gebhart/patrepeval huggingface dataset:
Assessment of cholinergic influences on a primary humoral immune response. (1992)

Cholinergic ligands can affect some lymphocyte functions, and binding of labelled cholinergic ligands to lymphocytes has been reported. However, the role of endogenous cholinergic stimulation in immunomodulation in vivo is unclear. It has been suggested that suppression of primary humoral immune responses in vivo by administration of organophosphorus compounds is caused by excessive cholinergic stimulation. If this is correct, it would demonstrate cholinergic immunomodulation in vivo and might serve as a useful model for the characterization of this phenomenon. In the present study, the organophosphorus insecticide parathion and its major metabolite, paraoxon, suppressed the primary IgM response to sheep red blood cells (SRBC) in vitro in Mishell-Dutton cultures at concentrations similar to those probably reached in vivo. In contrast, cholinergic agonists did not suppress the in vitro response, but tended to enhance it. However, antagonists also tended to enhance the response and the effects of agonists were not blocked by antagonists. Binding studies with a radiolabelled cholinergic antagonist ([3H-]QNB) did not indicate the presence of specific, saturable cholinergic receptors on lymphocytes. A membrane preparation from brain was used as a positive control, and specific, saturable binding was observed. These results suggest that suppression of primary immune responses in vivo by parathion is mediated at least in part by direct action of parathion and/or its major metabolite, paraoxon, on the immune system. The data provide no evidence that direct interaction of cholinergic ligands with the immune system contributes to parathion-induced immunosuppression. In fact, the absence of expected agonist-antagonist relationships in Mishell-Dutton cultures, the absence of saturable [3H]QNB binding, and puzzling inconsistencies in the literature on this subject cast doubt on the conclusion that lymphocytes express specific cholinergic receptors.
Integrated execution: A programming model for accelerators (2009)

The Cell Broadband Engine® (Cell/B.E.) processor was designed to provide a mix of central cores for control code and accelerators optimized for data processing. A heterogeneous design allows different processor elements to be optimized for specific functions and makes each processor element more area and power efficient. Cell/B.E. processor-based systems are the most powerful and the most power-efficient systems in the world, as represented by the Top500™ and Green500 lists. This paper offers a new view of the architectural design choices that were made in consideration of software usability and application development for the Cell/B.E. processor. Specifically, we explore the concept of integrated executables that allow a single application to execute across multiple heterogeneous processor elements. Hardware and software architectures were co-optimized to allow an application executing on multiple heterogeneous cores to efficiently communicate and share data, which is key to exploiting chip multiprocessors with ever-increasing numbers of cores.
Machine Tools (1994)

This chapter contains sections titled: Introduction Sensors and Actuators for Machine Tools Machine Tool Accuracy Computer Numerical Control Programmable Logic Control Machine Tool Control Bibliography
Design of the signal and data format for wide area augmentation of the Global Positioning System (2002)

The wide area augmentation system (WAAS) is being deployed by the Federal Aviation Administration (FAA) to augment the Global Positioning System (GPS) with additional ranging signals and a supporting ground network. The augmented system can be used as the primary position sensor for enroute through precision approach air navigation. Specifically, the WAAS provides the following three services: integrity monitoring to improve safety; a ranging function to improve time availability and continuity of service; and differential GPS corrections to improve accuracy. This paper describes the design of the WAAS signal and data format. It states the design objectives and describes the basic approach. Then, it analyzes the correction update rates, message duration, messaging rates and the use of forward error correction. This paper does not: give a basic description of the WAAS, analyze the non-interference properties of the signal, or give a description of the data fields.
Alkoxyamine C–ON Bond Homolysis: Stereoelectronic Effects (2006)

