gebhart/patrepeval huggingface dataset:
In Silico and Structural Analyses Demonstrate That Intrinsic Protein Motions Guide T Cell Receptor Complementarity Determining Region Loop Flexibility (2018)

T-cell immunity is controlled by T cell receptor (TCR) binding to peptide major histocompatibility complexes (pMHCs). The nature of the interaction between these two proteins has been the subject of many investigations because of its central role in immunity against pathogens, cancer, in autoimmunity, and during organ transplant rejection. Crystal structures comparing unbound and pMHC-bound TCRs have revealed flexibility at the interaction interface, particularly from the perspective of the TCR. However, crystal structures represent only a snapshot of protein conformation that could be influenced through biologically irrelevant crystal lattice contacts and other factors. Here, we solved the structures of three unbound TCRs from multiple crystals. Superposition of identical TCR structures from different crystals revealed some conformation differences of up to 5 Å in individual complementarity determining region (CDR) loops that are similar to those that have previously been attributed to antigen engagement. We then used a combination of rigidity analysis and simulations of protein motion to reveal the theoretical potential of TCR CDR loop flexibility in unbound state. These simulations of protein motion support the notion that crystal structures may only offer an artifactual indication of TCR flexibility, influenced by crystallization conditions and crystal packing that is inconsistent with the theoretical potential of intrinsic TCR motions.
Using the Time-Domain Characterization for Estimation Continuous Blood Pressure via Neural Network Method (2017)

The new method with back-propagation neural network is expected to be capable of continuous measurement of blood pressures with noninvasive, cuffless strain blood pressure sensor. The eight time-domain characterizations estimate systolic blood pressure and diastolic blood pressure via BPNN leading to a satisfactory accuracy of the BP sensor. The BP sensor is used on human wrist to collect the continuously pulse signal for measuring blood pressures. To assist the sensor, a readout circuit is devised with a Wheatstone bridge, amplifier, filter, and a digital signal processor. The results of SBP and DBP are 4.27±4.98 mmHg and 3.86±5.35 mmHg, respectively. The errors of blood pressure pass the criteria for Association for the Advancement of Medical Instrumentation (AAMI) method 2 and the British Hypertension Society (BHS) Grade B.
Development of a Model Predictive Airpath Controller for a Diesel Engine on a High-Fidelity Engine Model with Transient Thermal Dynamics (2022)

This paper presents the results of a model predictive controller (MPC) development for diesel engine air-path regulation. The control objective is to track the intake manifold pressure and exhaust gas recirculation (EGR) rate targets by manipulating the EGR valve and variable geometry turbine (VGT) while satisfying state and control constraints. The MPC controller is designed and verified using a high-fidelity engine model in GT-Power. The controller exploits a low-order rate-based linear parameter-varying (LPV) model for prediction which is identified from transient response data generated by the GT-Power model. It is shown that transient engine thermal dynamics influence the airpath dynamics, specifically the intake manifold pressure response, however, MPC demonstrates robustness against inaccuracies in modeling these thermal dynamics. In particular, we show that MPC can be successfully implemented using a rate-based prediction model with two inputs (EGR and VGT positions) identified from data with steady-state wall temperature dynamics, however, closed-loop performance can be improved if a prediction model (i) is identified from data with transient thermal dynamics, and (ii) has the fuel injection rate as extra model input. Further, the MPC calibration process across the engine operating range to achieve improved performance is addressed. As the MPC calibration is shown to be sensitive to the operating conditions, a fast calibration process is proposed.
PLGA/PEG Nanoparticles Loaded with Cyclodextrin-Peganum harmala Alkaloid Complex and Ascorbic Acid with Promising Antimicrobial Activities (2022)

