AoP-LSE: Antioxidant Proteins Classification Using Deep Latent Space Encoding of Sequence Features

2021 ◽  
Vol 43 (3) ◽  
pp. 1489-1501
Author(s):  
Muhammad Usman ◽  
Shujaat Khan ◽  
Seongyong Park ◽  
Jeong-A Lee
Keyword(s):  
Feature Space ◽  
Vital Role ◽  
Computational Method ◽  
The Novel ◽  
Novel Proteins ◽  
Discriminating Power ◽  
Latent Space ◽  
Antioxidant Proteins ◽  
Class Labels ◽  
Space Encoding

It is of utmost importance to develop a computational method for accurate prediction of antioxidants, as they play a vital role in the prevention of several diseases caused by oxidative stress. In this correspondence, we present an effective computational methodology based on the notion of deep latent space encoding. A deep neural network classifier fused with an auto-encoder learns class labels in a pruned latent space. This strategy has eliminated the need to separately develop classifier and the feature selection model, allowing the standalone model to effectively harness discriminating feature space and perform improved predictions. A thorough analytical study has been presented alongwith the PCA/tSNE visualization and PCA-GCNR scores to show the discriminating power of the proposed method. The proposed method showed a high MCC value of 0.43 and a balanced accuracy of 76.2%, which is superior to the existing models. The model has been evaluated on an independent dataset during which it outperformed the contemporary methods by correctly identifying the novel proteins with an accuracy of 95%.

scholarly journals ECM-LSE: Prediction of Extracellular Matrix Proteins Using Deep Latent Space Encoding of k-Spaced Amino Acid Pairs

2021 ◽  
Vol 9 ◽  
Author(s):  
Ubaid M. Al-Saggaf ◽  
Muhammad Usman ◽  
Imran Naseem ◽  
Muhammad Moinuddin ◽  
Ahmad A. Jiman ◽  
...  
Keyword(s):  
Amino Acid ◽  
Vital Role ◽  
Cellular Functions ◽  
Structural Support ◽  
Ecm Proteins ◽  
Latent Space ◽  
Machine Learning Approach ◽  
Wet Lab ◽  
Living Tissues ◽  
Space Encoding

Extracelluar matrix (ECM) proteins create complex networks of macromolecules which fill-in the extracellular spaces of living tissues. They provide structural support and play an important role in maintaining cellular functions. Identification of ECM proteins can play a vital role in studying various types of diseases. Conventional wet lab–based methods are reliable; however, they are expensive and time consuming and are, therefore, not scalable. In this research, we propose a sequence-based novel machine learning approach for the prediction of ECM proteins. In the proposed method, composition of k-spaced amino acid pair (CKSAAP) features are encoded into a classifiable latent space (LS) with the help of deep latent space encoding (LSE). A comprehensive ablation analysis is conducted for performance evaluation of the proposed method. Results are compared with other state-of-the-art methods on the benchmark dataset, and the proposed ECM-LSE approach has shown to comprehensively outperform the contemporary methods.

scholarly journals A Mathematical Model of Contact Tracing during the 2014–2016 West African Ebola Outbreak

Mathematics ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 608
Author(s):  
Danielle Burton ◽  
Suzanne Lenhart ◽  
Christina J. Edholm ◽  
Benjamin Levy ◽  
Michael L. Washington ◽  
...  
Keyword(s):  
Mathematical Model ◽  
Disease Management ◽  
Ebola Virus ◽  
Virus Disease ◽  
Infected Individual ◽  
Vital Role ◽  
West African ◽  
Contact Tracing ◽  
The Novel ◽  
Using Data

