gebhart/patrepeval huggingface dataset:
BIOPHYSICAL INVESTIGATIONS OF THE THREE-WAY JUNCTION IN PHI29-LIKE BACTERIOPHAGE PROHEAD RNA (2017)

The knowledge gained from biophysical studies of RNA can contribute to basic research and inform new directions for translational research. In particular, information that develops the relationships among RNA energetics, physiologic stability, and structure can contribute to better predictions of RNA structure from sequence and guide the rational design of functional supramolecular structures such as targeted therapeutics. A conserved three-way junction (3WJ) in noncoding viral prohead or packaging RNA (pRNA) uniquely captures many aspects of RNA structure and function and represents a model system for studying these relationships. This dissertation presents thermodynamics for pRNA 3WJs. Phylogenetically related 3WJs have a wide range of thermodynamic stabilities, and some sequences are more stable than a phi29 3WJ sequence that is used commonly in RNA nanotechnology. The range of thermodynamic stabilities observed is not explained fully by differences in sequence at the 3WJ core.\n\nThe prototype phi29 pRNA sequence is used commonly in nanotechnology, for example as a nanoparticle delivery vector for therapeutic drugs. Related sequences are underexplored. The successful translation of phi29-alternative 3WJs into clinical practice will depend on energetic stability and the ability to overcome several key physiological barriers. This dissertation also presents 3WJ stabilities in human blood serum and in cells. Energetic and physiologic stabilities are not always correlated, but some 3WJs are both more thermodynamically stable and more stable in serum than the phi29 3WJ. The results of cell uptake studies support the idea that phi29-alternative 3WJs may be useful in nanotechnology, for example, in stabilizing RNAs for drug delivery.\n\nThe coaxial stacking of helices across RNA 3WJs can be thermodynamically favorable and may account for some of the observed differences in 3WJ stabilities. Transmission electron microscopy (TEM) data for a helix-extended construct indicate that helices are distributed equally around the phi29 3WJ. The determination of the relative orientation of helices around the pRNA 3WJ can help shed light on how sequence and secondary structure at the 3WJ core influence global structure and may provide insight into why some 3WJs are more energetically and physiologically stable than others.\n\nThe work presented here contributes to parameters for better RNA structure prediction from sequence, expands the number of useful building blocks for RNA nanotechnology, and provides a method for further investigating structural mechanisms underlying pRNA stability and self-assembly.
Inter-track interference cancelation in presence of frequency offset for shingled magnetic recording (2013)

The enormous growth of consumer electronic industry is driving the need for achieving ultra-high areal storage densities. Shingled magnetic recording (SMR) is a promising high density storage technique where shingles are created by overlapping tracks for increasing the track per inch (TPI) and achieving higher areal densities. High TPI values, however, introduce sidetrack interference in the equalized output of the center track sensed through the read head. The problem of removing interference from the center track signal can be formulated as estimating pulse shapes of sidetracks assuming sidetracks are decodable. In this paper, we first propose a solution using the correlation method for estimating the pulse shape and the phase-misalignment. The correlation method fails when there is a frequency offset present from sidetracks. Furthermore, we devise a solution based on the least mean square (LMS) algorithm which can provide time varying estimates of the sidetrack pulse shapes and remove the interference from the center track signal. Experimental and simulation results which corroborate the analysis of the proposed algorithm, demonstrate that the proposed algorithm outperforms other techniques and gives the minimum bit error rate (BER). The complexity of the proposed algorithm is low and it can be easily implemented on the hardware.
Sensor-assisted ALOHA for wireless networks (2002)

A neural network-based system for stabilizing ALOHA random access networks is described. A grid of sensors is used to gather energy measurements for a neural network. The neural network has been trained to estimate the number of colliding users in a given slot, supporting an algorithm that tracks the number of backlogged users in the system.
Varanus: More-with-less fault localization in data centers (2012)

