Search results for: temporal sequences

Authors: Alireza Mirrashid, Mohammad Khoshbin, Ali Atghaei, Hassan Shahbazi

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In various industries, smoke and fire are two of the most important threats in the workplace. One of the common methods for detecting smoke and fire is the use of infrared thermal and smoke sensors, which cannot be used in outdoor applications. Therefore, the use of vision-based methods seems necessary. The problem of smoke and fire detection is spatiotemporal and requires spatiotemporal solutions. This paper presents a method that uses spatial features along with temporal-based features to detect smoke and fire in the scene. It consists of three main parts; the task of each part is to reduce the error of the previous part so that the final model has a robust performance. This method also uses transformer modules to increase the accuracy of the model. The results of our model show the proper performance of the proposed approach in solving the problem of smoke and fire detection and can be used to increase workplace safety.

Keywords: attention, fire detection, smoke detection, spatio-temporal

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Authors: T. Pedersen, A. Lindfeldt

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The minimum dwell time is an important part of railway timetable planning. Due to its stochastic behaviour, the minimum dwell time should be considered to create resilient timetables. While there has been significant focus on how to determine and estimate dwell times, to our knowledge, little research has been carried out regarding temporal and running direction variations of these. In this paper, we examine how the minimum dwell time varies depending on temporal factors such as the time of day, day of the week and time of the year. We also examine how it is affected by running direction and station type. The minimum dwell time is estimated by means of track occupation data. A method is proposed to ensure that only minimum dwell times and not planned dwell times are acquired from the track occupation data. The results show that on an aggregated level, the average minimum dwell times in both running directions at a station are similar. However, when temporal factors are considered, there are significant variations. The minimum dwell time varies throughout the day with peak hours having the longest dwell times. It is also found that the minimum dwell times are influenced by weekday, and in particular, weekends are found to have lower minimum dwell times than most other days. The findings show that there is a potential to significantly improve timetable planning by taking minimum dwell time variations into account.

Keywords: minimum dwell time, operations quality, timetable planning, track occupation data

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Authors: Khaled A. Abdel-Sater

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There are four areas of the temporal lobe. Primary auditory area (areas 41 and 42); it is for the perception of auditory impulse, auditory association area (area 22, 21, and 20): Areas 21 and 20 are for understanding and interpretation of auditory sensation, recognition of language, and long-term memories. Area 22, also called Wernicke’s area, and a sensory speech centre. It is for interpretation of auditory and visual information, formation of thoughts in the mind, and choice of words to be used. Ideas and thoughts originate in it. The limbic system is a part of cortical and subcortical structure forming a ring around the brainstem. Cortical structures are the orbitofrontal area, subcallosal gyrus, cingulate gyrus, parahippocampal gyrus, and uncus. Subcortical structures are the hypothalamus, hippocampus, amygdala, septum, paraolfactory area, anterior nucleus of the thalamus portions of the basal ganglia. There are several physiological functions of the limbic system, including regulation of behavior, motivation, and emotion.

Keywords: limbic system, motivation, emotions, temporal lobe

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Authors: Adam Rosiński

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This paper discusses an experiment conducted with two groups of participants, composed of musicians and non-musicians, in order to investigate the impact of the speed of a sound sequence and the order of sounds on the grouping of sounds into sequences of six tones. Significant differences were observed between musicians and non-musicians with respect to the threshold sequence speed at which the sequence was split into two streams. The differences in the results for the two groups suggest that the musical education of the participating listeners may be a vital factor. The criterion of musical education should be taken into account during experiments so that the results obtained are reliable, uniform, and free from interpretive errors.

Keywords: auditory scene analysis, education, hearing, psychoacoustics

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Authors: Dongwon Lee, Sunmyeng Kim

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Underwater acoustic networks (UANs) have become a very active research area in recent years. Compared with wireless networks, UANs are characterized by the limited bandwidth, long propagation delay and high channel dynamic in acoustic modems, which pose challenges to the design of medium access control (MAC) protocol. The characteristics severely affect network performance. In this paper, we study a MS-MAC (Multi-Sender MAC) protocol in order to improve network performance. The proposed protocol exploits temporal reuse by learning the propagation delays to neighboring nodes. A source node locally calculates the transmission schedules of its neighboring nodes and itself based on the propagation delays to avoid collisions. Performance evaluation is conducted using simulation, and confirms that the proposed protocol significantly outperforms the previous protocol in terms of throughput.

