gebhart/patrepeval huggingface dataset:
Identification and Validation of Novel Small Molecule Disruptors of HuR-mRNA Interaction (2015)

HuR, an RNA binding protein, binds to adenine- and uridine-rich elements (ARE) in the 3'-untranslated region (UTR) of target mRNAs, regulating their stability and translation. HuR is highly abundant in many types of cancer, and it promotes tumorigenesis by interacting with cancer-associated mRNAs, which encode proteins that are implicated in different tumor processes including cell proliferation, cell survival, angiogenesis, invasion, and metastasis. Drugs that disrupt the stabilizing effect of HuR upon mRNA targets could have dramatic effects on inhibiting cancer growth and persistence. In order to identify small molecules that directly disrupt the HuR-ARE interaction, we established a fluorescence polarization (FP) assay optimized for high throughput screening (HTS) using HuR protein and an ARE oligo from Musashi RNA-binding protein 1 (Msi1) mRNA, a HuR target. Following the performance of an HTS of ∼6000 compounds, we discovered a cluster of potential disruptors, which were then validated by AlphaLISA (Amplified Luminescent Proximity Homogeneous Assay), surface plasmon resonance (SPR), ribonucleoprotein immunoprecipitation (RNP IP) assay, and luciferase reporter functional studies. These compounds disrupted HuR-ARE interactions at the nanomolar level and blocked HuR function by competitive binding to HuR. These results support future studies toward chemical probes for a HuR function study and possibly a novel therapy for HuR-overexpressing cancers.
Two-Photon Endoscopy: State of the Art and Perspectives (2021)

In recent years, the demand for non-destructive deep-tissue imaging modalities has led to interest in multiphoton endoscopy. In contrast to bench top systems, multiphoton endoscopy enables subcellular resolution imaging in areas not reachable before. Several groups have recently presented their development towards the goal of producing user friendly plug and play system, which could be used in biological research and, potentially, clinical applications. We first present the technological challenges, prerequisites, and solutions in two-photon endoscopic systems. Secondly, we focus on the applications already found in literature. These applications mostly serve as a quality check of the built system, but do not answer a specific biomedical research question. Therefore, in the last part, we will describe our vision on the enormous potential applicability of adult two-photon endoscopic systems in biological and clinical research. We will thus bring forward the concept that two-photon endoscopy is a sine qua non in bringing this technique to the forefront in clinical applications.
Early Life Lead Exposure Causes Gender-Specific Changes in the DNA Methylation Profile of DNA Extracted from Dried Blood Spots (2015)

In this pilot study, we measured the 5mC profiles of DNA extracted from dried blood spots (DBS) in a cohort of 43 children (25 males and 18 females; ages from 3 months to 5 years) from Detroit. Result & Discussion: We found that the effect of Pb-exposure on the 5-mC profiles can be separated into three subtypes: affected methylation loci which are conserved irrespective of the sex of the child (conserved); affected methylation loci unique to males (male-specific); and affected methylation loci unique to females (female-specific).
Simulation-based Assessment of Various Dual-Stage Boosting Systems in Terms of Performance and Fuel Economy Improvements (2009)

&lt;div class="htmlview paragraph"&gt;Diesel engines have been used in large vehicles, locomotives and ships as more efficient alternatives to the gasoline engines. They have also been used in small passenger vehicle applications, but have not been as popular as in other applications until recently. The two main factors that kept them from becoming the major contender in the small passenger vehicle applications were the low power outputs and the noise levels.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;A combination of improved mechanical technologies such as multiple injection, higher injection pressure, and advanced electronic control has mostly mitigated the problems associated with the noise level and changed the public notion of the Diesel engine technology in the latest generation of common-rail designs. The power output of the Diesel engines has also been improved substantially through the use of variable geometry turbines combined with the advanced fuel injection technology. However, recent trend in automotive industry suggests that the dual-stage boosting is also essential to further improve the power output of the Diesel engine to the level comparable to that of the other engine technologies. The advantage of the dual-stage boosting system over the single-stage system is the increase in the rated output while simultaneously improving the steady-state torque at low engine speeds and the transient response of the Diesel engine by rapidly building up boost pressure.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;In this study, several different types of dual-stage boosting systems are evaluated with a physics-based zero-dimensional Diesel engine system simulation in terms of their steady-state and transient performance characteristics and fuel economy improvements. The dual-stage boosting systems evaluated in the study include a boosting system with two fixed geometry turbochargers at both the high pressure and low pressure stages, and several hybrid boosting systems in which the high pressure turbocharger is replaced with a screw type supercharger, an electrical compressor, and a variable geometry turbocharger. A dual-stage boosting system with early intake valve closing (EIVC) strategy is also evaluated. Each alternative system exhibits unique tradeoffs and improvements in terms of performance and fuel economy compared to the dual-stage boosting system with fixed geometry turbochargers at both high and low stages.&lt;/div&gt;
Development and Characterization of V-PLEX® TH17 Cytokine. Assays (2017)

