Miracle-dz/UniFAR-FTUs huggingface dataset:
Intracellular calcium, preconditioning and regulation of cellular respiration in heart

Heart muscle has to work constantly throughout the life and its energy metabolism is heavily dependent on a continuous supply of oxygen. Energy metabolism must be effectively regulated to meet the demands of changing workloads in different circumstances. If the oxygen supply is interrupted, the function of the heart is easily disturbed and cells injured. Calcium metabolism is of great importance in these pathological conditions. In this thesis respiratory regulation was studied by non-destructive optical methods in mouse heart. The myoglobin-deficient mouse was used as an experimental model to avoid the artefact caused by intracellular myoglobin. Results show that increased consumption of energy and oxygen lead to concomitant reduction of cytochrome aa3 and oxidation of flavoproteins. This finding supports the view that cell respiration in intact myocardium is dominantly regulated at the level of the respiratory chain. The intracellular Ca2+ accumulation during ischemia is one of the major causes of irreversible ischemia-reperfusion injury. Ischemic preconditioning (IPC) has been shown to protect the heart muscle significantly from ischemic damage. In this thesis Ca2+ accumulation during ischemia and reperfusion was studied in perfused rat heart using Fura-2 as a fluorescent Ca2+ indicator. As there is a significant decrease in intracellular pH during prolonged ischemia, the pH-dependency of Fura-2 signal was taken into account. It was found that IPC attenuates Ca2+accumulation during ischemia and this was connected to a decrease in mitochondrial membrane potential. Both IPC and the pharmacologically induced preconditioning with the mitoKATP opener diaxozide were shown to be associated with increased production of superoxide monitored by means of lucigenin chemiluminescence. The superoxide production correlated with the oxidation-reduction state of flavoproteins. We also describe here a method for measuring of intracellular free Ca2+ in mouse heart during ischemia by simultaneous monitoring of Fura-2 and the pH probe BCECF fluorescence by means of dual wavelength excitation of both probes. The paradoxical decrease of Fura-2 fluorescence during ischemia indicating decreasing intracellular Ca2+ concentration was due to the pH effect on the dissociation constant of the Fura-2-Ca2+ complex. When the pH-dependency of Fura-2 was compensated, an extensive Ca2+ accumulation during ischemia was detected. Much of the previous literature on this subject must be re-evaluated because the pH-dependency of intracellular Ca2+ probes has been largely overlooked.
Culture-independent analysis of bacterial community composition during bioremediation of crude oil-polluted soil.

Aim: To use cultivation-independent techniques based on DGGE of PCR-amplified 16S rRNA gene and to evaluate bacterial community composition during bioremediation of crude oil-polluted soil. Study Design : Molecular fingerprints of bacterial populations involved in the active phase of crude oil biodegradation were generated with DGGE after 16S rRNA gene amplification. Place and Duration of Study: Department of Microbiology and Plant Pathology, University of Pretoria, South Africa, between March and August 2008. Methodology: Crude oil-degrading bacteria in soil microcosms contaminated with 4% crude oil and then biostimulated with nitrogen-phosphorus-potassium inorganic fertilizer (NPK: designated PN soil), calcium ammonium nitrate (designated PU soil) and poultry droppings (designated PP soil) respectively were characterized with PCR of the gene for the small subunit (SSU) of the bacterial ribosome. Total culturable heterotrophic and hydrocarbon utilizing bacteria were enumerated using plate count and Bushnell Haas media. Total organic carbon content was measured throughout the study period to indirectly determine the effect of Lite 2.01. Sequence identification was performed using BLAST. Results: Dendogram of the DGGE bands constructed using Jaccard coefficient algorithm revealed that communities from PU and PP-amended soils each formed distinct clades whereas PN treated soil showed less association when compared with PU and PP respectively. Fifty distinct bands were excised, reamplified by PCR and sequenced. Sequence analysis revealed the presence of phylogenetically distinct known hydrocarbon degrading bacteria like Corynebacterium spp. , Dietzia spp. , Janibacter sp. low G+C Gram positive bacterial clones Nocardioides spp. , Rhodococcus erythropolis and uncultured bacterial clones. Forty successful sequence data obtained from the excised DGGE bands were submitted to GenBank database under accession numbers GU451069 to GU451108. Chromatograms of the residual hydrocarbons in test treatments and controls showed that biodegradation occurred markedly in treated soils in this order PN>PU>PP while no significant loss was observed in the oil-contaminated control on days zero and 42 respectively. Bacterial counts increased significantly in PN, PU and PP treatments and not in controls PC and OC. Total organic carbon increased appreciably in PN, PU and PP respectively from day zero to day 28. Electron micrographs of microbial consortia in the nutrient-amended soils revealed presence of active populations induced by biostimulation as against the sparsely populated controls. Conclusion: The results suggest that nutrient amendment stimulates and selects indigenous soil bacteria that are able to degrade petroleum hydrocarbons.
Relationship between range of the euphotic zone and visibility of Secchi disc in three lakes of Łęczna - Włodawa lake district

