Search results for: fixation sequence

Authors: Lara Dutil-Fafard, Caroline Rhéaume, Patrick Archambault, Daniel Lafond, Neal W. Pollock

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Improving resources for medical autonomy of astronauts in prolonged space missions, such as a Mars mission, requires not only technology development, but also decision-making support systems. The Advanced Crew Medical System - Medical Condition Requirements study, funded by the Canadian Space Agency, aimed to create knowledge content and a scenario-based query capability to support medical autonomy of astronauts. The key objective of this study was to create a prototype tool for identifying medical infrastructure requirements in terms of medical knowledge, skills and materials. A multicriteria decision-making method was used to prioritize the highest risk medical events anticipated in a long-term space mission. Starting with those medical conditions, event sequence diagrams (ESDs) were created in the form of decision trees where the entry point is the diagnosis and the end points are the predicted outcomes (full recovery, partial recovery, or death/severe incapacitation). The ESD formalism was adapted to characterize and compare possible outcomes of medical conditions as a function of available medical knowledge, skills, and supplies in a given mission scenario. An extensive literature review was performed and summarized in a medical condition database. A PostgreSQL relational database was created to allow query-based evaluation of health outcome metrics with different medical infrastructure scenarios. Critical decision points, skill and medical supply requirements, and probable health outcomes were compared across chosen scenarios. The three medical conditions with the highest risk rank were acute coronary syndrome, sepsis, and stroke. Our efforts demonstrate the utility of this approach and provide insight into the effort required to develop appropriate content for the range of medical conditions that may arise.

Keywords: decision support system, event-sequence diagram, exploration mission, medical autonomy, scenario-based queries, space medicine

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Authors: Lien Gysens, Bert Vanmechelen, Maarten Haspeslagh, Piet Maes, Ann Martens

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Bovine papillomavirus (BPV) types 1 and 2 play a central role in the etiology of the most common neoplasm in horses, the equine sarcoid. The unknown mechanism behind the unique variety in a clinical presentation on the one hand and the host-dependent clinical outcome of BPV-1 infection, on the other hand, indicate the involvement of additional factors. Earlier studies have reported the potential functional significance of intratypic sequence variants, along with the existence of sarcoid-sourced BPV variants. Therefore, intratypic sequence variation seems to be an important emerging viral factor. This study aimed to give a broad insight in sarcoid-sourced BPV variation and explore its potential association with disease presentation. In order to do this, a nanopore sequencing approach was successfully optimized for screening a wide spectrum of clinical samples. Specimens of each tumour were initially screened for BPV-1/-2 by quantitative real-time PCR. A custom-designed primer set was used on BPV-positive samples to amplify the complete viral genome in two multiplex PCR reactions, resulting in a set of overlapping amplicons. For phylogenetic analysis, separate alignments were made of all available complete genome sequences for BPV-1/-2. The resulting alignments were used to infer Bayesian phylogenetic trees. We found substantial genetic variation among sarcoid-derived BPV-1, although this variation could not be linked to disease severity. Several of the BPV-1 genomes had multiple major deletions. Remarkably, the majority of the cluster within the region coding for late viral genes. Together with the extensiveness (up to 603 nucleotides) of the described deletions, this suggests an altered function of L1/L2 in disease pathogenesis. By generating a significant amount of complete-length BPV genomes, we succeeded in introducing next-generation sequencing into veterinary research focusing on the equine sarcoid, thus facilitating the first report of both nanopore-based sequencing of complete sarcoid-sourced BPV-1/-2 and the simultaneous nanopore sequencing of multiple complete genomes originating from a single clinical sample.

Keywords: Bovine papillomavirus, equine sarcoid, horse, nanopore sequencing, phylogenetic analysis

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Authors: Salina Yahya Saddick

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Ovarian cancer remains the most lethal gynecological malignancy due to the lack of highly sensitive and specific screening tools for detection of early-stage disease. The OSE provides the progenitor cells for 90% of human ovarian cancers. Recent morphologic, immunohistochemical and molecular genetic studies have led to the development of a new paradigm for the pathogenesis and origin of epithelial ovarian cancer (EOC) based on a ualistic model of carcinogenesis that divides EOC into two broad categories designated Types I and II which are characterized by specific mutations, including KRAS, BRAF, ERBB2, CTNNB1, PTEN PIK3CA, ARID1A, and PPPR1A, which target specific cell signaling pathways. Type 1 tumors rarely harbor TP53. type I tumors are relatively genetically stable and typically display a variety of somatic sequence mutations that include KRAS, BRAF, PTEN, PIK3CA CTNNB1 (the gene encoding beta catenin), ARID1A and PPP2R1A but very rarely TP53 . The cancer stem cell (CSC) hypothesis postulates that the tumorigenic potential of CSCs is confined to a very small subset of tumor cells and is defined by their ability to self-renew and differentiate leading to the formation of a tumor mass. Potential protein biomarker miRNA, are promising biomarkers as they are remarkably stable to allow isolation and analysis from tissues and from blood in which they can be found as free circulating nucleic acids and in mononuclear cells. Recently, genomic anaylsis have identified biomarkers and potential therapeutic targets for ovarian cancer namely, FGF18 which plays an active role in controlling migration, invasion, and tumorigenicity of ovarian cancer cells through NF-κB activation, which increased the production of oncogenic cytokines and chemokines. This review summarizes update information on epithelial ovarian cancers and point out to the most recent ongoing research.

