gebhart/patrepeval huggingface dataset:
Molecular Interactions in Interleukin and Toll-like Receptor Signaling Pathways (2014)

The ability of a single protein fold to make multi-modal interactions with itself and others for transmitting biological signals across multiple receptor families is a recurring theme in signal transduction. The Toll/IL-1 receptor (TIR) domain represents an evolutionarily conserved alpha-beta Flavodoxin-like protein fold [1], which has evolved complex multifaceted molecular interactions capable of transmitting a variety of developmental and immunological signals. In mammals, TIR domains are found on both interleukin-1 receptors (IL-1Rs) and Toll-like receptors (TLRs), as well as in cytoplasmic signaling adaptors and endogenous regulatory proteins. Appropriate TIR-TIR mediated immune interactions result in cytokine responses, pathogen clearance and host immune protection, while inappropriate signaling can lead to autoimmunity, inflammation and death. In the past decade, a number of three-dimensional structures of individual TIR domains have been elucidated. When coupled with the wealth of information from mutagenesis, genetic and peptide studies, this structural data provides additional insight to the molecular mechanisms underlying signal transduction mediated by interactions between TIR domains. Owing to their ability to regulate both innate and adaptive immune responses in a variety of organisms including humans, TIR domain-mediated molecular interactions are of intense interest for therapies targeting autoimmunity, cancer and emerging host-pathogen interactions. Here, we review progress in the development of peptides, peptidomimetics and small molecules designed to regulate TIR-dependent signaling in the context of recent advances in structural and molecular studies of TIR domain proteins and their interactions.
The highest levels of purine catabolic enzymes in mice are present in the proximal small intestine. (1993)

Recent studies on the tissue distribution and developmental regulation of adenosine deaminase (ADA) activity in mice show that very high ADA levels exist in the murine alimentary tract (tongue, esophagus, forestomach, proximal small intestine) and at the fetal-maternal interface. To understand the role of ADA in these tissues, we measured the levels of three other enzymes involved in purine catabolism, purine nucleoside phosphorylase (PNP), guanine deaminase (GDA), and xanthine dehydrogenase (XDH), to see how their levels correlated with ADA activity. Our results show that the highest level of PNP, GDA, and XDH is present in the proximal small intestine. Levels of these purine catabolic enzymes are much lower in the tongue, esophagus, forestomach, and fetal-maternal interface in marked contrast to ADA distribution. We also determined mRNA levels encoding PNP, XDH, and ADA in a variety of tissues. Tissue-specific differences in PNP, XDH, and ADA activity correlated with RNA abundance, indicating that the regulation of gene expression is at the level of mRNA production. Thus, ADA is part of a purine catabolic pathway leading to the production of uric acid that is present at the highest known level in the proximal small intestine. ADA may have additional roles in other tissues.
Equalization Digital On-Channel Repeater for Single Frequency Network Composition of ATSC Terrestrial Digital TV Broadcasting (2004)

In this paper we consider technological requirements to broadcast digital television signals using single frequency networks (SFN) in the Advanced Television Systems Committee (ATSC) transmission systems and propose equalization digital on-channel repeater (EDOCR) that overcomes the limitations of conventional digital on-channel repeaters (DOCRs). Since there are no forward error correction (FEC) decoder and encoder, the EDOCR does not have an ambiguity problem. In addition, since an adaptive equalizer in the EDOCR removes multi-path signals, additive white Gaussian noise (A WGN), and feedback signal due to low antenna isolation, the EDOCR may have good output signal quality with high power.
Genetic landscape of clear cell endometrial cancer and the era of precision medicine (2017)

The increased understanding of the genetic landscape of clear cell endometrial cancer should guide the development of precision medicine strategies to improve survival. See also pages 3261‐8.
Gold Nanorods as Plasmonic Nanotransducers: Distance-Dependent Refractive Index Sensitivity (2012)

