Search results for: gene name recognition

Authors: Aileen Editha

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The legal recognition of property rights over human genes is a divisive topic to which there is no resolution. As a frequently discussed topic, scholars and practitioners often highlight the inadequacies of a proprietary regime. However, little has been said in regard to the nature of human genetic materials (HGMs). This paper proposes approaching the issue of property over HGMs from an alternative perspective that looks at the personal and social value and valuation of HGMs. This paper will highlight how the unique and unresolved status of HGMs is incompatible with the main tenets of property and, consequently, contributes to legal ambiguity and uncertainty in the regulation of property rights over human genes. HGMs are perceived as part of nature and a free-for-all while also being within an individual’s private sphere. Additionally, it is also considered to occupy a unique “not-private-nor-public” status. This limbo-like position clashes with property’s fundamental characteristic that relies heavily on a clear public/private dichotomy. Moreover, as property is intrinsically linked to the legal recognition of one’s personhood, this irresolution benefits some while disadvantages others. In particular, it demands the publicization of once-private genes for the “common good” but subsequently encourages privatization (through labor) of these now-public genes. This results in the gain of some (already privileged) individuals while enabling the disenfranchisement of members of minority groups, such as Indigenous communities. This paper will discuss real and intellectual property rights over human genes, such as the right to income or patent rights, in Canada and the US. This paper advocates for a sui generis approach to governing rights and interests over human genes that would not rely on having a strict public/private dichotomy. Not only would this improve legal certainty and clarity, but it would also alleviate—or, at the very least, minimize—the role that the current law plays in further entrenching existing systemic inequalities. Despite the specificity of this topic, this paper argues that there are broader lessons to be learned. This issue is an insightful case study on the interconnection of various principles in law, society, and property, and what must be done when discordance between one or more of those principles has detrimental societal outcomes. Ultimately, it must be remembered that property is an adaptable and malleable instrument that can be developed to ensure it contributes to equity and flourishing.

Keywords: property rights, human genetic materials, critical legal scholarship, systemic inequalities

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Authors: Abdelkhalek Bakkari

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Image segmentation is a critical step in image processing and pattern recognition. In this paper, we proposed a new robust automatic image classification based on a dynamic fuzzy c-means algorithm and mathematical morphology. The proposed segmentation algorithm (DFCM_MM) has been applied to MR perfusion images. The obtained results show the validity and robustness of the proposed approach.

Keywords: segmentation, classification, dynamic, fuzzy c-means, MR image

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Authors: Amandeep Kaur

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Digital Image processing is a fundamental tool to perform various operations on the digital images for pattern recognition, noise removal and feature extraction. In this paper noise removal technique has been described for various types of noises. This paper comprises discussion about various noises available in the image due to different environmental, accidental factors. In this paper, various de-noising approaches have been discussed that utilize different wavelets and filters for de-noising. By analyzing various papers on image de-noising we extract that wavelet based de-noise approaches are much effective as compared to others.

Keywords: de-noising techniques, edges, image, image processing

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Authors: Naima Mohammadi

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The present paper critically reports on the emergency of Iranian international students in a large public university in Italy. Although the most sizeable diaspora of Iranians dates back to the 1979 revolution, a huge wave of Iranian female students travelled abroad after the Iranian Green Movement (2009) due to the intensification of gender discrimination and Islamization. To explore the experience of Iranian female students at an Italian public university, two complementary methods were adopted: a focus group and individual interviews. Focus groups yield detailed collective conversations and provide researchers with an opportunity to observe the interaction between participants, rather than between participant and researcher, which generates data. Semi-structured interviews allow participants to share their stories in their own words and speak about personal experiences and opinions. Research participants were invited to participate through a public call in a Telegram group of Iranian students. Theoretical and purposive sampling was applied to select participants. All participants were assured that full anonymity would be ensured and they consented to take part in the research. A two-hour focus group was held in English with participants in the presence and some online. They were asked to share their motivations for studying in Italy and talk about their experiences both within and outside the university context. Each of these interviews lasted from 45 to 60 minutes and was mostly carried out online and in Farsi. The focus group consisted of 8 Iranian female post-graduate students. In analyzing the data a blended approach was adopted, with a combination of deductive and inductive coding. According to research findings, although 9/11 was the beginning of the West’s challenges against Muslims, the nuclear threats of Islamic regimes promoted the toughest international sanctions against Iranians as a nation across the world. Accordingly, carrying an Iranian identity contributes to social, political, and economic exclusion. Research findings show that geopolitical factors such as international sanctions and Islamophobia, and a lack of reciprocity in terms of recognition, have created a sense of stigmatization for veiled and unveiled Iranian female students who are the largest groups of ‘non-European Muslim international students’ enrolled in Italian universities. Participants addressed how their nationality has devalued their public image and negatively impacted their self-confidence and self-realization in academia. They highlighted the experience of an unwelcoming atmosphere by different groups of people and institutes, such as receiving marked students’ badges, rejected bank account requests, failed visa processes, secondary security screening selection, and hyper-visibility of veiled students. This study corroborates the need for institutions to pay attention to geopolitical factors and religious diversity in student recruitment and provide support mechanisms and access to basic rights. Accordingly, it is suggested that Higher Education Institutions (HEIs) have a social and moral responsibility towards the discrimination and both social and academic exclusion of Iranian students.

