gebhart/patrepeval huggingface dataset:
Adeno-Associated Virus Serotype-Specific Inverted Terminal Repeat Sequence Role in Vector Transgene Expression (2020)

Adeno-associated viral vectors have been successfully used in laboratory and clinical settings for efficient gene delivery. In these vectors, 96% of the adeno-associated virus (AAV) genome is replaced with a gene cassette of interest, leaving only the 145 bp inverted terminal repeat (ITR) sequences. These cis-elements, primarily from AAV serotype 2, are required for genome rescue, replication, packaging, and vector persistence. Previous work from our lab and others have demonstrated that the AAV ITR2 sequence has inherent transcriptional activity, which may confound intended transgene expression in therapeutic applications. Currently, AAV capsids are extensively study for vector contribution; however, a comprehensive analysis of ITR promoter activity of various AAV serotypes has not been described to date. Here, the transcriptional activity of AAV ITRs from different serotypes (1-4, 6, and 7) was compared in numerous cell lines and a mouse model. Under the conditions used here, all ITRs tested were capable of promoting transgene expression both <i>in vitro</i> and <i>in vivo</i>. However, we observed three classes of AAV ITR expression <i>in vitro</i>. Class I ITRs (AAV2 and 3) generated the highest level, whereas class II (AAV 4) had intermediate levels, and class III (AAV1 and 6) had the lowest levels. These expression levels were consistent across multiple cell lines. Only ITR7 demonstrated cell-type dependent transcriptional activity. <i>In vivo</i>, all classes had promoter activity. Next-generation sequencing revealed multiple transcriptional start sites that originated from the ITR sequence, with most arising from within the Rep binding element. The collective results demonstrate that the serotype ITR sequence may have multiple levels of influence on transgene expression cassettes independent of promoter selection.
TH‐C‐220‐01: Pilot Study for the Development of Clinical Microbeam Radiation Therapy Using a Carbon Nanotube Field Emission Micro‐CT Scanner (2011)

Purpose: The possibilities of microbeam radiation therapy (MRT) up until now have mainly been studied using synchrotron sources due to their high flux (100s Gy/sec) and approximately parallel X‐ray paths. We wish to show that both of these advantages are also attainable with the use of carbon nanotube (CNT) field emission based X‐ray source arrays, and that by using this type of source a compact MRT system may be possible. Methods: The study was performed with our CNT micro‐CT scanner (100μm focal spot). A microbeam collimator alignment assembly with the capability to collimate and superimpose beams coming from different gantry positions was fabricated and attached to the scanner. Two orthogonal dosimetric films (Gafchromic EBT2) were embedded inside a cylindrical phantom to record the MRT dose distribution. Microbeams were fired at this target from 44 different entry angles to simulate an array of sources. In a separate experiment, phantom translation was used to simulate multiple parallel beams. Results: Forty‐four beams were superimposed in the phantom to produce a single microbeam dose profile with a FWHM of 310m (expected value was 280μm) indicating proper collimator alignment. A new MRT‐ specific tube was proposed and commissioned based on the preliminary experimental results and the corresponding Monte Carlo simulations. The estimated dose rate for this proposed tube was calculated to be over 100 Gy/sec from these initial measurements. Also, during the multiple beam simulation, a reasonable peak to valley dose ratio (∼12) was found when the translation distance was roughly 4x the beam width. Conclusions: We have shown that it will not only be possible to create microbeams with our CNT sources, but that the flexibility of these field emission sources will open the field of MRT study to the larger research community and possibly bring effective and compact MRT devices to the clinical environment.
Design, Synthesis and Evaluation of Novel N-Substituted-[Benzoylamino]-5-Ethyl-1,2,3,6-Tetrahydropyridines as Potential Anti-Cancer Agents (2019)

Four novel N-substituted [benzoylamino]-5-ethyl-1,2,3,6-tetrahydropyridines were synthesized, purified, and characterized. The four tetrahydropyridine analogs exhibited some anti-cancer activity. Based on the molecular modeling studies, EH3 was expected to have the best antiproliferative activity due to having the highest docking score for ERα. However, EH2 had the best antiproliferative activity. Nevertheless, the biological screening and molecular modeling can provide insight to help with the design of more biologically active compounds as potential anti-cancer agents.
Simplified holographic associative memory using enhanced nonlinear processing with a thermoplastic plate (1991)

