gebhart/patrepeval huggingface dataset:
Reservoir-Based Fracture Optimization Approach (2004)

Abstract A new methodology to obtain the optimum fracture treatment design for a wide range of reservoir conditions has been developed and successfully implemented. The approach discussed here significantly reduces the time required to evaluate an optimum design and limits the materials considered to only those that are appropriate for the reservoir conditions. These improvements make it an ideal methodology for real-time re-design of fracture treatments after feedback from minifrac data has been implemented. This innovative fracture design methodology has capability to determine appropriate fracture conductivity and an economic optimum fracture length while reconciling these with actual fracture growth behavior in the reservoir. The technique incorporates the following simple, automated steps: Selects the most cost-effective fluid that will meet a minimum apparent viscosity requirement at a specified shear rate and temperature condition from a large industry fluid library to ensure that the proppant will be placed within the pay zone.Selects a proppant that will provide the required fracture conductivity at the cheapest cost from a large industry library.Determines the proppant concentration that is required at the wellbore to achieve a user-specified dimensionless conductivity criterion for a range of fracture lengths.Evaluates economic criteria such as net present value (NPV) and return on investment (ROI) for different fracture lengths by comparing fracture treatment cost and revenues from production response.Determines the optimum fracture conductivity profile that will have a uniform pressure drop down the fracture. The conductivity is adjusted for potential losses from non-Darcy and multi-phase flow, gel damage, embedment, and other proppant damage effects.Iterates a fracture treatment schedule that will result in the best fit of the optimum conductivity profile. The methodology can help optimize fracture treatments in any type of environment. The technique is simple and can be run quickly in a real-time environment after a minifrac is conducted to make changes to the propped fracture treatment. The procedure has been implemented in a commercially available fracture design program.
Neutralizing Antibody Response to Hepatitis C Virus (2011)

A critical first step in a "rational vaccine design" approach for hepatitis C virus (HCV) is to identify the most relevant mechanisms of immune protection. Emerging evidence provides support for a protective role of virus neutralizing antibodies, and the ability of the B cell response to modify the course of acute HCV infection. This has been made possible by the development of in vitro cell culture models, based on HCV retroviral pseudotype particles expressing E1E2 and infectious cell culture-derived HCV virions, and small animal models that are robust tools in studies of antibody-mediated virus neutralization. This review is focused on the immunogenic determinants on the E2 glycoprotein mediating virus neutralization and the pathways in which the virus is able to escape from immune containment. Encouraging findings from recent studies provide support for the existence of broadly neutralization antibodies that are not associated with virus escape. The identification of conserved epitopes mediating virus neutralization that are not associated with virus escape will facilitate the design of a vaccine immunogen capable of eliciting broadly neutralizing antibodies against this highly diverse virus.
Java Based Symbolic Circuit Solver For Electrical Engineering Curriculum (2012)

The interactive technical electronic book, TechEBook, currently under development at the University of Central Florida (UCF), introduces a paradigm shift by replacing the traditional electrical engineering course with topic-driven modules that provide a useful tool for engineers and scientists. The TechEBook comprises the two worlds of classical circuit books and interactive operating platforms such as iPads, laptops and desktops. The TechEBook provides an interactive applets screen that holds many modules, each of which has a specific application in the self learning process.   This paper describes one of the interactive techniques in the TechEBook known as Symbolic Circuit Solver (SymCirc). The SymCirc develops a versatile symbolic based linear circuit with a switches solver. The solver works by accepting a Netlist and the element that the user wants to find the voltage across or current on, as input parameters. Then it either produces the plot or the time domain expression of the output. Frequency domain plots or Symbolic Transfer Functions are also produced. The solver gets its input from a Web-based GUI circuit drawer developed at UCF. Typical simulation tools that electrical engineers encounter are numerical in nature, that is, when presented with an input circuit they iteratively solve the circuit across a set of small time steps. The result is represented as a data set of output versus time, which can be plotted for further inspection. Such results do not help users understand the ultimate nature of circuits as Linear Time Invariant systems with a finite dimensional basis in the solution space. SymCirc provides all simulation results as time domain expressions composed of the basic functions that exclusively include exponentials, sines, cosines and/or t raised to any power.   This paper explains the motivation behind SymCirc, the Graphical User Interface front end and how the solver actually works. The paper also presents some examples and results to better explain the concept.
Human-computer interaction using gesture recognition and 3D hand tracking (2002)