Antimicrobial drugs face numerous challenges, including drug resistance, systemic toxic effects, and poor bioavailability. To date, treatment choices are limited, which warrants the search for novel potent antivirals, including those extracted from natural products. The seeds of <i>Peganum harmala</i> L. (<i>Zygophyllaceae</i> family) have been reported to have antimicrobial, antifungal, and anticancer activities. In the present study, a 2-hydroxy propyl-β-cyclodextrin (HPβCD)/harmala alkaloid-rich fraction (HARF) host-guest complex was prepared using a thin-film hydration method to improve the water solubility and bioavailability of HARF. The designed complex was then co-encapsulated with ascorbic acid into PLGA nanoparticles coated with polyethylene glycol (HARF-HPßCD/AA@PLGA-PEG NPs) using the W/O/W multiple emulsion-solvent evaporation method. The average particle size, PDI, and zeta potential were 207.90 ± 2.60 nm, 0.17 ± 0.01, and 31.6 ± 0.20 mV, respectively. The entrapment efficiency for HARF was 81.60 ± 1.20% and for ascorbic acid was 88 ± 2.20%. HARF-HPßCD/AA@PLGA-PEG NPs had the highest antibacterial activity against <i>Staphylococcus aureus</i> and <i>Escherichia coli</i> (MIC of 0.025 mg/mL). They also exhibited high selective antiviral activity against the H1N1 influenza virus (IC50 2.7 μg/mL) without affecting the host (MDCK cells). In conclusion, the co-encapsulation of HPCD-HARF complex and ascorbic acid into PLGA-PEG nanoparticles significantly increased the selective H1N1 killing activity with minimum host toxic effects.
Motor Carrier Electromagnetic Noise Caused by PWM Pulse Modifying Technique of DC Bus Current Detection (2019)

This paper describes the carrier electromagnetic noise caused by PWM pulse modifying technique of DC bus current detection. It is cleared from theoretical analysis that the influence factors of carrier harmonics are DC voltage, self-inductance and pulse modifying width. As estimated the carrier electromagnetic noise, we propose the new evaluation index of radiation area electromagnetic force to multiply the radial electromagnetic force and gap surface area. The proposed evaluation index can be estimated the increase of carrier electromagnetic noise within 1.5dB error by experiment. Also, the one phase pulse modifying method to reduce the carrier electromagnetic noise is proposed. The effect of this method was demonstrated in the experiment.
Neurofilaments are non-essential elements of toxicant-induced reductions in fast axonal transport: pulse labeling in CNS neurons. (2000)

Acrylamide (ACR) and g-diketones (g-DK) produce distal sensory-motor neuropathy in a variety of species, including humans. The specific molecular site and mechanism of toxicant action leading to specific morphological and behavioral abnormalities requires definition. The relative roles of fast anterograde axonal transport and neurofilaments (NF) are investigated using optic nerves of mice, with and without axonal neurofilaments. Segmental analysis, following pulse labeling with 3H-leucine into the vitreous body, was used to detect changes in fast anterograde transport in the optic nerve and tract. Single injections of ACR significantly reduced the quantity of radiolabeled proteins transported in both transgenic (lacking NF) and non-transgenic (containing NF) mice by 68.4% and 46.2%, respectively. Similarly, single injections of 2,5-hexanedione (2,5-HD) reduced the quantity of radiolabeled transport in transgenic and non-transgenic mice by 55.2% and 47.1%, respectively. Equimolar doses of propionamide and 3,4-hexanedione (non-neurotoxic analogues of ACR and 2,5-HD, respectively) produced no changes in the quantity or apparent rate of optic nerve transport. Additionally, no differences in quantity or apparent rate of transport between transgenic and non-transgenic animals were observed under control or experimental conditions. Therefore, ACR and 2,5-HD reduce the quantity of fast anterograde axonal transport in mouse CNS axons in a comparable amount to previously reported reductions in rat PNS axons. The absence of axonal neurofilaments had no effect on normal fast transport. Furthermore, the presence or absence of neurofilaments did not alter the effect of these toxicants on fast axonal transport. We conclude that toxicant-induced reductions in fast axonal transport are unrelated to ACR and g-diketone effects on NF or their accumulation.
Role of Atomic Structure on Exciton Dynamics and Photoluminescence in NIR Emissive InAs/InP/ZnSe Quantum Dots (2022)

