Search results for: somatic sequence mutations

Authors: Moaawia Abdulgader Gdara

Abstract:

This work presents a study of Carbone dioxide generation and migration in the Bahi sandstone reservoir over the EPSA 120/136 (conc 72). En Naga Sub Basin, Sirte Basin Libya. The Lower Cretaceous Bahi Sandstone is the result of deposition that occurred between the start of the Cretaceous rifting that formed the area's Horsts, Grabens and Cenomanian marine transgression. Bahi sediments were derived mainly from those Nubian sediments exposed on the structurally higher blocks, transported short distances into newly forming depocenters such as the En Naga Sub-basin and were deposited by continental processes over the Sirte Unconformity (pre-Late Cretaceous surface) Bahi Sandstone facies are recognized in the En Naga Sub-basin within different lithofacies distribution over this sub-base. One of the two lithofacies recognized in the Bahi is a very fine to very coarse, subangular to angular, pebbly and occasionally conglomeratic quartz sandstone, which is commonly described as being compacted but friable. This sandstone may contain pyrite and minor kaolinite. This facies was encountered at 11,042 feet in F1-72 well, and at 9,233 feet in L1-72. Good, reservoir quality sandstones are associated with paleotopographic highs within the sub-basin and around its margins where winnowing and/or deflationary processes occurred. The second Bahi Lithofacies is a thinly bedded sequence dominated by shales and siltstones with subordinate sandstones and carbonates. The sandstones become more abundant with depth. This facies was encountered at 12,580 feet in P1 -72 and at 11,850 feet in G1a -72. This argillaceous sequence is likely the Bahi sandstone's lateral facies equivalent deposited in paleotopographic lows, which received finer-grained material. The Bahi sandstones are generally described as a good reservoir rock, which after prolific production tests for the drilled wells makes Bahi sandstones the principal reservoir rocks for CO₂ where large volumes of CO₂ gas have been discovered in the Bahi Formation on and near EPSA 120/136, (conc 72). CO₂ occurs in this area as a result of the igneous activity of the Al Harouge Al Aswad complex. Igneous extrusive have been pierced in the subsurface and are exposed at the surface. Bahi CO₂ prospectivity is thought to be excellent in the central to western areas of EPSA 120/136 (CONC 72) where there are better reservoir quality sandstones associated with Paleostructural highs. Condensate and gas prospectivity increases to the east as the CO₂ productivity decreases with distance away from the Al Haruj Al Aswad igneous complex. To date, it has not been possible to accurately determine the volume of these strategically valuable reserves, although there are positive indications that they are very large. Three main structures (Barrut I, En Naga A and En Naga O) are thought to be prospective for the lower Cretaceous Bahi sandstone development. These leads are the most attractive on EPSA 120/136 for the deep potential.

Keywords: En Naga Sub Basin, Al Harouge Al Aswad's Igneous complex, carbon dioxide generation, migration in the Bahi sandstone reservoir, lower cretaceous Bahi Sandstone

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Authors: Moaawia Abdulgader Gdara

Abstract:

This work presents a study of carbon dioxide generation and migration in the Bahi sandstone reservoir over the EPSA 120/136 (conc 72), En Naga Sub Basin, Sirte Basin, Libya. The Lower Cretaceous Bahi Sandstone is the result of deposition that occurred between the start of the Cretaceous rifting that formed the area's Horsts, Grabens, and Cenomanian marine transgression. Bahi sediments were derived mainly from those Nubian sediments exposed on the structurally higher blocks, transported short distances into newly forming depocenters such as the En Naga Sub-basin, and were deposited by continental processes over the Sirte Unconformity (pre-Late Cretaceous surface). Bahi Sandstone facies are recognized in the En Naga Sub-basin within different lithofacies distributed over this sub-base. One of the two lithofacies recognized in the Bahi is a very fine to very coarse, subangular to angular, pebbly, and occasionally conglomeratic quartz sandstone, which is commonly described as being compacted but friable. This sandstone may contain pyrite, minor kaolinite. This facies was encountered at 11,042 feet in F1-72 well and at 9,233 feet in L1-72. Good, reservoir quality sandstones are associated with paleotopographic highs within the sub-basin and around its margins where winnowing and/or deflationary processes occurred. The second Bahi Lithofacies is a thinly bedded sequence dominated by shales and siltstones with subordinate sandstones and carbonates. The sandstones become more abundant with depth. This facies was encountered at 12,580 feet in P1 -72 and at 11,850 feet in G1a -72. This argillaceous sequence is likely the Bahi sandstone's lateral facies equivalent deposited in paleotopographic lows, which received finer grained material. The Bahi sandstones are generally described as a good reservoir rock, which after prolific production tests for the drilled wells that makes Bahi sandstones the principal reservoir rocks for CO₂ where large volumes of CO₂ gas have been discovered in the Bahi Formation on and near EPSA 120/136, (conc 72). CO₂ occurs in this area as a result of the igneous activity of the Al Harouge Al Aswad complex. Igneous extrusive have been pierced in the subsurface and are exposed at the surface. Bahi CO₂ prospectivity is thought to be excellent in the central to western areas of EPSA 120/136 (CONC 72), where there are better reservoir quality sandstones associated with Paleostructural highs. Condensate and gas prospectivity increases to the east as the CO₂ prospectivity decreases with distance away from the Al Haruj Al Aswad igneous complex. To date, it has not been possible to accurately determine the volume of these strategically valuable reserves, although there are positive indications that they are very large. Three main structures (Barrut I, En Naga A, and En Naga O) are thought to be prospective for the lower Cretaceous Bahi sandstone development. These leads are the most attractive on EPSA 120/136 for the deep potential.

