gebhart/patrepeval huggingface dataset:
Carbon Nanotubes: Carbon Nanotube Based High Resolution Holograms (Adv. Mater. 44/2012) (2012)

By using carbon nanotubes as the smallest possible scattering element, light can be diffracted in a highly controlled manner to produce a 2D image, as reported by Haider Butt and co-workers on page OP331. An array of carbon nanotubes is elegantly patterned to produce a high resolution hologram. In response to incident light on the hologram, a high contrast and wide field of view “CAMBRIDGE” image is produced.
Antibody production in mice. VI. Effect of anti-carrier antibody on cellular co-operation in the primary anti-hapten antibody response. (1974)

We studied the effect of passively administered anti-carrier and anti-hapten antibodies on the primary anti-hapten antibody response to hapten—carrier conjugates in mice. Bacterial α-amylase (BαA), Taka-amylase A (TAA) and keyhole limpet haemocyanin (KLH) were used as carrier molecules, and 2,4-dinitrophenyl (DNP) group was used as a haptenic determinant. Three groups of mice were injected intravenously with anti-carrier antiserum, anti-hapten antiserum and normal serum as the control, respectively, immediately after the immunization with the hapten—carrier conjugate. The primary anti-carrier antibody response was markedly suppressed by the passively administered anti-carrier antibody but not anti-hapten antibody. However, the primary anti-hapten antibody response was suppressed not only by passively administered anti-hapten antibody but also by the injection of anti-carrier antibody in an early period after the immunization. When anti-carrier antibody was given twice 0 and 7 days after immunization, the primary anti-hapten antibody response was markedly suppressed and the suppressive effect was observed even at a later period. In contrast, anti-hapten antibody given by the same schedule as above suppressed only the primary anti-hapten antibody response, but not the anti-carrier antibody response. Passively administered anti-carrier antibody did not suppress carrier-specific helper cell development, but still suppressed the development of B memory cells and antibody formation against carrier determinants. The antigen dose required for the development of B-cell memory was much higher than that necessary for the stimulation of T cells. Passively administered anti-carrier antibody clearly inhibited the cellular cooperation between carrier-committed helper cells and hapten-specific B cells and the augmented primary anti-hapten antibody response induced by carrier-primed T cells was clearly abolished. Furthermore, mice preimmunized with carrier showed significantly lower anti-hapten antibody response following the hapten—carrier challenge. Moreover, development of hapten-specific memory cells was also suppressed. Thus, even in the non-specific antibody-induced suppression by anti-carrier antibody, negative feedback effect of a B-cell product with anti-carrier specificity exclusively regulates the B-cell line development and differentiation.
Analytical Validation of a Highly Quantitative, Sensitive, Accurate, and Reproducible Assay (HERmark®) for the Measurement of HER2 Total Protein and HER2 Homodimers in FFPE Breast Cancer Tumor Specimens (2010)

We report here the results of the analytical validation of assays that measure HER2 total protein (H2T) and HER2 homodimer (H2D) expression in Formalin Fixed Paraffin Embedded (FFPE) breast cancer tumors as well as cell line controls. The assays are based on the VeraTag technology platform and are commercially available through a central CAP-accredited clinical reference laboratory. The accuracy of H2T measurements spans a broad dynamic range (2-3 logs) as evaluated by comparison with cross-validating technologies. The measurement of H2T expression demonstrates a sensitivity that is approximately 7-10 times greater than conventional immunohistochemistry (IHC) (HercepTest). The HERmark assay is a quantitative assay that sensitively and reproducibly measures continuous H2T and H2D protein expression levels and therefore may have the potential to stratify patients more accurately with respect to response to HER2-targeted therapies than current methods which rely on semiquantitative protein measurements (IHC) or on indirect assessments of gene amplification (FISH).
A Cross-Species Analysis in Pancreatic Neuroendocrine Tumors Reveals Molecular Subtypes with Distinctive Clinical, Metastatic, Developmental, and Metabolic Characteristics (2015)

This study involves a comprehensive cross-species integrated analysis of multi-omics profiles and histology to stratify PanNETs into subtypes with distinctive characteristics. We provide support for the RIP1-TAG2 mouse model as representative of its cognate human cancer with prospects to better understand PanNET heterogeneity and consider future applications of personalized cancer therapy.
Pharmacogenetics of warfarin safety and effectiveness in children (2013)

