Search results for: antigenic variants

Authors: Khadijat T. Bamigbade, Olufade F. W. Onifade

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The field of automatic facial expression analysis has been an active research area in the last two decades. Its vast applicability in various domains has drawn so much attention into developing techniques and dataset that mirror real life scenarios. Many techniques such as Local Binary Patterns and its variants (CLBP, LBP-TOP) and lately, deep learning techniques, have been used for facial expression recognition. However, the problem of occlusion has not been sufficiently handled, making their results not applicable in real life situations. This paper develops a simple, yet highly efficient method tagged Local Binary Pattern-Histogram of Gradient (LBP-HOG) with occlusion detection in face image, using a multi-class SVM for Action Unit and in turn expression recognition. Our method was evaluated on three publicly available datasets which are JAFFE, CK, SFEW. Experimental results showed that our approach performed considerably well when compared with state-of-the-art algorithms and gave insight to occlusion detection as a key step to handling expression in wild.

Keywords: automatic facial expression analysis, local binary pattern, LBP-HOG, occlusion detection

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Authors: R. Remya

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We consider an M/M/1 multiple variant vacation queueing system and working vacation with waiting server. Here, comparing considering three models. First model, working vacation is taken after the server has exhaustively served all the customers in the system and waits random amount of time. After completing a working vacation, the server will wait for a random period of time before going on vacation. Then it goes to finite number of vacations same way. After end of J th vacation server waits in busy or served immediately. Second model, working vacation is taken after the server has exhaustively served all the customers in the system and waits random amount of time. Third model, working vacation is taken after the server has exhaustively served all the customers in the system and waits random amount of time. It is expected that service times and vacation lengths are exponentially distributed . We provide a steady-state solution and cost comparison for the stated models.

Keywords: vacation, working vacation, waiting server, steady state analysis, cost analysis

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Authors: Tatiana R. Simonyan, Elena A. Protasova, Anastasia V. Mamontova, Eugene G. Maksimov, Konstantin A. Lukyanov, Alexey M. Bogdanov

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Here, we describe two variants of the calcium indicators based on the GCaMP sensitive core and BrUSLEE fluorescent protein (GCaMP-BrUSLEE and GCaMP-BrUSLEE-145). In contrast to the conventional GCaMP6-family indicators, these fluorophores are characterized by the well-marked responsiveness of their fluorescence decay kinetics to external calcium concentration both in vitro and in cellulo. Specifically, we show that the purified GCaMP-BrUSLEE and GCaMP-BrUSLEE-145 exhibit three-component fluorescence decay kinetics, with the amplitude-normalized lifetime component (t3*A3) of GCaMP-BrUSLEE-145 changing four-fold (500-2000 a.u.) in response to a Ca²⁺ concentration shift in the range of 0—350 nM. Time-resolved fluorescence microscopy of live cells displays the two-fold change of the GCaMP-BrUSLEE-145 mean lifetime upon histamine-stimulated calcium release. The aforementioned Ca²⁺-dependence calls considering the GCaMP-BrUSLEE-145 as a prospective Ca²⁺-indicator with the signal read-out in the time domain.

Keywords: calcium imaging, fluorescence lifetime imaging microscopy, fluorescent proteins, genetically encoded indicators

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Authors: Josef Wolfartsberger, Michael Heiml, Georg Schwarz, Sabrina Egger

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Growing individualization and higher numbers of variants in industrial assembly products raise the complexity of manufacturing processes. Technical assistance systems considering both procedural and human factors allow for an increase in product quality and a decrease in required learning times by supporting workers with precise working instructions. Due to varying needs of workers, the presentation of working instructions leads to several challenges. This paper presents an approach for a multi-modal visualization application to support assembly work of complex parts. Our approach is integrated within an interconnected assistance system network and supports the presentation of cloud-streamed textual instructions, images, videos, 3D animations and audio files along with multi-modal user interaction, customizable UI, multi-platform support (e.g. tablet-PC, TV screen, smartphone or Augmented Reality devices), automated text translation and speech synthesis. The worker benefits from more accessible and up-to-date instructions presented in an easy-to-read way.

Keywords: assembly, assistive technologies, augmented reality, manufacturing, visualization

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Authors: Kenneth Fon Mbah, Arash Habibi Lashkari, Ali A. Ghorbani

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Phishing e-mails are a security issue that not only annoys online users, but has also resulted in significant financial losses for businesses. Phishing advertisements and pornographic e-mails are difficult to detect as attackers have been becoming increasingly intelligent and professional. Attackers track users and adjust their attacks based on users’ attractions and hot topics that can be extracted from community news and journals. This research focuses on deceptive Phishing attacks and their variants such as attacks through advertisements and pornographic e-mails. We propose a framework called Phishing Alerting System (PHAS) to accurately classify e-mails as Phishing, advertisements or as pornographic. PHAS has the ability to detect and alert users for all types of deceptive e-mails to help users in decision making. A well-known email dataset has been used for these experiments and based on previously extracted features, 93.11% detection accuracy is obtainable by using J48 and KNN machine learning techniques. Our proposed framework achieved approximately the same accuracy as the benchmark while using this dataset.

