gebhart/patrepeval huggingface dataset:
Impact of Lipid Physical State on the Oxidation of Methyl Linolenate in Oil-in-Water Emulsions (2005)

The purpose of this research was to examine the influence of the physical state of lipids on iron-promoted oxidation of methyl linolenate in octadecane oil-in-water emulsions. Octadecane and methyl linolenate oil-in-water emulsions were prepared that contained droplets having the octadecane as either liquid or solid. The physical state of the octadecane was confirmed by a differential scanning calorimeter (DSC). The effect of the physical state of the lipid on oxidation rates was determined as a function of iron concentration (80 and 160 microM), pH (3.0 or 7.0), emulsifier type, and cooling rate. Oxidation of methyl linolenate was determined by lipid hydroperoxides and thiobarbituric acid reactive substances (TBARS). Emulsions containing solid octadecane had higher rates of lipid hydroperoxide and TBARS formation than those containing liquid octadecane. The rate at which the emulsions were cooled had no influence on oxidation rates. Oxidation rates in both emulsions increased with increasing iron concentration and decreasing pH. Oxidation rates were lowest in emulsions with cationic droplet membranes (dodecyl trimethylammonium bromide-stabilized), presumably due to the repulsion of iron from the oxidizable methyl linolenate in the emulsion droplet core. These results suggest that upon crystallization of octadecane, the liquid methyl linolenate migrated to the emulsion droplet surface, where it was more prone to oxidation because it was in closer contact with the iron ions in the aqueous phase.
Adaptive Clipping in JEM (2017)

This paper presents an adaptive clipping technique with optimized syntax in the video coding Joint Exploratory Model (JEM), which exploits the signal characteristics of the video sequence. The component-wise clipping bounds are coded for each slice. Two encoding methods leveraging the efficiency of the proposed technique are then described. The first one consists in modeling the errors induced by the clipping process in the Rate Distortion Optimization. The second one aims at reducing the cost of transform coefficients by smoothing the residuals. Finally, experimental results are provided and several variants are discussed.
Machine Learning Benchmarks and Random Forest Regression (2004)

Breiman (2001a,b) has recently developed an ensemble classification and regression approach that displayed outstanding performance with regard prediction error on a suite of benchmark datasets. As the base constituents of the ensemble are tree-structured predictors, and since each of these is constructed using an injection of randomness, the method is called ‘random forests’. That the exceptional performance is attained with seemingly only a single tuning parameter, to which sensitivity is minimal, makes the methodology all the more remarkable. The individual trees comprising the forest are all grown to maximal depth. While this helps with regard bias, there is the familiar tradeoff with variance. However, these variability concerns were potentially obscured because of an interesting feature of those benchmarking datasets extracted from the UCI machine learning repository for testing: all these datasets are hard to overfit using tree-structured methods. This raises issues about the scope of the repository.With this as motivation, and coupled with experience from boosting methods, we revisit the formulation of random forests and investigate prediction performance on real-world and simulated datasets for which maximally sized trees do overfit. These explorations reveal that gains can be realized by additional tuning to regulate tree size via limiting the number of splits and/or the size of nodes for which splitting is allowed. Nonetheless, even in these settings, good performance for random forests can be attained by using larger (than default) primary tuning parameter values.
Hydrogen/Deuterium Exchange Mass Spectrometry and Site-Directed Disulfide Cross-Linking Suggest an Important Dynamic Interface between the Two Lysostaphin Domains (2013)

