gebhart/patrepeval huggingface dataset:
Abstract B76: Targeting Mcl-1 for radiosensitization of pancreatic cancers (2015)

Abstract In order to identify targets whose inhibition may enhance the efficacy of chemoradiation in pancreatic cancer and, thus, improve survival in patients with locally advanced pancreatic cancer, we conducted an siRNA library screen of 8,800 genes. We identified Mcl-1 (myeloid cell leukemia-1), an anti-apoptotic member of the Bcl-2 family, as a target for sensitizing pancreatic cancer cells to gemcitabine-radiation. Thus, we investigated Mcl-1 inhibition by genetic (siRNA) and pharmacological (small molecule) approaches as a radiosensitizing strategy in pancreatic cancer cells. Mcl-1 depletion by siRNA radiosensitized BxPC-3, Panc-1, and MiaPaCa-2 cells with radiation enhancement ratios (RER) of 1.5±0.06, 1.4±0.03, and 1.3±0.01, respectively, and caused Caspase-3 activation and PARP cleavage. We next tested the ability of the recently identified, selective, small molecule inhibitor of Mcl-1, UMI-77 (Abulwerdi F et al., Mol Cancer Ther, 2014), to inhibit the anti-apoptotic functions of Mcl-1 and radiosensitize in pancreatic cancer cells. Consistent with inhibition of Mcl-1 anti-apoptotic function, UMI-77 (1-5uM) caused dissociation of Mcl-1 from the pro-apoptotic protein Bak. Under these same conditions, UMI-77 produced significant radiosensitization in BxPC-3 and Panc-1 cells (RER: 1.5±0.1 and 1.3±0.04, respectively; P&amp;lt;0.05) with minimal radiosensitization of MiaPaCa-2 cells (1.2±0.07). Since Mcl-1 expression levels are highest in BxPC-3 and Panc-1 cells and lowest in MiaPaCa-2 cells, these results suggest that elevated Mcl-1 protein levels may be a biomarker for radiosensitization by Mcl-1 inhibition. In addition, radiosensitization by UMI-77 was associated with Caspase-3 activation, PARP cleavage, and increased sub-G1 DNA content. In contrast, ABT-737, a well-established inhibitor of Bcl-2, Bcl-XL, and Bcl-w, failed to radiosensitize pancreatic cancer cells suggesting the unique importance of Mcl-1 in radiation survival. Taken together, these results validate Mcl-1 as a target for radiosensitization of pancreatic cancer cells and demonstrate the efficacy of small molecules which displace Mcl-1 from Bak/Bax as radiosensitizers in pancreatic cancer. Furthermore, these results support continued investigation of UMI-77 and its analogues in animal models and in combination with gemcitabine-radiation as a strategy for radiation and chemoradiation sensitization of pancreatic cancers. Citation Format: Qiang Zhang, Dongping Wei, Jason Schreiber, Tasneem Kausar, Theodore Lawrence, Yi Sun, Zaneta Nikolovska-Coleska, Meredith A. Morgan. Targeting Mcl-1 for radiosensitization of pancreatic cancers. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Innovations in Research and Treatment; May 18-21, 2014; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2015;75(13 Suppl):Abstract nr B76.
Highly active lipase immobilized on biogenous iron oxide via an organic bridging group: the dramatic effect of the immobilization support on enzymatic function (2011)

Iron-oxidizing bacteria, Leptothrix ochracea, produce biogenous iron oxide (BIO), while the heat treatment of BIO gives its magnetized material (m-BIO). In this study, they were chemically modified with silane coupling agents to give organic–inorganic hybrid materials, which were then used as immobilization supports for enzymes. BIO-M, which was prepared by modifying BIO with 3-methacryloxypropyltrimethoxysilane, was found to be the best immobilization support. The immobilized lipases showed remarkably high catalytic activity; for example, Burkholderia cepacialipase (BCL) immobilized on BIO-M showed a turnover frequency of 33 000 h−1 for 1-phenylethanol (1a). m-BIO-M, which was prepared by modifying m-BIO with 3-methacryloxypropyltrimethoxysilane, was also used as an immobilization support. Although the lipases immobilized on m-BIO-M showed lower catalytic activity than those immobilized on BIO-M, the former could be separated and reused easily by using a magnet. These immobilized enzymes could be recycled at least five times and are environmentally benign biocatalysts.
Silicon impurity-induced layer disordering of AlGaN/AlN superlattices (2010)

