gebhart/patrepeval huggingface dataset:
An Algebraic Approach to Signaling Cascades with n Layers (2010)

Posttranslational modification of proteins is key in transmission of signals in cells. Many signaling pathways contain several layers of modification cycles that mediate and change the signal through the pathway. Here, we study a simple signaling cascade consisting of n layers of modification cycles, such that the modified protein of one layer acts as modifier in the next layer. Assuming mass-action kinetics and taking the formation of intermediate complexes into account, we show that the steady states are solutions to a polynomial in one variable, and in fact that there is exactly one steady state for any given total amounts of substrates and enzymes. We demonstrate that many steady state concentrations are related through rational functions, which can be found recursively. For example, stimulus-response curves arise as inverse functions to explicit rational functions. We show that the stimulus-response curves of the modified substrates are shifted to the left as we move down the cascade. Further, our approach allows us to study enzyme competition, sequestration and how the steady state changes in response to changes in the total amount of substrates. Our approach is essentially algebraic and follows recent trends in the study of posttranslational modification systems.
Online Half Diminished-Reality Imaging Using Multiple RGB-D Sensors for Remote Control Robot (2015)

This paper presents a methodology to compose half-diminished reality images for operating remote control robots. At sites for disaster response, robots are desired to achieve various tasks. However, operators have problems concerned with camera images shown to them for controlling robots. For example, operators have to understand the environment by comparing many display images from multiple cameras, because the robot arm itself occludes target work objects in main camera image. Half-Diminished Reality technique is used for seeing through foreground objects and viewing occluded backgrounds. We have applied the technique to remote operating. In this paper, a fast algorithm to estimate the background image is proposed. Furthermore, an online half-diminished viewing system for remote control is constructed. In the experiment, we confirmed the validity of proposed method with three RGB-D sensors and a robot arm : The proposed method could display online half-diminished reality images to the operator to see through the target work objects occluded by the robot arm.
Contrast detection is enhanced by non-stochastic, high-frequency transcranial alternating current stimulation with triangle and sine waveform (2022)

Abstract Stochastic Resonance (SR) describes a phenomenon where an additive noise (stochastic carrier-wave) enhances the signal transmission in a nonlinear system. In the nervous system, nonlinear properties are present from the level of single ion channels all the way to perception and appear to support the emergence of SR. For example, SR has been repeatedly demonstrated for visual detection tasks, also by adding noise directly to cortical areas via transcranial random noise stimulation (tRNS). We mathematically show that high-frequency, non-stochastic, periodic signals can yield resonance-like effects with linear transfer and infinite signal-to-noise ratio at the output. Here we tested this prediction empirically and investigated whether non-random, high-frequency, transcranial alternating current stimulation (hf-tACS) applied to visual cortex could induce resonance-like effects and enhance performance on a visual detection task. We demonstrated in 28 participants that applying 80 Hz triangular-waves or sine-waves with hf-tACS reduced visual contrast detection threshold for optimal brain stimulation intensities. The influence of hf-tACS on contrast sensitivity was equally effective to tRNS-induced modulation, demonstrating that both hf-tACS and tRNS can reduce contrast detection thresholds. Our findings suggest that a resonance-like mechanism can also emerge when non-stochastic electrical waveforms are applied via hf-tACS. New &amp; Noteworthy Our findings extend our understanding of neuromodulation induced by noninvasive electrical stimulation. We provide first evidence showing acute online benefits of hf-tACS triangle and hf-tACS sine targeting the primary visual cortex (V1) on visual contrast detection in accordance with the resonance-like phenomenon. The ‘non-stochastic’ hf-tACS and ‘stochastic’ hf-tRNS are equally effective in enhancing visual contrast detection.
30.1: Flexible Image Sensor Made of a‐Si:H TFTs on Metal Foil (2008)

Abstract We have developed a flexible image sensor using hydrogenated amorphous silicon thin film transistor (a‐Si:H TFT) on metal foil. The metal foil was treated by electrolytic polishing and thus its RMS surface roughness was reduced from 1205 to 71.6 Å. The sensor has 160 × 128 pixels, where a pixel has one switching TFT, one sensor TFT and a storage capacitor. A clear image was demonstrated on the metal foil using conventional pixel having two transistors and one cap.
Pentaarylcyclopentadienyl Iron, Cobalt, and Nickel Halides (2016)

