Search results for: shotgun metagenomic sequence analysis

Authors: Rubin Dan, Xingcai Wang, Ziyang Chen

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A chaotic time series noise reduction method based on the fusion of the local projection method, wavelet transform, and particle swarm algorithm (referred to as the LW-PSO method) is proposed to address the problem of false recognition due to noise in the recognition process of chaotic time series containing noise. The method first uses phase space reconstruction to recover the original dynamical system characteristics and removes the noise subspace by selecting the neighborhood radius; then it uses wavelet transform to remove D1-D3 high-frequency components to maximize the retention of signal information while least-squares optimization is performed by the particle swarm algorithm. The Lorenz system containing 30% Gaussian white noise is simulated and verified, and the phase space, SNR value, RMSE value, and K value of the 0-1 test method before and after noise reduction of the Schreiber method, local projection method, wavelet transform method, and LW-PSO method are compared and analyzed, which proves that the LW-PSO method has a better noise reduction effect compared with the other three common methods. The method is also applied to the classical system to evaluate the noise reduction effect of the four methods and the original system identification effect, which further verifies the superiority of the LW-PSO method. Finally, it is applied to the Chengdu rainfall chaotic sequence for research, and the results prove that the LW-PSO method can effectively reduce the noise and improve the chaos recognition rate.

Keywords: Schreiber noise reduction, wavelet transform, particle swarm optimization, 0-1 test method, chaotic sequence denoising

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Authors: Abu Salim Mustafa

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The comparisons of mycobacterial genomes have identified several Mycobacterium tuberculosis-specific genomic regions that are absent in other mycobacteria and are known as regions of differences. Due to M. tuberculosis-specificity, the peptides encoded by these regions could be useful in the specific diagnosis of tuberculosis. To explore this possibility, overlapping synthetic peptides corresponding to 39 proteins predicted to be encoded by genes present in regions of differences were tested for antibody-reactivity with sera from tuberculosis patients and healthy subjects. The results identified four immunodominant peptides corresponding to four different proteins, with three of the peptides showing significantly stronger antibody reactivity and rate of positivity with sera from tuberculosis patients than healthy subjects. The fourth peptide was recognized equally well by the sera of tuberculosis patients as well as healthy subjects. Predication of antibody epitopes by bioinformatics analyses using ABCpred server predicted multiple linear epitopes in each peptide. Furthermore, peptide sequence analysis for sequence identity using BLAST suggested M. tuberculosis-specificity for the three peptides that had preferential reactivity with sera from tuberculosis patients, but the peptide with equal reactivity with sera of TB patients and healthy subjects showed significant identity with sequences present in nob-tuberculous mycobacteria. The three identified M. tuberculosis-specific immunodominant peptides may be useful in the serological diagnosis of tuberculosis.

Keywords: genomic regions of differences, Mycobacterium tuberculossis, peptides, serodiagnosis

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Authors: A. Shoiynbek, K. Kozhakhmet, P. Menezes, D. Kuanyshbay, D. Bayazitov

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Speech emotion recognition has received increasing research interest all through current years. There was used emotional speech that was collected under controlled conditions in most research work. Actors imitating and artificially producing emotions in front of a microphone noted those records. There are four issues related to that approach, namely, (1) emotions are not natural, and it means that machines are learning to recognize fake emotions. (2) Emotions are very limited by quantity and poor in their variety of speaking. (3) There is language dependency on SER. (4) Consequently, each time when researchers want to start work with SER, they need to find a good emotional database on their language. In this paper, we propose the approach to create an automatic tool for speech emotion extraction based on facial emotion recognition and describe the sequence of actions of the proposed approach. One of the first objectives of the sequence of actions is a speech detection issue. The paper gives a detailed description of the speech detection model based on a fully connected deep neural network for Kazakh and Russian languages. Despite the high results in speech detection for Kazakh and Russian, the described process is suitable for any language. To illustrate the working capacity of the developed model, we have performed an analysis of speech detection and extraction from real tasks.

Keywords: deep neural networks, speech detection, speech emotion recognition, Mel-frequency cepstrum coefficients, collecting speech emotion corpus, collecting speech emotion dataset, Kazakh speech dataset

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Authors: Maryam Beiranvand, Sajad Yaghoubi

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Background: Some microbes can colonize plants’ inner tissues without causing obvious damage and can even produce useful bioactive substances. In the present study, the diversity of the endophytic bacteria associated with medicinal plants from Iran was investigated by culturing techniques, molecular gene identification, as well as measuring them for antibacterial activity. Results: In the spring season from 2013 to 2014, 35 herb pharmacology samples were collected, sterilized, meshed, and then cultured on selective media culture. A total of 199 endophytic bacteria were successfully isolated from 35 tissue cultures of medical plants, and sixty-seven out of 199 bacterial isolates were subjected to identification by the 16S rRNA gene sequence analysis method. Based on the sequence similarity gene and phylogenetic analyses, these isolates were grouped into five classes, fourteen orders, seventeen families, twenty-one genera, and forty strains. The most abundant group of endophytic bacteria was actinobacterial, consisting of thirty-two (47%) out of 67 bacterial isolates. Ten (22.3%) out of 67 bacterial isolates remained unidentified and classified at the genus level. The signature of the 16S rRNA gene formed a distinct line in a phylogenetic tree showing that they might be new species of bacteria. One (5.2%) out of 67 bacterial isolates was still not well categorized. Forty-two out of 67 strains were candidates for antimicrobial activity tests. Nineteen (45%) out of 42 strains showed antimicrobial activity multidrug-resistance (MDR); thirteen (68%) out of 19 strains were allocated to classes actinobacteria. Four (21%) out of 19 strains belonged to the Bacillaceae family, one (5.2%) out of 19 strains was the Paenibacillaceae family, and one (5.2%) out of 19 strains belonged to the Pseudomonadaceae family. The other twenty-three strains did not show inhibitory activities. Conclusions: Our research showed a high-level phylogenetic diversity and the intoxicating antibiotic activity of endophytic bacteria in the herb pharmacology of Iran.

