gebhart/patrepeval huggingface dataset:
A Flexible Space-Time Coding System with Unequal Error Protection (2005)

Most multimedia source coders exhibit unequal bit error sensitivity. Efficient transmission system design should therefore incorporate the use of matching unequal error protection (UEP). In this paper, we present and evaluate a flexible space-time coding system with unequal error protection. Multiple transmit and receive antennas and bit-interleaved coded modulation techniques are used combined with rate compatible punctured convolutional codes. A near optimum iterative receiver is employed with a multiple-in multiple-out inverse mapper and a MAP decoder as component decoders. We illustrate how the UEP system gain can be achieved either as a power or bandwidth gain compared to the equal error protection system (EEP) for the identical source and equal overall quality for both the UEP and EEP systems. An example with two/three transmit and two receive antennas using 8PSK modulation is given for the block fading channel.
‘Hardcore’ OX40+immunosuppressive regulatory T cells in hepatic cirrhosis and cancer (2014)

Human regulatory T cells (Tregs) comprise an array of distinct subsets displaying diverse functions in response to microenvironmental signals. Here, we review our recent findings demonstrating the preferential accumulation of uncommitted, Th1-like and OX40<sup>-</sup> Tregs in non-cirrhotic tissues in contrast to the presence of committed, Th1-suppressing and OX40<sup>+</sup> Tregs in cirrhotic and tumor contexts in human liver affected by chronic hepatitis C.
In Vitro Engineering Using Acyl-Derivatized tRNAs (2003)

Incorporation of fluorescently labeled or otherwise modified amino acids into proteins is potentially useful in a variety of ways, including monitoring the folding of the nascent protein chain, measuring posttranslational conformational changes and binding of substrates, and determining structure-function relationships. One of the most successful techniques for incorporating fluorescent amino acids into proteins has been to use aminoacyl-tRNAs in which the α-amino group has been acylated with a fluorescent moiety producing an N-acylaminoacyl-tRNA derivative (1). These derivatives have been used in then own right to study tRNA binding sites on the ribosome (2). Such derivatives, with their acylated amino groups, can only serve as donors in protein synthesis and thus can only be incorporated at the N-terminus. Nevertheless they have been very useful in studying the poly (U)1-directed synthesis of polyphenylalanine, polyserine, and polyalanine, the latter two using synthetic tRNAs whose anticodons had been changed to AAA (3). By incorporating coumarin-labeled phenylalanine or alanine at the N-terminus of such nascent chains, we were able to study by fluorescence, the interactions of the nascent chains with the ribosome as a function of chain length (4,5). More recently, using an efficient coupled transcription/translation system from Escherichia coli (6), we have incorporated coumarin-labeled methionine from tRNAf Met into several proteins. The fluorescent probe has been instrumental in studying interactions of those proteins with molecular chaperones (7).
Theoretical analysis of the sensor effect of cantilever piezoelectric benders (1999)

Piezoelectric bending mode elements such as bimorph and unimorph benders can be used as both actuation and sensing elements for a wide range of applications. As actuation elements, these devices convert electric input energy into output mechanical energy. As sensing elements, they convert external mechanical stimuli into electrical charge or voltage. In this article, the sensing effect of cantilever mounted piezoelectric bimorph unimorph and triple layer benders subjected to external mechanical excitations are discussed. General analytical expressions relating generated electric voltage (or charge) to the applied mechanical input excitations (moment M, tip force F, and body force p) are derived based on the constitutive equations of these bending devices. It is found that the clamping effect of each component in the bender devices decreases the dielectric constant. The bimorph bender has a higher voltage sensitivity than the unimorph or triple layer bender with the same geometrical dimensions. The dependence of voltage and charge sensitivities on the thickness ratio and the Young’s modulus ratio of the elastic layer and piezoelectric layer under different conditions are discussed and compared for the unimorph and triple layer benders.
Latchup in CMOS from single particles (1990)

