Search results for: picking sequence

Authors: Manendra Singh Parihar, Sandip Ghosh Chowdhury

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Austenitic stainless steels are widely used and give a good combination of properties. When this steel is plastically deformed, a phase transformation of the metastable Face Centred Cubic Austenite to the stable Body Centred Cubic (α’) or to the Hexagonal close packed (ԑ) martensite may occur, leading to the enhancement in the mechanical properties like strength. The work was based on variant selection and corresponding texture analysis for the strain induced martensitic transformation during deformation of the parent austenite FCC phase to form the product HCP and the BCC martensite phases separately, obeying their respective orientation relationships. The automated method for reconstruction of the parent phase orientation using the EBSD data of the product phase orientation is done using the MATLAB and TSL-OIM software. The method of triplets was used which involves the formation of a triplet of neighboring product grains having a common variant and linking them using a misorientation-based criterion. This led to the proper reconstruction of the pre-transformation phase orientation data and thus to its microstructure and texture. The computational speed of current method is better compared to the previously used methods of reconstruction. The reconstruction of austenite from ԑ and α’ martensite was carried out for multiple samples and their IPF images, pole figures, inverse pole figures and ODFs were compared. Similar type of results was observed for all samples. The comparison gives the idea for estimating the correct sequence of the transformation i.e. γ → ε → α’ or γ → α’, during deformation of AISI 304 austenitic stainless steel.

Keywords: variant selection, reconstruction, EBSD, austenitic stainless steel, martensitic transformation

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Authors: Cornelia-Eugenia Munteanu

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From a psychological perspective, psychopathology is the area of clinical psychology that has at its core psychological assessment and psychotherapy. In day-to-day clinical practice, psychodiagnosis and psychotherapy are used independently, according to their intended purpose and their specific methods of application. The paper explores how the Minnesota Multiphasic Personality Inventory-2 (MMPI-2) and Mini Mental State Examination-2 (MMSE-2) psychological tools contribute to enhancing the effectiveness of cognitive behavioral psychotherapy (CBT). This combined approach, psychotherapy in conjunction with assessment of personality and cognitive functions, is illustrated by two cases, a severe depressive episode with psychotic symptoms and a mixed anxiety-depressive disorder. The order in which CBT, MMPI-2, and MMSE-2 were used in the diagnostic and therapeutic process was determined by the particularities of each case. In the first case, the sequence started with psychotherapy, followed by the administration of blue form MMSE-2, MMPI-2, and red form MMSE-2. In the second case, the cognitive screening with blue form MMSE-2 led to a personality assessment using MMPI-2, followed by red form MMSE-2; reapplication of the MMPI-2 due to the invalidation of the first profile, and finally, psychotherapy. The MMPI-2 protocols gathered useful information that directed the steps of therapeutic intervention: a detailed symptom picture of potentially self-destructive thoughts and behaviors otherwise undetected during the interview. The memory loss and poor concentration were confirmed by MMSE-2 cognitive screening. This combined approach, psychotherapy with psychological assessment, aligns with the trend of adaptation of the psychological services to the everyday life of contemporary man and paves the way for deepening and developing the field.

Keywords: assessment, cognitive behavioral psychotherapy, MMPI-2, MMSE-2, psychopathology

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Authors: Xiaogang Li, Jieqiong Miao

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As for the problem of the grey forecasting model prediction accuracy is low, an improved grey prediction model is put forward. Firstly, use trigonometric function transform the original data sequence in order to improve the smoothness of data , this model called SGM( smoothness of grey prediction model), then combine the improved grey model with support vector machine , and put forward the grey support vector machine model (SGM - SVM).Before the establishment of the model, we use trigonometric functions and accumulation generation operation preprocessing data in order to enhance the smoothness of the data and weaken the randomness of the data, then use support vector machine (SVM) to establish a prediction model for pre-processed data and select model parameters using genetic algorithms to obtain the optimum value of the global search. Finally, restore data through the "regressive generate" operation to get forecasting data. In order to prove that the SGM-SVM model is superior to other models, we select the battery life data from calce. The presented model is used to predict life of battery and the predicted result was compared with that of grey model and support vector machines．For a more intuitive comparison of the three models, this paper presents root mean square error of this three different models .The results show that the effect of grey support vector machine (SGM-SVM) to predict life is optimal, and the root mean square error is only 3.18%. Keywords: grey forecasting model, trigonometric function, support vector machine, genetic algorithms, root mean square error

Keywords: Grey prediction model, trigonometric functions, support vector machines, genetic algorithms, root mean square error

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Authors: Ngonidzashe Mangoma, Caroline Marigold Sebata

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The release of cyanide-rich effluents from gold mines, and other industries, into the environment, is a global concern considering the well-known metabolic effects of cyanide in all forms of life. Such effluents need to be treated to remove cyanide, among other pollutants, before their disposal. This study aimed at investigating the possible use of bacteria in the biological removal of cyanide from cyanide-rich effluents. Firstly, cyanide-degrading bacteria were isolated from gold mine effluents and characterised. The isolates were then tested for their ability to grow in the presence of cyanide and their tolerance to increasing levels of the compound. To evaluate each isolate’s cyanide-degrading activities, isolates were grown in the simulated and actual effluent, and a titrimetric method was used to quantify residual cyanide over a number of days. Cyanide degradation efficiency (DE) was then calculated for each isolate. Identification of positive isolates involved 16S rRNA gene amplification and sequence analysis through BLAST. Six cyanide-utilising bacterial strains were isolated. Two of the isolates were identified as Klebsiella spp. while the other two were shown to be different strains of Clostridium bifermentans. All isolates showed normal growth in the presence of cyanide, with growth being inhibited at 700 mg/L cyanide and beyond. Cyanide degradation efficiency for all isolates in the simulated effluent ranged from 79% to 97%. All isolates were able to remove cyanide from actual gold mine effluent with very high DE values (90 – 94%) being recorded. Isolates obtained in this study were able to efficiently remove cyanide from both simulated and actual effluent. This observation clearly demonstrates the feasibility of the biological removal of cyanide from cyanide-rich gold mine effluents and should, therefore, motivate research towards the possible large-scale application of this technology.

