gebhart/patrepeval huggingface dataset:
Thermal Magnetic Field Noise Limits Resolution in Transmission Electron Microscopy (2013)

The resolving power of an electron microscope is determined by the optics and the stability of the instrument. Recently, progress has been obtained towards subångström resolution at beam energies of 80 kV and below but a discrepancy between the expected and achieved instrumental information limit has been observed. Here we show that magnetic field noise from thermally driven currents in the conductive parts of the instrument is the root cause for this hitherto unexplained decoherence phenomenon. We demonstrate that the deleterious effect depends on temperature and at least weakly on the type of material.
Formation of Specially Shaped Plating Film by Nickel-Copper Alloy Electrodeposition (2022)

In this study, Ni-Cu electrodeposited film with three-dimensional structures was formed by controlling potential using a plating solution which is a mixture of Ni amidosulfate and Cu sulfate. When the concentration ratio of Ni amidosulfate to Cu sulfate was set to 150-450:15 (g/L) and the potential was set to -1.0 to -1.5 V, the electrodeposited film had dendritic morphology.
Modeling of the stress-strain state for a disk and a shaft from different Ni-based alloys during welding under shear pressing (2018)

The stress-strain state in a disk and a shaft made of different heat-resistant Ni-based alloys during pressure welding is analyzed by the finite element method. The disk and the shaft have a complimentary cone shape, and during welding the shaft is inserted into the disk or in-serted and simultaneously rotated. In the first case, a single component shear deformation is re-alized, while in the second case, one has a two-component shear deformation in the welding zone. The cone angle of 5° can be recommended, because in this case the plastic deformation in the welding zone is about 3%, which is typically sufficient for obtaining a reliable joint.
Resonant Acoustic MEMS Wake-Up Switch (2018)

We have designed a novel microelectromechanical systems (MEMS) resonant acoustic wake-up switch which is actuated by ambient sound waves, using zero power while waiting for a signal at its resonant frequency and less than 10 nW when the signal is detected. The system uses a battery to charge a capacitor through MEMS switches activated only by the target signals. The sensor is of rotational design allowing it to be insensitive to linear vibration and static gravity forces. Analysis and experimental results maximizing the Q of these resonators in air are presented. A simple, novel fabrication process is presented which uses silicon-on-insulator bonded wafers and still provides metal-metal electrical contacts. These devices have successfully detected 80-Hz sound as low as 0.005 Pa rms (48-dB SPL // 20 μ Pa) from a generator.
D-109 Defining a potent new class of latency reversing agents devoid of toxicity and detrimental cell activation that enhance CTL/NK cell killing (2018)

Despite long-term administration of antiretroviral therapy (ART), HIV-1 persists in a broadly distributed latent reservoir mainly comprised of resting CD4+ T cells. Cells harboring latent provirus typically display little to no HIV-1 gene expression and thus remain invisible to the immune system. To achieve a durable sustained viral remission in HIV-infected patients off ART (a functional cure), it will be important to both “reduce the size of the reservoir and to control viral rebound by eliciting an effective immune response capable of restraining viral spread from the smaller reservoir. This approach will likely require the combined use of potent and safe latency-reversing agent (LRA) and a therapeutic HIV vaccine. Our recent studies have shown that activators of the AKT/mTOR pathway form a promising group of LRAs. Our interest has focused on two small molecules, SB-216763 and Tideglusib that commonly inhibit glycogen synthase kinase-3 (GSK-3). This inhibition triggers a metabolic shift to glycolysis and results in sequential activation of mTORC2, AKT, and mTORC1. Both compounds are known to have high tissue penetration including the brain. We found that these GSK-3 inhibitors potently activate latent HIV-1 in both a tissue-based model of HIV latency formed in primary CD4 T cells, and in CD4 T cells isolated from HIV-infected patients. In some experiments, these agents are more potent than anti-CD3/anti-CD28 antibodies even though the GSK-3 inhibitors do not appear to induce T cell activation (measured by changes in CD69 and CD25 expression). Finally, in contrast to the undesirable compromise of CTL/NK function associated with many first generation LRAs (PKC activators, HDAC inhibitors), the GSK-3 inhibitors actually enhance CTL and NK cell effector function. In summary, our findings reveal GSK-3 inhibitors as an interesting new class of potent, safe, non-cell activating LRAs. Next, it will be key to define their activity in vivo using SIV-infected macaques on suppressive ART. The fact that tideglusib is already in phase II human trials for myotonic dystrophy and autism could accelerate its ultimate testing as an LRA in HIV-infected patients.
Cytoplasmic Signalling by Major Histocompatibility Class-I Proteins Modulates Synaptic Glutamate Receptors (2023)

