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Nicolle A, Deng S, Ihme M, Kuzhagaliyeva N, Ibrahim EA, Farooq A. Mixtures Recomposition by Neural Nets: A Multidisciplinary Overview. J Chem Inf Model 2024; 64:597-620. [PMID: 38284618 DOI: 10.1021/acs.jcim.3c01633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Artificial Neural Networks (ANNs) are transforming how we understand chemical mixtures, providing an expressive view of the chemical space and multiscale processes. Their hybridization with physical knowledge can bridge the gap between predictivity and understanding of the underlying processes. This overview explores recent progress in ANNs, particularly their potential in the 'recomposition' of chemical mixtures. Graph-based representations reveal patterns among mixture components, and deep learning models excel in capturing complexity and symmetries when compared to traditional Quantitative Structure-Property Relationship models. Key components, such as Hamiltonian networks and convolution operations, play a central role in representing multiscale mixtures. The integration of ANNs with Chemical Reaction Networks and Physics-Informed Neural Networks for inverse chemical kinetic problems is also examined. The combination of sensors with ANNs shows promise in optical and biomimetic applications. A common ground is identified in the context of statistical physics, where ANN-based methods iteratively adapt their models by blending their initial states with training data. The concept of mixture recomposition unveils a reciprocal inspiration between ANNs and reactive mixtures, highlighting learning behaviors influenced by the training environment.
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Affiliation(s)
- Andre Nicolle
- Aramco Fuel Research Center, Rueil-Malmaison 92852, France
| | - Sili Deng
- Massachusetts Institute of Technology, Cambridge 02139, Massachusetts, United States
| | - Matthias Ihme
- Stanford University, Stanford 94305, California, United States
| | | | - Emad Al Ibrahim
- King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Aamir Farooq
- King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
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Wang X, Meng X, Dong Y, Song C, Sui F, Lu X, Mei X, Fan Y, Liu Y. Differential protein analysis of saline-alkali promoting the oil accumulation in Nitzschia palea. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:11. [PMID: 38282018 PMCID: PMC10823674 DOI: 10.1186/s13068-023-02451-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/16/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND The increasingly severe salinization of the aquatic environment has led to serious damage to the habitats of aquatic organisms. Benthic diatoms are commonly employed as indicator species for assessing water quality and serve as a reflection of the overall health of the aquatic ecosystem. Nitzschia palea is a common diatom found in freshwater, with high oil content, rapid reproductive rate, and it is a commonly dominant species in various rivers. RESULTS The results showed that after 4 days (d) of saline-alkali stress, the cell density and chlorophyll a content of Nitzschia palea reached their maximum values. Therefore, we selected Nitzschia palea under 4 d stress for Tandem Mass Tag (TMT) quantitative proteomic analysis to explore the molecular adaptation mechanism of freshwater diatoms under saline-alkali stress. Totally, 854 proteins were enriched, of which 439 differentially expressed proteins were identified. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and subcellular fractionation analysis revealed that these proteins were mainly enriched in the photosynthesis pathway, citric acid cycle (TCA cycle), fatty acid synthesis, and glutathione cycle. CONCLUSIONS This study aims to reveal the physiological, biochemical and proteomic mechanisms of salt and alkali tolerance and molecular adaptation of Nitzschia palea under different saline-alkali concentrations. This study showed that Nitzschia palea is one candidate of the environmental friendly, renewable bioenergy microalgae. Meantime, Nitzschia palea reveals for the proteome of the freshwater and provides the basis, it became a model algal species for freshwater diatoms.
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Affiliation(s)
- Xintong Wang
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China
| | - Xianghong Meng
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China
| | - Yanlong Dong
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China
| | - Chunhua Song
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China
| | - Fengyang Sui
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China
| | - Xinxin Lu
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China
| | - Xiaoxue Mei
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China
| | - Yawen Fan
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China.
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin, China.
| | - Yan Liu
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China.
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin, China.