Keywords: cyanide effluent, bioremediation, Clostridium bifermentans, Klebsiella spp, environment

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Authors: Vijaykumar M. Baragi, Ramtilak Gattu, Gabriela Trifan, John L. Woodard, K. Meyers, Tim S. Halstead, Eric Hipple, Ewart Mark Haacke, Randall R. Benson

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NFL players, by virtue of their exposure to repetitive head injury, are at least twice as likely to develop Alzheimer's disease (AD) and dementia as the general population. Early recognition and intervention prior to onset of clinical symptoms could potentially avert/delay the long-term consequences of these diseases. Since AD is thought to have a long preclinical incubation period, the aim of the current research was to determine whether former NFL players, referred to a depression center, showed evidence of incipient dementia in their structural imaging prior to diagnosis of dementia. Thus, to identify neuroimaging markers of AD, against which former NFL players would be compared, we conducted a comprehensive volumetric analysis using a cohort of early stage AD patients (ADNI) to produce a set of brain regions demonstrating sensitivity to early AD pathology (i.e., the “AD fingerprint”). A cohort of 46 former NFL players’ brain MRIs were then interrogated using the AD fingerprint. Brain scans were done using a T1-weighted MPRAGE sequence. The Free Surfer image analysis suite (version 6.0) was used to obtain the volumetric and cortical thickness data. A total of 55 brain regions demonstrated significant atrophy or ex vacuo dilatation bilaterally in AD patients vs. healthy controls. Of the 46 former NFL players, 19 (41%) demonstrated a greater than expected number of atrophied/dilated AD regions when compared with age-matched controls, presumably reflecting AD pathology.

Keywords: alzheimers, neuroimaging biomarkers, traumatic brain injury, free surfer, ADNI

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Authors: Boroka Gács, Tibor Szolcsányi, Árpad Csathó

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Background: Individuals frequently show habituation to repeated noxious heat. However, given the defensive function of human pain processing, it is reasonable to assume that individuals imagine that they would become increasingly sensitive to repeated thermal pain stimuli. To the best of the authors' knowledge, no previous studies have, however, been addressed to this assumption. Therefore, in the current study, we investigated how healthy human individuals imagine the intensity of repeated thermal pain stimulations, and compared this with the intensity ratings given after physically induced thermal pain trials. Methods: Healthy participants (N = 20) gave pain intensity ratings in two conditions: imagined and real thermal pain. In the real pain condition thermal pain stimuli of two intensities (minimal and moderate pain) were delivered in four consecutive trials. The duration of the peak temperature was 20s, and stimulation was always delivered to the same location. In each trial, participants rated the pain intensity twice, 5s and 15s after the onset of the peak temperature. In the imagined pain condition, participants were subjected to a reference pain stimulus and then asked to imagine and rate the same sequence of stimulations as in the induced pain condition. Results: Ratings of imagined pain and physically induced pain followed opposite courses over repeated stimulation: Ratings of imagined pain indicated sensitization whereas ratings for physically induced pain indicated habituation. The findings were similar for minimal and moderate pain intensities. Conclusions: The findings suggest that, rather than habituating to pain, healthy individuals imagine that they would become increasingly sensitive to repeated thermal pain stimuli.

Keywords: habituation, imagined pain, pain perception, thermal stimulation

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Authors: Giorgio Visentin, Alexei A. Buchachenko

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Recent proposals to use Yb dimer as an optical clock and as a sensor for non-Newtonian gravity imply the knowledge of its interaction potential. Here, the ground-state Born-Oppenheimer Yb₂ potential energy curve is represented by a semi-analytical function, consisting of short- and long-range contributions. For the former, the systematic ab initio all-electron exact 2-component scalar-relativistic CCSD(T) calculations are carried out. Special care is taken to saturate diffuse basis set component with the atom- and bond-centered primitives and reach the complete basis set limit through n = D, T, Q sequence of the correlation-consistent polarized n-zeta basis sets. Similar approaches are used to the long-range dipole and quadrupole dispersion terms by implementing the CCSD(3) polarization propagator method for dynamic polarizabilities. Dispersion coefficients are then computed through Casimir-Polder integration. The semiclassical constraint on the number of the bound vibrational levels known for the ¹⁷⁴Yb isotope is used to scale the potential function. The scaling, based on the most accurate ab initio results, bounds the interaction energy of two Yb atoms within the narrow 734 ± 4 cm⁻¹ range, in reasonable agreement with the previous ab initio-based estimations. The resulting potentials can be used as the reference for more sophisticated models that go beyond the Born-Oppenheimer approximation and provide the means of their uncertainty estimations. The work is supported by Russian Science Foundation grant # 17-13-01466.

Keywords: ab initio coupled cluster methods, interaction potential, semi-analytical function, ytterbium dimer

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Authors: Suruchi Shukla, Shantanu Prakash, Amita Jain

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Introduction: Arboviral diseases are one of the most common causes of viral hemorrhagic fever (VHF). Of which, Dengue and Chikungunya pose a significant health problem in India. Arbovirus has a tendency to cross the territories and emerge in the new region. Considering the above issues, in the current study active surveillance was conducted among viral hemorrhagic fever (VHF) cases reported from Uttar Pradesh (UP), India. We studied the arboviral etiology of VHF; mainly Dengue, Chikungunya, and ZIKA. Methods: Clinical samples of 465 suspected VHF cases referred to tertiary care referral center of UP, India were enrolled in the study during a period from 15th May 2016 to 9th March 2018. Serum specimens were collected and analyzed for the presence of Dengue, Chikungunya, and ZIKA either by serology and/or by molecular assays. Results: Of all tested, 165 (35.4%) cases were positive for either Dengue or Chikungunya. Dengue (21.2%) was found to be the most prevalent, followed by Chikungunya, (6.6%). None of the cases tested positive for ZIKA virus. Serum samples of 35 (7.5%) cases were positive for both Dengue and Chikungunya. DEN-2 serotype was the most predominant serotype. Phylogenetic and sequence analysis of DEN-2 strains showed 100% clustering with the Cosmopolitan genotype strain. Bleeding from several sites, jaundice, abdominal pain, arthralgia, haemoconcentration, and thrombocytopenia were significantly higher in dengue hemorrhagic cases. However, the rash was significantly more common in Chikungunya patients. Most of the Dengue and Chikungunya positive cases (Age group 6-40 years) were seen in post monsoon season (September to November). Conclusion: Only one-third of total VHF cases are positive for either Dengue/Chikungunya or both. This necessitates the screening of other etiologies capable of causing hemorrhagic manifestations.

