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Rupert A. Collins Giulia Trauzzi Katherine M. Maltby Thomas I. Gibson Frances C. Ratcliffe Jane Hallam Sophie Rainbird James Maclaine Peter A. Henderson David W. Sims Stefano Mariani Martin J. Genner 《Journal of fish biology》2021,99(4):1446-1454
The accuracy and reliability of DNA metabarcoding analyses depend on the breadth and quality of the reference libraries that underpin them. However, there are limited options available to obtain and curate the huge volumes of sequence data that are available on public repositories such as NCBI and BOLD. Here, we provide a pipeline to download, clean and annotate mitochondrial DNA sequence data for a given list of fish species. Features of this pipeline include (a) support for multiple metabarcode markers; (b) searches on species synonyms and taxonomic name validation; (c) phylogeny assisted quality control for identification and removal of misannotated sequences; (d) automatically generated coverage reports for each new GenBank release update; and (e) citable, versioned DOIs. As an example we provide a ready-to-use curated reference library for the marine and freshwater fishes of the U.K. To augment this reference library for environmental DNA metabarcoding specifically, we generated 241 new MiFish-12S sequences for 88 U.K. marine species, and make available new primer sets useful for sequencing these. This brings the coverage of common U.K. species for the MiFish-12S fragment to 93%, opening new avenues for scaling up fish metabarcoding across wide spatial gradients. The Meta-Fish-Lib reference library and pipeline is hosted at https://github.com/genner-lab/meta-fish-lib . 相似文献
13.
Giovanni Benelli Santosh Revadi Adriano Carpita Giulia Giunti Alfio Raspi Gianfranco Anfora Angelo Canale 《Biological Control》2013,64(2):116-124
Psyttalia concolor (Szépligeti) is a koinobiont larval-pupal endoparasitoid of many Tephritidae of great economic importance, such as the medfly, Ceratitis capitata (Wiedemann). In several species of parasitoids it has been demonstrated that the mated females are strongly attracted by specific volatiles from insect-damaged plants. Yet the role of olfactory cues deriving from C. capitata-infested fruits on the female’s decision during the P. concolor host location was poorly investigated. In the present study, the responses of P. concolor females to either healthy or C. capitata-infested fruits was studied through behavioral assays. Volatiles emitted by healthy and infested fruits were SPME-sampled and analyzed by gas chromatography–mass spectrometry (GC–MS). The attractiveness of the identified volatiles was assessed and their electrophysiological activity was analyzed through gas-chromatography coupled with electroantennography (GC-EAD). P. concolor preferred infested peaches and apples over healthy ones, either when visual and olfactory or only olfactory cues were given. Nine compounds were found as exclusive of infested peaches, with respect to healthy ones, and seven of them evoked electrophysiological responses. In apples only quantitative changes in volatile emissions were observed after the medfly infestation. The emissions of 1-butyl butylate, 1-hexyl acetate and 1-butyl esanoate increased in infested apples, whereas 1-hexyl (E)-2-methyl butenoate decreased significantly. Among apple volatiles, 1-butyl butylate, 2-methyl-1-butyl acetate, 1-hexyl acetate, 2-methyl-1-butyl 2-methylbutanoate, 1-butyl hexanoate and 1-hexyl (E)-2-methyl butenoate elicited responses in female antennae. Synthetic blends reproducing the odors emitted by infested peaches and apples elicited strong attraction towards P. concolor females. For both fruits, the blend attractiveness was mainly due to some specific electrophysiological active chemicals: ethyl octanoate, decanal and 4-decanolide for peach, and 1-butyl butylate and 1-butyl hexanoate for apple. The responses induced by the identified fruit volatiles to P. concolor females allow us to suppose that they play a role as short-range attractants during host location. 相似文献
14.
The Cannabinoid Receptor Type 2 as Mediator of Mesenchymal Stromal Cell Immunosuppressive Properties
Francesca Rossi Maria Ester Bernardo Giulia Bellini Livio Luongo Antonella Conforti Iolanda Manzo Francesca Guida Luigia Cristino Roberta Imperatore Stefania Petrosino Bruno Nobili Vincenzo Di Marzo Franco Locatelli Sabatino Maione 《PloS one》2013,8(11)
Mesenchymal stromal cells are non-hematopoietic, multipotent progenitor cells producing cytokines, chemokines, and extracellular matrix proteins that support hematopoietic stem cell survival and engraftment, influence immune effector cell development, maturation, and function, and inhibit alloreactive T-cell responses. The immunosuppressive properties of human mesenchymal stromal cells have attracted much attention from immunologists, stem cell biologists and clinicians.Recently, the presence of the endocannabinoid system in hematopoietic and neural stem cells has been demonstrated. Endocannabinoids, mainly acting through the cannabinoid receptor subtype 2, are able to modulate cytokine release and to act as immunosuppressant when added to activated T lymphocytes.In the present study, we have investigated, through a multidisciplinary approach, the involvement of the endocannabinoids in migration, viability and cytokine release of human mesenchymal stromal cells.We show, for the first time, that cultures of human mesenchymal stromal cells express all of the components of the endocannabinoid system, suggesting a potential role for the cannabinoid CB2 receptor as a mediator of anti-inflammatory properties of human mesenchymal stromal cells, as well as of their survival pathways and their capability to home and migrate towards endocannabinoid sources. 相似文献
15.
