gebhart/patrepeval huggingface dataset:
Effects of C-1-substituted glucose analogue on the activation states of glycogen synthase and glycogen phosphorylase in rat hepatocytes (1995)

A series of glucose-analogue inhibitors of glycogen phosphorylase b (GPb) has been designed, synthesized and investigated in crystallographic binding and kinetic studies. The aim is to produce a compound that may exert more effective control over glycogen metabolism than the parent glucose molecule and which could alleviate hyperglycaemia in Type-II diabetes. N-Acetyl-beta-D-glucopyranosylamine (1-GlcNAc) has a Ki for muscle GPb in crude extracts of 30 microM, 367-fold lower than that of beta-D-glucose [Board, Hadwen and Johnson (1995) Eur. J. Biochem. 228, 753-761]. In the current work, the effects of 1-GlcNAc on the activation states of GP and glycogen synthase (GS) in cell-free preparations and in isolated hepatocytes are reported. In gel-filtered extracts of liver, which lack ATP for kinase activity, 1-GlcNAc produced a rapid and time-dependent inactivation of GP with a subsequent activation of GS. Effects of 1-GlcNAc on both enzymes were stronger than those of glucose, with 0.8 mM 1-GlcNAc being equipotent with 50 mM glucose. At 1 mM, 1-GlcNAc enhanced the dephosphorylation of exogenous GPa by liver extracts (600%) and by muscle extracts (75%). This represents an approximately 500-fold improvement on glucose for the liver activity and 40-fold for the muscle activity. In whole hepatocytes, 1-GlcNAc showed an approximately 5-fold enhancement of glucose effects for GP inactivation but failed to elicit activation of GS. Glucose-induced activation of GS in whole hepatocytes was reversed by subsequent addition of 1-GlcNAc. However, when GS activation was achieved via the adenosine analogue and kinase inhibitor, 5'-iodotubercidin (ITU), subsequent addition of 1-GlcNAc allowed continued activation of GS. Phosphorylation of 1-GlcNAc in rat hepatocytes was established using radiolabelled material. The rate of phosphorylation was 1.60 nmol/min per 10(6) cells at 20 mM 1-GlcNAc but was reduced by the presence of 50 microM ITU (0.775 nmol/min per 10(6) cells). It is suggested that the phosphorylated derivative of 1-GlcNAc formed in hepatocytes is 1-GlcNAc 6-phosphate and that the presence of this species is responsible for the failure of 1-GlcNAc to activate GS. The relative importance of the reduction in concentration of GPa versus increased glucose 6-phosphate levels for activation of GS is discussed.
Virtually tasty: An investigation of the effect of ambient lighting and 3D-shaped taste stimuli on taste perception in virtual reality (2022)

Taste perception is influenced by sensory information not only about the food itself but also about the external environment where the food is tasted. Prior studies have shown that both visual attributes of the environment (e.g., light colour, location) and the shape associated to food (e.g., plates, cutlery) can influence people's taste perception and expectations. However, previous studies are typically based on non-edible shapes usually shown as 2D images or presented as 3D tangible objects aimed to be perceived by subjects' hand. Therefore, the effect of mouthfeel of differently shaped foods on taste perception remains unclear. Capitalising on the advantages of virtual reality (VR) to manipulate multisensory features, we explore the effects of coloured (red, blue, neutral) virtual environments on the taste (sweet, neutral) perception of differently shaped taste samples (rounded/spiky shapes according to the Kiki-Bouba paradigm). Overall, our results showed increased ratings of sweetness when participants tasted Bouba-shaped samples (rounded) relative to Kiki-shaped samples (spiky) suggesting that tactile attributes perceived inside the mouth can influence sweetness perception. Furthermore, we concluded that lighting colour in a virtual setting might dampen experiences of sweetness. However, this effect may only be present when there is a cross-modal correspondence with taste. Based on our findings, we conclude by describing considerations for designing eating experiences in VR.
Application of holography to fluid flow measurements using bacteriorhodopsin (bR) (2004)

