Search results for: Breast cancer genes

Authors: Ryeong-Hyeon Kim, Ah-Reum Lee, Seong-Soo Roh, Gyo-Nam Kim

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Appropriate regulation of melanogenesis is important for the management of skin pigmentation-related disease. Although several beneficial effects of fisetin (3,7,3’,4’-tetrahydroxyflavone) have been reported, the precise role and molecular mechanisms of fisetin in skin health both remain unclear. Here, we induced melanogenesis of HRM2 mice (n=7/group) by UVB irradiation for 20 days. UVB-induced HRM2 mice showed that the significantly increased melanin accumulation, however, fisetin treatment (25mg and 50mg/kg of body weight) dose-dependently and significantly inhibits UVB-induced melanogenesis. In line with this, fisetin treatment effectively down-regulated m RNA and expression levels of tyrosinase, TRP2, and MITF. In addition, our inhibitor assay revealed the down-regulated melanogenic marker genes by fisetin treatment were mediated with connective tissue growth factor (CCN2)/TGF-β signaling pathway. Useful information is provided for development of functional foods using fisetin for skin health.

Keywords: connective tissue growth factor, fisetin, melanogenesis, skin, TGF-beta

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Authors: Chamin Chimyang

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The fast-changing global trend and declining forest region have impacted agricultural lands; animals, especially birds, might become one of the major pests in the near future and go neglected or unreported in many kinds of literature and events, which is mainly because of bird infestation being a pocket-zone problem. This bird infestation can be attributed to the balding of the forest region and the decline in their foraging hotspot due to anthropogenic activity. There are many ways to keep away the birds from agricultural fields, both conventional and non-conventional. But the question here is whether the traditional approach of bird scarring methods such as scare-crows are effective enough. There are many traits in rice that are supposed to keep the birds away from foraging in paddy fields, and the selection of such traits might be rewarding, such as the angle of the flag leaf from the stem, grain size, novelty of any trait in that particular region and also an awning. Awning, as such, is a very particular trait on which negative selection was imposed to such an extent that there has been a decline in the nucleotide responsible for the said trait. Thus, in this particular session, histology, genetics, genes behind the trait and how awns might be one of the solutions to the problem stated above will be discussed in detail.

Keywords: bird infestation, awning, negative selection, domestication

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Authors: Peder O. Laugen Heggdal, Oyvind Nordvik, Jonas Brannstrom, Flemming Vassbotn, Anne Kari Aarstad, Hans Jorgen Aarstad

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Background: Hearing loss (HL) affect people of all ages and stages in life. To author's best knowledge, if patients with an HL have reduced Generic Quality of life (QoL), has yet not been answered. Aim: The aim of the present study was to investigate the relationship between HL and generic and disease-specific Health Related Quality of Life (HRQoL) in adult patients (aged 18–78 years) with an HL, seeking Hearing Aid (HA). Material and Methods: 158 adult (aged 18-78 years) patients with HL, referred for HA fitting at Haukeland University Hospital in western Norway, participated in the study. Both first-time users, as well as patients referred for HA renewals, were included. First-time users had been pre-examined by an Ear Nose and Throat specialist. The questionnaires were answered before the actual HA fitting procedure. The pure-tone average (PTA; frequencies 0.5, 1, 2 and 4 kHz) was determined for each ear. The generic European Organization for Research and Treatment of Cancer (EORTC) Quality of Life Questionnaire general part and a shortened version of the Abbreviated Profile of Hearing Aid Benefit (APHAB) were answered. In addition, EORTC HRQoL answers from a general population and patients with former head and neck cancer served as comparison. Results: In general, no lowered HRQoL scores were determined among HL patients compared to the general population. Patients with unilateral HL to some extent showed lower HRQoL than those with bilateral HL (social function and fatigue). The APHAB scores correlated significantly with the EORTC HRQoL scores. By stepwise linear regression analysis, the APHAB scores were scored secondary to PTA (best ear), cognitive and physical function. Conclusion: HRQoL scores in HL patients, in general, seems to be at the population level, but the unilateral HL patients scored to some extent lower than the bilateral HI patients. APHAB and generic QoL scores levels are associated. Both HRQoL and APHAB scores are generated more complexly than anticipated.

Keywords: quality of life, hearing loss, hearing impairment, distress, depression, anxiety, hearing aid

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Authors: Nam-Kuk Kim, Jin Kim, Soomin Park, Changhee Lee, Mijin Chu, Seong-Hun Lee

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In this study, we conducted whole genome re-sequencing of 10 cultivars originated from five countries including Korea, China, India, Pakistan and Ethiopia with Sesamum indicum (Zhongzho No. 13) genome as a reference. Almost 80% of the whole genome sequences of the reference genome could be covered by sequenced reads. Numerous SNP and InDel were detected by bioinformatic analysis. Among these variants, 266,051 SNPs were identified as unique to countries. Pakistan and Ethiopia had high densities of SNPs compared to other countries. Three main clusters (cluster 1: Korea, cluster 2: Pakistan and India, cluster 3: Ethiopia and China) were recovered by neighbor-joining analysis using all variants. Interestingly, some variants were detected in DGAT1 (diacylglycerol O-acyltransferase 1) and FADS (fatty acid desaturase) genes, which are known to be related with fatty acid synthesis and metabolism. These results can provide useful information to understand the regional characteristics and develop DNA markers for origin discrimination of sesame.

Keywords: Sesamum indicum, NGS, SNP, DNA marker

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Authors: Fuad M. Alkoot

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Different experimental technologies such as microarray sequencing have been proposed to generate high-resolution genetic data, in order to understand the complex dynamic interactions between complex diseases and the biological system components of genes and gene products. However, the generated samples have a very large dimension reaching thousands. Therefore, hindering all attempts to design a classifier system that can identify diseases based on such data. Additionally, the high overlap in the class distributions makes the task more difficult. The data we experiment with is generated for the identification of autism. It includes 142 samples, which is small compared to the large dimension of the data. The classifier systems trained on this data yield very low classification rates that are almost equivalent to a guess. We aim at reducing the data dimension and improve it for classification. Here, we experiment with applying a multistage PCA on the genetic data to reduce its dimensionality. Results show a significant improvement in the classification rates which increases the possibility of building an automated system for autism detection.

