Search results for: functional annotation analysis

Authors: Shuo Mu, Guangzhi Jiang, Jinsa Chen

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The analysis of Indel for RNA sequencing of clinical samples is easily affected by sequencing experiment errors and software selection. In order to improve the efficiency and accuracy of analysis, we developed an automatic reporting system for Indel recognition and annotation based on image snapshot of transcriptome reads alignment. This system includes sequence local-assembly and realignment, target point snapshot, and image-based recognition processes. We integrated high-confidence Indel dataset from several known databases as a training set to improve the accuracy of image processing and added a bioinformatical processing module to annotate and filter Indel artifacts. Subsequently, the system will automatically generate data, including data quality levels and images results report. Sanger sequencing verification of the reference Indel mutation of cell line NA12878 showed that the process can achieve 83% sensitivity and 96% specificity. Analysis of the collected clinical samples showed that the interpretation accuracy of the process was equivalent to that of manual inspection, and the processing efficiency showed a significant improvement. This work shows the feasibility of accurate Indel analysis of clinical next-generation sequencing (NGS) transcriptome. This result may be useful for RNA study for clinical samples with microsatellite instability in immunotherapy in the future.

Keywords: automatic reporting, indel, next-generation sequencing, NGS, transcriptome

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Authors: Chia-Feng Lu, Yuh-Jen Wang, Yu-Te Wu, Sui-Hing Yan

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This study aimed at investigating whether the functional brain networks constructed using the initial EEG (obtained when patients first visited hospital) can be correlated with the progression of cognitive decline calculated as the changes of mini-mental state examination (MMSE) scores between the latest and initial examinations. We integrated the time–frequency cross mutual information (TFCMI) method to estimate the EEG functional connectivity between cortical regions, and the network analysis based on graph theory to investigate the organization of functional networks in aMCI. Our finding suggested that higher integrated functional network with sufficient connection strengths, dense connection between local regions, and high network efficiency in processing information at the initial stage may result in a better prognosis of the subsequent cognitive functions for aMCI. In conclusion, the functional connectivity can be a useful biomarker to assist in prediction of cognitive declines in aMCI.

Keywords: cognitive decline, functional connectivity, MCI, MMSE

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Authors: Paul Shize Li, Frank Alber

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A fundamental task of clinical genomics is to unravel the functions of genes and their associations with disorders. Although experimental biology has made efforts to discover and elucidate the molecular mechanisms of individual genes in the past decades, still about 40% of human genes have unknown functions, not to mention the diseases they may be related to. For those biologists who are interested in a particular gene with unknown functions, a powerful computational method tailored for inferring the functions and disease relevance of uncharacterized genes is strongly needed. Studies have shown that genes strongly linked to each other in multiple biological networks are more likely to have similar functions. This indicates that the densely connected subgraphs in multiple biological networks are useful in the functional and phenotypic annotation of uncharacterized genes. Therefore, in this work, we have developed an integrative network approach to identify the frequent local clusters, which are defined as those densely connected subgraphs that frequently occur in multiple biological networks and consist of the query gene that has few or no disease or function annotations. This is a local clustering algorithm that models multiple biological networks sharing the same gene set as a three-dimensional matrix, the so-called tensor, and employs the tensor-based optimization method to efficiently find the frequent local clusters. Specifically, massive public gene expression data sets that comprehensively cover dynamic, physiological, and environmental conditions are used to generate hundreds of gene co-expression networks. By integrating these gene co-expression networks, for a given uncharacterized gene that is of biologist’s interest, the proposed method can be applied to identify the frequent local clusters that consist of this uncharacterized gene. Finally, those frequent local clusters are used for function and disease annotation of this uncharacterized gene. This local tensor clustering algorithm outperformed the competing tensor-based algorithm in both module discovery and running time. We also demonstrated the use of the proposed method on real data of hundreds of gene co-expression data and showed that it can comprehensively characterize the query gene. Therefore, this study provides a new tool for annotating the uncharacterized genes and has great potential to assist clinical genomic diagnostics.

Keywords: local tensor clustering, query gene, gene co-expression network, gene annotation

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Authors: Luv Sharma

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Sex determination has been the most intriguing puzzle for forensic pathologists and anthropologists, for which efforts have been made for a long. Sexual dimorphism is well established in the adult pelvis, and it is known to provide the highest level of information about sexual dimorphism. This study was conducted to know whether this dimorphism exists in fetal bones or not. A total of 34 pairs of fetal pelvis bones (22 males and 12 Females), ages ranging from 4 months to full term, were collected from unidentified dead fetuses brought to the Department of Forensic Medicine for routine medicolegal autopsies to study for sexual dimorphism in the Department of Anatomy, Pt. BD Sharma PGIMS, Rohtak. Samples were divided into 2 age groups, and various metric parameters were recorded with the help of a digital vernier caliper. Data obtained was subjected to descriptive and discriminant functional analysis. Results of Descriptive and Discriminant Functional Analysis showed that sex determination can be done with 100% accuracy by using different combinations of parameters of fetal ilium. This study illustrates that sexual dimorphism exists from early fetal life after mid-pregnancy; it can be clearly established by discriminant functional analysis.