Abstract Alkoxyamines and persistent nitroxides are important regulators of nitroxide‐mediated radical polymerization (NMP) reactions. Because polymerization times decrease with an increase in the rate constant for the homolysis of the C–ON bond between the polymer chain and the nitroxyl moiety, the factors influencing the cleavage rate constant are of considerable interest. Therefore, it was interesting to check whether the methyl effect (+17 kJ/mol for each methyl added onto the carbon atom of the C–ON bond) observed in the TEMPO‐based alkoxyamine series was also observed in the SG1 [ N ‐ tert ‐butyl‐ N ‐(1‐diethoxyphosphoryl‐2,2‐dimethylpropyl)aminoxyl] series. Moreover, we extended the incremental substituent scale proposed earlier and confirmed the versatility of the multiparameter analysis developed in previous work. X‐ray and natural bond orbital (NBO) analyses of several SG1‐CHMeCOOR alkoxyamines showed that the difference in reactivity between the ( RR / SS ) and ( RS / SR ) diastereoisomers is caused by a n σ →σ* interaction between the n σ lone pair of the oxygen atom of the ester bond and the σ* orbital of the cleaved O–C bond. Furthermore, a compilation of the effects — steric, polar, stabilizing, long‐distance polar and long‐distance reverse steric — of the leaving alkyl radical on the value of k d for C–ON bond homolysis led us to question the one‐step mechanism. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2006)
From the Guest Editor… (2005)

Graphical representations have played a central role in decision analysis. Although decision trees remain popular, more general graphical languages can be used to encode relationships among variables of a decision basis. Influence diagrams, introduced in the late 1970s, provide a general graphical representation for decision analysis. We publish, in this first of two volumes of a special issue of Decision Analysis, the original manuscript on influence diagrams, along with a retrospective by the authors. We also include two new articles focusing respectively on the use of graphical models for group coordination challenges and on handling the unintended side effects of interventions.
Stem Cell Rejuvenation by Restoration of Youthful Metabolic Compartmentalization (2021)

Stem cell dysfunction is a hallmark of aging. Much recent study suggests that epigenetic changes play a critical role in the loss of stem cell function with age. However, the underlying mechanisms require elucidation. A recent report describes a process by which mild mitochondrial stress associated with aging causes lysosomal-mediated decreases in CiC, the mitochondrial citrate transporter, in bone marrow-derived mesenchymal stem cells (MSCs). This, in turn, results in a deficit of acetyl-CoA in the nucleus and hypoacetylation of histones. The altered epigenome results in skewered stem cell differentiation favoring adipogenesis and disfavoring osteogenesis, which is problematic given the role the MSCs play in maintaining the integrity of bone tissue. Restoration of nuclear acetyl-CoA by either ectopic expression of CiC or acetate supplementation of MSCs in culture rejuvenates the MSC, restoring the potential to efficiently differentiate along the osteogenic lineage. Citrate, which has recently been reported to extend lifespan in Drosophila, chemically incorporates acetyl-CoA and may prove useful to restore cytoplasmic and nuclear acetyl-CoA levels. The general applicability of the CiC defect in old cells, particularly stem cells, should be established.
Data from Composite Three-Marker Assay for Early Detection of Kidney Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; Early detection of renal cell carcinoma using serum/plasma biomarkers remains challenging. To validate clinical performance of potential candidate markers for kidney tumors, three-marker assay composed of nicotinamide &lt;i&gt;N&lt;/i&gt;-methyltransferase (NNMT), L-plastin (LCP1), and nonmetastatic cells 1 protein (NM23A) was evaluated.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Methods:&lt;/b&gt; Patients with kidney cancer and control group were included in the clinical evaluation. Participants were divided into cohorts representing the training group of control group including healthy and benign tumors (&lt;i&gt;n&lt;/i&gt; = 102) and patients with kidney cancer (&lt;i&gt;n&lt;/i&gt; = 87) that were used to identify criteria for scoring. Then, we developed a three-marker assay that was validated with a cohort of test group samples (&lt;i&gt;n&lt;/i&gt; = 100). A scoring method based on the cut-point of each of the three markers was used to evaluate the diagnostic performance of the marker combination.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Plasma levels of NNMT, LCP1, and NM23A were highly elevated in patients with kidney cancer (&lt;i&gt;P&lt;/i&gt; &lt; 0.0001). In 289 blind sample tests with control subjects (&lt;i&gt;n&lt;/i&gt; = 175) and patients with kidney cancer (&lt;i&gt;n&lt;/i&gt; = 114), the diagnostic accuracy of NNMT alone and the three-marker assay was 0.913 and 0.932, respectively. When 90% specificity was defined, the sensitivity of NNMT and the three-marker assay was 71.9% and 95.7%, respectively. The predictive value of the three-marker assay was 87.2% (+PPV) and 97% (−PPV).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; The composite assay with NNMT, LCP1, and NM23A was a promising novel serum marker assay for the early detection of malignant kidney tumors covering subtypes of RCC with high diagnostic characteristics.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Impact:&lt;/b&gt; NNMT/LCP1/NM23A triple markers could be a helpful screening assay to detect early RCC. &lt;i&gt;Cancer Epidemiol Biomarkers Prev; 22(3); 390–8. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Dynamic behaviors of water droplets on superhydrophobic polyester films and woven and knitted fabrics (2022)