The measurements of the intensity and distribution of photosynthetic active radiation (PAR), were conducted in three lakes with different trophy and morphometry. One affirmed, that in spite high correlation between range of euphotic zone and visibility of Secchi disc, the value of conversion rate ZEUF/ZSD had changed since 1,4 to 5. Low values were in lake Rogóźno during blue-green algae bloom in metalimnion. However high values were in polimictic lake Głębokie Uścimowskie and lake Krasne and they be connected with large quantity of suspensions from sediments in water.
Private land and public goods: process lessons from habitat conservation planning.

In our interconnected, shared-power world, we have the challenge of balancing the rights of using privately held forest resources with publically held rights regarding environmental quality. Private property rights are a fundamental value in the history of our society and are firmly imbedded in both our Constitution and common law (Flick, 1994). More recently, environmental stewardship has grown to also become an important American value and has been incorporated into policy and law through numerous environmental statutes. These private and public rights have not been well integrated but rather have collided, forming deep divisions between people and between and among various institutions including government, the private sector and interest groups within our civic society (Shannon, 1991; Boyte, 1994; Yaffee, 1994; Snow, 2001). These divisions have put in place an adversarial culture and incentives of gridlock common to natural resource policy during the last 30 years (Dukes, 1996; Ostermeier, 1999). The reality of our existence is that we live in a systems world and that we are becoming increasingly more interconnected. Conceptually we recognize this interconnection and the need for cooperation, but our history, culture and incentives in our market-dominated society push us toward competition. This is the paradox of our times, ‘we preach cooperation while we practice competition’ (Yaffee, 1998). In this chapter, we evaluate the process of Habitat Conservation Planning under the Endangered Species Act (ESA) to better understand how private and public rights regarding privately held forest resources might be integrated and balanced. In the evaluation we focus on how decision making is conducted in Habitat Conservation Planning and do not evaluate the plans themselves. Our interest is in the process of conservation planning and what we can learn from these processes about the challenges of balancing private and public rights regarding private forest lands.
Consequences From the Redistribution of Urban Poverty During the 1990s: A Cautionary Tale

Conventional wisdom notwithstanding, the recent spatial redistribution of the urban poor does not necessarily bode well for the future. During the 1990s, the share of metropolitan population living in census tracts with high percentages (more than 40%) of poverty indeed fell significantly, but the shares with 10% to 20% and 20% to 40% poverty rates each rose 1 percentage point. These latter shifts are worrisome because many neighborhoods may have been pushed over their thresholds where poverty concentrations start to create significant external effects for neighbors.
Hollow cathode effect modified time-dependent global model and high-power impulse magnetron sputtering discharge and transport in cylindrical cathode

