NN'-diacetylchitobiase activity in Tay-Sachs disease and Sandhoff's disease.
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ABSTRACT:
SUBMITTER: Stirling JL
PROVIDER: S-EPMC1168118 | biostudies-other | 1974 Aug
REPOSITORIES: biostudies-other
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Project description:BackgroundBreast cancer is the most common cancer which causes significant morbidity and mortality among women worldwide. Lack of medical facilities for early detection, therapeutic strategies for treatment and side effects due to pharmacological compounds have encompassed the need for new therapies mostly from natural sources. A lot of components have been identified from different snake venoms as therapeutic agents. A group of polypeptides (60-70 amino acid residues) called cytotoxins or cardiotoxins present in an elapid family of snakes have a wide variety of pharmaceutical actions and have the tendency to damage a wide variety of cells including cancerous cells. The aim of the present study was to evaluate the cytotoxic effect of NN-32 protein toxin purified from Indian Spectacled Cobra venom against human breast cancer cell lines (MCF-7 and MDA-MB-231).MethodsThe NN-32 toxin was purified by ion exchange chromatography and further by RP-HPLC. The potential anticancer effects of the NN-32 toxin on MCF-7 and MDA-MB-231 cells were evaluated using MTT, anti-proliferation, neutral red (NR) uptake and Lactate Dehydrogenase (LDH) release assay.ResultsThe ion exchange chromatography showed various peaks among fraction no. 35 showing cytotoxic activity and this fraction showed a single peak with retention time 3.6 mins by HPLC using C18 column. The NN-32 toxin induced cytotoxicity in MCF-7 and MDA-MB-231 cells with the IC50 value of 2.5 and 6.7 μg/ml respectively. The NN-32 showed significant cytotoxicity to both the cell lines along with low cytotoxicity to MCF-10A (normal breast epithelial) cells. The cytotoxic effect was further confirmed by the anti-proliferative, NR uptake and LDH release assays.ConclusionThe purified toxin NN-32 from Naja naja venom showed cytotoxic activity against MCF-7 (ER+) and MDA-MB-231(ER-) cells in both dose dependent and time dependent manner.
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Project description:BackgroundDrug repositioning is an emerging approach in pharmaceutical research for identifying novel therapeutic potentials for approved drugs and discover therapies for untreated diseases. Due to its time and cost efficiency, drug repositioning plays an instrumental role in optimizing the drug development process compared to the traditional de novo drug discovery process. Advances in the genomics, together with the enormous growth of large-scale publicly available data and the availability of high-performance computing capabilities, have further motivated the development of computational drug repositioning approaches. More recently, the rise of machine learning techniques, together with the availability of powerful computers, has made the area of computational drug repositioning an area of intense activities.ResultsIn this study, a novel framework SNF-NN based on deep learning is presented, where novel drug-disease interactions are predicted using drug-related similarity information, disease-related similarity information, and known drug-disease interactions. Heterogeneous similarity information related to drugs and disease is fed to the proposed framework in order to predict novel drug-disease interactions. SNF-NN uses similarity selection, similarity network fusion, and a highly tuned novel neural network model to predict new drug-disease interactions. The robustness of SNF-NN is evaluated by comparing its performance with nine baseline machine learning methods. The proposed framework outperforms all baseline methods ([Formula: see text] = 0.867, and [Formula: see text]=0.876) using stratified 10-fold cross-validation. To further demonstrate the reliability and robustness of SNF-NN, two datasets are used to fairly validate the proposed framework's performance against seven recent state-of-the-art methods for drug-disease interaction prediction. SNF-NN achieves remarkable performance in stratified 10-fold cross-validation with [Formula: see text] ranging from 0.879 to 0.931 and [Formula: see text] from 0.856 to 0.903. Moreover, the efficiency of SNF-NN is verified by validating predicted unknown drug-disease interactions against clinical trials and published studies.ConclusionIn conclusion, computational drug repositioning research can significantly benefit from integrating similarity measures in heterogeneous networks and deep learning models for predicting novel drug-disease interactions. The data and implementation of SNF-NN are available at http://pages.cpsc.ucalgary.ca/ tnjarada/snf-nn.php .
