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121.
Sebastian Tarcz 《European journal of protistology》2013,49(1):50-61
Paramecium novaurelia Beale and Schneller, 1954, was first found in Scotland and is known to occur mainly in Europe, where it is the most common species of the P. aurelia complex. In recent years, two non-European localities have been described: Turkey and the United States of America. This article presents the analysis of intraspecific variability among 25 strains of P. novaurelia with the application of ribosomal and mitochondrial loci (ITS1-5.8S-ITS2, 5′ large subunit rDNA (5′LSU rDNA) and cytochrome c oxidase subunit 1 (COI) mtDNA). The mean distance observed for all of the studied P. novaurelia sequence pairs was p = 0.008/0.016/0.092 (ITS1-5.8S-ITS2/5′LSU rDNA/COI). Phylogenetic trees (NJ/MP/BI) based on a comparison of all of the analysed sequences show that the studied strains of P. novaurelia form a distinct clade, separate from the P. caudatum outgroup, and are divided into two clusters (A and B) and two branches (C and D). The occurrence of substantial genetic differentiation within P. novaurelia, confirmed by the analysed DNA fragments, indicates a rapid evolution of particular species within the Paramecium genus. 相似文献
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123.
Anja Engleder Elisabeth Haring Sebastian Kirchhof Werner Mayer 《Journal of Zoological Systematics and Evolutionary Research》2013,51(2):132-143
Eremiadinae, one of three subfamilies of Lacertidae, are distributed throughout Asia and Africa. Previous phylogenetic studies suggested that one of the main groups of Eremiadinae (the Ethiopian clade) consist of two clades with predominately East‐African and South‐African distribution. Yet, especially the latter one, which includes the genera Pedioplanis, Meroles, Ichnotropis, Tropidosaura and Australolacerta, was not well supported in the molecular phylogenetic analysis. In this study, we analysed the phylogenetic relationships among the genera of the ‘South African clade’ to assess whether this group actually forms a highly supported clade and to address questions concerning the monophyly of the genera. We sequenced sections of the widely used mitochondrial genes coding for 16S rRNA, 12S rRNA and cytochrome b (altogether 2045 bp) as well as the nuclear genes c‐mos, RAG‐1, PRLR, KIF24, EXPH5 and RAG‐2 (altogether 4473 bp). The combined data set increased the support values for several nodes considerably. Yet, the relationships among five major lineages within the ‘South African clade’ are not clearly resolved even with this large data set. We interpret this as a ‘hard polytomy’ due to fast radiation within the South African lacertids. The combined tree based on nine marker genes provides strong support for the ‘South African Clade’ and its sister group relationship with the ‘East African Clade’. Our results confirm the genus Tropidosaura as a monophylum, while Ichnotropis is paraphyletic in our trees: Ichnotropis squamulosa appears more closely related to Meroles than to Ichnotropis capensis. Furthermore, the monophyly of Meroles is questionable as well. Based on our results, I. squamulosa should be transferred from Ichnotropis into the genus Meroles. Also, the two species of Australolacerta (A. australis and A. rupicola) are very distantly related and the genus is perhaps paraphyletic, too. Finally we propose a phylogeographical scenario in the context of palaeoclimatic data and compare it with a previously postulated hypothesis. 相似文献
124.
Although medicinal leeches have long been used as treatment for various ailments because of their potent anticoagulation factors, neither the full diversity of salivary components that inhibit coagulation, nor the evolutionary selection acting on them has been thoroughly investigated. Here, we constructed expressed sequence tag libraries from salivary glands of two species of medicinal hirudinoid leeches, Hirudo verbana and Aliolimnatis fenestrata, and identified anticoagulant‐orthologs through BLASTx searches. The data set then was augmented by the addition of a previously constructed EST library from the macrobdelloid leech Macrobdella decora. The identified orthologs then were compared and contrasted with well‐characterized anticoagulants from a variety of leeches with different feeding habits, including non‐sanguivorous species. Moreover, four different statistical methods for predicting signatures of positive and negative evolutionary pressures were used for 10 rounds each to assess the level and type of selection acting on the molecules as a whole and on specific sites. In total, sequences showing putative BLASTx‐orthology with five and three anticoagulant‐families were recovered in the A. fenestrata and H. verbana EST libraries respectively. Selection pressure analyses predicted high levels of purifying selection across the anticoagulant diversity, although a few isolated sites showed signatures of positive selection. This study represents a first attempt at mapping the anticoagulant repertoires in a comparative fashion across several leech families. 相似文献
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126.
