gebhart/patrepeval huggingface dataset:
Modeling the Internet and the Web: Probabilistic Method and Algorithms (2003)

Preface. 1 Mathematical Background. 1.1 Probability and Learning from a Bayesian Perspective. 1.2 Parameter Estimation from Data. 1.3 Mixture Models and the Expectation Maximization Algorithm. 1.4 Graphical Models. 1.5 Classification. 1.6 Clustering. 1.7 Power--Law Distributions. 1.8 Exercises. 2 Basic WWW Technologies. 2.1 Web Documents. 2.2 Resource Identifiers: URI, URL, and URN. 2.3 Protocols. 2.4 Log Files. 2.5 Search Engines. 2.6 Exercises. 3 Web Graphs. 3.1 Internet and Web Graphs. 3.2 Generative Models for the Web Graph and Other Networks. 3.3 Applications. 3.4 Notes and Additional Technical References. 3.5 Exercises. 4 Text Analysis. 4.1 Indexing. 4.2 Lexical Processing. 4.3 Content--Based Ranking. 4.4 Probabilistic Retrieval. 4.5 Latent Semantic Analysis. 4.6 Text Categorization. 4.7 Exploiting Hyperlinks. 4.8 Document Clustering. 4.9 Information Extraction. 4.10 Exercises. 5 Link Analysis. 5.1 Early Approaches to Link Analysis. 5.2 Nonnegative Matrices and Dominant Eigenvectors. 5.3 Hubs and Authorities: HITS. 5.4 PageRank. 5.5 Stability. 5.6 Probabilistic Link Analysis. 5.7 Limitations of Link Analysis. 6 Advanced Crawling Techniques. 6.1 Selective Crawling. 6.2 Focused Crawling. 6.3 Distributed Crawling. 6.4 Web Dynamics. 7 Modeling and Understanding Human Behavior on the Web. 7.1 Introduction. 7.2 Web Data and Measurement Issues. 7.3 Empirical Client--Side Studies of Browsing Behavior. 7.4 Probabilistic Models of Browsing Behavior. 7.5 Modeling and Understanding Search Engine Querying. 7.6 Exercises. 8 Commerce on the Web: Models and Applications. 8.1 Introduction. 8.2 Customer Data on theWeb. 8.3 Automated Recommender Systems. 8.4 Networks and Recommendations. 8.5 Web Path Analysis for Purchase Prediction. 8.6 Exercises. Appendix A: Mathematical Complements. A.1 Graph Theory. A.2 Distributions. A.3 Singular Value Decomposition. A.4 Markov Chains. A.5 Information Theory. Appendix B: List of Main Symbols and Abbreviations. References. Index.
Urokinase‐Type Plasminogen Activator, an Endogenous Antibiotic (2005)

Urokinase-type plasminogen activator (uPA) is a serine protease that not only displays fibrinolytic function but also modulates innate and adaptive immune responses. In the present study, we assessed whether uPA acts as an endogenous antibiotic. It has been demonstrated that uPA inhibits growth of Staphylococcus aureus both in vivo and in vitro. Importantly, the bactericidal properties of uPA are associated with the serine protease domain of the molecule but are not dependent on its plasminogen-activation potential and cannot be inhibited by plasminogen activator inhibitor type 1 (PAI-1). In a murine infection model, uPA treatment alleviated staphylococcal sepsis by inhibiting bacterial growth. To further evaluate the changes in uPA levels during the course of staphylococcal infection, total uPA and active uPA levels were analyzed in plasma and in kidney homogenates. Expression of total uPA was constant, but PAI-1 levels were dramatically increased in plasma and in kidney homogenates during the course of staphylococcal infection. After infection with staphylococci, the level of metabolically active uPA was unaltered in plasma but was significantly decreased in kidney homogenates. Active uPA levels were inversely related to PAI-1 levels and to bacterial loads in kidney homogenates. In conclusion, we report that uPA acts as an endogenous antibacterial substance that might constitute the first line of host defense against staphylococcal infection. The decreased active uPA levels in infected organs might be due to the dramatically increased PAI-1 production during S. aureus infection.
Dietary intake measurements (2005)

