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  1. Gene isolation using degenerate primers targeting protein motif: A laboratory exercise
    Yeo BPH, Foong LC, Tam SM, Lee V, Hwang SS
    Biochem Mol Biol Educ, 2018 01;46(1):47-53.
    PMID: 29131478 DOI: 10.1002/bmb.21089
    Structures and functions of protein motifs are widely included in many biology-based course syllabi. However, little emphasis is placed to link this knowledge to applications in biotechnology to enhance the learning experience. Here, the conserved motifs of nucleotide binding site-leucine rich repeats (NBS-LRR) proteins, successfully used for the isolation and characterization of many plant resistance gene analogues (RGAs), is featured in the development of a series of laboratory experiments using important molecular biology techniques. A set of previously isolated RGA sequences is used as the model for performing sequence alignment and visualising 3D protein structure using current bioinformatics programs (Clustal Omega and Argusdock software). A pair of established degenerate primer sequences is provided for the prediction of targeted amino acids sequences in the RGAs. Reverse transcription-polymerase chain reaction (RT-PCR) is used to amplify RGAs from total RNA samples extracted from the tropical wild relative of black pepper, Piper colubrinum (Piperaceae). This laboratory exercise enables students to correlate specific DNA sequences with respective amino acid codes and the interaction between conserved motifs of resistance genes with putatively targeted proteins. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):47-53, 2018.
    Matched MeSH terms: Software
  2. Distal Femoral Rotation Correlates With Proximal Tibial Joint Line Obliquity: A Consideration for Kinematic Total Knee Arthroplasty
    Ng CK, Chen JY, Yeh JZY, Ho JPY, Merican AM, Yeo SJ
    J Arthroplasty, 2018 06;33(6):1936-1944.
    PMID: 29395720 DOI: 10.1016/j.arth.2017.12.025
    BACKGROUND: We hypothesized that there is a correlation between the distal femoral rotation and proximal tibial joint line obliquity in nonarthritic knees. This has significance for kinematic knee arthroplasty, in which the target knee alignment desired approximates the knee before disease.

    METHODS: Fifty computed tomography scans of nonarthritic knees were evaluated using three-dimensional image processing software. Four distal femoral rotational axes were determined in the axial plane: the transepicondylar axis (TEA), transcondylar axis (TCA), posterior condylar axis (PCA), and a line perpendicular to Whiteside's anterior-posterior axis. Then, angles were measured relative to the TEA. Tibial joint line obliquity was measured as the angle between the proximal tibial plane and a line perpendicular to the axis of the tibia.

    RESULTS: There was a strong positive correlation between PCA-TEA and tibial joint line obliquity (r = 0.68, P < .001) as well as TCA-TEA and tibial joint line obliquity (r = 0.69, P < .001). In addition, the tibial joint line obliquity and TCA-TEA angles were similar, 3.7° ± 2.2° (mean ± standard deviation) and 3.5° ± 1.7°, respectively (mean difference, 0.2° ± 0.2°; P = .369).

    CONCLUSION: Both PCA-TEA and TCA-TEA strongly correlated with proximal tibial joint line obliquity indicating a relationship between distal femoral rotational geometry and proximal tibial inclination. These findings could imply that the native knee in flexion attempts to balance the collateral ligaments toward a rectangular flexion space. A higher tibial varus inclination is matched with a more internally rotated distal femur relative to the TEA.

    Matched MeSH terms: Software
  3. Fulltext Factors prognosticating the outcome of decompressive craniectomy in severe traumatic brain injury: A Malaysian experience
    Sharda P, Haspani S, Idris Z
    Asian J Neurosurg, 2014 Oct-Dec;9(4):203-12.
    PMID: 25685217 DOI: 10.4103/1793-5482.146605
    OBJECTIVE: The objective of this prospective cohort study was to analyse the characteristics of severe Traumatic Brain Injury (TBI) in a regional trauma centre Hospital Kuala Lumpur (HKL) along with its impact of various prognostic factors post Decompressive Craniectomy (DC).
