Search results for: deletion 13q14

Authors: D. Estrella, A. Silva, R. Zapata, H. Rubio

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A total of 100 primary caregivers (mothers, fathers, grandparents) with at least one child or grandchild with a diagnosis of congenital bilateral profound deafness were assessed in order to evaluate the functionality of families with a deaf member, who was evaluated by specialists in audiology, molecular biology, genetics and psychology. After confirmation of the clinical diagnosis, DNA from the patients and parents were analyzed in search of the 35delG deletion of the GJB2 gene to determine who possessed the mutation. All primary caregivers were provided psychological support, regardless of whether or not they had the mutation, and prior and subsequent, the family APGAR test was applied. All parents, grandparents were informed of the results of the genetic analysis during the psychological intervention. The family APGAR, after psychological and genetic counseling, showed that 14% perceived their families as functional, 62% moderately functional and 24% dysfunctional. This shows the importance of psychological support in family functionality that has a direct impact on the quality of life of these families.

Keywords: deafness, psychological support, family, adaptation to disability

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Authors: Camille Rault, Mark Bahr

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The aim of the present study was to develop a contemporaneous instrument measuring adolescent’s subjective well-being (SWB). The instrument development underwent a three-phase pilot study. Phase one (N = 31) used a qualitative approach to generate domains of SWB relevant to adolescents. During the second phase (N = 22), items were tested targeting these domains. Finally, the third phase (N = 22) assisted in addition, deletion and refinement according to the first two phases of the pilot. A total of 49 items were retained for the final version of the instrument. The Contemporary Adolescent Well-Being Scale (CAWBS) was administered to 1071 school children (599 girls) aged between ten to 18 years old (M = 14,70; SD = 1.45) from Queensland, Australia. Results confirmed the seven-factor construct hypothesized and explained 45% of the variance. The questionnaire pertained to seven domains of adolescent’s SWB, namely; Overall life satisfaction; Bullying; Body image; Social connectedness; Activities; Control appraisal; and Negative feelings. Reliability was shown to be acceptable with Cronbach’s alpha ranging from .58 to .89. Future research should refine the CAWBS and investigate the psychometric properties of this instrument.

Keywords: adolescence, construct validity, instrument, subjective well-being

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Authors: A. Satty, H. Mwambi

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Much clinical trials data-based research are characterized by the unavoidable problem of dropout as a result of missing or erroneous values. This paper aims to review some of the various techniques to address the dropout problems in longitudinal clinical trials. The fundamental concepts of the patterns and mechanisms of dropout are discussed. This study presents five general techniques for handling dropout: (1) Deletion methods; (2) Imputation-based methods; (3) Data augmentation methods; (4) Likelihood-based methods; and (5) MNAR-based methods. Under each technique, several methods that are commonly used to deal with dropout are presented, including a review of the existing literature in which we examine the effectiveness of these methods in the analysis of incomplete data. Two application examples are presented to study the potential strengths or weaknesses of some of the methods under certain dropout mechanisms as well as to assess the sensitivity of the modelling assumptions.

Keywords: incomplete longitudinal clinical trials, missing at random (MAR), imputation, weighting methods, sensitivity analysis

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Authors: Alhadi Bustaman, Soeganda Formalidin, Titin Siswantining

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DNA microarray technology is used to analyze thousand gene expression data simultaneously and a very important task for drug development and test, function annotation, and cancer diagnosis. Various clustering methods have been used for analyzing gene expression data. However, when analyzing very large and heterogeneous collections of gene expression data, conventional clustering methods often cannot produce a satisfactory solution. Biclustering algorithm has been used as an alternative approach to identifying structures from gene expression data. In this paper, we introduce a transform technique based on singular value decomposition to identify normalized matrix of gene expression data followed by Mixed-Clustering algorithm and the Lift algorithm, inspired in the node-deletion and node-addition phases proposed by Cheng and Church based on Agglomerative Hierarchical Clustering (AHC). Experimental study on standard datasets demonstrated the effectiveness of the algorithm in gene expression data.

Keywords: agglomerative hierarchical clustering (AHC), biclustering, gene expression data, lymphoma, singular value decomposition (SVD)

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Authors: Neda Razavi Kaleibar, Bahloul Salmani

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The present study dealt with the multimodal analysis of two cinematic adaptations of The Great Gatsby as intersemiotic translation. The assessment in this study went beyond the faithfulness based on repetition, addition, deletion, and creation which limit the analysis from other aspects. In fact, this research aimed to pinpoint the role of multimodality in examining the intersemiotic translations of the novel into film by means of analyzing different applied modes. Through a qualitative type of research, the analysis was conducted based on the theory proposed by Burn as Kineikonic mode theory derived from the concept of multimodality. The results of the study revealed that due to the applied modes, each adaptation represents a sense and meaning different from the other one. Analyzing the results and discussions, it was concluded that not only the modes have an undeniable role in film adaptations, but rather multimodal analysis including different nonverbal modes can be a useful and functional choice for analyzing the intersemiotic translations.