In this study, the behaviors of water droplets on superhydrophobic polyester (PET) films as well as on woven and knitted fabrics with different surface microstructures were analyzed. The water droplet volume, height of release ( h), and surface inclination were modified to study the dynamic behavior of water droplets using a pressure balance and the Weber number ( We). The droplet volume did not affect the static contact angle. However, the shedding and sliding angles decreased with an increase in droplet volume. The water droplets rebounded on the surface of the superhydrophobic PET films with nano-roughness regardless of the surface inclination angle or h. However, the water droplets with h = 10 cm were pinned on the horizontal surfaces of the woven and knitted fabrics with micro-sized pores, where the dynamic pressure ( Pd) exceeded the capillary pressure. On an inclined surface, the water droplets rebounded on the surface of the woven fabric, owing to a decrease in Pd and an increase in the surface inclination angle. However, on the surface of the knitted fabric, pinning was observed even when the surface was tilted, regardless of the inclination angle. The sliding velocity of the droplets after rebound decreased in the following order: film, knitted fabric, woven fabric. With an increase in the inclination angle of the surface and the droplet volume, the sliding velocity increased, which was accompanied by a decrease in vertical impact velocity ( V) and an increase in the gravitational force. In terms of We, the droplets with a low We rebounded on all superhydrophobic surfaces, whereas the droplets with a high We were pinned on the surface of the woven and knitted fabrics.
Intracellular Signal Transduction Evoked by Low-Density Lipoprotein in Vascular Smooth Muscle Cells (2015)

Low-density lipoprotein (LDL) is a well-known causal factor in the development of arteriosclerosis. In the present study, we evaluated LDL-evoked cellular signal transduction in cultured rat vascular smooth muscle cells (VSMC). The addition of LDL at concentrations of more than 50 ng/ml, and apolipoprotein B (Apo-B) at more than 5 ng/ml, induced rapid but transient increases in the inositol 1,4,5-trisphosphate (InsP3) level, and caused rapid phasic and subsequent tonic increases in cytosolic free Ca2+ concentration [( Ca2+]i) in a dose-dependent manner in VSMC. LDL and Apo-B also caused transient acidification followed by Na(+)-dependent and amiloride-sensitive alkalization of the cells due to stimulation of a Na+/H+ exchanger. The enhancement of thymidine incorporation induced by the addition of LDL correlated well with the degree of increment of [Ca2+]i increases by the lipoprotein. These results suggest that an increase in [Ca2+]i mediated by InsP3 and intracellular alkalization may function as an important signal for enhanced DNA synthesis induced by LDL in VSMC.
Epitome inpainting with in-loop residue coding for image compression (2014)

This paper describes a novel image coding scheme based on epitome inpainting. An epitome containing a factorized texture representation of the image is first coded and transmitted. The decoded epitome is then inpainted by propagating its structure and texture with extended H.264 Intra directional prediction modes and advanced neighbor embedding methods. The blocks to be inpainted are processed according to an adaptive scanning order which adapts to the image content and gives a higher priority to the blocks having strong structures. The inpainting step has been incorporated in the coding loop of an H.264 encoder, leading to a bitrate saving of up to 48.12% with respect to H.264 intra.
Virus-driven Inflammation Is Associated With the Development of bNAbs in Spontaneous Controllers of HIV (2017)

