gebhart/patrepeval huggingface dataset:
Abstract 4520: The effect of EPZ011989, an enhancer of Zeste homolog 2 inhibitor, in acute myeloid leukemia (2016)

Abstract Enhancer of Zeste Homolog 2 (EZH2) is a catalytic core subunit of the Polycomb repressive complex 2, PRC2. EZH2 catalyzes the tri-methylation of lysine 27 on histone H3 (H3K27me3) which often results in the silencing of associated gene promoters. The over-expression of EZH2 is associated with cancer progression and poor prognosis in solid tumors and hematological malignances. EZH2 mutations in lymphoma generally are activating whereas those in myelodysplasia and acute myeloid leukemia are typically loss of function. Additionally, EZH2 mutations are not isolated to a hotspot and therefore discerning phenotype is challenging. The purpose of this study was to determine if the inhibition of EZH2 induces cell differentiation or apoptosis in AML, and to determine the significance of EZH2 mutations in AML patients. As H3K27me3 deposition is catalyzed by EZH2, we hypothesized that analysis of H3K27me3 levels could differentiate an inactivating EZH2 mutation. We analyzed H3K27me3 levels in AML patient samples with wild type (N = 5) and mutant (N = 3) EZH2, and found that overall H3K27me3 is reduced in the mutant patient samples. Furthermore, the sample with the highest variant allele frequency (VAF) of the EZH2 mutation had noticeably lower levels of H3K27me3 compared to those that had a lower VAF. This finding demonstrates that diminished H3K27me3 levels can predict the presence of an inactivating EZH2 mutation in AML cells. We next assessed if the EZH2 tool molecule EPZ011989 produced a similar phenotype in wild-type EZH2 AML cell lines (Kasumi-1, MOLM-13, and MV4-11). EPZ011989 inhibited H3K27me3 in all of the cell lines at a concentration of 0.625 μM after only four days of treatment. At these concentrations and this time point we demonstrated no change in viability among these three cell lines and only minimal proliferation inhibition in MV4-11 and MOLM-13 cells. Longer time points are currently being investigated as EZH2 inhibitors often induce anti-proliferative effects only after longer incubation periods. Therefore, our results support that inactivation of EZH2 with EZP011989 in AML cell lines induces the same cell-biochemical consequence (i.e. H3K27me3 loss) associated with EZH2 mutations in AML patients. This potentially will allow diverse pharmacologic studies in cell lines relative to gene targets and also synergistic lethality studies utilizing genetic and pharmacologic screening techniques to potentially develop therapeutic agents to treat this subtype of AML. Citation Format: Sydney Fobare, Cecelia Miller, Shelley J. Orwick, Heike Keilhack, Erin Hertlein, John C. Byrd. The effect of EPZ011989, an enhancer of Zeste homolog 2 inhibitor, in acute myeloid leukemia. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4520.
Coherent Manipulation of Electron Spins in the{Cu3}Spin Triangle Complex Impregnated in Nanoporous Silicon (2012)

We report on coherent manipulation of electron spins in an antiferromagnetically coupled spin triangle ${{\mathrm{Cu}}_{3}\mathrm{\text{\ensuremath{-}}}X}$ ($X=\mathrm{As}$, Sb) impregnated in freestanding nanoporous silicon (NS) by using 240 GHz microwave pulses. Rabi oscillations are observed and the spin coherence time is found to be ${T}_{2}=1066\text{ }\text{ }\mathrm{ns}$ at 1.5 K. This demonstrates that the ${{\mathrm{Cu}}_{3}\mathrm{\text{\ensuremath{-}}}X}\mathrm{\text{:}}\mathrm{NS}$ hybrid material provides a promising scheme for implementing spin-based quantum gates. By measuring the spin relaxation times of samples with different symmetries and environments we give evidence that a spin chirality is the main decoherence source of spin triangle molecules.
Discovery of Tetrahydropyridopyrimidines as Irreversible Covalent Inhibitors of KRAS-G12C with In Vivo Activity (2018)