A simplified holographic associative memory by enhanced nonlinear recording using a thermoplastic plate is described. The system is based on two new concepts: The system utilizes the second-order diffraction instead of the first-order diffraction, and to enhance the second-order diffraction efficiency, a novel angle-tuning recording using a thermoplastic plate is employed. As a result, the size of the system is reduced by one half with a remarkable increase (as much as approximately 100 times) in light efficiency compared with that of the conventional systems, and the need for critical alignment is eliminated. Experimental results demonstrating the performance of the system are provided.
Vision-based pose computation: robust and accurate augmented reality tracking (2003)

Vision-based tracking systems have advantages for augmented reality (AR) applications. Their registration can be very accurate, and there is no delay between the motions of real and virtual scene elements. However, vision-based tracking often suffers from limited range, intermittent errors, and dropouts. These shortcomings are due to the need to see multiple calibrated features or fiducials in each frame. To address these shortcomings, features in the scene can be dynamically calibrated and pose calculations can be made robust to noise and numerical instability. In this paper, we survey classic vision-based pose computations and present two methods that offer increased robustness and accuracy in the context of real-time AR tracking.
Single-Vector Calibration of Wind-Tunnel Force Balances (2003)

An improved method of calibrating a wind-tunnel force balance involves the use of a unique load application system integrated with formal experimental design methodology. The Single-Vector Force Balance Calibration System (SVS) overcomes the productivity and accuracy limitations of prior calibration methods. A force balance is a complex structural spring element instrumented with strain gauges for measuring three orthogonal components of aerodynamic force (normal, axial, and side force) and three orthogonal components of aerodynamic torque (rolling, pitching, and yawing moments). Force balances remain as the state-of-the-art instrument that provide these measurements on a scale model of an aircraft during wind tunnel testing. Ideally, each electrical channel of the balance would respond only to its respective component of load, and it would have no response to other components of load. This is not entirely possible even though balance designs are optimized to minimize these undesirable interaction effects. Ultimately, a calibration experiment is performed to obtain the necessary data to generate a mathematical model and determine the force measurement accuracy. In order to set the independent variables of applied load for the calibration 24 NASA Tech Briefs, October 2003 experiment, a high-precision mechanical system is required. Manual deadweight systems have been in use at Langley Research Center (LaRC) since the 1940s. These simple methodologies produce high confidence results, but the process is mechanically complex and labor-intensive, requiring three to four weeks to complete. Over the past decade, automated balance calibration systems have been developed. In general, these systems were designed to automate the tedious manual calibration process resulting in an even more complex system which deteriorates load application quality. The current calibration approach relies on a one-factor-at-a-time (OFAT) methodology, where each independent variable is incremented individually throughout its full-scale range, while all other variables are held at a constant magnitude. This OFAT approach has been widely accepted because of its inherent simplicity and intuitive appeal to the balance engineer. LaRC has been conducting research in a modern design of experiments (MDOE) approach to force balance calibration. Formal experimental design techniques provide an integrated view to the entire calibration process covering all three major aspects of an experiment; the design of the experiment, the execution of the experiment, and the statistical analyses of the data. In order to overcome the weaknesses in the available mechanical systems and to apply formal experimental techniques, a new mechanical system was required. The SVS enables the complete calibration of a six-component force balance with a series of single force vectors.
Next Generation Titanium Alloys for Elevated Temperature Service. (1991)

There are many ongoing U.S, aerospace programs which have identified requirements for higher temperature capability from conventional titanium alloys, In order to meet these requirements, two new titanium alloys have been developed. A near alpha alloy, designated "Ti-1100" (Ti-6Al-2.7Sn~IZr- 0.4Mo-0,45Si), is a modification of the well knownTi-6242S alloy (Ti-6Al-2Sn~Zr-2Mo-0.1 Si), It offers roughly a 55'C (1 OO'F) creep advantage over the older alloy and is currently being considered for sheet metal and forging applications in both turbine engine and airframe applications. On the other hand, a metastable beta alloy designated "Beta-21 S" (Ti-1 5M0-2.7Nb-3AI-0.2Si) has shown exceptional promise as a matrix in metal matrix composites for high temperature applications. Its key attributes are its ease of processing in foil production and its excellent oxidation resistance. This paper will review the development of these alloys and some of their more important mechanical properties,
Friction reducing properties of onion-like carbon based lubricant under high contact pressure (2012)