Keywords: En Naga Sub Basin, Al Harouge Al Aswad’s Igneous Complex, carbon dioxide generation and migration in the Bahi sandstone reservoir, lower cretaceous Bahi sandstone

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Authors: E. Koyuncu

Abstract:

The problem of Order Acceptance and Scheduling (OAS) is defined as a joint decision of which orders to accept for processing and how to schedule them. Any linear programming model representing real-world situation involves the parameters defined by the decision maker in an uncertain way or by means of language statement. Fuzzy data can be used to incorporate vagueness in the real-life situation. In this study, a fuzzy mathematical model is proposed for a single machine OAS problem, where the orders are defined by their fuzzy due dates, fuzzy processing times, and fuzzy sequence dependent setup times. The signed distance method, one of the fuzzy ranking methods, is used to handle the fuzzy constraints in the model.

Keywords: fuzzy mathematical programming, fuzzy ranking, order acceptance, single machine scheduling

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Authors: Aouiche Abdelaziz, Soudani Mouhamed Salah, Aouiche El Moundhe

Abstract:

The present paper addresses the utilization of Artificial Neural Networks (ANNs) and Fuzzy Inference Systems (FISs) for the identification and control of dynamical systems with some degree of uncertainty. Because ANNs and FISs have an inherent ability to approximate functions and to adapt to changes in input and parameters, they can be used to control systems too complex for linear controllers. In this work, we show how ANNs and FISs can be put in order to form nets that can learn from external data. In sequence, it is presented structures of inputs that can be used along with ANNs and FISs to model non-linear systems. Four systems were used to test the identification and control of the structures proposed. The results show the ANNs and FISs (Back Propagation Algorithm) used were efficient in modeling and controlling the non-linear plants.

Keywords: non-linear systems, fuzzy set Models, neural network, control law

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Authors: Andrew Shugyo Daijo Bonnici

Abstract:

Core-Self Intelligence (CSI) is an absolutely still, non-verbal, non-cerebral intelligence. Our still core-self intelligence is felt at our body's center point of gravity, just an inch below our navel, deep within our lower abdomen. The still sub-quantum depth of core-Self remains untouched by the conditioning influences of family, society, culture, religion, and spiritual views that shape our personalities and ego-self identities. As core-Self intelligence is inborn and unconditioned, it exists within all human beings regardless of age, race, color, creed, mental acuity, or national origin. Our core-self intelligence functions as a wise and compassionate guide that advances our health and well-being, our mental clarity and emotional resiliency, our fearless peace and behavioral wisdom, and our ever-deepening compassion for self and others. Although our core-Self, with its absolutely still non-judgmental intelligence, operates far beneath the functioning of our ego-self identity and our thinking mind, it effectively coexists with our passing thoughts, all of our figuring and thinking, our logical and rational way of knowing, the ebb and flow of our feelings, and the natural or triggered emergence of our emotions. When we allow our whole inner somatic awareness to gently sink into the intelligent center point of gravity within our lower abdomen, the felt arising of our core- Self’s inborn stillness has a serene and relaxing effect on our ego-self and thinking mind. It naturally slows down the speedy passage of our involuntary thoughts, diminishes our ego-self's defensive and reactive functioning, and decreases narcissistic reflections on I, me, and mine. All of these healthy cognitive benefits advance our innate wisdom and compassion, facilitate our personal and interpersonal growth, and liberate the ever-fresh wonder and curiosity of our beginner's heartmind. In conclusion, by studying, exploring, and researching our core-Self intelligence, psychologists and psychotherapists can unlock new avenues for advancing the farther reaches of our mental, emotional, and spiritual health and well-being, our innate behavioral wisdom and boundless empathy, our lucid compassion for self and others, and our unwavering confidence in the still guiding light of our core-Self that exists at the abdominal center point of all human beings.

Keywords: intelligence, transpersonal, beginner’s heartmind, compassionate wisdom

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Authors: Farideh Halakou, Emel Sen, Attila Gursoy, Ozlem Keskin

Abstract:

Protein–Protein Interactions (PPIs) mediate major biological processes in living cells. The study of PPIs as networks and analyze the network properties contribute to the identification of genes and proteins associated with diseases. In this study, we have created the sub-networks of brain and lung metastasis from primary tumor in breast cancer. To do so, we used seed genes known to cause metastasis, and produced their interactions through a network-topology based prioritization method named GUILDify. In order to have the experimental support for the sub-networks, we further curated them using STRING database. We proceeded by modeling structures for the interactions lacking complex forms in Protein Data Bank (PDB). The functional enrichment analysis shows that KEGG pathways associated with the immune system and infectious diseases, particularly the chemokine signaling pathway, are important for lung metastasis. On the other hand, pathways related to genetic information processing are more involved in brain metastasis. The structural analyses of the sub-networks vividly demonstrated their difference in terms of using specific interfaces in lung and brain metastasis. Furthermore, the topological analysis identified genes such as RPL5, MMP2, CCR5 and DPP4, which are already known to be associated with lung or brain metastasis. Additionally, we found 6 and 9 putative genes that are specific for lung and brain metastasis, respectively. Our analysis suggests that variations in genes and pathways contributing to these different breast metastasis types may arise due to change in tissue microenvironment. To show the benefits of using structural PPI networks instead of traditional node and edge presentation, we inspect two case studies showing the mutual exclusiveness of interactions and effects of mutations on protein conformation which lead to different signaling.

