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Fulltext TranCEP: Predicting the substrate class of transmembrane transport proteins using compositional, evolutionary, and positional information

Alballa M, Aplop F, Butler G

PLoS One, 2020;15(1):e0227683.
PMID: 31935244 DOI: 10.1371/journal.pone.0227683

Transporters mediate the movement of compounds across the membranes that separate the cell from its environment and across the inner membranes surrounding cellular compartments. It is estimated that one third of a proteome consists of membrane proteins, and many of these are transport proteins. Given the increase in the number of genomes being sequenced, there is a need for computational tools that predict the substrates that are transported by the transmembrane transport proteins. In this paper, we present TranCEP, a predictor of the type of substrate transported by a transmembrane transport protein. TranCEP combines the traditional use of the amino acid composition of the protein, with evolutionary information captured in a multiple sequence alignment (MSA), and restriction to important positions of the alignment that play a role in determining the specificity of the protein. Our experimental results show that TranCEP significantly outperforms the state-of-the-art predictors. The results quantify the contribution made by each type of information used.

Matched MeSH terms: Software
Occurrence and Molecular Characterization of Squash leaf curl Phillipines virus in Taiwan

Tsai WS, Shih SL, Green SK, Jan FJ

Plant Dis, 2007 Jul;91(7):907.
PMID: 30780410 DOI: 10.1094/PDIS-91-7-0907A

Whitefly-transmitted, cucurbit-infecting begomoviruses (genus Begomovirus, family Geminiviridae) have been detected on cucurbit crops in Bangladesh, China, Egypt, Israel, Malaysia, Mexico, the Philippines, Thailand, United States, and Vietnam. Pumpkin plants showing leaf curling, blistering, and yellowing symptoms were observed in the AVRDC fields (Tainan, Taiwan) during 2001 and in nearby farmers' fields during 2005. Two samples from symptomatic plants were collected in 2001 and six collected in 2005. Viral DNAs were extracted (2), and the PCR, with previously described primers, was used to detect the presence of begomoviral DNA-A (4), DNA-B (3), and associated satellite DNA (1). Begomoviral DNA-A was detected in one of the 2001 samples and in all 2005 samples. The PCR-amplified 1.5 kb viral DNA-A from one positive sample each from the 2001 and 2005 collections was cloned and sequenced. On the basis of the 1.5-kb DNA-A sequences, specific primers were designed to completely sequence the DNA-A component. The overlap between fragments obtained using primer walking ranged from 43 to 119 bp with 100% nt identities. The complete DNA-A sequences were determined for the two isolates as 2,734 bp (2001) (GenBank Accession No. DQ866135) and 2,733 bp (2005) (GenBank Accession No. EF199774). Sequence comparisons and analyses were performed using the DNAMAN Sequence Analysis Software (Lynnon Corporation, Vaudreuil, Quebec, Canada). The DNA-A of the begomovirus isolates each contained the conserved nanosequence-TAATATTAC and six open reading frames, including two in the virus sense and four in the complementary sense. On the basis of a 99% shared nucleotide sequence identity, they are considered isolates of the same species. BLASTn analysis and a comparison of the sequence with others available in the GenBank database ( http://www.ncbi.nlm.nih.gov ) indicated that the Taiwan virus shared its highest nt identity (more than 95%) with the Squash leaf curl Philippines virus (GenBank Accession No. AB085793). Virus-associated satellite DNA was not found in any of the samples. DNA-B was found in both samples, providing further evidence that the virus was the same as the bipartite Squash leaf curl Philippines virus. To our knowledge, this is the first report of Squash leaf curl Philippines virus in Taiwan. References: (1) R. W. Briddon et al. Virology 312:106, 2003. (2) R. L. Gilbertson et al. J. Gen. Virol. 72:2843, 1991. (3) S. K. Green et al. Plant Dis. 85:1286, 2001. (4) M. R. Rojas et al. Plant Dis. 77:340, 1993.