    MATERIALS AND METHODS: Duration of the study was of 13 months in HKL. 110 consecutive patients undergoing DC and remained in our centre were recruited. They were then analysed categorically with standard analytical software.
    RESULTS: Age group have highest range between 12-30 category with male preponderance. Common mechanism of injury was motor vehicle accident involving motorcyclist. Univariate analysis showed statistically significant in referral area (P = 0.006). In clinical evaluation statistically significant was the motor score (P = 0.040), pupillary state (P = 0.010), blood pressure stability (P = 0.013) and evidence of Diabetes Insipidus (P < 0.001). In biochemical status the significant statistics included evidence of coagulopathy (P < 0.001), evidence of acidosis (P = 0.003) and evidence of hypoxia (P = 0.030). In Radiological sector, significant univariate analysis proved in location of the subdural clot (P < 0.010), location of the contusion (P = 0.045), site of existence of both type of clots (P = 0.031) and the evidence of edema (P = 0.041). The timing of injury was noted to be significant as well (P = 0.061). In the post operative care was, there were significance in the overall stability in intensive care (P < 0.001), the stability of blood pressure, cerebral perfusion pressure, pulse rates and oxygen saturation (all P < 0.001)seen individually, post operative ICP monitoring in the immediate (P = 0.002), within 24 hours (P < 0.001) and within 24-48 hours (P < 0.001) period, along with post operative pupillary size (P < 0.001) and motor score (P < 0.001). Post operatively, radiologically significant statistics included evidence of midline shift post operatively in the CT scan (P < 0.001). Multivariate logistic regression with stepwise likelihood ratio (LR) method concluded that hypoxia post operatively (P = 0.152), the unmaintained Cerebral Perfusion Pressure (CPP) (P = 0.007) and unstable blood pressure (BP) (P = <0.001). Poor outcome noted 10.2 times higher in post operative hypoxia [OR10.184; 95% CI: 0.424, 244.495]. Odds of having poor outcome if CPP unmaintained was 13.8 times higher [OR: 13.754; CI: 2.050, 92.301]. Highest predictor of poor outcome was the unstable BP, 32 times higher [OR 31.600; CI: 4.530, 220440].
    CONCLUSION: Our series represent both urban and rural population, noted to be the largest series in severe TBI in this region. Severe head injury accounts for significant proportion of neurosurgical admissions, resources with its impact on socio-economic concerns to a growing population like Malaysia. This study concludes that the predictors of outcome in severe TBI post DC were postoperative hypoxia, unmaintained cerebral perfusion pressure and unstable blood pressure as independent predictors of poor outcome. Key words: Decompressive craniectomy, prognostication of decompressive craniectomy, prognostication of severe head injury, prognostication of traumatic brain injury, severe head injury, severe traumatic brain injury, traumatic brain injury.
    KEYWORDS: Decompressive craniectomy; prognostication of decompressive craniectomy; prognostication of severe head injury; prognostication of traumatic brain injury; severe head injury; severe traumatic brain injury; traumatic brain injury
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  4. Esophagogastric junction morphology and contractile integral on high-resolution manometry in asymptomatic healthy volunteers: An international multicenter study
    Rogers BD, Rengarajan A, Abrahao L, Bhatia S, Bor S, Carlson DA, et al.
    Neurogastroenterol Motil, 2021 06;33(6):e14009.
    PMID: 33094875 DOI: 10.1111/nmo.14009
    BACKGROUND: Esophagogastric junction contractile integral (EGJ-CI) and EGJ morphology are high-resolution manometry (HRM) metrics that assess EGJ barrier function. Normative data standardized across world regions and HRM manufacturers are limited.

