Search results for: picking sequence

Authors: Julius M. Ndambuki, Gislar E. Kifanyi, Samuel N. Odai, Charles Gyamfi

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Conjunctive management of surface and groundwater resources is a challenging task due to the spatial and temporal variability nature of hydrology as well as hydrogeology of the water storage systems. Surface water-groundwater hydrogeology is highly uncertain; thus it is imperative that this uncertainty is explicitly accounted for, when managing water resources. Various methodologies have been developed and applied by researchers in an attempt to account for the uncertainty. For example, simulation-optimization models are often used for conjunctive water resources management. However, direct application of such an approach in which all realizations are considered at each iteration of the optimization process leads to a very expensive optimization in terms of computational time, particularly when the number of realizations is large. The aim of this paper, therefore, is to introduce and apply an efficient approach referred to as Retrospective Optimization Approximation (ROA) that can be used for optimizing conjunctive use of surface water and groundwater over a multiple hydrogeological model simulations. This work is based on stochastic simulation-optimization framework using a recently emerged technique of sample average approximation (SAA) which is a sampling based method implemented within the Retrospective Optimization Approximation (ROA) approach. The ROA approach solves and evaluates a sequence of generated optimization sub-problems in an increasing number of realizations (sample size). Response matrix technique was used for linking simulation model with optimization procedure. The k-means clustering sampling technique was used to map the realizations. The methodology is demonstrated through the application to a hypothetical example. In the example, the optimization sub-problems generated were solved and analysed using “Active-Set” core optimizer implemented under MATLAB 2014a environment. Through k-means clustering sampling technique, the ROA – Active Set procedure was able to arrive at a (nearly) converged maximum expected total optimal conjunctive water use withdrawal rate within a relatively few number of iterations (6 to 7 iterations). Results indicate that the ROA approach is a promising technique for optimizing conjunctive water use of surface water and groundwater withdrawal rates under hydrogeological uncertainty.

Keywords: conjunctive water management, retrospective optimization approximation approach, sample average approximation, uncertainty

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Authors: Sundus Mona, Atif Adnan, Babar Ali, Fareeha Arshad, Allah Rakha

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Molecular diversity is the variation in the abundance of species. Forensic entomology is a neglected field in Pakistan. Insects collected from the crime scene should be handled by forensic entomologists who are currently virtually non-existent in Pakistan. Correct identification of insect specimen along with knowledge of their biodiversity can aid in solving many problems related to complicated forensic cases. Inadequate morphological identification and insufficient thermal biological studies limit the entomological utility in Forensic Medicine. Recently molecular identification of entomological evidence has gained attention globally. DNA barcoding is the latest and established method for species identification. Only proper identification can provide a precise estimation of postmortem intervals. Arthropods are known to be the first tourists scavenging on decomposing dead matter. The objective of the proposed study was to identify species by molecular techniques and analyze their phylogenetic importance with barcoded necrophagous insect species of early succession on human cadavers. Based upon this identification, the study outcomes will be the utilization of established DNA bar codes to identify carrion feeding insect species for concordant estimation of post mortem interval. A molecular identification method involving sequencing of a 658bp ‘barcode’ fragment of the mitochondrial cytochrome oxidase subunit 1 (CO1) gene from collected specimens of unknown dipteral species from cadavers of Lahore was evaluated. Nucleotide sequence divergences were calculated using MEGA 7 and Arlequin, and a neighbor-joining phylogenetic tree was generated. Three species were identified, Chrysomya megacephala, Chrysomya saffranea, and Chrysomya rufifacies with low genetic diversity. The fixation index was 0.83992 that suggests a need for further studies to identify and classify forensically relevant insects in Pakistan. There is an exigency demand for further research especially when immature forms of arthropods are recovered from the crime scene.

Keywords: molecular diversity, DNA barcoding, species identification, forensically relevant

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Authors: Ian Campbell, Gillian Mitchell, Paul James, Na Li, Ella Thompson

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The genetic cause of the majority of multiple-case breast cancer families remains unresolved. Next generation sequencing has emerged as an efficient strategy for identifying predisposing mutations in individuals with inherited cancer. We are conducting whole exome sequence analysis of germ line DNA from multiple affected relatives from breast cancer families, with the aim of identifying rare protein truncating and non-synonymous variants that are likely to include novel cancer predisposing mutations. Data from more than 200 exomes show that on average each individual carries 30-50 protein truncating mutations and 300-400 rare non-synonymous variants. Heterogeneity among our exome data strongly suggest that numerous moderate penetrance genes remain to be discovered, with each gene individually accounting for only a small fraction of families (~0.5%). This scenario marks validation of candidate breast cancer predisposing genes in large case-control studies as the rate-limiting step in resolving the missing heritability of breast cancer. The aim of this study is to screen genes that are recurrently mutated among our exome data in a larger cohort of cases and controls to assess the prevalence of inactivating mutations that may be associated with breast cancer risk. We are using the Agilent HaloPlex Target Enrichment System to screen the coding regions of 168 genes in 1,000 BRCA1/2 mutation-negative familial breast cancer cases and 1,000 cancer-naive controls. To date, our interim analysis has identified 21 genes which carry an excess of truncating mutations in multiple breast cancer families versus controls. Established breast cancer susceptibility gene PALB2 is the most frequently mutated gene (13/998 cases versus 0/1009 controls), but other interesting candidates include NPSR1, GSN, POLD2, and TOX3. These and other genes are being validated in a second cohort of 1,000 cases and controls. Our experience demonstrates that beyond PALB2, the prevalence of mutations in the remaining breast cancer predisposition genes is likely to be very low making definitive validation exceptionally challenging.

Keywords: predisposition, familial, exome sequencing, breast cancer

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Authors: Xianming Chen, Yu Lei, Meinan Wang

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The dikaryotic basidiomycete fungus, Puccinia striiformis, causes stripe rust, one of the most important diseases of wheat and barley worldwide. The pathogen is largely reproduced asexually, and asexual recombination has been hypothesized to be one of the mechanisms for the pathogen variations. To test the hypothesis and understand the genetic process of asexual recombination, somatic recombinant isolates were obtained under controlled conditions by inoculating susceptible host plants with a mixture of equal quantity of urediniospores of isolates with different virulence patterns and selecting through a series of inoculation on host plants with different genes for resistance to one of the parental isolates. The potential recombinant isolates were phenotypically characterized by virulence testing on the set of 18 wheat lines used to differentiate races of the wheat stripe rust pathogen, P. striiformis f. sp. tritici (Pst), for the combinations of Pst isolates; or on both sets of the wheat differentials and 12 barley differentials for identifying races of the barley stripe rust pathogen, P. striiformis f. sp. hordei (Psh) for combinations of a Pst isolate and a Psh isolate. The progeny and parental isolates were also genotypically characterized with 51 simple sequence repeat and 90 single-nucleotide polymorphism markers. From nine combinations of parental isolates, 68 potential recombinant isolates were obtained, of which 33 (48.5%) had similar virulence patterns to one of the parental isolates, and 35 (51.5%) had virulence patterns distinct from either of the parental isolates. Of the 35 isolates of distinct virulence patterns, 11 were identified as races that had been previously detected from natural collections and 24 were identified as new races. The molecular marker data confirmed 66 of the 68 isolates as recombinants. The percentages of parental marker alleles ranged from 0.9% to 98.9% and were significantly different from equal proportions in the recombinant isolates. Except for a couple of combinations, the greater or less contribution was not specific to any particular parental isolates as the same parental isolates contributed more to some of the progeny isolates but less to the other progeny isolates in the same combination. The unequal contributions by parental isolates appear to be a general role in somatic recombination for the stripe rust fungus, which may be used to distinguish asexual recombination from sexual recombination in studying the evolutionary mechanisms of the highly variable fungal pathogen.