This paper demonstrates the use of bacteriorhodopsin (bR) as the holographic recording medium for a holographic particle image velocimetry (HPIV) system. Using an off-axis hologram in bR, double-exposed images of particles in a turbulent flow are recorded. A high numerical aperture configuration (NA = 0.75) ensures a maximal signal intensity of the holographic recordings. Using a CCD the real particle images, that were reconstructed in the original object space, were digitized. The reconstructed image has a theoretical depth of focus of 4.73 µm and a diffraction-limited resolution of 0.43 µm. Using a priori knowledge about the flow, the flow pattern is extracted from the double-exposed particle images. A liquid crystal shutter was employed during the reconstruction in order to minimize photo-induced erasure. Details of the experimental set-up, as well as the difficulties which were encountered during this investigation, are discussed in this paper. The paper also discusses various multiplexing methods and their suitability for use with bR to remove directional ambiguity in HPIV.
Objective Evaluation of Pain Perception in Patients with Schizophrenia (1994)

The pain thresholds of patients with schizophrenia often seem to differ from those of healthy subjects. In the present study we assessed the pain thresholds of ten patients with schizophrenia, and of ten controls, by measuring the leg flexion nociceptive reflex threshold: the stimulation threshold at which this reflex is triggered, is known to be correlated with the pain threshold. Our conclusion is that, in most cases, the increase in pain threshold is the result of 'attitude' and not of alterations in brain function.
Supramolecular Platform Stabilizing Growth Factors (2018)

High concentrations of supplemented growth factors can cause oversaturation and adverse effects in in vitro and in vivo studies, though these supraphysiological concentrations are often required due to the low stability of growth factors. Here we demonstrate the stabilization of TGF-β1 and BMP4 using supramolecular polymers. Inspired by heparan sulfate, sulfonated peptides were presented on a supramolecular polymer to allow for noncovalent binding to growth factors in solution. After mixing with excipient molecules, both TGF-β1 and BMP4 were shown to have a prolonged half-life compared to the growth factors free in solution. Moreover, high cellular response was measured by a luciferase assay, indicating that TGF-β1 remained highly active upon binding to the supramolecular assembly. The results demonstrate that significant lower concentrations of growth factors can be used when supramolecular polymers bearing growth factor binding moieties are implemented. This approach can also be exploited in hydrogel systems to control growth factor release.
Medium access design for LTE in unlicensed band (2015)

In this paper, a medium access protocol suitably adapted for the operation of Long term evolution (LTE) in unlicensed band (LTE-U) is proposed. The MAC design considers the impact of LTE-U on the devices operating in unlicensed band, such as WiFi and legacy LTE. The LTE-U design differences from the legacy LTE system, an inherently a synchronized, tightly controlled system are explored. The performance of LTE-U is studied via a detailed system level simulator implementation and 3GPP simulation test scenarios. We show that our proposed MAC design enables high throughput in unlicensed band and achieves co-existence with the incumbent systems. Moreover, the use of channel reservation mechanisms is shown to improve LTE-U cell edge performance.
Iterative wirability and performance improvement for FPGAs (1993)

In FPGAs, routing resources are fixed and their usage is constrained by the location of antifuses. This severely limits the ability to make accurate wirability and timing predictions at the placement level. There is a need, therefore, for a layout flow in which an incremental placer changes the layout based on post-layout timing and wirability analysis. In this paper we consider such an incremental placer. Up to 29% improvement in timing has been obtained for a set of industrial designs and MCNC benchmark examples.
Preparation of Multilayer Biodegradable Nanofibers by Triaxial Electrospinning (2013)

A biodegradable, multilayer nanofiber structure has been successfully developed by using a self-designed and fabricated triaxial electrospinning system using gelatin as the sheath and core layers and poly(ε-caprolactone) (PCL) as the middle layer. The triaxial structure was investigated by confocal fluorescence microscopy (CFM) and focused ion beam and field-emission scanning electron microscopy (FIB-FESEM). The ability to fabricate the multilayered nanofibers efficiently with different biodegradable polymers will enable this triaxial electrospinning technique to have wider applications in biotechnology.
Crystallographic insights into the self‐assembly of KLVFF amyloid‐beta peptides (2017)