Keywords: PCA, gene expression, dimensionality reduction, classification, autism

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Authors: Selim M. Khan

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Indoor air quality is strongly influenced by the presence of radioactive radon (222Rn) gas. Indeed, exposure to high 222Rn concentrations is unequivocally linked to DNA damage and lung cancer and is a worsening issue in North American and European built environments, having increased over time within newer housing stocks as a function of as yet unclear variables. Indoor air radon concentration can be influenced by a wide range of environmental, structural, and behavioral factors. As some of these factors are quantitative while others are qualitative, no single statistical model can determine indoor radon level precisely while simultaneously considering all these variables across a complex and highly diverse dataset. The ability of AI- machine (deep) learning to simultaneously analyze multiple quantitative and qualitative features makes it suitable to predict radon with a high degree of precision. Using Canadian and Swedish long-term indoor air radon exposure data, we are using artificial deep neural network models with random weights and polynomial statistical models in MATLAB to assess and predict radon health risk to human as a function of geospatial, human behavioral, and built environmental metrics. Our initial artificial neural network with random weights model run by sigmoid activation tested different combinations of variables and showed the highest prediction accuracy (>96%) within the reasonable iterations. Here, we present details of these emerging methods and discuss strengths and weaknesses compared to the traditional artificial neural network and statistical methods commonly used to predict indoor air quality in different countries. We propose an artificial deep neural network with random weights as a highly effective method for assessing and predicting indoor radon.

Keywords: radon, radiation protection, lung cancer, aI-machine deep learnng, risk assessment, risk prediction, Europe, North America

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Authors: Misty Attwood, Helgi Schioth

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Transmembrane proteins are important components in many essential cell processes such as signal transduction, cell-cell signalling, transport of solutes, structural adhesion activities, and protein trafficking. Due to their involvement in diverse critical activities, transmembrane proteins are implicated in different disease pathways and hence are the focus of intense interest in understanding functional activities, their pathogenesis in disease, and their potential as pharmaceutical targets. Further, as the structure and function of proteins are correlated, investigating a group of proteins with the same tertiary structure, i.e., the same number of transmembrane regions, may give understanding about their functional roles and potential as therapeutic targets. In this in silico bioinformatics analysis, we identify and comprehensively characterize the previously unstudied group of proteins with five transmembrane-spanning regions (5TM). We classify nearly 60 5TM proteins in which 31 are members of ten families that contain two or more family members and all members are predicted to contain the 5TM architecture. Furthermore, nine singlet proteins that contain the 5TM architecture without paralogues detected in humans were also identifying, indicating the evolution of single unique proteins with the 5TM structure. Interestingly, more than half of these proteins function in localization activities through movement or tethering of cell components and more than one-third are involved in transport activities, particularly in the mitochondria. Surprisingly, no receptor activity was identified within this family in sharp contrast with other TM families. Three major 5TM families were identified and include the Tweety family, which are pore-forming subunits of the swelling-dependent volume regulated anion channel in astrocytes; the sidoreflexin family that acts as mitochondrial amino acid transporters; and the Yip1 domain family engaged in vesicle budding and intra-Golgi transport. About 30% of the proteins have enhanced expression in the brain, liver, or testis. Importantly, 60% of these proteins are identified as cancer prognostic markers, where they are associated with clinical outcomes of various tumour types, indicating further investigation into the function and expression of these proteins is important. This study provides the first comprehensive analysis of proteins with 5TM regions and provides details of the unique characteristics and application in pharmaceutical development.

Keywords: 5TM, cancer prognostic marker, drug targets, transmembrane protein

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Authors: Fei Ye, Åsa Barrefelt, Manuchehr Abedi-Valugerdi, Khalid M. Abu-Salah, Salman A. Alrokayan, Mamoun Muhammed, Moustapha Hassan

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With appropriate encapsulation in functional nanoparticles drugs are more stable in physiological environment and the kinetics of the drug can be more carefully controlled and monitored. Furthermore, targeted drug delivery can be developed to improve chemotherapy in cancer treatment, not only by enhancing intracellular uptake by target cells but also by reducing the adverse effects in non-target organs. Inorganic imaging agents, delivered together with anti-cancer drugs, enhance the local imaging contrast and provide precise diagnosis as well as evaluation of therapy efficacy. We have developed biodegradable polymeric vesicles as a nanocarrier system for multimodal bio-imaging and anticancer drug delivery. The poly (lactic-co-glycolic acid) PLGA) vesicles were fabricated by encapsulating inorganic imaging agents of superparamagnetic iron oxide nanoparticles (SPION), manganese-doped zinc sulfide (MN:ZnS) quantum dots (QDs) and the anticancer drug busulfan into PLGA nanoparticles via an emulsion-evaporation method. T2-weighted magnetic resonance imaging (MRI) of PLGA-SPION-Mn:ZnS phantoms exhibited enhanced negative contrast with r2 relaxivity of approximately 523 s-1 mM-1 Fe. Murine macrophage (J774A) cellular uptake of PLGA vesicles started fluorescence imaging at 2 h and reached maximum intensity at 24 h incubation. The drug delivery ability PLGA vesicles was demonstrated in vitro by release of busulfan. PLGA vesicles degradation was studied in vitro, showing that approximately 32% was degraded into lactic and glycolic acid over a period of 5 weeks. The biodistribution of PLGA vesicles was investigated in vivo by MRI in a rat model. Change of contrast in the liver could be visualized by MRI after 7 min and maximal signal loss detected after 4 h post-injection of PLGA vesicles. Histological studies showed that the presence of PLGA vesicles in organs was shifted from the lungs to the liver and spleen over time.

Keywords: biodegradable polymers, multifunctional nanoparticles, quantum dots, anticancer drugs

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Authors: H. Sakamoto, S. Kurosawa, M. Suzuki, S. Oguri

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In Arabidopsis, several genes encoding proteins with ankyrin repeats and trans-membrane domains (AtANKTM) have been identified as mediators of biotic and abiotic stress responses. It has been known that the expression of an AtANKTM gene, At2g24600, is induced in response to abiotic stress and that there are four splicing variants derived from this locus. In this study, by RT-PCR and sequencing analysis, an unknown splicing variant of the At2g24600 transcript was identified. Based on differences in the predicted amino acid sequences, the five splicing variants are divided into three groups. The three predicted proteins are highly homologous, yet have different numbers of ankyrin repeats and trans-membrane domains. It is generally considered that ankyrin repeats mediate protein-protein interaction and that the number of trans-membrane domains affects membrane topology of proteins. The protein variants derived from the At2g24600 locus may have different molecular functions each other.