Abstract AMPA-type glutamate receptors (AMPARs) and major histocompatibility complex class I (MHC-I) proteins regulate synaptic signalling. Here we describe the importance of the cytoplasmic tail of MHC-I for its role in the central nervous system (CNS) in synaptic signalling and the modulation of synaptic glutamate receptor expression. We demonstrate that Y321F mutation of the conserved cytoplasmic tyrosine in MHC-I affects expression of the AMPAR, GluA2/3, and alters phosphorylation of a number of kinases, including Fyn, Lyn, p38, ERK1/2, JNK1/2/3, and p70 S6 kinase. These data elucidate the important role of MHC-1 on AMPAR function and modifications to the cytoplasmic tail of MHC-1 can alter synaptic strength, plasticity and learning and memory.
Design and control of femtosecond lasers for optical clocks and the synthesis of low-noise optical and microwave signals (2003)

This paper describes recent advances in the design and control of femtosecond laser combs for their use in optical clocks and in the synthesis of low-noise microwave and optical signals. The authors present a compact and technically simple femtosecond laser that directly emits a broad continuum and shows that it can operate continuously on the timescale of days as the phase-coherent "clockwork" of an optical clock. They further demonstrate phase locking of an octave-spanning frequency comb to an optical frequency standard at the millihertz level. As verified through heterodyne measurements with an independent optical frequency standard, this provides a network of narrow optical modes with linewidths at the level of /spl les/150 Hz, presently limited by measurement noise. Finally, they summarize their progress in using the femtosecond laser comb to transfer the stability and low phase-noise optical oscillators to the microwave domain.
INCREASED FREE PLASMA CORTICOSTERONE AND ADRENAL HYPERACTIVITY ASSOCIATED WITH GRAFT-VERSUS-HOST DISEASE (1983)

This study profiles adrenal function in 14-day-old neonatal and adult rats with graft-versus-host disease (GVHD). Measurements of adrenal function included total serum corticosterone, the relative percentage of free corticosterone (a measure of biologically active hormone), adrenal cholesterol content, adrenal weights, and adrenal histology. Diseased animals in both age groups displayed a shift from the protein-bound to the free corticosterone fraction, with, surprisingly, no change in total serum corticosterone titers. We discuss the possibility that such a shift toward the biologically active, free-hormone pool results in a physiologic hyperglucocorticoidism that might contribute to the progress of GVHD. Compared with littermate controls, diseased adults had enlarged adrenals. In neonates with GVHD, no adrenal hypertrophy was evident, yet decreased adrenal cholesterol content and associated depletion of adrenal lipid droplets--evidence of adrenal hyperactivity--were identified. The GVHD must be responsible for the observed alterations in adrenal function because treatment of affected animals with alloantiserum directed against donor cells halted the disease and elevated the cholesterol content toward control levels. The possible contribution of adrenal dysfunction to the pathogenesis of secondary manifestations of GVHD is discussed.
Abstract 1871: Novel conditionally active bispecific HER2 x CD3 T cell engager targeting solid tumors (2023)