<i>KRAS</i> is the most frequently mutated driver oncogene in human cancer, and KRAS mutations are commonly associated with poor prognosis and resistance to standard treatment. The ability to effectively target and block the function of mutated KRAS has remained elusive despite decades of research. Recent findings have demonstrated that directly targeting KRAS-G12C with electrophilic small molecules that covalently modify the mutated codon 12 cysteine is feasible. We have discovered a series of tetrahydropyridopyrimidines as irreversible covalent inhibitors of KRAS-G12C with in vivo activity. The PK/PD and efficacy of compound <b>13</b> will be highlighted.
Comparison of Time to Recurrence of Instability After Open and Arthroscopic Bankart Repair Techniques (2016)

Delayed time to recurrence after open Bankart repair suggests that the open technique may be more suited to withstand the high stress and demands of a heavy-duty profession (contact athletes and heavy manual labor).
Achieving Ultralow Turn-On Voltages in Organic Thin-Film Transistors: Investigating Fluoroalkylphosphonic Acid Self-Assembled Monolayer Hybrid Dielectrics (2019)

The properties of organic thin-film transistors (TFTs) and thus their ability to address specific circuit design requirements depend greatly on the choice of the materials, particularly the organic semiconductor and the gate dielectric. For a particular organic semiconductor, the TFT performance must be reviewed for different combinations of substrates, fabrication conditions, and the choice of the gate dielectric in order to achieve the optimum TFT and circuit characteristics. We have fabricated and characterized organic TFTs based on the small-molecule organic semiconductor 2,7-diphenyl[1]benzothieno[3,2-<i>b</i>][1]benzothiophene in combination with an ultrathin hybrid gate dielectric consisting of aluminum oxide and a self-assembled monolayer. Fluoroalkylphosphonic acids with chain lengths ranging from 6 to 14 carbon atoms have been used to form the self-assembled monolayer in the gate dielectric, and their influence on the TFT characteristics has been studied. By optimizing the fabrication conditions, a turn-on voltage of 0 V with an on/off current ratio above 10<sup>6</sup> has been achieved, in combination with charge-carrier mobilities up to 0.4 cm<sup>2</sup>/V s on flexible plastic substrates and 1 cm<sup>2</sup>/V s on silicon substrates.
Hiding information inside structured shapes (2010)

This paper describes a new technique for embedding a message within structured shapes. It is desired that any changes in the shape owing to the embedded message are invisible to a casual observer but detectable by a specialized decoder. The message embedding algorithm represents shape outlines as a set of cubic Bezier curves and straight line segments. By slightly perturbing the Bezier curves, a single shape can spawn a library of similar-looking shapes each corresponding to a unique message. This library is efficiently stored using Adaptively Sampled Distance Fields (ADFs) which also facilitate rendering of the modified shapes at the desired resolution and fidelity. Given any modified shape, a forensic detector applies Procrustes analysis to determine the embedded message. Results of an extensive subjective test confirm that the shape modifications are indeed unobtrusive. Further, to test the recovery of the message bits in noisy physical environments, a text document is put through a print-photocopy-scan process. Message recovery is found to be stable even after multiple rounds of photocopying.
Pilot power management in radio network planning for WCDMA networks (2005)

The high price of auction-based 3G licences and the growing competition in telecommunications market is putting enormous pressure on manufacturers and operators to configure the next-generation mobile network in the most cost-effective way possible providing high quality 3G services. Therefore, aiming to improve overall network performance and to ensure efficient utilization of network resources, radio network planning and optimization became even more important thar. in previous generation networks. On the other hand, in 3G networks, due to support of multiple services, high data rates, low frequency reuse, higher spectral loading and interference levels, and much uncertainty about future traffic growth. these processes became more challenging tasks.This thesis addresses the problem of pilot power optimization in WCDMA (Wideband Code Division Multiple Access) networks studying such issues as a trade-off between coverage of the service area and pilot power consumption, load balancing, and soft handover control. In the thesis, the author presents a number of pilot power optimization models, discusses the solution approaches. and reports numerical results obtained for test networks of various sizes based on real planning scenarios.
Relation of Tubular Interstitial Disease to Renal Function (2015)

