gebhart/patrepeval huggingface dataset:
Optical and electronic design for a high-performance surface plasmon resonance imager (2004)

Surface plasmon resonance (SPR) imaging is a versatile technique for detection, quantification, and visualization of bio-molecular binding events which have spatial structure. In this paper, we describe the design principles which we are applying toward construction of a new high-performance SPR imager. We briefly review the basic principles of SPR biosensing and SPR imaging, and discuss the goals for the new design. We focus on two main goals, refractive index (RI) resolution and mechanical simplicity. We address RI resolution as a signal-to-noise issue, using simulations to determine how to maximize the signal (i.e. changes in intensity due to binding events) and minimize the noise. Specific attention is paid to the dominant effects of shot noise. Design concepts for collimating and imaging optics which reduce or eliminate the need for mechanical adjustment are presented. Ray-tracing analysis of the collimating optics is used for detailed analysis of collimator performance.
Functional Proteomic Analysis of Lipid Raft Kinase Complexes (2009)

Abstract : A series of studies from our laboratories suggested that survival signaling in prostate cancer cells is mediated, in part, through lipid raftresident Akt. I have hypothesized that the lipid raft-resident Akt in prostate tumor cells is a privileged Akt population that mediates cell survival by interacting with discrete subsets of regulatory proteins and by transmitting signals that are unique to the lipid raft environment. Many components in lipid raft-resident Akt complexes and Akt pathways are likely to be palmitoylated, given that a number of key signaling molecules are palmitoylated and that palmitoyl proteins have been proposed to be enriched in lipid rafts. As an approach into the analysis of Akt signaling through lipid rafts, in year 1 of this project I developed a novel, proteomic method of palmitoyl protein analysis, which resulted in many interesting and unanticipated biological findings. In addition, our group has very recently reported that EGF stimulation or accumulation of Akt1 in lipid rafts resulted in the rapid formation of secreted microvesicles, which are capable of activating phosphotyrosine and Akt pathway signaling as well as stimulating proliferation and migration in recipient cells. Functional palmitoylproteomics analysis suggested that certain palmitoyl proteins actively participate in transmitting EGFR-Akt signaling. The protein acyltransferases and acylprotein thioesterases regulating the palmitoylation levels of these key palmitoyl proteins may be novel targets for the inhibition of EGFR-Akt signaling, which can be exploited for the treatment of advanced prostate cancer.
TEMPERATURE DEPENDENCE OF MAGNETO-OPTICAL EFFECT IN MAGNETIC FLUIDS (1987)

Temperature dependence of magnetic birefringence of magnetic fluids under a magnetic field H was studied. Temperature dependence of the phase difference θ between the two modes of the rays with polarization parallel and perpendicular to the field H was found to obey the generalized Curie-Weiss law, or θ∝ (T-T0(H))-1 where T is the temperature of the magnetic fluid. The function T0 of H satisfies the empirical formula, T0 (H) ∝ exp (-αH), where α is a constant.
Genome-Wide mRNA and microRNA Profiling of the NCI 60 Cell-Line Screen and Comparison of FdUMP[10] with Fluorouracil, Floxuridine, and Topoisomerase 1 Poisons (2010)

A profile of microRNA (miRNA) and mRNA expression patterns across the NCI-60 cell-line screen was analyzed to identify expression signatures that correlate with sensitivity to FdUMP[10], fluorouracil (5FU), floxuridine (FdU), topotecan, and irinotecan. Genome-wide profile analyses revealed FdUMP[10] resembles FdU most closely and shows dissimilarities with 5FU. FdUMP[10] had the largest dynamic range of any of these drugs across the NCI-60 indicative of cancer cell-specific activity. Genes involved in endocytosis, such as clathrin (CLTC), SNF8, annexin A6 (ANXA6), and amyloid protein-binding 2 (APPBP2) uniquely correlated with sensitivity to FdUMP[10], consistent with a protein-mediated cellular uptake of FdUMP[10]. Genes involved in nucleotide metabolism were enriched for the three fluoropyrimidine drugs, with the expression profile for 5FU correlated to an RNA-mediated cytotoxic mechanism, whereas expression of glycosyltransferases (XYLT2) that use UDP sugars as substrates and the nucleoside diphosphatase and metastasis suppressor NM23 (NME1) were associated with FdUMP[10] sensitivity. Topotecan and irinotecan had significant negative correlations with miR-24, a miRNA with a high aggregate P(CT) score for topoisomerase 1 (Top1). Our results reveal significant new correlations between FdUMP[10] and Top1 poisons, as well as new information on the unique cytotoxic mechanism and genomic signature of FdUMP[10].
Component Analysis of Pressure Drop and Ventilation Variability (1984)

