gebhart/patrepeval huggingface dataset:
7S Nerve growth factor .alpha. and .gamma. subunits are closely related proteins (1984)

The polypeptide composition and partial amino acid sequence of the 7S nerve growth factor (NGF) alpha subunit have been determined. Residues in 76 unique positions corresponding to 35% of the molecule were identified. The sequence shows that the NGF alpha subunit is closely related to the NGF gamma subunit and thus a member of the same protein family as the serine proteases. This finding is unexpected since the NGF alpha subunit is devoid of detectable protease activity. However, the NGF alpha subunit differs in one important respect from the NGF gamma subunit and related serine proteases. The highly conserved amino-terminal activation cleavage structure, common to most serine proteases, has been deleted, and an uncleaved activation peptide remains attached to the amino terminus of the mature NGF alpha subunit. It is suggested that this feature is causally related to the apparent lack of proteolytic activity.
Prion disease susceptibility is affected by β-structure folding propensity and local side-chain interactions in PrP (2010)

Prion diseases occur when the normally α-helical prion protein (PrP) converts to a pathological β-structured state with prion infectivity (PrP(Sc)). Exposure to PrP(Sc) from other mammals can catalyze this conversion. Evidence from experimental and accidental transmission of prions suggests that mammals vary in their prion disease susceptibility: Hamsters and mice show relatively high susceptibility, whereas rabbits, horses, and dogs show low susceptibility. Using a novel approach to quantify conformational states of PrP by circular dichroism (CD), we find that prion susceptibility tracks with the intrinsic propensity of mammalian PrP to convert from the native, α-helical state to a cytotoxic β-structured state, which exists in a monomer-octamer equilibrium. It has been controversial whether β-structured monomers exist at acidic pH; sedimentation equilibrium and dual-wavelength CD evidence is presented for an equilibrium between a β-structured monomer and octamer in some acidic pH conditions. Our X-ray crystallographic structure of rabbit PrP has identified a key helix-capping motif implicated in the low prion disease susceptibility of rabbits. Removal of this capping motif increases the β-structure folding propensity of rabbit PrP to match that of PrP from mouse, a species more susceptible to prion disease.
Negative Solvatochromism of an Anionic Thiazole‐Based Dye (2013)

Keep it small, flat, and easy: The synthesis of an unconventional strong solvatochromic dye is presented. The solvatochromic and NMR behavior of the anionic chromophore was characterized and the compound might be used as a sensor. The thiazol-4-olate donor group is derived from the oxyluciferin of fireflies and strongly influences the electronic properties of the dye. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Better Patch Stitching for Parametric Surface Reconstruction (2020)

Recently, parametric mappings have emerged as highly effective surface representations, yielding low reconstruction error. In particular, the latest works represent the target shape as an atlas of multiple mappings, which can closely encode object parts. Atlas representations, however, suffer from one major drawback: The individual mappings are not guaranteed to be consistent, which results in holes in the reconstructed shape or in jagged surface areas. We introduce an approach that explicitly encourages global consistency of the local mappings. To this end, we introduce two novel loss terms. The first term exploits the surface normals and requires that they remain locally consistent when estimated within and across the individual mappings. The second term further encourages better spatial configuration of the mappings by minimizing novel stitching error. We show on standard benchmarks that the use of normal consistency requirement outperforms the baselines quantitatively while enforcing better stitching leads to much better visual quality of the reconstructed objects as compared to the state-of-the-art.
Analysis of Concept and Incentives for Digital Content Superdistribution (2007)

Despite the huge popularity of peer-to-peer distribution and yet again growing interest towards superdistribution, there is no consensus among researchers regarding the appropriate definition of superdistribution or its different types. There is a similar lack of consistence in the definition of the relation between superdistribution and peer-to-peer distribution. The objective of this paper is to develop a classification system for superdistribution that is useful to researchers from various disciplinary perspectives and takes into account the different ways how superdistribution can be realized. We also present some statistics about general acceptance of superdistribution as a distribution method for commercial and user-created content.
The visual comparison of three sequences (1991)

Scientists (particularly biologists) currently lack effective tools for comparing multiple sequences of numbers or symbols. This paper describes a method of visual comparison which provides the scientist with a new and unique tool to study the qualitative relationships between three such sequences. The program displays a three-dimensional shape containing the sequence similarities and differences, which manifest themselves as simple geometric shapes and colors that a human observer can easily detect and classify. The method presents all possible correlations to the user, giving it a considerable advantage over existing sequence comparison tools which only search for a programmed subset of all possible correlations. Thus, using this technique, researchers may detect sequence similarities which available analytic methods might completely overlook. The program can also filter out undesirable or insignificant correlations, letting the user focus full attention on the more interesting sequence relationships. The technique enjoys facile adaptation to a wide range of applications, including DNA and protein sequence analysis, speech analysis, signal processing, text comparison, and image analysis.
Peptide Mapping by Two-Dimensional Thin-Layer Electrophoresis-Thin-Layer Chromatography (1996)

