gebhart/patrepeval huggingface dataset:
Using Microseisms to Monitor Hydraulic Fractures Within the Bakken Formation of North Dakota (2010)

The Mississippian-Devonian Bakken Formation is a relatively tight mixed carbonate – clastic sequence in the Williston Basin of North Dakota. Although production can exceed 1000 BOPD, hydraulic fracturing is necessary to induce economic production. In late 2007 seven (7) operators along with Schlumberger formed a consortium for the purpose of applying the best available technologies to examine the geologic factors and the drilling and completion principles that affect production. As part of this, three (3) horizontal wells (each 4000 feet in length) were drilled 1500 feet apart into the Middle Bakken Member. Schlumberger positioned an array of 16 triaxial geophones, spaced 100 feet apart, in the middle lateral (Nesson State 42X-36) to monitor the microseismic activity during the hydraulic fracturing of the two (2) outside wells. Different hydraulic fracturing methods were applied in each stage; ranging from a single treatment in the northern lateral (Nesson State 41X-36) to a six (6) staged treatment with swell packers in the southern lateral (Nesson State 44X-36). The microseismic events were studied in the context of our geologic understanding of the area, comparison to the distributions of radioactive and chemical tracers and a reservoir simulation to develop a robust interpretation of effectiveness of the hydraulic fracture treatments. In addition to the microseismic monitoring conducted by Schlumberger, three other microseismic monitoring arrays were installed and monitored. The results of the various monitoring efforts varied dramatically and these differences are worthy of examination.
Near-infrared in vivo fluorescence sensor with integrated dielectric emission filter (2009)

We present a monolithically integrated near-infrared fluorescence sensor incorporating a dielectric emission filter for in vivo applications. We successfully integrated a dielectric emission filter (OD3) onto a low-noise detector and sensed 50nM fluorescent dye concentration.
Nucleotide sequence of a 55 kbp region from the right end of the genome of a pathogenic African swine fever virus isolate (Malawi LIL20/1) (1994)

The nucleotide sequence of a 55098 bp region from the right end of the genome of a virulent African swine fever virus (ASFV) isolate (Malawi LIL20/1) has been determined. Translation of the sequence identified 67 major open reading frames (ORFs) which are closely spaced and read from both DNA strands. At six positions intergenic tandem repeat arrays are found. Comparison of the predicted amino acid sequences of encoded proteins with protein sequence databases identified a number of homologies. These include three subunits of RNA polymerase, a protein with homology to transcription factor SII (TFSII), a DNA ligase, two subunits of mRNA capping enzyme, a DNA topoisomerase type II, a dUTPase, a protein kinase, three helicases, a ubiquitin-conjugating enzyme, a protein with homology to the nif S and nif S-like proteins identified in some bacteria and Saccharomyces cerevisiae, a protein with homology to both a myeloid differentiation primary response antigen (MyD116) and to a herpes simplex virus-encoded neurovirulence-associated protein (ICP34.5), a protein with homology to the ASFV-encoded structural protein p22, two proteins with homology to copies of the ASFV-encoded multigene family 360 and one protein with homology to the ASFV-encoded multigene family 110. Four genes encode proteins which have homology to each other and constitute a new multigene family (MGF100). Nine ORFs encode proteins which contain predicted transmembrane domains. The possible functions of these predicted ASFV-encoded proteins are discussed and the evolutionary relationship of ASFV to other viruses are considered. Despite the similarities in genome structure and replication strategy of ASFV with poxviruses, sequence similarity between them is low and the organization of ASFV-encoded genes is not colinear with that of the orthopoxviruses.
Electrochemical and Structural Studies on Microcrystals of the (C60)x(CTV) Inclusion Complexes (x = 1, 1.5; CTV = cyclotriveratrylene) (2001)