Keywords: Iranian diaspora, female students, recognition theory, inclusive university

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Authors: Likith Reddy Pinninti, Fredrik Ribsskog Staven, Leslie Robert Noble, Jorge Manuel de Oliveira Fernandes, Deepti Manjari Patel, Torstein Kristensen

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Understanding fish behavior is essential to improve animal welfare in aquaculture research. Behavioral traits can have a strong influence on fish health and habituation. To identify the genes and biological pathways responsible for lumpfish behavior, we performed an experiment to understand the interspecies relationship (mutualism) between the lumpfish and salmon. Also, we tested the correlation between the gene expression data vs. observational/physiological data to know the essential genes that trigger stress and swimming behavior in lumpfish. After the de novo assembly of the brain transcriptome, all the samples were individually mapped to the available lumpfish (Cyclopterus lumpus L.) primary genome assembly (fCycLum1.pri, GCF_009769545.1). Out of ~16749 genes expressed in brain samples, we found 267 genes to be statistically significant (P > 0.05) found only in odor and control (1), model and control (41) and salmon and control (225) groups. However, genes with |LogFC| ≥0.5 were found to be only eight; these are considered as differentially expressed genes (DEG’s). Though, we are unable to find the differential genes related to the behavioral traits from RNA-Seq data analysis. From the correlation analysis, between the gene expression data vs. observational/physiological data (serotonin (5HT), dopamine (DA), 3,4-Dihydroxyphenylacetic acid (DOPAC), 5-hydroxy indole acetic acid (5-HIAA), Noradrenaline (NORAD)). We found 2495 genes found to be significant (P > 0.05) and among these, 1587 genes are positively correlated with the Noradrenaline (NORAD) hormone group. This suggests that Noradrenaline is triggering the change in pigmentation and skin color in lumpfish. Genes related to behavioral traits like rhythmic, locomotory, feeding, visual, pigmentation, stress, response to other organisms, taxis, dopamine synthesis and other neurotransmitter synthesis-related genes were obtained from the correlation analysis. In KEGG pathway enrichment analysis, we find important pathways, like the calcium signaling pathway and adrenergic signaling in cardiomyocytes, both involved in cell signaling, behavior, emotion, and stress. Calcium is an essential signaling molecule in the brain cells; it could affect the behavior of fish. Our results suggest that changes in calcium homeostasis and adrenergic receptor binding activity lead to changes in fish behavior during stress.

Keywords: behavior, De novo, lumpfish, salmon

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Authors: Reham Banwair, Lana Alshehri, Sara Hadrawi

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The purpose of this project is to identify user satisfaction with the AI functions on Snapchat, in order to generate improvement proposals that allow its development within the app. To achieve this, a qualitative analysis was carried out through interviews to people who usually use the application, revealing their satisfaction or dissatisfaction with the usefulness of the AI. In addition, the background of the company and its introduction in these algorithms were analyzed. Furthermore, the characteristics of the three main functions of AI were explained: identify songs, solve mathematical problems, and recognize plants. As a result, it was obtained that 50% still do not know the characteristics of AI, 50% still believe song recognition is not always correct, 41.7% believe that math problems are usually accurate and 91.7% believes the plant detection tool is working properly.

Keywords: artificial intelligence, scanning, Snapchat, machine learning

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Authors: Jamileh Ahmed, Helena Hernandez, Gabriel De Erausquin

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H1N1 virus susceptibility of iPSC-derived DA neurons from schizophrenia patients and controls will compared. C57/BL-6 fibroblasts were reprogrammed into iPSCs using a lenti-viral vector containing SOKM genes. Pluripotency verification with the AP assay and immunocytochemistry ensured iPSC presence. The experimental outcome of ISPCs from DA neuron differentiation will be discussed in the Results section. Fibroblasts from patients and controls will be reprogrammed into iPSCs using a sendai-virus vector containing SOKM. IPSCs will be characterized using the AP assay, immunocytochemistry and RT-PCR. IPSCs will then be differentiated into DA neurons. Gene methylation will be compared for both groups with custom-designed microarrays.

Keywords: schizophrenia, iPSCs, stem cells, neuroscience

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Authors: Yasser Y. Lenis, Amy Jo Montgomery, Diego F. Carrillo-Gonzalez

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Introduction: The use of didactic instruments in different learning environments plays a pivotal role in enhancing the level of knowledge in veterinary science students. The direct instruction of basic animal reproduction concepts in students enrolled in veterinary medicine programs allows them to elucidate the biological and molecular mechanisms that perpetuate the animal species in an ecosystem. Therefore, universities must implement didactic strategies that facilitate the teaching and learning processes for students and, in turn, enrich learning environments. Objective: to evaluate the effect of the use of a didactic textbook on the level of theoretical knowledge in embryo-maternal recognition for veterinary medicine students. Methods: the participants (n=24) were divided into two experimental groups: control (Ctrl) and treatment (Treat). Both groups received 4 hours of theoretical training regarding the basic concepts in bovine embryo-maternal recognition. However, the Treat group was also exposed to a guided lecture and the activity play-to-learn from a cow reproduction didactic textbook. A pre-test and a post-test were applied to assess the prior and subsequent knowledge in the participants. Descriptive statistics were applied to identify the success rates for each of the tests. Afterwards, a repeated measures model was applied where the effect of the intervention was considered. Results: no significant difference (p>0,05) was observed in the number of right answers for groups Ctrl (54,2%±12,7) and Treat (40,8%±16,8) in the pre-test. There was no difference (p>0,05) compering the number of right answers in Ctrl pre-test (54,2%±12,7) and post-test (60,8±18,8). However, the Treat group showed a significant (p>0,05) difference in the number of right answers when comparing pre-test (40,8%±16,8) and post-test (71,7%±14,7). Finally, after the theoretical training and the didactic activity in the Treat group, an increase of 10.9% (p<0,05) in the number of right answers was found when compared with the Ctrl group. Conclusion: the use of didactic tools that include guided lectures and activities like play-to-learn from a didactic textbook enhances the level of knowledge in an animal reproduction course for veterinary medicine students.