Keywords: alternative splicing, ankyrin repeats, trans-membrane domains, arabidopsis

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Authors: Husham Bayazed

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Purpose of Presentation: Obesity and overweight are among the biggest health challenges of the 21st century, according to the WHO. Obviously, obese individuals suffer different courses of disease – from infections and allergies to cancer- and even respond differently to some treatment options. Of note, obesity often seems to predispose and triggers several secondary diseases such as diabetes, arteriosclerosis, or heart attacks. Since decades it seems that immunological signals gear inflammatory processes among obese individuals with the aforementioned conditions. This review aims to shed light how obesity sparks or rewire the immune system and predisposes to such unpleasant health outcomes. Moreover, lessons from the Covid-19 pandemic ascertain that people living with pre-existing conditions such as obesity can develop severe acute respiratory syndrome (SARS), which needs to be elucidated how obesity and its adjuvant inflammatory process distortion contribute to enhancing severe COVID-19 consequences. Recent Findings: In recent clinical studies, obesity was linked to alter and sparks the immune system in different ways. Adipose tissue (AT) is considered as a secondary immune organ, which is a reservoir of tissue-resident of different immune cells with mediator release, making it a secondary immune organ. Adipocytes per se secrete several pro-inflammatory cytokines (IL-6, IL-4, MCP-1, and TNF-α ) involved in activation of macrophages resulting in chronic low-grade inflammation. The correlation between obesity and T cells dysregulation is pivotal in rewiring the immune system. Of note, autophagy occurrence in adipose tissues further rewire the immune system due to flush and outburst of leptin and adiponectin, which are cytokines and influencing pro-inflammatory immune functions. These immune alterations among obese individuals are collectively incriminated in triggering several metabolic disorders and playing role in increasing cancers incidence and susceptibility to different infections. During COVID-19 pandemic, it was verified that patients with pre-existing obesity being at greater risk of suffering severe and fatal clinical outcomes. Beside obese people suffer from increased airway resistance and reduced lung volume, ACE2 expression in adipose tissue seems to be high and even higher than that in lungs, which spike infection incidence. In essence, obesity with pre-existence of pro-inflammatory cytokines such as LI-6 is a risk factor for cytokine storm and coagulopathy among COVID-19 patients. Summary: It is well documented that obesity is associated with chronic systemic low-grade inflammation, which sparks and alter different pillars of the immune system and triggers different metabolic disorders, and increases susceptibility of infections and cancer incidence. The pre-existing chronic inflammation in obese patients with the augmented inflammatory response against the viral infection seems to increase the susceptibility of these patients to developing severe COVID-19. Although the new weight loss drugs and bariatric surgery are considered as breakthrough news for obesity treatment, but preventing is easier than treating it once it has taken hold. However, obesity and immune system link new insights dispute the role of immunotherapy and regulating immune cells treating diet-induced obesity.

Keywords: immunity, metabolic disorders, cancer, COVID-19

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Authors: Mohd Adil, Rosina Khan, Asad U. Khan, Vasantha Rupasinghe HP

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The study examined the effects of Syzygium aromaticum extracts on the virulence properties of Streptococcus mutans. The activity of glucosyltransferases in the presence of crude and diethylether fraction was reduced to 80% at concentration 78.12μg/ml and 39.06μg/ml respectively. The glycolytic pH drop by S. mutans cells was also disrupted by these extracts without affecting the bacterial viability. Microscopic analysis revealed morphological changes of the S. mutans biofilms, indicating that these plant extracts at sub-MICs could significantly affect the ability of S. mutans to form biofilm with distorted extracellular matrix. Furthermore, with the help of quantitative RT-PCR, the expression of different genes involved in adherence, quorum sensing, in the presence of these extracts were down regulated. The crude and active fractions were found effective in preventing caries development in rats. The data showed that S. aromaticum holds promise as a naturally occurring source of compounds that may prevent biofilm-related oral diseases.

Keywords: biofilm, quorum sensing, Streptococcus mutans, Syzygium aromaticum extract

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Authors: Nichole Haag, Kimberly Velk, Tyler McCune, Chun Wu

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Methicillin/multiple-resistant Staphylococcus aureus (MRSA) are infectious bacteria that are resistant to common antibiotics. A previous in silico study in our group has identified a hypothetical protein SAV1226 as one of the potential drug targets. In this study, we reported the bioinformatics characterization, as well as cloning, expression, purification and kinetic assays of hypothetical protein SAV1226 from methicillin/vancomycin-resistant Staphylococcus aureus Mu50 strain. MALDI-TOF/MS analysis revealed a low degree of structural similarity with known proteins. Kinetic assays demonstrated that hypothetical protein SAV1226 is neither a domain of an ATP dependent dihydroxyacetone kinase nor of a phosphotransferase system (PTS) dihydroxyacetone kinase, suggesting that the function of hypothetical protein SAV1226 might be misannotated on public databases such as UniProt and InterProScan 5.

Keywords: Methicillin-resistant Staphylococcus aureus, dihydroxyacetone kinase, essential genes, drug target, phosphoryl group donor

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Authors: Ihtisham Bukhari

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In the current study, we enrolled a 46, XY phenotypically female patient bearing testes in her inguinal canal. DNA sequencing of the AR gene detected a missense mutation C.1715A > G (p. Y572C) in exon 2 which is already known to cause Complete androgen insensitivity syndrome (CAIS). We further studied the effects of this mutation on the testicular histopathology of the patient. No spermatocytes were seen in the surface spreading of testicular tissues while H&E staining showed that seminiferous tubules predominantly have only Sertoli cells. To confirm this meiotic failure is likely due to the current AR mutation we performed mRNA expression of genes associated with AR pathway, expression and location of the associated proteins in testicular tissues. Western blot and real-time PCR data showed that the patient had high levels of expression of AMH, SOX9, and INNB in testis. Tubules were stained with SOX9 and AMH which revealed Sertoli cell maturation arrest. Therefore, we suggest that AR mutation enhances AMH expression which ultimately leads to failure in the maturation of Sertoli cells and failure in spermatogenesis.