Keywords: cinematic adaptation, intersemiotic translation, kineikonic mode, multimodality

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Authors: Hazha Hidayat, Shayma Ibrahim

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Folate metabolism plays a crucial role in the normal development of the neonatal central nervous system. It is regulated by MTHFR gene polymorphism. Any factors, which will affect this metabolism either by hereditary or gene mutation will lead to many mental disorders. The purpose of this study was to investigate whether MTHFR gene mutation contributes to the development of mental retardation and CP combined with mental retardation in Erbil city. DNA was isolated from the peripheral blood samples of 40 cases suffering from mental retardation (MR) and CP combined with MR were recruited, sequence the 4, 6, 7, 8 exons of the MTHFR gene were done to identify the variants. Exons were amplified by PCR technique and then sequenced according to Sanger method to show the differences with MTHFR reference sequences. We observed (14) mutations in 4, 6, 7, 8 exons in the MTHFR gene associated with Cerebral Palsy combined with mental retardation included deletion, insertion, Substitution. The current study provides additional evidence that multiple variations in the MTHFR gene are associated with mental retardation and Cerebral Palsy.

Keywords: methylenetetrahydrofolate reductase (MTHFR) gene, SNPs, homocysteine, sequencing

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Authors: Vadim E. Levit, Eugen Mandrescu

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A graph is well-covered if all its maximal independent sets are of the same size. A well-covered graph is 1-well-covered if deletion of every vertex of the graph leaves it well-covered. It is known that a graph without isolated vertices is 1-well-covered if and only if every two disjoint independent sets are included in two disjoint maximum independent sets. Well-covered graphs are related to combinatorial commutative algebra (e.g., every Cohen-Macaulay graph is well-covered, while each Gorenstein graph without isolated vertices is 1-well-covered). Our intent is to construct several infinite families of 1-well-covered graphs using the following known graph operations: corona, join, and rooted product of graphs. Adopting some known techniques used to advantage for well-covered graphs, one can prove that: if the graph G has no isolated vertices, then the corona of G and H is 1-well-covered if and only if H is a complete graph of order two at least; the join of the graphs G and H is 1-well-covered if and only if G and H have the same independence number and both are 1-well-covered; if H satisfies the property that every three pairwise disjoint independent sets are included in three pairwise disjoint maximum independent sets, then the rooted product of G and H is 1-well-covered, for every graph G. These findings show not only how to generate some more families of 1-well-covered graphs, but also that, to this aim, sometimes, one may use graphs that are not necessarily 1-well-covered.

Keywords: maximum independent set, corona, concatenation, join, well-covered graph

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Authors: Chapman Eze Nnadozie

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Relational databases constitute a very vital tool for the effective management and administration of both personal and organizational data. Data access ranges from a single user database management software to a more complex distributed server system. This paper intends to appraise the use a programming language extension like structured query language (SQL) to establish links to a relational database (Microsoft Access 2013) using Visual C++ 9 programming language environment. The methodology used involves the creation of tables to form a database using Microsoft Access 2013, which is Object Linking and Embedding (OLE) database compliant. The SQL command is used to query the tables in the database for easy extraction of expected records inside the visual C++ environment. The findings of this paper reveal that records can easily be accessed and manipulated to filter exactly what the user wants, such as retrieval of records with specified criteria, updating of records, and deletion of part or the whole records in a table.

Keywords: data access, database, database management system, OLE, programming language, records, relational database, software, SQL, table

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Authors: Emmanuel Uba, Lily Chimuanya, Maryam Tar

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Orthographic engineering is no longer the preserve of the Short Messaging Service (SMS), which is characterised by limited space. Such stylistic creativity or deviation is fast creeping into real-time messaging, popularly known as Instant Messaging (IM), despite the large number of characters allowed. This occurs at various linguistic levels: phonology, morphology, syntax, etc. Nigerians are not immune to this linguistic stylisation. This study investigates the phonological and meta-phonological conventions of the messages sent and received via WhatsApp by Nigerian graduates. This is ontological study of 250 instant messages collected from 98 graduates from different ethnic groups in Nigeria. The selection and analysis of the messages are based on figure and ground principle. The results reveal the use of accent stylisation, phoneme substitution, blending, consonantisation (a specialised form of deletion targeting vowels), numerophony (using a figure/number, usually 1-10, to represent a word or syllable that has the same sound) and phonetic respelling in the IMs sent by Nigerians. The study confirms the existence of linguistic creativity.

