Miracle-dz/UniFAR-FTUs huggingface dataset:
Time Accurate Simulation: Making a PC Behave Like a 8-Bit Embedded CPU

When developing embedded systems, developers often use simulation techniques to allow development to proceed without access to the target hardware. To make use of the high quality development tools available on the PC platform, one popular simulation method is to compile the code intended for the target system to run on the PC, allowing the development of the software to proceed on the PC without use of the final target system. For a distributed system, each target node is given its own process on the host PC, with software on the PC simulating the communications network. We have extended one such simulation environment to include the aspect of relative and absolute processing speed of the target systems, allowing for a more accurate simulation where not only functional but also timing-related bugs can be found and diagnosed. The absolute time mode makes the software on the PC run at the same speed as the real target, thus allowing the mixing of simulated nodes with real target hardware in the same system setup. The method is applicable to any embedded processor, as long as it is significantly slower than the PC. ∗ This work was performed within the Advanced Software Technology competence center (ASTEC, http://www.docs.uu.se/astec), supported by the Swedish National Innovation Systems’ Administration (VINNOVA, http://www.vinnova.se). Jakob is an industrial PhD student at IAR Systems (http://www.iar.com) and Uppsala university, sharing his time between research and development work. � Uppsala University, Dept. of Information Technology, Technical Report 2002-024. Submitted to RTAS 2002 and accepted as a poster, but none of the authors was able to attend and present the poster, thus not published. The system has been implemented and tested on standard PCs running the Windows NT operating system, and is currently being used in industrial projects.
DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein

WRKY proteins, defined by the conserved WRKYGQK sequence, are comprised of a large superfamily of transcription factors identified specifically from the plant kingdom. This superfamily plays important roles in plant disease resistance, abiotic stress, senescence as well as in some developmental processes. In this study, the Arabidopsis WRKY1 was shown to be involved in the salicylic acid signaling pathway and partially dependent on NPR1; a C-terminal domain of WRKY1, AtWRKY1-C, was constructed for structural studies. Previous investigations showed that DNA binding of the WRKY proteins was localized at the WRKY domains and these domains may define novel zinc-binding motifs. The crystal structure of the AtWRKY1-C determined at 1.6 Å resolution has revealed that this domain is composed of a globular structure with five β strands, forming an antiparallel β-sheet. A novel zinc-binding site is situated at one end of the β-sheet, between strands β4 and β5. Based on this high-resolution crystal structure and site-directed mutagenesis, we have defined and confirmed that the DNA-binding residues of AtWRKY1-C are located at β2 and β3 strands. These results provided us with structural information to understand the mechanism of transcriptional control and signal transduction events of the WRKY proteins.
Properties of an Inwardly Rectifying ATP-sensitive K+ Channel in the Basolateral Membrane of Renal Proximal Tubule

The potassium conductance of the basolateral membrane (BLM) of proximal tubule cells is a critical regulator of transport since it is the major determinant of the negative cell membrane potential and is necessary for pump-leak coupling to the Na+,K+-ATPase pump. Despite this pivotal physiological role, the properties of this conductance have been incompletely characterized, in part due to difficulty gaining access to the BLM. We have investigated the properties of this BLM K+ conductance in dissociated, polarized Ambystoma proximal tubule cells. Nearly all seals made on Ambystoma cells contained inward rectifier K+ channels (γslope, in = 24.5 ± 0.6 pS, γchord, out = 3.7 ± 0.4 pS). The rectification is mediated in part by internal Mg2+. The open probability of the channel increases modestly with hyperpolarization. The inward conducting properties are described by a saturating binding–unbinding model. The channel conducts Tl+ and K+, but there is no significant conductance for Na+, Rb+, Cs+, Li+, NH4 +, or Cl−. The channel is inhibited by barium and the sulfonylurea agent glibenclamide, but not by tetraethylammonium. Channel rundown typically occurs in the absence of ATP, but cytosolic addition of 0.2 mM ATP (or any hydrolyzable nucleoside triphosphate) sustains channel activity indefinitely. Phosphorylation processes alone fail to sustain channel activity. Higher doses of ATP (or other nucleoside triphosphates) reversibly inhibit the channel. The K+ channel opener diazoxide opens the channel in the presence of 0.2 mM ATP, but does not alleviate the inhibition of millimolar doses of ATP. We conclude that this K+ channel is the major ATP-sensitive basolateral K+ conductance in the proximal tubule.
Emergent Behavior in Lung Structure and Function Lung tissue mechanics as an emergent phenomenon

