gebhart/patrepeval huggingface dataset:
Accurate modeling of the intramolecular electrostatic energy of proteins (1995)

Abstract The (ϕ, ψ) energy surface of blocked alanine ( N ‐acetyl–N′‐methyl alanineamide) was calculated at the Hartree‐Fock (HF)/6‐31G* level using ab initio molecular orbital theory. A collection of six electrostatic models was constructed, and the term electrostatic model was used to refer to (1) a set of atomic charge densities, each unable to deform with conformation; and (2) a rule for estimating the electrostatic interaction energy between a pair of atomic charge densities. In addition to two partial charge and three multipole electrostatic models, this collection includes one extremely detailed model, which we refer to as nonspherical CPK. For each of these six electrostatic models, parameters—in the form of partial charges, atomic multipoles, or generalized atomic densities—were calculated from the HF/6‐31G* wave functions whose energies define the ab initio energy surface. This calculation of parameters was complicated by a problem that was found to originate from the locking in of a set of atomic charge densities, each of which contains a small polarization‐induced deformation from its idealized unpolarized state. It was observed that the collective contribution of these small polarization‐induced deformations to electrostatic energy differences between conformations can become large relative to ab initio energy differences between conformations. For each of the six electrostatic models, this contribution was reduced by an averaging of atomic charge densities (or electrostatic energy surfaces) over a large collection of conformations. The ab initio energy surface was used as a target with respect to which relative accuracies were determined for the six electrostatic models. A collection of 42 more complete molecular mechanics models was created by combining each of our six electrostatic models with a collection of seven models of repulsion + dispersion + intrinsic torsional energy, chosen to provide a representative sample of functional forms and parameter sets. A measure of distance was defined between model and ab initio energy surfaces; and distances were calculated for each of our 42 molecular mechanics models. For most of our 12 standard molecular mechanics models, the average error between model and ab initio energy surfaces is greater than 1.5 kcal/mol. This error is decreased by (1) careful treatment of the nonspherical nature of atomic charge densities, and (2) accurate representation of electrostatic interaction energies of types 1—2 and 1—3. This result suggests an electrostatic origin for at least part of the error between standard model and ab initio energy surfaces. Given the range of functional forms that is used by the current generation of protein potential functions, these errors cannot be corrected by compensating for errors in other energy components. © 1995 by John Wiley & Sons, Inc.
Objetive Video Quality Metrics: A Performance Analysis (2006)

Publication in the conference proceedings of EUSIPCO, Florence, Italy, 2006
A probabilistic approach to automatic keyword indexing. Part II. An algorithm for probabilistic indexing (1975)

Abstract In Part I of this study,* a mixture of two Poisson distributions was examined as a model of specialty word distribution. Formulas expressing the three parameters of the model in terms of empirical frequency statistics were derived, and a statistical measure intended to identify specialty words, consistent with the model, was proposed. In the present paper, Part II of the study, a probabilistic model of keyword indexing is outlined, and some of the consequences of the model are examined. An algorithm defining a measure of indexability is developed‐a measure intended to reflect the relative significance of words in documents. The measure is evaluated and is found to consistently produce indexes superior to those produced by another measure which had previously been identified in the literature as producing the best results.
Spectrophotometric Characterization of Behavior and the Predominant Species of Flavonoids in Physiological Buffer: Determination of Solubility, Lipophilicity and Anticancer Efficacy (2008)

