Miracle-dz/UniFAR-FTUs huggingface dataset:
Data-driven reduced order modelling of tide-induced sand bars in confined channels

<div>Tidal bars are bed forms in tidal channels that have a wave-like structure in both the along-channel and cross-channel direction. They are found in tidal channels all around the globe, for example, in the Western Scheldt in the Netherlands, the Exe Estuary in England, the Ord River Estuary in Australia and the Venice Lagoon in Italy. Typically, tidal bars are several meters high, have wavelengths of 1-15 km and migration speeds of meters per day. Understanding their dynamics is important as they are invaluable for many living organisms (e.g., migrating birds) but they hamper marine traffic. </div><div>&#160;</div><div> <div>It has been shown, by means of a linear stability analysis, that these bars emerge due to inherent feedbacks between the tidal currents and the erodible bed. When the bars mature, their dynamics becomes nonlinear. Schramkowski et al. (2004) applied a bifurcation analysis to analyse the bar dynamics, but their method was limited to small bottom friction. Here, we developed a numerical (time integration) model that simulates the nonlinear dynamics and the corresponding (stable) equilibrium patterns for realistic parameter values. </div> <div>&#160;</div> <div> <div>Using the output of the numerical model we derive a reduced order model with a method called SINDy (Brunton et al., 2016). Loiseau and Brunton (2018) showed that from output of complex numerical models simulating fully nonlinear fluid flows, SINDy can identify small systems of equations which govern the complex flows. Here we show that, for parameters regimes where the dynamics is weakly nonlinear, SINDy finds a Landau type equation that reproduces the tidal bar dynamics well. The Landau equation is a nonlinear ordinary differential equation in terms of the Fourier amplitude of the pattern that initially has the largest growth rate. The form of this equation corresponds with the one that is expected from the symmetry of the patterns. Also, the application of SINDy to the fully nonlinear dynamics of tidal bars will be discussed. </div> <div>&#160;</div> <div>&#160;</div> <div> <div>Brunton, S.L. , Proctor, J.L. , and Kutz, J.N. (2016). Discovering governing equations from data by sparse identification of nonlinear dynamical systems. Proceedings of the National Academy of Sciences, 113(15):3932-3937. </div> <div>Loiseau, J.-C. and Brunton, S.L. (2018). Constrained sparse Galerkin regression. Journal of Fluid Mechanics, 838:42-67. </div> <div>Schramkowski, G.P., Schuttelaars, H.M. , and de Swart, H.E. (2004). Nonlinear channel-shoal dynamics in long tidal embayments. Ocean Dynamics, 54(3):399-407. </div> </div> </div> </div>
Cardiac Functions & Lipid Profile In Obese Children & Adolescents

Background: Obesity is a disease which results from genetic or lifestyle factors. Such diseases are called Non communicable diseases. The epidemic of obesity among youth is spreading at an alarming rate due to lack of physical activity, dietary habits. The percentage of youths who are at risk of becoming overweight continues to increase. National data indicates that 16% of children aged six to nineteen years are overweight. (1) Considering the high prevalence of obesity among children and adolescents and its associated cardiovascular complications like hypertension, left ventricular hypertrophy, increased left ventricular mass, decreased left ventricular ejection fraction, the present study was planned to assess cardiac functions and lipid profile in obese children and adolescents. Early detection and intervention can help in reducing the complications associated with obesity. Objective: Primary objective is to assess cardiac functions and lipid profile in obese children and adolescents. Methodology: 100 obese children and adolescents in the age group 6-18 years were taken after excluding obese children with evidence of endocrine disease, malformation syndromes and iatrogenic obesity (drug treatments). Results: In the present study 7% subjects were hypertensive while 8% were prehypertensive. 71.43% children with hypertension were performing physical activity for < 30 min in 1-3 days/week while 49.11% normotensive children were performing physical activity for > 30 min per day. 3% obese children were having abnormal LVEF on 2DECHO . All the 3 obese children with abnormal LVEF were having physical activity less than 30 min in 1-3 days /week and the difference was statistically significant. All the three children with abnormal LVEF were hypertensive and the difference was statistically significant. 6% children were having raised serum cholesterol >190mg/dl. Serum triglyceride >150mg/dl was observed in 17% obese children. HDL level <20mg/dl was observed in 7% children while LDL above 130mg/dl was observed in 6% children. The proportion among male and female children was comparable. Conclusion: Cardiovascular complications of adulthood in obese children and adolescents may be prevented by early identification and intervention in the form of healthy life style, dietary intake and physical activity.
The Drosophila ERG channel seizure plays a role in the neuronal homeostatic stress response

