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Background
Plasmid DNA molecules are closed circular molecules that are widely used in life sciences, particularly in gene therapy research. Monte Carlo methods have been used for several years to simulate the conformational behavior of DNA molecules. In each iteration these simulation methods randomly generate a new trial conformation, which is either accepted or rejected according to a criterion based on energy calculations and stochastic rules. These simulation trials are generated using a method based on crankshaft motion that, apart from some slight improvements, has remained the same for many years.Results
In this paper, we present a new algorithm for the deformation of plasmid DNA molecules for Monte Carlo simulations. The move underlying our algorithm preserves the size and connectivity of straight-line segments of the plasmid DNA skeleton. We also present the results of three experiments comparing our deformation move with the standard and biased crankshaft moves in terms of acceptance ratio of the trials, energy and temperature evolution, and average displacement of the molecule. Our algorithm can also be used as a generic geometric algorithm for the deformation of regular polygons or polylines that preserves the connections and lengths of their segments.Conclusion
Compared with both crankshaft moves, our move generates simulation trials with higher acceptance ratios and smoother deformations, making it suitable for real-time visualization of plasmid DNA coiling. For that purpose, we have adopted a DNA assembly algorithm that uses nucleotides as building blocks. 相似文献95.
H. Lemriss Martins Sim?es P S. Lemriss M. Butin A. Ibrahimi S. El Kabbaj JP Rasigade F. Laurent 《Standards in genomic sciences》2014,9(3):1118-1127
Staphylococcus capitis is a coagulase-negative staphylococcus (CoNS) commonly found in the human microflora. Recently, a clonal population of Staphylococcus capitis (denominated NRCS-A) was found to be a major cause of late-onset sepsis (LOS) in several neonatal intensive care units in France. Here, we report the complete genome sequence and annotation of the prototype Staphylococcus capitis NCRS-A strain CR01. The 2,504,472 bp long genome (1 chromosome and no plasmids) exhibits a G+C content of 32.81%, and contains 2,468 protein-coding and 59 tRNA genes and 4 rRNA genes. 相似文献
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97.
Y Novik LM Ryan DG Haller R Asbury JP Dutcher A Schutt 《Cancer immunology, immunotherapy : CII》1999,16(4):261-266
The study was a Phase II randomized study to evaluate the efficacy of new agents for the treatment of advanced gastric carcinoma.
Patients were randomized to receive single agent chemotherapy with mitoxantrone, etoposide, aclacinomycin-A or spirogermanium.
The patients were stratified by prior use of chemotherapy, prior doxorubicin use and ECOG performance status. Patients with
a history of cardiac disease or prior doxorubicin exceeding a dose of 400 mg/m2 were restrictively randomized to sopirogermanium or etoposide only. One hundred and fourteen patients were registered for
the study. Among 98 evaluable patients there were only two partial responses (both in the etoposide arm), and one complete
response in the mitoxantrone arm. The median survival on the study was 3.3 months. One hundred and six patients were analyzable
for toxicity. There were four treatment-related deaths and four life-threatening toxicities. Because of low response rates
and relatively high toxicities the studied compounds were not deemed worth further investigation for advanced gastric cancer. 相似文献
98.
JP Reyes A Huanosta-Gutiérrez A López-Rodríguez A Martínez-Torres 《Channels (Austin, Tex.)》2015,9(2):88-95
We studied the effects of mutations of positively charged amino acid residues in the pore of X. tropicalis TMEM16A calcium-activated chloride channels: K613E, K628E, K630E; R646E and R761E. The activation and deactivation kinetics were not affected, and only K613E showed a lower current density. K628E and R761E affect anion selectivity without affecting Na+ permeation, whereas K613E, R646E and the double mutant K613E + R646E affect anion selectivity and permeability to Na+. Furthermore, altered blockade by the chloride channel blockers anthracene-9-carboxylic acid (A-9-C), 4, 4''-Diisothiocyano-2,2''-stilbenedisulfonic acid (DIDS) and T16inh-A01 was observed. These results suggest the existence of 2 binding sites for anions within the pore at electrical distances of 0.3 and 0.5. These sites are also relevant for anion permeation and blockade. 相似文献
99.
C Tardif H Maamar M Balfin JP Belaich 《Journal of industrial microbiology & biotechnology》2001,27(5):271-274
Electropermeabilization of Clostridium cellulolyticum was optimized using ATP leakage assays. Electrotransformation was then performed under optimized conditions (6 to 7.5 kV
cm−1 field strength applied during 5 ms to a mixture containing methylated plasmids and late exponential phase cell suspensions
(10 molecules:1 cell) in a sucrose-containing buffer). Transformants were only obtained when 7 or 7.5 kV cm−1 pulses were applied. Transformation efficiencies evaluated from the growth curves of transformed cells were between 105 and 107 transformants per microgram of plasmid DNA for five different replicon-based plasmids. Restriction nuclease digestion patterns
of pJIR418 purified from transformed Clostridia and Escherichia coli were indistinguishable, indicating that heterologous DNA was structurally stable in the Clostridium strain. Copy numbers of 130, 70 and 10 were estimated from purification yield for pCTC1, pKNT19 and pJIR418, respectively.
Journal of Industrial Microbiology & Biotechnology (2001) 27, 271–274.
Received 12 September 2000/ Accepted in revised form 25 November 2000 相似文献
100.
Evolutionary transfer of ORF-containing group I introns between different subcellular compartments (chloroplast and mitochondrion) 总被引:8,自引:2,他引:8
Turmel M; Cote V; Otis C; Mercier JP; Gray MW; Lonergan KM; Lemieux C 《Molecular biology and evolution》1995,12(4):533-545
We describe here a case of homologous introns containing homologous open
reading frames (ORFs) that are inserted at the same site in the large
subunit (LSU) rRNA gene of different organelles in distantly related
organisms. We show that the chloroplast LSU rRNA gene of the green alga
Chlamydomonas pallidostigmatica contains a group I intron (CpLSU.2)
encoding a site-specific endonuclease (I-CpaI). This intron is inserted at
the identical site (corresponding to position 1931-1932 of the Escherichia
coli 23S rRNA sequence) as a group I intron (AcLSU.m1) in the mitochondrial
LSU rRNA gene of the amoeboid protozoon Acanthamoeba castellanii. The
CpLSU.2 intron displays a remarkable degree of nucleotide similarity in
both primary sequence and secondary structure to the AcLSU.m1 intron;
moreover, the Acanthamoeba intron contains an ORF in the same location
within its secondary structure as the CpLSU.2 ORF and shares with it a
strikingly high level of amino acid similarity (65%; 42% identity). A
comprehensive survey of intron distribution at site 1931 of the chloroplast
LSU rRNA gene reveals a rather restricted occurrence within the
polyphyletic genus Chlamydomonas, with no evidence of this intron among a
number of non- Chlamydomonad green algae surveyed, nor in land plants. A
parallel survey of homologues of a previously described and similar
intron/ORF pair (C. reinhardtii chloroplast CrLSU/A. castellanii
mitochondrial AcLSU.m3) also shows a restricted occurrence of this intron
(site 2593) among chloroplasts, although the intron distribution is
somewhat broader than that observed at site 1931, with site-2593 introns
appearing in several green algal branches outside of the Chlamydomonas
lineage. The available data, while not definitive, are most consistent with
a relatively recent horizontal transfer of both site-1931 and site- 2593
introns (and their contained ORFs) between the chloroplast of a
Chlamydomonas-type organism and the mitochondrion of an Acanthamoeba- like
organism, probably in the direction chloroplast to mitochondrion. The data
also suggest that both introns could have been acquired in a single event.
相似文献