The objectives of this study were to investigate the behavior of flavonoids in an aqueous physiological buffer and to determine the structural and functional group substitution which is responsible for their anticancer action. The deprotonated anionic form of 7 flavonoids can easily be determined using spectrophotometry, and owing to its charged state, is highly soluble in aqueous physiological buffer and is not prone to aggregation. The protonated form of these 7 flavonoids is much less soluble and tends to aggregate following precipitation. For all flavonoids studied except catechin and 5,5 -dihydroxy-6,7,3 ,4 -tetramethoxyflavone, it was possible to determine the rates of deprotonation; pKa value of eriodictyol, apigenin, kaempferol, quercetin, WP 279, and WP 283 was equal to 7. 00, 8.72, 7.86, 8.30, 7.70 and 9.90, respectively. The methoxyl group substitutions in place of hydrogen atoms and/or hydroxyl groups at various positions of carbon atoms in ring A, B and C particularly WP 283 resulted in an increase in the solubility, lipophilicity, and specifically its anticancer efficacy (by 60-fold). The neutral forms of flavonoids are predominantly active molecules and the active sites responsible for anticancer activity are found in ring A and C, especially C4=O, C5-OH and C2=C3.
The Potential Impact of Zinc Supplementation on COVID-19 Pathogenesis (2020)

During the current corona pandemic, new therapeutic options against this viral disease are urgently desired. Due to the rapid spread and immense number of affected individuals worldwide, cost-effective, globally available, and safe options with minimal side effects and simple application are extremely warranted. This review will therefore discuss the potential of zinc as preventive and therapeutic agent alone or in combination with other strategies, as zinc meets all the above described criteria. While a variety of data on the association of the individual zinc status with viral and respiratory tract infections are available, study evidence regarding COVID-19 is so far missing but can be assumed as was indicated by others and is detailed in this perspective, focusing on re-balancing of the immune response by zinc supplementation. Especially, the role of zinc in viral-induced vascular complications has barely been discussed, so far. Interestingly, most of the risk groups described for COVID-19 are at the same time groups that were associated with zinc deficiency. As zinc is essential to preserve natural tissue barriers such as the respiratory epithelium, preventing pathogen entry, for a balanced function of the immune system and the redox system, zinc deficiency can probably be added to the factors predisposing individuals to infection and detrimental progression of COVID-19. Finally, due to its direct antiviral properties, it can be assumed that zinc administration is beneficial for most of the population, especially those with suboptimal zinc status.
Antiviral Activity of Suramin: Inhibitory Effect on Japanese Encephalitis Virus Replication. (1996)

Suramin, a polysulfonated naphthylurea, has been used for the treatment of trypanosomias and onchocerciasis, and is a potent inhibitor of nucleic acid polymerase including reverse transcriptase and DNA polymerase. This drug is used to examine an antiviral activity in the case of Japanese encephalitis virus (JEV) infection. Japanese encephalitis occurs in endemic and epidemic form over a wide area of Asia, at least tens of thousands of cases occur annually in East Asia. Although the vaccine against JEV is widely used, we have no antiviral drugs against JEV replication. Here we describe an antiviral activity of suramin on JEV replication in the cultured cells. In the presence of 50 μg/ml suramin, virus yields in human neuroblastoma cell line, IMR-32, reduced to 0.1% of control level. JEV growth in human hepatoma cell line, HepG2, was also inhibited, but inhibitory effect of suramin was lower than in IMR-32. The difference of inhibitory effects between host cells suggests that some host factors were involved in the process of inhibition of JEV growth. By Western blot analysis, it was clarified that expressions of JEV proteins, NS3 and E were markedly reduced by the treatment of suramin at 50-200 μg/ml. Especially the expression of E protein seems to be sensitive against suramin treatment. On the other hand, JEV-RNA level in the cells treated with suramin was not so different from control level, and in vitro JEV-RNA synthesis was also not inhibited by the addition of suramin. These results suggest that suramin inhibits virus replication through the influence to viral protein production, not to viral RNA synthesis.
Internal Cardioversion of Chronic Atrial Fibrillation in Patients (1997)