Keywords: molecular markers, Puccinia striiformis, somatic recombination, stripe rust

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Authors: Surbhi Surbhi, Andrea Erni, Gunter Meister, Harold Cremer, Christophe Beclin

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MicroRNAs (miRNAs) are short 20-23 nucleotide long non-coding RNAs; there are 2605 miRNA in humans and 1936 miRNA in mouse in total (miRBase). The nervous system expresses the most abundant miRNA and most diverse. MiRNAs play a role in many steps during neurogenesis, like cell proliferation, differentiation, neural patterning, axon pathfinding, etc. Moreover, in vitro studies suggested a role in the regulation of local translation at the synapse, thus controlling neuronal plasticity. However, due to the specific structure of miRNA molecules, an in-vivo confirmation of the general role of miRNAs in the control of neuronal plasticity is still pending. For example, their small size and their high level of sequence homology make difficult the analysis of their cellular and sub-cellular localization in-vivo by in-situ hybridization. Moreover, it was found that only 40% of the expressed miRNA molecules in a cell are included in RNA-Induced Silencing Complexes (RISC) and, therefore, involved in inhibitory interactions while the rest is silent. Definitively, the development of new tools is needed to have a better understanding of the cellular function of miRNAs, in particular their role in neuronal plasticity. Here we describe a new technique called in-vivo AGO-APP designed to investigate miRNA expression and function in-vivo. This technique is based on the expression of a small peptide derived from the human RISC-complex protein TNRC6B, called T6B, which binds all known Argonaute (Ago) proteins with high affinity allowing the efficient immunoprecipitation of AGO-bound miRNAs. We have generated two transgenic mouse lines conditionally expressing T6B either ubiquitously in the cell or targeted at the synapse. A comparison of the repertoire of miRNAs immuno-precipitated from mature neurons of both mouse lines will provide us with a list of miRNAs showing a specific activity at the synapse. The physiological role of these miRNAs will be subsequently addressed through gain and loss of function experiments.

Keywords: RNA-induced silencing complexes, TNRC6B, miRNA, argonaute, synapse, neuronal plasticity, neurogenesis

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Authors: Sonia Sassi, Mostapha Tarfaoui, Hamza Ben Yahia

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In this investigation, an experimental technique in which the dynamic response, damage kinetic and heat dissipation are measured simultaneously during high strain rates on adhesively bonded joints materials. The material used in this study is widely used in the design of structures for military applications. It was composed of a 45° Bi-axial fiber-glass mat of 0.286 mm thickness in a Polyester resin matrix. In adhesive bonding, a NORPOL Polyvinylester of 1 mm thickness was used to assemble the composite substrate. The experimental setup consists of a compression Split Hopkinson Pressure Bar (SHPB), a high-speed infrared camera and a high-speed Fastcam rapid camera. For the dynamic compression tests, 13 mm x 13 mm x 9 mm samples for out-of-plane tests were considered from 372 to 1030 s-1. Specimen surface is controlled and monitored in situ and in real time using the high-speed camera which acquires the damage progressive in specimens and with the infrared camera which provides thermal images in time sequence. Preliminary compressive stress-strain vs. strain rates data obtained show that the dynamic material strength increases with increasing strain rates. Damage investigations have revealed that the failure mainly occurred in the adhesive/adherent interface because of the brittle nature of the polymeric adhesive. Results have shown the dependency of the dynamic parameters on strain rates. Significant temperature rise was observed in dynamic compression tests. Experimental results show that the temperature change depending on the strain rate and the damage mode and their maximum exceed 100 °C. The dependence of these results on strain rate indicates that there exists a strong correlation between damage rate sensitivity and heat dissipation, which might be useful when developing damage models under dynamic loading tacking into account the effect of the energy balance of adhesively bonded joints.

Keywords: adhesive bonded joints, Hopkinson bars, out-of-plane tests, dynamic compression properties, damage mechanisms, heat dissipation

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Authors: H. Alijani, M. Jabari, S. Matroodi, H. Zolqarnein, A. Sharafi, I. Zamani

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Actinomycetes, Gram-positive bacteria, are interesting as a main producer of secondary metabolites and are important industrially and pharmaceutically. The marine environment is a potential source for new actinomycetes, which can provide novel bioactive compounds and industrially important enzymes. The aims of this study were to isolate and identify novel actinomycetes from Persian Gulf sediments and screen these isolates for the production of secondary metabolites, especially antibiotics, Using phylogenetic (16S rRNA gene sequence), morphological and biochemical analyses. 15 different actinomycete strains from Persian Gulf sediments at a depth of 5-10 m were identified. DNA extraction was done using Cinnapure DNA Kit. PCR amplification of 16S rDNA gene was performed using F27 and R1492 primers. Phylogenetic tree analysis was performed using the MEGA 6 software. Most of the isolated strains belong to the genus namely Streptomyces (14), followed by Nocardiopsis (1). Antibacterial assay of the isolates supernatant was performed using a standard disc diffusion assay with replication (n=3). The results of disk diffusion assay showed that most active strain against Proteus volgaris and Bacillus cereus was AMJ1 (16.46±0.2mm and 13.78±0.2mm, respectively), against Salmonella sp. AMJ7 was the most effective strain (10.13±0.2mm), and AMJ1 and AHA5 showed more inhibitory activity against Escherichia coli (8.04±0.02 mm and 8.2±0.03 ). The AMJ6 strain showed best antibacterial activity against Klebsiella sp. (8.03±0.02mm). Antifungal activity of AMJ2 showed that it was most active strain against complex (16.05±0.02mm) and against Aspergillus flavus strain AMJ1 was most active strain (16.4±0.2mm) and highest antifungal activity against Trichophyton mentagrophytes, Microsporum gyp serum and Candida albicans, were shown by AHA1 (21.03±0.02mm), AHA3 and AHA7 (18±0.03mm), AMJ6 (21.03±0.2mm) respectively. Our results revealed that the marine actinomycetes of Persian Gulf sediments were potent source of novel antibiotics and bioactive compounds and indicated that the antimicrobial metabolites were extracellular. Most of the secondary metabolites and antibiotics are extracellular in nature and extracellular products of actinomycetes show potent antimicrobial activities.

Keywords: antibacterial activity, antifungal activity, marine actinomycetes, Persian Gulf

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Authors: Jovian Cheung, Thomas Kwok, Victor Wong

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Buildings are entwined with smart city developments. Building performance relies heavily on electrical and mechanical (E&M) systems and services accounting for about 40 percent of global energy use. By cohering the advancement of technology as well as energy and operation-efficient initiatives into the buildings, people are enabled to raise building performance and enhance the sustainability of the built environment in their daily lives. Digital transformation in the buildings is the profound development of the city to leverage the changes and opportunities of digital technologies To optimize the building performance, intelligent power quality and energy management system is developed for transforming data into actions. The system is formed by interfacing and integrating legacy metering and internet of things technologies in the building and applying big data techniques. It provides operation and energy profile and actionable insights of a building, which enables to optimize the building performance through raising people awareness on E&M services and energy consumption, predicting the operation of E&M systems, benchmarking the building performance, and prioritizing assets and energy management opportunities. The intelligent power quality and energy management system comprises four elements, namely the Integrated Building Performance Map, Building Performance Dashboard, Power Quality Analysis, and Energy Performance Analysis. It provides predictive operation sequence of E&M systems response to the built environment and building activities. The system collects the live operating conditions of E&M systems over time to identify abnormal system performance, predict failure trends and alert users before anticipating system failure. The actionable insights collected can also be used for system design enhancement in future. This paper will illustrate how intelligent power quality and energy management system provides operation and energy profile to optimize the building performance and actionable insights to revitalize an existing building into a smart building. The system is driving building performance optimization and supporting in developing Hong Kong into a suitable smart city to be admired.

