at the log-phase and the death rate at the stationary phase were modified for older ages. The average and maximum ages changed slightly when either the conjugation rate or the proportion of transplantation was somewhat lowered. Although they changed considerably when such parameters as the immaturity period, conjugation rate and death rate were extremely modified, no clones with the age over 230 fissions appeared in any simulations. These results indicate the robustness of the model, which provides us with fresh insight into the structural system of the clonal lifespan of P. caudatum in nature. 相似文献
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Choi MH Kim SH Chung JH Jang HJ Eom JH Chung BS Sohn WM Chai JY Hong ST 《The Journal of parasitology》2006,92(2):236-241
The cercaria morphology of Echinochasmus japonicus was investigated using light and scanning electron microscopy. Cercariae, liberated from naturally infected snails (Parafossarulus manchouricus), had ovoid bodies and diminutive tails. The cercaria tegument was covered with minute spines. Four type II sensory papillae were observed on the dorsal side of the oral sucker, and type I papillae were distributed on the dorsal tegument surfaces. When cercariae were kept in the same bath as the freshwater fish, Pseudorasbora parva, which were free from trematode infections, parasites encysted only in the gills of fishes at day 4 postinfection (PI). The outermost metacercaria wall was fully formed in host tissues at day 7 PI. Adult worms were recovered from the intestines of rats, chicks, and ducks 28 days after experimental exposure to metacercariae. The head crown of the adult was armed with 24 collar spines, which were interrupted dorsal to the oral sucker, and the species was identified as E. japonicus. 相似文献
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Yuki Kawakami Shiori Hirano Mai Kinoshita Akemi Otsuki Toshiko Suzuki-Yamamoto Makiko Suzuki Masumi Kimoto Sae Sasabe Mitsuo Fukushima Koji Kishimoto Takashi Izumi Toru Oga Shuh Narumiya Mitsuaki Sugahara Masashi Miyano Shozo Yamamoto Yoshitaka Takahashi 《Biochimica et Biophysica Acta (BBA)/General Subjects》2014