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81.
82.
Jennifer Van Grol Cecilia Subauste Rosa M. Andrade Koh Fujinaga Julie Nelson Carlos S. Subauste 《PloS one》2010,5(7)
Autophagy is a homeostatic mechanism of lysosomal degradation. Defective autophagy has been linked to various disorders such as impaired control of pathogens and neurodegeneration. Autophagy is regulated by a complex array of signaling pathways that act upstream of autophagy proteins. Little is known about the role of altered regulatory signaling in disorders associated with defective autophagy. In particular, it is not known if pathogens inhibit autophagy by modulation of upstream regulatory pathways. Cells infected with HIV-1 blocked rapamycin-induced autophagy and CD40-induced autophagic killing of Toxoplasma gondii in bystander (non-HIV-1 infected) macrophage/monocytic cells. Blockade of autophagy was dependent on Src-Akt and STAT3 triggered by HIV-1 Tat and IL-10. Neutralization of the upstream receptors VEGFR, β-integrin or CXCR4, as well as of HIV-1 Tat or IL-10 restored autophagy in macrophage/monocytic cells exposed to HIV-1-infected cells. Defective autophagic killing of T. gondii was detected in monocyte-derived macrophages from a subset of HIV-1+ patients. This defect was also reverted by neutralization of Tat or IL-10. These studies revealed that a pathogen can impair autophagy in non-infected cells by activating counter-regulatory pathways. The fact that pharmacologic manipulation of cell signaling restored autophagy in cells exposed to HIV-1-infected cells raises the possibility of therapeutic manipulation of cell signaling to restore autophagy in HIV-1 infection. 相似文献
83.
Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated 总被引:3,自引:1,他引:2
It has long been known, from the distribution of multiple amino acid
replacements, that not all amino acids of a sequence are replaceable. More
recently, the phenomenon was observed at the nucleotide level in
mitochondrial DNA even after allowing for different rates of transition and
transversion substitutions. We have extended the search to globin gene
sequences from various organisms, with the following results: (1) Nearly
every data set showed evidence of invariable nucleotide positions. (2) In
all data sets, substitution rates of transversions and transitions were
never in the ratio of 2/1, and rarely was the ratio even constant. (3) Only
rarely (e.g., the third codon position of beta hemoglobins) was it possible
to fit the data set solely by making allowance for the number of invariable
positions and for the relative rates of transversion and transition
substitutions. (4) For one data set (the second codon position of beta
hemoglobins) we were able to simulate the observed data by making the
allowance in (3) and having the set of covariotides (concomitantly variable
nucleotides) be small in number and be turned over in a stochastic manner
with a probability that was appreciable. (5) The fit in the latter case
suggests, if the assumptions are correct and at all common, that current
procedures for estimating the total number of nucleotide substitutions in
two genes since their divergence from their common ancestor could be low by
as much as an order of magnitude. (6) The fact that only a small fraction
of the nucleotide positions differ is no guarantee that one is not
seriously underestimating the total amount of divergence (substitutions).
(7) Most data sets are so heterogeneous in their number of transition and
transversion differences that none of the current models of nucleotide
substitution seem to fit them even after (a) segregation of coding from
noncoding sequences and (b) splitting of the codon into three subsets by
codon position. (8) These frequently occurring problems cannot be seen
unless several reasonably divergent orthologous genes are examined
together.
相似文献
84.
Bayesian adaptive sequence alignment algorithms 总被引:3,自引:1,他引:2
The selection of a scoring matrix and gap penalty parameters continues to
be an important problem in sequence alignment. We describe here an
algorithm, the 'Bayes block aligner, which bypasses this requirement.
Instead of requiring a fixed set of parameter settings, this algorithm
returns the Bayesian posterior probability for the number of gaps and for
the scoring matrices in any series of interest. Furthermore, instead of
returning the single best alignment for the chosen parameter settings, this
algorithm returns the posterior distribution of all alignments considering
the full range of gapping and scoring matrices selected, weighing each in
proportion to its probability based on the data. We compared the Bayes
aligner with the popular Smith-Waterman algorithm with parameter settings
from the literature which had been optimized for the identification of
structural neighbors, and found that the Bayes aligner correctly identified
more structural neighbors. In a detailed examination of the alignment of a
pair of kinase and a pair of GTPase sequences, we illustrate the
algorithm's potential to identify subsequences that are conserved to
different degrees. In addition, this example shows that the Bayes aligner
returns an alignment-free assessment of the distance between a pair of
sequences.
相似文献
85.