Impurity-induced layer disordering is demonstrated in Al0.1Ga0.9N/AlN superlattices grown by metal-organic vapor phase epitaxy. During growth at temperatures as low as 885 °C and under post growth annealing at 1000 °C in N2 the heterointerfaces of Si-doped (Si concentration &amp;gt;8×1019 cm−3) superlattices exhibit layer disordering (intermixing) while the unintentionally doped superlattices remain stable. Shifts in the intersubband energy transitions and scanning transmission electron microscope images showing changes in the layer abruptness are used to verify layer disordering due to Si diffusion in Al0.1Ga0.9N/AlN superlattices.
An M-dwarf star in the transition disk of Herbig HD 142527; Physical parameters and orbital elements (2015)

HD 142527A is one of the most studied Herbig Ae/Be stars with a transitional disk, as it has the largest imaged gap in any protoplanetary disk: the gas is cleared from 30 to 90 AU. The HD142527 system is also unique in that it has a stellar companion with a small mass compared to the mass of the primary star. This factor of ~20 in mass ratio between the two objects makes this binary system different from any other YSO. The HD142527 system could therefore provide a valuable test bed. This low-mass stellar object may be responsible for both the gap and dust trapping observed by ALMA at longer distances. We observed this system with the NACO and GPI instruments using the aperture masking technique. Aperture masking is ideal for providing high dynamic range even at very small angular separations. We present the spectral energy distribution for HD142527A and B. Brightness of the companion is now known from the R band up to the M' band. We also followed the orbital motion of HD 142527B over a period of more than two years. The SED of the companion is compatible with a T=3000+/-100K object in addition to a 1700K blackbody environment (likely a circus-secondary disk). From evolution models, we find that it is compatible with an object of mass 0.13+/-0.03Msun, radius 0.90+/-0.15Rsun, and age $1.0^{+1.0}_{-0.75}$Myr. This age is significantly younger than the age previously estimated for HD142527A. Computations to constrain the orbital parameters found a semi major axis of $140^{+120}_{-70}$mas, an eccentricity of 0.5+/-0.2, an inclination of 125+/-15 degrees, and a position angle of the right ascending node of -5+/-40 degrees. Inclination and position angle of the ascending node are in agreement with an orbit coplanar with the inner disk, not coplanar with the outer disk. Despite its high eccentricity, it is unlikely that HD142527B is responsible for truncating the inner edge of the outer disk.
Effects of Time and Growth Media on Short-Chain Fatty Acid Production by Bacteroides fragilis (1975)

Gas-liquid chromatography was used to monitor the evolution of short chain fatty acids by Bacteroides fragilis in five media. Acetic and succinic acids, the prominent end products encountered, were readily detected within 24 h. Propionic, isobutyric, isovaleric, and lactic acids were usually recorded in more limited quantities. Maximum rates of bacterial multiplication, glucose catabolism, and end-production coincided with the first 24 h in carbohydrate-supplemented media. Extended incubation (672 h) favored substantial succinate increases in three of five media. These observations suggest that incubation time and composition of the medium are important determinants in short chain fatty acid production by B. fragilis.
Synthesis and Preliminary Evaluation of Biological Activity of Glycoconjugates Analogues of Acyclic Uridine Derivatives (2018)

Herein we present the methodology for obtaining glycosyltransferase inhibitors, analogues of natural enzyme substrates of donor-type: UDP-glucose and UDP-galactose. The synthesis concerned glycoconjugates, nucleoside analogues containing an acyclic ribose mimetic linked to a uracil moiety in their structure. The biological activity of the synthesised compounds was determined on the basis of their ability to inhibit the model enzyme action of β-1,4-galactosyltransferase from bovine milk. The obtained results allowed to expand and supplement the existing library of synthetic compounds that are able to regulate the biological activity of enzymes from the GT class.
Discovery of a Tetracyclic Quinoxaline Derivative as a Potent and Orally Active Multifunctional Drug Candidate for the Treatment of Neuropsychiatric and Neurological Disorders (2014)