Abstract Human epidermal growth factor receptor 2 (HER2) is overexpressed in multiple cancers and is associated with poor prognosis. Despite the outstanding improvement in survival with the introduction of anti-HER2 therapies, therapeutic benefit is limited by many resistance mechanisms and toxicities. Clinical trials of therapeutics redirecting T cell activity to HER2+ tumors have highlighted the apparent risk of on-target, off-tumor adverse effects for this target, as HER2 is also expressed in normal epithelia. Using BioAtla’s Conditionally Active Biologic (CAB) platform, we have developed a HER2 x CAB-CD3 bispecific antibody that was engineered to bind with high affinity to the CD3 receptor and induce T cell activation under conditions that mimic the tumor microenvironment, but with reduced binding in physiological conditions. Both in vitro and in vivo efficacy data for a CAB T cell engager (TCE) targeting HER2 will be presented. Our data will demonstrate that HER2 x CAB-CD3 bispecific antibody promotes cytotoxicity of HER2+ cancer cells in vitro and induces complete regression of tumor growth in vivo. The HER2 x CAB-CD3 bispecific antibody has higher potency in inducing primary T cell activation measured by means of cytokine release and cancer cell cytotoxicity under acidic conditions compared to the non-CAB benchmark bispecific antibody. The generation of CAB bispecific antibodies with activity in the disease microenvironment minimizes on-target, off-tumor toxicities, thereby enabling higher potency-TCEs for targeting drug resistant, low expressing-HER2+ tumors. In summary, the use of CAB technology expands the universe of targets for drug development by generating a new class of potent CAB T-cell engagers with increased safety margin for potentially enhanced therapeutic indices in the clinic. Citation Format: Ana Paula Cugnetti, Haizhen Liu, Patricia McNeeley, Christina Wheeler, Matthew Lucas, Charles Xing, Solmarie Joyner, Kyrie Johnson, Kathryn Woodard, Wei Zhou, Cathy Chang, Gerhard Frey, William J. Boyle, Jay M. Short. Novel conditionally active bispecific HER2 x CD3 T cell engager targeting solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1871.
Cramér–Rao Lower Bound on AoA Estimation Using an RF Lens-Embedded Antenna Array (2018)

In this letter, we investigate the Cramér-Rao lower bound (CRLB) on angle of arrival (AoA) estimation of an RF lens-embedded antenna array. We first derive an expression for the received signal, in terms of intrinsic lens characteristics, using an RF lens-embedded antenna array. As the AoA changes, the received signal through the RF lens also changes in amplitude. This differentiates the RF lens-embedded antenna array from a conventional uniform linear array (ULA) without an RF lens. Based on this property, we next derive the CRLB on AoA estimation and confirm that the CRLB of an RF lens-embedded antenna array may be better than the CRLB for a conventional ULA in a certain desired range. The results can be used as a guideline for designing RF lens-embedded antenna arrays in fifth generation localization.
A Cautionary View of the use of Cyclic Prefix on CDMA Systems (2006)

We call attention to the fact that, under certain conditions, the signal-to-noise ratio loss for a given E <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</sub> /N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> value and the spectral efficiency degradation caused by cyclic prefix (CP) insertion may outweigh its benefits that is intersymbol interference elimination and better equalization when compared to an equivalent CDMA system without CP and with similar complexity frequency domain equalizer. In this paper, we analyze how such conditions (channel length and its frequency selectivity, E <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</sub> /N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> , number of active codes and equalizer length) affect the performance of both approaches in chip level equalization context
EDL-291, a novel isoquinoline, presents antiglioblastoma effects in vitro and in vivo (2012)

To investigate the effectiveness of EDL-291, a 6,7-dimethoxy-1-[4-(4-methoxypyridin-3-yl)benzyl]-1,2,3,4-tetrahydroisoquinoline dihydrochloride compound, in inhibiting the survival of glioblastoma in vitro and in vivo. Dose-response curves were generated to determine the EC50 in rat and human glioblastoma cell lines by treatment with different dilutions of EDL-291. To evaluate the architecture of the glioblastoma cells after treatment with EDL-291, the rat and human glioblastoma cells were stained with Mito Tracker Green FM. To determine whether autophagy was induced in EDL-291-treated glioblastoma cells, both rat and human glioblastoma cell lines were stained with acridine orange and light chain-3 immunoblots were performed. The efficacy of EDL-291 was monitored in vivo using a rat glioblastoma model. Rat glioblastoma cells were transplanted into an intracranial rat model, followed by infusions of saline, a low dose of EDL-291 (20 mg/kg for the first half hour, followed by 40 mg/kg EDL-291 in saline for 4 h), or a high dose of EDL-291 (60 mg/kg for the first half hour, followed by 90 mg/kg EDL-291 for 4 h). EDL-291 inhibits glioblastoma in vitro by destroying the mitochondria as shown with Mito Tracker Green FM. Acridine orange staining and light chain-3 immunoblots suggest that autophagy is induced when glioblastoma cells are treated with EDL-291. In vivo, a low dosage of EDL-291 is sufficient and effective in reducing glioblastoma tumor size. EDL-291 selectively induces cell death in rat and human glioblastoma cell lines by the induction of autophagy. EDL-291 exhibits antiglioblastoma effects both in vitro and in vivo.
Raman Spectra of Graphite Oxide and Functionalized Graphene Sheets (2007)