Keywords: intelligent buildings, internet of things technologies, big data analytics, predictive operation and maintenance, building performance

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Authors: Laribi-Habchi Hasiba, Bouanane-Darenfed Amel, Drouiche Nadjib, Pausse André, Mameri Nabil

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Chitin, a linear 1, 4-linked N-acetyl-d-glucosamine (GlcNAc) polysaccharide is the major structural component of fungal cell walls, insect exoskeletons and shells of crustaceans. It is one of the most abundant naturally occurring polysaccharides and has attracted tremendous attention in the fields of agriculture, pharmacology and biotechnology. Each year, a vast amount of chitin waste is released from the aquatic food industry, where crustaceans (prawn, crab, Shrimp and lobster) constitute one of the main agricultural products. This creates a serious environmental problem. This linear polymer can be hydrolyzed by bases, acids or enzymes such as chitinase. In this context an extracellular chitinase (ChiA-65) was produced and purified from a newly isolated LHH100. Pure protein was obtained after heat treatment and ammonium sulphate precipitation followed by Sephacryl S-200 chromatography. Based on matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS) analysis, the purified enzyme is a monomer with a molecular mass of 65,195.13 Da. The sequence of the 27 N-terminal residues of the mature ChiA-65 showed high homology with family-18 chitinases. Optimal activity was achieved at pH 4 and 75◦C. Among the inhibitors and metals tested p-chloromercuribenzoic acid, N-ethylmaleimide, Hg2+ and Hg + completelyinhibited enzyme activity. Chitinase activity was high on colloidal chitin, glycol chitin, glycol chitosane, chitotriose and chitooligosaccharide. Chitinase activity towards synthetic substrates in the order of p-NP-(GlcNAc) n (n = 2–4) was p-NP-(GlcNAc)2> p-NP-(GlcNAc)4> p-NP-(GlcNAc)3. Our results suggest that ChiA-65 preferentially hydrolyzed the second glycosidic link from the non-reducing end of (GlcNAc) n. ChiA-65 obeyed Michaelis Menten kinetics the Km and kcat values being 0.385 mg, colloidal chitin/ml and5000 s−1, respectively. ChiA-65 exhibited remarkable biochemical properties suggesting that this enzyme is suitable for bioconversion of chitin waste.

Keywords: Bacillus licheniformis LHH100, characterization, extracellular chitinase, purification

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Authors: Mina Kalantarzadeh, Claire Lockie-Williams, Caroline Howard

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DNA barcoding is increasingly used for identification of medicinal plants worldwide. In the last decade, a large number of DNA barcodes have been generated, and their application in species identification explored. The success of DNA barcoding process relies on the accuracy of the results from polymerase chain reaction (PCR) amplification step which could be negatively affected due to a presence of inhibitors or degraded DNA in herbal samples. An established DNA reference material can be used to support molecular characterisation protocols and prove system suitability, for fast and accurate identification of plant species. The present study describes the use of a novel reference material, the trnH-psbA British Pharmacopoeia Nucleic Acid Reference Material (trnH-psbA BPNARM), which was produced to aid in the identification of Ocimum tenuiflorum L., a widely used herb. During DNA barcoding of O. tenuiflorum, PCR amplifications of isolated DNA produced inconsistent results, suggesting an issue with either the method or DNA quality of the tested samples. The trnH-psbA BPNARM was produced and tested to check for the issues caused during PCR amplification. It was added to the plant material as control DNA before extraction and was co-extracted and amplified by PCR. PCR analyses revealed that the amplification was not as successful as expected which suggested that the amplification is affected by presence of inhibitors co-extracted from plant materials. Various potential issues were assessed during DNA extraction and optimisations were made accordingly. A DNA barcoding protocol for O. tenuiflorum was published in the British Pharmacopoeia 2016, which included the reference sequence. The trnH-psbA BPNARM accelerated degradation test which investigates the stability of the reference material over time demonstrated that it has been stable when stored at 56 °C for a year. Using this protocol and trnH-psbA reference material provides a fast and accurate method for identification of O. tenuiflorum. The optimisations of the DNA extraction using the trnH-psbA BPNARM provided a signposting method which can assist in overcoming common problems encountered when using molecular methods with medicinal plants.

Keywords: degradation, DNA extraction, nucleic acid reference material, trnH-psbA

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Authors: Sana Hamdi, Emna Bouazizi, Sami Faiz

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In recent years, real-time spatial applications, like location-aware services and traffic monitoring, have become more and more important. Such applications result dynamic environments where data as well as queries are continuously moving. As a result, there is a tremendous amount of real-time spatial data generated every day. The growth of the data volume seems to outspeed the advance of our computing infrastructure. For instance, in real-time spatial Big Data, users expect to receive the results of each query within a short time period without holding in account the load of the system. But with a huge amount of real-time spatial data generated, the system performance degrades rapidly especially in overload situations. To solve this problem, we propose the use of data partitioning as an optimization technique. Traditional horizontal and vertical partitioning can increase the performance of the system and simplify data management. But they remain insufficient for real-time spatial Big data; they can’t deal with real-time and stream queries efficiently. Thus, in this paper, we propose a novel data partitioning approach for real-time spatial Big data named VPA-RTSBD (Vertical Partitioning Approach for Real-Time Spatial Big data). This contribution is an implementation of the Matching algorithm for traditional vertical partitioning. We find, firstly, the optimal attribute sequence by the use of Matching algorithm. Then, we propose a new cost model used for database partitioning, for keeping the data amount of each partition more balanced limit and for providing a parallel execution guarantees for the most frequent queries. VPA-RTSBD aims to obtain a real-time partitioning scheme and deals with stream data. It improves the performance of query execution by maximizing the degree of parallel execution. This affects QoS (Quality Of Service) improvement in real-time spatial Big Data especially with a huge volume of stream data. The performance of our contribution is evaluated via simulation experiments. The results show that the proposed algorithm is both efficient and scalable, and that it outperforms comparable algorithms.

Keywords: real-time spatial big data, quality of service, vertical partitioning, horizontal partitioning, matching algorithm, hamming distance, stream query

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Authors: I-Hui Hsieh, Yu-Hsuan Hu

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The powerful effect of music is often associated with changes in physiological responses such as heart rate and respiration. Previous studies demonstrate that Mayer waves of blood pressure, the spontaneous rhythm occurring at 0.1 Hz, corresponds to a progressive crescendo of the musical phrase. However, music contain dynamic changes in temporal and spectral features. As such, it remains unclear which aspects of musical structures optimally affect synchronization of cardiovascular rhythms. This study investigates the independent contribution of spectral pattern, temporal pattern, and dissonance level on synchronization of cardiovascular rhythms. The regularity of acoustical patterns occurring at a periodic rhythm of 0.1 Hz is hypothesized to elicit the strongest coherence of cardiovascular rhythms. Music excerpts taken from twelve pieces of Western classical repertoire were modulated to contain varying degrees of pattern regularity of the acoustic envelope structure. Three levels of dissonance were manipulated by varying the harmonic structure of the accompanying chords. Electrocardiogram and photoplethysmography signals were recorded for 5 minutes of baseline and simultaneously while participants listen to music excerpts randomly presented over headphones in a sitting position. Participants were asked to indicate the pleasantness of each music excerpt by adjusting via a slider presented on screen. Analysis of the Fourier spectral power of blood pressure around 0.1 Hz showed a significant difference between music excerpts characterized by spectral and temporal pattern regularity compared to the same content in random pattern. Phase coherence between heart rate and blood pressure increased significantly during listening to spectrally-regular phrases compared to its matched control phrases. The degree of dissonance of the accompanying chord sequence correlated with level of coherence between heart rate and blood pressure. Results suggest that low-level auditory features of music can entrain coherence of autonomic physiological variables. These findings have potential implications for using music as a clinical and therapeutic intervention for regulating cardiovascular functions.