Keywords: Ilium, fetus, sex determination, morphometric

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Authors: Ih-Ching Hsu

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Inspired by the so called Jacobi Identity (x y) z + (y z) x + (z x) y = 0, the following class of functional equations EQ I: F [F (x, y), z] + F [F (y, z), x] + F [F (z, x), y] = 0 is proposed, researched and generalized. Research methodologies begin with classical methods for functional equations, then evolve into discovering of any implicit algebraic structures. One of this paper’s major findings is that EQ I, under two additional conditions F (x, x) = 0 and F (x, y) + F (y, x) = 0, proves to be a fundamental functional equation for Lie Algebras. Existence of non-trivial solutions for EQ I can be proven by defining F (p, q) = [p q] = pq –qp, where p and q are quaternions, and pq is the quaternion product of p and q. EQ I can be generalized to the following class of functional equations EQ II: F [G (x, y), z] + F [G (y, z), x] + F [G (z, x), y] = 0. Concluding Statement: With a major finding proven, and non-trivial solutions derived, this research paper illustrates and provides a new functional equation scheme for studies in two major areas: (1) What underlying algebraic structures can be defined and/or derived from EQ I or EQ II? (2) What conditions can be imposed so that conditional general solutions to EQ I and EQ II can be found, investigated and applied?

Keywords: fundamental functional equation, generalized functional equations, Lie algebras, quaternions

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Authors: E. Grochowska-Niedworok, K. Brukało, M. Kardas

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The aim of this study was to analyze and evaluate the consumption of functional food by consumers by: age, sex, formal education level, place of residence and diagnosed diseases. The study employed an ad hoc questionnaire in a group of 300 inhabitants of Upper Silesia voivodship. Knowledge of functional food among the group covered in the study was far from satisfactory. The choice of functional food was of intuitive character. In addition, the group covered was more likely to choose pharmacotherapy instead of diet-related prevention then, which can be associated with presumption of too distant effects and a long period of treatment.

Keywords: consumer choice, functional food, healthy lifestyle, consumer knowledge

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Authors: Hala Raslan, Noha Eltaweel, Hanaa Rasmi, Solaf Kamel, May Magdy, Sherif Ismail, Khalda Amr

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Introduction: Rheumatoid arthritis (RA) is an inflammatory, autoimmune disorder with progressive joint damage. Osteoarthritis (OA) is a degenerative disease of the articular cartilage that shows multiple clinical manifestations or symptoms resembling those of RA. Genetic predisposition is believed to be a principal etiological factor for RA and OA. In this study, we aimed to measure the expression of the top deregulated miRNAs that might be the cause of pathogenesis in both diseases, according to our latest NGS analysis. Six of the deregulated miRNAs were selected as they had multiple target genes in the RA pathway, so they are more likely to affect the RA pathogenesis.Methods: Eighty cases were recruited in this study; 45 rheumatoid arthiritis (RA), 30 osteoarthiritis (OA) patients, as well as 20 healthy controls. The selection of the miRNAs from our latest NGS study was done using miRwalk according to the number of their target genes that are members in the KEGG RA pathway. Total RNA was isolated from plasma of all recruited cases. The cDNA was generated by the miRcury RT Kit then used as a template for real-time PCR with miRcury Primer Assays and the miRcury SYBR Green PCR Kit. Fold changes were calculated from CT values using the ΔΔCT method of relative quantification. Results were compared RA vs Controls and OA vs Controls. Target gene prediction and functional annotation of the deregulated miRNAs was done using Mienturnet. Results: Six miRNAs were selected. They were miR-15b-3p, -128-3p, -194-3p, -328-3p, -542-3p and -3180-5p. In RA samples, three of the measured miRNAs were upregulated (miR-194, -542, and -3180; mean Rq= 2.6, 3.8 and 8.05; P-value= 0.07, 0.05 and 0.01; respectively) while the remaining 3 were downregulated (miR-15b, -128 and -328; mean Rq= 0.21, 0.39 and 0.6; P-value= <0.0001, <0.0001 and 0.02; respectively) all with high statistical significance except miR-194. While in OA samples, two of the measured miRNAs were upregulated (miR-194 and -3180; mean Rq= 2.6 and 7.7; P-value= 0.1 and 0.03; respectively) while the remaining 4 were downregulated (miR-15b, -128, -328 and -542; mean Rq= 0.5, 0.03, 0.08 and 0.5; P-value= 0.0008, 0.003, 0.006 and 0.4; respectively) with statistical significance compared to controls except miR-194 and miR-542. The functional enrichment of the selected top deregulated miRNAs revealed the highly enriched KEGG pathways and GO terms. Conclusion: Five of the studied miRNAs were greatly deregulated in RA and OA, they might be highly involved in the disease pathogenesis and so might be future therapeutic targets. Further functional studies are crucial to assess their roles and actual target genes.