Suki B, Bates JH. Lung tissue mechanics as an emergent phenomenon. J Appl Physiol 110: 1111–1118, 2011. First published January 6, 2011; doi:10.1152/japplphysiol.01244. 2010. —The mechanical properties of lung parenchymal tissue are both elastic and dissipative, as well as being highly nonlinear. These properties cannot be fully understood, however, in terms of the individual constituents of the tissue. Rather, the mechanical behavior of lung tissue emerges as a macroscopic phenomenon from the interactions of its microscopic components in a way that is neither intuitive nor easily understood. In this review, we first consider the quasi-static mechanical behavior of lung tissue and discuss computational models that show how smooth nonlinear stress-strain behavior can arise through a percolation-like process in which the sequential recruitment of collagen fibers with increasing strain causes them to progressively take over the load-bearing role from elastin. We also show how the concept of percolation can be used to link the pathologic progression of parenchymal disease at the micro scale to physiological symptoms at the macro scale. We then examine the dynamic mechanical behavior of lung tissue, which invokes the notion of tissue resistance. Although usually modeled phenomenologically in terms of collections of springs and dashpots, lung tissue viscoelasticity again can be seen to reflect various types of complex dynamic interactions at the molecular level. Finally, we discuss the inevitability of why lung tissue mechanics need to be complex.
Proteomics in Ménière disease

Ménière's disease (MD) is a disorder of the inner ear characterized by an insidious onset and aspecific symptoms, such as dizziness, vertigo, tinnitus, and hearing loss, that may become very debilitating. The presence of endolymphatic hydrops is a common feature in MD patients, but the pathophysiology is still largely unknown. In this study, we have used a proteomics‐driven approach to identify potential biomarkers of MD. To this end, plasma was obtained from whole blood of 16 individuals previously diagnosed as suffering from MD and compared to plasma from healthy donors. A depletion of the highly abundant proteins (i.e., albumin, IgG, transferrin, etc.) was performed in order to enhance the chance of detection of the less represented ones, therefore reducing the noise‐background. Two‐dimensional gel electrophoresis, followed by in‐gel tryptic digestion of the selected spots and LC‐MS/MS analysis, allowed us to identify a set of proteins whose expression appears to be differentially modulated in patients versus controls. In particular: complement factor H and B, fibrinogen alpha and gamma chains, beta‐actin and pigment epithelium derived factor are over expressed; on the other hand, the levels of beta‐2 glycoprotein‐1, vitamin D binding protein and apolipoprotein‐1 are significantly decreased in the plasma of MD‐affected individuals. Even though preliminary and not necessarily linked directly to the molecular pathogenesis of the disease, our original findings suggest that a molecular signature, represented by the plasma protein profile previously described, might represent a potentially powerful, innovative and not invasive tool for early diagnosis and clinical management of MD patients. J. Cell. Physiol. 227: 308–312, 2012. © 2011 Wiley Periodicals, Inc.
Thrombosis of the cerebral veins and sinuses.