Neuronal physiology is particularly sensitive to acute stressors that affect excitability, many of which can trigger seizures and epilepsies. Although intrinsic neuronal homeostasis plays an important role in maintaining overall nervous system robustness and its resistance to stressors, the specific genetic and molecular mechanisms that underlie these processes are not well understood. Here we used a reverse genetic approach in Drosophila to test the hypothesis that specific voltage-gated ion channels contribute to neuronal homeostasis, robustness, and stress resistance. We found that the activity of the voltage-gated potassium channel seizure (sei), an ortholog of the mammalian ERG channel family, is essential for protecting flies from acute heat-induced seizures. Although sei is broadly expressed in the nervous system, our data indicate that its impact on the organismal robustness to acute environmental stress is primarily mediated via its action in excitatory neurons, the octopaminergic system, as well as glia. Furthermore, our studies suggest that human mutations in the human ERG channel (hERG), which have been primarily implicated in the cardiac Long QT Syndrome (LQTS), may also contribute to the high incidence of seizures in LQTS patients via a cardiovascular-independent neurogenic pathway. Author Summary Neurons are extremely sensitive to diverse environmental stressors, including rapid changes in the ambient temperature. To buffer stress, all animals have evolved diverse physiological mechanisms to protect neuronal activity from acute and chronic stressors, and failures of these safeguards often lead to hyperexcitability, episodic seizures, and chronic epilepsy. Although seizures and related syndromes are common, their underlying molecular and genetic factors, and their interactions with environmental triggers, remain mostly unknown. Here, we show that in the fruit fly, mutations in the ERG voltage-gated potassium channel seizure (sei), an ortholog of the human hERG channel that has been previously implicated in the cardiac Long-QT syndrome, could also increase seizure susceptibility. We demonstrate that in addition to its cardiac expression, the sei channel is broadly expressed in the nervous system, specifically localized to axonal projections, and is specifically required in excitatory and modulatory neurons, as well as non-neuronal glia for maintaining organismal resistance to heat-induced seizures. Thus, our work suggests that the previously reported increase in seizure susceptibility in individuals with mutations in hERG are likely directly related to its neuronal action, independent of its cardiac function.
Bioremediation of Petroleum Hydrocarbons Contaminated Soil using Bio piles System

This study was focused on biotreatment of soil which polluted by petroleum compounds (Diesel) which caused serious environmental problems. One of the most effective and promising ways to treat diesel-contaminated soil is bioremediation. It is a choice that offers the potential to destroy harmful pollutants using biological activity. Four bacterial strains were isolated from diesel contaminated soil samples. The isolates were identified by the Vitek 2 system, as Sphingomonas paucimobilis, Pentoae species, Staphylococcus aureus, and Enterobacter cloacae. The potential of biological surfactant production was tested using the Sigma 703D stand-alone tensiometer showed that these isolates are biological surfactant producers. The better results of the surface tension reduction test were obtained using the mixed bacterial culture which reduced the surface tension of the medium from 66mN/m to 33.89mN/m. For further evidence of the biodegradation effect of these isolates individually and as a mixed culture, which was supported by the use of Gas-Chromatography technology confirming the occurrence of biodegradation. The capability of mixed bacterial culture was examined to remediate the diesel contaminated soil in bio piles system. Two pilot scale bio piles (25 kg soil each) were constructed containing soils contaminated with approximately 2140 mg/kg total petroleum hydrocarbons (TPHs). Both systems were equipped with oxygen to provide aerobic conditions, incubated at ambient temperature and weekly sampling within 35 days (during summer season). Overall 75.71 % of the total petroleum hydrocarbons were removed from the amended soil and 33.18 % of the control soil at the end of study period. The study concluded that the ex-situ bioremediation (bio piles) is a good option for treating the soil contaminated with diesel as economical and environmentally friendly.
Characteristics of the Protein Complexes and Pores Formed by Bacillus cereus Hemolysin BL