We report the synthesis and structure-activity relationships of a class of tetracyclic butyrophenones that exhibit potent binding affinities to serotonin 5-HT(2A) and dopamine D2 receptors. This work has led to the discovery of 4-((6bR,10aS)-3-methyl-2,3,6b,9,10,10a-hexahydro-1H,7H-pyrido[3',4':4,5]pyrrolo[1,2,3-de]quinoxalin-8-yl)-1-(4-fluorophenyl)-butan-1-one 4-methylbenzenesulfonate (ITI-007), which is a potent 5-HT(2A) antagonist, postsynaptic D2 antagonist, and inhibitor of serotonin transporter. This multifunctional drug candidate is orally bioavailable and exhibits good antipsychotic efficacy in vivo. Currently, this investigational new drug is under clinical development for the treatment of neuropsychiatric and neurological disorders.
Octahedral Bipyridine and Bipyrimidine Dioxomolybdenum(VI) Complexes: Characterization, Application in Catalytic Epoxidation, and Density Functional Mechanistic Study (2002)

Complexes of the general formula [MoO(2)X(2)L(2)] (X=Cl, Br, Me; L(2)=bipy, bpym) have been prepared and fully characterized, including X-ray crystallographic investigations of all six compounds. Additionally, the highly soluble complex [MoO(2)Cl(2)(4,4'-bis(hexyl)-2,2'-bipyridine)] has been synthesized. The reaction of the complexes with tert-butyl hydroperoxide (TBHP) is an equilibrium reaction, and leads to MoV(I) eta(1)-alkylperoxo complexes that selectively catalyze the epoxidation of olefins. Neither the Mo-X bonds nor the Mo-N bonds are cleaved during this reaction. These experimental results are supported by theoretical calculations, which show that the attack of TBHP at the Mo center through the X-O-N face is energetically favored and the TBHP hydrogen atom is transferred to a terminal oxygen of the Mo=O moiety. After the attack of the olefin on the Mo-bound peroxo oxygen atom, epoxide and tert-butyl alcohol are formed. The latter compound acts as a competitive inhibitor for the TBHP attack, and leads to a significant reduction in the catalytic activity with increasing reaction time.
Abstract 424: Loss of Sirt2 Protects Against Pressure Overload- and Ischemic Reperfusion Injury-induced Cardiac Dysfunction (2020)

Introduction: Sirtuins are NAD+ dependent deacetylases and critical regulators of energy metabolism and response to oxidative stress. Sirtuin2 (SIRT2) is a cytoplasmic member of the sirtuin family, and has been shown to regulate cellular iron homeostasis through deacetylation of nuclear factor erythroid-derived 2-related factor 2 (NRF2). However, whether SIRT2-NRF2 pathway is involved in the development of heart failure remains unknown. Methods and results: To investigate the functional role of SIRT2 in the response to cardiac stress, SIRT2 knockout (KO) mice and their littermate controls were subjected to pressure overload by transverse aortic constriction (TAC). SIRT2 KO had normal appearance and cardiovascular parameters at baseline. However, in response to TAC, Sirt2 -/- mice displayed resistance to the pathological hypertrophic response, whereas wild type (WT) mice developed cardiac hypertrophy and heart failure. In addition, SIRT2 KO mice displayed less cardiac damage after /reperfusion injury. SIRT2 knockdown in neonatal rat cardiomyocytes (NRCM) reduced reactive oxygen species (ROS) production and cell death after H2O2 treatment. Since cellular oxidative stress is one of major contributor of cardiac dysfunction caused by both I/R injury and pressure overload, we examined whether NRF2 is associated with SIRT2-mediated cardiac response to oxidative stress. Levels of NRF2 was upregulated in NRCM with SIRT2 knockdown and treated with H2O2 compared to wild type (WT) cells. Moreover, NRF2 is translocated into the nucleus and its anti-oxidant target proteins are upregulated in NRCM with SIRT2 knockdown. SIRT2 was also found to bind and deacetylate NRF2 directly as determined by co-immunoprecipitation studies. This led to a reduction of its nuclear translocation and transcriptional activity. Finally, knockdown of both SIRT2 and NRF2 diminished the effects of SIRT2 knockdown on ROS production and cellular damage. Conclusion: These results indicate that SIRT2 contributes to pressure overload and I/R injury induced heart impairment in mice, and promotes oxidative stress injury in cardiomyocytes via deacetylating NRF2 and altering its activity.
Red organic light emitting device made from triphenylene hexaester and perylene tetraester (2001)

