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81.
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Amanda R. Goldberg Courtney J. Conway David C. Tank Kimberly R. Andrews Digpal S. Gour Lisette P. Waits 《Ecology and evolution》2020,10(14):7627-7643
In herbivores, survival and reproduction are influenced by quality and quantity of forage, and hence, diet and foraging behavior are the foundation of an herbivore's life history strategy. Given the importance of diet to most herbivores, it is imperative that we know the species of plants they prefer, especially for herbivorous species that are at risk for extinction. However, it is often difficult to identify the diet of small herbivores because: (a) They are difficult to observe, (b) collecting stomach contents requires sacrificing animals, and (c) microhistology requires accurately identifying taxa from partially digested plant fragments and likely overemphasizes less‐digestible taxa. The northern Idaho ground squirrel (Urocitellus brunneus) is federally threatened in the United States under the Endangered Species Act. We used DNA metabarcoding techniques to identify the diet of 188 squirrels at 11 study sites from fecal samples. We identified 42 families, 126 genera, and 120 species of plants in the squirrel's diet. Our use of three gene regions was beneficial because reliance on only one gene region (e.g., only trnL) would have caused us to miss >30% of the taxa in their diet. Northern Idaho ground squirrel diet differed between spring and summer, frequency of many plants in the diet differed from their frequency within their foraging areas (evidence of selective foraging), and several plant genera in their diet were associated with survival. Our results suggest that while these squirrels are generalists (they consume a wide variety of plant species), they are also selective and do not eat plants relative to availability. Consumption of particular genera such as Perideridia may be associated with higher overwinter survival. 相似文献
84.
A road map for molecular ecology 总被引:1,自引:0,他引:1
Rose L. Andrew Louis Bernatchez Aurélie Bonin C. Alex. Buerkle Bryan C. Carstens Brent C. Emerson Dany Garant Tatiana Giraud Nolan C. Kane Sean M. Rogers Jon Slate Harry Smith Victoria L. Sork Graham N. Stone Timothy H. Vines Lisette Waits Alex Widmer Loren H. Rieseberg 《Molecular ecology》2013,22(10):2605-2626
The discipline of molecular ecology has undergone enormous changes since the journal bearing its name was launched approximately two decades ago. The field has seen great strides in analytical methods development, made groundbreaking discoveries and experienced a revolution in genotyping technology. Here, we provide brief perspectives on the main subdisciplines of molecular ecology, describe key questions and goals, discuss common challenges, predict future research directions and suggest research priorities for the next 20 years. 相似文献
85.
Vonn Walter Xiaoying Yin Matthew D. Wilkerson Christopher R. Cabanski Ni Zhao Ying Du Mei Kim Ang Michele C. Hayward Ashley H. Salazar Katherine A. Hoadley Karen Fritchie Charles G. Sailey Mark C. Weissler William W. Shockley Adam M. Zanation Trevor Hackman Leigh B. Thorne William D. Funkhouser Kenneth L. Muldrew Andrew F. Olshan Scott H. Randell Fred A. Wright Carol G. Shores D. Neil Hayes 《PloS one》2013,8(2)
Head and neck squamous cell carcinoma (HNSCC) is a frequently fatal heterogeneous disease. Beyond the role of human papilloma virus (HPV), no validated molecular characterization of the disease has been established. Using an integrated genomic analysis and validation methodology we confirm four molecular classes of HNSCC (basal, mesenchymal, atypical, and classical) consistent with signatures established for squamous carcinoma of the lung, including deregulation of the KEAP1/NFE2L2 oxidative stress pathway, differential utilization of the lineage markers SOX2 and TP63, and preference for the oncogenes PIK3CA and EGFR. For potential clinical use the signatures are complimentary to classification by HPV infection status as well as the putative high risk marker CCND1 copy number gain. A molecular etiology for the subtypes is suggested by statistically significant chromosomal gains and losses and differential cell of origin expression patterns. Model systems representative of each of the four subtypes are also presented. 相似文献
86.