Keywords: figure and ground principle, instant messaging, linguistic stylisation, meta-phonology

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Authors: Bong Borero Lumabao

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This qualitative research is a study on the lines of Fliptop talks performed by the Fliptop rappers employing Finnegan’s (2008) discourse analysis. This paper aimed to analyze the phonological, morphological, and semantic features of the fliptop talk, to explore the structures in the lines of Fliptop among Filipino youth, and to uncover the various insights that can be gained from it. The corpora of the study included all the 20 Fliptop Videos downloaded from the Youtube Channel of Fliptop. Results revealed that Fliptop contains phonological features such as assonance, consonance, deletion, lengthening, and rhyming. Morphological features include acronym, affixation, blending, borrowing, code-mixing and switching, compounding, conversion or functional shifts, and dysphemism. Semantics presented the lexical category, meaning, and words used in the fliptop talks. Structure of Fliptop revolves on the personal attack (physical attributes), attack on the bars (rapping skills), extension: family members and friends, antithesis, profane words, figurative languages, sexual undertones, anime characters, homosexuality, and famous celebrities involvement.

Keywords: discourse analysis, fliptop talks, filipino youth, fliptop videos, Philippines

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Authors: Chao Wu

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Thioredoxin reductase 2 is a mitochondrial enzyme that belongs to the cellular defense against oxidative stress. We deleted mitochondrial Txnrd2 in a KrasG12D-driven pancreatic tumor model. Despite an initial increase in precursor lesions, tumor incidence decreased significantly. We isolated cancer cell lines from these genetically engineered mice and observed an impaired proliferation and colony formation. Reactive Oxygen Species, as determined by DCF fluorescence, were increased. We detected a higher mitochondrial copy number in Txnrd2-deficient cells (KTP). However, measurement of mitochondrial bioenergetics showed no impairment of mitochondrial function and comparable O₂-consumption and extracellular acidification rates. In addition, the mitochondrial complex composition was affected in Txnrd2 deleted cell lines. To gain better insight into the role of Txnrd2, we deleted Txnrd2 in clones from parental KrasG12D cell lines using Crispr/Cas9 technology. The deletion was confirmed by western blot and activity assay. Interestingly, and in line with previous RNA expression analysis, we saw changes in EMT markers in Txnrd2 deleted cell lines and control cell lines. This might help us explain the reduced tumor incidence in KrasG12D; Txnrd2∆panc mice.

Keywords: PDAC, TXNRD2, epithelial-to-mesenchymal-transition, ROS

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Authors: Fhajema Kunso

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People who live in the same region and who seemed to speak the same language still vary in some aspects of their language. The variation may occur in terms of pronunciation, lexicon, morphology, and syntax. This qualitative study described the phonological, morphological, and lexical variations of the Maguindanaon language among the ten Maguindanao municipalities. Purposive sampling, in-depth interviews, focus group discussion, and sorting and classifying of words according to phonological and morphological as well as lexical structures in data analysis were employed. The variations occurred through phonemic changes and other phonological processes and morphological processes. Phonological processes consisted of vowel lengthening and deletion while morphological processes included affixation, borrowing, and coinage. In the phonological variation, it was observed that there were phonemic changes in one dialect to another. For example, there was a change of phoneme /r/ to /l/. The phoneme /r/ was most likely to occur in Kabuntalan like /biru/, /kurIt/, and /kɘmɅr/ whereas in the rest of the dialects these were /bilu/, /kuIɪt/, and /kɘmɅl/ respectively. Morphologically, the affixation was the main way to know the tenses. For example, the root sarig (expect) when inserted with im becomes simarig, i.e. s + im + arig = simarig (expected). Lexical variation also existed in the Maguindanaon language. Results revealed that the variation in phonology, morphology, and lexicon were observed to be associated primarily on geographic distribution.

Keywords: applied linguistics, language, lexicon, Maguindanao, morphology, Philippines, phonology, processes, qualitative, variation

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Authors: K. Ali, M. F. Qamar, M. A. Zaman, M. Younus, I. Khan, S. Ehtisham-ul-Haque, R. Tamkeen, M. I. Rashid, Q. Ali

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This study centers on molecular identification of Haemonchus contortus and isolation of Benz-imidazoles (BZ) resistant strains. Different abattoirs’ of two geographic regions of Punjab (Pakistan) were frequently visited for the collection of worms. Out of 1500 (n=1500) samples that were morphologically confirmed as H. contortus, 30 worms were subjected to molecular procedures for isolation of resistant strains. Resistant worms (n=8) were further subjected to DNA gene sequencing. Bio edit sequence alignment editor software was used to detect the possible mutation, deletion, replacement of nucleotides. Genetic diversity was noticed and genetic variation existing in β-tubulin isotype 1 of the H. contortus population of small ruminants of different regions considered in this study. H. contortus showed three different type of genetic sequences. 75%, 37.5%, 25% and 12.5% of the studied samples showed 100% query cover and identity with isolates and clones of China, UK, Australia and other countries, respectively. Interestingly the neighbor countries such as India and Iran haven’t many similarities with the Pakistani isolates. Thus, it suggests that population density of same genetic makeup H. contortus is scattered worldwide rather than clustering in a single region.