Single-particle latchup in bulk CMOS was examined using heavy ions, a californium fission source, and a pulsed laser. Experiments with the laser demonstrated that latchup triggering was caused by secondary photocurrent in either the vertical or lateral parasitic transistor. Charge diffusion is shown to be important for bipolar transistor responses in latchup, which in turn makes it important to have uniform charge deposition for depths of 10 mu m or more. Californium sources have insufficient range, which causes cross sections measured with californium to be much lower than cross sections from heavy ion experiments.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Catalytic Sandmeyer Bromination (2007)

An efficient catalyst system for Sandmeyer bromination is proposed. Aryl bromides and dibromides can be obtained with excellent yield by this synthetic protocol.
Small RNAs derived from the 5′ end of tRNA can inhibit protein translation in human cells (2013)

Recently, it has been shown that tRNA molecules can be processed into small RNAs that are derived from both the 5' and 3' termini. To date, the function of these tRNA fragments (tRFs) derived from the 5' end of tRNA has not been investigated in depth. We present evidence that conserved residues in tRNA, present in all 5' tRFs, can inhibit the process of protein translation without the need for complementary target sites in the mRNA. These results implicate 5' tRFs in a new mechanism of gene regulation by small RNAs in human cells.
The Immunoglobulin Heavy Chain Constant Region Affects Kinetic and Thermodynamic Parameters of Antibody Variable Region Interactions with Antigen (2007)

A central dogma in immunology is that antibody specificity is a function of the variable (V) region. However serological analysis of IgG(1), IgG(2a), and IgG(2b) switch variants of murine monoclonal antibody (mAb) 3E5 IgG(3) with identical V domains revealed apparent specificity differences for Cryptococcus neoformans glucuronoxylomannan (GXM). Kinetic and thermodynamic binding properties of mAbs 3E5 to a 12-mer peptide mimetic of GXM revealed differences in the affinity of these mAbs for a monovalent ligand, a result that implied that the constant (C) region affects the secondary structure of the antigen binding site, thus accounting for variations in specificity. Structural models of mAbs 3E5 suggested that isotype-related differences in binding resulted from amino acid sequence polymorphisms in the C region. This study implies that isotype switching is another mechanism for generating diversity in antigen binding and that isotype restriction of certain antibody responses may reflect structural constraints imposed by C region on V region binding. Furthermore, isotype affected the polyreactivity of V region identical antibodies, implying a role for C region in determining self-reactivity.
Combined Surface and Volume Templating of Highly Porous Nanocast Carbon Monoliths (2005)

Abstract Nanocast carbon monoliths exhibiting a three‐ or four‐modal porosity have been prepared by one‐step impregnation, using silica monoliths containing a bimodal porosity as the scaffold. Combined volume and surface templating, together with the controlled synthesis of the starting silica monoliths used as the scaffold, enables a flexible means of pore‐size control on several length scales simultaneously. The monoliths were characterized by nitrogen sorption, scanning electron microscopy, transmission electron microscopy, and mercury porosimetry. It is shown that the carbon monoliths represent a positive replica of the starting silica monoliths on the micrometer length scale, whereas the volume‐templated mesopores are a negative replica of the silica scaffold. In addition to the meso‐ and macropores, the carbon monoliths also exhibit microporosity. The different modes of porosity are arranged in a hierarchical structure‐within‐structure fashion, which is thought to be optimal for applications requiring a high surface area in combination with a low pressure drop over the material.
A HapMap harvest of insights into the genetics of common disease (2008)

The International HapMap Project was designed to create a genome-wide database of patterns of human genetic variation, with the expectation that these patterns would be useful for genetic association studies of common diseases. This expectation has been amply fulfilled with just the initial output of genome-wide association studies, identifying nearly 100 loci for nearly 40 common diseases and traits. These associations provided new insights into pathophysiology, suggesting previously unsuspected etiologic pathways for common diseases that will be of use in identifying new therapeutic targets and developing targeted interventions based on genetically defined risk. In addition, HapMap-based discoveries have shed new light on the impact of evolutionary pressures on the human genome, suggesting multiple loci important for adapting to disease-causing pathogens and new environments. In this review we examine the origin, development, and current status of the HapMap; its prospects for continued evolution; and its current and potential future impact on biomedical science.
Sarpogrelate, a Selective 5-HT2A Serotonergic Receptor Antagonist, Inhibits Serotonin-Induced Coronary Artery Spasm in a Porcine Model (2000)

