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1.
Ribosomal (r)RNA and rDNA have been golden molecular markers in microbial ecology. However, it remains poorly understood how ribotype copy number (CN)‐based characteristics are linked with diversity, abundance, and activity of protist populations and communities observed at organismal levels. Here, we applied a single‐cell approach to quantify ribotype CNs in two ciliate species reared at different temperatures. We found that in actively growing cells, the per‐cell rDNA and rRNA CNs scaled with cell volume (CV) to 0.44 and 0.58 powers, respectively. The modeled rDNA and rRNA concentrations thus appear to be much higher in smaller than in larger cells. The observed rRNA:rDNA ratio scaled with CV0.14. The maximum growth rate could be well predicted by a combination of per‐cell ribotype CN and temperature. Our empirical data and modeling on single‐cell ribotype scaling are in agreement with both the metabolic theory of ecology and the growth rate hypothesis, providing a quantitative framework for linking cellular rDNA and rRNA CNs with body size, growth (activity), and biomass stoichiometry. This study also demonstrates that the expression rate of rRNA genes is constrained by cell size, and favors biomass rather than abundance‐based interpretation of quantitative ribotype data in population and community ecology of protists.  相似文献   
2.

Background

The study of nuclear architecture using Chromosome Conformation Capture (3C) technologies is a novel frontier in biology. With further reduction in sequencing costs, the potential of Hi-C in describing nuclear architecture as a phenotype is only about to unfold. To use Hi-C for phenotypic comparisons among different cell types, conditions, or genetic backgrounds, Hi-C data processing needs to be more accessible to biologists.

Results

HiCdat provides a simple graphical user interface for data pre-processing and a collection of higher-level data analysis tools implemented in R. Data pre-processing also supports a wide range of additional data types required for in-depth analysis of the Hi-C data (e.g. RNA-Seq, ChIP-Seq, and BS-Seq).