The development of bright, near-infrared-emissive quantum dots (QDs) is a necessary requirement for the realization of important new classes of technology. Specifically, there exist significant needs for brighter, heavy metal-free, near-infrared (NIR) QDs for applications with high radiative efficiency that span diverse applications, including down-conversion emitters for high-performance luminescent solar concentrators. We use a combination of theoretical and experimental approaches to synthesize bright, NIR luminescent InAs/InP/ZnSe QDs and elucidate fundamental material attributes that remain obstacles for development of near-unity NIR QD luminophores. First, using Monte Carlo ray tracing, we identify the atomic and electronic structural attributes of InAs core/shell, NIR emitters, whose luminescence properties can be tailored by synthetic design to match most beneficially those of high-performance, single-band-gap photovoltaic devices based on important semiconductor materials, such Si or GaAs. Second, we synthesize InAs/InP/ZnSe QDs based on the optical attributes found to maximize LSC performance and develop methods to improve the emissive qualities of NIR emitters with large, tunable Stokes ratios, narrow emission linewidths, and high luminescence quantum yields (here reaching 60 ± 2%). Third, we employ atomistic electronic structure calculations to explore charge carrier behavior at the nanoscale affected by interfacial atomic structures and find that significant exciton occupation of the InP shell occurs in most cases despite the InAs/InP type I bulk band alignment. Furthermore, the density of the valence band maximum state extends anisotropically through the (111) crystal planes to the terminal InP surfaces/interfaces, indicating that surface defects, such as unpassivated phosphorus dangling bonds, located on the (111) facets play an outsized role in disrupting the valence band maximum and quenching photoluminescence.
The application of parameter identification methods with competing systems to model a human interface device (2003)

Identification methods are applied to experimental data (hand motion) from a design study on a human interface system. The internal model of the Kalman filter employed for the state estimation implicitly utilizes two competing systems (involving an agonist and an antagonist human muscle actuator). The parameters (parsimonious representation) are obtained by minimizing the sums of the squares of the output error residuals, which are tested for whiteness. This technique is a generalization of a method borrowed from pharmacological studies.
Measurement of CP observables in $B^{\pm} to D^{(*)}K^{\pm}$ and $B^{\pm} \to D^{(*)}\pi^{\pm}$ decays using two-body D final states (2020)

Abstract: Measurements of CP observables in B± → D(*)K± and B± → D(*)π± decays are presented, where D(∗) indicates a neutral D or D∗ meson that is an admixture of meson and anti-meson states. Decays of the D(∗) meson to the Dπ0 and Dγ final states are partially reconstructed without inclusion of the neutral pion or photon. Decays of the D meson are reconstructed in the K±π∓, K+K−, and π+π− final states. The analysis uses a sample of charged B mesons produced in proton-proton collisions and collected with the LHCb experiment, corresponding to integrated luminosities of 2.0, 1.0, and 5.7 fb−1 taken at centre-of-mass energies of 7, 8, and 13 TeV, respectively. The measurements of partially reconstructed B± → D(*)K± and B± → D(∗)π± with D → K∓π± decays are the first of their kind, and a first observation of the B± → Dπ0D∗π± decay is made with a significance of 6.1 standard deviations. All CP observables are measured with world-best precision, and in combination with other LHCb results will provide strong constraints on the CKM angle γ.
In Vitro Reassortment between Endemic H1N2 and 2009 H1N1 Pandemic Swine Influenza Viruses Generates Attenuated Viruses (2012)

The pandemic H1N1 (pH1N1) influenza virus was first reported in humans in the spring of 2009 and soon thereafter was identified in numerous species, including swine. Reassortant viruses, presumably arising from the co-infection of pH1N1 and endemic swine influenza virus (SIV), were subsequently identified from diagnostic samples collected from swine. In this study, co-infection of swine testicle (ST) cells with swine-derived endemic H1N2 (MN745) and pH1N1 (MN432) yielded two reassortant H1N2 viruses (R1 and R2), both possessing a matrix gene derived from pH1N1. In ST cells, the reassortant viruses had growth kinetics similar to the parental H1N2 virus and reached titers approximately 2 log(10) TCID(50)/mL higher than the pH1N1 virus, while in A549 cells these viruses had similar growth kinetics. Intranasal challenge of pigs with H1N2, pH1N1, R1 or R2 found that all viruses were capable of infecting and transmitting between direct contact pigs as measured by real time reverse transcription PCR of nasal swabs. Lung samples were also PCR-positive for all challenge groups and influenza-associated microscopic lesions were detected by histology. Interestingly, infectious virus was detected in lung samples for pigs challenged with the parental H1N2 and pH1N1 at levels significantly higher than either reassortant virus despite similar levels of viral RNA. Results of our experiment suggested that the reassortant viruses generated through in vitro cell culture system were attenuated without gaining any selective growth advantage in pigs over the parental lineages. Thus, reassortant influenza viruses described in this study may provide a good system to study genetic basis of the attenuation and its mechanism.
Latent, Thermally Activated Organic Catalysts for the On‐Demand Living Polymerization of Lactide (2005)