Transvenous internal cardioversion of chronic AF using a right atrium (RA) coronary sinus (CS) vector requires more energy than cardioversion of paroxysmal AF. Chronic AF is not terminated in 25% of patients using biphasic shocks up to 10 J. We therefore evaluated efficacy, safety, and tolerability of internal cardioversion using a "unipolar" configuration (RA to skin patch) and biphasic shocks in patients with long-lasting AF and different heart disease. In each patient, biphasic R wave synchronous shocks were delivered between a large defibrillating surface area electrode in the RA and a skin patch in the left prepectoral position. Defibrillation protocol started with a test shock of 0.4 J. Shocks were repeated and increased until termination of AF or a maximum of 34 J. Sedation was used when the patient described the shock as painful. This study included 11 patients with a mean age of 67 +/- 8 years (range 56-83). AF duration was > or = 1 month in all patients with a mean duration of 11 +/- 11 months (range 2-36). Underlying heart disease was present in all patients and the mean left atrial dimension was 43 +/- 9 mm (range 26-57). AF was terminated in 10 of 11 patients (91%) with a mean delivered energy of the successful shocks of 18.7 +/- 8.7 J (median energy 16.9 J; range 7.3-32.5) and a mean leading edge voltage of 564 +/- 129 V. The mean shock impedance at the defibrillation threshold was 71 +/- 13 omega (range 59-103). A total of 131 shocks were delivered without any complication and proarrhythmia episodes. We conclude that low energy "unipolar" internal cardioversion is a simple, safe, and effective technique for termination of chronic AF in patients with heart disease. The procedure is often tolerated under light sedation.
Thermal Stress and Strain in a GaN Epitaxial Layer Grown on a Sapphire Substrate by the MOCVD Method (2010)

In this article we have studied the existence of stress and strain in a Si-doped GaN (2μm)/sapphire structure grown by the metal-organic chemical vapour deposition (MOCVD) method and tried to model the parameters. The presence of stress in our sample is supported by an E2 Raman shift mode (Δω) of about 1.25 cm^(-1). To find the amount of biaxial basal plane stress we performed two techniques, XRD and film bending by a profilometer. The XRD technique confirmed that the GaN layer has a hexagonal structure with the lattice constants of c=5.1825A and a=3.187A. Our theoretical calculations show that this layer suffers a biaxial stress (σ(subscript α)) of about 0.175±0.003 GPa. The profilometer data analysis also leads to a compatible value of 0.12±0.04 GPa. These parameters altogether suggest the relation Δω=7.1±0.1σcm^(-1)/GPa for this layer.
Exposure of RNA Templates and Encapsidation of Spliced Viral RNA Are Influenced by the Arginine-Rich Domain of Human Hepatitis B Virus Core Antigen (HBcAg 165-173) (2005)

Previously, human hepatitis B virus (HBV) mutant 164, which has a truncation at the C terminus of the HBV core antigen (HBcAg), was speculated to secrete immature genomes. For this study, we further characterized mutant 164 by different approaches. In addition to the 3.5-kb pregenomic RNA (pgRNA), the mutant preferentially encapsidated the 2.2-kb or shorter species of spliced RNA, which can be reverse transcribed into double-stranded DNA before virion secretion. We observed that mutant 164 produced less 2.2-kb spliced RNA than the wild type. Furthermore, it appeared to produce at least two different populations of capsids: one encapsidated a nuclease-sensitive 3.5-kb pgRNA while the other encapsidated a nuclease-resistant 2.2-kb spliced RNA. In contrast, the wild-type core-associated RNA appeared to be resistant to nuclease. When arginines and serines were systematically restored at the truncated C terminus, the core-associated DNA and nuclease-resistant RNA gradually increased in both size and signal intensity. Full protection of encapsidated pgRNA from nuclease was observed for HBcAg 1-171. A full-length positive-strand DNA phenotype requires positive charges at amino acids 172 and 173. Phosphorylation at serine 170 is required for optimal RNA encapsidation and a full-length positive-strand DNA phenotype. RNAs encapsidated in Escherichia coli by capsids of HBcAg 154, 164, and 167, but not HBcAg 183, exhibited nuclease sensitivity; however, capsid instability after nuclease treatment was observed only for HBcAg 164 and 167. A new hypothesis is proposed here to highlight the importance of a balanced charge density for capsid stability and intracapsid anchoring of RNA templates.
Investigation of graphene based miniaturized terahertz antenna for novel substrate materials (2015)

