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Numerical solution of first order stiff ordinary differential equations using fifth order block backward differentiation formulas

NOR AIN AZEANY MOHD NASIR, Zarina Bibi Ibrahim, Khairil Iskandar Othman, Mohamed Suleiman

Sains Malaysiana, 2012;41:489-492.

This paper describes the development of a two-point implicit code in the form of fifth order Block Backward Differentiation Formulas (BBDF(5)) for solving first order stiff Ordinary Differential Equations (ODEs). This method computes the approximate solutions at two points simultaneously within an equidistant block. Numerical results are presented to compare the efficiency of the developed BBDF(5) to the classical one-point Backward Differentiation Formulas (BDF). The results indicated that the BBDF(5) outperformed the BDF in terms of total number of steps, accuracy and computational time.

Matched MeSH terms: Cell Differentiation
Transformation and differentiation of henstock-wiener integrals

elvira pederes de lara-tuprio, Varayu boonpogkrong

Sains Malaysiana, 2017;46:2549-2554.

n this paper, transformation and differentiation of Henstock-Wiener integrals are discussed. The approach is by Riemann sums. The idea is more transparent than that of classical Wiener integral.

Matched MeSH terms: Cell Differentiation
Decellularized extracellular matrix of human umbilical vein endothelial cells promotes endothelial differentiation of stem cells from exfoliated deciduous teeth

Gong T, Heng BC, Xu J, Zhu S, Yuan C, Lo EC, et al.

J Biomed Mater Res A, 2017 04;105(4):1083-1093.
PMID: 28076902 DOI: 10.1002/jbm.a.36003

Dental stem cells can serve as a potential source of functional endothelial cells for tissue engineering applications, but the endothelial-lineage differentiation efficiency is rather low even with growth factors and mechanical stimuli, which greatly limits their clinical applications. This is partly due to the deficiency of standard two-dimensional (2-D) culture systems, which is unable to recapitulate the three-dimensional (3-D) in vivo milieu that is rich in extracellular matrix. Hence, we extracted decellularized extracellular matrix from human umbilical vein endothelial cells (HUVECs-DECM) to provide a bioactive substratum conducive to the endothelial differentiation of dental stem cells. Compared to cells plated on tissue culture polystyrene (TCP), stem cells from exfoliated deciduous teeth (SHED) cultured on the HUVECs-DECM demonstrated more regular arrangement and elongated morphology. HUVECs-DECM significantly enhanced the rapid adhesion and proliferation rates of SHED, as demonstrated by WST-8 assay and immunocytochemistry indicating higher expression levels of vinculin by newly adherent SHED on HUVECs-DECM versus TCP. In addition, there was twofold to fivefold higher mRNA expression levels of endothelial-specific markers CD31 and VEGFR-2 in SHED after seven days of culture on DECM versus TCP. Functional testing with in vitro matrigel angiogenesis assay identified more capillary-like structure formation with significantly higher tubule length in SHED induced by DECM versus TCP. Hence, the results of this study provide a better understanding of the unique characteristics of cell-specific ECM and demonstrated the potential use of HUVECs-DECM as a culture substratum conducive for stimulating the endothelial differentiation of SHED for therapeutic angiogenic applications. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1083-1093, 2017.

Matched MeSH terms: Cell Differentiation*
Macrophage polarization in THP-1 cell line and primary monocytes: A systematic review