Keywords: Haemonchus contortus, Benzimidazole resistant, β-tubulin-1 gene, abattoirs

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Authors: Bimrisha Mali

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The present study investigates the type of errors English as a second language (ESL) learners produce using the definite article ‘the’. The participants were provided a questionnaire on the learner's ability test. The questionnaire consists of three cloze tests and two free composition tests. Each participant's response was received in the form of written data. A total of 78 participants from three government schools participated in the study. The participants are high-school students from Rural Assam. Assam is a north-eastern state of India. Their age ranged between 14-15. The medium of instruction and the communication among the students take place in the local language, i.e., Assamese. Pit Corder’s steps for conducting error analysis have been followed for the analysis procedure. Four types of errors were found (1) deletion of the definite article, (2) use of the definite article as modifiers as adjectives, (3) incorrect use of the definite article with singular proper nouns, (4) substitution of the definite article by the indefinite article ‘a’. Classifiers in Assamese that express definiteness is used with nouns, adjectives, and numerals. It is found that native language (L1) transfer plays a pivotal role in the learners’ errors. The analysis reveals the learners' inability to acquire the semantic connotation of definiteness in English due to native language (L1) interference.

Keywords: definite article error, l1 transfer, error analysis, ESL

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Authors: Mir Hussain Nawaz, Lyudmila Nedyalkova, Haizhong Zhu, Wael M. Rabeh

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In this study, we aim to biochemically and structurally characterize the interactions of human HK2 with the mitochondria in addition to the role of its N-terminal domain in catalysis and stability of the full-length enzyme. Here, we solved the crystal structure of human HK2 in complex with glucose and glucose-6-phosphate (PDB code: 2NZT), where it is a homodimer with catalytically active N- and C-terminal domains linked by a seven-turn α-helix. Different from the inactive N-terminal domains of isozymes 1 and 3, the N- domain of HK2 not only capable to catalyze a reaction but it is responsible for the thermodynamic stabilizes of the full-length enzyme. Deletion of first α-helix of the N-domain that binds to the mitochondria altered the stability and catalytic activity of the full-length HK2. In addition, we found the linker helix between the N- and C-terminal domains to play an important role in controlling the catalytic activity of the N-terminal domain. HK2 is a major step in the regulation of glucose metabolism in cancer making it an ideal target for the development of new anticancer therapeutics. Characterizing the structural and molecular mechanisms of human HK2 and its role in cancer metabolism will accelerate the design and development of new cancer therapeutics that are safe and cancer specific.

Keywords: cancer metabolism, enzymology, drug discovery, protein stability

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Authors: H. Merhni, A. Sbiti, I. Ratbi, A. Sefiani

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The proximal spinal muscular atrophy (SMA) is a group of neuromuscular disorders characterized by progressive muscle weakness due to the degeneration and loss of anterior motor neurons of the spinal cord. Depending on the age of onset of symptoms and their evolution, four types of SMA, varying in severity, result in a mutations of the SMN gene (survival of Motor neuron). We have analyzed the DNA of 295 patients referred to our genetic counseling; since January 1996 until October 2014; for suspected SMA. The homozygous deletion of exon 7 of the SMN gene was found in 133 patients; of which, 40.6% were born to consanguineous parents. In countries like Morocco, where the frequency of heterozygotes for SMA is high, genetic testing should be offered as first-line and, after careful clinical assessment, especially in newborns and infants with congenital hypotonia unexplained and prognosis compromise. The molecular diagnosis of SMA allows a quick and certainly diagnosis, provide adequate genetic counseling for families at risk and suggest, for couples who want prenatal diagnosis. The analysis of the SMN gene is a perfect example of genetic testing with an excellent cost/benefit ratio that can be of great interest in public health, especially in low-income countries. We emphasize in this work for the benefit of the generalization of molecular diagnosis of SMA by the technique of PCR-enzymatic digestion in other centers in Morocco.

Keywords: Exon7, PCR-digestion, SMA, SMN gene

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Authors: Mehrnoosh Pirhayati

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Translation can be affected by different meta-textual factors of target context such as ideology, politics, and culture. So, the rule of fidelity, or being faithful to the source text, can be ignored by the translator. On the other hand, critical discourse analysis, derived from applied linguistics, is entered into the field of translation studies and used by scholars for revealing hidden deviations and possible roots of manipulations. This study focused on the famous Persian translation of the bestseller book, “A**hole No More,” written by XavierCrement 1990, performed by Mahmud Farjami to comparatively and critically analyze it with its corresponding English original book. The researcher applied Pirhayati’s model and framework of translation criticism at the textual and semiotic levels for this qualitative study. It should be noted that Kress and Van Leeuwen’s semiotic model, along with Machin’s model of typographical analysis, was also used at the semiotic level. The results of the comparisons and analyses indicate thatthis Persian translation of the book is affected by the factors of ideology and economics and reveal that the Islamic attitude causes the translator to employ some strategies such as substitution and deletion. Those who may benefit from this research are translation trainers, students of translation studies, critics, and scholars.