Matched MeSH terms: Software
A new approach for arrhythmia classification using deep coded features and LSTM networks

Yildirim O, Baloglu UB, Tan RS, Ciaccio EJ, Acharya UR

Comput Methods Programs Biomed, 2019 Jul;176:121-133.
PMID: 31200900 DOI: 10.1016/j.cmpb.2019.05.004

BACKGROUND AND OBJECTIVE: For diagnosis of arrhythmic heart problems, electrocardiogram (ECG) signals should be recorded and monitored. The long-term signal records obtained are analyzed by expert cardiologists. Devices such as the Holter monitor have limited hardware capabilities. For improved diagnostic capacity, it would be helpful to detect arrhythmic signals automatically. In this study, a novel approach is presented as a candidate solution for these issues.
METHODS: A convolutional auto-encoder (CAE) based nonlinear compression structure is implemented to reduce the signal size of arrhythmic beats. Long-short term memory (LSTM) classifiers are employed to automatically recognize arrhythmias using ECG features, which are deeply coded with the CAE network.
RESULTS: Based upon the coded ECG signals, both storage requirement and classification time were considerably reduced. In experimental studies conducted with the MIT-BIH arrhythmia database, ECG signals were compressed by an average 0.70% percentage root mean square difference (PRD) rate, and an accuracy of over 99.0% was observed.
CONCLUSIONS: One of the significant contributions of this study is that the proposed approach can significantly reduce time duration when using LSTM networks for data analysis. Thus, a novel and effective approach was proposed for both ECG signal compression, and their high-performance automatic recognition, with very low computational cost.

Matched MeSH terms: Software
Patients with congenital hypothyroidism demonstrate different altered expression of plasma fibrinogen and haptoglobin polypeptide chains

Yong PH, Junit SM, Harun F, Hashim OH

Clin Biochem, 2006 Feb;39(2):126-32.
PMID: 16412408

To compare the plasma protein profiles of treated and untreated congenital hypothyroidism (CH) patients with those of normal control infants.

Matched MeSH terms: Software
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
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
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
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

Matched MeSH terms: Software
Science stars of East Asia

Cyranoski D, Law YH, Ong S, Phillips N, Zastrow M

Nature, 2018 06;558(7711):502-510.
PMID: 29950631 DOI: 10.1038/d41586-018-05506-1
Matched MeSH terms: Speech Recognition Software*
Fulltext Allele-specific polymerase chain reaction for the detection of Alzheimer's disease-related single nucleotide polymorphisms

Darawi MN, Ai-Vyrn C, Ramasamy K, Hua PP, Pin TM, Kamaruzzaman SB, et al.

BMC Med Genet, 2013;14:27.
PMID: 23419238 DOI: 10.1186/1471-2350-14-27

The incidence of Alzheimer's disease, particularly in developing countries, is expected to increase exponentially as the population ages. Continuing research in this area is essential in order to better understand this disease and develop strategies for treatment and prevention. Genome-wide association studies have identified several loci as genetic risk factors of AD aside from apolipoprotein E such as bridging integrator (BIN1), clusterin (CLU), ATP-binding cassette sub-family A member 7 (ABCA7), complement receptor 1 (CR1) and phosphatidylinositol binding clathrin assembly protein (PICALM). However genetic research in developing countries is often limited by lack of funding and expertise. This study therefore developed and validated a simple, cost effective polymerase chain reaction based technique to determine these single nucleotide polymorphisms.

