gebhart/patrepeval huggingface dataset:
Adaptive optimization of run-to-run controllers: the EWMA example (2000)

This paper presents a recursive scheme for optimizing the gain of an exponentially weighted moving average (EWMA) controller under stability constraints. The objective is to minimize the asymptotic mean square error in the output with minimal a priori information. The algorithm hinges on a simple representation of the optimal EWMA gain. Both step and drift disturbances are considered. It is shown that the gain sequence generated by the algorithm always yields a stable system. Furthermore, this sequence is shown to converge to a suboptimal value. Extensions to the algorithm to the case where there is model uncertainty are also presented. The algorithm is verified via simulation. Data from a manufacturing implementation are presented.
Self-diffusion of a polystyrene-polyisoprene block copolymer (1996)

Forced Rayleigh scattering (FRS) has been used to measure the self-diffusion coefficient, D, of a lamellar-forming polystyrene-polyisoprene diblock copolymer (MPS = 1.0 X 104, MPI = 1.3 X 104) as a function of temperature. The measurements traverse the order-disorder transition (ODT), which occurs at 160°C. There is no obvious change in either D or the temperature dependence of D at the ODT, in agreement with measurements on several other systems. Electron microscopy confirms that the sample in the ordered state is quenched, with no long-range orientation of lamellae, and a typical grain size well below 1 μm. In contrast to previous measurements on a similar styrene-isoprene diblock, these FRS signals are well-described by single exponential decays; this may be largely attributed to differences in average grain size. The temperature dependence of D is modeled with several empirical expressions, based on the known monomeric friction factors for pure polystyrene and pure polyisoprene, but without quantitative success. These results underscore the need for a greater understanding of the composition and temperature dependences of local friction in polymer mixtures. © 1996 John Wiley & Sons, Inc.
Comparison of image-assisted versus traditional fundus examination (2013)

Image-assisted fundus examination may enhance detection of retinal lesions compared with traditional fundus examination alone.
Spatial and Spectral Effects in Continuous-Wave Intracavity Raman Lasers (2014)

We develop an analytic model to explore spatial and spectral effects in intracavity Raman lasers. The effects of deterioration of the spatial and spectral properties of the fundamental and Stokes fields on the laser performance are derived. We quantify how the fundamental field strength can be used to diagnose the behavior of the system, and apply this tool to key prior experimental results.
Characterization of Rhodopsin P23H-Induced Retinal Degeneration in aXenopus laevisModel of Retinitis Pigmentosa (2006)

These results support a role for rhoP23H misfolding and inner segment accumulation in rod death, possibly by ER overload or other cellular stress pathways rather than by altered rhodopsin signal transduction or aggresome formation.
Biochemical and Thermodynamic Characterization of Compounds That Bind to RNA Hairpin Loops:  Toward an Understanding of Selectivity (2006)

Elucidation of the molecular forces governing small molecule-RNA binding is paramount to the progress of rational design strategies. The extensive characterization of the aminoglycoside-16S rRNA A-site interaction has deepened our understanding of how aminoglycosides bind to their target and exert their antimicrobial effects. However, to date no other RNA binding compounds have undergone such rigorous evaluation, and in general the origins of small molecule-RNA binding remain a mystery. We recently reported the identification of small molecules, dimers of 2-deoxystreptamine, which are able to bind selectively to RNA tetraloops and octaloops, respectively [Thomas, Liu, and Hergenrother (2005) J. Am. Chem. Soc. 127, 12434-12435]. Described herein is the biochemical and biophysical characterization of the RNA binding properties of the most selective compound, B-12, as well as closely related analogues. These studies further substantiate that B-12 is indeed selective for RNA octaloop sequences and indicate that the origin of this selectivity may lie in B-12's unusual binding mode, in which entropic factors are major contributors to the overall binding energy. In fact, isothermal titration calorimetry (ITC) experiments indicate that the binding of B-12 and most of its analogues is associated with a strong entropic contribution to the total binding energy. This is in stark contrast to the aminoglycosides, for which favorable enthalpy typically provides the driving force for binding. These studies are the first to examine small molecule-RNA hairpin loop binding in detail and are a necessary step toward the design of compounds that are specific binders for a given RNA sequence.
Primary Malignant Tumors of the Heart: Four Cardiovascular Hormones Decrease the Number and DNA Synthesis of Human Angiosarcoma Cells (2006)

