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41.
Wastewater treatment is one of the largest scale and arguably the most commercially important biotechnological process in the world. Bacterial breakdown of waste materials facilitates the safe disposal of effluents into receiving water bodies. Given this significance, research has focused on identifying the keystone species on which efficient treatment is based. However, unravelling the microbial diversity within such systems has proven difficult. This is highlighted by our lack of detailed knowledge of the microbial interactions within these complex populations, limiting our ability to fully exploit bacterial degradative abilities. Even with the incorporation of new emerging molecular techniques, there have been no investigations linking genetic sequence to microbial function and successful treatment operation. To reach this goal, researchers need the ability to identify, enumerate and monitor the metabolic functions of subpopulations within these complex bacterial communities. Flow cytometry (FCM) combined with fluorescence-based molecular identification techniques provides a method for such studies. Moreover, single-cell sorting provides a unique opportunity to identify and remove individual cells of interest. Laboratory culture of sorted cells is often possible and permits the use of more traditional microbiological techniques to backup molecular investigations. Utilising this approach will advance our understanding of wastewater treatment processes and help maintain and enhance plant operation to improve efficiency. 相似文献
42.
Dunsmore BC Jacobsen A Hall-Stoodley L Bass CJ Lappin-Scott HM Stoodley P 《Journal of industrial microbiology & biotechnology》2002,29(6):347-353
Biofilms of sulphate-reducing Desulfovibrio sp. EX265 were grown in square section glass capillary flow cells under a range of fluid flow velocities from 0.01 to 0.4
m/s (wall shear stress, τw, from 0.027 to 1.0 N/m2). In situ image analysis and confocal scanning laser microscopy revealed biofilm characteristics similar to those reported for aerobic
biofilms. Biofilms in both flow cells were patchy and consisted of cell clusters separated by voids. Length-to-width ratio
measurements (l
c:w
c) of biofilm clusters demonstrated the formation of more “streamlined” biofilm clusters (l
c:w
c=3.03) at high-flow velocity (Reynolds number, Re, 1200), whereas at low-flow velocity (Re 120), the l
c:w
c of the clusters was approximately 1 (l
c:w
c of 1 indicates no elongation in the flow direction). Cell clusters grown under high flow were more rigid and had a higher
yield point (the point at which the biofilm began to flow like a fluid) than those established at low flow and some biofilm
cell aggregates were able to relocate within a cluster, by travelling in the direction of flow, before attaching more firmly
downstream.
Received 01 February 2002/ Accepted in revised form 16 July 2002 相似文献
43.
Christopher D. Clegg Jan D. van Elsas Jonathan M. Anderson Hilary M. Lappin-Scott 《FEMS microbiology ecology》1994,15(1-2):161-168
Abstract The effects of a terrestrial isopod, Porcellio scaber , on the survival of a genetically modified pseudomonad were studied. Pseudomonas fluorescens KTG was inoculated onto ash leaf litter and supplied to populations of P. scaber . Plate counts were lower in fresh faeces than the ash leaf litter for P. fluorescens KTG, and higher counts were detected in the faeces for the total bacterial population. When faeces were aged by incubation for up to 7 days at 15–17°C, plate counts for P. fluorescens KTG increased during the first day to a level similar to those in the corresponding ash leaf litter, and remained relatively constant thereafter. The total bacterial population in the faeces continued to increase steadily over the 7 days, whilst remaining at a constant level in the ash leaf litter during the same period. Counts of bacteria in faecal material showed that P. fluorescens KTG was present for 6 days after the isopods had fed on inoculated litter although transit times of food through the gut were as little as 5 h. The implications for GEMMO dispersal of bacterial retention in the gut is considered. The polymerase chain reaction was utilised in the detection of the inserted DNA. Positive amplification of the inserted DNA sequence of P. fluorescens KTG was achieved in ash leaf litter, fresh faeces, and faeces from animal which were supplied uninoculated litter for one day after feeding on the inoculated litter. However, plate counts were more sensitive than the polymerase chain reaction in detecting P. fluorescens KTG in the faeces. Our findings suggest that when the GEMMO is ingested by the woodlouse it can survive within the guts and faeces. This has implications for risk assessment of genetically modified bacteria in terrestrial environments. 相似文献
44.