Keywords: cardiovascular rhythms, coherence, dissonance, pattern regularity

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Authors: Ayman K. El Essawy, Amal M. Hosny, Hala M. Abu Shady

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The rapid detection of TB and drug resistance, both optimizes treatment and improves outcomes. In the current study, respiratory specimens were collected from 155 patients. Conventional susceptibility testing and MIC determination were performed for rifampicin (RIF) and isoniazid (INH). Genotype MTBDRplus assay, which is a molecular genetic assay based on the DNA-STRIP technology and specific gene sequencing with primers for rpoB, KatG, and mab-inhA genes were used to detect mutations associated with resistance to rifampicin and isoniazid. In comparison to other categories, most of rifampicin resistant (61.5%) and isoniazid resistant isolates (47.1%) were from patients relapsed in treatment. The genotypic profile (using Genotype MTBDRplus assay) of multi-drug resistant (MDR) isolates showed missing of katG wild type 1 (WT1) band and appearance of mutation band katG MUT2. For isoniazid mono-resistant isolates, 80% showed katG MUT1, 20% showed katG MUT1, and inhA MUT1, 20% showed only inhA MUT1. Accordingly, 100% of isoniazid resistant strains were detected by this assay. Out of 17 resistant strains, 16 had mutation bands for katG distinguished high resistance to isoniazid. The assay could clearly detect rifampicin resistance among 66.7% of MDR isolates that showed mutation band rpoB MUT3 while 33.3% of them were considered as unknown. One mono-resistant rifampicin isolate did not show rifampicin mutation bands by Genotype MTBDRplus assay, but it showed an unexpected mutation in Codon 531 of rpoB by DNA sequence analysis. Rifampicin resistance in this strain could be associated with a mutation in codon 531 of rpoB (based on molecular sequencing), and Genotype MTBDRplus assay could not detect the associated mutation. If the results of Genotype MTBDRplus assay and sequencing were combined, this strain shows hetero-resistance pattern. Gene sequencing of eight selected isolates, previously tested by Genotype MTBDRplus assay, could detect resistance mutations mainly in codon 315 (katG gene), position -15 in inhA promotes gene for isoniazid resistance and codon 531 (rpoB gene) for rifampicin resistance. Genotyping techniques allow distinguishing between recurrent cases of reinfection or reactivation and supports epidemiological studies.

Keywords: M. tuberculosis, rpoB, KatG, inhA, genotype MTBDRplus

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Authors: S. Sreeja, Radhakrishnan R. Nair, Noble Gracious, Sreeja S. Nair, M. Radhakrishna Pillai

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Background: Tacrolimus is a potent immunosuppressant clinically used for the long term treatment of antirejection of transplanted organs in liver and kidney transplant recipients though dose optimization is poorly managed. However, So far no study has been carried out on the South Indian kidney transplant patients. The objective of this study is to evaluate the potential influence of a functional polymorphism in CYP3A5*3 gene on tacrolimus physiological availability/dose ratio in South Indian renal transplant patients. Materials and Methods: Twenty five renal transplant recipients receiving tacrolimus were enrolled in this study. Their body weight, drug dosage, and therapeutic concentration of Tacrolimus were observed. All patients were on standard immunosuppressive regime of Tacrolimus-Mycophenolate mofetil along with steroids on a starting dose of Tac 0.1 mg/kg/day. CYP3A5 genotyping was performed by PCR followed with RFLP. Conformation of RFLP analysis and variation in the nucleotide sequence of CYP3A5*3 gene were determined by direct sequencing using a validated automated generic analyzer. Results: A significant association was found between tacrolimus per dose/kg/d and CYP3A5 gene (A6986G) polymorphism in the study population. The CYP3A5 *1/*1, *1/*3 and *3/*3 genotypes were detected in 5 (20 %), 5 (20 %) and 15 (60 %) of the 25 graft recipients, respectively. CYP3A5*3 genotypes were found to be a good predictor of tacrolimus Concentration/Dose ratio in kidney transplant recipients. Significantly higher L/D was observed among non-expressors 9.483 ng/mL(4.5- 14.1) as compared with the expressors 5.154 ng/mL (4.42-6.5 ) of CYP3A5. Acute rejection episodes were significantly higher for CYP3A5*1 homozygotes compared to patients with CYP3A5*1/*3 and CYP3A5*3/*3 genotypes (40 % versus 20 % and 13 %, respectively ). The dose normalized TAC concentration (ng/ml/mg/kg) was significantly lower in patients having CYP3A5*1/*3 polymorphism. Conclusion: This is the first study to extensively determine the effect of CYP3A5*3 genetic polymorphism on tacrolimus pharmacokinetics in South Indian renal transplant recipients and also shows that majority of our patients carry mutant allele A6986G in CYP3A5*3 gene. Identification of CYP3A5 polymorphism prior to transplantation could contribute to evaluate the appropriate initial dosage of tacrolimus for each patient.

Keywords: kidney transplant patients, CYP3A5 genotype, tacrolimus, RFLP

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Authors: Ahilya Singh, Brad Carte, Ramesh Subramani, William Aalbersberg

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A total of 37 actinomycete strains were purified from 25 Solomon Islands marine sediments using four different types of isolation media. Among them, 54% of the strains had obligate requirement of seawater for growth. The ethyl acetate extract of 100 ml fermentation product of each strain was screened for antimicrobial activity against multidrug resistant human pathogens and cytotoxic activity against brine shrimps. A total of 67% of the ethyl acetate extracts showed antimicrobial and/or cytotoxic activities. A strain F-1915 was selected for isolation and evaluation of bioactive compound(s) based on its bioactive properties and chemical profile analysis using the LC-MS. The strain F-1915 was identified to have 96% sequence similarity to Streptomyces violaceusniger on the basis of 16S rDNA sequences using BLAST analysis. The 16S rDNA revealed that the strain F-1915 is a new member of MAR4 clade of actinomycetes. The MAR4 clade is an interesting clade of actinomycetes known for the production of pharmaceutically important hybrid isoprenoid compounds. The ethyl acetate extract of the fermentation product of this strain was purified by silica gel column chromatography and afforded the isolation of one bioactive pure compound. Based on the 1D and 2D NMR spectral data of compound 1 it was identified as a new mono-brominated phenazinone, Marinophenazimycin A, a structure which has already been studied by external collaborators at Scripps Institution of Oceanography but is yet to be published. Compound 1 displayed significant antimicrobial activity against drug resistant human pathogens. The minimum inhibitory concentration (MIC) of compound 1 was against Methicillin Resistant Staphylococcus aureus (MRSA) was about 1.9 μg/ml and MIC recorded against Amphotericin Resistant Candida albicans (ARCA) was about 0.24 μg/ml. The bioactivity of compound 1 against ARCA was found to be better than the standard antifungal agent amphotericin B. Compound 1 however did not show any cytotoxic activity against brine shrimps.