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Santos MM, Costa TC, Mendes TAO, Dutra LL, Silva DNL, Araújo RD, Serão NVL, Rennó LN, Silva YFRS, Detmann E, Martín-Tereso J, Carvalho IP, Gionbelli MP, Duarte MS. Can the post-ruminal urea release impact liver metabolism, and nutritional status of beef cows at late gestation? PLoS One 2023; 18:e0293216. [PMID: 37856443 PMCID: PMC10586634 DOI: 10.1371/journal.pone.0293216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/07/2023] [Indexed: 10/21/2023] Open
Abstract
We aimed to evaluate the effects of post-ruminal supply of urea (PRU) on nutritional status, and liver metabolism of pregnant beef cows during late gestation. Twenty-four Brahman dams, pregnant from a single sire, and weighing 545 kg ± 23 kg were confined into individual pens at 174 ± 23 d of gestation, and randomly assigned into one of two dietary treatments up to 270 d of gestation: Control (CON, n = 12), consisting of a basal diet supplemented with conventional urea, where the cows were fed with diets containing 13.5 g conventional urea per kg dry matter; and PRU (PRU, n = 12), consisting of a basal diet supplemented with a urea coated to extensively prevent ruminal degradation while being intestinally digestible, where the cows were fed with diets containing 14,8 g urea protected from ruminal degradation per kg dry matter. Post-ruminal supply of urea reduced the urine levels of 3-methylhistidine (P = 0.02). There were no differences between treatments for dry matter intake (DMI; P = 0.76), total digestible nutrient (TDN) intake (P = 0.30), and in the body composition variables, such as, subcutaneous fat thickness (SFT; P = 0.72), and rib eye area (REA; P = 0.85). In addition, there were no differences between treatments for serum levels of glucose (P = 0.87), and serum levels of glucogenic (P = 0.28), ketogenic (P = 0.72), glucogenic, and ketogenic (P = 0.45) amino acids, neither for urea in urine (P = 0.51) as well as urea serum (P = 0.30). One the other hand, enriched pathways were differentiated related to carbohydrate digestion, and absorption, glycolysis, pyruvate metabolism, oxidative phosphorylation, pentose phosphate pathway, and biosynthesis of amino acids of the exclusively expressed proteins in PRU cows. Shifting urea supply from the rumen to post-ruminal compartments decreases muscle catabolism in cows during late gestation. Our findings indicate that post-ruminal urea supplementation for beef cows at late gestation may improve the energy metabolism to support maternal demands. In addition, the post-ruminal urea release seems to be able to trigger pathways to counterbalance the oxidative stress associated to the increase liver metabolic rate.
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Affiliation(s)
- Marta M. Santos
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
- Muscle Biology, and Nutrigenomics Laboratory, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Thaís C. Costa
- Muscle Biology, and Nutrigenomics Laboratory, Universidade Federal de Viçosa, Viçosa, MG, Brazil
- Department of Animal Science, Universidade Federal de Lavras, Lavras, MG, Brazil
| | - Tiago A. O. Mendes
- Department of Biochemistry, and Molecular Biology, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Luana L. Dutra
- Department of Biochemistry, and Molecular Biology, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Davi N. L. Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
- Muscle Biology, and Nutrigenomics Laboratory, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Renato D. Araújo
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
- Muscle Biology, and Nutrigenomics Laboratory, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Nick V. L. Serão
- StatsGaze Data Science Solutions, Liverpool, NY, United States of America
| | - Luciana N. Rennó
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Yamê F. R. S. Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Edenio Detmann
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | | | | | - Mateus P. Gionbelli
- Department of Animal Science, Universidade Federal de Lavras, Lavras, MG, Brazil
| | - Marcio S. Duarte
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
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Alvarez-Rivera E, Ortiz-Hernández EJ, Lugo E, Lozada-Reyes LM, Boukli NM. Oncogenic Proteomics Approaches for Translational Research and HIV-Associated Malignancy Mechanisms. Proteomes 2023; 11:22. [PMID: 37489388 PMCID: PMC10366845 DOI: 10.3390/proteomes11030022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/09/2023] [Accepted: 06/29/2023] [Indexed: 07/26/2023] Open
Abstract
Recent advances in the field of proteomics have allowed extensive insights into the molecular regulations of the cell proteome. Specifically, this allows researchers to dissect a multitude of signaling arrays while targeting for the discovery of novel protein signatures. These approaches based on data mining are becoming increasingly powerful for identifying both potential disease mechanisms as well as indicators for disease progression and overall survival predictive and prognostic molecular markers for cancer. Furthermore, mass spectrometry (MS) integrations satisfy the ongoing demand for in-depth biomarker validation. For the purpose of this review, we will highlight the current developments based on MS sensitivity, to place quantitative proteomics into clinical settings and provide a perspective to integrate proteomics data for future applications in cancer precision medicine. We will also discuss malignancies associated with oncogenic viruses such as Acquire Immunodeficiency Syndrome (AIDS) and suggest novel mechanisms behind this phenomenon. Human Immunodeficiency Virus type-1 (HIV-1) proteins are known to be oncogenic per se, to induce oxidative and endoplasmic reticulum stresses, and to be released from the infected or expressing cells. HIV-1 proteins can act alone or in collaboration with other known oncoproteins, which cause the bulk of malignancies in people living with HIV-1 on ART.