Keywords: epithelial ovarian cancers, somatic sequence mutations, cancer stem cell (CSC), potential protein, biomarker, genomic analysis, FGF18 biomarker

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Authors: Klára Gajdošíková

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The aim of this study was to examine the quiet eye method and its components using the mobile eye tracking device. Quiet eye training was proven to be beneficial for different sports, including golf. The main idea of this method is to prolong your fixations on a specific place in order to improve your performance. The shot examined in this study is called putt. Its importance is based on its role on a golf course because, many times, it is the last putt that decides whether you win or lose. Quiet eye training helps players be more focused under pressure, control their attention and overall improve their putting success. Six highly skilled golfers with a handicap ranging from - 4 to + 4, aged 23 to 26, participated in a pilot study with the usage of an eye-tracking device. The study took place in an indoor training area at the golf club Hostivař. Crosstabs showed significant differences between individuals' laterality and their gaze into AOI - areas of interest (middle part of the ball, top of the ball, bottom of the ball, back side of the ball). Statistically significant differences were also discovered between the mean fixation duration of participants with AOI on the middle part of the ball and all other AOIs. The results of this study helped us understand the examined phenomena and showed us the next aim in future quiet eye research. Future research should focus on examining a quiet eye on the golf course. Applying a quiet eye and therefore changing the way we concentrate might be beneficial for coaches and players themselves.

Keywords: eye tracking, golf, laterality, quiet eye

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Authors: Don Anushka Sandaruwan Elvitigala, P. D. S. U. Wickramasinghe, Jehee Lee

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Cystatins are a large superfamily of proteins which act as reversible inhibitors of cysteine proteases. Papain proteases and cysteine cathepsins are predominant substrates of cystatins. Cystatin superfamily can be further clustered into three groups as Stefins, Cystatins, and Kininogens. Among them, stefines are also known as family 1 cystatins which harbors cystatin Bs and cystatin As. In this study, a homologue of family one cystatins more close to cystatin Bs was identified from Korean black rockfish (Sebastes schlegeli) using a prior constructed cDNA (complementary deoxyribonucleic acid) database and designated as RfCyt1. The full-length cDNA of RfCyt1 consisted of 573 bp, with a coding region of 294 bp. It comprised a 5´-untranslated region (UTR) of 55 bp, and 3´-UTR of 263 bp. The coding sequence encodes a polypeptide consisting of 97 amino acids with a predicted molecular weight of 11kDa and theoretical isoelectric point of 6.3. The RfCyt1 shared homology with other teleosts and vertebrate species and consisted conserved features of cystatin family signature including single cystatin-like domain, cysteine protease inhibitory signature of pentapeptide (QXVXG) consensus sequence and N-terminal two conserved neighboring glycine (⁸GG⁹) residues. As expected, phylogenetic reconstruction developed using the neighbor-joining method showed that RfCyt1 is clustered with the cystatin family 1 members, in which more closely with its teleostan orthologues. An SYBR Green qPCR (quantitative polymerase chain reaction) assay was performed to quantify the RfCytB transcripts in different tissues in healthy and immune stimulated fish. RfCyt1 was ubiquitously expressed in all tissue types of healthy animals with gill and spleen being the highest. Temporal expression of RfCyt1 displayed significant up-regulation upon infection with Aeromonas salmonicida. Recombinantly expressed RfCyt1 showed concentration-dependent papain inhibitory activity. Collectively these findings evidence for detectable protease inhibitory and immunity relevant roles of RfCyt1 in Sebastes schlegeli.

Keywords: Sebastes schlegeli, family 1 cystatin, immune stimulation, expressional modulation

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Authors: Norhidayu Muhamad Zain

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Gelatin, a purified protein derived mostly from porcine and bovine sources, is used widely in food manufacturing, pharmaceutical, and cosmetic industries. However, the presence of any porcine-related products are strictly forbidden for Muslim and Jewish consumption. Therefore, analytical methods offering reliable results to differentiate the sources of gelatin are needed. The aim of this study was to differentiate the sources of gelatin (porcine and tilapia fish) using Fourier transform infrared- attenuated total reflection (FTIR-ATR) combined with two dimensional infrared (2DIR) correlation analysis. Porcine gelatin (PG) and tilapia fish gelatin (FG) samples were diluted in distilled water at concentrations ranged from 4-20% (w/v). The samples were then analysed using FTIR-ATR and 2DIR correlation software. The results showed a significant difference in the pattern map of synchronous spectra at the region of 1000 cm⁻¹ to 1100 cm⁻¹ between PG and FG samples. The auto peak at 1080 cm⁻¹ that attributed to C-O functional group was observed at high intensity in PG samples compared to FG samples. Meanwhile, two auto peaks (1080 cm⁻¹ and 1030 cm⁻¹) at lower intensity were identified in FG samples. In addition, using 2D correlation analysis, the original broad water OH bands in 1D IR spectra can be effectively differentiated into six auto peaks located at 3630, 3340, 3230, 3065, 2950 and 2885 cm⁻¹ for PG samples and five auto peaks at 3630, 3330, 3230, 3060 and 2940 cm⁻¹ for FG samples. Based on the rule proposed by Noda, the sequence of the spectral changes in PG samples is as following: NH₃⁺ amino acid > CH₂ and CH₃ aliphatic > OH stretch > carboxylic acid OH stretch > NH in secondary amide > NH in primary amide. In contrast, the sequence was totally in the opposite direction for FG samples and thus both samples provide different 2D correlation spectra ranged from 2800 cm-1 to 3700 cm⁻¹. This method may provide a rapid determination of gelatin source for application in food, pharmaceutical, and cosmetic products.