Mohd Yasin ZN, Mohd Idrus FN, Hoe CH, Yvonne-Tee GB

Differentiation, 2022;128:67-82.
PMID: 36370526 DOI: 10.1016/j.diff.2022.10.001

Macrophages derived from human monocytic leukemia THP-1 cell line are often used as the alternative of human primary macrophage. However, the polarization method of THP-1 to macrophages varies between different laboratories, which may unknowingly affect the relevance of research output across research groups. In this regard, a systematic search was developed in Pubmed, BioOne, Scopus, and Science Direct to identify articles focusing on THP-1 polarization into M1 and M2 macrophages. All selected articles were read and discussed by two independent reviewers. The selection process was based on selected keywords on the title, abstract and full-text level. A total of 85 articles were selected and categorized based on the field of studies, method of THP-1 differentiation, and markers or genes expressed upon differentiation. THP-1 derived macrophages were mainly used together with primary monocyte-derived macrophages in cellular inflammation studies, while it was commonly employed alone in cancer research. THP-1 derived macrophages are also of paramount importance in biomaterials studies to prevent unfavorable immune responses in-vivo. We explored various methods of THP-1 differentiation and suggested several common genes encountered to characterize M1 and M2 macrophages differentiated from THP-1. The systematic review highlights the relevance of using THP-1 derived macrophage as a useful alternative to primary macrophage. Although it is not possible to derive a standard method of THP-1 polarization into M1 and M2 macrophages from this review, it may lead researchers to obtain reproducible polarization protocol based on commonly used stimulants and markers of differentiation.

Matched MeSH terms: Cell Differentiation/genetics
Block backward differentiation formulas for solving first order fuzzy differential equations under generalized differentiability

Iskandar Shah Mohd Zawawi, Zarina Bibi Ibrahim

Sains Malaysiana, 2016;45:989-998.

In this paper, the fully implicit 2-point block backward differentiation formula and diagonally implicit 2-point block
backward differentiation formula were developed under the interpretation of generalized differentiability concept for
solving first order fuzzy differential equations. Some fuzzy initial value problems were tested in order to demonstrate the
performance of the developed methods. The approximated solutions for both methods were in good agreement with the
exact solutions. The numerical results showed that the diagonally implicit method outperforms the fully implicit method
in term of accuracy.

Matched MeSH terms: Cell Differentiation
Identification of biomarkers for periodontal disease using the immunoproteomics approach

Kerishnan JP, Mohammad S, Alias MS, Mu AK, Vaithilingam RD, Baharuddin NA, et al.

PeerJ, 2016;4:e2327.
PMID: 27635317 DOI: 10.7717/peerj.2327

Periodontitis is one of the most common oral diseases associated with the host's immune response against periodontopathogenic infection. Failure to accurately diagnose the stage of periodontitis has limited the ability to predict disease status. Therefore, we aimed to look for reliable diagnostic markers for detection or differentiation of early stage periodontitis using the immunoprotemic approach.

Matched MeSH terms: Cell Differentiation
Fulltext Solving delay differential equations by using implicit 2-point block backward differentiation formula

Heng, S.C., Ibrahim, Z.B., Suleiman, M., Ismail, F.

Pertanika Journal of Science & Technology, 2013;21(1):37-44.
MyJurnal

In this paper, an implicit 2-point Block Backward Differentiation formula (BBDF) method was considered for solving Delay Differential Equations (DDEs). The method was implemented by using a constant stepsize via Newton Iteration. This implicit block method was expected to produce two points simultaneously. The efficiency of the method was compared with the existing classical 1-point Backward Differentiation Formula (BDF) in terms of execution time and accuracy.

Matched MeSH terms: Cell Differentiation
Fulltext Block backward differentiation formulas for solving second order fuzzy differential equations

Tiaw, Kah Fookand, Zarina Bibi Ibrahim

MATEMATIKA, 2017;33(2):215-226.
MyJurnal

In this paper, we study the numerical method for solving second order Fuzzy
Differential Equations (FDEs) using Block Backward Differential Formulas (BBDF)
under generalized concept of higher-order fuzzy differentiability. Implementation of
the method using Newton iteration is discussed. Numerical results obtained by BBDF
are presented and compared with Backward Differential Formulas (BDF) and exact
solutions. Several numerical examples are provided to illustrate our methods.

Matched MeSH terms: Cell Differentiation
Fulltext The immortal amoeba: a useful model to study cellular differentiation processes?