Keywords: animal reproduction, pedagogic, level of knowledge, learning environment

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Authors: Panagiota Katsikouli, William Hamilton Byrne, Thomas Gammeltoft-Hansen, Tijs Slaats

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An individual who demonstrates a well-founded fear of persecution or faces real risk of being subjected to torture is eligible for asylum. In Danish law, the exact legal thresholds reflect those established by international conventions, notably the 1951 Refugee Convention and the 1950 European Convention for Human Rights. These international treaties, however, remain largely silent when it comes to how states should assess asylum claims. As a result, national authorities are typically left to determine an individual’s legal eligibility on a narrow basis consisting of an oral testimony, which may itself be hampered by several factors, including imprecise language interpretation, insecurity or lacking trust towards the authorities among applicants. The leaky ground, on which authorities must assess their subjective perceptions of asylum applicants' credibility, questions whether, in all cases, adjudicators make the correct decision. Moreover, the subjective element in these assessments raises questions on whether individual asylum cases could be afflicted by implicit biases or stereotyping amongst adjudicators. In fact, recent studies have uncovered significant correlations between decision outcomes and the experience and gender of the assigned judge, as well as correlations between asylum outcomes and entirely external events such as weather and political elections. In this study, we analyze a publicly available dataset containing approximately 8,000 summaries of asylum cases, initially rejected, and re-tried by the Refugee Appeals Board (RAB) in Denmark. First, we look for variations in the recognition rates, with regards to a number of applicants’ features: their country of origin/nationality, their identified gender, their identified religion, their ethnicity, whether torture was mentioned in their case and if so, whether it was supported or not, and the year the applicant entered Denmark. In order to extract those features from the text summaries, as well as the final decision of the RAB, we applied natural language processing and regular expressions, adjusting for the Danish language. We observed interesting variations in recognition rates related to the applicants’ country of origin, ethnicity, year of entry and the support or not of torture claims, whenever those were made in the case. The appearance (or not) of significant variations in the recognition rates, does not necessarily imply (or not) bias in the decision-making progress. None of the considered features, with the exception maybe of the torture claims, should be decisive factors for an asylum seeker’s fate. We therefore investigate whether the decision can be predicted on the basis of these features, and consequently, whether biases are likely to exist in the decisionmaking progress. We employed a number of machine learning classifiers, and found that when using the applicant’s country of origin, religion, ethnicity and year of entry with a random forest classifier, or a decision tree, the prediction accuracy is as high as 82% and 85% respectively. tentially predictive properties with regards to the outcome of an asylum case. Our analysis and findings call for further investigation on the predictability of the outcome, on a larger dataset of 17,000 cases, which is undergoing.

Keywords: asylum adjudications, automated decision-making, machine learning, text mining

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Authors: Fereydoon Bondarian, Samira Shaygan

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Today, many nutritionists recommend the consumption of plants, fruits, and vegetables to provide the antioxidants needed by the body because the use of plant antioxidants usually causes fewer side effects and better treatment. Natural antioxidants increase the power of plasma antioxidants and reduce the incidence of some diseases, such as cancer. Bad lifestyles and environmental factors play an important role in increasing the incidence of cancer. In this study, different extracts of white teas taken from two types of tea available in Iran (clone 100 and Chinese hybrid) due to the presence of a hydroxyl functional group in their structure to inhibit free radicals and anticancer properties, using 3 aqueous, methanolic and aqueous-methanolic methods were used. The total polyphenolic content was calculated using the Folin-Ciocalcu method, and the percentage of inhibition and trapping of free radicals in each of the extracts was calculated using the DPPH method. With the help of high-performance liquid chromatography, a small amount of each catechin in the tea samples was obtained. Clone 100 white tea was found to be the best sample of tea in terms of all the examined attributes (total polyphenol content, antioxidant properties, and individual amount of each catechin). The results showed that aqueous and aqueous-methanolic extracts of Clone 100 white tea have the highest total polyphenol content with 27.59±0.08 and 36.67±0.54 (equivalent gallic acid per gram dry weight of leaves), respectively. Due to having the highest level of different groups of catechin compounds, these extracts have the highest property of inhibiting and trapping free radicals with 66.61±0.27 and 71.74±0.27% (mg/l) of the extracted sample against ascorbic acid). Using the MTT test, the inhibitory effect of clone 100 white tea extract in inhibiting the growth of HCT-116 colon cancer cells was investigated and the best time and concentration treatments were 500, 150 and 1000 micrograms in 8, 16 and 24 hours, respectively. To investigate gene expression changes, selected genes, including tumorigenic genes, proto-oncogenes, tumor suppressors, and genes involved in apoptosis, were selected and analyzed using the real-time PCR method and in the presence of concentrations obtained for white tea. White tea extract at a concentration of 1000 μg/ml 3 times 16, 8, and 24 hours showed the highest growth inhibition in cancer cells with 53.27, 55.8, and 86.06%. The concentration of 1000 μg/ml aqueous extract of white tea under 24-hour treatment increased the expression of tumor suppressor genes compared to the normal sample.