Keywords: acoustic channel, MAC, temporal reuse, UAN

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Authors: T. Padma, Jayashree S. Pillai

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Random entities are an essential component in any cryptographic application. The suitability of a number theory based novel pseudorandom sequence called Pseudorandom Partial Quotient Sequence (PPQS) generated from the continued fraction expansion of irrational numbers, in cryptographic applications, is analyzed in this paper. An approach to build the algorithm around a hard mathematical problem has been considered. The PQ sequence is tested for randomness and its suitability as a cryptographic key by performing randomness analysis, key sensitivity and key space analysis, precision analysis and evaluating the correlation properties is established.

Keywords: pseudorandom sequences, key sensitivity, correlation, security analysis, randomness analysis, sensitivity analysis

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Authors: H. Ali, A. Whitehead

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Providing a panoramic view of famous landmarks around the world offers artistic and historic value for historians, tourists, and researchers. Exploring the history of famous landmarks by presenting a comprehensive view of a temporal panorama merged with geographical and historical information presents a unique challenge of dealing with images that span a long period, from the 1800’s up to the present. This work presents the concept of temporal panorama through a timeline display of aligned historic and modern images for many famous landmarks. Utilization of this panorama requires a collection of hundreds of thousands of landmark images from the Internet comprised of historic images and modern images of the digital age. These images have to be classified for subset selection to keep the more suitable images that chronologically document a landmark’s history. Processing of historic images captured using older analog technology under various different capturing conditions represents a big challenge when they have to be used with modern digital images. Successful processing of historic images to prepare them for next steps of temporal panorama creation represents an active contribution in cultural heritage preservation through the fulfillment of one of UNESCO goals in preservation and displaying famous worldwide landmarks.

Keywords: cultural heritage, image registration, image subset selection, registered image similarity, temporal panorama, timescapes

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Authors: Jung Ho Yang, Yong Soo Kim

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Electrical units are operated by electrical and electronic components. An environmental test sequence is useful for testing electrical units to reduce reliability issues. This study introduces test sequence guidelines based on relevant principles and considerations for electronic testing according to international standard IEC-60068-1 and the United States military standard MIL-STD-810G. Then, test sequences were proposed based on the descriptions for each test. Finally, General Motors (GM) specification GMW3172 was interpreted and compared to IEC-60068-1 and MIL-STD-810G.

Keywords: reliability, environmental test sequence, electrical units, IEC 60068-1, MIL-STD-810G

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Authors: Arianne Van Der Wal, Femke Van Horen, Amir Grinstein

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Consumers in today’s world are confronted with the alarming consequences of unsustainable behavior such as pollution and resource degradation. In addition, they are facing an increase in uncertainty due to, for instance, economic instability and terror attacks. Although these two problems are central to consumers’ lives, occur on a global scale, and have significant impact on the world’s political, economic, environmental, and social landscapes, they have not been systematically studied in tandem before. Contributing to research on persuasion and pro-social behavior, this paper shows in five studies (three experimental studies and one field study) that the two problems are intertwined. We demonstrate that uncertainty leads to lower sustainable behavior in comparison to certainty (Studies 1 and 2) and that this is due to consumers displaying higher levels of temporal discounting (i.e., adopting a more immediate orientation; Study 2). Finally, providing valuable implications for policy makers and responsible marketers, we show that emphasizing the immediate benefits of sustainable behavior during uncertainty buffers the negative effect (Studies 3 and 4).