S?ren Franzenburg Sebastian Fraune Philipp M Altrock Sven Künzel John F Baines Arne Traulsen Thomas CG Bosch 《The ISME journal》2013,7(4):781-790
Animals are colonized by complex bacterial communities. The processes controlling community membership and influencing the establishment of the microbial ecosystem during development are poorly understood. Here we aimed to explore the assembly of bacterial communities in Hydra with the broader goal of elucidating the general rules that determine the temporal progression of bacterial colonization of animal epithelia. We profiled the microbial communities in polyps at various time points after hatching in four replicates. The composition and temporal patterns of the bacterial communities were strikingly similar in all replicates. Distinct features included high diversity of community profiles in the first week, a remarkable but transient adult-like profile 2 weeks after hatching, followed by progressive emergence of a stable adult-like pattern characterized by low species diversity and the preponderance of the Betaproteobacterium Curvibacter. Intriguingly, this process displayed important parallels to the assembly of human fecal communities after birth. In addition, a mathematical modeling approach was used to uncover the organizational principles of this colonization process, suggesting that both, local environmental or host-derived factor(s) modulating the colonization rate, as well as frequency-dependent interactions of individual bacterial community members are important aspects in the emergence of a stable bacterial community at the end of development. 相似文献
127.
Sebastian Ullrich Phillip Bremer Christine Neumann-Grutzeck Helge Otto Christoph Rüther Cay Uwe von Seydewitz Gerd Peter Meyer Keihan Ahmadi-Simab Joachim R?ther Barbara Hogan Wolfgang Schwenk Roman Fischbach J?rg Caselitz Jochen Puttfarcken Susanne Huggett Petra Tiedeken Jordan Pober Nancy C. Kirkiles-Smith Friedrich Hagenmüller 《PloS one》2013,8(2)
Objectives
Shiga-toxin producing O157:H7 Entero Haemorrhagic E. coli (STEC/EHEC) is one of the most common causes of Haemolytic Uraemic Syndrome (HUS) related to infectious haemorrhagic colitis. Nearly all recommendations on clinical management of EHEC infections refer to this strain. The 2011 outbreak in Northern Europe was the first to be caused by the serotype O104:H4. This EHEC strain was found to carry genetic features of Entero Aggregative E. coli (EAEC) and extended spectrum β lactamase (ESBL). We report symptoms and complications in patients at one of the most affected centres of the 2011 EHEC O104 outbreak in Northern Germany.Methods
The courses of patients admitted to our hospital due to bloody diarrhoea with suspected EHEC O104 infection were recorded prospectively. These data include the patients’ histories, clinical findings, and complications.Results
EHEC O104 infection was confirmed in 61 patients (female = 37; mean age: 44±2 years). The frequency of HUS was 59% (36/61) in our cohort. An enteric colonisation with co-pathogens was found in 57%. Thirty-one (51%) patients were treated with plasma-separation/plasmapheresis, 16 (26%) with haemodialysis, and 7 (11%) with Eculizumab. Patients receiving antibiotic treatment (n = 37; 61%) experienced no apparent change in their clinical course. Twenty-six (43%) patients suffered from neurological symptoms. One 83-year-old patient died due to comorbidities after HUS was successfully treated.Conclusions
EHEC O104:H4 infections differ markedly from earlier reports on O157:H7 induced enterocolitis in regard to epidemiology, symptomatology, and frequency of complications. We recommend a standard of practice for clinical monitoring and support the renaming of EHEC O104:H4 syndrome as “EAHEC disease”. 相似文献128.