Ahmed Khan N, Baqir H, Siddiqui R

Pathog Glob Health, 2015;109(7):305-6.
PMID: 26878933 DOI: 10.1080/20477724.2015.1103504
Matched MeSH terms: Cell Differentiation*
Stem Cell Therapies for Reversing Vision Loss

Higuchi A, Kumar SS, Benelli G, Alarfaj AA, Munusamy MA, Umezawa A, et al.

Trends Biotechnol, 2017 11;35(11):1102-1117.
PMID: 28751147 DOI: 10.1016/j.tibtech.2017.06.016

Current clinical trials that evaluate human pluripotent stem cell (hPSC)-based therapies predominantly target treating macular degeneration of the eyes because the eye is an isolated tissue that is naturally weakly immunogenic. Here, we discuss current bioengineering approaches and biomaterial usage in combination with stem cell therapy for macular degeneration disease treatment. Retinal pigment epithelium (RPE) differentiated from hPSCs is typically used in most clinical trials for treating patients, whereas bone marrow mononuclear cells (BMNCs) or mesenchymal stem cells (MSCs) are intravitreally transplanted, undifferentiated, into patient eyes. We also discuss reported negative effects of stem cell therapy, such as patients becoming blind following transplantation of adipose-derived stem cells, which are increasingly used by 'stem-cell clinics'.

Matched MeSH terms: Cell Differentiation*
Fulltext Gene expression profiles for in vitro human stem cell differentiation into osteoblasts and osteoclasts: a systematic review

Zainal Ariffin SH, Lim KW, Megat Abdul Wahab R, Zainal Ariffin Z, Rus Din RD, Shahidan MA, et al.

PeerJ, 2022;10:e14174.
PMID: 36275474 DOI: 10.7717/peerj.14174

BACKGROUND: There have been promising results published regarding the potential of stem cells in regenerative medicine. However, the vast variety of choices of techniques and the lack of a standard approach to analyse human osteoblast and osteoclast differentiation may reduce the utility of stem cells as a tool in medical applications. Therefore, this review aims to systematically evaluate the findings based on stem cell differentiation to define a standard gene expression profile approach.
METHODS: This review was performed following the PRISMA guidelines. A systematic search of the study was conducted by retrieving articles from the electronic databases PubMed and Web of Science to identify articles focussed on gene expression and approaches for osteoblast and osteoclast differentiation.
RESULTS: Six articles were included in this review; there were original articles of in vitro human stem cell differentiation into osteoblasts and osteoclasts that involved gene expression profiling. Quantitative polymerase chain reaction (qPCR) was the most used technique for gene expression to detect differentiated human osteoblasts and osteoclasts. A total of 16 genes were found to be related to differentiating osteoblast and osteoclast differentiation.
CONCLUSION: Qualitative information of gene expression provided by qPCR could become a standard technique to analyse the differentiation of human stem cells into osteoblasts and osteoclasts rather than evaluating relative gene expression. RUNX2 and CTSK could be applied to detect osteoblasts and osteoclasts, respectively, while RANKL could be applied to detect both osteoblasts and osteoclasts. This review provides future researchers with a central source of relevant information on the vast variety of gene expression approaches in analysing the differentiation of human osteoblast and osteoclast cells. In addition, these findings should enable researchers to conduct accurately and efficiently studies involving isolated human stem cell differentiation into osteoblasts and osteoclasts.

Matched MeSH terms: Cell Differentiation/genetics
Fulltext Stem cell imaging through convolutional neural networks: current issues and future directions in artificial intelligence technology