This paper describes a real time system for human-computer interaction through gesture recognition and three dimensional hand-tracking. Using two cameras that are focused at the user's hand the system recognizes three gestures and tracks the hand in three dimensions. The system can simultaneously track two fingers (thumb and pointing finger) and output their poses. The pose for each finger consists of three positional coordinates and two angles (azimuth and elevation). By moving the thumb and the pointing finger in 3D, the user can control 10 degrees of freedom in a smooth and natural fashion. We have used this system as a multi-dimensional input-interface to computer games, terrain navigation software and graphical editors. In addition to providing 10 degrees of control, our system is much more natural and intuitive to use compared to traditional input devices. The system is user independent, and operates at the rate of 60 Hz.
Identification of a Metastasis-Specific MicroRNA Signature in Human Colorectal Cancer (2015)

We discovered a metastasis-specific miRNA signature in pCRCs and discovered novel tissue- and serum-based CRC metastasis-specific miRNA biomarkers through intensive validation. These unique miRNAs may be clinically applicable to predict prognosis and distant metastasis in CRC.
Monoclonal antibodies detect different distribution patterns of IL-8 receptor A and IL-8 receptor B on human peripheral blood leukocytes. (1994)

mAbs previously reported to be specific for IL-8R type A (IL-8R-A) and mAbs specific for IL-8R type B (IL-8R-B), which are described in this paper, were used to investigate the expression of each receptor on various types of cells. We generated mAbs specific for IL-8R-B, 4D1, and 10H2 by immunizing mice with 293 cells that expressed IL-8R-B and by selecting hybridoma cell lines that secreted mAbs that bind to human neutrophils. Flow cytometry showed that mAbs 4D1 and 10H2 were specific for IL-8R-B, as determined by their exclusive binding to 293-27 cells that expressed IL-8R-B, but not to 293-71 cells that expressed IL-8R-A. Epitopes recognized by these IL-8R-B-specific mAbs were shown to be within the N-terminal residues 1-18 of the IL-8R-B on the basis of their binding to various N-terminal peptides, as measured by ELISA. These IL-8R-B-specific mAbs were able to inhibit up to 90 and 50% of the 125I-labeled IL-8 binding to 293-27 cells and human neutrophils, respectively. The combination of mAb 9H1 (anti-IL-8R-A) and mAb 10H2 (anti-IL-8R-B) inhibited approximately 70% of 125I-labeled IL-8 binding to human neutrophils. Flow cytometry showed a wide range of donor variation in the expression levels of IL-8R-A and IL-8R-B on various human peripheral blood leukocytes. All neutrophils, all monocytes, and 5 to 25% of total lymphocytes (CD8+ T cells and CD56+ NK cells) expressed IL-8R. Neutrophils expressed the highest level of both IL-8R-A and IL-8R-B, at an approximately equal ratio, whereas monocytes and IL-8R+ lymphocytes expressed higher levels of IL-8R-B than IL-8R-A. Double-color flow cytometric analysis showed that 7 to 42% of CD8+ T cells and 39 to 76% of CD56+ NK cells, but no CD 20+ B cells or CD4+ T cells, expressed IL-8R.
Immunization of Humans with Recombinant Pneumococcal Surface Protein A (rPspA) Elicits Antibodies That Passively Protect Mice from Fatal Infection with<i>Streptococcus pneumoniae</i>Bearing Heterologous PspA (2000)

