gebhart/patrepeval huggingface dataset:
The human papillomavirus E7 oncoprotein can uncouple cellular differentiation and proliferation in human keratinocytes by abrogating p21<sup>Cip1</sup>-mediated inhibition of cdk2 (1997)

The high risk human papillomaviruses (HPVs) are associated etiologically with the majority of human cervical carcinomas. These HPVs encode two viral oncoproteins, E6 and E7, which are expressed consistently in cervical cancers. The function of these viral oncoproteins during a productive infection is to ensure viral replication in cells that have normally withdrawn from the cell division cycle and are committed to terminal differentiation. Expression of the E7 oncoprotein has been shown to lead to the abrogation of various negative growth regulatory signals, including a p53-mediated G1 growth arrest, TGFbeta-mediated growth inhibition, and quiescence of suprabasal keratinocytes. Here we describe a novel mechanism by which E7 can uncouple cellular proliferation and differentiation. In contrast to normal, differentiating keratinocytes, HPV-16 E7-expressing keratinocytes show delayed cellular differentiation and elevated cdk2 kinase activity despite high levels of p21(Cip1) and association of p21(Cip1) with cdk2. We show that the HPV E7 protein can interact with p21(Cip1) and abrogate p21(Cip1)-mediated inhibition of cyclin A and E-associated kinase activities. Based on these findings, we propose that this capacity of the HPV E7 oncoprotein to overcome p21(Cip1)-mediated inhibition of cdk2 activity during keratinocyte differentiation contributes to the ability of E7 to allow for cellular DNA synthesis in differentiated keratinocytes.
Multiscale Grid Design and Upscaling for a Full Field Tight Gas Reservoir Model on a Next Generation Simulator (2013)

Abstract Reservoir management and simulation of tight gas reservoirs pose several interesting technical challenges. Accurate simulation estimates of the effectiveness of multi-stage fracturing, well rates, the interaction between multiple fractures, and between the reservoir and fractures requires high resolution gridding near the well. These predictions have been achieved in the past through the design of LGR (Local Grid Refinement) grids, or through the use of fractured well indices or cell permeabilities. The latter techniques are based upon steady state concepts and are less able to resolve well rate transients compared to the use of LGR grids. Decisions on well counts, spacing, and timing also depend upon the interaction between wells. These simulations face specific challenges due to the geology of these reservoirs: in addition to the permeability being low, the connectivity of these reservoirs is intermittent due to the three dimensional spatial patterns of sand deposition and subsequent diagenesis. If these reservoir models are over-averaged or not carefully upscaled, the barriers between sands and internal heterogeneity will be lost, leading to far too optimistic estimates of lateral continuity and under-estimates of infill requirements. The need for accurate flow simulation of these systems has led to the development of spatially adaptive upscaling techniques that honor the vertical discontinuities of the sands in the design of the coarsened simulation grid and which also preserves the heterogeneity within sands. In the current study, these two approaches have been combined, providing a model with both high resolution and computational efficiency. Starting with a high resolution 3D geologic model, the simulation grid is designed using refinement at the fractured wells, and successively coarsened away from the well, leading to an unstructured numerical problem. Away from the wells, the vertical coarsening utilizes the "pillar-based" adaptive coarsening of Zhou and King, 2011. Simulation is performed using a next generation unstructured commercial simulator. We will report upon the performance of the different techniques in terms of accuracy, computational efficiency, and how they are impacted by different implementations of the multiscale simulation grid design.
The Development of an Efficient Multipurpose Bean Pod Mottle Virus Viral Vector Set for Foreign Gene Expression and RNA Silencing  (2010)