Keywords: phishing e-mail, phishing detection, anti phishing, alarm system, machine learning

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Authors: Halima Benazzouz

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It is often believed that British English and American English are the foremost varieties of the English Language serving as reference norms for other varieties;that is the reason why they have obviously been compared and contrasted.Meanwhile,the terms “British English” and “American English” are used differently by different people to refer to: 1) Two national varieties each subsuming regional and other sub-varieties standard and non-standard. 2) Two national standard varieties in which each one is only part of the range of English within its own state, but the most prestigious part. 3) Two international varieties, that is each is more than a national variety of the English Language. 4) Two international standard varieties that may or may not each subsume other standard varieties.Furthermore,each variety serves as a reference norm for users of the language elsewhere. Moreover, without a clear identification, as primarily belonging to one variety or the other, British English(Br.Eng) and American English (Am.Eng) are understood as national or international varieties. British English and American English are both “variants” and “varieties” of the English Language, more similar than different.In brief, the following may justify general categories of difference between Standard American English (S.Am.E) and Standard British English (S.Br.e) each having their own sociolectic value: A difference in pronunciation exists between the two foremost varieties, although it is the same spelling, by contrast, a divergence in spelling may be recognized, eventhough the same pronunciation. In such case, the same term is different but there is a similarity in spelling and pronunciation. Otherwise, grammar, syntax, and punctuation are distinctively used to distinguish the two varieties of the English Language. Beyond these differences, spelling is noted as one of the chief sources of variation.

Keywords: Greek, Latin, French pronunciation expert, varieties of English language

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Authors: Jae Woong Sull

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Lipid levels are related to the risk of cardiovascular diseases. Cholesterol ester transfer protein (CETP) gene is one of the candidate genes of cardiovascular diseases. A total of 2,304 persons were chosen from a Hospital (N=4,294) in South Korea. Female subjects with the CG/GG genotype had a 2.03 -fold (p=0.0001) higher risk of having abnormal HDL cholesterol levels (<40 mg/dL) than subjects with the CC genotype. Male subjects with the CG/GG genotype had a 1.34 -fold (p=0.0019) higher risk than subjects with the CC genotype. When analyzed by body mass index, the association with CETP was much stronger in male subjects with BMI>=25.69 (OR=1.55, 95% CI: 1.15-2.07, P=0.0037) than in male lean subjects. When analyzed by family history of diabetes, the association with CETP was much stronger in male subjects with positive family history of low physical activity (OR=4.82, 95% CI: 1.86-12.5, P=0.0012) than in male subjects with negative family history of diabetes. This study clearly demonstrates that genetic variants in CETP influence HDL cholesterol levels in Korean adults.

Keywords: CETP, diabetes, obesity, polymorphisms

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Authors: Yasaswi Palagummi, Sareh Rowlands

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Generalised Zero-Shot Learning, often known as GZSL, is an advanced variant of zero-shot learning in which the samples in the unseen category may be either seen or unseen. GZSL methods typically have a bias towards the seen classes because they learn a model to perform recognition for both the seen and unseen classes using data samples from the seen classes. This frequently leads to the misclassification of data from the unseen classes into the seen classes, making the task of GZSL more challenging. In this work of ours, to solve the GZSL problem, we propose an approach leveraging the Shifted Window based Self-Attention in the Swin Transformer (Swin-GZSL) to work in the inductive GSZL problem setting. We run experiments on three popular benchmark datasets: CUB, SUN, and AWA2, which are specifically used for ZSL and its other variants. The results show that our model based on Swin Transformer has achieved state-of-the-art harmonic mean for two datasets -AWA2 and SUN and near-state-of-the-art for the other dataset - CUB. More importantly, this technique has a linear computational complexity, which reduces training time significantly. We have also observed less bias than most of the existing GZSL models.

Keywords: generalised, zero-shot learning, inductive learning, shifted-window attention, Swin transformer, vision transformer

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Authors: Safa Abusara Mohammed Ali, Mohammed Khair Abdallah, Gurdon A. Brockmann, M. Reissmann

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The aim of the study was the characterization of DGAT1 variants in Sudanese dairy cattle breeds. In this study, we examined 94 Kenana and 91 Butana dairy cattle from two regions of Sudan. We genotyped the DGAT1 sequence variant AJ318490.1:g.10433/10434 AA>GC that leads to the Lysine – Alanine substitution at position 232 (K232A) in the protein and the VNTR polymorphism in the promoter region. Genotyping was performed by allele specific PCR and PCR fragment lengths determination, respectively. In both breeds, the DGAT1 Lysine variant (232K) that is associated with high fat and protein content as well as high fat yield in other breeds is the high frequent allele. The frequencies of the 232K allele were 96.3% and 84.6% in Kenana and Butana breeds, respectively. At the DGAT1 promoter VNTR locus, four alleles containing four to seven repeats of the 18 bp motif were found in both breeds. The highest frequent allele was the VNTR allele 3 containing five repeats with 60.4 % and 57.5 % in Kenana and Butana breeds, respectively. In conclusion, the two examined Sudanese dairy cattle breeds do not differ in allele frequencies at the DGAT1 locus.