High-power impulse magnetron sputtering boasts high ionization, large coating density, and good film adhesion but suffers from drawbacks such as low deposition rates, unstable discharge, and different ionization rates for different materials. Herein, a cylindrical cathode in which the special cathode shape introduces the hollow cathode effect to enhance the discharge is described. To study the discharge performance of the cylindrical cathode, a hollow cathode effect modified time-dependent global model is established to fit the discharge current pulses. The simulation results indicate that the cylindrical cathode has relatively large Hall parameters of 24 (700 V) to 26 (1000 V). Compared to the planar cathode, the cylindrical cathode has a larger plasma density as a result of the hollow cathode effect. In addition, the ionization rate and ion return probability increase by about 3.0% and 4.3%, respectively. Particle transport derived from the plasma diffusion model shows that the magnetic field enables further diffusion of ions than atoms, resulting in nearly pure ion deposition on the substrate. The deposition rate and ion current measured experimentally support the simulation model and results, and this model provides a universal platform to simulate plasma systems with similar structures.
Improving the throughput of transportation networks with a time-optimization routing strategy

ABSTRACT Traffic congestion, a common and complicated phenomenon in urban transportation systems, is attracting increasing attention from researchers in Geographical Information Science (GIS) and other fields. In this study, we illustrate a general mechanism that reveals the relationship between travel time and dynamic traffic conditions. We measure a vehicle’s travel time to its destination along any path, where the travel time is calculated based on the path length and on the real-time traffic volume and transport capacity of each road segment on the path. On the basis of this measurement, we present a simple dynamic routing strategy that allows each vehicle to dynamically choose the path to its destination while imposing the minimum travel time. The application of our routing algorithm to the Chengdu street network, Barabási–Albert scale-free network and Erdös–Rényi random network shows that the proposed strategy remarkably improves network throughput and balances traffic load distribution. Our findings suggest that mining the time mechanism of network transport is important to explore efficient time-optimization routing algorithms to enhance the transport capacity of urban street networks and other kinds of networks.
Face Labelings of Graphs

The thesis deals with the problem of labeling the vertices, edges and faces of a plane graph in such a way that the label of a face and the labels of vertices and edges surrounding that face add up to a weight of that face. A labeling of a plane graph is called d-antimagic if for every positive integer s, the s-sided face weights form an arithmetic progression with a difference d. Such a labeling is called super if the smallest possible labels appear on the vertices. The thesis is devoted to study of super d-antimagic labelings of type (1, 1, 1) for antiprisms and disjoint union of prisms. We consider the antiprism and prism as three cycle parts: the outer cycle, the inner cycle and the middle cycle. To label the inner, the outer and the middle cycles we use the edge-antimagic total labelings and the vertex-antimagic total labelings. These labelings combine to a resulting super d-antimagic labeling of type (1, 1, 1) for the required values of difference d.
THE OPTIMAL INFLATION TARGET IN AN ECONOMY WITH LIMITED ENFORCEMENT

We formulate a central bank's problem of selecting an optimal long-run inflation rate as the choice of a distorting tax by a planner who wishes to maximize discounted stationary utility for a heterogeneous population of infinitely lived households in an economy with constant aggregate income and public information. Households are segmented into agents who store value in currency alone and agents who have access to both currency and loans. We show that the optimum inflation rate is positive, because inflation reduces the value of the outside option for credit agents and raises their debt limits.
In vitro arrow cane (Gynerium sagitatum Aubl.) multiplication in double phase medium

Arrow cane (Gynerium sagitatum Aubl.) is a Poaceae species used as fiber source to make traditional and valuable handmade craftsmanship by indigenous communities in Northern Colombia. Since no commercial crops are established fiber needs are taken from natural plant populations affecting ecosystem. A micropropagation protocol to clonally multiply large quantities of arrow cane plant material for planting commercial crops has been developed; however, micropropagated plants are costly compared to naturally extracted plant material. To reduce micropropagated plants costs, in the present research a double phase medium formulation along with continuous shoot culture with no periodic transfers to fresh medium was compared to semisolid medium system with subculture every four weeks with respect to multiplication rate and costs of micropropagated plants. The results showed that continuous culture of explants with double phase medium and no periodic transfers resulted in higher multiplication rates and larger shoots compared to shoots cultured using the conventionalsemisolid medium system and transfer to fresh medium every four weeks. Plants from both, semisolid and double phase culture system, fully adapted and recovered when transferred to ex vitro conditions. The cost analysis showed that double phase cultured shoots are ≥20% less expensive.
Guaranteed Passive Joel PhilliDs Balancin ! Order Ret Transformations for Model luction

