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1.
Background
DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. Fast deployment of new methods as well as a combination of predefined, easy to apply methods with programmer's access to the data are important requirements for any analysis framework. Mayday is an open source platform with emphasis on visual data exploration and analysis. Many built-in methods for clustering, machine learning and classification are provided for dissecting complex datasets. Plugins can easily be written to extend Mayday's functionality in a large number of ways. As Java program, Mayday is platform-independent and can be used as Java WebStart application without any installation. Mayday can import data from several file formats, database connectivity is included for efficient data organization. Numerous interactive visualization tools, including box plots, profile plots, principal component plots and a heatmap are available, can be enhanced with metadata and exported as publication quality vector files. 相似文献2.
3.
Lydie M. Dupont Hans Peter Linder Florian Rommerskirchen Enno Schefuß 《Journal of Biogeography》2011,38(6):1059-1068
Aim To test whether the radiation of the extremely rich Cape flora is correlated with marine‐driven climate change. Location Middle to Late Miocene in the south‐east Atlantic and the Benguela Upwelling System (BUS) off the west coast of South Africa. Methods We studied the palynology of the thoroughly dated Middle to Late Miocene sediments of Ocean Drilling Program (ODP) Site 1085 retrieved from the Atlantic off the mouth of the Orange River. Both marine upwelling and terrestrial input are recorded at this site, which allows a direct correlation between changes in the terrestrial flora and the marine BUS in the south‐east Atlantic. Results Pollen types from plants of tropical affinity disappeared, and those from the Cape flora gradually increased, between 10 and 6 Ma. Our data corroborate the inferred dating of the diversification in Aizoaceae c. 8 Ma. Main conclusions Inferred vegetation changes for the Late Miocene south‐western African coast are the disappearance of Podocarpus‐dominated Afromontane forests, and a change in the vegetation of the coastal plain from tropical grassland and thicket to semi‐arid succulent vegetation. These changes are indicative of an increased summer drought, and are in step with the development of the southern BUS. They pre‐date the Pliocene uplift of the East African escarpment, suggesting that this did not play a role in stimulating vegetation change. Some Fynbos elements were present throughout the recorded period (from 11 Ma), suggesting that at least some elements of this vegetation were already in place during the onset of the BUS. This is consistent with a marine‐driven climate change in south‐western Africa triggering substantial radiation in the terrestrial flora, especially in the Aizoaceae. 相似文献
4.
Florian Witzmann 《Acta zoologica》2011,92(3):281-302
Witzmann F. (2011). Morphological and histological changes of dermal scales during the fish‐to‐tetrapod transition. —Acta Zoologica (Stockholm) 92 : 281–302. The gastral scales of limbed tetrapodomorphs evolved from the ‘elpistostegid’‐type of scale by an enlargement and differentiation of the articulation facets and a shortening and broadening of the keel. These changes caused a tighter connection between gastral scales within a scale row and a greater overlap between the rows. Dorsal round scales of limbed tetrapodomorphs developed from a gastral scale‐type by an alteration of the ontogenetic pathway. The posterolateral direction of scale rows in ‘elpistostegids’ was retained in the gastral scalation of most limbed tetrapodomorphs, whereas the arrangement of round dorsal scales is modified to a transverse orientation. Both gastral and dorsal scales of limbed tetrapodomorphs consist solely of parallel‐fibred bone with circumferential growth marks. The proportionally larger overlap surfaces of gastral scales and their mode of articulation in the ventral midline indicate that the body of limbed tetrapodomorphs might have been more flexible than that of their finned relatives. The alteration of dermal scales was one of the most rapid morphological changes during the fish‐to‐tetrapod transition. Once established, gastral and dorsal scales were retained as a conservative character in different lineages of basal tetrapods, in both the amphibian and the amniote lineages. 相似文献
5.