Bacillus cereus Hemolysin BL is a tripartite toxin responsible for a diarrheal type of food poisoning. Open questions remain regarding its mode of action, including the extent to which complex formation prior to cell binding contributes to pore-forming activity, how these complexes are composed, and the properties of the pores formed in the target cell membrane. Distinct complexes of up to 600 kDa were found on native gels, whose structure and size were primarily defined by Hbl B. Hbl L1 and L2 were also identified in these complexes using Western blotting and an LC-MS approach. LC-MS also revealed that many other proteins secreted by B. cereus exist in complexes. Further, a decrease of toxic activity at temperatures ≥60 °C was shown, which was unexpectedly restored at higher temperatures. This could be attributed to a release of Hbl B monomers from tight complexation, resulting in enhanced cell binding. In contrast, Hbl L1 was rather susceptible to heat, while heat treatment of Hbl L2 seemed not to be crucial. Furthermore, Hbl-induced pores had a rather small single-channel conductance of around 200 pS and a probable channel diameter of at least 1 nm on planar lipid bilayers. These were highly instable and had a limited lifetime, and were also slightly cation-selective. Altogether, this study provides astonishing new insights into the complex mechanism of Hbl pore formation, as well as the properties of the pores.
Geodesic Vulnerability Approach for Identification of Critical Buses in Power Systems

One of the most critical issues in the evaluation of power systems is the identification of critical buses. For this purpose, this paper proposes a new methodology that evaluates the substitution of the power flow technique by the geodesic vulnerability index to identify critical nodes in power grids. Both methods are applied comparatively to demonstrate the scope of the proposed approach. The applicability of the methodology is illustrated using the IEEE 118-bus test system as a case study. To identify the critical components, a node is initially disconnected, and the performance of the resulting topology is evaluated in the face of simulations for multiple cascading faults. Cascading events are simulated by randomly removing assets on a system that continually changes its structure with the elimination of each component. Thus, the classification of the critical nodes is determined by evaluating the resulting performance of 118 different topologies and calculating the damage area for each of the disintegration curves of cascading failures. In summary, the feasibility and suitability of complex network theory are justified to identify critical nodes in power systems.
Development of a Gallium-Containing One-Bead One-Compound Peptide Library for the Discovery of New Molecular Imaging Probes

II CO-AUTHORSHIP STATEMENT . III ACKNOWLEDGMENTS . V TABLE OF CONTENTS . VI LIST OF TABLES . IX LIST OF FIGURES . X LIST OF SCHEMES . XIV LIST OF ABBREVIATIONS . XV 1 CHAPTER 1: INTRODUCTION . 1 1.1 MOLECULAR IMAGING . 1 1.2 PET AND SPECT IMAGING AGENTS . 4 1.3 GA AS AN IMAGING ENTITY . 8 1.4 PEPTIDES AS TARGETING ENTITIES . 10 1.5 DISCOVERY AND DEVELOPMENT OF PEPTIDE-BASED IMAGING AGENTS . 13 1.6 ONE-BEAD ONE-COMPOUND PEPTIDE LIBRARIES . 18 1.7 SEQUENCE DECONVOLUTION AND IDENTIFICATION OF PEPTIDE SEQUENCES . 21 1.8 [GA]DOTA PEPTIDE LIBRARIES . 23 1.9 THESIS RATIONALE . 25 2 CHAPTER 2: SYNTHESIS, COORDINATION AND SEQUENCE DECONVOLUTION OF A [GA]DOTA-OCTAPEPTIDE . 27 2.
Temperature dependence of the uptake coefficients of nitric acid, hydrochloric acid and nitrogen oxide (N2O5) by water droplets