Objectives To assess the contribution of CYP2C9 / VKORC1 genotypes and variation in other genes involved in warfarin biotransformation and coagulation pathways to warfarin‐related outcomes in children. Furthermore, to validate the performance of a previously published pediatric pharmacogenetics‐dosing model when predicting the required dose in an independent cohort of children. Methods Clinical and genetic data was collected from 93 patients ≤18 years of age who received warfarin therapy. Genotyping was performed using a custom 96 SNP genotyping assay. Results Together, VKORC1 –1639G/A and CYP2C9 *2/*3 accounted for 21.1% of dose variability. There was a strong correlation (R 2 =0.64; P &lt;0.001) between actual and predicted warfarin dose using a pediatric pharmacogenetics‐dosing model. VKORC1 genotype also had a significant impact on time to therapeutic INR ( P =0.047), time to INR&gt;;4 ( P =0.028), and risk of over‐anticoagulation (INR&gt;;4) during the initiation of therapy (odds ratio, 3.3; P =0.014). An additional variant in CYP2C9 (rs7089580) was significantly associated with warfarin dose in a multivariate model. Conclusions This study confirms the importance of VKORC1/CYP2C9 genotype for warfarin outcomes in children and validates a pediatric‐specific genotype‐based dosing algorithm. Research funding provided by CIHR‐DSEN and CFI.
Monolithic Integration of Nanoscale Solid Oxide Fuel Cell Membranes onto Polymer Scaffolds through Stress Control (2013)

Ultrathin fast-ion conducting oxide membranes are of broad interest to a range of energy conversion technologies. We demonstrate a low-temperature (<30 °C) process for controlling internal stress in an archetypal fast-ion conductor, crystalline Y2O3-doped ZrO2 (YDZ), which allows us to form stable suspended nanomembranes akin to those fabricated at high temperature (>550 °C). Such a low-temperature synthesis method then enables us to monolithically integrate the suspended oxide-ion conducting membranes onto polyimide (Kapton by DuPont), a polymer with vastly different physical properties than that of a ceramic. Integrated functional heterostructure solid oxide fuel cells operable below the glass transition temperature of the polymer are demonstrated. Our results describe a mechanistic low-temperature processing route for forming stable multifunctional membrane structures, applicable to the realization of various energy conversion and sensing devices and structural skins for miniature autonomous systems.
Design and Validation of a Gammaray Scanning System for Measuring Irradiated Nuclear Fuel (2022)

A prototype gamma-ray scanning system was designed to perform post-irradiation measurements of nuclear fuel at Idaho National Laboratory (INL). The system is composed of a coaxial high-purity germanium (HPGe) detector, a collimator, and mechanical positioning stages that translate the fuel sample across the front of the collimator. This paper documents the design process, modeling and the laboratory characterization performed to validate the system. The modeling of the system was done using the Monte Carlo N-Particle code with vendor-supplied design specifications, dimensional measurements, and x-ray radiographs of the HPGe detector. The characterization included measurements of calibrated radiation sources in different geometries, and calculations for absolute efficiency and dead time. Benchmark measurements were performed by scanning an irradiated fuel rodlet containing ten pellets of 4.9% enriched UO2 in zirconium alloy. These results were compared to simulated spectra to further help characterize the detector model. One goal of the system is to determine the number of fissions per gram of UO2 in the fuel; comparison of the results from this prototype system's assay of the irradiated fuel rodlet are in agreement with previously estimated results.
High Dynamic Range Processing for Magnetic Resonance Imaging (2013)

We have developed and tested a method to apply HDR processing to MR images. The increased dynamic range of HDR-MR images as compared to standard T1- and T2-weighted images minimizes feature loss caused by magnetization recovery or low SNR.
PD-L1 blockade enhances anti-tumor efficacy of NK cells (2018)