Keywords: breast cancer, metastasis, PPI networks, protein conformational changes

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Authors: Regina Bowler

Abstract:

Rationale & Aims: Complementary interventions such as mindfulness-meditation, gratitude, and self-affirmation are often used by therapists to treat stress. Many studies have been conducted using these interventions either individually or adjunctively with regard to stress. However, there has been little work comparing these interventions to investigate which of them is the most effective in treating stress. This study aims to compare these interventions and to determine which of them has the strongest perceived and physiological impact on stress. Participants: 120 law students preparing to take the bar exam: 3 experimental groups of 30 individuals, 1 control group of 30 individuals. Methods: One day prior to administering the interventions, baseline salivary cortisol samples will be taken, and the participants will complete the perceived stress scale (Cohen et al., 1983). Thirty days prior to the bar exam, each experimental group will be given an intervention to practice. Interventions will be practiced once in the morning after waking and once at night at bedtime. In group one, each participant will do a recorded three-minute mindfulness meditation. In group two, each participant will practice gratitude by writing down three things he/she/they are grateful for. In group three, each participant will practice affirmation by writing three sentences affirming his/her/their core values. The control group will not have an intervention to practice. Starting experimental day 1, upon waking and prior to practicing the intervention, the participants will take a salivary cortisol sample. Then they will practice their given intervention. Every night, before going to bed, the participants will practice their given intervention for a second time. The participants will practice their interventions and take salivary cortisol samples for 28 days. After each seven-day period (days 7, 14, 21, 28), the participants will fill out a brief questionnaire about the effects their intervention has on their stress, daily life, and relationships with themselves and others. On day 29, the participants will take a final salivary cortisol sample and will fill out the Perceived Stress Scale (Cohen et al., 1983). Applications of findings: Findings from this study would inform therapists of best practices when working with clients with stress. Moreover, therapists will gain knowledge of how individuals perceive these interventions and their impact on stress, daily life, somatic symptoms, and relationships with self and others. Thus, therapists will be able to administer these interventions with more precision to the stress-related contexts and issues their clients bring.

Keywords: stress, mindfulness-meditation, gratitude, affirmations, complementary interventions

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Authors: Murat Emre, Zeynep Tufekcioglu

Abstract:

Objective: We describe a patient with late onset phenylketonuria which presented with rapidly progressive dementia and parkinsonism that were reversible after management. Background: Phenylketonuria is an autosomal recessive disorder due to mutations in the phenylalanine hydroxlase gene. It normally presents in childhood, in rare cases, however, it may have its onset in adulthood and may mimic other neurological disorders. Case description: A previously normal functioning, 59 year old man was admitted for blurred vision, cognitive impairment and gait difficulty which emerged over the past eight months. In neurological examination he had brisk reflexes, slow gait and left-dominant parkinsonism. Mini-mental state examination score was 25/30, neuropsychological testing revealed a dysexecutive syndrome with constructional apraxia and simultanagnosia. In cranial MRI there were bilateral diffuse hyper-intense lesions in parietal and occipital white matter with no significant atrophy. Electroencephalography showed diffuse slowing with predominance of teta waves. In cerebrospinal fluid examination protein level was slightly elevated (61mg/dL), oligoclonal bands were negative. Electromyography was normal. Routine laboratory examinations for rapidly progressive dementia and parkinsonism were also normal. Serum amino acid levels were determined to explore metabolic leukodystrophies and phenylalanine level was found to be highly elevated (1075 µmol/L) with normal tyrosine (61,20 µmol/L). His cognitive impairment and parkinsonian symptoms improved following three months of phenylalanine restricted diet. Conclusions: Late onset phenylketonuria is a rare, potentially reversible cause of rapidly progressive parkinsonism with dementia. It should be considered in the differential diagnosis of patients with suspicious features.

Keywords: dementia, neurology, Phenylketonuria, rapidly progressive parkinsonism

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Authors: A. S. Cheliyan, S. K. Bhattacharyya

Abstract:

Dynamic Positioning System (DPS) is employed in marine vessels of the offshore oil and gas industry. It is a computer controlled system to automatically maintain a ship’s position and heading by using its own thrusters. Reliability assessment of the same can be analyzed through conventional fault tree. However, the complex behaviour like sequence failure, redundancy management and priority of failing of events cannot be analyzed by the conventional fault trees. The Dynamic Fault Tree (DFT) addresses these shortcomings of conventional Fault Tree by defining additional gates called dynamic gates. Monte Carlo based simulation approach has been adopted for the dynamic gates. This method of realistic modeling of DPS gives meaningful insight into the system reliability and the ability to improve the same.