Keywords: MiRNAs, expression, rheumatoid arthritis, osteoarthritis

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Authors: Olakunle Moses Makanjuola, Adebola Ajayi

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Noodles are made from unleavened dough, rolled flat and cut into shapes. The instant noodle market is growing fast in Asian countries and is gaining popularity in the western market. This project reports on the proximate functional and sensory evaluation of different brands of instant noodles in Nigeria. The comparisons were based on proximate functional and sensory evaluation of the product. The result obtained from the proximate analysis showed that sample QHR has the highest moisture content, sample BMG has the highest protein content, sample CPO has the highest fat content, sample. The obtained result from the functional properties showed that sample BMG (Dangote noodles) had the highest volume increase after cooking due to its high swelling capacity, high water absorption capacity and high hydration capacity. Sample sensory analysis of the noodles showed that all the samples are of significant difference (at P < 0.05) in terms of colour, texture, and aroma but there is no significant difference in terms of taste and overall acceptability. Sample QHR (Indomie noodles) is the most preferred by the panelists.

Keywords: proximate, functional, sensory evaluation, noodles

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Authors: L. Kamandulytė-Merfeldienė

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The paper deals with the main issues of methodology of the Corpus of Spoken Lithuanian which was started to be developed in 2006. At present, the corpus consists of 300,000 grammatically annotated word forms. The creation of the corpus consists of three main stages: collecting the data, the transcription of the recorded data, and the grammatical annotation. Collecting the data was based on the principles of balance and naturality. The recorded speech was transcribed according to the CHAT requirements of CHILDES. The transcripts were double-checked and annotated grammatically using CHILDES. The development of the Corpus of Spoken Lithuanian has led to the constant increase in studies on spontaneous communication, and various papers have dealt with a distribution of parts of speech, use of different grammatical forms, variation of inflectional paradigms, distribution of fillers, syntactic functions of adjectives, the mean length of utterances.

Keywords: CHILDES, corpus of spoken Lithuanian, grammatical annotation, grammatical disambiguation, lexicon, Lithuanian

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Authors: Neda Lovričević, Đilda Pečarić, Josip Pečarić

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The Jensen functional in its discrete form is brought in relation to the Csiszar divergence functional, this time via its monotonicity property. This approach presents a generalization of the previously obtained results that made use of interpolating Jensen-type inequalities. Thus the monotonicity property is integrated with the Zipf-Mandelbrot law and applied to f-divergences for probability distributions that originate from the Csiszar divergence functional: Kullback-Leibler divergence, Hellinger distance, Bhattacharyya distance, chi-square divergence, total variation distance. The Zipf-Mandelbrot and the Zipf law are widely used in various scientific fields and interdisciplinary and here the focus is on the aspect of the mathematical inequalities.

Keywords: Jensen functional, monotonicity, Csiszar divergence functional, f-divergences, Zipf-Mandelbrot law

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Authors: Vun Yee Thien, Kenneth Francis Rodrigues, Clemente Michael Vui Ling Wong, Wilson Thau Lym Yong

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Transcriptomes associated with the process of photosynthesis have offered insights into the mechanism of gene regulation in terrestrial plants; however, limited information is available as far as macroalgae are concerned. This investigation aims to decipher the underlying mechanisms associated with photosynthesis in the red alga, Kappaphycus alvarezii, by performing a differential expression analysis on a de novo assembled transcriptomes. Comparative analysis of gene expression was designed to examine the alteration of light qualities and its effect on physiological mechanisms in the red alga. High-throughput paired-end RNA-sequencing was applied to profile the transcriptome of K. alvarezii irradiated with different wavelengths of light (blue 492-455 nm, green 577-492 nm and red 780-622 nm) as compared to the full light spectrum, resulted in more than 60 million reads individually and assembled using Trinity and SOAPdenovo-Trans. The transcripts were annotated in the NCBI non-redundant (nr) protein, SwissProt, KEGG and COG databases with a cutoff E-value of 1e-5 and nearly 30% of transcripts were assigned to functional annotation by Blast searches. Differential expression analysis was performed using edgeR. The DEGs were designated to six categories: BL (blue light) regulated, GL (green light) regulated, RL (red light) regulated, BL or GL regulated, BL or RL regulated, GL or RL regulated, and either BL, GL or RL regulated. These DEGs were mapped to terms in KEGG database and compared with the whole transcriptome background to search for genes that regulated by light quality. The outcomes of this study will enhance our understanding of molecular mechanisms underlying light-induced responses in red algae.