Ramakrishna RR, Abd Hamid Z, Wan Zaki WMD, Huddin AB, Mathialagan R

PeerJ, 2020;8:e10346.
PMID: 33240655 DOI: 10.7717/peerj.10346

Stem cells are primitive and precursor cells with the potential to reproduce into diverse mature and functional cell types in the body throughout the developmental stages of life. Their remarkable potential has led to numerous medical discoveries and breakthroughs in science. As a result, stem cell-based therapy has emerged as a new subspecialty in medicine. One promising stem cell being investigated is the induced pluripotent stem cell (iPSC), which is obtained by genetically reprogramming mature cells to convert them into embryonic-like stem cells. These iPSCs are used to study the onset of disease, drug development, and medical therapies. However, functional studies on iPSCs involve the analysis of iPSC-derived colonies through manual identification, which is time-consuming, error-prone, and training-dependent. Thus, an automated instrument for the analysis of iPSC colonies is needed. Recently, artificial intelligence (AI) has emerged as a novel technology to tackle this challenge. In particular, deep learning, a subfield of AI, offers an automated platform for analyzing iPSC colonies and other colony-forming stem cells. Deep learning rectifies data features using a convolutional neural network (CNN), a type of multi-layered neural network that can play an innovative role in image recognition. CNNs are able to distinguish cells with high accuracy based on morphologic and textural changes. Therefore, CNNs have the potential to create a future field of deep learning tasks aimed at solving various challenges in stem cell studies. This review discusses the progress and future of CNNs in stem cell imaging for therapy and research.

Matched MeSH terms: Cell Differentiation
Fulltext Neural Commitment of Embryonic Stem Cells through the Formation of Embryoid Bodies (EBs)

Liyang G, Abdullah S, Rosli R, Nordin N

Malays J Med Sci, 2014 Sep-Oct;21(5):8-16.
PMID: 25977628 MyJurnal

An embryonic stem cell (ESC) is a good tool to generate neurons in vitro and can be used to mimic neural development in vivo. It has been widely used in research to examine the role of cell signalling during neuronal development, test the effects of drugs on neurons, and generate a large population of functional neurons. So far, a number of protocols have been established to promote the differentiation of ESCs, such as direct and indirect differentiation. One of the widely used protocols to generate neurons is through the spontaneous formation of multicellular aggregates known as embryonic bodies (EBs). However, for some, it is not clear why EB protocol could be the protocol of choice. EB also is known to mimic an early embryo; hence, knowing the similarities between EB and an early embryo is essential, particularly the information on the players that promote the formation of EBs or the aggregation of ESCs. This review paper focuses on these issues and discusses further the generation of neural cells from EBs using a well-known protocol, the 4-/4+ protocol.

Matched MeSH terms: Cell Differentiation
Fulltext Fabrication of a Multiplexed Artificial Cellular MicroEnvironment Array

Mashimo Y, Yoshioka M, Tokunaga Y, Fockenberg C, Terada S, Koyama Y, et al.

J Vis Exp, 2018 09 07.
PMID: 30247461 DOI: 10.3791/57377

Cellular microenvironments consist of a variety of cues, such as growth factors, extracellular matrices, and intercellular interactions. These cues are well orchestrated and are crucial in regulating cell functions in a living system. Although a number of researchers have attempted to investigate the correlation between environmental factors and desired cellular functions, much remains unknown. This is largely due to the lack of a proper methodology to mimic such environmental cues in vitro, and simultaneously test different environmental cues on cells. Here, we report an integrated platform of microfluidic channels and a nanofiber array, followed by high-content single-cell analysis, to examine stem cell phenotypes altered by distinct environmental factors. To demonstrate the application of this platform, this study focuses on the phenotypes of self-renewing human pluripotent stem cells (hPSCs). Here, we present the preparation procedures for a nanofiber array and the microfluidic structure in the fabrication of a Multiplexed Artificial Cellular MicroEnvironment (MACME) array. Moreover, overall steps of the single-cell profiling, cell staining with multiple fluorescent markers, multiple fluorescence imaging, and statistical analyses, are described.

Matched MeSH terms: Cell Differentiation
Fulltext Three dimensional microcarrier system in mesenchymal stem cell culture: a systematic review

Koh B, Sulaiman N, Fauzi MB, Law JX, Ng MH, Idrus RBH, et al.