Keywords: catechin, gene expression, suppressor genes, colon cell line

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Authors: Y. Saylan, F. Yılmaz, A. Denizli

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Rheumatoid arthritis (RA) which is the most common autoimmune disorder of the body's own immune system attacking healthy cells. RA has both articular and systemic effects.Until now romatiod factor (RF) assay is used the most commonly diagnosed RA but it is not specific. Anti-cyclic citrullinated peptide (anti-CCP) antibodies are IgG autoantibodies which recognize citrullinated peptides and offer improved specificity in early diagnosis of RA compared to RF. Anti-CCP antibodies have specificity for the diagnosis of RA from 91 to 98% and the sensitivity rate of 41-68%. Molecularly imprinted polymers (MIP) are materials that are easy to prepare, less expensive, stable have a talent for molecular recognition and also can be manufactured in large quantities with good reproducibility. Molecular recognition-based adsorption techniques have received much attention in several fields because of their high selectivity for target molecules. Quartz crystal microbalance (QCM) is an effective, simple, inexpensive approach mass changes that can be converted into an electrical signal. The applications for specific determination of chemical substances or biomolecules, crystal electrodes, cover by the thin films for bind or adsorption of molecules. In this study, we have focused our attention on combining of molecular imprinting into nanofilms and QCM nanosensor approaches and producing QCM nanosensor for anti-CCP, chosen as a model protein, using anti-CCP imprinted nanofilms. For this aim, anti-CCP imprinted QCM nanosensor was characterized by Fourier transform infrared spectroscopy, atomic force microscopy, contact angle measurements and ellipsometry. The non-imprinted nanosensor was also prepared to evaluate the selectivity of the imprinted nanosensor. Anti-CCP imprinted QCM nanosensor was tested for real-time detection of anti-CCP from aqueous solution. The kinetic and affinity studies were determined by using anti-CCP solutions with different concentrations. The responses related with mass shifts (Δm) and frequency shifts (Δf) were used to evaluate adsorption properties and to calculate binding (Ka) and dissociation (Kd) constants. To show the selectivity of the anti-CCP imprinted QCM nanosensor, competitive adsorption of anti-CCP and IgM was investigated.The results indicate that anti-CCP imprinted QCM nanosensor has a higher adsorption capabilities for anti-CCP than for IgM, due to selective cavities in the polymer structure.

Keywords: anti-CCP, molecular imprinting, nanosensor, rheumatoid arthritis, QCM

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Authors: Seok Woo Chang, Kee Yeon Kum, Kwang Shik Bae, WooCheol Lee

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Aim: The objective of this study was to compare the biocompatibilities and mineralization potential of ProRoot MTA and newly developed calcium phosphate based cement, Capseal. Materials and Methods: The biocompatibilities and mineralization-related gene expressions (Bone sialoprotein (BSP) and osteocalcin (OCN)) of ProRoot MTA and Capseal were also compared by a methylthiazol tetrazolium (MTT) assay and reverse transcription-polymerization chain reaction (RT-PCR) analysis on 1, 3, and 7 days, respectively. Empty rings were used as control group. The results were statistically analyzed by Kruskal-Wallis test with a Bonferroni correction. P-value of < 0.05 was considered significant. Results: The biocompatibilities of ProRoot MTA and Capseal were equally favorable. ProRoot MTA and Capseal affected the messenger RNA expression of osteocalcin and osteonectin. Conclusions: Based on the results, both ProRoot MTA and Capseal could be a useful biomaterial in clinical endodontics.

Keywords: biocompatibility, calcium silicate cement, MTT, RT-PCR

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Authors: Valeria Velasco, Ana M. Bonilla, José L. Vergara, Alcides Lofa, Jorge Campos, Pedro Rojas-García

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Staphylococcus aureus is both commensal bacterium and opportunistic pathogen that can cause different diseases in humans and can rapidly develop antimicrobial resistance. Since this bacterium has the ability to colonize the nares and skin of humans and animals, there is a risk of contamination of food in different steps of the food chain supply. Emerging strains have been detected in food-producing animals and meat, such as methicillin-resistant S. aureus (MRSA). The aim of this study was to determine the prevalence and oxacillin susceptibility of S. aureus in the pork chain supply in Chile and to suggest some natural antimicrobials for control. A total of 487 samples were collected from pigs (n=332), carcasses (n=85), and retail pork meat (n=70). Presumptive S. aureus colonies were isolated by selective enrichment and culture media. The confirmation was carried out by biochemical testing (Api® Staph) and molecular technique PCR (detection of nuc and mecA genes, associated with S. aureus and methicillin resistance, respectively). The oxacillin (β-lactam antibiotic that replaced methicillin) susceptibility was assessed by minimum inhibitory concentration (MIC) using the Epsilometer test (Etest). A preliminary assay was carried out to test thymol, carvacrol, oregano essential oil (Origanum vulgare L.), Maqui or Chilean wineberry extract (Aristotelia chilensis (Mol.) Stuntz) as anti-staphylococcal agents using the disc diffusion method at different concentrations. The overall prevalence of S. aureus in the pork chain supply reached 33.9%. A higher prevalence of S. aureus was determined in carcasses (56.5%) than in pigs (28.3%) and pork meat (32.9%) (P ≤ 0.05). The prevalence of S. aureus in pigs sampled at farms (40.6%) was higher than in pigs sampled at slaughterhouses (23.3%) (P ≤ 0.05). The contamination of no packaged meat with S. aureus (43.1%) was higher than in packaged meat (5.3%) (P ≤ 0.05). The mecA gene was not detected in S. aureus strains isolated in this study. Two S. aureus strains exhibited oxacillin resistance (MIC ≥ 4µg/mL). Anti-staphylococcal activity was detected in solutions of thymol, carvacrol, and oregano essential oil at all concentrations tested. No anti-staphylococcal activity was detected in Maqui extract. Finally, S. aureus is present in the pork chain supply in Chile. Although the mecA gene was not detected, oxacillin resistance was found in S. aureus and could be attributed to another resistance mechanism. Thymol, carvacrol, and oregano essential oil could be used as anti-staphylococcal agents at low concentrations. Research project Fondecyt No. 11140379.

