Search results for: inter simple sequence repeat

Authors: Sujit Kumar

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Historicity of inter-caste relations can be traced in the early stages of evolution of rural community in the Indian society. These have witnessed vicissitudes during long drawn interactions between caste groups. Inter-caste relations evolved in a more organized form in the guise of Jajmani system. This is a system of permanent and hereditary inter-caste relations and gives a kaleidoscopic view of socio-economic relations among various caste groupings. Universality of its prevalence in rural India for centuries is well recognized and documented. But it has been undergoing metamorphic change in some regions and changing at a slower pace in the others during post-independence period. An empirical study was conducted with the objectives to know whether Jajmani system is in vogue in the rural areas and type and intensity of socio-economic ties among different caste categories and to find out the change in inter-caste relations, if any owing to industrialization and modernization. Information was elicited from 225 respondents using interview schedule designed for this purpose. It is discernible that in majority of cases, inter-caste social relations which find better expression on the occasions like marriage, death, birth and festivals etc. among Brahmins and lower castes vis-à-vis other caste categories have grown weak. The data further unearth that economic relations as maintained on the occasions of marriage, sacred thread ceremony, mundan sacrament, birthday, death, yajna, katha, routine hair cut, manufacture and repair of various iron, earthen, wooden and leather articles between members of higher castes (general category) and lower castes (scheduled castes) are moderate but weak in case of Other Backward Classes vis-à-vis all other caste categories. Overwhelming majority of informants believe that decline in hereditary occupations, depreciation of old products and services and their availability from the market being made by industry are main reasons in descending order for change in inter caste relations. Modernization, westernization, industrialization, transportation and communications, growing materialism and consumerism together have brought change in relations among caste groups affecting about a billion population inhabiting rural India.

Keywords: inter-caste, Jajmani, sacrament, Yajna

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Authors: Mudawamah Mudawamah, Muhammad Z. Fadli, Gatot Ciptadi, Aulanni’am

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Canary breeders have spread throughout Indonesian regions for the low-middle society and become an income source for them. The interesting phenomenon of the canary market is the feather colours become one of determining factor for the price. The advantages of this research were contributed to the molecular database as a base of selection and mating for the Indonesia canary breeder. The research method was experiment with the genome obtained from canary blood isolation. The genome did the PCR amplification with PMEL marker followed by sequencing. Canaries were used 24 heads of light and dark colour feathers. Research data analyses used BioEdit and Network 4.6.0.0 software. The results showed that all samples were amplification with PMEL gene with 500 bp fragment length. In base sequence of 40 was found Cytosine(C) in the light colour canaries, while the dark colour canaries was obtained Thymine (T) in same base sequence. Sequence results had 286-415 bp fragment and 10 haplotypes. The conclusions were the PMEL gene (gene of white pigment) was likely to be used PMEL gene to detect molecular genetic variation of dark and light colour feather.

Keywords: canary, haplotype, PMEL, sequence

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Authors: Mehmet Yildiz, Mehmet Kale

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The primary aim of the present study was to identify the bilateral balance asymmetries when comparing the dominant (DL) vs. the non-dominant leg (NDL) in the collegian soccer players. The secondary aim was to compare the inter-limb asymmetry index (ASI) when differentiating by kicking preference (right-dominant vs. left-dominant). 34 right-dominant leg (RightDL) (age:21.12±1.85, height:174.50±5.18, weight:69.42±6.86) and 23 left-dominant leg (LeftDL), (age:21.70±2.03, height:176.2±6.27, weight:68.73±5.96) collegian football players were tested for bilateral static and dynamic balance. Balance ability was assessed by measuring centre of pressure deviation on a single leg. Single leg static and dynamic balance scores and inter-limb asymmetry index (ASI) were determined. Student t tests were used for the comparison of dominant and nondominant leg balance scores and RightDL and LeftDL football players’ inter-limb asymmetry index of the balance scores. The results showed that there were significant differences in the dynamic balance scores in favour of the nondominant leg, (DL:738±211 vs. NDL:606±226, p < 0.01). Also, it has been seen that LeftDL players have significantly higher inter-limb asymmetry index when compared with rightDL players for both static (rightDL:-7.07±94.91 vs. leftDL:-183.19±354.05, p < 0.01) and dynamic (rightDL: 1.73±49.65 vs. leftDL:27.08±23.34, p < 0.05) balance scores. In conclusion, bilateral dynamic balance asymmetries may be affected using single leg predominantly in the mobilization workouts. Because of having higher inter-limb asymmetry index, left-dominant leg players may be screened and trained to minimize balance asymmetry.

