gebhart/patrepeval huggingface dataset:
Quantitative Competitive Reverse Transcription-PCR for Quantification of Dengue Virus RNA (2000)

A quantitative competitive reverse transcription-PCR assay was developed to quantify dengue virus RNA in this study. The main features include a primer pair targeting a highly conserved region in the capsid and the addition of competing RNA that contains an internal deletion to provide a stringent internal control for quantification. It can be utilized to quantify RNA isolated from the four dengue virus serotypes but not RNA isolated from other flaviviruses, including Japanese encephalitis virus and hepatitis C virus, both prevalent in Asia. It can also be used to quantify dengue virus RNA isolated from the plasma of infected individuals. The sensitivity of the assay was estimated to be 10 to 50 copies of RNA per reaction, and twofold differences in virus titer are distinguishable. This assay is a convenient, sensitive, and accurate method for quantification and can be used to further understanding of the pathogenesis of dengue virus infection.
Recent developments in transparent spinel ceramic and composite windows (2013)

The U.S. Naval Research Laboratory has pioneered the development of sintering processes for making highly transparent optical ceramics. For example, we have demonstrated the fabrication of record low absorption loss spinel as an exit window for High Energy Laser systems and rare earth doped Y<sub>2</sub>O<sub>3</sub> and Lu<sub>2</sub>O<sub>3</sub> for solid-state ceramic lasers. We have also developed thick spinel windows for submarine photonic masts and predicted the performance of an imaging system using testing and modeling. More recently, we have developed a novel approach of hot pressing where a transparent ceramic is produced in the net shape without requiring post polishing. This technology will result in significant cost savings associated with polishing the final optical element. We are also developing motheye structures on spinel surface to provide rugged anti-reflective solutions. We had earlier identified a Barium GalloGermanate (BGG) glass with matching index and expansion coefficient to spinel. We had demonstrated fabrication of a laminated dome for the Joint Air to Ground Missile (JAGM) program and the technology was transitioned to industry. We have pushed this technology further by developing a BGG glass – spinel ceramic transparent micro-composite, which can be processed well below spinel sintering temperatures. To address the relatively lower strength of BGG glass compared with spinel, we developed an ion-exchange process and achieved strengths up to 450 MPa. This paper gives a summary of our recent findings.
Phytosterol nanoparticles with reduced crystallinity generated using nanoporous starch aerogels (2016)

Phytosterol nanoparticles with reduced crystallinity were generated by impregnation of the phytosterols into nanoporous starch aerogels using supercritical carbon dioxide.
D-BigBand: sensing GHZ-wide non-sparse spectrum on commodity radios (2014)

This paper presents D-BigBand, a system that senses a GHz-wide spectrum in real time using ADCs sampling at only tens of MS/s speed. It is an advanced version of our previous work, BigBand, which senses GHz-wide sparse spectrum using commodity radios. However, unlike BigBand that requires the spectrum to be sparse, D-BigBand does not assume sparsity utilization of the spectrum. This is particularly important for the spectrum under 2GHz which is typically not sparse, crowded with different wireless technologies like TV broadcasting, mobile, AM radios, etc. The key idea of D-BigBand is to run sparse recovery on the changes of the spectrum: since only a small fraction of the spectrum is likely to change its occupancy over short intervals of a few milliseconds, the changes of the spectrum is sparse and we can apply sparse recovery to it. Our evaluation shows that D-BigBand works even if 95% of the spectrum is occupied.
Image-based street-side city modeling (2009)

We propose an automatic approach to generate street-side 3D photo-realistic models from images captured along the streets at ground level. We first develop a multi-view semantic segmentation method that recognizes and segments each image at pixel level into semantically meaningful areas, each labeled with a specific object class, such as building, sky, ground, vegetation and car. A partition scheme is then introduced to separate buildings into independent blocks using the major line structures of the scene. Finally, for each block, we propose an inverse patch-based orthographic composition and structure analysis method for façade modeling that efficiently regularizes the noisy and missing reconstructed 3D data. Our system has the distinct advantage of producing visually compelling results by imposing strong priors of building regularity. We demonstrate the fully automatic system on a typical city example to validate our methodology.
Ray-Triangle Intersection Algorithm for Modern CPU Architectures (2007)