It's all about control: Alcohol adducts of stable N-heterocyclic carbenes function as excellent single-component catalysts/initiators for the ring-opening polymerization of lactide (see scheme). This polymerization can be reversibly terminated simply by modulating the temperature. The use of multifunctional macroinitiators enables the synthesis of more complex polymer architectures. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z500723_s.pdf or from the author. 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.
Inhibiting Isoprenylation Suppresses FcεRI-Mediated Mast Cell Function and Allergic Inflammation (2023)

IgE-mediated mast cell activation is a driving force in allergic disease in need of novel interventions. Statins, long used to lower serum cholesterol, have been shown in multiple large-cohort studies to reduce asthma severity. We previously found that statins inhibit IgE-induced mast cell function, but these effects varied widely among mouse strains and human donors, likely due to the upregulation of the statin target, 3-hydroxy-3-methylgutaryl-CoA reductase. Statin inhibition of mast cell function appeared to be mediated not by cholesterol reduction but by suppressing protein isoprenylation events that use cholesterol pathway intermediates. Therefore, we sought to circumvent statin resistance by targeting isoprenylation. Using genetic depletion of the isoprenylation enzymes farnesyltransferase and geranylgeranyl transferase 1 or their substrate K-Ras, we show a significant reduction in FcεRI-mediated degranulation and cytokine production. Furthermore, similar effects were observed with pharmacological inhibition with the dual farnesyltransferase and geranylgeranyl transferase 1 inhibitor FGTI-2734. Our data indicate that both transferases must be inhibited to reduce mast cell function and that K-Ras is a critical isoprenylation target. Importantly, FGTI-2734 was effective in vivo, suppressing mast cell-dependent anaphylaxis, allergic pulmonary inflammation, and airway hyperresponsiveness. Collectively, these findings suggest that K-Ras is among the isoprenylation substrates critical for FcεRI-induced mast cell function and reveal isoprenylation as a new means of targeting allergic disease.
Ultrasound holography for noninvasive imaging of buried defects and interfaces for advanced interconnect architectures (2009)

Imaging high resolution subsurface defects nondestructively in advanced interconnect structures and devices is a challenge and no known metrology tools are available to identify such defects in a nondestructive way at nanometer level. Monitoring these defects necessitate the understanding of their growth mechanism of these interconnects as well as defect formation. We report here the application of scanning near field ultrasound holography by imaging buried defects in copper interconnects and low-K dielectric materials. Defects in these copper lines such as voids and delaminations appear as regions of dark contrast in ultrasound holography imaging due to large acoustic impedance mismatch at the voids. Identification of these buried defects in these interconnect architectures in a nondestructive way will open up unique opportunities in using this technique to detect subsurface defects and material imperfections.
Interstitial Lung Disease: NHLBI Workshop on the Primary Prevention of Chronic Lung Diseases (2014)

Population-based, longitudinal studies spanning decades linking risk factors in childhood, adolescence and early adulthood to incident clinical interstitial lung disease (ILD) events in late adulthood have not been performed. In addition, no observational or randomized clinical trials have been conducted; therefore, there is presently no evidence to support the notion that reduction of risk factor levels in early life prevents ILD events in adult life. Primary prevention strategies are host-directed interventions designed to modify adverse risk factors (i.e., smoking) with the goal of preventing the development of ILD, whereas primordial prevention for ILD can be defined as the elimination of external risk factors (i.e., environmental pollutants). As no ILD primary prevention studies have been previously conducted, we propose that research studies that promote implementation of primary prevention strategies could, over time, make a subset of ILD preventable. Herein, we provide a number of initial steps required for the future implementation of prevention strategies; this statement discusses the rationale and available evidence that support potential opportunities for primordial and primary prevention, as well as fertile areas for future research of preventive intervention in ILD.
Effects of Interferon, Ribavirin, and Iminosugar Derivatives on Cells Persistently Infected with Noncytopathic Bovine Viral Diarrhea Virus (2004)