Keywords: de novo transcriptome sequencing, differential gene expression, Kappaphycus alvareziired, red alga

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Authors: Wen-jing Shan

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The Chinese annotated edition of “Experience and education: The 60th anniversary edition,” originally written in English by John Dewey (1859-1952), was published in 2015 by this author. A report of the process and results of the translation and annotation of the book is the purpose of this paper. It is worth mentioning that the original 1938 edition was considered as the best concise statement on education by John Dewey, one the most important educational theorists of the twentieth century. One of the features of this The 60th anniversary edition is that the original publisher, Kappa Delta Pi International Honor Society, invited four contemporary Deweyan scholars who had been awarded the Society’s Laureate Scholar to write a review of the book published by Dewey, who was the first to receive this honor. The four scholars are Maxine Greene(1917-2014), Philip W. Jackson(1928-2015), Linda Darling-Hammond(1951-), and O. L. Davis, Jr.(1928-). The original 1938 edition, the best concise statement on education by the most important educational theorist of the twentieth century, was translated into Chinese for five times after its publication in the U.S.A, three in the 1940s, one in the 1990s, and one in 2010s. Nonetheless, the five translations have few or no annotations and have some flaws of mis-interpretations and lack of information. The author retranslated and annotated the book to make the interpretations more faithful, expressive, and elegant, and providing the readers with more understanding and more correct information. This author started the project of translation and annotation sponsored by Taiwan Ministry of Science and Technology in August 2011 and finished and published by July 2015. The work, the author, did was divided into three stages. First, in the preparatory stage of the project, the summary of each chapter, the rationale of the book, the textual commentary, the development of the original and Chinese editions, and reviews and criticisms, as well as Dewey’s biography and bibliography were initially investigated. Secondly, on the basis of the above preliminary work, the translation with annotation of Experience and Education, an epitome of Dewey’s biography and bibliography, a chronology, and a critical introduction for the Experience and Education were written. In the critical introduction, Dewey’s philosophy of experience and educational ideas will be examined along the timeline of human thought. And the vast literature about Dewey and his work will be instrumental to reveal the historical significance of Experience and Education on the modern age and make the critical introduction more knowledgeable. Third, the final stage took another two years to review and revise the draft of the work and send it for publication. There are two parts in the book. The first part is a scholarly introduction including Dewey’s chronicle (in short form), Dewey’s mind, people and life, the importance of “Experience and education”, the necessity of re-translation and re-annotation of “Experience and education” into Chinese. The second part is the re-translation and re-annotation version, including Dewey’s “Experience and education” and four papers written by contemporary scholars.

Keywords: John Dewey, experience and education: the 60th anniversary edition, translation, annotation

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Authors: Preetham Shankapal, Jill King, Kori Murray, Corby Martin, Paula Giselman, Jason Hicks, Owen Carmicheal

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Activation of reward and satiety networks in the brain while processing palatable food cues, as well as functional connectivity during rest has been studied using functional Magnetic Resonance Imaging of the brain in various obesity phenotypes. However, functional connectivity within the reward and satiety network during food cue processing is understudied. 14 obese individuals underwent two fMRI scans during viewing of Macronutrient Picture System images. Each scan included two blocks of images of High Sugar/High Fat (HSHF), High Carbohydrate/High Fat (HCHF), Low Sugar/Low Fat (LSLF) and also non-food images. Seed voxels within seven food reward relevant ROIs: Insula, putamen and cingulate, precentral, parahippocampal, medial frontal and superior temporal gyri were isolated based on a prior meta-analysis. Beta series correlation for task-related functional connectivity between these seed voxels and the rest of the brain was computed. Voxel-level differences in functional connectivity were calculated between: first and the second scan; individuals who saw novel (N=7) vs. Repeated (N=7) images in the second scan; and between the HC/HF, HSHF blocks vs LSLF and non-food blocks. Computations and analysis showed that during food image viewing, reward network ROIs showed significant functional connectivity with each other and with other regions responsible for attentional and motor control, including inferior parietal lobe and precentral gyrus. These functional connectivity values were heightened among individuals who viewed novel HS/HF images in the second scan. In the second scan session, functional connectivity was reduced within the reward network but increased within attention, memory and recognition regions, suggesting habituation to reward properties and increased recollection of previously viewed images. In conclusion it can be inferred that Functional Connectivity within reward network and between reward and other brain regions, varies by important experimental conditions during food photography viewing, including habituation to shown foods.

