Search results for: phenotype transition

Authors: Shivani Sharma, Prashant Saxena, Inamul Hasan Madar

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Since the time of Darwin, it has been considered that genetic change is the direct indicator of variation in phenotype. But a few studies in system biology in the past years have proposed that epigenetic developmental processes also affect the phenotype thus shifting the focus from a linear genotype-phenotype map to a non-linear G-P map. In this paper, we attempt at explaining the evolution of colour vision in mammals by taking LWS/ Long-wave sensitive gene under consideration.

Keywords: evolution, phenotypes, epigenetics, LWS gene, G-P map

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Authors: Huilan Yao, Huaixin Zhang

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Simulations of the transition flow of model propellers are important for predicting hydrodynamic performance and studying scale effects. In this paper, the transition flow of a model propeller under different loadings are simulated using a transition model provided by STAR-CCM+, and the influence of turbulence intensity (TI) on the transition, especially friction and pressure components of propeller performance, was studied. Before that, the transition model was applied to simulate the transition flow of a flat plate and an airfoil. Predicted transitions agree well with experimental results. Then, the transition model was applied for propeller simulations in open water, and the influence of TI was studied. Under the heavy and moderate loadings, thrust and torque of the propeller predicted by the transition model (different TI) and two turbulence models are very close and agree well with measurements. However, under the light loading, only the transition model with low TI predicts the most accurate results. Above all, the friction components of propeller performance predicted by the transition model with different TI have obvious difference.

Keywords: transition flow, model propellers, hydrodynamic performance, numerical simulation

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Authors: Abderahman Efhialelbum

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The period since the fall of the Berlin Wall on November 9, 1989, and the collapse of the former Soviet Union in December 1985 has seen a major change in the economies and labour markets of Eastern Europe. The events also had reverberating effects across Asia and South America and parts of Africa, including Libya. This article examines the typologies and the models of transition economies. Also, it sheds light on the Libyan transition in particular and the impact of Qadhafi’s regime on the transition process. Finally, it illustrates how the Libyan transition process followed the trajectory of other countries using economic indicators such as free trade, property rights, and inflation.

Keywords: transition, economy, typology, model, Libya

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Authors: Han Bai, Tong Zhang, Lemei Yu, Doudou Xie, Liang Zhao

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Road transition design on freeway tunnel entrance and exit is one vital factor in realizing smooth transition and improving traveling safety for vehicles. The goal of this research is to develop a horizontal road transition design tool that considers the transition technology of traffic capacity consistency to explore its accommodation mechanism. The influencing factors of capacity are synthesized and a modified capacity calculation model focusing on the influence of road width and lateral clearance is developed based on the VISSIM simulation to calculate the width of road transition sections. To keep the traffic capacity consistency, the right side of the transition section of the tunnel entrance and exit is divided into three parts: front arc, an intermediate transition section, and end arc; an optimization design on each transition part is conducted to improve the capacity stability and horizontal alignment transition. A case study on the Panlong Tunnel in Ji-Qing freeway illustrates the application of the tool.

Keywords: traffic safety, road transition, freeway tunnel, traffic capacity

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Authors: S. Pradhan, D. Pradhan, G. Tripathy

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Anti-estrogen treatment resistant is a noteworthy reason for disease relapse and mortality in estrogen receptor alpha (ERα)- positive breast cancers. Tamoxifen or estrogen withdrawal increases the dependance of breast malignancy cells on INT3 signaling. Here, we researched the contribution of Quercetin and INT3 signaling in endocrine resistant breast cancer cells. Methods: We utilized two models of endocrine therapies resistant (ETR-) breast cancer: tamoxifen-resistant (TamR) and long term estrogen-deprived (LTED) MCF7 cells. We assessed the migratory and invasive limit of these cells by Transwell assay. Expression of epithelial to mesenchymal transition (EMT) controllers and in addition INT3 receptors and targets were assessed by real-time PCR and western blot analysis. Besides, we tried in vitro anti-Quercetin monoclonal antibodies (mAbs) and gamma secretase inhibitors (GSIs) as potential EMT reversal therapeutic agents. At last, we created stable Quercetin over expessing MCF7 cells and assessed their EMT features and response to tamoxifen. Results:We found that ETR cells acquired an epithelial to mesenchymal transition (EMT) phenotype and showed expanded levels of Quercetin and INT3 targets. Interestingly, we detected higher level of INT3 however lower levels of INT31 and INT32 proposing a switch to targeting through distinctive INT3 receptors after obtaining of resistance. Anti-Quercetin monoclonal antibodies and the GSI PF03084014 were effective in obstructing the Quercetin/INT3 axis and in part inhibiting the EMT process. As a consequence of this, cell migration and invasion were weakened and the stem cell like population was considerably decreased. Genetic hushing of Quercetin and INT3 prompted proportionate impacts. Finally, stable overexpression of Quercetin was adequate to make MCF7 lethargic to tamoxifen by INT3 activation. Conclusions: ETR cells express abnormal amounts of Quercetin and INT3, whose actuation eventually drives invasive conduct. Anti-Quercetin mAbs and GSI PF03084014 lessen expression of EMT molecules decreasing cellular invasiveness. Quercetin overexpression instigates tamoxifen resistance connected to obtaining of EMT phenotype. Our discovering propose that focusing on Quercetin and/or INT3 warrants further clinical assessment as substantial therapeutic methodologies in endocrine-resistant breast cancer.

