Miracle-dz/UniFAR-FTUs huggingface dataset:
Universität Des Saarlandes Fachrichtung 6.1 – Mathematik Monotonicity of Implicit Finite Difference Methods for Hyperbolic Conservation Laws Monotonicity of Implicit Finite Difference Methods for Hyperbolic Conservation Laws

Hyperbolic conservation laws (HCLs) are a class of partial differential equations that model transport processes. Many important phenomena in natural sciences are described by them. In this paper we consider finite difference methods for the approximation of HCLs. As HCLs describe an evolution in time, one may distinguish explicit and implicit schemes by the corresponding time integration mechanism employed by them. Explicit numerical schemes are well-analysed. In the explicit setting, the monotonicity property of a method is the key to approximate the physically relevant entropy solution of a HCL. However, there does not exist a rigorous general approach to implicit monotone methods in the literature up to now. In the current work, this open issue is addressed. We propose monotonicity conditions for fully implicit schemes, and we prove that they are meaningful. The relation between an implicit monotone scheme and a discrete entropy inequality is constructed in a similar fashion as in the classic explicit approach of Crandall and Majda. The convergence of implicit monotone schemes is verified in a framework that does not rely on a compactness property of the underlying function space. All proofs are given for the case of a scalar HCL in multiple space dimensions. They can easily be extended to HCLs with source terms or specialised to the 1-D case. We apply the developed notion of monotonicity by investigating implicit variants of some well known explicit monotone schemes. As a surprising result, a stability restriction on the time step size may arise. This contradicts the usual intuition that implicit schemes give unconditional stability. Such a restriction is established for the implicit Lax-Friedrichs scheme, and it is illustrated by numerical tests.
Spectacle: Faster and more accurate chromatin state annotation using spectral learning

Recently, a wealth of epigenomic data has been generated by biochemical assays and next-generation sequencing (NGS) technologies. In particular, histone modification data generated by the ENCODE project and other large-scale projects show specific patterns associated with regulatory elements in the human genome. It is important to build a unified statistical model to decipher the patterns of multiple histone modifications in a cell type to annotate chromatin states such as transcription start sites, enhancers and transcribed regions rather than to map histone modifications individually to regulatory elements. Several genome-wide statistical models have been developed based on hidden Markov models (HMMs). These methods typically use the Expectation-Maximization (EM) algorithm to estimate the parameters of the model. Here we used spectral learning, a state-of-the-art parameter estimation algorithm in machine learning. We found that spectral learning plus a few (up to five) iterations of local optimization of the likelihood outper-forms the standard EM algorithm. We also evaluated our software implementation called Spectacle on independent biological datasets and found that Spectacle annotated experimentally defined functional elements such as enhancers significantly better than a previous state-of-the-art method. Spectacle can be downloaded from https://github.com/jiminsong/Spectacle.
Beta-adrenergic blockade in the management of acute thyrotoxic crisis, tachycardia and arrhythmias.

TACHYCARDIA is a characteristic feature of thyrotoxicosis at all ages, but the older the patient the more frequent the occurrence of atrial fibrillation. Treatment of thyrotoxicosis is followed by slowing of heart rate and more than half of the thyrotoxic patients with atrial fibrillation, who are treated with anti-thyroid drugs or surgery (Sandler & Wilson, 1959) or radioactive iodine therapy (Staffurth, Gibberd & Hilton, 1965) revert to sinus rhythm. Until thyrotoxicosis is controlled the tachycardia is resistant to digitalis therapy unless a larger dose is employed (McMichael, 1963) and this feature may itself indicate the diagnosis of occult thyrotoxicosis (Cookson, 1959). Even shifts in the protein-binding of thyroxine may play a part in supraventricular tachycardias (Schatz, 1967). The circulatory features of thyrotoxicosis are usually a marked feature of the thyrotoxic crisis or storm, when tachycardia is associated with hyperpyrexia, diarrhoea, psychiatric disturbance, muscle weakness and profuse sweating (Ingbar, 1966). Urgent control of the tachycardia, cardiac arrhythmias and the hypermetabolic state are occasionally required, notably when a fully established crisis develops. In this situation blockade of the sympathetic nervous system or depletion of tissue stores of catecholamines may be of value. The first reports of a striking improvement in patients with thyrotoxic crisis were those treated by epidural block (Crile, 1929) and later using spinal anaesthesia (Knight, 1945). It was suggested that the circulatory changes were due to increased peripheral responsiveness to catecholamines (Brewster et al., 1956), no evidence being found for an absolute increase in their output (Wisewell et al., 1963). Reserpine was found to be effective in controlling thyrotoxic symptoms (Canary et al., 1959) and sympathetic blockade by guanethidine has been used increasingly (Degroot et al., 1961; Leak, 1963; Waldstein et al., 1964) with similar success. Recently propranolol has been tried in thyrotoxic tachycardia,
Role of Glutathione in Detoxification of Copper and Cadmium by Yeast Cells Having Different Abilities to Express Cup1 Protein