Keywords: dairy cattle, DGAT1, Kenana, Butana.

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Authors: Rebecca Owusu Coffie, Atakelty Hailu

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Variants of production frontier models have emerged, however, only a limited number of them are applied in empirical research. Hence the effects of these alternative frontier models are not well understood, particularly within sub-Saharan Africa. In this paper, we apply recent advances in the production frontier to examine levels of technical efficiency and efficiency drivers. Specifically, we compare the heteroscedastic parametric and the semiparametric stochastic smooth coefficient (SPSC) models. Using rice production data from Ghana, our empirical estimates reveal that alternative specification of efficiency estimators results in either downward or upward bias in the technical efficiency estimates. Methodologically, we find that the SPSC model is more suitable and generates high-efficiency estimates. Within the parametric framework, we find that parameterization of both the mean and variance of the pre-truncated function is the best model. For the drivers of technical efficiency, we observed that longer farm distances increase inefficiency through a reduction in labor productivity. High soil quality, however, increases productivity through increased land productivity.

Keywords: pre-truncated, rice production, smooth coefficient, technical efficiency

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Authors: Sri Mahan Borah

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The issue of migration and displacement is considered so sensitive that states have often linked it with their sovereignty, independence and even existence. Therefor, even in the era of globalisation no nation-state is ready to compromise with its territorial boundaries. The problem of migration and displacement has generated a range of socio-political, economic, ethnic, and communal tensions in India in general and northeastern States in particular. In such situation it becomes unpreventable to look over the issue so that a viable elucidation may emerge. The present paper is an attempt to understand the impact of Bangladeshi and Nepali migration to North-Eastern states of India through historical and analytical methods. In this course it will look into the emergence of the migration and displacement problem, its causes, impacts on security and other issues of national interest especially when the migration is illegal and poses multi-layered challenges to the Indian state. The nature of migration from these countries to India has been dissimilar. This is because of their different historical backgrounds, geographical variants, ethno-religious affinities, political systems and bilateral arrangements with India. It concludes inter alia that, India’s borders with Bangladesh and Nepal must be regulated and that resident migrants need to be strategically dealt with, keeping in mind age-old relationships with these countries and, more importantly, the nature and construct of our geography.

Keywords: migration, displacement, North-East, India

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Authors: Jae Woong Sull, Sun Ha Jee

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High-density lipoprotein (HDL) cholesterol levels are associated with decreased risk of coronary artery disease. Several genome-wide association studies (GWAS) for HDL cholesterol levels have implicated cholesterol ester transfer protein (CETP) as possibly causal. We tested for the association between single nucleotide polymorphisms (SNPs) in CETP gene and HDL cholesterol levels in Korean population. Subjects were selected from the Korean Metabolic Syndrome Research Initiative study in the Bundang-Gu area. A total of 2,304 individuals from Bundang-Gu were recruited in 2008. Other subjects were selected from the Severance Hospital (N=4,294). SNP rs6499861 in the CETP gene was associated with mean HDL cholesterol levels (effect per allele -2.044 mg/dL, p=7.23×10-7). Subjects with the CG/GG genotype had a 1.46 -fold (range 1.24–1.72-fold) higher risk of having abnormal HDL cholesterol levels (<40 mg/dL) than subjects with the CC genotype. When analyzed by gender, the association of CETP was stronger in women than in men. When analyzed by physical activity behavior, the association with CETP was much stronger in male subjects with low physical activity (OR=1.54, 95% CI: 1.23-1.92, P=0.0001) than in male subjects with high physical activity. This study clearly demonstrates that genetic variants in CETP influence HDL cholesterol levels in Korean adults.

Keywords: CETP, HDL cholesterol, physical activity, polymorphisms

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Authors: Christoph Speer

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Decentralized ventilation systems should combine a small and economical design with high aerodynamic and thermal efficiency. The Counter Flow Heat Recovery Fan (CHRF) provides the ability to meet these requirements by using only one cross flow fan with a large number of blades to generate both airflows and which simultaneously acts as a regenerative counter flow heat exchanger. The successful development of the first laboratory prototype has shown the potential of this ventilation system. Occurring condensate on the surfaces of the fan blades during the cold and dry season can be recovered through the characteristic mode of operation. Hence the CHRF provides the possibility to avoid the need for frost protection and condensate drain. Through the implementation of system-specific solutions for flow balancing and summer bypass the required functionality is assured. The scalability of the CHRF concept allows the use in renovation as well as in new buildings from single-room devices through to systems for office buildings. High aerodynamic and thermal efficiency and the lower number of required mechatronic components should enable a reduction in investment as well as operating costs. The rotor is the key component of the system, the requirements and possible implementation variants are presented.

