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A study on discrete wavelet-based noise removal from EEG signals

Asaduzzaman K, Reaz MB, Mohd-Yasin F, Sim KS, Hussain MS

Adv Exp Med Biol, 2010;680:593-9.
PMID: 20865544 DOI: 10.1007/978-1-4419-5913-3_65

Electroencephalogram (EEG) serves as an extremely valuable tool for clinicians and researchers to study the activity of the brain in a non-invasive manner. It has long been used for the diagnosis of various central nervous system disorders like seizures, epilepsy, and brain damage and for categorizing sleep stages in patients. The artifacts caused by various factors such as Electrooculogram (EOG), eye blink, and Electromyogram (EMG) in EEG signal increases the difficulty in analyzing them. Discrete wavelet transform has been applied in this research for removing noise from the EEG signal. The effectiveness of the noise removal is quantitatively measured using Root Mean Square (RMS) Difference. This paper reports on the effectiveness of wavelet transform applied to the EEG signal as a means of removing noise to retrieve important information related to both healthy and epileptic patients. Wavelet-based noise removal on the EEG signal of both healthy and epileptic subjects was performed using four discrete wavelet functions. With the appropriate choice of the wavelet function (WF), it is possible to remove noise effectively to analyze EEG significantly. Result of this study shows that WF Daubechies 8 (db8) provides the best noise removal from the raw EEG signal of healthy patients, while WF orthogonal Meyer does the same for epileptic patients. This algorithm is intended for FPGA implementation of portable biomedical equipments to detect different brain state in different circumstances.
Acute Lung Injury: Disease Modelling and the Therapeutic Potential of Stem Cells

Lian J, Lin J, Zakaria N, Yahaya BH

Adv Exp Med Biol, 2020;1298:149-166.
PMID: 32424492 DOI: 10.1007/5584_2020_538

Acute lung injury (ALI) is a severe clinical condition with high morbidity and mortality that usually results in the development of multiple organ dysfunction. The complex pathophysiology of ALI seems to provide a wide range of targets that offer numerous therapeutic options. However, despite extensive studies of ALI pathophysiology and treatment, no effective pharmacotherapy is available. Increasing evidence from both preclinical and clinical studies supports the preventive and therapeutic effects of mesenchymal stem cells (MSCs) for treating ALI. As cell-based therapy poses the risk of occlusion in microvasculature or unregulated growth, MSC-derived extracellular vesicles (MSC-EVs) have been extensively studied as a new therapeutic strategy for non-cell based therapy. It is widely accepted that the therapeutic properties of MSCs are derived from soluble factors with paracrine or endocrine effects, and EVs are among the most important paracrine or endocrine vehicles that can deliver various soluble factors with a similar phenotype as the parent cell. Therapeutic effects of MSCs have been reported for various delivery approaches, diverse doses, multiple origins, and different times of administration, and MSC-EVs treatment may include but is not limited to these choices. The mechanisms by which MSCs and MSC-EVs may contribute to ALI treatment remain elusive and need further exploration. This review provides an overview of preclinical studies that support the application of MSC-EVs for treating ALI, and it discusses emerging opportunities and their associated challenges.
Adipose-Derived Mesenchymal Stem Cells Promote Growth and Migration of Lung Adenocarcinoma Cancer Cells

