gebhart/patrepeval huggingface dataset:
Comparing two colorimetric AuNPs-based assays for direct detection of unamplified hepatitis C virus RNA in clinical specimens (2013)

Background. Two different approaches for direct detection of unamplified hepatitis C virus (HCV) RNA have been developed using two types of spherical gold nanoparticles (AuNPs); negatively charged AuNPs [1] and cationic AuNPs [2]. Both assays have demonstrated good clinical performance, cost-effectiveness and short turnaround time compared to routine amplification-based molecular assays. AuNPs-based assays utilize the phenomenon of surface plasmon resonance (SPR) which is the origin of the unique optical properties of AuNPs and responsible for their color change from red to blue upon aggregation. However, the assay's target detection mechanism differs according to the surface charge of AuNPs. Methods. In this work, a total of 22 serum samples (11 HCV-positive, 11 HCV-negative) were characterized using real-time PCR and tested using both AuNPs-based approaches to compare and evaluate their performance in direct colorimetric HCV RNA detection. Negatively charged spherical AuNPs were synthesized using the citrate reduction method [3], and cationic spherical AuNPs were synthesized as described previously [4]. The prepared AuNPs were characterized using UV spectrophotometry and scanning electron microscopy. Total RNA was extracted from the serum samples, and real-time HCV PCR was performed. The extracted RNA was then assayed using the anionic AuNPs. For the cationic AuNPs approach, a modified extraction protocol that employed magnetic nanoparticles and a specificity-conferring HCV-specific oligonucleotide was used prior to addition of the cationic AuNPs. Results. The turnaround time using anionic AuNPs was about an hour, while that using cationic AuNPs was about 45 minutes. The anionic AuNP assay detected 90.9% and 81.8% of positive and negative samples; respectively. The cationic AuNP assay detected 90.9% and 100% of positive and negative HCV samples, respectively. Conclusion. The cationic AuNP assay showed better clinical performance than anionic AuNP assay for detection of unamplified HCV RNA in serum, particularly to rule out viral infection, which warrants further investigation. References: References 1. Shawky SM, Bald D, Azzazy HME. Direct detection of unamplified hepatitis C virus RNA using unmodified gold nanoparticles. Clin Biochem 2010;43: 1163-8. 2. Shawky SM, Guirgis BSS, Azzazy HME. Specific detection of unamplified HCV RNA using colloidal cationic gold nanoparticles. 19th International Symposium on Hepatitis C Virus and Related Viruses. Venice, Italy, 2012. 3. Storhoff JJ, Elghanian R, Mucic RC, Mirkin CA, Letsinger RL. One-pot colorimetric differentiation of polynucleotides with single base imperfections using gold nanoparticle probes. J Am Chem Soc 1998;120:1959-64. 4. Huang X JP, El-Sayed IH, El-Sayed MA. Gold nanoparticles: interesting optical properties and recent applications in cancer diagnostics and therapy. Nanomed 2007;2.
Kinetics of Peptide Amidase and its Application for the Resolution of Racemates (1997)

The chemical synthesis of various N-protected amino acid amides was carried out. These compounds served as substrates to determine the V max and KM values for the deamidation catalyzed by the peptide amidase from Citrus sinensis and Stenotrophomonas maltophilia, respectively, and to investigate the influence of the side chain of the amino acid on the performance of the enzymatic hydrolysis. The enzymatic resolution of racemic N-acetyl amino acids amides yielded N-acetyl-L-amino acids in optical purity ≧ 99% at complete conversion.
Quadruply Hydrogen Bonded Cytosine Modules for Supramolecular Applications (2006)

In view of the range of properties required from supramolecular materials, there is clearly a need for new strong quadruple hydrogen bonded modules, which can be used in polymer or copolymer synthesis via the self- or hetero-association of complimentary units. A cytosine-based module has been prepared for supramolecular applications using a straightforward synthetic approach. The cytosine module was designed such that it does not undergo tautomeric changes observed with ureidopyrimidinones. The cytosine module was capable of forming quadruple hydrogen bonded assemblies both in solution and in the solid state, and the structure of the dimeric self-assembled unit was confirmed by single-crystal X-ray and solution NMR techniques. The dimerization constant was estimated to be greater than 9 x 106 M-1 in deuterated benzene. The capacity of the cytosine-based module to strongly hetero-associate with the ureidopyrimidinone module was demonstrated, and a supramolecular polymer of a bifunctional unit incorporating the cytosine module and PEG-based linker was described.
Hardware implementation for scalable lookahead Regular Expression detection (2010)