Detecting and localizing performance faults is crucial for operating large enterprise data centers. This problem is relatively straightforward to solve if each entity (applications, servers, business processes) within the data center can be instrumented and monitored explicitly. Unfortunately, such instrument-everything approach is often not tenable because of the limits imposed by enterprises on the permissible amounts of instrumentation intrusiveness and monitoring overhead. In this paper, we address the problem of achieving high accuracy of detecting and localizing performance faults in data centers, while minimizing the required instrumentation intrusiveness and overhead. We present novel algorithms for solving three key subproblems: (1) How many monitors are required and where should they be placed within the data center? (2) Given the proposed instrumentation plan, how to detect the existence of performance faults accurately? and (3) How to localize the root-cause of the fault? We demonstrate the effectiveness of our approach for a real-world data center topology as well as through extensive simulations.
A New Type of Conformal Antenna Using Magnetic Flux Channels (2014)

Under SBIR-funded contracts [1 & 2], researchers at JEM Engineering and Arizona State University have demonstrated the critical components of a new class of physically small antenna that utilizes a magneto-dielectric composite material having a high magnetic flux conductivity [3]. The magnetic material is placed into flux channels which are made from a metallo-dielectric substrate. The substrate can be placed directly onto a conducting platform skin and its thickness is on the order of one hundredth of a wavelength or less. This paper introduces a novel realization of such a flux channel antenna by winding a thin composite tape about a mandrel [4]. The number of turns is potentially several thousand as the composite tape thickness is only a half mil (13 microns). Measured gains (IEEE) for a magnetic loop, which is equivalent to an electric monopole, of -5 to +4 dBiL were demonstrated from 225 - 600 MHz by a prototype antenna that measured 0.25" high by 16" diameter.
Probabilistic Resource Allocation for Opportunistic Spectrum Access (2010)

Opportunistic spectrum access (OSA) in cognitive radio (CR) networks significantly improves spectrum efficiency by allowing secondary usage of licensed spectrum. In this paper, we propose a probabilistic resource allocation approach to further exploit the flexibility of OSA. Based on the probabilities of channel availability obtained from spectrum sensing, the proposed approach optimizes channel and power allocation in a multi-channel environment. The given algorithm maximizes the overall utility of a CR network and ensures sufficient protection of licensed users from unacceptable interference, which also supports diverse quality-of-service requirements and enables a distributed implementation in multi-user networks. Both analytical and simulation results demonstrate the effectiveness of this approach as well as its advantage over conventional approaches that rely upon the hard decisions on channel availability.
Simple method for the complete characterization of an optical pulse (1998)

A novel and simple method to measure the amplitude and the phase of optical pulses is presented. The technique basically involves modulating the optical pulse train in a particular manner and then directly examining the resultant optical spectrum. This experimental measurement technique, which is extremely accurate and sensitive and can be implemented with an all-fiber setup, permits direct measurement of the phase of the optical signal in the frequency domain. Experimental results demonstrate the use of this measurement technique for characterizing optical pulses at 10 GHz from a gain-switched laser diode.
Modelling of an innovative rail conveyor system (2016)

Belt conveyors are regarded as the most common material handling systems in the modern world due to their ability to handle a vast range of bulk materials. Modern belt conveyors are used in a wide range of industries ranging from food manufacturing to power generation. Although belt conveyors have been around for centuries, their principle structure have been unchanged. In this paper a novel type of conveyor system is taken into account and a mathematical model that allows the analysis of the dynamic states of the proposed belt conveyor is presented. The novel conveyor system identified as the rail conveyor implements a cart based propagation technique abandoning the traditional idlers. The simulation model is conceived by adopting a finite number of elements consisting of springs, masses, and dampers for various forces existing in the belt and other structures of the rail conveyor. Each rheological model comprised of elements described later in this paper are formulated to characterize innate qualities such as viscoelastic behavior of the belt and resistance forces experienced by the carts in the rail conveyor system.
Cytotoxic withanolide constituents of Physalis longifolia (2012)