Persistent infection with hepatitis C virus (HCV) is a major cause of chronic hepatitis in humans. In chronic carriers, the viral infection induces liver damage that predisposes the patient for cirrhosis and can lead to hepatocellular carcinoma. Current chemotherapies are limited to alpha interferon (IFN-alpha) used either alone or in combination with ribavirin (RBV). In addition to its limited efficacy, this treatment is frequently poorly tolerated because of its side effects. The urgently needed development of new drugs is made difficult by the lack of an in vitro or in vivo infectivity model, and no cell line has been found so far to reliably and reproducibly support HCV infection. For this reason, the closely related pestivirus bovine viral diarrhea virus (BVDV) has sometimes been used as a surrogate in vitro infectivity model. In this study we used an MDBK cell line persistently infected with noncytopathic BVDV to assess the antiviral effect of IFN-alpha and RBV, the two drugs currently in clinical use against HCV. The same system was then used to evaluate the potential of two classes of iminosugar derivates to clear noncytopathic BVDV infection from MDBK cells. We show that treatment with long-alkyl-chain deoxynojirimycin derivatives, which are inhibitors of the endoplasmic reticulum (ER)-resident alpha-glucosidases, can greatly reduce the amount of secreted enveloped viral RNA. Long-alkyl-chain deoxygalactonojirimycin derivatives, which do not inhibit ER alpha-glucosidases, were less potent but still more effective in this system than IFN-alpha or ribavirin.
LTE Uplink icin DFT-tabanli kanal kestirimcide sizma azaltimi Leakage reduction in DFT-based channel estimation for LTE Uplink (2010)

Abstract Channel estimation is an integral part of receiver designs in co-herent OFDM systems. Moreover channel estimation is a chal-lenging problem in wireless systems, due to time variation ofthe multipath channel. In this paper, a time domain channelestimation method for rapidly time varying channel in LTE Up-link, which we have been proposed previously is further studiedin the presence of guard band and multiple access. Since thepresence of guard band and multiple access results in leakage,we therefore propose a new approach to reduce leakage on thenumber of taps which are to be tracked by Kalman Filter. 1. Giris¸ Dik frekans bolmeli c¨ ¸ogullama (OFDM) ve OFDM-tabanli˘modulasyon ve c¨ ¸oklu eris¸im teknikleri (OFDMA ve SC-FDMA gibi) frekans sec¸ici kanallarda veri iletis¸imi kabiliyeti,mukemmel spektral verimlili¨ ˘gi, y ¨uksek de ˘gis ¸kenlige sahip˘kanal ve c¸evresel s¸artlara uyum saglayabilmesi gibi˘ ¨ozelliklerinedeniyle c¸ok ilgi c¸ekmektedir. Ozellikle, kullanicilarin kanal¨tecr¨ubesine dayali olarak alttas ¸iyicilarin kullanicilara tahsisininuyumlu ve optimal planlama ile yapilabilmesi OFDM-benzerimodulasyon tekniklerinin¨ ust¨ ¨un ozelliklerindendir.¨Diger bir c˘ ¸ok evreuyumlu sayisal kablosuz alicilar gibi,kanal kestirim evreuyumlu OFDM-benzeri sistemler alicitasariminin ayrilmaz bir parc¸asidir. C¸okyollu kanalin zamanla
Early life stress disrupts intestinal homeostasis via NGF-TrkA signaling (2019)

Early childhood is a critical period for development, and early life stress may increase the risk of gastrointestinal diseases including irritable bowel syndrome (IBS). In rodents, neonatal maternal separation (NMS) induces bowel dysfunctions that resemble IBS. However, the underlying mechanisms remain unclear. Here we show that NMS induces expansion of intestinal stem cells (ISCs) and their differentiation toward secretory lineages including enterochromaffin (EC) and Paneth cells, leading to EC hyperplasia, increased serotonin production, and visceral hyperalgesia. This is reversed by inhibition of nerve growth factor (NGF)-mediated tropomyosin receptor kinase A (TrkA) signalling, and treatment with NGF recapitulates the intestinal phenotype of NMS mice in vivo and in mouse intestinal organoids in vitro. Mechanistically, NGF transactivates Wnt/β-catenin signalling. NGF and serotonin are positively correlated in the sera of diarrhea-predominant IBS patients. Together, our findings provide mechanistic insights into early life stress-induced intestinal changes that may translate into treatments for gastrointestinal diseases.