Keywords: bilateral balance, asymmetries, dominant leg, leg preference

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Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Khaoula Hidouri, Ali Benhmidene, Bechir Chouachi

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The purification of brackish seawater becomes a necessity and not a choice against demographic and industrial growth especially in third world countries. Two models can be used in this work: simple solar still and simple solar still coupled with a heat pump. In this research, the productivity of water by Simple Solar Distiller (SSD) and Simple Solar Distiller Hybrid Heat Pump (SSDHP) was determined by the orientation, the use of heat pump, the simple or double glass cover. The productivity can exceed 1.2 L/m²h for the SSDHP and 0.5 L/m²h for SSD model. The result of the global efficiency is determined for two models SSD and SSDHP give respectively 30%, 50%. The internal efficiency attained 35% for SSD and 60% of the SSDHP models. Convective heat coefficient can be determined by attained 2.5 W/m²°C and 0.5 W/m²°C respectively for SSDHP and SSD models.

Keywords: productivity, efficiency, convective heat coefficient, SSD model, SSDHPmodel

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Authors: Xiao Zhou, Jianlin Cheng

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A single amino acid mutation can have a significant impact on the stability of protein structure. Thus, the prediction of protein stability change induced by single site mutations is critical and useful for studying protein function and structure. Here, we presented a deep learning network with the dropout technique for predicting protein stability changes upon single amino acid substitution. While using only protein sequence as input, the overall prediction accuracy of the method on a standard benchmark is >85%, which is higher than existing sequence-based methods and is comparable to the methods that use not only protein sequence but also tertiary structure, pH value and temperature. The results demonstrate that deep learning is a promising technique for protein stability prediction. The good performance of this sequence-based method makes it a valuable tool for predicting the impact of mutations on most proteins whose experimental structures are not available. Both the downloadable software package and the user-friendly web server (DNpro) that implement the method for predicting protein stability changes induced by amino acid mutations are freely available for the community to use.

Keywords: bioinformatics, deep learning, protein stability prediction, biological data mining

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Authors: Dong Tran, Thanh Dac Van, Ly Le

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Hemagglutinin (HA) and Neuraminidase (NA) play an important role in host immune evasion across influenza virus evolution process. The correlation between HA and NA evolution in respect to epitopic evolution and drug interaction has yet to be investigated. In this study, combining of sequence to structure evolution and statistical analysis on epitopic/binding site specificity, we identified potential therapeutic features of HA and NA that show specific antibody binding site of HA and specific binding distribution within NA active site of current inhibitors. Our approach introduces the use of sequence variation and molecular interaction to provide an effective strategy in establishing experimental based distributed representations of protein-protein/ligand complexes. The most important advantage of our method is that it does not require complete dataset of complexes but rather directly inferring feature interaction from sequence variation and molecular interaction. Using correlated sequence analysis, we additionally identified co-evolved mutations associated with maintaining HA/NA structural and functional variability toward immunity and therapeutic treatment. Our investigation on the HA binding specificity revealed unique conserved stalk domain interacts with unique loop domain of universal antibodies (CR9114, CT149, CR8043, CR8020, F16v3, CR6261, F10). On the other hand, NA inhibitors (Oseltamivir, Zaninamivir, Laninamivir) showed specific conserved residue contribution and similar to that of NA substrate (sialic acid) which can be exploited for drug design. Our study provides an important insight into rational design and identification of novel therapeutics targeting universally recognized feature of influenza HA/NA.

Keywords: influenza virus, hemagglutinin (HA), neuraminidase (NA), sequence evolution

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Authors: Amel Ourici

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An electrical machine failure that is not identified in an initial stage may become catastrophic and it may suffer severe damage. Thus, undetected machine faults may cascade in it failure, which in turn may cause production shutdowns. Such shutdowns are costly in terms of lost production time, maintenance costs, and wasted raw materials. Doubly fed induction generators are used mainly for wind energy conversion in MW power plants. This paper presents a detection of an inter turn stator fault in a doubly fed induction machine whose stator and rotor are supplied by two pulse width modulation (PWM) inverters. The method used in this article to detect this fault, is based on Park’s Vector Approach, using a neural network.

Keywords: doubly fed induction machine, PWM inverter, inter turn stator fault, Park’s vector approach, neural network

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Authors: Yoonjung An, Yongtae Park

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Offering a Product-Service System (PSS) is a well-accepted strategy that companies may adopt to provide a set of systemic solutions to customers. PSSs were initially provided in a simple form but now take diversified and complex forms involving multiple services, products and technologies. With the growing interest in the PSS, frameworks for the PSS development have been introduced by many researchers. However, most of the existing frameworks fail to examine various relations existing in a complex PSS. Since designing a complex PSS involves full integration of multiple products and services, it is essential to identify not only product-service relations but also product-product/ service-service relations. It is also equally important to specify how they are related for better understanding of the system. Moreover, as customers tend to view their purchase from a more holistic perspective, a PSS should be developed based on the whole system’s requirements, rather than focusing only on the product requirements or service requirements. Thus, we propose a framework to develop a complex PSS that is coordinated fully with the requirements of both worlds. Specifically, our approach adopts a multi-domain matrix (MDM). A MDM identifies not only inter-domain relations but also intra-domain relations so that it helps to design a PSS that includes highly desired and closely related core functions/ features. Also, various dependency types and rating schemes proposed in our approach would help the integration process.