of the cerebral veins and sinuses is a distinct cere-brovascular disorder that, unlike arterial stroke, most often affects young adults and children. The symptoms and clinical course are highly variable. A teenag-er who has had recent headaches after starting oral contraception, a woman who has had seizures after delivery in the obstetrical ward, and a comatose man with a dilated pupil in the emergency room all may have sinus thrombosis. The estimated annual in-cidence is 3 to 4 cases per 1 million population and up to 7 cases per 1 million among children. About 75 percent of the adult patients are women. During the past decade, increased awareness of the diagnosis, improved neuroimaging techniques, and more effective treatment have improved the prognosis. More than 80 percent of all patients now have a good neurologic outcome. This review summarizes recent insights into the pathogenesis of sinus thrombosis, risk factors, and clinical and radiologic diagnosis and discusses the current evidence and controversies about the best treatment.
Assessment of HER-2/Neu Status by Immunohistochemistry and Fluorescence In Situ Hybridization in Mammary Paget Disease and Underlying Carcinoma

HER-2/Neu overexpression is seen in 20% to 30% of invasive breast carcinomas and has been reported in as many as 80% of high-grade infiltrating carcinomas. Earlier studies have suggested that 100% of the tumor cells in mammary Paget disease show overexpression of HER-2 protein. We undertook this study to assess HER-2 status of mammary Paget disease and of the underlying breast carcinoma, when present, by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). Formalin-fixed, paraffin-embedded tissue from 20 cases of mammary Paget disease were analyzed for HER-2 status by IHC and FISH. IHC for estrogen receptor (ER) was also performed. The patients ranged in age from 34 to 88 years, with a mean age of 62 years. Eighty percent of the cases showed strong overexpression (3+) of HER-2 protein by IHC, and all of these cases showed more than 5-fold amplification of the HER-2 gene by FISH. The remaining 4 cases, which were negative for HER-2/Neu by IHC, showed no amplification by FISH. All of the latter cases expressed ER, whereas no case that overexpressed HER-2 expressed ER. Sixteen cases had an underlying tumor, which was in situ in 6 cases. The underlying tumors were identical to the Paget disease with respect to their HER-2/Neu overexpression by both IHC and FISH. HER-2 overexpression was identified in 80% of our cases of Paget disease. There was 100% concordance between HER-2 protein overexpression by immunohistochemistry and gene amplification in both the Paget and the underlying tumor. Moreover, all of the cases negative for HER-2 overexpression expressed ER, whereas those positive for HER-2 did not.
Influence of Peak and Trough Levels of Opioid Maintenance Therapy on Driving Aptitude

To evaluate driving aptitude and traffic-relevant performance at peak and trough medication levels in opioid-dependent patients receiving maintenance therapy with either buprenorphine (mean: 13.4 mg) or methadone (52.7 mg) and a medication-free control group, the Addiction Clinic at Medical University Vienna conducted a prospective, open-label trial where 40 opioid-dependent patients maintained either on buprenorphine or methadone were assessed regarding their traffic-relevant performance. Using the standardized Act and React Testsystem (ART) 2020 Standard test battery, traffic-relevant performance was analysed 1.5 h (peak level) and 20 h (trough level) after administration of opioid maintenance therapy. Results showed that patients at trough level had a significantly higher percentage of incorrect reactions (p = 0.03) and more simple errors (p = 0.02) than patients at peak level as well as methadone-maintained patients at peak level tended to perform less well than buprenorphine-maintained patients in some of the test items, e.g. methadone-maintained patients at trough level had a higher number of delayed reactions in the RST3 phase 2 test (p = 0.09) and answered fewer questions correctly in the visual structuring ability test (p = 0.04). This investigation indicates that opioid-maintained patients did not differ significantly at peak vs.trough level in the majority of the investigated items and that both substances do not appear to affect traffic-relevant performance dimensions when given as a maintenance therapy in a population where concomitant consumption would be excluded.
A hierarchical bin-based legalizer for standard-cell designs with minimal disturbance