    METHODS: Our aim was to determine normative EGJ metrics in a large international cohort of healthy volunteers undergoing HRM (Medtronic, Laborie, and Diversatek software) acquired from 16 countries in four world regions. EGJ-CI was calculated by the same two investigators using a distal contractile integral-like measurement across the EGJ for three respiratory cycles and corrected for respiration (mm Hg cm), using manufacturer-specific software tools. EGJ morphology was designated according to Chicago Classification v3.0. Median EGJ-CI values were calculated across age, genders, HRM systems, and regions.

    RESULTS: Of 484 studies (28.0 years, 56.2% F, 60.7% Medtronic studies, 26.0% Laborie, and 13.2% Diversatek), EGJ morphology was type 1 in 97.1%. Median EGJ-CI was similar between Medtronic (37.0 mm Hg cm, IQR 23.6-53.7 mm Hg cm) and Diversatek (34.9 mm Hg cm, IQR 22.1-56.1 mm Hg cm, P = 0.87), but was significantly higher using Laborie equipment (56.5 mm Hg cm, IQR 35.0-75.3 mm Hg cm, P 

    Matched MeSH terms: Software
  5. Fulltext Adding glycaemic index and glycaemic load functionality to DietPLUS, a Malaysian food composition database and diet intake calculator
    Shyam S, Wai TN, Arshad F
    Asia Pac J Clin Nutr, 2012;21(2):201-8.
    PMID: 22507605
    This paper outlines the methodology to add glycaemic index (GI) and glycaemic load (GL) functionality to food DietPLUS, a Microsoft Excel-based Malaysian food composition database and diet intake calculator. Locally determined GI values and published international GI databases were used as the source of GI values. Previously published methodology for GI value assignment was modified to add GI and GL calculators to the database. Two popular local low GI foods were added to the DietPLUS database, bringing up the total number of foods in the database to 838 foods. Overall, in relation to the 539 major carbohydrate foods in the Malaysian Food Composition Database, 243 (45%) food items had local Malaysian values or were directly matched to International GI database and another 180 (33%) of the foods were linked to closely-related foods in the GI databases used. The mean ± SD dietary GI and GL of the dietary intake of 63 women with previous gestational diabetes mellitus, calculated using DietPLUS version3 were, 62 ± 6 and 142 ± 45, respectively. These values were comparable to those reported from other local studies. DietPLUS version3, a simple Microsoft Excel-based programme aids calculation of diet GI and GL for Malaysian diets based on food records.
    Matched MeSH terms: Software
  6. Fulltext Bibliography of clinical research in Malaysia: methods and brief results
    Teng CL, Zuhanariah MN, Ng CS, Goh CC
    Med J Malaysia, 2014 Aug;69 Suppl A:4-7.
    PMID: 25417946
    This article describes the methodology of this bibliography. A search was conducted on the following: (1) bibliographic databases (PubMed, Scopus, and other databases) using search terms that maximize the retrieval of Malaysian publications; (2) Individual journal search of Malaysian healthrelated journals; (3) A targeted search of Google and Google Scholar; (4) Searching of Malaysian institutional repositories; (5) Searching of Ministry of Health and Clinical Research Centre website. The publication years were limited to 2000- 2013. The citations were imported or manually entered into bibliographic software Refworks. After removing duplicates, and correcting data entry errors, PubMed's Medical Subject Headings (MeSH terms) were added. Clinical research is coded using the definition "patient-oriented-research or research conducted with human subjects (or on material of human origin) for which the investigator directly interacts with the human subjects at some point during the study." A bibliography of citations [n=2056] that fit the criteria of clinical research in Malaysia in selected topics within five domains was generated: Cancers [589], Cardiovascular diseases [432], Infections [795], Injuries [142], and Mental Health [582]. This is done by retrieving citations with the appropriate MESH terms, as follow: For cancers (Breast Neoplasms; Colorectal Neoplasms; Uterine Cervical Neoplasms), for cardiovascular diseases (Coronary Disease; Hypertension; Stroke), for infections (Dengue; Enterovirus Infections, HIV Infections; Malaria; Nipah Virus; Tuberculosis), for injuries (Accidents, Occupational; Accidents, Traffic; Child Abuse; Occupational Injuries), for mental health (Depression; Depressive Disorder; Depressive Disorder, Major; Drug Users; Psychotic Disorders; Suicide; Suicide, Attempted; Suicidal Ideation; Substance- Related Disorders).