The electrochemical reduction of microcrystals of (C60)x(CTV) (x = 1, 1.5; CTV = cyclotriveratrylene) complexes adhered to electrode surfaces in contact with CH3CN (0.10 mol L-1 Bu4NClO4) results in initial formation of (C60-)x(CTV) which is followed by the liberation of the reduced fullerene anion from the CTV cavity. The released fullerene anion then reacts with the Bu4N+ electrolyte cation to form surface-confined (Bu4N)C60 species which can in turn be further reduced to solid-state and/or solution-phase multi-charged fullerene anions or oxidized to C60(solid). The expelled CTV diffuses from the surface of the electrode into the bulk solution to form (Bu4N+)(CTV) species. The peak potential for one-electron reduction of solid (C60)x(CTV) is positively shifted by about 50 mV (x = 1) or 80 mV (x = 1.5) relative to the value for pure C60 microcrystals. These and results with other supramolecular complexes available in the literature suggest that the contact area between host and guest molecules as well as the position of high electron density area of the host are important factors that stabilize the host−guest complexes during/after the addition of electrons to the fullerene. The improved crystal structure determination of (C60)(CTV)(toluene)0.5 using X-ray diffraction data at 173 K shows a two-dimensional close packed array of fullerenes with a third of these devoid of CTV.
Narrow-line Cooling and Determination of the Magic Wavelength of Cd (2019)

We experimentally and theoretically determine the magic wavelength of the (5s^{2})^{1}S_{0}-(5s5p)^{3}P_{0} clock transition of ^{111}Cd to be 419.88(14) and 420.1(7) nm. To perform Lamb-Dicke spectroscopy of the clock transition, we use narrow-line laser cooling on the ^{1}S_{0}-^{3}P_{1} transition to cool the atoms to 6 μK and load them into an optical lattice. Cadmium is an attractive candidate for optical lattice clocks because it has a small sensitivity to blackbody radiation and its efficient narrow-line cooling mitigates higher order light shifts. We calculate the blackbody shift, including the dynamic correction, to be fractionally 2.83(8)×10^{-16} at 300 K, an order of magnitude smaller than that of Sr and Yb. We also report calculations of the Cd ^{1}P_{1} lifetime and the ground state C_{6} coefficient.
AntWall (2018)

Mobile devices have become an essential part of our every-day lives but are also suffering from various privacy and security risks. The ease of app development has led to a plethora of apps that employ poor security practices and often expose personal identifiers to remote servers. Moreover, these privacy exposures often come from third-party libraries that are leveraged by multiple apps, leading to cross-app tracking of users. This tracking is typically used to serve personalized ads, which cost the user extra data and take up screen real estate. In this demo, we will showcase AntWall, a system for preventing exposures of personal information and blocking ads.
Introduction to VR technology (2003)

This tutorial provides a fast paced introduction to the technologies of virtual reality, providing a foundation to comprehend the other activities at VR2003. Attendees will learn the component technologies that allow for the creation and experience of desktop and immersive virtual worlds. Each technology topic will provide a definition, brief introduction to the methods and issues, example systems, and references for further investigation (background, research, and commercial). Topics will include the basic hardware and software technologies and also touch on design issues such as usability and story elements.
Isotypic Restriction of the Antibody Response to Human Immunodeficiency Virus (1988)

HIV-infected individuals progress toward AIDS despite the early elicitation of a specific immune response. Analysis of the isotypic distribution of HIV-specific antibodies appears of special interest for two reasons: first, isotypic diversity is partly under the control of antigen-specific T-helper cells, the very cells infected by HIV; second, isotype determines antibody functions, effector (neutralization, antibody-dependent complement, or cell-mediated cytotoxicity) as well as blocking functions. We have investigated by Western blot analysis the isotypic profile of the antibody response to HIV structural proteins (env, gag, pol) and to the nonstructural protein F (3' orf), which is absent from the virion and might primarily target infected cells. In 115 asymptomatic individuals, infected by sexual contact (homosexual men) or intravenously (hemophiliacs), the response to gag-products was polyisotypic, including IgM, IgG1, IgG3 and IgA; the response to F was more restricted (IgM, IgG1, IgA) and the response to env strikingly restricted to the IgG1 isotype, suggesting different regulatory mechanisms in the B-cell response to these proteins. The isotypic distribution was also influenced by the route of infection, IgG4 and IgE (gag-specific) being exclusively elicited in the hemophiliac group. Finally, observations of potential diagnostic interest were made in a limited number of at-risk individuals; these included the presence of gag- and pol-specific IgM or IgA in the absence of any HIV-specific IgG isotypes; and the presence of gag- and F-specific antibodies in the absence of env-specific antibodies, suggesting the early occurrence of both isotypic and antigenic selection mechanisms during the course of HIV infection.
Waveform Optimization for Wireless Power Transfer with Power Amplifier and Energy Harvester Non-Linearities (2021)