We investigate Raman spectra of graphite oxide and functionalized graphene sheets with epoxy and hydroxyl groups and Stone-Wales and 5-8-5 defects by first-principles calculations to interpret our experimental results. Only the alternating pattern of single-double carbon bonds within the sp2 carbon ribbons provides a satisfactory explanation for the experimentally observed blue shift of the G band of the Raman spectra relative to graphite. To obtain these single-double bonds, it is necessary to have sp3 carbons on the edges of a zigzag carbon ribbon.
Supplementary Figure Legends 1-5 from FGFR Genetic Alterations Predict for Sensitivity to NVP-BGJ398, a Selective Pan-FGFR Inhibitor (2023)

&lt;p&gt;PDF file - 139K&lt;/p&gt;
ChemInform Abstract: Oxocompostelline and Oxocularine, Structure and Synthesis. (1983)

Abstract Das aus (Ia) durch saure Debenzylierung erhaltene Phenol (Ib) sowie die analoge Dimethyl‐Verbindung (Ic) werden mit Dimsyl‐Natrium zu Gemischen aus (II) und (III) cyelisiert.
Complex Permittivity Extraction Method of a Thin Coating: EM Properties of a Graphene- Based Film on a Composite Layer (2018)

In the design of innovative nanomaterials for electromagnetic (EM) field absorption and shielding a crucial issue is the experimental characterization of the complex effective permittivity of non-uniform layered materials or electrically thin lossy layers. This paper proposes a technique to retrieve the complex relative permittivity of a thin lossy coating supported by a dielectric substrate through transmission/reflection measurements in a rectangular waveguide. A 2-port network de-embedding method is applied to remove the EM contribution of the substrate, and the so obtained scattering parameters of the film are used in the modified Nicolson- Ross-Weir algorithm to extract the complex permittivity. The method, validated by simulations, is applied to characterize a glass-fiber reinforced composite coated with a thin coating made of graphene nanoplatelets (GNPs)-polymer composite. Finally, the reflection properties of radar absorbing panels, constituted by several bilayers of GNP-coated GFRC are investigated in the range 12.4-18 GHz.
Juvenile mild traumatic brain injury elicits distinct spatiotemporal astrocyte responses (2019)

Mild-traumatic brain injury (mTBI) represents ~80% of all emergency room visits and increases the probability of developing long-term cognitive disorders in children. To date, molecular and cellular mechanisms underlying post-mTBI cognitive dysfunction are unknown. Astrogliosis has been shown to significantly alter astrocytes' properties following brain injury, potentially leading to significant brain dysfunction. However, such alterations have never been investigated in the context of juvenile mTBI (jmTBI). A closed-head injury model was used to study jmTBI on postnatal-day 17 mice. Astrogliosis was evaluated using glial fibrillary acidic protein (GFAP), vimentin, and nestin immunolabeling in somatosensory cortex (SSC), dentate gyrus (DG), amygdala (AMY), and infralimbic area (ILA) of prefrontal cortex in both hemispheres from 1 to 30 days postinjury (dpi). In vivo T2-weighted-imaging (T2WI) and diffusion tensor imaging (DTI) were performed at 7 and 30 dpi to examine tissue level structural alterations. Increased GFAP-labeling was observed up to 30 dpi in the ipsilateral SSC, the initial site of the impact. However, vimentin and nestin expression was not perturbed by jmTBI. The morphology of GFAP positive cells was significantly altered in the SSC, DG, AMY, and ILA up to 7 dpi that some correlated with magnetic resonance imaging changes. T2WI and DTI values were significantly altered at 30 dpi within these brain regions most prominently in regions distant from the impact site. Our data show that jmTBI triggers changes in astrocytic phenotype with a distinct spatiotemporal pattern. We speculate that the presence and time course of astrogliosis may contribute to pathophysiological processes and long-term structural alterations following jmTBI.
Helicobacter pylori Sialic Acid-Specific Surface Lectin Associated with Pathogenecity Island cag PAI (2015)

