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61.
Motivation
In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size.Results
Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data.Availability
Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS. 相似文献62.
Helen Atterby James N. Aegerter Graham C. Smith Christine M. Conyers Theodore R. Allnutt Manuel Ruedi Alan D. MacNicoll 《European Journal of Wildlife Research》2010,56(1):67-81
The Daubenton’s bat is widespread and common in the UK and countries bordering the English Channel and North Sea. European
bat lyssavirus 2 (EBLV-2), a rabies virus, has been detected in Daubenton’s bats in the UK and continental Europe. Investigating
the relatedness of colonies and gene flow between these regions would allow regional estimates of the movement of Daubenton’s
bats and thus the potential for disease transmission. The genetic structure of the Daubenton’s bat in western Europe was investigated
by analysing variability at eight microsatellite loci. Genetic diversity was found to be high at all sites (H
E = 0.73–0.84), with little differentiation between bats sampled in the UK and continental Europe. Mantel tests indicated a
significant correlation between geographic distance and pair-wise F
ST (P = 0.000), between colonies sampled in Scotland and northern England. However, this was not continuous throughout the sampled
range, with evidence of panmixia within the area sampled in continental Europe. Assignment tests show no evidence that the
(potential) EBLV-2 sero-positive and virus positive bats were more likely to have originated from the continental rather than
UK populations. There is no sufficient significant genetic differentiation amongst most UK and continental colonies to conclude
that EBLV-2 is maintained in the UK by immigration. Results show that it is likely to be maintained at a low endemic level
within the UK. The relative genetic uniformity of UK and continental populations implies that there is no migration barrier
to EBLV-2, between these regions. 相似文献
63.
64.
Haptoglobin (Hp) is a hemoglobin-binding plasma protein consisting of two types of chains, called α and β, which originate
from a common polypeptide. In humans, but not in other mammals, Hp has been shown to occur in two allelic forms, Hp1 and Hp2,
which differ in the length of the α-chain. The longer α-chain (in Hp2) seems to have arisen by an internal duplication of
a gene segment coding for almost the entire α-chain of Hp1. In this article we show that Hp of cow (Bos taurus) contains an α-chain, the structure of which is similar to that of the human Hp2 α-chain. Furthermore, comparison of the
structure of bovine Hp and human Hp2 suggests that the bovine gene arose by a duplication of the gene segment homologous to that duplicated in human Hp2. However, a phylogenetic analysis indicates that the two genes were formed independently. The evolutionary pressure that
has led to the fixation of the Hps with a longer α-chain is not known.
Reviewing
Editor: Dr. Manyuan Long 相似文献
65.
Two-dimensional (15)N-heteronuclear single-quantum coherence (HSQC) NMR studies with a di-domain (lipoyl domain+ linker+ peripheral subunit-binding domain) of the dihydrolipoyl acetyltransferase (E2) component of the pyruvate dehydrogenase complex of Bacillus stearothermophilus allowed a molecular comparison of the need for lipoic acid to be covalently attached to the lipoyl domain in order to undergo reductive acetylation by the pyruvate decarboxylase (E1) component, in contrast with the ability of free lipoic acid to serve as substrate for the dihydrolipoyl dehydrogenase (E3) component. Tethering the lipoyl domain to the peripheral subunit-binding domain in a complex with E1 or E3 rendered the system more like the native enzyme complex, compared with the use of a free lipoyl domain, yet of a size still amenable to investigation by NMR spectroscopy. Recognition of the tethered lipoyl domain by E1 was found to be ensured by intensive interaction with the lipoyl-lysine-containing beta-turn and with residues in the protruding loop close to the beta-turn. The size and sequence of this loop varies significantly between species and dictates the lipoylated lipoyl domain as the true substrate for E1. In contrast, with E3 the main interaction sites on the tethered lipoyl domain were revealed as residues Asp41 and Ala43, which form a conserved sequence motif, DKA, around the lipoyl-lysine residue. No domain specificity is observed at this step and substrate channelling in the complex thus rests on the recognition of the lipoyl domain by the first enzyme, E1. The cofactor, thiamine diphosphate, and substrate, pyruvate, had distinct but contrasting effects on the E1/di-domain interaction, whereas NAD(+) and NADH had negligible effect on the E3/di-domain interaction. Tethering the lipoyl domain did not significantly change the nature of its interaction with E1 compared with a free lipoyl domain, indicative of the conformational freedom allowed by the linker in the movement of the lipoyl domain between active sites. 相似文献
66.