Fourier transform infrared investigation of the Escherichia coli methionine aporepressor 总被引:3,自引:0,他引:3
P W Yang H H Mantsch J L Arrondo I Saint-Girons Y Guillou G N Cohen O Barzu 《Biochemistry》1987,26(10):2706-2711
This study represents the first physicochemical analysis of the recently cloned methionine repressor protein (Met aporepressor) from Escherichia coli. Infrared spectrometry was used to investigate the secondary structure and the hydrogen-deuterium exchange behavior of the E. coli Met aporepressor. The secondary structure of the native bacterial protein was derived by analysis of the amide I mode. The amide I band contour was found to consist of five major component bands (at 1625, 1639, 1653, 1665, and 1676 cm-1) which reflect the presence of various substructures. The relative areas of these component bands are consistent with a high alpha-helical content of the peptide chain secondary structure in solution (43%) and a small amount of beta-sheet structure (7%). The remaining substructure is assigned to turns (10%) and to unordered (or less ordered) structures (40%). The temperature dependence of the infrared spectra of native Met aporepressor in D2O medium over the temperature interval 20-80 degrees C indicates that there are two discrete thermal events: the first thermal event, centered at 42 degrees C, is associated with the hydrogen-deuterium exchange of the hard-to-exchange alpha-helical peptide bonds accompanied by a partial denaturation of the protein, while the second event, centered around 50 degrees C, represents the irreversible thermal denaturation of the protein. 相似文献
6.
Shaw S. Somers Julian F. Dye Pierre J. Guillou 《Cancer immunology, immunotherapy : CII》1991,33(4):217-222
Summary Serum-free supernatants from the human melanoma cell line G361 contain a factor that can potently suppress the generation of tumouricidal lymphokine-activated killer (LAK) cells in response to interleukin-2. To characterise the suppressive factor of tumour origin we performed a number of physicochemical and functional comparisons with another immunosuppressive protein, transforming growth factor (TGF). The bioactivity of tumour-derived suppressor factor (TDSF), assayed by suppression of LAK cell generation, was unaffected by a reducing agent but lost when denatured with a chaotropic agent. In contrast, TGF was inactivated by reduction but not denaturation. TDSF lost bioactivity in conditions of pH less than 4, whereas TGF showed no loss of activity. The TDSF moiety has an estimated pI of 4.3 and a molecular mass of 69–87 kDa. This differs from published values of pI 9.5, and 25 kDa molecular mass for TGF. Anti-TGF antiserum reversed the effects of TGF but did not affect the suppression of LAK cell generation caused by TDSF. These findings provide compelling evidence that the TDSF moiety is not TGF, and may be a novel immunoregulatory cytokine. 相似文献
7.
C Capdeville F el Bouhtoury R M Parache R G Boulu J Guillou J Atkinson 《Life sciences》1990,47(6):539-546
Global cerebral ischemia (four vessel model) was induced in renovascular hypertensive rats (two kidney, one clip model) chronically treated with intraperitoneal administration of angiotensin I converting enzyme inhibitors, either captopril (100 mg/kg per day) or Wy-44,655 (10 mg/kg per day). Mortality following cerebral ischemia was higher in renovascular hypertensive rats than in normotensive controls. Reduction of blood pressure with captopril or Wy-44,655, lowered mortality. In surviving renovascular hypertensive and normotensive rats cerebral ischemia induced hyperactivity and lesions of the CA1 area of the hippocampus. Prolonged treatment with captopril--but not with Wy-44,655--reduced hyperactivity and the extent of the CA1 lesions. In conclusion, hypertension increases mortality following cerebral ischemia but does not affect the extent of brain injury in survivors. Prior treatment with converting enzyme inhibitors lowers mortality. Treatment with captopril attenuates brain injury in survivors. 相似文献
8.
