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Perruzza D, Bernabò N, Rapino C, Valbonetti L, Falanga I, Russo V, Mauro A, Berardinelli P, Stuppia L, Maccarrone M, Barboni B. Artificial Neural Network to Predict Varicocele Impact on Male Fertility through Testicular Endocannabinoid Gene Expression Profiles. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3591086. [PMID: 30539009 PMCID: PMC6258097 DOI: 10.1155/2018/3591086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/01/2018] [Indexed: 02/07/2023]
Abstract
The relationship between varicocele and fertility has always been a matter of debate because of the absence of predictive clinical indicators or molecular markers able to define the severity of this disease. Even though accumulated evidence demonstrated that the endocannabinoid system (ECS) plays a central role in male reproductive biology, particularly in the testicular compartment, to date no data point to a role for ECS in the etiopathogenesis of varicocele. Therefore, the present research has been designed to investigate the relationship between testicular ECS gene expression and fertility, using a validated animal model of experimental varicocele (VAR), taking advantage of traditional statistical approaches and artificial neural network (ANN). Experimental induction of VAR led to a clear reduction of spermatogenesis in left testes ranging from a mild (Johnsen score 7: 21%) to a severe (Johnsen score 4: 58%) damage of the germinal epithelium. However, the mean number of new-borns recorded after two sequential matings was quite variable and independent of the Johnsen score. While the gene expression of biosynthetic and degrading enzymes of AEA (NAPE-PLD and FAAH, respectively) and of 2-AG (DAGLα and MAGL, respectively), as well as their binding cannabinoid receptors (CB1 and CB2), did not change between testes and among groups, a significant downregulation of vanilloid (TRPV1) expression was recorded in left testes of VAR rats and positively correlated with animal fertility. Interestingly, an ANN trained by inserting the left and right testicular ECS gene expression profiles (inputs) was able to predict varicocele impact on male fertility in terms of mean number of new-borns delivered (outputs), with a very high accuracy (average prediction error of 1%). The present study provides unprecedented information on testicular ECS gene expression patterns during varicocele, by developing a freely available predictive ANN model that may open new perspectives in the diagnosis of varicocele-associated infertility.
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Affiliation(s)
- Davide Perruzza
- Faculty of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Nicola Bernabò
- Faculty of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Cinzia Rapino
- Faculty of Veterinary Medicine, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Luca Valbonetti
- Faculty of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Ilaria Falanga
- Faculty of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Valentina Russo
- Faculty of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Annunziata Mauro
- Faculty of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Paolo Berardinelli
- Faculty of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Liborio Stuppia
- Department of Psychological, Health and Territorial Sciences, School of Medicine and Health Sciences, University “G. d'Annunzio” of Chieti and Pescara, 66100 Chieti, Italy
| | - Mauro Maccarrone
- Department of Medicine, Campus Bio-Medico University of Rome, 00128 Rome, Italy
- European Center for Brain Research, IRCCS Santa Lucia Foundation, 00164 Rome, Italy
| | - Barbara Barboni
- Faculty of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
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Reaching optimized parameter set: protein secondary structure prediction using neural network. Neural Comput Appl 2016. [DOI: 10.1007/s00521-015-2150-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Houška J, Peña-Méndez EM, Hernandez-Fernaud JR, Salido E, Hampl A, Havel J, Vaňhara P. Tissue profiling by nanogold-mediated mass spectrometry and artificial neural networks in the mouse model of human primary hyperoxaluria 1. J Appl Biomed 2014. [DOI: 10.1016/j.jab.2013.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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Armano G, Ledda F. Exploiting intrastructure information for secondary structure prediction with multifaceted pipelines. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2012; 9:799-808. [PMID: 22201070 DOI: 10.1109/tcbb.2011.159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Predicting the secondary structure of proteins is still a typical step in several bioinformatic tasks, in particular, for tertiary structure prediction. Notwithstanding the impressive results obtained so far, mostly due to the advent of sequence encoding schemes based on multiple alignment, in our view the problem should be studied from a novel perspective, in which understanding how available information sources are dealt with plays a central role. After revisiting a well-known secondary structure predictor viewed from this perspective (with the goal of identifying which sources of information have been considered and which have not), we propose a generic software architecture designed to account for all relevant information sources. To demonstrate the validity of the approach, a predictor compliant with the proposed generic architecture has been implemented and compared with several state-of-the-art secondary structure predictors. Experiments have been carried out on standard data sets, and the corresponding results confirm the validity of the approach. The predictor is available at http://iasc.diee.unica.it/ssp2/ through the corresponding web application or as downloadable stand-alone portable unpack-and-run bundle.