Matched MeSH terms: Software*
Computerized segmentation and measurement of chronic wound images

Ahmad Fauzi MF, Khansa I, Catignani K, Gordillo G, Sen CK, Gurcan MN

Comput Biol Med, 2015 May;60:74-85.
PMID: 25756704 DOI: 10.1016/j.compbiomed.2015.02.015

An estimated 6.5 million patients in the United States are affected by chronic wounds, with more than US$25 billion and countless hours spent annually for all aspects of chronic wound care. There is a need for an intelligent software tool to analyze wound images, characterize wound tissue composition, measure wound size, and monitor changes in wound in between visits. Performed manually, this process is very time-consuming and subject to intra- and inter-reader variability. In this work, our objective is to develop methods to segment, measure and characterize clinically presented chronic wounds from photographic images. The first step of our method is to generate a Red-Yellow-Black-White (RYKW) probability map, which then guides the segmentation process using either optimal thresholding or region growing. The red, yellow and black probability maps are designed to handle the granulation, slough and eschar tissues, respectively; while the white probability map is to detect the white label card for measurement calibration purposes. The innovative aspects of this work include defining a four-dimensional probability map specific to wound characteristics, a computationally efficient method to segment wound images utilizing the probability map, and auto-calibration of wound measurements using the content of the image. These methods were applied to 80 wound images, captured in a clinical setting at the Ohio State University Comprehensive Wound Center, with the ground truth independently generated by the consensus of at least two clinicians. While the mean inter-reader agreement between the readers varied between 67.4% and 84.3%, the computer achieved an average accuracy of 75.1%.

Matched MeSH terms: Software
Improving detection of obstructive sleep apnoea by overnight oximetry in children using pulse rate parameters

Sahadan DZ, Davey MJ, Horne RS, Nixon GM

Sleep Breath, 2015 Dec;19(4):1409-14.
PMID: 25739713 DOI: 10.1007/s11325-014-1108-4

PURPOSE: Overnight oximetry is a simple tool for investigation of obstructive sleep apnoea (OSA) in children, but only severe cases will be detected, and children with obstructive events resulting in arousal, but not desaturation, will have a normal (inconclusive) result. We hypothesised that pulse rate rises using pulse rate indices per hour (PRI) and pulse rate standard deviation (PR-SD) automatically calculated from commercially available software would improve oximetry as a diagnostic tool.
METHODS: Children having home overnight oximetry for suspected OSA were identified over 12 months, and those with a normal result who went on to have polysomnography (PSG) were included. Oximetry, including PR-SD and PRI (rises of 8, 10 and 15 beats/min per hour), was analyzed using commercially available software. PR parameters were compared between those with OSA (obstructive apnoea-hypopnoea index (OAHI) >1 event/h) and those without OSA.
RESULTS: One hundred sixteen children had normal oximetry, of whom 93 (median age 4.5 years; 55 % M) had PSG. Fifty-seven of 93 (61 %) children had OSA (median OAHI 4.5 events/h, range 1.1-24). PR-SD was not different between the OSA and non-OSA groups (p = 0.87). PRI tended to be higher in those with OSA, but there was considerable overlap between the groups: PRI-8 (mean ± SD 58.5 ± 29.0/h in OSA group vs 48.6 ± 20.2/h in non-OSA group, p = 0.07), PRI-10 (45.1 ± 25.0 vs 36.2 ± 16.7, p = 0.06) and PRI-15 (24.4 ± 14.5 vs 18.9 ± 9.0, p = 0.04). A PRI-15 threshold of >35/h had specificity of 97 % for OSA.
CONCLUSION: The PRI-15 shows promise as an indicator of OSA in children with normal oximetry.

Matched MeSH terms: Software
Fulltext Analysis of human bradykinin receptor gene and endothelial nitric oxide synthase gene polymorphisms in end-stage renal disease among malaysians

Vasudevan R, Ismail P, Jaafar N, Mohamad N, Etemad E, Wan Aliaa W, et al.