Pneumococcal surface protein A (PspA), a cross-reactive protein expressed by all pneumococci, is known to elicit an antibody in animals that can passively protect mice from infection with Streptococcus pneumoniae. A phase I trial with recombinant PspA showed the protein to be immunogenic in humans. Pre- and postimmune serum samples from this trial were examined, and human antibody to PspA could protect mice from pneumococcal infection. The serum samples of subjects immunized twice with 125 microg of PspA had >100 times as much antibody per milliliter as was required to consistently protect mice from fatal infection (1.3 microg/dose). At least 98% of PspAs fall into PspA sequence/serologic families 1 or 2. Human antibodies elicited by a family 1 PspA protected against infection with S. pneumoniae expressing either family 1 or 2 PspAs and with strains of all 3 capsular types tested: 3, 6A, and 6B. These studies suggest that PspA may have efficacy as a human vaccine.
Supporting anti-terrorist analyst teams using agents with shared RPD process (2004)

Antiterrorist analysts often need to work in teams with the requirement to analyze voluminous amounts of dynamic information in order to assess potential terrorist threats. Analysts have a high cognitive demand complicated by factors that typically the information has restrict access and requires special expertise for interpretation. The goal of this research is to enhance team performance by modeling and implementing a cognitive agent architecture capable of proactively seeking, linking and sharing information using knowledge and experience distributed among team members. The agent architecture is empowered by a collaborative RPD model - a novel team-based naturalistic decision making process derived from Klein's recognition-primed decision framework.
Analytical model of the nonlinear dynamics of cantilever tip-sample surface interactions for various acoustic atomic force microscopies (2008)

An analytical model is developed of the interaction of the cantilever tip of an atomic force microscope with the sample surface that treats the cantilever and sample as independent systems coupled by a nonlinear force acting between the cantilever tip and a volume element of the sample surface. To maintain equilibrium, the volume element is subjected to a restoring force from the remainder of the sample. The model accounts for the positions on the cantilever of the cantilever tip, laser probe, and excitation force (if any). The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a matrix iteration procedure. Solutions are obtained for the phase and amplitude signals generated by various acoustic atomic force microscope (A-AFM) techniques including force modulation microscopy, atomic force acoustic microscopy, ultrasonic force microscopy, heterodyne force microscopy, resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM), and amplitude modulation--atomic force microscopy (AM-AFM) (intermittent contact mode). The solutions are used to obtain a quantitative measure of A-AFM image contrast resulting from variations in the Young modulus of the sample. Applications of the model to measurements of LaRC™-CP2 polyimide film using RDF-AFUM and AM-AFM images predict maximum variations in the Young modulus of 24% and 18%, respectively, over a common scan area. Both predictions are in good agreement with the value of 21% obtained from independent mechanical stretching measurements of the polyimide sheet material.
An analytics approach to traffic analysis in network virtualization (2014)

Network virtualization has been propounded as a diversifying attribute of the future inter-networking paradigm. However, monitoring and troubleshooting operational virtual networks can be a daunting task, due to their size, distributed state, and additional complexity introduced by network virtualization. We propose an analytics approach for the analysis of network traces collected across hypervisors and switches. To re-organize individual trace events into path-wise slices that represent the life-cycle of individual packets, we first present a trace slicing scheme. Then, we develop a path characterization scheme to extract feature matrices from those trace slices. Using those feature metrics, we develop a set of trace analysis algorithms to cluster, rank, query, and verify packet traces. We have developed the analytics approach in a SDN network management tool, and presented evaluation results to show how it can enable visibility and effective problem diagnosis in a SDN network.
Side-chain-to-tail cyclization of ribosomally derived peptides promoted by aryl and alkyl amino-functionalized unnatural amino acids (2016)