Lysostaphin is a peptidoglycan hydrolase secreted by Staphylococcus simulans. It can specifically lyse Staphylococcus aureus and is being tested as a novel antibacterial agent. The protein contains an N-terminal catalytic domain and a C-terminal cell wall targeting domain. Although the two domains from homologous enzymes were structurally determined, the structural organization of lysostaphin domains remains unknown. We used hydrogen/deuterium exchange mass spectrometry (H/DX-MS) and site-directed disulfide cross-linking to probe the interface between the lysostaphin catalytic and targeting domains. H/DX-MS-mediated comparison of peptides from full-length lysostaphin and the separated domains identified four peptides of lower solvent accessibility in the full-length protein. Cross-linking analysis using cysteine pair substitutions within those peptides showed that two pairs of cysteines can form disulfide bonds, supporting the domain association role of the targeted peptides. The cross-linked mutant exhibited a binding capacity to S. aureus that was similar to that of the wild-type protein but reduced bacteriolytic activity probably because of restraint in conformation. The diminished activity was further reduced with increasing NaCl concentrations that can cause contractions of bacterial peptidoglycan. The lytic activity, however, could be fully recovered by reducing the disulfide bonds. These results suggest that lysostaphin may require dynamic association of the two domains for coordinating substrate binding and target cleavage on the elastic peptidoglycan. Our study will help develop site-specific PEGylated lysostaphin to treat systemic S. aureus infections.
Paper Reduction of OFDM Signals Using Selective Mapping With TURBO Codes (2011)

promising candidate for high performance 4G broadband wireless communications. One main disadvantage of OFDM is the high peak-to-average power ratio (PAPR) of the transmitter's output signal. Selected-Mapping (SLM) scheme which does not require the transmission of side information and can reduce the peak to average power ratio (PAPR) in turbo coded orthogonal frequency division multiplexing (OFDM) system is proposed. Simulation results show that the system can achieve significant reduction in PAPR and satisfactory bit error rate performance over AWGN channels.
Immunomodulation by Processed Animal Feed: The Role of Maillard Reaction Products and Advanced Glycation End-Products (AGEs) (2018)

The immune system provides host protection to infection with pathogenic organisms, while at the same time providing tolerance upon exposure to harmless antigens. Thus, an impaired immune function is associated with increased susceptibility to infections with increased disease severity and thereby necessitating the therapeutic use of antibiotics. Livestock performance and feed efficiency, in addition to their health status, are dependent on the microbial load of their gut, the barrier function of the intestinal epithelium and the activity of the mucosal immune system, all of which can be modulated by dietary components. The majority of feeds that are consumed in pets and livestock have been processed. Processing promotes a non-enzymatic reaction between proteins and sugars called Maillard reaction (MR). Maillard reaction products (MRPs) and advanced Maillard reaction products (AGEs) determine taste, smell, and color of many food products therefore the MR is highly relevant for the feed industry. MRPs interact with different types of immune receptors, including the receptor for advanced glycation end products (RAGE) and immunomodulatory potential of feed proteins can be modified by Maillard reaction. This MR has become an important concern since MRPs/AGEs have been shown to contribute to increasing prevalence of diet-related chronic inflammatory states in the gut with negative health consequences and performance. The immunomodulatory effects of dietary MRPs and AGEs in livestock and pet animals are far less well-described, but widely considered to be similar to the relevant concepts and mechanisms obtained in the human field. This review will highlight immunological mechanisms underlying initiation of the innate and adaptive immune responses by MRPs/AGEs present in animal feeds, which are currently not completely understood. Bridging this knowledge gap, and taking advantage of progress in the human field, will significantly improve nutritional quality of feed and increase the prevention of diet-mediated inflammation in animals.
Composition, decomposition and model checking of pushdown processes (1995)

Rapid changes of protein phosphorylation play a crucial role in the regulation of many cellular processes. Being post-translationally modified, phosphoproteins are often present in quite low abundance and tend to co-exist with their unphosphorylated isoform within the cell. To make their identification more practicable, the use of enrichment protocols is often required. The enrichment strategies can be performed either at the level of phosphoproteins or at the level of phosphopeptides. Both approaches have their advantages and disadvantages. Most enriching strategies are based on chemical modifications, affinity chromatography to capture peptides and proteins containing negatively charged phosphate groups onto a positively charged matrix, or immunoprecipitation by phospho-specific antibodies.In this article, the most up-to-date enrichment techniques are discussed, taking into account their optimization, and highlighting their advantages and disadvantages. Moreover, these methods are compared to each other, revealing their complementary nature in providing comprehensive coverage of the phosphoproteome.
Experimental Methods in Ventilation (2008)