In this study, carbon based nanomaterials such as onion-like carbon (OLC), carbon nanotube and buckminsterfullerene (or buckyball) (C60) have been investigated as nanocolloidal additives for liquid lubricants. When tested under a range of contact pressures from 0·51 to 1·10 GPa, OLC provided the best overall friction reducing property in synthetic lubricant, although the friction reducing properties of all nanocarbon materials were dependent on the contact pressure. Detailed transmission electron microscopy revealed that the OLC kept its original structure intact and induced the formation during sliding of a thin ‘tribofilm’ composed of OLC, nanosized wear debris, amorphous carbon and graphitic layers on the wear debris. This tribofilm seems to be responsible for reduced friction under boundary conditions.
Cost-Effective and Selective Fluorescent Chemosensor (Pyr-NH@SiO2 NPs) for Mercury Detection in Seawater (2022)

The release of mercury into the environment has adverse effects on humans and aquatic species, even at very low concentrations. Pyrene and its derivatives have interesting fluorescence properties that can be utilized for mercury (Hg<sup>2+</sup>) ion sensing. Herein, we reported the highly selective pyrene-functionalized silica nanoparticles (Pyr-NH@SiO<sub>2</sub> NPs) for chemosensing mercury (Hg<sup>2+</sup>) ions in a seawater sample. The Pyr-NH@SiO<sub>2</sub> NPs were synthesized via a two-step protocol. First, a modified Stöber method was adopted to generate amino-functionalized silica nanoparticles (NH<sub>2</sub>@SiO<sub>2</sub> NPs). Second, 1-pyrenecarboxylic acid was coupled to NH<sub>2</sub>@SiO<sub>2</sub> NPs using a peptide coupling reaction. As-synthesized NH<sub>2</sub>@SiO<sub>2</sub> NPs and Pyr-NH@SiO<sub>2</sub> NPs were thoroughly investigated by <sup>1</sup>H-NMR, FTIR, XRD, FESEM, EDS, TGA, and BET surface area analysis. The fluorescent properties were examined in deionized water under UV-light illumination. Finally, the developed Pyr-NH@SiO<sub>2</sub> NPs were tested as a chemosensor for Hg<sup>2+</sup> ions detection in a broad concentration range (0-50 ppm) via photoluminescence (PL) spectroscopy. The chemosensor can selectively detect Hg<sup>2+</sup> ions in the presence of ubiquitous ions (Na<sup>+</sup>, K<sup>+</sup>, Ca<sup>2+</sup>, Mg<sup>2+</sup>, Ba<sup>2+</sup>, Ag<sup>+</sup>, and seawater samples). The quenching of fluorescence properties with Hg<sup>2+</sup> ions (LOD: 10 ppb) indicates that Pyr-NH@SiO<sub>2</sub> NPs can be effectively utilized as a promising chemosensor for mercury ion detection in seawater environments.
Localization of high-molecular-weight adhesion proteins of nontypeable Haemophilus influenzae by immunoelectron microscopy (1994)

A family of high-molecular-weight (HMW) surface-exposed proteins important in the attachment of nontypeable Haemophilus influenzae (NTHi) to human epithelial cells was previously identified (J. W. St. Geme III, S. Falkow, and S. J. Barenkamp, Proc. Natl. Acad. Sci. USA 90:2875-2879, 1993). In the present investigation, indirect immunogold labeling and electron microscopy were used to localize these proteins on three clinical isolates of NTHi, mutants deficient in expression of one or both HMW proteins, and embedded sections of human oropharyngeal cells after incubation with NTHi strain 12. The filamentous material comprising the proteins was labeled with monoclonal antibodies directed against two prototype HMW proteins (HMW1 and HMW2) of prototype NTHi strain 12. Gold labeling was observed as a cap or discrete aggregate off one pole or centrally along one long axis of the bacterial cell. Heavily labeled, non-bacterial-cell-associated, disk-like aggregates of the HMW proteins were frequently noted in both bacterial preparations as well as in association with the oropharyngeal cell surface and intracellularly. Mutants demonstrated diminished labeling or an absence thereof, respectively, which correlated well with their previously demonstrated reduced ability or inability to adhere to Chang conjunctival epithelial cells in vitro. The Haemophilus HMW proteins share antigenic determinants with and demonstrate amino acid sequence similarity to the filamentous hemagglutinin protein of Bordetella pertussis, a critical adhesin of that organism. The studies presented here demonstrate that the Haemophilus proteins and B. pertussis filamentous hemagglutinin show impressive morphologic and perhaps additional functional similarity.
Development of Highly Nonlinear Fibers for Optical Signal Processing (2003)

