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91.
Justine Collier 《Molecular microbiology》2010,77(1):11-14
Cell division in Gram‐negative bacteria involves the co‐ordinated invagination of the three cell envelope layers to form two new daughter cell poles. This complex process starts with the polymerization of the tubulin‐like protein FtsZ into a Z‐ring at mid‐cell, which drives cytokinesis and recruits numerous other proteins to the division site. These proteins are involved in Z‐ring constriction, inner‐ and outer‐membrane invagination, peptidoglycan remodelling and daughter cell separation. Three papers in this issue of Molecular Microbiology, from the teams of Lucy Shapiro, Martin Thanbichler and Christine Jacobs‐Wagner, describe a novel protein, called DipM for Division Involved Protein with LysM domains, that is required for cell division in Caulobacter crescentus. DipM localizes to the mid‐cell during cell division, where it is necessary for the hydrolysis of the septal peptidoglycan to remodel the cell wall. Loss of DipM results in severe defects in cell envelope constriction, which is deleterious under fast‐growth conditions. State‐of‐the‐art microscopy experiments reveal that the peptidoglycan is thicker and that the cell wall is incorrectly organized in DipM‐depleted cells compared with wild‐type cells, demonstrating that DipM is essential for reorganizing the cell wall at the division site, for envelope invagination and cell separation in Caulobacter. 相似文献
92.
Background
One of the major challenges in the field of vaccine design is to predict conformational B-cell epitopes in an antigen. In the past, several methods have been developed for predicting conformational B-cell epitopes in an antigen from its tertiary structure. This is the first attempt in this area to predict conformational B-cell epitope in an antigen from its amino acid sequence.Results
All Support vector machine (SVM) models were trained and tested on 187 non-redundant protein chains consisting of 2261 antibody interacting residues of B-cell epitopes. Models have been developed using binary profile of pattern (BPP) and physiochemical profile of patterns (PPP) and achieved a maximum MCC of 0.22 and 0.17 respectively. In this study, for the first time SVM model has been developed using composition profile of patterns (CPP) and achieved a maximum MCC of 0.73 with accuracy 86.59%. We compare our CPP based model with existing structure based methods and observed that our sequence based model is as good as structure based methods.Conclusion
This study demonstrates that prediction of conformational B-cell epitope in an antigen is possible from is primary sequence. This study will be very useful in predicting conformational B-cell epitopes in antigens whose tertiary structures are not available. A web server CBTOPE has been developed for predicting B-cell epitope http://www.imtech.res.in/raghava/cbtope/. 相似文献93.
Common dandelions (Taraxacum officinale Weber, sensu lato; Asteraceae) introduced to North America form an assemblage of asexual (agamospermous), clonal lineages derived from Eurasian mixed sexual and asexual populations. We investigated whether selection for more pollution tolerant clonal lineages occurs at polluted sites and selection for more pollution intolerant lineages occurs at unpolluted sites. We tested the above hypothesis by performing reciprocal greenhouse productivity experiments in which unique dandelion clones (12 clones, identified by DNA fingerprinting, from each site type) sampled from two unpolluted and two polluted (moderately enhanced Cu, Pb and Zn soil concentrations) sites were grown pairwise in both unpolluted (nutrient solution only) and polluted (nutrient solution + Cu, Pb and Zn) media (n?=?48 paired tests for each media type). Dandelion clones from polluted sites produced fewer and smaller leaves, shorter roots and smaller root diameters, reduced shoot and root dry weights, and reduced total biomass compared to clones from unpolluted sites when clones were grown in unpolluted-media (P?≤?0.05). In contrast, clones taken from unpolluted sites were shown to produce significantly fewer and shorter leaves, shorter roots and smaller root diameters, reduced shoot and root dry weights, reduced total biomass, a reduced shoot : root biomass ratio, and have much lower survival compared to clones from polluted sites when both were grown in polluted-media (P?≤?0.05). These results reveal that there was increased selection against unpolluted-site clonal lineages in polluted-media and against polluted-site clonal lineages in unpolluted-media. Across all treatments, clones from unpolluted sites growing in unpolluted-media had the highest proximate measures of fitness. Overall, these findings provide insight into the relationships among anthropogenic environmental contamination and the consequent effects of selective forces acting on dandelion clones and their population genetic architecture. 相似文献
94.
95.
Gary L. Larson Robert L. Hoffman Bruce R. Hargreaves Robert W. Collier 《Hydrobiologia》2007,574(1):141-148
We addressed potential sources of error in estimating the water clarity of mountain lakes by investigating the use of beam
transmissometer measurements to estimate Secchi disk depth. The optical properties Secchi disk depth (SD) and beam transmissometer
attenuation (BA) were measured in Crater Lake (Crater Lake National Park, Oregon, USA) at a designated sampling station near
the maximum depth of the lake. A standard 20 cm black and white disk was used to measure SD. The transmissometer light source
had a nearly monochromatic wavelength of 660 nm and a path length of 25 cm. We created a SD prediction model by regression
of the inverse SD of 13 measurements recorded on days when environmental conditions were acceptable for disk deployment with
BA averaged over the same depth range as the measured SD. The relationship between inverse SD and averaged BA was significant
and the average 95% confidence interval for predicted SD relative to the measured SD was ±1.6 m (range = −4.6 to 5.5 m) or ±5.0%.