Anti-PD-1/anti-PD-L1 therapies have shown success in cancer treatment but responses are limited to ~ 15% of patients with lymphocyte infiltrated, PD-L1 positive tumors. Hence, strategies that increase PD-L1 expression and tumor infiltration should make more patients eligible for PD-1/PD-L1 blockade therapy, thus improving overall outcomes. PD-L1 expression on tumors is induced by IFNγ, a cytokine secreted by NK cells. Therefore, we tested if PM21-particle expanded NK cells (PM21-NK cells) induced expression of PD-L1 on tumors and if anti-PD-L1 treatment enhanced NK cell anti-tumor efficacy in an ovarian cancer model. Studies here showed that PM21-NK cells secrete high amounts of IFNγ and that adoptively transferred PM21-NK cells induce PD-L1 expression on SKOV-3 cells <i>in vivo</i>. The induction of PD-L1 expression on SKOV-3 cells coincided with the presence of regulatory T cells (Tregs) in the abdominal cavity and within tumors. In <i>in vitro</i> experiments, anti-PD-L1 treatment had no direct effect on cytotoxicity or cytokine secretion by predominantly PD-1 negative PM21-NK cells in response to PD-L1<sup>+</sup> targets. However, significant improvement of NK cell anti-tumor efficacy was observed <i>in vivo</i> when combined with anti-PD-L1. PD-L1 blockade also resulted in increased <i>in vivo</i> NK cell persistence and retention of their cytotoxic phenotype. These results support the use of anti-PD-L1 in combination with NK cell therapy regardless of initial tumor PD-L1 status and indicate that NK cell therapy would likely augment the applicability of anti-PD-L1 treatment.
Partial MMSE-ML detection for coded MIMO systems (2014)

We propose computationally efficient MIMO detection scheme which can provide accurate soft decision information to the decoder. The detection process has two stages. The proposed scheme first detects MIMO symbols using MMSE method, and calculates noise variances of each detected symbol. Next, the detected symbols are demodulated in bits by maximum likelihood method respectively. The proposed scheme greatly reduces the complexity due to its computational algorithm compared to the maximum likelihood MIMO detection which exhaustively searches for the soft decision information.
A Polymorphism in the Serotonin Receptor 3A (HTR3A) Gene and Its Association With Harm Avoidance in Women (2003)

The C178T polymorphism in the HTR3A gene may affect the personality trait of harm avoidance in women.
Aero Engine Concepts Beyond 2030: Part 1—The Steam Injecting and Recovering Aero Engine (2020)

Abstract Recognizing the attention currently devoted to the environmental impact of aviation, this three-part publication series introduces two new aircraft propulsion concepts for the timeframe beyond 2030. This first part focuses on the steam injecting and recovering aero engine (SIRA) concept. Exhaust heat generated steam is injected into the combustion chamber. By use of a condenser, installed behind the steam generator, the water is recovered from the exhaust gas–steam mixture. Both lead to a noticeable increase in specific power compared to a conventional gas turbine and, foremost, to a significant increase in thermodynamic efficiency. The proposed concept is expected to reduce fuel burn and carbon dioxide (CO2) emissions by about 15% and nitrogen oxides (NOx) formation can be almost completely avoided compared to state-of-the-art engines of the same technology level. Moreover, the described concept has the potential to drastically reduce or even avoid the formation of condensation trails. Thus, the SIRA concept operated with sustainable aviation fuels offers the potential for climate-neutral aviation. Based on consistent thermodynamic descriptions, preliminary designs and initial performance studies, the potentials of the concepts are analyzed. Complementarily, a detailed discussion on concrete engineering solutions considers the implementation into aircraft. Finally, the impact on emissions is outlined.
Immunoglobulin G Fc Receptor Polymorphisms and Clinical Course in Follicular Lymphoma Patients. (2004)

Abstract Patients with low-grade B cell lymphoma, such as follicular lymphoma usually have an indolent clinical course. In most of the cases, patients do not require therapy at the time of diagnosis. Instead, patients can be monitored from months to years before the need for therapy. However, the time interval from diagnosis to the first therapy in these patients can vary significantly. In addition, the overall clinical course is heterogeneous in these patients with variable length of survival after diagnosis. The pathobiological basis of this hetergenisity is not known. We have recently found that IgG Fc receptor (FcγR) polymorphisms correlated with clinical outcome after immunotherapies in patients with follicular lymphoma. In one case, FcγRIIIa 158 V/F and FcγRIIa 131 H/R polymorphisms predicted the response to anti-CD20 antibody, rituximab therapy probably due to their role in the antibody-dependent cellular cytotoxicity. One question is whether the FcγR polymorphisms are correlated with the general clinical course of follicular lymphoma due toq their role in innate immunity. We therefore tested if FcγRIIIa 158 V/F, FcγRIIa 131 H/R and FcγRIIb 232 I/T polymorphisms predict clinical course of a group of 307 patients with follicular lymphoma. None of the three FcγR polymorphisms tested correlated with the time interval from diagnosis to first therapy, or with overall survival in this group of patients. We then tested whether FcγR polymorphisms have predictive value on clinical response to chemotherapy. Of 307 patients, only 158 patients received chemotherapy alone as first therapy, while the rest of the patients have received additional idiotype vaccination or rituximab. In the analysis of these 158 patients, there was no correlation between the FcγR polymorphisms and response rate to chemotherapy or time to progression after chemotherapy. Our results did not find any association between the three FcγR polymorphisms tested and clinical course of disease or response to chemotherapy in patients with follicular lymphoma, suggesting that the predictive value of FcγR polymorphisms on the clinical responses to rituximab is specific to the monoclonal antibody therapy.
Collocated Finite Volume Scheme for Scalable Simulation of Induced Seismicity (2022)

