Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational Metabolic Modeling of Cellular Growth : From Bacteria to Cancer

Constraint-based modeling (CBM) has been very commonly used for metabolic network analysis, and currently, dozens of genome-scale models amenable for CBM analysis are available for various multi-cellular and unicellular organisms. Cell division rate (growth rate) is a widely used estimate of the fitness of unicellular organisms, and aiming to follow this principle, the popular CBM method „flux balance analysis‟ (FBA), predicts metabolic behavior of an organism by maximizing the growth-demand of a predefined set of essential biomass precursors, allowing maximal growth rate. However, ignoring the growth demand for the synthesis of intermediate metabolites required for balancing their dilution, leads FBA to false predictions in some cases. In chapter ‎2 we present a new method to address this problem, resulting in improved metabolic phenotype predictions. Despite the fact that FBA is frequently used for unicellular organisms, it has been rarely applied for multi-cellular ones, as single cells in a multi-cellular system cannot be considered to maximize their own individual growth rates. Nevertheless, for some cell types, and specifically for cancer cells, growth rate maximization can be a good proxy for the single cell‟s objective and for identifying the cell‟s most likely metabolic rate. Recently, it has been suggested that a classical hallmark of cancer metabolism, the Warburg effect, is a consequence of the cell‟s adaptation to fast proliferation. In chapter ‎3 we rigorously study this hypothesis and show that applying an FBA variant accounting for both stoichiometry and enzyme kinetics on the human metabolic model, predicts that the Warburg effect is a direct outcome of the metabolic adjustment of cancer cells to facilitate the uptake and incorporation of nutrients into biomass.
Numerical Simulation of Force Convection in a Channel with Porous Part

In the present work, two dimensional laminar flow and convective heat transfer between two parallel plates of a symmetric channel were simulated using Lattice Boltzmann Method (LBM). The channel was filled partially with a porous block. The BrinkmanForchheimer model was used for porous zone. The effects of various parameters such as Reynolds number and porosity on the channel flow and thermal profiles were investigated. It was found that all these parameters have significant influence on thermal field of the channel in certain conditions.
Translationally controlled tumor protein acts as a guanine nucleotide dissociation inhibitor on the translation elongation factor eEF1A

Recently, we demonstrated that the expression levels of the translationally controlled tumor protein (TCTP) were strongly down-regulated at the mRNA and protein levels during tumor reversion/suppression and by the activation of p53 and Siah-1. To better characterize the function of TCTP, a yeast two-hybrid hunt was performed. Subsequent analysis identified the translation elongation factor, eEF1A, and its guanine nucleotide exchange factor, eEF1Bβ, as TCTP-interacting partners. In vitro and in vivo studies confirmed that TCTP bound specifically eEF1Bβ and eEF1A. Additionally, MS analysis also identified eEF1A as a TCTP interactor. Because eEF1A is a GTPase, we investigated the role of TCTP on the nucleotide exchange reaction of eEF1A. Our results show that TCTP preferentially stabilized the GDP form of eEF1A, and, furthermore, impaired the GDP exchange reaction promoted by eEF1Bβ. These data suggest that TCTP has guanine nucleotide dissociation inhibitor activity, and, moreover, implicate TCTP in the elongation step of protein synthesis.
ADAPTIVE ACQUISITION TECHNIQUES FOR PLANAR NEAR-FIELD ANTENNA MEASUREMENTS

The use of adaptive acquisition techniques to reduce the overall test time in planar near-field antenna measurements is described. A decision function is used to track the accuracy of a measurement as the data acquisition proceeds, and to halt such acquisition when this is considered sufficient for the measured quantity of importance. Possible decision functions are defined and compared. Several test cases are presented to show that significant test time reduction is possible when compared to traditional acquisition schemes.
Characterization of a double probe for local pulse wave velocity assessment

Local pulse-wave velocity (PWV) is an accurate indicator of the degree of arteriosclerosis (stiffness) in an artery, providing a direct characterization of the properties of its wall. Devices currently available for local PWV measurement are mainly based on ultrasound systems and have not yet been generalized to clinical practice since they require high technical expertise and most of them are limited in precision, due to the lack of reliable signal processing methods. The present work describes a new type of probe, based on a double-headed piezoelectric (PZ) sensor. The principle of PWV measurement involves determination of the pulse transit time between the signals acquired simultaneously by both PZs, placed 23 mm apart. The double probe (DP) characterization is accomplished in three main studies, carried out in a dedicated test bench system, capable of reproducing a range of clinically relevant properties of the cardiovascular system. The first study refers to determination of the impulse response (IR) for each PZ sensor, whereas the second one explores the existence of crosstalk between both transducers. In the last one, DP time resolution is inferred from a set of three different algorithms based on (a) the maximum of cross-correlation function, (b) the maximum amplitude detection and (c) the zero-crossing point identification. These values were compared with those obtained by the reference method, which consists of the simultaneous acquisition of pressure waves by means of two pressure sensors. The new probe demonstrates good performance on the test bench system and results show that the signals do not exhibit crosstalk. A good agreement was also verified between the PWV obtained from the DP signals (19.55 ± 2.02 ms−1) and the PWV determined using the reference method (19.26 ± 0.04 ms−1). Although additional studies are still required, this probe seems to be a valid alternative to local PWV stand-alone devices.
Evaluation and Improvements of Cloud and Precipitation Physics in the Operational Hurricane WRF Model at NOAA/EMC