Keywords: actinomycetes, antimicrobial activity, brominated phenazine, MAR4 clade, marine natural products, multidrug resistent, 1D and 2D NMR

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Authors: Young Ah Kim, Hyunsoo Kim, Eun-Jeong Yoon, Young Hee Seo, Kyungwon Lee

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Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli from food animals are considered as a reservoir for transmission of ESBL genes to human. The aim of this study is to assess the prevalence and molecular epidemiology of ESBL-producing E. coli colonization in pigs, farm workers, and farm environments to elucidate the transmission of multidrug-resistant clones from animal to human. Nineteen pig farms were enrolled across the country in Korea from August to December 2017. ESBL-producing E. coli isolates were detected in 190 pigs, 38 farm workers, and 112 sites of farm environments using ChromID ESBL (bioMerieux, Marcy l'Etoile, France), directly (stool or perirectal swab) or after enrichment (sewage). Antimicrobial susceptibility tests were done with disk diffusion methods and blaTEM, blaSHV, and blaCTX-M were detected with PCR and sequencing. The genomes of the four CTX-M-55-producing E. coli isolates from various sources in one farm were entirely sequenced to assess the relatedness of the strains. Whole genome sequencing (WGS) was performed with PacBio RS II system (Pacific Biosciences, Menlo Park, CA, USA). ESBL genotypes were 85 CTX-M-1 group (one CTX-M-3, 23 CTX-M-15, one CTX-M-28, 59 CTX-M-55, one CTX-M-69) and 60 CTX-M-9 group (41 CTX-M-14, one CTX-M-17, one CTX-M-27, 13 CTX-M-65, 4 CTX-M-102) in total 145 isolates. The rectal colonization rates were 53.2% (101/190) in pigs and 39.5% (15/38) in farm workers. In WGS, sequence types (STs) were determined as ST69 (E. coli PJFH115 isolate from a human carrier), ST457 (two E. coli isolates PJFE101 recovered from a fence and PJFA1104 from a pig) and ST5899 (E. coli PJFA173 isolate from the other pig). The four plasmids encoding CTX-M-55 (88,456 to 149, 674 base pair), whether it belonged to IncFIB or IncFIC-IncFIB type, shared IncF backbone furnishing the conjugal elements, suggesting of genes originated from same ancestor. In conclusion, the prevalence of ESBL-producing E. coli in swine farms was surprisingly high, and many of them shared common ESBL genotypes of clinical isolates such as CTX-M-14, 15, and 55 in Korea. It could spread by horizontal transfer between isolates from different reservoirs (human-animal-environment).

Keywords: Escherichia coli, extended-spectrum β-lactamase, prevalence, whole genome sequencing

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Authors: Mohammed H. Abu-Dieyeh, Mohammad M. Zalloum

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Plant growth-promoting rhizobacteria (PGPR) are known to enhance plant growth and/or reduce plant damage due to soil-borne pathogens. Tomato is the highest consumable vegetable world-wide including Jordan. Fusarium oxysporum is a pathogen that causes well-known damages and losses to many vegetable crops including tomato. In this study, purification of 112 isolates of PGPR strains from rhizosphere environment of different regions in Jordan was accomplished. All bacterial isolates were In-vitro screened for antagonistic effects against F. oxysporum. The eleven most effective isolates that caused 30%-50% in-vitro growth reduction of F. oxysporum were selected. 8 out of 11 of these isolates were collected from Al-Halabat (arid-land). 7 isolates of Al-Halabat exerted 40-54% In-vitro growth reduction of F. oxysporum. Four-week-old seedlings of tomato cultivar (Anjara, the most susceptible indigenous cultivar to F. oxysporum) treated with PGPR5 (Bacillus amyloliquefaciens), and exposed to F. oxysporum, showed no disease symptoms and no significant changes in biomasses or chlorophyll contents indicating a non-direct mechanism of action of PGPR on tomato plants. However PGPR3 (Bacillus sp.), PGPR4 (Bacillus cereus), and PGPR38 (Paenibacillus sp.) treated plants or PGPR treated and exposed to F. oxysporum showed a significant increasing growth of shoot and root biomasses as well as chlorophyll contents of leaves compared to control untreated plants or plants exposed to the fungus without PGPR treatment. A significant increase in number of flowers per plant was also recorded in all PGPR treated plants. The characterization of rhizobacterial strains were accomplished using 16S rRNA gene sequence analysis in addition to microscopic characterization. Further research is necessary to explore the potentiality of other collected PGPR isolates on tomato plants in addition to investigate the efficacy of the identified isolates on other plant pathogens and then finding a proper and effective methods of formulation and application of the successful isolates on selected crops.

Keywords: antagonism, arid land, growth promoting, rhizobacteria, tomato

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Authors: Hyeon-Kyo Lim, Tong-Il Jang, Yong-Hee Lee

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For an operator in a nuclear power plant, human error is one of the most dreaded factors that may result in unexpected accidents. The possibility of human errors may be low, but the risk of them would be unimaginably enormous. Thus, for accident prevention, it is quite indispensable to analyze the influence of any factors which may raise the possibility of human errors. During the past decades, not a few research results showed that performance of human operators may vary over time due to lots of factors. Among them, stress is known to be an indirect factor that may cause human errors and result in mental illness. Until now, not a few assessment tools have been developed to assess stress level of human workers. However, it still is questionable to utilize them for human performance anticipation which is related with human error possibility, because they were mainly developed from the viewpoint of mental health rather than industrial safety. Stress level of a person may go up or down with work time. In that sense, if they would be applicable in the safety aspect, they should be able to assess the variation resulted from work time at least. Therefore, this study aimed to compare their applicability for safety purpose. More than 10 kinds of work stress tools were analyzed with reference to assessment items, assessment and analysis methods, and follow-up measures which are known to close related factors with work stress. The results showed that most tools mainly focused their weights on some common organizational factors such as demands, supports, and relationships, in sequence. Their weights were broadly similar. However, they failed to recommend practical solutions. Instead, they merely advised to set up overall counterplans in PDCA cycle or risk management activities which would be far from practical human error prevention. Thus, it was concluded that application of stress assessment tools mainly developed for mental health seemed to be impractical for safety purpose with respect to human performance anticipation, and that development of a new assessment tools would be inevitable if anyone wants to assess stress level in the aspect of human performance variation and accident prevention. As a consequence, as practical counterplans, this study proposed a new scheme for assessment of work stress level of a human operator that may vary over work time which is closely related with the possibility of human errors.