Keywords: CHRF, counter flow heat recovery fan, decentralized ventilation system, renovation

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Authors: Karam Ignaim, Joao M. Fernandes, Andre L. Ferreira

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Mapping the artifacts coming from a set of similar products family developed in an ad-hoc manner to make up the resulting software product line (SPL) plays a key role to maintain the consistency between requirements and code. This paper presents a feature mapping approach that focuses on tracing the artifact coming from the migration process, the current feature model (FM), to the other artifacts of the resulting SPL, the reference architecture, and code. Thus, our approach relates each feature of the current FM to its locations in the implementation code, using the reference architecture as an intermediate artifact (as a centric point) to preserve consistency among them during an SPL evolution. The approach uses a particular artifact (i.e., traceability tree) as a solution for managing the mapping process. Tool support is provided using friendlyMapper. We have evaluated the feature mapping approach and tool support by putting the approach into practice (i.e., conducting a case study) of the automotive domain for Classical Sensor Variants Family at Bosch Car Multimedia S.A. The evaluation reveals that the mapping approach presented by this paper fits the automotive domain.

Keywords: feature location, feature models, mapping, software product lines, traceability

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Authors: Abdul-Razak Inusah

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The study is a cross-sectional investigation of issues in Dagbanli Phonology, a Mabia language spoken in the Northern Region of Ghana. The issues investigated and assessed for the purpose of Dagbanli phonology are the status of the velar fricatives [x, ɣ] and the flap [ɾ] across Dagbanli dialects. The ethnographic approach is employed to solicit the primary data from bucolic Dagbanli speech communities. The descriptive method is engaged for the analysis of the primary data available. The investigation reveals that the dialects have the velar fricatives [x, ɣ] confined to specific segmental contexts with a particular inventory stricture. The flap[ɾ] is noticed to occur mostly in intervocalic but entirely missing in Dagbanli indigenous words in word-initial. The velar fricatives [x, ɣ] and the flap[ɾ] are observed to be non-contrastive and only suffice as dialectal allophones in the language. The paper shows evidence of coalesce of non-coronal labial /m/ and coronal fricative /s/ to produce dorsal fricative [x] in intervocalic and coalesce of stem final stop /ɡ/ and suffix onset fricative /s/ to yield the dorsal fricative [x], a finding which shows the status of the segment [x] in Dagbanli phonology. The paper concludes that the segments [x], [ɣ] and [ɾ] are positional variants of /ɡ+s/ or /m+s/, /ɡ/ and /d/.

Keywords: Dagbani, phonology, dialect, segment, fricatives, coalesce

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Authors: Xueying Zhao, Ke Ma, Hui Li, Yu Cao, Fan Yang, Qingwen Xu, Wenbin Liu

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Massively parallel sequencing (MPS) technologies allow high-throughput sequencing analyses with a relatively affordable price and have gradually been applied to forensic casework. MPS technology identifies short tandem repeat (STR) loci based on sequence so that repeat motif variation within STRs can be detected, which may help one to infer the origin of the mutation in some cases. Here, we report on one case with one three-step mismatch (D18S51) in family trios based on both capillary electrophoresis (CE) and MPS typing. The alleles of the alleged father (AF) are [AGAA]₁₇AGAG[AGAA]₃ and [AGAA]₁₅. The mother’s alleles are [AGAA]₁₉ and [AGAA]₉AGGA[AGAA]₃. The questioned child’s (QC) alleles are [AGAA]₁₉ and [AGAA]₁₂. Given that the sequence variants in repeat regions of AF and mother are not observed in QC’s alleles, the QC’s allele [AGAA]₁₂ was likely inherited from the AF’s allele [AGAA]₁₅ by loss of three repeat [AGAA]. Besides, two new alleles of D18S51 in this study, [AGAA]₁₇AGAG[AGAA]₃ and [AGAA]₉AGGA[AGAA]₃, have not been reported before. All the results in this study were verified using Sanger-type sequencing. In summary, the MPS typing method can offer valuable information for forensic genetics research and play a promising role in paternity testing.

