gebhart/patrepeval huggingface dataset:
Differential DNA Hypermethylation of Critical Genes Mediates the Stage-Specific Tobacco Smoke-Induced Neoplastic Progression of Lung Cancer (2005)

Promoter DNA methylation status of six genes in samples derived from 27 bronchial epithelial cells and matching blood samples from 22 former/current smokers and five nonsmokers as well as 49 primary non-small cell lung cancer samples with corresponding blood controls was determined using methylation-specific PCR (MSP). Lung tumor tissues showed a significantly higher frequency of promoter DNA methylation in p16, MGMT, and DAPK (P < 0.05; Fisher's exact test). p16 promoter DNA methylation in tumors was observed at consistently higher levels when compared with all the other samples analyzed (P = 0.001; Fisher's exact test). ECAD and DAPK exhibited statistically insignificant differences in their levels of DNA methylation among the tumors and bronchial epithelial cells from the smokers. Interestingly, similar levels of methylation were observed in bronchial epithelial cells and corresponding blood from smokers for all four genes (ECAD, p16, MGMT, and DAPK) that showed smoking/lung cancer-associated methylation changes. In summary, our data suggest that targeted DNA methylation silencing of ECAD and DAPK occurs in the early stages and that of p16 and MGMT in the later stages of lung cancer progression. We also provide preliminary evidence that peripheral lymphocytes could potentially be used as a surrogate for bronchial epithelial cells to detect altered DNA methylation in smokers.
High-performance many-core networking (2015)

Operating systems play a key role in providing general purpose services to upper layer applications at the highest available performance level. The two design requirements --- generality and performance --- are however in contention: the more general purpose a service layer is, the more overhead it incurs in accessing domain-specific high-performance features provided by the layers beneath it. This trade-off comes to manifest in modern computer systems as the state-of-the-art has evolved from architectures with a few number of cores to systems employing a very large number of cores (many-core systems). Such evolution has rendered the networking layer in current operating systems inefficient as its general purpose design deprives it from a proper use of the large number of cores. In this paper we introduce DNAC (Dynamic Network Acceleration for Many-Core), a high-performance abstraction layer designed to target the maximum network performance available from the network interface in many-core general purpose operating systems.
A Model-Scale Wind-Tunnel Study of Main Rotor/Propeller Interference (2016)

A model-scale wind tunnel test was conducted to determine propulsive efficiency and relative vibration levels of a tail mounted propeller in the wake of a powered rotor and generic fuselage. Six-component propeller loads were measured for all test points with a focus on thrust and torque. Propeller and main rotor operating conditions were set to mimic low- and highspeed vehicle flight operations, simulating speeds from 105 kts to 200 kts. A total pressure wake survey conducted without the propeller installed was used to determine the propeller plane inflow characteristics. Propeller operation had no measureable effect on rotor trim whereas the main rotor states significantly altered the propeller performance. All propeller positions showed a propulsive efficiency increase relative to the isolated propeller data when operated in the rotor wake. No position showed noticeable vibration levels higher or lower than another. The highest propulsive efficiency was measured for the mid-height propeller position.
Using Hybrid Propulsion Autonomous Marine Vehicles to Better Characterize Geomagnetic Fields Offshore (2016)

