gebhart/patrepeval huggingface dataset:
Abstract P3-03-03: DNA Mutation as a Biomarker for Tracking Circulating Tumor Cells and Disseminated Tumor Cells in Breast Cancer Metastases (2010)

Abstract Introduction: Most cancer deaths are caused by metastatic disease. Tumor cells exit the primary tumor and travel through blood and/or lymphatic channels to distant sites. Circulating tumor cells (CTCs) from blood and disseminated tumor cells (DTCs) from bone marrow may play key roles in the metastatic process. Primary tumor heterogeneity and how the metastatic process evolves over time may confound the study of metastatic biology. To better distinguish the cells of origin in metastases, we developed new methodologies to isolate single tumor cells from tissues, blood, and bone marrow for DNA and RNA analyses. We compared these analyses in individual cells from primary and metastatic tumors, CTCs and DTCs. Materials and Methods: Single tumor cell suspensions from primary and metastatic tissues were prepared from fresh human specimens or mouse xenografts. Single cells were isolated from blood, bone marrow, or single tumor cell suspensions from tissue using EpCAM-conjugated microbeads and the MagSweeper, a device invented by our group. Unbounded microbeads were removed and the single cells were placed into individual PCR tubes for further nucleic acid analyses. Live CTCs and DTCs from some breast cancer patients were cultured for further testing. Single cell DNA mutational analyses were performed by multiplex PCR sequencing. Single cell transcriptional profiling was performed by multiplex qRT-PCR. Single tumor cells with mutations were compared among multiple compartments: primary tumor, metastatic tumor, blood and bone marrow. Array CGH analysis was used to focus single cell analysis on genes in potential areas of DNA deletion or amplification. Xenograft mouse models were generated using primary or tumor tissues and single cells were compared. Results: Single tumor cells from fresh or fixed solid tumor tissues were successfully isolated for nucleic acid analyses. CTCs and DTCs isolated by MagSweeper from breast cancer patients could be isolated live and cultured or injected for growth in xenografts. Single cell DNA mutation analysis of the PIK3CA gene was identified in 3/27 breast cancer patients, showing the mutation in only 45/178 single tumor cells. Sequential PIK3CA mutational analyses of CTCs, DTCs, and metastases showed that DTCs better reflected the mutational status of metastases at time points earlier in the metastatic process. Discussion: Our results indicate that isolating single tumor cells from tumor tissues, blood, and bone marrow provides detailed information about different tumor compartments in individual cancer patients. Single cell DNA mutational analysis can provide a biomarker for tracking CTCs and DTCs over time during the metastatic process. Based on our initial findings, we postulate that the bone marrow serves as a tumor cell reservoir for early metastatic spread in breast cancer. Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-03-03.
A Research Roadmap for Substantially Improving Safety for Transit Buses through Autonomous Braking Assistance for Operators (2016)

The purpose of this paper is to lay the groundwork for development of autonomous collision avoidance and autonomous emergency braking for transit buses. Although significant progress is being made in bringing autonomous collision avoidance and autonomous emergency braking to automobiles and trucks, the transit industry is being left behind. Bus transit is one of the safest ways to travel in the United States. Bus passengers are more than three times safer than automobile passengers when comparing the rate of fatalities per 100 million passenger miles. However, buses can be made even safer. Data from the Federal Transit Administration (FTA) National Transit Database (NTD) show that buses and vanpools have been involved in 85,391 collisions, experienced 1,340 fatalities, 201,382 injuries between 2002 and 2014, and created expenditures for casualty and liability expenses of $5.7 billion between 2002 and 2013. Included in these data are 56 fatalities and 16,312 injuries involving bus transit workers. The authors lay out a draft research roadmap for the adaptation to buses of proven technology that has been shown to reduce collisions and claims for automobiles. The objectives are first to educate the industry on the magnitude of the problem, second, to provide a draft program that would lead to the desired outcomes, and third, to seek stakeholder involvement to refine the program and support to seek funding for it.
Cobalt−Xantphos-Catalyzed, LiCl-Mediated Preparation of Arylzinc Reagents from Aryl Iodides, Bromides, and Chlorides (2011)