Keywords: medical plant, endophytic bacteria, antimicrobial activity, whole genome sequencing analysis

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Authors: Yanyan Wang

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This paper on second language teaching and learning uses conversation analysis (CA) approach and focuses on how second language learners of Chinese do repair when making clarification requests. In order to demonstrate their behavior in interaction, a comparison was made to study the differences between native speakers of Chinese with non-native speakers of Chinese. The significance of the research is to make second language teachers and learners aware of repair and how to seek clarification. Utilizing the methodology of CA, the research involved two sets of naturally occurring recordings, one of native speaker students and the other of non-native speaker students. Both sets of recording were telephone talks between students and teachers. There were 50 native speaker students and 50 non-native speaker students. From multiple listening to the recordings, the parts with repairs for clarification were selected for analysis which included the moments in the talk when students had problems in understanding or hearing the speaker and had to seek clarification. For example, ‘Sorry, I do not understand ‘and ‘Can you repeat the question? ‘were the parts as repair to make clarification requests. In the data, there were 43 such cases from native speaker students and 88 cases from non-native speaker students. The non-native speaker students were more likely to use repair to seek clarification. Analysis on how the students make clarification requests during their conversation was carried out by investigating how the students initiated problems and how the teachers repaired the problems. In CA term, it is called other-initiated self-repair (OISR), which refers to student-initiated teacher-repair in this research. The findings show that, in initiating repair, native speaker students pay more attention to mutual understanding (inter-subjectivity) while non-native speaker students, due to their lack of language proficiency, pay more attention to their status of knowledge (epistemic) switch. There are three major differences: 1, native Chinese students more often initiate closed-class OISR (seeking specific information in the request) such as repeating a word or phrases from the previous turn while non-native students more frequently initiate open-class OISR (not specifying clarification) such as ‘sorry, I don’t understand ‘. 2, native speakers’ clarification requests are treated by the teacher as understanding of the content while non-native learners’ clarification requests are treated by teacher as language proficiency problem. 3, native speakers don’t see repair as knowledge issue and there is no third position in the repair sequences to close repair while non-native learners take repair sequence as a time to adjust their knowledge. There is clear closing third position token such as ‘oh ‘ to close repair sequence so that the topic can go back. In conclusion, this paper uses conversation analysis approach to compare differences between native Chinese speakers and non-native Chinese learners in their ways of conducting repair when making clarification requests. The findings are useful in future Chinese language teaching and learning, especially in teaching pragmatics such as requests.

Keywords: conversation analysis (CA), clarification request, second language (L2), teaching implication

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Authors: David Levy

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The newly released Distributed System Interface 3 (DSI3) Bus Standard specification defines 3 modulation levels from which 16 valid symbols are coded. This structure creates power consumption variations depending on the transmitted data of a factor of more than 2 between minimum and maximum. The power generation unit has to consider therefore the worst case maximum consumption all the time and be built accordingly. This paper proposes a method to reduce both the average current consumption and worst case current consumption. The transmitter randomizes the data using several pseudo-random sequences. It then estimates the energy consumption of the generated frames and selects to transmit the one which consumes the least. The transmitter also prepends the index of the pseudo-random sequence, which is not randomized, to allow the receiver to recover the original data using the correct sequence. We show that in the case that the frame occupies most of the DSI3 synchronization period, we achieve average power consumption reduction by up to 13% and the worst case power consumption is reduced by 17.7%.

Keywords: DSI3, energy, power consumption, randomization

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Authors: Hamdi Omar Omar, Hela Fakhfakh, Chokri Yaich

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This work reflects the integration of different techniques, such as field sampling and observations, magnetic susceptibility measurement, cyclostratigaraphy and sequence stratigraphy. The combination of these results allows us to reconstruct the environmental evolution of the Sidi Khalif Formation in the North-South Axis (NOSA), aged of Upper Tithonian, Berriasian and Lower Valanginian. Six sedimentary facies were identified and are primarily influenced by open marine sedimentation receiving increasing terrigenous influx. Spectral analysis, based on MS variation (for the outcropped section) and wireline logging gamma ray (GR) variation (for the sub-area section) show a pervasive dominance of 405-kyr eccentricity cycles with the expression of 100-kyr eccentricity, obliquity and precession. This study provides (for the first time) a precise duration of 2.4 myr for the outcropped Sidi Khalif Formation with a sedimentation rate of 5.4 cm/kyr and the sub-area section to 3.24 myr with a sedimentation rate of 7.64 cm/kyr. We outlined 27 5th-order depositional sequences, 8 Milankovitch depositional sequences and 2 major 3rd-order cycles for the outcropping section, controlled by the long eccentricity (405 kyr) cycles and the precession index cycles. This study has demonstrated the potential of MS and GR to be used as proxies to develop an astronomically calibrated time-scale for the Mesozoic era.

Keywords: Berriasian, magnetic susceptibility, orbital tuning, Sidi Khalif Formation

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Authors: Wanatchapong Kongkaew

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This paper proposes an application of probabilistic technique, namely Gaussian process regression, for estimating an optimal sequence of the single machine with total weighted tardiness (SMTWT) scheduling problem. In this work, the Gaussian process regression (GPR) model is utilized to predict an optimal sequence of the SMTWT problem, and its solution is improved by using an iterated local search based on simulated annealing scheme, called GPRISA algorithm. The results show that the proposed GPRISA method achieves a very good performance and a reasonable trade-off between solution quality and time consumption. Moreover, in the comparison of deviation from the best-known solution, the proposed mechanism noticeably outperforms the recently existing approaches.