Plant viral vectors are valuable tools for heterologous gene expression, and because of virus-induced gene silencing (VIGS), they also have important applications as reverse genetics tools for gene function studies. Viral vectors are especially useful for plants such as soybean (Glycine max) that are recalcitrant to transformation. Previously, two generations of bean pod mottle virus (BPMV; genus Comovirus) vectors have been developed for overexpressing and silencing genes in soybean. However, the design of the previous vectors imposes constraints that limit their utility. For example, VIGS target sequences must be expressed as fusion proteins in the same reading frame as the viral polyprotein. This requirement limits the design of VIGS target sequences to open reading frames. Furthermore, expression of multiple genes or simultaneous silencing of one gene and expression of another was not possible. To overcome these and other issues, a new BPMV-based vector system was developed to facilitate a variety of applications for gene function studies in soybean as well as in common bean (Phaseolus vulgaris). These vectors are designed for simultaneous expression of multiple foreign genes, insertion of noncoding/antisense sequences, and simultaneous expression and silencing. The simultaneous expression of green fluorescent protein and silencing of phytoene desaturase shows that marker gene-assisted silencing is feasible. These results demonstrate the utility of this BPMV vector set for a wide range of applications in soybean and common bean, and they have implications for improvement of other plant virus-based vector systems.
Frequency Modulated Gyroscopes (2013)

MEMS gyroscopes for consumer devices, such as smartphones and tablets, suffer from high power consumption and drift which precludes their use in inertial navigation applications. Conventional MEMS gyroscopes detect Coriolis force through measurement of very small displacements on a sense axis, which requires low-noise, and consequently high-power, electronics. The sensitivity of the gyroscope is improved through mode-matching, but this introduces many other problems, such as low bandwidth and unreliable scale factor. Additionally, the conventional Coriolis force detection method is very sensitive to asymmetries in the mechanical transducer because the rate signal is derived from only the sense axis. Parasitic coupling between the drive and sense axis introduces unwanted bias errors which could be rejected by a perfectly symmetric readout scheme.In this thesis, I present frequency modulated (FM) gyroscopes that overcome the above limitations. FM gyroscopes operate the mechanical transducer in a perfectly symmetric way: each transducer axis is continuously driven to maintain a constant envelope oscillation. The rate is detected as changes in the frequencies of oscillations of the two axes. Frequency readout offers superior scale factor reliability in comparison to amplitude readout. For pendulum type gyroscopes, the scale factor is a dimensionless constant equal to 1 Hz (or cycle per second) per 360 deg/s.FM gyroscopes are trivial to mode-match. Oscillation frequencies of both axes can be continually monitored and matched through electrostatic tuning. The FM gyroscope receives the same improved sensitivity benefit from mode-matching as the conventional gyroscope, without the drawbacks of limited bandwidth or unreliable scale factor.Because of the symmetry, compatibility with mode-matching, and ease of frequency readout, the FM gyroscopes promise to improve the power dissipation and drift of MEMS gyroscopes.
Optoacoustic monitoring of blood hemoglobin concentration: a pilot clinical study (2005)

The optoacoustic technique is noninvasive, has high spatial resolution, and potentially can be used to measure the total hemoglobin concentration ([THb]) continuously and accurately. We performed in vitro measurements in blood and in vivo tests in healthy volunteers. Our clinical protocol included rapid infusion of intravenous saline to simulate rapid change in the [THb] during fluid therapy or surgery. Optoacoustic measurements were made from the wrist area overlying the radial artery for more than 1 h. The amplitude of the optoacoustic signal generated in the radial artery closely followed the [THb] measured directly in concurrently collected blood samples.
Moderately hard, memory-bound functions (2005)

A resource may be abused if its users incur little or no cost. For example, e-mail abuse is rampant because sending an e-mail has negligible cost for the sender. It has been suggested that such abuse may be discouraged by introducing an artificial cost in the form of a moderately expensive computation. Thus, the sender of an e-mail might be required to pay by computing for a few seconds before the e-mail is accepted. Unfortunately, because of sharp disparities across computer systems, this approach may be ineffective against malicious users with high-end systems, prohibitively slow for legitimate users with low-end systems, or both. Starting from this observation, we research moderately hard functions that most recent systems will evaluate at about the same speed. For this purpose, we rely on memory-bound computations. We describe and analyze a family of moderately hard, memory-bound functions, and we explain how to use them for protecting against abuses.
A Novel Development Infrastructure for Scalable Video Coding/Transcoding Applications (2016)