A cobalt-Xantphos-catalyzed, LiCl-mediated system has been developed for the direct and expedient preparation of arylzinc reagents in THF from the corresponding aryl iodides, bromides, and chlorides. Owing to the use of THF as a versatile solvent, the thus-formed arylzinc reagents displayed a high degree of compatibility with a variety of conventional as well as newly emerging metal-catalyzed cross-coupling reactions.
Complement C3 Deficiency Leads to Accelerated Amyloid Plaque Deposition and Neurodegeneration and Modulation of the Microglia/Macrophage Phenotype in Amyloid Precursor Protein Transgenic Mice (2008)

Complement factor C3 is the central component of the complement system and a key inflammatory protein activated in Alzheimer's disease (AD). Previous studies demonstrated that inhibition of C3 by overexpression of soluble complement receptor-related protein y in an AD mouse model led to reduced microgliosis, increased amyloid beta (Abeta) plaque burden, and neurodegeneration. To further address the role of C3 in AD pathology, we generated a complement C3-deficient amyloid precursor protein (APP) transgenic AD mouse model (APP;C3(-/-)). Brains were analyzed at 8, 12, and 17 months of age by immunohistochemical and biochemical methods and compared with age-matched APP transgenic mice. At younger ages (8-12 months), no significant neuropathological differences were observed between the two transgenic lines. In contrast, at 17 months of age, APP;C3(-/-) mice showed significant changes of up to twofold increased total Abeta and fibrillar amyloid plaque burden in midfrontal cortex and hippocampus, which correlated with (1) significantly increased Tris-buffered saline (TBS)-insoluble Abeta(42) levels and reduced TBS-soluble Abeta(42) and Abeta(40) levels in brain homogenates, (2) a trend for increased Abeta levels in the plasma, (3) a significant loss of neuronal-specific nuclear protein-positive neurons in the hippocampus, and (4) differential activation of microglia toward a more alternative phenotype (e.g., significantly increased CD45-positive microglia, increased brain levels of interleukins 4 and 10, and reduced levels of CD68, F4/80, inducible nitric oxide synthase, and tumor necrosis factor). Our results suggest a beneficial role for complement C3 in plaque clearance and neuronal health as well as in modulation of the microglia phenotype.
Conceptualization of Purposeful Games (2017)

This document presents a summary of my research as a doctoral student. The topic of my research is "Conceptualization of Purposeful Games". I am interested in knowing how designers conceptualize games that resolve the duality of fun and purpose effectively. I have conducted pilot studies and the results are encouraging. This document presents my research situation, research question, my approach to answering this question, and the expected contributions of the research.
Contribution of Accelerated Body Masses to Able-Bodied Gait (2003)

A video-based system was able to determine the net effect of the external forces with the summation of the mass-acceleration products during able-bodied gait. The trunk and lower limbs were the dominant body segments responsible for the production of external forces during able-bodied gait, whereas the thighs contributed more to the ground reaction force than the foot and shank for forward progression in able-bodied gait.
Inhibition of Tissue Factor (TF) Pathway Blunts Hepatic Tumor Development in a Rat Colorectal Cancer Model. (2007)

Abstract Occurrence of hepatic metastasis (HM) is the leading cause of death in colorectal cancer, making their prevention a major challenge. Tissue factor (TF), the principal initiator of coagulation after binding to its ligand, coagulation factor FVIIa, is expressed by most colorectal cancer cells, and has been demonstrated to be associated to tumor invasion and metastasis. The aim of this study was to analyze the effects of inhibition of the TF pathway in a rat model of HM of colorectal cancer. Methods DHDK12 Pro B cells (20.106 cells), a tumor cell line established from chemically induced colon carcinoma in BDIX rats, were injected in the portal vein of syngenic rats. Inhibition of TF was achieved in 19 rats (treat ment group) through intraperitoneal injection of active site-inactivated factor VIIa (FFR-FVIIa, Novo Nordisk, Denmark) (10μg/g, once a day from day 3 to day 8 after HM induction). Additionally, 18 rats underwent cancer cell infusion according to the same procedure, without FFR-FVIIa treatment (control group). Rats were sacrificed at day 14. Results In the control group, infusion of cancer cells resulted in the development of macroscopical hepatic tumors in 17 out of 18 rats. In rats treated by FFR-FVIIa, no macroscopical or histological hepatic tumors were visible on the liver surface in 16 out of 19 rats (p=0.002, versus control group). Conclusion These results suggest that blockage of TF with proteolytically inactive FFR-VIIa inhibits hepatic tumor development at an early stage of tumoral development and TF is a target for adjuvant therapy in the prevention of HM.
SideTrack (2009)