Keywords: quercetin, INT3, mesenchymal transition, MCF7 breast cancer cells

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Authors: Zaw Min Tun

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The paper focuses on the spacecraft’s trajectory transition from interplanetary hyperbolic orbit to the planet’s orbit using the aerobraking in the atmosphere of the planet. A considerable mass of fuel is consumed during the spacecraft transition from the planet’s gravitation assist trajectory into the planet’s satellite orbit. To reduce the fuel consumption in this transition need to slow down the spacecraft’s velocity in the planet’s atmosphere and reduce its orbital transition time. The paper is devoted to the use of the planet’s atmosphere for slowing down the spacecraft during its transition into the satellite orbit with uncertain atmospheric parameters. To reduce the orbital transition time of the spacecraft is controlled by the change of attack angles’ values at the aerodynamic deceleration path and adjusting the minimum flight altitude of the spacecraft at the pericenter of the planet’s upper atmosphere.

Keywords: aerobraking, atmosphere of the planet, orbital transition time, Spacecraft’s trajectory

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Authors: Joris Zufferey, Roderick John Lawrence

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This paper provides an overview of the state of the art about the positive health impacts of exposure to natural outdoor environments. It presents the results of a “review of reviews” in terms of empirical evidence and identifies some key questions. Finally, the authors stress the need to develop more interdisciplinary and systemic contributions. This synthesis of empirical research has been done as part of the EU- FP7 PHENOTYPE research project.

Keywords: Exposure, environment, phenotype, salutogenic effects

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Authors: Mansi Srivastava, Uzma Saqib, Adnan Naim, Anjali Roy, Dongfang Liu, Deepak Bhatnagar, Ravinder Ravinder, Mirza S. Baig

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Macrophages polarize to proinflammatory M1 or anti-inflammatory M2 states with distinct physiological functions. This transition within the M1 to M2 phenotypes decides the nature, duration, and severity of an inflammatory response. However, inspite of a substantial understanding of the fate of these phenotypes, the underlying molecular mechanisms are not well understood. We have investigated the role of Neuronal nitric oxide synthase (NOS1) mediated regulation of Activator protein 1 (AP-1) transcription factor in macrophages as a critical effector of macrophage phenotypic change. Activator protein 1 (AP-1) is a group of dimeric transcription factors composed of jun, Fos, and ATF family proteins. We determined that NOS1-derived nitric oxide (NO) facilitate Fos and jun interaction which induces IL12 & IL23 expression. Pharmacological inhibition of NOS1 inhibits Fos and jun interaction but increases ATF2 and Fos dimerization. Switching of Fos and jun dimer to ATF2 and jun dimerization switches phenotype from IL–12high IL-23high IL-10low to IL–12low IL-23lowIL-10high phenotype, respectively. Together, these findings highlight a key role of the TLR4-NOS1-AP1 signaling axis in regulating macrophage polarization.

Keywords: inflammation, macrophage, lipopolysaccharide (LPS), proinflammatory cytokines, activator protein 1 (AP-1), neuronal nitric oxide synthase (NOS1)

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Authors: Edina Koch, Péter Hudacsek

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In railways transition zone is present at the boundaries of zones with different stiffness. When a train rides from an embankment onto a stiff structure, such as a bridge, tunnel or culvert, an abrupt change in the support stiffness occurs possibly inducing differential settlements. This in long term can yield to the degradation of the tracks and foundations in the transition zones. A number of techniques have been proposed or implemented to provide gradual stiffness transition at the problem zones, such as methods to ensure gradually changing pad stiffness, application of long sleepers or installation of auxiliary rails in the transition zone. Aim of the research presented in this paper is to analyze the 3D and the dynamic effects induced by the passing train over an area where significant difference in the support stiffness exists. The effects were analyzed for different arrangements associated with certain differential settlement mitigation strategies of the transition zones.

