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41.
RNA Aminoacylation Mediated by Sequential Action of Two Ribozymes and a Nonactivated Amino Acid 下载免费PDF全文
Dr. Jiacui Xu Dr. Bettina Appel Darko Balke Claudia Wichert Prof. Dr. Sabine Müller 《Chembiochem : a European journal of chemical biology》2014,15(8):1200-1209
In the transition from the RNA world to the modern DNA/protein world, RNA‐catalyzed aminoacylation might have been a key step towards early translation. A number of ribozymes capable of aminoacylating their own 3′ termini have been developed by in vitro selection. However, all of those catalysts require a previously activated amino acid—typically an aminoacyl‐AMP—as substrate. Here we present two ribozymes connected by intermolecular base pairing and carrying out the two steps of aminoacylation: ribozyme 1 loads nonactivated phenylalanine onto its phosphorylated 5′ terminus, thereby forming a high‐energy mixed anhydride. Thereafter, a complex of ribozymes 1 and 2 is formed by intermolecular base pairing, and the “activated” phenylalanine is transferred from the 5′ terminus of ribozyme 1 to the 3′ terminus of ribozyme 2. This kind of simple RNA aminoacylase complex was engineered from previously selected ribozymes possessing the two required activities. RNA aminoacylation with a nonactivated amino acid as described here is advantageous to RNA world scenarios because initial amino acid activation by an additional reagent (in most cases, ATP) and an additional ribozyme would not be necessary. 相似文献
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43.
Natasa Boban Marija Tonkic Danijela Budimir Darko Modun Davorka Sutlovic Volga Punda-Polic Mladen Boban 《Journal of food science》2010,75(5):M322-M326
Abstract: While the antimicrobial effectiveness of wine is well documented, relative contributions of the wine components to its antimicrobial activity is controversial. To separate the role of wine phenolics, ethanol, and pH from other wine constituents, the antimicrobial effects of intact wine were compared to that of phenols-stripped wine, dealcoholized wine, ethanol, and low pH applied separately and in combination, against 2 common foodborne pathogens, Salmonella enterica serovar Enteritidis and Escherichia coli. All samples were biochemically characterized with respect to their total phenolics and resveratrol content, antioxidant capacity, ethanol content, and pH. Antioxidative activity of the samples corresponded to their total phenolics content. Except for respective controls, pH and ethanol content were similar in all samples. The order of antibacterial activity of the samples was: intact wine > phenols-stripped wine > dealcoholized wine > combination of ethanol and low pH > low pH > ethanol. Separate application of ethanol or low pH showed negligible antibacterial activity while their combination showed synergistic effect. Antibacterial activity of the samples could not be related to their total phenolics and resveratrol content, antioxidant capacity, ethanol content, or pH. Our study indicates that antimicrobial activity of complex solutions such as intact wine cannot be exclusively attributed to its phenolic or nonphenolic constituents, nor can the antimicrobial activity of wine be predicted on the basis of its particular components. 相似文献
44.
This article presents an agent‐based fuzzy cognitive map (ABFCM) developed injecting the concept of multi‐agent system (MAS) into the fuzzy cognitive map (FCM). Fuzzy cognitive map is used for qualitative modeling and simulation. Compared to the FCM, the ABFCM enables different inference algorithms in each node enabling simulation of systems with diverse behavior concepts. Each map node can exhibit individual, more or less intelligent, behavior and still can interact with other nodes to conclude on system behavior. Resulting method also enables automatic results interpretation adding additional intelligence to a classic FCM. Explanation of the obtained system architecture with FCM and MAS integration is presented in the article. The experimental results in the article are obtained with the ABFCM prototype, developed on the basis of ABFCM structure given in the article. Multi‐agent technology can bring new properties into existing fields and methods, like in the ABFCM case. © 2010 Wiley Periodicals, Inc. 相似文献
45.
In this paper we show how to use two‐colored pixels as a generic tool for image processing. We apply two‐colored pixels as a basic operator as well as a supporting data structure for several image processing applications. Traditionally, images are represented by a regular grid of square pixels with one constant color each. In the two‐colored pixel representation, we reduce the image resolution and replace blocks of N × N pixels by one square that is split by a (feature) line into two regions with constant colors. We show how the conversion of standard mono‐colored pixel images into two‐colored pixel images can be computed efficiently by applying a hierarchical algorithm along with a CUDA‐based implementation. Two‐colored pixels overcome some of the limitations that classical pixel representations have, and their feature lines provide minimal geometric information about the underlying image region that can be effectively exploited for a number of applications. We show how to use two‐colored pixels as an interactive brush tool, achieving realtime performance for image abstraction and non‐photorealistic filtering. Additionally, we propose a realtime solution for image retargeting, defined as a linear minimization problem on a regular or even adaptive two‐colored pixel image. The concept of two‐colored pixels can be easily extended to a video volume, and we demonstrate this for the example of video retargeting. 相似文献
46.