Atomicity is a key correctness specification for multithreaded programs. Prior dynamic atomicity analyses include precise tools, which report an error if and only if the observed trace is not serializable; and imprecise tools, which generalize from the observed trace to report errors that might occur on other traces, but which may also report false alarms.
Toward automated cochlear implant insertion using tubular manipulators (2016)

During manual cochlear implant electrode insertion the surgeon is at risk to damage the intracochlear fine-structure, as the electrode array is inserted through a small opening in the cochlea blindly with little force-feedback. This paper addresses a novel concept for cochlear electrode insertion using tubular manipulators to reduce risks of causing trauma during insertion and to automate the insertion process. We propose a tubular manipulator incorporated into the electrode array composed of an inner wire within a tube, both elastic and helically shaped. It is our vision to use this manipulator to actuate the initially straight electrode array during insertion into the cochlea by actuation of the wire and tube, i.e. translation and slight axial rotation. In this paper, we evaluate the geometry of the human cochlea in 22 patient datasets in order to derive design requirements for the manipulator. We propose an optimization algorithm to automatically determine the tube set parameters (curvature, torsion, diameter, length) for an ideal final position within the cochlea. To prove our concept, we demonstrate that insertion can be realized in a follow-the-leader fashion for 19 out of 22 cochleas. This is possible with only 4 different tube/wire sets.
Use of azide and hydrogen peroxide as an inhibitor for endogenous peroxidase in the immunoperoxidase method. (1987)

We describe a simple and effective method for inhibition of endogenous peroxidase activity in the immunoperoxidase technique. Specimens are pre-treated with a mixture of azide and hydrogen peroxide, which is then followed by an indirect immunoperoxidase procedure. Comparison studies showed no significant loss of antigenicity or morphological details by this pre-treatment. The method is most useful for evaluating cell-specific antigens on specimens that have abundant endogenous peroxidase activity, such as blood and bone marrow.
Thyroid Hormone Transport by the Heterodimeric Human System L Amino Acid Transporter (2001)

Transport of thyroid hormone across the cell membrane is required for thyroid hormone action and metabolism. We have investigated the possible transport of iodothyronines by the human system L amino acid transporter, a protein consisting of the human 4F2 heavy chain and the human LAT1 light chain. Xenopus oocytes were injected with the cRNAs coding for human 4F2 heavy chain and/or human LAT1 light chain, and after 2 d were incubated at 25 C with 0.01-10 microM [(125)I]T(4), [(125)I]T(3), [(125)I]rT(3), or [(125)I]3,3'-diiodothyronine or with 10-100 microM [(3)H]arginine, [(3)H]leucine, [(3)H]phenylalanine, [(3)H]tyrosine, or [(3)H]tryptophan. Injection of human 4F2 heavy chain cRNA alone stimulated the uptake of leucine and arginine due to dimerization of human 4F2 heavy chain with an endogenous Xenopus light chain, but did not affect the uptake of other ligands. Injection of human LAT1 light chain cRNA alone did not stimulate the uptake of any ligand. Coinjection of cRNAs for human 4F2 heavy chain and human LAT1 light chain stimulated the uptake of phenylalanine > tyrosine > leucine > tryptophan (100 microM) and of 3,3'-diiodothyronine > rT(3) approximately T(3) > T(4) (10 nM), which in all cases was Na(+) independent. Saturation analysis provided apparent Michaelis constant (K(m)) values of 7.9 microM for T(4), 0.8 microM for T(3), 12.5 microM for rT(3), 7.9 microM for 3,3'-diiodothyronine, 46 microM for leucine, and 19 microM for tryptophan. Uptake of leucine, tyrosine, and tryptophan (10 microM) was inhibited by the different iodothyronines (10 microM), in particular T(3). Vice versa, uptake of 0.1 microM T(3) was almost completely blocked by coincubation with 100 microM leucine, tryptophan, tyrosine, or phenylalanine. Our results demonstrate stereospecific Na(+)-independent transport of iodothyronines by the human heterodimeric system L amino acid transporter.
LES of Vaporizing Gasoline Sprays Considering Multi-Injection Averaging and Grid-Convergent Mesh Resolution (2015)