Zakaria N, Yahaya BH

Adv Exp Med Biol, 2020;1292:83-95.
PMID: 31916234 DOI: 10.1007/5584_2019_464

INTRODUCTION: Mesenchymal stem cells (MSCs) have been used in cancer therapy as vehicles to deliver therapeutic materials such as drugs, apoptosis inducers and cytokines due to their ability to migrate and home at the tumour site. Furthermore, MSCs have been genetically engineered to produce anticancer molecules such as TRAIL that can induce apoptosis of cancer cells. However, MSCs' presence in the tumour microenvironment has shown to be involved in promoting tumour growth and progression. Therefore, the roles of MSCs either promoting or suppressing tumorigenesis need to be investigated.
METHODS: Human adipose-derived MSCs (Ad-MSCs) and A549 cells are co-cultured together in indirect co-culture system using Transwell insert. Following co-culture, both cells were analysed in terms of growth rate, migration ability, apoptosis and gene expression for genes involved in migration and stemness characteristics.
RESULTS: The result shows that Ad-MSCs promoted the growth of A549 cells when indirectly co-cultured for 48 and 72 h. Furthermore, Ad-MSCs significantly enhanced the migration rate of A549 cells. The increased in migration rate was in parallel with the significant increase of MMP9. There are no significant changes observed in the expression of TWIST2, CDH2 and CDH1, genes involved in the epithelial-to-mesenchymal transition (EMT). Ad-MSCs also protect A549 cancer cells from undergoing apoptosis and increase the survival of cancer cells.
CONCLUSION: Secretion of soluble factors from Ad-MSCs has been shown to promote the growth and metastatic characteristics of A549 cancer cells. Therefore, the use of Ad-MSCs in cancer therapy needs to be carefully evaluated in the long-term aspect.
An MLP neural network for ECG noise removal based on Kalman filter

Moein S

Adv Exp Med Biol, 2010;680:109-16.
PMID: 20865492 DOI: 10.1007/978-1-4419-5913-3_13

In this paper, application of Artificial Neural Network (ANN) for electrocardiogram (ECG) signal noise removal has been investigated. First, 100 number of ECG signals are selected from Physikalisch-Technische Bundesanstalt (PTB) database and Kalman filter is applied to remove their low pass noise. Then a suitable dataset based on denoised ECG signal is configured and used to a Multilayer Perceptron (MLP) neural network to be trained. Finally, results and experiences are discussed and the effect of changing different parameters for MLP training is shown.
An Overview of Circular RNAs

Awasthi R, Singh AK, Mishra G, Maurya A, Chellappan DK, Gupta G, et al.

Adv Exp Med Biol, 2018 9 28;1087:3-14.
PMID: 30259353 DOI: 10.1007/978-981-13-1426-1_1

Circular RNAs (cirRNAs) are long, noncoding endogenous RNA molecules and covalently closed continuous loop without 5'-3' polarity and polyadenylated tail which are largely concentrated in the nucleus. CirRNA regulates gene expression by modulating microRNAs and functions as potential biomarker. CirRNAs can translate in vivo to link between their expression and disease. They are resistant to RNA exonuclease and can convert to the linear RNA by microRNA which can then act as competitor to endogenous RNA. This chapter summarizes the evolutionary conservation and expression of cirRNAs, their identification, highlighting various computational approaches on cirRNA, and translation with a focus on the breakthroughs and the challenges in this new field.
Anticoagulation Therapy in Patients with Chronic Kidney Disease

Saheb Sharif-Askari F, Syed Sulaiman SA, Saheb Sharif-Askari N

Adv Exp Med Biol, 2017;906:101-114.
PMID: 27628006

Patients with chronic kidney disease (CKD) are at increased risk for both thrombotic events and bleeding. The early stages of CKD are mainly associated with prothrombotic tendency, whereas in its more advanced stages, beside the prothrombotic state, platelets can become dysfunctional due to uremic-related toxin exposure leading to an increased bleeding tendency. Patients with CKD usually require anticoagulation therapy for treatment or prevention of thromboembolic diseases. However, this benefit could easily be offset by the risk of anticoagulant-induced bleeding. Treatment of patients with CKD should be based on evidence from randomized clinical trials, but usually CKD patients are excluded from these trials. In the past, unfractionated heparins were the anticoagulant of choice for patients with CKD because of its independence of kidney elimination. However, currently low-molecular-weight heparins have largely replaced the use of unfractionated heparins owing to fewer incidences of heparin-induced thrombocytopenia and bleeding. We undertook this review in order to explain the practical considerations for the management of anticoagulation in these high risk population.
Arsenic-Induced Sex Hormone Disruption: An Insight into Male Infertility