Keywords: family trios analysis, forensic casework, ion torrent personal genome machine (PGM), massively parallel sequencing (MPS)

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Authors: Khaoula Azraiel, Mohamed Mehdi Abassi, Amel Sadraoui, Walid Hammami, Azouz Msaddek, Imed Cheikh, Maria Mancebo, Elisabet Perez-Navarro, Antonio Caruz, Henda Triki, Ahlem Djebbi

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IL28B rs12979860 genotype is confirmed as an important predictor of response to peginterferon/ribavirin therapy in patients with chronic hepatitis C (CHC). IFNL4 ss469415590 is a newly discovered polymorphism that could also affect the sustained virological response (SVR). The aim of this study was to evaluate the association of IL28B and IFNL4 genotypes with peginterferon/ribavirin treatment response in Tunisians patients with CHC and to determine which of these SNPs, was the stronger marker. A total of 120 patients were genotyped for both rs12979860 and ss469415590 polymorphisms. The association of each genetic marker with SVR was analyzed and comparison between the two SNPs was calculated by logistic regression models. For rs12979860, 69.6% of patients with CC, 41.8% with CT and 42.8% with TT achieved SVR (p = 0.003). Regarding ss469415590, 70.4% of patients with TT/TT genotype achieved SVR compared to 42.8% with TT/ΔG and 37.5% with ΔG /ΔG (p = 0.002). The presence of CC and TT/TT genotypes was independently associated with treatment response with an OR of 3.86 for each. In conclusion, both IL28B rs12979860 and IFNL4 ss469415590 variants were associated with response to pegIFN/RBV in Tunisian patients, without any additional benefit in performance for IFNL4. Our results are different from those detected in Sub-Saharan Africa countries.

Keywords: Hepatitis C virus, IFNL4, IL28B, Peginterferon/ribavirin, polymorphism

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Authors: Hidayatul Fitri, Petr Šařec

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The use of organic fertilizer is increasing nowadays, and the application must be conducted accurately to provide the right benefits for plants and maintain soil health. Improper application of fertilizers can cause problems for both plants and the environment. This study investigated the liquid organic fertilizer application, particularly digestate, varied into different application doses concerning mitigation of adverse environmental impacts, improving water infiltration ability, and crop yields. The experiment was established into eight variants with different digestate doses, conducted on emission monitoring and soil physical properties. As a result, the digestate application with shallow injection (5 cm in depth) was confirmed as an appropriate technique for applying liquid fertilizer into the soil. Gas emissions resulted in low concentration and declined gradually over time, obviously proved from the experiment conducted under two measurements immediately after application and the next day. Applied various doses of liquid digestate fertilizer affected the emission concentrations of NH3 volatilization, differing significantly and decreasing about 40% from the first to second measurement. In this study, winter wheat crop production significantly increases under digestate application with additional N fertilizer. This study suggested the long-term application of digestate to obtain more alteration of soil properties such as bulk density, penetration resistance, and hydraulic conductivity.

Keywords: liquid organic fertilizer, digestate, application, ammonia, emission

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Authors: Nazmul Shahadat, Anthony S. Maida

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In recent years, hypercomplex inspired neural networks improved deep CNN architectures due to their ability to share weights across input channels and thus improve cohesiveness of representations within the layers. The work described herein studies the effect of replacing existing layers in an Axial Attention ResNet with their quaternion variants that use cross-channel weight sharing to assess the effect on image classification. We expect the quaternion enhancements to produce improved feature maps with more interlinked representations. We experiment with the stem of the network, the bottleneck layer, and the fully connected backend by replacing them with quaternion versions. These modifications lead to novel architectures which yield improved accuracy performance on the ImageNet300k classification dataset. Our baseline networks for comparison were the original real-valued ResNet, the original quaternion-valued ResNet, and the Axial Attention ResNet. Since improvement was observed regardless of which part of the network was modified, there is a promise that this technique may be generally useful in improving classification accuracy for a large class of networks.

Keywords: axial attention, representational networks, weight sharing, cross-channel correlations, quaternion-enhanced axial attention, deep networks

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Authors: Adinarayana Badveeti, Mohammad Shafi Mir

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In Srinagar City, in India, traffic congestion is a condition on transport networks that occurs as use increases and is characterized by slower speeds, longer trip times, and increased vehicular queuing. Traffic congestion is conventionally measured using indicators such as roadway level-of-service, the Travel Time Index and their variants. Several measures have been taken in order to counteract congestion like road pricing, car pooling, improved traffic management, etc. While new road construction can temporarily relieve congestion in the longer term, it simply encourages further growth in car traffic through increased travel and a switch away from public transport. The full paper report, on which this abstract is based, aims to provide policymakers and technical staff with the real-time data, conceptual framework and guidance on some of the engineering tools necessary to manage congestion in such a way as to reduce its overall impact on individuals, families, communities, and societies dynamic, affordable, liveable and attractive urban regions will never be free of congestion. Road transport policies, however, should seek to manage congestion on a cost-effective basis with the aim of reducing the burden that excessive congestion imposes upon travellers and urban dwellers throughout the urban road network.