Keywords: androgen receptor, spermatogenesis, infertility, Sertoli cell only syndrome

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Authors: Ilknur Tuncer, Nihayet Bizsel

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The studies in bacterial diversity and antimicrobial resistance in coastal areas are important to understand the variability in the community structures and metabolic activities. In the present study, antimicrobial susceptibility and phylogenetic analysis of bacteria isolated from stations with different depths and influenced by terrestrial and marine fluxes in eastern Aegean Sea were illustrated. 51% of the isolates were found as resistant and 14% showed high MAR index indicating the high-risk sources of contamination in the environment. The resistance and the intermediate levels and high MAR index of the study area were 38–60%, 11–38% and 0–40%, respectively. According to 16S rRNA gene analysis, it was found that the isolates belonged to two phyla Firmicutes and Gammaproteobacteria with the genera Bacillus, Halomonas, Oceanobacillus, Photobacterium, Pseudoalteromonas, Psychrobacter, and Vibrio. 47% of Bacillus strains which were dominant among all isolates were resistant. In addition to phylogenetically diverse bacteria, the variability in resistance, intermediate and high MAR index levels of the study area indicated the effect of geographical differences.

Keywords: bacterial diversity, multiple antibiotic resistance, 16S rRNA genes, Aegean Sea

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Authors: Emad M.Abdullat, Hasan A. Ader-Rahman, Rayyan Al Ali, Arwa.A.Hudaib

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This retrospective study aims to determine the epidemiological features of such deaths in one of the general teaching hospitals in Jordan with a focus on weaning practices and its relation to sucking as major factors underlying the mechanism of choking in infants and young children. The study utilized a retrospective design to review the records of forensic cases due to foreign body aspiration examined at the forensic department at the Jordan University Hospital. A total of 27 cases of choking in the pediatric age group were retrieved from the reports of the autopsy cases dissected. All cases of children who died due to chocking by foreign bodies were under 11 years old. Choking by food materials constituted (44.4%) of cases under 3 years of age while choking by non-food material were less prevalent under 3 years of age and comprising 18.5% of the cases. Health care personnel and parents need to be aware that introduction of solid food, unlike exclusive breast or formula-milk feeding, can have serious consequences if occurring in inappropriate timing or consistency during early childhood physical and functional development. Parents need to be educated regarding the appropriate timing and process of weaning.

Keywords: chocking, infants, weaning practices, young children

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Authors: A. O. Ogunkeyede, D. Amuchi, A. A. Adebayo

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Heavy metal contaminations in soil have received great attention. Anthropogenic activities such as vehicular emission, industrial activities and constructions have resulted in elevated concentration of heavy metals in the surface soils. The metal particles can be free from the surface soil when they are disturbed and re-entrained in air, which necessitated the need to investigate surface soil at market environment where adults and children are present on daily basis. This study assesses concentration of heavy metal pollution, ecological and health risk factors in surface soil at Effurun market. 8 samples were collected at household material (EMH), fish (EMFs), fish and commodities (EMF-C), Abattoir (EMA 1 & 2), fruit sections (EMF 1 & 2) and lastly main road (EMMR). The samples were digested and analyzed in triplicate for contents of Lead (Pb), Nickel (Ni), Cadmium (Cd) and Copper (Cu). The mean concentration of the Pb mg/kg (112.27 ± 1.12) and Cu mg/kg (156.14 ± 1.10) were highest in the abattoir section (EMA 1). The mean concentrations of the heavy metal were then used to calculate the ecological and health risk for people within the market. Pb contamination at EMMR, EMF 2, EMFs were moderately while Pb shows considerable contamination at EMH, EMA 1, EMA 2 and EMF-C sections of the Effurun market. The ecological risk factor varies between low to moderate pollution for Pb and EMA 1 has the highest potential ecological risk that falls within moderate pollution. The hazard quotient results show that dermal exposure pathway is the possible means of heavy metal exposure to the traders while ingestion is the least sources of exposure to adult. The ingestion suggested that children around the EMA 1 have the highest possible exposure to children due to hand-to-mouth and object-to-mouth behaviour. The results further show that adults at the EMA1 will have the highest exposure to Pb due to inhalation during burning of cow with tyre that contained Pb and Cu. The carcinogenic risk values of most sections were higher than acceptable values, while Ni at EMMR, EMF 1 & 2, EMFs and EMF-C sections that were below the acceptable values. The cancer risk for inhalation exposure pathway for Pb (1.01E+17) shows a significant level of contamination than all the other sections of the market. It suggested that the people working at the Abattoir were very prone to cancer risk.

Keywords: carcinogenic, ecological, heavy metal, risk

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Authors: Mohamed Moussaoui, Mouna Baassi, Soukayna Baammi, Hatim Soufi, Mohammed Salah, Rachid Daoud, Achraf EL Allali, Mohammed Elalaoui Belghiti, Said Belaaouad

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The present study aims to investigate the quantitative structure-activity relationship (QSAR) of a series of Thiazole derivatives reported as anticancer agents (hepatocellular carcinoma), using principally the electronic descriptors calculated by the density functional theory (DFT) method and by applying the multiple linear regression method. The developed model showed good statistical parameters (R²= 0.725, R²ₐ𝒹ⱼ= 0.653, MSE = 0.060, R²ₜₑₛₜ= 0.827, Q²𝒸ᵥ = 0.536). The energy of the highest occupied molecular orbital (EHOMO) orbital, electronic energy (TE), shape coefficient (I), number of rotatable bonds (NROT), and index of refraction (n) were revealed to be the main descriptors influencing the anti-cancer activity. Additional Thiazole derivatives were then designed and their activities and pharmacokinetic properties were predicted using the validated QSAR model. These designed molecules underwent evaluation through molecular docking (MD) and molecular dynamic (MD) simulations, with binding affinity calculated using the MMPBSA script according to a 100 ns simulation trajectory. This process aimed to study both their affinity and stability towards Cyclin-Dependent Kinase 2 (CDK2), a target protein for cancer disease treatment. The research concluded by identifying four CDK2 inhibitors - A1, A3, A5, and A6 - displaying satisfactory pharmacokinetic properties. MDs results indicated that the designed compound A5 remained stable in the active center of the CDK2 protein, suggesting its potential as an effective inhibitor for the treatment of hepatocellular carcinoma. The findings of this study could contribute significantly to the development of effective CDK2 inhibitors.