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Affiliation(s)
- Giuliano Armano
- Department of Electrical and Electronic Engineering, University of Cagliari, Piazza d’Armi, Cagliari 09123, Italy.
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Bettella F, Rasinski D, Knapp EW. Protein Secondary Structure Prediction with SPARROW. J Chem Inf Model 2012; 52:545-56. [DOI: 10.1021/ci200321u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Francesco Bettella
- Freie Universität
Berlin,
Institut für Chemie, Fabeckstr. 36a, D-14195 Berlin, Germany
- deCODE genetics, Sturlugata
8, 101 Reykjavik, Iceland
| | - Dawid Rasinski
- Freie Universität
Berlin,
Institut für Chemie, Fabeckstr. 36a, D-14195 Berlin, Germany
| | - Ernst Walter Knapp
- Freie Universität
Berlin,
Institut für Chemie, Fabeckstr. 36a, D-14195 Berlin, Germany
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Arabnia HR, Tran QN. Improved prediction of MHC class I binders/non-binders peptides through artificial neural network using variable learning rate: SARS corona virus, a case study. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 696:223-9. [PMID: 21431562 PMCID: PMC7123181 DOI: 10.1007/978-1-4419-7046-6_22] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Abstract
Fundamental step of an adaptive immune response to pathogen or vaccine is the binding of short peptides (also called epitopes) to major histocompatibility complex (MHC) molecules. The various prediction algorithms are being used to capture the MHC peptide binding preference, allowing the rapid scan of entire pathogen proteomes for peptide likely to bind MHC, saving the cost, effort, and time. However, the number of known binders/non-binders (BNB) to a specific MHC molecule is limited in many cases, which still poses a computational challenge for prediction. The training data should be adequate to predict BNB using any machine learning approach. In this study, variable learning rate has been demonstrated for training artificial neural network and predicting BNB for small datasets. The approach can be used for large datasets as well. The dataset for different MHC class I alleles for SARS Corona virus (Tor2 Replicase polyprotein 1ab) has been used for training and prediction of BNB. A total of 90 datasets (nine different MHC class I alleles with tenfold cross validation) have been retrieved from IEDB database for BNB. For fixed learning rate approach, the best value of AROC is 0.65, and in most of the cases it is 0.5, which shows the poor predictions. In case of variable learning rate, of the 90 datasets the value of AROC for 76 datasets is between 0.806 and 1.0 and for 7 datasets the value is between 0.7 and 0.8 and for rest of 7 datasets it is between 0.5 and 0.7, which indicates very good performance in most of the cases.
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Affiliation(s)
- Hamid R. Arabnia
- Dept. Computer Science, University of Georgia, Athens, 30602-7404 Georgia USA
| | - Quoc-Nam Tran
- , Department of Computer Science, Lamar University, Beaumont, 77710 Texas USA
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Soam SS, Khan F, Bhasker B, Mishra BN. Prediction of MHC class I binding peptides using probability distribution functions. Bioinformation 2009; 3:403-8. [PMID: 19759816 PMCID: PMC2732036 DOI: 10.6026/97320630003403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 03/31/2009] [Accepted: 04/19/2009] [Indexed: 11/23/2022] Open
Abstract
Binding of peptides to specific Major Histo-compatibility Complex (MHC) molecule is important for understanding immunity and has applications to vaccine discovery and design of immunotherapy. Artificial neural networks (ANN) are widely used by predictions tools to classify the peptides as binders or non-binders (BNB). However, the number of known binders to a specific MHC molecule is limited in many cases, which poses a computational challenge for prediction of BNB and hence, needs improvement in learning of ANN. Here, we describe, the application of probability distribution functions to initialize the weights and biases of the artificial neural network in order to predict HLA-A*0201 binders and non-binders. The 10-fold cross validation has been used to validate the results. It is evident from the results that the A(ROC) for 90% of test cases for Weibull, Uniform and Rayleigh distributions is in the range 0.90-1.0. Further, the standard deviation for AROC was minimum for Weibull distribution, and may be used to train the artificial neural network for HLA-A*0201 MHC Class-I binders and non-binders prediction.