Abstract This chapter describes different experimental methods related to the function of ventilation. Methods of thermal comfort are also treated. A classical, comprehensive review paper on this subject is found in Hitchin and Wilson (1967). Much information provided by this paper is still valid, although today the standard technology is digital, not analogue. In this chapter we examine a range of developments in the field since Hitchin and Wilson's paper. With arrays of sensors in digital cameras and heat cameras, etc., we can record velocities, temperatures and concentrations over whole fields in space instead of point-wise. Adding tracers that follow air movement is a qualitative visualization method that has now become a quantitative method for recording velocities over large fields. Optical techniques such as laser Doppler anemometry are now a standard technique for recording the velocity vector at a specific point. Passive tracer gas techniques enable one to take measurements in the field without tying up expensive and bulky equipment. There has been a shift from pure technical issues to a focus on people. Concern about air quality has led to development of manikins that can breathe. Instruments for assessing thermal comfort have been developed that combine the effect of radiation, velocity and temperature in an index.
Refinement of severely incomplete structures with maximum likelihood inBUSTER–TNT (2004)

BUSTER-TNT is a maximum-likelihood macromolecular refinement package. BUSTER assembles the structural model, scales observed and calculated structure-factor amplitudes and computes the model likelihood, whilst TNT handles the stereochemistry and NCS restraints/constraints and shifts the atomic coordinates, B factors and occupancies. In real space, in addition to the traditional atomic and bulk-solvent models, BUSTER models the parts of the structure for which an atomic model is not yet available ('missing structure') as low-resolution probability distributions for the random positions of the missing atoms. In reciprocal space, the BUSTER structure-factor distribution in the complex plane is a two-dimensional Gaussian centred around the structure factor calculated from the atomic, bulk-solvent and missing-structure models. The errors associated with these three structural components are added to compute the overall spread of the Gaussian. When the atomic model is very incomplete, modelling of the missing structure and the consistency of the BUSTER statistical model help structure building and completion because (i) the accuracy of the overall scale factors is increased, (ii) the bias affecting atomic model refinement is reduced by accounting for some of the scattering from the missing structure, (iii) the addition of a spatial definition to the source of incompleteness improves on traditional Luzzati and sigmaA-based error models and (iv) the program can perform selective density modification in the regions of unbuilt structure alone.
A 40/50 GHz diplexer realized with three dimensional copper micromachining (2008)

This paper describes the design and measurement of a millimeter-wave (40/50GHz) diplexer fabricated using a three dimensional metal micromachining process. The measured diplexer has channels at 40.8 GHz and 51.1 GHz with fractional bandwidths of 2.36 GHz (5.8%) and 2.07 GHz (4.05%) and midband insertion loss of 1.58 dB and 3.52 dB, respectively. The diplexer measures 7.0 mm × 3.9 mm × 0.745 mm. It is fabricated from two comb line filters realized with microfabricated stripline resonators. The three-dimensional copper metal micromachining process utilized to fabricate the diplexer has demonstrated integration with active components and the diplexer is fabricated on wafer with a variety of other passive components.
Structural requirements for the growth factor activity of the amino-terminal domain of urokinase. (1992)

