Search results for: molecular diagnosis

Authors: Rumana Keyani, Haleema Sadia, Asia Nosheen, Rabia Naz, Humaira Yasmin, Sidra Zahoor

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Tomato is a significant crop of the world and is one of the staple foods of Pakistan. A vast number of plant pathogens from simple viruses to complex parasites cause diseases in tomatoes but fungal infection in our country is quite high. Sometimes the symptoms are too harsh destroying the crop altogether. Countries like our own with continuously increasing massive population and limited resources cannot afford such an economic loss. There is an array of morphological, genetic, biochemical and molecular processes involved in plant resistance mechanisms to biotic stress. The study of different metabolic pathways like Jasmonic acid (JA) pathways and most importantly signaling molecules like ROS/RNS and their redoxin enzymes i.e. TRX and NRX is crucial to disease management, contributing to healthy plant growth. So, improving tolerance in crop plants against biotic stresses is a dire need of our country and world as whole. In the current study, fungal pathogenic strains Alternaria solani and Rhizoctonia solani were used to inoculate tomatoes to check the defense responses of tomato plant against these pathogens at molecular as well as phenotypic level with jasmonic acid and spermidine pretreatment. All the growth parameters (root and shoot length, dry and weight root, shoot weight measured 7 days post-inoculation, exhibited that infection drastically declined the growth of the plant whereas jasmonic acid and spermidine assisted the plants to cope up with the infection. Thus, JA and Spermidine treatments maintained comparatively better growth factors. Antioxidant assays and expression analysis through real time quantitative PCR following time course experiment at 24, 48 and 72 hours intervals also exhibited that activation of JA defense genes and a polyamine Spermidine helps in mediating tomato responses against fungal infection when used alone but the two treatments combined mask the effect of each other.

Keywords: fungal infection, jasmonic acid defence, tomato, spermidine

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Authors: Mohammad Nazri Abdul Bahari, Nurshafika Mohd Sakeh, Siti Nor Akmar Abdullah

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Basal stem rot (BSR) is the most devastating disease in oil palm. Among the oil palm pathogenic fungi, the most prevalent and virulent species associated with BSR is Ganoderma boninense. Early detection of G. boninense attack in oil palm wherein physical symptoms has not yet appeared can offer opportunities to prevent the spread of the necrotrophic fungus. However, poor understanding of molecular defense responses and roles of antifungal metabolites in oil palm against G. boninense has complicated the resolving measures. Hence, characterization of defense-related molecular responses and production of antifungal compounds during early interaction with G. boninense is of utmost important. Four month-old oil palm (Elaeis guineensis) seedlings were artificially infected with G. boninense-inoculated rubber wood block via sitting technique. RNA of samples were extracted from roots and leaves tissues at 0, 3, 7 and 11 days post inoculation (d.p.i) followed with sequencing using RNA-Seq method. Differentially-expressed genes (DEGs) of oil palm-G. boninense interaction were identified, while changes in metabolite profile will be scrutinized related to the DEGs. The RNA-Seq data generated a total of 113,829,376 and 313,293,229 paired-end clean reads from untreated (0 d.p.i) and treated (3, 7, 11 d.p.i) samples respectively, each with two biological replicates. The paired-end reads were mapped to Elaeis guineensis reference genome to screen out non-oil palm genes and subsequently generated 74,794 coding sequences. DEG analysis of phytohormone biosynthetic genes in oil palm roots revealed that at p-value ≤ 0.01, ethylene and jasmonic acid may act in antagonistic manner with salicylic acid to coordinate defense response at early interaction with G. boninense. Findings on metabolite profiling of G. boninense-infected oil palm roots and leaves are hoped to explain the defense-related compounds elicited by Elaeis guineensis in response to G. boninense colonization. The study aims to shed light on molecular defense response of oil palm at early interaction with G. boninense and promote prevention measures against Ganoderma infection.

Keywords: Ganoderma boninense, metabolites, phytohormones, RNA-Seq

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Authors: Rajvir Kaur, Jeewani Anupama Ginige

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With recent trends in Big Data and advancements in Information and Communication Technologies, the healthcare industry is at the stage of its transition from clinician oriented to technology oriented. Many people around the world die of cancer because the diagnosis of disease was not done at an early stage. Nowadays, the computational methods in the form of Machine Learning (ML) are used to develop automated decision support systems that can diagnose cancer with high confidence in a timely manner. This paper aims to carry out the comparative evaluation of a selected set of ML classifiers on two existing datasets: breast cancer and cervical cancer. The ML classifiers compared in this study are Decision Tree (DT), Support Vector Machine (SVM), k-Nearest Neighbor (k-NN), Logistic Regression, Ensemble (Bagged Tree) and Artificial Neural Networks (ANN). The evaluation is carried out based on standard evaluation metrics Precision (P), Recall (R), F1-score and Accuracy. The experimental results based on the evaluation metrics show that ANN showed the highest-level accuracy (99.4%) when tested with breast cancer dataset. On the other hand, when these ML classifiers are tested with the cervical cancer dataset, Ensemble (Bagged Tree) technique gave better accuracy (93.1%) in comparison to other classifiers.

Keywords: artificial neural networks, breast cancer, classifiers, cervical cancer, f-score, machine learning, precision, recall

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Authors: Ligia Florio, João Mauricio Castaldelli-Maia

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Background: Food addiction (FA) emerged in the 1990s as a possible contributor to the increasing prevalence of obesity and overweight, in conjunction with changing food environments and mental health conditions. However, FA is not yet listed as one of the disorders in the DSM-5 and/or the ICD-11. Although there are controversies and debates in the literature about the classification and construct of FA, the most common approach to access it is the use of a research tool - the Yale Food Addiction Scale (YFAS) - which approximates the concept of FA to the concept diagnosis of dependence on psychoactive substances. There is a need to explore the dimensional phenotypes accessed by YFAS in different population groups for a better understanding and scientific support of FA diagnoses. Methods: The primary objective of this project was to investigate the construct validity of the FA concept by mYFAS 2.0 in individuals who underwent bariatric surgery (n = 100) at the Hospital Estadual Mário Covas since 2011. Statistical analyzes were conducted using the STATA software. In this sense, structural or factor validity was the type of construct validity investigated using exploratory factor analysis (EFA) and item response theory (IRT) techniques. Results: EFA showed that the one-dimensional model was the most parsimonious. The IRT showed that all criteria contributed to the latent structure, presenting discrimination values greater than 0.5, with most presenting values greater than 2. Conclusion: This study reinforces a FA dimension in patients who underwent bariatric surgery. Within this dimension, we identified the most severe and discriminating criteria for the diagnosis of FA.