We present an algorithm for determining if a ray intersects a triangle interior; and computing intersection point parameters as well as distance of intersection in response to the ray intersecting a triangle interior. Particularly a variation of a hybrid test having all benefits of Plücker and projected barycentric tests is proposed. The test is also vectorized using SIMD instructions for efficient handling ray packets. It is essential for achieving high ray tracing performance on modern CPUs. Our implementation also detects axis-orthogonal triangles and processing them separately. For maximum performance we also introduce a method for triangle representation, using only necessary pre-computed values. We also present inherently thread-safe and memory efficient alternative of mailboxing to avoid unnecessary intersection tests for ray packet in case when many leaves share the same triangle.
The Chiral Qubit: quantum computing with chiral anomaly (2019)

The quantum chiral anomaly enables a nearly dissipationless current in the presence of chirality imbalance and magnetic field -- this is the Chiral Magnetic Effect (CME), observed recently in Dirac and Weyl semimetals. Here we propose to utilize the CME for the design of qubits potentially capable of operating at THz frequency, room temperature, and the coherence time to gate time ratio of about $10^4$. The proposed "Chiral Qubit" is a micron-scale ring made of a Weyl or Dirac semimetal, with the $|0\rangle$ and $|1\rangle$ quantum states corresponding to the symmetric and antisymmetric superpositions of quantum states describing chiral fermions circulating along the ring clockwise and counter-clockwise. A fractional magnetic flux through the ring induces a quantum superposition of the $|0\rangle$ and $|1\rangle$ quantum states. The entanglement of qubits can be implemented through the near-field THz frequency electromagnetic fields.
Diagnosis of Intermittent Scan Chain Faults Through a Multistage Neural Network Reasoning Process (2019)

Diagnosis of intermittent scan chain failures still remains a hard problem. In this article, we demonstrate that the use of artificial neural networks (ANNs) can lead to significantly higher accuracy. The key of this method is a multistage process incorporating ANNs with gradually refined focuses. During this process, the final fault suspect is elected through multiple rounds of ANN inference, instead of just one round. At each stage, identification of a proper Affine Group, used as the “candidate set of scan cells for the next round of ANN inference,” will influence the final diagnostic accuracy. Thus, we propose a validation-based learning procedure for Affine Group derivation to further boost the final diagnostic accuracy. The experimental results on benchmark circuits have shown that this method is, on the average, 17.46% more accurate than a state-of-the-art commercial tool for intermittent stuck-at-0 faults.
Estrogen Regulation of Human Osteoblastic Cell Proliferation and Differentiation* (1997)

Estrogen (E2) has been shown to prevent bone loss among postmenopausal women. The molecular mechanism(s) by which this is accomplished is not clear. The discovery of E2 receptor (ER) in osteoblasts and osteoclasts has implicated these cells as direct targets for E2. Previous studies on the effects of E2 on osteoblastic cells in vitro or in organ culture present conflicting results, possibly due to heterogeneity in cell types, stage of differentiation, ER levels, and/or species differences. The effects of E2 on gene expression during various stages of human osteoblast cell differentiation has not been investigated extensively. In this study we employed a newly developed human fetal osteoblastic cell line (hFOB/ER9) that contains high levels of ER to examine the effects of E2 on osteoblast proliferation and differentiation. The basal levels and E2 effects on the expression of various extracellular matrix proteins were also characterized throughout different stages of differentiation. These stages include a proliferative/relatively undifferentiated stage (day 6), a matrix maturation stage (days 10-14), and a mineralization/calcified nodule stage (day 18). During the stage of rapid cell proliferation, E2 treatment of hFOB/ER9 cells resulted in a dose-dependent decrease in [3H]thymidine incorporation to a maximum of 72% compared to the vehicle control value. Treatment of hFOB/ER9 cells with 10(-9) M E2 for 48 h resulted in an increase in alkaline phosphatase (AP) activity throughout cell differentiation. The magnitude of AP induction varied from approximately 200-500%. In contrast, E2 decreased osteocalcin protein levels to a minimum of 54% compared to the vehicle control value. The steady state messenger RNA levels for AP increased and osteocalcin decreased after E2 treatment, similar to the responses observed at the protein level. At all stages, there was little or no effect of E2 on type I collagen protein levels or osteonectin steady state messenger RNA levels. The E2 responses on hFOB/ER9 cell matrix protein expression and cell proliferation were mediated through the ER, as cultures cotreated with a 100-fold molar excess of a type II anti-E2 (ICI 182,780) abrogated these effects. These results support the hypothesis that E2 does have an effect on osteoblastic differentiation by decreasing hFOB/ER9 cell proliferation and differentially regulating extracellular matrix expression.
Validation of vortex flowmeters (2002)