Florian J. Schweigert Wayne T. Stobo Hermann Zucker 《Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology》1990,159(6):649-654
Summary Vitamin E levels in serum, liver and blubber (subcutaneous adipose tissue) were determined for 66 male and female grey seals of varying age in the pupping colony on Sable Island in the Northwest Atlantic by high-performance liquid chromatography (HPLC). Fatty acid concentrations were determined for all blubber specimens. Adult males and pups had significantly higher levels of vitamin E and cholesterol in serum than females and juveniles. A close relationship between vitamin E and cholesterol in serum could be observed. Suckling pups had significantly higher levels of vitamin E in liver (191 mg·kg–1) than juveniles and adults (21–41 mg·kg–1). Levels of vitamin E in blubber showed an age-dependent increase, with the highest levels being found in adult males; overall, these levels were much lower than in man. Vitamin E levels in blubber and liver of lactating females were only half that of adult males. This might be due to an intensive transfer of vitamin E from mother to pup during lactation, a process which may also explain the much higher levels of vitamin E in serum and liver of nursing pups. The low levels of vitamin E in blubber of seals might be a result of its high percentage of unsaturated fatty acids (79%). Highest percentage was represented by 18:1, 16:1, 22:6 and 16:0. Pups had lower values of monounsaturated, and a higher percentage of saturated fatty acids compared to mothers. 相似文献
9.
Native disulfide bonds greatly accelerate secondary structure formation in the folding of lysozyme. 总被引:3,自引:3,他引:0 下载免费PDF全文
To assess the respective roles of local and long-range interactions during protein folding, the influence of the native disulfide bonds on the early formation of secondary structure was investigated using continuous-flow circular dichroism. Within the first 4 ms of folding, lysozyme with intact disulfide bonds already had a far-UV CD spectrum reflecting large amounts of secondary structure. Conversely, reduced lysozyme remained essentially unfolded at this early folding time. Thus, native disulfide bonds not only stabilize the cfinal conformation of lysozyme but also provide, in early folding intermediates, the necessary stabilization that favors the formation of secondary structure. 相似文献
10.
Summary Despite extensive discussions during the last 20 years stromatolites are still used by many geologists as unequivocal indicators
of very shallow-water conditions. We investigated four stratigraphic units from the Lower and Middle Jurassic of southern
Germany (Posidonien-Schiefer, Amaltheen-Ton) and of the Northern Calcareous Alps (Adneter Kalk, Klauskalk), which were formerly
interpreted as shallow marine sediments by some authors due to the occurrence of stromatolites. Our interpretations of the
macro-, micro- and ultrafacies of these sediments are not compatible with shallow-water settings. We therefore propose a deep-marine,
aphotic origin of these stromatolites.
Former interpretations of the Posidonien-Schiefer as a shallow-water deposit are mainly based on the occurrence of stromatolites.
We favour the model of a temporarily stagnant, deep, aphotic basin for these planktonrich sediments. Particles resembling
ooids, but lying within mudstones cannot be taken as evidence for shallow agitated water. They either formed within the mud
or are allochthonous.
The deep-water setting of the red limestone of the Alpine Early and Middle Jurassic is indicated by a lack of platform-typical
components like coated grains and phototrophic benthos and by shells of plankton and nekton forming a major part of the sediment.
Stromatolites occur on the steep slope of a drowned Rhaetian reef with an estimated relief of 50–100 m and immediately below
and within radiolarian limestones, deposited below the aragonite compensation depth (ACD).
The aphotic stromatolites show some morphological differences to their shallow water counterparts. In all of our sections
they occurred during intervals of reduced sedimentation. They form only thin horizons and probably grew very slowly. Mineralizations
by Fe−Mn oxides and phosphate are very common. The presence of a microbial film is evident from binding of sedimentary particles,
but the nature of the microbes is not known. Growth habits within the very distinct environments of red limestone and black
shales show some common features, but also clear differences.
The microproblematicumFrutexites
Maslov is a very common component in deep-water stromatolites, but may also itself form small crusts or dendrolites. It occurs in
two different forms. Opaque, slender forms with indistinct outlines probably grew within the weakly lithified sediment. Thicker,
transparent forms with well defined outlines are found in cavities and probably also grew on the seafloor. Well preserved
specimens display an internal fabric of radially arranged fibres of Fe−Mn oxides and calcite. It is suggested that calcite
or aragonite were one original mineralogy ofFrutexites, which was later replaced by Fe−Mn oxides or phosphate.
It is not certain whetherFrutexites is an organic, biomineralized structure or an inorganic mineralization, but the variable mineralogy and growth forms in different
environments point to an organic origin. But even if organic, the occurrence in cryptic habitats and negative phototactic
growth-directions make it clear thatFrutexites was not phototrophic. 相似文献