Abstract Th17 cytokines are important mediators of the host defense against infection and are increasingly investigated for their role in autoimmune disorders and immune regulation at mucosal surfaces. Here we describe the development, characterization, and analytical validation of a multiplexed immunoassay panel for seven Th17 cytokines, IL-17A, IL-21, IL-22, IL-23, IL-27, IL-31, and MIP-3alpha, on MSD’s V-PLEX platform. To efficiently and rapidly identify potential antibody pairs, biotinylated capture antibodies and detection antibodies conjugated with SULFO-TAG™ label were screened on MSD’s U-PLEX® platform, which enables the solution phase assembly of capture antibody arrays. Subsequent development used printed arrays of capture antibodies. Antibody concentrations, calibrator curve linearity, dynamic range, specificity, matrix tolerance, and assay robustness were analyzed for each assay during development. Calibration curves demonstrated a three-log dynamic range while achieving a lower limit of quantitation (LLOQ) of less than 1 pg/mL for most assays. Control samples for the assays had CVs of less than 10%. Dilution linearity and spike recovery studies in serum, plasma, urine, and cell culture media were conducted to demonstrate matrix compatibility. Spiked matrix samples were typically found to recover between 80%–120% of the expected value. Cross-reactivity was shown to be less than 0.3% between assays within the panel and less than 0.5% when panned against more than 30 other blood-related biomarkers. These validated, multiplexed assays provide sensitive measurement of Th17 cytokines in a variety of matrices and can be used as part of a researcher’s pre-clinical and clinical studies.
New Radical Allylation Reactions Using 2-Bromo-3-(phenylthio)propene and Their Application to the Synthesis of Carbocyclic Compounds (1996)

A study on the application of vinyl radical cyclization via free radical allylation reaction in the synthesis of various carbocyclic compounds is described. In connection with this study, a new allyl transfer reagent, 2-bromo-3-(phenylthio)propene 1 is developed and it was shown that vinyl radical cyclization through free radical allylation reaction using reagent 1 provides a valuable approach to carbocyclic systems with a reactive exo-alkylidene moiety, which is advantageous for further transformations.
29Si MAS-NMR study of hydrated cement paste and mortar with varying content of fly ash (2006)

This study presents 29 Si magic-angle-spinning nuclear magnetic resonance (MAS-NMR) measurements that trace the cement hydration process in both cement paste as well as mortar specimens made from Type I ordinary Portland cement, when the cement content was replaced by 0, 20, 40, 55 and 70% by weight of high lime fly ash. The specimens were cured by continuous immersion in potable water for 3, 7, 14, 28, 90 and 180 days at a laboratory temperature of 21°C (69·8°F). The results show that values of the degree of hydration (%) and the compressive strength generally decreased with increasing content of high lime fly ash. Beyond 28 days of curing time, a progressive increase in the degree of hydration (%), that was comparable with that of the control specimens occurred in the cement paste specimens containing 20, 40, and 55% high lime fly ash. This indicates delayed pozzolanic reactivity of the high lime fly ash that started after 28 days of curing time and reached optimal value at 90 days of curing time. Moreover, throughout the curing ages of this study, the cement paste as well as the mortar specimens containing 20 % high lime fly ash indicated values of degree of hydration (%) and compressive strength that were close and comparable with those of the control specimens without high lime fly ash.
IgA dominates the early neutralizing antibody response to SARS-CoV-2 (2020)