Giulia Falivelli Erika Mathes Lisabeth Elena Rubio de la Torre Gizeh Perez-Tenorio Giovanna Tosato Ombretta Salvucci Elena B. Pasquale 《PloS one》2013,8(11)
The Eph receptor tyrosine kinases mediate juxtacrine signals by interacting “in trans” with ligands anchored to the surface of neighboring cells via a GPI-anchor (ephrin-As) or a transmembrane segment (ephrin-Bs), which leads to receptor clustering and increased kinase activity. Additionally, soluble forms of the ephrin-A ligands released from the cell surface by matrix metalloproteases can also activate EphA receptor signaling. Besides these trans interactions, recent studies have revealed that Eph receptors and ephrins coexpressed in neurons can also engage in lateral “cis” associations that attenuate receptor activation by ephrins in trans with critical functional consequences. Despite the importance of the Eph/ephrin system in tumorigenesis, Eph receptor-ephrin cis interactions have not been previously investigated in cancer cells. Here we show that in cancer cells, coexpressed ephrin-A3 can inhibit the ability of EphA2 and EphA3 to bind ephrins in trans and become activated, while ephrin-B2 can inhibit not only EphB4 but also EphA3. The cis inhibition of EphA3 by ephrin-B2 implies that in some cases ephrins that cannot activate a particular Eph receptor in trans can nevertheless inhibit its signaling ability through cis association. We also found that an EphA3 mutation identified in lung cancer enhances cis interaction with ephrin-A3. These results suggest a novel mechanism that may contribute to cancer pathogenesis by attenuating the tumor suppressing effects of Eph receptor signaling pathways activated by ephrins in trans. 相似文献
16.
Valeria Rimoldi Giulia Soldà Rosanna Asselta Silvia Spena Cristiana Stuani Emanuele Buratti Stefano Duga 《PloS one》2013,8(3)
Most pathological pseudoexon inclusion events originate from single activating mutations, suggesting that many intronic sequences are on the verge of becoming exons. However, the precise mechanisms controlling pseudoexon definition are still largely unexplored. Here, we investigated the cis-acting elements and trans-acting regulatory factors contributing to the regulation of a previously described fibrinogen gamma-chain (FGG) pseudoexon, which is activated by a deep-intronic mutation (IVS6-320A>T). This pseudoexon contains several G-run elements, which may be bound by heterogeneous nuclear ribonucleoproteins (hnRNPs) F and H. To explore the effect of these proteins on FGG pseudoexon inclusion, both silencing and overexpression experiments were performed in eukaryotic cells. While hnRNP H did not significantly affect pseudoexon splicing, hnRNP F promoted pseudoexon inclusion, indicating that these two proteins have only partially redundant functions. To verify the binding of hnRNP F and the possible involvement of other trans-acting splicing modulators, pulldown experiments were performed on the region of the pseudoexon characterized by both a G-run and enrichment for exonic splicing enhancers. This 25-bp-long region strongly binds hnRNP F/H and weakly interacts with Serine/Arginine-rich protein 40, which however was demonstrated to be dispensable for FGG pseudoexon inclusion in overexpression experiments. Deletion analysis, besides confirming the splicing-promoting role of the G-run within this 25-bp region, demonstrated that two additional hnRNP F binding sites might instead function as silencer elements. Taken together, our results indicate a major role of hnRNP F in regulating FGG pseudoexon inclusion, and strengthen the notion that G-runs may function either as splicing enhancers or silencers of the same exon. 相似文献
17.