Serotonin is one of the most important vasoactive substances and has been implicated in the pathogenesis of coronary artery spasm and of acute coronary syndrome. We have recently demonstrated that local and long-term treatment with interleukin-1beta(IL-1beta) causes coronary arteriosclerotic changes and hyperconstrictive responses to serotonin in pigs in vivo. However, it remains to be examined which serotonergic (5-HT) receptor subtype mediates coronary spasm and whether alterations in serotonergic receptors are involved in the abnormality. In this study, we examined the inhibitory effect of sarpogrelate, a selective 5-HT2A serotonergic receptor antagonist, on the serotonin-induced coronary spasm as well as the possible alterations of serotonergic receptors in our porcine model. A segment of the porcine coronary artery was carefully dissected and aseptically wrapped with cotton mesh absorbing IL-1beta-bound microbeads from the adventitia. Two weeks after the procedure, angiographic study was performed, followed by binding assay for 5-HT1B and 5-HT2A serotonergic receptors and reverse transcription-polymerase chain reaction (RT-PCR) analysis for mRNA of those receptors. Angiographic study showed coronary vasospastic responses to serotonin at the IL-1beta-treated site. Sarpogrelate dose-dependently inhibited the serotonin-induced coronary spasm, but it did not affect the prostaglandin F2alpha-induced vasoconstriction. Radiolabeled receptor-binding assay showed that receptor affinity or receptor number of the 5-HT1B, or 5-HT2A receptors did not differ significantly between the spastic and the control sites. Furthermore, RT-PCR analysis showed that the expression of neither 5-HT2A nor 5-HT1B receptor mRNA was significantly altered at the spastic site. These results indicate that serotonin-induced coronary spasm is mediated primarily by 5-HT2A receptor in our porcine model, although the 5-HT2A receptor was not up-regulated, suggesting that alteration in the signal-transduction pathway for vascular smooth muscle contraction beyond the 5-HT2A receptor plays a primary role in the pathogenesis of coronary spasm in our porcine model.
Column Packings for Modern Liquid Chromatography (1973)

Journal Article Column Packings for Modern Liquid Chromatography Get access R. E. Leitch, R. E. Leitch Search for other works by this author on: Oxford Academic PubMed Google Scholar J. J. DeStefano J. J. DeStefano E. I. du Pont de Nemours & Co., Inc., Biochemicals Department, Experimental Station, Wilmington, Delaware 19898 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Chromatographic Science, Volume 11, Issue 3, March 1973, Pages 105–113, https://doi.org/10.1093/chromsci/11.3.105 Published: 01 March 1973 Article history Received: 11 January 1973 Published: 01 March 1973
Application of New Least-Squares Methods for the Quantitative Infrared Analysis of Multicomponent Samples (1982)

Improvements have been made in previous least-squares regression analyses of infrared spectra for the quantitative estimation of concentrations of multicomponent mixtures. Spectral baselines are fitted by least-squares methods, and overlapping spectral features are accounted for in the fitting procedure. Selection of peaks above a threshold value reduces computation time and data storage requirements. Four weighted least-squares methods incorporating different baseline assumptions were investigated using FT-IR spectra of the three pure xylene isomers and their mixtures. By fitting only regions of the spectra that follow Beer's Law, accurate results can be obtained using three of the fitting methods even when baselines are not corrected to zero. Accurate results can also be obtained using one of the fits even in the presence of Beer's Law deviations. This is a consequence of pooling the weighted results for each spectral peak such that the greatest weighting is automatically given to those peaks that adhere to Beer's Law. It has been shown with the xylene spectra that semiquantitative results can be obtained even when all the major components are not known or when expected components are not present. This improvement over previous methods greatly expands the utility of quantitative least-squares analyses.
Robotics-driven printing of curved 3D structures for manufacturing cardiac therapeutic devices (2015)