Keywords: fMRI, functional connectivity, task-based, beta series correlation

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Authors: Jialin Ma, Jia Meng

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Genomic features, the genome-based coordinates, are commonly used for the representation of biological features such as genes, RNA transcripts and transcription factor binding sites. For the analysis of RNA-related genomic features, such as RNA modification sites, a common task is to correlate these features with transcript components (5'UTR, CDS, 3'UTR) to explore their distribution characteristics in terms of transcriptomic coordinates, e.g., to examine whether a specific type of biological feature is enriched near transcription start sites. Existing approaches for performing these tasks involve the manipulation of a gene database, conversion from genome-based coordinate to transcript-based coordinate, and visualization methods that are capable of showing RNA transcript components and distribution of the features. These steps are complicated and time consuming, and this is especially true for researchers who are not familiar with relevant tools. To overcome this obstacle, we develop a dedicated web app TARF, which represents web toolkit for annotating RNA-related genomic features. TARF web tool intends to provide a web-based way to easily annotate and visualize RNA-related genomic features. Once a user has uploaded the features with BED format and specified a built-in transcript database or uploaded a customized gene database with GTF format, the tool could fulfill its three main functions. First, it adds annotation on gene and RNA transcript components. For every features provided by the user, the overlapping with RNA transcript components are identified, and the information is combined in one table which is available for copy and download. Summary statistics about ambiguous belongings are also carried out. Second, the tool provides a convenient visualization method of the features on single gene/transcript level. For the selected gene, the tool shows the features with gene model on genome-based view, and also maps the features to transcript-based coordinate and show the distribution against one single spliced RNA transcript. Third, a global transcriptomic view of the genomic features is generated utilizing the Guitar R/Bioconductor package. The distribution of features on RNA transcripts are normalized with respect to RNA transcript landmarks and the enrichment of the features on different RNA transcript components is demonstrated. We tested the newly developed TARF toolkit with 3 different types of genomics features related to chromatin H3K4me3, RNA N6-methyladenosine (m6A) and RNA 5-methylcytosine (m5C), which are obtained from ChIP-Seq, MeRIP-Seq and RNA BS-Seq data, respectively. TARF successfully revealed their respective distribution characteristics, i.e. H3K4me3, m6A and m5C are enriched near transcription starting sites, stop codons and 5’UTRs, respectively. Overall, TARF is a useful web toolkit for annotation and visualization of RNA-related genomic features, and should help simplify the analysis of various RNA-related genomic features, especially those related RNA modifications.

Keywords: RNA-related genomic features, annotation, visualization, web server

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Authors: Ian Walsh, Terry Nguyen-Khuong, Christopher H. Taron, Pauline M. Rudd

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Glycoproteins and their covalently bonded glycans play critical roles in the immune system, cell communication, disease and disease prognosis. Ultra performance liquid chromatography (UPLC) coupled with mass spectrometry is conventionally used to qualitatively and quantitatively characterise glycan structures in a given sample. Exoglycosidases are enzymes that catalyze sequential removal of monosaccharides from the non-reducing end of glycans. They naturally have specificity for a particular type of sugar, its stereochemistry (α or β anomer) and its position of attachment to an adjacent sugar on the glycan. Thus, monitoring the peak movements (both in the UPLC and MS1) after application of exoglycosidases provides a unique and effective way to annotate sugars with high detail - i.e. differentiating positional and linkage isomers. Manual annotation of an exoglycosidase experiment is difficult and time consuming. As such, with increasing sample complexity and the number of exoglycosidases, the analysis could result in manually interpreting hundreds of peak movements. Recently, we have implemented pattern recognition software for automated interpretation of UPLC-MS1 exoglycosidase digestions. In this work, we explain the software, indicate how much time it will save and provide example usage showing the annotation of positional and linkage isomers in Immunoglobulin G, apolipoprotein J, and simple glycan standards.

Keywords: bioinformatics, automated glycan assignment, liquid chromatography, mass spectrometry

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Authors: Youn-Sung Kim, Hye-Mi Kim, Sang-Hoon Seo, Jaden Cha

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This International standard IEC 61508 sets out a generic approach for all safety lifecycle activities for systems comprised of electrical/electronic/programmable electronic (E/E/PE) elements that are used to perform safety functions. The control unit in stage control system is safety related facilities to control state and speed for stage system running, and it performs safety-critical function by stage control system. The controller unit is part of safety loops corresponding to the IEC 61508 and classified as logic part in the safety loop. In this paper, we analyze using FMEDA (Failure Mode Effect and Diagnostic Analysis) to verification for fault tolerance methods and functional safety of control unit. Moreover, we determined SIL (Safety Integrity Level) for control unit according to the safety requirements defined in IEC 61508-2 based on an analyzed functional safety.