ABSTRACT Although copper is an essential metal and cadmium is an environmental pollutant, both are toxic when present in excess. Metallothionein and glutathione are two of the key components that participate in detoxification of copper and cadmium. In the present study the role of glutathione in resistance to copper and cadmium was investigated with the yeast Saccharomyces cerevisiae. The yeast cells used in this study have different abilities to produce glutathione and Cup1 protein, the yeast metallothionein homolog encoded by CUP1 gene. It was demonstrated that Cup1 protein plays a dominant role in buffering excess copper, and yeast does not depend on glutathione to reduce copper toxicity whether it possesses single or multiple copies of CUP1. In fact, excess copper can cause glutathione oxidation and depletion and damage the glutathione system. On the other hand, it was indicated that Cup1 protein is an important cadmium-detoxifying component, and the glutathione system can positively respond to cadmium. In yeast containing single or multiple copies of CUP1, glutathione is an indispensable line of defense against cadmium. Yeast having glutathione and no Cup1 protein is not able to grow in medium containing excess copper, but can tolerate higher concentrations of cadmium. In addition, it was found that yeast, independent of glutathione, can efficiently remove excess copper, whereas it cannot promptly eliminate accumulated cadmium regardless of having glutathione or not.
Class I Chitinase and β-1,3-Glucanase Are Differentially Regulated by Wounding, Methyl Jasmonate, Ethylene, and Gibberellin in Tomato Seeds and Leaves1

Class I chitinase (Chi9) and β-1,3-glucanase (GluB) genes are expressed in the micropylar endosperm cap of tomato (Lycopersicon esculentum) seeds just before radicle emergence through this tissue to complete germination. In gibberellin (GA)-deficient mutant (gib-1) seeds, expression of Chi9 and GluB mRNA and protein is dependent upon GA. However, as expression occurs relatively late in the germination process, we investigated whether the genes are induced indirectly in response to tissue wounding associated with endosperm cap weakening and radicle protrusion. Wounding and methyl jasmonate (MeJA) induced Chi9 expression, whereas ethylene, abscisic acid, sodium salicylate, fusicoccin, or β-aminobutyric acid were without effect. Chi9 expression occurred only in the micropylar tissues when seeds were exposed to MeJA or were wounded at the chalazal end of the seed. Expression of Chi9, but not GluB, mRNA was reduced in germinating seeds of the jasmonate-deficient defenseless1 tomato mutant and could be restored by MeJA treatment. Chi9 expression during germination may be associated with “wounding” from cell wall hydrolysis and weakening in the endosperm cap leading to radicle protrusion, and jasmonate is involved in the signaling pathway for this response. Among these treatments and chemicals (other than GA), only MeJA and wounding induced a low level of GluB expression in gib-1 seeds. However, MeJA, wounding, and particularly ethylene induced both genes in leaves, whereas GA induced only Chi9 in leaves. Although normally expressed simultaneously during tomato seed germination, Chi9 and GluB genes are regulated distinctly and tissue specifically by hormones and wounding.
First-principles calculations of the magnetic and electronic structures of MnP under pressure