Background: Understanding the mechanism(s) by which broadly neutralizing antibodies (bNAbs) emerge naturally following infection is crucial for the development of a protective vaccine against human immunodeficiency virus (HIV). Although previous studies have implicated high viremia and associated immune activation as potential drivers for the development of bNAbs, here we sought to unlink the effect of these 2 parameters by evaluating the key inflammatory predictors of bNAb development in HIV-infected individuals who spontaneously control HIV in the absence of antiretroviral therapy (“controllers”). Methods: The breadth of antibody-mediated neutralization against 11 tier 2 or 3 viruses was assessed in 163 clade B spontaneous controllers of HIV. Plasma levels of 17 cytokines were screened in the same set of subjects. The relationship of the inflammatory signature was assessed in the context of viral blips or viral RNA levels in peripheral blood or gastrointestinal biopsies from aviremic controllers (<50 copies RNA/mL) and in the context of viral sequence diversity analysis in the plasma of viremic controllers (<50–2000 copies RNA/mL). Results: A unique inflammatory profile, including high plasma levels of CXCL13, sCD40L, IP10, RANTES, and TNFα, was observed in HIV controllers who developed bNAbs. Interestingly, viral load and tissue viremia, but not intermittent viral blips, were associated with these cytokine profiles. However, viral diversity was not significantly associated with increased breadth in controllers. Conclusion: These results suggest that low antigenic diversity in the setting of a unique inflammatory profile associated with antigen persistence may be linked to the evolution of neutralizing antibody breadth. Keywords: neutralizing antibodies, inflammation, HIV vaccine.
Realizing the benefits of user-level channel diversity (2005)

Channel or path diversity is known to improve performance in physical layer designs, channel access strategies, path switching mechanisms, etc. In this paper, we focus on "user-level" mechanisms that operate simply by distributing packet transmissions across multiple channels. We seek to understand when, why, and to what extent this can be of benefit, and equally important, whether these benefits can be realized with as little of an added cost as possible. In that context, our main contribution is not so much in identifying optimal policies for leveraging channel diversity, but in introducing the concept of channel "equivalence" and demonstrating that channel diversity yields substantial benefits mostly when channels are approximately equivalent. We build on this finding to investigate the robustness of these improvements against errors in the characterization of the available channels or changes in their characteristics. We also explore the sensitivity of the results as the number of available channels varies. The findings of the paper demonstrate that by allowing packet transmissions from multiple users to intelligently share channels, it is possible to improve overall performance and robustness through simple and portable user-level mechanisms.
Development of a phonetic system for large vocabulary Arabic speech recognition (2007)

This paper describes the development of an Arabic speech recognition system based on a phonetic dictionary. Though phonetic systems have been previously investigated, this paper makes a number of contributions to the understanding of how to build these systems, as well as describing a complete Arabic speech recognition system. The first issue considered is discriminative training when there are a large number of pronunciation variants for each word. In particular, the loss function associated with Minimum Phone Error (MPE) training is examined. The performance and combination of phonetic and graphemic acoustic models are then compared on both Broadcast News (BN) and Broadcast Conversation (BC) data. The final contribution of the paper is a simple scheme for automatically generating pronunciations for use in training and reducing the phonetic out-of-vocabulary rate. The paper concludes with a description and results from using phonetic and graphemic systems in a multipass/ combination framework.
Foton geïnduceerd etsen van koper en vorming van koper nanodraden (2008)

status: Published
The Werner Syndrome Gene Product Co-purifies with the DNA Replication Complex and Interacts with PCNA and Topoisomerase I (1999)