Keywords: Gaussian process regression, iterated local search, simulated annealing, single machine total weighted tardiness

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Authors: Ibrahim Ilker Ozyigit, Ertugrul Filiz, Ilhan Dogan

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An in silico analysis of Brachypodium distachyon, Triticum aestivum, Festuca arundinacea, Lolium perenne, Hordeum vulgare subsp. vulgare of the Pooideaea was performed based on complete chloroplast genomes including rbcL coding and trnH-psbA intergenic spacer regions alone to compare phylogenetic resolving power. Neighbor-joining, Minimum Evolution, and Unweighted Pair Group Method with arithmetic mean methods were used to reconstruct phylogenies with the highest bootstrap supported the obtained data from whole chloroplast genome sequence. The highest and lowest values from nucleotide diversity (π) analysis were found to be 0.315813 and 0.043495 in rbcL coding region in chloroplast genome and complete chloroplast genome, respectively. The highest transition/transversion bias (R) value was recorded as 1.384 in complete chloroplast genomes. F. arudinacea-L. perenne clade was uncovered in all phylogenies. Sequences of rbcL and trnH-psbA regions were not able to resolve the Pooideae phylogenies due to lack of genetic variation.

Keywords: chloroplast DNA, Pooideae, phylogenetic analysis, rbcL, trnH-psbA

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Authors: Maria Neagu

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This paper presents the heat and mass driven natural convection succession in a Darcy thermally stratified porous medium that embeds a vertical semi-infinite impermeable wall of constant heat flux and concentration. The scale analysis of the system determines the two possible maps of the heat and mass driven natural convection sequence along the wall as a function of the process parameters. These results are verified using the finite differences method applied to the conservation equations.

Keywords: finite difference method, natural convection, porous medium, scale analysis, thermal stratification

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Authors: Atif Zafar, Fan Haijun

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A sequence of different Reservoir Engineering methods and tools in reservoir characterization and field development are presented in this paper. The real data of Jin Gas Field of L-Basin of Pakistan is used. The basic concept behind this work is to enlighten the importance of well test analysis in a broader way (i.e. reservoir characterization and field development) unlike to just determine the permeability and skin parameters. Normally in the case of reservoir characterization we rely on well test analysis to some extent but for field development plan, the well test analysis has become a forgotten tool specifically for locations of new development wells. This paper describes the successful implementation of well test analysis in Jin Gas Field where the main uncertainties are identified during initial stage of field development when location of new development well was marked only on the basis of G&G (Geologic and Geophysical) data. The seismic interpretation could not encounter one of the boundary (fault, sub-seismic fault, heterogeneity) near the main and only producing well of Jin Gas Field whereas the results of the model from the well test analysis played a very crucial rule in order to propose the location of second well of the newly discovered field. The results from different methods of well test analysis of Jin Gas Field are also integrated with and supported by other tools of Reservoir Engineering i.e. Material Balance Method and Volumetric Method. In this way, a comprehensive way out and algorithm is obtained in order to integrate the well test analyses with Geological and Geophysical analyses for reservoir characterization and field development. On the strong basis of this working and algorithm, it was successfully evaluated that the proposed location of new development well was not justified and it must be somewhere else except South direction.

Keywords: field development plan, reservoir characterization, reservoir engineering, well test analysis

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Authors: Abdoulie K. Ceesay

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Within the sequence of the whole genome, it is known that 99.9% of the human genome is similar, whilst our difference lies in just 0.1%. Among these minor dissimilarities, the most common type of genetic variations that occurs in a population is SNP, which arises due to nucleotide substitution in a protein sequence that leads to protein destabilization, alteration in dynamics, and other physio-chemical properties’ distortions. While causing variations, they are equally responsible for our difference in the way we respond to a treatment or a disease, including various cancer types. There are two types of SNPs; synonymous single nucleotide polymorphism (sSNP) and non-synonymous single nucleotide polymorphism (nsSNP). sSNP occur in the gene coding region without causing a change in the encoded amino acid, while nsSNP is deleterious due to its replacement of a nucleotide residue in the gene sequence that results in a change in the encoded amino acid. Predicting the effects of cancer related nsSNPs on protein stability, function, and dynamics is important due to the significance of phenotype-genotype association of cancer. In this thesis, Data of 5 oncogenes (ONGs) (AKT1, ALK, ERBB2, KRAS, BRAF) and 5 tumor suppressor genes (TSGs) (ESR1, CASP8, TET2, PALB2, PTEN) were retrieved from ClinVar. Five common in silico tools; Polyphen, Provean, Mutation Assessor, Suspect, and FATHMM, were used to predict and categorize nsSNPs as deleterious, benign, or neutral. To understand the impact of each variation on the phenotype, Maestro, PremPS, Cupsat, and mCSM-NA in silico structural prediction tools were used. This study comprises of in-depth analysis of 10 cancer gene variants downloaded from Clinvar. Various analysis of the genes was conducted to derive a meaningful conclusion from the data. Research done indicated that pathogenic variants are more common among ONGs. Our research also shows that pathogenic and destabilizing variants are more common among ONGs than TSGs. Moreover, our data indicated that ALK(409) and BRAF(86) has higher benign count among ONGs; whilst among TSGs, PALB2(1308) and PTEN(318) genes have higher benign counts. Looking at the individual cancer genes predisposition or frequencies of causing cancer according to our research data, KRAS(76%), BRAF(55%), and ERBB2(36%) among ONGs; and PTEN(29%) and ESR1(17%) among TSGs have higher tendencies of causing cancer. Obtained results can shed light to the future research in order to pave new frontiers in cancer therapies.