Four cardiovascular hormones decrease the number of angiosarcoma cells within 24 h via inhibition of DNA synthesis mediated in part by cyclic GMP.
Leukemic B-cell precursors express functional receptors for human interleukin-3 (1989)

The purpose of this study was to analyze the expression of functional interleukin-3 (IL-3) receptors on leukemic B-cell precursors (BCPs) from 12 BCP acute lymphoblastic leukemia (ALL) patients and five BCP ALL cell lines. The specific binding of biosynthetically labeled 35S-recombinant (r) IL-3 to freshly obtained leukemic marrow blasts was initially investigated. In five of 12 BCP ALL cases, the binding of 35S-rIL-3 was markedly blocked by excess cold rIL-3, and the percentage of inhibitable binding ranged from 53% to 78% (mean +/- SE = 65% +/- 4%). In these cases, the cell-bound radioactivity ranged from 146 cpm/10(7) cells to 1,433 cpm/10(7) cells (mean +/- SE = 627 +/- 250 cpm/10(7) cells), indicating that 1 to 14 femtomole (mean +/- SE = 6 +/- 2 fms) of [35S]rIL-3/10(7) cells were specifically bound (= 60 to 840 molecules per cell). rIL-3 stimulated the proliferative activity of leukemic BCPs in a dose-dependent fashion without inducing differentiation, and the half-maximal stimulatory activity was observed at a concentration of 17 to 34 pmol/L. Fluorescence-activated cell sorter (FACS)-isolated virtually pure populations of CD10+CD19+ leukemic BCPs from two BCP ALL patients, as well as from two of five BCP ALL cell lines, showed a marked proliferative response to highly purified rIL-3, providing formal evidence that the observed IL-3 responses were not mediated by accessory cells. There was a high correlation between [35S]rIL-3 binding and proliferative response in colony assays, indicating that functional IL-3 receptors were detected in ligand binding assays. Scatchard plot analysis of the specific equilibrium binding data for IL-3-responsive leukemic BCPs from one BCP ALL patient and two BCP ALL cell lines yielded a straight linear regression line, indicating the existence of a single class of 60 to 210 high-affinity IL-3 binding sites/cell. The calculated apparent affinity constant (Ka) values ranged from 3.6 x 10(9) to 5.9 x 10(9) mol/L-1. Hence, the concentration of IL-3 required to produce 50% maximal receptor occupancy (Kd) was in the range of 168 to 280 pmol/L. These concentrations are approximately tenfold higher than those required to induce 50% maximal proliferative response from leukemic BCPs in colony assays, indicating that low receptor occupancy is sufficient for growth stimulation of leukemic BCPs by rIL-3. In comparison, less than 10 to 20 IL-3 molecules/cell were bound to IL-3 unresponsive leukemic BCPs even when the concentration of free-[35S]rIL-3 was as high as 2 nmol/L.(ABSTRACT TRUNCATED AT 400 WORDS)
cDNA cloning and deduced amino acid sequence of prothrombin activator (ecarin) from Kenyan Echis carinatus venom (1995)

The complete amino acid sequence of ecarin is deduced from the nucleotide sequence of a cDNA clone isolated by screening a venomous gland cDNA library of Kenyan Echis carinatus. The cDNA sequence with 2379 base pairs encodes an open reading frame of 616 amino acids with a remarkable sequence homology to the putative precursor protein of trigramin from Trimeresurus gramineus venom (61% identity) and a large hemorrhagin, jararhagin, from the pit viper Bothrops jararaca venom (62% identity). Thus, ecarin, as well as jararhagin and trigramin, is translated as a precursor protein, which may be processed posttranslationally. The ecarin proprotein has a "cysteine switch" motif (-Pro-Lys-Met-Cys-Gly-Val-) similar to that involved in the activation of matrix metalloproteinase zymogens. The processed mature protein consists of 426 amino acid residues (residues 191-616), showing the strongest sequence similarity with that of Russell's viper venom factor X activator (RVV-X) heavy chain (64% identity). Like RVV-X heavy chain, ecarin contains metalloproteinase, disintegrin, and cysteine-rich domains. The metalloproteinase domain has a typical zinc-chelating sequence (-His-Glu-Xaa-Xaa-His-Xaa-Xaa-Gly-Xaa-Xaa-His-), as found in crayfish astacin. In the disintegrin domain of ecarin, the Arg-Gly-Asp sequence is replaced by Arg-Asp-Asp, as found in the disintegrin domains of RVV-X heavy chain (Arg-Asp-Glu) and a guinea pig sperm fusion protein, PH-30 beta (Thr-Asp-Glu). These findings show that while there are structural and evolutionary relationships among these proteins, each has a unique functional activity.
Experiments in Digital Video for Workstations (1989)