Keywords: dynamic positioning system, dynamic fault tree, Monte Carlo simulation, reliability assessment

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Authors: Petr Šimek

Abstract:

This work deals with the problem of synchronization of bus frames during transmission using USB (Universal Serial Bus). The principles for synchronization between USB and the non-deterministic CAN (Controller Area Network) bus will be described here. Furthermore, the work deals with ensuring the time sequence of communication frames when receiving from multiple communication bus channels. The structure of a general object for storing frames from different types of communication buses, such as CAN and LIN (Local Interconnect Network), will be described here. Finally, an evaluation of the communication throughput of bus frames for USB High speed will be performed. The creation of this architecture was based on the analysis of the communication of control units with a large number of communication buses. For the design of the architecture, a test HW with a USB-HS interface was used, which received previously known messages, which were compared with the received result. The result of this investigation is the block architecture of the control program for test HW ensuring correct data transmission via the USB bus.

Keywords: analysis, CAN, interface, LIN, synchronization, USB

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Authors: Jorge Maestre Vidal, Ana Lucila Sandoval Orozco, Luis Javier García Villalba

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With the increase in popularity of mobile devices, new and varied forms of malware have emerged. Consequently, the organizations for cyberdefense have echoed the need to deploy more effective defensive schemes adapted to the challenges posed by these recent monitoring environments. In order to contribute to their development, this paper presents a malware detection strategy for mobile devices based on sequence alignment algorithms. Unlike the previous proposals, only the system calls performed during the startup of applications are studied. In this way, it is possible to efficiently study in depth, the sequences of system calls executed by the applications just downloaded from app stores, and initialize them in a secure and isolated environment. As demonstrated in the performed experimentation, most of the analyzed malicious activities were successfully identified in their boot processes.

Keywords: android, information security, intrusion detection systems, malware, mobile devices

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Authors: David Mafullul, Jiang Lei, Edward Goacher, Jibin Francis

Abstract:

PURPOSE: Timely decompressive surgery for cauda equina syndrome (CES) is dependent on efficient referral pathways for patients presenting at local primary or secondary centres to tertiary spinal centres in the United Kingdom (UK). Identifying modifiable points of delay within this process is important as minimising time between presentation and surgery may improve patient outcomes. This study aims to analyse whether adequacy of referral impacts on time to surgery in CES. MATERIALS AND METHODS: Data from all cases of confirmed CES referred to a single tertiary UK hospital between August 2017 to December 2019, via a suspected CES e-referral pathway, were obtained retrospectively. Referral adequacy was defined by the inclusion of sufficient information to determine the presence or absence of several NICE ‘red flags’. Correlation between referral adequacy and delay from referral-to-surgery was then analysed. RESULTS: In total, 118 confirmed CES cases were included. Adequate documentation for saddle anaesthesia was associated with reduced delays of more than 48 hours from referral-to-surgery [X2(1, N=116)=7.12, p=.024], an effect partly attributable to these referrals being accepted sooner [U=16.5; n1=27, n2=4, p=.029, r=.39]. Other red flags had poor association with delay. Referral adequacy was better for somatic red flags [bilateral sciatica (97.5%); severe or progressive bilateral neurological deficit of the legs (95.8%); saddle anaesthesia (91.5%)] compared to autonomic red flags [loss of anal tone (80.5%); urinary retention (79.7%); faecal incontinence or lost sensation of rectal fullness (57.6%)]. Although referral adequacy for urinary retention was 79.7%, only 47.5% of referrals documented a post-void residual numerical value. CONCLUSIONS: Adequate documentation of saddle anaesthesia in e-referrals is associated with reduced delay-to-surgery for confirmed CES, partly attributable to these referrals being accepted sooner. Other red flags had poor association with delay to surgery. Referral adequacy for autonomic red flags, including documentation for post-void residuals, has significant room for improvement.

Keywords: cauda equina, cauda equina syndrome, neurosurgery, spinal surgery, decompression, delay, referral, referral adequacy

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Authors: Tze Jin Wong, Lee Feng Koo, Pang Hung Yiu

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Lenstra’s attack uses Chinese remainder theorem as a tool and requires a faulty signature to be successful. This paper reports on the security responses of fourth and sixth order Lucas based (LUC_4,6) cryptosystem under the Lenstra’s attack as compared to the other two Lucas based cryptosystems such as LUC and LUC₃ cryptosystems. All the Lucas based cryptosystems were exposed mathematically to the Lenstra’s attack using Chinese Remainder Theorem and Dickson polynomial. Result shows that the possibility for successful Lenstra’s attack is less against LUC_4,6 cryptosystem than LUC₃ and LUC cryptosystems. Current study concludes that LUC_4,6 cryptosystem is more secure than LUC and LUC₃ cryptosystems in sustaining against Lenstra’s attack.

Keywords: Lucas sequence, Dickson polynomial, faulty signature, corresponding signature, congruence

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Authors: A. Hocine, A. Ghouaoula, S. M. Medjdoub, M. Cherifi

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The present paper proposed a meso–macro model describing the mechanical behaviour composite laminates of staking sequence [+θ/-θ]s under tensil loading. The behaviour of a layer is ex-pressed through elasticity coupled to damage. The elastic strain is due to the elasticity of the layer and can be modeled by using the classical laminate theory, and the laminate is considered as an orthotropic material. This means that no coupling effect between strain and curvature is considered. In the present work, the damage is associated to cracking of the matrix and parallel to the fibers and it being taken into account by the changes in the stiffness of the layers. The anisotropic damage is completely described by a single scalar variable and its evolution law is specified from the principle of maximum dissipation. The stress/strain relationship is investigated in plane stress loading.