Keywords: QSAR, ADMET, Thiazole, anticancer, molecular docking, molecular dynamic simulations, MMPBSA calculation

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Authors: M. Omer Faruk, A. M. A. M. Zonaed Siddiki, M. Fazal Karim, Md. Masuduzzaman, S. Chowdhury, Md. Shafiqul Islam, M. Alamgir Hossain

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The dog tapeworms Echinococcus granulosus develop hydatid cysts in various organs in human and domestic animals worldwide including Bangladesh. The aim of this study was to identify and characterize the genotype of E. granulosus isolated from cattle using 12S rRNA and Cytochrome oxidase 1 (COX 1) genes. A total of 43 hydatid cyst samples were collected from 390 examined cattle samples derived from slaughterhouses. Among them, three cysts were fertile. Genomic DNA was extracted from germinal membrane and/or protoscoleces followed by PCR amplification of mitochondrial 12S rRNA and Cytochrome oxidase 1 gene fragments. The sequence data revealed existence of G1 (64.28%) and possible G3 (21.43%) genotypes for the first time in Bangladesh. The study indicates that common sheep strain G1 is the dominant subtype of E. granulosus in Chittagong region of Bangladesh. This will increase our understanding of the epidemiology of hydatidosis in the southern part of the country and will be useful to plan suitable control measures in the long run.

Keywords: Echinococcus granulosus, Cox1, 12S rRNA, molecular characterization, Bangladesh

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Authors: Vishwesh Kulkarni, Nikhil Bellarykar

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Cellular complexity stems from the interactions among thousands of different molecular species. Thanks to the emerging fields of systems and synthetic biology, scientists are beginning to unravel these regulatory, signaling, and metabolic interactions and to understand their coordinated action. Reverse engineering of biological networks has has several benefits but a poor quality of data combined with the difficulty in reproducing it limits the applicability of these methods. A few years back, many of the commonly used predictive algorithms were tested on a network constructed in the yeast Saccharomyces cerevisiae (S. cerevisiae) to resolve this issue. The network was a synthetic network of five genes regulating each other for the so-called in vivo reverse-engineering and modeling assessment (IRMA). The network was constructed in S. cereviase since it is a simple and well characterized organism. The synthetic network included a variety of regulatory interactions, thus capturing the behaviour of larger eukaryotic gene networks on a smaller scale. We derive a new set of algorithms by solving a nonlinear optimization problem and show how these algorithms outperform other algorithms on these datasets.

Keywords: synthetic gene network, network identification, optimization, nonlinear modeling

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Authors: Tripureshwari Paul

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We are born with nature molded by nurture. Studies have confirmed the productive role of genes and environment on an individual. This study examines the relationship of parental genotype values on the intellectual ability of their children. Keeping in mind that academic achievement-learning capacity of student through normative education, a function of exposure to family environment and pathology with intellectual quotient of the individual. Purposive sampling was used and children between ages 11 and 12 years and their respective parents were involved. Raven’s Standard Progressive Matrices (RSPM), Family Pathology Scale (FPS) and Family Environment Scale (FES) were administered. The results found significant relationship of Offspring IQ to Parental IQ, maternal IQ demonstrating higher values of correlation. Female IQ was significant to maternal IQ and male IQ was significant to paternal IQ. With Academic Achievement not significantly correlated to IQ, it was determined that Competitive framework, freedom to expression and Recreational Orientation in family affect a child’s intellectual performance.

Keywords: academic achievement, environment, family environment, family pathology, genotype, intelligence quotient, maternal IQ, paternal IQ

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Authors: Grâce Chidikofan, François Pinta, A. Benoist, G. Volle, J. Valette

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Statement of the Problem: biomass gasification systems may be relevant for decentralized power generation from recoverable agricultural and wood residues available in rural areas. In recent years, many systems have been implemented in all over the world as especially in Cambodgia, India. Although they have many positive effects, these systems can also affect the environment and human health. Indeed, during the process of biomass gasification, black wastewater containing tars are produced and generally discharged in the local environment either into the rivers or on soil. However, in most environmental assessment studies of biomass gasification systems, the impact of these releases are underestimated, due to the difficulty of identification of their chemical substances. This work deal with the analysis of the environmental impacts of tars from wood gasification in terms of human toxicity cancer effect, human toxicity non-cancer effect, and freshwater ecotoxicity. Methodology: A Life Cycle Assessment (LCA) approach was adopted. The inventory of tars chemicals substances was based on experimental data from a downdraft gasification system. The composition of six samples from two batches of raw materials: one batch made of tree wood species (oak+ plane tree +pine) at 25 % moisture content and the second batch made of oak at 11% moisture content. The tests were carried out for different gasifier load rates, respectively in the range 50-75% and 50-100%. To choose the environmental impacts assessment method, we compared the methods available in SIMAPRO tool (8.2.0) which are taking into account most of the chemical substances. The environmental impacts for 1kg of tars discharged were characterized by ILCD 2011+ method (V.1.08). Findings Experimental results revealed 38 important chemical substances in varying proportion from one test to another. Only 30 are characterized by ILCD 2011+ method, which is one of the best performing methods. The results show that wood species or moisture content have no significant impact on human toxicity noncancer effect (HTNCE) and freshwater ecotoxicity (FWE) for water release. For human toxicity cancer effect (HTCE), a small gap is observed between impact factors of the two batches, either 3.08E-7 CTUh/kg against 6.58E-7 CTUh/kg. On the other hand, it was found that the risk of negative effects is higher in case of tar release into water than on soil for all impact categories. Indeed, considering the set of samples, the average impact factor obtained for HTNCE varies respectively from 1.64 E-7 to 1.60E-8 CTUh/kg. For HTCE, the impact factor varies between 4.83E-07 CTUh/kg and 2.43E-08 CTUh/kg. The variability of those impact factors is relatively low for these two impact categories. Concerning FWE, the variability of impact factor is very high. It is 1.3E+03 CTUe/kg for tars release into water against 2.01E+01 CTUe/kg for tars release on soil. Statement concluding: The results of this study show that the environmental impacts of tars emission of biomass gasification systems can be consequent and it is important to investigate the ways to reduce them. For environmental research, these results represent an important step of a global environmental assessment of the studied systems. It could be used to better manage the wastewater containing tars to reduce as possible the impacts of numerous still running systems all over the world.