Summary An increasing number of geo-energy applications require the quantitative prediction of hydromechanical response in subsurface. Integration of mass, momentum, and energy conservation laws becomes essential for performance and risk analysis of enhanced geothermal systems, stability assessment of CO2 sequestration and hydrogen storage, resolving the issue of induced seismicity. The latter problem is of particular interest because it exposes safety risks to people and surface infrastructure. Implicit coupling of conservation laws is computationally demanding and the solution procedure often uses different numerical methods for different laws that complicates simulation. Recently developed Finite Volume (FV) schemes for poromechanics present a unified approach for the modeling of conservation laws in geo-energy applications. Contact mechanics at faults requires special attention due to the inequality constraints it imposes and nonlinear friction laws that strongly affect the occurrence of seismicity. We develop a cell-centered FV scheme for the purpose of integrated simulation in Delft Advanced Research Terra Simulator (DARTS) platform. The scheme proposes a unified numerical framework capable to resolve conservation laws in a fully implicit manner using a single collocated grid. Coupled multi-point flux and multi-point stress approximations provide mass, momentum, and heat fluxes at the faces of the computational grid. We use a conformal discrete fracture model to incorporate faults, where the multi-point approximations of fluxes respect the discontinuity in displacements. The block-partitioned preconditioner that takes the advantage of linear structure of the coupled problem is developed to facilitate the performance of the simulation. The proposed numerical scheme are validated against analytical and numerical solutions in a number of test cases. The convergence and stability of the schemes are investigated. It is found that the developed scheme is indeed accurate, stable, and efficient. Thereafter, we demonstrate the applicability of the approach to model fault reactivation at the laboratory scale. In a core injection test, we validate the results of simulation against experimental measurements. Next, we investigate the performance of the different preconditioning strategies. The proposed block-partitioned preconditioning strategy demonstrates the scalability and efficiency of the numerical framework.
Enhanced Electrochemical Stability of Quasi-Solid-State Electrolyte Containing SiO2 Nanoparticles for Li-O2 Battery Applications (2015)

A stable electrolyte is required for use in the open-packing environment of a Li-O2 battery system. Herein, a gelled quasi-solid-state electrolyte containing SiO2 nanoparticles was designed, in order to obtain a solidified electrolyte with a high discharge capacity and long cyclability. We successfully fabricated an organic-inorganic hybrid matrix with a gelled structure, which exhibited high ionic conductivity, thereby enhancing the discharge capacity of the Li-O2 battery. In particular, the improved electrochemical stability of the gelled cathode led to long-term cyclability. The organic-inorganic hybrid matrix with the gelled structure played a beneficial role in improving the ionic conductivity and long-term cyclability and diminished electrolyte evaporation. The experimental and theoretical findings both suggest that the preferential binding between amorphous SiO2 and polyethylene glycol dimethyl ether (PEGDME) solvent led to the formation of the solidified gelled electrolyte and improved electrochemical stability during cycling, while enhancing the stability of the quasi-solid state Li-O2 battery.
Advanced Lung Cancer Screening: An Individualized Molecular Nanotechnology Approach (2014)