Manganese monophosphide (MnP) shows complicated magnetic states varying with both temperature and pressure. We calculate the magnetic and electronic structures of MnP at different pressures using first-principles methods and obtain spiral ground states whose propagation vector changes from the c-axis at low pressure to the b-axis at high pressure. In between, we find a ferromagnetic state, as observed in the experimental phase diagram. The propagation vector of the spiral states is found to vary nonmonotonically with pressure, consistent with neutron measurements. Our results indicate that the complicated magnetic phase diagram originates from a delicate competition between neighboring exchange interactions between the Mn-ions. At all pressures, the electronic structures indicate the existence of quasi-one-dimensional charge carriers, which appear in the ferromagnetic state and become gapped in the spiral state, and anisotropic three-dimensional charge carriers. We argue that this two-fluid behavior originates from the special crystal structure of MnP and may be relevant for understanding the pairing mechanism of the superconductivity at the border of the high pressure spiral phase.
In Vivo Measurements of Brain Glucose Transport Using the Reversible Michaelis–Menten Model and Simultaneous Measurements of Cerebral Blood Flow Changes during Hypoglycemia

Glucose is the major substrate that sustains normal brain function. When the brain glucose concentration approaches zero, glucose transport across the blood–brain barrier becomes rate limiting for metabolism during, for example, increased metabolic activity and hypoglycemia. Steady-state brain glucose concentrations in α-chloralose anesthetized rats were measured noninvasively as a function of plasma glucose. The relation between brain and plasma glucose was linear at 4.5 to 30 mmol/L plasma glucose, which is consistent with the reversible Michaelis–Menten model. When the model was fitted to the brain glucose measurements, the apparent Michaelis-Menten constant, Kt, was 3.3 ± 1.0 mmol/L, and the ratio of the maximal transport rate relative to CMRglc, Tmax/CMRglc, was 2.7 ± 0.1. This Kt is comparable to the authors' previous human data, suggesting that glucose transport kinetics in humans and rats are similar. Cerebral blood flow (CBF) was simultaneously assessed and constant above 2 mmol/L plasma glucose at 73 ± 6 mL 100 g−1 min−1. Extrapolation of the reversible Michaelis–Menten model to hypoglycemia correctly predicted the plasma glucose concentration (2.1 ± 0.6 mmol/L) at which brain glucose concentrations approached zero. At this point, CBF increased sharply by 57% ± 22%, suggesting that brain glucose concentration is the signal that triggers defense mechanisms aimed at improving glucose delivery to the brain during hypoglycemia.
Evaluation of informed consent: a pilot study.

AIM This paper is a report of a study to describe and analyse the use of informed consent in clinical research, from the point of view of voluntary adult research participants, in order to develop and test an interview schedule for the evaluation of informed consent. BACKGROUND Informed consent is one of the central ethical research principles in healthcare research, but empirical research on this topic is still scarce. To evaluate and develop the ethical quality of scientific research, there is a need to explore the meaning and implications of informed consent for research participants. METHOD The data were collected in 2004 by interviews using an interview schedule created for this study by the first author and discussed in a multidisciplinary group. The response rate was 81%. The sample consisted of 32 patients with a metabolic syndrome who were participants in a project evaluating the effects of betaine on cardiovascular risk factors. FINDINGS Participants stated that the key elements of informed consent are information, understanding and decision-making, and that competence is an essential factor in the reception and understanding of information and making an independent decision about participation. Our interview schedule was found to be useful in the investigation of informed consent. CONCLUSION This study strengthened the perception that more extensive research about research participants is needed.
The Cost Barrier to Peritoneal Dialysis in the Developing World—An Asian Perspective