Keywords: human error, human performance, work stress, assessment tool, time-variant, accident prevention

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Authors: Mukolwe D. Lubembe, Odongo O. David, Githaka Naftali, Kanduma Esther, Marinda Oosthuizen, Kgomotso P. Sibeko

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Theileriosis is a tick-borne disease of cattle caused by an apicomplexan protozoan parasite of the genus Theileria. In eastern and southern Africa, Theileria infections in cattle are caused by the species Theileria parva whose natural reservoir is the African buffalo (Syncerus caffer). Currently, East Coast Fever (ECF) caused by the cattle-derived Theileria parva is still a major problem in eastern Africa and some parts of southern Africa but not in South Africa following its eradication in the 1950s. However, Corridor disease (CD) caused by the buffalo-derived Theileria parva still remains a concern in South Africa. The diversity of Theileria parva in South Africa in comparison to other affected countries is poorly defined yet its known to be the survival strategy of this parasite. We assessed the antigenic diversity of Theileria parva isolates from Buffalo and cattle at the wildlife-livestock interface comparing samples from South Africa, Zimbabwe, Kenya, Tanzania, and Uganda. Antigenic epitopes of eight schizont antigen genes (Tp1, Tp3, Tp4, Tp5, Tp6, Tp7, Tp8 and Tp10) were amplified by PCR from genomic DNA extracted from blood samples collected from cattle and buffalo at the wildlife-livestock interface. Amplicons were purified and then sequenced on NGS platform. Full length open reading frames (ORFs) of two schizont antigen genes (Tp2 and Tp9) and one sporozoite antigen gene, p67 were also amplified from genomic DNA. Amplicons were then purified and cloned for sequencing. Analysis was based on sequence differences in the genes. Preliminary results show an extensively diverse population of Theileria parva circulating in buffalo and cattle populations at the wildlife-livestock interface. Diversity of the antigen genes contributes to the evasion of the immune system of the host by Theileria parva. This possess a concern in that, some of the Theileria parva populations may re-assort and become adapted to cattle to cause a form of theileriosis that is as fatal as ECF in areas where ECF was eradicated or is absent

Keywords: Theileria parva, east coast fever, corridor diseases, antigen genes, diversity

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Authors: Feixiong Chen, Naoufel Haddour, Marie Frenea-Robin, Yves MéRieux, Yann Chevolot, Virginie Monnier

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Neonatal thrombopenia occurs when the mother generates antibodies against her baby’s platelet antigens. It is particularly critical for newborns because it can cause coagulation troubles leading to intracranial hemorrhage. In this case, diagnosis must be done quickly to make platelets transfusion immediately after birth. Before transfusion, platelet antigens must be tested carefully to avoid rejection. The majority of thrombopenia (95 %) are caused by antibodies directed against Human Platelet Antigen 1a (HPA-1a) or 5b (HPA-5b). The common method for antigen platelets detection is polymerase chain reaction allowing for identification of gene sequence. However, it is expensive, time-consuming and requires significant blood volume which is not suitable for newborns. We propose to develop a point-of-care device based on double functionalized magnetic colloids with 1) antibodies specific to antigen platelets and 2) highly sensitive electroactive molecules in order to be detected by an electrochemical microsensor. These magnetic colloids will be used first to isolate platelets from other blood components, then to capture specifically platelets bearing HPA-1a and HPA-5b antigens and finally to attract them close to sensor working electrode for improved electrochemical signal. The expected advantages are an assay time lower than 20 min starting from blood volume smaller than 100 µL. Our functionalization procedure based on amine dendrimers and NHS-ester modification of initial carboxyl colloids will be presented. Functionalization efficiency was evaluated by colorimetric titration of surface chemical groups, zeta potential measurements, infrared spectroscopy, fluorescence scanning and cyclic voltammetry. Our results showed that electroactive molecules and antibodies can be immobilized successfully onto magnetic colloids. Application of a magnetic field onto working electrode increased the detected electrochemical signal. Magnetic colloids were able to capture specific purified antigens extracted from platelets.

Keywords: Magnetic Nanoparticles , Electroactive Molecules, Antibody, Platelet

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Authors: Masahiro Nochi

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This study explores the process in which a Japanese child with congenital blindness deepens understanding of the condition of being “unable to see” and develops the idea of “blind self,” despite having no direct experience of vision. The rehabilitation activities of a child with a congenital visual impairment that were video-recorded from 1 to 6 years old were analyzed qualitatively. The duration of the video was about 80 hours. The recordings were transcribed verbatim, and the episodes in which the child used the words related to the act of “looking” were extracted. Detailed transcripts were constructed referencing the notations of conversation analysis. Characteristics of interactions in those episodes were identified and compared longitudinally. Results showed that the child used the expression "look" under certain interaction patterns and her body expressions and interaction with adults developed in conjunction with the development of language use. Four stages were identified. At the age of 1, interactions involving “look” began to occur. The child said "Look" in the sequence: the child’s “Look,” an adult’s “I’m looking,” certain performances by the child, and the adult’s words of praise. At the age of 3, the child began to behave in accordance with the spatial attributes of the act of "looking," such as turning her face to the adult’s voice before saying, “Look.” She also began to use the expression “Keep looking,” which seemed to reflect her understanding of the temporality of the act of “looking.” At the age of 4, the use of “Look” or “Keep looking” became three times more frequent. She also started to refer to the act of looking in the future, such as “Come and look at my puppy someday.” At the age of 5, she moved her hands toward the adults when she was holding something she wanted to show them. She seemed to understand that people could see the object more clearly when it was in close priximity. About that time, she began to say “I cannot see” to her mother, which suggested a heightened understanding of her own blindness. The findings indicate that as she grew up, the child came to utilize nonverbal behavior before and after the order "Look" to make the progress of the interaction with adults even more certain. As a result, actions that reflect the characteristics of the sighted person's visual experience were incorporated into the interaction chain. The purpose of "Look," with which she intended to attract the adult's attention at first, changed and became something that requests a confirmation she was unable to make herself. It is considered that such a change in the use of the word as well as interaction with sighted adults reflected her heightened self-awareness as someone who could not do what sighted people could do easily. A blind child can gradually deepen their understanding of their own characteristics of blindness among sighted people around them. The child can also develop “blind self” by learning how to interact with others even without direct visual experiences.

Keywords: blindness, child development, conversation analysis, self-concept

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Authors: Sarra K. Ikhlef, Onita Basu

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Natural organic matter (NOM) removal efficiency using drinking water treatment biological filters can be highly influenced by backwashing conditions. Backwashing has the ability to remove the accumulated biomass and particles in order to regenerate the biological filters' removal capacity and prevent excessive headloss buildup. A lab scale system consisting of 3 biological filters was used in this study to examine the implications of different backwash strategies on biological filtration performance. The backwash procedures were evaluated based on their impacts on dissolved organic carbon (DOC) removals, biological filters’ biomass, backwash water volume usage, and particle removal. Results showed that under nutrient limited conditions, the simultaneous use of air and water under collapse pulsing conditions lead to a DOC removal of 22% which was significantly higher (p>0.05) than the 12% removal observed under water only backwash conditions. Employing a bed expansion of 20% under nutrient supplemented conditions compared to a 30% reference bed expansion while using the same amount of water volume lead to similar DOC removals. On the other hand, utilizing a higher bed expansion (40%) lead to significantly lower DOC removals (23%). Also, a backwash strategy that reduced the backwash water volume usage by about 20% resulted in similar DOC removals observed with the reference backwash. The backwash procedures investigated in this study showed no consistent impact on biological filters' biomass concentrations as measured by the phospholipids and the adenosine tri-phosphate (ATP) methods. Moreover, none of these two analyses showed a direct correlation with DOC removal. On the other hand, dissolved oxygen (DO) uptake showed a direct correlation with DOC removals. The addition of the extended terminal subfluidization wash (ETSW) demonstrated no apparent impact on DOC removals. ETSW also successfully eliminated the filter ripening sequence (FRS). As a result, the additional water usage resulting from implementing ETSW was compensated by water savings after restart. Results from this study provide insight to researchers and water treatment utilities on how to better optimize the backwashing procedure for the goal of optimizing the overall biological filtration process.

