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1.
A simulation approach for power calculation in large cohort studies based on multistate models
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Bastian Jenny Jan Beyersmann Martin Schumacher 《Biometrical journal. Biometrische Zeitschrift》2018,60(4):671-686
Realistic power calculations for large cohort studies and nested case control studies are essential for successfully answering important and complex research questions in epidemiology and clinical medicine. For this, we provide a methodical framework for general realistic power calculations via simulations that we put into practice by means of an R‐based template. We consider staggered recruitment and individual hazard rates, competing risks, interaction effects, and the misclassification of covariates. The study cohort is assembled with respect to given age‐, gender‐, and community distributions. Nested case‐control analyses with a varying number of controls enable comparisons of power with a full cohort analysis. Time‐to‐event generation under competing risks, including delayed study‐entry times, is realized on the basis of a six‐state Markov model. Incidence rates, prevalence of risk factors and prefixed hazard ratios allow for the assignment of age‐dependent transition rates given in the form of Cox models. These provide the basis for a central simulation‐algorithm, which is used for the generation of sample paths of the underlying time‐inhomogeneous Markov processes. With the inclusion of frailty terms into the Cox models the Markov property is specifically biased. An “individual Markov process given frailty” creates some unobserved heterogeneity between individuals. Different left‐truncation‐ and right‐censoring patterns call for the use of Cox models for data analysis. p‐values are recorded over repeated simulation runs to allow for the desired power calculations. For illustration, we consider scenarios with a “testing” character as well as realistic scenarios. This enables the validation of a correct implementation of theoretical concepts and concrete sample size recommendations against an actual epidemiological background, here given with possible substudy designs within the German National Cohort. 相似文献
2.
PurposeAt introduction in 2014, dose calculation for the first MLC on a robotic SRS/SBRT platform was limited to a correction-based Finite-Size Pencil Beam (FSPB) algorithm. We report on the dosimetric accuracy of a novel Monte Carlo (MC) dose calculation algorithm for this MLC, included in the Precision™ treatment planning system.MethodsA phantom was built of one slab (5.0 cm) of lung-equivalent material (0.09…0.29 g/cc) enclosed by 3.5 cm (above) and 5 cm (below) slabs of solid water (1.045 g/cc). This was irradiated using rectangular (15.4 × 15.4 mm2 to 53.8 × 53.7 mm2) and two irregular MLC-fields. Radiochromic film (EBT3) was positioned perpendicular to the slabs and parallel to the beam. Calculated dose distributions were compared to film measurements using line scans and 2D gamma analysis.ResultsMeasured and MC calculated percent depth dose curves showed a characteristic dose drop within the low-density region, which was not correctly reproduced by FSPB. Superior average gamma pass rates (2%/1 mm) were found for MC (91.2 ± 1.5%) compared to FSPB (55.4 ± 2.7%). However, MC calculations exhibited localized anomalies at mass density transitions around 0.15 g/cc, which were traced to a simplification in electron transport. Absence of these anomalies was confirmed in a modified build of the MC engine, which increased gamma pass rates to 96.6 ± 1.2%.ConclusionsThe novel MC algorithm greatly improves dosimetric accuracy in heterogeneous tissue, potentially expanding the clinical use of robotic radiosurgery with MLC. In-depth, independent validation is paramount to identify and reduce the residual uncertainties in any software solution. 相似文献
3.
The role of the polypeptide matrix in electron transfer processes in proteins has been studied in two distinct systems: first
in a protein where the induced ET is artificial, and second as part of the catalytic cycle of an enzyme. Azurins are structurally
well-characterized blue single-copper proteins consisting of a rigid β-sheet polypeptide matrix. We have determined rate constants
and activation parameters for intramolecular long-range electron transfer between the disulfide radical anions (generated
by pulse radiolysis) and the copper(II) centre as a function of driving force and nature of the intervening medium in a large
number of wild-type and single-site-mutated proteins. In ascorbate oxidase, for which the three-dimensional structure is equally
well characterized, the internal ET from the type-I Cu(I) to the trinuclear Cu(II) centre has been studied. We find that the
results correlate well with distance through well-defined pathways using a through-bond electron tunnelling mechanism.
Received: 2 January 1997 / Accepted: 6 February 1997 相似文献
4.
In order to be able to simulate long time and large space scale properties of polymer melts one has to resort to coarse grained models, for example by subdividing all polymers into parts and restricting attention to the center of mass positions and velocities of these parts. The dynamics of these variables is governed by Langevin equations in which the free energy obtained by integrating the remaining variables provides the potential of the conservative forces. In general this leads to many particle interactions on the coarse-grained level. Methods suggested in the literature to represent these many particle interactions by effective two body interactions are reviewed and a new method, based on the Gibbs-Bogoliubov inequality, is proposed. The reason why none of these methods is able to reproduce the pressure of the underlying atomistic model is discussed. 相似文献
5.
