gebhart/patrepeval huggingface dataset:
P1‐073: Specific detection of soluble amyloid beta oligomers using conformationally dynamic pronucleon™ peptides (2009)

We have previously reported the use of small conformationally dynamic peptides (Pronucleon™ peptides) that enable the detection of beta sheet amyloid proteins associated with Alzheimer's disease (AD). These fluorescently-labeled peptides undergo a sequence-specific conformational rearrangement in the presence of Abeta aggregates, resulting in a change in their fluorescence profile that can be monitored using standard laboratory instrumentation (Adlyfe's “misfolded” protein detection [MPD] assay). The development of Pronucleon™ peptides to detect soluble amyloid beta (Abeta) oligomers (which are reported to be the neurotoxic species likely to be the cause of AD), would be a unique and valuable contribution to the field. To aid in development of an effective in vitro diagnostic test to measure neurotoxic Abeta species, we produced two distinct types of soluble oligomers: SDS-derived and DMEM/F12 media-induced oligomers. We have developed a formulation to maximize their stability, and extensively characterized them with respect to size distribution, ThT reactivity, and structural properties. We have also optimized the design of our Pronucleon peptides to enhance solubility, and alter the pH and salt-sensitivity of their conformational states in order to optimize their ability to detect oligomers under clinically relevant conditions. The ability of Pronucleon peptides to detect oligomers was assessed using Adlyfe's MPD assay as well as by independent direct binding methods. We will also evaluate the performance of Pronucleon peptide variants with CSF clinical samples. Both synthetic Abeta oligomer preparations are robust and stable for up to six months in our current formulation. Preliminary experimental data showed that Pronucleon peptides interact specifically with both oligomer types. Circular dichroism spectroscopy demonstrated that several Pronucleon peptide variants are conformationally dynamic, and that their structural properties can be controlled by altering assay conditions. We have optimized the design of Pronucleon peptides to detect synthetic Abeta oligomers in our MPD assay, and are continuing to design peptide variants that enhance the assay's specificity and dynamic range. The development of stable oligomer products will be expanded to include other potentially clinically relevant types (e.g. dimers) that can be broadly used in AD research.
Microcanonical processing methodology for ECG and intracardial potential: application to atrial fibrillation (2012)

Cardiac diseases are the principal cause of human morbidity and mortality in the western world. The electric potential of the heart is a highly complex signal emerging as a result of nontrivial flow conduction, hierarchical structuring and multiple regulation mechanisms. Its proper accurate analysis becomes of crucial importance in order to detect and treat arrhythmias or other abnormal dynamics that could lead to life-threatening conditions. To achieve this, advanced nonlinear processing methods are needed: one example here is the case of recent advances in the Microcanonical Multiscale Formalism. The aim of the present paper is to recapitulate those advances and extend the analyses performed, specially looking at the case of atrial fibrillation. We show that both ECG and intracardial potential signals can be described in a model-free way as a fast dynamics combined with a slow dynamics. Sharp differences in the key parameters of the fast dynamics appear in different regimes of transition between atrial fibrillation and healthy cases. Therefore, this type of analysis could be used for automated early warning, also in the treatment of atrial fibrillation particularly to guide radiofrequency ablation procedures.
Experiments on a Segmented Axial Relativistic Magnetron Fed by a Split Cathode (2022)

We have recently confirmed that a magnetron fed by a split cathode operates as well as when a solid cathode is applied. With a split cathode no microwave pulse shortening appears. We have also shown that a magnetron built from anode block segments separated by longitudinal slits, allows fast magnetic field penetration and does not influence the magnetron operation. This allows the use of a pulsed, much lower power system, to charge the coil supplying the required axial insulating magnetic field. The result is a compact light weight and repetitive system with considerably higher overall electrical efficiency. We present new experiments using our Linear Induction Accelerator as the magnetron power source.
QUANTITATIVE TRAIT LOCI ANALYSIS OF PHOTOINHIBITION UNDER CHILLING STRESS IN TOMATO (2000)

ISHS XXV International Horticultural Congress, Part 11: Application of Biotechnology and Molecular Biology and Breeding - Gene Expression and Molecular Breeding, Genome Analysis. QUANTITATIVE TRAIT LOCI ANALYSIS OF PHOTOINHIBITION UNDER CHILLING STRESS IN TOMATO
Heterogeneity of antibodies reactive with the dominant antigen of Actinobacillus actinomycetemcomitans (1997)