Keywords: traffic congestion, modeling, traffic management, travel time index

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Authors: Supanan Chansap, Werachon Cheukamud, Pornanan Kueakhai, Narin Changklungmoa

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Fasciola species (Fasciola spp.) is caused fasciolosis in ruminants such as cattle, sheep, and buffalo. Fasciola gigantica (F.gigantica) commonly infects tropical regions. Fasciola hepatica (F.hepatica) in temperate regions. Liver fluke infection affects livestock economically, for example, reduced milk and meat production, weight loss, sterile animals. Currently, Triclabendazole is used to treat liver flukes. However, liver flukes have also been found to be resistant to drugs in countries. Therefore, vaccination is an attractive alternative to prevent liver fluke infection. Peptide vaccines are new vaccine technologies that mimic epitope antigens that trigger an immune response. An interesting antigen used in vaccine production is catepsin L, a family of proteins that play an important role in the life of the parasite in the host. This study aims to identify immunogenic regions of protein and construct a multi-epidetope vaccine using an immunoinformatic tool. Fasciola gigantica Cathepsin L1 (FgCatL1), Fasciola gigantica Cathepsin L1G (FgCatL1G), and Fasciola gigantica Cathepsin L1H (FgCatL1H) were predicted B-cell and Helper T lymphocytes (HTL) by Immune Epitope and Analysis Resource (IEDB) servers. Both B-cell and HTL epitopes aligned with cathepsin L of the host and Fasciola hepatica (F. hepatica). Epitope groups were selected from non-conserved regions and overlapping sequences with F. hepatica. All overlapping epitopes were linked with the GPGPG and KK linker. GPGPG linker was linked between B-cell epitope. KK linker was linked between HTL epitope and B-cell and HTL epitope. The antigenic scores of multi-epitope peptide vaccine was 0.7824. multi-epitope peptide vaccine was non-allergen, non-toxic, and good soluble. Multi-epitope peptide vaccine was predicted tertiary structure and refinement model by I-Tasser and GalaxyRefine server, respectively. The result of refine structure model was good quality that was generated by Ramachandran plot analysis. Discontinuous and linear B-cell epitopes were predicted by ElliPro server. Multi-epitope peptide vaccine model was two and seven of discontinuous and linear B-cell epitopes, respectively. Furthermore, multi-epitope peptide vaccine was docked with Toll-like receptor 2 (TLR-2). The lowest energy ranged from -901.3 kJ/mol. In summary, multi-epitope peptide vaccine was antigenicity and probably immune response. Therefore, multi-epitope peptide vaccine could be used to prevent F. gigantica infections in the future.

Keywords: fasciola gigantica, Immunoinformatic tools, multi-epitope, Vaccine

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Authors: Ognjen Vukovic

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Chern-Simons equation represents the cornerstone of quantum physics. The question that is often asked is if the aforementioned equation can be successfully applied to the interaction in international financial markets. By analysing the time series in financial theory, it is proved that Chern-Simons equation can be successfully applied to financial time-series. The aforementioned statement is based on one important premise and that is that the financial time series follow the fractional Brownian motion. All variants of Chern-Simons equation and theory are applied and analysed. Financial theory time series movement is, firstly, topologically analysed. The main idea is that exchange rate represents two-dimensional projections of three-dimensional Brownian motion movement. Main principles of knot theory and topology are applied to financial time series and setting is created so the Chern-Simons equation can be applied. As Chern-Simons equation is based on small particles, it is multiplied by the magnifying factor to mimic the real world movement. Afterwards, the following equation is optimised using Solver. The equation is applied to n financial time series in order to see if it can capture the interaction between financial time series and consequently explain it. The aforementioned equation represents a novel approach to financial time series analysis and hopefully it will direct further research.

Keywords: Brownian motion, Chern-Simons theory, financial time series, econophysics

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Authors: Purva Mishra, Rajesh Potlia, Kuljeet Singh Sandhu

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The role of glycyl residues in the protein structure has lingered within the research community for the last several decades. Glycyl residue is the only amino acid that is achiral due to the lack of a side chain and can, therefore, exhibit Ramachandran conformations that are disallowed for L-amino acids. The structural and functional significance of glycyl residues with L-disallowed conformation, however, remains obscure. Through statistical analysis of various datasets, we found that the glycyls with L-disallowed conformations are over-represented at disease-associated sites and tend to be evolutionarily conserved. The mutations of L-disallowed glycyls tend to destabilize the native conformation, reduce protein solubility, and promote inter-molecular aggregations. We uncovered a structural motif referred to as “β-crescent” formed around the L-disallowed glycyl, which prevents β-sheet aggregation by disrupting the alternating pattern of β-pleats. The L-disallowed conformation of glycyls also holds predictive power to infer the pathogenic missense variants. Altogether, our observations highlight that the L-disallowed conformation of glycyls is selected to facilitate native folding and prevent inter-molecular aggregations. The findings may also have implications for designing more stable proteins and prioritizing the genetic lesions implicated in diseases.