Abstract Mathematical models were derived that describe the variability of ventilation and pressure drop as functions of cigarette design specifications and the variabilities of cigarette components. These models and the graphical isovariation contour representation have several important potential applications for quality control and improvement. For example, the models can be used in cigarette performance studies to determine the relative contributions of each source of variability and to identify the largest source of variability. The models can be used in quality improvement to target programs for maximum effectiveness and to set realistic goals for quality improvement. The quantitative variability values that the models produce can also be used to establish acceptance limits for the variabilities of the cigarette components which control ventilation and pressure drop variability within specified limits. These applications and the insight into the causes of variability that these models can provide should make them a valuable tool for improving the uniformity of cigarette performance.
International Education Year (1969)

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Rituximab for the Treatment of Thymoma-Associated and De Novo Myasthenia Gravis: 3 Cases and Review (2009)

These observations support the concept that rituximab may be helpful for the treatment of MG. Remissions in patients with or without thymoma are achievable with rituximab given in combination with commonly used modalities. Furthermore, rituximab is not necessarily contraindicated for the treatment of MG in patients being treated for thymoma. Controlled studies are called for to define its role in the treatment of refractory MG.
Comparison of heat-affected zones due to nanosecond and femtosecond laser pulses using transmission electronic microscopy (2002)

This letter presents a method aimed at quantifying the dimensions of the heat-affected zone (HAZ), produced during nanosecond and femtosecond laser–matter interactions. According to this method, 0.1 μm thick Al samples were microdrilled and observed by a transmission electronic microscopy technique. The holes were produced at laser fluences above the ablation threshold in both nanosecond and femtosecond regimes (i.e., 5 and 2 J/cm2, respectively). The grain size in the samples was observed near the microholes. The main conclusion is that a 40 μm wide HAZ is induced by the nanosecond pulses, whereas the femtosecond regime does not produce any observable HAZ. It turns out that the width of the femtosecond HAZ is less than 2 μm, which is our observation limit.
Marital Status in Relation to Kaposi's Sarcoma, Non-Hodgkin's Lymphoma, and Anal Cancer in the Pre-AIDS Era (1996)

Persons with human immunodeficiency virus/AIDS are at high risk of Kaposi's sarcoma (KS), non-Hodgkin lymphoma (NHL), and possibly anal cancers. To examine whether this risk preceded the AIDS epidemic, we used pre-AIDS era data from the Surveillance, Epidemiology, and End Results program (excluding Connecticut) from 1973 to 1976, and the Connecticut Tumor Registry from 1940 to 1976. We compared risk of being single (a surrogate to identify men who might be homosexual) to those ever married, using a case control matching study with up to 10 controls per case. Overall, no excess risk was observed for KS (risk ratio for men 20-59 years old: 1.00; 95% confidence interval 0.218-3.61), but there was a suggestion of higher risk (4.00; 0.54-29.48) in 1973-1976, the period just before the AIDS epidemic. The NHL risk (0.85; 0.74-0.99) was slightly low, but for anal cancer the risk ratio of being single was significantly high both in men 20-59 years old (5.68) and older men (2.78) long before the AIDS epidemic. If the excess risk was solely due to being homosexual, the actual relative risk in the subset who were homosexual must have been much higher, given that only a fraction of the single men would have been homosexual. As comparison groups to verify the methodology, we used colon (no association with marital status) and prostatic cancer (decreased in single men), with findings as reported in other studies. Thus, single men may have been at an excess risk of KS (but a slightly low risk of NHL) just before the AIDS epidemic and have been at excess risk of anal cancer for many years before the AIDS epidemic.
Conformational differences between the Pfr and Pr states in <i>Pseudomonas aeruginosa</i> bacteriophytochrome (2009)

Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria by means of reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here, we report the crystal structure of the Q188L mutant of Pseudomonas aeruginosa bacteriophytochrome (PaBphP) photosensory core module, which exhibits altered photoconversion behavior and different crystal packing from wild type. We observe two distinct chromophore conformations in the Q188L crystal structure that we identify with the Pfr and Pr states. The Pr/Pfr compositions, varying from crystal to crystal, seem to correlate with light conditions under which the Q188L crystals are cryoprotected. We also compare all known Pr and Pfr structures. Using site-directed mutagenesis, we identify residues that are involved in stabilizing the 15Ea (Pfr) and 15Za (Pr) configurations of the biliverdin chromophore. Specifically, Ser-261 appears to be essential to form a stable Pr state in PaBphP, possibly by means of its interaction with the propionate group of ring C. We propose a "flip-and-rotate" model that summarizes the major conformational differences between the Pr and Pfr states of the chromophore and its binding pocket.
Testing of the Katrix rotary lobe expander for distributed concentrating solar combined heat and power systems (2014)

Abstract In this article, we present performance results and analysis of a novel rotary lobe expander device. This is part of a larger research effort into the analysis and design of a small‐scale solar system that would compete with available distributed technologies for heat and electricity generation. To choose an appropriate working fluid and components for a distributed concentrating solar combined heat and power (DCS‐CHP) system, we compared many different working fluids, collectors, and expander choices. Of the expanders analyzed, including piston expanders, radial inflow turbines, Tesla turbines, screw expanders, and scroll expanders, the rotary lobe expander shows the greatest promise in small‐scale power applications due to its high efficiency in expanding fluids over large pressure ratios and its low cost to manufacture. This article focuses on testing of a prototype small‐scale expander that was chosen because, to date, no suitable commercial product of less than 10 kW has been found for this application. Initial testing was completed with air to get results that should be indicative of future testing with steam. The test system consists of a compressed air expander (a prototype designed by Katrix, Inc. of Australia) connected to an induction motor driven by a variable frequency drive (VFD) that enables expander testing at varying shaft speeds. Results of the expander testing are reported isentropic efficiencies of 22–25%, thermomechanical efficiencies of 80–95%, and pressure ratios of 6–11 at the tested speeds. Despite mixed results from this particular expander, future refinements could lead to a new class of expanders with low cost and high performance for use in solar combined heat and power and waste‐heat recovery.
MeCP2 driven transcriptional repression in vitro: selectivity for methylated DNA, action at a distance and contacts with the basal transcription machinery (2000)

The pathways for selective transcriptional repression of methylated DNA templates by the methyl-CpG-binding protein MeCP2 have been investigated using a purified in vitro transcription system that does not assemble chromatin. MeCP2 selectively inhibits transcription complex assembly on methylated DNA but does not destabilize a pre-assembled transcription complex. MeCP2 functions to repress transcription at a distance of >500 bp from the transcription start site. The transcription repression domain (TRD) of MeCP2 will repress transcription in vitro when fused to a heterologous Gal4 DNA-binding domain. The TRD associates with TFIIB. Exogenous TFIIB does not relieve transcriptional repression established by either intact MeCP2 or a Gal4-TRD fusion protein under these in vitro conditions, nor does the addition of histone deacetylase inhibitors. We find that the transcriptional repression established by both MeCP2 and the Gal4-TRD fusion protein in vitro also correlates with selective assembly of large nucleoprotein complexes. The formation of such complexes reflects a local concentration of DNA-bound transcriptional repressor that may stabilize a state of repression even in the presence of exogenous transcriptional machinery.
A comparative study of matrix measures for maximum likelihood texture classification (1991)