To provide a concise summary of field and laboratory methods for the measurement of dietary intake with particular reference to the assessment of energy and protein intake and to the pitfalls and difficulties that may be encountered in practice when implementing the methods both in the field and under laboratory conditions.
CHRONOBIOLOGY OF HIGH BLOOD PRESSURE. (2007)

BIOCOS, the project aimed at studying BIOlogical systems in their COSmos, has obtained a great deal of expertise in the fields of blood pressure (BP) and heart rate (HR) monitoring and of marker rhythmometry for the purposes of screening, diagnosis, treatment, and prognosis. Prolonging the monitoring reduces the uncertainty in the estimation of circadian parameters; the current recommendation of BIOCOS requires monitoring for at least 7 days. The BIOCOS approach consists of a parametric and a non-parametric analysis of the data, in which the results from the individual subject are being compared with gender- and age-specified reference values in health.Chronobiological designs can offer important new information regarding the optimization of treatment by timing its administration as a function of circadian and other rhythms.New technological developments are needed to close the loop between the monitoring of blood pressure and the administration of antihypertensive drugs.
Combined prospective and retrospective correction to reduce motion‐induced image misalignment and geometric distortions in EPI (2012)

Despite rigid-body realignment to compensate for head motion during an echo-planar imaging time-series scan, nonrigid image deformations remain due to changes in the effective shim within the brain as the head moves through the B(0) field. The current work presents a combined prospective/retrospective solution to reduce both rigid and nonrigid components of this motion-related image misalignment. Prospective rigid-body correction, where the scan-plane orientation is dynamically updated to track with the subject's head, is performed using an active marker setup. Retrospective distortion correction is then applied to unwarp the remaining nonrigid image deformations caused by motion-induced field changes. Distortion correction relative to a reference time-frame does not require any additional field mapping scans or models, but rather uses the phase information from the echo-planar imaging time-series itself. This combined method is applied to compensate echo-planar imaging scans of volunteers performing in-plane and through-plane head motions, resulting in increased image stability beyond what either prospective or retrospective rigid-body correction alone can achieve. The combined method is also assessed in a blood oxygen level dependent functional MRI task, resulting in improved Z-score statistics.
Temperature dependence of the capacitance of a ferroelectric material (2007)

We present an alternate version of the undergraduate laboratory experiment developed by Dixon [Am. J. Phys. 75, 1038–1045 (2007)] that is suitable for second-year students. We study the temperature variation of the capacitance of a ferroelectric ceramic derived from barium titanate, the Ba(Ti0.9Sn0.1)O3 solid solution. The ratio of tin to titanium is chosen to provide a convenient Curie temperature near 50°C. Using careful temperature control and real-time capacitance measurements, we track the time evolution of the capacitance in response to temperature changes at 5Hz for runs that last up to a day. At temperatures well above the Curie temperature, TC, the capacitance relaxation is well-described by a single exponential decay. Near TC, the relaxation is linear in the logarithm of time over more than three decades. For T&gt;TC, the permittivity deviates from the Curie–Weiss law and follows another phenomenological form commonly used to describe relaxor perovskite-ceramic capacitors.
Hydrogen Ions Kill Brain at Concentrations Reached in Ischemia (1987)

Elevation of brain glucose before the onset of nearly complete ischemia leads to increased lactic acid within brain. When excessive, such acidosis may be a necessary factor for converting selective neuronal loss to brain infarction from nearly complete ischemia. To examine the potential neurotoxicity of excessive lactic acid concentrations, we microinjected (0.5 microliter/min) 150 mM sodium lactate solutions (adjusted to 6.50-4.00 pH) for 20 min into parietal cortex of anesthetized rats. Interstitial pH (pH0) was monitored with hydrogen ion-selective microelectrodes. Animals were allowed to recover for 24 h before injection zones were examined with the light microscope. Injectants produced brain necrosis in a histological pattern resembling ischemic infarction only when pH0 was less than or equal to 5.30. Nonlethal injections showed only needle tract injuries. Abrupt deterioration of brain acid-base homeostatic mechanisms correlated with necrosis since pH0 returned to baseline more slowly after lethal tissue injections than after nonlethal ones. The slowed return of pH0 to baseline after the severely acidic injections may reflect altered function of plasma membrane antiport systems for pH regulation and loss of brain hydrogen ion buffers.
Complexity constrained rate-distortion optimization of sign language video using an objective intelligibility metric (2007)