The selection of appropriate substrate material acts as a performance regulator for miniaturized graphene patch antenna. The substrate material not only controls the transport properties of graphene but also influences the resonant properties of the graphene patch antenna. The edge fed microstrip line graphene based rectangular patch antenna is designed here for operating in the frequency range 2.67–2.92 THz for wireless applications. The performance is investigated for silicon nitride, aluminum oxide, boron nitride, silica and quartz substrate materials on the basis of return loss, voltage standing wave ratio (VSWR), absorption cross section, bandwidth and radiation efficiency. The comparison of results shows that silicon nitride exhibits overall excellent performance by the virtue of having higher bandwidth and radiation efficiency as compared to other chosen substrate materials.
Phase Locality Detection Using a Branch Trace Buffer for Efficient Profiling in Dynamic Optimization (2002)

Abstract Efficient profiling is a major challenge for dynamic optimization because the profiling overhead contributes to the total execution time. In order to identify program hot spots for runtime optimization, the profiler in a dynamic optimizer must detect new execution phases and subsequent phase changes. Current profiling approaches used in prototype dynamic optimizers are interpretation or instrumentation based. They have eithervery high overhead, or generate poor quality profiles. We use the branch trace buffer and the hardware performance monitoring features provided in the IA -64 architecture to detect new execution phases and phase changes. The branch trace buffer records the last few branch instructions executed before an event based interrupt is generated. Using the branch trace buffer, our profiler continuously samples execution paths leading to critical performance events, such as cache misses and pipeline stalls. A set of frequently executed traces and their respective performancecharacteristics within a time interval are considered as an execution phase. Since such phases tend to repeat over time, a dynamic optimizer can exploit the phase locality to drive optimization. We check for new phases and phase changes at the end of each time interval. Although a new phase or a changed phase can be a candidate for optimization, our phase detector delays the invocation of the optimizer until a relatively stable phase is detected. We report the effectiveness of various phase detection methods using Spec2000int as the benchmark. Our results indicate branch trace based phase detection can be suitable for dynamic binary optimizers.
Two-dimensional LMS adaptive filter incorporating a local-mean estimator for image processing (1993)

An adaptive scheme is proposed whereby a local-mean estimation substructure is incorporated to overcome the problem of the 2-D least-mean-square (LMS) adaptive filter in dealing with signals having a nonzero mean, especially with abrupt variations (edges), which is a typical feature of practical images. The advantages of this scheme over the direct use of the 2-D LMS are considered. As a direct application, the scheme is used for adaptive cancellation of an artifact disturbance in an image. A method of implementing the local-mean estimation substructure with the edge-preserving property is introduced. Using this local-mean estimator, the scheme is applied to enhancement of images disturbed by wideband noise. All of the application examples illustrate some useful feature of the 2-D LMS adaptive filter in image processing and the improved performance of the scheme.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Reorder Buffer Design for High Performance Processors (2012)

Modern reorder buffers (ROBs) were conceived to improve processor performance by allowing instruction execution out of the original program order and run ahead of sequential instruction code exploiting existing instruction level parallelism (ILP). The ROB is a functional structure of a processor execution engine that supports speculative execution, physical register recycling, and precise exception recovering. Traditionally, the ROB is considered as a monolithic circular buffer with incoming instructions at the tail pointer after the decoding stage and completing instructions at the head pointer after the commitment stage. The latter stage verifies instructions that have been dispatched, issued, executed, and are not completed speculatively. This paper presents a design of distributed reorder buffer microarchitecture by using small structures near building blocks which work together, using the same tail and head pointer values on all structures for synchronization. The reduction of area, and therefore, the reduction of power and delay make this design suitable for both embedded and high performance microprocessors.
General shape distributions in a plane (1991)