Fourteen new withanolides, <b>1</b>–<b>14</b>, named withalongolides A–N, respectively, were isolated\nfrom\nthe aerial parts of <i>Physalis longifolia</i> together\nwith eight known compounds (<b>15</b>–<b>22</b>). The structures of compounds <b>1</b>–<b>14</b> were elucidated through spectroscopic techniques and chemical methods.\nIn addition, the structures of withanolides <b>1</b>, <b>2</b>, <b>3</b>, and <b>6</b> were confirmed by X-ray\ncrystallographic analysis. Using a MTS viability assay, eight withanolides\n(<b>1</b>, <b>2</b>, <b>3</b>, <b>7</b>, <b>8</b>, <b>15</b>, <b>16</b>, and <b>19</b>)\nand four acetylated derivatives (<b>1a</b>, <b>1b</b>, <b>2a</b>, and <b>2b</b>) showed potent cytotoxicity against\nhuman head and neck squamous cell carcinoma (JMAR and MDA-1986), melanoma\n(B16F10 and SKMEL-28), and normal fetal fibroblast (MRC-5) cells with\nIC<sub>50</sub> values in the range between 0.067 and 9.3 μM.
Development of Subunit Vaccines That Provide High-Level Protection and Sterilizing Immunity against Acute Inhalational Melioidosis (2017)

<i>Burkholderia pseudomallei</i>, the etiologic agent of melioidosis, causes severe disease in humans and animals. Diagnosis and treatment of melioidosis can be challenging, and no licensed vaccines currently exist. Several studies have shown that this pathogen expresses a variety of structurally conserved protective antigens that include cell surface polysaccharides and cell-associated and cell-secreted proteins. Based on those findings, such antigens have become important components of the subunit vaccine candidates that we are currently developing. In the present study, the 6-deoxyheptan capsular polysaccharide (CPS) from <i>B. pseudomallei</i> was purified, chemically activated, and covalently linked to recombinant CRM197 diphtheria toxin mutant (CRM197) to produce CPS-CRM197. Additionally, tandem nickel-cobalt affinity chromatography was used to prepare highly purified recombinant <i>B. pseudomallei</i> Hcp1 and TssM proteins. Immunization of C57BL/6 mice with CPS-CRM197 produced high-titer IgG and opsonizing antibody responses against the CPS component of the glycoconjugate, while immunization with Hcp1 and TssM produced high-titer IgG and robust gamma interferon-secreting T cell responses against the proteins. Extending upon these studies, we found that when mice were vaccinated with a combination of CPS-CRM197 and Hcp1, 100% of the mice survived a lethal inhalational challenge with <i>B. pseudomallei</i> Remarkably, 70% of the survivors had no culturable bacteria in their lungs, livers, or spleens, indicating that the vaccine formulation had generated sterilizing immune responses. Collectively, these studies help to better establish surrogates of antigen-induced immunity against <i>B. pseudomallei</i> as well as provide valuable insights toward the development of a safe, affordable, and effective melioidosis vaccine.
Development of CMOS Active Pixel Image Sensors for Low Cost Commercial Applications (1994)

The Jet Propulsion Laboratory, under sponsorship from the NASA Office of Advanced Concepts and Technology, has been developing a second-generation solid-state image sensor technology. Charge-coupled devices (CCDs) are a well-established first generation image sensor technology. For both commercial and NASA applications, CCDs have numerous short comings. In response, the active pixel sensor (APS) technology has been under research. The major advantages of APS technology are the ability to integrate on-chip timing, control, signal-processing and analog-to-digital converter functions, reduced sensitivity to radiation effects, low power operation, and random access readout. JPL has been exploring a complementary metal-oxide-semiconductor (CMOS) APS technology. CMOS is a widely used microelectronics technology for microprocessors, memory devices and application specific integrated circuits (ASICs). Use of CMOS for image sensors can reduce fabrication costs by over a factor of three compared to CCD image sensors. Thus, the JPL-developed technology has widespread appeal for low cost commercial applications such as video phones, computer input devices, surveillance and robotics. The JPL CMOS APS technology is being successfully transferred to industry. The sensors feature TTL-compatible operation (5 volts or less), random accessibility, 75 dB dynamic range, fixed pattern noise less than 0.1 %, read noise in the 15-25 electron r.m.s. range, and low power. This paper will discuss the development of CMOS APS technology, its performance characteristics, and its application to low cost commercial products. 1.
Reduction of Electrostatic Control Voltage with a Tri-Electrode Actuator (2017)