The serotype b-specific carbohydrate antigen (SbAg) of Actinobacillus actinomycetemcomitans Y4 is reported to be the O antigen of lipopolysaccharide, and the highest titers of serum antibody reactive with A. actinomycetemcomitans in early-onset periodontitis (EOP) patients bind SbAg. These high titers of serum antibody reactive with SbAg are associated with a lesser extent and severity of periodontal disease. The aim of this study was to determine if a limited number of genes code for anti-SbAg antibodies as has been shown for immunoglobulin G (IgG) reactive with the type b polysaccharide from Haemophilus influenzae. Serum IgG reactive with the SbAg was prepared from 20 high-titer EOP patients by affinity chromatography. The IgG subclass concentrations were determined, and heterogeneity was analyzed by isoelectric focusing (IEF). IgG2 was the dominant subclass (83% of total IgG) in the anti-SbAg IgG fraction and represented an average of 1.33% of total serum IgG2. The IgG2 reactive with SbAg was isolated from the affinity-purified IgG fraction by affinity chromatography with protein A and subclass-specific monoclonal antibodies. On IEF gels, only 4 to 20 bands were observed in the anti-SbAg IgG fractions, indicating limited heterogeneity. N-terminal amino acid sequence analysis of eight representative anti-SbAg IgG2 preparations indicated that variable heavy and light chains consisted largely of V(H)III and V(kappa)II, respectively. However, a significant fraction of anti-SbAg may use V(H) and V(lambda) genes with blocked N termini. In short, these findings indicate that IgG reactive with SbAg is very much like the antibody reactive with H. influenzae type b polysaccharide. Similarities include IgG2 dominance, limited bands on IEF gels, supporting an oligoclonal response, and use of genes from V(H)III and V(kappa)II regions.
Topical clustering of search results (2012)

Search results clustering (SRC) is a challenging algorithmic problem that requires grouping together the results returned by one or more search engines in topically coherent clusters, and labeling the clusters with meaningful phrases describing the topics of the results included in them.
Antibody Mediated Depletion of iNKT Cells Protects Against Hypoxia-Induced Pulmonary Injury in a Murine Model of Sickle Cell Disease (2014)

Abstract Background: Painful vaso-occlusive crises (pVOC) are caused by the polymerization of sickle deoxyhemoglobin, red cell sickling and vaso-occlusion. Vaso-occlusion is exacerbated by an inflammatory cascade that is initiated by iNKT cell activation. Townes sickle cell mice have mouse globins replaced by human globins, including the mutant human sickle b-globin gene (SS). NKT-14 is a monoclonal antibody directed specifically to the mouse invariant T cell receptor (iTCR). The antibody is a chimeric mouse IgG2a that, when bound to the mouse iNKT cell, promotes a rapid, specific and long lasting (&gt; 14 days) depletion. Aims: Our primary goal was to determine if selective iNKT cell depletion with NKT-14 reduces lung inflammation and injury in response to hypoxia-induced RBC sickling in Townes SS mice. Methods: Hypoxic pulmonary injury was induced by placing mice in 8% O2 (Coy Lab products)followed by reoxygenation. Some mice were subject to a second period of hypoxia and continuously monitored to determine carotid Hb-saturation (Starr MouseOx). Total cell numbers and activation state of iNKT cells and neutrophils in lung were determined by FACS. Pulmonary vascular leak was quantified with Evans Blue dye. Results: Twelve hours of 8% hypoxia followed 4 hours of reoxygenation (H/R) was found to produce non-lethal lung inflammation and injury in SS mice. Compared to isotype Ab controls, injection of four mice with 100µg/mouse of NKT-14 Ab three days prior to HR was found to decrease the number of pulmonary iNKT cells by 91% (P &lt; 0.01). Following H/R, NKT-14 Ab treatment resulted in a significant 65% decrease in lung neutrophil accumulation (Fig. A, P &lt; 0.01), and a 54% decrease in pulmonary vascular leak (Fig. B, P &lt; 0.05). In addition, arterial Hb-Sat during a second exposure of SS mice to hypoxia was improved (Fig. C). Figure 1 Figure 1. Conclusions: Selective depletion of mouse iNKT cells by injection of NKT-14 Ab three days prior to H/R results in substantial reductions in pulmonary inflammation, vascular leak and injury as measured by Hb-Sat in SS mice. The results suggest that prophylactic Ab-mediated depletion of iNKT cells in humans with SCD may be useful for reducing the incidence and severity of pVOC and acute chest syndrome. Disclosures Schaub: NKT Therapeutics Inc: Employment, Equity Ownership. Scheuplein:NKT Therapeutics Inc: Employment, Equity Ownership. Mashal:NKT Therapeutics Inc: Employment, Equity Ownership.
<title>User's guide to IR detectors</title> (2001)