Keywords: safety function, failure mode effect, IEC 61508-2, diagnostic analysis, stage control system

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Authors: Harihara Subramaniam Salem Chandrasekaran

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Scrum framework is built upon emphasises on self-management and cross-functionality around which the framework is built upon. However, in reality, many organisations that adapt scrum are having functional structures and hierarchy. In such cases, the scrum teams are built with a mixture of people from different functionalities to deliver specific products and projects. For instance, every scrum team would be having a designer, developer or tester, etc.; who will make their own contribution to an increment. This results in people centric dependencies for delivering an increment and thus creating bottlenecks at certain times. This paper presents in detail how functional silos are a challenge to the scrum teams and hinder the incremental deliver of value to customers. The study has been conducted with 14 individuals from the software industry from different functional departments, and the findings summarize that functional silos are naturally formed due to the organizational dynamics and hierarchy and the mindset of being confined within the silos is detrimental to the fundamental values of agile and scrum. The paper also sheds light on what the individuals propose to overcome the silo mindset within the scrum team and focus on continuous improvement in delivery excellence.

Keywords: agile, scrum, cross-functional, functional silos

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Authors: Sadiq Aminu, Ahmed Lamido

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This research studies Barack Obama’s second inaugural speech using Halliday’s Systemic Functional Grammar (SFG). SFG is a text grammar which describes how language is used, so that the meaning of the text can be better understood. The primary source of data in this research work is Barack Obama’s second inaugural speech which was obtained from the internet. The analysis of the speech was based on the ideational and textual metafunctions of Systemic Functional Grammar. Specifically, the researcher analyses the Process Types and Participants (ideational) and the Theme/Rheme (textual). It was found that material process (process of doing) was the most frequently used ‘Process type’ and ‘We’ which refers to the people of America was the frequently used ‘Theme’. Application of the SFG theory, therefore, gives a better meaning to Barack Obama’s speech.

Keywords: ideational, metafunction, rheme, textual, theme

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Authors: Parvin Malhami

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The purpose of the present study was to investigate the effects of two functional and functional stretching methods of the leg muscles on a selection of kinematical and kinetic indicators among women with ankle instability. Twenty-four persons were targeted and randomly divided into the functional exercise (8 persons), extra-functional exercise (8 persons) and control (8 persons) groups on the basis of inclusion and exclusion criteria. The experimental groups received stretching for eight weeks, 3 sessions each week, and the control group merely performed its daily activities. Then, in order to measure the pre -test and post -test variables, the dorsi flexion, Plantar flexion and ground reaction force were investigated and measured. Data were analyzed using paired T-test and independent T-tests at a significant level of 0.05. All statistical analyses were conducted using SPSS 25 software. The results of the T-test showed the significant effect of eight weeks of functional and Extra functional exercises on dorsi Flexion, Plantar Flexion and ground reaction force. (P≤ 0/001). The results of this study showed that the implementation of the functional and Extra-functional exercise protocol had an impact on the amount of Ankle dorsi Flexion and the Plantar felxion of women with an ankle instability. It was also found that muscle flexibility following the stretch ability of the gastrocnemius muscles facilitates the walking of the wrist installation by affecting the amount of wrist flexion, so these people are recommended to use the functional and extra-functional exercise protocol.

Keywords: functional stretching, extra functional stretching, dorsi flexion, plantar flexion

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Authors: Ewa Flaczyk, Monika Przeor, Joanna Kobus-Cisowska, Józef Korczak

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The aim of this paper was to collect the information concerning the most popular raw plant materials of antidiabetic activity, in a context of functional food developing production. The elaboration discusses morphological elements possible for an application in functional food production of the plants such as: common bean, ginger, Ceylon cinnamon, white mulberry, fenugreek, French lilac, ginseng, jambolão, and bitter melon. An activity of bioactive substances contained in these raw plant materials was presented, pointing their antiglycemic and also hypocholesterolemic, antiarthritic, antirheumatic, antibacterial, and antiviral activity in the studies on humans and animals. Also the genesis of functional food definition was presented.