Keywords: obesity, food addiction, bariatric surgery, regain

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Authors: Elmira Ghanbari, Jan Van Esch, Stephen J. Picken, Sahil Aggarwal

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Organogels are formed by the assembly of low molecular weight gelators (LMWG) into fibrous structures. The assembly of these molecules into crystalline fibrous structures occurs as a result of reversible interactions such as π-stacking, hydrogen-bonding, and van der Waals interactions. Bisamide organogelators with two amide groups have been used as one of LMWGs which show efficient assembly behavior via hydrogen bonding for network formation, the formation of a crystalline network for solvent entrapment. In this study, different bisamide gelators with different lengths of alkyl chains have been added to the bisamide parent gels. The effect of the addition of bisamide additives on the gelation of bisamide gels is described. Investigation of the thermal properties of the gels by differential scanning calorimetry and dropping ball techniques indicated that the bisamide gels can be formed by the addition of a high concentration of the second bisamide components. The microstructure of the gels with different gelator components has been visualized with scanning electron microscopy (SEM) which has shown systematic woven, platelet-like, and a combination of those morphologies for different gels. Examining the addition of a range of bisamide additives with different structural characteristics than the parent bisamide gels has confirmed the effect of the molecular structure on the morphology of the bisamide gels and their final properties.

Keywords: bisamide organogelator additives, gel morphology, gel properties, self-assembly

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Authors: Hyunsik Park

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As the rate of cerebrovascular disease increases in old populations, the prevalence rate of vascular dementia would be expected. Therefore, authors designed this study to find out the possibility of somatosensory evoked potentials(SSEP) as a parameter for early diagnosis and prognosis prediction of vascular dementia in cortical vascular dementia patients. 21 patients who met the criteria for vascular dementia according to DSM-IV,ICD-10and NINDS-AIREN with the history of recent cognitive impairment, fluctuation progression, and neurologic deficit. We subdivided these patients into two groups; a mild dementia and a severe dementia groups by MMSE and CDR score; and analysed comparison between normal control group and patient control group who have been cerebrovascular attack(CVA) history without dementia by using N20 latency and amplitude of median nerve. In this study, mild dementia group showed significant differences on latency and amplitude with normal control group(p-value<0.05) except patient control group(p-value>0.05). Severe dementia group showed significant differences both normal control group and patient control group.(p-value<0.05, <001). Since no significant difference has founded between mild dementia group and patient control group, SSEP has limitation to use for early diagnosis test. However, the comparison between severe dementia group and others showed significant results which indicate SSEP can predict the prognosis of vascular dementia in cortical vascular dementia patients.

Keywords: SSEP, cortical vascular dementia, N20 latency, N20 amplitude

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Authors: Abdulwahab Kammon, Tan Sheau Wei, Abdul Rahman Omar, Abdunaser Dayhum, Ibrahim Eldghayes, Monier Sharif

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Infectious bronchitis virus (IBV) is a very dynamic and evolving virus which causing major economic losses to the global poultry industry. Recently, the Libyan poultry industry faced severe outbreak of respiratory distress associated with high mortality and dramatic drop in egg production. Tracheal and cloacal swabs were analyzed for several poultry viruses. IBV was detected using SYBR Green I real-time PCR detection based on the nucleocapsid (N) gene. Sequence analysis of the partial N gene indicated high similarity (~ 94%) to IBV strain 3382/06 that was isolated from Taiwan. Even though the IBV strain 3382/06 is more similar to that of the Mass type H120, the isolate has been implicated associated with intertypic recombinant of 3 putative parental IBV strains namely H120, Taiwan strain 1171/92 and China strain CK/CH/LDL/97I. Complete sequencing and antigenicity studies of the Libya IBV strains are currently underway to determine the evolution of the virus and its importance in vaccine induced immunity. In this paper, we documented for the first time the presence of possibly variant IBV strain from Libya which required a dramatic change in the vaccination program.

Keywords: Libya, infectious bronchitis, molecular characterization, viruses, vaccine

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Authors: Lee Rui, Rajeev Ramachandran

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The approach to recurrent fevers in the paediatric or adolescent age group is not a straightforward one. Causes range from infectious diseases to rheumatological conditions to endocrinopathies, and are usually accompanied by weight loss rather than weight gain. We present an interesting case of a 16-year-old girl brought by her mother to the General Pediatrics Clinic for concerns of recurrent fever paired with significant weight gain over 1.5 years, with no identifiable cause found despite extensive work-up by specialists ranging from Rheumatologists to Oncologists. This case provides a learning opportunity on the approach to weight gain paired with persistent fevers in a paediatric population, one which is not commonly encountered and prompts further evaluation and consideration of less common diagnoses. In a span of 2 years, the girl’s weight had increased from 55 kg at 13 years old (75th centile) to 73.9 kg at 16 years old (>97th centile). About 1 year into her rapid weight gain, she started developing recurrent fevers of documented temperatures > 37.5 – 38.6 every 2-3 days, resulting in school absenteeism when she was sent home after temperature-taking in school found her to be febrile. The rapid onset of weight gain paired with unexplained fevers prompted the treating physician to consider the diagnosis of ROHHAD syndrome. Rapid onset obesity with hypoventilation, hypothalamic dysfunction and autonomic dysregulation (ROHHAD) syndrome is a rare disorder first described in 2007. It is characterized by dysfunction of the autonomic and endocrine system, characterized by hyperphagia and rapid-onset weight gain. This rapid weight gain is classically followed by hypothalamic manifestations with neuroendocrine deficiencies, hypo-ventilatory breathing abnormalities, and autonomic dysregulation. ROHHAD is challenging to diagnose with and diagnosis is made based mostly on clinical judgement. However if truly diagnosed, the condition is characterized by high morbidity and mortality rates. Early recognition of sleep disorders breathing and targeted therapeutic interventions helps limit morbidity and mortality associated with ROHHAD syndrome. This case poses an interesting diagnostic challenge and a diagnosis of ROHHAD has to be considered, given the serious complications that can come with disease progression while conditions such as Munchausen’s or drug fever remain as diagnoses of exclusion until we have exhausted all other possible conditions.