Modeling, identification, and validation of models for predictive ammonia control in a wastewater treatment plant--a case study 总被引:1,自引:0,他引:1
The aim of this work is to develop the ammonia models that could be used for model predictive control (MPC) of nitrification process in a wastewater treatment plant. First, a reduced nonlinear model is presented, which is based on expression for nitrification reaction rate in activated sludge model No. 1 and modified for attached biomass processes, while second, a linear black-box model is shown. The data used for model identification were collected during several weeks of experiments on a real plant so that good identification data were obtained. The designed models were validated based on open loop simulations and predictions. Validation results show that the reduced nonlinear model performs better compared to the linear model, however, both models show relatively large errors compared to the real plant data. Hence, a closed loop simulation study was performed to see the differences between the performance of model predictive controller using previously estimated linear and nonlinear models and a standard proportional integral (PI) controller. From the simulation study results it was seen that in spite of relatively large model errors the MPC algorithms give better results in terms of ammonia removal compared to the PI controller, while MPC with the nonlinear model shows additional improvements over the MPC with the linear model. 相似文献
47.
Darko Veberič 《Computer Physics Communications》2012,183(12):2622-2628
48.
Darko Bosnakovski David Oyler Ana Mitanoska Madison Douglas Elizabeth T. Ener Ahmed S. Shams Michael Kyba 《International journal of molecular sciences》2022,23(4)
FSHD is caused by loss of silencing of the DUX4 gene, but the DUX4 protein has not yet been directly detected immunohistologically in affected muscle, raising the possibility that DUX4 expression may occur at time points prior to obtaining adult biopsies for analysis, with consequent perturbations of muscle being responsible for disease progression. To test the extent to which muscle can regenerate following DUX4-mediated degeneration, we employed an animal model with reversible DUX4 expression, the iDUX4pA;HSA mouse. We find that muscle histology does recover substantially after DUX4 expression is switched off, with the extent of recovery correlating inversely with the duration of prior DUX4 expression. However, despite fairly normal muscle histology, and recovery of most cytological parameters, the fibroadipogenic progenitor compartment, which is significantly elevated during bouts of fiber-specific DUX4 expression, does not return to basal levels, even many weeks after a single burst of DUX4 expression. We find that muscle that has recovered from a DUX4 burst acquires a propensity for severe fibrosis, which can be revealed by subsequent cardiotoxin injuries. These results suggest that a past history of DUX4 expression leads to maintained pro-fibrotic alterations in the cellular physiology of muscle, with potential implications for therapeutic approaches. 相似文献
49.
Milena Todorovic Balint Jelena Jelicic Biljana Mihaljevic Jelena Kostic Bojana Stanic Bela Balint Nadja Pejanovic Bojana Lucic Natasa Tosic Irena Marjanovic Maja Stojiljkovic Teodora Karan-Djurasevic Ognjen Perisic Goran Rakocevic Milos Popovic Sava Raicevic Jelena Bila Darko Antic Bosko Andjelic Sonja Pavlovic 《International journal of molecular sciences》2016,17(5)
The existence of a potential primary central nervous system lymphoma-specific genomic signature that differs from the systemic form of diffuse large B cell lymphoma (DLBCL) has been suggested, but is still controversial. We investigated 19 patients with primary DLBCL of central nervous system (DLBCL CNS) using the TruSeq Amplicon Cancer Panel (TSACP) for 48 cancer-related genes. Next generation sequencing (NGS) analyses have revealed that over 80% of potentially protein-changing mutations were located in eight genes (CTNNB1, PIK3CA, PTEN, ATM, KRAS, PTPN11, TP53 and JAK3), pointing to the potential role of these genes in lymphomagenesis. TP53 was the only gene harboring mutations in all 19 patients. In addition, the presence of mutated TP53 and ATM genes correlated with a higher total number of mutations in other analyzed genes. Furthermore, the presence of mutated ATM correlated with poorer event-free survival (EFS) (p = 0.036). The presence of the mutated SMO gene correlated with earlier disease relapse (p = 0.023), inferior event-free survival (p = 0.011) and overall survival (OS) (p = 0.017), while mutations in the PTEN gene were associated with inferior OS (p = 0.048). Our findings suggest that the TP53 and ATM genes could be involved in the molecular pathophysiology of primary DLBCL CNS, whereas mutations in the PTEN and SMO genes could affect survival regardless of the initial treatment approach. 相似文献
50.
Application of a Genetic Algorithm for the Optimization of a Complex Reservoir System in Tunisia 总被引:2,自引:2,他引:0
Mohamed Hedi Louati Sihem Benabdallah Fethi Lebdi Darko Milutin 《Water Resources Management》2011,25(10):2387-2404
A genetic algorithm (GA) model is developed and used for optimizing the allocation of water resources within a complex multiple
reservoir system located in Tunisia. The GA model considers two objectives: the water allocation to demand centers and the
salinity level of the water supply to end users. These two objectives are combined into a single objective function using
a weighting factor approach. Five different cases (representing five different weighting factor combinations) were analyzed
by the GA model to produce the “optimum” allocation of water resources for each case. The generated solutions exhibited low
variability. The results are then compared using a range of system performance indicators to measure reliability, resilience,
and vulnerability. The evaluation of the system performance is an essential step to help system managers identify the preferred
allocation strategy and it provides a comprehensive insight into system behavior. 相似文献