Keywords: biomass gasification, life cycle analysis, LCA, environmental impact, tars

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Authors: Ashwani Kumar Aggarwal

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NIR Light is non-ionizing and can pass easily through living tissues such as breast without any harmful effects. Therefore, use of NIR light for imaging the biological tissue and to quantify its optical properties is a good choice over other invasive methods. Optical tomography involves two steps. One is the forward problem and the other is the reconstruction problem. The forward problem consists of finding the measurements of transmitted light through the tissue from source to detector, given the spatial distribution of absorption and scattering properties. The second step is the reconstruction problem. In X-ray tomography, there is standard method for reconstruction called filtered back projection method or the algebraic reconstruction methods. But this method cannot be applied as such, in optical tomography due to highly scattering nature of biological tissue. A hybrid algorithm for reconstruction has been implemented in this work which takes into account the highly scattered path taken by photons while back projecting the forward data obtained during Monte Carlo simulation. The reconstructed image suffers from blurring due to point spread function. This blurred reconstructed image has been enhanced using a digital filter which is optimal in mean square sense.

Keywords: least-squares optimization, filtering, tomography, laser interaction, light scattering

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Authors: Witri Pratiwi, Shopa Nur Fauzah, Dini Norviatin

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WHO recommends breastfeeding exclusively for infants aged 0 to 6 months because breast milk is the best nutrition. There are several factors associated with the success of exclusive breastfeeding. This study aims to determine the factors associated with the success of exclusive breastfeeding. A cross-sectional study was conducted at 6 community health centers in Cirebon City, Indonesia. Primary data were obtained from a validated questionnaire given to mothers who have children aged 6 to 24 months. A total of 326 mothers participated in this study. Two hundred and eighteen (66.9%) mothers gave exclusive breastfeeding to their babies, and 108 (33.1%) did not give exclusive breastfeeding. The baby gender (p=0.240), birth weight (p=0.436), and place of birth (0.137) were not related to exclusive breastfeeding. Mode of delivery (p=0.029) and early initiation of breastfeeding (p=0.001) were significantly associated with exclusive breastfeeding. Infants with early initiation of breastfeeding are three times more likely to get exclusive breastfeeding compared to those who do not get breastfeeding early (p=0.001; OR=3.696 [95% CI 1.764 – 7.746]). Early initiation of breastfeeding is the most important factor in determining the success of exclusive breastfeeding. Promotion and education on the importance of early breastfeeding initiation to prospective mothers, families, and health workers are expected to be improved.

Keywords: early initiation of breastfeeding, exclusive breastfeeding, mode of delivery, Indonesia

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Authors: Bianca Peterson, Tomasz J. Sańko, Carlos C. Bezuidenhout, Johnnie Van Den Berg

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Busseola fusca (Fuller) (Lepidoptera: Noctuidae), the maize stem borer, is a major pest in sub-Saharan Africa. It causes economic damage to maize and sorghum crops and has evolved non-recessive resistance to genetically modified (GM) maize expressing the Cry1Ab insecticidal toxin. Since B. fusca is a non-model organism, very little genomic information is publicly available, and is limited to some cytochrome c oxidase I, cytochrome b, and microsatellite data. The biology of B. fusca is well-described, but still poorly understood. This, in combination with its larval-specific behavior, may pose problems for limiting the spread of current resistant B. fusca populations or preventing resistance evolution in other susceptible populations. As part of on-going research into resistance evolution, B. fusca larvae were collected from Bt and non-Bt maize in South Africa, followed by RNA isolation (15 specimens) and sequencing on the Illumina HiSeq 2500 platform. Quality of reads was assessed with FastQC, after which Trimmomatic was used to trim adapters and remove low quality, short reads. Trinity was used for the de novo assembly, whereas TransRate was used for assembly quality assessment. Transcript identification employed BLAST (BLASTn, BLASTp, and tBLASTx comparisons), for which two libraries (nucleotide and protein) were created from 3.27 million lepidopteran sequences. Several transcripts that have previously been implicated in Cry toxin resistance was identified for B. fusca. These included aminopeptidase N, cadherin, alkaline phosphatase, ATP-binding cassette transporter proteins, and mitogen-activated protein kinase. MEGA7 was used to align these transcripts to reference sequences from Lepidoptera to detect mutations that might potentially be contributing to Cry toxin resistance in this pest. RSEM and Bioconductor were used to perform differential gene expression analysis on groups of B. fusca larvae challenged and unchallenged with the Cry1Ab toxin. Pairwise expression comparisons of transcripts that were at least 16-fold expressed at a false-discovery corrected statistical significance (p) ≤ 0.001 were extracted and visualized in a hierarchically clustered heatmap using R. A total of 329,194 transcripts with an N50 of 1,019 bp were generated from the over 167.5 million high-quality paired-end reads. Furthermore, 110 transcripts were over 10 kbp long, of which the largest one was 29,395 bp. BLAST comparisons resulted in identification of 157,099 (47.72%) transcripts, among which only 3,718 (2.37%) were identified as Cry toxin receptors from lepidopteran insects. According to transcript expression profiles, transcripts were grouped into three subclusters according to the similarity of their expression patterns. Several immune-related transcripts (pathogen recognition receptors, antimicrobial peptides, and inhibitors) were up-regulated in the larvae feeding on Bt maize, indicating an enhanced immune status in response to toxin exposure. Above all, extremely up-regulated arylphorin genes suggest that enhanced epithelial healing is one of the resistance mechanisms employed by B. fusca larvae against the Cry1Ab toxin. This study is the first to provide a resource base and some insights into a potential mechanism of Cry1Ab toxin resistance in B. fusca. Transcriptomic data generated in this study allows identification of genes that can be targeted by biotechnological improvements of GM crops.

Keywords: epithelial healing, Lepidoptera, resistance, transcriptome

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Authors: Prajna Paramita Naik, Sujit Kumar Bhutia