The principle behind peptide mapping is straightforward: If two proteins have the same primary structures, then cleavage of each protein with a specific protease or chemical cleavage reagent will yield identical peptide fragments. However, if the proteins have different primary structures, and then the cleavage will generate unrelated peptides. The similarity or dissimilarity of the proteins’ primary structure is reflected in the similarity or dissimilarity of the peptide fragments. Separation of peptides by 2D thin-layer electrophoresis-thin-layer chromatography (2D TLE-TLC) results in very high resolution of the peptides, making subtle comparisons possible. There are four phases to the 2D TLE-TLC peptide mapping process: 1. Identification and purification of the proteins to be compared; 2. Radiolabeling of the proteins, and thus the peptide fragments, to minimize the quantity of protein required; 3. Cleavage of the proteins with specific endopeptidic reagents, either chemical or enzymatic; and 4. Separation and visualization of the peptide fragments for comparison.
In vivo comparison of myocardial T1 with T2 and T2* in thalassaemia major (2013)

In patients with iron overload, myocardial T2 and T1 are correlated with T2*. In patients with low or normal myocardial iron concentration, other factors become dominant in affecting T2* values as shown by scattered T2* data. Myocardial T1 correlates linearly with T2 measurements in all patients suggesting that these two relaxation parameters avoid extrinsic magnetic field inhomogeneity effects and may potentially provide improved myocardial tissue characterization.
Crystal Growth and Scintillation Properties of Ce Doped ${\rm Gd}_{3}({\rm Ga},{\rm Al})_{5}{\rm O}_{12}$ Single Crystals (2012)

Ce1%, 2% and 3% doped Gd <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> (Ga,Al) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sub> (GAGG) single crystals were grown by the Cz method. Luminescence and scintillation properties were measured. Light yield change along the growth direction and effects of Ce concentration on scintillation properties in Ce:GAGG were studied. Ce <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> 5d-4f emission within 520-530 nm was observed in the Ce:GAGG crystals. The Ce1%:GAGG sample with 3×3×1 mm size showed the highest light yield of 46000 photon/MeV. The energy resolution was 7.8%@662 keV. With increasing solidification fraction, the LY were decreased. It is proposed that the increase of Ga concentration along the growth direction is the main cause of the decrease of LY. The scintillation decay times were accelerated with increasing Ce concentration in the Ce:GAGG crystals. The scintillation decay times were 92.0 ns, 79.1 ns and 68.3 ns in the Ce1, 2 and 3% GAGG, respectively.
Elastography in Chronic Liver Disease: Modalities, Techniques, Limitations, and Future Directions (2016)

Chronic liver disease has multiple causes, many of which are increasing in prevalence. The final common pathway of chronic liver disease is tissue destruction and attempted regeneration, a pathway that triggers fibrosis and eventual cirrhosis. Assessment of fibrosis is important not only for diagnosis but also for management, prognostic evaluation, and follow-up of patients with chronic liver disease. Although liver biopsy has traditionally been considered the reference standard for assessment of liver fibrosis, noninvasive techniques are the emerging focus in this field. Ultrasound-based elastography and magnetic resonance (MR) elastography are gaining popularity as the modalities of choice for quantifying hepatic fibrosis. These techniques have been proven superior to conventional cross-sectional imaging for evaluation of fibrosis, especially in the precirrhotic stages. Moreover, elastography has added utility in the follow-up of previously diagnosed fibrosis, the assessment of treatment response, evaluation for the presence of portal hypertension (spleen elastography), and evaluation of patients with unexplained portal hypertension. In this article, a brief overview is provided of chronic liver disease and the tools used for its diagnosis. Ultrasound-based elastography and MR elastography are explored in depth, including a brief glimpse into the evolution of elastography. Elastography is based on the principle of measuring tissue response to a known mechanical stimulus. Specific elastographic techniques used to exploit this principle include MR elastography and ultrasonography-based static or quasistatic strain imaging, one-dimensional transient elastography, point shear-wave elastography, and supersonic shear-wave elastography. The advantages, limitations, and pitfalls of each modality are emphasized. <sup>©</sup>RSNA, 2016.
Involvement of the ERK1/2 Pathway During Oxytocin-Induced PGF2alpha Production in the Bovine Endometrial Epithelial Cell Line bEEL. (2009)

