gebhart/patrepeval huggingface dataset:
Utilization of Nonviral Sequences for Minus-Strand DNA Transfer and Gene Reconstitution during Retroviral Replication (2000)

Minus-strand DNA transfer, an essential step in retroviral reverse transcription, is mediated by the two repeat (R) regions in the viral genome. It is unclear whether R simply serves as a homologous sequence to mediate the strand transfer or contains specific sequences to promote strand transfer. To test the hypothesis that the molecular mechanism by which R mediates strand transfer is based on homology rather than specific sequences, we examined whether nonviral sequences can be used to facilitate minus-strand DNA transfer. The green fluorescent protein (GFP) gene was divided into GF and FP fragments, containing the 5' and 3' portions of GFP, respectively, with an overlapping F fragment (85 bp). FP and GF were inserted into the 5' and 3' long terminal repeats, respectively, of a murine leukemia virus-based vector. Utilization of the F fragment to mediate minus-strand DNA transfer should reconstitute GFP during reverse transcription. Flow cytometry analyses demonstrated that GFP was expressed in 73 to 92% of the infected cells, depending on the structure of the viral construct. This indicated that GFP was reconstituted at a high frequency; molecular characterization further confirmed the accurate reconstitution of GFP. These data indicated that nonviral sequences could be used to efficiently mediate minus-strand DNA transfer. Therefore, placement and homology, not specific sequence context, are the important elements in R for minus-strand DNA transfer. In addition, these experiments demonstrate that minus-strand DNA transfer can be used to efficiently reconstitute genes for gene therapy applications.
Techniques and applications for guest-language safepoints (2015)

Safepoints are a virtual machine mechanism that allows one thread to suspend other threads in a known state so that runtime actions can be performed without interruption and with data structures in a consistent state. Many virtual machines use safepoints as a mechanism to provide services such as stop-the-world garbage collection, debugging, and modification to running code such as installing or replacing classes. Languages implemented on these virtual machines may have access to these services, but not directly to the safepoint mechanism itself. We show that safepoints have many useful applications for the implementation of guest languages running on a virtual machine. We describe an API for using safepoints in languages that were implemented under the Truffle language implementation framework on the Java Virtual Machine and show several applications of the API to implement useful guest-language functionality. We present an efficient implementation of this API, when running in combination with the Graal dynamic compiler. We also demonstrate that our safepoints cause zero overhead with respect to peak performance and statistically insignificant overhead with respect to compilation time. We compare this to other techniques that could be used to implement the same functionality and demonstrate the large overhead that they incur.
Reactive power, imbalance and harmonics compensation using d-statcom with a dissipativity-based controller (2002)

We present a solution to the problem of reactive power compensation and harmonic compensation in a general case when both the source voltages and the load currents are unbalanced and contain an arbitrary number of harmonics. For the compensation purpose, a d-statcom is connected in parallel to inject the required currents, so that from the source terminals the same apparent resistance is observed in all phases and at all frequencies. A controller based on the ideas of passivity theory, to which we have added adaptation to compensate for the unavoidable uncertainty in some of the parameters, is suggested as a solution. One of the major advantages of this solution compared to conventional ones is that we are able to perform precise tracking (also for high order harmonics) even in the presence of a relatively low switching frequency, i.e., in presence of an active filter with limited bandwidth. Simulation results are provided to illustrate the performance of our controller.
Rewriting Schemes for Flash Memory (2015)

Flash memory is a leading storage media with excellent features such as random access and
high storage density. However, it also faces significant reliability and endurance challenges.
In flash memory, the charge level in the cells can be easily increased, but removing charge
requires an expensive erasure operation. In this thesis we study rewriting schemes that
enable the data stored in a set of cells to be rewritten by only increasing the charge level
in the cells. We consider two types of modulation scheme; a convectional modulation based
on the absolute levels of the cells, and a recently-proposed scheme based on the relative cell
levels, called rank modulation. The contributions of this thesis to the study of rewriting
schemes for rank modulation include the following: we •propose a new method of rewriting in rank modulation, beyond the previously proposed
method of “push-to-the-top”; •study the limits of rewriting with the newly proposed method, and derive a tight upper
bound of 1 bit per cell; •extend the rank-modulation scheme to support rankings with repetitions, in order to
improve the storage density; •derive a tight upper bound of 2 bits per cell for rewriting in rank modulation with
repetitions; •construct an efficient rewriting scheme that asymptotically approaches the upper bound
of 2 bit per cell. The next part of this thesis studies rewriting schemes for a conventional absolute-levels
modulation. The considered model is called “write-once memory” (WOM). We focus on
WOM schemes that achieve the capacity of the model. In recent years several capacity-achieving
WOM schemes were proposed, based on polar codes and randomness extractors.
The contributions of this thesis to the study of WOM scheme include the following: we •propose a new capacity-achievingWOM scheme based on sparse-graph codes, and show
its attractive properties for practical implementation; •improve the design of polarWOMschemes to remove the reliance on shared randomness
and include an error-correction capability. The last part of the thesis studies the local rank-modulation (LRM) scheme, in which a
sliding window going over a sequence of real-valued variables induces a sequence of permutations.
The LRM scheme is used to simulate a single conventional multi-level flash cell.
The simulated cell is realized by a Gray code traversing all the relative-value states where,
physically, the transition between two adjacent states in the Gray code is achieved by using
a single “push-to-the-top” operation. The main results of the last part of the thesis are two
constructions of Gray codes with asymptotically-optimal rate.
Building Usable Menu-Based Natural Language Interfaces To Databases (1983)