A state-of-the-art spray modeling methodology, recently presented by Senecal et al. [1,2,3], is applied to Large Eddy Simulations (LES) of vaporizing gasoline sprays. Simulations of non-combusting Spray G (gasoline fuel) from the Engine Combustion Network are performed. Adaptive mesh refinement (AMR) with cell sizes from 0.09 mm to 0.5 mm are utilized to demonstrate grid convergence of the dynamic structure LES model for the gasoline sprays. Grid settings are recommended to optimize the accuracy/runtime tradeoff for LES-based spray simulations at different injection pressure conditions typically encountered in gasoline direct injection (GDI) applications. Twenty different realizations are simulated by changing the random number seed used in the spray sub-models. It is shown that for global quantities such as spray penetration, comparing a single LES simulation to experimental data is reasonable. Through a detailed analysis using the relevance index (RI) criteria, recommendations are made regarding the minimum number of LES realizations required for accurate prediction of the gasoline sprays.
Selective synthesis of zigzag-type aligned carbon nanotubes on SiC (0 0 0 −1) wafers (2002)

Zigzag-type carbon nanotubes have been selectively produced by surface decomposition of a well-polished SiC single crystal. The SiC wafer was heated to 1500 °C at a very small heating rate under vacuum. Transmission electron microscopy (TEM) and electron diffraction patterns revealed that almost all the well-aligned carbon nanotubes formed perpendicular to the SiC (0 0 0 −1) surface were double-walled and of zigzag type. The results of high-resolution electron microscopy (HREM) indicate that the zigzag type structure evolves from the Si–C hexagonal networks in the SiC crystal by the collapse of carbon layers remaining after the process of decomposition.
Rate of Penetration Optimization using Moving Horizon Estimation (2016)

Increase of drilling safety and reduction of drilling operation costs, especially improvement of drilling efficiency, are two important considerations in the oil and gas industry. The rate of penetration (ROP, alternatively called as drilling speed) is a critical drilling parameter to evaluate and improve drilling safety and efficiency. ROP estimation has an important role in drilling optimization as well as interpretation of all stages of the well life cycle. In this paper, we use a moving horizon estimation (MHE) method to estimate ROP as well as other drilling parameters. In the MHE formulation the states are estimated by a forward simulation with a pre-estimating observer. Moreover, it considers the constraints of states/outputs in the MHE problem. It is shown that the estimation error is with input-to-state stability. Furthermore, the ROP optimization (to achieve minimum drilling cost/drilling energy) concerning with the efficient hole cleaning condition and downhole environmental stability is presented. The performance of the methodology is demonstrated by one case study.
Uptake of Pharmaceutical and Personal Care Products by Soybean Plants from Soils Applied with Biosolids and Irrigated with Contaminated Water (2010)