Countries in Asia vary significantly in culture and socioeconomic status. Dialysis costs and reimbursement structures are significant factors in decisions about the rates and modalities of renal replacement therapy. From our survey of Asian nephrologists conducted in 2001, a number of observations can be made. In many developing countries, the annual cost of continuous ambulatory peritoneal dialysis (CAPD) is greater than the per-capita gross national income (GNI). The median cost of a 2-L bag of peritoneal dialysis (PD) fluid is around US$5. The absolute cost of PD fluid among countries with significant differences in per-capita GNI actually varies very little. Thus, most renal failure patients can be expected to have problems accessing PD therapy in developing countries in Asia. In countries with unequal reimbursement policies for PD versus hemodialysis, a lack of incentive to prescribe PD also exists. Automated PD is nearly non existent in many developing countries in Asia. Some possible ways to reduce the cost barriers to PD in those countries include • individual governments providing more public funding for treating dialysis patients; • dialysate-producing companies reducing the cost of their products; • physicians using appropriately smaller exchange volumes (3 x 2 L) in some Asian patients with smaller body sizes and with residual renal function; and • reducing the complication rate for PD (for example, peritonitis) thereby reducing the costs required for treatment and hospitalization.
Effect of Bagasse ash reinforcement on the wear behaviour of Al-Cu-Mg/Bagasse ash particulate composites

The efiect of Bagasse ash (BAp) particle reinforcement on the wear behavior of Al-CuMg alloy has been studied. Bagasse ash particles were varied from 0 wt pct{10 wt pct with interval of 2 wt pct. Unlubricated pin-on disc tests were conducted to examine the wear behaviour of the aluminium alloy/Bagasse ash particulate composites. The tests were conducted at varying loads, from 5 to 20 N and sliding speeds of 1.26 m/s, 2.51 m/s, 3.77 m/s and 5.02 m/s for a constant sliding distance of 5000 m. The results showed that the wear rates of the Al-Cu-Mg/BAp composites are lower than that of the matrix alloy and further decrease with increasing Bagasse ash content. Wear rate increases as the sliding speed and applied load increase. The microstructure of the worn surface revealed that a large amount of plastic deformation appeared on the surface of the unreinforced alloy. While Bagasse ash reinforced Al-Cu-Mg alloy showed worn out surface that is not smooth, and grooves, scratches and parallel lines were observed. A combination of adhesion and delamination wear was in operation. These results show that improve wear properties is achievable for the aluminium alloy by the addition of Bagasse ash particles as reinforcement material.
Experimental and Numerical Investigation on the Interaction Between Ar Flow Channel and Ar Plasma Jet at Atmospheric Pressure

In this paper, the interaction between Ar flow channel and atmospheric pressure plasma jet (APPJ) is investigated quantitatively by combining 3-D species transport simulation and optical schlieren observation together. The turbulence model, gravity force, and electrostatic force model are included into the Ar flow channel simulation. It is found that, with the increment of the Ar flow rate, the plasma plume reaches the maximum length at 3.5 L/min and then decreases sharply, which is corresponding to the Ar flow status. The simulations of the Ar flow channel show good agreement with the captured schlieren images. At small flow rates, the Ar flow channel bends downward due to the gravity. Under laminar flow, the high Ar mole fraction region near the axis of the Ar flow channel increases with the flow rate. However, the Ar flow presents as twist and radial diffusion, and the Ar mole fraction decreases rapidly when the Ar flow transits into turbulence, which leads the length of the Ar plasma plume to decrease sharply correspondingly. The plasma plume bestows the Ar flow channel a forward momentum, which decreases the curvature of bending downward and reinforces the twist and instability of the Ar flow channel under turbulence flow. By coupling the optical emission spectra and flow channel investigation together, it is revealed that Ar APPJ propagates along the core of the conelike flow channel. The Ar mole fractions at the head of the plasma plume are about 0.985 and 0.45 under laminar and turbulence flow, respectively.
Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genes