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Project description:Metagenomic sequencing of the rumen of 11 nn from Scotland
| PRJEB42306 | ENA
Project description:PurposeRecently, several attempts were conducted to transfer deep learning to medical image reconstruction. An increasingly number of publications follow the concept of embedding the computed tomography (CT) reconstruction as a known operator into a neural network. However, most of the approaches presented lack an efficient CT reconstruction framework fully integrated into deep learning environments. As a result, many approaches use workarounds for mathematically unambiguously solvable problems.MethodsPYRO-NN is a generalized framework to embed known operators into the prevalent deep learning framework Tensorflow. The current status includes state-of-the-art parallel-, fan-, and cone-beam projectors, and back-projectors accelerated with CUDA provided as Tensorflow layers. On top, the framework provides a high-level Python API to conduct FBP and iterative reconstruction experiments with data from real CT systems.ResultsThe framework provides all necessary algorithms and tools to design end-to-end neural network pipelines with integrated CT reconstruction algorithms. The high-level Python API allows a simple use of the layers as known from Tensorflow. All algorithms and tools are referenced to a scientific publication and are compared to existing non-deep learning reconstruction frameworks. To demonstrate the capabilities of the layers, the framework comes with baseline experiments, which are described in the supplementary material. The framework is available as open-source software under the Apache 2.0 licence at https://github.com/csyben/PYRO-NN.ConclusionsPYRO-NN comes with the prevalent deep learning framework Tensorflow and allows to setup end-to-end trainable neural networks in the medical image reconstruction context. We believe that the framework will be a step toward reproducible research and give the medical physics community a toolkit to elevate medical image reconstruction with new deep learning techniques.
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Project description:Hyperbolic neural networks have been popular in the recent past due to their ability to represent hierarchical data sets effectively and efficiently. The challenge in developing these networks lies in the nonlinearity of the embedding space namely, the Hyperbolic space. Hyperbolic space is a homogeneous Riemannian manifold of the Lorentz group which is a semi-Riemannian manifold, i.e. a manifold equipped with an indefinite metric. Most existing methods (with some exceptions) use local linearization to define a variety of operations paralleling those used in traditional deep neural networks in Euclidean spaces. In this paper, we present a novel fully hyperbolic neural network which uses the concept of projections (embeddings) followed by an intrinsic aggregation and a nonlinearity all within the hyperbolic space. The novelty here lies in the projection which is designed to project data on to a lower-dimensional embedded hyperbolic space and hence leads to a nested hyperbolic space representation independently useful for dimensionality reduction. The main theoretical contribution is that the proposed embedding is proved to be isometric and equivariant under the Lorentz transformations, which are the natural isometric transformations in hyperbolic spaces. This projection is computationally efficient since it can be expressed by simple linear operations, and, due to the aforementioned equivariance property, it allows for weight sharing. The nested hyperbolic space representation is the core component of our network and therefore, we first compare this representation - independent of the network - with other dimensionality reduction methods such as tangent PCA, principal geodesic analysis (PGA) and HoroPCA. Based on this equivariant embedding, we develop a novel fully hyperbolic graph convolutional neural network architecture to learn the parameters of the projection. Finally, we present experiments demonstrating comparative performance of our network on several publicly available data sets.