Werner syndrome (WS) is a recessive disorder characterized by genomic instability and by the premature onset of a number of age-related diseases. To understand the molecular basis of this disease, we deleted a segment of the murine Wrn gene and created Wrn-deficient embryonic stem (ES) cells. At the molecular level, wild type-but not mutant-WS protein co-purifies through a series of centrifugation, chromatography, and sucrose gradient steps with the well characterized 17 S multiprotein DNA replication complex. Furthermore, wild type WS protein co-immunoprecipitates with a prominent component of the multiprotein replication complex, proliferating cell nuclear antigen (PCNA). In vitro studies also indicate that PCNA binds to a region in the N terminus portion of the WS protein containing a potential 3'-5' exonuclease domain. Finally, human WS protein also co-immunoprecipitates with both PCNA and topoisomerase I. These results suggest that the WS protein interacts with several components of the DNA replication fork.
Effect of Microwave Blanching on the Yield and Quality of Canned Mushrooms (1986)

ABSTRACT Shrinkage of mushrooms during blanching and retorting processes was studied using microwave and boiling water blanching treatments. A microwave blanching treatment of 4 min 40 sec at the high setting in a microwave oven was compared to a 7 min, boiling water, conventional blanching treatment. Data showed that the microwave blanching process was superior with respect to yield, allowing for a significant (p &lt; 0.01) increase in net yield (3.41%) for three trials. Color and sensory analyses of the canned mushrooms showed that the two treatments were not significantly different (p&lt;0.05) with respect to flavor, texture, color and overall acceptability.
Broadcast-Enabled Massive Multicore Architectures: A Wireless RF Approach (2015)

Broadcast traditionally has been regarded as a prohibitive communication transaction in multiprocessor environments. Nowadays, such a constraint largely drives the design of architectures and algorithms all-pervasive in diverse computing domains, directly and indirectly leading to diminishing performance returns as the many-core era is approaching. Novel interconnect technologies could help revert this trend by offering, among others, improved broadcast support, even in large-scale chip multiprocessors. This article outlines the prospects of wireless on-chip communication technologies pointing toward low-latency (a few cycles) and energy-efficient broadcast (a few picojoules per bit). It also discusses the challenges and potential impact of adopting these technologies as key enablers of unconventional hardware architectures and algorithmic approaches, in the pathway of significantly improving the performance, energy efficiency, scalability, and programmability of many-core chips.
Frequency multiplexed raster neural networks 1: Theory (1989)

In the first part of this paper we present frequency multiplexed raster (FMR) optical implementation of neural networks. A hidden difficulty for hardware (optical and electronic) implementation is that the dimension of the synaptic matrix is twice that of the input and output matrices or vectors. For 2-D images, which is we believe one of the greatest potentialities of neural networks, the synaptic matrix is 4-D and cannot be directly implemented in optics. We propose FMR as a method to fold this matrix into a 2-D format. In the second part of this paper we describe the system built in our laboratory showing the feasibility of FMR optical neural networks. The system is built from an optical input module, a fixed synaptic matrix coded on a transparency, a CCD camera, and a microcomputer which performs the thresholding and feedback operations. In a later stage the fixed matrix will be replaced by a programmable matrix.
Structure–Activity Relationships in Human Toll-like Receptor 8-Active 2,3-Diamino-furo[2,3-c]pyridines (2012)

In our ongoing search toward identifying novel and synthetically simpler candidate vaccine adjuvants, we hypothesized that the imidazo[1,2-a]pyrazines, readily accessible via the Groebke–Blackburn–Bienaymé multicomponent reaction, would possess sufficient structural similarity with TLR7/8-agonistic imidazoquinolines. With pyridoxal as the aldehyde component, furo[2,3-c]pyridines, rather than the expected imidazo[1,2-a]pyridines, were obtained, which were characterized by NMR spectroscopy and crystallography. Several analogues were found to activate TLR8-dependent NF-κB signaling. In a focused library of furo[2,3-c]pyridines, a distinct SAR was observed with varying substituents at C2. In human PBMCs, none of the furo[2,3-c]pyridines showed any proinflammatory cytokine induction but upregulated several chemokine ligand genes. In immunization studies in rabbits, the most active compound showed prominent adjuvantic effects. The complete lack of proinflammatory cytokine induction coupled with strong adjuvantic activity of the novel furo[2,3-c]pyridines render this hitherto unknown chemotype an attractive class of compounds which are expected to be devoid of local or systemic reactogenicity.