Humoral immune responses are typically characterized by primary IgM antibody responses followed by secondary antibody responses associated with immune memory and composed of IgG, IgA, and IgE. Here, we measured acute humoral responses to SARS-CoV-2, including the frequency of antibody-secreting cells and the presence of SARS-CoV-2-specific neutralizing antibodies in the serum, saliva, and bronchoalveolar fluid of 159 patients with COVID-19. Early SARS-CoV-2-specific humoral responses were dominated by IgA antibodies. Peripheral expansion of IgA plasmablasts with mucosal homing potential was detected shortly after the onset of symptoms and peaked during the third week of the disease. The virus-specific antibody responses included IgG, IgM, and IgA, but IgA contributed to virus neutralization to a greater extent compared with IgG. Specific IgA serum concentrations decreased notably 1 month after the onset of symptoms, but neutralizing IgA remained detectable in saliva for a longer time (days 49 to 73 post-symptoms). These results represent a critical observation given the emerging information as to the types of antibodies associated with optimal protection against reinfection and whether vaccine regimens should consider targeting a potent but potentially short-lived IgA response.
Single InGaN nanocolumn spectroscopy (2015)

We report on the spectroscopy of single InGaN/GaN nanocolumns that are site-controlled nanostructures allowing for pixel-like large-scale integration. A single nanocolumn shows several narrow photoluminescence peaks at around 600 nm at 20–90 K, the linewidth of which ranges between 0.3 and 10 meV. We have observed an interesting temperature dependence of the integrated intensity, the maximum being around 40–70 K, which suggests the existence of efficient carrier injection channels from localized states. The results show that the optical properties of single nanocolumns are favorable for the future large-scale integration of single-photon emitters and qubits.
Periprocedural and Late Complications (2011)

This chapter contains sections titled: Cardiac tamponade Thromboembolic events PV stenosis PN injury Atrioesophageal fistula Periesophageal vagal injury Vascular complications Acute coronary artery injury Air emboli Catheter entrapment in the MV or PV Organized left atrial tachyarrhythmias after AF ablation Adverse impact on atrial contractility Radiation exposure during catheter ablation of AF References
Space harmonic analysis of integrated optic modulators with periodic electrodes (1992)

The frequency response of integrated optic modulators with traveling wave electrodes is limited by the phase velocity mismatch between the optical and RF signals. At millimeter wave frequencies the short electrodes that must be used to avoid this phase mismatch severely reduce the modulator sensitivity. One approach that provides high frequency modulators with increased sensitivity is the use of periodic intermittent interaction (PII) electrodes and enhanced periodic phase reversal (EPPR) electrodes. In this paper, the RF signal on the electrode is represented as a summation of traveling wave space harmonics. The electrode geometry is adjusted so that the phase velocity of the dominant space harmonic equals the phase velocity of the optical signal at the design frequency. General velocity-matching conditions are derived for both the PII and the EPPR modulators; the bandpass frequency response is then calculated by adding the individual responses of all space harmonics traveling down the electrode. Design examples are provided of periodic electrodes for LiNbO3 and GaAs modulators for operation at 35 GHz. Finally, a practical method for velocity-matching is described that requires only the two-port characterization of an individual electrode unit section.
Simulation of electrostatic ion instabilities in the presence of parallel currents and transverse electric fields (1989)

A spatially two-dimensional electrostatic PIC simulation code was used to study the stability of a plasma equilibrium characterized by a localized transverse dc electric field and a field-aligned drift for L is much less than Lx, where Lx is the simulation length in the x direction and L is the scale length associated with the dc electric field. It is found that the dc electric field and the field-aligned current can together play a synergistic role to enable the excitation of electrostatic waves even when the threshold values of the field aligned drift and the E x B drift are individually subcritical. The simulation results show that the growing ion waves are associated with small vortices in the linear stage, which evolve to the nonlinear stage dominated by larger vortices with lower frequencies.
2D-3D PIC Code Benchmarking/Anchoring Comparisons For a Novel RFQ/RFI LINAC Design (2018)