We present a new tri-electrode topology for reducing the control voltage for electrostatic actuators. Conventional parallel plate actuators are dual-electrode systems, formed by the MEMS structure and the drive electrode. By placing a perforated intermediate electrode between these elements, a tri-electrode configuration is formed. This topology enables a low voltage on the intermediate electrode to modulate the electrostatic force on the MEMS device, while the higher voltage on the drive electrode remains fixed. Results presented show that in comparison to conventional parallel plate electrostatic actuators, the intermediate electrode’s modulating voltage can be as low as 20% of normal, while still providing the full actuation stroke.
Mueller calculus and perfect polarization conversion modes in liquid crystal displays (2001)

We introduce a 4×4 Mueller matrix for describing the polarization states of a liquid crystal cell. Using this Mueller matrix, it is possible to derive conditions whereby a linearly polarized input can be converted to either a perfectly linearly or perfectly circularly polarized output. These are called the perfect polarization conversion (PPC) conditions. These PPC conditions can be used in many different ways. For example, based on these PPC conditions, polarization mode switching schemes can be derived for the analysis of most liquid crystal displays.
Revised structure of brevifoliol and some baccatin VI derivatives (1993)

Brevifoliol and some baccatin VI derivatives have been shown to have a rearranged 11(15→1)abeo-taxane skeleton and not a taxane skeleton as originally reported, making abeo-taxanes an emerging major structural type of taxoids.
SU‐F‐T‐505: A Novel Approach for Sparing Critical Organs at Risk for Cancer Patients Undergoing Radiation Oncology Treatments (2016)

Purpose: A major goal of an effective radiation treatment plan is to deliver the maximum dose to the tumor while minimizing radiation exposure to the surrounding normal structures. For example, due to the radiation exposure to neighboring critical structures during prostate cancer treatment, a significant increase in cancer risk was observed for the bladder (77%) and the rectum (105%) over the following decade. Consequently, an effective treatment plan necessitates limiting the exposure to such organs which can best be achieved by physically displacing the organ at‐risk. The goal of this study is to present a prototype for an organ re‐positioner device designed and fabricated to physically move the rectum away from the path of radiation beam during external beam and brachytherapy treatments. This device affords patient comfort and provides a fully controlled motion to safely relocate the rectum during treatment. Methods: The NiTi shape memory alloy was designed and optimized for manufacturing a rectal re‐positioner device through cooling and heating the core alloy for its shaping. This has been achieved through a prototyped custom designed electronic circuit in order to induce the reversible austenitic transformation and was tested rigorously to ensure the integrity of the actuated motion in displacement of the target anatomy. Results: The desirable NiTi shape‐setting was configured for easy insertion and based on anatomical constraint. When the final prototype was evaluated, accuracy and precision of the maximum displacement and temperature changes revealed that the device could safely be used within the target anatomy. Conclusion: The organ re‐positioner device is a promising tool that can be implemented in clinical setting. It provides a controlled and safe displacement of the delicate organ(s) at risk. The location of the organ being treated could also be identified using conventional onboard imaging devices or MV imaging available on‐board most modern clinical accelerators.
Automatic plagiarism detection for spoken responses in an assessment of English language proficiency (2016)

This paper addresses the task of automatically detecting plagiarized responses in the context of a test of spoken English proficiency for non-native speakers. Text-to-text content similarity features are used jointly with speaking proficiency features extracted using an automated speech scoring system to train classifiers to distinguish between plagiarized and non-plagiarized spoken responses. A large data set drawn from an operational English proficiency assessment is used to simulate the performance of the detection system in a practical application. The best classifier on this heavily imbalanced data set resulted in an F1-score of 0.706 on the plagiarized class. These results indicate that the proposed system can potentially be used to improve the validity of both human and automated assessment of non-native spoken English.
Recent advances in compact broadly tunable external-cavity quantum cascade lasers (ECqcL) (2009)

