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91.
S Timothy Motley John M Picuri Chris D Crowder Jeremiah J Minich Steven A Hofstadler Mark W Eshoo 《BMC genomics》2014,15(1)
Background
Next-generation sequencing sample preparation requires nanogram to microgram quantities of DNA; however, many relevant samples are comprised of only a few cells. Genomic analysis of these samples requires a whole genome amplification method that is unbiased and free of exogenous DNA contamination. To address these challenges we have developed protocols for the production of DNA-free consumables including reagents and have improved upon multiple displacement amplification (iMDA).Results
A specialized ethylene oxide treatment was developed that renders free DNA and DNA present within Gram positive bacterial cells undetectable by qPCR. To reduce DNA contamination in amplification reagents, a combination of ion exchange chromatography, filtration, and lot testing protocols were developed. Our multiple displacement amplification protocol employs a second strand-displacing DNA polymerase, improved buffers, improved reaction conditions and DNA free reagents. The iMDA protocol, when used in combination with DNA-free laboratory consumables and reagents, significantly improved efficiency and accuracy of amplification and sequencing of specimens with moderate to low levels of DNA. The sensitivity and specificity of sequencing of amplified DNA prepared using iMDA was compared to that of DNA obtained with two commercial whole genome amplification kits using 10 fg (~1-2 bacterial cells worth) of bacterial genomic DNA as a template. Analysis showed >99% of the iMDA reads mapped to the template organism whereas only 0.02% of the reads from the commercial kits mapped to the template. To assess the ability of iMDA to achieve balanced genomic coverage, a non-stochastic amount of bacterial genomic DNA (1 pg) was amplified and sequenced, and data obtained were compared to sequencing data obtained directly from genomic DNA. The iMDA DNA and genomic DNA sequencing had comparable coverage 99.98% of the reference genome at ≥1X coverage and 99.9% at ≥5X coverage while maintaining both balance and representation of the genome.Conclusions
The iMDA protocol in combination with DNA-free laboratory consumables, significantly improved the ability to sequence specimens with low levels of DNA. iMDA has broad utility in metagenomics, diagnostics, ancient DNA analysis, pre-implantation embryo screening, single-cell genomics, whole genome sequencing of unculturable organisms, and forensic applications for both human and microbial targets. 相似文献92.
EB Adamah-Biassi Y Zhang H Jung S Vissapragada RJ Miller ML Dubocovich 《The journal of histochemistry and cytochemistry》2014,62(1):70-84
The pineal hormone melatonin activates two G-protein coupled receptors (MT1 and MT2) to regulate in part biological functions. The MT1 and MT2 melatonin receptors are heterogeneously distributed in the mammalian brain including humans. In the mouse, only a few reports have assessed the expression of the MT1 melatonin receptor expression using 2-iodomelatonin binding, in situ hybridization and/or polymerase chain reaction (PCR). Here, we described a transgenic mouse in which red fluorescence protein (RFP) is expressed under the control of the endogenous MT1 promoter, by inserting RFP cDNA at the start codon of MTNR1a gene within a bacterial artificial chromosome (BAC) and expressing this construct as a transgene. The expression of RFP in the brain of this mouse was examined either directly under a fluorescent microscope or immunohistochemically using an antibody against RFP (RFP-MT1). RFP-MT1 expression was observed in many brain regions including the subcommissural organ, parts of the ependyma lining the lateral and third ventricles, the aqueduct, the hippocampus, the cerebellum, the pars tuberalis, the habenula and the habenula commissure. This RFP-MT1 transgenic model provides a unique tool for studying the distribution of the MT1 receptor in the brain of mice, its cell-specific expression and its function in vivo. 相似文献
93.
Cheng H Lundy DeMello KM Li J Sakya SM Ando K Kawamura K Kato T Rafka RJ Jaynes BH Ziegler CB Stevens R Lund LA Mann DW Kilroy C Haven ML Nimz EL Dutra JK Li C Minich ML Kolosko NL Petras C Silvia AM Seibel SB 《Bioorganic & medicinal chemistry letters》2006,16(8):2076-2080
The discovery of heteroaryl-phenyl-substituted pyrazole derivatives as canine selective COX-2 inhibitors is described. Structure-activity relationship (SAR) studies of this class of compounds led to the identification of compound 1 which demonstrated a canine whole blood COX-2 inhibitory IC50 of 12 nM and selectivity ratio of COX-1/COX-2 greater than 4000-fold. 相似文献
94.
Marcel ML Cunha Anderson J Franzen Sergio H Seabra Marcelo H Herbst Ney V Vugman Luana P Borba Wanderley de Souza Sonia Rozental 《BMC microbiology》2010,10(1):80
Background
The pathogenic fungus Fonsecaea pedrosoi constitutively produces the pigment melanin, an important virulence factor in fungi. Melanin is incorporated in the cell wall structure and provides chemical and physical protection for the fungus. 相似文献95.
Jeffrey W. Corbett Kevin D. Freeman-Cook Richard Elliott Felix Vajdos Francis Rajamohan Darcy Kohls Eric Marr Hailong Zhang Liang Tong Meihua Tu Sharad Murdande Shawn D. Doran Janet A. Houser Wei Song Christopher J. Jones Steven B. Coffey Leanne Buzon Martha L. Minich Kenneth J. Dirico Susan Tapley William Esler 《Bioorganic & medicinal chemistry letters》2010,20(7):2383-2388
Screening Pfizer’s compound library resulted in the identification of weak acetyl-CoA carboxylase inhibitors, from which were obtained rACC1 CT-domain co-crystal structures. Utilizing HTS hits and structure-based drug discovery, a more rigid inhibitor was designed and led to the discovery of sub-micromolar, spirochromanone non-specific ACC inhibitors. Low nanomolar, non-specific ACC-isozyme inhibitors that exhibited good rat pharmacokinetics were obtained from this chemotype. 相似文献
96.
M K Sharp G M Pantalos L Minich L Y Tani E C McGough J A Hawkins 《Journal of applied physiology》2000,88(6):2227-2239
Flow and pressure measurements were performed in the ascending aortas of six pediatric patients ranging in age from 1 to 4 yr and in weight from 7.2 to 16.4 kg. From these measurements, input impedance was calculated. It was found that total vascular resistance decreased with increasing patient weight and was approximately one to three times higher than those of adults. Conductance per unit weight was relatively constant but was approximately three times higher than for adults. Strong inertial character was observed in the impedance of four of the six patients. Among a three-element and two four-element lumped-parameter models, the model with characteristic aortic resistor (R(c)) and inertance in series followed by parallel peripheral resistor (R(p)) and compliance fitted the data best. R(p) decreased with increasing patient weight and was one to three times higher than in adults, and R(c) decreased with increasing patient weight and was 2 to 15 times higher. The R(p)-to-R(c) ratio differed significantly between infants and children vs. adults. The results suggested that R(p) developed more rapidly with patient weight than did R(c). Compliance values increased with increasing patient weight and were 3 to 16 times lower than adult values. 相似文献
97.
The administration of L-tryptophan-[3-14C] to Phalaris arundinacea L. (Vantage strain) for 9 days resulted in the formation of radioactive gramine (8.2% absolute incorporation). A systematic degradation of the alkaloid indicated that essentially all its activity was located on the methylene group, indicating that its biosynthesis is the same as that occurring in Hordeum species and Lupinus hartwegii. 相似文献
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