Keywords: tumor suppressor genes (TSGs), oncogenes (ONGs), non synonymous single nucleotide polymorphism (nsSNP), single nucleotide polymorphism (SNP)

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Authors: A. Ferasat, S. Rostampour Yasouri

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Seasonal flu is a highly contagious infection caused by influenza viruses. These viruses undergo genetic changes that result in new epidemics across the globe. Medical attention is crucial in severe cases, particularly for the elderly, frail, and those with chronic illnesses, as their immune systems are often weaker. The purpose of this study was to detect new subtypes of the influenza A virus rapidly using a specific RT-PCR method based on the HA gene (hemagglutinin). In the winter and spring of 2022_2023, 120 embryonated egg samples were cultured, suspected of seasonal influenza. RNA synthesis, followed by cDNA synthesis, was performed. Finally, the PCR technique was applied using a pair of specific primers designed based on the HA gene. The PCR product was identified after purification, and the nucleotide sequence of purified PCR products was compared with the sequences in the gene bank. The results showed a high similarity between the sequence of the positive samples isolated from the patients and the sequence of the new strains isolated in recent years. This RT-PCR technique is entirely specific in this study, enabling the detection and multiplication of influenza and its subspecies from clinical samples. The RT-PCR technique based on the HA gene, along with sequencing, is a fast, specific, and sensitive diagnostic method for those infected with influenza viruses and its new subtypes. Rapid molecular diagnosis of influenza is essential for suspected people to control and prevent the spread of the disease to others. It also prevents the occurrence of secondary (sometimes fatal) pneumonia that results from influenza and pathogenic bacteria. The critical role of rapid diagnosis of new strains of influenza is to prepare a drug vaccine against the latest viruses that did not exist in the community last year and are entirely new viruses.

Keywords: influenza, molecular diagnosis, patients, RT-PCR technique

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Authors: Nemat Sokhandan Bashir

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Threats from viruses to agricultural crops could be even larger than the losses caused by the other pathogens because, in many cases, the viral infection is latent but crucial from an epidemic point of view. Wild vegetation can be a source of many viruses that eventually find their destiny in crop plants. Although often asymptomatic in wild plants due to adaptation, they can potentially cause serious losses in crops. Therefore, exploring viruses in wild vegetation is very important. Recently, omics have been quite useful for exploring plant viruses from various plant sources, especially wild vegetation. For instance, we have discovered viruses such as Ambrossia asymptomatic virus I (AAV-1) through the application of metagenomics from Oklahoma Prairie Reserve. Accordingly, extracts from randomly-sampled plants are subjected to high speed and ultracentrifugation to separated virus-like particles (VLP), then nucleic acids in the form of DNA or RNA are extracted from such VLPs by treatment with phenol—chloroform and subsequent precipitation by ethanol. The nucleic acid preparations are separately treated with RNAse or DNAse in order to determine the genome component of VLPs. In the case of RNAs, the complementary cDNAs are synthesized before submitting to DNA sequencing. However, for VLPs with DNA contents, the procedure would be relatively straightforward without making cDNA. Because the length of the nucleic acid content of VPLs can be different, various strategies are employed to achieve sequencing. Techniques similar to so-called "chromosome walking" may be used to achieve sequences of long segments. When the nucleotide sequence data were obtained, they were subjected to BLAST analysis to determine the most related previously reported virus sequences. In one case, we determined that the novel virus was AAV-l because the sequence comparison and analysis revealed that the reads were the closest to the Indian citrus ringspot virus (ICRSV). AAV—l had an RNA genome with 7408 nucleotides in length and contained six open reading frames (ORFs). Based on phylogenies inferred from the replicase and coat protein ORFs of the virus, it was placed in the genus Mandarivirus.

Keywords: wild, plant, novel, metagenomics

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Authors: Imad H. Hameed, Mohammad A. Jebor, Ammera J. Omer

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The aim of this research is to study the mitochonderial coding region by using the Sanger sequencing technique and establish the degree of variation characteristic of a fragment. FTA® Technology (FTA™ paper DNA extraction) utilized to extract DNA. Portion of coding region encompassing positions 11719 –12384 amplified in accordance with the Anderson reference sequence. PCR products purified by EZ-10 spin column then sequenced and Detected by using the ABI 3730xL DNA Analyzer. Five new polymorphic positions 11741, 11756, 11878, 11887 and 12133 are described may be suitable sources for identification purpose in future. The calculated value D= 0.95 and RMP=0.048 of the genetic diversity should be understood as high in the context of coding function of the analysed DNA fragment. The relatively high gene diversity and a relatively low random match probability were observed in Iraq population. The obtained data can be used to identify the variable nucleotide positions characterized by frequent occurrence which is most promising for various identifications.