The preparation of new stable half-sandwich transition metal complexes, having a bulky cyclopentadienyl ligand C5(C6H4-4-Et)5 (Cp(Ar1)) or C5(C6H4-4-nBu)5 (Cp(Ar2)), is reported. The tetrahydrofuran (THF) adduct [Cp(Ar1)Fe(μ-Br)(THF)]2 (1a) was synthesized by reacting K[Cp(Ar1)] with [FeBr2(THF)2] in THF, and its molecular structure was determined by X-ray crystallography. Complex 1a easily loses its coordinated THF molecules under vacuum to form the solvent-free complex [Cp(Ar1)Fe(μ-Br)]2 (1b). The analogous complexes [Cp(Ar1)Co(μ-Br)]2 (2), [Cp(Ar1)Ni(μ-Br)]2 (3), and [Cp(Ar2)Ni(μ-Br)]2 (4) were synthesized from CoBr2 and [NiBr2(1,2-dimethoxyethane)]. The mononuclear, low-spin cobalt(III) and nickel(III) complexes [Cp(Ar2)MI2] (5, M = Co; 6, M = Ni) were prepared by reacting the radical Cp(Ar2) with NiI2 and CoI2. The complexes were characterized by NMR and UV-vis spectroscopies and by elemental analyses. Single-crystal X-ray structure analyses revealed that the dimeric complexes 1a, 1b, and 3 have a planar M2Br2 core, whereas 2 and 4 feature a puckered M2Br2 ring.
ChemInform Abstract: SYNTHESIS OF 1,2‐DIHYDROINDOLO(1,7‐AB)(1,5)BENZODIAZEPINES AND RELATED STRUCTURES. A NEW HETEROCYCLIC RING SYSTEM (1980)

Abstract Aus den Indolinen (I) und den 2‐Fluornitrobenzolen (II) entstehen die Kondensate (III), die zu den Amino‐phenyl‐Verbindungen (IV) reduziert und dann zu (V) acyliert werden.
Single-exposure complementary aperture phase microscopy with polarization encoding (2012)

We introduce a single-exposure widefield system of producing phase gradient images by dividing the illumination and detection apertures into two oblique complementary components and encoding them using polarization. A Wollaston prism splits the images formed by the two respective aperture halves to allow both components to be simultaneously imaged by a single camera. By producing images characteristically similar to differential interference contrast while using a darkfield illumination scheme, sensitivity to weak phase gradients is improved.
Developmental regulation of MHC II expression and transport in human plasmacytoid-derived dendritic cells (2008)

Plasmacytoid predendritic cells (pDCs) play a key role in antiviral immunity through their capacity to produce large amounts of type I interferons in response to Toll-like receptor triggering, and to differentiate into dendritic cells (DCs). However, their antigen processing and presentation pathways remain poorly characterized. In this study, we analyzed major histocompatibility complex class II (MHC II) synthesis and transport in primary human pDCs. We show that stimulation of pDCs with influenza virus leads to a sustained neosynthesis of MHC II molecules, which rapidly accumulate in antigen loading compartments organized around the microtubule organization center. MHC II endocytosis as well as antigen internalization remain active during the entire process of pDC differentiation into DCs, suggesting a capacity to constantly renew surface peptide-MHC II complexes. Formation of the intracellular pool of MHC II in activated pDCs is nuclear factor-kappaB-dependent and associated with acquisition of a dendritic phenotype, but independent of the IRF7-type I interferon-dependent pathway, suggesting that innate and adaptive functions of pDCs are differentially regulated. Our data demonstrate that the regulation of MHC II expression and transport is drastically different in pDCs compared with conventional DCs, indicating distinct and potentially complementary immunoregulatory functions.
Curcuminoids and<i>Boswellia serrata</i>extracts combination decreases tendinopathy symptoms: findings from an open-label post-observational study (2020)