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Affiliation(s)
- Eduardo Alvarez-Rivera
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR 00960, USA
| | - Emanuel J. Ortiz-Hernández
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR 00960, USA
| | - Elyette Lugo
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR 00960, USA
| | | | - Nawal M. Boukli
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR 00960, USA
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The Zipf–Poisson-stopped-sum distribution with an application for modeling the degree sequence of social networks. Comput Stat Data Anal 2020. [DOI: 10.1016/j.csda.2019.106838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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Abstract
Metaproteomics can provide critical information about biological systems, but peptides are found within a complex background of other peptides. This complex background can change across samples, in some cases drastically. Cofragmentation, the coelution of peptides with similar mass to charge ratios, is one factor that influences which peptides are identified in an LC-MS/MS experiment: it is dependent on the nature and complexity of this dynamic background. Metaproteomics applications are particularly susceptible to cofragmentation-induced bias; they have vast protein sequence diversity and the abundance of those proteins can span many orders of magnitude. We have developed a mechanistic model that determines the number of potentially cofragmenting peptides in a given sample (called cobia, https://github.com/bertrand-lab/cobia ). We then used previously published data sets to validate our model, showing that the resulting peptide-specific score reflects the cofragmentation "risk" of peptides. Using an Antarctic sea ice edge metatranscriptome case study, we found that more rare taxonomic and functional groups are associated with higher cofragmentation bias. We also demonstrate how cofragmentation scores can be used to guide the selection of protein- or peptide-based biomarkers. We illustrate potential consequences of cofragmentation for multiple metaproteomic approaches, and suggest practical paths forward to cope with cofragmentation-induced bias.
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Affiliation(s)
- J Scott P McCain
- Department of Biology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
| | - Erin M Bertrand
- Department of Biology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
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Sato S, Horikawa M, Kondo T, Sato T, Setou M. A power law distribution of metabolite abundance levels in mice regardless of the time and spatial scale of analysis. Sci Rep 2018; 8:10315. [PMID: 29985415 PMCID: PMC6037760 DOI: 10.1038/s41598-018-28667-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 06/26/2018] [Indexed: 11/29/2022] Open
Abstract
Biomolecule abundance levels change with the environment and enable a living system to adapt to the new conditions. Although, the living system maintains at least some characteristics, e.g. homeostasis. One of the characteristics maintained by a living system is a power law distribution of biomolecule abundance levels. Previous studies have pointed to a universal characteristic of biochemical reaction networks, with data obtained from lysates of multiple cells. As a result, the spatial scale of the data related to the power law distribution of biomolecule abundance levels is not clear. In this study, we researched the scaling law of metabolites in mouse tissue with a spatial scale of quantification that was changed stepwise between a whole-tissue section and a single-point analysis (25 μm). As a result, metabolites in mouse tissues were found to follow the power law distribution independently of the spatial scale of analysis. Additionally, we tested the temporal changes by comparing data from younger and older mice. Both followed similar power law distributions, indicating that metabolite composition is not diversified by aging to disrupt the power law distribution. The power law distribution of metabolite abundance is thus a robust characteristic of a living system regardless of time and space.