Natural language interfaces to databases are not in couunon use today for two main reasons: they are difficult to use and they are expensive to build and maintain. This paper presents a functional overview of a new kind of natural language interface that goes far in overcoming both of these problems. The “ease-of-use” problem is solved by wedding a menu-based interaction technique to a traditional semantic graaauar-driven natural language system. Using this approach, all user queries are “understood” by the system. The “creation and maintenance problem” is solved by designing a core grannnar with parameters supplied by the data dictionary and then automatically generating semantic graumars covering some selected subpart of the user’s data. Automatically generated natural language interfaces offer the user an attractive way to group semantically related tables together, to model a user’s access rights, and to model a user's view of supported joins paths in a database.
Volume holographic correlator (1991)

An optical correlator with a volume hologram as a matched filter is usually not shift-invariant in both directions. If the input image is shifted along the degeneracy direction, correlation peak can still be obtained. 1,2 But if the input image is shifted perpendicular to the direction of degeneracy, there will be no correlation peak from the Bragg mismatch. We propose a 2-D shift-invariant optical correlator with a volume hologram as a matched filter. The shift-invariance along the degeneracy direction is obtained directly through Fourier transform. In the direction perpendicular to that of degeneracy, the image is shifted to obtain the correlation peak. Image shifting is achieved by deflecting the plane waves (Fourier components) at the Fourier plane. Either a rotating mirror or a Bragg cell can be employed as the deflector. Other methods to achieve image shifting that may be potentially applicable are also discussed. In addition, the amount of shift-invariance along the degeneracy direction is evaluated. The result shows that the amount of shift-invariance depends on the size of the image, focal length and also the angle between the reference and object beams. The combination of degeneracy and image shifting provides the 2-D shift-invariant optical correlation.
Extracting library-based object-oriented applications (2000)

In an increasingly popular model of software distribution, software is developed in one computing environment and deployed in other environments by transfer over the internet. Extraction tools perform a static whole-program analysis to determine unused functionality in applications in order to reduce the time required to download applications. We have identified a number of scenarios where extraction tools require information beyond what can be inferred through static analysis: software distributions other than complete applications, the use of reflection, and situations where an application uses separately developed class libraries. This paper explores these issues, and introduces a modular specification language for expressing the information required for extraction. We implemented this language in the context of Jax, an industrial-strength application extractor for Java, and present a small case study in which different extraction scenarios are applied to a commercially available library-based application.
Coronary Vasoactivity of Novel N<sup>6</sup>-Substituted Adenosines (1991)

Abstract Previous studies of the structure-coronary vasoactivity relationships of adenosines substituted at N-6 identified certain simple alkyl and aralkyl groups that can promote activity and others that reduce activity. The present study shows that such alkyl and aryl moieties, when combined in an N-6 substituent, can contribute additively to coronary vasoactivity.
Robust production of virus‐like particles and monoclonal antibodies with geminiviral replicon vectors in lettuce (2011)

Pharmaceutical protein production in plants has been greatly promoted by the development of viral-based vectors and transient expression systems. Tobacco and related Nicotiana species are currently the most common host plants for the generation of plant-made pharmaceutical proteins (PMPs). Downstream processing of target PMPs from these plants, however, is hindered by potential technical and regulatory difficulties owing to the presence of high levels of phenolics and toxic alkaloids. Here, we explored the use of lettuce, which grows quickly yet produces low levels of secondary metabolites and viral vector-based transient expression systems to develop a robust PMP production platform. Our results showed that a geminiviral replicon system based on the bean yellow dwarf virus permits high-level expression in lettuce of virus-like particles (VLP) derived from the Norwalk virus capsid protein and therapeutic monoclonal antibodies (mAbs) against Ebola and West Nile viruses. These vaccine and therapeutic candidates can be readily purified from lettuce leaves with scalable processing methods while fully retaining functional activity. Furthermore, this study also demonstrated the feasibility of using commercially produced lettuce for high-level PMP production. This allows our production system to have access to unlimited quantities of inexpensive plant material for large-scale production. These results establish a new production platform for biological pharmaceutical agents that are effective, safe, low cost, and amenable to large-scale manufacturing.
A Novel Rubbing Encryption Algorithm and the Implementation of a Web Based One-Time Password Token (2010)