Nonlinear optical phenomena occurring in optical fibers result in noise and wave- form distortion that are factors in signal degradation. It is therefore desirable that nonlinear phenomena in fibers used as the transmission path be reduced as much as possible. On the other hand consideration is being given to methods of optical signal processing that make use of the nonlinear phenomena occurring in the fibers. For example, by actively making use of such nonlinear phenomena as four-wave mixing (FWM) and self-phase modulation (SPM), it is possible to combine optical signals of multiple wavelengths to achieve wavelength conversion, pulse compression and the like 1)~4) . Such techniques for utilizing nonlinear phenomena are con- sidered promising in terms of the next generation of high-speed optical signal processing and long-haul optical transmission. A highly nonlinear optical fiber has been developed for wave- length conversion using FWM that has a dispersion slope of 0.02 ps/nm2/km or less. This fiber relaxes the dependence of the pump wavelength in wavelength conversion using FWM, broaden- ing the conversion bandwidth. We also report on a polarization-maintaining highly nonlinear fiber and a highly nonlinear fiber with reduced clad diameter. ABSTRACT
Exomic sequencing of pancreatic neuroendocrine tumors: Detection of alterations in chromatin remodeling and mTOR pathway genes. (2011)

10501 Background: Pancreatic Neuroendocrine Tumors (PanNETs) are a rare but clinically important form of pancreatic neoplasia but relatively little is known about the molecular genetics of this disease. Methods: To explore the genetic basis of PanNETs, we determined the exomic sequences of ten non-familial PanNETs and then screened the most commonly mutated genes in 58 additional PanNETs. Results: We found frequently mutated genes implicated in chromatin remodeling: 44% of the tumors had somatic inactivating mutations in MEN-1, which encodes menin, a component of a histone methyltransferase complex; and 43% had mutations in genes encoding either of the two subunits of a transcription/chromatin remodeling complex consisting of DAXX (death-domain associated protein) and ATRX (alpha thalassemia/mental retardation syndrome X-linked). In a multivariate analysis adjusting for WHO classification, mutations in the MEN1 (HR 0.30; 95% CI 0.1-0.9; p=0.03) and DAXX/ATRX (HR 0.23; 95% CI 0.07-0.75; p=0.02) genes, alone or in combination (HR 0.11; 95% CI 0.02-0.55; p=0.01), were associated with better prognosis. Interestingly, tumors without mutations in MEN1 or DAXX/ATRX were primarily from patients with PanNETs localized to the pancreas (p=0.006). We also found mutations in genes in the mTOR (mammalian target of rapamycin) pathway in 14% of the tumors that included mutations in PIK3CA, PTEN and TSC2. Conclusions: Taken together, these findings could potentially be used to stratify patients with PanNETs and help determine which patients may benefit from treatment with mTOR inhibitors.
In Vivo Bacteriophages’ Application for the Prevention and Therapy of Aquaculture Animals–Chosen Aspects (2022)