The major concems in state-of-the-art model reduction algorithms are: achieving accurate models of sufficiently small size, numerically stable and efficient generation of the models, and preservation of system properties such as passivity. Algorithms such as PRIMA generate guaranteed-passive models, for systems with special intemal structure, using numerically stable and efficient Krylov-subspace iterations. Truncated Balanced Realization (TBR) algorithms, as used to date in the design automation community, can achieve smaller models with better error control, but do not necessarily preserve passivity. In this paper we show how to construct TBR-like methods that guarantee passive reduced models and in addition are applicable to state-space systems with arbitrary intemal structure. Categories 8z Subject Descriptors: B.7. 2 Simulation, B.8. 2 Performance Analysis & Design Aids, 1.6 Simulation & Modeling. General Terms: Algorithms, Performance, Design,
NBER WORKING PAPER SERIES THE HARROD-BALASSA-SAMUELSON HYPOTHESIS: REAL EXCHANGE RATES AND THEIR LONG-RUN EQUILIBRIUM

Jordà is grateful for the support from the Spanish MICINN National Grant SEJ2007-6309 and the hospitality of the Federal Reserve Bank of San Francisco during preparation of this manuscript. Taylor also gratefully acknowledges research support from the Center for the Evolution of the Global Economy at the University of California, Davis. The views expressed herein are those of the authors and do not necessarily reflect the views of the National Bureau of Economic Research.
Multi-parameter optimization of a loose focusing high flux high-harmonic beamline

We perform a multi-dimensional parameter scan in the generation of high-order harmonics, with the main purpose to find the macroscopic conditions that optimize the harmonic yield in a specific spectral domain, around 40 eV for this particular case. The scanned parameters are the laser pulse energy, gas pressure, interaction cell position relative to focus and the cell length, while the fixed parameters are chosen to model a loose focusing configuration which is used in many existing laboratories. We performed the simulations with a 3D non-adiabatic model complemented by a detailed analysis of the phase matching mechanisms involved in an efficient harmonic generation. Based on the results we identify a range of parameter combinations that lead to a high yield in the specified spectral domain. The method and results presented here can be the framework for the design and construction of high flux high-order harmonic generation beamlines.
A HYDRO-CLIMATIC MODELING FRAMEWORK FOR ADAPTIVE WATER RESOURCES MANAGEMENT IN THE GREAT LAKES BASIN

This dissertation addresses water resources decision making in the Great Lakes Basin by developing a multi-model framework for climate change impact assessment, including integrated climate and hydrologic modeling. Physically based watershed models, using soil moisture accounting and temperature index (degree-day) snowmelt algorithms, are developed, calibrated and validated to simulate baseflow, snowmelt, and surface runoff under historic conditions. Comparison with an existing model of the Great Lakes basin, the NOAA Large Basin Runoff Model (LBRM), showed improvements resulting from the increased spatial resolution and use of a more process-based snow algorithm in the Hydrologic Engineering Center’s Hydrologic Modeling System (HECHMS). As an alternative to the physically based hydrologic models, and particularly appealing for ungauged basins or locations where record lengths are short, regional regression models are developed to directly predict selected streamflow quantiles, using physical basin characteristics as well as meteorological variables output by general circulation models (GCMs). Hydrologic responses are evaluated based on different combinations of hydro-climatic modeling approaches, when driven using GCM outputs. The model results, presented in a probabilistic context of multi-model predictions, provide insights to potential model weaknesses, including comparatively low runoff predictions from hydrologic models using temperature proxy potential evapotranspiration (PET) approaches and limited accuracy of regional regression models for small, groundwater-dominated watersheds. Additional insights are gained by replacing the temperature-proxy PET method with an approach that maintains a consistent energy budget between the climate and hydrologic models. Hydrologic projections for the Great Lakes watersheds under future climates are evaluated using the model with a consistent energy budget, and differences in responses are explained by differences in watershed characteristics, aridity index, and the future climate projections. It is proposed that these hydrologic projections inform adaptive water resources decision making through a multi-stage decision model, and applications to water withdrawal permitting and BMP implementation are described. The framework developed herein demonstrates an integrated analysis of climate change impact assessment and will potentially be useful for researchers, water managers, and regulators as an aid to decision making and policy implementation.
Simultaneous Measurements of Site Locations by GPS Interferometers Referred to VLBI and SLR Sites in Japan.