Keywords: sustainable behavior, uncertainty, temporal discounting, framing

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Authors: Kalyan S. Ghosh, B. L. Dhananjaya

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Snake bite causes fatal injuries in multi-organs and even many deaths due to several adverse physiological effects of various phospholipases (PLA2s) present in snake venom. Though these PLA2s bear highly homologues sequences and also structure but exhibit a different extent of those pharmacological effects. In this study, we have explored the difference in the neurotoxicity of two PLA2 namely PLA2-V, PLA2-VIIIa present in the venom from Vipera russellii. Bioinformatics studies on sequences of these two proteins along with detailed structural comparison enable us to explore the differences unambiguously. The identification of the residues involved in neurotoxicity will further lead towards proper designing of inhibitors against such killing effects of the venom.

Keywords: electrostatic potential, homology modeling, hydrophobicity, neurotoxicity, Phospholipase A2

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Authors: Khen Cohen, Daniel Yankelevich, David Mendlovic, Dan Raviv

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We present a 3D stereo system for high-resolution sensing in both the spatial and the temporal domains by combining a frame-based camera and an event-based camera. We establish a method to merge both devices into one unite system and introduce a calibration process, followed by a correspondence technique and interpolation algorithm for 3D reconstruction. We further provide quantitative analysis about our system in terms of depth resolution and additional parameter analysis. We show experimentally how our system performs temporal super-resolution up to effectively 1ms and can detect fast-moving objects and human micro-movements that can be used for micro-expression analysis. We also demonstrate how our method can extract colored events for an event-based camera without any degradation in the spatial resolution, compared to a colored filter array.

Keywords: DVS-CIS stereo vision, micro-movements, temporal super-resolution, 3D reconstruction

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Authors: JingWei Yu, Hong Yang Yu

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At present, the increasingly serious air pollution in various cities of China has made people pay more attention to the air quality index(hereinafter referred to as AQI) of their living areas. To face this situation, it is of great significance to predict air pollution in heavily polluted areas. In this paper, based on the time series model of LSTM, a spatiotemporal prediction model of PM2.5 concentration in Mianyang, Sichuan Province, is established. The model fully considers the temporal variability and spatial distribution characteristics of PM2.5 concentration. The spatial correlation of air quality at different locations is based on the Air quality status of other nearby monitoring stations, including AQI and meteorological data to predict the air quality of a monitoring station. The experimental results show that the method has good prediction accuracy that the fitting degree with the actual measured data reaches more than 0.7, which can be applied to the modeling and prediction of the spatial and temporal distribution of regional PM2.5 concentration.

Keywords: LSTM, PM2.5, neural networks, spatio-temporal prediction

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Authors: Shahrzad Mohammadi, Ghasem Boshrouei Sharq

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All seismic design codes are based on the determination of the design earthquake without taking into account the effects of aftershocks in the design practice. In regions with a high level of seismicity, the occurrence of several aftershocks of various magnitudes and different time lags is very likely. This research aims to estimate the collapse capacity of a 10-story steel bundled tube moment frame subjected to as-recorded seismic sequences. The studied structure is designed according to the seismic regulations of the fourth revision of the Iranian code of practice for the seismic-resistant design of buildings (Code No.2800). A series of incremental dynamic analyses (IDA) is performed up to the collapse level of the intact structure. Then, in order to demonstrate the effects of aftershock events on the collapse vulnerability of the building, aftershock IDA analyzes are carried out. To gain deeper insight, collapse fragility curves are developed and compared for both series. Also, a study on the influence of various ground motion characteristics on collapse capacity is carried out. The results highlight the importance of considering the decisive effects of aftershocks in seismic codes due to their contribution to the occurrence of collapse.

Keywords: IDA, aftershock, bundled tube frame, fragility assessment, GM characteristics, as-recorded seismic sequences

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Authors: Balaji Ganesh Rajagopal, Subramanian Appavu alias Balamurugan, Ayyalraj Midhun Kumar, Krishnan Nallaperumal

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Intelligent Transportation System is an Emerging area to solve multiple transportation problems. Several forms of inputs are needed in order to solve ITS problems. Advanced Traveler Information System (ATIS) is a core and important ITS area of this modern era. This involves travel time forecasting, efficient road map analysis and cost based path selection, Detection of the vehicle in the dynamic conditions and Traffic congestion state forecasting. This Article designs and provides an algorithm for traffic data generation which can be used for the above said ATIS application. By inputting the real world traffic situation in the form of video sequences, the algorithm determines the Traffic density in terms of congestion, number of vehicles in a given path which can be fed for various ATIS applications. The Algorithm deduces the key frame from the video sequences and follows the Blob detection, Identification and Tracking using connected components algorithm to determine the correlation between the vehicles moving in the real road scene.