The guidance for the first time user toward proper selection and use of infrared detectors for applications in industrial inspection, process control and laser measurements are presented. The properties of two primary detectors, thermal detectors and photon detectors, are compared. Thermal detectors absorb the energy of the photon as heat and photon detectors use the energy of the photon to increase the energy of a charge carrier.
An Experimentally Validated Finite Element Model of the Lower Limb to Investigate the Efficacy of Blast Mitigation Systems (2021)

Improvised explosive devices (IEDs) used in the battlefield cause damage to vehicles and their occupants. The injury burden to the casualties is significant. The biofidelity and practicality of current methods for assessing current protection to reduce the injury severity is limited. In this study, a finite-element (FE) model of the leg was developed and validated in relevant blast-loading conditions, and then used to quantify the level of protection offered by a combat boot. An FE model of the leg of a 35 years old male cadaver was developed. The cadaveric leg was tested physically in a seated posture using a traumatic injury simulator and the results used to calibrate the FE model. The calibrated model predicted hindfoot forces that were in good correlation (using the CORrelation and Analysis or CORA tool) with data from force sensors; the average correlation and analysis rating (according to ISO18571) was 0.842. The boundary conditions of the FE model were then changed to replicate pendulum tests conducted in previous studies which impacted the leg at velocities between 4 and 6.7 m/s. The FE model results of foot compression and peak force at the proximal tibia were within the experimental corridors reported in the studies. A combat boot was then incorporated into the validated computational model. Simulations were run across a range of blast-related loading conditions. The predicted proximal tibia forces and associated risk of injury indicated that the combat boot reduced the injury severity for low severity loading cases with higher times to peak velocity. The reduction in injury risk varied between 6 and 37% for calcaneal minor injuries, and 1 and 54% for calcaneal major injuries. No injury-risk reduction was found for high severity loading cases. The validated FE model of the leg developed here was able to quantify the protection offered by a combat boot to vehicle occupants across a range of blast-related loading conditions. It can now be used as a design and as an assessment tool to quantify the level of blast protection offered by other mitigation technologies.
A 0.5ps 1.4mW 50MS/s Nyquist bandwidth time amplifier based two-step flash-ΔΣ time-to-digital converter (2016)

We propose a 50-MS/s two-step flash-ΔΣ time-to-digital converter (TDC) using stable time amplifiers (TAs). The TDC demonstrates low-levels of shaped quantization noise. The system is simulated in 40-nm CMOS and consumes 1.3 mA from a 1.1 V supply. The bandwidth is broadened to Nyquist rate. At frequencies below 25 MHz, the integrated TDC error is as low as 143 fsrms, which is equal to an equivalent TDC resolution of 0.5 ps.
Analysis of Supersonic and Transonic Panel Flutter Using a Fluid-Structure Coupling Algorithm (2014)

In order to analyze the supersonic and transonic panel flutter behaviors quantitatively and accurately, a fluid-structure coupling algorithm based on the finite element method (FEM) is proposed to study the two-dimensional panel flutter problem. First, the Von Kármán's large deformation is used to model the panel, and the high speed airflow is approached by the Euler equations. Then, the equation of panel is discretized spatially by the standard Galerkin FEM, and the equations of fluid are discretized by the characteristic-based split finite element method (CBS-FEM) with dual time stepping; thus, the numerical oscillation encountered frequently in the numerical simulation of flow field could be removed efficiently. Further, a staggered algorithm is used to transfer the information on the interface between the fluid and the structure. Finally, the aeroelastic behaviors of the panel in both the supersonic and transonic airflows are studied in details. And the results show that the system can present the flat and stable, simple harmonic oscillation, buckling, and inharmonic oscillation states at Mach 2, considering the effect of the pretightening force; at Mach 1.2, as the panel loses stability, the ensuing limit cycle oscillation is born; at Mach 0.8 and 0.9, positive and negative bucklings are the typical states of the panel as it loses its stability. Further, the transonic stability boundary is obtained and the transonic bucket is precisely captured. More, this algorithm can be applied to the numerical analysis of other complicated problems related to aeroelasticity.
Posttransplantation Diabetes (2002)