Keywords: coding region, Iraq, mitochondrial DNA, polymorphic positions, sanger technique

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Authors: Pranjali Sharma, Swati Neogi

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Composite pressure vessels are low weight structures mainly used in a variety of applications such as automobiles, aeronautics and chemical engineering. Fiber reinforced polymer (FRP) composite materials offer the simplicity of design and use, high fuel storage capacity, rapid refueling capability, excellent shelf life, minimal infrastructure impact, high safety due to the inherent strength of the pressure vessel, and little to no development risk. Apart from these preliminary merits, the subsidized weight of composite vessels over metallic cylinders act as the biggest asset to the automotive industry, increasing the fuel efficiency. The result is a lightweight, flexible, non-explosive, and non-fragmenting pressure vessel that can be tailor-made to attune with specific applications. The winding pattern of the composite over-wrap is a primary focus while designing a pressure vessel. The critical stresses in the system depend on the thickness, angle and sequence of the composite layers. The composite over-wrap is wound over a plastic liner, whose geometry can be varied for the ease of winding. In the present study, we aim to optimize the FRP vessel geometry that provides an ease in winding and also aids in weight reduction for enhancing the vessel performance. Finite element analysis is used to study the effect of dome geometry, yielding a design with maximum value of burst pressure and least value of vessel weight. The stress and strain analysis of different dome ends along with the cylindrical portion is carried out in ANSYS 19.2. The failure is predicted using different failure theories like Tsai-Wu theory, Tsai-Hill theory and Maximum stress theory. Corresponding to a given winding sequence, the optimum dome geometry is determined for a fixed internal pressure to identify the theoretical value of burst pressure. Finally, this geometry is used to decrease the number of layers to reach the set value of safety in accordance with the available safety standards. This results in decrease in the weight of the composite over-wrap and manufacturing cost of the pressure vessel. An improvement in the overall weight performance of the pressure vessel gives higher fuel efficiency for its use in automobile applications.

Keywords: Compressed Gas Storage, Dome geometry, Theoretical Analysis, Type-4 Composite Pressure Vessel, Improvement in Vessel Weight Performance

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Authors: R. Sulakshana, R. Lakshmi

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Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR associate (CRISPR/Cas) is an adaptive immunity system found in bacteria and archaea. It has been modified to serve as a potent gene editing tool. Moreover, it has found widespread use in the field of genome research because of its accessibility and low cost. Several bioinformatics methods have been created to aid in the construction of specific single guide RNA (sgRNA), which is highly active and crucial to CRISPR/Cas performance. Various Cas proteins, including Cas1, Cas2, Cas9, and Cas12, have been used to create genome engineering tools because of their programmable sequence specificity. Class 1 and 2 CRISPR/Cas systems, as well as the processes of all known Cas proteins (including Cas9 and Cas12), are discussed in this review paper. In addition, the various CRISPR methodologies and their tools so far discovered are discussed. Finally, the challenges and issues in the CRISPR system along with future works, are presented.

Keywords: gene editing tool, Cas proteins, CRISPR, guideRNA, programmable sequence

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Authors: Eun-Ji Lee, Hye-Sung Park, Chan-Jung Lee, Won-Sik Kong

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We analyzed the DNA sequence of the ITS (Internal Transcribed Spacer) region of the 18S ribosomal gene and compared it with the gene sequence of T. fuciformis and Hypoxylon sp. in the BLAST database. The sequences of collected T. fuciformis and Hypoxylon sp. have over 99% homology in the T. fuciformis and Hypoxylon sp. sequence BLAST database. In order to select the optimal medium for T. fuciformis, five kinds of a medium such as Potato Dextrose Agar (PDA), Mushroom Complete Medium (MCM), Malt Extract Agar (MEA), Yeast extract (YM), and Compost Extract Dextrose Agar (CDA) were used. T. fuciformis showed the best growth on PDA medium, and Hypoxylon sp. showed the best growth on MCM. So as to investigate the optimum pH and temperature, the pH range was set to pH4 to pH8 and the temperature range was set to 15℃ to 35℃ (5℃ degree intervals). Optimum culture conditions for the T. fuciformis growth were pH5 at 25℃. Hypoxylon sp. were pH6 at 25°C. In order to confirm the most suitable carbon source, we used fructose, galactose, saccharose, soluble starch, inositol, glycerol, xylose, dextrose, lactose, dextrin, Na-CMC, adonitol. Mannitol, mannose, maltose, raffinose, cellobiose, ethanol, salicine, glucose, arabinose. In the optimum carbon source, T. fuciformis is xylose and Hypoxylon sp. is arabinose. Using the column test, we confirmed sawdust a suitable for T. fuciformis, since the composition of sawdust affects the growth of fruiting bodies of T. fuciformis. The sawdust we used is oak tree, pine tree, poplar, birch, cottonseed meal, cottonseed hull. In artificial cultivation of T. fuciformis with sawdust medium, T. fuciformis and Hypoxylon sp. showed fast mycelial growth on mixture of oak tree sawdust, cottonseed hull, and wheat bran.

Keywords: cultivation, optimal condition, tremella fuciformis, nutritional source

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Authors: Khaled Mahmud Gaddah

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Cretaceous deposits in the southeast of the Sirt Basin of Libya occur in several grabens that formed during a major phase of rifting related to the opening of the Tethys. They include continental deposits of Early Cretaceous age that belong to the Nubian Formation and marginal to fully marine deposits of Late Cretaceous age that belong to the Lidam Formation and transitional beds. The sequence was extensively sampled from twenty-two boreholes and palynologically analysed. Much of the sequence is barren. However, subordinate shales in all formations yield diverse assemblages of poorly to well preserved and thermally middle to post mature palynomorphs. Most of the assemblages contain non-marine palynomorphs (spores, pollen, and freshwater algae), although some contain rare marine elements (dinoflagellate cysts and acritarchs). The palynofloras enabled the recognition of six assemblage zones of the late Barremian-Turonian age based on the dominant and base/top occurrences of stratigraphically useful palynomorphs: AI (Afropollisspp.-Aequitriraditesspinulosus) of late Barremian age; AIIa (Scenedesmusbifidus-S. sp.) of late Barremian?-early Aptian age; AIIb (Afropollisoperculatus-A. zonatus) of Aptian age; AIII (Crybelosporitespannuceus-Afropollisjardinus) of early Albian age; AIV (Subtilisphaera sp.-Lophosphaeridiumspp.) of Cenomanian-?Turonian age; AIV (Pediastrumbifidites-Leiosphaeridiaspp.) of Cenomanian?-Turonian age. These assemblages are comparable to others from Northern Gondwana (particularly from Libya and Egypt) and correspond to established Cretaceous palynofloral provinces. Palynofacies analysis is used to interpret the depositional environments, and five palynofacies types are recognised that reflect increasing marine influence up section.