Owing to the facile tunability of the localized surface plasmon resonance wavelength (LSPR) and large refractive index sensitivity, gold nanorods (AuNR) are of high interest as plasmonic nanotransducers for label-free biological sensing. We investigate the influence of gold nanorod dimensions on distance-dependent LSPR sensitivity and electromagnetic (EM) decay length using electrostatic layer-by-layer (LbL) assembly of polyelectrolytes. The electromagnetic decay length was found to increase linearly with both nanorod length and diameter, although to variable degrees. The rate of EM decay length increase with nanorod diameter is significantly higher compared to that of the length, indicating that diameter is a convenient handle to tune the EM decay length of gold nanorods. The ability to precisely measure the EM decay length of nanostructures enables the rational selection of plasmonic nanotransducer dimensions for the particular biosensing application.
System technology co-optimization and design challenges for 3D IC (2022)

As Moore's law fades and scaling of logic, memory and interconnects diverge, 3D integration technologies have become one of the primary approaches to maintaining performance gains in SoCs and SiPs. To fully exploit the system-level performance gains from 3D, we need to co-optimize the 3D system design for the 3D integration technology used, as well as solve the major physical design challenges of system partitioning, power delivery, thermals, and timing for 3D ICs. In this paper we will cover the system technology co-optimization and design challenges for 3D ICs from high-performance 3D CPU to many-core 3D system design.
The Impact of CO2 Evolved from VC and FEC during Formation of Graphite Anodes in Lithium-Ion Batteries (2019)

Additives such as vinylene carbonate (VC) and fluoroethylene carbonate (FEC) are commonly added to lithium-ion battery electrolytes in order to form a solid electrolyte interphase (SEI) on the anode, suppressing continuous solvent reduction. In this work, we directly compare VC and FEC by analyzing the SEI with FTIR and XPS, and the evolved gases with on-line electrochemical mass spectrometry (OEMS) in different model systems. Since both additives evolve mainly CO2 during formation, the effect of CO2 as an additive is compared to the addition of VC and FEC. While Li2CO3 is as expected the main SEI compound found due to the added CO2, surprisingly no CO was detected in the gas phase of such cells. Based on FTIR, NMR and OEMS analyses of cells filled with 13C labeled CO2, we suggest a mechanism explaining the beneficial effects of CO2 and hence also of CO2 evolving additives in lithium-ion battery cells. While the generation of polycarbonate from FEC or VC reduction is observed, the generation of Li2CO3 may be as important as the generation of polycarbonate.
Heat Exchangers Design Under Variable Overall Heat Transfer Coefficient: Improved Analytical and Numerical Approaches (2010)

In typical heat exchanger design methods it is generally assumed that the overall heat transfer coefficient is constant and uniform; however, the heat transfer coefficients on the hot and cold sides of the heat exchanger may vary with flow Reynolds number, surface geometries, fluid thermophysical properties, and other factors. In this article we present simple analytical and numerical methods for calculating heat transfer area for data sets introduced earlier in the literature. For the analytical methods presented in the article, the variation in the overall heat transfer coefficient with the local hot and cold fluid temperature difference is expressed as a power-law model and as a general polynomial model. The procedure for calculating the heat transfer area with the power-law model is explained with respect to a simple closed-form solution, while the polynomial model can also provide an analytical solution that seems to be quite accurate for the data sets examined. It is also shown that a Chebyshev numerical integration scheme that requires four points compared to the Simpson method of three points is quite accurate (within 1% of the exact value).
Proteins and antibodies in serum, plasma, and whole blood—size characterization using asymmetrical flow field-flow fractionation (AF4) (2018)