Vicky Wang-Wei Tsai Laurence Macia Heiko Johnen Tamara Kuffner Rakesh Manadhar Sebastian Beck J?rgensen Ka Ki Michelle Lee-Ng Hong Ping Zhang Liyun Wu Christopher Peter Marquis Lele Jiang Yasmin Husaini Shu Lin Herbert Herzog David A. Brown Amanda Sainsbury Samuel N. Breit 《PloS one》2013,8(2)
The TGF-b superfamily cytokine MIC-1/GDF15 circulates in all humans and when overproduced in cancer leads to anorexia/cachexia, by direct action on brain feeding centres. In these studies we have examined the role of physiologically relevant levels of MIC-1/GDF15 in the regulation of appetite, body weight and basal metabolic rate. MIC-1/GDF15 gene knockout mice (MIC-1−/−) weighed more and had increased adiposity, which was associated with increased spontaneous food intake. Female MIC-1−/− mice exhibited some additional alterations in reduced basal energy expenditure and physical activity, possibly owing to the associated decrease in total lean mass. Further, infusion of human recombinant MIC-1/GDF15 sufficient to raise serum levels in MIC-1−/− mice to within the normal human range reduced body weight and food intake. Taken together, our findings suggest that MIC-1/GDF15 is involved in the physiological regulation of appetite and energy storage. 相似文献
129.
Model-based prediction is dependent on many choices ranging from the sample collection and prediction endpoint to the choice of algorithm and its parameters. Here we studied the effects of such choices, exemplified by predicting sensitivity (as IC50) of cancer cell lines towards a variety of compounds. For this, we used three independent sample collections and applied several machine learning algorithms for predicting a variety of endpoints for drug response. We compared all possible models for combinations of sample collections, algorithm, drug, and labeling to an identically generated null model. The predictability of treatment effects varies among compounds, i.e. response could be predicted for some but not for all. The choice of sample collection plays a major role towards lowering the prediction error, as does sample size. However, we found that no algorithm was able to consistently outperform the other and there was no significant difference between regression and two- or three class predictors in this experimental setting. These results indicate that response-modeling projects should direct efforts mainly towards sample collection and data quality, rather than method adjustment. 相似文献
130.
Hansi Weissensteiner Margot Haun Sebastian Sch?nherr Mathias Neuner Lukas Forer Günther Specht Anita Kloss-Brandst?tter Florian Kronenberg Stefan Coassin 《PloS one》2013,8(3)
Single nucleotide polymorphisms (SNPs) play a prominent role in modern genetics. Current genotyping technologies such as Sequenom iPLEX, ABI TaqMan and KBioscience KASPar made the genotyping of huge SNP sets in large populations straightforward and allow the generation of hundreds of thousands of genotypes even in medium sized labs. While data generation is straightforward, the subsequent data conversion, storage and quality control steps are time-consuming, error-prone and require extensive bioinformatic support. In order to ease this tedious process, we developed SNPflow. SNPflow is a lightweight, intuitive and easily deployable application, which processes genotype data from Sequenom MassARRAY (iPLEX) and ABI 7900HT (TaqMan, KASPar) systems and is extendible to other genotyping methods as well. SNPflow automatically converts the raw output files to ready-to-use genotype lists, calculates all standard quality control values such as call rate, expected and real amount of replicates, minor allele frequency, absolute number of discordant replicates, discordance rate and the p-value of the HWE test, checks the plausibility of the observed genotype frequencies by comparing them to HapMap/1000-Genomes, provides a module for the processing of SNPs, which allow sex determination for DNA quality control purposes and, finally, stores all data in a relational database. SNPflow runs on all common operating systems and comes as both stand-alone version and multi-user version for laboratory-wide use. The software, a user manual, screenshots and a screencast illustrating the main features are available at http://genepi-snpflow.i-med.ac.at. 相似文献