Keywords: inter-domain relations, intra-domain relations, multi-domain matrix, product-service system design

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Authors: Atef Ibrahim, Hamed Elsimary, Abdullah Aljumah, Fayez Gebali

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This paper presents a novel semi-systolic array architecture for an optimized parallel sequence alignment algorithm. This architecture has the advantage that it can be modified to be reused for multiple pass processing in order to increase the number of processing elements that can be packed into a single FPGA and to increase the number of sequences that can be aligned in parallel in a single FPGA. This resolves the potential problem of many FPGA resources left unused for designs that have large values of short read length. When using the previously published conventional hardware design. FPGA implementation results show that, for large values of short read lengths (M>128), the proposed design has a slightly higher speed up and FPGA utilization over the the conventional one.

Keywords: bioinformatics, genome sequence alignment, re-sequencing applications, systolic array

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Authors: Anésio de Leles Ferreira Filho, Wesley Rodrigues de Oliveira, Jéssica Santoro Gonçalves, Jorge Andrés Cormane Angarita

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The increase in electric power demand in face of environmental issues has intensified the participation of renewable energy sources such as photovoltaics, in the energy matrix of various countries. Due to their operational characteristics, they can generate time-varying harmonic and inter-harmonic distortions. For this reason, the application of methods of measurement based on traditional Fourier analysis, as proposed by IEC 61000-4-7, can provide inaccurate results. Considering the aspects mentioned herein, came the idea of the development of this work which aims to present the results of a comparative evaluation between a methodology arising from the combination of the Prony method with the Kalman filter and another method based on the IEC 61000-4-30 and IEC 61000-4-7 standards. Employed in this study were synthetic signals and data acquired through measurements in a 50kWp photovoltaic installation.

Keywords: harmonics, inter-harmonics, iec61000-4-7, parametric estimators, photovoltaic generation

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Authors: N. Zeinalzadeh, Mahdi Sadeghi

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Enterotoxigenic Escherichia coli (ETEC) is the most common cause of non-inflammatory diarrhea in the developing countries, resulting in approximately 20% of all diarrheal episodes in children in these areas. ST is one of the most important virulence factors and CFA/I is one of the frequent colonization factors that help to process of ETEC infection. ST and CfaB (CFA/I subunit) are among vaccine candidates against ETEC. So, ST because of its small size is not a good immunogenic in the natural form. However to increase its immunogenic potential, here we explored candidate positions for ST insertion in CfaB sequence. After bioinformatics analysis, one of the candidate positions was selected and the chimeric gene (cfaB*st) sequence was synthesized and expressed in E. coli BL21 (DE3). The chimeric recombinant protein was purified with Ni-NTA columns and characterized with western blot analysis. The residue 74-75 of CfaB sequence could be a good candidate position for ST and other epitopes insertion.

Keywords: bioinformatics, CFA/I, enterotoxigenic E. coli, ST toxoid

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Authors: Abdullah Alaklabi, Ibrahim A. Arif, Sameera O. Bafeel, Ahmad H. Alfarhan, Anis Ahamed, Jacob Thomas, Mohammad A. Bakir

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Diospyros mespiliformis (Hochst. ex A.DC.; Ebenaceae) is a large deciduous medicinal plant. This plant species is currently listed as endangered in Saudi Arabia. Molecular identification of this plant species based on short sequence regions (571 and 664 bp) of plastid rbcL (ribulose-1, 5-biphosphate carboxylase) gene was investigated in this study. The endangered plant specimens were collected from Al-Baha, Saudi Arabia (GPS coordinate: 19.8543987, 41.3059349). Phylogenetic tree inferred from the rbcL gene sequences showed that this species is very closely related with D. brandisiana. The close relationship was also observed among D. bejaudii, D. Philippinensis and D. releyi (≥99.7% sequence homology). The partial rbcL gene sequence region (571 bp) that was amplified by rbcL primer-pair rbcLaF-rbcLaR failed to discriminate D. mespiliformis from the closely related plant species, D. brandisiana. In contrast, primer-pair rbcL1F-rbcL724R yielded longer amplicon, discriminated the species from D. brandisiana and demonstrated nucleotide variations in 3 different sites (645G>T; 663A>C; 710C>G). Although D. mespiliformis (EU980712) and D. brandisiana (EU980656) are very closely related species (99.4%); however, studied specimen showed 100% sequence homology with D. mespiliformis and 99.6% with D. brandisiana. The present findings showed that rbcL short sequence region (664 bp) of plastid rbcL gene, amplified by primer-pair rbcL1F-rbcL724R, can be used for authenticating samples of D. mespiliforformis and may provide help in authentic identification and management process of this medicinally valuable endangered plant species.