Keywords: 2 dimensional infrared (2DIR) correlation analysis, Fourier transform infrared- attenuated total reflection (FTIR-ATR), porcine gelatin, tilapia fish gelatin

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Authors: Abu S. Mustafa, Mohammad W. Khan, Faraz Shaheed Khan, Nazima Habibi

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Brucellosis is a zoonotic disease of worldwide prevalence. There are at least four species and several strains of Brucella that cause human disease. Brucella genomes have very limited variation across strains, which hinder strain identification using classical molecular techniques, including PCR and 16 S rDNA sequencing. The aim of this study was to perform whole genome sequencing of clinical isolates of Brucella and perform bioinformatics and comparative genomics analyses to determine the existence of genetic differences across the isolates of a single Brucella species and strain. The draft sequence data were generated from 15 clinical isolates of Brucella melitensis (biovar 2 strain 63/9) using MiSeq next generation sequencing platform. The generated reads were used for further assembly and analysis. All the analysis was performed using Bioinformatics work station (8 core i7 processor, 8GB RAM with Bio-Linux operating system). FastQC was used to determine the quality of reads and low quality reads were trimmed or eliminated using Fastx_trimmer. Assembly was done by using Velvet and ABySS softwares. The ordering of assembled contigs was performed by Mauve. An online server RAST was employed to annotate the contigs assembly. Annotated genomes were compared using Mauve and ACT tools. The QC score for DNA sequence data, generated by MiSeq, was higher than 30 for 80% of reads with more than 100x coverage, which suggested that data could be utilized for further analysis. However when analyzed by FastQC, quality of four reads was not good enough for creating a complete genome draft so remaining 11 samples were used for further analysis. The comparative genome analyses showed that despite sharing same gene sets, single nucleotide polymorphisms and insertions/deletions existed across different genomes, which provided a variable extent of diversity to these bacteria. In conclusion, the next generation sequencing, bioinformatics, and comparative genome analysis can be utilized to find variations (point mutations, insertions and deletions) across different genomes of Brucella within a single strain. This information could be useful in surveillance and epidemiological studies supported by Kuwait University Research Sector grants MI04/15 and SRUL02/13.

Keywords: brucella, bioinformatics, comparative genomics, whole genome sequencing

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Authors: Nurulhikma Md Isa, Intan Elya Suka, Nur Farhana Roslan, Chew Bee Lynn

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The evolutionarily conserved N-end rule pathway marks proteins for degradation by the Ubiquitin Proteosome System (UPS) based on the nature of their N-terminal residue. Proteins with a destabilizing N-terminal residue undergo a series of condition-dependent N-terminal modifications, resulting in their ubiquitination and degradation. Intensive research has been carried out in Arabidopsis previously. The group VII Ethylene Response Factor (ERFs) transcription factors are the first N-end rule pathway substrates found in Arabidopsis and their role in regulating oxygen sensing. ERFs also function as central hubs for the perception of gaseous signals in plants and control different plant developmental including germination, stomatal aperture, hypocotyl elongation and stress responses. However, nothing is known about the role of this pathway during fruit development and ripening aspect. The plant model system Arabidopsis cannot represent fleshy fruit model system therefore tomato is the best model plant to study. PROTEOLYSIS6 (PRT6) is an E3 ubiquitin ligase of the N-end rule pathway. Two homologs of PRT6 sequences have been identified in tomato genome database using the PRT6 protein sequence from model plant Arabidopsis thaliana. Homology search against Ensemble Plant database (tomato) showed Solyc09g010830.2 is the best hit with highest score of 1143, e-value of 0.0 and 61.3% identity compare to the second hit Solyc10g084760.1. Further homology search was done using NCBI Blast database to validate the data. The result showed best gene hit was XP_010325853.1 of uncharacterized protein LOC101255129 (Solanum lycopersicum) with highest score of 1601, e-value 0.0 and 48% identity. Both Solyc09g010830.2 and uncharacterized protein LOC101255129 were genes located at chromosome 9. Further validation was carried out using BLASTP program between these two sequences (Solyc09g010830.2 and uncharacterized protein LOC101255129) to investigate whether they were the same proteins represent PRT6 in tomato. Results showed that both proteins have 100 % identity, indicates that they were the same gene represents PRT6 in tomato. In addition, we used two different RNAi constructs that were driven under 35S and Polygalacturonase (PG) promoters to study the function of PRT6 during tomato developmental stages and ripening processes.

Keywords: ERFs, PRT6, tomato, ubiquitin

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Authors: Pranjali Sharma, Swati Neogi

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

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

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Authors: Isabel Moscol, Carlos J. Díaz, Ciro Rodríguez

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Hip replacement becomes necessary when a person suffers severe pain or considerable functional limitations and the best option to enhance their quality of life is through the replacement of the damaged joint. One of the main components in femoral prostheses is the stem which distributes the loads from the joint to the proximal femur. To preserve more bone stock and avoid weakening of the diaphysis, a short starting stem was selected, generated from the intramedullary morphology of the patient's femur. It ensures the implantability of the design and leads to geometric delimitation for personalized optimization with machine learning (ML) and metaheuristic algorithms. The present study attempts to design a cementless short stem to make the strain deviation before and after implantation close to zero, promoting its fixation and durability. Regression models developed to estimate the percentage change of maximum principal stresses were used as objective optimization functions by the metaheuristic algorithm. The latter evaluated different geometries of the short stem with the modification of certain parameters in oblique sections from the osteotomy plane. The optimized geometry reached a global stress shielding (SS) of 18.37% with a determination factor (R²) of 0.667. The predicted results favour implantability integration in the short stem optimization to effectively reduce SS in the proximal femur.