In vitro concentrative transport of PAH-3H was evaluated in human renal biopsies by section freeze-dry autoradiography. Renal cortical tissue obtained by biopsy was incubated in vitro in medium containing PAH-3H, and section freeze-dry autoradiographs prepared. The autoradiographs demonstrated that the number of proximal tubules which accumulate PAH-3H in vitro varies inversely with the amount of tubular interstitial disease and directly with glomerular filtration rate. In order to further examine the mechanisms of tubular-interstitial disease, we have developed a technique for simultaneous fluorescent microscopy and autoradiography in single freeze-dried sections. This technique permits evaluation of the relationship between concentrative transport and immunoglobulin deposition in individual tubules and should increase our knowledge of the biologic significance of immunoglobulin deposits in proximal tubules.
The leishmanicidal activity of oleuropein (2016)

Different datasets on which the conclusions of the manuscript rely.
Extending Effective Area of Fundamental Mode in Optical Fibers (2009)

High power fiber lasers have become well established in many commercial realms. However, the amplification of ultrafast pulses to higher pulse energies in ytterbium-doped fibers remains very challenging due to nonlinear effects. We have demonstrated a new class of optical fibers based on resonantly enhanced leakage channels to extend the effective mode area of conventional single mode fibers by over two orders of magnitudes. This new class of fibers paves the way for a new breed of diffraction-limited kW-level ultrafast lasers, which can usher in a new age of high peak and average power ultrafast laser science as well as many new industrial applications in material processing.
2781. Statistical Modeling to Predict Maternal RSV Vaccine Efficacy from Neutralizing Titers (2019)

Abstract Background In the United States, respiratory syncytial virus (RSV) is the leading cause of respiratory-related hospitalization in infants. The well-studied efficacy of the prophylactic monoclonal antibody, palivizumab, at preventing RSV disease in the highest risk infants provides proof of mechanism that serum neutralizing antibody protects against RSV. The expense and burden of monthly antibody injections limit the utility of palivizumab, leaving a large unmet medical need. Maternal immunization, with transplacental transfer of antibodies to the fetus, is an alternative, highly practical approach to protect many more infants. Methods Levels of protection by known palivizumab serum concentrations provide a basis for predicting maternal RSV vaccine efficacy in infants based on serum neutralizing antibody titers elicited in vaccine clinical trials, using statistical modeling to compensate for differences between palivizumab prophylaxis and maternal immunization. The model adjusts for the dependency of maternal vaccine responses on pre-immunization RSV neutralizing titers, exponential decay of maternal antibodies in infants, and exponentially decreasing airway resistance (reducing RSV disease risk) as infants grow. Results The rates of severe RSV disease by age projected from the model match the pattern of US infant hospitalization for RSV, with a peak at 1.5 months of age. The model relates vaccine-elicited increases in maternal RSV neutralizing titers to predicted reductions in severe RSV disease in infants from 0 to 6 months of age. Conclusion Statistical modeling of maternal RSV vaccine efficacy based on elicited RSV neutralizing titers provides a rational basis for decision-making during RSV vaccine development. Disclosures All authors: No reported disclosures.
Performance of amplify-and-forward relay networks with interference-limited destination in rician fading environments (2014)

A study on the effect of co-channel interference (CCI) on the performance of fixed-gain amplify-and-forward (AF) relay networks is presented in this paper. The analysis assumes a noise-limited relay and an interference-limited destination. Furthermore, both the source-relay, the relay-destination channels of the desired user and interferers' channels are assumed to follow the Rician distribution. Approximate but accurate expressions are derived in this work for the outage probability and the average symbol error rate (SER) for independent non-identically distributed (i.n.d.) and independent identically distributed (i.i.d.) cases of desired user channels. Furthermore, a look into the asymptotical high signal-to-noise ratio (SNR) performance has been taken and the diversity order and coding gain of the considered system are determined. The accuracy of the analytical results are validated by Monte-Carlo simulations. Findings show that when the second hop SNR is kept fixed, a noise floor appears in the results and hence, a zero diversity gain is achieved by the system. Also, results illustrate that the system performance is dominated by interference affecting the worst hop. Finally, findings illustrated the inaccuracy of approximating the Rician fading by the Nakagami-m model in systems with Line-of-Sight (LoS) components.
Phase Stability Measurement of an Optical Two-Tone Signal Applied to a Signal Reference Source for Millimeter and Sub-Millimeter Wave Interferometer (2006)