Keywords: palynology, palynomorphs, palynofacies, tethys, sirt basin

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Authors: Leyla Esfandiari

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Rapid, sensitive detection of nucleic acid (NA) molecules of specific sequence is of interest for a range of diverse health-related applications such as screening for genetic diseases, detecting pathogenic microbes in food and water, and identifying biological warfare agents in homeland security. Sequence-specific nucleic acid detection platforms rely on base pairing interaction between two complementary single stranded NAs, which can be detected by the optical, mechanical, or electrochemical readout. However, many of the existing platforms require amplification by polymerase chain reaction (PCR), fluorescent or enzymatic labels, and expensive or bulky instrumentation. In an effort to address these shortcomings, our research is focused on utilizing the cutting edge nanotechnology and microfluidics along with resistive pulse electrical measurements to design and develop a cost-effective, handheld and highly-sensitive nanopore-based sensor for point-of-care medical diagnostics.

Keywords: diagnostics, nanopore, nucleic acids, sensor

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Authors: Pavan K. Rallabandi, Kailash C. Patidar

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In this paper, we present an optimization technique or a learning algorithm using the hybrid architecture by combining the most popular sequence recognition models such as Recurrent Neural Networks (RNNs) and Hidden Markov models (HMMs). In order to improve the sequence or pattern recognition/ classification performance by applying a hybrid/neural symbolic approach, a gradient descent learning algorithm is developed using the Real Time Recurrent Learning of Recurrent Neural Network for processing the knowledge represented in trained Hidden Markov Models. The developed hybrid algorithm is implemented on automata theory as a sample test beds and the performance of the designed algorithm is demonstrated and evaluated on learning the deterministic finite state automata.

Keywords: hybrid systems, hidden markov models, recurrent neural networks, deterministic finite state automata

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Authors: Tereza Branyšová, Martina Kračmarová, Kateřina Demnerová, Michal Ďurovič, Hana Stiborová

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Microbial deterioration threatens all objects of cultural heritage, including audio-visual materials. Fungi are commonly known to be the main factor in audio-visual material deterioration. However, although being neglected, bacteria also play a significant role. In addition to microbial contamination of materials, it is also essential to analyse air as a possible contamination source. This work aims to identify bacterial species in the archives of the Czech Republic that occur on audio-visual materials as well as in the air in the archives. For sampling purposes, the smears from the materials were taken by sterile polyurethane sponges, and the air was collected using a MAS-100 aeroscope. Metagenomic DNA from all collected samples was immediately isolated and stored at -20 °C. DNA library for the 16S rRNA gene was prepared using two-step PCR and specific primers and the concentration step was included due to meagre yields of the DNA. After that, the samples were sent to the University of Fairbanks, Alaska, for Illumina MiSeq sequencing. Subsequently, the analysis of the sequences was conducted in R software. The obtained sequences were assigned to the corresponding bacterial species using the DADA2 package. The impact of air contamination and the impact of different photosensitive layers that audio-visual materials were made of, such as gelatine, albumen, and collodion, were evaluated. As a next step, we will take a deeper focus on air contamination. We will select an appropriate culture-dependent approach along with a culture-independent approach to observe a metabolically active species in the air. Acknowledgment: This project is supported by grant no. DG18P02OVV062 of the Ministry of Culture of the Czech Republic.

Keywords: cultural heritage, Illumina MiSeq, metagenomics, microbial identification

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Authors: Petr Šimek

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This work deals with the problem of synchronization of bus frames during transmission using USB (Universal Serial Bus). The principles for synchronization between USB and the non-deterministic CAN (Controller Area Network) bus will be described here. Furthermore, the work deals with ensuring the time sequence of communication frames when receiving from multiple communication bus channels. The structure of a general object for storing frames from different types of communication buses, such as CAN and LIN (Local Interconnect Network), will be described here. Finally, an evaluation of the communication throughput of bus frames for USB High speed will be performed. The creation of this architecture was based on the analysis of the communication of control units with a large number of communication buses. For the design of the architecture, a test HW with a USB-HS interface was used, which received previously known messages, which were compared with the received result. The result of this investigation is the block architecture of the control program for test HW ensuring correct data transmission via the USB bus.