45.
Antibodies to citrullinated proteins and differences in clinical progression of rheumatoid arthritis
van der Helm-van Mil AH Verpoort KN Breedveld FC Toes RE Huizinga TW 《Arthritis research & therapy》2005,7(5):R949-R958
Antibodies to citrullinated proteins (anti-cyclic-citrullinated peptide [anti-CCP] antibodies) are highly specific for rheumatoid
arthritis (RA) and precede the onset of disease symptoms, indicating a pathogenetic role for these antibodies in RA. We recently
showed that distinct genetic risk factors are associated with either anti-CCP-positive disease or anti-CCP-negative disease.
These data are important as they indicate that distinct pathogenic mechanisms are underlying anti-CCP-positive disease or
anti-CCP-negative disease. Likewise, these observations raise the question of whether anti-CCP-positive RA and anti-CCP-negative
RA are clinically different disease entities. We therefore investigated whether RA patients with anti-CCP antibodies have
a different clinical presentation and disease course compared with patients without these autoantibodies. In a cohort of 454
incident patients with RA, 228 patients were anti-CCP-positive and 226 patients were anti-CCP-negative. The early symptoms,
tender and swollen joint count, and C-reactive protein level at inclusion, as well as the swollen joint count and radiological
destruction during 4 years of follow-up, were compared for the two groups. There were no differences in morning stiffness,
type, location and distribution of early symptoms, patients' rated disease activity and C-reactive protein at inclusion between
RA patients with and without anti-CCP antibodies. The mean tender and swollen joint count for the different joints at inclusion
was similar. At follow-up, patients with anti-CCP antibodies had more swollen joints and more severe radiological destruction.
Nevertheless, the distribution of affected joints, for swelling, bone erosions and joint space narrowing, was similar. In
conclusion, the phenotype of RA patients with or without anti-CCP antibodies is similar with respect to clinical presentation
but differs with respect to disease course. 相似文献
46.
Sofie HM Manders Wietske Kievit Eddy Adang Herman L Brus Hein J Bernelot Moens Andre Hartkamp Lidy Hendriks Elisabeth Brouwer Henk Visser Harald E Vonkeman Jos Hendrikx Tim L Jansen Rene Westhovens Mart AFJ van de Laar Piet LCM van Riel 《Arthritis research & therapy》2015,17(1)
IntroductionFor patients with rheumatoid arthritis (RA) whose treatment with a tumour necrosis factor inhibitor (TNFi) is failing, several biological treatment options are available. Often, another TNFi or a biological with another mode of action is prescribed. The objective of this study was to compare the effectiveness and cost-effectiveness of three biologic treatments with different modes of action in patients with RA whose TNFi therapy is failing.MethodsWe conducted a pragmatic, 1-year randomised trial in a multicentre setting. Patients with active RA despite previous TNFi treatment were randomised to receive abatacept, rituximab or a different TNFi. The primary outcome (Disease Activity Score in 28 joints) and the secondary outcomes (Health Assessment Questionnaire Disability Index and 36-item Short Form Health Survey scores) were analysed using linear mixed models. Cost-effectiveness was analysed on the basis of incremental net monetary benefit, which was based on quality-adjusted life-years (calculated using EQ-5D scores), and all medication expenditures consumed in 1 year. All analyses were also corrected for possible confounders.ResultsOf 144 randomised patients, 5 were excluded and 139 started taking abatacept (43 patients), rituximab (46 patients) or a different TNFi (50 patients). There were no significant differences between the three groups with respect to multiple measures of RA outcomes. However, our analysis revealed that rituximab therapy is significantly more cost-effective than both abatacept and TNFi over a willingness-to-pay range of 0 to 80,000 euros.ConclusionsAll three treatment options were similarly effective; however, when costs were factored into the treatment decision, rituximab was the best option available to patients whose first TNFi treatment failed. However, generalization of these costs to other countries should be undertaken carefully.