Keywords: culvert, dynamic load, HS small model, railway transition zone

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Authors: Yuhang Wang

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As energy is vital to industrial productivity and human existence, ensuring energy security becomes a critical government responsibility. The Chinese government has implemented the energy transition to safeguard China’s energy security. Throughout this progression, the Chinese government has faced numerous obstacles. This article seeks to describe the causes of China’s energy transition barriers and the steps taken by the Chinese government to overcome them.

Keywords: energy transition, energy market, fragmentation, path dependency

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Authors: A. Ozel

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The ductile to brittle transition temperature is a very important criterion that is used for selection of materials in some applications, especially in low-temperature conditions. For that reason, in this study transition temperature of as-cast and austempered unalloyed ductile iron in the temperature interval from -60 to +100 degrees C have been investigated. The microstructures of samples were examined by light microscope. The impact energy values obtained from the experiments were found to depend on the austempering time and temperature.

Keywords: Austempered Ductile Iron (ADI), Charpy test, microstructure, transition temperature

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Authors: Hiroyuki Aoki

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The glass transition phenomenon has been extensively studied for a long time. The glass transition of polymer materials is assigned to the transition of the dynamics of the chain backbone segment. However, the detailed mechanism of the transition behavior of the segmental motion is still unclear. In the current work, the single molecule detection technique was employed to reveal the trajectory of the molecular motion of the single polymer chain. The center segment of poly(butyl methacrylate) chain was labeled by a perylenediimide dye molecule and observed by a highly sensitive fluorescence microscope in a defocus condition. The translational and rotational diffusion of the center segment in a single polymer chain was analyzed near the glass transition temperature. The direct observation of the individual polymer chains revealed the intermittent behavior of the segmental motion, indicating the spatial inhomogeneity.

Keywords: glass transition, molecular motion, polymer materials, single molecule

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Authors: S. Bentata, W. Benstaali, A. Abbad, H. A. Bentounes, B. Bouadjemi

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The full potential linear augmented plane wave (FPLAPW) based on density-functional theory (DFT) is employed to study the electronic, magnetic and optical properties of some transition metals doped ZnSe. Calculations are carried out by varying the doped atoms. Four 3D transition elements were used as a dopant: Cr, Mn, Co and Cu in order to induce spin polarization. Our results show that, Mn and Cu-doped ZnSe could be used in spintronic devices only if additional dopants are introduced, on the contrary, transition elements showing delocalized quality such as Cr, and Co doped ZnSe might be promising candidates for application in spintronic.

Keywords: spin-up, spin-down, magnetic properties, transition metal, composite materials

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Authors: Sombol Mokhles

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This paper tries to show the prospects of utilising (big)data for enabling just the transition of diverse cities. Our key purpose is to offer a framework of applications and implications of utlising (big) data in comparing sustainability transitions across different cities. Relying on the cosmopolitan comparison, this paper explains the potential application of (big) data but also its limitations. The paper calls for adopting a data-driven and just perspective in including different cities around the world. Having a just and inclusive approach at the front and centre ensures a just transition with synergistic effects that leave nobody behind.

Keywords: big data, just sustainable transition, cosmopolitan city comparison, cities

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Authors: Madhu Sarwan, Ritu Dubey, Sadhna Singh

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We have investigated the structural phase transition from Zinc-Blende (ZB) to Rock-Salt (RS) structure of TlxGa1-xAs by using Interaction Potential Model (IPM). The IPM consists of Coulomb interaction, Three-Body Interaction (TBI), Van Der Wall (vdW) interaction and overlap repulsive short range interaction. The structural phase transition has been computed by using the vegard’s law. The volume collapse is also computed for this alloy. We have also investigated the second order elastic constants with composition for the alloy TlxGa1-xAs.

Keywords: III-V alloy, elastic moduli, phase transition, semiconductors

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Authors: Namrata Yaduvanshi, Shilpa Kapoor, Pooja Pawar, Sadhna Singh

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In the present paper, we have investigated the high-pressure structural phase transition and elastic properties of cerium mononitride. We studied theoretically the structural properties of this compound (CeN) by using the Improved Interaction Potential Model (IIPM) approach. This compound exhibits first order crystallographic phase transition from NaCl (B1) to tetragonal (BCT) phase at 37 GPa. The phase transition pressures and associated volume collapse obtained from present potential model (IIPM) show a good agreement with available theoretical data.