Many pharmaceuticals and personal care products (PPCPs) are commonly found in biosolids and effluents from wastewater treatment plants. Land application of these biosolids and the reclamation of treated wastewater can transfer those PPCPs into the terrestrial and aquatic environments, giving rise to potential accumulation in plants. In this work, a greenhouse experiment was used to study the uptake of three pharmaceuticals (carbamazepine, diphenhydramine, and fluoxetine) and two personal care products (triclosan and triclocarban) by an agriculturally important species, soybean (Glycine max (L.) Merr.). Two treatments simulating biosolids application and wastewater irrigation were investigated. After growing for 60 and 110 days, plant tissues and soils were analyzed for target compounds. Carbamazepine, triclosan, and triclocarban were found to be concentrated in root tissues and translocated into above ground parts including beans, whereas accumulation and translocation for diphenhydramine and fluoxetine was limited. The uptake of selected compounds differed by treatment, with biosolids application resulting in higher plant concentrations, likely due to higher loading. However, compounds introduced by irrigation appeared to be more available for uptake and translocation. Degradation is the main mechanism for the dissipation of selected compounds in biosolids applied soils, and the presence of soybean plants had no significant effect on sorption. Data from two different harvests suggest that the uptake from soil to root and translocation from root to leaf may be rate limited for triclosan and triclocarban and metabolism may occur within the plant for carbamazepine.
216-64: Slow Septal Conduction Is Key In LBBB Patient-Specifc Models (2016)

Ejection fraction (EF) determines eligibility for CRT in heart failure patients (Pts) with left bundle branch block (LBBB). Since EF by echocardiography (Echo) may be hampered by technical difficulties it would be of interest to have an alternative for Pts with LBBB. Previous studies have shown good correlation between EF and systolic time intervals (STI), including pre-ejection period (PEP), left ventricular ejection time (LVET) and the ratio PEP/ LVET, but they were done mostly in Pts with narrow QRS.
Achromatic flat focusing lens based on dispersion engineering of spoof surface plasmon polaritons (2017)

In this letter, we first analyze the dispersion relation for achromatic focusing and obtain the achromatic focusing conditions for discretized unit cells of flat lenses. Then, we propose to engineer the dispersion of spoof surface plasmon polaritons (SSPPs) to satisfy the achromatic focusing conditions. Metallic blades structures are utilized to achieve the linear dispersion response by tailoring the weak dispersion region of SSPPs. A broadband achromatic flat focusing lens (AFFL) is implemented with delicate combinations of the blade structures. A prototype was designed, fabricated, and measured. Both the simulated and experimental results demonstrate that the proposed AFFL can achieve achromatic focusing from 7.5 to 9.0 GHz under the normal incidence.
Size Effects on the Stabilization of Ultrafine Zirconia Nanoparticles (2002)

The spontaneous oxidation of crystallized ZrAu at room temperature leads to the formation of ultrafine monoclinic zirconia (MZ) particles (about 3.6 nm in diameter). The presence of tetragonal phase (TZ), generally observed in very small zirconia particles, was investigated by X-ray diffraction and Raman experiments but was not observed. Thermodynamical calculations considering the finite size effects in zirconia were introduced to explain the formation of pure MZ considering experimental and theoretical surface energies. The results of these calculations associated with the near equilibrium conditions used for synthesis demonstrate that the monoclinic structure is the stable crystallographic structure of zirconia nanocrystals at room temperature.
Особенности применения самоорганизующихся нейронных сетей для анализа отклика однокристальной мультисенсорной системы идентификации газов (2009)

The pattern recognition technique based on self-organizing neural networks is considered to be applied to «e-nose» single-crystal multisensor system exposed to odors emitting by meat of different quality. The methodic to advance the level of the data recognition is suggested. It is shown that application of the technique based on Kohonen map modeling allows us to increase the correct recognition and classification of the different groups of experimental data up to 90 %.
Integrated Weld Automation for Gas Turbine Blades (1991)

The automation of turbine blade welding provides both metallurgical benefits and production advantages. Heat-affected zone cracking in sensitive superalloys, such as IN738 and IN100, can be eliminated or greatly reduced by optimizing process control, and higher production yields can be achieved when welding jet engine blades. However, the successful implementation of automated processes requires careful consideration and engineering of the technology package. In particular, the equipment packager must be experienced in the technology associated with turbine blade welding and incorporate appropriate tooling, measurement system, power source and robotic controls. An example of a welding system for high pressure blade tips is presented which required the development and integration of a novel vision system to measure the thickness of the squealer wall, in order to select the appropriate welding parameters. Several practical applications of the technology are demonstrated on turbine blades exhibiting typical dimensional and metallurgical variations.