In this work, a hierarchical bin-based legalization approach, HiBinLegalizer, is developed to legalize standard cells with minimal movement. First, a chip is divided into several bins with equal size. Then, starting with the most crowed unlegalized bin, a merging procedure for bins is used to integrate bins into a cross-shape region or a square-shape region until the cell density in that region is less than a specific cell-density-threshold. After that, an efficient legalization method which simultaneously preserves the cell orders in each row and minimizes the weighted sum of movement distances is developed to legalize cells in that region to limit the movable scope. To improve the legalization quality, HiBinLegalizer refreshes the positions of legalized cells during legalization. The legalizing procedure is repeated until all cells are non-overlapped. Compared with the state-of-the-art method, Abacus, HiBin-Legalizer can reduce the total movement of cells to be 48% in average and save the largest movement of cells to be 140% in average. Moreover, HiBinLegalizer can reduce the HPWL by 47% and obtain average 1.11x runtime speed up.
Plasma Immersion Ion Implantation With Lithium Atoms

A new method was developed to produce lithium plasma for plasma immersion ion implantation. Initially, an argon glow discharge with operation pressure ranging from 2 times 10-1 to 1 mbar is generated by negatively polarizing an electrode from -400 to -1500 V. Small pieces of metallic lithium that are 99.9% pure fill the top of a conic crucible, with a depth of 2 cm, in electric contact with the electrode. Argon ions from the plasma are used to bombard this target, where heat is created by the momentum transfer from the impacting ions to the crucible. By controlling the operation pressure and the electrode voltage polarization, it is possible to easily heat the crucible to temperatures above the lithium melting point (180degC), causing its evaporation. Lithium atoms are then ionized, mainly due to collisions, with argon ions moving toward the crucible. Double Langmuir probe measurements indicated variation in the density of the discharge from 4 times 109 cm-3 to 1010 cm-3 after lithium evaporation. Silicon wafer pieces immersed in this mixed plasma were submitted to repetitive negative high-voltage pulses (3 kV/6 mus/2.5 kHz) to accelerate plasma ions. High strain in the treated layers was measured by high-resolution X-ray diffraction. Photoluminescence intensity increased after annealing. X-ray photoelectron spectrometry measurement revealed lithium implantation in silicon with an atomic concentration of 78% on the top surface and a penetration depth of about 75 nm.
Effects of osmotic stress on antioxidant enzymes activities in leaf discs of PSAG12-IPT modified gerbera

Leaf senescence is often caused by water deficit and the chimeric gene PSAG12-IPT is an auto-regulated gene delaying leaf senescence. Using in vitro leaf discs culture system, the changes of contents of chlorophylls, carotenoids, soluble protein and thiobarbituric acid reactive substance (TBARS) and antioxidant enzymes activities were investigated during leaf senescence of PSAGl2-IPT modified gerbera induced by osmotic stress compared with the control plant (wild type). Leaf discs were incubated in 20%, 40% (w/v) polyethylene glycol (PEG) 6 000 nutrient solution for 20 h under continuous light [130 μmol/(m2·s)]. The resultsshowed that the contents of chlorophylls, carotenoids and soluble protein were decreased by osmotic stress with the decrease beingmore pronounced at 40% PEG, but that, at the same PEG concentration the decrease in the transgenic plants was significantly lower than that in the control plant. The activities of superoxide dismutase (SOD), catalases (CAT), ascorbate peroxidase (APX), guaiacol peroxidase (GPX) and dehydroascorbate reductase (DHAR) were stimulated by PEG treatment. However, the increaseswere higher in PSAG12-IPT transgenic plants than in the control plants, particularly at 40% PEG treatment. Lipid peroxidation (TBARS content) was increased by PEG treatment with the increase being much lower in transgenic plant than in the control plant. It could be concluded that the increases in the activities of antioxidant enzymes including SOD, CAT, APX, GPX and DHAR were esponsible for the delay of leaf senescence induced by osmotic stress.
Sendmail Without the Superuser