Keywords: phase transition, volume collapse, elastic constants, three body interaction

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Authors: Fatma Koksal Cakirlar, Murat Gunaydin, Nevri̇ye Gonullu, Nuri Kiraz

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During the last few decades, the increasing prevalence of methicillin resistant-CoNS isolates has become a common problem worldwide. Macrolide-lincosamide-streptogramin B (MLSB) antibiotics are effectively used for the treatment of CoNS infections. However, resistance to MLSB antibiotics is prevalent among staphylococci. The aim of this study is to determine species distribution and the incidence of inducible clindamycin resistance in CoNS isolates caused nosocomial bacteremia in our hospital. Between January 2014 and October 2015, a total of 484 coagulase-negative CoNS isolates were isolated from blood samples of patients with true bacteremia who were hospitalized in intensive care units and in other departments of Istanbul University Cerrahpasa Medical Hospital. Blood cultures were analyzed with the BACTEC 9120 system (Becton Dickinson, USA). The identification and antimicrobial resistance of isolates were determined by Phoenix automated system (BD Diagnostic Systems, Sparks, MD). Inducible clindamycin resistance was detected using D-test. The species distribution was as follows: Staphylococcus epidermidis 211 (43%), S. hominis 154 (32%), S. haemolyticus 69 (14%), S. capitis 28 (6%), S. saprophyticus 11 (2%), S. warnerii 7 (1%), S. schleiferi 5 (1%) and S. lugdunensis 1 (0.2%). Resistance to methicillin was detected in 74.6% of CoNS isolates. Methicillin resistance was highest in S.hemoliticus isolates (89%). Resistance rates of CoNS strains to the antibacterial agents, respectively, were as follows: ampicillin 77%, gentamicin 20%, erythromycin 71%, clindamycin 22%, trimethoprim-sulfamethoxazole 45%, ciprofloxacin 52%, tetracycline 34%, rifampicin 20%, daptomycin 0.2% and linezolid 0.2%. None of the strains were resistant to vancomycin and teicoplanin. Fifteen (3%) CoNS isolates were D-test positive, inducible MLSB resistance type (iMLSB-phenotype), 94 (19%) were constitutively resistant (cMLSB -phenotype), and 237 (46,76%) isolates were found D-test negative, indicating truly clindamycin-susceptible MS phenotype (M-phenotype resistance). The incidence of iMLSB-phenotypes was higher in S. epidermidis isolates (4,7%) compared to other CoNS isolates.

Keywords: bacteremia, inducible MLSB resistance phenotype, methicillin-resistant, staphylococci

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Authors: Phimsupha Kokchang, Divine Ifransca Wijaya

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The energy transition is crucial for mitigating climate change and achieving sustainable development and resilience. As the energy transition advances, generation Z is entering the economic world and will soon be responsible for taking care of the environment. This study aims to investigate the factors influencing generation Z’s pro-environmental behavior to support the energy transition. The theory of planned behavior approach was combined with the pro-environmental behavior concept to examine generation Z’s support toward the energy transition through participating in activism, using energy from renewable sources, opting for energy-efficient utilities or vehicles, and influencing others. Data were collected through an online questionnaire of 400 respondents aged 18-26 living in Jakarta, Indonesia. Partial least square structural equation modeling (PLS-SEM) using SmartPLS 3.0 software was used to analyze the reliability and validity of the measurement model. The results show that attitude, subjective norms, and perceived behavior control positively correlate with generation Z’s pro-environmental behavior to support the energy transition. This finding could enhance understanding and provide insights to formulate effective strategies and policies to increase generation Z’s support towards the energy transition. This study contributes to the energy transition discussion as it is included in the Sustainable Development Goals, as well as pro-environmental behavior and theory of planned behavior literature.

Keywords: energy transition, pro-environmental behavior, theory of planned behavior, generation Z

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Authors: Angelina Anani, Ignacio Ortiz Flores, Haitao Li

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The use of underground mining methods have increased significantly over the past decades. This increase has also been spared on by several mines transitioning from surface to underground mining. However, determining the transition depth can be a challenging task, especially when coupled with production schedule optimization. Several researchers have simplified the problem by excluding operational features relevant to production schedule optimization. Our research objective is to investigate the extent to which operational features of transition mines accounted for affect the optimal production schedule. We also provide a framework for factors to consider in production schedule optimization for transition mines. An integrated mixed-integer linear programming (MILP) model is developed that maximizes the NPV as a function of production schedule and transition depth. A case study is performed to validate the model, with a comparative sensitivity analysis to obtain operational insights.