    Matched MeSH terms: Software
  7. Fulltext First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene
    Mohamoud HS, Hussain MR, El-Harouni AA, Shaik NA, Qasmi ZU, Merican AF, et al.
    Comput Math Methods Med, 2014;2014:904052.
    PMID: 24723968 DOI: 10.1155/2014/904052
    GalNAc-T1, a key candidate of GalNac-transferases genes family that is involved in mucin-type O-linked glycosylation pathway, is expressed in most biological tissues and cell types. Despite the reported association of GalNAc-T1 gene mutations with human disease susceptibility, the comprehensive computational analysis of coding, noncoding and regulatory SNPs, and their functional impacts on protein level, still remains unknown. Therefore, sequence- and structure-based computational tools were employed to screen the entire listed coding SNPs of GalNAc-T1 gene in order to identify and characterize them. Our concordant in silico analysis by SIFT, PolyPhen-2, PANTHER-cSNP, and SNPeffect tools, identified the potential nsSNPs (S143P, G258V, and Y414D variants) from 18 nsSNPs of GalNAc-T1. Additionally, 2 regulatory SNPs (rs72964406 and #x26; rs34304568) were also identified in GalNAc-T1 by using FastSNP tool. Using multiple computational approaches, we have systematically classified the functional mutations in regulatory and coding regions that can modify expression and function of GalNAc-T1 enzyme. These genetic variants can further assist in better understanding the wide range of disease susceptibility associated with the mucin-based cell signalling and pathogenic binding, and may help to develop novel therapeutic elements for associated diseases.
    Matched MeSH terms: Software
  8. Fulltext PASS-predicted Vitex negundo activity: antioxidant and antiproliferative properties on human hepatoma cells--an in vitro study
    Kadir FA, Kassim NM, Abdulla MA, Yehye WA
    BMC Complement Altern Med, 2013;13:343.
    PMID: 24305067 DOI: 10.1186/1472-6882-13-343
    Hepatocellular carcinoma is a common type of tumour worldwide with a high mortality rate and with low response to current cytotoxic and chemotherapeutic drugs. The prediction of activity spectra for the substances (PASS) software, which predicted that more than 300 pharmacological effects, biological and biochemical mechanisms based on the structural formula of the substance was efficiently used in this study to reveal new multitalented actions for Vitex negundo (VN) constituents.
    Matched MeSH terms: Software
  9. Fulltext Impacts of Nonsynonymous Single Nucleotide Polymorphisms of Adiponectin Receptor 1 Gene on Corresponding Protein Stability: A Computational Approach
    Saleh MA, Solayman M, Paul S, Saha M, Khalil MI, Gan SH
    Biomed Res Int, 2016;2016:9142190.
    PMID: 27294143 DOI: 10.1155/2016/9142190
    Despite the reported association of adiponectin receptor 1 (ADIPOR1) gene mutations with vulnerability to several human metabolic diseases, there is lack of computational analysis on the functional and structural impacts of single nucleotide polymorphisms (SNPs) of the human ADIPOR1 at protein level. Therefore, sequence- and structure-based computational tools were employed in this study to functionally and structurally characterize the coding nsSNPs of ADIPOR1 gene listed in the dbSNP database. Our in silico analysis by SIFT, nsSNPAnalyzer, PolyPhen-2, Fathmm, I-Mutant 2.0, SNPs&GO, PhD-SNP, PANTHER, and SNPeffect tools identified the nsSNPs with distorting functional impacts, namely, rs765425383 (A348G), rs752071352 (H341Y), rs759555652 (R324L), rs200326086 (L224F), and rs766267373 (L143P) from 74 nsSNPs of ADIPOR1 gene. Finally the aforementioned five deleterious nsSNPs were introduced using Swiss-PDB Viewer package within the X-ray crystal structure of ADIPOR1 protein, and changes in free energy for these mutations were computed. Although increased free energy was observed for all the mutants, the nsSNP H341Y caused the highest energy increase amongst all. RMSD and TM scores predicted that mutants were structurally similar to wild type protein. Our analyses suggested that the aforementioned variants especially H341Y could directly or indirectly destabilize the amino acid interactions and hydrogen bonding networks of ADIPOR1.