Keywords: farjami (2013), Ideology, manipulation, pirhayati's (2013) model of translation criticism, Xavier crement (1990)

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Authors: Gordon Wong

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This paper shows how the task of disk defragmentation can be handled by modern operating systems in a transparent, automated, efficient, and confined way through user's file-access patterns. Since files tend to gradually fragment from time to time through file creation, deletion, growth, and shrinking, the problem gets even worse when a disk becomes so fragmented that file accesses cannot be made reasonably efficient without performing the operation of defragmentation for the "entire" disk, which is done manually by the user by launching the disk defragmentation utility program normally bundled with the operating system. In this paper, we argue that the disk defragmentation problem described can be solved without having to manually use the utility program to defragment the entire disk. The argument is based on the observation that system users tend to access certain files in a particular time interval like the way observed for programs exhibiting temporal locality of memory references during their execution. The task of disk defragmentation can be initiated and acted upon for those files contained in the current file-access locality detected and identified by the operating system. The paper also discusses how to use the locality of file references approach to quantitatively measure and determine the locality of user's file access patterns on which the task of disk defragmentation is based.

Keywords: operating systems, disk defragmentation, locality of file accesses, system performance

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Authors: Zi-Han Li, Lu Fang, Liang Wu, Dong-Yuan Chang, Manyuan Dong, Liang Ji, Qi Zhang, Ming-Hui Zhao, Sydney C. W. Tang, Lemin Zheng, Min Chen

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Uncoupling of mitochondrial respiration by chemical uncouplers has proven effective in ameliorating obesity, insulin resistance, and hyperglycemia, which were risk factors for diabetic nephropathy (DN). Recently, we found that ANXA1 could improve mitochondrial function to mitigate DN progression. However, the underlying mechanism is not fully clear yet. Here, we identified uncoupling protein 1 (UCP1), an inner membrane protein of mitochondria, as a key to mitochondrial homeostasis improved by ANXA1. Specifically, ANXA1 attenuated mitochondrial dysfunction via appropriately upregulating UCP1 by stabilizing its transcription factor GATA binding protein 3 (GATA3) by combining it with thioredoxin. Moreover, specific overexpression of UCP1 in the renal cortex rescued renal injuries in diabetic Anxa1-KO mice. UCP1 deletion aggravated renal injuries in HFD/STZ-induced diabetic mice. Mechanistically, UCP1 reduced mitochondrial fission through the aristaless-related homeobox (ARX)/cardiolipin synthase 1 (CRLS1) pathway. Therapeutically, CL316243, a UCP1 agonist, could attenuate established DN in db/db mice. This work established an alternative principle to harness the power of uncouplers for the treatment of DN.

Keywords: diabetic nephropathy, uncoupling protein 1, mitochondrial homeostasis, cardiolipin metabolism

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Authors: Zi-Han Li, Lu Fang, Liang Wu, Dong-Yuan Chang, Manyuan Dong, Liang Ji, Qi Zhang, Ming-Hui Zhao, Sydney C.W. Tang, Lemin Zheng, Min Chen

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Uncoupling of mitochondrial respiration by chemical uncouplers has proven effective in ameliorating obesity, insulin resistance, and hyperglycemia, which were risk factors for diabetic nephropathy (DN). Recently, it was found that annexin A1(ANXA1) could improve mitochondrial function to mitigate DN progression. However, the underlying mechanism is not fully clear yet. Here, it was identified that uncoupling protein 1 (UCP1), an inner membrane protein of mitochondria, as a key to mitochondrial homeostasis improved by ANXA1. Specifically, ANXA1 attenuated mitochondrial dysfunction via appropriately upregulating UCP1 by stabilizing its transcription factor GATA binding protein 3 (GATA3) through combining with thioredoxin. Moreover, specific overexpression of UCP1 in renal cortex rescued renal injuries in diabetic Anxa1-KO mice. UCP1 deletion aggravated renal injuries in HFD/STZ-induced diabetic mice. Mechanistically, UCP1 reduced mitochondrial fission through the aristaless-related homeobox (ARX)/cardiolipin synthase 1 (CRLS1) pathway. Therapeutically, CL316243, a UCP1 agonist, could attenuate established DN in db/db mice. This work established a novel principle to harness the power of uncouplers for the treatment of DN.

Keywords: diabetic nephropathy, uncoupling protein 1, mitochondrial homeostasis, cardiolipin metabolism

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Authors: Byeong-Uk Lim, Young-Ran Song, Sang-Ho Baik