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Affiliation(s)
- Shumpei Sato
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Makoto Horikawa
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
- International Mass Imaging Center, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Takeshi Kondo
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
- International Mass Imaging Center, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Tomohito Sato
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Mitsutoshi Setou
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.
- International Mass Imaging Center, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.
- Preeminent Medical Photonics Education & Research Center, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.
- Department of Anatomy, The University of Hong Kong, 6/F, William MW Mong Block 21 Sassoon Road, Pokfulam, Hong Kong SAR, China.
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Hooper CM, Stevens TJ, Saukkonen A, Castleden IR, Singh P, Mann GW, Fabre B, Ito J, Deery MJ, Lilley KS, Petzold CJ, Millar AH, Heazlewood JL, Parsons HT. Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1202-1217. [PMID: 29024340 PMCID: PMC5863471 DOI: 10.1111/tpj.13743] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/25/2017] [Accepted: 09/28/2017] [Indexed: 05/20/2023]
Abstract
Measuring changes in protein or organelle abundance in the cell is an essential, but challenging aspect of cell biology. Frequently-used methods for determining organelle abundance typically rely on detection of a very few marker proteins, so are unsatisfactory. In silico estimates of protein abundances from publicly available protein spectra can provide useful standard abundance values but contain only data from tissue proteomes, and are not coupled to organelle localization data. A new protein abundance score, the normalized protein abundance scale (NPAS), expands on the number of scored proteins and the scoring accuracy of lower-abundance proteins in Arabidopsis. NPAS was combined with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment markers was developed, enabling independent verification of in silico estimates for relative organelle abundance. Estimation of relative organelle abundance was found to be reproducible and consistent over a range of tissues and growth conditions. In silico abundance estimations and localization data have been combined into an online tool, multiple marker abundance profiling, available in the SUBA4 toolbox (http://suba.live).
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Affiliation(s)
- Cornelia M. Hooper
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaPerthWA6009Australia
| | | | - Anna Saukkonen
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QRUK
| | - Ian R. Castleden
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaPerthWA6009Australia
| | - Pragya Singh
- Joint BioEnergy InstituteLawrence Berkeley National LaboratoryBerkeleyCA94702USA
| | - Gregory W. Mann
- Joint BioEnergy InstituteLawrence Berkeley National LaboratoryBerkeleyCA94702USA
| | - Bertrand Fabre
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QRUK
| | - Jun Ito
- Joint BioEnergy InstituteLawrence Berkeley National LaboratoryBerkeleyCA94702USA
| | - Michael J Deery
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QRUK
| | | | | | - A. Harvey Millar
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaPerthWA6009Australia
| | - Joshua L. Heazlewood
- Joint BioEnergy InstituteLawrence Berkeley National LaboratoryBerkeleyCA94702USA
- School of BioSciencesThe University of MelbourneMelbourneVIC3010Australia
| | - Harriet T. Parsons
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QRUK
- Copenhagen University, Plant and Environmental SciencesFrederiksberg1871Denmark
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A Bayesian algorithm for detecting differentially expressed proteins and its application in breast cancer research. Sci Rep 2016; 6:30159. [PMID: 27444576 PMCID: PMC4957118 DOI: 10.1038/srep30159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 06/28/2016] [Indexed: 02/07/2023] Open
Abstract
Presence of considerable noise and missing data points make analysis of mass-spectrometry (MS) based proteomic data a challenging task. The missing values in MS data are caused by the inability of MS machines to reliably detect proteins whose abundances fall below the detection limit. We developed a Bayesian algorithm that exploits this knowledge and uses missing data points as a complementary source of information to the observed protein intensities in order to find differentially expressed proteins by analysing MS based proteomic data. We compared its accuracy with many other methods using several simulated datasets. It consistently outperformed other methods. We then used it to analyse proteomic screens of a breast cancer (BC) patient cohort. It revealed large differences between the proteomic landscapes of triple negative and Luminal A, which are the most and least aggressive types of BC. Unexpectedly, majority of these differences could be attributed to the direct transcriptional activity of only seven transcription factors some of which are known to be inactive in triple negative BC. We also identified two new proteins which significantly correlated with the survival of BC patients, and therefore may have potential diagnostic/prognostic values.
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