Keywords: viral hemorrhagic fever, dengue, chikungunya, zika, India

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Authors: Mourad Bédir, Sami Khomsi, Hakim Gabtni, Hajer Azaiez, Ramzi Gharsalli, Riadh Chebbi

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Eastern Tunisia is a semi-arid area; located in the northern Africa plate; southern Mediterranean side. It is facing water scarcity, overexploitation, and decreasing of water quality of phreatic water table. Water supply and storage will not respond to the demographic and economic growth and demand. In addition, only 5 109 m3 of rainwater from 35 109 m3 per year renewable rain water supply can be retained and remobilized. To remediate this water deficiency, researches had been focused to near new subsurface deep aquifers resources. Among them, Upper Miocene sandstone deposits of Béglia, Saouaf, and Somaa Formations. These sandstones are known for their proven Hydrogeologic and hydrocarbon reservoir characteristics in the Tunisian margin. They represent semi-confined to confined aquifers. This work is based on new integrated approaches of seismic stratigraphy, seismic tectonics, and hydrogeology, to highlight and characterize these reservoirs levels for aquifer exploitation in semi-arid area. As a result, five to six third order sequence deposits had been highlighted. They are composed of multi-layered extended sandstones reservoirs; separated by shales packages. These reservoir deposits represent lowstand and highstand system tracts of these sequences, which represent lowstand and highstand system tracts of these sequences. They constitute important strategic water resources volumes for the region.

Keywords: Tunisia, Hydrogeology, sandstones, basin, seismic, aquifers, modeling

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Authors: Hu Ding, Kai Liu, Guoan Tang

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The Chinese Loess Plateau suffers from serious gully erosion induced by natural and human causes. Gully features detection including gully-affected area and its two dimension parameters (length, width, area et al.), is a significant task not only for researchers but also for policy-makers. This study aims at gully-affected area detection in three catchments of Chinese Loess Plateau, which were selected in Changwu, Ansai, and Suide by using unmanned aerial vehicle (UAV). The methodology includes a sequence of UAV data generation, image segmentation, feature calculation and selection, and random forest classification. Two experiments were conducted to investigate the influences of segmentation strategy and feature selection. Results showed that vertical and horizontal root-mean-square errors were below 0.5 and 0.2 m, respectively, which were ideal for the Loess Plateau region. The segmentation strategy adopted in this paper, which considers the topographic information, and optimal parameter combination can improve the segmentation results. Besides, the overall extraction accuracy in Changwu, Ansai, and Suide achieved was 84.62%, 86.46%, and 93.06%, respectively, which indicated that the proposed method for detecting gully-affected area is more objective and effective than traditional methods. This study demonstrated that UAV can bridge the gap between field measurement and satellite-based remote sensing, obtaining a balance in resolution and efficiency for catchment-scale gully erosion research.

Keywords: unmanned aerial vehicle (UAV), object-analysis image analysis, gully erosion, gully-affected area, Loess Plateau, random forest

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Authors: Abdul Muqsit Abbasi, Ibrahim Chhipa, Asad Anwer, Saad Farooq, Hassan Berry, Sonu Kumar, Sundar Ali, Muhammad Owais Mahmood, Areeb Ur Rehman, Bahram Baloch

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Accurate translation between structurally diverse languages, such as Arabic and English, presents a critical challenge in natural language processing due to significant linguistic and cultural differences. This paper investigates the effectiveness of Facebook’s mBART model, fine-tuned specifically for sequence-tosequence (seq2seq) translation tasks between Arabic and English, and enhanced through advanced refinement techniques. Our approach leverages the Alef Dataset, a meticulously curated parallel corpus spanning various domains to capture the linguistic richness, nuances, and contextual accuracy essential for high-quality translation. We further refine the model’s output using advanced language models such as GPT-3.5 and GPT-4, which improve fluency, coherence, and correct grammatical errors in translated texts. The fine-tuned model demonstrates substantial improvements, achieving a BLEU score of 38.97, METEOR score of 58.11, and TER score of 56.33, surpassing widely used systems such as Google Translate. These results underscore the potential of mBART, combined with refinement strategies, to bridge the translation gap between Arabic and English, providing a reliable, context-aware machine translation solution that is robust across diverse linguistic contexts.

Keywords: natural language processing, machine translation, fine-tuning, Arabic-English translation, transformer models, seq2seq translation, translation evaluation metrics, cross-linguistic communication

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Authors: D. Shehu, Z. Alias

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Glutathione S-transferases (GSTs) are family of enzymes that function in the detoxification of variety of electrophilic substrates. In the present work, we report a novel zeta-like GST (designated as KKSG9) from the biphenyl/polychlorobiphenyl degrading organism Acidovorax sp. KKS102. KKSG9 possessed low sequence similarity but similar biochemical properties to zeta class GSTs. The gene for KKSG9 was cloned, purified and biochemically characterized. Functional analysis showed that the enzyme exhibits wider substrate specificity compared to most zeta class GSTs by reacting with 1-chloro-2,4-dinitrobenzene (CDNB), p-nitrobenzyl chloride (NBC), ethacrynic acid (EA), hydrogen peroxide, and cumene hydroperoxide (CuOOH). The enzyme also displayed dehalogenation function against dichloroacetate (a common substrate for zeta class GSTs) in addition to permethrin, and dieldrin. The functional role of Tyr12 was also investigated by site-directed mutagenesis. The mutant (Y12C) displayed low catalytic activity and dehalogenation function against all the substrates when compared with the wild type. Kinetic analysis using NBC and GSH as substrates showed that the mutant (Y12C) displayed a higher affinity for NBC when compared with the wild type, however, no significant change in GSH affinity was observed. These findings suggest that the presence of tyrosine residue in the motif might represent an evolutionary trend toward improving the catalytic activity of the enzyme. The enzyme as well could be useful in the bioremediation of various types of organochlorine pollutants.