Choudhury BP, Roychoudhury S, Sengupta P, Toman R, Dutta S, Kesari KK

Adv Exp Med Biol, 2022;1391:83-95.
PMID: 36472818 DOI: 10.1007/978-3-031-12966-7_6

Arsenic (As) is one of the most potent natural as well as anthropogenic metalloid toxicants that have various implications in the everyday life of humans. It is found in several chemical forms such as inorganic salt, organic salt, and arsine (gaseous form). Although it is mostly released via natural causes, there are many ways through which humans come in contact with As. Drinking water contamination by As is one of the major health concerns in various parts of the world. Arsenic exposure has the ability to induce adverse health effects including reproductive problems. Globally, around 15% of the couples are affected with infertility, of which about 20-30% are attributed to the male factor. Arsenic affects the normal development and function of sperm cells, tissue organization of the gonads, and also the sex hormone parameters. Stress induction is one of the implications of As exposure. Excessive stress leads to the release of glucocorticoids, which impact the oxidative balance in the body leading to overproduction of reactive oxygen species (ROS). This may in turn result in oxidative stress (OS) ultimately interfering with normal sperm and hormonal parameters. This study deals with As-induced OS and its association with sex hormone disruption as well as its effect on sperm and semen quality.
Asynchronous brain machine interface-based control of a wheelchair

Hema CR, Paulraj MP, Yaacob S, Adom AH, Nagarajan R

Adv Exp Med Biol, 2011;696:565-72.
PMID: 21431597 DOI: 10.1007/978-1-4419-7046-6_57

A brain machine interface (BMI) design for controlling the navigation of a power wheelchair is proposed. Real-time experiments with four able bodied subjects are carried out using the BMI-controlled wheelchair. The BMI is based on only two electrodes and operated by motor imagery of four states. A recurrent neural classifier is proposed for the classification of the four mental states. The real-time experiment results of four subjects are reported and problems emerging from asynchronous control are discussed.
Benign Disorders of the Breast in Pregnancy and Lactation

Taib NA, Rahmat K

Adv Exp Med Biol, 2020;1252:43-51.
PMID: 32816261 DOI: 10.1007/978-3-030-41596-9_6

Benign cystic or solid lumps frequently occur in the breasts of young women, and consequently can also be seen during pregnancy and lactation. Simple cysts do not increase the risk of malignancy. The current management is routine follow-up. Complex cysts are thick walled or contain a mass, and should be followed by a US-guided biopsy and then treated similar to any non-gravid, non-lactating patient.Galactoceles can be detected during the last trimester of pregnancy and during or after stopping lactation. Aspiration can be done to confirm the content. Co-existence of galactocele and malignancy is extremely rare, and the key is to follow up until it resolves.Fibroadenoma is the most frequent lesion found during pregnancy and lactation. Management is usually conservative after triple assessment. Surgery is usually not recommended in pregnant and lactating women unless rapid increase in size occurs or there is discordance in the triple assessment.Lactating adenomas are sometimes interpreted as a variant of fibroadenoma . They can naturally disappear at the end of pregnancy or lactation. Management is usually conservative, and an excisional biopsy is only mandated if it is rapidly enlarging or if there is discordance in the triple assessment.Gestational gigantomastia is a rare condition consisting of diffuse severe hypertrophy of both breasts during pregnancy . Mastectomy and reconstruction may rarely be required in such cases.
Biobanking of Human Mesenchymal Stem Cells: Future Strategy to Facilitate Clinical Applications