Biofilm Formation by and Antifungal Susceptibility of Candida Isolates from Urine 总被引:2,自引:0,他引:2
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N. Jain R. Kohli E. Cook P. Gialanella T. Chang B. C. Fries 《Applied microbiology》2007,73(6):1697-1703
Biofilm formation (BF) in the setting of candiduria has not been well studied. We determined BF and MIC to antifungals in Candida spp. isolates grown from urine samples of patients and performed a retrospective chart review to examine the correlation with risk factors. A total of 67 Candida spp. isolates were grown from urine samples from 55 patients. The species distribution was C. albicans (54%), C. glabrata (36%), and C. tropicalis (10%). BF varied greatly among individual Candida isolates but was stable in sequential isolates during chronic infection. BF also depended on the growth medium and especially in C. albicans was significantly enhanced in artificial urine (AU) compared to RPMI medium. In nine of the C. albicans strains BF was 4- to 10-fold higher in AU, whereas in three of the C. albicans strains and two of the C. glabrata strains higher BF was measured in RPMI medium than in AU. Determination of the MICs showed that planktonic cells of all strains were susceptible to amphotericin B (AMB) and caspofungin (CASPO) and that three of the C. glabrata strains and two of the C. albicans strains were resistant to fluconazole (FLU). In contrast, all biofilm-associated adherent cells were resistant to CASPO and FLU. The biofilms of 14 strains (28%) were sensitive to AMB (MIC50 of <1 μg/ml). Correlation between degree of BF and MIC of AMB was not seen in RPMI grown biofilms but was present when grown in AU. A retrospective chart review demonstrated no correlation of known risk factors of candiduria with BF in AU or RPMI. We conclude that BF is a stable characteristic of Candida strains that varies greatly among clinical strains and is dependent on the growth medium. Resistance to AMB is associated with higher BF in AU, which may represent the more physiologic medium to test BF. Future studies should address whether in vitro BF can predict treatment failure in vivo. 相似文献
67.
Llorenç Milà i Canals Christian Bauer Jochen Depestele Alain Dubreuil Ruth Freiermuth Knuchel Gérard Gaillard Ottar Michelsen Ruedi Müller-Wenk Bernt Rydgren 《The International Journal of Life Cycle Assessment》2007,12(1):5-15
Background, Aim and Scope
Land use by agriculture, forestry, mining, house-building or industry leads to substantial impacts, particularly on biodiversity
and on soil quality as a supplier of life support functions. Unfortunately there is no widely accepted assessment method so
far for land use impacts. This paper presents an attempt, within the UNEP-SETAC Life Cycle Initiative, to provide a framework
for the Life Cycle Impact Assessment (LCIA) of land use.
Materials and Methods:
This framework builds from previous documents, particularly the SETAC book on LCIA (Lindeijer et al. 2002), developing essential
issues such as the reference for occupation impacts; the impact pathways to be included in the analysis; the units of measure
in the impact mechanism (land use interventions to impacts); the ways to deal with impacts in the future; and bio-geographical
differentiation.
Results:
The paper describes the selected impact pathways, linking the land use elementary flows (occupation; transformation) and parameters
(intensity) registered in the inventory (LCI) to the midpoint impact indicators and to the relevant damage categories (natural
environment and natural resources). An impact occurs when the land properties are modified (transformation) and also when
the current man-made properties are maintained (occupation).