Sign language users are eager for the freedom and convenience of video communication over cellular devices. Compression of sign language video in this setting offers unique challenges. The low bitrates available make encoding decisions extremely important, while the power constraints of the device limit the encoder complexity. The ultimate goal is to maximize the intelligibility of the conversation given the rate-constrained cellular channel and power constrained encoding device. This paper uses an objective measure of intelligibility, based on subjective testing with members of the Deaf community, for rate-distortion optimization of sign language video within the H.264 framework. Performance bounds are established by using the intelligibility metric in a Lagrangian cost function along with a trellis search to make optimal mode and quantizer decisions for each macroblock. The optimal QP values are analyzed and the unique structure of sign language is exploited in order to reduce complexity by three orders of magnitude relative to the trellis search technique with no loss in rate-distortion performance. Further reductions in complexity are made by eliminating rarely occuring modes in the encoding process. The low complexity SL optimization technique increases the measured intelligibility up to 3.5 dB, at fixed rates, and reduces rate by as much as 60% at fixed levels of intelligibility with respect to a rate control algorithm designed for aesthetic distortion as measured by MSE.
Changes in the voltage profile of Li/<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Li</mml:mi></mml:mrow><mml:mrow><mml:mn>1</mml:mn><mml:mo>+</mml:mo><mml:mi mathvariant="italic">x</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Mn</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn><mml:mi mathvariant="normal">−</mml:mi><mml:mi mathvariant="italic">x</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mrow><mml:mn>4</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>cells as a function of<i>x</i> (1996)

${\mathrm{Li}}_{1+\mathit{x}}$${\mathrm{Mn}}_{2\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{O}}_{4}$ is a very promising candidate as the cathode material in state-of-the-art Li-ion rechargeable batteries. The ability to retain the initial capacity of the electrochemical cell upon cycling depends on the amount of the excess Li, represented as x in ${\mathrm{Li}}_{1+\mathit{x}}$${\mathrm{Mn}}_{2\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{O}}_{4}$. Thus it is important to measure the voltage profiles of Li/${\mathrm{Li}}_{1+\mathit{x}}$${\mathrm{Mn}}_{2\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{O}}_{4}$ electrochemical cells carefully as a function of x. The twin peaks in the derivative curve, -dy/dV versus V, where y denotes the amount of intercalated Li, are found to be weakened with increasing x. With a simple lattice-gas model, we show that the two peaks in the derivative curve are consistent with order-disorder phase transitions of Li ions, and the weakening of the peaks with increasing x is due to the presence of intercalated Li atoms pinned to the excess Li atoms which are substituted for Mn in the host lattice. \textcopyright{} 1996 The American Physical Society.
Type XVII collagen gene mutations in junctional epidermolysis bullosa and prospects for gene therapy (2003)

Non-Herlitz junctional epidermolysis bullosa (nH-JEB) is caused predominantly by mutations leading to premature stop codons on both alleles of the type XVII collagen gene (COL17A1). The analysis of mutations in this gene has provided a means of correlating genotype with phenotype of nH-JEB patients. The phenotype of nH-JEB is characterized by generalized blistering of skin and mucous membranes with atrophic scarring and nail dystrophy. Atrophic alopecia is a distinct feature of nH-JEB patients, but one that is not associated with the severity of the disease at other sites. Enamel hypoplasia and pitting of the teeth are also characteristic for nH-JEB and can be used to facilitate the correct diagnosis in children with a blistering skin disease. Analysis of the biological consequences of mutations in the COL17A1 gene has shown that most patients lack type XVII collagen mRNA due to nonsense-mediated mRNA decay. Patients with these mutations can therefore be a target for corrective gene therapy using vectors coding for full-length type XVII collagen. Proof of principle for this approach has recently been demonstrated. The analysis of naturally occurring phenomena of gene correction in the COL17A1 gene provides evidence for other mechanisms of gene correction in genetic diseases. For example, exclusion of an exon carrying a mutation can lead to a milder phenotype of nH-JEB than predicted by the original mutation. In addition, we have gained data suggesting that COL17A1 exons harbouring pathogenic mutations can also be repaired by trans-splicing, i.e. aligning corrected RNA sequences to introns in the vicinity of faulty exons in the COL17A1 premtRNA.
Morphological evidence of the continuum between necrosis and apoptosis in model of anoxia <i>in vitro</i> (2003)