The analysis of aggregates of therapeutic proteins is crucial in order to ensure efficacy and patient safety. Typically, the analysis is performed in the finished formulation to ensure that aggregates are not present. An important question is, however, what happens to therapeutic proteins, with regard to oligomerization and aggregation, after they have been administrated (i.e., in the blood). In this paper, the separation of whole blood, plasma, and serum is shown using asymmetric flow field-flow fractionation (AF4) with a minimum of sample pre-treatment. Furthermore, the analysis and size characterization of a fluorescent antibody in blood plasma using AF4 are demonstrated. The results show the suitability and strength of AF4 for blood analysis and open new important routes for the analysis and characterization of therapeutic proteins in the blood.
The capacity region of a class of deterministic interference channels (Corresp.) (1982)

The capacity region of a class of deterministic discrete memoryless interference channels is established. In this class of channels the outputs <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Y_{1}</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Y_{2}</tex> are (deterministic) functions of the inputs <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X_{1}</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X_{2}</tex> such that <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">H(Y_{1}|X_{1})=H(V_{2})</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">H(Y_{2}|X_{2})=H(V_{l})</tex> for all product probabiliW distributions on <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X_{1}X_{2}</tex> , where <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V_{1}</tex> is a function of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X_{1}</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V_{2}</tex> a function of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X_{2}</tex> . The capacity, region for the case in which <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V_{2} \equiv 0</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Y_{1}</tex> depends randomly on <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X_{1}</tex> is also obtained and illustrated with an example.
Immune Cell‐Mediated Vasomotor Dysfunction in Large Vessels During Hypercholesterolemia (2006)

Hypercholesterolemia, a risk factor for the development of atherosclerosis, elicits inflammation and endothelial cell dysfunction in large arteries. The adaptive immune system has been implicated in the development of lesions, but it remains unclear whether lymphocytes contribute to the early hypercholesterolemia‐induced arterial dysfunction. Our hypothesis was that hypercholesterolemia elicits large vessel endothelial dysfunction through an immune‐mediated mechanism. Wire myography was employed to assess vasodilation and constriction responses of aortic rings in four groups of mice: wild‐type (WT) mice on a normal diet, WT mice on a high cholesterol diet for 2 weeks (HC), lymphocyte deficient (SCID) mice on HC, and a SCID‐HC group that received splenocytes from WT mice 5 days prior to observation. Endothelium‐independent contraction to phenylephrine did not differ between the groups. Aortic rings also exhibited similar endothelial‐independent dilation responses to sodium nitroprusside regardless of diet or immune‐competency. In contrast, HC led to an impaired endothelium‐dependent vasodilation response to acetylcholine in WT mice. This hypercholesterolemia‐induced dysfunction was absent in lymphocyte‐deficient mice. However, administration of splenocytes to immunodeficient SCID‐HC mice restored the hypercholesterolemia‐induced impairment of endothelium‐dependent vasodilation. Our findings indicate that lymphocytes contribute to hypercholesterolemia‐induced endothelial cell dysfunction in large arteries long before the development of atherosclerotic plaques. (Supported by R01 HL26441
Durch faziale Traumata induzierte Schädelbasisverletzungen (2007)

Einleitung: Ziel dieser Studie war die Erstellung eines Schädelbasis-Modells, mit dem die Kraftübertragung von Gesichtstraumata auf die Schädelbasis simuliert werden kann. Schwerpunkt war die mögliche Verletzung der Dura durch Deformation der benachbarten knöchernen Strukturen. Das Einreisen der Dura ist nicht immer direkt nach dem Trauma ersichtlich. Dies kann zu gravierenden Problemen und vital bedrohlich Folgeschäden (z.B. Meningitis) führen.
High-resolution control of optical phase for code-empowered networking (2006)

The ability to modify the individual optical phases of close-spaced, phase-locked laser lines underlies spectrally phase encoded optical-CDMA networks offering signal obscurity and scrambling, passive code-exchange and routing, and spectral efficiency comparable to DWDM
Unwrapping the eye for visible-spectrum gaze tracking on wearable devices (2013)