Keywords: underground mining, transition mines, mixed-integer linear programming, production schedule

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Authors: Josephine Hai, Jie Jiang, Karen M. Lyons

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Of the musculoskeletal tissues, tendon is least understood in terms of biological development. The current study examines Cysteine-rich angiogenic inducer 61, or CCN1, a member of the CCN family of secreted matricellular proteins that regulate cell behavior via intercellular signaling. Though CCN1 is notable in limiting fibrosis by inducing senescence in fibroblasts, little is known about its role in normal fibrous tissue, where it may be essential to the development of ECM-rich structures like tendons. We found that CCN1 knockout mice (using limb-specific Prx1-Cre) exhibited clubfoot and waddling gaits, a unique phenotype not described in any other mutant to date. Histological analysis showed that the Achilles and patellar tendons, where we previously found high CCN1 expression in adult reporter mice, were thicker and denser in the Prx1-Cre knockouts than in their wildtype littermates. We then hypothesized that CCN1 is required directly in tendon progenitor cells for normal tendon development and generated tendon-specific CCN1 knockout mice using Scx-Cre. We observed similar Achilles/patellar tendon morphology among the Scx-Cre and Prx1-Cre mutants, indicating that the phenotype is a direct result of CCN1’s loss in tendon. To further study phenotype onset and progression, we will histologically characterize these tendons across different developmental time-points. We will also perform RNA-seq and qPCR to analyze tenocyte gene expression and expect fibrotic marker upregulation in the Scx-Cre mutants if CCN1 is required to maintain a normal tendon phenotype. Thus, our study aims to elucidate the molecular mechanisms underlying tendon formation and maintenance. Understanding tendons at the most basic level invites novel approaches to tendon repair.

Keywords: development, matricellular, musculoskeletal, tendon

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Authors: Hadda Krarcha, S. Messaasdi

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In order to investigate Hafnium transition metal alloys HfM (M= Co, Ir, Os,Pt, Rh, Ru) phase diagrams in the region of 50/50% atomic ratio, we performed ab initio Full-Potential Linearized Augmented Plane Waves calculations of the enthalpies of formation of HfM compounds at B2 (CsCl) structure type. The obtained enthalpies of formation are discussed and compared to some of the existing models and available experimental data.

Keywords: enthalpy of formation, transition metal, binarry compunds, hafnium

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Authors: Amal Ait El Djoudi

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A thermodynamical model of coexisting hadronic and quark–gluon plasma (QGP) phases is used to study the thermally driven deconfining phase transition occurring between the two phases. A color singlet partition function is calculated for the QGP phase with two massless quarks, as in our previous work, but now the finite extensions of the hadrons are taken into account in the equation of state of the hadronic phase. In the present work, the finite-size effects on the system are examined by probing the behavior of some thermodynamic quantities, called response functions, as order parameter, energy density and their derivatives, on a range of temperature around the transition at different volumes. It turns out that the finiteness of the system size has as effects the rounding of the transition and the smearing of all the singularities occurring in the thermodynamic limit, and the additional finite-size effect introduced by the requirement of exact color-singletness involves a shift of the transition point. This shift as well as the smearing of the transition region and the maxima of both susceptibility and specific heat show a scaling behavior with the volume characterized by scaling exponents. Another striking result is the large similarity noted between the behavior of these response functions and that of the cumulants of the probability density. This similarity is worked to try to extract information concerning the occurring phase transition.

Keywords: equation of state, thermodynamics, deconfining phase transition, quark–gluon plasma (QGP)

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Authors: Nikolay E. Dubinin

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Pair-interaction approximations allow to consider a different states of condensed matter from a single position. At the same time, description of an effective pair interaction in transition metal is a hard task since the d-electron contribution to the potential energy in this case is non-pairwise in principle. There are a number of models for transition-metal effective pair potentials. Here we use the Wills-Harrison (WH) approach to calculate pair potentials for Fe, Co, and Ni in crystalline, liquid, and nano states. Last is especially interesting since nano particles of pure transition metals immobilized on the dielectric matrices are widely used in different fields of advanced technologies: as carriers and transmitters of information, as an effective catalytic materials, etc. It is found that the minimum of the pair potential is deeper and oscillations are stronger in nano crystalline state in comparison with the liquid and crystalline states for all metals under consideration.