Keywords: Acidovorax sp. KKS102, bioremediation, glutathione s-transferase, site-directed mutagenesis, zeta

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Authors: Amita Jain, Shantanu Prakash, Suruchi Shukla

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Introduction: Acute encephalitis syndrome (AES) is a complex multi etiology syndrome posing a great public health problem in the northern part of India. Japanese encephalitis (JE) virus is an established etiology of AES in this region. Recently, Scrub typhus (ST) is being recognized as an emerging aetiology of AES in JE endemic belt. This study was conducted to establish the direct evidence of Central nervous system invasion by Orientia tsutsugamushi leading to AES. Methodology: A total of 849 cases with clinical diagnosis of AES were enrolled from six districts (Deoria and its adjoining area) of the traditional north Indian Japanese encephalitis (JE) belt. Serum and Cerebrospinal fluid samples were collected and tested for major agent causing acute encephalitis. AES cases either positive for anti-ST IgM antibodies or negative for all tested etiologies were investigated for ST-DNA by real-time PCR. Results: Of these 505 cases, 250 patients were laboratory confirmed for O. tsutsugamushi infection either by anti-ST IgM antibodies positivity (n=206) on serum sample or by ST-DNA detection by real-time PCR assay on CSF sample (n=2) or by both (n=42).Total 29 isolate could be sequenced for 56KDa gene. Conclusion: All the strains were found to cluster with Gilliam strains. The majority of the isolates showed a 97–99% sequence similarity with Thailand and Cambodian strains. Gilliam strain of O.tsusugamushi is an emerging as one of the major aetiologies leading to AES in northern part of India.

Keywords: acute encephalitis syndrome, O. tsutsugamushi, Gilliam strain, North India, cerebrospinal fluid

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Authors: Keiko Naito, Y. Nakashima, S. Yamauchi, Y. Kunitani, Y. Ishigami, K. Numata, M. Mizobe, Y. Homma, J. Takahashi, T. Inoue, T. Shiga, H. Funakoshi

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Background: A presence of severe acidemia, defined as pH < 7.2, is common during endotracheal intubation for critically ill patients in the emergency department (ED). Severe acidemia is widely recognized as a predisposing factor for intubation failure. However, it is unclear that acidemic condition itself actually makes endotracheal intubation more difficult. We aimed to evaluate if a presence of severe acidemia before intubation is associated with the lower first attempt intubation success rate in the ED. Methods: This is a retrospective observational cohort study in the ED of an urban hospital in Japan. The collected data included patient demographics, such as age, sex, and body mass index, presence of one or more factors of modified LEMON criteria for predicting difficult intubation, reasons for intubation, blood gas levels, airway equipment, intubation by emergency physician or not, and the use of the rapid sequence intubation technique. Those with any of the following were excluded from the analysis: (1) no blood gas drawn before intubation, (2) cardiopulmonary arrest, and (3) under 18 years of age. The primary outcome was the first attempt intubation success rates between a severe acidemic patients (SA) group and a non-severe acidemic patients (NA) group. Logistic regression analysis was used to test the first attempt success rates for intubations between those two groups. Results: Over 5 years, a total of 486 intubations were performed; 105 in the SA group and 381 in the NA group. The univariate analysis showed that the first attempt intubation success rate was lower in the SA group than in the NA group (71.4% vs 83.5%, p < 0.01). The multivariate logistic regression analysis identified that severe acidemia was significantly associated with the first attempt intubation failure (OR 1.9, 95% CI 1.03-3.68, p = 0.04). Conclusions: A presence of severe acidemia before endotracheal intubation lowers the first attempt intubation success rate in the ED.

Keywords: acidemia, airway management, endotracheal intubation, first-attempt intubation success rate

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Authors: Indu Bhushan Sharma, Rashmi Saraswat

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The thermotolerant, solvent stable and alkalophilic lipase producing bacterial strain was isolated from the water sample of the foothills of Trikuta Mountain in Kakryal (Reasi district) in Jammu and Kashmir, India. The lipase-producing microorganisms were screened using tributyrin agar plates. The selected microbe was optimized for maximum lipase production by subjecting to various carbon and nitrogen sources, incubation period and inoculum size. The selected strain was identified as Bacillus subtilis strain kakrayal_1 (BSK_1) using 16S rRNA sequence analysis. Effect of pH, temperature, metal ions, detergents and organic solvents were studied on lipase activity. Lipase was found to be stable over a pH range of 6.0 to 9.0 and exhibited maximum activity at pH 8. Lipolytic activity was highest at 37°C and the enzyme activity remained at 60°C for 24hrs, hence, established as thermo-tolerant. Production of lipase was significantly induced by vegetable oil and the best nitrogen source was found to be peptone. The isolated Bacillus lipase was stimulated by pre-treatment with Mn2+, Ca2+, K+, Zn2+, and Fe2+. Lipase was stable in detergents such as triton X 100, tween 20 and Tween 80. The 100% ethyl acetate enhanced lipase activity whereas, lipase activity were found to be stable in Hexane. The optimization resulted in 4 fold increase in lipase production. Bacillus lipases are ‘generally recognized as safe’ (GRAS) and are industrially interesting. The inducible alkaline, thermo-tolerant lipase exhibited the ability to be stable in detergents and organic solvents. This could be further researched as a potential biocatalyst for industrial applications such as biotransformation, detergent formulation, bioremediation and organic synthesis.

Keywords: bacillus, lipase, thermotolerant, alkalophilic

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Authors: Shweta Singh, Sudaman Katti

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The most well-known sequence models make use of complex recurrent neural networks in an encoder-decoder configuration. The model used in this research makes use of a transformer, which is based purely on a self-attention mechanism, without relying on recurrence at all. More specifically, encoders and decoders which make use of self-attention and operate based on a memory, are used. In this research work, results for various 3D visual and non-visual reinforcement learning tasks designed in Unity software were obtained. Convolutional neural networks, more specifically, nature CNN architecture, are used for input processing in visual tasks, and comparison with standard long short-term memory (LSTM) architecture is performed for both visual tasks based on CNNs and non-visual tasks based on coordinate inputs. This research work combines the transformer architecture with the proximal policy optimization technique used popularly in reinforcement learning for stability and better policy updates while training, especially for continuous action spaces, which are used in this research work. Certain tasks in this paper are long horizon tasks that carry on for a longer duration and require extensive use of memory-based functionalities like storage of experiences and choosing appropriate actions based on recall. The transformer, which makes use of memory and self-attention mechanism in an encoder-decoder configuration proved to have better performance when compared to LSTM in terms of exploration and rewards achieved. Such memory based architectures can be used extensively in the field of cognitive robotics and reinforcement learning.