Wearable devices with gaze tracking can assist users in many daily-life tasks. When used for extended periods of time, it is desirable that such devices do not employ active illumination for safety reasons and to minimize interference from other light sources such as the sun. Most non active-illumination methods for gaze tracking attempt to locate the iris contour by fitting an ellipse. Although the camera projection causes the iris to appear as an ellipse in the eye image, it is actually a circle on the eye surface. Instead of searching for an ellipse in the eye image, the method proposed in this paper searches for a circle on the eye surface. To this end, the method calibrates a three-dimensional eye model based on the location of the corners of the eye. Using the 3D eye model, an input image is first transformed so that the eye's spherical surface is warped into a plane, thus “unwrapping” the eye. The iris circle is then detected on the unwrapped image by a three-step robust circle-fitting procedure. The location of the circle corresponds to the gaze orientation on the outside image. The method is fast to calibrate and runs in realtime. Extensive experimentation on embedded hardware and comparisons with alternative methods demonstrate the effectiveness of the proposed solution.
Expression of the WT1 Wilms' tumor gene by normal and malignant human melanocytes (1994)

We report expression of the wt1 (Wilms' tumor) gene by cultured human melanoma cells. Using RNA polymerase chain reaction analysis, wt1 transcripts were detected in 7 of 9 melanoma cell lines but not in 5 normal melanocyte strains. In Northern blot analysis, steady-state wt1 mRNA levels were found in 2 of 4 melanoma lines but not in normal melanocytes. Sequence analysis of the wt1 cDNA expressed by melanoma cell line WM 902-B revealed the presence of 4 previously published splice variants but no evidence for mutations in the coding region. Previous work has shown that WT1 modulates transcription after binding to the early growth response (EGR)-1 sites present in the platelet-derived growth factor (PDGF)-A chain promoter; the PDGF-A chain gene is known to be expressed by various melanoma cell lines. Based on these findings, we studied the relationship of wt1 and PDGF-A chain gene expression in melanoma cell lines. Co-expression of the wt1 and the PDGF-A chain genes was observed in 2 melanoma cell lines with mutated p53 but not in 2 melanoma cell lines with wild-type p53; this result is consistent with a previous report showing that, in the context of absent or mutated p53, WT1 acts as a transcriptional activator, whereas in the presence of wild-type p53 it acts as a repressor.
Minimizing aggregation latency under the physical interference model in Wireless Sensor Networks (2012)

Wireless Sensor Networks (WSNs) have been widely recognized as a promising technology that can enhance various aspects of today's electric power systems, making them a vital component of the smart grid. Efficient aggregation of data collected by sensors is crucial for a successful WSN-based smart grid application. Existing works on the Minimum Latency Aggregation Scheduling (MLAS) problem in WSNs usually adopt the protocol interference model, which is a tremendous simplification of the physical reality faced in wireless networks. In contrast, the more realistic physical interference model has been proved to have the potential to increase the network capacity. In this paper, we propose a distributed algorithm to minimize the data aggregation latency under the physical interference model, which jointly considers routing, power assignment and transmission scheduling. We theoretically prove that our algorithm solves the MLAS problem correctly and the latency is bounded by √ 3(K + 1) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> (Δ + log √2/K+1) + 6K <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> + 4K + 2, where K is a model-specific 2 constant and Δ is the logarithm of the ratio between the lengths of the longest and shortest links in the network. Simulation results demonstrate that our algorithm can significantly reduce the aggregation latency compared to other schemes under the physical interference model. In networks where n nodes are uniformly distributed, our algorithm achieves an average latency between O(log <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> n) and O(log <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> n). We also discuss how to improve the energy efficiency through load-balancing techniques.
Structure–activity relationship of GPR15L peptide analogues and investigation of their interaction with the GPR15 receptor (2023)