Cardiovascular disease (CVD) is the leading cause of death in the United States. 3D printing technology has increasingly paved its way into cardiovascular applications, in particular for manufacturing cardiac therapeutic devices. However, currently available commercial 3D printers and those under development exclusively work by successively depositing layers of material using axis-aligned slicing methods, thus need unacceptably high demand of support materials and even fail fabricating for some complex cardiovascular structures, not to mention printing for the purpose of repairing an existing abnormal strictures. To solve this problem, we propose and develop a novel and robust robotics-driven printing system, consisting of a robotic arm and an extruder tool to allow printing along trajectories on any curved surface. Given the target structure, a new set of algorithms for robot toolpath planning was implemented, which include mesh parameterization, distance transform, contouring and smooth interpolation. Using both simulation and actual physical testing, we showed our system can successfully print layers of the target structure on curved geometry by following planned tool paths and depositing materials. In this paper, we describe our methodology and algorithm pipeline, compare and analyze the printing results of different techniques, and most importantly, envision the promising future extension of our robotics-driven printing system in manufacturing cardiac therapeutic devices.
Polypeptide halomethyl ketones bind to serine proteases as analogs of the tetrahedral intermediate. X-ray crystallographic comparison of lysine- and phenylalanine-polypeptide chloromethyl ketone-inhibited subtilisin. (1976)

1. A detailed study of cytochrome C oxidse activity with Keilin-Hartree particles and purified beef heart enzyme, at low ionic strength and low cytochrome C concentrations, showed biphasic kinetics with apparent Km1 = 5 x 10(-8) M, and apparent Km2 = 0.35 to 1.0 x 10(-6) M. Direct binding studies with purified oxidase, phospholipid-containing as well as phospholipid-depleted, demonstrated two sites of interaction of cytochrome c with the enzyme, with KD2 less than or equal to 10(-7) M, and KD2 = 10(-6) M. 2...
Iron Starvation and Culture Age Activate Metacaspases and Programmed Cell Death in the Marine Diatom Thalassiosira pseudonana (2007)

In the modern ocean, phytoplankton maintain extremely high primary production/biomass ratios, indicating that they bloom, die, and are replaced weekly. The molecular mechanisms regulating cellular mortality and turnover are largely unknown, even though they effectively short-circuit carbon export to the deep ocean and channel primary productivity to microbial food webs. Here, we present morphological, biochemical, and molecular evidence of caspase-mediated, autocatalytic programmed cell death (PCD) in the diatom Thalassiosira pseudonana in response to iron starvation. Transmission electron microscopy revealed internal degradation of nuclear, chloroplastic, and mitochondrial organelles, all while the plasma membranes remained intact. Cellular degradation was concomitant with dramatic decreases in photosynthetic efficiency, externalization of phosphatidylserine, and significantly elevated caspase-specific activity, with the addition of a broad-spectrum caspase inhibitor rescuing cells from death. A search of the T. pseudonana genome identified six distinct putative metacaspases containing a conserved caspase domain structure. Quantitative reverse transcription-PCR and Western blot analysis revealed differential gene and protein expression of T. pseudonana metacaspases, some of which correlated with physiological stress and caspase activity. Taken together with the recent discovery of the metacaspase-mediated viral infection of phytoplankton (K. D. Bidle, L. Haramaty, J. Barcelos-Ramos, and P. G. Falkowski, Proc. Natl. Acad. Sci. USA 104:6049-6054, 2007), our findings reveal a key role for metacaspases in the turnover of phytoplankton biomass in the oceans. Furthermore, given that Fe is required for photosynthetic electron transfer and is chronically limiting in a variety of oceanic systems, including high-nutrient low-chlorophyll regions, our findings provide a potential ecological context for PCD in these unicellular photoautotrophs.
Identification of microRNAs in the cerebrospinal fluid as biomarker for the diagnosis of glioma (2011)