Saturated red light emission from organic light emitting diodes is less common than emission in the green or the blue. Most organic red light emitting devices are based on rare earth complexes, mainly europium, which are known to exhibit stability problems. The present article describes new diodes made of indium tin oxide-coated glass/triphenylene hexaether/perylene tetraester/aluminum. The band diagram was determined by ultraviolet photoemission spectroscopy, cyclic voltammetry, scanning tunneling microscopy, and absorbance measurements. The interfaces between electrodes and organic layers were investigated by x-ray photoelectron spectroscopy. The current–voltage and luminance–voltage characteristics are very reproducible from device to device, with an emission peak at 620 nm and a full width at half maximum of 80 nm, a current rectification ratio of about 30, I∼V2 at low voltages and I∼Lum∼V6 at higher voltages.
Detection of genetically modified maize DNA fragments in the intestinal contents of pigs fed StarLink CBH351. (2003)

We tried to detect DNA fragments derived from maize in the intestinal contents of pigs fed genetically modified (GM) StarLink CBH351 maize (SL) or non-GM maize. Intestinal contents of 8 SL and 8 non-GM maize-fed pigs were collected at slaughter, and the genes of the recombinant cry9C and the maize intrinsic zein (Zel) were assayed by polymerase chain reaction (PCR) 3 times with a total of 4 primer pairs of different expected lengths. The cry9C gene (either 103 or 170 bp) was detected in the rectal contents (with a frequency of 25-37.5%) and in the cecal contents (25-50%) of the pigs fed SL. In a similar fashion, the zein (Zel) gene (either 242 or 329 bp) was detected in the rectal contents (with a frequency of 31.3%) and in the cecal contents (25-37.5%) of pigs fed on SL non-GM maize. These results suggested that ingested DNA was not totally degraded, but is present in a form detectable by PCR.
Dissolution of dissolving pulp in alkaline solvents after steam explosion pretreatments (2011)

Abstract In this project different aqueous based solvent systems were investigated for the dissolution of steam exploded (STEX) dissolving pulps prior to a coagulation step for preparation of textile fibers. The pulp samples studied could, to a large degree, be dissolved in a NaOH/urea/thiourea system, but there are always residuals, irrespective of the conditions. The dissolution process appeared to be kinetically controlled, as prolonged retention time decreased the amount of residuals. A pre-cooled NaOH/urea/thiourea system, and a retention time of 60 h generated the lowest amount (6%) of residuals of the STEX pretreated dissolving pulp studied. Some fundamental results are described and a model for dissolution of dissolving pulp fibers is proposed.
Nonblocking k-compare-single-swap (2003)

The current literature o .ers two extremes of nonblocking software synchronization support for concurrent data structure design:intricate designs of specific structures based on single-location operations such as compare-and-swap (CAS), and general-purpose multilocation transactional memory implementations. While the former are sometimes efficient, they are invariably hard to extend and generalize. The latter are .exible and general, but costly. This paper aims at a middle ground:reasonably efficient multilocation operations that are general enough to reduce the design difficulties of algorithms based on CAS alone. We present an obstruction-free implementation of an atomic k-location-compare single-swap (KCSS)operation. KCSS allows for simple nonblocking manipulation of linked data structures by overcoming the key algorithmic difficulty in their design: making sure that while a pointer is being manipulated, neighboring parts of the data structure remain unchanged. Our algorithm is efficient in the common uncontended case: A successful k location KCSS operation requires only two CAS operations, two stores, and 2 k noncached loads when there is no contention. We therefore believe our results lend themselves to efficient and flexible nonblocking manipulation of list-based data structures in today's architectures.
A Carbazole Derivative Synthesis for Stabilizing the Quadruplex Structure (2003)

Abstract A new molecule of 3,6‐Bis(1‐methyl‐4‐vinylpyridium iodine)carbazole ( BMVC ) was synthesized for stabilizing the quadruplex structure of human telomeric sequence of d(T 2 AG 3 ) 4 in vitro . Mixing BMVC with the DNA can raise the melting temperature of the d(T 2 AG 3 ) 4 by ∼ 13 °C, implying that BMVC could be a useful telomerase inhibitor. In addition, the fluorescence of the BMVC increased significantly upon interacting with the d(T 2 AG 3 ) 4 which may be useful as a G‐quadruplex specific marker.
Photonic Damascene Process for Low-Loss, High-Confinement Silicon Nitride Waveguides (2018)