Abstract This paper describes a study conducted to develop new capabilities for offshore geomagnetic surveying. To conduct the research we equipped two (2) new generation autonomous marine vehicles (AMVs) with towed marine magnetometers. This paper describes the validation study of the measurement system offshore between 2013 and 2015 that compares a regular pattern with main, tie and perimeter lines. It was investigated whether the new AMV was suitable for use as a "base station" to monitor time variations of the disturbance field. The geomagnetic data measured by the vehicles from May 11 - 14, 2015 was analyzed and compared against data obtained from the USGS Honolulu Geomagnetic Observatory (HON). Highly sensitive sensors were used to establish the minimum required separation between the AMV and the magnetic sensor payload. Directional drilling requires accurate knowledge of the geomagnetic field direction and strength in the wellbore. To compute wellbore azimuth, the measurement while drilling (MWD) tool takes a measurement of the magnetic field and then the directional driller compares it with the geomagnetic field reference in order to position the wellbore in real-time while drilling. By utilizing the AMV we were able to accurately map the crustal field direction and strength in the area of interest where the drilling activity for oil and gas will take place. This study shows that the AMV is ideally suited to carry out geomagnetic surveys in offshore remote locations. Correction for the disturbance field is essential for crustal field mapping that requires a base station recording the variations of the disturbance field. A second AMV circulating at a fixed location provides a more accurate base station than a land-based station. This is due to two factors: The land- based station is further away from the measurement site and the disturbance fields are different on land than in the ocean, due to the different electrical conductivity of the subsurface. The new generation AMV offers distinct advantages for data collection in offshore environments. Their low cost compared to seaborne or airborne vehicle allow them to be deployed in tandem and collect data repeatedly over predefined areas yielding accurate measurements to determine the disturbance and crustal fields. It solves the problem of accurately mapping the geomagnetic reference field in offshore locations that previously unknown of.
Silver Clusters Embedded in Glass as a Perennial High Capacity Optical Recording Medium (2010)

Three-dimensional optical recording by laser-induced fluorescent silver clusters is demonstrated in glass. The fluorescence properties of these stable clusters can be altered, depending on the glass recording exposure conditions. A “Blu-ray”-like drive enables readout of the information inside the glass without cross-talk and photobleaching (see figure). This original recording medium can provide an answer to the societal problem of long-term high-density data storage.
Entflechtung überlagernder Multipletts in zweidimensionalen NMR‐Korrelationsspektren durch selektive Inversion der Spins der Kopplungspartner (1990)

Saubere und einfache zweidimensionale Multiplettmuster anstelle von überlagernden Multipletts können mit einem NMR‐Experiment erhalten werden, das mit selektiven Pulsen eine kleine Region des Spektrums herausgreift. Die Muster eines ausgewählten Multipletts werden dabei durch Veränderung der scheinbaren Vorzeichen der Kopplungskonstanten manipuliert. Diese Technik eignet sich nicht nur um überlagernde Signale zu trennen, sondern auch zum Testen von Hypothesen bezüglich des untersuchten Kopplungsnetzwerkes.
Molecular Friction as a Tool to Identify Functionalized Alkanethiols (2010)

By using the nanografting method, well-defined nanoscale patches of alkanethiols were constructed in a self-assembled monolayer (SAM) matrix on an atomically flat gold (Au(111)) surface. A series of nanografted patches, composed of alkanethiols with different end groups (-CH(3), -CF(3), -OH, -SH, -COOH, and -NH(2)), were analyzed in detail by a combination of atomic force microscopy (AFM) height and quantitative lateral friction measurements. By constructing a series of nanografted patches of methyl-terminated thiols with various chain lengths, it was shown that the absolute friction of the nanografted patches was always smaller than that of the surrounding SAM matrix, demonstrating that, because of the spatially confined self-assembly during nanografting, SAMs show less defects. In addition, the friction gradually increased for decreasing alkane chain length as expected, although a subtle odd-even effect was observed. The study of thiols with functionalized end groups (-CF(3), -OH, -SH, -COOH, and -NH(2)) gave specific insights in orientation, packing, and structure of the molecules in the SAMs. Depending on the thiol end groups, these nanografted patches exhibited large and specific differences in lateral friction force, which offers the unique possibility to use the friction as a molecular recognition tool for thiol-based self-assembled monolayers.
Atomic-scale investigations on the wet etching kinetics of GeversusSiGe in acidic H2O2solutions: a postoperandosynchrotron XPS analysis (2020)

In this atomic-scale study on wet etching, the importance of surface chemistry, in particular the nature of the surface oxides, is demonstrated for technologically relevant group IV semiconductors, Ge and SiGe.
B cell convergence to distinct broadly reactive epitopes revealed by chimeric hemagglutinin vaccination (2022)