Keywords: antimicrobials, mecA gen, nuc gen, oxacillin susceptibility, pork meat

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Authors: Senol Dogan, Gunay Karli

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Identification of relevant publications based on a Medline query is time-consuming and error-prone. An all based process has the potential to solve this problem without any manual work. To the best of our knowledge, our study is the first to investigate the ability of machine learning to identify relevant articles accurately. 5 different machine learning algorithms were tested using 23 predictors based on several metadata fields attached to publications. We find that the Boosted model is the best-performing algorithm and its overall accuracy is 96%. In addition, specificity and sensitivity of the algorithm is 97 and 93%, respectively. As a result of the work, we understood that we can apply the same procedure to understand cancer gene expression big data.

Keywords: prediction of publications, machine learning, algorithms, bariatric surgery, comparison of algorithms, boosted, tree, logistic regression, ANN model

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Authors: Christelle E. Chua, Alicia L. Ho

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The development of a panel of differential gene expression signatures has been of interest in the field of biomarker discovery for radiation exposure. In the absence of the availability of exposed human subjects, lymphocyte cell lines have often been used as a surrogate to human whole blood, when performing ex vivo irradiation studies. The extent of variation between different lymphocyte cell lines is currently unclear, especially with regard to the expression of extracellular miRNA. This study compares the expression profile of extracellular miRNA isolated from different lymphocyte cell lines. It also compares the profile of miRNA obtained when different exosome isolation kits are used. Lymphocyte cell lines were created using lymphocytes isolated from healthy adult males of similar racial descent (Chinese American and Chinese Singaporean) and immortalised with Epstein-Barr virus. The cell lines were cultured in exosome-free cell culture media for 72h and the cell culture supernatant was removed for exosome isolation. Two exosome isolation kits were used. Total exosome isolation reagent (TEIR, ThermoFisher) is a polyethylene glycol (PEG)-based exosome precipitation kit, while ExoSpin (ES, Cell Guidance Systems) is a PEG-based exosome precipitation kit that includes an additional size exclusion chromatography step. miRNA from the isolated exosomes were isolated using miRNEASY minikit (Qiagen) and analysed using nCounter miRNA assay (Nanostring). Principal component analysis (PCA) results suggested that the overall extracellular miRNA expression profile differed between the lymphocyte cell line originating from the Chinese American donor and the cell line originating from the Chinese Singaporean donor. As the gender, age and racial origins of both donors are similar, this may suggest that there are other genetic or epigenetic differences that account for the variation in extracellular miRNA gene expression in lymphocyte cell lines. However, statistical analysis showed that only 3 miRNA genes had a fold difference > 2 at p < 0.05, suggesting that the differences may not be of that great a significance as to impact overall conclusions drawn from different cell lines. Subsequent analysis using cell lines from other donors will give further insight into the reproducibility of results when difference cell lines are used. PCA results also suggested that the method of exosome isolation impacted the expression profile. 107 miRNA had a fold difference > 2 at p < 0.05. This suggests that the inclusion of an additional size exclusion chromatography step altered the subset of the extracellular vesicles that were isolated. In conclusion, these results suggest that extracellular miRNA can be isolated and analysed from exosomes derived from lymphocyte cell lines. However, care must be taken in the choice of cell line and method of exosome isolation used.

Keywords: biomarker, extracellular miRNA, isolation methods, lymphocyte cell line

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Authors: Kriddikorn Kaewwongsri, Nikom Suvonvorn

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In the deep south of Thailand, checkpoints for people verification are necessary for the security management of risk zones, such as official buildings in the conflict area. In this paper, we propose an automatic checkpoint system that verifies persons using information from ID cards and facial features. The methods for a person’s information abstraction and verification are introduced based on useful information such as ID number and name, extracted from official cards, and facial images from videos. The proposed system shows promising results and has a real impact on the local society.

Keywords: face comparison, card recognition, OCR, checkpoint system, authentication

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Authors: Fakhrosadat Sajjadian

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The majority of deaths in cancer patients are caused by distant metastasis. Breast cancer shows a unique spread pattern, often affecting bone, liver, lung, and brain. Breast cancer can be categorized into various subtypes according to gene expression patterns, and these subtypes exhibit specific preferences for organs where metastasis occurs. Breast tumors with luminal characteristics have a preference for spreading to the bone, whereas basal-like breast cancer (BLBC) shows a tendency to metastasize to the lungs. Still, the mechanisms behind this particular pattern of metastasis in organs have yet to be fully understood. In this evaluation, we will outline the latest progress in molecular signaling pathways and treatment methods for breast cancer lung metastasis.

Keywords: lung cancer, liver cancer, diagnosis, BLBC, metastasis

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Authors: Alsu F. Saifitdinova, Alexey S. Komissarov, Svetlana A. Galkina, Elena I. Koshel, Maria M. Kulak, Stephen J. O'Brien, Elena R. Gaginskaya