Eleven additional sample dates tested the accuracy of the predictive model. The average 95% confidence interval for these
sample dates was ±0.7 m (range = −3.5 to 3.8 m) or ±2.2%. The 1996–2000 time-series means for measured and predicted SD varied
by 0.1 m, and the medians varied by 0.5 m. The time-series mean annual measured and predicted SD’s also varied little, with
intra-annual differences between measured and predicted mean annual SD ranging from −2.1 to 0.1 m. The results demonstrated
that this prediction model reliably estimated Secchi disk depths and can be used to significantly expand optical observations
in an environment where the conditions for standardized SD deployments are limited. 相似文献
96.
In order to evaluate hydrocarbon inputs to Crater Lake from anthropogenic and natural sources, samples of water, aerosol,
surface slick and sediment were collected and analyzed by gas chromatography-mass spectrometry (GC-MS) for determination of
their aliphatic and aromatic hydrocarbon concentrations and compositions. Results show that hydrocarbons originate from both
natural (terrestrial plant waxes and algae) and anthropogenic (petroleum use) sources and are entering the lake through direct
input and atmospheric transport. The concentrations of petroleum hydrocarbons range from low to undetectable. The distributions
and abundances of n-alkanes, polycyclic aromatic hydrocarbons (PAH) and unresolved complex mixture (UCM) from petroleum are similar for all surface
slick sampling sites. The estimated levels of PAH in surface slicks range from 7–9 ng/m2 which are low. Transport of petroleum-derived hydrocarbons from the lake surface has resulted in their presence in some sediments,
particularly near the boat operations mooring (total petroleum HC = 1440 μg/kg, dry wt. compared to naturally derived n-alkanes, 240 μg/kg, dry wt.). The presence of biomarkers such as the tricyclic terpanes, hopanes and steranes in shallow
sediments further confirms petroleum input from boat traffic. In the deep lake sediments, petroleum hydrocarbon concentrations
were very low (16 μg/kg, dry wt.). Very low concentrations of PAH were detected in shallow sediments (17–40 μg/kg at 5 m depth
near the boat operations) and deep sediments (3–15 μg/kg at 580 m depth). The individual PAH concentrations in sediments (μg/kg
or ppb range) are at least three orders of magnitude less than reported threshold effects levels (mg/kg or ppm range, test
amphipod Hyalella azteca). Therefore, no adverse effects are expected to occur in benthic biota exposed to these sediments. Boating activities are leaving a detectable level of petroleum in surface waters and lake sediments but these concentrations are very low. 相似文献
97.
Seasonal nutrient and plankton dynamics in a physical-biological model of Crater Lake 总被引:1,自引:1,他引:0
Katja Fennel Robert Collier Gary Larson Greg Crawford Emmanuel Boss 《Hydrobiologia》2007,574(1):265-280
A coupled 1D physical-biological model of Crater Lake is presented. The model simulates the seasonal evolution of two functional
phytoplankton groups, total chlorophyll, and zooplankton in good quantitative agreement with observations from a 10-year monitoring
study. During the stratified period in summer and early fall the model displays a marked vertical structure: the phytoplankton
biomass of the functional group 1, which represents diatoms and dinoflagellates, has its highest concentration in the upper
40 m; the phytoplankton biomass of group 2, which represents chlorophyta, chrysophyta, cryptomonads and cyanobacteria, has
its highest concentrations between 50 and 80 m, and phytoplankton chlorophyll has its maximum at 120 m depth. A similar vertical
structure is a reoccurring feature in the available data. In the model the key process allowing a vertical separation between
biomass and chlorophyll is photoacclimation. Vertical light attenuation (i.e., water clarity) and the physiological ability
of phytoplankton to increase their cellular chlorophyll-to-biomass ratio are ultimately determining the location of the chlorophyll
maximum. The location of the particle maxima on the other hand is determined by the balance between growth and losses and
occurs where growth and losses equal. The vertical particle flux simulated by our model agrees well with flux measurements
from a sediment trap. This motivated us to revisit a previously published study by Dymond et al. (1996). Dymond et al. used a box model to estimate the vertical particle flux and found a discrepancy by a factor 2.5–10 between
their model-derived flux and measured fluxes from a sediment trap. Their box model neglected the exchange flux of dissolved
and suspended organic matter, which, as our model and available data suggests is significant for the vertical exchange of
nitrogen. Adjustment of Dymond et al.’s assumptions to account for dissolved and suspended nitrogen yields a flux estimate
that is consistent with sediment trap measurements and our model. 相似文献
98.
Background
Annotations that describe the function of sequences are enormously important to researchers during laboratory investigations and when making computational inferences. However, there has been little investigation into the data quality of sequence function annotations. Here we have developed a new method of estimating the error rate of curated sequence annotations, and applied this to the Gene Ontology (GO) sequence database (GOSeqLite). This method involved artificially adding errors to sequence annotations at known rates, and used regression to model the impact on the precision of annotations based on BLAST matched sequences.Results
We estimated the error rate of curated GO sequence annotations in the GOSeqLite database (March 2006) at between 28% and 30%. Annotations made without use of sequence similarity based methods (non-ISS) had an estimated error rate of between 13% and 18%. Annotations made with the use of sequence similarity methodology (ISS) had an estimated error rate of 49%.Conclusion
While the overall error rate is reasonably low, it would be prudent to treat all ISS annotations with caution. Electronic annotators that use ISS annotations as the basis of predictions are likely to have higher false prediction rates, and for this reason designers of these systems should consider avoiding ISS annotations where possible. Electronic annotators that use ISS annotations to make predictions should be viewed sceptically. We recommend that curators thoroughly review ISS annotations before accepting them as valid. Overall, users of curated sequence annotations from the GO database should feel assured that they are using a comparatively high quality source of information. 相似文献99.
100.