Keywords: Ramachandran plot, β-sheet, protein stability, protein aggregation

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Authors: Xinyuan Chen, Mohd Nizam Husen, Zhongmei Zhou, Gongde Guo, Wei Gao

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Temporal Knowledge Graph Completion (TKGC) has attracted increasing attention for its enormous value; however, existing models lack capabilities to capture both local interactions and global dependencies simultaneously with evolutionary dynamics, while the latest achievements in convolutions and Transformers haven't been employed in this area. What’s more, periodic patterns in TKGs haven’t been fully explored either. To this end, a multi-stage hybrid architecture with convolution-backed Transformers is introduced in TKGC tasks for the first time combining the Hawkes process to model evolving event sequences in a continuous-time domain. In addition, the seasonal-trend decomposition is adopted to identify periodic patterns. Experiments on six public datasets are conducted to verify model effectiveness against state-of-the-art (SOTA) methods. An extensive ablation study is carried out accordingly to evaluate architecture variants as well as the contributions of independent components in addition, paving the way for further potential exploitation. Besides complexity analysis, input sensitivity and safety challenges are also thoroughly discussed for comprehensiveness with novel methods.

Keywords: temporal knowledge graph completion, convolution, transformer, Hawkes process, periodicity

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Authors: Laila Seada, Hanan Oreiby, Fawaz Al Rashid, Ashraf Negm

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Background and Objective: In most areas of the world, the incidence of thyroid cancer has been increasing over the last decade, mostly due to a combination of early detection of the neoplasm resulting from sensitive procedures and increased population exposure to radiation and unrecognized carcinogens. Methods: Cases of thyroid cancer have been retrieved from the cancer registry at King Khalid Hospital during the period from August 2012 to April 2016. Age, gender and histopathologic types have been recorded. Results: Thyroid carcinoma ranked as the second most common malignancy in females (25%) after breast cancer (31%). It constituted 20.8% of all newly diagnosed cancer cases. As for males, it ranked the 4^th type of malignancy after gastrointestinal cancer, lymphomas and soft tissue sarcomas. Mean age for females and males was 38.7 +/- 13.2 and 60.25 +/- 11.5 years, respectively, and the difference between the two groups was statistically significant (p value = 0.0001). Fifty-five (82%) were papillary carcinomas including 10 follicular variant of papillary (FVPC), and eight papillary micro carcinomas (PMC) and two tall cell/oncocytic variants. Follicular carcinomas constituted two (3.1%), while two (3.1%) were anaplastic, and two (3.1%) were medullary. Conclusion: Thyroid cancer incidence in Hail is ranking as the 2^nd most common female malignancy similar to other regions in the Kingdom. However, this high incidence contrasts with much lower rates worldwide.

Keywords: thyroid, hail, papillary, microcarcinoma

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Authors: Fern Baedyananda, Arkom Chaiwongkot, Somchai Niruthisard, Nakarin Kitkumthorn, Parvapan Bhattarakosol

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High-risk human papillomavirus (HPV) infections cause transformation of the host cells by down-regulating and inhibiting host regulatory proteins such as p53 and pRb by overexpressing the viral oncoproteins E6 and E7. However, the E1 protein which is the only enzyme encoded by HPV has also been shown to cause DNA instability leading to the integration of the virus into the host genome and triggering carcinogenic events. A 63bp duplication in the E1 helicase region has been detected in European patients. However, the clinical prognosis of these patients is still controversial. This study was performed to determine the presence of the HPV-16 E1 63bp duplication in patient cervical samples in Thai women and determine the sequence of the variant in the Thai population. Detection of the HPV-16 E1 duplication in the helicase region was performed in 90 patient cell samples across normal, cervical intraepithelial neoplasia I-III, and squamous cervical carcinoma stages by PCR. The PCR products were purified and sequenced to determine the presence of duplication variants.The variant form was found in 10% of all CIN 1 patients. In this study, the presence of the 63 bp duplication variant in the Thai population was found to be present and was further characterized. Interestingly, all samples that exhibited the variant form of HPV-16 E1 were classified as CIN I. Presence of the variant, constricted to mild dysplasia signifies the importance of HPV-16 E1 in carcinogenesis.