Cell Biosci, 2020;10:75.
PMID: 32518618 DOI: 10.1186/s13578-020-00438-8

Stem cell-based regenerative medicine is a promising approach for tissue reconstruction. However, a large number of cells are needed in a typical clinical study, where conventional monolayer cultures might pose a limitation for scale-up. The purpose of this review was to systematically assess the application of microcarriers in Mesenchymal Stem Cell cultures. A comprehensive search was conducted in Medline via Ebscohost, Pubmed, and Scopus, and relevant studies published between 2015 and 2019 were selected. The literature search identified 53 related studies, but only 14 articles met the inclusion criteria. These include 7 utilised commercially available microcarriers, while the rest were formulated based on different surface characteristics, all of which are discussed in this review. Current applications of microcarriers were focused on MSC expansion and induction of MSCs into different lineages. These studies demonstrated that MSCs could proliferate in a microcarrier culture system in-fold compared to monolayer cultures, and the culture system could simulate a three-dimensional environment which induces cell differentiation. However, detailed studies are still required before this system were to be adapted into the scale of GMP manufacturing.

Matched MeSH terms: Cell Differentiation
Role of circular RNAs in determining the fate of mesenchymal stem cells

Wong RSY, Cheong SK

Malays J Pathol, 2021 Aug;43(2):241-250.
PMID: 34448788

Ribonucleic acid (RNA) has been well-understood for its linear form for many years. With advances in high-throughput sequencing, there is an increasing focus on circular RNAs (circRNAs) recently. Although they were previously regarded as splicing error by-products, research has shown that they play a pivotal role in many cellular processes, one of which is the control of stem cell differentiation and fate. On the other hand, decades of research have demonstrated the promising therapeutic potential of mesenchymal stem cells (MSCs). To this end, there is a growing body of research on the role of circRNAs in the determination of the fate of MSCs. This review critically examines the current evidence and consolidates key findings from studies that explore the involvement of circRNAs in the regulation of MSC differentiation.

Matched MeSH terms: Cell Differentiation
Current developments and therapeutic potentials of exosomes from induced pluripotent stem cells-derived mesenchymal stem cells

Aldoghachi AF, Loh JK, Wang ML, Yang YP, Chien CS, Teh HX, et al.

J Chin Med Assoc, 2023 Apr 01;86(4):356-365.
PMID: 36762931 DOI: 10.1097/JCMA.0000000000000899

Mesenchymal stem cells (MSCs) are multipotent cells derived from adult human tissues that have the ability to proliferate in vitro and maintain their multipotency, making them attractive cell sources for regenerative medicine. However, MSCs reportedly show limited proliferative capacity with inconsistent therapeutic outcomes due to their heterogeneous nature. On the other hand, induced pluripotent stem cells (iPSC) have emerged as an alternative source for the production of various specialized cell types via their ability to differentiate from all three primary germ layers, leading to applications in regenerative medicine, disease modeling, and drug therapy. Notably, iPSCs can differentiate into MSCs in monolayer, commonly referred to as induced mesenchymal stem cells (iMSCs). These cells show superior therapeutic qualities compared with adult MSCs as the applications of the latter are restricted by passage number and autoimmune rejection when applied in tissue regeneration trials. Furthermore, increasing evidence shows that the therapeutic properties of stem cells are a consequence of the paracrine effects mediated by their secretome such as from exosomes, a type of extracellular vesicle secreted by most cell types. Several studies that investigated the potential of exosomes in regenerative medicine and therapy have revealed promising results. Therefore, this review focuses on the recent findings of exosomes secreted from iMSCs as a potential noncell-based therapy.

Matched MeSH terms: Cell Differentiation
Fulltext Platelet rich concentrate promotes early cellular proliferation and multiple lineage differentiation of human mesenchymal stromal cells in vitro

Shani S, Ahmad RE, Naveen SV, Murali MR, Puvanan K, Abbas AA, et al.