Yong KW, Choi JR, Wan Safwani WK

Adv Exp Med Biol, 2016;951:99-110.
PMID: 27837557

Human mesenchymal stem cells (hMSCs), a type of adult stem cells that hold great potential in clinical applications (e.g., regenerative medicine and cell-based therapy) due to their ability to differentiate into multiple types of specialized cells and secrete soluble factors which can initiate tissue repair and regulate immune response. hMSCs need to be expanded in vitro or cryopreserved to obtain sufficient cell numbers required for clinical applications. However, long-term in vitro culture-expanded hMSCs may raise some biosafety concerns (e.g., chromosomal abnormality and malignant transformation) and compromised functional properties, limiting their use in clinical applications. To avoid those adverse effects, it is essential to cryopreserve hMSCs at early passage and pool them for off-the-shelf use in clinical applications. However, the existing cryopreservation methods for hMSCs have some notable limitations. To address these limitations, several approaches have to be taken in order to produce healthy and efficacious cryopreserved hMSCs for clinical trials, which remains challenging to date. Therefore, a noteworthy amount of resources has been utilized in research in optimization of the cryopreservation methods, development of freezing devices, and formulation of cryopreservation media to ensure that hMSCs maintain their therapeutic characteristics without raising biosafety concerns following cryopreservation. Biobanking of hMSCs would be a crucial strategy to facilitate clinical applications in the future.
Collagen Type I: A Versatile Biomaterial

Chowdhury SR, Mh Busra MF, Lokanathan Y, Ng MH, Law JX, Cletus UC, et al.

Adv Exp Med Biol, 2018 10 26;1077:389-414.
PMID: 30357700 DOI: 10.1007/978-981-13-0947-2_21

Collagen type I is the most abundant matrix protein in the human body and is highly demanded in tissue engineering, regenerative medicine, and pharmaceutical applications. To meet the uprising demand in biomedical applications, collagen type I has been isolated from mammalians (bovine, porcine, goat and rat) and non-mammalians (fish, amphibian, and sea plant) source using various extraction techniques. Recent advancement enables fabrication of collagen scaffolds in multiple forms such as film, sponge, and hydrogel, with or without other biomaterials. The scaffolds are extensively used to develop tissue substitutes in regenerating or repairing diseased or damaged tissues. The 3D scaffolds are also used to develop in vitro model and as a vehicle for delivering drugs or active compounds.
Computer-Aided Antibody Design: An Overview

Choong YS, Lee YV, Soong JX, Law CT, Lim YY

Adv Exp Med Biol, 2017;1053:221-243.
PMID: 29549642 DOI: 10.1007/978-3-319-72077-7_11

The use of monoclonal antibody as the next generation protein therapeutics with remarkable success has surged the development of antibody engineering to design molecules for optimizing affinity, better efficacy, greater safety and therapeutic function. Therefore, computational methods have become increasingly important to generate hypotheses, interpret and guide experimental works. In this chapter, we discussed the overall antibody design by computational approches.
Contribution of kinin system to the antihypertensive action of angiotensin converting enzyme inhibitors

Sharma JN

Adv Exp Med Biol, 1989;247A:197-205.
PMID: 2690588
Current Perspectives on Nasopharyngeal Carcinoma

Lee HM, Okuda KS, González FE, Patel V

Adv Exp Med Biol, 2019;1164:11-34.
PMID: 31576537 DOI: 10.1007/978-3-030-22254-3_2

Of the ~129,079 new cases of nasopharyngeal carcinoma (NPC) and 72,987 associated deaths estimated for 2018, the majority will be geographically localized to South East Asia, and likely to show an upward trend annually. It is thought that disparities in dietary habits, lifestyle, and exposures to harmful environmental factors are likely the root cause of NPC incidence rates to differ geographically. Genetic differences due to ethnicity and the Epstein Barr virus (EBV) are likely contributing factors. Pertinently, NPC is associated with poor prognosis which is largely attributed to lack of awareness of the salient symptoms of NPC. These include nose hemorrhage and headaches and coupled with detection and the limited therapeutic options. Treatment options include radiotherapy or chemotherapy or combination of both. Surgical excision is generally the last option considered for advanced and metastatic disease, given the close proximity of nasopharynx to brain stem cell area, major blood vessels, and nerves. To improve outcome of NPC patients, novel cellular and in vivo systems are needed to allow an understanding of the underling molecular events causal for NPC pathogenesis and for identifying novel therapeutic targets and effective therapies. While challenges and gaps in current NPC research are noted, some advances in targeted therapies and immunotherapies targeting EBV NPCs are discussed in this chapter, which may offer improvements in outcome of NPC patients.
Digital image processing and analysis for activated sludge wastewater treatment