Keywords: Diospyros mespiliformis, endangered plant, identification partial rbcL

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Authors: Rajkumar Ghosh

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The Chaura Thrust, located in Himachal Pradesh, India, is a prominent geological feature that exhibits characteristics of an out-of-sequence thrust fault. This paper explores the geological setting of Himachal Pradesh, focusing on the Chaura Thrust's unique characteristics, its classification as an out-of-sequence thrust, and the implications of its presence in the region. The introduction provides background information on thrust faults and out-of-sequence thrusts, emphasizing their significance in understanding the tectonic history and deformation patterns of an area. It also outlines the objectives of the paper, which include examining the Chaura Thrust's geological features, discussing its classification as an out-of-sequence thrust, and assessing its implications for the region. The paper delves into the geological setting of Himachal Pradesh, describing the tectonic framework and providing insights into the formation of thrust faults in the region. Special attention is given to the Chaura Thrust, including its location, extent, and geometry, along with an overview of the associated rock formations and structural characteristics. The concept of out-of-sequence thrusts is introduced, defining their distinctive behavior and highlighting their importance in the understanding of geological processes. The Chaura Thrust is then analyzed in the context of an out-of-sequence thrust, examining the evidence and characteristics that support this classification. Factors contributing to the out-of-sequence behavior of the Chaura Thrust, such as stress interactions and fault interactions, are discussed. The geological implications and significance of the Chaura Thrust are explored, addressing its impact on the regional geology, tectonic evolution, and seismic hazard assessment. The paper also discusses the potential geological hazards associated with the Chaura Thrust and the need for effective mitigation strategies in the region. Future research directions and recommendations are provided, highlighting areas that warrant further investigation, such as detailed structural analyses, geodetic measurements, and geophysical surveys. The importance of continued research in understanding and managing geological hazards related to the Chaura Thrust is emphasized. In conclusion, the Chaura Thrust in Himachal Pradesh represents an out-of-sequence thrust fault that has significant implications for the region's geology and tectonic evolution. By studying the unique characteristics and behavior of the Chaura Thrust, researchers can gain valuable insights into the geological processes occurring in Himachal Pradesh and contribute to a better understanding and mitigation of seismic hazards in the area.

Keywords: chaura thrust, out-of-sequence thrust, himachal pradesh, geological setting, tectonic framework, rock formations, structural characteristics, stress interactions, fault interactions, geological implications, seismic hazard assessment, geological hazards, future research, mitigation strategies.

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Authors: Milind S. Patil, Purushottam S. Desale, Eknath R. Deore

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Thermal analysis of reheat, regenerative, inter-cooled gas turbine cycle is presented. Specific work output, thermal efficiency and SFC is simulated with respect to operating conditions. Analytical formulas were developed taking into account the effect of operational parameters like ambient temperature, compression ratio, compressor efficiency, turbine efficiency, regenerator effectiveness, pressure loss in inter cooling, reheating and regenerator. Calculations were made for wide range of parameters using engineering equation solver and the results were presented here. For pressure ratio of 12, regenerator effectiveness 0.95, and maximum turbine inlet temperature 1200 K, thermal efficiency decreases by 27% with increase in ambient temperature (278 K to 328 K). With decrease in regenerator effectiveness thermal efficiency decreases linearly. With increase in ambient temperature (278 K to 328 K) for the same maximum temperature and regenerator effectiveness SFC decreases up to a pressure ratio of 10 and then increases. Sharp rise in SFC is noted for higher ambient temperature. With increase in isentropic efficiency of compressor and turbine, thermal efficiency increases by about 40% for low ambient temperature (278 K to 298 K) however, for higher ambient temperature (308 K to 328 K) thermal efficiency increases by about 70%.

Keywords: gas turbine, reheating, regeneration, inter-cooled, thermal analysis

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Authors: Utpal Das, Sona Das