Natural selection can influence even the lowest level of biological organization, the atomic composition of biological macromolecules. In analysing genome-scale gene expression data, we find that ancestral yeast strains preferentially express proteins with low carbon content during carbon limitation, relative to strains selected in the laboratory under carbon limitation. The likely reason is that the artificially selected strains acquire adaptations that refine their response to the limitation or partly circumvent the limiting condition. This finding extends previous work which shows that natural selection can act on the atomic costs of proteins. We also show that genes with high carbon and nitrogen content are less likely to have duplicates, indicating that atomic composition also plays a role in evolution by gene duplication. Taken together, our results contribute to the emerging view that protein atomic composition influences genome and transcriptome evolution.
A temporal comparison of AltaVista Web searching

Major Web search engines, such as AltaVista, are essential tools in the quest to locate online information. This article reports research that used transaction log analysis to examine the characteristics and changes in AltaVista Web searching that occurred from 1998 to 2002. The research questions we examined are (1) What are the changes in AltaVista Web searching from 1998 to 2002? (2) What are the current characteristics of AltaVista searching, including the duration and frequency of search sessions? (3) What changes in the information needs of AltaVista users occurred between 1998 and 2002? The results of our research show (1) a move toward more interactivity with increases in session and query length, (2) with 70% of session durations at 5 minutes or less, the frequency of interaction is increasing, but it is happening very quickly, and (3) a broadening range of Web searchers' information needs, with the most frequent terms accounting for less than 1% of total term usage. We discuss the implications of these findings for the development of Web search engines.
Calcium Signals Driven by Single Channel Noise

Usually, the occurrence of random cell behavior is appointed to small copy numbers of molecules involved in the stochastic process. Recently, we demonstrated for a variety of cell types that intracellular Ca2+ oscillations are sequences of random spikes despite the involvement of many molecules in spike generation. This randomness arises from the stochastic state transitions of individual Ca2+ release channels and does not average out due to the existence of steep concentration gradients. The system is hierarchical due to the structural levels channel - channel cluster - cell and a corresponding strength of coupling. Concentration gradients introduce microdomains which couple channels of a cluster strongly. But they couple clusters only weakly; too weak to establish deterministic behavior on cell level. Here, we present a multi-scale modelling concept for stochastic hierarchical systems. It simulates active molecules individually as Markov chains and their coupling by deterministic diffusion. Thus, we are able to follow the consequences of random single molecule state changes up to the signal on cell level. To demonstrate the potential of the method, we simulate a variety of experiments. Comparisons of simulated and experimental data of spontaneous oscillations in astrocytes emphasize the role of spatial concentration gradients in Ca2+ signalling. Analysis of extensive simulations indicates that frequency encoding described by the relation between average and standard deviation of interspike intervals is surprisingly robust. This robustness is a property of the random spiking mechanism and not a result of control.
Tau forms in CSF as a reliable biomarker for progressive supranuclear palsy

Kuiperij, H Bea Verbeek, Marcel M Borroni, B Gardoni, F Malinverno, M Padovani, A Di Luca, M Comment Letter United States Neurology. 2011 Apr 19;76(16):1443; author reply 1443.
Coupling Neighboring Microgrids for Overload Management Based on Dynamic Multicriteria Decision-Making

A microgrid (MG) is expected to supply its local loads independently; however, due to intermittency of wind and solar-based energy resources as well as the load uncertainty, it is probable that the MG experiences power deficiency (overloading). This problem can be mitigated by coupling the overloaded MG to another neighboring MG that has surplus power. Considering a distribution network composed of several islanded MGs, defining the suitable MGs (alternative) to be coupled with the overloaded MG is a challenge. An MG overload management technique is developed in this paper, which first identifies the overloaded MG(s) and then selects the most suitable alternative. The alternative selection is based on different criteria, such as available surplus power, reliability, supply security, power loss, electricity cost, and CO2 emissions in the alternative MGs. Moreover, the frequency and voltage deviation in the system of coupled MGs are considered in the selection. A dynamic multicriteria decision-making algorithm is developed for this purpose. To contemplate the uncertainties in the considered distribution network, a cloud theory-based probabilistic analysis is deployed as the research framework and the performance of the developed technique is evaluated in MATLAB.