This paper describes experimental work in the use of digital video by computer workstations. The approach is essentially practical, since the aims of the research were to gain experience with the handling of video, and to investigate some of the systems aspects of its integration into the workstation environment. The motivation for the work is explained, along with the compromises which were necessary to make the work possible. The hardware and software tools used in the experimentation are described, and the experiences gained from the first trial applications are discussed. 1. Introduction Since its foundation in 1986, the Cambridge Olivetti Research Laboratory has been working heavily in the area of digital video. The work is based on the use of a high speed local area network with sufficient capacity to carry video traffic [Hopper88]. It also owes much to work done at the University of Cambridge Computer Laboratory, primarily the Cambridge Model Distributed System [Needham82] and ...
A Generalized Lyapunov Feature for Dynamical Systems on Riemannian Manifolds (2015)

Dynamic phenomena such as human activities, dynamic scenes, and moving crowds are commonly observed through visual sensors, resulting in feature trajectories sampled in time. Such phenomena can be accurately modeled by taking the temporal variations and changes into account. For problems where the trajectories are sufficiently different, elastic metrics can provide distances that are invariant to speed, but for more complex problems such as fine grained activity classification, one needs to exploit higher order dynamical properties. For features in the Euclidean space, applications such as crowd monitoring, dynamic scene recognition and human movement quality analysis have found a lot of success this way. In this paper we propose the largest Riemannian Lyapunov exponent (L-RLE), which is the first generalization of the largest Lyapunov exponent to Riemannian manifolds. The largest Lyapunov exponent is a classic measure to quantify the amount of chaos within signals in the Euclidean space, and allows us to exploit higher order dynamics for various applications. We show the effectiveness of the L-RLE on two manifolds the Grassmann and the SO(3) lie group. By modeling human actions as dynamic processes evolving on Riemannian manifolds, we show that L-RLE can measure the amount of chaos within each action accurately. We show that our measure is a good generalization of largest Euclidean Lyapunov exponent (L-ELE), and is less susceptible to arbitrary distortions.
Pending Issues in the Modeling of Concentrator Solar Cells (2005)

The modelling of concentrator solar cells for real conditions of operation inside optical concentrators is a subject almost untreated. Consequently, this work highlights the main specifi c situations that should be included in a realistic modelling. The results of a 2-D modelling applied to the case of a 1000 sun GaAs concentrator solar cell inside a TIR-R concentrator are presented. The necessity of going towards a 3-D modelling is also stated. This task is being carried out now at IES-UPM. Keywords: concentrator cells, modelling, III-V semiconductors.
Biochemical and immunological characteristics of 4-1BB (CD137) receptor and ligand and potential applications in cancer therapy. (1999)

4-1BB (CD 137) is a member of the tumor necrosis factor receptor (TNFR) superfamily that is expressed primarily on activated T cells. Crosslinking of the 4-1BB receptor activates an intracellular signal cascade that leads to the activation of NF-kappaB and costimulation of T cell growth. Recent evidence indicates that 4-1BB may preferentially costimulate CD8+ T cell growth and induce cytolytic activity. The cytolytic activity induced by 4-1BB crosslinking is able to eradicate large, well-established, poorly immunogenic tumors and augments allogenic T cell responses in vivo. The 4-1BB/4-1BB ligand costimulatory pathway can provide an alternative T cell costimulatory pathway in the absence of CD28, but may physiologically function as a synergistic or complementary pathway to the CD28 costimulatory pathway. Only some of the basic immunological functions of 4-1BB/4-IBB ligand have been elucidated and much study is required to determine its exact role in T cell activation.
Binding and internalization of interleukin 1 by T cells. Direct evidence for high- and low-affinity classes of interleukin 1 receptor. (1986)