    Matched MeSH terms: Software
  10. Identification of reference genes for real-time polymerase chain reaction gene expression studies in Nile rats fed Water-Soluble Palm Fruit Extract
    Leow SS, Lee WK, Khoo JS, Teoh S, Hoh CC, Fairus S, et al.
    Mol Biol Rep, 2020 Dec;47(12):9409-9427.
    PMID: 33222119 DOI: 10.1007/s11033-020-06003-3
    The Nile rat (Arvicanthis niloticus) is a novel diurnal carbohydrate-sensitive rodent useful for studies on type 2 diabetes mellitus (T2DM) and the metabolic syndrome. Hepatic responses to T2DM and any interventions thereof can be evaluated via transcriptomic gene expression analysis. However, the study of gene expression via real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR) requires identification of stably expressed reference genes for accurate normalisation. This study describes the evaluation and identification of stable reference genes in the livers from Control Nile rats as well as those supplemented with Water-Soluble Palm Fruit Extract, which has been previously shown to attenuate T2DM in this animal model. Seven genes identified as having stable expression in RNA-Sequencing transcriptome analysis were chosen for verification using real-time RT-qPCR. Six commonly used reference genes from previous literature and two genes from a previous microarray gene expression study in Nile rats were also evaluated. The expression data of these 15 candidate reference genes were analysed using the RefFinder software which incorporated analyses performed by various algorithms. The Hpd, Pnpla6 and Vpp2 genes were identified as the most stable across the 36 samples tested. Their applicability was demonstrated through the normalisation of the gene expression profiles of two target genes, Cela1 and Lepr. In conclusion, three novel reference genes which can be used for robust normalisation of real-time RT-qPCR data were identified, thereby facilitating future hepatic gene expression studies in the Nile rat.
    Matched MeSH terms: Software
  11. Synthesis, SAR elucidations and molecular docking study of newly designed isatin based oxadiazole analogs as potent inhibitors of thymidine phosphorylase
    Javid MT, Rahim F, Taha M, Nawaz M, Wadood A, Ali M, et al.
    Bioorg Chem, 2018 09;79:323-333.
    PMID: 29803079 DOI: 10.1016/j.bioorg.2018.05.011
    Thymidine phosphorylase is an enzyme involved in pyrimidine salvage pathway that is identical to platelet-derived endothelial cell growth factor (PD-ECGF) and gliostatin. It is enormously up regulated in a variety of solid tumors. Furthermore, surpassing of TP level protects tumor cells from apoptosis and helps cell survival. Thus TP is identified as a prime target for developing novel anticancer therapies. A new class of exceptionally potent isatin based oxadiazole (1-30) has been synthesized and evaluated for thymidine phosphorylase inhibitory potential. All analogs showed potent thymidine phosphorylase inhibition when compared with standard 7-Deazaxanthine, 7DX (IC50 = 38.68 ± 1.12 µM). Molecular docking study was performed in order to determine the binding interaction of these newly synthesized compounds, which revealed that these synthesized compounds established stronger hydrogen bonding network with active site of residues as compare to the standard compound 7DX.
    Matched MeSH terms: Software
  12. Linked color imaging improves the visibility of various featured colorectal polyps in an endoscopist's visibility and color difference value
    Yoshida N, Naito Y, Yasuda R, Murakami T, Hirose R, Ogiso K, et al.