Using One-time Password (OTP) in a Two-factor Authentication (2FA) system is very popular nowadays. OTP function has been embedded into many devices such as standalone token, PC, PDA and cellular phone. The generated OTP code is entered into the login window to complete a user's authentication procedure. These tokens and devices do bear extra cost to the user. Deployment or support of such OTP tokens can not be fully done through Internet to reduce the expense and work load. And certain designs may compromise network security when token is lost or stolen. We propose a secure way to generate the OTP code by way of a web browser. A user does not need any electronic device on hand to obtain OTP for 2FA login. A new Rubbing Encryption Algorithm (REAL) is proposed as the base technology. Implementation method of such web-based OTP token is presented and analyzed. The token is licensed to a company to promote product sales. It operates through a web-browser with a REAL dynamic session key. It can be integrated into many secure Internet commerce applications as well.
X-ray zone plates fabricated using electron-beam and x-ray lithography (1979)

Fresnel zone plate patterns, free of spherical aberration, with diameters of up to 0.63 mm and linewidths as small as 1000 Å were fabricated on polyimide membrane x-ray masks using scanning electron beam lithography. Distortion of the electron beam scan raster was reduced to ?2500 Å over a 2×2 mm field by applying deflection corrections, while viewing the distortion using a Moiré method. CK x-ray lithography was used to replicate the zone plate pattern in thick PMMA over a 100 Å thick plating base on a glass substrate. Zones plates in 1.3 μm thick gold were fabricated by plating, and made free-standing by removal of the plating base and the supporting glass substrate. Zone plates were tested as imaging elements with visible light and soft x-rays.
Type-I Ge∕Ge1−x−ySixSny strained-layer heterostructures with a direct Ge bandgap (2004)

The electronic properties of Ge∕Ge1−x−ySixSny strained-layer heterostructures are predicted theoretically. It is found that a lattice-matched system with fully strained Ge layers and relaxed Ge1−x−ySixSny alloys can have a direct fundamental bandgap with spatial localization in the Ge layers (type I). The Si and Sn concentrations for which such a direct bandgap obtains are close to those that have already been experimentally demonstrated [M. Bauer, C. Ritter, P. A. Crozier, J. Ren, J. Menendez, G. Wolf, and J. Kouvetakis, Appl. Phys. Lett. 83, 2163 (2003)]. The required level of tensile strain in the Ge layers is compatible with Si–Ge technology. The predicted direct bandgap values are as high as 0.6eV.
Segmentation and Fracture Detection in X-ray images for Traumatic Pelvic Injury (2010)

Due to the risk of complications such as hemorrhage, severe pelvic trauma is associated with a high mortality rate. Prompt medical treatment is therefore vital. However, the complexity of the injuries can make successful diagnosis and treatment challenging. By generating predictions and recommendations based on patient data, computer-aided decision support systems have the potential to assist physicians in improving outcomes. However, no current system considers features automatically extracted from medical images. This dissertation describes a system to extract diagnostic features from pelvic X-ray images that can be used as input to the prediction process; specifically, the presence of fracture and quantitative measures of displacement. Feature extraction requires prior identification of separate structures of interest within the pelvis. The proposed system therefore incorporates a hierarchical segmentation algorithm which is able to automatically extract multiple structures in a single pass, using a combination of anatomical knowledge and computational techniques such as directed Hough Transform. This algorithm also applies a novel Spline/ASM segmentation method which combines cubic spline interpolation with a deformable model approach which maintains curved contours and provides local control over segmentation. In order for the proposed system to be used as a component in a computerized decision support system, segmentation is designed to be entirely automatic. Furthermore, Spline/ASM is suitable for many other segmentation applications where the objects of interest show curved contours. After successful segmentation, fracture detection is performed on the pelvic ring and pubis structures, using an algorithm based on wavelet transform, anatomical information and boundary tracing. A method is also developed to calculate quantitative measures of symphysis pubis displacement that may indicate pelvic instability and prove useful in identifying fracture patterns. Finally, X-ray features are combined with patient demographics and physiological scores for generation of predictive rules for injury severity, with promising current results. This indicates the potential diagnostic value of the extracted features, and in turn the usefulness of the proposed radiograph analysis component in a larger decision support system.
Photorefractive optical lock-in vibration spectral measurement (1997)