Keywords: pediatrics, endocrine, weight gain, recurrent fever, adolescent

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Authors: Saad Chahba, Rabia Sehab, Ahmad Akrad, Cristina Morel

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Nowadays, the electric machines used in urban electric vehicles are, in most cases, three-phase electric machines with or without a magnet in the rotor. Permanent Magnet Synchronous Machine (PMSM) and Induction Machine (IM) are the main components of drive trains of electric and hybrid vehicles. These machines have very good performance in healthy operation mode, but they are not redundant to ensure safety in faulty operation mode. Faced with the continued growth in the demand for electric vehicles in the automotive market, improving the reliability of electric vehicles is necessary over the lifecycle of the electric vehicle. Multiphase electric machines respond well to this constraint because, on the one hand, they have better robustness in the event of a breakdown (opening of a phase, opening of an arm of the power stage, intern-turn short circuit) and, on the other hand, better power density. In this work, a diagnosis approach using a neural network for an open circuit fault or more of a five-phase induction machine is developed. Validation on the simulator of the vehicle drivetrain, at reduced power, is carried out, creating one and more open circuit stator phases showing the efficiency and the reliability of the new approach to detect and to locate on-line one or more open phases of a five-induction machine.

Keywords: electric vehicle drivetrain, multiphase drives, induction machine, control, open circuit (OC) fault diagnosis, artificial neural network

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Authors: Hamza Javar Magnier, Leslie V. Woodcock

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It has been reported that at temperatures above the critical there is no “continuity of liquid and gas”, as originally hypothesized by van der Waals. Rather, both gas and liquid phases, with characteristic properties as such, extend to supercritical temperatures. Each phase is bounded by the locus of a percolation transition, i.e. a higher-order thermodynamic phase change associated with percolation of gas clusters in a large void, or liquid interstitial vacancies in a large cluster. Between these two-phase bounds, it is reported there exists a mesophase that resembles an otherwise homogeneous dispersion of gas micro-bubbles in liquid (foam) and a dispersion of liquid micro-droplets in gas (mist). Such a colloidal-like state of a pure one-component fluid represents a hitherto unchartered equilibrium state of matter besides pure solid, liquid or gas. Here we provide compelling evidence, from molecular dynamics (MD) simulations, for the existence of this supercritical mesophase and its colloidal nature. We report preliminary results of computer simulations for a model fluid using a simplistic representation of atoms or molecules, i.e. a hard-core repulsion with an attraction so short that the atoms are referred to as “adhesive spheres”. Molecular clusters, and hence percolation transitions, are unambiguously defined. Graphics of color-coded clusters show colloidal characteristics of the supercritical mesophase.

Keywords: critical phenomena, mesophase, supercritical, square-well, critical parameters

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Authors: B. Gonzalez-Yebra, H. Barajas, P. Palomares, M. Hernandez, O. Torres, M. Ayala, A. L. González, G. Vazquez-Ortiz, M. L. Guzman

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Leukemia arises by molecular alterations of the normal hematopoietic stem cell (HSC) transforming it into a leukemic stem cell (LSC) with high cell proliferation, self-renewal, and cell differentiation. Chronic myeloid leukemia (CML) originates from an LSC-leading to elevated proliferation of myeloid cells and acute lymphoblastic leukemia (ALL) originates from an LSC development leading to elevated proliferation of lymphoid cells. In both cases, LSC can be identified by multicolor flow cytometry using several antibodies. However, to date, LSC levels in peripheral blood (PB) are not established well enough in ALL and CML patients. On the other hand, the detection of the minimal residue disease (MRD) in leukemia is mainly based on the identification of the mRNA bcr-abl gene in CML patients and some other genes in ALL patients. There is no a properly biomarker to detect MDR in both types of leukemia. The objective of this study was to determine mRNA bcr-abl and the percentage of LSC in peripheral blood of patients with CML and ALL and identify a possible association between the amount of LSC in PB and clinical data. We included in this study 19 patients with Leukemia. A PB sample was collected per patient and leukocytes were obtained by Ficoll gradient. The immunophenotype for LSC CD34+ was done by flow cytometry analysis with CD33, CD2, CD14, CD16, CD64, HLA-DR, CD13, CD15, CD19, CD10, CD20, CD34, CD38, CD71, CD90, CD117, CD123 monoclonal antibodies. In addition, to identify the presence of the mRNA bcr-abl by RT-PCR, the RNA was isolated using TRIZOL reagent. Molecular (presence of mRNA bcr-abl and LSC CD34+) and clinical results were analyzed with descriptive statistics and a multiple regression analysis was performed to determine statistically significant association. In total, 19 patients (8 patients with ALL and 11 patients with CML) were analyzed, 9 patients with de novo leukemia (ALL = 6 and CML = 3) and 10 under treatment (ALL = 5 and CML = 5). The overall frequency of mRNA bcr-abl was 31% (6/19), and it was negative in ALL patients and positive in 80% in CML patients. On the other hand, LSC was determined in 16/19 leukemia patients (%LSC= 0.02-17.3). The Novo patients had higher percentage of LSC (0.26 to 17.3%) than patients under treatment (0 to 5.93%). The amount of LSC was significantly associated with the amount of LSC were: absence of treatment, the absence of splenomegaly, and a lower number of leukocytes, negative association for the clinical variables age, sex, blasts, and mRNA bcr-abl. In conclusion, patients with de novo leukemia had a higher percentage of circulating LSC than patients under treatment, and it was associated with clinical parameters as lack of treatment, absence of splenomegaly and a lower number of leukocytes. The mRNA bcr-abl detection was only possible in the series of patients with CML, and molecular detection of LSC could be identified in the peripheral blood of all leukemia patients, we believe the identification of circulating LSC may be used as biomarker for the detection of the MRD in leukemia patients.

