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71.
Tracking down human contamination in ancient human teeth 总被引:1,自引:0,他引:1
Sampietro ML Gilbert MT Lao O Caramelli D Lari M Bertranpetit J Lalueza-Fox C 《Molecular biology and evolution》2006,23(9):1801-1807
DNA contamination arising from the manipulation of ancient calcified tissue samples is a poorly understood, yet fundamental, problem that affects the reliability of ancient DNA (aDNA) studies. We have typed the mitochondrial DNA hypervariable region I of the only 6 people involved in the excavation, washing, and subsequent anthropological and genetic study of 23 Neolithic remains excavated from Granollers (Barcelona, Spain) and searched for their presence among the 572 clones generated during the aDNA analyses of teeth from these samples. Of the cloned sequences, 17.13% could be unambiguously identified as contaminants, with those derived from the people involved in the retrieval and washing of the remains present in higher frequencies than those of the anthropologist and genetic researchers. This finding confirms, for the first time, previous hypotheses that teeth samples are most susceptible to contamination at their initial excavation. More worrying, the cloned contaminant sequences exhibit substitutions that can be attributed to DNA damage after the contamination event, and we demonstrate that the level of such damage increases with time: contaminants that are >10 years old have approximately 5 times more damage than those that are recent. Furthermore, we demonstrate that in this data set, the damage rate of the old contaminant sequences is indistinguishable from that of the endogenous DNA sequences. As such, the commonly used argument that miscoding lesions observed among cloned aDNA sequences can be used to support data authenticity is misleading in scenarios where the presence of old contaminant sequences is possible. We argue therefore that the typing of those involved in the manipulation of the ancient human specimens is critical in order to ensure that generated results are accurate. 相似文献
72.
Noy A Meyer T Rueda M Ferrer C Valencia A Pérez A de la Cruz X López-Bes JM Pouplana R Fernandez-Recio J Luque FJ Orozco M 《Journal of biomolecular structure & dynamics》2006,23(4):447-456
Analysis, storage, and transfer of molecular dynamic trajectories are becoming the bottleneck of computer simulations. In this paper we discuss different approaches for data mining and data processing of huge trajectory files generated from molecular dynamic simulations of nucleic acids. 相似文献
73.
beta-lactam antibiotics induce the SOS response and horizontal transfer of virulence factors in Staphylococcus aureus 下载免费PDF全文
Maiques E Ubeda C Campoy S Salvador N Lasa I Novick RP Barbé J Penadés JR 《Journal of bacteriology》2006,188(7):2726-2729
Antibiotics that interfere with DNA replication and cell viability activate the SOS response. In Staphylococcus aureus, the antibiotic-induced SOS response promotes replication and high-frequency horizontal transfer of pathogenicity island-encoded virulence factors. Here we report that β-lactams induce a bona fide SOS response in S. aureus, characterized by the activation of the RecA and LexA proteins, the two master regulators of the SOS response. Moreover, we show that β-lactams are capable of triggering staphylococcal prophage induction in S. aureus lysogens. Consequently, and as previously described for SOS induction by commonly used fluoroquinolone antibiotics, β-lactam-mediated phage induction also resulted in replication and high-frequency transfer of the staphylococcal pathogenicity islands, showing that such antibiotics may have the unintended consequence of promoting the spread of bacterial virulence factors. 相似文献
74.
Sandrine Vuillaumier-Barrot Céline Bouchet-Séraphin Malika Chelbi Louise Devisme Samuel Quentin Steven Gazal Annie Laquerrière Catherine Fallet-Bianco Philippe Loget Sylvie Odent Dominique Carles Anne Bazin Jacqueline Aziza Alix Clemenson Fabien Guimiot Maryse Bonnière Sophie Monnot Christine Bole-Feysot Jean-Pierre Bernard Laurence Loeuillet Marie Gonzales Koryna Socha Bernard Grandchamp Tania Attié-Bitach Férechté Encha-Razavi Nathalie Seta 《American journal of human genetics》2012,91(6):1135-1143
Cobblestone lissencephaly is a peculiar brain malformation with characteristic radiological anomalies. It is defined as cortical dysplasia that results when neuroglial overmigration into the arachnoid space forms an extracortical layer that produces agyria and/or a “cobblestone” brain surface and ventricular enlargement. Cobblestone lissencephaly is pathognomonic of a continuum of autosomal-recessive diseases characterized by cerebral, ocular, and muscular deficits. These include Walker-Warburg syndrome, muscle-eye-brain disease, and Fukuyama muscular dystrophy. Mutations in POMT1, POMT2, POMGNT1, LARGE, FKTN, and FKRP identified these diseases as alpha-dystroglycanopathies. Our exhaustive screening of these six genes, in a cohort of 90 fetal cases, led to the identification of a mutation in only 53% of the families, suggesting that other genes might also be involved. We therefore decided to perform a genome-wide study in two multiplex families. This allowed us to identify two additional genes: TMEM5 and ISPD. Because TMEM has a glycosyltransferase domain and ISPD has an isoprenoid synthase domain characteristic of nucleotide diP-sugar transferases, these two proteins are thought to be involved in the glycosylation of dystroglycan. Further screening of 40 families with cobblestone lissencephaly identified nonsense and frameshift mutations in another four unrelated cases for each gene, increasing the mutational rate to 64% in our cohort. All these cases displayed a severe phenotype of cobblestone lissencephaly A. TMEM5 mutations were frequently associated with gonadal dysgenesis and neural tube defects, and ISPD mutations were frequently associated with brain vascular anomalies. 相似文献
75.