An optical photorefractive frequency-domain method is described for measuring displacement amplitude and phase of vibrating surfaces. The method is applicable to diffusely scattering surfaces and usable in either a point-detection or imaging configuration. The method utilizes an optical lock-in approach to measure phase modulation of light scattered from continuously vibrating surfaces. Picometer displacement sensitivities have been demonstrated over a frequency range of 100 Hz to greater than 100 kHz. The response of the spectral method is independent of the vibration frequency above the photorefractive cutoff frequency. Two methods are described that produce a readout beam intensity that is a direct function of the vibration amplitude suitable for imaging.
Multiprotein HIV Type 1 Clade B DNA/MVA Vaccine: Construction, Safety, and Immunogenicity in Macaques (2004)

Recently, a simian/human immunodeficiency virus (SHIV) vaccine consisting of priming with a Gag-Pol-Env-expressing DNA and boosting with a Gag-Pol-Env-expressing recombinant modified vaccinia Ankara (rMVA) has successfully controlled a virulent SHIV challenge in a macaque model. In this, and the accompanying paper, we report on the construction and testing of a Gag-Pol-Env DNA/MVA vaccine for HIV-1/AIDS. The DNA vaccine, pGA2/JS2, expresses aggregates of Gag proteins and includes safety mutations that render it integration, reverse transcription, and packaging defective. The rMVA vaccine, MVA/HIV 48, is integration and reverse transcription defective and has a truncated Env to enhance expression on the plasma membrane. In a study in rhesus macaques, priming with pGA2/JS2 and boosting with MVA/HIV 48 raised high frequencies of T cells for Gag and Env and lower frequencies of T cells for PR, RT, and Tat. Stimulations with five peptide pools for Gag and seven peptide pools for Env revealed epitopes for cellular immune responses throughout Gag and Env. On average, CD4 T cells from the vaccinated animals recognized 7.1 peptide pools and CD8 T cells, 3.2 peptide pools. Both the height and the breadth of the elicited cellular response provide hope that this multiprotein DNA/MVA vaccine will successfully control clade B isolates of HIV-1, as well as contribute to the control of other clades and recombinant forms of HIV-1/AIDS.
Ultra-Low-Loss Reduced-Clad Fiber with Attenuation less than 0.16 dB/km (2022)

We have prototyped optical fibers with cladding and coating diameters of 1 00 and 160 µm, respectively, with an attenuation less than 0.16 dB/km. This geometry mitigates microbending sensitivity sufficiently well to enable ultra-low-loss performance.
Taper structures for coupling into photonic crystal slab waveguides (2003)

We present an adiabatic taper design in three dimensions for coupling light into photonic crystal defect waveguides in a square lattice of circular dielectric rods. The taper is a two-stage structure in which the first stage makes the transition from a dielectric waveguide to a coupled-cavity waveguide. The second stage subsequently transforms the waveguide mode from an index-guided mode to a band-gap-guided mode. We discuss differences between the two-dimensional device and its three-dimensional slab version.
Wavelength conversion using semiconductor optical amplifiers in differential Mach-Zehnder interferometer with tunable input coupler (2009)

A monolithically-integrated wavelength converter on an InP platform with a semiconductor optical amplifier in each arm of a differential Mach-Zehnder interferometer is presented. The data input has a tunable coupler that adjusts the splitting ratio of the optical power sent to each arm. Wavelength conversion at 40 Gbit/s is demonstrated and a conversion penalty of <2 dB is found when less optical power is sent to the delayed arm.
Effect of dapagliflozin in DAPA-HF according to background glucose-lowering therapy (2020)

<b>Objective</b>: To determine whether the benefits of dapagliflozin in patients with heart failure and reduced ejection fraction (HFrEF) and type 2 diabetes in DAPA-HF varied by background glucose-lowering therapy (GLT). <p><b>Research design and methods: </b>We examined the effect of study treatment by the use or not of GLT, and by GLT classes and combinations. The primary outcome was a composite of worsening HF (hospitalization or urgent visit requiring intravenous therapy) or cardiovascular death. </p> <p><b>Results</b>: In the 2139 type 2 diabetes patients, the effect of dapagliflozin on the primary outcome was consistent by GLT use/no use (hazard ratio 0.72 [95%CI 0.58-0.88] versus 0.86 [0.60-1.23]; P-interaction=0.39) and across GLT classes. </p> <p><b>Conclusions</b>: In DAPA-HF, dapagliflozin improved outcomes irrespective of use/no use of GLT or by GLT type used in patients with type 2 diabetes and HFrEF.</p>