Keywords: traffic transportation, traffic density estimation, blob identification and tracking, relative velocity of vehicles, correlation between vehicles

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Authors: Kumar Y., Suman D., Sumathi

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Introduction: Burns to the face account for between one-fourth and one-third of all burns. The loss of an eyebrow due to a burn or infection can have negative physical and psychological consequences for patients because eyebrows have a critical functional and aesthetic role on the face. Plastic surgeons face unique challenges in reconstructing eyebrows due to their complex anatomy and variations within genders. As a general rule, there are three techniques for reconstructing the eyebrow: superficial temporal artery island flap, a composite graft from the scalp, and mini or micro follicular grafts from the scalp. In situations where a sufficient amount of subcutaneous tissue is not available and the defect is big such as the case of burns, flaps like the superficial temporal artery scalp flap remain reliable options. In 2018, a 17-year-old female patient presented to the department of Burns Plastic and reconstructive Surgery of Guru Teg Bahadur Hospital, Delhi, India. A scald-burn injury to the face occurred two years before admission, resulting in bilateral eyebrow loss. We reconstructed the bilateral eyebrows using bilateral scalp island flaps based on the posterior branch of the superficial temporal artery. The reconstructed eyebrows successfully assumed a desirable shape and exhibited a natural appearance, which was consistent with preoperative expectations and the patient stated that she was more comfortable with her social relationships. Among the current treatment procedures, the superficial temporal artery island flap continues to be a versatile option for reconstructing the eyebrows after alopecia, especially in cases of burns. Results: During the 30 days follow-up period, the scalp island flap remained vascularised with normal hair growth, without complications. The reconstructed eyebrows successfully assumed a desirable shape and exhibited a natural appearance; the patient stated that she was more comfortable with her social relationships. Conclusion: In this case report, we demonstrated how scalp island flaps pedicled by the superficial temporal artery could be performed very safely and reliably to create new eyebrows.

Keywords: alopecia, burns, eyebrow, flap, superficial temporal artery

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Authors: Asher John Mohan, Krishna K. L.

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Objectives: (1) To assess the extent of memory impairment induced by Phenytoin (PHT) at normal and reduced dose on temporal lobe epileptic mice. (2) To evaluate the protective effect of Levetiracetam (LEV) on aggravation of memory impairment in temporal lobe epileptic mice by PHT. Materials and Methods: Albino mice of either sex (n=36) were used for the study for a period of 64 days. Convulsions were induced by intraperitoneal administration of pilocarpine 280 mg/kg on every 6th day. Radial arm maze (RAM) was employed to evaluate the memory impairment activity on every 7th day. The anticonvulsant and memory impairment activity were assessed in PHT normal and reduced doses both alone and in combination with LEV. RAM error scores and convulsive scores were the parameters considered for this study. Brain acetylcholine esterase and glutamate were determined along with histopathological studies of frontal cortex. Results: Administration of PHT for 64 days on mice has shown aggravation of memory impairment activity on temporal lobe epileptic mice. Although the reduction in PHT dose was found to decrease the degree of memory impairment the same decreased the anticonvulsant potency. The combination with LEV not only brought about the correction of impaired memory but also replaced the loss of potency due to the reduction of the dose of the antiepileptic drug employed. These findings were confirmed with enzyme and neurotransmitter levels in addition to histopathological studies. Conclusion: This study thus builds a foundation in combining a nootropic anticonvulsant with an antiepileptic drug to curb the adverse effect of memory impairment associated with temporal lobe epilepsy. However further extensive research is a must for the practical incorporation of this approach into disease therapy.