<b>Background:</b> To investigate the effects of 1-month treatment in addition to standard care with a food supplement containing both <i>Curcuma longa</i> and <i>Boswellia serrata</i> extracts on tendinopathy symptoms.<b>Method:</b> This open-label, non-controlled, post-observational study included 670 patients suffering from tendinopathy recruited at different sites by Belgian general practitioners. Patients received a medical prescription for 1-month treatment with two tablets twice a day of a pharmaceutical grade food supplement containing both <i>C. longa</i> and <i>B. serrata</i> extracts. Pain and functional limitation were evaluated using a visual analog scale at the inclusion and 1-month treatment later. Patient satisfaction, concomitant drugs intake and side effects were also recorded.<b>Results:</b> After 1-month treatment, pain and functional limitation were significantly improved whatever the cause of tendinopathy, its localization, and the duration of symptoms. The pain score decreased from 6.16 ± 1.53 to 2.98 ± 1.64 (<i>p</i> < .0001), yielding a drop of 51.6% and the functional limitation score fell after 1-month treatment from 5.96 ± 1.73 to 2.88 ± 1.67 (<i>p</i> < .0001) corresponding to a drop of 51.6%. The percentage of patients taking at least one concomitant treatment at the end of the treatment period had decreased from 81.3% to 61.8% (<i>p</i> < .0001). Only 43 (6.5%) patients reported side effects. No severe adverse effects related to the product were reported.<b>Conclusion:</b> The combination of <i>C. longa</i> and <i>B. serrata</i> extracts improves symptoms in patients suffering of tendinopathy and shows a good safety. Although its effect will have to be confirmed in randomized controlled trials, it can be considered as a helpful support of standard symptomatic treatments for tendinopathies. HighlightsTendinopathy is a common disease representing 30% of all consultations with a general practitioner for musculoskeletal disorders.The combination of Curcuminoids and <i>Boswellia</i><i>serrata</i> extracts are efficient on tendinopathy symptoms in support of standard symptomatic treatments.The combination of Curcuminoids and <i>B. Serrata</i> extract is safe and can be administrated for at least 1 month in addition of analgesic and non-steroidal anti-inflammatory drugs.
ChemInform Abstract: Sceliphrolactam, a Polyene Macrocyclic Lactam from a Wasp‐Associated Streptomyces sp. (2011)

Abstract Title compound (I) shows antifungal activity against amphotericin B‐resistant Candida albicans.
Quantizing Euclidean Motions via Double-Coset Decomposition (2019)

Concepts from mathematical crystallography and group theory are used here to quantize the group of rigid-body motions, resulting in a “motion alphabet” with which robot motion primitives are expressed. From these primitives it is possible to develop a dictionary of physical actions. Equipped with an alphabet of the sort developed here, intelligent actions of robots in the world can be approximated with finite sequences of characters, thereby forming the foundation of a language in which robot motion is articulated. In particular, we use the discrete handedness-preserving symmetries of macromolecular crystals (known in mathematical crystallography as Sohncke space groups) to form a coarse discretization of the space SE(3) of rigid-body motions. This discretization is made finer by subdividing using the concept of double-coset decomposition. More specifically, a very efficient, equivolumetric quantization of spatial motion can be defined using the group-theoretic concept of a double-coset decomposition of the form Γ\SE(3)/Δ, where Γ is a Sohncke space group and Δ is a finite group of rotational symmetries such as those of the icosahedron. The resulting discrete alphabet is based on a very uniform sampling of SE(3) and is a tool for describing the continuous trajectories of robots and humans. An efficient coarse-to-fine search algorithm is presented to round off any motion sampled from the continuous group of motions to the nearest element of our alphabet. It is shown that our alphabet and this efficient rounding algorithm can be used as a geometric data structure to accelerate the performance of other sampling schemes designed for desirable dispersion or discrepancy properties. Moreover, the general “signals to symbols” problem in artificial intelligence is cast in this framework for robots moving continuously in the world.
Determination of plasma temperature and electron density of iron in iron slag samples using laser induced breakdown spectroscopy (2016)

Plasma temperature and electron density of iron in iron slag samples taken from a local plant is studied. Optimal experimental conditions were evaluated using Nd: YAG laser at 1064 nm. Some toxic elements were identified and quantitative measurements were also made. Plasma temperature and electron density were estimated using standard equations and well resolved iron spectral lines in the 229.06-358.11 nm region at 10, 20, 30 and 40 mJ laser pulse energy with 4.5 μs delay time. These parameters were found to increase with increase in laser pulse energy. The Boltzmann distribution and experimentally measured line intensities support the assumption that the laser-induced plasma was in local thermal equilibrium. It is worth mentioning that iron and steel sector generates tons of solid waste and residues annually containing variety of contaminants which can be harmful to the environment and therefore knowledge, proper analysis and investigation of such iron slag is important.
Phase Equilibria of HFC Mixtures:  Binary Mixtures of Trifluoromethane + 1,1-Difluoroethane and Trifluoromethane + 1,1,1-Trifluoroethane at 283.15 and 293.15 K (2002)