Recent advances in commercially available quantum cascade semiconductor materials providing laser gain in the 3- 12μm regime have been developed. This enables wavelength tunable, narrow linewidth external cavity quantum cascade laser (ECqcL) sources operating above room temperature to be realized with high yield. Daylight has combined these materials with advanced coating and attach technologies, mid-IR micro-optics and telecom-style packaging to yield compact, hermetically-sealed lasers. In addition, ultra-broad tuning ranges (>250 wavenumbers) have been demonstrated from a commercially available product platform. Meanwhile, phase continuous tuning capabilities have been achieved to provide the ability to perform wavelength modulation spectroscopy in the mid-IR from similar commercial platforms. When integrated and optimized with new room temperature mid-IR detectors and modern low power embedded digital signal processing electronics, the resulting sensor platform can provide significant advantages. These include multispecies fingerprint identification at real-time update rates (10 Hz). Daylight will review the most recent progress in ECqcL devices as well as describe their portable, battery-operated Swept Sensor<sup>TM</sup> technology based upon this platform.
Second‐order matrix pencil‐based phasor measurement algorithm for P‐class PMUs (2020)

Phasor measurement units (PMUs) have made real‐time monitoring and control of power systems possible, thanks to their time synchronisation and fast reporting rate. It is critical that the PMUs can track the dynamics of complex power systems accurately. In this study, a measurement bandwidth extraction method based on signal reconstruction is proposed to filter the out‐of‐band signals without extra response time. The synthetic phasor is modelled by the second‐order Taylor's series expansion. A matrix pencil‐based fast phasor measurement algorithm is proposed for P‐class PMUs. Simulation and experiment results show that the accuracy and the response time of the proposed algorithm meet the requirements of the IEEE standard. Field data test shows that out‐of‐band signals have been reduced and the dynamic change of power system can be accurately reflected by phasor estimations. All results demonstrate that the proposed algorithm is suitable for P‐class PMUs in complex power systems.
Defining coverage views to improve functional coverage analysis (2004)

Coverage analysis is used to monitor the quality of the verification process. Reports provided by coverage tools help users identify areas in the design that have not been adequately tested. Because of their sheer size, the analysis of large coverage models can be an intimidating and time-consuming task. Practically, it can only be done by focusing on specific parts of the model. This paper presents a method for defining views onto the coverage data of cross-product functional coverage models. The proposed method allows users to focus on certain aspects of the coverage data to extract relevant, useful information, thereby improving the quality of the coverage analysis. A number of examples are provided that show how the proposed method improved the verification of actual designs.
Polyanions and Glucose as Osmotic Agents in Simulated Peritoneal Dialysis (1983)

Peritoneal dialysis solutions contain glucose as an osmotic agent to obtain ultrafiltration. Due to rapid absorption, glucose does not sustain high ultrafiltration during long exchanges. Nonabsorbable polyanions might be effective as osmotic agents when suspended in electrolyte solution. Concentrations of freely diffusible ions should be in Gibbs-Donnan equilibrium with plasma electrolytes. The ideal proportion of diffusable to polymerbound cation concentrations is unknown. To obtain concentrations of free ions in equilibrium with plasma, it is assumed that the polymer solution dialyzed against a polyelectrolyte solution of the desired composition (with hydraulic pressure higher on the polymer side) will approach the same thermodynamic activity as the electrolyte solution. Subsequently, if transmembrane pressure is released, osmotic ultrafiltration will occur in proportion to the hydrostatic pressure applied during polymer solution preparation. Polyacrylate solution so prepared was compared with a commercial dextrose dialysis solution in an in vitro simulation of peritoneal dialysis. With dwell times up to 24 h, sustained ultrafiltration with polymer was observed, whereas, with dextrose, ultrafiltration ceased after 8 h. Concentrations of diffusible bivalent cations in polyacrylate were lower than intended due to avid polymer complexing; however, dextran sulfate solutions were developed to contain desired concentrations of diffusible electrolytes. The conclusion is that some polymer solutions might be useful in clinical settings when high sustained ultrafiltration is needed.