Keywords: analysis, CAN, interface, LIN, synchronization, USB

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Authors: Monika Soni, Shovonlal Bhowmick, Chandra Bhattacharya, Jitendra Sharma, Prafulla Dutta, Jagadish Mahanta

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Aedes aegypti and Aedes albopictus are considered as two major vectors to transmit dengue virus. In North-east India, two states viz. Assam and Arunachal Pradesh are known to be high endemic zone for dengue and Chikungunya viral infection. The taxonomical classification of medically important vectors are important for mapping of actual evolutionary trends and epidemiological studies. However, misidentification of mosquito species in field-collected mosquito specimens could have a negative impact which may affect vector-borne disease control policy. DNA barcoding is a prominent method to record available species, differentiate from new addition and change of population structure. In this study, a combined approach of a morphological and molecular technique of DNA barcoding was adopted to explore sequence variation in mitochondrial cytochrome c oxidase subunit I (COI) gene within dengue vectors. The study has revealed the map distribution of the dengue vector from two states i.e. Assam and Arunachal Pradesh, India. Approximate five hundred mosquito specimens were collected from different parts of two states, and their morphological features were compared with the taxonomic keys. The analysis of detailed taxonomic study revealed identification of two species Aedes aegypti and Aedes albopictus. The species aegypti comprised of 66.6% of the specimen and represented as dominant dengue vector species. The sequences obtained through standard DNA barcoding protocol were compared with public databases, viz. GenBank and BOLD. The sequences of all Aedes albopictus have shown 100% similarity whereas sequence of Aedes aegypti has shown 99.77 - 100% similarity of COI gene with that of different geographically located same species based on BOLD database search. From dengue prevalent different geographical regions fifty-nine sequences were retrieved from NCBI and BOLD databases of the same and related taxa to determine the evolutionary distance model based on the phylogenetic analysis. Neighbor-Joining (NJ) and Maximum Likelihood (ML) phylogenetic tree was constructed in MEGA6.06 software with 1000 bootstrap replicates using Kimura-2-Parameter model. Data were analyzed for sequence divergence and found that intraspecific divergence ranged from 0.0 to 2.0% and interspecific divergence ranged from 11.0 to 12.0%. The transitional and transversional substitutions were tested individually. The sequences were deposited in NCBI: GenBank database. This observation claimed the first DNA barcoding analysis of Aedes mosquitoes from North-eastern states in India and also confirmed the range expansion of two important mosquito species. Overall, this study insight into the molecular ecology of the dengue vectors from North-eastern India which will enhance the understanding to improve the existing entomological surveillance and vector incrimination program.

Keywords: COI, dengue vectors, DNA barcoding, molecular identification, North-east India, phylogenetics

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Authors: Janet Holland

Abstract:

Eye tracking is a great way to triangulate multiple data sources for deeper, more complete knowledge of how instructional materials are really being used and emotional connections made. Using sensor based biometrics provides a detailed local analysis in real time expanding our ability to collect science based data for a more comprehensive level of understanding, not previously possible, for teaching and learning. The knowledge gained will be used to make future improvements to instructional materials, tools, and interactions. The literature has been examined and a preliminary pilot test was implemented to develop a methodology for research in Instructional Design and Technology. Eye tracking now offers the addition of objective metrics obtained from eye tracking and other biometric data collection with analysis for a fresh perspective.

Keywords: area of interest, eye tracking, biometrics, fixation, fixation count, fixation sequence, fixation time, gaze points, heat map, saccades, time to first fixation

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Authors: Kenneth D. Aiello, M. Simeone, Manfred Laubichler

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It is increasingly difficult to analyze emerging scientific fields as contemporary scientific fields are more dynamic, their boundaries are more porous, and the relational possibilities have increased due to Big Data and new information sources. In biomedicine, where funding, medical categories, and medical jurisdiction are determined by distinct boundaries on biomedical research fields and definitions of concepts, ambiguity persists between the microbiome, metabolome, and metagenome research fields. This ambiguity continues despite efforts by institutions and organizations to establish parameters on the core concepts and research discourses. Further, the explosive growth of microbiome, metabolome, and metagenomic research has led to unknown variation and covariation making application of findings across subfields or coming to a consensus difficult. This study explores the evolution and variation of knowledge within the microbiome, metabolome, and metagenome research fields related to ambiguous scholarly language and commensurable theoretical frameworks via a semantic analysis of key concepts and narratives. A computational historical framework of cultural evolution and large-scale publication data highlight the boundaries and overlaps between the competing scientific discourses surrounding the three research areas. The results of this study highlight how discourse and language distribute power within scholarly and scientific networks, specifically the power to set and define norms, central questions, methods, and knowledge.

Keywords: biomedicine, conceptual change, history of science, philosophy of science, science of science, sociolinguistics, sociology of knowledge

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Authors: Po-Jung Huang, Chi-Ching Lee, Bertrand Chin-Ming Tan, Yuan-Ming Yeh, Julie Lichieh Chu, Tin-Wen Chen, Cheng-Yang Lee, Ruei-Chi Gan, Hsuan Liu, Petrus Tang

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Whole-exome sequencing focuses on the protein coding regions of disease/cancer associated genes based on a priori knowledge is the most cost-effective method to study the association between genetic alterations and disease. Recent advances in high throughput sequencing technologies and proteomic techniques has provided an opportunity to integrate genomics and proteomics, allowing readily detectable mutated peptides corresponding to mutated genes. Since sequence database search is the most widely used method for protein identification using Mass spectrometry (MS)-based proteomics technology, a mutant proteome database is required to better approximate the real protein pool to improve disease-associated mutated protein identification. Large-scale whole exome/genome sequencing studies were launched by National Cancer Institute (NCI), Broad Institute, and The Cancer Genome Atlas (TCGA), which provide not only a comprehensive report on the analysis of coding variants in diverse samples cell lines but a invaluable resource for extensive research community. No existing database is available for the collection of mutant protein sequences related to the identified variants in these studies. CMPD is designed to address this issue, serving as a bridge between genomic data and proteomic studies and focusing on protein sequence-altering variations originated from both germline and cancer-associated somatic variations.