Keywords: convolutional neural networks, reinforcement learning, self-attention, transformers, unity

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Authors: O. H. Gebril, N. A. Meguid

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Background: Iron had been a focus of interest recently as a main exaggerating factor for oxidative stresses in the central nervous system and a link to various neurological disorders is suspected. Many studies with various techniques showed evidence of disturbed iron-related proteins in the cell in human and animal models of neurodegenerative disorders. Also, linkage to significant pathological changes had been evidenced e.g. apoptosis and cell signaling. On the other hand, the role of iron in neurodevelopmental disorders is still unclear. With increasing prevalence of autism worldwide, some changes in iron parameters and its stores were documented in many studies. This study includes Haemochromatosis HFE gene polymorphisms (p.H63D and p.C282Y) and ferroportin gene (SLC40A1) Q248H polymorphism in autism and control children. Materials and Methods: Whole genome DNA was extracted; p.H63D and p.C282Y genotyping was studied using specific sequence amplification followed by restriction enzyme digestion on a sample of autism patients (25 cases) and twenty controls. Results: The p.H63D is seen more than the C282Y among both autism and control samples, with no significant association of p.H63D or p.C282Y polymorphism and autism was revealed. Also, no association with Q248H polymorphism was evidenced. Conclusion: The study results do not prove the role of cellular iron genes polymorphisms as risk factors for neurodevelopmental disorders, and in turn highlights the specificity of cellular iron related pathways in neurodegeneration. These results demand further gene expression studies to elucidate the main pathophysiological pathways that are disturbed in autism and other neurodevelopmental disorders.

Keywords: iron, neurodevelopmental, oxidative stress, haemohromatosis, ferroportin, genes

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Authors: Maxime Merheb, Rachel Matar

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Retrieving ancient DNA sequences which in return permit the entire genome sequencing from fossils have extraordinarily improved in recent years, thanks to sequencing technology and other methodological advances. In any case, the quest to search for ancient DNA is still obstructed by the damage inflicted on DNA which accumulates after the death of a living organism. We can characterize this damage into three main categories: (i) Physical abnormalities such as strand breaks which lead to the presence of short DNA fragments. (ii) Modified bases (mainly cytosine deamination) which cause errors in the sequence due to an incorporation of a false nucleotide during DNA amplification. (iii) DNA modifications referred to as blocking lesions, will halt the PCR extension which in return will also affect the amplification and sequencing process. We can clearly see that the issues arising from breakage and coding errors were significantly decreased in recent years. Fast sequencing of short DNA fragments was empowered by platforms for high-throughput sequencing, most of the coding errors were uncovered to be the consequences of cytosine deamination which can be easily removed from the DNA using enzymatic treatment. The methodology to repair DNA sequences is still in development, it can be basically explained by the process of reintroducing cytosine rather than uracil. This technique is thus restricted to amplified DNA molecules. To eliminate any type of damage (particularly those that block PCR) is a process still pending the complete repair methodologies; DNA detection right after extraction is highly needed. Before using any resources into extensive, unreasonable and uncertain repair techniques, it is vital to distinguish between two possible hypotheses; (i) DNA is none existent to be amplified to begin with therefore completely un-repairable, (ii) the DNA is refractory to PCR and it is worth to be repaired and amplified. Hence, it is extremely important to develop a non-enzymatic technique to detect the most degraded DNA.

Keywords: ancient DNA, DNA barcodong, enzymatic repair, PCR

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Authors: Wan Liu, Haibo Wang, Cathy Huang, Zhiwu Tan, Zhiwei Chen

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The tremendous diversity of HIV-1 has been a major challenge for an effective AIDS vaccine development. Mosaic approach presents the potential for vaccine design aiming for global protection. The mosaic antigen of HIV-1 Gag allows antigenic breadth for vaccine-elicited immune response against a wider spectrum of viral strains. However, the enhancement of immune response using vaccines is dependent on the strategy used. Heterologous prime/boost regimen has been shown to elicit high levels of immune responses. Here, we investigated whether priming using plasmid DNA with electroporation followed by boosting with the live replication-competent modified vaccinia virus vector TianTan (MVTT) combined with the mosaic antigenic sequence could elicit a greater and broader antigen-specific response against HIV-1 Gag in mice. When compared to DNA or MVTT alone, or MVTT/MVTT group, DNA/MVTT group resulted in coincidentally high frequencies of broadly reactive, Gag-specific, polyfunctional, long-lived, and cytotoxic CD8+ T cells and increased anti-Gag antibody titer. Meanwhile, the vaccination could upregulate PD-1+, and Tim-3+ CD8+ T cell, myeloid-derived suppressive cells and Treg cells to balance the stronger immune response induced. Importantly, the prime/boost vaccination could help control the EcoHIV and mesothelioma AB1-gag challenge. The stronger protective Gag-specific immunity induced by a Mosaic DNA/MVTT vaccine corroborate the promise of the mosaic approach, and the potential of two acceptably safe vectors to enhance anti-HIV immunity and cancer prevention.