Isothermal vapor−liquid equilibria for the binary mixtures of trifluoromethane (R-23) + 1,1-difluoroethane (HFC-152a) and trifluoromethane + 1,1,1-trifluoroethane (HFC-143a) were measured at 283.15 and 293.15 K. The experiments were carried out with a circulation-type equilibrium apparatus with the measurement of temperature, pressure, and the compositions of the liquid and vapor phases. The experimental data were correlated with the Peng−Robinson equation of state using the Wong and Sandler mixing rules and the Carnahan−Starling−Desantis (CSD) equation of state. Calculated results with these equations showed good agreement with the experimental data, but the Peng−Robinson equation of state gave more accurate predictions for the binary systems. Azeotropic behavior has not been found in either of these mixtures.
0170 Shifting to Earlier Sleep Times during Sleep Extension: The Impact on Total Sleep Time and Self-Reported Fatigue and Stress (2018)

Sleep extension is associated with a positive impact on immune function, cognitive performance, and mood. However, it also requires either an earlier bedtime, later arise time, or both. In this study, we utilized natural variability in sleep bedtimes in a healthy population participating in a 7-day sleep extension paradigm to explore the impact of shifting bedtimes. Twenty-seven healthy adults (20–39 yrs) participated in a two-phase study. During Phase 1, habitual bedtimes were recorded via actigraphy at home for two weeks. Phase 2 consisted of an in-lab portion with two conditions: 1) Sleep Extension: 7 consecutive nights (2100 bedtime, 10h time-in-bed), and 2) Sleep Deprivation (40h of total deprivation). Sleep shift times were assessed by quantifying the degree to which habitual bedtimes were shifted to 2100 in the sleep extension condition. Self-reported fatigue and stress were assessed using the Fatigue Visual Analogue Scale (FVAS) and Stress Visual Analogue Scale (SVAS). Greater shifts in habitual bedtime was associated with higher self-reported fatigue (but not stress [r=0.19, p=0.34]) after one subsequent night of sleep deprivation (r=0.41, p=0.03). Sleep shift time was not linked to total sleep time (TST) during the sleep extension phase (r=-0.20, p=0.32). Additionally, sleep shift time was not correlated with self-reported fatigue (r=0.42, p=0.83) or stress (r=0.05, p=0.82) after 7 nights of sleep extension. Shifts in habitual bedtimes do not appear to impact total sleep time or self-reported fatigue and stress in healthy adults undergoing sleep extension in a laboratory setting. However, we found that greater shifts in habitual bedtimes prior to sleep manipulation were associated with greater self-reported fatigue after a night of sleep deprivation. These results suggest that shifting bedtimes may have an impact on fatigue that is unmasked during sleep deprivation. Department of Defense Military Operational Medicine Research Program (MOMRP).
Control of a VSC-diode bridge combination for industrial rectifier applications (2014)

This paper discusses the suitability of a voltage source converter (VSC)-diode bridge combination as a rectifier in industrial applications. This particular rectifier arrangement consists of a full rated diode bridge rectifier and a partially rated two-level voltage source auxiliary converter. This combination helps achieve power conversion at medium voltage with low voltage switching devices, improve current quality through pulse width modulation (PWM) operation and smoothen the dc-link voltage by transferring the ripples to the dc-side of the auxiliary converter. Moreover, this topology can be extended by replacing the two-level auxiliary converter with a multilevel converter such as diode-clamped three-level converter to achieve higher voltage levels and better power quality requirements. Apart from that, there is a possibility of interfacing energy storage devices through the dc-side of the auxiliary converter to mitigate power fluctuations. Control strategies and modulation techniques that are specific to the topology for different operating scenarios are simulated in MATLAB/Simulink. Simulation results are presented to verify the operation of the proposed topology.
Analysis of penalized likelihood reconstruction for PET kinetic quantification (2007)