    Int J Colorectal Dis, 2017 Sep;32(9):1253-1260.
    PMID: 28725959 DOI: 10.1007/s00384-017-2855-z
    PURPOSE: Linked color imaging (LCI) by laser endoscopy is a novel narrow band light observation. In this study, we analyzed the efficacy of LCI for improving the various featured colorectal polyp's visibility utilizing a subjective endoscopist's visibility scoring and objective color difference (CD) value.

    METHODS: We retrospectively reviewed two pictures both with white light (WL) and LCI for 54 consecutive neoplastic polyps 2-20 mm in size. All pictures were evaluated by four endoscopists according to a published polyp visibility score from four (excellent visibility) to one (poor visibility). Additionally, we calculated CD value between each polyp and surrounding mucosa in LCI and WL using an original software.

    RESULTS: The mean polyp visibility scores of LCI (3.11 ± 1.05) were significantly higher than those of WL (2.50 ± 1.09, P 

    Matched MeSH terms: Software
  13. Tokyo Guidelines 2018: initial management of acute biliary infection and flowchart for acute cholangitis
    Miura F, Okamoto K, Takada T, Strasberg SM, Asbun HJ, Pitt HA, et al.
    J Hepatobiliary Pancreat Sci, 2018 Jan;25(1):31-40.
    PMID: 28941329 DOI: 10.1002/jhbp.509
    The initial management of patients with suspected acute biliary infection starts with the measurement of vital signs to assess whether or not the situation is urgent. If the case is judged to be urgent, initial medical treatment should be started immediately including respiratory/circulatory management if required, without waiting for a definitive diagnosis. The patient's medical history is then taken; an abdominal examination is performed; blood tests, urinalysis, and diagnostic imaging are carried out; and a diagnosis is made using the diagnostic criteria for cholangitis/cholecystitis. Once the diagnosis has been confirmed, initial medical treatment should be started immediately, severity should be assessed according to the severity grading criteria for acute cholangitis/cholecystitis, and the patient's general status should be evaluated. For mild acute cholangitis, in most cases initial treatment including antibiotics is sufficient, and most patients do not require biliary drainage. However, biliary drainage should be considered if a patient does not respond to initial treatment. For moderate acute cholangitis, early endoscopic or percutaneous transhepatic biliary drainage is indicated. If the underlying etiology requires treatment, this should be provided after the patient's general condition has improved; endoscopic sphincterotomy and subsequent choledocholithotomy may be performed together with biliary drainage. For severe acute cholangitis, appropriate respiratory/circulatory management is required. Biliary drainage should be performed as soon as possible after the patient's general condition has been improved by initial treatment and respiratory/circulatory management. Free full articles and mobile app of TG18 are available at: http://www.jshbps.jp/modules/en/index.php?content_id=47. Related clinical questions and references are also included.
    Matched MeSH terms: Software Design
  14. Fulltext The efficacy and safety of intramuscular injections of methylcobalamin in patients with chronic nonspecific low back pain: a randomised controlled trial
    Chiu CK, Low TH, Tey YS, Singh VA, Shong HK
    Singapore Med J, 2011 Dec;52(12):868-73.
    PMID: 22159928
    INTRODUCTION: Chronic, nonspecific low back pain is a difficult ailment to treat and poses an economic burden in terms of medical expenses and productivity loss. The aim of this study was to determine the efficacy and safety of intramuscular metylcobalamin in the treatment of chronic nonspecific low back pain.
    METHODS: This was a double-blinded, randomised, controlled experimental study. 60 patients were assigned to either the methylcobalamin group or the placebo group. The former received intramuscular injections of 500 mcg parenteral methylcobalamin in 1 ml solution three times a week for two weeks, and the placebo group received 1 ml normal saline. Patients were assessed with Oswestry Disability Index questionnaire Version 2.0 and Visual Analogue Scale pain score. They were scored before commencement of the injections and at two months interval.