Balkan J. Med. Genet., 2014 Jun;17(1):37-40.
PMID: 25741213 DOI: 10.2478/bjmg-2014-0023

The aim of this study was to determine the association of the c.894G>T; p.Glu298Asp polymorphism and the variable number tandem repeat (VNTR) polymorphism of the endothelial nitric oxide synthase (eNOS) gene and c.181C>T polymorphism of the bradykinin type 2 receptor gene (B2R) in Malaysian end-stage renal disease (ESRD) subjects. A total of 150 ESRD patients were recruited from the National Kidney Foundation's (NKF)dialysis centers in Malaysia and compared with 150 normal healthy individuals. Genomic DNA was extracted from buccal cells of all the subjects. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was carried out to amplify the products and the restricted fragments were separated by agarose gel electrophoresis. Statistical analyses were carried out using software where a level of p <0.05 was considered to be statistically significant. The genotypic and allelic frequencies of the B2R gene (c.181C>T, 4b/a) and eNOS gene (c.894G>T) polymorphisms were not statistically significant (p >0.05) when compared to the control subjects. The B2R and eNOS gene polymorphisms may not be considered as genetic susceptibility markers for Malaysian ESRD subjects.

Matched MeSH terms: Software
Fulltext Automatic frequency controller for power amplifiers used in bio-implanted applications: issues and challenges

Hannan MA, Hussein HA, Mutashar S, Samad SA, Hussain A

Sensors (Basel), 2014;14(12):23843-70.
PMID: 25615728 DOI: 10.3390/s141223843

With the development of communication technologies, the use of wireless systems in biomedical implanted devices has become very useful. Bio-implantable devices are electronic devices which are used for treatment and monitoring brain implants, pacemakers, cochlear implants, retinal implants and so on. The inductive coupling link is used to transmit power and data between the primary and secondary sides of the biomedical implanted system, in which efficient power amplifier is very much needed to ensure the best data transmission rates and low power losses. However, the efficiency of the implanted devices depends on the circuit design, controller, load variation, changes of radio frequency coil's mutual displacement and coupling coefficients. This paper provides a comprehensive survey on various power amplifier classes and their characteristics, efficiency and controller techniques that have been used in bio-implants. The automatic frequency controller used in biomedical implants such as gate drive switching control, closed loop power control, voltage controlled oscillator, capacitor control and microcontroller frequency control have been explained. Most of these techniques keep the resonance frequency stable in transcutaneous power transfer between the external coil and the coil implanted inside the body. Detailed information including carrier frequency, power efficiency, coils displacement, power consumption, supplied voltage and CMOS chip for the controllers techniques are investigated and summarized in the provided tables. From the rigorous review, it is observed that the existing automatic frequency controller technologies are more or less can capable of performing well in the implant devices; however, the systems are still not up to the mark. Accordingly, current challenges and problems of the typical automatic frequency controller techniques for power amplifiers are illustrated, with a brief suggestions and discussion section concerning the progress of implanted device research in the future. This review will hopefully lead to increasing efforts towards the development of low powered, highly efficient, high data rate and reliable automatic frequency controllers for implanted devices.

Matched MeSH terms: Software
Fulltext In vitro porcine blood-brain barrier model for permeability studies: pCEL-X software pKa(FLUX) method for aqueous boundary layer correction and detailed data analysis

Yusof SR, Avdeef A, Abbott NJ

Eur J Pharm Sci, 2014 Dec 18;65:98-111.
PMID: 25239510 DOI: 10.1016/j.ejps.2014.09.009