Keywords: antiglycemic activity, raw plant materials, functional food, food, nutritional sciences

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Authors: Mahdi Jalili

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Functional connectivity in the human brain can be represented as a network using electroencephalography (EEG) signals. Network representation of EEG time series can be an efficient vehicle to understand the underlying mechanisms of brain function. Brain functional networks – whose nodes are brain regions and edges correspond to functional links between them – are characterized by neurobiologically meaningful graph theory metrics. This study investigates the degree to which graph theory metrics are sex dependent. To this end, EEGs from 24 healthy female subjects and 21 healthy male subjects were recorded in eyes-closed resting state conditions. The connectivity matrices were extracted using correlation analysis and were further binarized to obtain binary functional networks. Global and local efficiency measures – as graph theory metrics– were computed for the extracted networks. We found that male brains have a significantly greater global efficiency (i.e., global communicability of the network) across all frequency bands for a wide range of cost values in both hemispheres. Furthermore, for a range of cost values, female brains showed significantly greater right-hemispheric local efficiency (i.e., local connectivity) than male brains.

Keywords: EEG, brain, functional networks, network science, graph theory

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Authors: Najiba Ouled Omar, Azza Harbaoui, Henda Ben Ghezala

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Current research practices sentiment analysis with a focus on social networks, DEfi Fouille de Texte (DEFT) (Text Mining Challenge) evaluation campaign focuses on opinion mining and sentiment analysis on social networks, especially social network Twitter. It aims to confront the systems produced by several teams from public and private research laboratories. DEFT offers participants the opportunity to work on regularly renewed themes and proposes to work on opinion mining in several editions. The purpose of this article is to scrutinize and analyze the works relating to opinions mining and sentiment analysis in the Twitter social network realized by DEFT. It examines the tasks proposed by the organizers of the challenge and the methods used by the participants.

Keywords: opinion mining, sentiment analysis, emotion, polarity, annotation, OSEE, figurative language, DEFT, Twitter, Tweet

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Authors: Shengzhu Cao, Hui Zhou, Gan Wu, Lanxi Wanhg, Kaifeng Zhang, Rui Wang, Hu Wang

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The functional micro and nanostructures, which can endow material surface with unique properties such as super-absorptance, hydrophobic and drag reduction. Recently, femtosecond laser ablation has been demonstrated to be a promising technology for surface functional micro and nanostructures fabrication. In this paper, using femtosecond laser ablation processing technique, we fabricated functional micro and nanostructures on Ti and Al alloy surfaces, test results showed that processed surfaces have 82%~96% absorptance over a broad wavelength range from ultraviolet to infrared. The surface function properties, which determined by micro and nanostructures, could be modulated by variation laser parameters. These functional surfaces may find applications in such areas as photonics, plasmonics, spaceborne devices, thermal radiation sources, solar energy absorbers and biomedicine.

Keywords: surface functional, micro and nanostructures, femtosecond laser, ablation

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Authors: S. Srednyak

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We study a class of functional partial differential equations(FPDEs). This class is suggested by Quantum Field Theory. We derive general properties of solutions to such equations. In particular, we demonstrate that they lead to systems of coupled integral equations with singular kernels. We show that solutions to such hierarchies can be sought among functions with regular singularities at a countable set of subvarieties of the physical space. We also develop a formal analogy of basic constructions of differential geometry on functional manifolds, as this is necessary for in depth study of FPDEs. We also consider the case of linear overdetermined systems of functional differential equations and show that it can be completely solved in terms of formal solutions of a functional equation that is a functional analogy of a system of determined algebraic equations. This development leads us to formally define the functional analogy of algebraic geometry, which we call functional algebraic geometry. We study basic properties of functional algebraic varieties. In particular, we investigate the case of a formally discrete set of solutions. We also define and study functional analogy of discriminants. In the case of fully determined systems such that the defining functionals have regular singularities, we demonstrate that formal solutions can be sought in the class of functions with regular singularities. This case provides a practical way to apply our results to physics problems.

Keywords: functional equations, quantum field theory, holomorphic functions, Yang Mills mass gap problem, quantum chaos

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Authors: Roham Rafiee, Hadi Hesamsadat

Abstract:

In this study, a parametric finite element modeling is developed to analyze failure modes of FRP pipes subjected to internal pressure. First-ply failure pressure and functional failure pressure was determined by a progressive damage modeling and then it is validated using experimental observations. The influence of both winding angle and fiber volume fraction is studied on the functional failure of FRP pipes and it corresponding pressure. It is observed that despite the fact that increasing fiber volume fraction will enhance the mechanical properties, it will be resulted in lower values for functional failure pressure. This shortcoming can be compensated by modifying the winding angle in angle plies of pipe wall structure.