Keywords: stem cells, leukemia, biomarkers, flow cytometry

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Authors: Abu Salim Mustafa

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The comparisons of mycobacterial genomes have identified several Mycobacterium tuberculosis-specific genomic regions that are absent in other mycobacteria and are known as regions of differences. Due to M. tuberculosis-specificity, the peptides encoded by these regions could be useful in the specific diagnosis of tuberculosis. To explore this possibility, overlapping synthetic peptides corresponding to 39 proteins predicted to be encoded by genes present in regions of differences were tested for antibody-reactivity with sera from tuberculosis patients and healthy subjects. The results identified four immunodominant peptides corresponding to four different proteins, with three of the peptides showing significantly stronger antibody reactivity and rate of positivity with sera from tuberculosis patients than healthy subjects. The fourth peptide was recognized equally well by the sera of tuberculosis patients as well as healthy subjects. Predication of antibody epitopes by bioinformatics analyses using ABCpred server predicted multiple linear epitopes in each peptide. Furthermore, peptide sequence analysis for sequence identity using BLAST suggested M. tuberculosis-specificity for the three peptides that had preferential reactivity with sera from tuberculosis patients, but the peptide with equal reactivity with sera of TB patients and healthy subjects showed significant identity with sequences present in nob-tuberculous mycobacteria. The three identified M. tuberculosis-specific immunodominant peptides may be useful in the serological diagnosis of tuberculosis.

Keywords: genomic regions of differences, Mycobacterium tuberculossis, peptides, serodiagnosis

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Authors: Seyed Hassan Moosa-kazemi, Jalal Mohammadi Soleimani, Hassan Vatandoost, Mohammad Hassan Shirazi, Sara Hajikhani, Roonak Bakhtiari, Morteza Akbari, Siamak Hydarzadeh

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Malaria is an infectious disease and considered most important health problems in the southeast of Iran. Iran is elimination malaria phase and new tool need to vector control. Paraterasgenesis is a new way to cut of life cycle of the malaria parasite. In this study, the microflora of the surface and gut of various stages of Anopheles fluviatilis James as one of the important malaria vector was studied using biochemical and molecular techniques during 2013-2014. Twelve bacteria species were found including; Providencia rettgeri, Morganella morganii, Enterobacter aerogenes, Pseudomonas oryzihabitans, Citrobacter braakii، Citrobacter freundii، Aeromonas hydrophila، Klebsiella oxytoca, Citrobacter koseri, Serratia fonticola، Enterobacter sakazakii and Yersinia pseudotuberculosis. The species of Alcaligenes faecalis, Providencia vermicola and Enterobacter hormaechei were identified in various stages of the vector and confirmed by biochemical and molecular techniques. We found Providencia rettgeri proper candidate for paratransgenesis.

Keywords: Anopheles fluviatilis, bacteria, malaria, Paraterasgenesis, Southern Iran

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Authors: Rubina Ghani, Sehrish Zia, Afifa Fatima Rafique, Shaista Emad

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Background: Cancer is a leading cause of death worldwide, with breast cancer being the most common cancer in women. Pakistan has the highest rate of breast cancer cases among Asian countries. Early and accurate diagnosis is crucial for treatment outcomes and quality of life. Method: It is a case-control study with a sample size of 150. There were 100 suspected cancer cases, 25 healthy controls, and 25 diagnosed cancer cases. To analyze SSAT-1 mRNA expression in whole blood, Zymo Research Quick-RNA Miniprep and Innu SCRIPT—One Step RT-PCR Syber Green kits were used. Patients were divided into three groups: 100 suspected cancer cases, 25 controls, and 25 confirmed breast cancer cases. Result: The total mRNA was isolated, and the expression of SSAT-1 was measured using RT-qPCR. The threshold cycle (Ct) values were used to determine the amount of each mRNA. Ct values were then calculated by taking the difference between the CtSSAT-1 and Ct GAPDH, and further Ct values were calculated with the median absolute deviation for all the samples within the same experimental group. Samples that did not correlate with the results were taken as outliers and excluded from the analysis. The relative fold change is shown as 2^-Ct values. Suspected cases showed a maximum fold change of 32.24, with a control fold change of 1.31. Conclusion: The study reveals an overexpression of SSAT-1 in breast cancer. Furthermore, we can use SSAT-1 as a diagnostic, prognostic, and therapeutic marker for early diagnosis of cancer.

Keywords: breast cancer, spermidine/spermine, qPCR, mRNA

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Authors: Viacheslav Sushko, Viktor Sushko

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Pre-cancerous breast diseases are pathological changes that precede the appearance of adenocarcinoma. The most common benign breast disease is mastopathy. We examined the life and disease history of 114 women aged 58-69 who were diagnosed with adenocarcinoma of the breast at different stages of development. They filled out the Reeder Scale to determine the level of stress. The results of the study revealed that 62 of them had mastopathy at the age of 30-45 years old. These women refused surgical treatment for mastopathy. Five to six years before their diagnosis of adenocarcinoma of the mammary gland, 84 women had experienced severe stress (death of a beloved close relative, torture accompanied by rape, prolonged stay in extreme conditions (under bombardment and bombardment). In the assessment of data from completed Reeder scales, 114 women had a high level of mental stress, with a score from 1-1.72. The 84 women who suffered from severe stress showed overeating or a significant decrease in food intake, insomnia, apathy, increased irritability and restlessness, loss of interest in sexual relationships, forgetfulness, difficulty in performing routine work, prolonged uncontrollable headaches, unexplained fatigue, heart pain, reduced capacity for work. In conclusion, it is important to provide psychotherapy for breast cancer patients as the diagnosis, and the different stages of treatment are very stressful. It is also advisable to see a psychiatrist at an early stage and prevent distress and treat precancerous breast disease.

Keywords: breast cancer, distress, mastopathy, severe stress

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Authors: Thangaraj Arasakumar, Athar Ata, Palathurai Subramaniam Mohan

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A series of novel 4-quinolone-3-carboxylic acid grafted spiropyrrolidines as new type of antibacterial agents were synthesized via multicomponent 1,3-dipolar cycloaddition reaction of an azomethine ylides with a newly prepared (E)-4-oxo-6-(3-phenyl-acryloyl)-1,4-dihydro-quinoline-3-carboxylic acids in high regioselectivity with good yields. The structure of cycloadduct characterized by FT IR, mass, 1H, 13C, 2D NMR techniques and elemental analysis. Structure and spectrometry of compound 8a has been investigated theoretically by using HF and DFT approach at B3LYP, M05-2x/6-31G* levels of theories. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. A good agreement is found between the measured and calculated values. The DFT studies support the molecular mechanism of this cycloaddition reaction and determine the molecular electrostatic potential and thermodynamic properties. Furthermore, the antibacterial activities of synthesized compounds were evaluated against Gram-positive bacteria (Staphylococcus aureus, Bacillus subtilis) and Gram-negative bacteria strains (Escherichia coli, Klebsiella pneumoniae). Among 21 compounds screened, 8f and 8p were found to be more active against tested bacteria.