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InAs/GaSb type-II superlattice (T2SL) Mid-wave infrared (MWIR) focal plane arrays (FPAs) have recently seen rapid development. However, in small pixel size large format FPAs, the occurrence of high mesa sidewall surface leakage current is a major constraint necessitating proper surface passivation. A simple pixel isolation technique in InAs/GaSb T2SL detector arrays without the conventional mesa etching has been proposed to isolate the pixels by forming a more resistive higher band gap material from the SL, in the inter-pixel region. Here, a single step femtosecond (fs) laser anneal of the T2SL structure of the inter-pixel T2SL regions, have been used to increase the band gap between the pixels by QW-intermixing and hence increase isolation between the pixels. The p-i-n photodiode structure used here consists of a 506nm, (10 monolayer {ML}) InAs:Si (1x10¹⁸cm⁻³)/(10ML) GaSb SL as the bottom n-contact layer grown on an n-type GaSb substrate. The undoped absorber layer consists of 1.3µm, (10ML)InAs/(10ML)GaSb SL. The top p-contact layer is a 63nm, (10ML)InAs:Be(1x10¹⁸cm⁻³)/(10ML)GaSb T2SL. In order to improve the carrier transport, a 126nm of graded doped (10ML)InAs/(10ML)GaSb SL layer was added between the absorber and each contact layers. A 775nm 150fs-laser at a fluence of ~6mJ/cm² is used to expose the array where the pixel regions are masked by a Ti(200nm)-Au(300nm) cap. Here, in the inter-pixel regions, the p+ layer have been reactive ion etched (RIE) using CH₄+H₂ chemistry and removed before fs-laser exposure. The fs-laser anneal isolation improvement in 200-400μm pixels due to spatially selective quantum well intermixing for a blue shift of ~70meV in the inter-pixel regions is confirmed by FTIR measurements. Dark currents are measured between two adjacent pixels with the Ti(200nm)-Au(300nm) caps used as contacts. The T2SL quality in the active photodiode regions masked by the Ti-Au cap is hardly affected and retains the original quality of the detector. Although, fs-laser anneal of p+ only etched p-i-n T2SL diodes show a reduction in the reverse dark current, no significant improvement in the full RIE-etched mesa structures is noticeable. Hence for a 128x128 array fabrication of 8μm square pixels and 10µm pitch, SU8 polymer isolation after RIE pixel delineation has been used. X-n+ row contacts and Y-p+ column contacts have been used to measure the optical response of the individual pixels. The photo-response of these 8μm and other 200μm pixels under a 2ns optical pulse excitation from an Optical-Parametric-Oscillator (OPO), shows a peak responsivity of ~0.03A/W and 0.2mA/W, respectively, at λ~3.7μm. Temporal response of this detector array is seen to have a fast response ~10ns followed typical slow decay with ringing, attributed to impedance mismatch of the connecting co-axial cables. In conclusion, response times of a few ns have been measured in 8µm pixels of a 128x128 array. Although fs-laser anneal has been found to be useful in increasing the inter-pixel isolation in InAs/GaSb T2SL arrays by QW inter-mixing, it has not been found to be suitable for passivation of full RIE etched mesa structures with vertical walls on InAs/GaSb T2SL.

Keywords: band-gap blue-shift, fs-laser-anneal, InAs/GaSb T2SL, Inter-pixel isolation, ns-Response, photodiode array

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Authors: Aika Umemuro, Mitsuru Sato, Mizuki Narita, Saya Hori, Saya Sakurai, Tomomi Nakayama, Ayano Nakazawa, Toshihiro Ogura

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Mammography requires the detection of very small calcifications, and physicians search for microcalcifications by magnifying the images as they read them. The mouse is necessary to zoom in on the images, but this can be tiring and distracting when many images are read in a single day. Therefore, an image magnification system combining an eye-detector and a simple electroencephalograph (EEG) scanner was devised, and its operability was evaluated. Two experiments were conducted in this study: the measurement of eye-detection error using an eye-detector and the measurement of the time required for image magnification using a simple EEG scanner. Eye-detector validation showed that the mean distance of eye-detection error ranged from 0.64 cm to 2.17 cm, with an overall mean of 1.24 ± 0.81 cm for the observers. The results showed that the eye detection error was small enough for the magnified area of the mammographic image. The average time required for point magnification in the verification of the simple EEG scanner ranged from 5.85 to 16.73 seconds, and individual differences were observed. The reason for this may be that the size of the simple EEG scanner used was not adjustable, so it did not fit well for some subjects. The use of a simple EEG scanner with size adjustment would solve this problem. Therefore, the image magnification system using the eye-detector and the simple EEG scanner is useful.

Keywords: EEG scanner, eye-detector, mammography, observers

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Authors: Cheikh Bamba Dione, Alla Lo, Elhadji Mamadou Nguer, Siley O. Ba

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In this paper, we propose two neural machine translation (NMT) systems (French-to-Wolof and Wolof-to-French) based on sequence-to-sequence with attention and transformer architectures. We trained our models on a parallel French-Wolof corpus of about 83k sentence pairs. Because of the low-resource setting, we experimented with advanced methods for handling data sparsity, including subword segmentation, back translation, and the copied corpus method. We evaluate the models using the BLEU score and find that transformer outperforms the classic seq2seq model in all settings, in addition to being less sensitive to noise. In general, the best scores are achieved when training the models on word-level-based units. For subword-level models, using back translation proves to be slightly beneficial in low-resource (WO) to high-resource (FR) language translation for the transformer (but not for the seq2seq) models. A slight improvement can also be observed when injecting copied monolingual text in the target language. Moreover, combining the copied method data with back translation leads to a substantial improvement of the translation quality.