A strategy for the production of side-chain-to-tail cyclic peptides from ribosomally derived polypeptide precursors is reported. Two genetically encodable unnatural amino acids, bearing either an aryl or alkyl amino group, were investigated for their efficiency toward promoting the formation of medium to large-sized peptide macrocycles via intein-mediated side-chain-to-C-terminus cyclization. While only partial cyclization was observed with precursor proteins containing para-amino-phenylalanine, efficient peptide macrocyclization could be achieved using O-2-aminoethyl-tyrosine as the reactive moiety. Conveniently, the latter was generated upon quantitative, post-translational reduction of the azido-containing counterpart, O-2-azidoethyl-tyrosine, directly in E. coli cells. This methodology could be successfully applied for the production of a 12 mer cyclic peptide with enhanced binding affinity for the model target protein streptavidin as compared to the acyclic counterpart (KD: 5.1 μM vs. 22.4 μM), thus demonstrating its utility toward the creation and investigation of novel, functional macrocyclic peptides.
Hot gas desulfurization sorbent and method (1991)

A multiple metal oxide sorbent supported on a zeolite of substantially silicon oxide is used for the desulfurization of process gas streams, such as from a coal gasifier, at temperatures in the range of about 1200[degrees] to about 1600[degrees]F. The sorbent is provided by a mixture of copper oxide and manganese oxide and preferably such a mixture with molybdenum oxide. The manganese oxide and the molybdenum are believed to function as promoters for the reaction of hydrogen sulfide with copper oxide. Also, the manganese oxide inhibits the volatilization of the molybdenum oxide at the higher temperatures.
Sizing the streaming media cluster solution for a given workload (2004)

The goal of the proposed benchmarking and capacity planning framework is to evaluate the amount of resources needed for processing a given workload while meeting the specified performance requirements. There are two essential components in our capacity planning framework: (i) the capacity measurements of different hardware and software solutions using a specially designed set of media benchmarks; and (ii) a media service workload profiler, called MediaProf, which extracts a set of quantitative and qualitative parameters characterizing the service demand. The capacity planning tool matches the requirements of the media service workload profile, SLA and configuration constraints to produce the best available cost/performance solution. In case of a multi-node configuration, the capacity planner performs a cluster sizing evaluation by taking into account the choice of load balancing solution.
COMP: Compiler Optimizations for Manycore Processors (2014)

Applications executing on multicore processors can now easily offload computations to many core processors, such as Intel Xeon Phi coprocessors. However, it requires high levels of expertise and effort to tune such offloaded applications to realize high-performance execution. Previous efforts have focused on optimizing the execution of offloaded computations on many core processors. However, we observe that the data transfer overhead between multicore and many core processors, and the limited device memories of many core processors often constrain the performance gains that are possible by offloading computations. In this paper, we present three source-to-source compiler optimizations that can significantly improve the performance of applications that offload computations to many core processors. The first optimization automatically transforms offloaded codes to enable data streaming, which overlaps data transfer between multicore and many core processors with computations on these processors to hide data transfer overhead. This optimization is also designed to minimize the memory usage on many core processors, while achieving the optimal performance. The second compiler optimization re-orders computations to regularize irregular memory accesses. It enables data streaming and factorization on many core processors, even when the memory access patterns in the original source codes are irregular. Finally, our new shared memory mechanism provides efficient support for transferring large pointer-based data structures between hosts and many core processors. Our evaluation shows that the proposed compiler optimizations benefit 9 out of 12 benchmarks. Compared with simply offloading the original parallel implementations of these benchmarks, we can achieve 1.16x-52.21x speedups.
Transmit diversity and equalization for power controlled wireless networks (1997)

A multitap transmit diversity scheme for the downlink is proposed where the transmit weight vectors are adjusted such that the SNR at each mobile is above a threshold. The proposed transmit diversity scheme can be applied to networks with multipath fading channels and in cases where the number of cochannels and multipaths are larger than the number of antenna elements.
Model-based evaluation of mechanisms and benefits of mainstream shortcut nitrogen removal processes (2015)