In ruminants, oxytocin (OT) initiates the pulsatile release of progstaglandin F2α (PGF2α) from the endometrial epithelial cells through the G protein coupled oxytocin receptor (OTR) that is up-regulated during the luteolytic phase. It has been proposed that the embryonic signal interferon tau exerts its antiluteolytic effect by disrupting the OT signaling axis. In this respect, we have studied the signaling pathway of OT-induced PGF2α production in bovine endometrial epithelial cell line (bEEL) using kinase inhibitors. Uncoupling OTR with suramin (100μM) inhibited OT (500nM)-induced PGF2α release confirming mediation through G protein subunits. OT induces intracellular Ca2+ mobilization suggesting Gαq/11 mediated signaling as was shown for myometrial OTRs. Surprisingly, however, neither the Ca2+ chelator BAPTA nor a PKC inhibitor had any effect on OT-induced PGF2α release. In contrast, the MEK inhibitor PD 98059 (10μM) and Raf1 inhibitor GW5074 (1μM) practically abolished OT-induced PGF2α production in bEEL cells, thus pointing at the involvement of the of ERK pathway. Inhibition of the small GTPase Ras by munanmyin (1μM) inhibited PGF2α by 50%; whereas LY 294002 (25μM) and AG1879 (10μM) inhibited OT-induced PGF2α production by 80-90% indicating the involvement of PI3K and Src, respectively. In addition, pertussis toxin (PTX 200 ngml-1) inhibited PGF2α production by 50% suggesting a role for Gαi/o; however, increasing intracellular cAMP by 8 bromo cAMP, forskolin or IBMX did not inhibit OT-induced PGF2α production suggesting involvement of Gαo rather than Gαi as the PTX sensitive subtype. Surprisingly, the inhibition of OT-induced PGF2α production was not accompanied by down regulation of COX2 expression. Therefore, phosphorylation of cPLA2, inhibition of COX2 activity, or uncoupling of PGF synthase from COX2 might be considered as alternate mechanisms behind the reduced PGF2α production. Our results suggest that OT-induced PGF2α production in bEEL cells is mediated principally through Gβ γ subunit initiating phosphorylation of downstream molecules such as PI3K, Src, Ras, Raf1, MEK and ERK kinases and co-regulated by PTX sensitive Gα. (poster)
Mechanical and electrical properties of cardiomyopathic hearts of Syrian hamsters (1989)

To determine whether the cardiomyopathy that develops in the Syrian hamster before the occurrence of congestive heart failure is associated with mechanical and electrical alterations consistent with myocardial dysfunction, left ventricular posterior papillary muscles of control and cardiomyopathic animals at 120 days of age were studied in vitro. Moreover, the electrocardiographic response to ouabain was investigated in vivo to analyze the arrhythmogenic potential of the cardiomyopathic heart to glycoside exposure. Results showed a decreased tension-generating ability of the myocardium in the diseased animals, which was accompanied by a prolongation of the timing parameters of contraction and an increase in the duration of the repolarization phase of the transmembrane action potential. Furthermore, the velocity of isotonic muscle shortening and relengthening was depressed at all physiological loads. Glycoside infusion elicited premature ventricular contractions, ventricular tachycardia, and ventricular fibrillation in diseased hamsters much earlier in time than in healthy controls. The impairment in mechanical performance in association with the abnormality in membrane electrical activity may be responsible for the progression of the disease process and the occurrence of lethal arrhythmias in this animal model.
Zeeman splitting of single semiconductor impurities in resonant tunneling heterostructures (1996)

Zeeman splitting of the ground state of single impurities in the quantum wells of resonant tunneling heterostructures is reported. We determine the absolute magnitude of the effective magnetic spin splitting factorg⊥* for a single impurity in a 44 Å Al0.27Ga0.73As/GaAs/Al0.27Ga0.73As quantum well to be 0.28±0.02. This system also allows for independent measurement of the electron tunneling rates through the two potential barriers and estimation of the occupation probability of the impurity state in the quantum well.
Smart Storytelling: Video and Text Risk Communication to Increase MFA Acceptability (2020)