Keywords: antibacterial activity, azomethine ylide, DFT calculation, spirooxindole

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Authors: S. Taghavi Kalajahi, A. Koerdt, T. Lund Skovhus

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Cathodic protection (CP) is an electrochemical method to control and manage corrosion in different industries and environments. CP which is widely used, especially in buried and sub-merged environments, which both environments are susceptible to microbiologically influenced corrosion (MIC). Most of the standards recommend performing CP using -800 mV, however, if MIC threats are high or sulfate reducing bacteria (SRB) is present, the recommendation is to use more negative potentials for adequate protection of the metal. Due to the lack of knowledge and research on the effectiveness of CP on MIC, to the author’s best knowledge, there is no information about what MIC threat is and how much more negative potentials should be used enabling adequate protection and not overprotection (due to hydrogen embrittlement risk). Recently, the development and cheaper price of molecular microbial methods (MMMs) open the door for more effective investigations on the corrosion in the presence of microorganisms, along with other electrochemical methods and surface analysis. In this work, using MMMs, the gene expression of SRB biofilm under different potentials of CP will be investigated. The specific genes, such as pH buffering, metal oxidizing, etc., will be compared at different potentials, enabling to determine the precise potential that protect the metal effectively from SRB. This work is the initial step to be able to standardize the recommended potential under MIC condition, resulting better protection for the infrastructures.

Keywords: cathodic protection, microbiologically influenced corrosion, molecular microbial methods, sulfate reducing bacteria

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Authors: El-Sohaimy Sobhy A., Androsova Natalia, Toshev Abuvali Djabarovec

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The conditions of the isolation of proteins from the hemp seeds were optimized in the current work. Moreover, the physicochemical and functional properties of hemp protein isolate were evaluated for its potential application in food manufacturing. The elastin protein is the most predominant protein in the protein profile with a molecular weight of 58.1 KDa, besides albumin, with a molecular weight of 31.5 KDa. The FTIR spectrum detected the absorption peaks of the amide I in 1750 and 1600 cm⁻¹, which pointed to C=O stretching while N-H was stretching at 1650-1580 cm⁻¹. The peak at 3250 was related to N-H stretching of primary aliphatic amine (3400-3300 cm⁻¹), and the N-H stretching for secondary (II) amine appeared at 3350-3310 cm⁻¹. Hemp protein isolate (HPI) was showed high content of arginine (15.52 g/100 g), phenylalanine+tyrosine (9.63 g/100 g), methionine + cysteine (5.49 g/100 g), leucine + isoleucine (5.21 g/100 g) and valine (4.53 g/100 g). It contains a moderate level of threonine (3.29 g/100 g) and lysine (2.50 g/100 g), with the limiting amino acid being a tryptophan (0.22 g/100 g HPI). HPI showed high water-holding capacity (4.5 ± 2.95 ml/g protein) and oil holding capacity (2.33 ± 1.88 ml/g) values. The foaming capacity of HPI was increased with increasing the pH values to reach the maximum value at pH 11 (67.23±3.20 %). The highest emulsion ability index of HPI was noted at pH 9 (91.3±2.57 m2/g) with low stability (19.15±2.03).

Keywords: Cannabis sativa ssp., protein isolate, isolation conditions, amino acid composition, chemical properties, functional properties

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Authors: Beata Lachtara, Renata Szewczyk, Katarzyna Bielinska, Kinga Wieczorek, Jacek Osek

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Listeria monocytogenes is an important human and animal pathogen that causes foodborne outbreaks. The bacteria may be present in different types of food: cheese, raw vegetables, sliced meat products and vacuum-packed sausages, poultry, meat, fish. The most common method, which has been used for the investigation of genetic diversity of L. monocytogenes, is PFGE. This technique is reliable and reproducible and established as gold standard for typing of L. monocytogenes. The aim of the study was characterization by molecular serotyping and PFGE analysis of L. monocytogenes strains isolated from fresh fish and fish products in Poland. A total of 301 samples, including fresh fish (n = 129) and fish products (n = 172) were, collected between January 2014 and March 2016. The bacteria were detected using the ISO 11290-1 standard method. Molecular serotyping was performed with PCR. The isolates were tested with the PFGE method according to the protocol developed by the European Union Reference Laboratory for L. monocytogenes with some modifications. Based on the PFGE profiles, two dendrograms were generated for strains digested separately with two restriction enzymes: AscI and ApaI. Analysis of the fingerprint profiles was performed using Bionumerics software version 6.6 (Applied Maths, Belgium). The 95% of similarity was applied to differentiate the PFGE pulsotypes. The study revealed that 57 of 301 (18.9%) samples were positive for L. monocytogenes. The bacteria were identified in 29 (50.9%) ready-to-eat fish products and in 28 (49.1%) fresh fish. It was found that 40 (70.2%) strains were of serotype 1/2a, 14 (24.6%) 1/2b, two (4.3%) 4b and one (1.8%) 1/2c. Serotypes 1/2a, 1/2b, and 4b were presented with the same frequency in both categories of food, whereas serotype 1/2c was detected only in fresh fish. The PFGE analysis with AscI demonstrated 43 different pulsotypes; among them 33 (76.7%) were represented by only one strain. The remaining 10 profiles contained more than one isolate. Among them 8 pulsotypes comprised of two L. monocytogenes isolates, one profile of three isolates and one restriction type of 5 strains. In case of ApaI typing, the PFGE analysis showed 27 different pulsotypes including 17 (63.0%) types represented by only one strain. Ten (37.0%) clusters contained more than one strain among which four profiles covered two strains; three had three isolates, one with five strains, one with eight strains and one with ten isolates. It was observed that the isolates assigned to the same PFGE type were usually of the same serotype (1/2a or 1/2b). The majority of the clusters had strains of both sources (fresh fish and fish products) isolated at different time. Most of the strains grouped in one cluster of the AscI restriction was assigned to the same groups in ApaI investigation. In conclusion, PFGE used in the study showed a high genetic diversity among L. monocytogenes. The strains were grouped into varied clonal clusters, which may suggest different sources of contamination. The results demonstrated that 1/2a serotype was the most common among isolates from fresh fish and fish products in Poland.