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Background: Regardless of the development multimodal treatment strategies, oral squamous cell carcinoma (OSCC) is often associated with a high rate of recurrence, metastasis and chemo- and radio- resistance. The present study inspected the relevance of CD44, ABCB1 and ADAM17 expression as a putative stem cell compartment in oral squamous cell carcinoma (OSCC) and deciphered the role of autophagy in regulating the expression of aforementioned proteins, stemness and chemoresistance. Methods: A retrospective analysis of CD44, ABCB1 and ADAM17 expression with respect to the various clinicopathological factors of sixty OSCC patients were determined via immunohistochemistry. The correlation among CD44, ABCB1 and ADAM17 expression was established. Sphere formation assay, flow cytometry and fluorescence microscopy were conducted to elucidate the stemness and chemoresistance nature of established cisplatin-resistant oral cancer cells (FaDu). The pattern of expression of CD44, ABCB1 and ADAM17 in parental (FaDu-P) and resistant FaDu cells (FaDu-CDDP-R) were investigated through fluorescence microscopy. Western blot analysis of autophagy marker proteins was performed to compare the status of autophagy in parental and resistant FaDu cell. To investigate the role of autophagy in chemoresistance and stemness, sphere formation assay, immunofluorescence and Western blot analysis was performed post transfection with siATG14 and the level of expression of autophagic proteins, mitochondrial protein and stemness-associated proteins were analyzed. The statistical analysis was performed by GraphPad Prism 4.0 software. p-value was defined as follows: not significant (n.s.): p > 0.05;*: p ≤ 0.05; **: p ≤ 0.01; ***: p ≤ 0.001; ****: p ≤ 0.0001 were considered statistically significant. Results: In OSCC, high CD44, ABCB1 and ADAM17 expression were significantly correlated with higher tumor grades and poor differentiation. However, the expression of these proteins was not related to the age and sex of OSCC patients. Moreover, the expression of CD44, ABCB1 and ADAM17 were positively correlated with each other. In vitro and OSCC tissue double labeling experiment data showed that CD44+ cells were highly associated with ABCB1 and ADAM17 expression. Further, FaDu-CDDP-R cells showed higher sphere forming capacity along with increased fraction of the CD44+ population and β-catenin expression FaDu-CDDP-R cells also showed accelerated expression of CD44, ABCB1 and ADAM17. A comparatively higher autophagic flux was observed in FaDu-CDDP-R against FaDu-P cells. The expression of mitochondrial proteins was noticeably reduced in resistant cells as compared to parental cells indicating the occurrence of autophagy-mediated mitochondrial degradation in oral cancer. Moreover, inhibition of autophagy was coupled with the decreased formation of orospheres suggesting autophagy-mediated stemness in oral cancer. Blockade of autophagy was also found to induce the restoration of mitochondrial proteins in FaDu-CDDP-R cells indicating the involvement of mitophagy in chemoresistance. Furthermore, a reduced expression of CD44, ABCB1 and ADAM17 was also observed in ATG14 deficient cells FaDu-P and FaDu-CDDP-R cells. Conclusion: The CD44+ ⁄ABCB1+ ⁄ADAM17+ expression in OSCC might be associated with chemoresistance and a putative CSC compartment. Further, the present study highlights the contribution of mitophagy in chemoresistance and confirms the potential involvement of autophagic regulation in acquisition of stem-like characteristics in OSCC.

Keywords: ABCB1, ADAM17, autophagy, CD44, chemoresistance, mitophagy, OSCC, stemness

Procedia PDF Downloads 192

Authors: Miceska Simona, Škof Erik, Frković Grazio Snježana, Jeričević Anja, Smrkolj Špela, Cvjetićanin Branko, Novaković Srdjan, Grčar Kuzmanov Biljana, Kloboves-Prevodnik Veronika

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Objectives: High-grade serous ovarian cancer (HGSOC) is characterized by the dissemination of the tumor cells (TC) in the peritoneal cavity forming malignant ascites at the time of diagnosis or recurrence. Still, cytology itself has been underutilized as a modality for the diagnosis of HGSOC from ascites, and histological examination from the tumor tissue is yet the only validated method used. The objective of this study was to evaluate the reliability of cytology in the diagnosis of HGSOC in relation to the histopathological examination. Methods: The study included 42 patients with histologically confirmed HGSOC, accompanied by malignant ascites. To confirm the malignancy of the TC in the ascites and to define their immunophenotype, immunohistochemical reaction (IHC) of the following antigens: Calretinin, MOC, WT1, PAX8, p53, p16 & Ki-67 was evaluated on ascites cytospins and tissue blocks. For complete cytological determination of HGSOC, BRCA 1/2 gene mutation was determined from ascites, tissue block, and blood. BRCA1/2 mutation from blood was performed to define the type of mutation, somatic vs germline. Results: Among 42 patients, the immunophenotype of HGSOC from ascites was confirmed in 36 cases (86%). For more profound analysis, the patients were divided in 3 groups regarding the number of TC present in the ascites: patients with less than 10% TC, 10% TC, and more than 10% TC. From all included patients, in the group with less than 10% TC, there were 10 cases, and only 5 of them(50%) showed HGSOC phenotype; 12 cases had equally 10% of TC, and 11 cases (92%) showed HGSOC phenotype; 20 cases had more than 10% TC and all of them (100%) confirmed the HGSOC immunophenotype from ascites. Only 33 patients were eligible for further BRCA1/2 analysis. Eleven BRCA1/2 mutations were detected from thetissue block: 6 germline and 5 somatic. In 2 cases with less than 10% TC, BRCA1/2 mutation was not detected; 4 cases had 10% TC, and 2 of them (50%) confirmed the mutation; 4 cases had more than 10% TC, and all showed 100% reliability with the tumor tissue. Conclusions: Cytology is a highly reliable method for determining the immunophenotype of HGSOC and BRCA1/2 mutation if more than 10% of tumor cells are present in the ascites. This may present an additional non-invasive clinical approach for fast and effective diagnose in the future, especially in inoperable conditions or relapses.

Keywords: cytology, ascites, high-grade serous ovarian cancer, immunophenotype, BRCA1/2

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Authors: John N. Idenyi, Hadimundeen Abdallah, Abigeal D. Adeyemi, Jonathan C. Eya

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Gut microbiomes play a significant role in the growth, metabolism, and health of fish. However, we know very little about the interactive effects of variations in dietary composition and temperature on rainbow trout gut microbiota. Exactly 288 rainbow trout weighing 45.6g ± 0.05 (average ± SD) were fed four isocaloric, isolipidic, and isonitrogenous diets comprising 40% crude protein and 20% crude lipid and formulated as 100 % animal-based protein (AP) and a blend of 50 fish oil (FO)/50 camelina oil (CO), 100 % AP and100 % CO, 100 % plant-based protein (PP) and a blend of 50FO/50CO or 100 % PP and 100 % CO in 14 or 18°C for 150 days. Gut content was analyzed using 16S rRNA gene and shotgun sequencing. The most abundant phyla identified regardless of diet were Tenericutes, Firmicutes, Proteobacteria, Spirochaetes, Bacteroidetes, and Actinobacteria, while Aeromonadaceae and Enterobacteriaceae were dominant families in 18°C. Moreover, gut microbes were dominated by genes relating to an amino acid, carbohydrate, fat, and energy metabolisms and influenced by temperature. The shared functional profiles for all the diets suggest that plant protein sources in combination with CO could be as good as the fish meal with 50/50 FO & CO in rainbow trout farming.