Keywords: anti-epileptic drug, Phenytoin, memory impairment, Pilocarpine

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Authors: Yijun Lai, Saber Khederzadeh, Lingshaung Han

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Species in Thunnus are organized due to the similarity between them. The closeness between T. maccoyii, T. thynnus, T. Tonggol, T. atlanticus, T. albacares, T. obsesus, T. alalunga, and T. orientails are in different degrees. However, the genetic pattern of differentiation has not been presented based on individuals yet, to the author’s best knowledge. Hence, we aimed to analyze the difference in individuals level of tuna species to identify the factors that contribute to the maternal lineage variety using Cytochrome c oxidase subunit I (COXI) gene sequences. Our analyses provided evidence of sharing lineages in the Thunnus. A phylogenetic analysis revealed that these lineages are basal to the other sequences. We also showed a close connection between the T. tonggol, T. thynnus, and T. albacares populations. Also, the majority of the T. orientalis samples were clustered with the T. alalunga and, then, T. atlanticus populations. Phylogenetic trees and migration modeling revealed high proximity of T. thynnus sequences to a few T. orientalis and suggested possible gene flow with T. tonggol and T. albacares lineages, while all T. obsesus samples indicated unique clustering with each other. Our results support the presence of old maternal lineages in Thunnus, as a legacy of an ancient wave of colonization or migration.

Keywords: Thunnus Tuna, phylogeny, maternal lineage, COXI gene

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Authors: Mahdy Elhusseiny, Richard Gearhart, Mariam Alyammahi

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In this study we analyse the impact of a number of major macroeconomic variables on industry-specific excess rates of return. In later specifications, we include time and recession fixed effects, to potentially capture time-specific trends that may have been changing over our panel. We have a number of results that bear mentioning. Seasonal and temporal factors found to have very large role in sector-specific excess returns. Increases in M1(money supply) decreases bank, insurance, real estate, and telecommunications, while increases industrial and transportation excess returns. The results indicate that the market return increases every sector-specific rate of return. The 2007 to 2009 recession significantly reduced excess returns in the bank, real estate, and transportation sectors.

Keywords: macroeconomic factors, industry returns, fixed effects, temporal factors

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Authors: Nkwanyang L. Takem, Christopher M. Agyingi

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Background and aim: An integrated interpretation of wireline logs and lithology of two selected wells (KF-1 and KF-2) of Kribi oil field within the southeastern offshore Douala/Kribi Campo Basin was carried out for sequence stratigraphic analysis of sediments penetrated by the wells. Methods: The stratigraphic units within the wells were subdivided into depositional sequences using characteristic well log patterns that were deposited between Tertiary Miocene to lower Cretaceous. Results: Nine (9) and eight (8) depositional sequences were identified respectively for KF-1 and KF-2. The sequences comprise LST (progradational packages), TSTs (retrogradational packages) and HSTs (aggradational packages), which reflect depositional systems deposited during different phases of base-level changes. The (LST) consists of Basin Floor Fans (BFF), Slope Fans and Channel Sands deposited when sea level was low and accommodation space lower than rate of sediment influx. TST consists of retrogradational marine shales deposited during high relative sea levels and when accommodation space was higher than rate of sediment influx. HST consisted of shoreface sands displaying mostly aggradational to progradational stacking patterns. Conclusion: The rapid facies changes between successive systems tracts provide potential stratigraphic traps. Reservoir stratification and continuity vary greatly between systems tracts and this enhanced development of stratigraphic traps in the area. Basin floor fans comprise sandstone of good reservoir quality, thus huge accumulation of HC can be trapped in this reservoirs.

Keywords: Douala-Kribi-Campo Basin, reservoirs, sequence strastigraphyy, system tracks

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Authors: A. T. Kuda, J. J. Dayya, A. Jimoh

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This paper investigates the fault detection and Isolation technique of measurement data sets from a three tank system using analytical model-based temporal redundancy which is based on residual generation using parity equations/space approach. It further briefly outlines other approaches of model-based residual generation. The basic idea of parity space residual generation in temporal redundancy is dynamic relationship between sensor outputs and actuator inputs (input-output model). These residuals where then used to detect whether or not the system is faulty and indicate the location of the fault when it is faulty. The method obtains good results by detecting and isolating faults from the considered data sets measurements generated from the system.