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This study aimed to develop yeast starters for scientific alcohol production and systematic quality control of whisky. A total of 389 yeast strains were isolated from traditional Korean fermentation starter (nuruk) and rice wine (makgeolli), and ten strains were finally selected for their high alcohol productivities, in which their alcohol productions were above 17.3% (v/v) during 10 days under two steps of glucose feeding condition (30% and then 15%, w/v). By 18s rDNA sequence analysis, all strains were identified as Saccharomyces cerevisiae (SC), and they can grow well under 50% (w/v) glucose and 10% (v/v) ethanol conditions. Furthermore, the capability of ten different SC strains to ferment rice wine for whisky was studied. Rice wine was fermented with only steamed rice, water, and two types of enzymes (glucoamylase and α-amylase) during 14 days at 25 °C, and then their oenological properties have been determined. As the results, the fermented rice wines indicated the final pH range of 4.24-4.38 and acidity range of 0.12-0.18. The highest ethanol production of 20.2% (v/v) was found in the fermentation with a SC-156 strain, whereas SC-92 (16.8%) and SC-119 (16.4%) showed significantly lowest ethanol productions. In addition, the residual sugar contents showed negative correlation with alcohol contents. Moreover, this study focused on nucleotide polymorphisms in the MSN2 and MSN4 genes to investigate the cause of the defective stress responses in yeast. Consequently, it was also confirmed that the deletion of the N termini of Msn4p from identified point mutations in SC-63, SC-95, SC-156, SC-158, and SC-160 strains.

Keywords: yeast, high-alcohol, whisky, rice wine

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Authors: M. Nakkuntod, S. Srinarang, K.W. Hilu

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Water lily (Nymphaea L.) is the largest genus of Nymphaeaceae. This family is composed of six genera (Nuphar, Ondinea, Euryale, Victoria, Barclaya, Nymphaea). Its members are nearly worldwide in tropical and temperate regions. The classification of some species in Nymphaea is ambiguous due to high variation in leaf and flower parts such as leaf margin, stamen appendage. Therefore, the phylogenetic relationships based on 18S rDNA were constructed to delimit this genus. DNAs of 52 specimens belonging to water lily family were extracted using modified conventional method containing cetyltrimethyl ammonium bromide (CTAB). The results showed that the amplified fragment is about 1600 base pairs in size. After analysis, the aligned sequences presented 9.36% for variable characters comprising 2.66% of parsimonious informative sites and 6.70% of singleton sites. Moreover, there are 6 regions of 1-2 base(s) for insertion/deletion. The phylogenetic trees based on maximum parsimony and maximum likelihood with high bootstrap support indicated that genus Nymphaea was a paraphyletic group because of Ondinea, Victoria and Euryale disruption. Within genus Nymphaea, subgenus Nymphaea is a basal lineage group which cooperated with Euryale and Victoria. The other four subgenera, namely Lotos, Hydrocallis, Brachyceras and Anecphya were included the same large clade which Ondinea was placed within Anecphya clade due to geographical sharing.

Keywords: nrDNA, phylogeny, taxonomy, waterlily

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Authors: Sanaa Bardaweel

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Inorganic polyphosphate (poly P) is present in all living forms tested to date, from each of the three kingdoms of life. Studied mainly in prokaryotes, poly P and its associated enzymes are vital in diverse basic metabolism, in at least some structural functions and, notably, in stress responses. These plentiful and unrelated roles for poly P are probably the consequence of its presence in life-forms early in evolution. The genomes of many bacterial species, including pathogens, encode a homologue of a major poly P synthetic enzyme, poly P kinase 1 (PPK1). Genetic deletion of ppk1 results in reduced poly P levels and loss of pathogens virulence towards protozoa and animals. Thus far, no PPK1 homologue has been identified in higher-order eukaryotes and, therefore, PPK1 represents a novel target for chemotherapy. The idea of the current study is to purify the PPK1 from Escherichia coli to homogeneity in order to study the effect of active site point mutations on PPK1 catalysis via the application of site-directed mutagenesis strategy. The knowledge obtained about the active site of PPK1 will be utilized to characterize the catalytic and kinetic mechanism of PPK1 with model substrates. Comprehensive understanding of the enzyme kinetic mechanism and catalysis will be used to design and screen a library of synthetic compounds for potential discovery of selective PPK1-inhibitors.

Keywords: antimicobial, Escherichia coli, inorganic polyphosphate, PPK1-inhibitors

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Authors: Daniel Fundi Murithi

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Missing data is a real bane in many surveys. To overcome the problems caused by missing data, partial deletion, and single imputation methods, among others, have been proposed. However, problems such as discarding usable data and inaccuracy in reproducing known population parameters and standard errors are associated with them. For regression and stochastic imputation, it is assumed that there is a variable with complete cases to be used as a predictor in estimating missing values in the other variable, and the relationship between the two variables is linear, which might not be realistic in practice. In this project, we estimate population total in presence of missing values in two-phase sampling. Instead of regression or stochastic models, non-parametric model based regression model is used in imputing missing values. Empirical study showed that nonparametric model-based regression imputation is better in reproducing variance of population total estimate obtained when there were no missing values compared to mean, median, regression, and stochastic imputation methods. Although regression and stochastic imputation were better than nonparametric model-based imputation in reproducing population total estimates obtained when there were no missing values in one of the sample sizes considered, nonparametric model-based imputation may be used when the relationship between outcome and predictor variables is not linear.