The overall goal of this project is to evaluate and improve the cloud and precipitation physics used in the operational Hurricane Weather Research and Forecast (HWRF) model developed in the Environmental Modeling Center (EMC) at the National Centers for Environmental Prediction (NCEP) of NOAA, achieving improved prediction of hurricane structure and intensity, including the size, by the HWRF model at NCEP/EMC.
The relationship of work stressors, coping and social support to psychological symptoms among female secretarial employees

A conceptual framework is advanced that assumes that psychological symptoms emerge within multiple contexts, such as the workplace, and are influenced by the interplay of individual and situational risk and protective factors over time. This framework was utilized to examine the impact of work and work-family role stressors, coping, and work-related social support on psychological symptoms among 239 female, secretarial employees in the USA, using both cross-sectional and longitudinal structural equation models. Work stressors and avoidance coping were viewed as risk factors, and active coping and social support as protective factors. Work stressors contributed substantially to increased symptoms, primarily through a direct pathway in the cross-sectional model, but also indirectly to both Time 1 and Time 2 symptoms (4 months later) via pathways through active and avoidance coping. In both models, avoidance coping also predicted increased symptoms. Avoidance coping also served to partially mediate the relationship between work stressors and symptoms in the cross-sectional model, but not in the longitudinal model. Active coping was related to fewer psychological symptoms in both models, thereby reducing the negative effect of work stressors on symptoms. Likewise, work-related social support served an indirect protective function by contributing to lower levels of reported work stressors and greater use of active coping. Work stressors but not active coping mediated the relationship between social support and symptoms. Implications for future research and workplace interventions are discussed.
STUDY OF CONSTITUTIVE MODELS FOR CYCLIC LIQUEFACTION IN SAND

Liquefaction induced by cyclic loading in the saturated loose granular deposit often proves to be catastrophic. UBCSAND and PM4SAND model were basically developed to meet the need arising for the numerical evaluation of the soil liquefaction. The concept with which each of these models was formulated is essentially different. The UBCSAND model is an effective stress model framed on the basis of classical plasticity theory. The PM4SAND model is developed based on bounding surface plasticity theory embracing the concept of critical state. It considers the bias in fabric orientation during the alternative dilation and contraction. The PM4SAND has recently emerged as a model that accounts for the soil behavior under monotonic and cyclic loading over a wide range of relative density and confining pressure reasonably well. The UBCSAND model has been commonly deployed for analyzing the seismic response of real time geotechnical structures while the PM4Sand model promises its ability in exhibiting the key features observed in laboratory simulations and continues to evolve as well. In this paper the formulation and characteristic response of both the model in predicting the soil behavior under cyclic loading is overviewed and the results of single element simulation of simple shear loading using PM4Sand is presented along with the data of Fraser river sand from the literature to facilitate a comparison of model the responses of UBCSAND and PM4SAND with laboratory observations.
The Measurement of Tidal Volumes in Spontaneously Breathing Children during General Anaesthesia using a Haloscale Infant Wright Respirometer

The accuracy of tidal volume measurements made with a Wright Haloscale infant respirometer in children breathing spontaneously during general anaesthesia was assessed by a bench test. The tidal volumes and peak flow rales of 20 spontaneously breathing, anaesthetised children were measured with a pneumotacho‐graph before and during surgery, and similar volumes, at the same flow rates, were delivered by a calibrated syringe simultaneously to the respirometer and a pneumotachograph. The results reveal that the mean (+ s.d.) peak gas flow rates of children aged 6 years and less, 7.5 (± 1.6) and 9.3 (±0.1) 1/min before surgery and during surgery respectively, are significantly less than the peak flow rates, 11.3 (± 1.0) and 11.9 (+ 1.5) before and during surgery, respectively, of children aged more than 6 years; and that the respirometer underestimates tidal volume by 10% when the peak flow rate is 11 1/min, and the percentage error in tidal volume estimation by the respirometer increases as the peak gas flow declines below 10 1/min.
Influence of process conditions on quality of spouted bed dried okara