Amyloidogenic peptide fragment KLVFF (H<sub>2</sub> N-Lys-Leu-Val-Phe-Phe-COOH, Aβ<sub>16-20</sub> ), the core-sequence of the polypeptide Aβ40, is a well-studied model for amyloid formation. However, due to its low crystallinity, detailed atomic information of KLVFF structure is lacking. Here we report the high-resolution single-crystal X-ray structure of two monohalogenated KLVFF derivatives, KLVFF(I) and KLVFF(Br). The obtained results highlight how halogenation is a good strategy to promote crystallization and facilitate the phase determination of KLVFF(I) and KLVFF(Br) fragments. Detailed structural studies on the packing features of both monohalogenated derivatives reveal the role of the halogen atoms showing that when they are positioned on the Phe aromatic moiety at the C-terminus they do not form halogen bonds and thus do not produce any extra stabilization of the β-sheet in the self-assembly process. The structural evidences gained from these studies corroborate the various polymorphic nanostructures of the halogenated variants of KLVFF and confirm the possibility to use halogenation as innovative strategy to tune the morphology of this pentapeptide.
Interaction of retinoids with steroid and peptide hormones in modulating morphological and functional differentiation of normal rat mammary epithelial cells. (1995)

The interaction of the retinoid RE80 with the lactogenic and mammogenic regulators of mammary gland development was investigated using a mammary epithelial cell (MEC) primary culture model in which cells from young virgin rats were cultured within a reconstituted basement membrane using defined serum-free medium. RE80 (10(-10) M) was able to substitute completely for epidermal growth factor and partially for hydrocortisone in stimulating both morphological and functional (casein accumulation) differentiation of the MEC. In contrast, the requirement of PRL for both differentiation processes was absolute. Furthermore, RE80 was found to abrogate the inhibitory effect of progesterone on casein accumulation and to act as an antiprogestin in terms of morphological effects. Under optimal medium conditions, RE80 also inhibited cell proliferation. This inhibition did not require epidermal growth factor, hydrocortisone, progesterone, or PRL, but, unexpectedly, was enhanced in medium deficient in or lacking hydrocortisone. Additionally, RE80 induced the death of differentiated MEC, an effect that was found to require hydrocortisone. These results suggest that retinoids may modulate transcription of the casein gene family, either directly by activation of the binding of retinoic acid receptors to the casein promoter or indirectly by modulation of the effects of other hormones. The antiproliferative effect of retinoid may also be direct or indirect by virtue of down-regulation of the receptors for one of the mitogenic hormones, possibly progesterone.
Nickel-Catalyzed, Carbonyl-Ene-Type Reactions:  Selective for Alpha Olefins and More Efficient with Electron-Rich Aldehydes (2006)

Described are several classes of unusual or unprecedented carbonyl-ene-type reactions, including those between alpha olefins and aromatic aldehydes. Catalyzed by nickel, these processes complement existing Lewis acid-catalyzed methods in several respects. Not only are monosubstituted alkenes, aromatic aldehydes, and tert-alkyl aldehydes effective substrates, but monosubstituted olefins also react faster than those that are more substituted, and large or electron-rich aldehydes are more effective than small or electron-poor ones. Conceptually, in the presence of a nickel-phosphine catalyst, the combination of off-the-shelf alkenes, silyl triflates, and triethylamine functions as a replacement for an allylmetal reagent.
Free‐breathing abdominal MRI improved by repeated k‐t‐subsampling and artifact‐minimization (ReKAM) (2017)

The ReKAM framework improves the quality of free-breathing abdominal MRI data, and is compatible with various MRI pulse sequences.
A Flexible Quadrature Coupler With Reconfigurable Frequency and Coupling Ratio in Switchable Coupling Direction (2019)

A highly reconfigurable and switchable quadrature coupler with simultaneous control in terms of operating frequency, coupling ratio, and coupling direction is presented. To start with, a prototype coupler based on an ideal admittance-inverter model is investigated, and a method to obtain the admittance-inverter values for an arbitrary coupling ratio is described. Next, a tunable-admittance-inverter network implemented with lumped inductors and varactors, which features reconfigurable operating frequency, and tunable-admittance-inverter value is discussed. The conceived reconfigurable coupler is then realized by replacing the ideal admittance inverters with the proposed tunable-admittance-inverter circuit to provide it with operating-frequency and coupling-ratio controllability. Furthermore, when exchanging the admittance-inverter values in the coupler, the coupling direction is switched from forward to backward. The proposed technique is further developed into a general design procedure for reconfigurable-coupler implementations with an arbitrary admittance-inverter-based network. Wilkinson power dividers with equal and unequal power-division ratios are also shown as examples. For experimental/demonstration purposes, a reconfigurable coupler prototype is fabricated and characterized. It demonstrates a tunable operating frequency from 1 to 1.5 GHz, a controllable power-division ratio between output ports from 1 to 0.7, and switchable operational direction between forward and backward.
Attosecond physics (2007)