The uptake of HNO{sub 3}, HCl, and N{sub 2}O{sub 5} by aqueous surfaces has been measured as a function of temperature over the range from 268 to 294 K. The experimental method employs a monodisperse train of droplets of 200-{mu}m diameter in a low-pressure flow reactor. The value of the uptake coefficient increases with decreasing temperature for each of these species. The similarity in the absolute values of {gamma} at all temperatures for HNO{sub 3}, HCl, and H{sub 2}O{sub 2} (previously reported) suggests that the uptake coefficient is a measure of the rate of physical solvation and is therefore identified as the mass accommodation coefficient. Therefore, the tropospheric cloud chemistry of these species will be determined by their solubility and aqueous-phase reactivity.
Role of sediment in the marine C cycle—insights from a coupled ocean-sediment model

<p>Fluxes of particles and solutes between deep ocean and marine sediment are essential in the biogeochemical cycles of carbon and nutrients, such as nitrogen, silicon and iron. On a millennial time scale, sediment accumulation connects the ocean with the surface lithosphere which impacts the climate through weathering. Despite the importance of sediments in the climate system, fluxes between ocean and sediment are poorly constrained and most of the ocean models use very simplified parameterisation based on some measurements on shelves. </p><p>Here we like to present the coupling of the marine biogeochemical model REcoM2 (Regional Ecosystem Model, version2) coupled with the sediment model MEDUSA (Model of Early Diagenesis in the Upper Sediment with Adaptable complexity) for a better understanding of the role of sediments in the marine carbon cycle. MEDUSA resolves chemical reactions and physical processes within the marine sediments. As REcoM allows deviations from the Redfield C:N ratio both in phytoplankton production and remineralisation, the molar ratio of carbon and nitrogen in sinking fluxes vary with time and depth. Our MEDUSA set-up is made to be able to deal with flexible stoichiometry in sinking fluxes by resolving two classes of organic matter with different C:N ratios and degradation rates. We performed model-data comparisons of calcite, opal and particulate organic matter in sediment for present-day to constrain the biological productivity and sinking behaviour of particles in water column, and studied the role of the marine carbon cycle for glacial carbon storage and the drawdown of atmospheric CO2 in simulations under glacial climate conditions. &#160;</p>
Facile real time detection of membrane colocalization of RAS superfamily GTPase proteins in living cells

Members of the RAS family of GTPases (KRAS4A, KRAS4B, HRAS, and NRAS) are the most frequently mutated oncogenes in human cancers. The CAAX motif in the C-terminal hypervariable region (HVR-CAAX domain) contains the cysteine residue that is critical for protein prenylation that enables RAS protein membrane localization, homodimer/oligomer formation, and activation of effector signaling and oncogenic activity. However, it remains unclear if RAS can interact with other prenylated proteins, and if so, how this impacts RAS function. Here we use a newly developed quantifiable Recombinase enhanced Bimolecular Luciferase Complementation strategy (ReBiL2.0) to investigate some of the requirements for RAS superfamily small GTPase protein interactions, and whether this requires cell membrane localization. ReBiL enables such analyses to be done at physiologic expression levels in living cells. Our results confirm that the C-terminal prenylated HVR-CAAX domain is sufficient to direct KRAS and heterologous proteins to colocalize in the cell membrane. We discovered that KRAS also colocalizes with a subset of small GTPase superfamily members including RAC1, RAC2 and DIRAS3 in a prenylation-dependent manner. KRAS colocalization or co-clustering with heterologous proteins can impact KRAS downstream signaling. ReBiL2.0 thus provides a rapid, simple and straightforward method to identify and characterize the colocalization of membrane-associated proteins and to discover agonists and antagonists thereof.
Production of MCM-41 Nanoparticles with Control of Particle Size and Structural Properties: Optimizing Operational Conditions during Scale-Up