Malignant gliomas are the most common and lethal primary intracranial tumors. To date, no reliable biomarkers for the detection and risk stratification of gliomas have been identified. Recently, we demonstrated significant levels of microRNAs (miRNAs) to be present in cerebrospinal fluid (CSF) samples from patients with primary CNS lymphoma. Because of the involvement of miRNA in carcinogenesis, miRNAs in CSF may serve as unique biomarkers for minimally invasive diagnosis of glioma. The objective of this pilot study was to identify differentially expressed microRNAs in CSF samples from patients with glioma as potential novel glioma biomarkers. With use of a candidate approach of miRNA quantification by reverse-transcriptase polymerase chain reaction (qRT-PCR), miRNAs with significant levels in CSF samples from patients with gliomas were identified. MiR-15b and miR-21 were differentially expressed in CSF samples from patients with gliomas, compared to control subjects with various neurologic disorders, including patients with primary CNS lymphoma and carcinomatous brain metastases. Receiver-operating characteristic analysis of miR-15b level revealed an area under the curve of 0.96 in discriminating patients with glioma from patients without glioma. Moreover, inclusion of miR-15b and miR-21 in combined expression analyses resulted in an increased diagnostic accuracy with 90% sensitivity and 100% specificity to distinguish patients with glioma from control subjects and patients with primary CNS lymphoma. In conclusion, the results of this pilot study demonstrate that miR-15b and miR-21 are markers for gliomas, which can be assessed in the CSF by means of qRT-PCR. Accordingly, miRNAs in the CSF have the potential to serve as novel biomarkers for the detection of gliomas.
Breast cancer detection using non-invasive near-field microwave nondestructive testing techniques (2004)

Early detection of breast cancer reduces the risk of death. In this investigation, the main goal is to explore the ability of near-field microwave techniques to detect tumors inside the breast using open-ended rectangular waveguide probes. The interaction of electromagnetic waves radiated from a rectangular waveguide into a multilayer structure is studied. Knowing the behavior of microwaves radiated from the waveguide, the phase and/or magnitude variations of the reflection coefficient at the waveguide aperture due to the presence of a tumor are calculated. Consequently, detection of a tumor can be attained. Various measurement optimization parameters are exploited to maximize the variations of the reflection coefficient. Results detailing the process of arriving at optimal measurement parameters are revealed and discussed to demonstrate the potential of such technique.
Identification of an Epitope on the Entamoeba histolytica 170-kD Lectin Conferring Antibody-mediated Protection against Invasive Amebiasis (1997)

The emergence of multidrug-resistant organisms and the failure to eradicate infection by a number of important pathogens has led to increased efforts to develop vaccines to prevent infectious diseases. However, the nature of the immune response to vaccination with a given antigen can be complex and unpredictable. An example is the galactose- and N-acetylgalactosamine-inhibitable lectin, a surface antigen of Entamoeba histolytica that has been identified as a major candidate in a vaccine to prevent amebiasis. Vaccination with the lectin can induce protective immunity to amebic liver abscess in some animals, but others of the same species exhibit exacerbations of disease after vaccination. To better understand this phenomenon, we used recombinant proteins corresponding to four distinct domains of the molecule, and synthetic peptides to localize both protective and exacerbative epitopes of the heavy chain subunit of the lectin. We show that protective immunity after vaccination can be correlated with the development of an antibody response to a region of 25 amino acid residues of the lectin, and have confirmed the importance of the antibody response to this region by passive immunization studies. In addition, we show that exacerbation of disease can be linked to the development of antibodies that bind to an NH2-terminal domain of the lectin. These findings are clinically relevant, as individuals who are colonized with E. histolytica but are resistant to invasive disease have a high prevalence of antibodies to the protective epitope(s), compared to individuals with a history of invasive amebiasis. These studies should enable us to develop an improved vaccine for amebiasis, and provide a model for the identification of protective and exacerbative epitopes of complex antigens.
The essence of senescence: Figure 1. (2010)

Almost half a century after the first reports describing the limited replicative potential of primary cells in culture, there is now overwhelming evidence for the existence of "cellular senescence" in vivo. It is being recognized as a critical feature of mammalian cells to suppress tumorigenesis, acting alongside cell death programs. Here, we review the various features of cellular senescence and discuss their contribution to tumor suppression. Additionally, we highlight the power and limitations of the biomarkers currently used to identify senescent cells in vitro and in vivo.