This study aimed to evaluate the spouted bed drying of okara with inert particles of polypropylene. A central composite rotatable design was carried out to verify the effect of drying air temperature and air flow on moisture content, techno-functional properties and trypsin inhibitors activity of dried product. Higher temperatures decreased emulsifying properties and trypsin inhibitor activity, probably due to thermal protein denaturation. In order to obtain a dried okara with maximum techno-functional properties and minimum moisture content and trypsin inhibitor activity, the optimal drying conditions were suggested: air temperature of 60ºC and air flow of 180 m3/h.Keywords: soy pulp; spouted bed drying; trypsin inhibitor activity; techno-functional properties; optimization
Expression of neurotrophin receptors during rat tooth development is developmentally regulated, independent of innervation, and suggests functions in the regulation of morphogenesis and innervation

Low‐affinity neurotrophin receptor (LANR) and trk receptor tyrosine kinases (trks) serve as low‐ and high‐affinity receptors for neurotrophins. Besides promoting the development and maintenance of the mammalian nervous system, it has been suggested that neurotrophins may have broader functions in the development of non‐neuronal tissues. To evaluate the possible roles of neurotrophic factors in tooth development, we performed a detailed examination of the expression patterns of neurotrophin receptors during development of the rat tooth from initiation to completion of crown morphogenesis. mRNA expression was studied by in situ hybridisation and LANR protein was localised by immunohistochemistry. Furthermore, dissected tooth germs were cultured in vitro to examine the role of trigeminal innervation in the expression of neurotrophin receptors. mRNAs for LANR, trkB, and trkC, but not trkA, were detected in developing teeth. LANR and the truncated form of trkB, which lacks the intracellular tyrosine kinase domain, were expressed throughout tooth morphogenesis and their expression patterns were largely non‐overlapping and changed spatio‐temporally. trkC was expressed after birth, and it was restricted to dental papilla mesenchyme. The expression of all receptors correlated with the development of innervation, but, in addition, the expression of LANR and trkB appeared to be associated with cell differentiation and epithelial‐mesenchymal interactions. The patterns of LANR, trkB, and trkC in teeth which underwent morphogenesis in organ culture were similar to those in vivo, which indicates that the expression of these neurotrophin receptors is not regulated by and does not depend on trigeminal innervation. The data suggest that neurotrophin receptors have roles in the development of tooth innervation, but that they also have non‐neuronal, organogenetic functions. © 1996 Wiley‐Liss, Inc.
ICAT ' 99 Portable Tactile Feedback Interface Using Air Jet

One of the authors have developed portable force feedback displays, to realize the use of force feedback for telerobotic and large-scale virtual environment applications. Tactile sensations as well as force sensations, however, are also required for initial contact detection to virtual objects, because force feedback does not come about prior to any manipulation tasks. In this paper, we have developed a portable tactile display using air jet on a trial purpose to give local shapes of virtual objects and have conducted an evaluation of the perceptual characteristics of the air jet stimulator and the two point difference threshold of index finger pads and thumb finger pads. The tactile display has a eight element array tactile stimulator. In our experiments, subjects are tested to see if they can perceived patterns presented with the device. Two test sets of a cubic geometry shape; the corners, the edge, and the plane surface of the cubic on a PC or a graphics workstation are used to present. It is experimentally verified that the portable display provides the sensation of contact.
Analysis of Exterior Acoustics using the Edge-based Smoothed Finite Element Method ( ES-FEM )

Solving acoustic problems governed by Helmholtz equation by standard finite method (FEM), the numerical dispersion error is not negligible when the wave increases due to the “overly-stiff” character of FEM. To overcome this numerical dispersion error, this paper uses the edge-based smoothed finite method (ES_FEM) to analyze the 2D exterior scattering problems. Linear triangle elements and is employed separately to mesh the 2D computational domain. Using gradient smoothing technology to build a relatively soft stiffness thus the numerical dispersion error can significantly decreased. In addition, the gradient smoothing technology transfers domain integrals involving gradient of shape function to simple boundary integrals involving only shape function, which can reduce computing cost. In order to model exterior acoustic problems defined in unbounded domains, the unbounded domain is truncated by an artificial boundary on which the non-reflecting boundary condition is imposed to replace the Somerfield condition at infinite. Examples for exterior scattering problems with known exact solutions are calculated to demonstrate the ES-FEM realization, result shows that the ES-FEM is also very accurate. Compared FEM calculation process and results, ES-FEM is more effective and could achieve much more accurate result in solving exterior acoustic problems, especially when number is large.
Future trends in earthquake-resistant design of structures