Hiroshi Monoi 《生物化学与生物物理学报:生物膜》1982,693(1):159-164
An electrostatic calculation suggests that when an ion is bound near the mouth of a channel penetrating a low-dielectric membrane, a counter ion may form an ion pair with this ion. The tendency towards ion-pair formation is remarkably enhanced at channel mouths by forces (image forces) arising from the charges induced on the boundaries between different dielectrics. The binding constant for the formation of ion-pairs of monovalent ions is estimated under the assumption that local interactions between the counter ion and the channel wall are negligibly small. It is of the order of 1–10 molal?1 or more for the binding of a Cl? (F?) counter ion to an () ion if appropriate conditions are fulfilled. The binding constant depends on the position of the binding site, the dimensions and geometries of the channel and channel mouth, and the state of ion loading of the channel, as well as the ionic species. The present results also indicate that when cation (anion) channels have anionic (cationic) groups as integrant parts of their channel walls, interactions between these charged groups and permeant ions are markedly enhanced by the image forces. 相似文献
6.
The influence of earthworms (Lumbricidae) on the nitrogen dynamics in the soil litter system of a deciduous forest 总被引:2,自引:0,他引:2
S. Scheu 《Oecologia》1987,72(2):197-201
Summary The influence of earthworms (Aporrectodea caliginosa (Savigny) and Lumbricus castaneus (Savigny)) on the rate of nitrogen net mineralization of the soil was studied in the laboratory and in the field. The additional mineralization of nitrogen cause by the burrowing activity of the substrat feeding earthworm A. caliginosa (N
L
)was directly correlated to the biomass of the lumbricids independently of their number. A rise in temperature caused an exponential increase in N
L
values. The Q
10 value of this process (2.18) was found to be much higher than that of the nitrogen mineralization without earthworms (Q
10=1.22). At 15°C the N
L
value caused by A. caliginosa was calculated to be about 250 g N g-1 fresh body wt d-1. Using the experimentally determined exponential relationship between temperature and N
L
values, the additional nitrogen mineralization caused by a population of A. caliginosa in a beechwood on limestone was calculated to be 4.23 kg ha-1 a-1.In contrast to A. caliginosa the litter dwelling species L. castaneus lost considerable amounts of biomass (56%) during the 4 week incubation period. Only 1/3 of the nitrogen equivalent to the weight loss of the animals was recovered in the mineral nitrogen pool.The addition of litter (old beech leaf litter, freshly fallen beech and ash leaf litter) had a pronounced effect on both nitrogen net mineralization and N
L
values of the soil. Presence of old beech leaves caused an increase in both values, wheres the other litter types effected a decrease in nitrogen net mineralization. Fragmented ash litter was found to have the most distinct effect on N
L
values (-69%) and nitrogen net mineralization (-74%). 相似文献
7.
8.
To obtain a satisfactory agreement between computed transition temperatures and those determined experimentally, we introduce explicitly water molecules which hydrate the polar headgroup of dipalmitoylphosphatidylethanolamine molecules. The calculated free energy curves as a function of the intermolecular interchain distance and the degree of hydration of the polar groups permit the determination of the transition of the phospholipid system from the gel to the liquid crystalline phase. The detailed structure of the hydration shell is defined using the supermolecular approach. 相似文献
9.
Summary A method for quantification of distances between amide hydrogens using only the 3D NOESY-HMQC experiment recorded on a 15N-labelled protein is presented. This method is based on an approximate expression of the NOE intensities between amide hydrogens obtained from continuum modelling of the non-amide spins; this expression is used in a distance calculation algorithm. The algorithm has been named CROWD, standing for Continuum approximation of Relaxati On path Ways between Dilute spins. This approximation as well as the CROWD algorithm are tested on a simulated case; the CROWD algorithm is then applied to experimental data, measured on a fragment of bacteriorhodopsin. 相似文献
10.
The internal cation levels of chloroplasts isolated from a green sea alga, Bryopsis maxima, were studied. Atomic absorption spectroscopy, combined with the determination of the sorbitol-impermeable and water-permeable spaces, revealed that chloroplasts contain an extremely high concentration of K+ and high levels of Na+, Mg2+ and Ca2+. A method was developed to estimate the thermodynamic activities of monovalent and divalent cations present in chloroplasts. pH changes induced by the addition of an ionophore (plus an H+ carrier), which makes the outer limiting membranes of chloroplasts permeable to both a cation and H+, were determined. Provided that the external pH was set equal to the internal pH, the internal concentration of the cation was estimated by determining the external cation concentration which gave rise to no electrochemical potential difference of the cation and hence no pH change on addition of the ionophore. The internal pH was determined by measuring distributions of radioactive methylamine and 5,5-dimethyloxazolidine-2,4-dione between the chloroplast and medium (Heldt, H.W., Werdan, K., Milovancev, M. and Geller, G. (1973) Biochim. Biophys. Acta 314, 224–241). The internal pH was also estimated by measuring pH changes caused by the disruption of the outer limiting membrane with Triton X-100. The results indicate that a significant part of the monovalent cations and most of the divalent cations are attracted into a diffuse layer adjacent to the negatively charged surfaces of membranes and proteins, or form complexes with organic and inorganic compounds present in the intact chloroplasts. 相似文献