Conclusions

HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes, their correlation to genomic and epigenomic features, and on comparative studies. It uses simple input and output formats and can therefore easily be integrated into existing workflows or combined with alternative tools.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0678-x) contains supplementary material, which is available to authorized users.  相似文献   
3.
大麦G-带变动性以及与染色粒的一致性分析   总被引:3,自引:1,他引:2  
以大麦为材料,进行了G-带带纹变动性分析以及G-带与减数分裂粗线期染色粒的比较。有丝分裂早中期至中期两个不同时期G-带带纹总数减少36%,染色体组的绝对长度缩短25%,带数减少的幅度大于染色体长度缩短的幅度。染色体组中每条染色体之间带纹减少的比例不尽相同,变幅在0.29-0.50之间。不同染色体绝对长度减少的幅度在0.27-3.70μ之间。从早中期至中期,每单位染色体绝对长度带数具相对减少的趋势。选择第6染色体进行的比较显示,减数分裂的染色粒与有丝分裂的G-带带纹之间具有很好的对应关系,G-带带纹和染色粒间的数目、位置和着色程度上都具一致性。对G-带性质和植物中G-带的应用等问题进行了讨论。  相似文献   
4.
通过和玉米杂交诱导硬粒小麦单倍体   总被引:6,自引:1,他引:5  
硬粒小麦(Triticum durum Desf.)DR147授以超甜玉米(Zea m ays L.) ss 7700的花粉后,在83.4% 的柱头上观察到花粉萌发及花粉管长入胚囊,有9.9% 的子房发生了卵细胞的单受精,1.9% 的子房发生了中央细胞的单受精,32.7% 的子房发生了双受精。尽管双受精后可同时形成胚和胚乳,但胚乳往往发育迟缓,甚至败育。硬粒小麦×玉米形成的杂合子核型高度不稳定,在最初的几次细胞分裂中,来自父本玉米的染色体逐步被排除,最后形成硬粒小麦单倍体胚。在授以玉米花粉4 h 后用100 ppm 2,4-D溶液浸蘸硬粒小麦穗部,可以有效地促进幼胚在缺乏胚乳或胚乳败育情况下的生长和发育。授粉9—13 d 后由533个硬粒小麦子房解剖出25个胚,得胚率为4.7% 。通过幼胚拯救获得11棵正常植株,植株获得率为2.1% 。根尖细胞染色体计数表明,它们为单倍体(2n= 2x= 14)。  相似文献   
5.
Sizing of the Leptospira genome by pulsed-field agarose gel electrophoresis   总被引:1,自引:0,他引:1  
Pulsed-field gel electrophoresis allowed the determination of the size of the genome of Leptospira, a bacterium of the spirochete family. The three restriction enzymes, NotI (5'GC/GGCCGC), NheI (5'G/CTAGC), ApaI (5'-GGGCC/C) generated DNA fragments of suitable size. The results are compatible with a size of 5000 kb for the chromosome of both the pathogenic and the saprophytic species of Leptospira.  相似文献   
6.
Unicellular protists can biomineralize spatially complex and functional shells. A typical cell of the photosynthetic synurophyte Mallomonas is covered by about 60–100 silica scales. Their geometric arrangement, the so-called scale case, mainly depends on the species and on the cell cycle. In this study, the scale case of the synurophyte Mallomonas was preserved in aqueous suspension using high-pressure freezing (HPF). From this specimen, a three-dimensional (3D) data set spanning a volume of about 25.6 μm × 19.2 μm × 4.2 μm with a voxel size of 12.5 nm × 12.5 nm × 25.0 nm was collected by Cryo-FIB SEM in 3 h and 24 min. SEM imaging using In-lens SE detection allowed to clearly differentiate between mineralized, curved scales of less than 0.2 μm thickness and organic cellular ultrastructure or vitrified ice. The three-dimensional spatial orientations and shapes of a minimum set of scales (N = 13) were identified by visual inspection, and manually segmented. Manual and automated segmentation approaches were comparatively applied to one arbitrarily selected reference scale using the differences in grey level between scales and other constituents. Computational automated routines and principal component analysis of the experimentally extracted data created a realistic mathematical model based on the Fibonacci pattern theory. A complete in silico scale case of Mallomonas was reconstructed showing an optimized scale coverage on the cell surface, similarly as it was observed experimentally. The minimum time requirements from harvesting the living cells to the final scale case determination by Cryo-FIB SEM and computational image processing are discussed.  相似文献   
7.
The flow of cerebrospinal fluid (CSF) in a patient-specific model of the subarachnoid space in a Chiari I patient was investigated using numerical simulations. The pulsating CSF flow was modeled using a time-varying velocity pulse based on peak velocity measurements (diastole and systole) derived from a selection of patients with Chiari I malformation. The present study introduces the general definition of the Reynolds number to provide a measure of CSF flow instability to give an estimate of the possibility of turbulence occurring in CSF flow. This was motivated by the fact that the combination of pulsating flow and the geometric complexity of the spinal canal may result in local Reynolds numbers that are significantly higher than the commonly used global measure such that flow instabilities may develop into turbulent flow in these regions. The local Reynolds number was used in combination with derived statistics to characterize the flow. The results revealed the existence of both local unstable regions and local regions with velocity fluctuations similar in magnitude to what is observed in fully turbulent flows. The results also indicated that the fluctuations were not self-sustained turbulence, but rather flow instabilities that may develop into turbulence. The case considered was therefore believed to represent a CSF flow close to transition.  相似文献   
8.
Use of single-sample genetic methods to estimate effective population size has skyrocketed in recent years. Although the underlying models assume discrete generations, they are widely applied to age-structured species. We simulated genetic data for 21 iteroparous animal and plant species to evaluate two untested hypotheses regarding performance of the single-sample method based on linkage disequilibrium (LD): (1) estimates based on single-cohort samples reflect the effective number of breeders in one reproductive cycle (Nb), and (2) mixed-age samples reflect the effective size per generation (Ne). We calculated true Ne and Nb, using the model species’ vital rates, and verified these with individual-based simulations. We show that single-cohort samples should be equally influenced by Nb and Ne and confirm this with simulated results: N^b was a linear (r2 = 0.98) function of the harmonic mean of Ne and Nb. We provide a quantitative bias correction for raw N^b based on the ratio Nb/Ne, which can be estimated from two or three simple life history traits. Bias-adjusted estimates were within 5% of true Nb for all 21 study species and proved robust when challenged with new data. Mixed-age adult samples produced downwardly biased estimates in all species, which we attribute to a two-locus Wahlund effect (mixture LD) caused by combining parents from different cohorts in a single sample. Results from this study will facilitate interpretation of rapidly accumulating genetic estimates in terms of both Ne (which influences long-term evolutionary processes) and Nb (which is more important for understanding eco-evolutionary dynamics and mating systems).  相似文献   
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