Keywords: carcinogenesis, cervical cancer, human papillomavirus, HPV-16 E1

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Authors: Tomas Barnak, Libor Matejka

Abstract:

The aim of this study is to create a standard application using multi-criteria evaluation in the field of forensic engineering. This situation can occur in the professional assessment in several cases such as when it is necessary to consider more criteria variant of the structural subsystems, more variants according to several criteria based on a court claim, which requires expert advice. A problematic situation arises when it is necessary to clearly determine the ranking of the options according to established criteria, and reduce subjective evaluation. For the procurement in the field of construction which is based on the prepared text of the law not only economic criteria but also technical, technological and environmental criteria will be determined. This fact substantially changes the style of evaluation of individual bids. For the above-mentioned needs of procurement, the unification of expert’s decisions and the use of multi-criteria assessment seem to be a reasonable option. In the case of experimental verification when using multi-criteria evaluation of alternatives construction subsystem the economic, technical, technological and environmental criteria will be compared. The core of the solution is to compare a selected number of set criteria, application methods and evaluation weighting based on the weighted values assigned to each of the criteria to use multi-criteria evaluation methods. The sequence of individual variations is determined by the evaluation of the importance of the values of corresponding criteria concerning expertise in the problematic of outside wall constructional subsystems.

Keywords: criteria, expertise, multi-criteria evaluation, outside wall subsystems

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Authors: Karthik Mittal

Abstract:

This study performs an unsupervised machine learning analysis to find clusters of related SNPs which highlight biological pathways that are important for the biological mechanisms of breast cancer. Studying genetic variations in isolation is illogical because these genetic variations are known to modulate protein production and function; the downstream effects of these modifications on biological outcomes are highly interconnected. After extracting the SNPs and their effect on different types of breast cancer using the MRBase library, two unsupervised machine learning clustering algorithms were implemented on the genetic variants: a k-means clustering algorithm and a hierarchical clustering algorithm; furthermore, principal component analysis was executed to visually represent the data. These algorithms specifically used the SNP’s beta value on the three different types of breast cancer tested in this project (estrogen-receptor positive breast cancer, estrogen-receptor negative breast cancer, and breast cancer in general) to perform this clustering. Two significant genetic pathways validated the clustering produced by this project: the MAPK signaling pathway and the connection between the BRCA2 gene and the ESR1 gene. This study provides the first proof of concept showing the importance of unsupervised machine learning in interpreting GWAS summary statistics.

Keywords: breast cancer, computational biology, unsupervised machine learning, k-means, PCA

Procedia PDF Downloads 117

Authors: Natarajan Vijayarangan, Viswanath Kumar Ganesan, G. Kumudhavalli

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This abstract figures out an uncertainty problem pertaining to evaluating business proposals or concept notes in an organisation. Let us consider business proposal evaluation process (BPEP) for execution of corporate research cum business projects in the organisation. Assume that two concept notes X and Y of BPEP are approved: one of them is a full-fledged type (100% financial approval given by the organisation) - X and other one is a conditional type (a partial financial approval given by the organisation) - Y. Then a penalty criteria has been introduced during the process. At the end of annual appraisal, if both of them complete as per the goals and objectives committed or figured out at the time of concept note submission, then both will get an incentive of $N from the organisation. If one of them doesn't fulfill the goals and objectives at the year-end appraisal, then d% reduction or cut will be levied on the project budget for the next year. If X fulfills the goals and objectives and Y doesn't , then X gets a gain of d% on Y's previous year budget and Y gets a loss of d% from the previous year budget for the next year. And vice-versa. Further, an incentive of $N will be given to those who gains. This process is a part of Necktie paradox and inherits an uncertainty principle on X or Y getting more than $N even if X or Y performs well.Solving the above problem and generalizing on finitely many concept notes will be a challenging task.

Keywords: concept notes, necktie paradox, annual appraisal, project budget and gain or loss

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Authors: A. Ameur Ameur, F. Chougrani, M. Halbouche

Abstract:

In order to characterize the sheep's milk, we analyzed and compared, in a first stage of our work, the physical and chemical characteristics in two Algerian sheep breeds: Hamra race and race Ouled Djellal breeding at the station the experimental ITELV Ain Hadjar (Saïda Province). Analyses are performed by Ekomilk Ultra-analyzer (EON TRADING LLC, USA), they focused on the pH, density, freezing, fat, total protein, solids-the total dry extract. The results obtained for these parameters showed no significant differences between the two breeds studied. The second stage of this work was the isolation and characterization of milk proteins. For this, we used the precipitation of caseins phi [pH 4.6]. For this, we used the precipitation of caseins Phi (pH 4.6). After extraction, purification and assay, both casein and serum protein fractions were then assayed by the Bradford method and controlled by polyacrylamide gel electrophoresis (PAGE) in the different conditions (native, in the presence of urea and in the presence of SDS). The electrophoretic pattern of milk samples showed the presence similarities of four major caseins variants (αs1-, αs2-β-and k-casein) and two whey proteins (β-lactoglobulin, α-lactalbumin) of two races Hamra and Ouled Djellal. But compared to bovine milk, they have helped to highlight some peculiarities as related to serum proteins (α La β Lg) as caseins, including αs1-Cn.

Keywords: Hamra, Ouled Djellal, protein polymorphism, sheep breeds

Procedia PDF Downloads 532