The 2014–2016 West African outbreak of Ebola Virus Disease (EVD) was the largest and most deadly to date. Contact tracing, following up those who may have been infected through contact with an infected individual to prevent secondary spread, plays a vital role in controlling such outbreaks. Our aim in this work was to mechanistically represent the contact tracing process to illustrate potential areas of improvement in managing contact tracing efforts. We also explored the role contact tracing played in eventually ending the outbreak. We present a system of ordinary differential equations to model contact tracing in Sierra Leonne during the outbreak. Using data on cumulative cases and deaths, we estimate most of the parameters in our model. We include the novel features of counting the total number of people being traced and tying this directly to the number of tracers doing this work. Our work highlights the importance of incorporating changing behavior into one’s model as needed when indicated by the data and reported trends. Our results show that a larger contact tracing program would have reduced the death toll of the outbreak. Counting the total number of people being traced and including changes in behavior in our model led to better understanding of disease management.

scholarly journals A novel missense variant c.G644A (p.G215E) of the RPGR gene in a Chinese family causes X-linked retinitis pigmentosa

2019 ◽  
Vol 39 (10) ◽  
Author(s):  
Jiewen Fu ◽  
Jingliang Cheng ◽  
Qi Zhou ◽  
Chunli Wei ◽  
Hanchun Chen ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
Expression Patterns ◽  
Missense Variant ◽  
Vital Role ◽  
Chinese Family ◽  
The Novel ◽  
Rna Seq ◽  
Targeted Next Generation Sequencing ◽  
Retinal Tissue ◽  
Eye Tissues

Abstract The mutations in patients with X-linked retinitis pigmentosa (xlRP) have not been well described in the Chinese population. In the present study, a five-generation Chinese retinitis pigmentosa (RP) family was recruited; targeted next-generation sequencing (TGS) was used to identify causative genes and Sanger sequencing for co-segregation. RNA-seq data analysis and revere transcriptional-polymerase chain reaction (RT-PCR) were applied to investigate gene expression patterns of RP GTPase regulator (RPGR) in human and Rpgr in mouse. A novel, hemizygous, deleterious and missense variant: c.G644A (p.G215E) in the RPGR gene (NM_000328.2) exon 7 of X-chromosome was identified in the proband, which was co-segregated with the clinical phenotypes in this family. RNA-seq data showed that RPGR is ubiquitously expressed in 27 human tissues with testis in highest, but no eye tissues data. Then the expressions for Rpgr mRNA in mice including eye tissues were conducted and showed that Rpgr transcript is ubiquitously expressed very highly in retina and testis, and highly in other eye tissues including lens, sclera, and cornea; and expressed highly in the six different developmental times of retinal tissue. Ubiquitous expression in different tissues from eye and very high expression in the retina indicated that RPGR plays a vital role in eye functions, particularly in retina. In conclusion, our study is the first to indicate that the novel missense variant c.G644A (p.G215E) in the RPGR gene might be the disease-causing mutation in this xlRP family, expanding mutation spectrum. These findings facilitate better understanding of the molecular pathogenesis of this disease; provide new insights for genetic counseling and healthcare.

scholarly journals C4orf41 and TTC-15 are mammalian TRAPP components with a role at an early stage in ER-to-Golgi trafficking

2011 ◽  
Vol 22 (12) ◽  
pp. 2083-2093 ◽  
Author(s):  
P. James Scrivens ◽  
Baraa Noueihed ◽  
Nassim Shahrzad ◽  
Sokunthear Hul ◽  
Stephanie Brunet ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Multidisciplinary Approach ◽  
Early Stage ◽  
Binary Interaction ◽  
The Novel ◽  
Novel Proteins ◽  
Bona Fide ◽  
Interaction Map ◽  
Equivalent Complex