Fundamental processes in atoms, molecules, as well as condensed matter are triggered or mediated by the motion of electrons inside or between atoms. Electronic dynamics on atomic length scales tends to unfold within tens to thousands of attoseconds (1 attosecond [as] = 10-18 s). Recent breakthroughs in laser science are now opening the door to watching and controlling these hitherto inaccessible microscopic dynamics. The key to accessing the attosecond time domain is the control of the electric field of (visible) light, which varies its strength and direction within less than a femtosecond (1 femtosecond = 1000 attoseconds). Atoms exposed to a few oscillations cycles of intense laser light are able to emit a single extreme ultraviolet (xuv) burst lasting less than one femtosecond. Full control of the evolution of the electromagnetic field in laser pulses comprising a few wave cycles have recently allowed the reproducible generation and measurement of isolated sub-femtosecond xuv pulses, demonstrating the control of microscopic processes (electron motion and photon emission) on an attosecond time scale. These tools have enabled us to visualize the oscillating electric field of visible light with an attosecond “oscilloscope”, to control single-electron and probe multi-electron dynamics in atoms, molecules and solids. Recent experiments hold promise for the development of an attosecond x-ray source, which may pave the way towards 4D electron imaging with sub-atomic resolution in space and time.
Nonblocked Midwest Guardrail System for Wire-Faced Walls of Mechanically Stabilized Earth (2011)

Wire-faced walls of mechanically stabilized earth (MSE) provide an economical method for building vertical structures for supporting roadways where local topography or high land costs preclude the use of conventional fill slopes. W-beam guardrail systems are often used for shielding high vertical drop-offs associated with MSE walls. For this study, the Midwest Guardrail System (MGS) was modified to decrease the overall width of the MSE wall structure. Dynamic component testing was used to determine the post–soil behavior of steel and wood posts embedded in compacted soil materials used for constructing wire-faced MSE walls as well as to evaluate the effects of sloped terrain and different installation methods. Twenty-six dynamic tests were performed to evaluate the propensity for MSE wall damage, to select post length, and to determine the preferred post material and section. The standard MGS was modified by removing the wood spacer blocks 12 in. (305 mm) deep and by incorporating W-beam backup plates. All other MGS features—including the W6 × 8.5 (W152 × 12.6) steel posts 6 ft (1.8 m) long, rail splices at midspan locations, the 31-in. (787-mm) top-mounting height, and the 75-in. (1,905-mm) post spacing—were maintained. The nonblocked MGS was installed with the posts driven at the slope break point of a 3H:1V fill slope. The modified MGS was successfully crash tested with both 1100C small car and 2270P pickup truck vehicles in accordance with Test Level 3 safety performance guidelines in the Manual for Assessing Safety Hardware. The MSE wall was not damaged during the testing programs. The nonblocked MGS is recommended for use with wire-faced MSE walls when they are placed at the slope break point of a 3H:1V fill slope. The modified MGS reduces the required width of the MSE wall, resulting in decreased construction costs.
Physical and functional interactions between SH2 and SH3 domains of the Src family protein tyrosine kinase p59fyn. (1994)