Waveform optimization has recently been shown to be a key technique to boost the efficiency and range of far-field wireless power transfer (WPT). Current research has optimized transmit waveform adaptive to channel state information (CSI) and accounting for energy harvester (EH)'s non-linearity but under the assumption of linear high power amplifiers (HPA) at the transmitter. This paper proposes a channel-adaptive waveform design strategy that optimizes the transmitter's input waveform considering both HPA and EH non-linearities. Simulations demonstrate that HPA's non-linearity degrades the energy harvesting efficiency of WPT significantly, while the performance loss can be compensated by using the proposed optimal input waveform.
Globally Optimal Beamforming for Rate Splitting Multiple Access (2021)

We consider globally optimal precoder design for rate splitting multiple access in Gaussian multiple-input single-output downlink channels with respect to weighted sum rate and energy efficiency maximization. The proposed algorithm solves an instance of the joint multicast and unicast beamforming problem and includes multicast-and unicast-only beamforming as special cases. Numerical results show that it outperforms state-of-the-art algorithms in terms of numerical stability and converges almost twice as fast.
Atmospheric transmission from an instrument measuring scatter at 1550 nm (2013)

The Naval Research Laboratory (NRL) has extensively investigated atmospheric effects on maritime lasercomm in both long term research studies and short term system demonstrations. A current effort is underway in the ONR Tactical Line-of-Sight Optical Communications (TALON) program to better characterize atmospheric transmission at 1550 nm in multiple climates to enable prediction of communication link performance. In order to allow long term unmanned measurements in these multiple climates, NRL developed a scattering-based 1550 nm transmission sensor similar in function to commercial visible wavelength visibility monitors. After the system was built and calibrated, it was deployed to a number of sites with various climate types to collect data over a 1-month period for each site. This paper describes the development of the instrument and the software. It also presents some of the collected data.
Abstract 2534: High-affinity small molecule inhibitors of the menin-MLL interaction reverse oncogenic transformation mediated by MLL fusion proteins in leukemia (2014)

Abstract The protein-protein interaction (PPI) between menin and Mixed Lineage Leukemia (MLL) plays a critical role in acute leukemias with translocations of MLL gene, and inhibition of this interaction with small molecules represents a new potential therapeutic strategy for the MLL leukemia patients. We identified novel small molecule inhibitors of the menin-MLL interaction with distinct molecular scaffolds by performing a High Throughput Screening (HTS) of over 300,000 compounds. Extensive medicinal chemistry efforts performed for two lead classes to improve inhibitory activity of these compounds resulted in menin-MLL inhibitors with low nanomolar binding affinities. The menin-inhibitor co-crystal structures revealed that these compounds directly bind to menin and closely mimic the key interactions of MLL with menin, resulting in their high binding affinity. Interestingly, the hydroxymethylpiperidine class of the menin-MLL inhibitors extends beyond the MLL binding region on menin, providing additional opportunity for their optimization. We combined extensive crystallography studies with structure-based design to perform rational optimization and scaffold modification to rapidly improve activity and modulate physicochemical properties of the menin-MLL inhibitors. Treatment of MLL leukemia cells with the most potent menin-MLL inhibitors we developed resulted in very effective and selective inhibition of cell proliferation, induced apoptosis and differentiation of these cells. These effects were associated with downregulation of Hoxa9 and Meis1 expression, the downstream targets of MLL fusion proteins required for their leukemogenicity, demonstrating a very specific mechanism of action for these newly developed menin-MLL inhibitors. In vivo studies are currently undergoing to assess the effect of these compounds on leukemia progression in animal models of MLL leukemia. Our studies provide a novel and very attractive scaffolds for further development as a new potential therapeutic approach for the MLL leukemia patients. Citation Format: Jolanta E. Grembecka, Shihan He, Timothy J. Senter, Dmitry Borkin, Jonathan Pollock, Changho Han, Sunil Kumar Upadhyay, Trupta Purohit, Hongzhi Miao, Rocco D. Gogliotti D. Gogliotti, Craig W. Lindsley, Tomasz Cierpicki, Shaun R. Stauffer. High-affinity small molecule inhibitors of the menin-MLL interaction reverse oncogenic transformation mediated by MLL fusion proteins in leukemia. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2534. doi:10.1158/1538-7445.AM2014-2534
Interval-Based Analysis of Software Processes (2001)