TRAPP is a multisubunit tethering complex implicated in multiple vesicle trafficking steps in Saccharomyces cerevisiae and conserved throughout eukarya, including humans. Here we confirm the role of TRAPPC2L as a stable component of mammalian TRAPP and report the identification of four novel components of the complex: C4orf41, TTC-15, KIAA1012, and Bet3L. Two of the components, KIAA1012 and Bet3L, are mammalian homologues of Trs85p and Bet3p, respectively. The remaining two novel TRAPP components, C4orf41 and TTC-15, have no homologues in S. cerevisiae. With this work, human homologues of all the S. cerevisiae TRAPP proteins, with the exception of the Saccharomycotina-specific subunit Trs65p, have now been reported. Through a multidisciplinary approach, we demonstrate that the novel proteins are bona fide components of human TRAPP and implicate C4orf41 and TTC-15 (which we call TRAPPC11 and TRAPPC12, respectively) in ER-to-Golgi trafficking at a very early stage. We further present a binary interaction map for all known mammalian TRAPP components and evidence that TRAPP oligomerizes. Our data are consistent with the absence of a TRAPP I–equivalent complex in mammalian cells, suggesting that the fundamental unit of mammalian TRAPP is distinct from that characterized in S. cerevisiae.

Supervised Determined Source Separation with Multichannel Variational Autoencoder

2019 ◽  
Vol 31 (9) ◽  
pp. 1891-1914 ◽  
Author(s):  
Hirokazu Kameoka ◽  
Li Li ◽  
Shota Inoue ◽  
Shoji Makino
Keyword(s):  
Source Separation ◽  
Generative Model ◽  
Separation Technique ◽  
Separation Performance ◽  
Unknown Parameters ◽  
Baseline Method ◽  
Latent Space ◽  
Variational Autoencoder ◽  
Training Examples ◽  
Class Labels

This letter proposes a multichannel source separation technique, the multichannel variational autoencoder (MVAE) method, which uses a conditional VAE (CVAE) to model and estimate the power spectrograms of the sources in a mixture. By training the CVAE using the spectrograms of training examples with source-class labels, we can use the trained decoder distribution as a universal generative model capable of generating spectrograms conditioned on a specified class index. By treating the latent space variables and the class index as the unknown parameters of this generative model, we can develop a convergence-guaranteed algorithm for supervised determined source separation that consists of iteratively estimating the power spectrograms of the underlying sources, as well as the separation matrices. In experimental evaluations, our MVAE produced better separation performance than a baseline method.

Wspólnoty kobiet w pisarstwie i życiu Anny Kowalskiej

Wielogłos ◽  
2020 ◽  
pp. 117-130
Author(s):  
Ewa Kraskowska
Keyword(s):  
Vital Role ◽  
The Novel ◽  
Agricultural Cooperative ◽  
Women's Communities

Women’s Communities in the Writing and Life of Anna Kowalska The article is devoted to the writing and biography of Anna Kowalska. The first part discusses the shared home of Maria Dąbrowska and Anna Kowalska, in which women hired as housekeepers played a vital role. Then the article briefly analyses Kowalska’s novel Safona (Sappho), which depicts the aging Greek female poet surrounded by her young protégées. The main focus is, however, on the novel Gruce (The Gruca family), co-published in 1936 by Anna Kowalska and her husband, Jerzy Kowalski. The novel was heavily revised by Kowalska and reprinted in 1961, and then in 1968. One of the side motifs of this vast work explores a women’s agricultural cooperative in a village near Lviv in the second half of the 1930s. The utopian projects of feminism and cooperativism are criticised here, while the entire novel fits in the “dark” formula of psychological and social (“populist” in the language of the era) realism, characteristic of that decade.

scholarly journals The Tryptophan Pathway Targeting Antioxidant Capacity in the Placenta

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
Kang Xu ◽  
Gang Liu ◽  
Chenxing Fu
Keyword(s):  
Oxidative Stress ◽  
Antioxidant Capacity ◽  
Fetal Development ◽  
Antioxidant Properties ◽  
Redox Status ◽  
Kynurenine Pathway ◽  
Vital Role ◽  
Tryptophan Metabolites ◽  
Antioxidant Proteins ◽  
Hydroxyanthranilic Acid