Discussion:
The size of impact is the difference between the effect on land quality from the studied case of land use and a suitable reference
land use on the same area (dynamic reference situation). The impact depends not only on the type of land use (including coverage
and intensity) but is also heavily influenced by the bio-geographical conditions of the area. The time lag between the land
use intervention and the impact may be large; thus land use impacts should be calculated over a reasonable time period after
the actual land use finishes, at least until a new steady state in land quality is reached.
Conclusions:
Guidance is provided on the definition of the dynamic reference situation and on methods and time frame to assess the impacts
occurring after the actual land use. Including the occupation impacts acknowledges that humans are not the sole users of land.
Recommendations and Perspectives:
The main damages affected by land use that should be considered by any method to assess land use impacts in LCIA are: biodiversity
(existence value); biotic production potential (including soil fertility and use value of biodiversity); ecological soil quality
(including life support functions of soil other than biotic production potential). Bio-geographical differentiation is required
for land use impacts, because the same intervention may have different consequences depending on the sensitivity and inherent
land quality of the environment where it occurs. For the moment, an indication of how such task could be done and likely bio-geographical
parameters to be considered are suggested. The recommendation of indicators for the suggested impact categories is a matter
of future research. 相似文献
68.
Wang P Tang H Fitzgibbon MP McIntosh M Coram M Zhang H Yi E Aebersold R 《Biostatistics (Oxford, England)》2007,8(2):357-367
Integrated liquid-chromatography mass-spectrometry (LC-MS) is becoming a widely used approach for quantifying the protein composition of complex samples. The output of the LC-MS system measures the intensity of a peptide with a specific mass-charge ratio and retention time. In the last few years, this technology has been used to compare complex biological samples across multiple conditions. One challenge for comparative proteomic profiling with LC-MS is to match corresponding peptide features from different experiments. In this paper, we propose a new method--Peptide Element Alignment (PETAL) that uses raw spectrum data and detected peak to simultaneously align features from multiple LC-MS experiments. PETAL creates spectrum elements, each of which represents the mass spectrum of a single peptide in a single scan. Peptides detected in different LC-MS data are aligned if they can be represented by the same elements. By considering each peptide separately, PETAL enjoys greater flexibility than time warping methods. While most existing methods process multiple data sets by sequentially aligning each data set to an arbitrarily chosen template data set, PETAL treats all experiments symmetrically and can analyze all experiments simultaneously. We illustrate the performance of PETAL on example data sets. 相似文献
69.
Thomas Kuilman Alessio Maiolica Molly Godfrey Noémie Scheidel Ruedi Aebersold Frank Uhlmann 《The EMBO journal》2015,34(1):81-96
The final event of the eukaryotic cell cycle is cytokinesis, when two new daughter cells are born. How the timing and execution of cytokinesis is controlled is poorly understood. Here, we show that downregulation of cyclin-dependent kinase (Cdk) activity, together with upregulation of its counteracting phosphatase Cdc14, controls each of the sequential steps of cytokinesis, including furrow ingression, membrane resolution and cell separation in budding yeast. We use phosphoproteome analysis of mitotic exit to identify Cdk targets that are dephosphorylated at the time of cytokinesis. We then apply a new and widely applicable tool to generate conditionally phosphorylated proteins to identify those whose dephosphorylation is required for cytokinesis. This approach identifies Aip1, Ede1 and Inn1 as cytokinetic regulators. Our results suggest that cytokinesis is coordinately controlled by the master cell cycle regulator Cdk together with its counteracting phosphatase and that it is executed by concerted dephosphorylation of Cdk targets involved in several cell biological processes. 相似文献
70.
Hubert Pausch Hermann Schwarzenbacher Johann Burgstaller Krzysztof Flisikowski Christine Wurmser Sandra Jansen Simone Jung Angelika Schnieke Thomas Wittek Ruedi Fries 《BMC genomics》2015,16(1)