Keywords: TCGA, cancer, mutant, proteome

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Authors: Sasan Talebnezhad, Parviz Hamidia

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GPC and RMS analysis showed no distinct difference between PE 100 On, Off, and Reference grade. But FTIR spectra and multiple endothermic peaks obtained from SSA analysis, attributed to heterogeneity of ethylene sequence length, lamellar thickness and also the non-uniformity of short chain branching, showed sharp discrepancy and proposed a blend structure of high-density polyethylenes in PE 100 grade. Catalysis along with process parameters dictates poly blend PE 100 structure. This in-reactor blend is a mixture of compatible co-crystallized phases with different crystalinity, forming a physical semi hard and soft segment network responsible for improved impact properties in PE 100 pipe grade. We propose a new approach for PE100 evaluation that is more efficient than normal microstructure characterization.

Keywords: HDPE, pipe grade, in-reactor blend, hard and soft segments

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Authors: Shazi Farooqui, Anupam Sharma

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The Mahi River (~600km long) is an important west flowing the river of Central India. It originates in Madhya Pradesh and starts flowing in NW direction and enters into the state of Rajasthan. It flows across southern Rajasthan and then enters into Gujarat and finally debouches in the Gulf of Cambay. In Gujarat state, it flows through all four geomorphic zones i.e. eastern upland zone, shallow buried piedmont zone, alluvial zone and coastal zone. In lower reaches and particularly when it is flowing under the coastal regime, it provides an opportunity to study – 1. Land–Sea interaction and role of relative sea level changes, 2. Coastal/estuarine geological process, 3. Landscape evolution in marginal areas and so on. The Late Quaternary deposits of Mainland Gujarat is appreciably studied by Chamyal and his group of MS University of Baroda, and they have established that the 30-35m thick sediment package of the Mainland Gujarat is comprised of marine, fluvial and aeolian sediments. It is also established that in the estuarine zone, the upper few meter thick sediments package is of marine nature. However, its thickness, characters and the depositional environment including the role of climate and tectonics is still not clearly defined. To understand few aspects of the above mentioned, in the present study, a 17m subsurface sediment core has been retrieved from the estuarine zone of Mahi river basin. The Multiproxy studies which include the textural analysis (grain size), Loss on ignition (LOI), Bulk and clay mineralogy and geochemical studies have been carried out. In the entire sedimentary sequence, the grain size largely varies from coarse sand to clay; however, a solitary gravel bed is also noticed. The lower part (depth 9-17m), is mainly comprised of sub equal proportion of sand and silt. The sediments mainly have bimodal and leptokurtic distribution and deposited in alternate sand-silt package, probably indicating flood deposits. Relatively low moisture (1.8%) and organic carbon (2.4%) with increased carbonate values (12%) indicate that conditions must have to remain oxidizing. The middle part (depth 9–6m) has a 1m thick gravel bed at the bottom and overlain by coarse sand to very fine sand showing fining upward sequence. The presence of gravel bed suggests some kind of tectonic activity resulting into change in base level or enhanced precipitation in the catchment region. The upper part (depth 6–0m; top part of sequence) mainly comprised of fine sand to silt size grains (with appreciable clay content). The sediment of this part is Unimodal and very leptokurtic in nature suggesting wave and winnowing process and deposited in low energy suspension environment. This part has relatively high moisture (2.1%) and organic carbon (2.7%) with decreased carbonate content (4.2%) indicating change in the depositional environment probably under estuarine conditions. The presence of chlorite along with smectite clay mineral further supports the significant marine contribution in the formation of upper part of the sequence.

Keywords: grain size, statistical analysis, clay minerals, late quaternary, LOI

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Authors: Reshu Saxena, R. K. Tripathi

Abstract:

HIV-1 transmission and spread involves significant host-virus interaction. Potential targets for prevention of HIV-1 lies at the site of mucosal barriers. Thus a better understanding of how HIV-1 infects target cells at such sites and lead their invasion is required, with prime focus on the host determinants regulating HIV-1 spread. HIV-1 Nef is important for viral infectivity and pathogenicity. It promotes HIV-1 replication, facilitating immune evasion by interacting with various host factors and altering cellular pathways via multiple protein-protein interactions. In this study nef was sequenced from HIV-1 patients, and showed specific mutations revealing sequence variability in nef. To explore the difference in Nef functionality based on sequence variability we have studied the effects of HIV-1 Nef in human SupT1 T cell line and (THP-1) monocyte-macrophage cell lines through proteomics approach. 2D-Gel Electrophoresis in control and Nef-transfected SupT1 cells demonstrated several differentially expressed proteins with significant modulation of alpha-enolase. Through further studies, effects of Nef on alpha-enolase regulation were found to be cell lineage-specific, being stimulatory in macrophages/monocytes, inhibitory in T cells and without effect in HEK-293 cells. Cell migration and invasion studies were employed to determine biological function affected by Nef mediated regulation of alpha-enolase. Cell invasion was enhanced in THP-1 cells but was inhibited in SupT1 cells by wildtype nef. In addition, the modulation of enolase and cell invasion remained unaffected by a unique nef variant. These results indicated that regulation of alpha-enolase expression and invasive property of host cells by Nef is sequence specific, suggesting involvement of a particular motif of Nef. To precisely determine this site, we designed a heptapeptide including the suggested alpha-enolase regulating sequence of nef and a nef mutant with deletion of this site. Macrophages/monocytes being the major cells affected by HIV-1 at mucosal barriers, were particularly investigated by the nef mutant and peptide. Both the nef mutant and heptapeptide led to inhibition of enhanced enolase expression and increased invasiveness in THP-1 cells. Together, these findings suggest a possible mechanism of host invasion by HIV-1 through Nef mediated regulation of alpha-enolase and identifies a potential therapeutic target for HIV-1 entry at mucosal barriers.

Keywords: HIV-1 Nef, nef variants, host-virus interaction, tissue invasion

Procedia PDF Downloads 384