Keywords: machine learning techniques, metaheuristic algorithms, short-stem design, stress shielding, hip replacement

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Authors: Milda Nainyte, Viktoras Masevicius

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Biological methylation is a methyl group transfer from S-adenosyl-L-methionine (AdoMet) onto N-, C-, O- or S-nucleophiles in DNA, RNA, proteins or small biomolecules. The reaction is catalyzed by enzymes called AdoMet-dependent methyltransferases (MTases), which represent more than 3 % of the proteins in the cell. As a general mechanism, the methyl group from AdoMet replaces a hydrogen atom of nucleophilic center producing methylated DNA and S-adenosyl-L-homocysteine (AdoHcy). Recently, DNA methyltransferases have been used for the sequence-specific, covalent labeling of biopolymers. Two types of MTase catalyzed labeling of biopolymers are known, referred as two-step and one-step. During two-step labeling, an alkylating fragment is transferred onto DNA in a sequence-specific manner and then the reporter group, such as biotin, is attached for selective visualization using suitable chemistries of coupling. This approach of labeling is quite difficult and the chemical hitching does not always proceed at 100 %, but in the second step the variety of reporter groups can be selected and that gives the flexibility for this labeling method. In the one-step labeling, AdoMet analog is designed with the reporter group already attached to the functional group. Thus, the one-step labeling method would be more comfortable tool for labeling of biopolymers in order to prevent additional chemical reactions and selection of reaction conditions. Also, time costs would be reduced. However, effective AdoMet analog appropriate for one-step labeling of biopolymers and containing cleavable bond, required for reduction of PCR interferation, is still not known. To expand the practical utility of this important enzymatic reaction, cofactors with activated sulfonium-bound side-chains have been produced and can serve as surrogate cofactors for a variety of wild-type and mutant DNA and RNA MTases enabling covalent attachment of these chains to their target sites in DNA, RNA or proteins (the approach named methyltransferase-directed Transfer of Activated Groups, mTAG). Compounds containing hex-2-yn-1-yl moiety has proved to be efficient alkylating agents for labeling of DNA. Herein we describe synthetic procedures for the preparation of N-biotinoyl-N’-(pent-4-ynoyl)cystamine starting from the coupling of cystamine with pentynoic acid and finally attaching the biotin as a reporter group. The synthesis of the first AdoMet based cofactor containing a cleavable reporter group and appropriate for one-step labeling was developed.

Keywords: adoMet analogs, DNA alkylation, cofactor, methyltransferases

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Authors: H. S. Kang

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Coupled electrical and optical model for conversion of electrical energy into coherent optical energy for transmitter-receiver link by solid state device is presented. Probability distribution for travelling laser beam switching time intervals and the number of switchings in the time interval is obtained. Selector function mapping is employed to regulate optical data transmission speed. It is established that regulated laser transmission from PhotoActive Laser transmitter follows principal of invariance. This considerably simplifies design of PhotoActive Laser Transmission networks.

Keywords: computational mathematics, finite difference Markov chain methods, sequence spaces, singularly perturbed differential equations

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Authors: Quan Li, Dongcai Shen, Zhengting Xiao, Xin Liu Mingrui Wu, Licheng Liu, Qin Li, Xianguo Li, Wentai Wang

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Direct electrocatalytic nitrogen oxidation (NOR) provides a promising alternative strategy for synthesizing high-value-added nitric acid from widespread N₂, which overcomes the disadvantages of the Haber-Bosch-Ostwald process. However, the NOR process suffers from the limitation of high N≡N bonding energy (941 kJ mol− ¹), sluggish kinetics, low efficiency and yield. It is a prerequisite to develop more efficient electrocatalysts for NOR. Herein, we synthesized double-shelled CeO₂ hollow spheres (D-CeO₂) and further modified with Ti₃C₂ MXene quantum dots (MQDs) for electrocatalytic N₂ oxidation, which exhibited a NO₃− yield of 71.25 μg h− ¹ mgcat− ¹ and FE of 31.80% at 1.7 V. The unique quantum size effect and abundant edge active sites lead to a more effective capture of nitrogen. Moreover, the double-shelled hollow structure is favorable for N₂ fixation and gathers intermediate products in the interlayer of the core-shell. The in-situ infrared Fourier transform spectroscopy confirmed the formation of *NO and NO₃− species during the NOR reaction, and the kinetics and possible pathways of NOR were calculated by density functional theory (DFT). In addition, a Zn-N₂ reaction device was assembled with D-CeO₂/MQDs as anode and Zn plate as cathode, obtaining an extremely high NO₃− yield of 104.57 μg h− ¹ mgcat− ¹ at 1 mA cm− ².

Keywords: electrocatalytic N₂ oxidation, nitrate production, CeO₂, MXene quantum dots, double-shelled hollow spheres

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Authors: Misbah Irshad, Faiza Sarfraz

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The problem of approximating surface to surface intersection is considered to be very important in computer aided geometric design and computer aided manufacturing. Although it is a complex problem to handle, its continuous need in the industry makes it an active topic in research. A technique for approximating intersection curves of two parametric surfaces is proposed, which extracts boundary points and turning points from a sequence of intersection points and interpolate them with the help of rational cubic spline functions. The proposed approach is demonstrated with the help of examples and analyzed by calculating error.