Keywords: composite pipe, functional failure, progressive modeling, winding angle

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Authors: Timothy William Lawrence

Abstract:

The goal of this paper is to research and categorize the four basic verb types found in the Spanish descriptive grammar book Método de los Relojes using verb clauses as representation as found in M.A.K. Halliday's Systemic-Functional Grammar with the purpose of establishing theoretical along with syntactical parallels and deviations between English and Spanish. Results confirm theoretical correlations exist therefore leading to an analysis of English grammar syntax resulting in delineating commonalities and differences from Spanish. Corpora searches were carried out on different patterns of syntactical structures confirming divergences in verb syntax, making it possible to establish parameters to adapt English verbs to the criteria of the four basic Método de los Relojes verb types.

Keywords: corpus studies, Método de los Relojes, structural-functional grammar, verb syntax

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Authors: Arenkala Kichu

Abstract:

This paper consolidates and tries to bring out the findings that investigated in Kohima and Mokokchung districts in Nagaland, which is in the northeastern part of India. The aim of this paper is to test the speaking and writing skills of the undergraduate learners who opt functional English as one of their papers. functional English is taught in just two colleges; Fazl Ali College and Kohima Colleges, out of 15 government and 36 private colleges in the state. This research (based on several observations made by Naga researchers) hypothesizes that functional English enhances competencies at the undergraduate level, which would open doors to work, learn more and better prospects. It is expected that learners in Functional English class, which follows the communicative language teaching method, might be the answers to those problems, as to why proficiency level still leaves much to be desired, in spite of the advent of the education over a hundred years ago. This type of teaching follows only in functional English class in these two colleges.

Keywords: enhancing competencies, speaking skills, undergraduate level, writing skills

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Authors: Charintorn Suwannawong, Tananpon Yavilas, Sopida Boonaneksap, Chotika Viriyarattanasak, Chairath Tangduangdee

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With increasing aging population and health conscious consumers, the demand for health promoting products such as functional foods, dietary supplements, and nutraceutical products has continuously increased in Thailand. Nevertheless, the strategic framework for regulatory functional food developments in Thailand is still unclear. The objective of this study was to survey stakeholders’ perspectives on three scopes, consisting of 1) the current status 2) obstacles, and 3) future trend for the development and production of functional foods in Thailand. A survey was conducted by interviewing ten experts from governmental organization, industrial sector and academic institute. The obtained results show that there is no established definition for functional foods in Thailand. There is a variety of raw materials that are capable to be potential ingredients for functional food production in Thailand and exported to global market. However, the scaling up technology into a commercial production is limited. Moreover, there is a need to establish the infrastructures, such as testing laboratory, and regulatory standards for quality control and ensuring product safety. This information is useful for government in the development of the strategic framework and policy statement on improvement of functional food industry in Thailand.

Keywords: functional foods, interview, perspective, Thailand

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Authors: Karolis Leonavičius, Dalius Kučiauskas, Dangiras Lukošius, Arnoldas Jasiūnas, Kostas Zdanys, Rokas Stanislovas, Emilis Gegevičius, Žana Kapustina, Juozas Nainys

Abstract:

Screening throughput is a common bottleneck in many research areas, including functional genomics, drug discovery, and directed evolution. High-throughput screening techniques can be classified into two main categories: (i) affinity-based screening and (ii) functional screening. The first one relies on binding assays that provide information about the affinity of a test molecule for a target binding site. Binding assays are relatively easy to establish; however, they reveal no functional activity. In contrast, functional assays show an effect triggered by the interaction of a ligand at a target binding site. Functional assays might be based on a broad range of readouts, such as cell proliferation, reporter gene expression, downstream signaling, and other effects that are a consequence of ligand binding. Screening of large cell or gene libraries based on direct activity rather than binding affinity is now a preferred strategy in many areas of research as functional assays more closely resemble the context where entities of interest are anticipated to act. Droplet sorting is the basis of high-throughput functional biological screening, yet its applicability is limited due to the technical complexity of integrating high-performance droplet analysis and manipulation systems. As a solution, the Droplet Genomics Styx platform enables custom droplet sorting workflows, which are necessary for the development of early-stage or complex biological therapeutics or industrially important biocatalysts. The poster will focus on the technical design considerations of Styx in the context of its application spectra.

Keywords: functional screening, droplet microfluidics, droplet sorting, dielectrophoresis

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Authors: Abdul Musaweer Habib, Habibul Hasan Mazumder, Saiful Islam, Sohel Sikder, Omar Faruk Sikder

Abstract:

The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1499 proteins of Fusobacterium nucleatum, which has no homolog in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the KEGG Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the 3-D structure of these three proteins. Finally, determination of ligand binding sites of the key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against Fusobacterium nucleatum.

Keywords: colorectal cancer, drug target, Fusobacterium nucleatum, homology modeling, ligands

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