Khan MB, Lee XY, Nisar H, Ng CA, Yeap KH, Malik AS

Adv Exp Med Biol, 2015;823:227-48.
PMID: 25381111 DOI: 10.1007/978-3-319-10984-8_13

Activated sludge system is generally used in wastewater treatment plants for processing domestic influent. Conventionally the activated sludge wastewater treatment is monitored by measuring physico-chemical parameters like total suspended solids (TSSol), sludge volume index (SVI) and chemical oxygen demand (COD) etc. For the measurement, tests are conducted in the laboratory, which take many hours to give the final measurement. Digital image processing and analysis offers a better alternative not only to monitor and characterize the current state of activated sludge but also to predict the future state. The characterization by image processing and analysis is done by correlating the time evolution of parameters extracted by image analysis of floc and filaments with the physico-chemical parameters. This chapter briefly reviews the activated sludge wastewater treatment; and, procedures of image acquisition, preprocessing, segmentation and analysis in the specific context of activated sludge wastewater treatment. In the latter part additional procedures like z-stacking, image stitching are introduced for wastewater image preprocessing, which are not previously used in the context of activated sludge. Different preprocessing and segmentation techniques are proposed, along with the survey of imaging procedures reported in the literature. Finally the image analysis based morphological parameters and correlation of the parameters with regard to monitoring and prediction of activated sludge are discussed. Hence it is observed that image analysis can play a very useful role in the monitoring of activated sludge wastewater treatment plants.
Enhanced optical flow field of left ventricular motion using quasi-Gaussian DCT filter

Riyadi S, Mustafa MM, Hussain A, Maskon O, Nor IF

Adv Exp Med Biol, 2011;696:461-9.
PMID: 21431586 DOI: 10.1007/978-1-4419-7046-6_46

Left ventricular motion estimation is very important for diagnosing cardiac abnormality. One of the popular techniques, optical flow technique, promises useful results for motion quantification. However, optical flow technique often failed to provide smooth vector field due to the complexity of cardiac motion and the presence of speckle noise. This chapter proposed a new filtering technique, called quasi-Gaussian discrete cosine transform (QGDCT)-based filter, to enhance the optical flow field for myocardial motion estimation. Even though Gaussian filter and DCT concept have been implemented in other previous researches, this filter introduces a different approach of Gaussian filter model based on high frequency properties of cosine function. The QGDCT is a customized quasi discrete Gaussian filter in which its coefficients are derived from a selected two-dimensional DCT. This filter was implemented before and after the computation of optical flow to reduce the speckle noise and to improve the flow field smoothness, respectively. The algorithm was first validated on synthetic echocardiography image that simulates a contracting myocardium motion. Subsequently, this method was also implemented on clinical echocardiography images. To evaluate the performance of the technique, several quantitative measurements such as magnitude error, angular error, and standard error of measurement are computed and analyzed. The final motion estimation results were in good agreement with the physician manual interpretation.
Functional Analysis of Circular RNAs

Shanmugapriya, Huda HA, Vijayarathna S, Oon CE, Chen Y, Kanwar JR, et al.

Adv Exp Med Biol, 2018 9 28;1087:95-105.
PMID: 30259360 DOI: 10.1007/978-981-13-1426-1_8

Circular RNAs characterize a class of widespread and diverse endogenous RNAs which are non-coding RNAs that are made by back-splicing events and have covalently closed loops with no polyadenylated tails. Various indications specify that circular RNAs (circRNAs) are plentiful in the human transcriptome. However, their participation in biological processes remains mostly undescribed. To date thousands of circRNAs have been revealed in organisms ranging from Drosophila melanogaster to Homo sapiens. Functional studies specify that these transcripts control expression of protein-coding linear transcripts and thus encompass a key component of gene expression regulation. This chapter provide a comprehensive overview on functional validation of circRNAs. Furthermore, we discuss the recent modern methodologies for the functional validation of circRNAs such as RNA interference (RNAi) gene silencing assay, luciferase reporter assays, circRNA gain-of-function investigation via overexpression of circular transcript assay, RT-q-PCR quantification, and other latest applicable assays. The methods described in this chapter are demonstrated on the cellular model.
Functional Genomics