Trial registration
Netherlands Trial Register number NTR1605. Registered 24 December 2008.Electronic supplementary material
The online version of this article (doi:10.1186/s13075-015-0630-5) contains supplementary material, which is available to authorized users. 相似文献47.
Improved Fluorescent In Situ Hybridization Method for Detection of Bacteria from Activated Sludge and River Water by Using DNA Molecular Beacons and Flow Cytometry 总被引:3,自引:1,他引:2 下载免费PDF全文
Fluorescent in situ hybridization (FISH) remains a key technique in microbial ecology. Molecular beacons (MBs) are self-reporting probes that have potential advantages over linear probes for FISH. MB-FISH strategies have been described using both DNA-based and peptide nucleic acid (PNA)-based approaches. Although recent reports have suggested that PNA MBs are superior, DNA MBs have some advantages, most notably cost. The data presented here demonstrate that DNA MBs are suitable for at least some FISH applications in complex samples, providing superior discriminatory power compared to that of corresponding linear DNA-FISH probes. The use of DNA MBs for flow cytometric detection of Pseudomonas putida resulted in approximately double the signal-to-noise ratio of standard linear DNA probes when using laboratory-grown cultures and yielded improved discrimination of target cells in spiked environmental samples, without a need for separate washing steps. DNA MBs were also effective for the detection and cell sorting of both spiked and indigenous P. putida from activated sludge and river water samples. The use of DNA MB-FISH presents another increase in sensitivity, allowing the detection of bacteria in environmental samples without the expense of PNA MBs or multilaser flow cytometry. 相似文献
48.
Ami M. Smith Deepak Sharma Hilary Lappin-Scott Sara Burton David H. Huber 《Applied microbiology and biotechnology》2014,98(5):2321-2334
The microbial community structure of a stable pilot-scale thermophilic continuous stirred tank reactor digester stabilized on poultry litter was investigated. This 40-m3 digester produced biogas with 57 % methane, and chemical oxygen demand removal of 54 %. Bacterial and archaeal diversity were examined using both cloning and pyrosequencing that targeted 16S rRNA genes. The bacterial community was dominated by phylum Firmicutes, constituting 93 % of the clones and 76 % of the pyrotags. Of the Firmicutes, class Clostridia (52 % pyrotags) was most abundant followed by class Bacilli (13 % pyrotags). The bacterial libraries identified 94 operational taxonomic units (OTUs) and pyrosequencing identified 577 OTUs at the 97 % minimum similarity level. Fifteen OTUs were dominant (≥2 % abundance), and nine of these were novel unclassified Firmicutes. Several of the dominant OTUs could not be classified more specifically than Clostridiales, but were most similar to plant biomass degraders, including Clostridium thermocellum. Of the rare pyrotag OTUs (<0.5 % abundance), 75 % were Firmicutes. The dominant methanogen was Methanothermobacter which has hydrogenotrophic metabolism, and accounted for >99 % of the archaeal clones. Based on the primary methanogen, as well as digester chemistry (high VA and ammonia levels), we propose that bacterial acetate oxidation is the primary pathway in this digester for the control of acetate levels. 相似文献
49.
Erin N Smith Kristen Jepsen Mahdieh Khosroheidari Laura Z Rassenti Matteo D’Antonio Emanuela M Ghia Dennis A Carson Catriona HM Jamieson Thomas J Kipps Kelly A Frazer 《Genome biology》2014,15(7)
Accurate allele frequencies are important for measuring subclonal heterogeneity and clonal evolution. Deep-targeted sequencing data can contain PCR duplicates, inflating perceived read depth. Here we adapted the Illumina TruSeq Custom Amplicon kit to include single molecule tagging (SMT) and show that SMT-identified duplicates arise from PCR. We demonstrate that retention of PCR duplicate reads can imply clonal evolution when none exists, while their removal effectively controls the false positive rate. Additionally, PCR duplicates alter estimates of subclonal heterogeneity in tumor samples. Our method simplifies PCR duplicate identification and emphasizes their removal in studies of tumor heterogeneity and clonal evolution.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0420-4) contains supplementary material, which is available to authorized users. 相似文献50.
Biofilms adhere to stay 总被引:3,自引:0,他引:3