The 57-mer full-length GPR15L(25-81) peptide has been identified as the principal endogenous agonist of the G protein-coupled receptor GPR15. Its main activity resides in the C-terminal 11-mer GPR15L(71-81), which has full efficacy but ~40-fold lower potency than the full-length peptide. Here, we systematically investigated the structure-activity relationship of GPR15L(71-81) by truncations/extensions, alanine-scanning, and N- and C-terminal capping. The synthesized peptide analogues were tested at GPR15 stably expressed in HEK293A cells using a homogenous time-resolved Förster resonance energy transfer-based G<sub>i</sub> cAMP functional assay. We show that the C-terminal α carboxyl group and the residues Leu<sup>78</sup> , Pro<sup>75</sup> , Val<sup>74</sup> , and Trp<sup>72</sup> are critical for receptor interaction and contribute significantly to the peptide potency. Furthermore, we tested the ability of GPR15L(71-81), C-terminally amidated GPR15L(71-81), and GPR15L(25-81) to activate the three GPR15 receptor mutants in a bioluminescence resonance energy transfer-based G protein activation assay. The results demonstrate that the Lys192 and Glu272 residues in GPR15 are important for the potency of the GPR15L peptide. Overall, our study identifies critical residues in the peptide and receptor sequences for future drug design.
Experimental Investigations of Planar Dielectric Disk Antennae (2005)

The results of experimental investigations of planar dielectric disk antennae with different dielectric substrates and radiating elements are represented. Geometric and electric parameters of antenna prototypes have been chosen in accordance with the theoretical calculations [1] to provide the conditions of the TM01 mode excitation in the electromagnetic structure under study. It has been determined that the use of substrates with different values of the permittivity gives rise to the change in the antenna patterns and the field intensity in their lobes. Moreover, the use of dielectric disks with high permittivity (εd = 90) provides an increase in the power radiated into the free space as well as a frequency band enhancement.
Peptide adsorption on a hydrophobic surface results from an interplay of solvation, surface, and intrapeptide forces (2008)

The hydrophobic effect, i.e., the poor solvation of nonpolar parts of molecules, plays a key role in protein folding and more generally for molecular self-assembly and aggregation in aqueous media. The perturbation of the water structure accounts for many aspects of protein hydrophobicity. However, to what extent the dispersion interaction between molecular entities themselves contributes has remained unclear. This is so because in peptide folding interactions and structural changes occur on all length scales and make disentangling various contributions impossible. We address this issue both experimentally and theoretically by looking at the force necessary to peel a mildly hydrophobic single peptide molecule from a flat hydrophobic diamond surface in the presence of water. This setup avoids problems caused by bubble adsorption, cavitation, and slow equilibration that complicate the much-studied geometry with two macroscopic surfaces. Using atomic-force spectroscopy, we determine the mean desorption force of a single spider-silk peptide chain as F = 58 +/- 8 pN, which corresponds to a desorption free energy of approximately 5 k(B)T per amino acid. Our all-atomistic molecular dynamics simulation including explicit water correspondingly yields the desorption force F = 54 +/- 15 pN. This observation demonstrates that standard nonpolarizable force fields used in classical simulations are capable of resolving the fine details of the hydrophobic attraction of peptides. The analysis of the involved energetics shows that water-structure effects and dispersive interactions give contributions of comparable magnitude that largely cancel out. It follows that the correct modeling of peptide hydrophobicity must take the intimate coupling of solvation and dispersive effects into account.
The IBM 2009 GALE Arabic speech transcription system (2011)

We describe the Arabic broadcast transcription system fielded by IBM in the GALE Phase 4 machine translation evaluation. Key advances over our Phase 3.5 system include improvements to context-dependent modeling in vowelized Arabic acoustic models; the use of neural-network features provided by the International Computer Science Institute; Model M language models; a neural network language model that uses syntactic and morphological features; and improvements to our system combination strategy. These advances were instrumental in achieving a word error rate of 8.9% on the Phase 4 evaluation set, and an absolute improvement of 1.6% word error rate over our 2008 system on the unsequestered Phase 3.5 evaluation data.