Normal 0 false false false MicrosoftInternetExplorer4 Helicobacter pylori bacterium causing gastritis, duodenitis, non-ulcer dyspepsia, adenocarcinoma, MALT lymphoma and now-a-days causing hepatocellular carcinoma and cholengiocarcinoma has been studied for its surface antigens. There are many virulence factors which have been studied since many years. Cag-PAI is the site for virulence and causes mixed infections. Sialic acid is a type of glycan which is a surface lectin associated with adherence to cell lines and other virulence factors studied in detail in H. pylori. Sialic acid dependency is been studied by performing heamagglutination studies. Sialidase activity was carried out by haemagglutination assay on H. pylori. Some strains were found Sia-dependent and many were found Sia-independent. CagA, VacA, VirD4 genes were identified by PCR in some strains and picB gene was not detected in the 19/20 strains analysed. Thus, it was found that Sia-dependent and Sia-independent strains of H. pylori were correlating with PCR strains analysed for virulent factors. H. pylori strains where in total 9/54 strains were Sia-dependent belonged to class I category and others to class II category. Haemagglutination and PCR analysis revealed pathogenecity in some strains. Therefore, if broad spectrum studies are carried out on a large scale, it will be very useful in the diagnosis and prognosis of the diseases caused by H. pylori. Keywords: H. pylori , haemagglutination, sialic acid, PCR, cag PAI Cite this Article Rupa Mulchandani, Hans-Olof Nilsson,  Torkel Wadstrom. Helicobacter pylori Sialic Acid-Specific Surface Lectin Associated with pathogenecity Island Cag PAI. Research & Reviews: Journal of Microbiology and Virology . 2015; 5(3): 10–17p.
Synthesis of 3,3′-(4<i>H</i>,4′<i>H</i>)-spirobi(2<i>H</i>-naphtho[1,2-<i>b</i>]pyran)-6,6′-dicarboxylic Acid and Its Optical Resolution (2008)

Abstract The synthesis and optical resolution of 3,3′-(4H,4′H)-spirobi(2H-naphtho[1,2-b]pyran)-6,6′-dicarboxylic acid were successfully accomplished. The formation of the spiro skeleton and the bromination of the aromatic ring were easily achieved in the presence of bromine. Optical resolution was achieved by amidation with l-valinol (2-amino-3-methyl-1-butanol).
Supplementary Figure Legend from Monoclonal Gammopathy of Undetermined Significance and Smoldering Multiple Myeloma: A Review of the Current Understanding of Epidemiology, Biology, Risk Stratification, and Management of Myeloma Precursor Disease (2023)

&lt;p&gt;PDF file - 31K&lt;/p&gt;
IL-18 Serum Levels in Patients with Obesity, Prediabetes and Newly Diagnosed Type 2 Diabetes. (2022)

Our data indicate that as the levels of IL-18 are increased the carbohydrate tolerance is deteriorated. However, the significance of IL-18 in the progression of diabetes mellitus and subsequent consequences requires further exploration.
Relay Redox and Lewis Acid Catalysis in the Titanocene‐ Catalyzed Multicomponent Assembly of 1,5‐Enynes (2013)

Abstract Herein we describe a direct, multicomponent assembly of 1,5‐enynes. The titanocene‐catalyzed coupling of an aryl aldehyde, iodoalkyne, and allylsilane enables the convergent and rapid synthesis of this versatile architectural motif in good to excellent yields.
Multimethodological Approach to Identification of Glycoproteins from the Proteome of <i>Francisella tularensis</i>, an Intracellular Microorganism (2010)

It appears that most glycoproteins found in pathogenic bacteria are associated with virulence. Despite the recent identification of novel virulence factors, the mechanisms of virulence in Francisella tularensis are poorly understood. In spite of its importance, questions about glycosylation of proteins in this bacterium and its potential connection with bacterial virulence have not been answered yet. In the present study, several putative Francisella tularensis glycoproteins were characterized through the combination of carbohydrate-specific detection and lectin affinity with highly sensitive mass spectrometry utilizing the bottom-up proteomic approach. The protein PilA that was recently found as being possibly glycosylated, as well as other proteins with designation as novel factors of virulence, were among the proteins identified in this study. The reported data compile the list of potential glycoproteins that may serve as a takeoff platform for a further definition of proteins modified by glycans, faciliting a better understanding of the function of protein glycosylation in pathogenicity of Francisella tularensis.
Image-guided high intensity focused ultrasound treatment for uterine leiomyomata (2003)

Thesis (Ph. D.)--University of Washington, 2003