Keywords: damage, behavior modeling, meso-macro model, composite laminate, membrane loading

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Authors: Khabat Barkhordari

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Hepatitis delta virus (HDV) is a RNA virus that needs the function of hepatitis B virus (HBV) for its propagation and assembly. Infection by HDV can occur spontaneously with HBV infection and cause acute hepatitis or develop as secondary infection in HBV suffering patients. Based on genome sequence analysis, HDV has several genotypes which show broad geographic and diverse clinical features. The aim of current study is determine the molecular epidemiology of hepatitis delta virus genotype in patients with positive HBsAg among different ethnic groups of Iran. This systematic review study reviews the results of different studies which examined 2000 Iranian patients with HBV infection from 2010 to 2015. Among 2000 patients in this study, 16.75 % were containing anti-HDV antibody and HDV RNA was found in just 1.75% cases. All of positive cases also have genotype I.

Keywords: HDV, genotype, epidemiology, distribution

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Authors: Janet Holland

Abstract:

Eye tracking is a great way to triangulate multiple data sources for deeper, more complete knowledge of how instructional materials are really being used and emotional connections made. Using sensor based biometrics provides a detailed local analysis in real time expanding our ability to collect science based data for a more comprehensive level of understanding, not previously possible, for teaching and learning. The knowledge gained will be used to make future improvements to instructional materials, tools, and interactions. The literature has been examined and a preliminary pilot test was implemented to develop a methodology for research in Instructional Design and Technology. Eye tracking now offers the addition of objective metrics obtained from eye tracking and other biometric data collection with analysis for a fresh perspective.

Keywords: area of interest, eye tracking, biometrics, fixation, fixation count, fixation sequence, fixation time, gaze points, heat map, saccades, time to first fixation

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Authors: Irtaza M. Syed, Kaamran Raahemifar

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This paper presents a model predictive control (MPC) of a utility interactive (UI) single phase inverter (SPI) for a photovoltaic (PV) system at residential/distribution level. The proposed model uses single-phase phase locked loop (PLL) to synchronize SPI with the grid and performs MPC control in a dq reference frame. SPI model consists of boost converter (BC), maximum power point tracking (MPPT) control, and a full bridge (FB) voltage source inverter (VSI). No PI regulators to tune and carrier and modulating waves are required to produce switching sequence. Instead, the operational model of VSI is used to synthesize sinusoidal current and track the reference. Model is validated using a three kW PV system at the input of UI-SPI in Matlab/Simulink. Implementation and results demonstrate simplicity and accuracy, as well as reliability of the model.

Keywords: phase locked loop, voltage source inverter, single phase inverter, model predictive control, Matlab/Simulink

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Authors: Majid Forghani, Michael Khachay

Abstract:

In genetics, the impact of neighboring amino acids on a target site is referred as the nearest-neighbor effect or simply neighbor effect. In this paper, a new method called wavelet particle decomposition representing the one-dimensional neighbor effect using wavelet packet decomposition is proposed. The main idea lies in known dependence of wavelet packet sub-bands on location and order of neighboring samples. The method decomposes the value of a signal sample into small values called particles that represent a part of the neighbor effect information. The results have shown that the information obtained from the particle decomposition can be used to create better model variables or features. As an example, the approach has been applied to improve the correlation of test and reference sequence distance with titer in the hemagglutination inhibition assay.

Keywords: antigenic variants, neighbor effect, wavelet packet, wavelet particle decomposition

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Authors: Catherine K. Derow

Abstract:

Possibly a slime mold somehow mutated or already was mutated at progeniture and so stayed as a metazoan when it developed into the fruiting stage and so the slime mold(s) we are evolved and similar to are genetically differ from the slime molds in existence now. This may be why there are genetic links between humans and other metazoa now alive and slime molds now alive but we are now divergent branches of the evolutionary tree compared to the original slime mold, or perhaps slime mold-like organisms, that gave rise to metazoan animalia and perhaps algae and plantae as slime molds were undifferentiated enough in many ways that could allow their descendants to evolve into these three separate phylogenetic categories. Or it may be a slime mold was born or somehow progenated as multicellular, as the particular organism was mutated enough to have say divided in a a 'pseudo-embryonic' stage, and this could have happened for algae, plantae as well as animalia or all the branches may be from the same line but the missing link might be covered in 'phylogenetic sequence comparison noise'.

Keywords: metazoan evolution, unicellular bridge to metazoans, evolution, slime mold

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Authors: Igor V. Grigoriev

Abstract:

Understanding of biological processes encoded in fungi is instrumental in addressing future food, feed, and energy demands of the growing human population. Genomics is a powerful and quickly evolving tool to understand these processes. The Fungal Genomics Program of the US Department of Energy Joint Genome Institute (JGI) partners with researchers around the world to explore fungi in several large scale genomics projects, changing the fungal genomics landscape. The key trends of these changes include: (i) rapidly increasing scale of sequencing and analysis, (ii) developing approaches to go beyond culturable fungi and explore fungal ‘dark matter,’ or unculturables, and (iii) functional genomics and multi-omics data integration. Power of comparative genomics has been recently demonstrated in several JGI projects targeting mycorrhizae, plant pathogens, wood decay fungi, and sugar fermenting yeasts. The largest JGI project ‘1000 Fungal Genomes’ aims at exploring the diversity across the Fungal Tree of Life in order to better understand fungal evolution and to build a catalogue of genes, enzymes, and pathways for biotechnological applications. At this point, at least 65% of over 700 known families have one or more reference genomes sequenced, enabling metagenomics studies of microbial communities and their interactions with plants. For many of the remaining families no representative species are available from culture collections. To sequence genomes of unculturable fungi two approaches have been developed: (a) sequencing DNA from fruiting bodies of ‘macro’ and (b) single cell genomics using fungal spores. The latter has been tested using zoospores from the early diverging fungi and resulted in several near-complete genomes from underexplored branches of the Fungal Tree, including the first genomes of Zoopagomycotina. Genome sequence serves as a reference for transcriptomics studies, the first step towards functional genomics. In the JGI fungal mini-ENCODE project transcriptomes of the model fungus Neurospora crassa grown on a spectrum of carbon sources have been collected to build regulatory gene networks. Epigenomics is another tool to understand gene regulation and recently introduced single molecule sequencing platforms not only provide better genome assemblies but can also detect DNA modifications. For example, 6mC methylome was surveyed across many diverse fungi and the highest among Eukaryota levels of 6mC methylation has been reported. Finally, data production at such scale requires data integration to enable efficient data analysis. Over 700 fungal genomes and other -omes have been integrated in JGI MycoCosm portal and equipped with comparative genomics tools to enable researchers addressing a broad spectrum of biological questions and applications for bioenergy and biotechnology.

Keywords: fungal genomics, single cell genomics, DNA methylation, comparative genomics

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Authors: Saul Estrin, Ute Stephan, Suncica Vujic

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Background and research question: Gender differences in pay are present at all organisational levels, including at the very top. One possible way for women to circumvent organizational norms and discrimination is to engage in entrepreneurship because, as CEOs of their own organizations, entrepreneurs largely determine their own pay. While commercial entrepreneurship plays an important role in job creation and economic growth, social entrepreneurship has come to prominence because of its promise of addressing societal challenges such as poverty, social exclusion, or environmental degradation through market-based rather than state-sponsored activities. This opens the research question whether social entrepreneurship might be a form of entrepreneurship in which the pay of men and women is the same, or at least more similar; that is to say there is little or no gender pay gap. If the gender gap in pay persists also at the top of social enterprises, what are the factors, which might explain these differences? Methodology: The Oaxaca-Blinder Decomposition (OBD) is the standard approach of decomposing the gender pay gap based on the linear regression model. The OBD divides the gender pay gap into the ‘explained’ part due to differences in labour market characteristics (education, work experience, tenure, etc.), and the ‘unexplained’ part due to differences in the returns to those characteristics. The latter part is often interpreted as ‘discrimination’. There are two issues with this approach. (i) In many countries there is a notable convergence in labour market characteristics across genders; hence the OBD method is no longer revealing, since the largest portion of the gap remains ‘unexplained’. (ii) Adding covariates to a base model sequentially either to test a particular coefficient’s ‘robustness’ or to account for the ‘effects’ on this coefficient of adding covariates might be problematic, due to sequence-sensitivity when added covariates are correlated. Gelbach’s decomposition (GD) addresses latter by using the omitted variables bias formula, which constructs a conditional decomposition thus accounting for sequence-sensitivity when added covariates are correlated. We use GD to decompose the differences in gaps of pay (annual and hourly salary), size of the organisation (revenues), effort (weekly hours of work), and sources of finances (fees and sales, grants and donations, microfinance and loans, and investors’ capital) between men and women leading social enterprises. Database: Our empirical work is made possible by our collection of a unique dataset using respondent driven sampling (RDS) methods to address the problem that there is as yet no information on the underlying population of social entrepreneurs. The countries that we focus on are the United Kingdom, Spain, Romania and Hungary. Findings and recommendations: We confirm the existence of a gender pay gap between men and women leading social enterprises. This gap can be explained by differences in the accumulation of human capital, psychological and social factors, as well as cross-country differences. The results of this study contribute to a more rounded perspective, highlighting that although social entrepreneurship may be a highly satisfying occupation, it also perpetuates gender pay inequalities.

Keywords: Gelbach’s decomposition, gender gap, returns to social entrepreneurship, values and preferences

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Authors: Sasan Talebnezhad, Parviz Hamidia

Abstract:

GPC and RMS analysis showed no distinct difference between PE 100 On, Off, and Reference grade. But FTIR spectra and multiple endothermic peaks obtained from SSA analysis, attributed to heterogeneity of ethylene sequence length, lamellar thickness and also the non-uniformity of short chain branching, showed sharp discrepancy and proposed a blend structure of high-density polyethylenes in PE 100 grade. Catalysis along with process parameters dictates poly blend PE 100 structure. This in-reactor blend is a mixture of compatible co-crystallized phases with different crystalinity, forming a physical semi hard and soft segment network responsible for improved impact properties in PE 100 pipe grade. We propose a new approach for PE100 evaluation that is more efficient than normal microstructure characterization.

Keywords: HDPE, pipe grade, in-reactor blend, hard and soft segments

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Authors: M. F. F. Ab Rashid, A. N. Mohd Rose, N. M. Z. Nik Mohamed, W. S. Wan Harun, S. A. Che Ghani

Abstract:

Traveling salesman problem with precedence constraint (TSPPC) is one of the most complex problems in combinatorial optimization. The existing algorithms to solve TSPPC cost large computational time to find the optimal solution. The purpose of this paper is to present an efficient genetic algorithm that guarantees optimal solution with less number of generations and iterations time. Unlike the existing algorithm that generates priority factor as chromosome, the proposed algorithm directly generates sequence of solution as chromosome. As a result, the proposed algorithm is capable of generating optimal solution with smaller number of generations and iteration time compare to existing algorithm.