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Affiliation(s)
- Sudhir Singh Soam
- Institute of Engineering & Technology, (A Constituent College of Uttar Pradesh Technical University, Lucknow) Lucknow, India
| | - Feroz Khan
- Institute of Engineering & Technology, (A Constituent College of Uttar Pradesh Technical University, Lucknow) Lucknow, India
| | - Bharat Bhasker
- Institute of Engineering & Technology, (A Constituent College of Uttar Pradesh Technical University, Lucknow) Lucknow, India
| | - Bhartendu Nath Mishra
- Institute of Engineering & Technology, (A Constituent College of Uttar Pradesh Technical University, Lucknow) Lucknow, India
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Sivan S, Filo O, Siegelmann H. Application of expert networks for predicting proteins secondary structure. ACTA ACUST UNITED AC 2007; 24:237-43. [PMID: 17236807 DOI: 10.1016/j.bioeng.2006.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2006] [Revised: 12/05/2006] [Accepted: 12/06/2006] [Indexed: 02/02/2023]
Abstract
The present study utilizes expert neural networks for the prediction of proteins secondary structure. We use three independent networks, one for each structure (alpha, beta and coil) as the first-level processing unit; decision upon the chosen structure for each residue is carried out by a second-level, post-processing unit, which utilizes the Chou and Fasman frequency values Falpha and Fbeta in order to strengthen and/or deplete the probability of the specific structure under investigation. The highest prediction case was 76%. Our method requires primitive computational means and a relatively small training set, while still been comparable to previous work. It is not meant to be an alternative to the determination of secondary structure by means of free energy minimization, integration of dynamic equations of motion or crystallography, which are expensive, time-consuming and complicated, but to provide additional constrains, which might be considered and incorporated into larger computing setups in order to reduce the initial search space for the above methods.
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Affiliation(s)
- Sarit Sivan
- Department of Biomedical Engineering, Technion, Israel Institute of Technology, IIT, Haifa 32000, Israel.
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Zhou HJ, Liu YK, Li Z, Yun D, Shun QL, Guo K. Analysing protein–protein interaction networks of human liver cancer cell lines with diverse metastasis potential. J Cancer Res Clin Oncol 2007; 133:663-72. [PMID: 17458561 DOI: 10.1007/s00432-007-0218-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 03/23/2007] [Indexed: 11/29/2022]
Abstract
PURPOSE Human hepatocellular carcinoma (HCC) is one of the most mortal tumor. In a previous study, we had constructed glycoprotein expression profiles and glycoprotein databases of three human liver cancer cell lines with diverse metastasis potential. In order to discover vital glycoproteins related to pathogenesis and metastasis of HCC, in this study we analyzed previous data with bioinformatic approach. METHODS We took previous data to draw the protein-protein interaction (PPI) networks of liver cell lines by searching IntACT database and then using Pajeck software. Further more, we compared the differences between the three PPI networks by drawing the PPI networks of differential glycoproteins and by naming differential display PPI networks. RESULTS Large numbers of proliferation and apoptosis-relative proteins interact with the differential glycoproteins, and among the differential glycoproteins there are many interactions. CONCLUSIONS We conclude that neither single nor several proteins cause malignant proliferation of liver cells. "Molecule groups" concept should be introduced into diagnosis and metastasis prediction of the HCC.
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Affiliation(s)
- Hai-Jun Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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Helmer-Citterich M, Casadio R, Guffanti A, Mauri G, Milanesi L, Pesole G, Valle G, Saccone C. Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society. BMC Bioinformatics 2005. [PMCID: PMC1866399 DOI: 10.1186/1471-2105-6-s4-s1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005, in Milan. This Editorial provides a brief overview of the Conference topics and introduces the peer-reviewed manuscripts accepted for publication in this Supplement.
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