Keywords: finite population total, missing data, model-based imputation, two-phase sampling

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Authors: Chinmayee Choudhury

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Human Melanocortin 4 Receptor (HMC4R) is one of the most potential drug targets for the treatment of obesity which controls the appetite. A deletion of the residues 88-92 in HMC4R is sometimes the cause of severe obesity in the humans. In this study, two homology models are constructed for the normal as well as mutated HMC4Rs and some phytochemicals present in Green Tea, Honey and Cinnamon have been docked to them to study their differential binding to the normal and mutated HMC4R as compared to the natural agonist α- MSH. Two homology models have been constructed for the normal as well as mutated HMC4Rs using the Modeller9v7. Some of the phytochemicals present in Green Tea, Honey, and Cinnamon, which have appetite suppressant activities are constructed, minimized and docked to these normal and mutated HMC4R models using ArgusLab 4.0.1. The mode of binding of the phytochemicals with the Normal and Mutated HMC4Rs have been compared. Further, the mode of binding of these phytochemicals with that of the natural agonist α- Melanocyte Stimulating Hormone(α-MSH) to both normal and mutated HMC4Rs have also been studied. It is observed that the phytochemicals Kaempherol, Epigallocatechin-3-gallate (EGCG) present in Green Tea and Honey, Isorhamnetin, Chlorogenic acid, Chrysin, Galangin, Pinocambrin present in Honey, Cinnamaldehyde, Cinnamyl acetate and Cinnamyl alcohol present in Cinnamon have capacity to form more stable complexes with the Mutated HMC4R as compared to α- MSH. So they may be potential agonists of HMC4R to suppress the appetite.

Keywords: HMC4R, α-MSH, docking, photochemical, appetite suppressant, homology modelling

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Authors: Alieh Farshbaf, Tayyeb Bahrami

Abstract:

Introduction: Cc-chemokine receptor-5 (CCR5) is known as a main co-receptor in human immunodeficiency virus type-1 (HIV-1) infection. Many studies showed 32bp deletion (Δ32) in CCR5 gene, provide natural resistance to HIV-1 infection in homozygous individuals. Inducing the resistance mechanism by CCR5 in HIV-1 infected patients eliminated many problems of highly-active-anti retroviral therapy (HAART) drugs like as low safety, side-effects and virus rebounding from latent reservoirs. New treatments solved some restrictions that are based on gene modification and cell therapy. Literature review: The stories of the “Berlin and Boston patients” showed autologous hematopoietic stem cells transplantation (HSCT) could provide effective cure of HIV-1 infected patients. Furthermore, gene modification by zinc finger nuclease (ZFN) demonstrated another successful result again. Despite the other studies for gene therapy by ∆32 genotype, there is another mutation -CCR5 ∆32/m303- that provides HIV-1 resistant. It is a heterozygote genotype for ∆32 and T→A point mutation at nucleotide 303. These results approved the key role of CCR5 gene. Conclusion: Recent studies showed immune gene therapy and cell therapy could provide effective cure for refractory disease like as HIV. Eradication of HIV-1 from immune system was not observed by HAART, because of reloading virus genome from latent reservoirs after stopping them. It is showed that CCR5 could induce natural resistant to HIV-1 infection by the new approaches based on stem cell transplantation and gene modifying.

Keywords: CCR5, HIV-1, stem cell, immune gene therapy, gene modification

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Authors: Hao-Wei Fu, Chung-Feng Kao

Abstract:

In the era of rapid technological advancement, information technology (IT) has become integral to modern life, exerting significant influence across diverse sectors and serving as a catalyst for development in various industries. Within agriculture, the integration of IT offers substantial benefits, notably enhancing operational efficiency. Real-time monitoring systems, for instance, have been widely embraced in agriculture, effectively improving crop management practices. This study specifically addresses the management of rice panicle fertilizer, presenting the development of a web application tailored to handle data associated with rice panicle fertilizer management. Leveraging the normalized difference red edge index, this application optimizes the quantity of rice panicle fertilizer used, providing recommendations to agricultural stakeholders and service providers in the agricultural information sector. The overarching objective is to minimize costs while maximizing yields. Furthermore, a robust database system has been established to store and manage relevant data for future reference in rice cultivation management. Additionally, the study utilizes the Representational State Transfer software architectural style to construct an application programming interface (API), facilitating data creation, retrieval, updating, and deletion for users via the HyperText Transfer Protocol methods. Future plans involve integrating this API with third-party services to incorporate it into larger frameworks, thus catering to the diverse requirements of various third-party services.