Keywords: fault detection, fault isolation, disturbing influences, system failure, parity equation/relation, structured parity equations

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Authors: Tyler Gill, Sophia Daniels

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The paper examines how accessing the spatial-temporal constrains of data will help inform policymakers and law enforcement officials. The authors utilize Chicago crime data from 2006-2016 to demonstrate how the Emerging Hot Spot Tool is an ideal hot spot clustering approach to analyze crime data. Traditional approaches include density maps or creating a spatial weights matrix to include the spatial-temporal constrains. This new approach utilizes a space-time implementation of the Getis-Ord Gi* statistic to visualize the data more quickly to make better decisions. The research will help complement socio-cultural research to find key patterns to help frame future policies and evaluate the implementation of prior strategies. Through this analysis, homicide trends and patterns are found more effectively and recommendations for use by non-traditional users of GIS are offered for real life implementation.

Keywords: crime mapping, emerging hot spot analysis, Getis-Ord Gi*, spatial-temporal analysis

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Authors: Simone Jane Dennis

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This paper leverages the spatial and temporal investigative strategy utilized by crime scene investigators – blood spatter work– to engage with the real and metaphorical memorialization of blood-soaked places. It uses this key trope with phenomenological sensibility, to trace the physical and temporal movement of blood outbound from the human body to sites beyond. Working backward, as crime scene investigators do, this paper traces the importance of both space and time and their confluence, to developing a comprehensive theory of violence. To do this work, the paper engages a range of geo-violent scales, from murder scenes to genocides, to both engage an extraordinarily replete literature of bloodshed across history and to move beyond analyses of how significance is assigned to the sites in which blood comes to rest to instead consider the importance of space and time to the structure of violence itself. It is in this regard that the kind of investigative work upon which blood spatter analysis depends is crucial: it engages time and space in reverse to understand the microscopic relations between bodies, places, and numerous (biological, clock, and seasonal) temporalities. Considering the circumstances under which blood escaped a body, the details of its destination in place, and the temporal circumstances of corporal departure, is crucial to making new knowledge about the peculiar temporality and spatiality of violence itself.

Keywords: blood, crime scenes, temporality, violence

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Authors: Yi-Lin Chen, Sheng-Jou Hung, Tsunglin Liu

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Adaptive immune system recognizes a wide range of antigens via expressing a large number of structurally distinct T cell and B cell receptor genes. The distinct receptor genes arise from complex rearrangements called V(D)J recombination, and constitute the immune repertoire. A common method of profiling immune repertoire is via amplifying recombined receptor genes using multiple primers and high-throughput sequencing. This multiplex-PCR approach is efficient; however, the resulting repertoire can be distorted because of primer bias. To eliminate primer bias, 5’ RACE is an alternative amplification approach. However, the application of RACE approach is limited by its low efficiency (i.e., the majority of data are non-regular receptor sequences, e.g., containing intronic segments) and lack of the convenient tool for analysis. We propose a computational tool that can correctly identify non-regular receptor sequences in RACE data via aligning receptor sequences against the whole gene instead of only the exon regions as done in all other tools. Using our tool, the remaining regular data allow for an accurate profiling of immune repertoire. In addition, a RACE approach is improved to yield a higher fraction of regular T-cell receptor sequences. Finally, we quantify the degree of primer bias of a multiplex-PCR approach via comparing it to the RACE approach. The results reveal significant differences in frequency of VJ combination by the two approaches. Together, we provide a new experimental and computation pipeline for an unbiased profiling of immune repertoire. As immune repertoire profiling has many applications, e.g., tracing bacterial and viral infection, detection of T cell lymphoma and minimal residual disease, monitoring cancer immunotherapy, etc., our work should benefit scientists who are interested in the applications.