Due to recent demand for playback of high quality video on mobile devices, there is the need for a scalable, error resilient framework with the ability to adjust to the network and receiver's specification. To cope with the bandwidth fluctuations in the network, the framework's scalability allows for high bit-rate video to be transcoded to a low bit-rate format while preserving quality as much as possible. The new High Efficiency Video Coding (HEVC/H.265) standard allows for high compression rates, however, it is computationally intensive. We propose a novel Development Infrastructure for Video coding/transcoding Applications (DIVA). This framework is capable of providing different quality of services (e.g., Bronze, Silver, Gold), and has some error-resilient capability. Taking advantage of IBM Platform Symphony, the computationally intensive task of HEVC encoding can be distributed on available local or cloud resources. Our experiments illustrate the feasibility of this approach.
Optimal Parameter Settings for Forward Error Correction Schemes for Multimedia Streaming over Wireless Networks (2005)

This paper investigates algorithms to determine an optimal choice of the FEC parameters (n, k) to mitigate the effects of packet loss due to buffer overflow at a wireless base station on multimedia traffic. We develop an analytic model of the considered network scenario that takes into account the traffic arrival rates, the channel loss characteristics, the size of the buffer at the wireless access point, and the influence of the FEC parameters on the packet loss. Applying the theory of recurrent linear equations, we present a new approach to establish a closed form solution of the underlying Markov model for the buffer occupancy and verify the analytical results via simulations
Elimination of Oxidation‐Induced Stacking Faults by Preoxidation Gettering of Silicon Wafers: I . Phosphorus Diffusion‐Induced Misfit Dislocations (1975)

In the present paper a preoxidation gettering procedure (called POGO) is described which prevents the formation and/or activation of stacking fault nucleation sites during oxidation. In this way the stacking faults and their possible device degrading influences are eliminated at the start of a processing schedule. In addition, the gettering medium is retained through all subsequent high temperature processing, thereby continuing to suppress the formation of stacking faults. The gettering of the nucleation sites, whether they be process induced, such as impurity precipitation, or native to the original crystal growth, such as vacancies or impurities, is achieved by the controlled introduction of interfacial misfit dislocations on the back side of the wafer. The dislocations interact with the stacking fault nucleation sites such that the nuclei diffuse from the active device side of the wafer to the line defects which are confined to within a few microns of the back surface.
A Golgi-localized two-photon probe for imaging zinc ions (2015)

We report a two-photon fluorescent probe which shows a strong two photon excited fluorescence enhancement in response to Zn(2+), easy loading into the cells, Golgi-localizing ability, low cytotoxicity, and high photostability. Two-photon microscopy imaging revealed that this probe allows for real-time monitoring of the changes in Golgi Zn(2+) as well as their 3D distributions in live cells and tissues.
Peer assisted VoD for set-top box based IP network (2007)

IP-enabled set-top boxes are becoming key devices in home entertainment networks. In addition to providing TV signals, STBs have been providing pay-per view service for a long time. But this service suffers from bandwidth requirements at the source server and has scaling problems. We propose a new design for providing a peer-assisted VoD service where peers co-operate in delivering the content to other peers. This design uses a Bittorrent like protocol for peer-to-peer topology management and DHT for data retrieval with low startup time, provision for VCR operation and admission control to guarantee QoS for subscribers. It utilizes the large storage of STBs for better viewing experience with reduced jitter and the underlying network architecture to do a location aware content fetching and reduce the expensive cross AS traffic over the Internet.
Functional Coherence of the Human Y Chromosome (1998)

Howard Hughes Medical Institute, Whitehead Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts. Science 1997;278:675-680.
A Multiport DC Power Flow Controller Embedded in Modular Multilevel DC Transformer (2022)