The performance of various matrix features in classifying synthetic and natural textures is compared by using the features directly in a maximum likelihood texture classifier. The matrix texture features examined are the spatial gray-level dependence matrix (SGLDM), the neighboring gray-level dependence matrix (NGLDM) and the neighboring spatial gray-level dependence matrix (NSGLDM). It is shown that, in general, for natural textures that are stochastic in nature, any of the texture features based on the NGLDM for distance (d) equal to 1 would be good choices as measures for texture classification. The parameter alpha should be chosen to maximize classification performance. For d=1, these measures require much fewer computations than the SGLDM with comparable performance. Also, the NGLDM-based measure require fewer computations for d=1 than for larger distances. For highly structured textures that may be characterized by large primitive elements, the NSGLDM can be used to extract texture information at larger distances while maintaining its relative computational efficiency.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Language model adaptation using cross-lingual information (2003)

The success of statistical language modeling techniques is crucially dependent on the availability of a large amount training text. For a language in which such large text collections are not available, methods have recently been proposed to take advantage of a resource-rich language, together with cross-lingual information retrieval and machine translation, to sharpen language models for the resource-deficient language. In this paper, we describe investigations into such language models for an automatic speech recognition system for Mandarin Broadcast News. By exploiting a large side-corpus of contemporaneous English news articles to adapt a static Chinese language model to the news story being transcribed, we demonstrate significant improvements in recognition accuracy. The improvement from using English text is greater when less Chinese text is available to estimate the static language model. We also compare our cross-lingual adaptation to monolingual topic-dependent language model adaptation, and achieve further gains by combining the two adaptation techniques.
Evolution of Catalysis in the Serine Proteases (1987)

The hydrolytic cleavage of peptide bonds by proteases is an ancient biochemical reaction prevalent in all forms of living organisms. Hydrolysis of a peptide substrate by a protease requires specificity in binding and catalytic efficiency. Certain constellations of amino acid residues comprise the substrate binding pocket, which in turn confers the unique substrate specificity of each enzyme. Productive binding of the substrate in this pocket positions the scissile bond next to a characteristic set of functional amino acid residues arranged in a particular conformation to form the active site. The active-site residues polarize the peptide bond by nucleophilic attack on the carbon-oxygen bond assisted by the donation of a proton to the peptide amide nitrogen. The evolution of this highly sophisticated protein "machine" has been the topic of previous studies involving protein sequencing, crystallography, and enzyme kinetics (Neurath 1984). A prototypic hydrolytic enzyme that has been the subject of many...
Naturally Arising CD25+CD4+ Regulatory T Cells in Maintaining Immunologic Self-Tolerance and Preventing Autoimmune Disease (2003)

A large body of evidence indicates that T cell-mediated dominant suppression of self-reactive T cells is indispensable for maintaining immunologic unresponsiveness to self-constituents (i.e., self-tolerance) and preventing autoimmune disease. CD25+CD4+ regulatory T cells naturally present in normal animals, in particular, engage in this function, as their reduction or functional abnormality leads to the development of autoimmune disease in otherwise normal animals. They are at least in part produced by the normal thymus as a functionally mature and distinct subpopulation of T cells. Recent studies have demonstrated that CD25+CD4+ regulatory T cells control not only autoimmune reactions but also other immune responses, including tumor immunity, transplantation tolerance and microbial infection. Thus, this unique population of regulatory T cells can be exploited to control pathological as well as physiological immune responses.
Solid-Phase Synthesis of Cyclic Peptides (1994)

Interest in cyclic peptides dates back almost half a century to the discovery that the antibiotic gramicidin S is a cyclic decapeptide (Consden et al., 1947). Since then, numerous naturally occurring cyclic antibiotics and toxins have been found. Many of these are homodetic, that is, with only peptide (lactam) linkages connecting the constituent amino acid residues, whereas others are heterodetic, and include other functions such as disulfide, ester (lactone), ether, or thioether bridges that contribute to the ring(s). Duplication of the natural cycles, and the introduction of unnatural rings, have attracted the attention of chemists because of the extra level of synthetic complexity of such endeavors. Concurrently, a variety of biological studies have suggested that cyclic structures may exhibit improved metabolic stabilities, increased potencies, better receptor selectivities, and more controlled bioavailabilities. Further, the constrained geometries of cyclic peptides are conducive to conformational investigations, and for modeling and/or “locking” key secondary structural elements in protein folding. Early synthetic work focused on peptides with a small ring size, particularly cyclic hexapeptides. With the development of improved methods for peptide synthesis, larger ring sizes and more complex targets have become accessible.
Mast cell–expressed orphan receptor CCRL2 binds chemerin and is required for optimal induction of IgE-mediated passive cutaneous anaphylaxis (2008)