Abstract Seasonal influenza virus vaccines provide modest protection against endemic viruses but lack effectiveness against pandemic-threat viruses. Therefore, new immunogens and vaccine platforms that induce antibodies against broadly protective epitopes are needed to provide robust protection against seasonal and novel influenza viruses. In a phase 1 clinical trial, the chimeric hemagglutinin (cHA) immunogen induced antibody responses against the conserved HA stalk domain. However, the landscape of the B cell specificities and subsets induced by this vaccine remain undetermined. Using single cell RNA-sequencing and repertoire sequencing, we identified that formulation of the cHA vaccine differentially induced B cell responses against distinct epitopes. Notably, those participants that received an inactivated vaccine with a squalene-based adjuvant had a greater proportion of B cells targeting two conserved neutralizing epitopes of the stalk domain: the central stalk and anchor epitopes. Moreover, participants that received an inactivated vaccine with adjuvant had distinct transcriptional B cell subsets, including an increase in atypical memory B cells. B cell clonal overlap between acute and memory timepoints was substantial, with several multi-donor clones that targeted distinct broadly protective epitopes. In addition, we identified stalk targeting germline antibodies that could neutralize recent pandemic H1N1 viruses. Altogether, our study reveals that the inactivated cHA vaccine with an oil-in-water adjuvant promotes B cell activation and maturation against broadly protective epitopes. Supported by National Institute of Allergy and Infectious Diseases (NIAID) National Institutes of Health grant numbers K99AI159136 (JJG), U19AI082724 (PCW), U19AI109946 (PCW), U19AI057266 (PCW), P01AI097092 (PP), R01AI145870-01 (PP), R21AI146529 (LC), and T32AI007244-36 (JH), the NIAID Centers of Excellence for Influenza Research and Surveillance (CEIRS) grant number HHSN272201400005C (PCW), HHSN272201400008C (LC, FK, PP), and the NIAD Centers of Excellence for Influenza Research and Response (CEIRR) grant number 75N93019R00028 (PCW, FK, PP). This work was also partially supported by the NIAID Collaborative Influenza Vaccine Innovation Centers (CIVIC; 75N93019C00051, FK, PP, ABW, PCW).
Evaluating treatment effectiveness under model misspecification: A comparison of targeted maximum likelihood estimation with bias-corrected matching (2014)

Statistical approaches for estimating treatment effectiveness commonly model the endpoint, or the propensity score, using parametric regressions such as generalised linear models. Misspecification of these models can lead to biased parameter estimates. We compare two approaches that combine the propensity score and the endpoint regression, and can make weaker modelling assumptions, by using machine learning approaches to estimate the regression function and the propensity score. Targeted maximum likelihood estimation is a double-robust method designed to reduce bias in the estimate of the parameter of interest. Bias-corrected matching reduces bias due to covariate imbalance between matched pairs by using regression predictions. We illustrate the methods in an evaluation of different types of hip prosthesis on the health-related quality of life of patients with osteoarthritis. We undertake a simulation study, grounded in the case study, to compare the relative bias, efficiency and confidence interval coverage of the methods. We consider data generating processes with non-linear functional form relationships, normal and non-normal endpoints. We find that across the circumstances considered, bias-corrected matching generally reported less bias, but higher variance than targeted maximum likelihood estimation. When either targeted maximum likelihood estimation or bias-corrected matching incorporated machine learning, bias was much reduced, compared to using misspecified parametric models.
PET imaging of neurokinin‐1 receptors with [18F]SPA‐RQ in human subjects: Assessment of reference tissue models and their test–retest reproducibility (2007)

[(18)F]SPA-RQ (substance P antagonist receptor quantifier) labels the substance P-preferring (NK(1)) receptor in human brain. A prior study showed that [(18)F]SPA-RQ brain uptake can be quantified with a reference tissue method and thereby avoid invasive blood sampling. The purposes of this study were to compare three different reference tissue methods and to assess test-retest reproducibility. Eight healthy subjects underwent two [(18)F]SPA-RQ scans. We calculated the binding potential (BP), which is proportional to receptor density, from both regional volume of interest and voxel-wise data. We compared three reference tissue methods: simplified reference tissue model, multilinear reference tissue model (MRTM), and its two-parameter version (MRTM2). The three methods generated equivalent values of regional BP, but MRTM2 was the most resistant to noise. Temporally stable values of BP were obtained with 240 min of imaging data. MRTM2 had excellent test-retest reproducibility, with high reliability (intraclass correlation > 0.9) and low variability (< 10%). In addition to regional volume of interest analysis, we also created parametric images of BP, variability, and reliability based on voxel-wise time-activity data. The reproducibility of parametric BP was also good, with variability < 20% and reliability > 0.7 in gray matter regions. In conclusion, a two-parameter reference tissue method (MRTM2) provided reproducible and reliable measurements of [(18)F]SPA-RQ brain uptake using 240 min of both regional and voxel-wise data.
Interaction of hydrogen peroxide and chlorine dioxide stages in ECF bleaching (1996)