Meshed dc or hybrid ac/dc distribution grids have attracted increasing interest lately and their power flow control is a major topic of study. Since the dc grids implemented with the existing power converters lack sufficient control freedoms for proper power flow adjustment, it is necessary to develop new dc power flow controllers (DCPFCs) to effectively mitigate power flow congestion and line losses by optimizing the power flow of the connected feeders. Unlike previously introduced solutions, in this article, we propose a DCPFC directly integrated in a modular multilevel dc transformer. The proposed DCPFC does not require external power supply and high-voltage isolation transformer, and features a simple structure, convenience for multiport extension and bidirectional power flow adjustment capability. The power flow control strategy and its energy balance scheme based on the phase-shifted modulation are elaborated. The proposed topology and its performance are verified through a scaled-down experimental platform under typical operating conditions.
The Contribution of an Animal Model Toward Uncovering Biological Risk Factors for PTSD (2006)

Clinical studies of posttraumatic stress disorder (PTSD) have elicited proposed risk factors for developing PTSD in the aftermath of stress exposure. Generally, these risk factors have arisen from retrospective analysis of premorbid characteristics of study populations. A valid animal model of PTSD can complement clinical studies and help to elucidate issues, such as the contribution of proposed risk factors, in ways which are not practicable in the clinical arena. Important qualities of animal models include the possibility to conduct controlled prospective studies, easy access to postmortem brains, and the availability of genetically manipulated subjects, which can be tailored to specific needs. When these qualities are further complemented by an approach which defines phenomenologic criteria to address the variance in individual response pattern and magnitude, enabling the animal subjects to be classified into definable groups for focused study, the model acquires added validity. This article presents an overview of a series of studies in such an animal model which examine the contribution of two proposed risk factors and the value of two early postexposure pharmacological manipulations on the prevalence rates of subjects displaying an extreme magnitude of behavioral response to a predator stress paradigm.
Effector-triggered immunity blocks pathogen degradation of an immunity-associated vesicle traffic regulator in <i>Arabidopsis</i> (2011)

Innate immunity in plants can be triggered by microbe- and pathogen-associated molecular patterns. The pathogen-associated molecular pattern-triggered immunity (PTI) is often suppressed by pathogen effectors delivered into the host cell. Plants can overcome pathogen suppression of PTI and reestablish pathogen resistance through effector-triggered immunity (ETI). An unanswered question is how plants might overcome pathogen-suppression of PTI during ETI. Findings described in this paper suggest a possible mechanism. During Pseudomonas syringae pathovar tomato (Pst) DC3000 infection of Arabidopsis, a host ADP ribosylation factor guanine nucleotide exchange factor, AtMIN7, is destabilized by the pathogen effector HopM1 through the host 26S proteasome. In this study, we discovered that AtMIN7 is required for not only PTI, consistent with the notion that Pst DC3000 degrades AtMIN7 to suppress PTI, but also ETI. The AtMIN7 level in healthy plants is low, but increases posttranscriptionally in response to activation of PTI. Whereas DC3000 infection led to degradation of AtMIN7, activation of ETI by three different effectors, AvrRpt2, AvrPphB, and HopA1, in Col-0 plants blocks the ability of Pst DC3000 to destabilize AtMIN7. Further analyses of bacterial translocation of HopM1 and AtMIN7 stability in HopM1 transgenic plants show that ETI prevents HopM1-mediated degradation of AtMIN7 inside the plant cell. Both AtMIN7 and HopM1 are localized to the trans-Golgi network/early endosome, a subcellular compartment that is not previously known to be associated with bacterial pathogenesis in plants. Thus, blocking pathogen degradation of trans-Golgi network/early endosome-associated AtMIN7 is a critical part of the ETI mechanism to counter bacterial suppression of PTI.
Video coding using pruned transforms and interleaving of multiple block (2008)