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The mystery of sex determination is one of the most ancient and still not solved until the end so far. In many species, sex determination is genetic and often accompanied by the presence of dimorphic sex chromosomes in the karyotype. Genomic sequencing gave the information about the gene content of sex chromosomes which allowed to reveal their origin from ordinary autosomes and to trace their evolutionary history. Female-specific W chromosome in birds as well as mammalian male-specific Y chromosome is characterized by the degeneration of gene content and the accumulation of repetitive DNA. Tandem repeats complicate the analysis of genomic data. Despite the best efforts chicken W chromosome assembly includes only 1.2 Mb from expected 55 Mb. Supplementing the information on the sex chromosome composition not only helps to complete the assembly of genomes but also moves us in the direction of understanding of the sex-determination systems evolution. A whole-genome survey to the assembly Gallus_gallus WASHUC 2.60 was applied for repeats search in assembled genome and performed search and assembly of high copy number repeats in unassembled reads of SRR867748 short reads datasets. For cytogenetic analysis conventional methods of fluorescent in situ hybridization was used for previously cloned W specific satellites and specifically designed directly labeled synthetic oligonucleotide DNA probe was used for bioinformatically identified repetitive sequence. Hybridization was performed with mitotic chicken chromosomes and manually isolated giant meiotic lampbrush chromosomes from growing oocytes. A novel chicken W specific satellite (GGAAA)n which is not co-localizes with any previously described classes of W specific repeats was identified and mapped with high resolution. In the composition of autosomes this repeat units was found as a part of upstream regions of gonad specific protein coding sequences. These findings may contribute to the understanding of the role of tandem repeats in sex specific differentiation regulation in birds and sex chromosome evolution. This work was supported by the postdoctoral fellowships from St. Petersburg State University (#1.50.1623.2013 and #1.50.1043.2014), the grant for Leading Scientific Schools (#3553.2014.4) and the grant from Russian foundation for basic researches (#15-04-05684). The equipment and software of Research Resource Center “Chromas” and Theodosius Dobzhansky Center for Genome Bioinformatics of Saint Petersburg State University were used.

Keywords: birds, lampbrush chromosomes, sex chromosomes, tandem repeats

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Authors: Khaldon Lweesy, Feryal Alskafi, Rabaa Hammad, Shaker Khanfar, Yara Alsukhni

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Electronic noses are devices designed to emulate the humane sense of smell by characterizing and differentiating odor profiles. In this study, we build a low-cost e-nose using an array module containing four different types of metal oxide semiconductor gas sensors. We used this system to create a profile for a meat specimen over three days. Then using a pattern recognition software, we correlated the odor of the specimen to its age. It is a simple, fast detection method that is both non-expensive and non-destructive. The results support the usage of this technology in food control management.

Keywords: e-nose, low cost, odor detection, food safety

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Authors: Ji Su Kim, Bo Ram Choi, Ju Yeon Cho, Hyukjin Lee

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Epidermal growth factor receptor (EGFR) 19 deletion mutation gene is over-expressed in carcinoma patient. EGFR 19 deletion mutation is known as typical biomarker of non-small cell lung cancer (NSCLC), which one section in the coding exon 19 of EGFR is deleted. Therefore, there have been many attempts over the years to detect EGFR 19 deletion mutation for replacing conventional diagnostic method such as PCR and tissue biopsy. We developed a simple and facile detection platform based on Rolling Circle Amplification (RCA), which provides highly amplified products in isothermal amplification of the ligated DNA template. Limit of detection (~50 nM) and a faster detection time (~30 min) could be achieved by introducing RCA.

Keywords: EGFR19, cancer, diagnosis, rolling circle amplification (RCA), hydrogel

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Authors: Seynabou Toure, Oumar Diop, Kidiyo Kpalma, Amadou S. Maiga

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Color and texture are the two most determinant elements for perception and recognition of the objects in an image. For this reason, color and texture analysis find a large field of application, for example in image classification and segmentation. But, the pioneering work in texture analysis was conducted on grayscale images, thus discarding color information. Many grey-level texture descriptors have been proposed and successfully used in numerous domains for image classification: face recognition, industrial inspections, food science medical imaging among others. Taking into account color in the definition of these descriptors makes it possible to better characterize images. Color texture is thus the subject of recent work, and the analysis of color texture images is increasingly attracting interest in the scientific community. In optical remote sensing systems, sensors measure separately different parts of the electromagnetic spectrum; the visible ones and even those that are invisible to the human eye. The amounts of light reflected by the earth in spectral bands are then transformed into grayscale images. The primary natural colors Red (R) Green (G) and Blue (B) are then used in mixtures of different spectral bands in order to produce RGB images. Thus, good color texture discrimination can be achieved using RGB under controlled illumination conditions. Some previous works investigate the effect of using different color space for color texture classification. However, the selection of the best performing color space in land-sea segmentation is an open question. Its resolution may bring considerable improvements in certain applications like coastline detection, where the detection result is strongly dependent on the performance of the land-sea segmentation. The aim of this paper is to present the results of a study conducted on different color spaces in order to show the best-performing color space for land-sea segmentation. In this sense, an experimental analysis is carried out using five different color spaces (RGB, XYZ, Lab, HSV, YCbCr). For each color space, the Haar wavelet decomposition is used to extract different color texture features. These color texture features are then used for Fusion of Over Segmentation (FOOS) based classification; this allows segmentation of the land part from the sea one. By analyzing the different results of this study, the HSV color space is found as the best classification performance while using color and texture features; which is perfectly coherent with the results presented in the literature.