Keywords: Listeria monocytogenes, molecular characteristic, PFGE, serotyping

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Authors: Shama Ranjan Barua, Tofazzal M. Rakib, Mohammad Alamgir Hossain, Tania Ferdushy, Sharmin Chowdhury

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Rotavirus is one of the main etiologies of neonatal diarrhea in bovine calves that causes significant economic loss in Bangladesh. The present study was carried out to investigate the pathology of neonatal enteritis in calves due to bovine rotavirus infection in south-eastern part of Bangladesh. Rotavirus was identified by using ELISA, RT-PCR (Reverse Transcription Polymerase Chain Reaction), real-time RT-PCR. We examined 12 dead calves with history of diarrhea during necropsy. Among 12 dead calves, in gross examination, 6 were found with pathological changes in intestine, 5 calves had congestion of small intestine and rest one had no distinct pathological changes. Intestinal contents and/or faecal samples of all dead calves were collected and examined to confirm the presence of bovine rotavirus A using Enzyme linked immunosorbant assay (ELISA), RT-PCR and real-time RT-PCR. Out 12 samples, 5 (42%) samples revealed presence of bovine rotavirus A in three diagnostic tests. The histopathological changes were found almost exclusively limited in the small intestine. The lesions of rotaviral enteritis ranged from slight to moderate shortening (atrophy) of villi in the jejunum and ileum with necrotic crypts. The villi were blunt and covered by immature epithelial cells. Infected cells, stained with Haematoxylin and Eosin staining method, showed characteristic syncytia and eosinophilc intracytoplasmic inclusion body. The presence of intracytoplasmic inclusion bodies in enterocytes is the indication of viral etiology. The presence of rotavirus in the affected tissues and/or lesions was confirmed by three different immunological and molecular tests. The findings of histopathological changes will be helpful in future diagnosis of rotaviral infection in dead calves.

Keywords: calves, diarrhea, pathology, rotavirus

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Authors: Purva Mishra, Rajesh Potlia, Kuljeet Singh Sandhu

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The role of glycyl residues in the protein structure has lingered within the research community for the last several decades. Glycyl residue is the only amino acid that is achiral due to the lack of a side chain and can, therefore, exhibit Ramachandran conformations that are disallowed for L-amino acids. The structural and functional significance of glycyl residues with L-disallowed conformation, however, remains obscure. Through statistical analysis of various datasets, we found that the glycyls with L-disallowed conformations are over-represented at disease-associated sites and tend to be evolutionarily conserved. The mutations of L-disallowed glycyls tend to destabilize the native conformation, reduce protein solubility, and promote inter-molecular aggregations. We uncovered a structural motif referred to as “β-crescent” formed around the L-disallowed glycyl, which prevents β-sheet aggregation by disrupting the alternating pattern of β-pleats. The L-disallowed conformation of glycyls also holds predictive power to infer the pathogenic missense variants. Altogether, our observations highlight that the L-disallowed conformation of glycyls is selected to facilitate native folding and prevent inter-molecular aggregations. The findings may also have implications for designing more stable proteins and prioritizing the genetic lesions implicated in diseases.

Keywords: Ramachandran plot, β-sheet, protein stability, protein aggregation

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Authors: L. I. Izhar, T. Stathaki, K. Howell

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Analyzing and interpreting of thermograms have been increasingly employed in the diagnosis and monitoring of diseases thanks to its non-invasive, non-harmful nature and low cost. In this paper, a novel system is proposed to improve diagnosis and monitoring of morphoea skin disorder based on integration with the published lines of Blaschko. In the proposed system, image registration based on global and local registration methods are found inevitable. This paper presents a modified normalized gradient cross-correlation (NGC) method to reduce large geometrical differences between two multimodal images that are represented by smooth gray edge maps is proposed for the global registration approach. This method is improved further by incorporating an iterative-based normalized cross-correlation coefficient (NCC) method. It is found that by replacing the final registration part of the NGC method where translational differences are solved in the spatial Fourier domain with the NCC method performed in the spatial domain, the performance and robustness of the NGC method can be greatly improved. It is shown in this paper that the hybrid NGC method not only outperforms phase correlation (PC) method but also improved misregistration due to translation, suffered by the modified NGC method alone for thermograms with ill-defined jawline. This also demonstrates that by using the gradients of the gray edge maps and a hybrid technique, the performance of the PC based image registration method can be greatly improved.

Keywords: Blaschko’s lines, image registration, morphoea, thermal imaging

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Authors: Arabi Abderrazak, Bourouba Nacerdine, Ayad Mouloud, Belaout Abdeslam

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In this paper, a new test technique of analog circuits using time mode simulation is proposed for the single catastrophic faults detection in analog circuits. This test process is performed to overcome the problem of catastrophic faults being escaped in a DC mode test applied to the inverter amplifier in previous research works. The circuit under test is a second-order low pass filter constructed around this type of amplifier but performing a function that differs from that of the previous test. The test approach performed in this work is based on two key- elements where the first one concerns the unique square pulse signal selected as an input vector test signal to stimulate the fault effect at the circuit output response. The second element is the filter response conversion to a square pulses sequence obtained from an analog comparator. This signal conversion is achieved through a fixed reference threshold voltage of this comparison circuit. The measurement of the three first response signal pulses durations is regarded as fault effect detection parameter on one hand, and as a fault signature helping to hence fully establish an analog circuit fault diagnosis on another hand. The results obtained so far are very promising since the approach has lifted up the fault coverage ratio in both modes to over 90% and has revealed the harmful side of faults that has been masked in a DC mode test.

Keywords: analog circuits, analog faults diagnosis, catastrophic faults, fault detection

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Authors: Hamidreza Akbari

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In this paper, for detection of inclined eccentricity in an induction motor, time–frequency analysis of the stator startup current is carried out. For this purpose, the discrete wavelet transform is used. Data are obtained from simulations, using winding function approach. The results show the validity of the approach for detecting the fault and discriminating with respect to other faults.