Keywords: backtranslation, low-resource language, neural machine translation, sequence-to-sequence, transformer, Wolof

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Authors: Yaser Maher Abdelaziz Hawa

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The Basic-ultrabasic rocks of Bou Azzer ophiolite complex in the Anti-atlas , Morrocco enclose some oxide and sulfide minerals as dissiminated traces. The oxide minerals show a wide variation in composition ranging from Cr-free. Titanomagnetite and ilmenite in the chilled margin gabbro of the upper part of the ophiolite sequence to Al-rich chromian spinel and pure magnetite enclosed in the serpentinized peridotite in the lower part of the sequence. Five mineral assemblages have been distinguished depending on the rock type of the ophiolite sequence. 1-Gersodorfite + Chalcopyrite + Al-Mg rich chromian spinel + pure magnetite, hosted by serpentinized peridotite. 2- Pyrite + Chalcopyrite, enclosed in metagabbro and overlying the ultrabasic cumulates. 3- Al-Fe rich Chromian spinel with rims of Al –rich chromian magnetite enclosed in wherlite. 4- Titanomagnetite replaced by sphene enclosed in marginal Gabbro. 5- Pyrrhotite exsolving Pentlandite + ilmenite + Ilmenite + Al- rich Chromian spinel + magnetite enclosed in fresh olivine olivine in the upper part of the ophiolite sequence.

Keywords: opaques, ophiolites, anti-atlas, morrocco

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Authors: Jingyuan Hu, Zhandong Liu

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CRISPR genome editing technology has transformed molecular biology by accurately targeting and altering an organism’s DNA. Despite the state-of-art precision of CRISPR genome editing, the imprecise mutation outcome and off-target effects present considerable risk, potentially leading to unintended genetic changes. Targeted deep sequencing, combined with bioinformatics sequence alignment, can detect such unwanted mutations. Nevertheless, the classical method, Needleman-Wunsch (NW) algorithm may produce false alignment outcomes, resulting in inaccurate mutation identification. The key to precisely identifying CRISPR-induced mutations lies in determining optimal parameters for the sequence alignment algorithm. Hidden Markov models (HMM) are ideally suited for this task, offering flexibility across CRISPR systems by leveraging forward-backward algorithms for parameter estimation. In this study, we introduce CRISPR-HMM, a statistical software to precisely call CRISPR-induced mutations. We demonstrate that the software significantly improves precision in identifying CRISPR-induced mutations compared to NW-based alignment, thereby enhancing the overall understanding of the CRISPR gene-editing process.

Keywords: CRISPR, HMM, sequence alignment, gene editing

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Authors: S. Raja Mohamed, M. H Shwehdi, D. Devaraj

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This paper is to present and discuss the new planned 380 kV transmission line performance under steady and transient states. Dynamic modeling and analysis of such inter-tie, which is, proposed to transfer energy from west to south and vice versa will be demonstrated and discussed. The west-central-south inter-tie links Al-Aula-Zaba-Tabuk-Tubajal-Jawf-Hail. It is essential to investigate the transient over-voltage to assure steady and stable transmission over such inter-tie. Saudi Electricity Company (SEC) has been improving its grid to make the whole country as an interconnected system. Already east, central and west were interconnected, yet mostly each is fed with its local generation. The SEC is planning to establish many inter-ties to strengthen the transient stability of its grid. The paper studies one of the important links of 380 kV, 220 km between Tabouk and Tubarjal, which is a step towards connecting the West with the South region. Modeling and analysis using some softwares will be utilized under different scenarios. Adoption of methods to stabilize and increase its power transmission are also discussed. Improvement of power system transients has been controlled by FACTS elements such the Static Var Compensators (SVC) receiving a wide interest since many technical studies have proven their effects on damping system oscillations and stability enhancement. Illustrations of the transient at each main generating or load bus will be checked in all inter-tie links. A brief review of possible means to solve the transient over-voltage problem using different FACTS element modeling will be discussed.

Keywords: transient stability, static var compensator, central-west interconnected system, damping controller, Saudi Electricity Company

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Authors: Kolesnik Nadezda A.

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The research aims to elaborate inter-organizational network relationships management model to maximize value co-creation. We propose a network management framework that requires evaluation of network partners with respect to their position and role in network; and elaboration of appropriate relationship development strategy with partners in network. Empirical research and approval is based on the case study method, including structured in-depth interviews with the companies from b2b market.