In this study, comparisons are made between several particle dynamics codes (namely CST Particle Studio, GPT, and upgraded PARMILA codes) in order to benchmark them. The structure used for the simulations is a novel 200 MHz, 2.5 MeV, CW RFQ/RFI LINAC designed by Ion Linac Systems (ILS). The structure design and parameters are provided, simulation techniques are explained, and results from all three code families are presented. These results are then compared with each other, identifying similarities and differences. Numerous parameters for comparison are used, including the transmission efficiency, Q-factor, E-field on axis, and beam properties. Preliminary anchoring between modeling and simulation performance predictions and experimental measurements will be provided.
High-Grade B-Cell Lymphoma (HGBL) with MYC and BCL2 and/or BCL6 Rearrangements Is Predominantly BCL6-Rearranged and BCL6-Expressing in Taiwan (2021)

This study investigated the epidemiological and clinical peculiarities of <i>BCL2</i> and <i>BCL6</i> rearrangement in patients with high grade B-cell lymphoma (HGBL) from Taiwan, compared with data from Western countries. Two hundred and eighty-two DLBCL cases from Taipei Medical University-affiliated hospitals (<i>n</i> = 179) and Tri-Service General Hospital (<i>n</i> = 103) were enrolled for this study. From the 282, 47 (16.7%) had <i>MYC</i> translocation; 24 of these harbored concurrent <i>BCL2</i> and/or <i>BCL6</i> translocation (double-hit, DH or triple-hit, TH). Twelve DH-HGBL cases had simultaneous <i>MYC</i> and <i>BCL6</i> translocations, 8 harbored <i>MYC</i> and <i>BCL2</i> rearrangement, while the remaining 4 patients exhibited TH. Together, 66.7% of DH/TH-HGBL patients were <i>BCL6</i> rearrangement positive. Among these <i>BCL6</i>-rearranged DH/TH-HGBL patients, only 6 (37.5%) overexpressed MYC and BCL6 proteins simultaneously, indicating that MYC-BCL6 co-overexpression may not be plausible surrogate biomarker for screening <i>BCL6</i>-rearranged DH-HGBL. By the end of year 5, all patients with TH-HGBL, <i>BCL2</i> DH-HGBL and all but one <i>BCL6</i> DH-HGBL cases had expired or were lost to follow-up. Progression-free survival (PFS) was longer for the non-DH/TH-HGBL group compared with the DH/TH-HGBL group. While the patients with <i>BCL2</i> DH-HGBL were lost to follow-up by day 800, their remaining TH-HGBL and <i>BCL6</i> DH-HGBL peers exhibited very poor PFS, regardless of age strata. More so, patients with <i>BCL6</i> rearrangement were 5.5-fold more likely associated with extranodal involvement compared with their BCL2-rearranged peers. Moreover, ~60.0% of the <i>BCL6</i>-rearranged DH-HGBL cases were non-GCB, suggesting that including screening for <i>BCL6</i> rearrangement in patients with the non-GCB phenotype may aid medical decision-making and therapeutic strategy. Contrary to contemporary data from western countries, 2 in every 3 patients with DH/TH-HGBL in Taiwan harbor <i>BCL6</i> rearrangement. Consistent with present findings, we recommend mandatory screening for <i>BCL6</i> rearrangement in patients with aggressive HGBL in Taiwan.
Clinical correlations of brain lesion distribution in multiple sclerosis (2009)

Periventricular lesions were related to disability. LL influenced relations between disability and lesion probability throughout the brain, suggesting interplay between lesional burden and its location in determining disability in MS.
ChemInform Abstract: TRANSFORMATION OF 2,2‐DIPHENYL‐2‐FLUORO‐2,3‐DIHYDRO‐1,3,2‐Λ5‐BENZOXAZAPHOSPHOLES. II. SYNTHESIS OF P,P‐DIPHENYLPHOSPHINIC AND ARYL AMIDES AND BENZOXAZAPHOSPHOLE DIMERS (1981)

Abstract Die Benzoxazaphosphole (I) hydrolysieren leicht zu den Phosphinsäurearylamiden (II).
Further results on sensor network localization using rigidity (2005)

Two further results, which extend the previous work on the use of rigidity in sensor network localization, are given. The previous work provided the conditions for the localization of an entire network in which some nodes know their locations and other nodes determine their locations by measuring the distances to their neighbors. First, the paper gives the conditions for partial localization of a subnetwork when an entire network is not localizable. Second, the paper gives the conditions for localization in which some nodes know their locations and other nodes determine their locations by measuring the bearings (angle of arrivals) to their neighbors rather than the distances.
PRODUCTION OF CARBON PRODUCTS USING A COAL EXTRACTION PROCESS (2005)