Keywords: induction machine, fault, DWT, electric

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Authors: Mbonigaba Swale

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Malaria is an infection or disease caused by parasites (Plasmodium Falciparum — causes severe Malaria, plasmodium Vivax, Plasmodium Ovale, and Plasmodium Malariae), transmitted by bites of infected anopheles (female) mosquitoes to humans. These vectors comprise of two types in Africa, particularly in Uganda, i.e. anopheles fenestus and Anopheles gambaie (‘example Anopheles arabiensis,,); feeds on man inside the house mainly at dusk, mid-night and dawn and rests indoors and makes them effective transmitters (vectors) of the disease. People in both urban and rural areas have consistently become prone to repetitive attacks of malaria, causing a lot of deaths and significantly increasing the poverty levels of the rural poor. Malaria is a national problem; it causes a lot of maternal pre-natal and antenatal disorders, anemia in pregnant mothers, low birth weights for the newly born, convulsions and epilepsy among the infants. Cumulatively, it kills about one million children every year in sub-Saharan Africa. It has been estimated to account for 25-35% of all outpatient visits, 20-45% of acute hospital admissions and 15-35% of hospital deaths. Uganda is the leading victim country, for which Rakai and Masaka districts are the most affected. So, it is not clear whether these abhorrent situations and episodes of recurrences and failure to cure from the disease are a result of poor diagnosis, prescription and dosing, treatment habits and compliance of the patients to the drugs or the ethical domain of the stake holders in relation to the main stream methodology of malaria management. The research is aimed at offering an alternative approach to manage and deal absolutely with problem by using a knowledge based software model of Artificial Intelligence (Al) that is capable of performing common-sense and cognitive reasoning so as to take decisions like the human brain would do to provide instantaneous expert solutions so as to avoid speculative simulation of the problem during differential diagnosis in the most accurate and literal inferential aspect. This system will assist physicians in many kinds of medical diagnosis, prescribing treatments and doses, and in monitoring patient responses, basing on the body weight and age group of the patient, it will be able to provide instantaneous and timely information options, alternative ways and approaches to influence decision making during case analysis. The computerized system approach, a new model in Uganda termed as “Software Aided Treatment” (SAT) will try to change the moral and ethical approach and influence conduct so as to improve the skills, experience and values (social and ethical) in the administration and management of the disease and drugs (combination therapy and generics) by both the patient and the health worker.

Keywords: knowledge based software, management, treatment, diagnosis

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Authors: Chandu Rathnayake, Isuri Anuradha

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Early detection and accurate diagnosis of lung diseases play a crucial role in improving patient prognosis. However, conventional diagnostic methods heavily rely on subjective symptom assessments and medical imaging, often causing delays in diagnosis and treatment. To overcome this challenge, we propose a novel lung disease prediction system that integrates patient symptoms and X-ray images to provide a comprehensive and reliable diagnosis.In this project, develop a mobile application specifically designed for detecting lung diseases. Our application leverages both patient symptoms and X-ray images to facilitate diagnosis. By combining these two sources of information, our application delivers a more accurate and comprehensive assessment of the patient's condition, minimizing the risk of misdiagnosis. Our primary aim is to create a user-friendly and accessible tool, particularly important given the current circumstances where many patients face limitations in visiting healthcare facilities. To achieve this, we employ several state-of-the-art algorithms. Firstly, the Decision Tree algorithm is utilized for efficient symptom-based classification. It analyzes patient symptoms and creates a tree-like model to predict the presence of specific lung diseases. Secondly, we employ the Random Forest algorithm, which enhances predictive power by aggregating multiple decision trees. This ensemble technique improves the accuracy and robustness of the diagnosis. Furthermore, we incorporate a deep learning model using Convolutional Neural Network (CNN) with the RestNet50 pre-trained model. CNNs are well-suited for image analysis and feature extraction. By training CNN on a large dataset of X-ray images, it learns to identify patterns and features indicative of lung diseases. The RestNet50 architecture, known for its excellent performance in image recognition tasks, enhances the efficiency and accuracy of our deep learning model. By combining the outputs of the decision tree-based algorithms and the deep learning model, our mobile application generates a comprehensive lung disease prediction. The application provides users with an intuitive interface to input their symptoms and upload X-ray images for analysis. The prediction generated by the system offers valuable insights into the likelihood of various lung diseases, enabling individuals to take appropriate actions and seek timely medical attention. Our proposed mobile application has significant potential to address the rising prevalence of lung diseases, particularly among young individuals with smoking addictions. By providing a quick and user-friendly approach to assessing lung health, our application empowers individuals to monitor their well-being conveniently. This solution also offers immense value in the context of limited access to healthcare facilities, enabling timely detection and intervention. In conclusion, our research presents a comprehensive lung disease prediction system that combines patient symptoms and X-ray images using advanced algorithms. By developing a mobile application, we provide an accessible tool for individuals to assess their lung health conveniently. This solution has the potential to make a significant impact on the early detection and management of lung diseases, benefiting both patients and healthcare providers.

Keywords: CNN, random forest, decision tree, machine learning, deep learning

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Authors: Aulanni’am Aulanni’am

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Incidence of Diabetes Mellitus (DM) progressively increasing it became a serious problem in Indonesia and it is a disease that government is priority to be addressed. The longer a person is suffering from diabetes the more likely to develop complications particularly diabetic patients who are not well maintained. Therefore, Incidence of Diabetes Mellitus needs to be done in the early diagnosis of pre-phase of the disease. In this pre-phase disease, already happening destruction of pancreatic beta cells and declining in beta cell function and the sign autoimmunity reactions associated with beta cell destruction. Type 1 DM is a multifactorial disease triggered by genetic and environmental factors, which leads to the destruction of pancreatic beta cells. Early marker of "beta cell autoreactivity" is the synthesis of autoantibodies against 65-kDa protein, which can be a molecule that can be detected early in the disease pathomechanism. The importance of early diagnosis of diabetic patients held in the phase of pre-disease is to determine the progression towards the onset of pancreatic beta cell destruction and take precautions. However, the price for this examination is very expensive ($ 150/ test), the anti-GAD65 abs examination cannot be carried out routinely in most or even in all laboratories in Indonesia. Therefore, production-based Rapid Test Recombinant Human Protein GAD65 with "Reverse Flow Immunchromatography Technique" in Indonesia is believed to reduce costs and improve the quality of care of patients with diabetes in Indonesia. Rapid Test Product innovation is very simple and suitable for screening and routine inspection of GAD65 autoantibodies. In the blood serum of patients with diabetes caused by autoimmunity, autoantibody-GAD65 is a major serologic marker to detect autoimmune reaction because their concentration level of stability.GAD65 autoantibodies can be found 10 years before clinical symptoms of diabetes. Early diagnosis is more focused to detect the presence autontibodi-GAD65 given specification and high sensitivity. Autoantibodies- GAD65 that circulates in the blood is a major indicator of the destruction of the islet cells of the pancreas. Results of research in collaboration with Biofarma has produced GAD65 autoantibodies based Rapid Test had conducted the soft launch of products and has been tested with the results of a sensitivity of 100 percent and a specificity between 90 and 96% compared with the gold standard (import product) which worked based on ELISA method.