In vitro blood-brain barrier (BBB) models from primary brain endothelial cells can closely resemble the in vivo BBB, offering valuable models to assay BBB functions and to screen potential central nervous system drugs. We have recently developed an in vitro BBB model using primary porcine brain endothelial cells. The model shows expression of tight junction proteins and high transendothelial electrical resistance, evidence for a restrictive paracellular pathway. Validation studies using small drug-like compounds demonstrated functional uptake and efflux transporters, showing the suitability of the model to assay drug permeability. However, one limitation of in vitro model permeability measurement is the presence of the aqueous boundary layer (ABL) resulting from inefficient stirring during the permeability assay. The ABL can be a rate-limiting step in permeation, particularly for lipophilic compounds, causing underestimation of the permeability. If the ABL effect is ignored, the permeability measured in vitro will not reflect the permeability in vivo. To address the issue, we explored the combination of in vitro permeability measurement using our porcine model with the pKa(FLUX) method in pCEL-X software to correct for the ABL effect and allow a detailed analysis of in vitro (transendothelial) permeability data, Papp. Published Papp using porcine models generated by our group and other groups are also analyzed. From the Papp, intrinsic transcellular permeability (P0) is derived by simultaneous refinement using a weighted nonlinear regression, taking into account permeability through the ABL, paracellular permeability and filter restrictions on permeation. The in vitro P0 derived for 22 compounds (35 measurements) showed good correlation with P0 derived from in situ brain perfusion data (r(2)=0.61). The analysis also gave evidence for carrier-mediated uptake of naloxone, propranolol and vinblastine. The combination of the in vitro porcine model and the software analysis provides a useful tool to better predict BBB permeability in vivo and gain better mechanistic information about BBB permeation.

Matched MeSH terms: Software
Fulltext Automatic detection and quantification of WBCs and RBCs using iterative structured circle detection algorithm

Alomari YM, Sheikh Abdullah SN, Zaharatul Azma R, Omar K

Comput Math Methods Med, 2014;2014:979302.
PMID: 24803955 DOI: 10.1155/2014/979302

Segmentation and counting of blood cells are considered as an important step that helps to extract features to diagnose some specific diseases like malaria or leukemia. The manual counting of white blood cells (WBCs) and red blood cells (RBCs) in microscopic images is an extremely tedious, time consuming, and inaccurate process. Automatic analysis will allow hematologist experts to perform faster and more accurately. The proposed method uses an iterative structured circle detection algorithm for the segmentation and counting of WBCs and RBCs. The separation of WBCs from RBCs was achieved by thresholding, and specific preprocessing steps were developed for each cell type. Counting was performed for each image using the proposed method based on modified circle detection, which automatically counted the cells. Several modifications were made to the basic (RCD) algorithm to solve the initialization problem, detecting irregular circles (cells), selecting the optimal circle from the candidate circles, determining the number of iterations in a fully dynamic way to enhance algorithm detection, and running time. The validation method used to determine segmentation accuracy was a quantitative analysis that included Precision, Recall, and F-measurement tests. The average accuracy of the proposed method was 95.3% for RBCs and 98.4% for WBCs.

Matched MeSH terms: Software
Fulltext Modeling and docking studies on novel mutants (K71L and T204V) of the ATPase domain of human heat shock 70 kDa protein 1

Elengoe A, Naser MA, Hamdan S

Int J Mol Sci, 2014;15(4):6797-814.
PMID: 24758925 DOI: 10.3390/ijms15046797

The purpose of exploring protein interactions between human adenovirus and heat shock protein 70 is to exploit a potentially synergistic interaction to enhance anti-tumoral efficacy and decrease toxicity in cancer treatment. However, the protein interaction of Hsp70 with E1A32 kDa of human adenovirus serotype 5 remains to be elucidated. In this study, two residues of ATPase domain of human heat shock 70 kDa protein 1 (PDB: 1 HJO) were mutated. 3D mutant models (K71L and T204V) using PyMol software were then constructed. The structures were evaluated by PROCHECK, ProQ, ERRAT, Verify 3D and ProSA modules. All evidence suggests that all protein models are acceptable and of good quality. The E1A32 kDa motif was retrieved from UniProt (P03255), as well as subjected to docking interaction with NBD, K71L and T204V, using the Autodock 4.2 program. The best lowest binding energy value of -9.09 kcal/mol was selected for novel T204V. Moreover, the protein-ligand complex structures were validated by RMSD, RMSF, hydrogen bonds and salt bridge analysis. This revealed that the T204V-E1A32 kDa motif complex was the most stable among all three complex structures. This study provides information about the interaction between Hsp70 and the E1A32 kDa motif, which emphasizes future perspectives to design rational drugs and vaccines in cancer therapy.