Goh HH, Ng CL, Loke KK

Adv Exp Med Biol, 2018 11 2;1102:11-30.
PMID: 30382566 DOI: 10.1007/978-3-319-98758-3_2

Functional genomics encompasses diverse disciplines in molecular biology and bioinformatics to comprehend the blueprint, regulation, and expression of genetic elements that define the physiology of an organism. The deluge of sequencing data in the postgenomics era has demanded the involvement of computer scientists and mathematicians to create algorithms, analytical software, and databases for the storage, curation, and analysis of biological big data. In this chapter, we discuss on the concept of functional genomics in the context of systems biology and provide examples of its application in human genetic disease studies, molecular crop improvement, and metagenomics for antibiotic discovery. An overview of transcriptomics workflow and experimental considerations is also introduced. Lastly, we present an in-house case study of transcriptomics analysis of an aromatic herbal plant to understand the effect of elicitation on the biosynthesis of volatile organic compounds.
Gingerol and Its Role in Chronic Diseases

Mohd Yusof YA

Adv Exp Med Biol, 2016;929:177-207.
PMID: 27771925

Since antiquity, ginger or Zingiber officinale, has been used by humans for medicinal purposes and as spice condiments to enhance flavor in cooking. Ginger contains many phenolic compounds such as gingerol, shogaol and paradol that exhibit antioxidant, anti-tumor and anti-inflammatory properties. The role of ginger and its constituents in ameliorating diseases has been the focus of study in the past two decades by many researchers who provide strong scientific evidence of its health benefit. This review discusses research findings and works devoted to gingerols, the major pungent constituent of ginger, in modulating and targeting signaling pathways with subsequent changes that ameliorate, reverse or prevent chronic diseases in human studies and animal models. The physical, chemical and biological properties of gingerols are also described. The use of ginger and especially gingerols as medicinal food derivative appears to be safe in treating or preventing chronic diseases which will benefit the common population, clinicians, patients, researchers, students and industrialists.
Greek Nurses' Perception of Hospital Ethical Climate: A Cross-Sectional Study

Fradelos EC, Latsou D, Alikari V, Papathanasiou IV, Roupa A, Balang V, et al.

Adv Exp Med Biol, 2021;1337:17-25.
PMID: 34972887 DOI: 10.1007/978-3-030-78771-4_3

This study aimed to examine Greek nurses' perceptions about hospital ethical climate and to investigate the possible difference of those perceptions regarding their demographic and work-related characteristics. The cross-sectional study design was employed in this study in which 286 nurses and nurse assistants participated. Data were collected by a sheet containing demographic and work-related characteristics and the Greek version of the Oslons' Hospital Ethical Climate Scale. IBM Statistical Package for Social Sciences 25 was used in data analysis. Frequencies, means, percentages, and standard deviations summarized the data. For the statistical differences, parametric tests were performed. Independent Samples t and Pearson correlation analysis were used to determine the relationship between the ethical climate of the hospital and the nurses' characteristics. The p-values 0.05 were considered statistically significant. The mean age of the nurses was 44 years (SD: 8.5 years; range 24-66 years). The majority of them were women (77.3%). A percent of 57.7% of the sample was married. Most positive perceptions were concerning managers (4.01) following by peers (3.82), patients (3.69), hospitals (3.29) while the least positive perceptions of the ethical climate were concerning the physicians (3.16). The factors associated with hospital ethical perception were: working experience and responsible position. The highest score of ethical climate reported to managers subscale, while the minimum score was related to physicians. In general, Greek nurses reported positive perceptions regarding hospital ethical climate. The positive ethical climate is associated with a better working environment, fewer nurses' experience of moral distress, fewer chances for nursing turnover, high quality of nursing care, and fewer errors in nursing practice.

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