Keywords: diabetes mellitus, GAD65 autoantibodies, rapid test, sensitivity, specificity

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Authors: Yasser Gaber, Mohamed Ismail, Serena Bisagni, Mohamad Takwa, Rajni Hatti-Kaul

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Enzymes are safe and selective catalysts. They skillfully catalyze chemical reactions; however, the native form is not usually suitable for industrial applications. Enzymes are therefore engineered by several techniques to meet the required catalytic task. Clopidogrel is recorded among the five best selling pharmaceutical in 2010 under the brand name Plavix. The commonly used route for production of the drug on an industrial scale is the synthesis of the racemic mixture followed by diastereomeric resolution to obtain the pure S isomer. The process consumes a lot of solvents and chemicals. We have evaluated a biocatalytic cleaner approach for asymmetric hydrolysis of racemic clopidogrel. Initial screening of a selected number of hydrolases showed only one enzyme EST to exhibit activity and selectivity towards the desired stereoisomer. As the crude EST is a mixture of several isoenzymes, a homology model of EST-1 was used in molecular dynamic simulations to study the interaction of the enzyme with R and S isomers of clopidogrel. Analysis of the geometric hindrances of the tetrahedral intermediates revealed a potential site for mutagenesis in order to improve the activity and the selectivity. Single point mutation showed dramatic increase in activity and inversion of the enantioselectivity (400 fold change in E value).

Keywords: biocatalysis, biotechnology, enzyme, protein engineering, molecular modeling

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Authors: Margarita S. Tikhonova, Alireza Baniasad, Anton G. Kalmykov, Georgy A. Kalmykov, Ralf Littke

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There is a high complexity in the pore structure of organic-rich rocks caused by the combination of inter-particle porosity from inorganic mineral matter and ultrafine intra-particle porosity from both organic matter and clay minerals. Fluids are retained in that pore space, but there are major uncertainties in how and where the fluids are stored and to what extent they are accessible or trapped in 'closed' pores. A large degree of tortuosity may lead to fractionation of organic matter so that the lighter and flexible compounds would diffuse to the reservoir whereas more complicated compounds may be locked in place. Additionally, parts of hydrocarbons could be bound to solid organic matter –kerogen– and mineral matrix during expulsion and migration. Larger compounds can occupy thin channels so that clogging or oil and gas entrapment will occur. Sequential extraction of applying different solvents is a powerful tool to provide more information about the characteristics of trapped organic matter distribution. The Upper Jurassic – Lower Cretaceous Bazhenov shale is one of the most petroliferous source rock extended in West Siberia, Russia. Concerning the variable mineral composition, pore space distribution and thermal maturation, there are high uncertainties in distribution and composition of organic matter in this formation. In order to address this issue geological and geochemical properties of 30 samples including mineral composition (XRD and XRF), structure and texture (thin-section microscopy), organic matter contents, type and thermal maturity (Rock-Eval) as well as molecular composition (GC-FID and GC-MS) of different extracted materials during sequential extraction were considered. Sequential extraction was performed by a Soxhlet apparatus using different solvents, i.e., n-hexane, chloroform and ethanol-benzene (1:1 v:v) first on core plugs and later on pulverized materials. The results indicate that the studied samples are mainly composed of type II kerogen with TOC contents varied from 5 to 25%. The thermal maturity ranged from immature to late oil window. Whereas clay contents decreased with increasing maturity, the amount of silica increased in the studied samples. According to molecular geochemistry, stored hydrocarbons in open and closed pore space reveal different geochemical fingerprints. The results improve our understanding of hydrocarbon expulsion and migration in the organic-rich Bazhenov shale and therefore better estimation of hydrocarbon potential for this formation.

Keywords: Bazhenov formation, bitumen, molecular geochemistry, sequential extraction

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Authors: S. M. Dankaka, N. Abdullahi

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Context: This research was conducted to isolate and identify phenol-tolerant bacteria from petroleum-contaminated sites in the northwestern part of Nigeria. Research Aim: The aim of this study was to identify bacteria with the ability to tolerate different phenol concentrations. Methodology: Samples were obtained from different petroleum-contaminated sites, and bacteria were cultured, followed by morphological, microscopic, and molecular identification. Isolates were grown on phenol-tolerant nutrient agar. The tolerant ability of the isolates was observed at 500 mg/L, 1000 mg/L, and 1500 mg/L concentrations of phenol. Findings: Two bacteria species (NWPK and NWPKD) were obtained. The total viable counts of phenol-utilizing bacteria from NWPK and NWPKD were 2.71x10⁷ and 4.0x10⁶ cfu/g, respectively. The NWPK showed its capacity to tolerate phenol at 2.3x10⁷, 2.5x10⁷, and 1.0x10⁷ cfu/g of 500, 1000, and 1500 mg/L of phenol concentration, respectively, while NWPKD tolerance ability was 1.5x10⁷, 3.8x10⁷ and 1.0x10⁷ cfu/g of 500, 1000 and 1500 mg/L of phenol respectively. The isolates were identified as Citrobacter and Acinetobacter species, respectively, based on 16S rRNA gene sequence analysis. Conclusion: The study found that these isolates showed the ability to withstand and survive high phenol concentrations in the environment.

Keywords: phenol tolerance, bacteria, petroleum contaminated sites, 16S rRNA

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