Matched MeSH terms: Software
New method for distance-based close following safety indicator

Sharizli AA, Rahizar R, Karim MR, Saifizul AA

Traffic Inj Prev, 2015;16(2):190-5.
PMID: 24827899 DOI: 10.1080/15389588.2014.921913

The increase in the number of fatalities caused by road accidents involving heavy vehicles every year has raised the level of concern and awareness on road safety in developing countries like Malaysia. Changes in the vehicle dynamic characteristics such as gross vehicle weight, travel speed, and vehicle classification will affect a heavy vehicle's braking performance and its ability to stop safely in emergency situations. As such, the aim of this study is to establish a more realistic new distance-based safety indicator called the minimum safe distance gap (MSDG), which incorporates vehicle classification (VC), speed, and gross vehicle weight (GVW).

Matched MeSH terms: Software
Skin dose measurements using radiochromic films, TLDS and ionisation chamber and comparison with Monte Carlo simulation

Alashrah S, Kandaiya S, Maalej N, El-Taher A

Radiat Prot Dosimetry, 2014 Dec;162(3):338-44.
PMID: 24300340 DOI: 10.1093/rpd/nct315

Estimation of the surface dose is very important for patients undergoing radiation therapy. The purpose of this study is to investigate the dose at the surface of a water phantom at a depth of 0.007 cm as recommended by the International Commission on Radiological Protection and International Commission on Radiation Units and Measurement with radiochromic films (RFs), thermoluminescent dosemeters and an ionisation chamber in a 6-MV photon beam. The results were compared with the theoretical calculation using Monte Carlo (MC) simulation software (MCNP5, BEAMnrc and DOSXYZnrc). The RF was calibrated by placing the films at a depth of maximum dose (d(max)) in a solid water phantom and exposing it to doses from 0 to 500 cGy. The films were scanned using a transmission high-resolution HP scanner. The optical density of the film was obtained from the red component of the RGB images using ImageJ software. The per cent surface dose (PSD) and percentage depth dose (PDD) curve were obtained by placing film pieces at the surface and at different depths in the solid water phantom. TLDs were placed at a depth of 10 cm in a solid water phantom for calibration. Then the TLDs were placed at different depths in the water phantom and were exposed to obtain the PDD. The obtained PSD and PDD values were compared with those obtained using a cylindrical ionisation chamber. The PSD was also determined using Monte Carlo simulation of a LINAC 6-MV photon beam. The extrapolation method was used to determine the PSD for all measurements. The PSD was 15.0±3.6% for RF. The TLD measurement of the PSD was 16.0±5.0%. The (0.6 cm(3)) cylindrical ionisation chamber measurement of the PSD was 50.0±3.0%. The theoretical calculation using MCNP5 and DOSXYZnrc yielded a PSD of 15.0±2.0% and 15.7±2.2%. In this study, good agreement between PSD measurements was observed using RF and TLDs with the Monte Carlo calculation. However, the cylindrical chamber measurement yielded an overestimate of the PSD. This is probably due to the ionisation chamber calibration factor that is only valid in charged particle equilibrium condition, which is not achieved at the surface in the build-up region.

Matched MeSH terms: Software
The interactive animated epilepsy education programme (IAEEP): how feasible, acceptable and practical is the technology to children?

Lua PL, Neni WS, Lee JK, Abd Aziz Z

Technol Health Care, 2013;21(6):547-56.
PMID: 24284547 DOI: 10.3233/THC-130758

Being well-informed and knowledgeable about their illnesses would be a great advantage to children with epilepsy (CWE). Subsequently, an effective education programme which could secure interest and simultaneously improve their awareness, knowledge and attitudes (AKA) is essential in enhancing well-being and health outcomes.

Matched MeSH terms: Software

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