Abstract Local signal generation with high phase stability is one of the key elements of an interferometer system. In the ALMA (Atacama Large Millimeter/submillimeter Array) project, we have plans to generate and transmit a micro/millimeter-wave LO (Local Oscillator) reference signal as an optical two-tone signal. To realize this, we introduce a method to generate an optical two-tone signal by double sideband suppressed carrier modulation with a lithium niobate ($\mathrm{LiNbO}_3$) Mach–Zehnder optical modulator. The phase instability of the LO signal causes a loss of coherence in the interferometer. We measured the phase instability and estimated the coherence loss while assuming the highest frequency of ALMA LO. The observed Allan standard deviation for 22 GHz was $1.9 \times 10^{-14}$ at 1 s. Additional noise was found at a longer time scale than 4 s; however, the reason is not well understood at this stage. If this additional noise was classified as white frequency noise, the estimated coherence loss was 5.2% when 938 GHz frequency and a 100-s integration time were assumed. On the other hand, if this additional noise was caused by some other effect, for example phase fluctuation of the amplifier, the coherence loss was estimated to be 0.33% at 938 GHz frequency (100 s).
Radioresistance in rhabdomyosarcomas: Much more than a question of dose (2022)

Management of rhabdomyosarcoma (RMS), the most common soft tissue sarcoma in children, frequently accounting the genitourinary tract is complex and requires a multimodal therapy. In particular, as a consequence of the advancement in dose conformity technology, radiation therapy (RT) has now become the standard therapeutic option for patients with RMS. In the clinical practice, dose and timing of RT are adjusted on the basis of patients' risk stratification to reduce late toxicity and side effects on normal tissues. However, despite the substantial improvement in cure rates, local failure and recurrence frequently occur. In this review, we summarize the general principles of the treatment of RMS, focusing on RT, and the main molecular pathways and specific proteins involved into radioresistance in RMS tumors. Specifically, we focused on DNA damage/repair, reactive oxygen species, cancer stem cells, and epigenetic modifications that have been reported in the context of RMS neoplasia in both <i>in vitro</i> and <i>in vivo</i> studies. The precise elucidation of the radioresistance-related molecular mechanisms is of pivotal importance to set up new more effective and tolerable combined therapeutic approaches that can radiosensitize cancer cells to finally ameliorate the overall survival of patients with RMS, especially for the most aggressive subtypes.
Introduction to the Special Issue on Processing Morphologically Rich Languages (2009)

The 12 papers in this special issue span a variety of speech and language processing applications highlighting the challenges and providing solutions for dealing with the morphological complexity of different languages.
Smart Networked Elements in Support of ISHM (2008)

At the core of ISHM is the ability to extract information and knowledge from raw data. Conventional data acquisition systems sample and convert physical measurements to engineering units, which higher-level systems use to derive health and information about processes and systems. Although health management is essential at the top level, there are considerable advantages to implementing health-related functions at the sensor level. The distribution of processing to lower levels reduces bandwidth requirements, enhances data fusion, and improves the resolution for detection and isolation of failures in a system, subsystem, component, or process. The Smart Networked Element (SNE) has been developed to implement intelligent functions and algorithms at the sensor level in support of ISHM.
Supplementary Figure 4 from A687V EZH2 Is a Driver of Histone H3 Lysine 27 (H3K27) Hypertrimethylation (2023)

&lt;p&gt;Supplementary Figure 4: Sanger sequencing chromatograms of EZH2 mutations in acute lymphoblastic leukemia cell lines&lt;/p&gt;
Origin of metastable oligomers and their effects on amyloid fibril self-assembly (2018)

Assembly of rigid amyloid fibrils with their characteristic cross-β sheet structure is a molecular signature of numerous neurodegenerative and non-neuropathic disorders. Frequently large populations of small globular amyloid oligomers (gOs) and curvilinear fibrils (CFs) precede the formation of late-stage rigid fibrils (RFs), and have been implicated in amyloid toxicity. Yet our understanding of the origin of these metastable oligomers, their role as on-pathway precursors or off-pathway competitors, and their effects on the self-assembly of amyloid fibrils remains incomplete. Using two unrelated amyloid proteins, amyloid-β and lysozyme, we find that gO/CF formation, analogous to micelle formation by surfactants, is delineated by a "critical oligomer concentration" (COC). Below this COC, fibril assembly replicates the sigmoidal kinetics of nucleated polymerization. Upon crossing the COC, assembly kinetics becomes biphasic with gO/CF formation responsible for the lag-free initial phase, followed by a second upswing dominated by RF nucleation and growth. RF lag periods below the COC, as expected, decrease as a power law in monomer concentration. Surprisingly, the build-up of gO/CFs above the COC causes a progressive increase in RF lag periods. Our results suggest that metastable gO/CFs are off-pathway from RF formation, confined by a condition-dependent COC that is distinct from RF solubility, underlie a transition from sigmoidal to biphasic assembly kinetics and, most importantly, not only compete with RFs for the shared monomeric growth substrate but actively inhibit their nucleation and growth.
Rotation barriers in condensed rings: an extension of Clar's stability rule (2005)