Sandrine Vuillaumier-Barrot Céline Bouchet-Séraphin Malika Chelbi Louise Devisme Samuel Quentin Steven Gazal Annie Laquerrière Catherine Fallet-Bianco Philippe Loget Sylvie Odent Dominique Carles Anne Bazin Jacqueline Aziza Alix Clemenson Fabien Guimiot Maryse Bonnière Sophie Monnot Christine Bole-Feysot Jean-Pierre Bernard Laurence Loeuillet Marie Gonzales Koryna Socha Bernard Grandchamp Tania Attié-Bitach Férechté Encha-Razavi Nathalie Seta 《American journal of human genetics》2012
76.
Harvesting the microalgae Phaeodactylum tricornutum with polyaluminum chloride, aluminium sulphate, chitosan and alkalinity-induced flocculation 总被引:1,自引:0,他引:1
Sema ?irin Rosa Trobajo Carles Ibanez Joan Salvadó 《Journal of applied phycology》2012,24(5):1067-1080
The purpose of this study was to explore efficient methods of harvesting the microalga Phaeodactylum tricornutum. Natural sedimentation experiments, performed at different light and temperature conditions, did not yield significant improvements in efficiency even after 1?week. When alkalinity-induced flocculation was performed, both the flocculation efficiency and the concentration factor dramatically improved at pH?=?9.75 (0.5–0.7 units over the original pH of the culture) after 10?min settling time. Sedimentation rates are documented at pH ranging between pH?9.75 and 11.0. The results of the application of two conventional flocculants used in wastewater treatment, polyaluminium chloride and aluminium sulphate, are also presented. Chitosan was also used as a natural flocculating agent to improve possible contamination problems in the downstream process. pH was adjusted in order to determine optimum flocculation efficiency of chitosan in combination with a high concentration factor. Satisfactory results were found with chitosan at an adjusted pH of 9.9 using concentrations as low as 20?mg?L?1, after testing a flocculant range of 5–200?mg?L?1. 相似文献
77.
78.
Via E Cardoner N Pujol J Martínez-Zalacaín I Hernández-Ribas R Urretavizacaya M López-Solà M Deus J Menchón JM Soriano-Mas C 《PloS one》2012,7(6):e38299
Melancholic depression is a biologically homogeneous clinical entity in which structural brain alterations have been described. Interestingly, reports of structural alterations in melancholia include volume increases in Cerebro-Spinal Fluid (CSF) spaces. However, there are no previous reports of CSF volume alterations using automated whole-brain voxel-wise approaches, as tissue classification algorithms have been traditionally regarded as less reliable for CSF segmentation. Here we aimed to assess CSF volumetric alterations in melancholic depression and their clinical correlates by means of a novel segmentation algorithm ('new segment', as implemented in the software Statistical Parametric Mapping-SPM8), incorporating specific features that may improve CSF segmentation. A three-dimensional Magnetic Resonance Image (MRI) was obtained from seventy patients with melancholic depression and forty healthy control subjects. Although imaging data were pre-processed with the 'new segment' algorithm, in order to obtain a comparison with previous segmentation approaches, tissue segmentation was also performed with the 'unified segmentation' approach. Melancholic patients showed a CSF volume increase in the region of the left Sylvian fissure, and a CSF volume decrease in the subarachnoid spaces surrounding medial and lateral parietal cortices. Furthermore, CSF increases in the left Sylvian fissure were negatively correlated with the reduction percentage of depressive symptoms at discharge. None of these results were replicated with the 'unified segmentation' approach. By contrast, between-group differences in the left Sylvian fissure were replicated with a non-automated quantification of the CSF content of this region. Left Sylvian fissure alterations reported here are in agreement with previous findings from non-automated CSF assessments, and also with other reports of gray and white matter insular alterations in depressive samples using automated approaches. The reliable characterization of CSF alterations may help in the comprehensive characterization of brain structural abnormalities in psychiatric samples and in the development of etiopathogenic hypotheses relating to the disorders. 相似文献
79.
80.
Jussi Pihlajamäki Carles Lerin Dorota Kaminska Sari Venesmaa Paula Itkonen Tanner Boes Thomas Floss Joshua Schroeder Farrell Dearie Sarah Crunkhorn Furkan Burak Josep C. Jimenez-Chillaron Tiina Kuulasmaa Pekka Miettinen Peter J. Park Imad Nasser Zhenwen Zhao Zhaiyi Zhang Yan Xu Wolfgang Wurst Mary Elizabeth Patti 《Cell metabolism》2012,15(3):267-269