A vortex-shedding flow meter produces an approximately sinewave signal whose average frequency is proportional to volumetric flow rate. The frequency of vortex shedding varies over a large range (up to 1:100), depending on the size of the flow meter. The conventional frequency-estimation method-a zero-crossing algorithm-fails at low flows, where the signal:noise ratio is poor. The paper describes a dual phase-locked loop structure that tracks the frequency over the flowmeter's full range with improved accuracy. The lock indicators associated with each PLL provide the SEVA metrics.
Spatio-temporal analysis for automatic contrast injection detection on angiography during trans-catheter aortic valve implantation (2011)

Registration of 3-D aortic model onto X-ray images provides anatomical details for optimal valve deployment in Trans-catheter aortic valve implantation (TAVI) procedures. Fast and automatic contrast detection in the aortic root in fluoroscopic sequences facilitates a seamless workflow by triggering 2-D/3-D registration automatically when necessary. In this paper, we propose an integrated spatial and temporal analysis on fluoroscopic sequences to improve the performance of the contrast feature curve based method in our previous work. For sequences with a high likelihood of containing contrasted aorta, a cascaded classifier is used to separate the contrasted aorta from the contrasted balloons. A local training procedure is then performed in sequences with contrasted aorta to identify the range of well-contrasted frames. Next, a multi-layer sparse Gabor feature based classifier is adopted to recognize faint contrast. Experiments on 69 sequences acquired during TAVI procedures achieved the correct classification rate of 12/12 for non-contrasted sequences and 56/57 for contrasted sequences.
Structure and synthesis of pyrrolomycin A. a chlorinated nitro-pyrrole antibiotic. (1981)

Pyrrolomycin A, a new antifungal antibiotic produced by an actinomycete, has a molecular formula C4H2N202Cl2. Its structure was determined to be 2, 3-dichloro-4-nitropyrrole by spectroscopic analysis and synthetic studies. Structure-activity relationships among the analogs of pyrrolomycin A are discussed.
Polyelectrolyte layer-by-layer deposition on nanoporous supports for ion selective membranes (2018)

This work demonstrates that the ionic selectivity and ionic conductivity of nanoporous membranes can be controlled independently <i>via</i> layer-by-layer (LbL) deposition of polyelectrolytes and subsequent selective cross-linking of these polymer layers. LbL deposition offers a scalable, inexpensive method to tune the ion transport properties of nanoporous membranes by sequentially dip coating layers of cationic polyethyleneimine and anionic poly(acrylic acid) onto polycarbonate membranes. The cationic and anionic polymers are self-assembled through electrostatic and hydrogen bonding interactions and are chemically crosslinked to both change the charge distribution and improve the intermolecular integrity of the deposited films. Both the thickness of the deposited coating and the use of chemical cross-linking agents influence charge transport properties significantly. Increased polyelectrolyte thickness increases the selectivity for cationic transport through the membranes while adding polyelectrolyte films decreases the ionic conductivity compared to an uncoated membrane. Once the nanopores are filled, no additional decrease in conductivity is observed with increasing film thickness and, upon cross-linking, a portion of the lost conductivity is recovered. The cross-linking agent also influences the ionic selectivity of the resulting polyelectrolyte membranes. Increased selectivity for cationic transport occurs when using glutaraldehyde as the cross-linking agent, as expected due to the selective cross-linking of primary amines that decreases the net positive charge. Together, these results inform deposition of chemically robust, highly conductive, ion-selective membranes onto inexpensive porous supports for applications ranging from energy storage to water purification.
Nitrite Reductase NirBD Is Induced and Plays an Important Role during <i>In Vitro</i> Dormancy of Mycobacterium tuberculosis (2013)