Growing evidence suggests that two modes of cell death, known as apoptosis and necrosis, are involved in postanoxic injury. The current opinion on these two types of cell death is that apoptosis and necrosis are not always the uniform and distinct events. The aim of this study was to determine ultrastructural criteria of postanoxic neuronal changes in model of anoxia in vitro . The organotypic cultures of rat hippocampus exposed to 10‐ and 20‐min of anoxic insult revealed the morphological features classic for both necrotic and apoptotic neuronal cell injury. Some neurones exhibited the typical necrotic lysis whereas others clearly reflected an active apoptotic form of cell death consisting of nuclear condensation with early preservation of cell membranes. However, numerous damaged cells shared both apoptotic and necrotic ultrastructural characteristics. These results evidenced the morphological continuum between apoptosis and necrosis under anoxia in vitro .
Towards a Graphene-Based Low Intensity Photon Counting Photodetector (2016)

Graphene is a highly promising material in the development of new photodetector technologies, in particular due its tunable optoelectronic properties, high mobilities and fast relaxation times coupled to its atomic thinness and other unique electrical, thermal and mechanical properties. Optoelectronic applications and graphene-based photodetector technology are still in their infancy, but with a range of device integration and manufacturing approaches emerging this field is progressing quickly. In this review we explore the potential of graphene in the context of existing single photon counting technologies by comparing their performance to simulations of graphene-based single photon counting and low photon intensity photodetection technologies operating in the visible, terahertz and X-ray energy regimes. We highlight the theoretical predictions and current graphene manufacturing processes for these detectors. We show initial experimental implementations and discuss the key challenges and next steps in the development of these technologies.
Dynamic rheological study of paraffin wax and its organoclay nanocomposites (2008)

Abstract Dynamic rheological data for paraffin wax and its organoclay nanocomposites are reported. Dynamic mechanical analysis of paraffin wax for temperatures ranging from −40 to 55°C showed a decrease of several orders of magnitude in the dynamic moduli and a significant shift toward viscous behavior, which resulted from the occurrence of two solid–solid phase transitions. In both the crystalline and mesophase regions, the dispersion of organoclay platelets in paraffin wax via ultrasonication increased the storage modulus, whereas the effect on the loss modulus was temperature‐dependent. The melt rheology data of the wax–clay nanocomposites at 70°C showed that the complex viscosities increased monotonically with clay addition and demonstrated shear‐thinning behavior for frequencies between 0.1 and 100 rad/s. The complex viscosity versus angular frequency data were well fit by a power‐law function for which the shear‐thinning exponent provides a gauge for the extent of clay exfoliation. The nanocomposites exhibited low‐frequency solid behavior, which indicated good exfoliation of the organoclay in the wax matrix. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008
Passive methods for suppressing acoustic resonance excitation in shallow rectangular cavities. (2014)