Keywords: immune repertoire, T-cell receptor, 5' RACE, high-throughput sequencing, sequence alignment

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Authors: Victor Prevost, Solene Landerneau, Michel Duhamel, Joel Sternheimer, Olivier Gallet, Pedro Ferrandiz, Marwa Mokni

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The search for homologous proteins is one of the ongoing challenges in biology and bioinformatics. Traditionally, a pair of proteins is thought to be homologous when they originate from the same ancestral protein. In such a case, their sequences share similarities, and advanced scientific research effort is spent to investigate this question. On this basis, we propose the Protein-Wave Alignment Tool (”P-WAT”) developed within the framework of the France Relance 2030 plan. Our work takes into consideration the mass-related wave aspect of protein biosynthesis, by associating specific frequencies to each amino acid according to its mass. Amino acids are then regrouped within their mass category. This way, our algorithm produces specific alignments in addition to those obtained with a common amino acid coding system. For this purpose, we develop the ”P-WAT” original algorithm, able to address large protein databases, with different attributes such as species, protein names, etc. that allow us to align user’s requests with a set of specific protein sequences. The primary intent of this algorithm is to achieve efficient alignments, in this specific conceptual frame, by minimizing execution costs and information loss. Our algorithm identifies sequence similarities by searching for matches of sub-sequences of different sizes, referred to as primers. Our algorithm relies on Boolean operations upon a dot plot matrix to identify primer amino acids common to both proteins which are likely to be part of a significant alignment of peptides. From those primers, dynamic programming-like traceback operations generate alignments and alignment scores based on an adjusted PAM250 matrix.

Keywords: protein, alignment, homologous, Genodic

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Authors: Hamidreza Saberkari, Mousa Shamsi, Hossein Ahmadi, Saeed Vaali, , MohammadHossein Sedaaghi

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In the recent years, using signal processing tools for accurate identification of the protein coding regions has become a challenge in bioinformatics. Most of the genomic signal processing methods is based on the period-3 characteristics of the nucleoids in DNA strands and consequently, spectral analysis is applied to the numerical sequences of DNA to find the location of periodical components. In this paper, a novel ensemble algorithm for gene selection in DNA sequences has been presented which is based on the combination of Goertzel algorithm and anti-notch filter (ANF). The proposed algorithm has many advantages when compared to other conventional methods. Firstly, it leads to identify the coding protein regions more accurate due to using the Goertzel algorithm which is tuned at the desired frequency. Secondly, faster detection time is achieved. The proposed algorithm is applied on several genes, including genes available in databases BG570 and HMR195 and their results are compared to other methods based on the nucleotide level evaluation criteria. Implementation results show the excellent performance of the proposed algorithm in identifying protein coding regions, specifically in identification of small-scale gene areas.

Keywords: protein coding regions, period-3, anti-notch filter, Goertzel algorithm

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

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

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

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Authors: Salihah Alghamdi, Surajit Ray

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Space-time data can be observed over irregularly shaped manifolds, which might have complex boundaries or interior gaps. Most of the existing methods do not consider the shape of the data, and as a result, it is difficult to model irregularly shaped data accommodating the complex domain. We used a method that can deal with space-time data that are distributed over non-planner shaped regions. The method is based on partial differential equations and finite element analysis. The model can be estimated using a penalized least squares approach with a regularization term that controls the over-fitting. The model is regularized using two roughness penalties, which consider the spatial and temporal regularities separately. The integrated square of the second derivative of the basis function is used as temporal penalty. While the spatial penalty consists of the integrated square of Laplace operator, which is integrated exclusively over the domain of interest that is determined using finite element technique. In this paper, we applied a spatio-temporal regression model with partial differential equations regularization (ST-PDE) approach to analyze a remote sensing data measuring the greenness of vegetation, measure by an index called enhanced vegetation index (EVI). The EVI data consist of measurements that take values between -1 and 1 reflecting the level of greenness of some region over a period of time. We applied (ST-PDE) approach to irregular shaped region of the EVI data. The approach efficiently accommodates the irregular shaped regions taking into account the complex boundaries rather than smoothing across the boundaries. Furthermore, the approach succeeds in capturing the temporal variation in the data.