The purpose of this DOE-funded effort is to develop technologies for carbon products from coal-derived feed-stocks. Carbon products can include precursor materials such as solvent extracted carbon ore (SECO) and synthetic pitch (Synpitch). In addition, derived products include carbon composites, fibers, foams and others.
High frame-rate MR-guided near-infrared tomography system to monitor breast hemodynamics (2011)

A near-infrared (NIR) tomography system with spectral-encoded sources at two wavelength bands was built to quantify the temporal contrast at 20 Hz bandwidth, while imaging breast tissue. The NIR system was integrated with a magnetic resonance (MR) machine through a custom breast coil interface, and both NIR data and MR images were acquired simultaneously. MR images provided breast tissue structural information for NIR reconstruction. Acquisition of finger pulse oximeter (PO) plethysmogram was synchronized with the NIR system in the experiment to offer a frequency-locked reference. The recovered absorption coefficients of the breast at two wavelengths showed identical temporal frequency as the PO output, proving this multi-modality design can recover the small pulsatile variation of absorption property in breast tissue related to the heartbeat. And it also showed the system's ability on novel contrast imaging of fast flow signals in deep tissue.
Sensors: An Optical Sensor for Volatile Amines Based on an Inkjet‐Printed, Hydrogen‐Bonded, Cholesteric Liquid Crystalline Film (Advanced Optical Materials 5/2014) (2014)

A green reflecting, hydrogen-bonded, cholesteric liquid crystal polymer film has been printed on a foil by C. W. M. Bastiaansen, A. P. H. J. Schenning, and co-workers. As demonstrated on page 459, this foil can be used as an optical sensor to detect volatile amines that are produced by decaying fish, resulting in a red color. The authors thank ICMS Animation Studio for preparing this cover image.
The microarchitecture of the synergistic processor for a cell processor (2005)

This paper describes an 11 FO4 streaming data processor in the IBM 90-nm SOI-low-k process. The dual-issue, four-way SIMD processor emphasizes achievable performance per area and power. Software controls most aspects of data movement and instruction flow to improve memory system performance and core performance density. The design minimizes instruction latency while providing for fine grain clock control to reduce power.
Texture discrimination: radiologist, machine and man (1991)

Over the last few years we have developed machine algorithms for detection and discrimination of liver disease from diagnostic ultrasound scans of the liver (Wagner, Insana & Brown, 1986; Insana et al., 1986a; Insana et al, 1986b; Wagner, Insana & Brown, 1987). Several diffuse disease conditions are manifested through very subtle changes in the texture of the image. In these cases the machine algorithms significantly outperform expert clinical readers of the images (Garra et al., 1989). The discrimination of textures by the machine depends principally on an analysis and partitioning of second-order statistical features such as the autocorrelation and power spectral estimators. This finding has prompted us to investigate whether the human visual system might be more limited in its performance of such second-order tasks than it is for the wide range of first-order tasks where it scores so well.
Terahertz backward wave oscillators (2006)

Terahertz backward wave oscillators (BWOs) are needed for spectroscopy applications from astrophysics to chemical and biological agent detection. A 600-700 GHz BWO is nearing completion that includes a depressed collector and high purity, quasi-optical, output beam. Design, fabrication, and results to date are presented.
Bacteriophages for managingShigellain various clinical and non-clinical settings (2013)

The control of shigellosis in humans enjoys a prominent position in the history of bacteriophage therapy. d’Herelle first demonstrated the efficacy of phage therapy by curing 4 patients of shigellosis, and several subsequent studies confirmed the ability of phages to reduce Shigella based infection. Shigella spp continue to cause millions of illnesses and deaths each year and the use of phages to control the disease in humans and the spread of the bacteria within food and water could point the way forward to the effective management of an infectious disease with global influence.
Supplementary Data from Yin Yang 1 Modulates Taxane Response in Epithelial Ovarian Cancer (2023)

Supplementary Data from Yin Yang 1 Modulates Taxane Response in Epithelial Ovarian Cancer