The flow-excited acoustic resonance in shallow rectangular cavities can be a source of severe noise and/or excessive vibration. This phenomenon is excited when one of the acoustic modes in the accommodating enclosure is coupled with the flow instabilities resulting from the shear layer formation at the cavity mouth. In this thesis, two passive methods for suppressing the flow-excited acoustic resonance phenomenon are addressed. The first passive method considers the edge geometry effect on the phenomenon. Several edge geometries including chamfered, round, and different configurations of spoilers are considered. The effect of the spoilers dimensions is investigated to provide criteria that help designing and optimizing spoilers. Some of the spoilers are found to be effective in suppressing the acoustic resonance excitation, while some other edges including chamfered and round edges result in shifting the resonance excitations to higher velocities with amplification in the acoustic pressure. To enrich the understanding of the suppression mechanism introduced by these passive methods, hotwire measurements are performed revealing the existence of orthogonal vortices interacting with the shear layer at the cavity mouth. The second passive method investigated is the effect of placing a high frequency vortex generator (control cylinder) in vicinity of the upstream edge of the cavity on the acoustic resonance excitation. The method is investigated experimentally and numerically. The effectiveness of the control cylinder method is studied by investigating different cylinder diameters and locations on both horizontal and vertical directions. It is found that locating the cylinder at relatively small height from the bottom wall and with a distance of 25.4 mm upstream the leading edge can significantly suppress the resonance excitation. To further understand the interaction between the cylinder vortex shedding and the shear layer at the cavity mouth and the influence on the shear layer thickness, a 2D numerical simulation using K-epsilon and Detached Eddy Simulation (DES) models has been carried out and compared to the experimental results. For both passive methods, the study included two cavities with different aspect ratios (L/D=1.0 and L/D=1.67, L: cavity length, D: cavity depth) to address the effectiveness of the methods with respect to the cavity depth. The methods are investigated in flow with Mach number up to 0.45. All different configurations investigated are compared to the base case which is the bare cavity with sharp edges installed upstream and downstream.
Research on Matrix Multiplication Based on the Combination of OpenACC and CUDA. (2016)

With the improvement of GPU’s general computing capacity, the use of parallel computing to solve some difficult problems with large amount of data and intensive computing tasks has become the trend of the times. In GPU general computing, CUDA and OpenCL have been widely used and studied. However, the two parallel programming models generally exist the weakness that whose API is too close to the underlying hardware, which makes programming inefficient and is not suitable for the large-scale parallel tasks that require rapid implementation. OpenACC is a relatively advanced and simple programming language, which can achieve rapid parallelization, but the computing effect of the program is relatively low (generally lower than CUDA). Therefore, this paper tries to combine CUDA and OpenACC for mixed parallelization. This way not only greatly reduces the workload of code conversion, but also has a computing performance no less than a pure CUDA program.
Dovitinib induces mitotic defects and activates the G<sub>2</sub><scp>DNA</scp> damage checkpoint (2013)

Dovitinib (TKI258; formerly CHIR-258) is an orally bioavailable inhibitor of multiple receptor tyrosine kinases. Interestingly, Dovitinib triggered a G2 /M arrest in cancer cell lines from diverse origins including HeLa, nasopharyngeal carcinoma, and hepatocellular carcinoma. Single-cell analysis revealed that Dovitinib promoted a delay in mitotic exit in a subset of cells, causing the cells to undergo mitotic slippage. Higher concentrations of Dovitinib induced a G2 arrest similar to the G2 DNA damage checkpoint. In support of this, DNA damage was triggered by Dovitinib as revealed by γ-H2AX and comet assays. The mitotic kinase CDK1 was found to be inactivated by phosphorylation in the presence of Dovitinib. Furthermore, the G2 arrest could be overcome by abrogation of the G2 DNA damage checkpoint using small molecule inhibitors of CHK1 and WEE1. Finally, Dovitinib-mediated G2 cell cycle arrest and subsequent cell death could be promoted after DNA damage repair was disrupted by inhibitors of poly(ADP-ribose) polymerases. These results are consistent with the recent finding that Dovitinib can also target topoisomerases. Collectively, these results suggest additional directions for use of Dovitinib, in particular with agents that target the DNA damage checkpoint.
An Edge Detection Algorithm Based on Improved CANNY Operator (2007)

Edge detection is an important aspect for image processing, and primary step of spatial data extraction in geography information system. For contour detection, this paper proposed the improved template algorithm, which is not only including the gradient directions of X and Y, but also the first order partial finite differences of directions 45 and 135 degree in calculating the amplitude values. These mostly improved the calculation accuracy of the amplitude values. In the non-maxima suppression process, the factor ratio of four quadrants of linear interpolation is improved to achieve better detection results. Experiments showed that this improved CANNY algorithm has better noise suppression and edge continuity.