Keywords: classification, coastline, color, sea-land segmentation

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Authors: Nazish Badar

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In early 2009, Pandemic type A (H1N1) Influenza virus emerged globally. Since then, it has continued circulation causing considerable morbidity and mortality. The purpose of this study was to evaluate the evolutionary changes in Influenza A (H1N1) pdm09 viruses from 2009-15 and their relevance with the current vaccine viruses. Methods: Respiratory specimens were collected with influenza-like illness and Severe Acute Respiratory Illness. Samples were processed according to CDC protocol. Sequencing and phylogenetic analysis of Haemagglutinin (HA) and neuraminidase (NA) genes was carried out comparing representative isolates from Pakistan viruses. Results: Between Jan2009 - Feb 2016, 1870 (13.2%) samples were positive for influenza A out of 14086. During the pandemic period (2009–10), Influenza A/ H1N1pdm 09 was the dominant strain with 366 (45%) of total influenza positives. In the post-pandemic period (2011–2016), a total of 1066 (59.6%) cases were positive Influenza A/ H1N1pdm 09 with co-circulation of different Influenza A subtypes. Overall, the Pakistan A(H1N1) pdm09 viruses grouped in two genetic clades. Influenza A(H1N1)pdm09 viruses only ascribed to Clade 7 during the pandemic period whereas viruses belong to clade 7 (2011) and clade 6B (2015) during the post-pandemic years. Amino acid analysis of the HA gene revealed mutations at positions S220T, I338V and P100S specially associated with outbreaks in all the analyzed strains. Sequence analyses of post-pandemic A(H1N1)pdm09 viruses showed additional substitutions at antigenic sites; S179N,K180Q (SA), D185N, D239G (CA), S202A (SB) and at receptor binding sites; A13T, S200P when compared with pandemic period. Substitution at Genetic markers; A273T (69%), S200P/T (15%) and D239G (7.6%) associated with severity and E391K (69%) associated with virulence was identified in viruses isolated during 2015. Analysis of NA gene revealed outbreak markers; V106I (23%) among pandemic and N248D (100%) during post-pandemic Pakistan viruses. Additional N-Glycosylation site; HA S179N (23%), NA I23T(7.6%) and N44S (77%) in place of N386K(77%) were only found in post-pandemic viruses. All isolates showed histidine (H) at position 275 in NA indicating sensitivity to neuraminidase inhibitors. Conclusion: This study shows that the Influenza A(H1N1)pdm09 viruses from Pakistan clustered into two genetic clades, with co-circulation of some variants. Certain key substitutions in the receptor binding site and few changes indicative of virulence were also detected in post-pandemic strains. Therefore, it is imperative to continue monitoring of the viruses for early identification of potential variants of high virulence or emergence of drug-resistant variants.

Keywords: Influenza A (H1N1) pdm09, evolutionary analysis, post pandemic period, Pakistan

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Authors: J. Branstett, V. Gagneux, A. Leleu, B. Levadoux, J. Pascale

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This paper presents the interface CONDUCTHOME which controls home automation systems with a Leap Motion using ‘invariant gesture protocols’. The function of this interface is to simplify the interaction of the user with its environment. A hardware part allows the Leap Motion to be carried around the house. A software part interacts with the home automation box and displays the useful information for the user. An objective of this work is the development a natural/invariant/simple gesture control interface to help elder people/people with disabilities.

Keywords: automation, ergonomics, gesture recognition, interoperability

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Authors: Yogesh Dalvi, Ruby Varghese, Nibu Varghese, C. K. Krishnan Nair

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Introduction: The Genus Phellinus, locally known as Phansomba is a well-known traditional folk medicine. Especially, in Western Ghats of India, many tribes use several species of Phellinus for various ailments related to teeth, throat, tongue, stomach and even wound healing. It is one of the few mushrooms which play a pivotal role in Ayurvedic Dravyaguna. Aim: The present study focuses on to investigate phytochemical analysis, antioxidant, and antitumor (in vitro and in vivo) potential of Phellinus robinae from South India, Kerala Material and Methods: The present study explores the following: 1. Phellinus samples were collected from Ranni, Pathanamthitta district of Kerala state, India from Artocarpus heterophyllus Lam. and species were identified using rDNA region. 2. The fruiting body was shadow dried, powdered and extracted with 50% alcohol using water bath at 60°C which was further condensed by rotary evaporator and lyophilized at minus 40°C temperature. 3. Secondary metabolites were analyzed by using various phytochemical screening assay (Hager’s Test, Wagner’s Test, Sodium hydroxide Test, Lead acetate Test, Ferric chloride Test, Folin-ciocalteu Test, Foaming Test, Benedict’s test, Fehling’s Test and Lowry’s Test). 4. Antioxidant and free radical scavenging activity were analyzed by DPPH, FRAP and Iron chelating assay. 5. The antitumor potential of Water alcohol extract of Phellinus (PAWE) is evaluated through In vitro condition by Trypan blue dye exclusion method in DLA cell line and In vivo by murine model. Result and Discussion: Preliminary phytochemical screening by various biochemical tests revealed presence of a variety of active secondary molecules like alkaloids, flavanoids, saponins, carbohydrate, protein and phenol. In DPPH and FRAP assay PAWE showed significantly higher antioxidant activity as compared to standard Ascorbic acid. While, in Iron chelating assay, PAWE exhibits similar antioxidant activity that of Butylated Hydroxytoluene (BHT) as standard. Further, in the in vitro study, PAWE showed significant inhibition on DLA cell proliferation in dose dependent manner and showed no toxicity on mice splenocytes, when compared to standard chemotherapy drug doxorubicin. In vivo study, oral administration of PAWE showed dose dependent tumor regression in mice and also raised the immunogenicity by restoring levels of antioxidant enzymes in liver and kidney tissue. In both in vitro and in vivo gene expression studies PAWE up-regulates pro-apoptotic genes (Bax, Caspases 3, 8 and 9) and down- regulates anti-apoptotic genes (Bcl2). PAWE also down regulates inflammatory gene (Cox-2) and angiogenic gene (VEGF). Conclusion: Preliminary phytochemical screening revealed that PAWE contains various secondary metabolites which contribute to its antioxidant and free radical scavenging property as evaluated by DPPH, FRAP and Iron chelating assay. PAWE exhibits anti-proliferative activity by the induction of apoptosis through a signaling cascade of death receptor-mediated extrinsic (Caspase8 and Tnf-α), as well as mitochondria-mediated intrinsic (caspase9) and caspase pathways (Caspase3, 8 and 9) and also by regressing angiogenic factor (VEGF) without any inflammation or adverse side effects. Hence, PAWE serve as a potential antioxidant and antitumor agent.