ScientificWorldJournal, 2014;2014:845293.
PMID: 25436230 DOI: 10.1155/2014/845293

Platelet rich concentrate (PRC) is a natural adjuvant that aids in human mesenchymal stromal cell (hMSC) proliferation in vitro; however, its role requires further exploration. This study was conducted to determine the optimal concentration of PRC required for achieving the maximal proliferation, and the need for activating the platelets to achieve this effect, and if PRC could independently induce early differentiation of hMSC. The gene expression of markers for osteocytes (ALP, RUNX2), chondrocytes (SOX9, COL2A1), and adipocytes (PPAR-γ) was determined at each time point in hMSC treated with 15% activated and nonactivated PRC since maximal proliferative effect was achieved at this concentration. The isolated PRC had approximately fourfold higher platelet count than whole blood. There was no significant difference in hMSC proliferation between the activated and nonactivated PRC. Only RUNX2 and SOX9 genes were upregulated throughout the 8 days. However, protein expression study showed formation of oil globules from day 4, significant increase in ALP at days 6 and 8 (P ≤ 0.05), and increased glycosaminoglycan levels at all time points (P < 0.05), suggesting the early differentiation of hMSC into osteogenic and adipogenic lineages. This study demonstrates that the use of PRC increased hMSC proliferation and induced early differentiation of hMSC into multiple mesenchymal lineages, without preactivation or addition of differentiation medium.

Matched MeSH terms: Cell Differentiation/physiology*
The proliferation and tenogenic differentiation potential of bone marrow-derived mesenchymal stromal cell are influenced by specific uniaxial cyclic tensile loading conditions

Nam HY, Pingguan-Murphy B, Amir Abbas A, Mahmood Merican A, Kamarul T

Biomech Model Mechanobiol, 2015 Jun;14(3):649-63.
PMID: 25351891 DOI: 10.1007/s10237-014-0628-y

It has been previously demonstrated that mechanical stimuli are important for multipotent human bone marrow-derived mesenchymal stromal cells (hMSCs) to maintain good tissue homeostasis and even to enhance tissue repair processes. In tendons, this is achieved by promoting the cellular proliferation and tenogenic expression/differentiation. The present study was conducted to determine the optimal loading conditions needed to achieve the best proliferation rates and tenogenic differentiation potential. The effects of mechanical uniaxial stretching using different rates and strains were performed on hMSCs cultured in vitro. hMSCs were subjected to cyclical uniaxial stretching of 4, 8 or 12 % strain at 0.5 or 1 Hz for 6, 24, 48 or 72 h. Cell proliferation was analyzed using alamarBlue[Formula: see text] assay, while hMSCs differentiation was analyzed using total collagen assay and specific tenogenic gene expression markers (type I collagen, type III collagen, decorin, tenascin-C, scleraxis and tenomodulin). Our results demonstrate that the highest cell proliferation is observed when 4 % strain [Formula: see text] 1 Hz was applied. However, at 8 % strain [Formula: see text] 1 Hz loading, collagen production and the tenogenic gene expression were highest. Increasing strain or rates thereafter did not demonstrate any significant increase in both cell proliferation and tenogenic differentiation. In conclusion, our results suggest that 4 % [Formula: see text] 1 Hz cyclic uniaxial loading increases cell proliferation, but higher strains are required for superior tenogenic expressions. This study suggests that selected loading regimes will stimulate tenogenesis of hMSCs.

Matched MeSH terms: Cell Differentiation*
Engineering physical microenvironment for stem cell based regenerative medicine

Han YL, Wang S, Zhang X, Li Y, Huang G, Qi H, et al.

Drug Discov Today, 2014 Jun;19(6):763-73.
PMID: 24508818 DOI: 10.1016/j.drudis.2014.01.015

Regenerative medicine has rapidly evolved over the past decade owing to its potential applications to improve human health. Targeted differentiations of stem cells promise to regenerate a variety of tissues and/or organs despite significant challenges. Recent studies have demonstrated the vital role of the physical microenvironment in regulating stem cell fate and improving differentiation efficiency. In this review, we summarize the main physical cues that are crucial for controlling stem cell differentiation. Recent advances in the technologies for the construction of physical microenvironment and their implications in controlling stem cell fate are also highlighted.

Matched MeSH terms: Cell Differentiation/physiology

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