Keywords: approximation, parametric surface, spline function, surface intersection

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Authors: Muhammad Haris, Syed Kamran Ali, Mubeen Islam, Tariq Mehmood, Faisal Shah

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Jacobabad Khairpur High, part of a Sukkur rift zone, is the separating boundary between Central and Southern Indus Basin, formed as a result of Post-Jurassic uplift after the deposition of Middle Jurassic Chiltan Formation. Habib Rahi Formation of Middle to Late Eocene outcrops in the vicinity of Jacobabad Khairpur High, a section at Rohri near Sukkur is measured in detail for lithofacies, microfacies, diagenetic analysis and sequence stratigraphy. Habib Rahi Formation is richly fossiliferous and consists of mostly limestone with subordinate clays and marl. The total thickness of the formation in this section is 28.8m. The bottom of the formation is not exposed, while the upper contact with the Sirki Shale of the Middle Eocene age is unconformable in some places. A section is measured using Jacob’s Staff method, and traverses were made perpendicular to the strike. Four different lithofacies were identified based on outcrop geology which includes coarse-grained limestone facies (HR-1 to HR-5), massive bedded limestone facies (HR-6 HR-7), and micritic limestone facies (HR-8 to HR-13) and algal dolomitic limestone facie (HR-14). Total 14 rock samples were collected from outcrop for detailed petrographic studies, and thin sections of respective samples were prepared and analyzed under the microscope. On the basis of Dunham’s (1962) classification systems after studying textures, grain size, and fossil content and using Folk’s (1959) classification system after reviewing Allochems type, four microfacies were identified. These microfacies include HR-MF 1: Benthonic Foraminiferal Wackstone/Biomicrite Microfacies, HR-MF 2: Foramineral Nummulites Wackstone-Packstone/Biomicrite Microfacies HR-MF 3: Benthonic Foraminiferal Packstone/Biomicrite Microfacies, HR-MF 4: Bioclasts Carbonate Mudstone/Micrite Microfacies. The abundance of larger benthic Foraminifera’s (LBF), including Assilina sp., A. spiral abrade, A. granulosa, A. dandotica, A. laminosa, Nummulite sp., N. fabiani, N. stratus, N. globulus, Textularia, Bioclasts, and Red algae indicates shallow marine (Tidal Flat) environment of deposition. Based on variations in rock types, grain size, and marina fauna Habib Rahi Formation shows progradational stacking patterns, which indicates coarsening upward cycles. The second order of sea-level rise is identified (spanning from Y-Persian to Bartonian age) that represents the Transgressive System Tract (TST) and a third-order Regressive System Tract (RST) (spanning from Bartonian to Priabonian age). Diagenetic processes include fossils replacement by mud, dolomitization, pressure dissolution associated stylolites features and filling with dark organic matter. The presence of the microfossils includes Nummulite. striatus, N. fabiani, and Assilina. dandotica, signify Bartonian to Priabonian age of Habib Rahi Formation.

Keywords: Jacobabad Khairpur High, Habib Rahi Formation, lithofacies, microfacies, sequence stratigraphy, diagenetic history

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Authors: Kiwon Yeom

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Change points are abrupt variations in a data sequence. Detection of change points is useful in modeling, analyzing, and predicting time series in application areas such as robotics and teleoperation. In this paper, a change point is defined to be a discontinuity in one of its derivatives. This paper presents a reliable method for detecting discontinuities within a three-dimensional trajectory data. The problem of determining one or more discontinuities is considered in regular and irregular trajectory data from teleoperation. We examine the geometric detection algorithm and illustrate the use of the method on real data examples.

Keywords: change point, discontinuity, teleoperation, abrupt variation

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Authors: J. Trarbach, S. Schosser, B. Vogt

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Decision-makers tend to prefer the first alternative over subsequent alternatives which is called the primacy effect. To reliably measure this effect, we conducted an experiment with real consequences for preference statements. Therefore, we elicit preferences of subjects using a rating scale, i.e. hypothetical preferences, and willingness to pay, i.e. real preferences, for two sequences of pain. Within these sequences, both overall intensity and duration of pain are identical. Hence, a rational decision-maker should be indifferent, whereas the primacy effect predicts a stronger preference for the first sequence. What we see is a primacy effect only for hypothetical preferences. This effect vanishes for real preferences.

Keywords: decision making, primacy effect, real incentives, willingness to pay

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Authors: Xiaoying Guo, Xiangyun Wang, Chunhua Jia

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Web page has been one of the most important way of knowing the world. Humans catch a lot of information from it everyday. Thus, understanding where human looks when they surfing the web pages is rather important. In normal scenes, the down-top features and top-down tasks significantly affect humans’ eye movement. In this paper, we investigated if the conventional visual salience algorithm can properly predict humans’ visual attractive region when they viewing the web pages. First, we obtained the eye movement data when the participants viewing the web pages using an eye tracker. By the analysis of eye movement data, we studied the influence of visual saliency and thinking way on eye-movement pattern. The analysis result showed that thinking way affect human’ eye-movement pattern much more than visual saliency. Second, we compared the results of web page visual salience region extracted by Itti model and Spectral Residual (SR) model. The results showed that Spectral Residual (SR) model performs superior than Itti model by comparison with the heat map from eye movements. Considering the influence of mind habit on humans’ visual region of interest, we introduced one of the most important cue in mind habit-fixation position to improved the SR model. The result showed that the improved SR model can better predict the human visual region of interest in web pages.