Keywords: biological filtration, backwashing, collapse pulsing, ETSW

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Authors: Bahor Bahriddinovna Turaeva

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The article provides a structural analysis of the titles of the famous Kyrgyz writer Chingiz Aitmatov’s creative works “The Day Lasts More Than a Hundred Years”, “Doomsday”. The author’s creative purpose in naming the work of art, the role of the elements of the plot, and the composition of the novels in revealing the essence of the title are explained. The criteria that are important in naming the author’s works in different genres are classified, and the titles that mean artistic time and artistic space are studied separately. Chronotope is being concerned as the literary-aesthetic category in world literary studies, expressing the scope of the universe interpretation, the author’s outlook and imagination regarding the world foundation, defining personages, and the composition means of expressing the sequence and duration of the events. A creative comprehension of the chronotope as a means of arranging the work composition, structure and constructing an epic field of the text demands a special approach to understanding the aesthetic character of the work. Since the chronotope includes all the elements of a fictional work, it is impossible to present the plot, composition, conflict, system of characters, feelings, and mood of the characters without the description of the chronotope. In the following development of the scientific-theoretical thought in the world, the chronotope is accepted to be one of the poetic means to demonstrate reality as well as to be a literary process that is basic for the expression of reality in the compositional construction and illustration of the plot relying on the writer’s intention and the ideological conception of the literary work. Literary time enables one to cognate the literary world picture created by the author in terms of the descriptive subject and object of the work. Therefore, one of the topical tasks of modern Uzbek literary studies is to describe historical evidence, event, the life of outstanding people, the chronology of the near past based on the literary time; on the example of the creative works of a certain period, creators or an individual writer are analyzed in separate or comparative-typological aspect.

Keywords: novel, title, chronotope, motive, epigraph, analepsis, structural analysis, plot line, composition

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Authors: Ghodratollah Rostami Paydar

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The Baba-Ali and Galali iron deposits are located in northwest Hamedan and the Iranian Sanandaj-Sirjan geological structural zone. The host rocks of these deposits are metavolcanosedimentary successions of Songhor stratigraphic series with permo-trriassic age. Field investigation, ore geometry, textures and structures and paragenetic sequence of minerals, all indicate that the ore minerals are crystallized in four stages: primary volcanosedimentary stage, secondary regional metamorphism with formation of ductile shear zones, contact metamorphism and metasomatism stage and the finally late hydrothermal mineralization within uplift and exposure. Totally 29 samples of sulfide, oxide-silicate and carbonate minerals of iron orees and gangue has been purified for stable isotope analysis. The isotope ratio data assure that occurrence of dynamothermal metamorphism in these areas typically involves a lengthy period of time, which results in a tendency toward isotopic homogenization specifically in O and H stable isotopes and showing the role of metamorphic waters in mineralization process. Measurement of δ34S (CDT) in first generation of pyrite is higher than another ones, so it confirms the volcanogenic origin of primary iron mineralization. δ13C data measurements in Galali carbonate country rocks show a marine origin. δ18O in magnetite and skarn forming silicates, δ18O and δ13C in limestone and skarn calcite and δ34S in sulphides are all consistent with the interaction of a magmatic-equilibrated fluid with Galali limestone, and a dominantly magmatic source for S. All these data imply skarn formation and mineralisation in a magmatic-hydrothermal system that maintained high salinity to relatively late stages resulting in the formation of the regional Na metasomatic alteration halo. Late stage hydrothermal quartz-calcite veinlets are important for gold mineralization, but the economic evaluation is required to detailed geochemical studies.

Keywords: iron, polygenetic, stable isotope, BabaAli, Galali

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Authors: Arpit Kumar Shrivastava, Subrat Kumar, Rajani Kanta Mohapatra, Priyadarshi Soumyaranjan Sahu

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Computational approaches to predict structure, function and other biological characteristics of proteins are becoming more common in comparison to the traditional methods in drug discovery. Cryptosporidiosis is a major zoonotic diarrheal disease particularly in children, which is caused primarily by Cryptosporidium hominis and Cryptosporidium parvum. Currently, there are no vaccines for cryptosporidiosis and recommended drugs are not effective. With the availability of complete genome sequence of C. hominis, new targets have been recognized for the development of effective and better drugs and/or vaccines. We identified a unique hypothetical epitopic protein in C. hominis genome through BLASTP analysis. A 3D model of the hypothetical protein was generated using I-Tasser server through threading methodology. The quality of the model was validated through Ramachandran plot by PROCHECK server. The functional annotation of the hypothetical protein through DALI server revealed structural similarity with human Transportin 3. Phylogenetic analysis for this hypothetical protein also showed C. hominis hypothetical protein (CUV04613) was the closely related to human transportin 3 protein. The 3D protein model is further subjected to virtual screening study with inhibitors from the Zinc Database by using Dock Blaster software. Docking study reported N-(3-chlorobenzyl) ethane-1,2-diamine as the best inhibitor in terms of docking score. Docking analysis elucidated that Leu 525, Ile 526, Glu 528, Glu 529 are critical residues for ligand–receptor interactions. The molecular dynamic simulation was done to access the reliability of the binding pose of inhibitor and protein complex using GROMACS software at 10ns time point. Trajectories were analyzed at each 2.5 ns time interval, among which, H-bond with LEU-525 and GLY- 530 are significantly present in MD trajectories. Furthermore, antigenic determinants of the protein were determined with the help of DNA Star software. Our study findings showed a great potential in order to provide insights in the development of new drug(s) or vaccine(s) for control as well as prevention of cryptosporidiosis among humans and animals.

Keywords: cryptosporidium hominis, hypothetical protein, molecular docking, molecular dynamics simulation

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Authors: Ayesha Sanjana Kawser Parsha

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S-acylation is an irreversible bond in which cysteine residues are linked to fatty acids palmitate (74%) or stearate (22%), either at the COOH or NH2 terminal, via a thioester linkage. There are several experimental methods that can be used to identify the S-palmitoylation site; however, since they require a lot of time, computational methods are becoming increasingly necessary. There aren't many predictors, however, that can locate S- palmitoylation sites in Arabidopsis Thaliana with sufficient accuracy. This research is based on the importance of building a better prediction tool. To identify the type of machine learning algorithm that predicts this site more accurately for the experimental dataset, several prediction tools were examined in this research, including the GPS PALM 6.0, pCysMod, GPS LIPID 1.0, CSS PALM 4.0, and NBA PALM. These analyses were conducted by constructing the receiver operating characteristics plot and the area under the curve score. An AI-driven deep learning-based prediction tool has been developed utilizing the analysis and three sequence-based input data, such as the amino acid composition, binary encoding profile, and autocorrelation features. The model was developed using five layers, two activation functions, associated parameters, and hyperparameters. The model was built using various combinations of features, and after training and validation, it performed better when all the features were present while using the experimental dataset for 8 and 10-fold cross-validations. While testing the model with unseen and new data, such as the GPS PALM 6.0 plant and pCysMod mouse, the model performed better, and the area under the curve score was near 1. It can be demonstrated that this model outperforms the prior tools in predicting the S- palmitoylation site in the experimental data set by comparing the area under curve score of 10-fold cross-validation of the new model with the established tools' area under curve score with their respective training sets. The objective of this study is to develop a prediction tool for Arabidopsis Thaliana that is more accurate than current tools, as measured by the area under the curve score. Plant food production and immunological treatment targets can both be managed by utilizing this method to forecast S- palmitoylation sites.