Earthquake-resistant design of structures has grown into a true multi-disciplinary field of engineering wherein many exciting developments are possible in the near future. Most notable among these are: (a) a complete probabilistic analysis and design approach; (b) performance-based design codes; (c) multiple annual probability hazard maps for response spectral accelerations and peak ground accelerations with better characterization of site soils, topography, near-field effects; (d) new structural systems and devices using non-traditional civil engineering materials and techniques; and (e) new refined analytical tools for reliable prediction of structural response, including nonlinearity, strength and stiffness degradation due to cyclic loads, geometry effects and more importantly, effects of soil–structure interaction. Some significant developments that the coming years will witness are discussed in this paper.
Improving enzymatic hydrolysis of hazelnut shells by alkaline peroxide ( APO ) pretreatment

Monomeric sugars from lignocellulosic biomass are generally produced by enzymatic hydrolysis. However, an effective pretreatment method is required to remove lignin from biomass and to increase accessibility of the enzymes to cellulose and hemicellulose. The efficiency of alkaline peroxide (APO) pretreatment method on digestibility of hazelnut shells was investigated. The biomass was pretreated with H2O2 (0, 2.0% and 4.0%, v/v) in 2% NaOH solution at different temperatures (30-6090 C) and pretreatment times (6, 24, 48 h). Considering the percent glucose recovery (81.86%), saccharification (85%) and cellulose digestion (98.74%), the optimum conditions for pretreatment were selected as an alkaline solution containing 2% H2O2, at 30°C and 6 hprocessing time. Keywords—Hazelnut shells, pretreatment, alkaline peroxide, ennzymatic hydrolysis
Modeling and Simulation of the Multi-module High Temperature Gas-cooled Reactor

The modular high temperature gas-cooled reactor (MHTGR) is characterized with the inherent safety. To enhance its economic benefit, the capital cost of MHTGR can be decreased by combining more reactor modules into one unit and realize the batch constructions in the concept of modularization. In the research and design of the multi-module reactors, one difficulty is to clarify the coupling effects of different modules in operating the reactors due to the shared feed water and main steam systems in the secondary loop. In the advantages of real-time simulation and coupling calculations of different modules and sub-systems, the operation of multi-module reactors can be studied and analyzed to understand the range and extent of the coupling effects. In the current paper, the engineering simulator for the multi-module reactors was realized and able to run in high performance computers, based on the research experience of the HTR-PM engineering simulator. The models were detailed introduced including the primary and secondary loops. The steady state of full power operation was demonstrated to show the good performance of six-module reactors. Typical dynamic processes, such as adjusting feed water flow rates and shutting down one reactor, were also tested to study the coupling effects in multi-module reactors.
Quantum physics , history , philosophy and NoS in traditional physics classrooms

History, philosophy and the nature of science (NoS) are advocated as important elements of science education. Quantum physics has been shown to motivate physics students due to its philosophical aspects, making the topic suited for learning activities that foster understanding of NoS and of the history and philosophy of physics. This paper discusses experiences from teaching senior high school quantum physics through such learning activities. Web-based teaching modules let students explore quantum physics through collaborative learning and historical and philosophical contexts. Data consists of seven focus groups with in total 40 participants from seven physics classrooms and one focus group with five teachers. Data were collected in 2014-2015 and analyzed qualitatively using a thematic approach, focusing on history, philosophy, NoS, motivation and physics classroom culture. Although students were motivated by physics history and philosophy, their recognition of these aspects and NoS as knowledge in its own right appears to have been limited by their enculturation into a traditional physics classroom oriented towards content knowledge, assessment and exams rather than physics history, context and processes. We suggest that physics history, philosophy and NoS learning goals and assessment criteria should be made more explicit to students, and assessment tools developed for teachers and exam developers. Introduction Understanding of the history, philosophy and nature of science (NoS) has long been advocated as an important element in science education (Abd-El-Khalick, 2013; Monk & Osborne, 1997). This is also reflected in curriculum documents such as the Next Generation Science Standards (NGSS, 2013). The Norwegian national curriculum for the optional physics subject for the final year of high school aims to help students “create an awareness that physics is part of our cultural heritage and that the subject must be viewed in a historical perspective” and strengthen their “ability to differentiate between scientifically-based knowledge and knowledge not based on scientific methods” (NDET, 2006). Quantum physics has been shown to motivate Norwegian physics students due to its philosophical aspects (Angell, Guttersrud, Henriksen, & Isnes, 2004), making the topic well suited as a starting point for implementing teaching and learning activities that foster understanding of NoS and of the historical and philosophical aspects of physics. This is also in accordance with learning goals in the Norwegian physic curriculum, which states for instance that students should be able to “give a qualitative account of how results from experiments with photoelectric effect, Compton scattering and the wave nature of particles represent a break with classical physics” and to “give an account of Heisenberg’s uncertainty relations, describe the phenomenon ‘entangled photons’ and give an account of their epistemological consequences” (NDET, 2006).