Keywords: web page salience region, eye-tracker, spectral residual, visual salience

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Authors: Maxence Queyrel, Edi Prifti, Alexandre Templier, Jean-Daniel Zucker

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Analysis of the human microbiome using metagenomic sequencing data has demonstrated high ability in discriminating various human diseases. Raw metagenomic sequencing data require multiple complex and computationally heavy bioinformatics steps prior to data analysis. Such data contain millions of short sequences read from the fragmented DNA sequences and stored as fastq files. Conventional processing pipelines consist in multiple steps including quality control, filtering, alignment of sequences against genomic catalogs (genes, species, taxonomic levels, functional pathways, etc.). These pipelines are complex to use, time consuming and rely on a large number of parameters that often provide variability and impact the estimation of the microbiome elements. Training Deep Neural Networks directly from raw sequencing data is a promising approach to bypass some of the challenges associated with mainstream bioinformatics pipelines. Most of these methods use the concept of word and sentence embeddings that create a meaningful and numerical representation of DNA sequences, while extracting features and reducing the dimensionality of the data. In this paper we present an end-to-end approach that classifies patients into disease groups directly from raw metagenomic reads: metagenome2vec. This approach is composed of four steps (i) generating a vocabulary of k-mers and learning their numerical embeddings; (ii) learning DNA sequence (read) embeddings; (iii) identifying the genome from which the sequence is most likely to come and (iv) training a multiple instance learning classifier which predicts the phenotype based on the vector representation of the raw data. An attention mechanism is applied in the network so that the model can be interpreted, assigning a weight to the influence of the prediction for each genome. Using two public real-life data-sets as well a simulated one, we demonstrated that this original approach reaches high performance, comparable with the state-of-the-art methods applied directly on processed data though mainstream bioinformatics workflows. These results are encouraging for this proof of concept work. We believe that with further dedication, the DNN models have the potential to surpass mainstream bioinformatics workflows in disease classification tasks.

Keywords: deep learning, disease prediction, end-to-end machine learning, metagenomics, multiple instance learning, precision medicine

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Authors: Hernández Eva Selene, Reyna Mary Carmen, Rivera Héctor, Barragán Irving

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We propose an approach that jointly addresses the layout of a facility and the scheduling of a sequence of jobs. In real production, these two problems are interrelated. However, they are treated separately in the literature. Our approach is an extension of the job shop problem with transportation delay, where the location of the machines is selected among possible sites. The model minimizes the makespan, using the short processing times rule with two algorithms; the first one considers all the permutations for the location of machines, and the second only a heuristic to select some specific permutations that reduces computational time. Some instances are proved and compared with literature.

Keywords: layout problem, job shop scheduling problem, concurrent scheduling and layout problem, metaheuristic

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Authors: C. A. Roberts, S. L. Mascaro, J. R. Gerrish, J. L. Horner

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Management-intensive Grazing (MiG) is a practice that rotates livestock through paddocks in a way that best matches the nutrient requirements of the animal to the yield and quality of the pasture. In the USA, MiG has been taught to livestock producers throughout the state of Missouri in 2- and 3-day workshops called “Missouri Grazing Schools.” The economic impact of these schools was quantified using IMPLAN software. The model included hectares of adoption, animal performance, carrying capacity, and input costs. To date, MiG, as taught in the Missouri Grazing Schools, has been implemented on more than 70,000 hectares in Missouri. The economic impact of these schools is presently $125 million USD per year added to the state economy. This magnitude of impact is the result not only of widespread adoption but also because of increased livestock carrying capacity; in Missouri, a capacity increase of 25 to 30% has been well documented. Additional impacts have been MiG improving forage quality and reducing the cost of feed and fertilizer. The environmental impact of MiG in the state of Missouri is currently being estimated. Environmental impact takes into account the reduction in the application of commercial fertilizers; in MiG systems, nitrogen is supplied by N fixation from legumes, and much of the P and K is recycled naturally by well-distributed manure. The environmental impact also estimates carbon sequestration and methane production; MiG can increase carbon sequestration and reduce methane production in comparison to default grazing practices and feedlot operations in the USA.

Keywords: agricultural education, forage quality, management-intensive grazing, nutrient cycling, stock density, sustainable agriculture

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Authors: Bing Zhang, Jingyi Zhang, Mudan Chen