The Src family protein tyrosine kinases participate in signalling through cell surface receptors that lack intrinsic tyrosine kinase domains. All nine members of this family possess adjacent Src homology (SH2 and SH3) domains, both of which are essential for repression of the enzymatic activity. The repression is mediated by binding between the SH2 domain and a C-terminal phosphotyrosine, and the SH3 domain is required for this interaction. However, the biochemical basis of functional SH2-SH3 interaction is unclear. Here, we demonstrate that when the SH2 and SH3 domains of p59fyn (Fyn) were present as adjacent domains in a single protein, binding of phosphotyrosyl peptides and proteins to the SH2 domain was enhanced, whereas binding of a subset of cellular polypeptide ligands to the SH3 domain was decreased. An interdomain communication was further revealed by occupancy with domain-specific peptide ligands: occupancy of the SH3 domain with a proline-rich peptide enhanced phosphotyrosine binding to the linked SH2 domain, and occupancy of the SH2 domain with phosphotyrosyl peptides enhanced binding of certain SH3-specific cellular polypeptides. Second, we demonstrate a direct binding between purified SH2 and SH3 domains of Fyn and Lck Src family kinases. Heterologous binding between SH2 and SH3 domains of closely related members of the Src family, namely, Fyn, Lck, and Src, was also observed. In contrast, Grb2, Crk, Abl, p85 phosphatidylinositol 3-kinase, and GTPase-activating protein SH2 domains showed lower or no binding to Fyn or Lck SH3 domains. SH2-SH3 binding did not require an intact phosphotyrosine binding pocket on the SH2 domain; however, perturbations of the SH2 domain induced by specific high-affinity phosphotyrosyl peptide binding abrogated binding of the SH3 domain. SH3-SH2 binding was observed in the presence of proline-rich peptides or when a point mutation (W119K) was introduced in the putative ligand-binding pouch of the Fyn SH3 domain, although these treatments completely abolished the binding to p85 phosphatidylinositol 3-kinase and other SH3-specific polypeptides. These biochemical SH2-SH3 interactions suggest novel mechanisms of regulating the enzymatic activity of Src kinases and their interactions with other proteins.
Linear Micromechanical Phased Arrays (2019)

Linear micromechanical optical phased arrays solve many of the problems facing their two-dimensional counter parts. In this paper we cover the basics of linear micromechanical phased arrays and show how their fundamental properties lead to desirable functional characteristics for optical applications. Experimental results on sheet microscopy with improved axial resolution demonstrates how the scanning performance of linear phased arrays can be combined with other scanning elements to create three dimensional images with high resolution at high speed.
A Multimodal Ca(II) Responsive Near IR-MR Contrast Agent Exhibiting High Cellular Uptake (2020)

Ca(II) ions are critical for the proper function of neurons by contributing to synaptic signaling and regulating neuronal plasticity. Dysregulation of Ca(II) is associated with a number of pathologies that cause neurodegeneration; therefore the ability to monitor Ca(II) intracellularly is an important target for molecular imaging. Contrast-enhanced MR imaging is a promising modality for imaging changes in Ca(II) concentrations. However, the majority of Ca(II) responsive MR agents are limited to the extracellular space or hindered by poor cellular uptake. Here, we describe a new class of multimodal, bioresponsive Ca(II) magnetic resonance agents that are coupled to the NIR probe IR-783. This new design is based on previous generations of our Ca(II) MR agents but overcomes two significant challenges: (1) the presence of the NIR probe dramatically increases cellular uptake of the agent and (2) provides histological validation of the MR signal using NIR fluorescence imaging. IR-783 targets organic anion transporter polypeptides, and we demonstrate that the agents are not toxic in HT-22 or U-87 MG cells up to 20 μM. The cellular uptake of complex <b>1</b> was measured to be greater than 16 femtomoles per cell (where ∼1 femtomole/cell is detectable in acquired MR images). Complex <b>1</b> is simultaneously detectable by both MR and NIR fluorescence imaging <i>in vitro</i> and is activated (turned on) by intracellular Ca(II) at concentrations between 1 and 10 μM.
Prediction of blood-based biomarkers and subsequent design of bisulfite PCR-LDR-qPCR assay for breast cancer detection (2020)

This report demonstrates the potential utilization of bisulfite PCR-LDR-qPCR assay, along with bioinformatically-driven biomarker discovery, in blood-based BrCa detection.
Virtual Rings on Highways: Traffic Control by Connected Automated Vehicles (2022)

This work gives introduction to traffic control by connected automated vehicles. The influence of vehicle control on vehicular traffic and traffic control strategies are discussed and compared. It is highlighted that vehicle-to-everything connectivity allows connected automated vehicles to access the state of the traffic behind them such that feedback can be utilized to mitigate evolving congestions. Numerical simulations demonstrate that such connectivity-based traffic control is beneficial for smoothness and energy efficiency of highway traffic. The dynamics and stability of traffic flow, under the proposed controllers, are analyzed in detail to construct stability charts that guide the selection of stabilizing control gains.