The synthesis of Mobil Composition of Matter 41 (MCM-41) mesoporous silica nanoparticles (MSNs) of controlled sizes and porous structure has been performed at laboratory and pilot plant scales. Firstly, the effects of the main operating conditions (TEOS –Tetraethyl ortosilicate– addition rate, nanoparticle maturation time, temperature, and CTAB –Cetrimonium bromide– concentration) on the synthesis at laboratory scale (1 L round-bottom flask) were studied via a Taguchi experimental design. Subsequently, a profound one-by-one study of operating conditions was permitted to upscale the process without significant particle enlargement and pore deformation. To achieve this, the temperature was set to 60 °C and the CTAB to TEOS molar ratio to 8. The final runs were performed at pilot plant scale (5 L cylindrical reactor with temperature and stirring speed control) to analyze stirring speed, type of impeller, TEOS addition rate, and nanoparticle maturation time effects, confirming results at laboratory scale. Despite slight variations on the morphology of the nanoparticles, this methodology provided MSNs with adequate sizes and porosities for biomedical applications, regardless of the reactor/scale. The process was shown to be robust and reproducible using mild synthesis conditions (2 mL⋅min−1 TEOS addition rate, 400 rpm stirred by a Rushton turbine, 60 min maturation time, 60 °C, 2 g⋅L−1 CTAB, molar ratio TEOS/CTAB = 8), providing ca. 13 g of prismatic short mesoporous 100–200 nm nanorods with non-connected 3 nm parallel mesopores.
Young water fractions at diverse time scales are driven by varying runoff generation processes in a Mediterranean small research catchment

The time water resides within a catchment has important implications for the water availability and quality for both ecosystem and human use. Here, we look at the short-term water transport using the concept of young water fraction (Fyw), defined as the proportion of water that is younger than 2-3 months. The study was conducted for the 0.56 Km 2 sub-humid Can Vila catchment (Vallcebre Research Catchments). During a period of over 58 months, the isotope ratios ( 2 H and
Impact of kangaroo care after caesarean section on paternal-infant attachment and involvement at 12 months: A longitudinal study in Turkey.

The mother's first meeting with the baby after the caesarean section is usually delayed due to the reasons arising from the mother and the baby in Turkey. Although there are many benefits of kangaroo care (KC) intervention between the mother and the newborn, there is a limited number of studies on the KC intervention between the newborn and the father after caesarean section in international literature, and there are none in Turkey. This study was carried out to determine the effect of fathers and infants who participated in KC, immediately after birth by caesarean section, on paternal-infant attachment and the fathers' involvement in infant care in the 12th month. The study was conducted as a longitudinal study with a control group. Initially, the sample consisted of 60 fathers. However, the study was completed with 48 fathers. KC intervention was practised to the couple of the father and the infant in the experimental group, while no practice was given to the control group. Fathers in the experimental group were told that they should continue to practice KC intervention at least two times a week until their baby will be 1-year-old. The data collection forms were given to fathers face-to-face in the first interview, and then through phone calls and emails after 12 months. The status of the fathers in the experimental group fathers' involvement in infant care of the baby (p = .005) was significantly higher than the control group. The mean score for the Postnatal Paternal-Infant Attachment Questionnaire (PPAQ), in fathers who participated in KC intervention, was higher than that of fathers who did not participate in the KC intervention (p < .005). The results of this study demonstrated that the paternal-infant attachment and the fathers' participation in infant care were more positive in fathers and babies who performed the KC intervention.
Protective Effects of Methanol Extract of Perilla Seed Meal against Oxidative Stress in HepG2 Cells

This study aimed to evaluate the protective effect of methanol extract of perilla seed meal (PSE) against oxidative stress induced by tert-butylhydroperoxide (t-BHP) in HepG2 cells. The total phenolics and flavonoid contents of PSE were 41.36 ± 1.00 mg gallic acid equivalents/g of residue and 38.20 ± 0.17 mg catechin equivalents/g of residue, respectively. Quantitative analysis of the major constituent phenolic acids and tocopherols was achieved by using high-performance liquid chromatography. PSE (10-100 μg/mL) pretreatment significantly prevented t-BHP-induced cytotoxicity in HepG2 cells. Oxidative damage induced by t-BHP was accompanied by glutathione depletion, ROS generation, and lipid peroxidation, which were all significantly ameliorated by PSE. The cytoprotective effect of PSE was attributed to the modulation of cellular antioxidant defense enzymes such as glutathione peroxidase, superoxide dismutase, glutathione reductase, and catalase. Collectively, the bioactive compounds of PSE were able to prevent oxidative stress through the enhancement of the antioxidant indices.