Mycobacterium tuberculosis is one of the strongest reducers of nitrate among all mycobacteria. Reduction of nitrate to nitrite, mediated by nitrate reductase (NarGHJI) of M. tuberculosis, is induced during the dormant stage, and the enzyme has a respiratory function in the absence of oxygen. Nitrite reductase (NirBD) is also functional during aerobic growth when nitrite is the sole nitrogen source. However, the role of NirBD-mediated nitrite reduction during the dormancy is not yet characterized. Here, we analyzed nitrite reduction during aerobic growth as well as in a hypoxic dormancy model of M. tuberculosis in vitro. When nitrite was used as the sole nitrogen source in the medium, the organism grew and the reduction of nitrite was evident in both hypoxic and aerobic cultures of M. tuberculosis. Remarkably, the hypoxic culture of M. tuberculosis, compared to the aerobic culture, showed 32- and 4-fold-increased expression of nitrite reductase (NirBD) at the transcription and protein levels, respectively. More importantly, a nirBD mutant of M. tuberculosis was unable to reduce nitrite and compared to the wild-type (WT) strain had a >2-log reduction in viability after 240 h in the Wayne model of hypoxic dormancy. Dependence of M. tuberculosis on nitrite reductase (NirBD) was also seen in a human macrophage-based dormancy model where the nirBD mutant was impaired for survival compared to the WT strain. Overall, the increased expression and essentiality of nitrite reductase in the in vitro dormancy models suggested that NirBD-mediated nitrite reduction could be critical during the persistent stage of M. tuberculosis.
Corrigendum: Space charge limited conduction mechanism in GaAsSb nanowires and the effect of <i>in-situ</i> annealing in ultra-high vacuum (2020 <i>Nanotechnology</i> 31 025205) (2020)

In this work, the first observation of the space charge limited conduction mechanism (SCLC) in GaAsSb nanowires (NWs) grown by Ga-assisted molecular beam epitaxial technique, and the effect of ultrahigh vacuum in-situ annealing have been investigated. The low onset voltage of the SCLC in the NW configuration has been advantageously exploited to extract trap density and trap distribution in the bandgap of this material system, using simple temperature dependent current-voltage measurements in both the ensemble and single nanowires. In-situ annealing in an ultra-high vacuum revealed significant reduction in the trap density from 1016 cm-3 in as-grown NWs to a low level of 7 * 1014 cm-3 and confining wider trap distribution to a single trap depth at 0.12 eV. A comparison of current conduction mechanism in the respective single nanowires using conductive atomic force microscopy (C-AFM) further confirms the SCLC mechanism identified in GaAsSb ensemble device to be intrinsic. Higher current observed in current mapping by C-AFM, increased 4K photoluminescence (PL) intensity along with reduced full-width half maxima and more symmetric PL spectra, reduced asymmetrical broadening and increased TO/LO mode in room temperature Raman spectra for in-situ annealed NWs again attest to effective annihilation of traps leading to the improved optical quality of NWs compared to as-grown NWs. Hence, the I-V-T analysis of the SCLC mechanism has been demonstrated to be a simple approach to obtain information on growth induced traps in the NWs.
Polymers for Chemical Sensors Using Hydrosilylation Chemistry (2001)

Sorbent and functionalized polymers play a key role in a diverse set of fields, including chemical sensors, separation membranes, solid phase extraction techniques, and chromatography. Sorbent polymers are critical to a number of sensor array or "electronic nose" systems. The responses of the sensors in the array give rise to patterns that can be used to distinguish one compound from another, provided that a sufficiently diverse set of sensing materials is present in the array. Figure 1 illustrates the concept of several sensors, each with a different sensor coating, giving rise to variable responses to an analyte that appear as a pattern in bar graph format. Using hydrosilylation as the bond-forming reaction, we have developed a versatile and efficient approach to developing sorbent polymers with diverse interactive properties for sensor applications. Both the chemical and physical properties of these polymers are predictable and tunable by design.
An Oracle for Tolerating and Detecting Asymmetric Races (2007)