Keywords: aquafeed, aquaculture, microbiome, rainbow trout

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Authors: K. Rhea Devaiah, B. S. Premalatha

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Background: Tonsillar Lingual sulcus is the area between the tonsils and the base of the tongue. The surgical resection of the lesions in the head and neck results in changes in speech and swallowing functions. The severity of the speech and swallowing problem depends upon the site and extent of the lesion, types and extent of surgery and also the flexibility of the remaining structures. Need of the study: This paper focuses on the importance of speech and swallowing rehabilitation in an individual with the lesion in the Tonsillar Lingual Sulcus and post-operative functions. Aim: Evaluating the speech and swallow functions post-intensive speech and swallowing rehabilitation. The objectives are to evaluate the speech intelligibility and swallowing functions after intensive therapy and assess the quality of life. Method: The present study describes a report of an individual aged 47years male, with the diagnosis of basaloid squamous cell carcinoma, left tonsillar lingual sulcus (pT2n2M0) and underwent wide local excision with left radical neck dissection with PMMC flap reconstruction. Post-surgery the patient came with a complaint of reduced speech intelligibility, and difficulty in opening the mouth and swallowing. Detailed evaluation of the speech and swallowing functions were carried out such as OPME, articulation test, speech intelligibility, different phases of swallowing and trismus evaluation. Self-reported questionnaires such as SHI-E(Speech handicap Index- Indian English), DHI (Dysphagia handicap Index) and SESEQ -K (Self Evaluation of Swallowing Efficiency in Kannada) were also administered to know what the patient feels about his problem. Based on the evaluation, the patient was diagnosed with pharyngeal phase dysphagia associated with trismus and reduced speech intelligibility. Intensive speech and swallowing therapy was advised weekly twice for the duration of 1 hour. Results: Totally the patient attended 10 intensive speech and swallowing therapy sessions. Results indicated misarticulation of speech sounds such as lingua-palatal sounds. Mouth opening was restricted to one finger width with difficulty chewing, masticating, and swallowing the bolus. Intervention strategies included Oro motor exercise, Indirect swallowing therapy, usage of a trismus device to facilitate mouth opening, and change in the food consistency to help to swallow. A practice session was held with articulation drills to improve the production of speech sounds and also improve speech intelligibility. Significant changes in articulatory production and speech intelligibility and swallowing abilities were observed. The self-rated quality of life measures such as DHI, SHI and SESE Q-K revealed no speech handicap and near-normal swallowing ability indicating the improved QOL after the intensive speech and swallowing therapy. Conclusion: Speech and swallowing therapy post carcinoma in the tonsillar lingual sulcus is crucial as the tongue plays an important role in both speech and swallowing. The role of Speech-language and swallowing therapists in oral cancer should be highlighted in treating these patients and improving the overall quality of life. With intensive speech-language and swallowing therapy post-surgery for oral cancer, there can be a significant change in the speech outcome and swallowing functions depending on the site and extent of lesions which will thereby improve the individual’s QOL.

Keywords: oral cancer, speech and swallowing therapy, speech intelligibility, trismus, quality of life

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Authors: Mohamed Boubekri

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Daylight in general and sunlight in particular are vital to life on earth, and it is not difficult to believe that their absence fosters conditions that promote disease. Through photosynthesis and other processes, sunlight provides photochemical ingredients necessary for our lives. There are fundamental biological, hormonal, and physiological functions coordinated by cycles that are crucial to life for cells, plants, animals, and humans. Many plants and animals, including humans, develop abnormal behaviors when sunlight is absent because their diurnal cycle is disturbed. Building​ codes disregard this aspect of daylighting when promulgating windows for buildings. This paper discusses the health aspects of daylighting design.

Keywords: daylighting, health, sunlight, sleep, disorders, circadian rythm, cancer

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Authors: Hossein Rassi, Marjan Moradi Fard, Samaneh Niko

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Human papillomavirus type 16 and 18 are closely associated with the development of human cervical carcinoma, which is one of the most common causes of cancer death in women worldwide. At present, HPV type 18 accounts for about 34 % of all HPV infections in Iran and the most promising vaccine against HPV infection is based on the L1 major capsid protein. The L1 protein of HPV18 has the capacity to self-assemble into capsomers or virus-like particles (VLPs) that are non-infectious, highly immunogenic and allowing their use in vaccine production. The methylotrophic yeast Pichia pastoris is an efficient and inexpensive expression system used to produce high levels of heterologous proteins. In this study we expressed HPV18 L1 VLPs in P. pastoris. The gene encoding the major capsid protein L1 of the high-risk HPV type 18 was isolated from Iranian patient by PCR and inserted into pTG19-T vector to obtain the recombinant expression vector pTG19-HPV18-L1. Then, the pTG19-HPV18-L1 was transformed into E. coli strain DH5α and the recombinant protein HPV18 L1 was expressed under IPTG induction in soluble form. The HPV18 L1 gene was excised from recombinant plasmid with XhoI and EcoRI enzymes and ligated into the yeast expression vector pPICZα linearized with the same enzymes, and transformed into P. pastoris. Induction and expression of HPV18 L1 protein was demonstrated by BMGY/BMMY and RT PCR. The parameters for induced cultivation for strain in P. pastoris KM71 with HPV16L1 were investigated in shaking flask cultures. After induced cultivation BMMY (pH 7.0) medium supplemented with methanol to a final concentration of 1.0% every 24 h at 37 degrees C for 96 h, the recombinant produced 78.6 mg/L of L1 protein. This work offers the possibility for the production of prophylactic vaccine for cervical carcinoma by P. pastoris for HPV-18 L1 gene. The VLP-based HPV vaccines can prevent persistent HPV18 infections and cervical cancer in Iran. The HPV-18 L1 gene was expressed successfully in E.coli, which provides necessary basis for preparing HPV-18 L1 vaccine in human. Also, HPV type 6 L1 proteins expressed in Pichia pastoris will facilitate the HPV vaccine development and structure-function study.

Keywords: Pichia pastoris, L1 virus-like particles, human papillomavirus type 18, biotechnology

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