Keywords: DNA/MVTT vaccine, EcoHIV, mosaic antigen, mesothelioma AB1-gag

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Authors: Muna Khushaim

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Aluminum-based alloys play a key role in modern engineering, especially in the aerospace industry. Introduction of solute atoms such as Li and Cu is the main approach to improve the strength in age-hardenable Al alloys via the precipitation hardening phenomenon. Knowledge of the decomposition process of the microstructure during the precipitation reaction is particularly important for future technical developments. The objective of this study is to investigate the nano-scale chemical composition in the Al-Cu, Al-Li and Al-Li-Cu during the early stage of the precipitation sequence and to describe whether this compositional difference correlates with variations in the observed precipitation kinetics. Comparing the random binomial frequency distribution and the experimental frequency distribution of concentrations in atom probe tomography data was used to investigate the early stage of decomposition in the different binary and ternary alloys which were experienced different heat treatments. The results show that an Al-1.7 at.% Cu alloy requires a long ageing time of approximately 8 h at 160 °C to allow the diffusion of Cu atoms into Al matrix. For the Al-8.2 at.% Li alloy, a combination of both the natural ageing condition (48 h at room temperature) and a short artificial ageing condition (5 min at 160 °C) induces increasing on the number density of the Li clusters and hence increase number of precipitated δ' particles. Applying this combination of natural ageing and short artificial ageing conditions onto the ternary Al-4 at.% Li-1.7 at.% Cu alloy induces the formation of a Cu-rich phase. Increasing the Li content in the ternary alloy up to 8 at.% and increasing the ageing time to 30 min resulted in the precipitation processes ending with δ' particles. Thus, the results contribute to the understanding of Al-alloy design.

Keywords: aluminum alloy, atom probe tomography, early stage, decomposition

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Authors: Patompong Satapornpong, Therdpong Tempark, Pawinee Rerknimitr, Jettanong Klaewsongkram, Chonlaphat Sukasem

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Dapsone (4, 4’-diaminodiphenyl sulfone, DDS) is broadly used for the treatment of inflammatory diseases and infections such as; leprosy, Pneumocystis jiroveci pneumonia in patients with HIV infection, neutrophilic dermatoses, dermatitis herpetiformis and autoimmune bullous disease. The severe cutaneous adverse drug reactions (SCARs) including, Stevens-Johnson syndrome (SJS), toxic epidermal necrolysis (TEN) and drug reaction with eosinophilia and systemic symptoms (DRESS) are rare but severe life-threatening adverse drug reactions. Dapsone is one of many culprit drugs induced SJS, TEN and DRESS. Notwithstanding, to our knowledge, there are no studies of the association of HLA class I alleles and dapsone-induced SCARs in non-leprosy Thai patients. This investigation was a prospective cohort study, which performed in a total of 45 non-leprosy patients. Fifteen patients of dapsone-induced SCARs were classified as following the RegiSCAR criteria, and 30 dapsone-tolerant controls were exposed to dapsone more than 6 months without any evidence of cutaneous reactions. The genotyping of HLA-A, -B and –C were performed using sequence-specific oligonucleotides (PCR-SSOs). The Ethics Committee of Ramathibodi hospital, Mahidol University, approved this study. Among all HLA class I alleles, HLA-A*24:07, HLA-B*13:01, HLA-B*15:02, HLA-C*03:04 and HLA-C*03:09 were significantly associated with dapsone-induced SCARs (OR = 10.55, 95% CI = 1.06 – 105.04, p = 0.0360; OR = 56.00, 95% CI = 8.27 – 379.22, p = 0.0001; OR = 7.00, 95% CI = 1.17 – 42.00, p = 0.0322; OR = 6.00, 95% CI = 1.24 – 29.07, p = 0.0425 and OR = 17.08, 95% CI = 0.82 – 355.45, p = 0.0321, respectively). Furthermore, HLA-B*13:01 allele had strong association with dapsone-induced SJS-TEN and DRESS when compared with dapsone-tolerant controls (OR = 42.00, 95% CI = 2.88 – 612.31, p = 0.0064 and OR = 63.00, 95% CI = 7.72 – 513.94 and p = 0.0001, respectively). Consequently, HLA-B*13:01 might serve as a pharmacogenetic marker for screening before initiating the therapy with dapsone for prevention of dapsone-induced SCARs.

Keywords: dapsone-induced SCARs, HLA-B*13:01, HLA class I alleles, severe cutaneous adverse reactions, Thai

Procedia PDF Downloads 233

Authors: Aid Abdelkrim

Abstract:

A method of fatigue damage accumulation based upon application of energy parameters of the fatigue process is proposed in the paper. Using this model is simple, it has no parameter to be determined, it requires only the knowledge of the curve W–N (W: strain energy density N: number of cycles at failure) determined from the experimental Wöhler curve. To examine the performance of nonlinear models proposed in the estimation of fatigue damage and fatigue life of components under random loading, a batch of specimens made of 6082 T 6 aluminium alloy has been studied and some of the results are reported in the present paper. The paper describes an algorithm and suggests a fatigue cumulative damage model, especially when random loading is considered. This work contains the results of uni-axial random load fatigue tests with different mean and amplitude values performed on 6082T6 aluminium alloy specimens. The proposed model has been formulated to take into account the damage evolution at different load levels and it allows the effect of the loading sequence to be included by means of a recurrence formula derived for multilevel loading, considering complex load sequences. It is concluded that a ‘damaged stress interaction damage rule’ proposed here allows a better fatigue damage prediction than the widely used Palmgren–Miner rule, and a formula derived in random fatigue could be used to predict the fatigue damage and fatigue lifetime very easily. The results obtained by the model are compared with the experimental results and those calculated by the most fatigue damage model used in fatigue (Miner’s model). The comparison shows that the proposed model, presents a good estimation of the experimental results. Moreover, the error is minimized in comparison to the Miner’s model.

Keywords: damage accumulation, energy model, damage indicator, variable loading, random loading

Procedia PDF Downloads 396

Authors: S. Khakurel, R. P. Dhakal, T. Z. Yeow

Abstract:

Downtime is one of the major sources (alongside damage and injury/death) of financial loss incurred by a structure in an earthquake. The length of downtime associated with a building after an earthquake varies depending on the time taken for the reaction (to the earthquake), decision (on the future course of action) and execution (of the decided course of action) phases. Post-earthquake assessment of buildings is a key step in the decision making process to decide the appropriate safety placarding as well as to decide whether a damaged building is to be repaired or demolished. The aim of the present study is to develop a model to quantify downtime associated with the post-earthquake building-assessment phase in terms of two parameters; i) duration of the different assessment phase; and ii) probability of different colour tagging. Post-earthquake assessment of buildings includes three stages; Level 1 Rapid Assessment including a fast external inspection shortly after the earthquake, Level 2 Rapid Assessment including a visit inside the building and Detailed Engineering Evaluation (if needed). In this study, the durations of all three assessment phases are first estimated from the total number of damaged buildings, total number of available engineers and the average time needed for assessing each building. Then, probability of different tag colours is computed from the 2010-11 Canterbury earthquake Sequence database. Finally, a downtime model for the post-earthquake building inspection phase is proposed based on the estimated phase length and probability of tag colours. This model is expected to be used for rapid estimation of seismic downtime within the Loss Optimisation Seismic Design (LOSD) framework.