Keywords: application programming interface, HyperText Transfer Protocol, nitrogen fertilizer intelligent management, web-based application

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Authors: Kyung-Tae Lee, Li Li Wang, Kwang-Woo Jung, Yong-Sun Bahn

Abstract:

Microtubules are involved in mechanical support, cytoplasmic organization as well as in a number of cellular processes by interacting with diverse microtubule-associated proteins (MAPs), such as plus-end tracking proteins, motor proteins, and tubulin-folding cofactors. A common feature of these proteins is the presence of a cytoskeleton-associated protein-glycine-rich (CAP-Gly) domain, which is evolutionarily conserved and generally considered to bind to α-tubulin to regulate functions of microtubules. However, there has been a dearth of research on CAP-Gly proteins in fungal pathogens, including Cryptococcus neoformans, which causes fatal meningoencephalitis globally. In this study, we identified five CAP-Gly proteins encoding genes in C. neoformans. Among these, Cgp1, encoded by CNAG_06352, has a unique domain structure that has not been reported before in other eukaryotes. Supporting the role of Cpg1 in microtubule-related functions, we demonstrate that deletion or overexpression of CGP1 alters cellular susceptibility to thiabendazole, a microtubule destabilizer, and Cgp1 is co-localized with cytoplasmic microtubules. Related to the cellular functions of microtubules, Cgp1 also governs maintenance of membrane stability and genotoxic stress responses. Furthermore, we demonstrate that Cgp1 uniquely regulates sexual differentiation of C. neoformans with distinct roles in the early and late stage of mating. Our domain analysis reveals that the CAP-Gly domain plays major roles in all the functions of Cgp1. Finally, the cgp1Δ mutant is attenuated in virulence. In conclusion, this novel CAP-Gly protein, Cgp1, has pleotropic roles in regulating growth, stress responses, differentiation and pathogenicity of C. neoformans.

Keywords: human fungal pathogen, CAP-Glycine protein, microtubule, meningoencephalitis

Procedia PDF Downloads 294

Authors: Jun Yang, Ching-Liang Hsieh, Yi-Wen Lin

Abstract:

Chronic inflammatory pain results from peripheral tissue injury or local inflammation to increase the release of protons, histamines, adenosine triphosphate, and several proinflammatory cytokines. Transient receptor potential vanilloid 1 (TRPV1) is involved in fibromyalgia, neuropathic, and inflammatory pain; however, its exact mechanisms in chronic inflammatory pain are still unclear. We investigate the analgesic effect of EA by injecting complete Freund’s adjuvant (CFA) in the hind paw of mice to induce chronic inflammatory pain ( > 14 d). Our results showed that EA significantly reduced chronic mechanical and thermal hyperalgesia in the chronic inflammatory pain model. Chronic mechanical and thermal hyperalgesia was also abolished in TRPV1−/− mice. TRPV1 increased in the dorsal root ganglion (DRG) and spinal cord (SC) at 2 weeks after CFA injection. The expression levels of downstream molecules such as pPKA, pPI3K, and pPKC increased, as did those of pERK, pp38, and pJNK. Transcription factors (pCREB and pNFκB) and nociceptive ion channels (Nav1.7 and Nav1.8) were involved in this process. Inflammatory mediators such as GFAP (Glial fibrillary acidic protein), S100B, and RAGE (Receptor for advanced glycation endproducts) were also involved. The expression levels of these molecules were reduced in EA (electroacupuncture) and TRPV1−/−mice but not in the sham EA group. The present study demonstrated that EA or TRPV1 gene deletion reduced chronic inflammatory pain through TRPV1 and related molecules. In addition, our data provided evidence to support the clinical use of EA for treating chronic inflammatory pain.

Keywords: auricular electric-stimulation, epileptic seizures, anti-inflammation, electroacupuncture

Procedia PDF Downloads 153

Authors: Etim, Victoria Enefiok, Dada, Oluseyi Akintunde, Bassey Okon

Abstract:

Phonological disorder is a serious and disturbing issue to many parents and teachers. Efforts towards resolving the problem have been undermined by other specific disabilities which were hidden to many regular and special education teachers. It is against this background that this study was motivated to provide data on the prevalence of phonological disorders in children with specific language impairment (CWSLI) as the first step towards critical intervention. The study was a survey of 15 CWSLI from St. Louise Inclusive schools, Ikot Ekpene in Akwa Ibom State of Nigeria. Phonological Processes Diagnostic Scale (PPDS) with 17 short sentences, which cut across the five phonological processes that were examined, were validated by experts in test measurement, phonology and special education. The respondents were made to read the sentences with emphasis on the targeted sounds. Their utterances were recorded and analyzed in the language laboratory using Praat Software. Data were also collected through friendly interactions at different times from the clients. The theory of generative phonology was adopted for the descriptive analysis of the phonological processes. Data collected were analyzed using simple percentage and composite bar chart for better understanding of the result. The study found out that CWSLI exhibited the five phonological processes under investigation. It was revealed that 66.7%, 80%, 73.3%, 80%, and 86.7% of the respondents have severe deficit in fricative stopping, velar fronting, liquid gliding, final consonant deletion and cluster reduction, respectively. It was therefore recommended that a nationwide survey should be carried out to have national statistics of CWSLI with phonological deficits and develop intervention strategies for effective therapy to remediate the disorder.

Keywords: language disorders, phonology, phonological processes, specific language impairment

Procedia PDF Downloads 166