Analysis of GPS phase observations carried out on December 6, 7, 8, 12, and 14, 1988, yielded the coordinate components of 11 observation sites in central Japan (Tsukuba, Shimosato and the others). As a fiducial point, either of Tsukuba or Shimosato was fixed, whose coordinates were determined by other previous studies using Very Long Baseline radio Interferometry (VLBI) and Satellite Laser Ranging (SLR), respectively. In order to evaluate accuracy of site coordinate determination with GPS measurement, we compared the coordinates determined by fixing Tsukuba with those by fixing Shimosato on December 8 and 14. The difference of the site positions between the VLBI and SLR referred analyses showed almost the same amount on each day, and the mean difference became about 1.33 m in length. On the other hand, the repeatability of the baseline vectors was less than about 0.87 m, which was smaller than the above differences. One of the most probable causes of such a large difference will be inconsistency between VLBI and SLR reference frames. Another one will be the error in the satellite ephemerides. Incomplete satellite constellation over Japan might be another one.
EVALUATION OF THE AIRPACT2 AIR QUALITY FORECAST SYSTEM FOR THE PACIFIC NORTHWEST

by Abdullah Al Mahmud, M.S. Washington State University December 2005 Chair: Brian K. Lamb AIRPACT2 is a numerical photochemical air quality modeling system that generates daily forecasts of hourly gas-phase mixing ratios of ozone (O3) and related species, including air toxic compounds, and particulate concentrations for the Pacific Northwest. The performance of the AIRPACT2 system has been evaluated in this work. The current AIRPACT2 system, which employs the second-generation CALGRID photochemical model, is undergoing conversion to utilize the third-generation CMAQ photochemical model. In anticipation of this change, an intercomparison between the CALGRID and the CMAQ model performances has also been completed. For both models, the forecast performance was assessed against observations from September and October 2003 using statistical measures including mean bias (MB), fractional bias (FB), mean error (ME), and fractional error (FE). The system predicted O3 quite accurately during an O3 episode that occurred during early September; but over-estimated O3 during non-episode periods later in the month. Although the CMAQ model produced performance results similar to the CALGRID model for the episode, CMAQ also predicted O3 quite well for non-episodes and for urban sites as compared to CALGRID. The current AIRPACT2 system yielded the following monthly statistics: MB of 14 ppb and FB of 40% for urban sites, and MB of 8 ppb and FB of 22% for semi-urban/rural sites, respectively. Using CMAQ in AIRPACT2 improved these statistics: MB of 0 ppb and FB of -
Frequency estimator by combination of phase difference method and interpolation algorithm

In the traditional time-shifting based phase difference method, considerable errors may be introduced by wrapped phase problem as long as translation coefficient tends to one even in a small-scale turbulence noise. In this paper, an improved frequency estimator is proposed to overcome the problem of wrapped phase by combination of phase difference method and interpolation algorithm. Compared with the traditional method of phase difference based on time-shifting, the improved algorithm can obtain an accurate estimate when translation coefficient exceeds one. Comparative studies were done by means of root-mean-square error over Cramer–Rao lower bound. According to the computer simulations, it is demonstrated that root-mean-square errors can cross Cramer–Rao lower bound if the translation coefficient is properly selected even in the case of the low signal-to-noise ratio, which implies that the proposed algorithm has a strong noise immunity. Finally, the advantage of the proposed algorithm is illustrated for the simulation signal which contained strong local random noise.