Paola Luciani Cristiana Deledda Susanna Benvenuti Roberta Squecco Ilaria Cellai Benedetta Fibbi Ilaria Maddalena Marone Corinna Giuliani Giulia Modi Fabio Francini Gabriella Barbara Vannelli Alessandro Peri 《PloS one》2013,8(8)
Exendin-4 is a molecule currently used, in its synthetic form exenatide, for the treatment of type 2 diabetes mellitus. Exendin-4 binds and activates the Glucagon-Like Peptide-1 Receptor (GLP-1R), thus inducing insulin release. More recently, additional biological properties have been associated to molecules that belong to the GLP-1 family. For instance, Peptide YY and Vasoactive Intestinal Peptide have been found to affect cell adhesion and migration and our previous data have shown a considerable actin cytoskeleton rearrangement after exendin-4 treatment. However, no data are currently available on the effects of exendin-4 on tumor cell motility. The aim of this study was to investigate the effects of this molecule on cell adhesion, differentiation and migration in two neuroblastoma cell lines, SH-SY5Y and SK-N-AS. We first demonstrated, by Extra Cellular Matrix cell adhesion arrays, that exendin-4 increased cell adhesion, in particular on a vitronectin substrate. Subsequently, we found that this molecule induced a more differentiated phenotype, as assessed by i) the evaluation of neurite-like protrusions in 3D cell cultures, ii) the analysis of the expression of neuronal markers and iii) electrophysiological studies. Furthermore, we demonstrated that exendin-4 reduced cell migration and counteracted anchorage-independent growth in neuroblastoma cells. Overall, these data indicate for the first time that exendin-4 may have anti-tumoral properties. 相似文献
18.
Adriano Redler Giorgio Di Rocco Domenico Giannotti Francesca Frezzotti Maria Giulia Bernieri Simona Ceccarelli Sirio D’Amici Enrica Vescarelli Anna Paola Mitterhofer Antonio Angeloni Cinzia Marchese 《PloS one》2013,8(8)
Fibroblast growth factor receptor-2 (FGFR-2) plays an important role in tumorigenesis. In thyroid cancer it has been observed a FGFR-2 down-modulation, but the role of this receptor has not been yet clarified. Therefore, we decided to examine the expression of both FGFR-2 isoform, FGFR-2-IIIb and FGFR-2-IIIc, in different histological thyroid variants such as hyperplasia, follicular adenoma and papillary carcinoma. Immunohistochemistry and quantitative Real-Time PCR analyses were performed on samples of hyperplasia, follicular adenoma and papillary carcinoma, compared with normal thyroid tissue. Thyroid hyperplasia did not show statistically significant reduction in FGFR-2 protein and mRNA levels. Interestingly, in both follicular adenoma and papillary carcinoma samples we observed a strongly reduced expression of both FGFR-2 isoforms. We speculate that FGFR-2 down-modulation might be an early event in thyroid carcinogenesis. Furthermore, we suggest the potential use of FGFR-2 as an early marker for thyroid cancer diagnosis. 相似文献
19.
Oecologia - Fluctuations in the abundance of main prey species might shape animal communities, by inducing numerical responses and dietary shifts in predators. Whether numerical responses and... 相似文献
20.
Gianluca
E.M. Boari Giulia Chiarini Silvia Bonetti Paolo Malerba Gianluca Bianco Cristina Faustini Federico Braglia-Orlandini Daniele Turini Vittoria Guarinoni Michele Saottini Sara Viola Giulia Ferrari-Toninelli Giancarlo Pasini Cristina Mascadri Bianca Bonzi Paolo Desenzani Claudia Tusi Eros Zanotti Matteo Nardin Damiano Rizzoni 《Bioscience reports》2020,40(12)
The aim of the present study was to simultaneously assess several potential predictors of outcome (co-morbidity, previous and in-hospital treatment, radiologic Brixia score) in patients with COVID-19.This retrospective cohort study included 258 consecutive patients with confirmed COVID-19 admitted to a medical ward at Montichiari Hospital, Brescia, Italy from February 28th to April 30rd, 2020. Patients had SARS-CoV-2 related pneumonia with respiratory failure, and were treated with hydroxychloroquine and lopinavir plus ritonavir. In some patients, additional treatment with tocilizumab, dexamethasone and enoxaparin was adopted. Outcomes (death or recovery) were assessed at the end of the discharge period or at the end of the follow-up (August 2020).During hospitalization, 59 patients died, while 6 died after discharge. The following variables were demonstrated to be associated with a worse prognosis: Radiologic Brixia score higher than 8, presence at baseline of hypertension, diabetes, chronic obstructive pulmonary disease, heart disease, cancer, previous treatment with ACE-inhibitors or anti-platelet drugs. Anticoagulant treatment during hospital admission with enoxaparin at a dose higher than 4000 U once daily was associated with a better prognosis.In conclusion, our study demonstrates that some co-morbidities and cardiovascular risk factors may affect prognosis. The radiologic Brixia score may be a useful tool to stratify the risk of death at baseline. Anticoagulant treatment with enoxaparin might be associated to a clinical benefit in terms of survival in patients with COVID-19. 相似文献