Exposure of passwords for authentication and access management is a ubiquitous and constant threat. Yet, reliable solutions, including multi-factor authentication (MFA), face issues with wide-spread adoption. Prior research shows that making MFA mandatory helps with tool adoption but is detrimental to users' mental models and leads to security-avoidance behavior. To explore feasible solutions, we implemented text-and video-based risk communication strategies to evaluate if either mode of risk communication was useful. We sought to explore users' technical biases to further examine the mental models that are associated with safer security habits. Our study of N = 620 participants found that users are aware of frequent security attacks, including phishing. We found that text- and video-based communication is often useful when information is aligned with individual actions and their consequences, which can range from benign to catastrophic. Shorter mental-model-aligned video snippets piqued user interest in MFA. On the other hand, detailed risk communication videos or textual descriptions improved users' understanding of MFA and the potential risks of non-usage. Our study indicates that, beyond usability and comprehensive education, risk communication offers the potential to increase MFA adoption.
RF displacement and strain sensing system for wireless structural health monitoring (2015)

Structural health monitoring (SHM) is a technology with worldwide interest that is vital to ensure the reliability of any structure while also protecting the safety of human life. Over the years, a lot of research has been conducted on this topic, proposing SHM methods that may be instrumental in understanding the condition of critical parts of a structure. These methods generally rely on wired and/or active technologies, which are not preferable since the wires disallow telemetric measurements and mean increased weight and space, while the active technologies require electric power in order to operate. Two of the most important damage indices of a building structure such as a reinforcing bar (rebar) are the strain and displacement forming either with time or a sudden impact like an earthquake.
Construire le sens d'un verbe dans son cadre pr edicatif (2011)

This paper presents a model of the construction of the meaning of what Jacques François calls a "predication", i.e." an expression containing a verbal predicate and its predicate frame" [our translation]. We define a distance between predications that takes into account semantic proximity between both verbs and predicate frames. This distance is explicitly computed from a synonym verb dictionary and a corpus distributional analysis. This work is an extension of a research program of Jacques François to which the authors collaborated a few years ago.
A Novel Caspase-1/Toll-like Receptor 4-independent Pathway of Cell Death Induced by Cytosolic Shigella in Infected Macrophages (2005)

Shigella-induced macrophage cell death is an important step in the induction of acute inflammatory responses that ultimately lead to bacillary dysentery. Cell death was previously reported to be dependent upon the activation of caspase-1 via interaction with IpaB secreted by intracellular Shigella, but in this study, we show that Shigella infection of macrophages can also induce cell death independent of caspase-1 or IpaB activity. Time-lapse imaging and electron microscopic analyses indicated that caspase-1-dependent and -independent cell death is morphologically indistinguishable and that both resemble necrosis. Analyses of Shigella mutants or Escherichia coli using co-infection with Listeria suggested that a component common to Gram-negative bacteria is involved in inducing caspase-1-independent cell death. Further studies revealed that translocation of bacterial lipid A into the cytosol of macrophages potentially mediates cell death. Notably, cell death induced by cytosolic bacteria was TLR4-independent. These results identify a novel cell death pathway induced by intracellular Gram-negative bacteria that may play a role in microbial-host interactions and inflammatory responses.
Effect of 2′-5′/3′-5′ phosphodiester linkage heterogeneity on RNA interference (2020)

We report on the synthesis of siRNAs containing both 2'-5'- and 3'-5'-internucleotide linkages and their effects on siRNA structure, function, and interaction with RNAi proteins. Screening of these siRNAs against their corresponding mRNA targets showed that 2'-5' linkages were well tolerated in the sense strand, but only at a few positions in the antisense strand. Extensive modification of the antisense strand minimally affected 5'-phosphorylation of the siRNA by kinases, however, it negatively affected siRNA loading into human AGO2. Modelling and molecular dynamics simulations were fully consistent with these findings. Furthermore, our studies indicated that the presence of a single 5'p-rN1-(2'-5')-N2 unit in the antisense strand does not alter the 'clover leaf' bend and sugar puckers that are critical for anchoring the 5'-phosphate to Ago 2 MID domain. Importantly, 2'-5'-linkages had the added benefit of abrogating immune-stimulatory activity of siRNAs. Together, these results demonstrate that 2'-5'/3'-5'-modified siRNAs, when properly designed, can offer an efficient new class of siRNAs with diminished immune-stimulatory responses.
Dual Wideband Printed Monopole Antenna for WLAN/WiMAX Applications (2007)

A novel printed monopole antenna with dual widebands is presented for simultaneously satisfying wireless local area network (WLAN) and worldwide interoperability for microwave access (WiMAX) applications. The antenna structure consists of a rectangular monopole with a microstrip feedline for excitation and a trapezoid conductor-backed plane for band broadening. The measured 10 dB bandwidth for return loss is from 2.01 to 4.27 GHz and 5.06 to 6.79 GHz, covering all the 2.4/5.2/5.8 GHz WLAN bands and 2.5/3.5/5.5 GHz WiMAX bands