The placenta plays a vital role in fetal development during pregnancy. Dysfunction of the placenta can be caused by oxidative stress and can lead to abnormal fetal development. Preventing oxidative stress of the placenta is thus an important measure to ensure positive birth outcomes. Research shows that tryptophan and its metabolites can efficiently clean free radicals (including the reactive oxygen species and activated chlorine). Consequently, tryptophan and its metabolites are suggested to act as potent antioxidants in the placenta. However, the mechanism of these antioxidant properties in the placenta is still unknown. In this review, we summarize research on the antioxidant properties of tryptophan, tryptophan metabolites, and metabolic enzymes. Two predicted mechanisms of tryptophan’s antioxidant properties are discussed. (1) Tryptophan could activate the phosphorylation of p62 after the activation of mTORC1; phosphorylated p62 then uncouples the interaction between Nrf2 and Keap1, and activated Nrf2 enters the nucleus to induce expressions of antioxidant proteins, thus improving cellular antioxidation. (2) 3-Hydroxyanthranilic acid, a tryptophan kynurenine pathway metabolite, changes conformation of Keap1, inducing the dissociation of Nrf2 and Keap1, activating Nrf2 to enter the nucleus and induce expressions of antioxidant proteins (such as HO-1), thereby enhancing cellular antioxidant capacity. These mechanisms may enrich the theory of how to apply tryptophan as an antioxidant during pregnancy, providing technical support for its use in regulating the pregnancy’s redox status and enriching our understanding of amino acids’ nutritional value.

scholarly journals SELECTING TARGET MARKET BY SIMILAR MEASURES IN INTERVAL INTUITIONISTIC FUZZY SET

2019 ◽  
Vol 25 (5) ◽  
pp. 934-950 ◽  
Author(s):  
Nguyen Xuan Thao ◽  
Truong Thi Thuy Duong
Keyword(s):  
Fuzzy Sets ◽  
Intuitionistic Fuzzy Set ◽  
Similarity Measures ◽  
Vital Role ◽  
Intuitionistic Fuzzy Sets ◽  
Target Market ◽  
The Novel ◽  
Market Selection ◽  
Intuitionistic Fuzzy ◽  
Decision Making Model

The selection of the target market plays vital role in promoting the marketing strategies of companies. We presented is a method for target market selection. We introduce some novel similarity measures between intuitionistic fuzzy sets and the novel similarity measures between interval-valued intuitionistic fuzzy sets. They are constructed by combining exponential and other functions. Finally, we introduce a multi-criteria decision making model to select target market by using the novel similarity measure of interval intuitionistic fuzzy sets.

scholarly journals Metals, non-metals and minerals: The complexity of bacterial selenate respiration

2012 ◽  
Vol 34 (5) ◽  
pp. 23-27
Author(s):  
Clive S. Butler
Keyword(s):  
Electron Transfer ◽  
Electron Acceptors ◽  
Elemental Selenium ◽  
The Novel ◽  
Novel Proteins ◽  
New Family ◽  
Recent Advances ◽  
Wide Range ◽  
Sequential Reduction ◽  
Shed Light

Metalloproteins and enzymes are an essential part of all respiratory electron-transfer chains and provide a pathway for electron transfer to terminal electron acceptors. Since bacteria can utilize a wide range of respiratory substrates, this variety of potential electron acceptors has facilitated the need for many different respiratory metalloproteins. Bacterial selenate respiration requires the sequential reduction of the selenium oxyanions selenate and selenite resulting in the precipitation of elemental selenium. The initial bioenergetic processes of selenate respiration are driven by metalloproteins utilizing cofactors containing iron and molybdenum. However, the assembly of the elemental selenium into selenium nanosphere crystals has shed light on a new family of proteins involved in selenium biomineralization. This article highlights some of the recent advances in our understanding of selenate respiration in the bacterium Thauera selenatis, with particular focus on the metalloproteins involved in selenate reduction and the novel proteins that function to deal with these insoluble selenium deposits. “As mineralogy constitutes a part of chemistry, it is clear that this arrangement of minerals must derive its principles from chemistry” Jöns Jacob Berzelius 1814

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