We report on fabrication of high-confinement and low loss silicon nitride (Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> ) waveguides using the photonic Damascene process. This process scheme represents a novel fabrication approach enabling reliable, wafer-scale fabrication of highconfinement optical waveguides. A reflow step of the silica preform reduces sidewall scattering to values not attainable with conventional etching, and reduces losses and backscattering significantly, resulting in a waveguide attenuation of 5.5 dB/m. We discuss the critical aspects of the process in detail and demonstrate the fabrication of high stress Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> waveguides with unprecedentedly large dimensions (1.75 μm × 1.425 μm) providing high-confinement at midinfrared wavelengths. A device characterization strategy allowing for systematic extraction of statistically relevant loss values is discussed and reveals the effects of the sidewall smoothing.
Next-generation multimodality of nutrigenomic cancer therapy: sulforaphane in combination with acetazolamide actively target bronchial carcinoid cancer in disabling the PI3K/Akt/mTOR survival pathway and inducing apoptosis (2021)

Combining SFN+AZ significantly inhibits the PI3K/Akt/mTOR pathway and significantly reducing 5-HT secretion in carcinoid syndrome.
Nonlinear Filter Evaluation for Estimating Vehicle Position and Velocity Using Satellites (1973)

Approximate nonlinear filtering theory is applied to the estimation of vehicle position and velocity in three demensions using sequential range measurements to three known locations. The particular case studied is a satellite air traffic control system which utilizes range measurements to two geostationary satellites and an altitude measurement. Three approximate filters are examined as suboptimal realizations of the minimum-variance filter and simulation results are presented to show that simple first-order approximation is an adequate representation. The parametric relationship between state covariance, measurement noise, vehicle maneuver structure, data rate, and system geometry is presented.
How to Enforce European eCall (2009)

Since early 2000 eCall is launched as a part of the eSafety initiative to help in fulfilling the goal of reducing the number of accidents and road victims in the European Union (EU). eCall, an automatic emergency call system that is triggered after a severe accident (e.g. with an airbag deployment) has been targeted to be available on new vehicles in the EU from 2010. A Memorandum of Understanding has been created but so far only 15 of the 27 EU member states have signed, but many companies have signed. Interestingly enough, even consumers are requesting safety functions on new vehicles. From today’s perspective a launch in 2010 seems unlikely, as too many open topics exist, mainly the lack of standardization and a viable business case – yes, protecting life and health requires reasonable investment that has to be recovered. Despite, there seem to be ways to enforce the eCall introduction, and after discussing eCall roadblocks from Continental’s perspective we will to inspire on how to remove these roadblocks.
Growth of the pulmonary artery after neonatal balloon dilatation of the right ventricular outflow tract in an infant with the tetralogy of Fallot and atrioventricular septal defect. (1989)

A two week old girl with tetralogy of Fallot and atrioventricular septal defect underwent palliation, for severe hypoxaemia, by balloon dilatation to the right ventricular outflow tract. This procedure was repeated once over the next eight months without complications. Serial right ventricular angiograms showed growth of the hypoplastic pulmonary ring ("annulus"), trunk, and arteries. Balloon dilatation is an alternative palliative procedure for patients with the tetralogy of Fallot which may promote growth of the pulmonary ring, trunk, and arteries.
Systematic analysis of human antibody response to ebolavirus glycoprotein reveals high prevalence of neutralizing public clonotypes (2022)

SUMMARY Understanding the human antibody response to emerging viral pathogens is key to epidemic preparedness. As the size of the B cell response to a pathogenic virus protective antigen is undefined, we performed deep paired heavy and light chain sequencing in EBOV-GP specific memory B cells, allowing analysis of the ebolavirus-specific antibody repertoire both genetically and functionally. This approach facilitated investigation of the molecular and genetic basis for evolution of cross-reactive antibodies by elucidating germline-encoded properties of antibodies to EBOV and identification of the overlap between antibodies in the memory B-cell and serum repertoire. We identified 73 public clonotypes to EBOV, 20% of which encoded antibodies with neutralization activity and capacity to protect in vivo . This comprehensive analysis of the public and private antibody repertoire provides insight into the molecular basis of the humoral immune response to EBOV-GP, which informs vaccine design of new vaccines and improved therapeutics.