    RESULTS: Of the 60 patients, 27 received the placebo injections and 33 were given methylcobalamin injections. A total of 58 patients were available for review at two months (placebo: n is 26; methylcobalamin: n is 32). There was a significant improvement in the Oswestry Disability Index and Visual Analogue Scale pain scores in the methylcobalamin group as compared with the placebo group (p-value less than 0.05). Only minor adverse reactions such as pain and haematoma at the injection sites were reported by some patients.
    CONCLUSION: Intramuscular methylcobalamin is both an effective and safe method of treatment for patients with nonspecific low back pain, both singly or in combination with other forms of treatment.
    Study site: Orthopaedic Clinic, Hospital Tuanku Jaafar, Seremban, Negeri Sembilan, Malaysia
    Matched MeSH terms: Software
  15. Fulltext A Fuzzy-C-Means-Clustering Approach: Quantifying Chromatin Pattern of Non-Neoplastic Cervical Squamous Cells
    Tang JR, Mat Isa NA, Ch'ng ES
    PLoS One, 2015;10(11):e0142830.
    PMID: 26560331 DOI: 10.1371/journal.pone.0142830
    Despite the effectiveness of Pap-smear test in reducing the mortality rate due to cervical cancer, the criteria of the reporting standard of the Pap-smear test are mostly qualitative in nature. This study addresses the issue on how to define the criteria in a more quantitative and definite term. A negative Pap-smear test result, i.e. negative for intraepithelial lesion or malignancy (NILM), is qualitatively defined to have evenly distributed, finely granular chromatin in the nuclei of cervical squamous cells. To quantify this chromatin pattern, this study employed Fuzzy C-Means clustering as the segmentation technique, enabling different degrees of chromatin segmentation to be performed on sample images of non-neoplastic squamous cells. From the simulation results, a model representing the chromatin distribution of non-neoplastic cervical squamous cell is constructed with the following quantitative characteristics: at the best representative sensitivity level 4 based on statistical analysis and human experts' feedbacks, a nucleus of non-neoplastic squamous cell has an average of 67 chromatins with a total area of 10.827 μm2; the average distance between the nearest chromatin pair is 0.508 μm and the average eccentricity of the chromatin is 0.47.
    Matched MeSH terms: Software
  16. Temporal patterns and source apportionment of nitrate-nitrogen leaching in a paddy field at Kelantan, Malaysia
    Hussain H, Yusoff MK, Ramli MF, Abd Latif P, Juahir H, Zawawi MA
    Pak J Biol Sci, 2013 Nov 15;16(22):1524-30.
    PMID: 24511695
    Nitrate-nitrogen leaching from agricultural areas is a major cause for groundwater pollution. Polluted groundwater with high levels of nitrate is hazardous and cause adverse health effects. Human consumption of water with elevated levels of NO3-N has been linked to the infant disorder methemoglobinemia and also to non-Hodgkin's disease lymphoma in adults. This research aims to study the temporal patterns and source apportionment of nitrate-nitrogen leaching in a paddy soil at Ladang Merdeka Ismail Mulong in Kelantan, Malaysia. The complex data matrix (128 x 16) of nitrate-nitrogen parameters was subjected to multivariate analysis mainly Principal Component Analysis (PCA) and Discriminant Analysis (DA). PCA extracted four principal components from this data set which explained 86.4% of the total variance. The most important contributors were soil physical properties confirmed using Alyuda Forecaster software (R2 = 0.98). Discriminant analysis was used to evaluate the temporal variation in soil nitrate-nitrogen on leaching process. Discriminant analysis gave four parameters (hydraulic head, evapotranspiration, rainfall and temperature) contributing more than 98% correct assignments in temporal analysis. DA allowed reduction in dimensionality of the large data set which defines the four operating parameters most efficient and economical to be monitored for temporal variations. This knowledge is important so as to protect the precious groundwater from contamination with nitrate.