Abstract The rotation barrier for a substituent OH in systems of condensed benzene rings was studied using density functional theory. The barrier height depends on the position of the hydroxy group and the number of independent benzene rings in the condensed ring system, in agreement with Clar's π‐electron sextet stability model. Investigating OH‐derivatized polycenes with as many as 19 condensed rings showed that increasing the total size of the system does not contribute significantly to the rotation barrier. Copyright © 2005 John Wiley &amp; Sons, Ltd.
Reactivity of Peroxynitrite and Nitric Oxide with LDL (2005)

Low density lipoprotein (LDL) oxidation by peroxynitrite is a complex process, finely modulated by control of peroxynitrite formation, LDL availability and free-radical scavenging by nitric oxide (*NO), ascorbate and alpha-tocopherol (alpha -TOH). In the presence of CO2, lipid targets are spared at the expense of surface constituents. Since surface damage may lead to oxidation-induced LDL aggregation and particle recognition by scavenger receptors, CO2 cannot be considered an inhibitor of peroxynitrite-dependent LDL modifications. Chromanols, urate and ascorbate cannot scavenge peroxynitrite in the vasculature, although intermediates of urate oxidation and high ascorbate concentrations may do soin vitro. Most if not all of the protection against peroxynitrite-induced LDL oxidation afforded by urate, ascorbate, chromanols and also*NO should be considered to depend on their free radical scavenging abilities, including inactivation of lipid peroxyl radicals (LOO),*NO2, and CO3*-; as well as their capacity to reduce high oxidation states of metal centers. Peroxynitrite direct interception by reduced manganese (II) porphyrins is possibly the most powerful although unspecific strategy to inhibit peroxynitrite reactions. In light of the recent demonstration of nitrated bioactive lipids in vivo, renewed interest in the mechanisms of peroxynitrite- and nitric oxide-mediated lipid nitration and nitrosation is guaranteed.
Synthesis of Reduced Transition-Metal Oxides with Hydroxylamine Hydrochloride (1998)

Addition of aqueous hydroxylamine hydrochloride in aqueous solutions of ammonium (MO4)n- salts at a fixed pH, maintained by adding HCl drops, has yielded amorphous, reduced oxides of intermediate valence such as VO2, Cr2O3, Fe3O4, MoO2, and (NH4)0.33WO3. The as-prepared products crystallize on heating to 300−500 °C.
Biologically Active Triterpenoids fromCephalaria ambrosioides (2009)

The roots of Cephalaria ambrosioides yielded a new triterpene, 6alpha-hydroxyhederagenic acid ( 1), in addition to the known triterpene hederagenic acid ( 2) and four corresponding saponins, leontoside A (or akeboside Stb) ( 3), kalopanax saponin A (or alpha-hederin) ( 4), saponin PG (or sapindoside B) ( 5), and dipsacoside B ( 6). Their structures have been elucidated on the basis of their spectral data (MS, 1 D and 2 D NMR) and by some chemical transformations. The extract and all isolated compounds were evaluated for their antimicrobial, molluscicidal and IN VITRO cytotoxic activities. All compounds showed strong antimicrobial activity (MIC values 1.80 - 2.50 microg/mL), with 5 and 6 exhibiting activities comparable to those of standard antibiotics. Moreover, compounds 3 - 5 were active against all assayed cancer cell lines, whereas compounds 3 and 4 exhibited higher activities against Biomphalaria Glabrata snails, with minimum inhibitory concentrations of 5.4 and 6.2 microg/mL, respectively.