In this report we describe, on the basis of direct IL-1 binding assays and IL-1 internalization studies, the existence of two classes of IL-1-R on a variety of T cell types. Cells of the EL4-6.1 thymoma express large numbers (approximately 20,000 per cell) of IL-1-R that have a Kd of approximately 300 pM for IL-1. Even though these receptors make up 98-99% of the total IL-1-R per cell, they appear to be nonfunctional, based on their inability to endocytose IL-1. A minor class of IL-1-R (200-400/cell) has an approximately 100-fold higher affinity for IL-1 (Kd, approximately 5 pM) and can rapidly internalize the ligand upon binding. All of the biological activity of IL-1 can be shown to occur via binding to high-affinity IL-1-R since the IL-1 concentration giving half-maximum biological activity in EL4-6.1 cells corresponds precisely to the Kd of this class of receptor. Other cell types, including normal T cells, also express both high- and low-affinity IL-1-R, but the absolute number of receptors per cell is considerably less.
Mechanisms of pancreatic beta-cell destruction in type I diabetes. (1989)

The pathogenetic mechanisms leading to beta-cell destruction and insulin-dependent diabetes mellitus (IDDM) are major histocompatibility complex (MHC) nonrestricted and are MHC associated and beta-cell specific. The macrophage peptide hormone interleukin 1 (IL-1) may be the primary MHC-nonrestricted beta-cell-destructive molecule. Beta-Cell death most likely results from free radical induction by IL-1. Thus, islet cell-specific antibodies and cytotoxic T-lymphocytes are secondary in importance and time. The potentiation of IL-1 effects on beta-cells by tumor necrosis factor alpha (TNF), another macrophage hormone controlled by a gene in the HLA region on chromosome 6, may account for the MHC association of IDDM. In the experimental model of IDDM etiopathogenesis described, release of beta-cell antigen, processed and presented by macrophages to helper T-lymphocytes, initiates a self-perpetuating and self-limiting circuit of cytokine production of which IL-1 is beta-cell cytotoxic. As postulated, the IL-1 effect is potentiated by TNF, whereas IL-1 and/or TNF production is controlled in a quantitative way by HLA-D genes.
Peptide Deformylase in Staphylococcus aureus : Resistance to Inhibition Is Mediated by Mutations in the Formyltransferase Gene (2000)

Peptide deformylase, a bacterial enzyme, represents a novel target for antibiotic discovery. Two deformylase homologs, defA and defB, were identified in Staphylococcus aureus. The defA homolog, located upstream of the transformylase gene, was identified by genomic analysis and was cloned from chromosomal DNA by PCR. A distinct homolog, defB, was cloned from an S. aureus genomic library by complementation of the arabinose-dependent phenotype of a P(BAD)-def Escherichia coli strain grown under arabinose-limiting conditions. Overexpression in E. coli of defB, but not defA, correlated to increased deformylase activity and decreased susceptibility to actinonin, a deformylase-specific inhibitor. The defB gene could not be disrupted in wild-type S. aureus, suggesting that this gene, which encodes a functional deformylase, is essential. In contrast, the defA gene could be inactivated; the function of this gene is unknown. Actinonin-resistant mutants grew slowly in vitro and did not show cross-resistance to other classes of antibiotics. When compared to the parent, an actinonin-resistant strain produced an attenuated infection in a murine abscess model, indicating that this strain also has a growth disadvantage in vivo. Sequence analysis of the actinonin-resistant mutants revealed that each harbors a loss-of-function mutation in the fmt gene. Susceptibility to actinonin was restored when the wild-type fmt gene was introduced into these mutant strains. An S. aureus Deltafmt strain was also resistant to actinonin, suggesting that a functional deformylase activity is not required in a strain that lacks formyltransferase activity. Accordingly, the defB gene could be disrupted in an fmt mutant.
123 I- m IBG Scintigraphy to Predict Inducibility of Ventricular Arrhythmias on Cardiac Electrophysiology Testing (2008)

The standard indices of (123)I-mIBG imaging (H/M and innervation-perfusion mismatch score) are not predictive of EP test results. The association of (123)I-mIBG SPECT defect severity with EP test inducibility in this exploratory study will require confirmation in a larger cohort of patients.
Proliferation of Intimal Smooth Muscle Cells (2000)