Schürmann A Schmidt M Asmus M Bayer S Fliegert F Koling S Massmann S Schilf C Subauste MC Voss M Jakobs KH Joost HG 《The Journal of biological chemistry》1999,274(14):9744-9751
ADP-ribosylation factor-related protein (ARP) is a membrane-associated GTPase with remote similarity to the family of ADP-ribosylation factors (ARF). In a yeast two-hybrid screen designed to identify proteins interacting with ARP, we isolated a partial cDNA of the ARF-specific guanine nucleotide exchange factor mSec7-1/cytohesin encoding its N terminus and most of the Sec7 domain (codons 1-200). ARP and ARP-Q79L (GTPase-negative ARP) exhibited a higher affinity to mSec7-1-(1-200) than ARP-T31N (nucleotide exchange-defective ARP) in the two-hybrid assay. Similarly, full-length [35S]mSec7-1/cytohesin was specifically adsorbed to glutathione-Sepharose loaded with glutathione S-transferase (GST)-ARP-Q79L, GST-ARP, or GST-ARP-T31N, the latter exhibiting the lowest binding affinity. Overexpression of ARP-Q79L, but not of ARP-T31N, in COS-7 cells reduced the fluorescence from co-expressed green fluorescent protein fused with mSec7-1/cytohesin or mSec7-2/ARNO in plasma membranes as detected by deconvolution microscopy. Recombinant ARP and ARP-Q79L, but not ARP-T31N, inhibited the phospholipase D (PLD) activity stimulated by mSec7-2/ARNO and ARF in a system of isolated membranes. Furthermore, transfection of HEK-293 cells with ARP or ARP-Q79L, but not ARP-T31N, inhibited the muscarinic acetylcholine receptor-3 induced PLD stimulation and translocation of ARF from cytosol to membranes. These data suggest that the GTP-bound form of ARP specifically binds mSec7-1/cytohesin, and that ARP may be involved in a pathway inhibiting the ARF-controlled activity of PLD. 相似文献
86.
87.
88.
Reta-Sánchez DG JS Serrato-Corona HM Quiroga-Garza A Gaytán-Mascorro JA Cueto-Wong 《Phyton》2015,84(2):262-271
Kenaf (Hibiscus cannabinus L.) forage potential can be enhanced through its regrowth capacity and higher production in narrow rows. A field experiment was conducted in Matamoros, Coahuila, Mexico, during 2 growing seasons (2004 and 2005) to study the effects of plant height and row spacing on kenaf forage potential with multiple harvests. This study evaluated the effects of (1) 2 plant heights at cutting (1.0-1.2 m and 1.8-2.0 m) and (2) 4 inter row spacings (0.19, 0.38, 0.57 and 0.76 m) using a 2 x 4 factorial arrangement of treatments in a completely randomized block design with 4 replications. Dry matter (DM) and crude protein (CP) yields, DM partitioning, neutral detergent fiber (NDF) and CP concentrations were determined. Heights at cutting × row spacing interactions were not significant for the monitored variables (p>0.05). Kenaf response to treatments was only relevant for main effects (p≤0.05). Row spacing and plant height affected DM and CP yields (p≤0.05), whereas only plant height affected chemical composition and DM partitioning (p≤0.05). Dry matter (17.0%-26.0%), and CP (12.4%-15.6%) yields were higher (p≤0.05) when plant heights had reached 1.8 to 2.0 m. Row spacing reduction from 0.76 m to 0.38 and 0.19 m increased DM yield (20.4-33.4%) and CP yield (24.2-38.5%) (p≤0.05). Kenaf forage potential increases when planted in narrow rows and harvested 2 or 3 times during the growing season. 相似文献
89.
Gutiérrez-Guzmán UN E Castellanos-Pérez JJ Q uiñones-Vera JS Serrato-Corona JJ Martínez-Ríos I Orona-Castillo I Chairez-Hernández 《Phyton》2015,84(2):312-318
A regression model was used to determine the relationship between aerial herbaceous biomass and vegetation coverage estimated by digital images. Four samplings (n=36 each date) of vegetation cover and herbaceous biomass were performed during the growing season in 2011 in a grassland dominated by Bouteloua gracilis in La Cieneguilla, Municipality of Villa Hidalgo, Durango. Average production of dry biomass was 37.36 ± 9.66 g/m2, and mean vegetation cover 30.02%. Dry biomass data were tested for normality using the test of Kolmogorov Smirnov, finding a lack of fit. The data were subjected to a logarithmic transformation and the model Ln(y) = 1.637926 + 0.08501X - 0.000586X2 with an adjusted R2 = 0.89 was found. In order to validate this model, another five samplings were carried out in 2013 at the same site during summer and autumn, using the same sampling size for each date as in 2011. Data collected in 2013 were analyzed with the model Ln (y) = β0 + β1X + β2X2. A comparison of regression coefficients was carried out between the 2011 and 2013 models with t (180+144-9-11-2=302, p<0.05) = 1.967. The results indicated that it is possible to use the 2011 regression model to estimate herbaceous aerial biomass from vegetation cover measurements with aerial photographs in La Cieneguilla site during summer and fall. 相似文献
90.
Sacha?AFT?van Hijum Anne?de Jong Richard?JS?Baerends Harma?A?Karsens Naomi?E?Kramer Rasmus?Larsen Chris?D?den Hengst Casper?J?Albers Jan?Kok Oscar?P?KuipersEmail author 《Genome biology》2005,6(4):P4