Mast cells contribute importantly to both protective and pathological IgE-dependent immune responses. We show that the mast cell-expressed orphan serpentine receptor mCCRL2 is not required for expression of IgE-mediated mast cell-dependent passive cutaneous anaphylaxis but can enhance the tissue swelling and leukocyte infiltrates associated with such reactions in mice. We further identify chemerin as a natural nonsignaling protein ligand for both human and mouse CCRL2. In contrast to other "silent" or professional chemokine interreceptors, chemerin binding does not trigger ligand internalization. Rather, CCRL2 is able to bind the chemoattractant and increase local concentrations of bioactive chemerin, thus providing a link between CCRL2 expression and inflammation via the cell-signaling chemerin receptor CMKLR1.
Improving the Performance of High-Density Platooning Using Vehicle Sensor-Based Doppler-Compensation Algorithms (2019)

This paper investigates the advantages of using communication supported by information from vehicle sensors to improve the performance of the High-Density Platooning (HDPL) application. HDPL is one of the most promising applications in the field of cooperative driving. The goal of this application is to improve fuel and road efficiency without impairing safety. The level of efficiency improvement depends on the instantaneous channel quality. Strong multipath components, which arise from other vehicles, traffic signs, and surrounding buildings in such a highly dynamic vehicular environment, significantly influence the instantaneous link quality between communicating vehicles in a platoon. An emerging concept of vehicle sensor-aided predictive communications has shown its potential to improve direct-link communication. In this paper, the applicability of this approach is evaluated in terms of inter-vehicle distance error, which reflects the difficulties that the control algorithm has to cope with in the communications conditions. The simulation results show that the proposed sensor-based approach significantly improves the platoon performance even if affected by multiple dynamic scattering reflections at the same time.
SHP-1 Deficient Mast Cells Are Hyperresponsive to Stimulation and Critical in Initiating Allergic Inflammation in the Lung (2009)

Phosphatase Src homology region 2 domain-containing phosphatase 1 (SHP-1)-deficient mice display an allergic asthma phenotype that is largely IL-13 and STAT6 dependent. The cell types responsible for the Th2 phenotype have not been identified. We hypothesized that SHP-1 deficiency leads to mast cell dysregulation and increased production and release of mediators and Th2 cytokines, leading to the allergic asthma phenotype. We examined SHP-1 regulation of mast cell differentiation, survival, and functional responses to stimulation using bone marrow-derived mast cells from viable motheaten (mev) mice. We assessed pulmonary phenotypical changes in mev mice on the mast cell-deficient Kit(W-Sh) genetic background. The results showed that SHP-1 deficiency led to increased differentiation and survival, but reduced proliferation, of mast cells. SHP-1-deficient mast cells produced and released increased amounts of mediators and Th2 cytokines IL-4 and -13 spontaneously and in response to H(2)O(2), LPS, and Fc epsilonI cross-linking, involving c-Kit-dependent and -independent processes. The Fc epsilonRI signaling led to binding of SHP-1 to linker for activation of T cells 2 and enhanced linker for activation of T cells 2 phosphorylation in mev bone marrow-derived mast cells. Furthermore, the number of mast cells in the lung tissue of mev mice was increased and mast cell production and release of Th2 cytokines were distinctly increased upon Fc epsilonRI stimulation. When backcrossed to the Kit(W-Sh) background, mev mice had markedly reduced pulmonary inflammation and Th2 cytokine production. These findings demonstrate that SHP-1 is a critical regulator of mast cell development and function and that SHP-1-deficient mast cells are able to produce increased Th2 cytokines and initiate allergic inflammatory responses in the lung.