High molecular weight urokinase-type plasminogen activator (uPA) in which proteolytic activity was inactivated (diisopropyl fluorophosphate (DFP)-uPA), its amino-terminal fragment (ATF, amino acids (aa) 1-143), and fucosylated and defucosylated growth factor domains (GFD, aa 4-43) were tested for growth-promoting effects and binding in human SaOS-2 osteosarcoma cells and U-937 lymphoma cells. DFP-uPA, ATF, and both the fucosylated and defucosylated GFD were capable of competing with 125I-ATF for binding to both SaOS-2 and U-937 cells. DFP-uPA, ATF, and fucosylated GFD were also mitogenic in SaOS-2 cells and increased cell numbers. However, defucosylated GFD was nonmitogenic in SaOS-2 cells and did not stimulate cell proliferation, even though it bound to these cells in a manner equivalent to the fucosylated GFD. A nonglycosylated high molecular weight uPA expressed and purified from Escherichia coli inhibited 125I-ATF binding to SaOS-2 cells but was also nonmitogenic. No mitogenic activity was observed in U-937 cells treated with the uPA forms capable of eliciting a mitogenic response in SaOS-2 cells. Proteolytically prepared kringle domain (aa 47-135) and low molecular weight uPA (aa 144-411) did not compete for 125I-ATF binding and did not elicit any mitogenic response in either of the cell lines tested. In addition, tissue plasminogen activator (tPA), which has been shown to be homologous to uPA in its growth factor domain and is also fucosylated, did not inhibit 125I-ATF binding nor elicit any mitogenic response. These results demonstrate that the GFD, implicated in binding to the uPA receptor, is also responsible for growth factor like activity in SaOS-2 cells and that the fucosylation at Thr18 within this domain may serve as a molecular trigger in eliciting this response.
Microfluidic Isolation of Leukocytes from Whole Blood for Phenotype and Gene Expression Analysis (2006)

Technologies that enable the isolation of cell subtypes from small samples of complex populations will greatly facilitate the implementation of proteomics and genomics to human diseases. Transcriptome analysis of blood requires the depletion of contaminating erythrocytes. We report an automated microfluidic device to rapidly deplete erythrocytes from whole blood via deionized water lysis and to collect enriched leukocytes for phenotype and genomic analyses. Starting with blood from healthy subjects, we demonstrate the utility of this microfluidic cassette and lysis protocol to prepare unstimulated leukocytes, and leukocytes stimulated ex vivo with Staphylococcal enterotoxin B, which mimics some of the cellular effects seen in patients with severe bacterial infections. Microarrays are used to assess the global gene expression response to enterotoxin B. The results demonstrate that this system can isolate unactivated leukocytes from small blood samples without any significant loss, which permits more information to be obtained from subsequent analysis, and will be readily applicable to clinical settings.
Psilocybin and Obsessive Compulsive Disorder (2014)

Obsessive Compulsive Disorder (OCD) is a psychiatric disorder with considerable morbidity and mortality. This condition disables many individuals and is often refractory to treatment. Research suggests that serotonin plays a role in OCD symptom reduction. We present a case of an individual who successfully used psilocybin, a serotonergic agent, to reduce the core symptoms of OCD for several years. Although not endorsing this form of treatment, we feel that the successful use of this agent highlights the role of serotonergic factors in OCD and the need for further, legitimate research into the value of psilocybin in the treatment of anxiety disorders.
Hardware-Assisted Run-Time Monitoring for Secure Program Execution on Embedded Processors (2006)

Embedded system security is often compromised when "trusted" software is subverted to result in unintended behavior, such as leakage of sensitive data or execution of malicious code. Several countermeasures have been proposed in the literature to counteract these intrusions. A common underlying theme in most of them is to define security policies at the system level in an application-independent manner and check for security violations either statically or at run time. In this paper, we present a methodology that addresses this issue from a different perspective. It defines correct execution as synonymous with the way the program was intended to run and employs a dedicated hardware monitor to detect and prevent unintended program behavior. Specifically, we extract properties of an embedded program through static program analysis and use them as the bases for enforcing permissible program behavior at run time. The processor architecture is augmented with a hardware monitor that observes the program's dynamic execution trace, checks whether it falls within the allowed program behavior, and flags any deviations from expected behavior to trigger appropriate response mechanisms. We present properties that capture permissible program behavior at different levels of granularity, namely inter-procedural control flow, intra-procedural control flow, and instruction-stream integrity. We outline a systematic methodology to design application-specific hardware monitors for any given embedded program. Hardware implementations using a commercial design flow, and cycle-accurate performance simulations indicate that the proposed technique can thwart several common software and physical attacks, facilitating secure program execution with minimal overheads
The structure of aquaporins (2006)