Aprilianto E. Wiria Firdaus Hamid Linda J. Wammes Maria M. M. Kaisar Linda May Margaretta A. Prasetyani Sitti Wahyuni Yenny Djuardi Iwan Ariawan Heri Wibowo Bertrand Lell Robert Sauerwein Gary T. Brice Inge Sutanto Lisette van Lieshout Anton J. M. de Craen Ronald van Ree Jaco J. Verweij Roula Tsonaka Jeanine J. Houwing-Duistermaat Adrian J. F. Luty Erliyani Sartono Taniawati Supali Maria Yazdanbakhsh 《PloS one》2013,8(3)
Background
Helminth infections are proposed to have immunomodulatory activities affecting health outcomes either detrimentally or beneficially. We evaluated the effects of albendazole treatment, every three months for 21 months, on STH, malarial parasitemia and allergy.Methods and Findings
A household-based cluster-randomized, double-blind, placebo-controlled trial was conducted in an area in Indonesia endemic for STH. Using computer-aided block randomization, 481 households (2022 subjects) and 473 households (1982 subjects) were assigned to receive placebo and albendazole, respectively, every three months. The treatment code was concealed from trial investigators and participants. Malarial parasitemia and malaria-like symptoms were assessed in participants older than four years of age while skin prick test (SPT) to allergens as well as reported symptoms of allergy in children aged 5–15 years. The general impact of treatment on STH prevalence and body mass index (BMI) was evaluated. Primary outcomes were prevalence of malarial parasitemia and SPT to any allergen. Analysis was by intention to treat. At 9 and 21 months post-treatment 80.8% and 80.1% of the study subjects were retained, respectively. The intensive treatment regiment resulted in a reduction in the prevalence of STH by 48% in albendazole and 9% in placebo group. Albendazole treatment led to a transient increase in malarial parasitemia at 6 months post treatment (OR 4.16(1.35–12.80)) and no statistically significant increase in SPT reactivity (OR 1.18(0.74–1.86) at 9 months or 1.37 (0.93–2.01) 21 months). No effect of anthelminthic treatment was found on BMI, reported malaria-like- and allergy symptoms. No adverse effects were reported.Conclusions
The study indicates that intensive community treatment of 3 monthly albendazole administration for 21 months over two years leads to a reduction in STH. This degree of reduction appears safe without any increased risk of malaria or allergies.Trial Registration
Controlled-Trials.com ISRCTN83830814 相似文献87.
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90.
Gloria Salazar Stephanie Zlatic Branch Craige Andrew A. Peden Jan Pohl Victor Faundez 《The Journal of biological chemistry》2009,284(3):1790-1802
The Hermansky-Pudlak syndrome is a disorder affecting endosome sorting.
Disease is triggered by defects in any of 15 mouse gene products, which are
part of five distinct cytosolic molecular complexes: AP-3, homotypic fusion
and vacuole protein sorting, and BLOC-1, -2, and -3. To identify molecular
associations of these complexes, we used in vivo cross-linking
followed by purification of cross-linked AP-3 complexes and mass spectrometric
identification of associated proteins. AP-3 was co-isolated with BLOC-1,
BLOC-2, and homotypic fusion and vacuole protein sorting complex subunits;
clathrin; and phosphatidylinositol-4-kinase type II α (PI4KIIα).
We previously reported that this membrane-anchored enzyme is a regulator of
AP-3 recruitment to membranes and a cargo of AP-3 (Craige, B.,
Salazar, G., and Faundez, V. (2008) Mol. Biol.