Keywords: traveling salesman problem, sequencing, genetic algorithm, precedence constraint

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Authors: Tahereh Habibi

Abstract:

The Oligocene carbonates are widespread along Fars Province, Zagros Basin, SW Iran. Distribution of planktonic and larger benthic foraminfera, stratal patterns and facies architecture are used as a tool to define microfacies and foraminiferal associations of these strata at Kavar Section. The presence of Nummulites spp. indicated the age of the sequence as Rupelian-Chattian (Nummulites vascus-Nummulites fichteli and Archaias asmaricus/hensoni-Miogypsinoides complanatus assemblage zones). The paleoenvironmental setting is interpreted as a homoclinal ramp environment according to the recognition of eight microfacies types. Four foraminiferal associations are recognized in the investigated ramp setting. They represent a salinity of 34-40 to 50 psu and higher than 50 psu in more restricted conditions. The depth ranges from 200 m as evidenced by the presence of planktonic foraminifera and to less than 30m in the more restricted inner ramp environment. Warm tropical and subtropical water with temperature of 18-25° C is proposed.

Keywords: foraminiferal associations, microfacies, oligocene, paleoecology

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Authors: Shweta Dhindhwal

Abstract:

Dopamine is an essential neurotransmitter in the central nervous system of all vertebrates and plays an important role in many processes such as motor function, learning and behavior, and sensory activity. One of the important functions of dopamine is release of pituitary hormones. It is synthesized from the amino acid tyrosine. Two types of dopamine receptors, D1-like and D2-like, have been reported in fish. The dopamine containing neurons are located in the olfactory bulbs, the ventral regions of the pre-optic area and tuberal hypothalamus. Distribution of the dopaminergic system has not been studied in the murrel, Channa punctatus. The present study deals with identification of D2 receptors in the brain of murrel. A phylogenetic tree has been constructed using partial sequence of D2 receptor. Distribution of putative dopaminergic neurons in the brain has been investigated. Also, formalin induced hypertrophy of neurosecretory cells in murrel has been studied.

Keywords: dopamine, fish, pre-optic area, murrel

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Authors: Alejandra Betancur Sánchez, Carmen Elena Zapata Sánchez, Juan Bautista López Ortiz

Abstract:

Adverse effects and increased air pollution has raised concerns about regulatory policies and has fostered the development of new air quality standards; this is due to the complexity of the composition and the poorly understood reactions in the atmospheric environment. Toxic compounds act as environmental agents having various effects, from irritation to death of cells and tissues. A toxic agent is defined an adverse response in a biological system. There is a particular class that produces some kind of alteration in the genetic material or associated components, so they are recognized as genotoxic agents. Within cells, they interact directly or indirectly with DNA, causing mutations or interfere with some enzymatic repair processes or in the genesis or polymerization of proteinaceous material involved in chromosome segregation. An air pollutant may cause or contribute to increased mortality or serious illness and even pose a potential danger to human health. The aim of this study was to evaluate the effect on the viability and the genotoxic potential on the cell lines CHO-K1 and Jurkat and peripheral blood of particulate matter PM T lymphocytes 2.5 obtained from filters collected three monitoring stations network air quality Aburrá Valley. Tests, reduction of MTT, trypan blue, NRU, comet assay, sister chromatid exchange (SCE) and chromosomal aberrations allowed evidence reduction in cell viability in cell lines CHO-K1 and Jurkat and damage to the DNA from cell line CHOK1, however, no significant effects were observed in the number of SCEs and chromosomal aberrations. The results suggest that PM2.5 material has genotoxic potential and can induce cancer development, as has been suggested in other studies.

Keywords: PM2.5, cell line Jurkat, cell line CHO-K1, cytotoxicity, genotoxicity

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Authors: Ali Akbar Attari, Ali Asghar Beheshti Shirazi

Abstract:

In this paper, we propose a blind and robust audio watermarking scheme based on spread spectrum in Discrete Wavelet Transform (DWT) domain. Watermarks are embedded in the low-frequency coefficients, which is less audible. The key idea is dividing the audio signal into small frames, and magnitude of the 6^th level of DWT approximation coefficients is modifying based upon the Direct Sequence Spread Spectrum (DSSS) technique. Also, the psychoacoustic model for enhancing in imperceptibility, as well as Savitsky-Golay filter for increasing accuracy in extraction, is used. The experimental results illustrate high robustness against most common attacks, i.e. Gaussian noise addition, Low pass filter, Resampling, Requantizing, MP3 compression, without significant perceptual distortion (ODG is higher than -1). The proposed scheme has about 83 bps data payload.