The ubiquitous members of the aquaporin (AQP) family form transmembrane pores that are either exclusive for water (aquaporins) or are also permeable for other small neutral solutes such as glycerol (aquaglyceroporins). The purpose of this review is to provide an overview of our current knowledge of AQP structures and to describe the structural features that define the function of these membrane pores. The review will discuss the mechanisms governing water conduction, proton exclusion and substrate specificity, and how the pore permeability is regulated in different members of the AQP family.
Design and Synthesis of Highly Sensitive Fluorogenic Substrates for Glutathione S-Transferase and Application for Activity Imaging in Living Cells (2008)

Here we report the development of fluorogenic substrates for glutathione S-transferase (GST), a multigene-family enzyme mainly involved in detoxification of endogenous and exogenous compounds, including drug metabolism. GST is often overexpressed in a variety of malignancies and is involved in the development of resistance to various anticancer drugs. Despite the medical significance of this enzyme, no practical fluorogenic substrates for fluorescence imaging of GST activity or for high-throughput screening of GST inhibitors are yet available. So, we set out to develop new fluorogenic substrates for GST. In preliminary studies, we found that 3,4-dinitrobenzanilide (NNBA) is a specific substrate for GST and established the mechanisms of its glutathionylation and denitration. Using these results as a basis for off/on control of fluorescence, we designed and synthesized new fluorogenic substrates, DNAFs, and a cell membrane-permeable variant, DNAT-Me. These fluorogenic substrates provide a dramatic fluorescence increase upon GST-catalyzed glutathionylation and have excellent kinetic parameters for the present purpose. We were able to detect nuclear localization of GSH/GST activity in HuCCT1 cell lines with the use of DNAT-Me. These results indicate that the newly developed fluorogenic substrates should be useful not only for high-throughput GST-inhibitor screening but also for studies on the mechanisms of drug resistance in cancer cells.
Dynamic Interplay between O-Linked N-Acetylglucosaminylation and Glycogen Synthase Kinase-3-dependent Phosphorylation (2007)

O-GlcNAcylation on serine and threonine side chains of nuclear and cytoplasmic proteins is dynamically regulated in response to various environmental and biological stimuli. O-GlcNAcylation is remarkably similar to O-phosphorylation and appears to have a dynamic interplay with O-phosphate in cellular regulation. A systematic glycoproteomics analysis of the affects of inhibiting specific kinases on O-GlcNAcylation should help reveal both the global and specific dynamic relationships between these two abundant post-translational modifications. Here we report the O-GlcNAc perturbations in response to inhibition of glycogen synthase kinase-3 (GSK-3), a pivotal kinase involved in many signaling pathways. By combining immunoaffinity chromatography and SILAC (stable isotope labeling with amino acids in cell culture)-based quantitative mass spectrometry, we identified 45 potentially O-GlcNAcylated proteins. Quantitative measurements indicated that at least 10 proteins had an apparent increase of O-GlcNAcylation upon GSK-3 inhibition by lithium, whereas surprisingly 19 other proteins showed decreases. O-GlcNAcylation changes on a subset of the proteins were confirmed by follow-up experiments. By combining a new O-GlcNAc peptide enrichment method and beta-elimination followed by Michael addition with DTT, we also mapped the O-GlcNAc site (Ser-55) of vimentin, which showed an apparent increase of O-GlcNAcylation upon GSK-3 inhibition. Based on the MS data, we further investigated potential roles of O-GlcNAc on host cell factor-1, a transcription co-activator, and showed that dynamic regulation of O-GlcNAcylation on host cell factor-1 influenced its subcellular distribution. Taken together, these data indicated the complex interplay between phosphorylation and O-GlcNAcylation that occurs within signaling networks.