Physicians should consider modification of immunosuppressive regimens to decrease the risk of PTD in high-risk transplant recipients. Randomized trials are needed to evaluate the use of oral glucose-lowering agents in transplant recipients, paying particular attention to interactions with immunosuppressive drugs.
Fast convergent algorithms for multi-kernel regression (2016)

Kernel ridge regression plays a central role in various signal processing and machine learning applications. Suitable kernels are often chosen as linear combinations of “basis kernels” by optimizing criteria under regularization constraints. Although such approaches offer reliable generalization performance, solving the associated min-max optimization problems face major challenges, especially with big data inputs. After analyzing the key properties of a convex reformulation, the present paper introduces an efficient algorithm based on a generalization of Nesterov's acceleration method, which achieves order-optimal convergence rate among first-order methods. Closed-form updates are derived for common regularizers. Experiments on real datasets corroborate considerable speedup advantages over competing algorithms.
Carbon Contamination Analysis and Its Effect on Extreme Ultra Violet Mask Imaging Performance Using Coherent Scattering Microscopy/<I>In-Situ</I> Accelerated Contamination System (2011)

The coherent scattering microscopy/in-situ accelerated contamination system (CSM/ICS) is a developmental metrology tool designed to analyze the impact of carbon contamination on the imaging performance. It was installed at 11B EUVL beam-line of the Pohang Accelerator Laboratory (PAL). Monochromatized 13.5 nm wavelength beam with Mo/Si multilayer mirrors and zirconium filters was used. The CSM/ICS is composed of the CSM for measuring imaging properties and the ICS for implementing acceleration of carbon contamination. The CSM has been proposed as an actinic inspection technique that records the coherent diffraction pattern from the EUV mask and reconstructs its aerial image using a phase retrieval algorithm. To improve the CSM measurement accuracy, optical and electrical noises of main chamber were minimized. The background noise level measured by CCD camera was approximately 8.5 counts (3 sigma) when the EUV beam was off. Actinic CD measurement repeatability was <1 A (3 sigma) at 17.5 nm line and space pattern. The influence of carbon contamination on the imaging properties can be analyzed by transferring EUV mask to CSM imaging center position after executing carbon contamination without a fine alignment system. We also installed photodiode and ellipsometry for in-situ reflectivity and thickness measurement. This paper describes optical design and system performance observed during the first phase of integration, including CSM imaging performance and carbon contamination analysis results.
3-O-tert-Butyldimethylsilyl-2,2′:5,6-di-O-isopropylidene-2-C-hydroxymethyl-D-1,4-gluconolactone (2004)

T = 150 K Mean '(CC) = 0.003 A R factor = 0.037 wR factor = 0.
Quantum electrodynamics of a nanocavity coupled with exciton complexes in a quantum dot (2009)

A comprehensive theory of the coupling between a nanocavity and exciton complexes in a quantum dot is developed, which successfully predicts the spectral triplet in the strong coupling regime that has been observed in several experiments but, which is unexpected according to conventional cavity quantum electrodynamics. The quantum anti-Zeno effect is found to play an essential role in the appearance of the central peak in the triplet under a low-excitation regime. The effect of hyperfine interactions is also discussed, which results in the cavity-mediated mixing of bright and dark exciton states. These results provide significant new insight into solid-state cavity quantum electrodynamics.
3-D Sidewall Interconnect Formation Climbing Over Self-Assembled KGDs for Large-Area Heterogeneous Integration (2017)