In this paper we investigate the exact shape distribution for general Gaussian labelled point configurations in two dimensions. The shape density is written in a closed form, in terms of Kendall's or Bookstein's shape variables. The distribution simplifies considerably in certain cases, including the complex normal, isotropic, circular Markov and equal means cases. Various asymptotic properties of the distribution are investigated, including a large variation distribution and the normal approximation for small variations. The triangle case is considered in particular detail, and we compare the density with simulated densities for some examples. Finally, we consider inference problems, with an application in biology.
Memory units in the Lincoln TX-2 (1957)

There are 3 high-speed live memories in TX-2; all are random access and all use ferrite cores. The largest is the 6 1/2-μsec cycle time "S" memory with 65,536 37-digit words. The "T" memory is entirely transistor driven; it has a capacity of 4096 37-digit words and a 5 1/2-μsec cycle time. The smallest and fastest is the "X" memory with a capacity of 64 19-digit words; external word selection and 2 cores per bit make possible an access time of 0.8 μsec and a cycle time of 4 μsec.
Regulation and regulatory parameters of histone modifications (1998)

Histone acetylation and phosphorylation destablizes nucleosome and chromatin structure. Relaxation of the chromatin fiber facilitates transcription. Coactivator complexes with histone acetyltransferase activity are recruited by transcription factors bound to enhancers or promoters. The recruited histone acetyltransferases may acetylate histone or nonhistone chromosomal proteins, resulting in the relaxation of chromatin structure. Alternatively, repressors recruit corepressor complexes with histone deacetylase activity, leading to condensation of chromatin.This review highlights the recent advances made in our understanding of the roles of histone acetyltransferases, histone deacetylases, histone kinases, and protein phosphatases in transcriptional activation and repression. Exciting reports revealing mechanistic connections between histone modifying activities and the RNA polymerase II machinery, the coupling of histone deacetylation and DNA methylation, the possible involvement of histone deacetylases in the organization of nuclear DNA, and the role of chromatin modulators in oncogenesis are discussed. J. Cell. Biochem. Suppls. 30/31:203–213, 1998. © 1998 Wiley-Liss, Inc.
Differentiated QoS for survivable WDM optical networks (2004)

Optical networks based on WDM technology have become a promising solution to realize transport networks that can meet the ever-increasing demand for bandwidth. As WDM networks carry a huge volume of traffic, maintaining a high level of survivability is an important and critical issue. The. development of GMPLS switching technology led to the direct integration of IP and WDM. In these IP-over-WDM networks different applications/end users need different levels of fault tolerance and differ in how much they are willing to pay for the service they get. The current trend in network development is moving toward a unified solution providing support for voice, data, and various multimedia services. Therefore, it imperative that WDM networks incorporate fault tolerance to single or multiple component failures, protection bandwidth, recovery time, and recovery granularity besides resource utilization and call acceptance ratio. This article presents a survey of various methods that have been proposed for providing service differentiation in survivable WDM networks and discuss their performance. Such methods are broadly classified under various paradigms such as differentiated reliability, R-connections, quality of protection, and quality of recovery.
Optimal regional pole placement for sun tracking control of high-concentration photovoltaic (HCPV) systems: case study (2010)

This paper proposes an optimal regional pole placement approach for sun tracking control of high-concentration photovoltaic systems. A static output feedback controller is designed to minimize an LQG cost function with a sector region pole constraint. The problem cannot be solved by LMI approach since it is a non-convex optimization problem. Based on the barrier method, we instead solve an auxiliary minimization problem to obtain an approximate solution. Simulation results show the benefit of our approach. Copyright © 2010 John Wiley & Sons, Ltd.
In service training in Zimbabwe : an analysis of relationships among education and training, industry, and the state (1990)

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Laplacian magic windows (2017)

A transparent sheet, flat to unaided vision but with a gentle surface relief, can concentrate light onto a screen with intensity reproducing any desired image: the sheet is a 'magic window'. When the ray deflections are sufficiently small that there are no caustics between the window and the screen, the image intensity is the Laplacian function of the relief height function—a very simple approximation to general freeform optics. Therefore the desired relief is obtained by solving Poisson's equation. Numerical simulations indicate that the Laplacian image approximation will apply to realistic situations.