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Fibre-reinforced polymer (FRP) composites have been extensively utilised in various industries due to their high specific strength, e.g., aerospace, renewable energy, automotive, and marine. However, they have relatively low electrical conductivity than metals, especially in the out-of-plane direction. Conductive metal strips or meshes are typically employed to protect composites when designing lightweight structures that may be subjected to lightning strikes, such as composite wings. Unfortunately, this approach downplays the lightweight advantages of FRP composites, thereby limiting their potential applications. Extensive studies have been undertaken to improve the electrical conductivity of FRP composites. The authors are amongst the pioneers who use through-thickness reinforcement (TTR) to tailor the electrical conductivity of composites. Compared to the conventional approaches using conductive fillers, the through-thickness reinforcement approach has been proven to be able to offer a much larger improvement to the through-thickness conductivity of composites. In this study, an advanced high-fidelity numerical modelling strategy is presented to investigate the effects of through-thickness reinforcement on both the in-plane and out-of-plane electrical conductivities of FRP composites. The critical micro-structural features of through-thickness reinforced composites incorporated in the modelling framework are 1) the fibre waviness formed due to TTR insertion; 2) the resin-rich pockets formed due to resin flow in the curing process following TTR insertion; 3) the fibre crimp, i.e., fibre distortion in the thickness direction of composites caused by TTR insertion forces. In addition, each interlaminar interface is described separately. An IMA/M21 composite laminate with a quasi-isotropic stacking sequence is employed to calibrate and verify the modelling framework. The modelling results agree well with experimental measurements for bothering in-plane and out-plane conductivities. It has been found that the presence of conductive TTR can increase the out-of-plane conductivity by around one order, but there is less improvement in the in-plane conductivity, even at the TTR areal density of 0.1%. This numerical tool provides valuable references as a design tool for through-thickness reinforced composites when exploring their electrical applications. Parametric studies are undertaken using the numerical tool to investigate critical parameters that affect the electrical conductivities of composites, including TTR material, TTR areal density, stacking sequence, and interlaminar conductivity. Suggestions regarding the design of electrical through-thickness reinforced composites are derived from the numerical modelling campaign.

Keywords: composite structures, design, electrical conductivity, numerical modelling, through-thickness reinforcement

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Authors: Shagufta Jabeen, Faez J. Firdaus Abdullah, Zunita Zakaria, Nurulfiza M. Isa, Yung C. Tan, Wai Y. Yee, Abdul R. Omar

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Pasteurella multocida (PM) is an important veterinary opportunistic pathogen particularly associated with septicemic pasteurellosis, pneumonic pasteurellosis and hemorrhagic septicemia in cattle and buffaloes. P. multocida serotype A has been reported to cause fatal pneumonia and septicemia. Pasteurella multocida subspecies multocida of serotype A Malaysian isolate PMTB2.1 was first isolated from buffaloes died of septicemia. In this study, the genome of P. multocida strain PMTB2.1 was sequenced using third-generation sequencing technology, PacBio RS2 system and analyzed bioinformatically via de novo analysis followed by in-depth analysis based on comparative genomics. Bioinformatics analysis based on de novo assembly of PacBio raw reads generated 3 contigs followed by gap filling of aligned contigs with PCR sequencing, generated a single contiguous circular chromosome with a genomic size of 2,315,138 bp and a GC content of approximately 40.32% (Accession number CP007205). The PMTB2.1 genome comprised of 2,176 protein-coding sequences, 6 rRNA operons and 56 tRNA and 4 ncRNAs sequences. The comparative genome sequence analysis of PMTB2.1 with nine complete genomes which include Actinobacillus pleuropneumoniae, Haemophilus parasuis, Escherichia coli and five P. multocida complete genome sequences including, PM70, PM36950, PMHN06, PM3480, PMHB01 and PMTB2.1 was carried out based on OrthoMCL analysis and Venn diagram. The analysis showed that 282 CDs (13%) are unique to PMTB2.1and 1,125 CDs with orthologs in all. This reflects overall close relationship of these bacteria and supports the classification in the Gamma subdivision of the Proteobacteria. In addition, genomic distance analysis among all nine genomes indicated that PMTB2.1 is closely related with other five Pasteurella species with genomic distance less than 0.13. Synteny analysis shows subtle differences in genetic structures among different P.multocida indicating the dynamics of frequent gene transfer events among different P. multocida strains. However, PM3480 and PM70 exhibited exceptionally large structural variation since they were swine and chicken isolates. Furthermore, genomic structure of PMTB2.1 is more resembling that of PM36950 with a genomic size difference of approximately 34,380 kb (smaller than PM36950) and strain-specific Integrative and Conjugative Elements (ICE) which was found only in PM36950 is absent in PMTB2.1. Meanwhile, two intact prophages sequences of approximately 62 kb were found to be present only in PMTB2.1. One of phage is similar to transposable phage SfMu. The phylogenomic tree was constructed and rooted with E. coli, A. pleuropneumoniae and H. parasuis based on OrthoMCL analysis. The genomes of P. multocida strain PMTB2.1 were clustered with bovine isolates of P. multocida strain PM36950 and PMHB01 and were separated from avian isolate PM70 and swine isolates PM3480 and PMHN06 and are distant from Actinobacillus and Haemophilus. Previous studies based on Single Nucleotide Polymorphism (SNPs) and Multilocus Sequence Typing (MLST) unable to show a clear phylogenetic relatedness between Pasteurella multocida and the different host. In conclusion, this study has provided insight on the genomic structure of PMTB2.1 in terms of potential genes that can function as virulence factors for future study in elucidating the mechanisms behind the ability of the bacteria in causing diseases in susceptible animals.

Keywords: comparative genomics, DNA sequencing, phage, phylogenomics

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Authors: Geetanjali Panda, Suvrakanti Chakraborty

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In this paper, Newton-like descent methods are proposed for unconstrained optimization problems, which use q-derivatives of the gradient of an objective function. First, a local scheme is developed with alternative sufficient optimality condition, and then the method is extended to a global scheme. Moreover, a variant of practical Newton scheme is also developed introducing a real sequence. Global convergence of these schemes is proved under some mild conditions. Numerical experiments and graphical illustrations are provided. Finally, the performance profiles on a test set show that the proposed schemes are competitive to the existing first-order schemes for optimization problems.