Changing the order of the hydrogen peroxide (P) and chlorine dioxide (D) stages in an ECF (elemental chlrorine free) bleach sequence was shown to affect the final brightness of kraft pulps. Application of a D(EOP)DPP bleach sequence to a southern softwood pulp produced consistently higher interstage and final brightnesses than a D(EOP)PDP sequence. These results were confirmed by bleaching a northern softwood and a eucalypt pulp using DEDP and DEPD sequences. In all cases, higher brightnesses were achieved when the second D state (D 2 ) preceded the P stage. The effect was especially evident with the hardwood pulp, where brightness of the DEDP pulp was three points higher than the DEPD pulp. NMR analysis of extracted lignin showed that the D 2 stage reduced the phenolic lignin content of softwood pulp by 60%, while the P stage had no effect. For the hardwood pulp, the D 2 stage reduced the phenolic lignin content by 90-95%. The greater bleaching efficiency of a DEDP sequence (compared with DEPD) is consistent with known reactivities of hydrogen peroxide and chlorine dioxide toward specific lignin structures. The D 2 stage lowers the phenolic lignin content of pulp while generating hydrogen peroxide-sensitive, nonphenolic lignin species. A followup P stage reacts effectively with this lignin. Application : explains why the second D stage should precede the first P stage in a kraft pulp bleaching sequence.
Involvement of the interleukin‐2 receptor γ subunit in interleukin‐4‐dependent activation of mouse hematopoietic cells and splenic B cells (1995)

Interleukin-4 (IL-4) has various activities on B cells and on hematopoietic cells. We previously reported that TUGm2, a monoclonal antibody to the gamma subunit of the IL-2 receptor (IL-2R gamma), inhibited IL-4-dependent proliferation of CTLL2, a cytotoxic T cell line. We proposed that IL-2R gamma is required for the functional IL-4 receptor (IL-4R) in T cells. In the present work, we further examined whether or not IL-2R gamma is involved in IL-4R function in mouse myeloid cell lines and splenic B cells. TUGm2 suppressed the IL-4-induced proliferation of BA/F3 or IC2 cells, as well as of purified splenic B cells. TUGm2 partially suppressed proliferation of B cells induced by the combination of IL-4 and anti-immunoglobulin M (IgM) antibody. In contrast, TUGm2 had no effect on proliferation of B cells induced by anti-IgM antibody alone or lipopolysaccharide (LPS). TUGm2 also inhibited IgE production induced by IL-4 of LPS-stimulated B cells. The induction of major histocompatibility complex class II molecules or CD23 by IL-4 was virtually unaffected by TUGm2 antibody. These results indicate that IL-2R gamma is differentially involved in various IL-4-dependent reactions.
Endocrine Profiles after Triggering of Final Oocyte Maturation with GnRH Agonist after Cotreatment with the GnRH Antagonist Ganirelix during Ovarian Hyperstimulation forin VitroFertilization (2002)