Technologies used in today's video coding standards have been designed and optimized mainly for standard definition (SD) resolutions and below. When moving to higher resolutions, data in video frames tend to become more correlated spatially. In this paper, we study how to take advantage of this phenomenon to lower computational requirements for high definition (HD) video coding. A coding method based on low complexity pruned transforms and interleaving of multiple transform coefficient blocks is proposed. An example implementation of this method in the context of H.264/AVC is also presented. Experimental results show that the proposed method maintains the high compression efficiency of H.264/AVC while significantly lowering the coding complexity of the codec.
Abstract 714: Direct Comparison of AAV Serotypes 1 9; Onset of Gene Expression, Time to Peak Expression, and Fate of Viral Genomes in Mice after Skeletal Muscle, and Tail Vein Injection (2006)

Background- Viral delivery vectors founded on the adeno-associated virus (AAV) serotype 2 platform are currently being evaluated for human gene transfer. All viral genes can be removed, resulting i...
Generation of Novel Bacterial Regulatory Proteins That Detect Priority Pollutant Phenols (2000)

The genetic systems of bacteria that have the ability to use organic pollutants as carbon and energy sources can be adapted to create bacterial biosensors for the detection of industrial pollution. The creation of bacterial biosensors is hampered by a lack of information about the genetic systems that control production of bacterial enzymes that metabolize pollutants. We have attempted to overcome this problem through modification of DmpR, a regulatory protein for the phenol degradation pathway of Pseudomonas sp. strain CF600. The phenol detection capacity of DmpR was altered by using mutagenic PCR targeted to the DmpR sensor domain. DmpR mutants were identified that both increased sensitivity to the phenolic effectors of wild-type DmpR and increased the range of molecules detected. The phenol detection characteristics of seven DmpR mutants were demonstrated through their ability to activate transcription of a lacZ reporter gene. Effectors of the DmpR derivatives included phenol, 2-chlorophenol, 2,4-dichlorophenol, 4-chloro-3-methylphenol, 2,4-dimethylphenol, 2-nitrophenol, and 4-nitrophenol.
Power Spectrum Analysis (2017)

Abstract We present a new, non-destructive electrical technique, Power Spectrum Analysis (PSA). PSA as described here uses off-normal biasing, an unconventional way of powering microelectronics devices. PSA with off-normal biasing can be used to detect subtle differences between microelectronic devices. These differences, in many cases, cannot be detected by conventional electrical testing. In this paper, we highlight PSA applications related to aging and counterfeit detection.
Application of vector scanning in focused ion beam photomask repair system (2008)

With continuous reduction in linewidth of the VLSI devices, the pattern integrity of photomasks becomes considerably more important than ever. Consequently, requirement for the defect repair technology on photomasks is more severe and strict. Focused ion beam (FIB) technology has been widely used for defect repairing in photomask industry. Therefore, the performance of the FIB mask repair tool has to be improved especially in repair accuracy and precision. The FIB repair processes are classified into two kinds; one is additive repair using FIB induced deposition for missing patterns, the other is subtractive repair using gas assisted FIB etching for extra patterns. In both processes, precursor gas is applied onto the processing area through a small nozzle. Thus, the repair processes are controlled by the FIB irradiation and the precursor gas supply. Important characteristics of the repairs, such as size, shape, and placement of the repair area, are defined by the FIB scanning control. As conventional FIB systems used raster type of beam scanning for the repair processes, the size, shape, and placement could be controlled with the unit of pixel size (typically about 6–12nm). However, in order to satisfy the recent requirement, more precise beam control is needed. The authors have developed a vector scanning system to meet the requirement. The vector scanning system enables us to control ion beams more precisely and more arbitrarily. Furthermore, unicursal beam scanning can be applied to the repair processes, which minimizes beam blanking times. By adopting the vector scanning, repair precision is improved. Additionally, sidewall angle of the repair region is also improved because the repair shape is formed without beam blanking.