A typical characteristic of complex embedded systems is their large software share that consists of software processes either being directly written in an implementation language like C, or being created from abstract modeling tools (e. g. Simulink or StateMate) using standard code generators, or being reused from previous designs (e. g. legacy code). A major challenge is the safe integration of these separately designed system parts. This paper focuses on the formal analysis of software processes with respect to their non-functional properties like timing or power consumption. The proposed approach yields safe upper and lower bounds on these properties and has advantages over previous work in terms of accuracy and efficiency. Further, it is shown how the results of this process-level analysis can be utilized to generate a model for the system-wide validation of non-functional properties. The applicability of the approach is demonstrated using an example of a filter process operating on a packet stream.
A comparative study of dopant activation in boron, BF/sub 2/, arsenic, and phosphorus implanted silicon (2002)

Ultra-low energy implants were used in combination with rapid thermal anneals in the temperature range 900/spl deg/C-1050/spl deg/C to study dopant activation in silicon. First, relatively long time anneals were performed in a conventional tungsten-based RTA to investigate the activation mechanisms. The activation was monitored using Hall measurement, where the rate of electrical activation was considered by measuring the time it takes to reach 50% activation. Using Arrhenius fits, an activation energy was extracted, and it was found that while boron has a mean activation energy for electrical activation of 4.7 eV in agreement with previous studies, arsenic and phosphorus have thermal activation energies of 3.6 eV and 4.1 eV, respectively. The 4.7 eV activation energy for boron is believed to be related to a point defect driven mechanism for electrical activation. Electrical activation of arsenic and phosphorus, however, seems to be related to dopant diffusion. In the second set of experiments, an arc lamp system was utilized to perform ultra-sharp spike anneals. For both dopants, it was found that for a given temperature, there is an optimum ramp-rate that produces the desired dopant activation and junction depth.
Structure–Activity Relationships of 33 Piperidines as Toxicants Against Female Adults of <I>Aedes aegypti</I> (Diptera: Culicidae) (2007)

Aedes aegypti (L.) (Diptera: Culicidae) is the primary vector of both dengue and yellow fever. Use of insecticides is one of the primary ways to control this medically important insect pest. However, few new insecticides have been developed for mosquito control in recent years. As a part of our collaborative effort to search for new insecticides to control mosquitoes, piperidine was used as base compound for further optimization. Herein, we report the structure-activity relationships of 33 piperidines against adult female Ae. aegypti. On the basis of 24-h LD50 values after topical application, the most toxic compound was 2-ethyl-piperidine, with an LD50 as low as 0.8 microg per mosquito. The toxicities of piperidine derivatives were significantly decreased when a benzyl moiety was attached to the carbon of the piperidine ring, with an LD50 value as high as 29.2 microg per mosquito. The toxicity order of three moieties attached to the carbon of the piperidine ring was ethyl- > methyl- > benzyl-derivatives. When the same moiety was attached to the piperidine ring, the carbon position to which the moiety was attached conferred different toxicity and the toxicity order was second carbon > third carbon > fourth carbon. Together, these preliminary results may be useful in guiding further piperidine ring modifications in the development of potential new insecticides.
Growing heterogeneous tumors in silico (2009)