In a randomized multicenter study, the efficacies of two different GnRH agonists were compared with that of hCG for triggering final stages of oocyte maturation after ovarian hyperstimulation for in vitro fertilization. Ovarian stimulation was conducted by recombinant FSH (Puregon), and the GnRH antagonist ganirelix (Orgalutran) was coadministered for the prevention of a premature LH rise. Luteal support was provided by daily progestin administration. Frequent blood sampling was performed at midcycle in the first 47 eligible subjects included in the current study, who were randomized for a single dose of 0.2 mg triptorelin (n = 17), 0.5 mg leuprorelin (n = 15), or 10,000 IU hCG (n = 15). Serum concentrations of LH, FSH, E2, and progesterone (P) were assessed at variable intervals. LH peaked at 4 h after both triptorelin and leuprorelin administration, with median LH levels of 130 and 107 IU/liter (P < 0.001), respectively. LH levels returned to baseline after 24 h. Subjects receiving hCG showed peak levels of 240 IU/liter hCG 24 h after administration. A rise in FSH to 19 IU/liter (P < 0.001) was noted in both GnRH agonist groups 8 h after injection. Within 24 h the areas under the curve for LH and FSH were significantly higher (P < 0.001) in both GnRH agonist groups compared with that for hCG. E2 and P levels were similar for all groups up to the day of oocyte retrieval. Luteal phase areas under the curve for P and E2 were significantly elevated (P < 0.001) in the hCG group. The mean (+/-SD) numbers of oocytes retrieved were 9.8 +/- 5.4, 8.7 +/- 4.5, and 8.3 +/- 3.3; the percentages of metaphase II oocytes were 72%, 85%, and 86%; and fertilization rates were 61%, 62%, and 56% in the triptorelin, leuprorelin, and hCG group, respectively (P = NS for all three comparisons). These findings support the effective induction of final oocyte maturation in both GnRH agonist groups. In summary, after treatment with the GnRH antagonist ganirelix for the prevention of premature LH surges, triggering of final stages of oocyte maturation can be induced effectively by a single bolus injection of GnRH agonist, as demonstrated by the induced endogenous LH and FSH surge and the quality and fertilization rate of recovered oocytes. Moreover, corpus luteum formation is induced by GnRH agonists with luteal phase steroid levels closer to the physiological range compared with hCG. This more physiological approach for inducing oocyte maturation may represent a successful and safer alternative for in vitro fertilization patients undergoing ovarian hyperstimulation.
C(sp3)–H Bond Hydroxylation Catalyzed by Myoglobin Reconstituted with Manganese Porphycene (2013)

Myoglobin reconstituted with manganese porphycene was prepared in an effort to generate a new biocatalyst and was characterized by spectroscopic techniques. The X-ray crystal structure of the reconstituted protein reveals that the artificial cofactor is located in the intrinsic heme-binding site with weak ligation by His93. Interestingly, the reconstituted protein catalyzes the H2O2-dependent hydroxylation of ethylbenzene to yield 1-phenylethanol as a single product with a turnover number of 13 at 25 °C and pH 8.5. Native myoglobin and other modified myoglobins do not catalyze C-H hydroxylation of alkanes. Isotope effect experiments yield KIE values of 2.4 and 6.1 for ethylbenzene and toluene, respectively. Kinetic data, log kobs versus BDE(C(sp(3))-H) for ethylbenzene, toluene, and cyclohexane, indicate a linear relationship with a negative slope. These findings clearly indicate that the reaction occurs via a rate-determining step that involves hydrogen-atom abstraction by a Mn(O) species and a subsequent rebound hydroxylation process which is similar to the reaction mechanism of cytochrome P450.
Relaxation Time of Short Wavelength Intersubband Transition in InGaAs/AlAs Quantum Wells (1998)

Linear and nonlinear light absorption characteristics of short-wavelength (near-infrared) intersubband transition in InGaAs/AlAs quantum wells are investigated for estimation of the intersubband relaxation time. Linear absorption measurements reveal that the intersubband absorption width is dominated by the inhomogeneous broadening caused by well-width fluctuations. Nonlinear absorption measurement results are analyzed by focusing on the inhomogeneous broadening and probe pulse width, which reveals that the intersubband energy relaxation time is as short as 1–10 ps. The observed relaxation time is of the same order as those of long wavelength (far-infrared) intersubband transitions. This result is expected to be useful for the ultrafast application of short-wavelength intersubband transition.
Raman Spectral Study of the Composition of Basic Silicate Solutions (1985)

Raman spectral data are reported for silicate solutions at varying hydroxide ion concentrations. The gradual change in the spectra is explained as being due to various monomeric, dimeric, cyclic, and polymeric silicate species in solution. Band assignments are made by comparison with the Raman spectra of phosphates and crystalline silicate minerals.
An Efficient and Highly Stereoselective Synthesis of New P‐Chiral 1,5‐Diphosphanylferrocene Ligands and Their Use in Enantioselective Hydrogenation. (2006)

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