To meet the nutritional requirements of our growing population, animal production must double by 2050, and due to the exhaustion of environmental capacity, any growth will have to come from aquaculture. Aquaculture is currently undergoing a dynamic development, but the intensification of production increases the risk of bacterial diseases. In recent years, there has been a drastic development in the resistance of pathogenic bacteria to antibiotics and chemotherapeutic agents approved for use, which has also taken place in aquaculture. Consequently, animal mortality and economic losses in livestock have increased. The use of drugs in closed systems is an additional challenge as it can damage biological filters. For this reason, there has been a growing interest in natural methods of combating pathogens. One of the methods is the use of bacteriophages both for prophylactic purposes and therapy. This work summarizes the diverse results of the in vivo application of bacteriophages for the prevention and control of bacterial pathogens in aquatic animals to provide a reference for further research on bacteriophages in aquaculture and to compare major achievements in the field.
Fluoroester Co-Solvents for Low-Temperature Li+ Cells (2009)

Electrolytes comprising LiPF6 dissolved in alkyl carbonate/fluoroester mixtures have been found to afford improved low-temperature performance and greater high-temperature resilience in rechargeable lithium-ion electrochemical cells. These and other electrolytes comprising lithium salts dissolved mixtures of esters have been studied in continuing research directed toward extending the lower limit of operating temperatures of such cells. This research at earlier stages, and the underlying physical and chemical principles, were reported in numerous previous NASA Tech Briefs articles. The purpose of the present focus on high-temperature resilience in addition to low-temperature performance is to address issues posed by the flammability of the esters and, at temperatures near the upper end (about 55 C) of their intended operating temperature range, by their high chemical reactivity. As used here, high-temperature resilience signifies, loosely, a desired combination of low flammability of an electrolyte mixture and the ability of a cell that contains the mixture to sustain a relatively small loss of reversible charge/discharge capacity during storage in the fully charged condition at high temperature. The selection of fluoroesters for study as candidate electrolyte solvent components to increase high-temperature resilience was prompted in part by the observation that like other halogenated compounds, fluoroesters have low flammability. The fluoroesters investigated in this study include trifluoroethyl butyrate (TFEB), ethyl trifluoroacetate (ETFA), trifluoroethyl acetate (TFEA), and methyl pentafluoropropionate (MPFP). Solvent mixtures were prepared by mixing these fluoroesters with two other esters: ethylene carbonate (EC) and ethyl methyl carbonate (EMC).
Energy-efficient timely transportation of long-haul heavy-duty trucks (2016)

We consider a timely transportation problem where a heavy-duty truck travels between two locations across the national highway system, subject to a hard deadline constraint. Our objective is to minimize the total fuel consumption of the truck, by optimizing both route planning and speed planning. The problem is important for cost-effective and environment-friendly truck operation, and it is uniquely challenging due to its combinatorial nature as well as the need of considering hard deadline constraint. We first show that the problem is NP-Complete; thus exact solution is computational prohibited unless P=NP. We then design a fully polynomial time approximation scheme (FPTAS) that attains an approximation ratio of 1 + ∈ with a network-size induced complexity of O(mn2/∈2), where m and n are the numbers of nodes and edges, respectively. While achieving highly-preferred theoretical performance guarantee, the proposed FPTAS still suffers from long running time when applying to national-wide highway systems with tens of thousands of nodes and edges. Leveraging elegant insights from studying the dual of the original problem, we design a fast heuristic solution with O(m + n log n) complexity. The proposed heuristic allows us to tackle the energy-efficient timely transportation problem on large-scale national highway systems. We further characterize a condition under which our heuristic generates an optimal solution. We observe that the condition holds in most of the practical instances in numerical experiments, justifying the superior empirical performance of our heuristic. We carry out extensive numerical experiments using real-world truck data over the actual U.S. highway network. The results show that our proposed solutions achieve 17% (resp. 14%) fuel consumption reduction, as compared to a fastest path (resp. shortest path) algorithm adapted from common practice.
Unsupervised Lexicon Acquisition from Speech and Text (2007)

When introducing a large vocabulary continuous speech recognition (LVCSR) system into a specific domain, it is preferable to add the necessary domain-specific words and their correct pronunciations selectively to the lexicon, especially in the areas where the LVCSR system should be updated frequently by adding new words. In this paper, we propose an unsupervised method of word acquisition in Japanese, where no spaces exist between words. In our method, by taking advantage of the speech of the target domain, we selected the domain-specific words among an enormous number of word candidates extracted from the raw corpora. The experiments showed that the acquired lexicon was of good quality and that it contributed to the performance of the LVCSR system for the target domain.