An in silico tool that can be utilized in the clinic to predict neoplastic progression and propose individualized treatment strategies is the holy grail of computational tumor modeling. Building such a tool requires the development and successful integration of a number of biophysical and mathematical models. In this paper, we work toward this long-term goal by formulating a cellular automaton model of tumor growth that accounts for several different inter-tumor processes and host-tumor interactions. In particular, the algorithm couples the remodeling of the microvasculature with the evolution of the tumor mass and considers the impact that organ-imposed physical confinement and environmental heterogeneity have on tumor size and shape. Furthermore, the algorithm is able to account for cell-level heterogeneity, allowing us to explore the likelihood that different advantageous and deleterious mutations survive in the tumor cell population. This computational tool we have built has a number of applications in its current form in both predicting tumor growth and predicting response to treatment. Moreover, the latent power of our algorithm is that it also suggests other tumor-related processes that need to be accounted for and calls for the conduction of new experiments to validate the model's predictions.
The Impact of Halogenated Phenylalanine Derivatives on NFGAIL Amyloid Formation (2020)

The hexapeptide hIAPP<sub>22-27</sub> (NFGAIL) is known as a crucial amyloid core sequence of the human islet amyloid polypeptide (hIAPP) whose aggregates can be used to better understand the wild-type hIAPP's toxicity to β-cell death. In amyloid research, the role of hydrophobic and aromatic-aromatic interactions as potential driving forces during the aggregation process is controversially discussed not only in case of NFGAIL, but also for amyloidogenic peptides in general. We have used halogenation of the aromatic residue as a strategy to modulate hydrophobic and aromatic-aromatic interactions and prepared a library of NFGAIL variants containing fluorinated and iodinated phenylalanine analogues. We used thioflavin T staining, transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) to study the impact of side-chain halogenation on NFGAIL amyloid formation kinetics. Our data revealed a synergy between aggregation behavior and hydrophobicity of the phenylalanine residue. This study introduces systematic fluorination as a toolbox to further investigate the nature of the amyloid self-assembly process.
Bio-inspired design of soft mechanisms using a toroidal hydrostat (2021)

Biology is replete with soft mechanisms of potential use for robotics. Here, we report that a soft, toroidal hydrostat can be used to perform three functions found in both living and engineered systems: gripping, catching, and conveying. We demonstrate a gripping mechanism that uses a tubular inversion to encapsulate objects within a crumpled elastic membrane under hydrostatic pressure. This mechanism produces gripping forces that depend predictably upon the geometric and materials properties of the system. We next demonstrate a catching mechanism akin to that of a chameleon’s tongue: the elasticity of the membrane is used to power a catapulting inversion process (≈400 m/s2) to capture flying objects (e.g., a bouncing ball). Finally, we demonstrate a conveying mechanism that passes objects through the center of the toroidal tube (∼1 cm/s) using a continuous inversion-eversion process. The hybrid hard-soft mechanisms presented here can be applied toward the integration of soft functionality into robotic systems.
The Minimum Spanning Tree Problem in the Phase Calibration for the Spatial FFT Interferometer (2000)

Achieving a Nyquist-rate direct-imaging observation using a spatial FFT interferometer, instrumental phase errors in transmission lines must be calibrated before the observation. We improved the phase-calibrating system in the Waseda FFT interferometer by increasing the number of simultaneous obtainable fringe baselines from 84 to 128, and using the algorithm of the minimum spanning tree problem in graph theory. As a result, the main-beam intensity of the interferometer became 1.6 times on average.
Low-Profile Distributed Cavity Resonators and Filters (2017)

In this paper, a new family of low-profile high quality factor cavity resonators, termed distributed resonators, is introduced. Initially, the theory of operation of the proposed distributed resonator is presented regarding two, three, and four coupled resonator elements. Based on this, a further-improved arrangement of resonator elements is proposed. It is shown that the height of the individual resonator can be controlled by the number of resonant elements and can be almost arbitrarily low. As an experimental verification, a three-pole filter operating at 1800 MHz with a bandwidth of 40 MHz is designed and fabricated. The individual resonator of this filter comprises 25 individual resonant elements, with an overall cavity height of 7 mm, or 15°, and an unloaded quality factor of 1900. The height of the presented filter is significantly lower than any other air-filled filter cavity solution available in the literature. The measured insertion loss of the filter is 0.5 dB, which is in excellent agreement with the theoretically predicted value of 0.4 dB.