Keywords: assessment, downtime, LOSD, Loss Optimisation Seismic Design, phase length, tag color

Procedia PDF Downloads 183

Authors: Manendra Singh Parihar, Sandip Ghosh Chowdhury

Abstract:

Austenitic stainless steels are widely used and give a good combination of properties. When this steel is plastically deformed, a phase transformation of the metastable Face Centred Cubic Austenite to the stable Body Centred Cubic (α’) or to the Hexagonal close packed (ԑ) martensite may occur, leading to the enhancement in the mechanical properties like strength. The work was based on variant selection and corresponding texture analysis for the strain induced martensitic transformation during deformation of the parent austenite FCC phase to form the product HCP and the BCC martensite phases separately, obeying their respective orientation relationships. The automated method for reconstruction of the parent phase orientation using the EBSD data of the product phase orientation is done using the MATLAB and TSL-OIM software. The method of triplets was used which involves the formation of a triplet of neighboring product grains having a common variant and linking them using a misorientation-based criterion. This led to the proper reconstruction of the pre-transformation phase orientation data and thus to its micro structure and texture. The computational speed of current method is better compared to the previously used methods of reconstruction. The reconstruction of austenite from ԑ and α’ martensite was carried out for multiple samples and their IPF images, pole figures, inverse pole figures and ODFs were compared. Similar type of results was observed for all samples. The comparison gives the idea for estimating the correct sequence of the transformation i.e. γ → ε → α’ or γ → α’, during deformation of AISI 304 austenitic stainless steel.

Keywords: variant selection, reconstruction, EBSD, austenitic stainless steel, martensitic transformation

Procedia PDF Downloads 489

Authors: Tiantian Li, Lusheng Wang, Zhaohui Zhan, Daming Zhu

Abstract:

In this paper, we propose two string problems, and study algorithms and complexity of various versions for those problems. Let S = {s₁, s₂, . . . , sₘ} be a set of m strings. A common substring of S is a substring appearing in every string in S. Given a set of m strings S = {s₁, s₂, . . . , sₘ} and a positive integer k, we want to find a set C of k common substrings of S such that the k common substrings in C appear in the same order and have no overlap among the m input strings in S, and the total length of the k common substring in C is maximized. This problem is referred to as the longest total length of k common substrings from m input strings (LCSS(k, m) for short). The other problem we study here is called the longest total length of a set of common substrings with length more than l from m input string (LSCSS(l, m) for short). Given a set of m strings S = {s₁, s₂, . . . , sₘ} and a positive integer l, for LSCSS(l, m), we want to find a set of common substrings of S, each is of length more than l, such that the total length of all the common substrings is maximized. We show that both problems are NP-hard when k and m are variables. We propose dynamic programming algorithms with time complexity O(k n₁n₂) and O(n₁n₂) to solve LCSS(k, 2) and LSCSS(l, 2), respectively, where n1 and n₂ are the lengths of the two input strings. We then design an algorithm for LSCSS(l, m) when every length > l common substring appears once in each of the m − 1 input strings. The running time is O(n₁²m), where n1 is the length of the input string with no restriction on length > l common substrings. Finally, we propose a fixed parameter algorithm for LSCSS(l, m), where each length > l common substring appears m − 1 + c times among the m − 1 input strings (other than s1). In other words, each length > l common substring may repeatedly appear at most c times among the m − 1 input strings {s₂, s₃, . . . , sₘ}. The running time of the proposed algorithm is O((n12ᶜ)²m), where n₁ is the input string with no restriction on repeats. The LSCSS(l, m) is proposed to handle whole chromosome sequence alignment for different strains of the same species, where more than 98% of letters in core regions are identical.

Keywords: dynamic programming, algorithm, common substrings, string

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Authors: Narjes Ebrahimi, Soheila Alyasin, Navid Nezafat, Hossein Esmailzadeh, Younes Ghasemi, Seyed Hesamodin Nabavizadeh

Abstract:

Immunotherapy with allergy vaccines is of great importance in allergen-specific immunotherapy. In recent years, B-cell epitope-based vaccines have attracted considerable attention and the prediction of epitopes is crucial to design these types of allergy vaccines. B-cell epitopes might be linear or conformational. The prerequisite for the identification of conformational epitopes is the information about allergens' tertiary structures. Bioinformatics approaches have paved the way towards the design of epitope-based allergy vaccines through the prediction of tertiary structures and epitopes. Mite allergens are one of the major allergy contributors. Several mite allergens can elicit allergic reactions; however, their structures and epitopes are not well established. So, B-cell epitopes of various groups of mite allergens (24 allergens in 6 allergen groups) were predicted in the present work. Tertiary structures of 17 allergens with unknown structure were predicted and refined with RaptorX and GalaxyRefine servers, respectively. The predicted structures were further evaluated by Rampage, ProSA-web, ERRAT and Verify 3D servers. Linear and conformational B-cell epitopes were identified with Ellipro, Bcepred, and DiscoTope 2 servers. To improve the accuracy level, consensus epitopes were selected. Fifty-four conformational and 133 linear consensus epitopes were predicted. Furthermore, overlapping epitopes in each allergen group were defined, following the sequence alignment of the allergens in each group. The predicted epitopes were also compared with the experimentally identified epitopes. The presented results provide valuable information for further studies about allergy vaccine design.