Quantification of tracer kinetics using dynamic positron emission tomography provides important information for understanding the physiological and biochemical processes in humans and animals. The common procedure is to reconstruct a sequence of dynamic images first, and then apply kinetic analysis to the time activity curve of a region of interest derived from the reconstructed images. Obviously, the choice of image reconstruction method and its parameters affect the accuracy of the time activity curve and hence the estimated kinetic parameters. This paper analyzes the effects of penalized likelihood image reconstruction on tracer kinetic parameter estimation. Approximate theoretical expressions are derived to study the bias, variance, and ensemble mean squares error of the estimated kinetic parameters. Computer simulations show that these formulae predict correctly the changes of these statistics as functions of the regularization parameter. It is found that the choice of the regularization parameter has a significant impact on kinetic parameter estimation, indicating proper selection of image reconstruction parameters is important for dynamic PET. A practical method has also been developed to use the theoretical formulae to guide the selection of the regularization parameter in dynamic PET image reconstruction.
A Serum Biomarker Panel Can Accurately Identify Mucosal Ulcers in Patients With Crohn’s Disease (2022)

The EHI was independently associated with ulcer size and accurately identified large or very large ulcers. A cutoff of 50 points can reliably rule in mucosal ulcers and allow for treatment adjustment. A cutoff of 20 points can reliably rule out mucosal ulcers and signal completion of treatment adjustment algorithms.
EUV mask pattern inspection for memory mask fabrication in 45-nm node and below (2006)

As the design rule continues to shrink towards 45 nm node and beyond, the lithographers need the new technologies such as immersion lithography and EUV lithography. Also the inspection specification on the printed reticle defects is becoming even more challenging for the reticles used in both lithography methods. The main purpose of this study is to investigate the pattern defect detection capability on EUV mask with the memory design patterns of 45 nm node and below in the DUV reticle inspection systems at our mask-shop and to compare those results with the absorber defect specification from the EUV lithography simulation in those design rules. In addition, we investigate the inspection capability on the pattern defects with the test optical mask designed in 45 nm node and below for the immersion lithography and compare the defect detection ability on the EUV mask and the optical mask in the current DUV reticle inspection equipment.
Recombinant Human Peroxisomal Targeting Signal Receptor PEX5 (1999)

Import of matrix proteins into peroxisomes requires two targeting signal-specific import receptors, Pex5p and Pex7p, and their binding partners at the peroxisomal membrane, Pex13p and Pex14p. Several constructs of human PEX5 have been overexpressed and purified by affinity chromatography in order to determine functionally important interactions and provide initial structural information. Sizing chromatography and electron microscopy suggest that the two isoforms of the human PTS1 receptor, PEX5L and PEX5S, form homotetramers. Surface plasmon resonance analysis indicates that PEX5 binds to the N-terminal fragment of PEX14-(1-78) with a very high affinity in the low nanomolar range. Stable complexes between recombinant PEX14-(1-78) and both the full-length and truncated versions of PEX5 were formed in vitro. Analysis of these complexes revealed that PEX5 possesses multiple binding sites for PEX14, which appear to be distributed throughout its N-terminal half. Coincidentally, this part of the molecule is also responsible for oligomerization, whereas the C-terminal half with its seven tetratricopeptide repeats has been reported to bind PTS1-proteins. A pentapeptide motif that is reiterated seven times in PEX5 is proposed as a determinant for the interaction with PEX14.
Adding art to STEM (2016)

The Communications Web site, http://cacm.acm.org, features more than a dozen bloggers in the BLOG@CACM community. In each issue of Communications , we'll publish selected posts or excerpts. twitter Follow us on Twitter at http://twitter.com/blogCACM http://cacm.acm.org/blogs/blog-cacm Perry R. Cook considers the career path that led him to STEAM.
MCH-12 Monolithically integration of GaN light-emitting diode and Si substrate with AlN/GaN superlattice as interlayer(Micro/Nanomechatronics IV,Technical Program of Oral Presentations) (2009)

InGaN/GaN p-i-n junction was deposited on GaN/Si template with AlN/GaN supperlattice as interlayer by molecular beam epitaxy. Different surface microstructure of the p-GaN was affected by the amount of Mg flux. Light-emitting diode was fabricated from the p-i-n junction. The crystal properties of InGaN/GaN p-i-n junction and the related light-emitting diode properties were investigated.