As an exercise in the application of the concept of least privilege, we have modified the pieces of an ordinary UNIX mail system, sendmail in particular, to require little or no privilege in their operation. No mail code runs with root or system IDs. In fact, the simplest configuration (local-only mail, with or without mandatory access controls) can run with no privilege or special access rights whatsoever, while even the most complex (multilevel network mail) can be done with minimal privilege requirements. While such modifications cannot guarantee the absence of security holes in mail, they should greatly limit their possible scope.
HDR Pathological Image Enhancement Based on Improved Bias Field Correction and Guided Image Filter

Pathological image enhancement is a significant topic in the field of pathological image processing. This paper proposes a high dynamic range (HDR) pathological image enhancement method based on improved bias field correction and guided image filter (GIF). Firstly, a preprocessing including stain normalization and wavelet denoising is performed for Haematoxylin and Eosin (H and E) stained pathological image. Then, an improved bias field correction model is developed to enhance the influence of light for high-frequency part in image and correct the intensity inhomogeneity and detail discontinuity of image. Next, HDR pathological image is generated based on least square method using low dynamic range (LDR) image, H and E channel images. Finally, the fine enhanced image is acquired after the detail enhancement process. Experiments with 140 pathological images demonstrate the performance advantages of our proposed method as compared with related work.
Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?

Cells must abide by a number of constraints. The environmental constrains of cellular behavior and physicochemical limitations affect cellular processes. To regulate and adapt their functions, cells impose constraints on themselves. Enumerating, understanding, and applying these constraints leads to a constraints‐based modeling formalism that has been helpful in converting conceptual models to computational models in biology. The continued success of the constraints‐based approach depends upon identification and incorporation of new constraints to more accurately define cellular capabilities. This review considers constraints in terms of environmental, physicochemical, and self‐imposed regulatory and evolutionary constraints with the purpose of refining current constraints‐based models of cell phenotype. © 2003 Wiley Periodicals, Inc.
Musical Pattern Design Using Contour Icons

This paper considers the use of Contour Icons in the design and implementation of musical patterns, for the purposes of detection and recognition. Research work had endeavoured to deliver musical patterns that were both distinct and memorable, and to this end a set of basic melodic shapes were introduced using a Sonification application called TrioSon that had been designed for the purpose. Existing work in the field (such as that concerning Earcon design [1]) has considered the mechanisms by which patterns may be made distinctive, but it is argued that separate consideration must be given to the method of making such patterns memorable. This work suggests that while segregation and detection can best be facilitated by the individuality of a patterns rhythm [2] and [3], the retention (and hence future recognition) of a musical pattern is concerned more with its melodic range [4] and contour [5] and [6]. The detection and comprehension of musical patterns based around basic shapes (known as Contour Icons) was tested, within Sonifications of simple data sets generated using TrioSon. A set of test patterns based on such factors as tonality and key was used for control purposes, with Contour Icons being introduced in the second set of tests. Results suggest that significant improvement was made due to the use of Contour Icons, with further work focusing on the many possibilities that such a design framework would suggest.
Comparison of The Quality of Percussive and Non-Percussive Sounds Separated From A Mixture of Instrumental Sounds

In this paper, we have investigated the quality of the separated non-percussive sound (Banjo) and compared its quality with separated percussive sound (Tabla) from a mixture of sounds of musical instruments Banjo and Tabla. The analysis of the result showed that the quality of the separated Banjo sound is satisfactory.
Syncretism and Fundamentalism: A Comparison

In several ways, syncretism and fundamentalism can be viewed as opposite reactions to the processes of modernization and globalization. Within religious contexts, syncretists and fundamentalists make different choices when confronted with alternatives and with challenges to the accepted practices of daily life. The power dimension is an important aspect for this comparison. But the study of these two modern religious phenomena also points to a similarity with a paradigmatic debate, the contrast between positivist and constructivist approaches. Though the comparison is not the most obvious, there are striking similarities between fundamentalists and positivists, on the one hand, and between constructivists and syncretists, on the other.