A laboratory and pilot plant scaled continuous stirred reactor separator for the production of ethanol from sugars, corn grits/starch or biomass streams

An improved bio-reactor has been developed to allow the high speed, continues, low energy conversion of various substrates to ethanol. The Continuous Stirred Reactor Separator (CSRS) incorporates gas stripping of the ethanol using a recalculating gas stream between cascading stirred reactors in series. We have operated a 4 liter lab scale unit, and built and operated a 24,000 liter pilot scale version of the bioreactor. High rates of fermentation are maintained in the reactor stages using a highly flocculent yeast strain. Ethanol is recovered from the stripping gas using a hydrophobic solvent absorber (isothermal), after which the gas is returned to the bioreactor. Ethanol can then be removed from the solvent to recover a highly concentrated ethanol product. We have applied the lab scale CSRS to sugars (glucose/sucrose), molasses, and raw starch with simultaneous saccharification and fermentation of the starch granules (SSF). The pilot scale CSRS has been operated as a cascade reactor using dextrins as a feed. Operating data from both the lab and pilot scale CSRS are presented. Details of how the system might be applied to cellulosics, with some preliminary data are also given

Image-Level and Group-Level Models for Drosophila Gene Expression Pattern Annotation

Background: Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment on the pace of biological discovery. It is thus imperative to design an automated system for efficient image annotation and comparison. Results: We present a computational framework to perform anatomical keywords annotation for Drosophila gene expression images. The spatial sparse coding approach is used to represent local patches of images in comparison with the well-known bag-of-words (BoW) method. Three pooling functions including max pooling, average pooling and Sqrt (square root of mean squared statistics) pooling are employed to transform the sparse codes to image features. Based on the constructed features, we develop both an image-level scheme and a group-level scheme to tackle the key challenges in annotating Drosophila gene expression pattern images automatically. To deal with the imbalanced data distribution inherent in image annotation tasks, the undersampling method is applied together with majority vote. Results on Drosophila embryonic expression pattern images verify the efficacy of our approach. Conclusion: In our experiment, the three pooling functions perform comparably well in feature dimension reduction. The undersampling with majority vote is shown to be effective in tackling the problem of imbalanced data. Moreover, combining sparse coding and image-level scheme leads to consistent performance improvement in keywords annotation

Learning Sparse Representations for Fruit Fly Gene Expression Pattern Image Annotation and Retreival

Background: Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughput images will provide novel insights into the functions, interactions, and networks of animal genes governing development. To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords. Results: In this article, we adapt advanced data mining and computer vision techniques to address the key challenges in annotating and retrieving fruit fly gene expression pattern images. To boost the performance of image annotation and retrieval, we propose representations integrating spatial information and sparse features, overcoming the limitations of prior schemes. Conclusions: We perform systematic experimental studies to evaluate the proposed schemes in comparison with current methods. Experimental results indicate that the integration of spatial information and sparse features lead to consistent performance improvement in image annotation, while for the task of retrieval, sparse features alone yields better results

Learning Sparse Representations for Fruit Fly Gene Expression Pattern Image Annotation and Retreival

Background: Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughput images will provide novel insights into the functions, interactions, and networks of animal genes governing development. To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords. Results: In this article, we adapt advanced data mining and computer vision techniques to address the key challenges in annotating and retrieving fruit fly gene expression pattern images. To boost the performance of image annotation and retrieval, we propose representations integrating spatial information and sparse features, overcoming the limitations of prior schemes. Conclusions: We perform systematic experimental studies to evaluate the proposed schemes in comparison with current methods. Experimental results indicate that the integration of spatial information and sparse features lead to consistent performance improvement in image annotation, while for the task of retrieval, sparse features alone yields better results

Adaptive Convolutional ReLUs

Rectified linear units (ReLUs) are currently the most popular activation function used in neural networks. Although ReLUs can solve the gradient vanishing problem and accelerate training convergence, it suffers from the dying ReLU problem in which some neurons are never activated if the weights are not updated properly. In this work, we propose a novel activation function, known as the adaptive convolutional ReLU (ConvReLU), that can better mimic brain neuron activation behaviors and overcome the dying ReLU problem. With our novel parameter sharing scheme, ConvReLUs can be applied to convolution layers that allow each input neuron to be activated by different trainable thresholds without involving a large number of extra parameters. We employ the zero initialization scheme in ConvReLU to encourage trainable thresholds to be close to zero. Finally, we develop a partial replacement strategy that only replaces the ReLUs in the early layers of the network. This resolves the dying ReLU problem and retains sparse representations for linear classifiers. Experimental results demonstrate that our proposed ConvReLU has consistently better performance compared to ReLU, LeakyReLU, and PReLU. In addition, the partial replacement strategy is shown to be effective not only for our ConvReLU but also for LeakyReLU and PReLU