Keywords: irregularly shaped domain, partial differential equations, finite element analysis, complex boundray

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Authors: Qurratulain Safdar

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Drought is a temporary aberration in contrast to aridity, as it is a permanent feature of climate. Virtually, it takes place in all types of climatic regions that range from high to low rainfall areas. Due to the wide latitudinal extent of Pakistan, there is seasonal and annual variability in rainfall. The south-central part of the country is arid and hyper-arid. This study focuses on the spatio-temporal analysis of droughts in arid and hyperarid region of Cholistan using the standardized precipitation index (SPI) approach. This study has assessed the extent of recurrences of drought and its temporal vulnerability to drought in Cholistan region. Initially, the paper described the geographic setup of the study area along with a brief description of the drought conditions that prevail in Pakistan. The study also provides a scientific foundation for preparing literature and theoretical framework in-line with the selected parameters and indicators. Data were collected both from primary and secondary data sources. Rainfall and temperature data were obtained from Pakistan Meteorology Department. By applying geostatistical approach, a standardized precipitation index (SPI) was calculated for the study region, and the value of spatio-temporal variability of drought and its severity was explored. As a result, in-depth spatial analysis of drought conditions in Cholistan area was found. Parallel to this, drought-prone areas with seasonal variation were also identified using Kriging spatial interpolation techniques in a GIS environment. The study revealed that there is temporal variation in droughts' occurrences both in time series and SPI values. The paper is finally concluded, and strategic plan was suggested to minimize the impacts of drought.

Keywords: Cholistan desert, climate anomalies, metrological droughts, standardized precipitation index

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Authors: S. M. Kulkarni, D. S. Bormane, S. L. Nalbalwar

Abstract:

The rapid development in the technology have dramatic impact on the medical health care field. Medical data base obtained with latest machines like CT Machine, MRI scanner requires large amount of memory storage and also it requires large bandwidth for transmission of data in telemedicine applications. Thus, there is need for video compression. As the database of medical images contain number of frames (slices), hence while coding of these images there is need of motion estimation. Motion estimation finds out movement of objects in an image sequence and gets motion vectors which represents estimated motion of object in the frame. In order to reduce temporal redundancy between successive frames of video sequence, motion compensation is preformed. In this paper three step search (TSS) block matching algorithm is implemented on different types of video sequences. It is shown that three step search algorithm produces better quality performance and less computational time compared with exhaustive full search algorithm.

Keywords: block matching, exhaustive search motion estimation, three step search, video compression

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Authors: Manju Kanu, Subrata Sinha, Surabhi Johari

Abstract:

Viral proteins of Ebola viruses belong to one of the best studied viruses; however no effective prevention against EBOV has been developed. Epitope-based vaccines provide a new strategy for prophylactic and therapeutic application of pathogen-specific immunity. A critical requirement of this strategy is the identification and selection of T-cell epitopes that act as vaccine targets. This study describes current methodologies for the selection process, with Ebola virus as a model system. Hence great challenge in the field of ebola virus research is to design universal vaccine. A combination of publicly available bioinformatics algorithms and computational tools are used to screen and select antigen sequences as potential T-cell epitopes of supertypes Human Leukocyte Antigen (HLA) alleles. MUSCLE and MOTIF tools were used to find out most conserved peptide sequences of viral proteins. Immunoinformatics tools were used for prediction of immunogenic peptides of viral proteins in zaire strains of Ebola virus. Putative epitopes for viral proteins (VP) were predicted from conserved peptide sequences of VP. Three tools NetCTL 1.2, BIMAS and Syfpeithi were used to predict the Class I putative epitopes while three tools, ProPred, IEDB-SMM-align and NetMHCII 2.2 were used to predict the Class II putative epitopes. B cell epitopes were predicted by BCPREDS 1.0. Immunogenic peptides were identified and selected manually by putative epitopes predicted from online tools individually for both MHC classes. Finally sequences of predicted peptides for both MHC classes were looked for common region which was selected as common immunogenic peptide. The immunogenic peptides were found for viral proteins of Ebola virus: epitopes FLESGAVKY, SSLAKHGEY. These predicted peptides could be promising candidates to be used as target for vaccine design.

Keywords: epitope, b cell, immunogenicity, ebola

Procedia PDF Downloads 315