Massively parallel chip assembly based on multi-interposer block concept is demonstrated for large-area heterogeneous system integration. The chips are aligned in parallel by liquid surface tension and assembled on the Si interposers through oxide-oxide bonding at room temperature without thermocompression. 3-D Cu sidewall interconnects (the width is approximately 20 μm) climbing over 100-μm-thick self-assembled chips are formed with a spin-on thick photoresist by electroplating. In addition, 3-D Cu interconnects with a width of nearly 10 μm are successfully formed across polyimide slopes formed on the sidewall of self-assembled chips. The electrical properties of the 3-D sidewall interconnects are characterized by the daisy chains, resistance distribution, and characteristic fluctuation of CMOS fabricated on the self-assembled chips.
A 3D Folded Power Inductor with PCB based technology for applications in the kW range (2019)

This paper presents an original 3D folded power inductor concept using Printed-Circuit-Board (PCB) technology. It is low cost for mass production and presents good reproducibility. A partial milling of the PCB is used to allow bending and building the inductor winding. A prototype is designed through an optimisation procedure. The frequency dependency of the series resistance, which widely impacts the losses in power converters, is investigated. Electrical and thermal tests are realised on the inductor to validate the applicability in power converters, e.g buck/boost inductor or EMI filter inductor, in particular differential mode inductor. These tests shows that the proposed inductor is a good candidate for power converters in the kW range.
Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers (2012)

Common inflammatome gene signatures as well as disease-specific signatures were identified by analyzing 12 expression profiling data sets derived from 9 different tissues isolated from 11 rodent inflammatory disease models. The inflammatome signature significantly overlaps with known drug targets and co-expressed gene modules linked to metabolic disorders and cancer. A large proportion of genes in this signature are tightly connected in tissue-specific Bayesian networks (BNs) built from multiple independent mouse and human cohorts. Both the inflammatome signature and the corresponding consensus BNs are highly enriched for immune response-related genes supported as causal for adiposity, adipokine, diabetes, aortic lesion, bone, muscle, and cholesterol traits, suggesting the causal nature of the inflammatome for a variety of diseases. Integration of this inflammatome signature with the BNs uncovered 151 key drivers that appeared to be more biologically important than the non-drivers in terms of their impact on disease phenotypes. The identification of this inflammatome signature, its network architecture, and key drivers not only highlights the shared etiology but also pinpoints potential targets for intervention of various common diseases.
Synthesis of 5-Bromopyridyl-2-magnesium Chloride and Its Application in the Synthesis of Functionalized Pyridines (2004)

[reaction: see text] The 5-bromopyridyl-2-magnesium chloride (2), which was not accessible previously, was efficiently synthesized for the first time via an iodo-magnesium exchange reaction with 5-bromo-2-iodopyridine (1). This reactive intermediate was allowed to react with a variety of electrophiles to afford a range of useful functionalized pyridine derivatives. Application of this methodology to 5-bromo-2-iodo-3-picoline provided a simple and economical synthesis of a key intermediate for the preparation of Lonafarnib, a potent anticancer agent.
The Impact of Electrode Dielectric Coating on the Insulation Integrity of GIS/GITL with Metallic Particle Contaminants (2002)

Coating the inside surface of GIS enclosures with a dielectric film reduces the deleterious effect of electrode surface roughness, impedes the development of metallic particle initiated microdischarges, increases the field required to lift particles, and reduces the charge acquired by particles, all of which help alleviate the adverse effect of contaminating metallic particles on insulation withstand. The performance of particle-contaminated compressed gas systems with dielectric coated electrodes is analyzed. Two mechanisms for the transfer of charge from electrodes to contaminating particles are considered, namely, conduction through the coating layer and microdischarges in the surrounding gas. This paper presents an electrostatic study of the particle lifting fields with dielectric covered electrodes. The overall breakdown strength of the system is evaluated and the results are discussed in the light of experimental findings.
Rapid Emergence of Potentially Transmissible Severe Acute Respiratory Syndrome Coronavirus 2 With Resistance to Combination Monoclonal Antibody Therapy (2023)

Abstract Prolonged coronavirus disease 2019 may generate new viral variants. We report an immunocompromised patient treated with monoclonal antibodies who experienced rebound of viral RNA and emergence of an antibody-resistant (&amp;gt;1000-fold) variant containing 5 mutations in the spike gene. The mutant virus was isolated from respiratory secretions, suggesting the potential for secondary transmission.