Keywords: inter-organizational networks, value co-creation, model, B2B market

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Authors: Lamin B Ceesay, Cecilia Rossignoli

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Inter-organizational collaboration is a growing phenomenon in both research and practice. The partnership between organizations enables firms to leverage external resources, experiences, and technology that lie with other firms. This collaborative practice is a source of improved business model performance, technological advancement, and increased competitive advantage for firms. However, the competitive intents, and even diverse institutional logics of firms, make inter-firm innovation-based partnership even more complex, and its governance more challenging. The purpose of this paper is to present a systematic review of research linking the inter-organizational relationship of firms with their innovation practice and specify the different project management issues and gaps addressed in previous research. To do this, we employed a systematic review of the literature on inter-organizational innovation using two complementary scholarly databases - ScienceDirect and Web of Science (WoS). Article scoping relies on the combination of keywords based on similar terms used in the literature:(1) inter-organizational relationship, (2) business network, (3) inter-firm project, and (4) innovation network. These searches were conducted in the title, abstract, and keywords of conceptual and empirical research papers done in English. Our search covers between 2010 to 2019. We applied several exclusion criteria including Papers published outside the years under the review, papers in a language other than English, papers neither listed in WoS nor ScienceDirect and papers that are not sharply related to the inter-organizational innovation-based partnership were removed. After all relevant search criteria were applied, a final list of 84 papers constitutes the data for this review. Our review revealed an increasing evolution of inter-organizational relationship research during the period under the review. The descriptive analysis of papers according to Journal outlets finds that International Journal of Project Management (IJPM), Journal of Industrial Marketing, Journal of Business Research (JBR), etc. are the leading journal outlets for research in the inter-organizational innovation project. The review also finds that Qualitative methods and quantitative approaches respectively are the leading research methods adopted by scholars in the field. However, literature review and conceptual papers constitute the least in the field. During the content analysis of the selected papers, we read the content of each paper and found that the selected papers try to address one of the three phenomena in inter-organizational innovation research: (1) project antecedents; (2) project management and (3) project performance outcomes. We found that these categories are not mutually exclusive, but rather interdependent. This categorization also helped us to organize the fragmented literature in the field. While a significant percentage of the literature discussed project management issues, we found fewer extant literature on project antecedents and performance. As a result of this, we organized the future research agenda addressed in several papers by linking them with the under-researched themes in the field, thus providing great potential to advance future research agenda especially, in the under-researched themes in the field. Finally, our paper reveals that research on inter-organizational innovation project is generally fragmented which hinders a better understanding of the field. Thus, this paper contributes to the understanding of the field by organizing and discussing the extant literature to advance the theory and application of inter-organizational relationship.

Keywords: inter-organizational relationship, inter-firm collaboration, innovation projects, project management, systematic review

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Authors: Masih Moore, Saeed Ziaei-Rad

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In this study, the stability characteristics of a bi-stable composite plate with different asymmetric composition are considered. The interest in bi-stable structures comes from their ability that these structures can have two different stable equilibrium configurations to define a discrete set of stable shapes. The structures can easily change the first stable shape to the second one by a simple snap action. The main purpose of the current research is to consider the effect of including resin layers on the stability characteristics of bi-stable laminates. To this end and In order to determine the magnitude of the loads that are responsible for snap through and snap back phenomena between two stable shapes of the laminate, a non-linear finite element method (FEM) is utilized. An experimental investigation was also carried out to study the critical loads that caused snapping between two different stable shapes. Several specimens were manufactured from T300/5208 graphite-epoxy with [0/90]T, [-30/60]T, [-20/70]T asymmetric stacking sequence. In order to create an accurate finite element model, different thickness of resin layers created during the manufacturing process of the laminate was measured and taken into account. The geometry of each lamina and the resin layers was characterized by optical microscopy from different locations of the laminates thickness. The exact thickness of each lamina and the resin layer in all specimens with [0/90]T,[-30/60]T, [-20/70]T stacking sequence were determined by using image processing technique.

Keywords: bi-stable laminates, finite element method, graphite-epoxy plate, snap behavior

Procedia PDF Downloads 224

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

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

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

Procedia PDF Downloads 363

Authors: Mohd Radzi Hilmi, Mohd Zulfaezal Che Azemin, Khairidzan Mohd Kamal, Azrin Esmady Ariffin, Mohd Izzuddin Mohd Tamrin, Norfazrina Abdul Gaffur, Tengku Mohd Tengku Sembok

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Purpose: The purpose of this study is to predict optical quality changes after pterygium surgery using tissue redness grading. Methods: Sixty-eight primary pterygium participants were selected from patients who visited an ophthalmology clinic. We developed a semi-automated computer program to measure the pterygium fibrovascular redness from digital pterygium images. The outcome of this software is a continuous scale grading of 1 (minimum redness) to 3 (maximum redness). The region of interest (ROI) was selected manually using the software. Reliability was determined by repeat grading of all 68 images and its association with contrast sensitivity function (CSF) and visual acuity (VA) was examined. Results: The mean and standard deviation of redness of the pterygium fibrovascular images was 1.88 ± 0.55. Intra- and inter-grader reliability estimates were high with intraclass correlation ranging from 0.97 to 0.98. The new grading was positively associated with CSF (p<0.01) and VA (p<0.01). The redness grading was able to predict 25% and 23% of the variance in the CSF and the VA respectively. Conclusions: The new grading of pterygium fibrovascular redness can be reliably measured from digital images and show a good correlation with CSF and VA. The redness grading can be used in addition to the existing pterygium grading.