Because races represent a hard-to-manage class of errors in concurrent programs, numerous approaches to detect them have been proposed and evaluated. We consider specifically asymmetric races, a subclass of race conditions, where a programmer’s thread correctly acquires and releases a lock for a specific variable, while another thread causes a race by improperly accessing this variable. We introduce ToleRace, an oracle that allows programs to either tolerate or detect asymmetric races based on local replication of shared state. ToleRace provides an approximation of atomicity in critical sections by creating local copies of shared variables when a critical section is entered and propagating the appropriate copy when the critical section is exited. We characterize the possible interleavings that can cause races and precisely describe the effect of ToleRace in each of these cases. We evaluate the theoretical aspects of the oracle and note that it could be implemented in hardware and/or software within a favorable range of overhead-to-benefit scenarios. 1.
Novel Aryloxyethyl Derivatives of 1-(1-Benzoylpiperidin-4-yl)methanamine as the Extracellular Regulated Kinases 1/2 (ERK1/2) Phosphorylation-Preferring Serotonin 5-HT<sub>1A</sub> Receptor-Biased Agonists with Robust Antidepressant-like Activity (2019)

Novel 1-(1-benzoylpiperidin-4-yl)methanamine derivatives were designed as "biased agonists" of serotonin 5-HT<sub>1A</sub> receptors. The compounds were tested in signal transduction assays (ERK1/2 phosphorylation, cAMP inhibition, Ca<sup>2+</sup> mobilization, and β-arrestin recruitment) which identified ERK1/2 phosphorylation-preferring aryloxyethyl derivatives. The novel series showed high 5-HT<sub>1A</sub> receptor affinity, >1000-fold selectivity versus noradrenergic α<sub>1</sub>, dopamine D<sub>2</sub>, serotonin 5-HT<sub>2A</sub>, histamine H<sub>1</sub>, and muscarinic M<sub>1</sub> receptors, and favorable druglike properties (CNS-MPO, Fsp<sup>3</sup>, LELP). The lead structure, (3-chloro-4-fluorophenyl)(4-fluoro-4-(((2-(pyridin-2-yloxy)ethyl)amino)methyl)piperidin-1-yl)methanone (17, NLX-204), displayed high selectivity in the SafetyScreen44 panel (including hERG channel), high solubility, metabolic stability, and Caco-2 penetration and did not block CYP3A4, CYP2D6 isoenzymes, or P-glycoprotein. Preliminary in vivo studies confirmed its promising pharmacokinetic profile. 17 also robustly stimulated ERK1/2 phosphorylation in rat cortex and showed highly potent (MED = 0.16 mg/kg) and efficacious antidepressant-like activity, totally eliminating immobility in the rat Porsolt test. These data suggest that the present 5-HT<sub>1A</sub> receptor-biased agonists could constitute promising antidepressant drug candidates.
High-density data-retention power gating structure using a four-terminal double-gate device (2007)

This paper presents a new power gating structure with robust data retention capability using only one single double-gate device to provide both power gating switch and virtual supply/ground diode clamp functions. The scheme reduces the transistor count, area, and capacitance of the power gating structure, thus improving circuit performance, power, and leakage. The scheme is compared to the conventional power gating structure via mixed-mode physics-based two-dimensional numerical simulations. Analysis of virtual ground bounce for the proposed scheme is also presented.
FM halftoning via block error diffusion (2002)

Error diffusion halftoning is a popular method of producing frequency modulated (FM) halftones. In FM halftoning the dot size and shape is fixed (equal to one pixel) and the dot frequency is varied in accordance to the graylevel values of the underlying grayscale image. We generalize error diffusion to produce FM halftones with user controlled dot size and shape using block quantization and a block filter in the feedback loop. We call this modified quantization and feedback process block error diffusion. The block filters are designed from well known scalar error filter prototypes and retain their properties. Further, we show that choosing a structured block filter results in an efficient parallel implementation of block error diffusion.