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Project description:Cloud computing enables users to outsource their databases and the computing functionalities to a cloud service provider to avoid the cost of maintaining a private storage and computational requirements. It also provides universal access to data, applications, and services without location dependency. While cloud computing provides many benefits, it possesses a number of security and privacy concerns. Outsourcing data to a cloud service provider in encrypted form may help to overcome these concerns. However, dealing with the encrypted data makes it difficult for the cloud service providers to perform some operations over the data that will especially be required in query processing tasks. Among the techniques employed in query processing task, the k-nearest neighbor method draws attention due to its simplicity and efficiency, particularly on massive data sets. A number of k-nearest neighbor algorithms for query processing task on a single encrypted database have been proposed. However, the performance of k-nearest neighbor algorithms on a single database may create accuracy and reliability problems. It is a fact that collaboration among different cloud service providers yields more accurate and more reliable results in query processing. By considering this fact, we focus on the k-nearest neighbor (k-NN) problem over two encrypted databases. We introduce a secure two-party k-NN interpolation protocol that enables a query owner to extract the interpolation of the k-nearest neighbors of a query point from two different databases outsourced to two different cloud service providers. We also show that our protocol protects the confidentiality of the data and the query point, and hides data access patterns. Furthermore, we conducted a number of experiment to demonstrate the efficiency of our protocol. The results show that the running time of our protocol is linearly dependent on both the number of nearest neighbours and data size.
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Project description: Not available
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Project description:Human action recognition is a trending topic in the field of computer vision and its allied fields. The goal of human action recognition is to identify any human action that takes place in an image or a video dataset. For instance, the actions include walking, running, jumping, throwing, and much more. Existing human action recognition techniques have their own set of limitations when it concerns model accuracy and flexibility. To overcome these limitations, deep learning technologies were implemented. In the deep learning approach, a model learns by itself to improve its recognition accuracy and avoids problems such as gradient eruption, overfitting, and underfitting. In this paper, we propose a novel parameter initialization technique using the Maxout activation function. Firstly, human action is detected and tracked from the video dataset to learn the spatial-temporal features. Secondly, the extracted feature descriptors are trained using the RBM-NN. Thirdly, the local features are encoded into global features using an integrated forward and backward propagation process via RBM-NN. Finally, an SVM classifier recognizes the human actions in the video dataset. The experimental analysis performed on various benchmark datasets showed an improved recognition rate when compared to other state-of-the-art learning models.
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Project description:Multiplex assays of variant effect (MAVEs) are a family of methods that includes deep mutational scanning experiments on proteins and massively parallel reporter assays on gene regulatory sequences. Despite their increasing popularity, a general strategy for inferring quantitative models of genotype-phenotype maps from MAVE data is lacking. Here we introduce MAVE-NN, a neural-network-based Python package that implements a broadly applicable information-theoretic framework for learning genotype-phenotype maps-including biophysically interpretable models-from MAVE datasets. We demonstrate MAVE-NN in multiple biological contexts, and highlight the ability of our approach to deconvolve mutational effects from otherwise confounding experimental nonlinearities and noise.
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Project description:The k-Nearest Neighbor (kNN) classifier represents a simple and very general approach to classification. Still, the performance of kNN classifiers can often compete with more complex machine-learning algorithms. The core of kNN depends on a "guilt by association" principle where classification is performed by measuring the similarity between a query and a set of training patterns, often computed as distances. The relative performance of kNN classifiers is closely linked to the choice of distance or similarity measure, and it is therefore relevant to investigate the effect of using different distance measures when comparing biomedical data. In this study on classification of cancer data sets, we have used both common and novel distance measures, including the novel distance measures Sobolev and Fisher, and we have evaluated the performance of kNN with these distances on 4 cancer data sets of different type. We find that the performance when using the novel distance measures is comparable to the performance with more well-established measures, in particular for the Sobolev distance. We define a robust ranking of all the distance measures according to overall performance. Several distance measures show robust performance in kNN over several data sets, in particular the Hassanat, Sobolev, and Manhattan measures. Some of the other measures show good performance on selected data sets but seem to be more sensitive to the nature of the classification data. It is therefore important to benchmark distance measures on similar data prior to classification to identify the most suitable measure in each case.
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