Keywords: contrast sensitivity, pterygium, redness, visual acuity

Procedia PDF Downloads 487

Authors: Wisam H. Benamer, Ehab A. Elfallah, Mohamed A. Elshaari, Farag A. Elshaari

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A challenge for laboratories is to provide bacterial identification and antibiotic sensitivity results within a short time. Hence, advancement in the required technology is desirable to improve timing, accuracy and quality. Even with the current advances in methods used for both phenotypic and genotypic identification of bacteria the need is there to develop method(s) that enhance the outcome of bacteriology laboratories in accuracy and time. The hypothesis introduced here is based on the assumption that the chromosome of any bacteria contains unique sequences that can be used for its identification and typing. The outcome of a pilot study designed to test this hypothesis is reported in this manuscript. Methods: The complete chromosome sequences of several bacterial species were downloaded to use as search targets for unique sequences. Visual basic and SQL server (2014) were used to generate a complete set of 18-base long primers, a process started with reverse translation of randomly chosen 6 amino acids to limit the number of the generated primers. In addition, the software used to scan the downloaded chromosomes using the generated primers for similarities was designed, and the resulting hits were classified according to the number of similar chromosomal sequences, i.e., unique or otherwise. Results: All primers that had identical/similar sequences in the selected genome sequence(s) were classified according to the number of hits in the chromosomes search. Those that were identical to a single site on a single bacterial chromosome were referred to as unique. On the other hand, most generated primers sequences were identical to multiple sites on a single or multiple chromosomes. Following scanning, the generated primers were classified based on ability to differentiate between medically important bacterial and the initial results looks promising. Conclusion: A simple strategy that started by generating primers was introduced; the primers were used to screen bacterial genomes for match. Primer(s) that were uniquely identical to specific DNA sequence on a specific bacterial chromosome were selected. The identified unique sequence can be used in different molecular diagnostic techniques, possibly to identify bacteria. In addition, a single primer that can identify multiple sites in a single chromosome can be exploited for region or genome identification. Although genomes sequences draft of isolates of organism DNA enable high throughput primer design using alignment strategy, and this enhances diagnostic performance in comparison to traditional molecular assays. In this method the generated primers can be used to identify an organism before the draft sequence is completed. In addition, the generated primers can be used to build a bank for easy access of the primers that can be used to identify bacteria.

Keywords: bacteria chromosome, bacterial identification, sequence, primer generation

Procedia PDF Downloads 167

Authors: Amy Gooden

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When human genomic data is considered, this is often done through only one dimension of the law, or the interplay between the various dimensions is not considered, thus providing an incomplete picture of the legal framework. This research considers and analyzes the various dimensions in South African law applicable to genomic sequence data – including property rights, personality rights, and intellectual property rights. The effective use of personal genomic sequence data requires the acknowledgement and harmonization of the rights applicable to such data.

Keywords: artificial intelligence, data, law, genomics, rights

Procedia PDF Downloads 116

Authors: Vyacheslav Furtak, Merja Roivainen, Olga Mirochnichenko, Majid Laassri, Bella Bidzhieva, Tatiana Zagorodnyaya, Vladimir Chizhikov, Konstantin Chumakov

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Molecular epidemiology and environmental surveillance are parts of a rational strategy to control infectious diseases. They have been widely used in the worldwide campaign to eradicate poliomyelitis, which otherwise would be complicated by the inability to rapidly respond to outbreaks and determine sources of the infection. The conventional scheme involves isolation of viruses from patients and the environment, followed by their identification by nucleotide sequences analysis to determine phylogenetic relationships. This is a tedious and time-consuming process that yields definitive results when it may be too late to implement countermeasures. Because of the difficulty of high-throughput full-genome sequencing, most such studies are conducted by sequencing only capsid genes or their parts. Therefore the important information about the contribution of other parts of the genome and inter- and intra-species recombination to viral evolution is not captured. Here we propose a new approach based on the rapid concentration of sewage samples with tangential flow filtration followed by deep sequencing and reconstruction of nucleotide sequences of viruses present in the samples. The entire nucleic acids content of each sample is sequenced, thus preserving in digital format the complete spectrum of viruses. A set of rapid algorithms was developed to separate deep sequence reads into discrete populations corresponding to each virus and assemble them into full-length consensus contigs, as well as to generate a complete profile of sequence heterogeneities in each of them. This provides an effective approach to study molecular epidemiology and evolution of natural viral populations.

Keywords: poliovirus, eradication, environmental surveillance, laboratory diagnosis

Procedia PDF Downloads 251