Keywords: S- palmitoylation, ROC PLOT, area under the curve, cross- validation score

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Authors: Ali Bahkali, Rayan Yousef Booq, Mohammad Khiyami

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Soil samples were collected from five different regions in the Kingdom of Saudi Arabia. Microbiological methods included dilution methods and pour plates to isolate and purify bacteria soil. The ability of isolates to develop biopolymer was investigated on petri dishes containing elements and substance concentrations stimulating developing biopolymer. Fluorescent stains, Nile red and Nile blue were used to stain the bacterial cells developing biopolymers. In addition, Sudan black was used to detect biopolymers in bacterial cells. The isolates which developed biopolymers were identified based on their gene sequence of 1 6sRNA and their ability to grow and synthesize PHAs on mineral medium supplemented with 1% dates molasses as the only carbon source under nitrogen limitation. During the study 293 bacterial isolates were isolated and detected. Through the initial survey on the petri dishes, 84 isolates showed the ability to develop biopolymers. These bacterial colonies developed a pink color due to accumulation of the biopolymers in the cells. Twenty-three isolates were able to grow on dates molasses, three strains of which showed the ability to accumulate biopolymers. These strains included Bacillus sp., Ralstonia sp. and Microbacterium sp. They were detected by Nile blue A stain with fluorescence microscopy (OLYMPUS IX 51). Among the isolated strains Ralstonia sp. was selected after its ability to grow on molasses dates in the presence of a limited nitrogen source was detected. The optimum conditions for formation of biopolymers by isolated strains were investigated. Conditions studied included, best incubation duration (2 days), temperature (30°C) and pH (7-8). The maximum PHB production was raised by 1% (v1v) when using concentrations of dates molasses 1, 2, 3, 4 and 5% in MSM. The best inoculated with 1% old inoculum (1= OD). The ideal extraction method of PHA and PHB proved to be 0.4% sodium hypochlorite solution, producing a quantity of polymer 98.79% of the cell's dry weight. The maximum PHB production was 1.79 g/L recorded by Ralstonia sp. after 48 h, while it was 1.40 g/L produced by R.eutropha ATCC 17697 after 48 h.

Keywords: bacteria forming polyhydroxyalkanoate, detection, molecular, Saudi Arabia

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Authors: Attila Kiss, Erzsébet Némedi, Zoltán Naár

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Due to the rapidly growing number of conscious customers in the recent years, more and more people look for products with positive physiological effects which may contribute to the preservation of their health. In response to these demands Food Science Research Institute of Budapest develops and introduces into the market new functional foods of guaranteed positive effect that contain bioactive agents. New, efficient technologies are also elaborated in order to preserve the maximum biological effect of the produced foods. The main objective of our work was the development of new functional biscuits fortified with physiologically beneficial ingredients. Bakery products constitute the base of the food nutrients’ pyramid, thus they might be regarded as foodstuffs of the largest consumed quantity. In addition to the well-known and certified physiological benefits of lysine, as an essential amino acid, a series of antioxidant type compounds is formed as a consequence of the occurring Maillard-reaction. Progress of the evoked Maillard-reaction was studied by applying diverse sugars (glucose, fructose, saccharose, isosugar) and lysine at several temperatures (120-170°C). Interval of thermal treatment was also varied (10-30 min). The composition and production technologies were tailored in order to reach the maximum of the possible biological benefits, so as to the highest antioxidant capacity in the biscuits. Out of the examined sugar components, theextent of the Maillard-reaction-driven transformation of glucose was the most pronounced at both applied temperatures. For the precise assessment of the antioxidant activity of the products FRAP and DPPH methods were adapted and optimised. To acquire an authentic and extensive mechanism of the occurring transformations, Maillard-reaction products were identified, and relevant reaction pathways were revealed. GC-MS and HPLC-MS techniques were applied for the analysis of the 60 generated MRPs and characterisation of actual transformation processes. 3 plausible major transformation routes might have been suggested based on the analytical result and the deductive sequence of possible occurring conversions between lysine and the sugars.

Keywords: Maillard-reaction, lysine, antioxidant activity, GC-MS and HPLC-MS techniques

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Authors: Noura El-Ahmady El-Naggar

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L-asparaginase is an important enzyme as therapeutic agents used in combination therapy with other drugs in the treatment of acute lymphoblastic leukemia in children. L-asparaginase producing actinomycete strain, NEAE-K, was isolated from soil sample and identified on the basis of morphological, cultural, physiological and biochemical properties, together with 16S rDNA sequence as new subsp. Streptomyces rochei subsp. chromatogenes NEAE-K and sequencing product (1532 bp) was deposited in the GenBank database under accession number KJ200343. The study was conducted to screen parameters affecting the production of L-asparaginase by Streptomyces rochei subsp. chromatogenes NEAE-K on solid state fermentation using Plackett–Burman experimental design. Sixteen different independent variables including incubation time, moisture content, inoculum size, temperature, pH, soybean meal+ wheat bran, dextrose, fructose, L-asparagine, yeast extract, KNO3, K2HPO4, MgSO4.7H2O, NaCl, FeSO4. 7H2O, CaCl2, and three dummy variables were screened in Plackett–Burman experimental design of 20 trials. The most significant independent variables affecting enzyme production (dextrose, L-asparagine and K2HPO4) were further optimized by the central composite design. As a result, a medium of the following formula is the optimum for producing an extracellular L-asparaginase by Streptomyces rochei subsp. chromatogenes NEAE-K from solid state fermentation: g/L (soybean meal+ wheat bran 15, dextrose 3, fructose 4, L-asparagine 8, yeast extract 2, KNO3 1, K2HPO4 2, MgSO4.7H2O 0.5, NaCl 0.1, FeSO4. 7H2O 0.02, CaCl2 0.01), incubation time 7 days, moisture content 50%, inoculum size 3 mL, temperature 30°C, pH 8.5.

Keywords: streptomyces rochei subsp. chromatogenes neae-k, 16s rrna, identification, solid state fermentation, l-asparaginase production, plackett-burman design, central composite design

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Authors: Anastasia Poliakova

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Harmful algal bloom (HAB) is a known negative phenomenon that is caused both by natural factors and anthropogenic influence. HABs can result in a series of deleterious effects, such as beach fouling, paralytic shellfish poisoning, mass mortality of marine species, and a threat to human health, especially if toxins pollute drinking water or occur nearby public resorts. In South China, the problem of HABs has an ultimately important meaning. For this study, we used a 1.5 m sediment core LAX-2018-2 collected in 2018 from the Zhanjiang Mangrove National Nature Reserve (109°03´E, 20°30´N), Guangdong Province, South China. High-resolution coastal environment reconstruction with a specific focus on the HABs history during the last ca 2500 yrs was attempted. Age control was performed with five radiocarbon dates obtained from benthic foraminifera. A total number of 71 dinoflagellate cyst types was recorded. The most common types found consistently throughout the sediment sequence were autotrophic Spiniferites spp., Spiniferites hyperacanthus and S. mirabilis, S. ramosus, Operculodinium centrocarpum sensu Wall and Dale 1966, Polysphaeridium zoharyi, and heterotrophic Brigantedinium ssp., cyst of Gymnodinium catenatum and cysts mixture of Protoperidinium. Three local dinoflagellate zones LAX-1 to LAX-3 were established based on the results of the constrained cluster analysis and data ordination; additionally, the middle zone LAX-2 was derived into two subzones, LAX-2a and LAX-2b based on the dynamics of toxic and heterotrophic cysts as well as on the significant changes (probability, P=0.89) in percentages of eutrophic indicators. The total cyst count varied from 106 to 410 dinocysts per slide, with 177 cyst types on average. Dinocyst assemblages are characterized by high values of the dost-depositional degradation index (kt) that varies between 3.6 and 7.6 (averaging 5.4), which is relatively high and is very typical for the areas with selective dinoflagellate cyst preservation that is related to bottom-water oxygen concentrations.

Keywords: reconstruction of palaeoenvironment, harmful algal blooms, anthropogenic influence on coastal zones, South China Sea

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