Cell
19,1415
-1426). Using cells deficient
in different Hermansky-Pudlak syndrome complexes, we identified that BLOC-1,
but not BLOC-2 or BLOC-3, deficiencies affect PI4KIIα inclusion into
AP-3 complexes. BLOC-1, PI4KIIα, and AP-3 belong to a tripartite
complex, and down-regulation of either PI4KIIα, BLOC-1, or AP-3
complexes led to similar LAMP1 phenotypes. Our analysis indicates that BLOC-1
complex modulates the association of PI4KIIα with AP-3. These results
suggest that AP-3 and BLOC-1 act, either in concert or sequentially, to
specify sorting of PI4KIIα along the endocytic route.Membranous organelles along the exocytic and endocytic pathways are each
defined by unique lipid and protein composition. Vesicle carriers communicate
and maintain the composition of these organelles
(2). Consequently defining the
machineries that specify vesicle formation, composition, and delivery are
central to understanding membrane protein traffic. Generally vesicle
biogenesis uses multiprotein cytosolic machineries to select membrane
components for inclusion in nascent vesicles
(2,
3). Heterotetrameric adaptor
complexes (AP-1 to AP-4) are critical to generate vesicles of specific
composition from the different organelles constituting the exocytic and
endocytic routes
(2-4).The best understood vesicle formation machinery in mammalian cells is the
one organized around the adaptor complex AP-2
(5). This complex generates
vesicles from the plasma membrane using clathrin. Our present detailed
understanding of AP-2 vesicle biogenesis mechanisms and interactions emerged
from a combination of organellar and in vitro binding proteomics
analyses together with the study of binary interactions in cell-free systems
(5-9).
In contrast, the vesicle biogenesis pathways controlled by AP-3 are far less
understood. AP-3 functions to produce vesicles that traffic selected membrane
proteins from endosomes to lysosomes, lysosome-related organelles, or synaptic
vesicles
(10-13).
AP-3 is one of the protein complexes affected in the Hermansky-Pudlak syndrome
(HPS;3 Online
Mendelian Inheritance in Man (OMIM) 203300). So far, mutations in any of 15
mouse or eight human genes trigger a common syndrome. This syndrome
encompasses defects that include pigment dilution, platelet dysfunction,
pulmonary fibrosis, and occasionally neurological phenotypes
(14,
15). All forms of HPS show
defective vesicular biogenesis or trafficking that affects lysosomes,
lysosome-related organelles (for example melanosomes and platelet dense
granules), and, in some of them, synaptic vesicles
(11-13).
Most of the 15 HPS loci encode polypeptides that assemble into five distinct
molecular complexes: the adaptor complex AP-3, HOPS, and the BLOC complexes 1,
2, and 3 (14). Recently binary
interactions between AP-3 and BLOC-1 or BLOC-1 and BLOC-2 suggested that
arrangements of these complexes could regulate membrane protein targeting
(16). Despite the abundance of
genetic deficiencies leading to HPS and genetic evidence that HPS complexes
may act on the same pathway in defined cell types
(17), we have only a partial
picture of protein interactions organizing these complexes and how they might
control membrane protein targeting.In this study, we took advantage of cell-permeant and reversible
cross-linking of HPS complexes followed by their immunoaffinity purification
to identify novel molecular interactions. Cross-linked AP-3 co-purified with
BLOC-1, BLOC-2, HOPS, clathrin, and the membrane protein PI4KIIα. We
previously identified PI4KIIα as a cargo and regulator of AP-3
recruitment to endosomes (1,
18). Using mutant cells
deficient in either individual HPS complexes or a combination of them, we
found that BLOC-1 facilitates the interaction of AP-3 and PI4KIIα. Our
studies demonstrate that subunits of four of the five HPS complexes co-isolate
with AP-3. Moreover BLOC-1, PI4KIIα, and AP-3 form a tripartite complex
as demonstrated by sequential co-immunoprecipitations as well as by similar
LAMP1 distribution phenotypes induced by down-regulation of components of this
tripartite complex. Our findings indicate that BLOC-1 complex modulates the
recognition of PI4KIIα by AP-3. These data suggest that AP-3, either in
concert or sequentially with BLOC-1, participates in the sorting of common
membrane proteins along the endocytic route. 相似文献