This grant utilizes complimentary approaches to improve the early detection of lung cancer, with each aim having independent goals and thus separate utility. Our goal is to explore whether detection of DNA methylation changes and enhanced CT evaluations will add to the specificity of lung cancer detection. In the first year of this proposal, we developed an improved panel of genes hypermethylated in lung cancer, with extraordinarily high specificity and sensitivity. These novel genes were used to develop sensitivity methylation specific PCR assays suitable for biologic fluid testing (sputum and plasma). We also optimized the processing of biologic samples to accomplish improved retention of DNA suitable for methylation detection. In the past year, we have combined this improved method with the newly developed PCR detection and begun to examine biologic fluids from patients with and without lung cancer. For plasma studies, we have examined 141 Cancer patients with plasma and 44 non-cancer patients. For sputum studies, we have examined 89 cancer patients for whom we collected sputum and 23 non-cancer patients with sputum (all with benign pulmonary nodules). Initial studies demonstrate the ability to detect differences in the presence of DNA methylation in cancers compared to controls. Will complete the analysis with an additional 72 Cancer positive and 32 non cancer subjects in the remainder of our funded work. In addition, we have utilized CT data sets of subjects with and without lung cancer to optimize CT as a potential screening tool beyond simply looking for lung nodules. We have data that suggests that parenchymal HU variability may be a potential marker of lung cancer. In combination with these molecular detection approaches, the parenchymal CT imaging approaches should lead to improved screening methods.
Automated Peak Detection and Matching Algorithm for Gas Chromatography−Differential Mobility Spectrometry (2011)

A gas chromatography-differential mobility spectrometer (GC-DMS) involves a portable and selective mass analyzer that may be applied to chemical detection in the field. Existing approaches examine whole profiles and do not attempt to resolve peaks. A new approach for peak detection in the 2D GC-DMS chromatograms is reported. This method is demonstrated on three case studies: a simulated case study; a case study of headspace gas analysis of Mycobacterium tuberculosis (MTb) cultures consisting of three matching GC-DMS and GC-MS chromatograms; a case study consisting of 41 GC-DMS chromatograms of headspace gas analysis of MTb culture and media.
Establishment of a Waldenstrom’s Macroglobulinemia Cell Line (BCWM.1) with Productive In Vivo Engraftment in SCID-hu Mice. (2005)

Abstract Waldenstrom’s Macroglobulinemia (WM) is incurable B-cell malignancy characterized by the infiltration of the bone marrow infiltration with lymphoplasmacytic cells (LPC) and the presence of an IgM monoclonal gammopathy. A significant impairment in understanding the biology and advancing therapeutics for WM has been the lack of a representative cell line and animal model. We therefore report on work accomplished in our laboratories in establishing the BWMC.1 cell line, which was derived from long term culture of CD19+ selected lymphoplasmacytic cells isolated from the bone marrow (BM) aspirate of a previously untreated 55-year-old female patient with IgMk secreting WM. BCWM.1 cells morphologically resembled LPC and had prominent nucleoli and ample cytoplasm by Wright-Giemsa staining, and were propagated in RPMI 1640 medium supplemented with 10% FBS. Phenotypic characterization by flow cytometric analysis demonstrated typical WM LPC characteristics: CD5−, CD10−, CD19+, CD20+, CD23+, CD27−, CD38+, CD138+, CD40+, CD52+, CD70+, CD117+, cIgM+, cIgG−, cIgA−, ck+, cl−. BCWM.1 cells also expressed the survival proteins APRIL and B-Lymphocyte Stimulator (B-LYS), and their receptors TACI, BCMA and BAFF-R. ELISA studies demonstrated secretion of IgMk in culture. Karyotypic and M-FISH studies did not demonstrate cytogenetic abnormalities. Molecular analysis of BCWM.1 cells confirmed clonality by determination of IgH rearrangements through FR1c/JHc amplification of genomic DNA. BCWM.1 cells were positive for LMP1 expression by histochemical staining and PCR analysis. Importantly, inoculation of BCWM.1 cells directly into the human BM milieu of SCID-hu mice resulted in engraftment of tumor cells and serum detection of human IgMk in four of five SCID-hu mice within two weeks. In contrast, subcutaneous injection of BCWM.1 cells in SCID mice did not lead to engraftment, suggesting a role for the human BM microenvironment in supporting the expansion of BCWM.1 cells. These studies therefore support the use of BCWM.1 cells as an appropriate model for the study of WM, which in conjunction with the SCID-hu mouse model may be used as a convenient model for studies focused on both the pathogenesis and development of targeted therapies for WM.