Keywords: antioxidant, antitumor, Dalton lymphoma ascites (DLA), fungi, Phellinus robinae

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Authors: S. Fröhlich, M. Herold, M. Allmer

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Early stage quantitative analysis of host cell protein (HCP) variations is challenging yet necessary for comprehensive bioprocess development. High resolution mass spectrometry (HRMS) provides a high-end technology for accurate identification alongside with quantitative information. Hereby we describe a flexible HRMS assay platform to quantify HCPs relevant in microbial expression systems such as E. Coli in both up and downstream development by means of MVDA tools. Cell pellets were lysed and proteins extracted, purified samples not further treated before applying the SMART tryptic digest kit. Peptides separation was optimized using an RP-UHPLC separation platform. HRMS-MSMS analysis was conducted on an Orbitrap Velos Elite applying CID. Quantification was performed label-free taking into account ionization properties and physicochemical peptide similarities. Results were analyzed using SIEVE 2.0 (Thermo Fisher Scientific) and SIMCA (Umetrics AG). The developed HRMS platform was applied to an E. Coli expression set with varying productivity and the corresponding downstream process. Selected HCPs were successfully quantified within the fmol range. Analysing HCP networks based on pattern analysis facilitated low level quantification and enhanced validity. This approach is of high relevance for high-throughput screening experiments during upstream development, e.g. for titer determination, dynamic HCP network analysis or product characterization. Considering the downstream purification process, physicochemical clustering of identified HCPs is of relevance to adjust buffer conditions accordingly. However, the technology provides an innovative approach for label-free MS based quantification relying on statistical pattern analysis and comparison. Absolute quantification based on physicochemical properties and peptide similarity score provides a technological approach without the need of sophisticated sample preparation strategies and is therefore proven to be straightforward, sensitive and highly reproducible in terms of product characterization.

Keywords: process analytical technology, mass spectrometry, process characterization, MVDA, pattern recognition

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Authors: Lev Bertovsky

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The purpose of this study was to determine the reasons for the formation of false testimony from witnesses and make recommendations on the recognition of such cases. During the studies, which were based on the achievements of professionals in the field of psychology, as well as personal investigative practice, the stages of perception of the information were studied, as well as the process of its reclaim from the memory and transmission to the communicator upon request. Based on the principles of the human brain, kinds of conscientious witness mistakes were systematized. Proposals were formulated for the optimization of investigative actions in cases where the witnesses make an honest mistake with respect to the effects previously observed by them.

Keywords: criminology, eyewitness testimony, honest mistake, information, investigator, investigation, questioning

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Authors: Sreerakuvandana Vandana

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Although the term third gender is relatively new, the language that is in use has already made its way to the concept of identity. With the vast recognition and the transparency in expressing their identity without a tint of embarrassment, it is highly essential to take into account the idea of “identity” and “language”. The community however picks up language as a tool to assert their presence in the “mainstream”, albeit contradictory practices. The paper is an attempt to see how Koti claims and tries to be a language just like any other language. With that, it also identifies how the community wants to be identified as a unique group, but yet want to remain grounded to the ‘mainstream’. The work is an attempt to bring out the secret language of the LGBT community and understand their desire to be recognized as "main stream." The paper is also an attempt to bring into light this language and see if it qualifies to be a language at all.

Keywords: identity, language, queer, transgender

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Authors: Amarjit Singh

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In this paper, a method for extraction of text subtitles in large video is proposed. The video data needs to be annotated for many multimedia applications. Text is incorporated in digital video for the motive of providing useful information about that video. So need arises to detect text present in video to understanding and video indexing. This is achieved in two steps. First step is text localization and the second step is text verification. The method of text detection can be extended to text recognition which finds applications in automatic video indexing; video annotation and content based video retrieval. The method has been tested on various types of videos.

Keywords: video, subtitles, extraction, annotation, frames

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Authors: Hamad Aljassmi, Sangwon Han

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Various solutions for preventing construction defects have been suggested. However, a construction company may have difficulties adopting all these suggestions due to financial and practical constraints. Based on this recognition, this paper aims to identify the most significant defect causes and formulate their defect generation mechanism in order to help a construction company to set priorities of its defect prevention strategies. For this goal, we conducted a questionnaire survey of 106 industry professionals and identified five most significant causes including: (1) organizational culture, (2) time pressure and constraints, (3) workplace quality system, (4) financial constraints upon operational expenses and (5) inadequate employee training or learning opportunities.

Keywords: defect, quality, failure, risk

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Authors: Nilubon Kurubanjerdjit, Nattakarn Iam-On, Ka-Lok Ng

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MicroRNAs are small non-coding RNA found in many different species. They play crucial roles in cancer such as biological processes of apoptosis and proliferation. The identification of microRNA-target genes can be an essential first step towards to reveal the role of microRNA in various cancer types. In this paper, we predict miRNA-target genes for lung cancer by integrating prediction scores from miRanda and PITA algorithms used as a feature vector of miRNA-target interaction. Then, machine-learning algorithms were implemented for making a final prediction. The approach developed in this study should be of value for future studies into understanding the role of miRNAs in molecular mechanisms enabling lung cancer formation.

Keywords: microRNA, miRNAs, lung cancer, machine learning, Naïve Bayes, SVM

Procedia PDF Downloads 379