Keywords: effective pair potential, nanocrystalline state, transition metal, Wills-Harrison approach

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Authors: Emily Gould, Walter Wehremeyer, David Greaves, Rodney Turtle

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This paper considers current thinking on the pathway for electric vehicles, identifying the development blocks of alternative innovation within the market and analyse technological lock-in. The relationship between transition pathways and technological lock-in is largely under-researched particularly in the field of e-mobility. This paper is based on a study with three commercial-urban fleets that examines strategic decisions in new technology adaption alongside vehicle procurement and driver perspective. The paper will analyse the fleet’s decision matrix upon electric vehicles and seek to understand the influence of company culture, strategy and technology applicability, within the context of transition pathways.

Keywords: electric vehicles, fleets, path dependencies, transition pathways

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Authors: Ali Bakari Mohammed

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Transitioning is a continuous process of radical change in a society which involves co-evolution of institutional, technological, socio-cultural, and ecological developments at different scales and levels. Transition management model is a methodology that influences structural change of complex systems over a period (0-30 years) by experimenting and implementing new techniques. A transition management in the context of groundwater is a radical change from the current operate and control system to a next generation integrated and sustainable system that takes into account quality protection and sustained supply into the future. This study evaluates the transition management model in adopting it as a viable tool for the attainment of sustainable groundwater management. The outcome of the evaluation shows that there are three levels (strategic, tactical and operational) of operating the transition management model. At the strategic level, long-term goals for sustainable groundwater management are formulated, at the tactical level activities such as inter institutional networking, negotiation, planning and financing are carried out, and at the operational level, transition experiments and strategic niche management are carried out at the societal level. Overall, different actors and set of activities are required to partake at each management level. The outcome of this paper will provide basis for the implementation of the Sustainable Development Goal (SDG) 6 in Nigeria.

Keywords: transition management, groundwater, sustainable management, tool, Nigeria

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Authors: Naim Suleyman Ting, Yakup Sahin, Ismail Aksoy

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This paper presents a zero voltage transition-zero current transition (ZVT-ZCT)-PWM DC-DC boost converter with direct power transfer. In this converter, the main switch turns on with ZVT and turns off with ZCT. The auxiliary switch turns on and off with zero current switching (ZCS). The main diode turns on with ZVS and turns off with ZCS. Besides, the additional current or voltage stress does not occur on the main device. The converter has features as simple structure, fast dynamic response and easy control. Also, the proposed converter has direct power transfer feature as well as excellent soft switching techniques. In this study, the operating principle of the converter is presented and its operation is verified for 1 kW and 100 kHz model.

Keywords: direct power transfer, boost converter, zero-voltage transition, zero-current transition

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Authors: Stoyan Nedeltchev, Markus Schubert

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The gas holdup fluctuations in a bubble column (0.15 m in ID) have been recorded by means of a conductivity wire-mesh sensor in order to extract information about the main transition velocities. These parameters are very important for bubble column design, operation and scale-up. For this purpose, the classical definition of the Shannon entropy was modified and used to identify both the onset (at UG=0.034 m/s) of the transition flow regime and the beginning (at UG=0.089 m/s) of the churn-turbulent flow regime. The results were compared with the Kolmogorov entropy (KE) results. A slight discrepancy was found, namely the transition velocities identified by means of the KE were shifted to somewhat higher (0.045 and 0.101 m/s) superficial gas velocities UG.

Keywords: bubble column, gas holdup fluctuations, modified Shannon entropy, Kolmogorov entropy

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Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Stoyan Nedeltchev, Markus Schubert

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By means of the ultrafast X-ray tomography facility, data were obtained at different superficial gas velocities U_G in a bubble column (0.1 m in ID) operated with an air-deionized water system at ambient conditions. Raw reconstructed images were treated by both the information entropy (IE) and the reconstruction entropy (RE) algorithms in order to identify the main transition velocities in a bubble column. The IE values exhibited two well-pronounced minima at U_G=0.025 m/s and U_G=0.085 m/s identifying the boundaries of the homogeneous, transition and heterogeneous regimes. The RE extracted from the central region of the column’s cross-section exhibited only one characteristic peak at U_G=0.03 m/s, which was attributed to the transition from the homogeneous to the heterogeneous flow regime. This result implies that the transition regime is non-existent in the core of the column.

Keywords: bubble column, ultrafast X-ray tomography, information entropy, reconstruction entropy

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