Basic fibroblast growth factor (FGF2) is a potent mitogen for medial smooth muscle cells and is necessary for their proliferation after balloon catheter injury; however, intimal smooth muscle cells do not require FGF2 for their proliferation, and they respond only weakly to exogenous FGF2. The present study examined the activation of extracellular signal-regulated kinase (ERK) signaling as well as the expression and activity of cell cycle proteins in FGF2-stimulated intimal smooth muscle cells. FGF2 activates ERKs 1 and 2, and Western blot analysis showed that cyclin D, cyclin E, and cyclin-dependent kinase (CDKs) 2 and 4 were expressed in intimal smooth muscle cells after FGF2 infusion. FGF2 stimulation, however, did not lead to phosphorylation of the retinoblastoma protein (Rb), CDK 2 activation, or expression of cyclin A. Western blot analysis showed that intimal smooth muscle cells express elevated levels of the cell cycle inhibitors p15(INK4b) and p27(Kip1), compared with medial smooth muscle cells, and that FGF2 stimulation does not reduce the level of these inhibitors. These studies suggest that despite activation of ERKs 1 and 2 and expression of the cell cycle activators, cyclin D and cyclin E, high levels of cell cycle inhibitors may inhibit cell cycle transit in FGF2-stimulated intimal smooth muscle cells.
Detection of chromosomal anomalies and c-myc gene amplification in the cribriform pattern of prostatic intraepithelial neoplasia and carcinoma by fluorescence in situ hybridization. (1997)

Grading of the cribriform pattern of prostate cancer is controversial, and the genetic changes are largely unknown. Furthermore, the pathogenetic relationship between the cribriform pattern of high-grade prostatic intraepithelial neoplasia (PIN) and cribriform carcinoma is poorly understood. We used fluorescence in situ hybridization with centromere-specific probes for chromosomes 7, 8, 10, 12, and Y and a region-specific probe for c-myc to evaluate genetic changes in matched foci of high-grade PIN (48 foci) and prostatic carcinoma (71 foci) in 25 whole-mount radical prostatectomy specimens from patients with metastatic cancer. These cases included 10 foci of cribriform PIN and 10 foci of cribriform cancer. Numeric chromosomal anomalies were found in 67 and 68% of the high-grade PIN and carcinoma foci, respectively. Extra copies of the c-myc gene were identified in 52 and 44% of the high-grade PIN and carcinoma foci, respectively. The cribriform pattern of cancer had a higher percentage of foci with gain of chromosomes 7, 12, and Y, loss of chromosome 8, and extra copies of c-myc gene than other Gleason Primary Patterns 3 and 4; there was no difference, however, for all paired comparisons of genetic changes between the cribriform pattern of cancer and Gleason Primary Pattern 5 cancer. Cribriform PIN and cribriform cancer generally exhibited similar anomalies, although the percentage of foci with gain of chromosomes 10 and 12 was higher in cribriform cancer. Our results indicate that the cribriform pattern of prostate cancer shares genetic changes with Gleason Primary Pattern 5 and that both contain more genetic changes than the cribriform pattern of PIN. These findings suggest that the cribriform pattern of prostate cancer has biologic similarity with Gleason Pattern 5 carcinoma and that the cribriform pattern of PIN is closely associated with the cribriform pattern of prostatic carcinoma.
Bimodal Surface Ligand Engineering: The Key to Tunable Nanocomposites (2012)

Tuning the dispersion of inorganic nanoparticles within organic matrices is critical to optimizing polymer nanocomposite properties and is intrinsically difficult due to their strong enthalpic incompatibility. Conventional attempts to use polymer brushes to control nanoparticle dispersion are challenged by the need for high graft density to reduce particle core-core attractions and the need for low graft density to reduce the entropic penalty for matrix penetration into the brush. We validated a parametric phase diagram previously reported by Pryamtisyn et al. (Pryamtisyn, V.; Ganesan, V.; Panagiotopoulos, A. Z.; Liu, H.; Kumar, S. K. Modeling the Anisotropic Self-Assembly of Spherical Polymer-Grafted Nanoparticles. J. Chem. Phys.2009, 131, 221102) for predicting dispersion of monomodal-polymer-brush-modified nanoparticles in polymer matrices. The theoretical calculation successfully predicted the experimental observation that the monomodal-poly(dimethyl siloxane) (PDMS)-brush-grafted TiO(2) nanoparticles can only be well dispersed within a small molecular weight silicone matrix. We further extended the parametric phase diagram to analyze the dispersion behavior of bimodal-PDMS-brush-grafted particles, which is also in good agreement with experimental results. Utilizing a bimodal grafted polymer brush design, with densely grafted short brushes to shield particle surfaces and sparsely grafted long brushes that favor the entanglement with matrix chains, we dispersed TiO(2) nanoparticles in high molecular weight commercial silicone matrices and successfully prepared thick (about 5 mm) transparent high-refractive-index TiO(2)/silicone nanocomposites.