Keywords: audio watermarking, spread spectrum, discrete wavelet transform, psychoacoustic, Savitsky-Golay filter

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Authors: Yuzhi Cai

Abstract:

This talk presents a Bayesian approach to quantile autoregressive (QAR) time series model estimation and forecasting. We establish that the joint posterior distribution of the model parameters and future values is well defined. The associated MCMC algorithm for parameter estimation and forecasting converges to the posterior distribution quickly. We also present a combining forecasts technique to produce more accurate out-of-sample forecasts by using a weighted sequence of fitted QAR models. A moving window method to check the quality of the estimated conditional quantiles is developed. We verify our methodology using simulation studies and then apply it to currency exchange rate data. An application of the method to the USD to GBP daily currency exchange rates will also be discussed. The results obtained show that an unequally weighted combining method performs better than other forecasting methodology.

Keywords: combining forecasts, MCMC, quantile modelling, quantile forecasting, predictive density functions

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Authors: Irene Capecchi, Tommaso Borghini, Iacopo Bernetti

Abstract:

One of the most common pieces of equipment still used today for pruning, felling, and processing trees is the chainsaw in forestry. However, chainsaw use highlights dangers and one of the highest rates of accidents in both professional and non-professional work. Felling is proportionally the most dangerous phase, both in severity and frequency, because of the risk of being hit by the plant the operator wants to cut down. To avoid this, a correct sequence of chainsaw cuts must be taught concerning the different conditions of the tree. Virtual reality (VR) makes it possible to virtually simulate chainsaw use without danger of injury. The limitations of the existing applications are as follow. The existing platforms are not symmetrical collaborative because the trainee is only in virtual reality, and the trainer can only see the virtual environment on a laptop or PC, and this results in an inefficient teacher-learner relationship. Therefore, most applications only involve the use of a virtual chainsaw, and the trainee thus cannot feel the real weight and inertia of a real chainsaw. Finally, existing applications simulate only a few cases of tree felling. The objectives of this research were to implement and test a symmetrical collaborative training application based on VR and mixed reality (MR) with the overlap between real and virtual chainsaws in MR. The research and training platform was developed for the Meta quest 2 head-mounted display. The research and training platform application is based on the Unity 3D engine, and Present Platform Interaction SDK (PPI-SDK) developed by Meta. PPI-SDK avoids the use of controllers and enables hand tracking and MR. With the combination of these two technologies, it was possible to overlay a virtual chainsaw with a real chainsaw in MR and synchronize their movements in VR. This ensures that the user feels the weight of the actual chainsaw, tightens the muscles, and performs the appropriate movements during the test allowing the user to learn the correct body posture. The chainsaw works only if the right sequence of cuts is made to felling the tree. Contact detection is done by Unity's physics system, which allows the interaction of objects that simulate real-world behavior. Each cut of the chainsaw is defined by a so-called collider, and the felling of the tree can only occur if the colliders are activated in the right order simulating a safe technique felling. In this way, the user can learn how to use the chainsaw safely. The system is also multiplayer, so the student and the instructor can experience VR together in a symmetrical and collaborative way. The platform simulates the following tree-felling situations with safe techniques: cutting the tree tilted forward, cutting the medium-sized tree tilted backward, cutting the large tree tilted backward, sectioning the trunk on the ground, and cutting branches. The application is being evaluated on a sample of university students through a special questionnaire. The results are expected to test both the increase in learning compared to a theoretical lecture and the immersive and telepresence of the platform.

Keywords: chainsaw, collaborative symmetric virtual reality, mixed reality, operator training

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Authors: Sergei Voychuk

Abstract:

Introduction: Adaptive response (AR) is a manifestation of radiation hormesis, which deal with the radiation resistance that may be increased with the pretreatment with small doses of radiation. In the current study, we evaluated the potency of radiofrequency EMF to induce the AR mechanisms and to increase a resistance to UV light. Methods: Saccharomyces cerevisiae yeast strains, which were created to study induction of mutagenesis and recombination, were used in the study. The strains have mutations in rad2 and rad54 genes, responsible for DNA repair: nucleotide excision repair (PG-61), postreplication repair (PG-80) and mitotic (crossover) recombination (T2). An induction of mutation and recombination are revealed due to the formation of red colonies on agar plates. The PG-61 and T2 are UV sensitive strains, while PG-80 is sensitive to ionizing radiation. Extremely high frequency electromagnetic field (EHF-EMF) was used. The irradiation was performed in floating mode and frequency changed during exposure from 57 GHz to 62 GHz. The power of irradiation was 100 mkW, and duration of exposure was 10 and 30 min. Treatment was performed at RT and then cells were stored at 28° C during 1 h without any exposure but after that they were treated with UV light (254nm) for 20 sec (strain T2) and 120 sec (strain PG-61 and PG-80). Cell viability and quantity of red colonies were determined after 5 days of cultivation on agar plates. Results: It was determined that EHF-EMF caused 10-20% decrease of viability of T2 and PG-61 strains, while UV showed twice stronger effect (30-70%). EHF-EMF pretreatment increased T2 resistance to UV, and decreased it in PG-61. The PG-80 strain was insensitive to EHF-EMF and no AR effect was determined for this strain. It was not marked any induction of red colonies formation in T2 and PG-80 strain after EHF or UV exposure. The quantity of red colonies was 2 times more in PG-61 strain after EHF-EMF treatment and at least 300 times more after UV exposure. The pretreatment of PG-61 with EHF-EMF caused at least twice increase of viability and consequent decrease of amount of red colonies. Conclusion: EHF-EMF may induce AR in yeast cells and increase their viability under UV treatment.

Keywords: Saccharomyces cerevisiae, EHF-EMF, UV light, adaptive response

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