Keywords: Descent algorithm, line search method, q calculus, Quasi Newton method

Procedia PDF Downloads 376

Authors: Naoki Ohshima, Ken Kaminishi

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Four types of dependencies, which are 'Finish-to-start', 'Finish-to-finish', 'Start-to-start' and 'Start-to-finish (S-F)' as logical relationship are modeled based on the definition by 'the predecessor activity is defined as an activity to come before a dependent activity in a schedule' in PMBOK. However, it is found a self-contradiction in the precedence diagram for S-F relationship by PMBOK. In this paper, author would like to validate logical relationship of S-F by Graph Theory and propose a new interpretation of the precedence diagram for S-F relationship.

Keywords: project time management, sequence activity, start-to-finish relationship, precedence diagram, PMBOK

Procedia PDF Downloads 241

Authors: A. B. Bolkhir, A. Elshafie, T. K. Yousif

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This paper highlights the methods of error estimation in finite element analysis (FEA) results. It indicates that the modeling error could be eliminated by performing finite element analysis with successively finer meshes or by extrapolating response predictions from an orderly sequence of relatively low degree of freedom analysis results. In addition, the paper eliminates the round-off error by running the code at a higher precision. The paper provides application in finite element analysis results. It draws a conclusion based on results of application of methods of error estimation.

Keywords: finite element analysis (FEA), discretization error, round-off error, mesh refinement, richardson extrapolation, monotonic convergence

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Authors: Cristóbal Moënne-Loccoz, Rodrigo C. Vergara, Vladimir López, Domingo Mery, Diego Cosmelli

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Our daily interaction with computational interfaces is plagued of situations in which we go from inexperienced users to experts through self-motivated exploration of the same task. In many of these interactions, we must learn to find our way through a sequence of decisions and actions before obtaining the desired result. For instance, when drawing cash from an ATM machine, choices are presented in a step-by-step fashion so that a specific sequence of actions must be performed in order to produce the expected outcome. But, as they become experts in the use of such interfaces, do users adopt specific search and learning strategies? Moreover, if so, can we use this information to follow the process of expertise development and, eventually, predict future actions? This would be a critical step towards building truly adaptive interfaces that can facilitate interaction at different moments of the learning curve. Furthermore, it could provide a window into potential mechanisms underlying decision-making behavior in real world scenarios. Here we tackle this question using a simple game interface that instantiates a 4-level binary decision tree (BDT) sequential decision-making task. Participants have to explore the interface and discover an underlying concept-icon mapping in order to complete the game. We develop a Hidden Markov Model (HMM)-based approach whereby a set of stereotyped, hierarchically related search behaviors act as hidden states. Using this model, we are able to track the decision-making process as participants explore, learn and develop expertise in the use of the interface. Our results show that partitioning the problem space into such stereotyped strategies is sufficient to capture a host of exploratory and learning behaviors. Moreover, using the modular architecture of stereotyped strategies as a Mixture of Experts, we are able to simultaneously ask the experts about the user's most probable future actions. We show that for those participants that learn the task, it becomes possible to predict their next decision, above chance, approximately halfway through the game. Our long-term goal is, on the basis of a better understanding of real-world decision-making processes, to inform the construction of interfaces that can establish dynamic conversations with their users in order to facilitate the development of expertise.

Keywords: behavioral modeling, expertise acquisition, hidden markov models, sequential decision-making

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Authors: Zouhair Issa Ahmed, Ahmed Abdulrasool Ahmed, Falah Hassan Abdulsada

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This paper presents a layout of a factory using Pro-Model simulation by choosing the best layout that gives the highest productivity and least work in process. The general problem is to find the best sequence in which jobs pass between the machines which are compatible with the technological constraints and optimal with respect to some performance criteria. The best simulation with Pro-Model program increased productivity and reduced work in process by balancing lines of production compared with the current layout of factory when productivity increased from 45 products to 180 products through 720 hours.

Keywords: scheduling, Pro-Model, simulation, balancing lines of production, layout planning, WIP

Procedia PDF Downloads 600

Authors: J. T. Manhire

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A tax authority wants to take actions it knows will foster the greatest degree of voluntary taxpayer compliance to reduce the “tax gap.” This paper suggests that even if a tax authority could attain a state of complete knowledge, there are constraints on whether and to what extent such actions would result in reducing the macro-level tax gap. These limits are not merely a consequence of finite agency resources. They are inherent in the system itself. To show that this is one possible interpretation of the tax gap data, the paper formulates known results in a different way by analyzing tax compliance as a population with a single covariate. This leads to a standard use of the logistic map to analyze the dynamics of non-compliance growth or decay over a sequence of periods. This formulation gives the same results as the tax gap studies performed over the past fifty years in the U.S. given the published margins of error. Limitations and recommendations for future work are discussed, along with some implications for tax policy.

Keywords: income tax, logistic map, tax compliance, tax law

Procedia PDF Downloads 97

Authors: O. Abusaeeda, J. P. O. Evans, D. Downes

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We demonstrate the synthesis of intermediary views within a sequence of X-ray images that exhibit depth from motion or kinetic depth effect in a visual display. Each synthetic image replaces the requirement for a linear X-ray detector array during the image acquisition process. Scale invariant feature transform, SIFT, in combination with epipolar morphing is employed to produce synthetic imagery. Comparison between synthetic and ground truth images is reported to quantify the performance of the approach. Our work is a key aspect in the development of a 3D imaging modality for the screening of luggage at airport checkpoints. This programme of research is in collaboration with the UK Home Office and the US Dept. of Homeland Security.

Keywords: X-ray, kinetic depth, KDE, view synthesis

Procedia PDF Downloads 234