Keywords: B-cell epitope, Immunotherapy, In silico prediction, Mite allergens, Tertiary structure

Procedia PDF Downloads 160

Authors: Sumeeta Khurana, Kirti Megha, Amit Gupta, Rakesh Sehgal

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Background: Amoebic keratitis is a painful vision threatening infection caused by a free living pathogenic amoeba Acanthamoeba. It can be misdiagnosed and very difficult to treat if not suspected early. The epidemiology of Acanthamoeba genotypes causing infection in our geographical area is not yet known to the best of our knowledge. Objective: To characterize Acanthamoeba isolates from amoebic keratitis patients. Methods: A total of 19 isolates obtained from patients with amoebic keratitis presenting to the Advanced Eye Centre at Postgraduate Institute of Medical Education and Research, a tertiary care centre of North India over a period of last 10 years were included. Their corneal scrapings, lens solution and lens case (in case of lens wearer) were collected for microscopic examination, culture and molecular diagnosis. All the isolates were maintained in the Non Nutrient agar culture medium overlaid with E.coli and 13 strains were axenised and maintained in modified Peptone Yeast Dextrose Agar. Identification of Acanthamoeba genotypes was based on amplification of diagnostic fragment 3 (DF3) region of the 18srRNA gene followed by sequencing. Nucleotide similarity search was performed by BLAST search of sequenced amplicons in GenBank database (http//www.ncbi.nlm.nih.gov/blast). Multiple Sequence alignments were determined by using CLUSTAL X. Results: Nine out of 19 Acanthamoeba isolates were found to belong to Genotype T4 followed by 6 isolates of genotype T11, 3 T5 and 1 T3 genotype. Conclusion: T4 is the predominant Acanthamoeba genotype in our geographical area. Further studies should focus on differences in pathogenicity of these genotypes and their clinical significance.

Keywords: Acanthamoeba, free living amoeba, keratitis, genotype, ocular

Procedia PDF Downloads 237

Authors: Lee Ping Ang, Salvatore Tomasello, Jun Wen, Marc S. Appelhans

Abstract:

With about 225 species, Zanthoxylum L. is the second most species rich genus in Rutaceae. It is the only genus with a pantropical distribution. Economically, it is used in several Asian countries as traditional medicine and spice. In the past Zanthoxylum was divided into two genera, the temperate Zanthoxylum sensu strictu (s.s.) and the (sub)tropical Fagara, due to the large differences in flower morphology: heterochlamydeous in Fagara and homochlamydeous in Zanthoxylum s.s.. This genus is much under studied and previous phylogenetic studies using Sanger sequencing did not resolve the relationships sufficiently. In this study, we use Hybrid Capture with a specially designed bait set for Zanthoxylum to sequence 347 putatively single-copy genes. The taxon sampling has been largely improved as compared to previous studies and the preliminary results will be based on 371 specimens representing 133 species from all continents and major island groups. Our preliminary results reveal similar tree topology as the previous studies while providing more details to the backbone of the phylogeny. The phylogenetic tree consists of four main clades: A) African/Malagasy clade, B) Z. asiaticum clade - a clade consisting widespread species occurring in (sub)tropical Asia and Africa as well as Madagascar, C) Asian/Pacific clade and D) American clade, which also includes the temperate Asian species. The merging of Fagara and Zanthoxylum is supported by our results and the homochlamydeous flowers of Zanthoxylum s.s. are likely derived from heterochlamydeous flowers. Several of the morphologically defined sections within Zanthoxylum are not monophyletic. The study dissemination will (1) introduce the framework of this project; (2) present preliminary results and (3) the ongoing progress of the study.

Keywords: Zanthoxylum, phylogenomic, hybrid capture, pantropical

Procedia PDF Downloads 72

Authors: Letizia Maria Drammis, Maria Antonella Brandimonte

Abstract:

The idea that people use space representations to think about time and number received support from several lines of research. However, how these representations develop in children and then shape space-time and space-number mappings is still a debated issue. In the present study, 40 children (20 pre-schoolers and 20 elementary-school children) performed 4 main tasks, which required the use of more concrete (non-symbolic) or more abstract (symbolic) space-time and space-number associations. In the non-symbolic conditions, children were required to order pictures of everyday-life events occurring in a specific temporal order (Temporal sequences) and of quantities varying in numerosity (Numerical sequences). In the symbolic conditions, they were asked to perform the typical time-to-position and number-to-position tasks by mapping time-related words and numbers onto lines. Results showed that children performed reliably better in the non-symbolic Time conditions than the symbolic Time conditions, independently of age, whereas only pre-schoolers performed worse in the Number-to-position task (symbolic) as compared to the Numerical sequence (non-symbolic) task. In addition, only older children mapped time-related words onto space following the typical left-right orientation, pre-schoolers’ performance being somewhat mixed. In contrast, mapping numbers onto space showed a clear left-right orientation, independently of age. Overall, these results indicate a cross-domain difference in the way younger and older children process time and number, with time-related tasks being more difficult than number-related tasks only when space-time tasks require symbolic representations.

Keywords: space-time associations, space-number associations, orientation, children

Procedia PDF Downloads 336

Authors: Hojjat Mohammadi, Randall Divito, Gary J. E. Kramer

Abstract:

Tunnelling and pipe jacking in very soft soils (fat clays), even with an Earth Pressure Balance tunnel boring machine (EPBM), can cause large ground displacements. In this study, the short-term and long-term ground and tunnel response is predicted for twin, pipe-jacked EPBM 3 meter diameter tunnels with a narrow pillar width. Initial modelling indicated complete closure of the annulus gap at the tail shield onto the centrifugally cast, glass-fiber-reinforced, polymer mortar jacking pipe (FRP). Numerical modelling was employed to simulate the excavation and support installation sequence, examine the ground response during excavation, confirm the adequacy of the pillar width and check the structural adequacy of the installed pipe. In the numerical models, Mohr-Coulomb constitutive model with the effect of unloading was adopted for the fat clays, while for the bedrock layer, the generalized Hoek-Brown was employed. The numerical models considered explicit excavation sequences and different levels of ground convergence prior to support installation. The well-studied excavation sequences made the analysis possible for this study on a very soft clay, otherwise, obtaining the convergency in the numerical analysis would be impossible. The predicted results indicate that the ground displacements around the tunnel and its effect on the pipe would be acceptable despite predictions of large zones of plastic behaviour around the tunnels and within the entire pillar between them due to excavation-induced ground movements.

Keywords: finite element modeling (FEM), pipe-jacked tunneling, very soft clay, EPBM

Procedia PDF Downloads 82