The main challenge in implementing shortcut nitrogen removal processes for mainstream wastewater treatment is the out-selection of nitrite oxidizing bacteria (NOB) to limit nitrate production. A model-based approach was utilized to simulate the impact of individual features of process control strategies to achieve NO(-)(2)-N shunt via NOB out-selection. Simulations were conducted using a two-step nitrogen removal model from the literature. Nitrogen shortcut removal processes from two case studies were modeled to illustrate the contribution of NOB out-selection mechanisms. The paper highlights a comparison between two control schemes; one was based on online measured ammonia and the other was based on a target ratio of 1 for ammonia vs. NOx (nitrate + nitrite) (AVN). Results indicated that the AVN controller possesses unique features to nitrify only that amount of nitrogen that can be denitrified, which promotes better management of incoming organics and bicarbonate for a more efficient NOB out-selection. Finally, the model was used in a scenario analysis, simulating hypothetical optimized performance of the pilot process. An estimated potential saving of 60% in carbon addition for nitrogen removal by implementing full-scale mainstream deammonification was predicted.
NLOS Identification and Mitigation for UWB Localization Systems (2007)

Non-line-of-sight (NLOS) identification and mitigation carries significant importance in wireless positioning systems. In this paper, the authors propose a novel NLOS identification technique based on the multipath channel statistics such as the kurtosis, the mean excess delay spread, and the root mean square delay spread. In particular, the IEEE 802.15.4a ultrawideband channel models are used as examples and the above statistics are found to be well modeled by log-normal random variables. Subsequently, a joint likelihood ratio test is developed for LOS/NLOS identification. Simulation results show that correct identification can be achieved with over 90% of the realizations for most channel models. A weighted least squares localization algorithm is also developed using the NLOS information, and accuracy gains with respect to a conventional least squares algorithm are demonstrated via Monte-Carlo simulations.
Abstract 1937: Development of microRNA-based prediction model of Trastuzumab treatment response for HER2-positive breast cancer using FFPE specimens. (2013)

Abstract [Background and Aim] Although Trastuzumab has been used for HER2(+) breast cancer, the treatment response of Trastuzumab therapy depends on unknown mechanisms among individual cases. In order to avoid unnecessary adverse events and to lighten financial burden, pre-treatment prediction of trastuzumab treatment response would be beneficial for patients. Thus, in this study, we develop a prediction algorithm using microRNA expression profile using formalin-fixed paraffin-embedded (FFPE) specimens of HER2(+) breast cancer. [Materials and Methods] Eighty-three breast cancer patients who underwent trastuzumab-chemo combined therapy before operations were enrolled with written informed consent. FFPE specimens of pre-treatment core needle biopsy samples were collected, and regions containing cancer and adjacent stromal cells were laser-microdissected. Total RNA samples extracted from the microdissected specimens were subjected for microRNA microarray (3D-Gene®, Toray, Japan) analysis. Among these 83 patients, 39 cases had pCR (definition: complete response in IDC regions regardless presence of DCIS without lymph node metastasis), and the other 44 cases did not. According to the pCR/non-pCR information, we develop a prediction model using 35 signature microRNAs by a SVM technique. Prediction accuracy assessed by Leave-one-out validation was AUROC=0.889. The 35 signature microRNAs for trastuzumab treatment response included 7 out of 8 let-7 family members and miR-125a-5p/b-5p, which were downregulated in pCR specimens. [Conclusion] microRNA profile could predict treatment response of trastuzumab-chemo combined therapy for HER2(+) breast cancer, and the developed prediction algorithm might be a useful tool for clinical decision making. Prediction Accuracy Outcome: non-pCR Outcome: pCR total Prediction: non-sensitive 35 6 41 Prediction: sensitive 9 33 42 total 44 39 83 Citation Format: Fumiaki Sato, Zhipeng Wang, Takayuki Ueno, Akira Myomoto, Satoko Takizawa, Feng Ling Pu, Norikazu Masuda, Yoshiki Mikami, Yoshiki Mikami, Kazuharu Shimizu, Shigehira Saji, Masakazu Toi. Development of microRNA-based prediction model of Trastuzumab treatment response for HER2-positive breast cancer using FFPE specimens. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1937. doi:10.1158/1538-7445.AM2013-1937