    Matched MeSH terms: Software
  17. MicroRNAs associated with tumour migration, invasion and angiogenic properties in A549 and SK-Lu1 human lung adenocarcinoma cells
    Ho CS, Yap SH, Phuah NH, In LL, Hasima N
    Lung Cancer, 2014 Feb;83(2):154-62.
    PMID: 24360396 DOI: 10.1016/j.lungcan.2013.11.024
    Dysregulation in miRNA expression contributes towards the initiation and progression of metastasis by regulating multiple target genes. In this study, variations in miRNA expression profiles were investigated between high and low invasive NSCLC cell lines followed by identification of miRNAs with targets governing NSCLC's metastatic potential.
    Matched MeSH terms: Software
  18. Fulltext Eukaryotic pathways targeted by the type III secretion system effector protein, BipC, involved in the intracellular lifecycle of Burkholderia pseudomallei
    Kang WT, Vellasamy KM, Vadivelu J
    Sci Rep, 2016 09 16;6:33528.
    PMID: 27634329 DOI: 10.1038/srep33528
    Burkholderia pseudomallei, the etiological agent for melioidosis, is known to secrete a type III secretion system (TTSS) protein into the host's internal milieu. One of the TTSS effector protein, BipC, has been shown to play an important role in the B. pseudomallei pathogenesis. To identify the host response profile that was directly or indirectly regulated by this protein, genome-wide transcriptome approach was used to examine the gene expression profiles of infected mice. The transcriptome analysis of the liver and spleen revealed that a total of approximately 1,000 genes were transcriptionally affected by BipC. Genes involved in bacterial invasion, regulation of actin cytoskeleton, and MAPK signalling pathway were over-expressed and may be specifically regulated by BipC in vivo. These results suggest that BipC mainly targets pathways related to the cellular processes which could modulate the cellular trafficking processes. The host transcriptional response exhibited remarkable differences with and without the presence of the BipC protein. Overall, the detailed picture of this study provides new insights that BipC may have evolved to efficiently manipulate host-cell pathways which is crucial in the intracellular lifecycle of B. pseudomallei.
    Matched MeSH terms: Software
  19. Fulltext MicroRNA Expression Profile of Neural Progenitor-Like Cells Derived from Rat Bone Marrow Mesenchymal Stem Cells under the Influence of IGF-1, bFGF and EGF
    Huat TJ, Khan AA, Abdullah JM, Idris FM, Jaafar H
    Int J Mol Sci, 2015;16(5):9693-718.
    PMID: 25938966 DOI: 10.3390/ijms16059693
    Insulin-like growth factor 1 (IGF-1) enhances cellular proliferation and reduces apoptosis during the early differentiation of bone marrow derived mesenchymal stem cells (BMSCs) into neural progenitor-like cells (NPCs) in the presence of epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF). BMSCs were differentiated in three groups of growth factors: (A) EGF + bFGF, (B) EGF + bFGF + IGF-1, and (C) without growth factor. To unravel the molecular mechanisms of the NPCs derivation, microarray analysis using GeneChip miRNA arrays was performed. The profiles were compared among the groups. Annotated microRNA fingerprints (GSE60060) delineated 46 microRNAs temporally up-regulated or down-regulated compared to group C. The expressions of selected microRNAs were validated by real-time PCR. Among the 46 microRNAs, 30 were consistently expressed for minimum of two consecutive time intervals. In Group B, only miR-496 was up-regulated and 12 microRNAs, including the let-7 family, miR-1224, miR-125a-3p, miR-214, miR-22, miR-320, miR-708, and miR-93, were down-regulated. Bioinformatics analysis reveals that some of these microRNAs (miR-22, miR-214, miR-125a-3p, miR-320 and let-7 family) are associated with reduction of apoptosis. Here, we summarize the roles of key microRNAs associated with IGF-1 in the differentiation of BMSCs into NPCs. These findings may provide clues to further our understanding of the mechanisms and roles of microRNAs as key regulators of BMSC-derived NPC maintenance.
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