Regular Expressions (RegExes) are widely used in various applications to identify strings of text. Their flexibility, however, increases the complexity of the detection system and often limits the detection speed as well as the total number of RegExes that can be detected using limited resources. The two classical detection methods, Deterministic Finite Automaton (DFA) and Non-Deterministic Finite Automaton (NFA), have the potential problems of prohibitively large memory requirements and a large number of concurrent operations, respectively. Although recent schemes addressing these problems to improve DFA and NFA are promising, they are inherently limited by their scalability, since they follow the state transition model in DFA and NFA, where the state transitions occur per each character of the input. We recently proposed a scalable RegEx detection system called Lookahead Finite Automata (LaFA) to solve these problems with three novel ideas: 1. Provide specialized and optimized detection modules to increase resource utilizations. 2. Systematically reordering the RegEx detection sequence to reduce number of concurrent operations. 3. Sharing states among automata for different RegExes to reduce resource requirements. In this paper, we propose an efficient hardware architecture and prototype design implementation based on LaFA. Our proof-of-concept prototype design is built on a fraction of a single commodity Field Programmable Gate Array (FPGA) chip and can accommodate up to twenty-five thousand (25k) RegExes. Using only 7% of the logic area and 25% of the memory on a Xilinx Virtex-4 FX100, the prototype design can achieve 2-Gbps (gigabits-per-second) detection throughput with only one detection engine. We estimate that 34-Gbps detection throughput can be achieved if the entire resources of a state-of-the-art FPGA chip are used to implement multiple detection engines.
Fast camera fingerprint matching in very large databases (2017)

Given a query image or video, or a known camera fingerprint, there is a lack of capabilities for fast identification of media, from a large repository of images and videos, that match the query fingerprint. This work introduces a new approach that improves the computation efficiency of pairwise camera fingerprint matching and incorporates group testing to make the search more effective. More specifically, we jointly leverage the individual strengths of composite fingerprints and fingerprint digests in a novel manner and design two methods that are superior to existing approaches. The results show that under very high-performance requirements, where the probability of correct identification is close to one with a false-positive rate of zero, the proposed search methods are 2-8 times faster than the state-of-art search methods.
Highly sensitive fluorescence detection on a biochip (2006)

A novel, generic lab-on-a-chip platform and associated readout instrumentation is presented. This high-sensitivity system has been developed for the efficient detection of surface-generated fluorescence in biomedical diagnostic applications. The proofof-principle polymer chip contains a 3×3 array of paraboloid elements designed to capture supercritical angle fluorescence (SAF) emitted from biorecognition zones on the top of each paraboloid. Each such element exhibits a fluorescence collection efficiency of 32%, comparable only to sophisticated microscope objectives of high numerical aperture. Furthermore, the chip optical design results in strict confinement of the fluorescence excitation to the surface. Consequently, this inexpensive chip combines the collecting power of modern microscopy optics with strong discrimination between surface and bulk fluorescence. The chip allows for simultaneous detection of 9 different targets (e.g. biomarkers) with very high sensitivity and also facilitates monitoring of receptor-ligand binding in real time. The chip is fabricated in the low fluorescence polymer Zeonor and is compatible with mass production via micro-injection moulding. The performance of the platform is demonstrated by application to a standard bioassay.
A Visual Analytics Approach to Understanding Spatiotemporal Hotspots (2009)

As data sources become larger and more complex, the ability to effectively explore and analyze patterns among varying sources becomes a critical bottleneck in analytic reasoning. Incoming data contain multiple variables, high signal-to-noise ratio, and a degree of uncertainty, all of which hinder exploration, hypothesis generation/exploration, and decision making. To facilitate the exploration of such data, advanced tool sets are needed that allow the user to interact with their data in a visual environment that provides direct analytic capability for finding data aberrations or hotspots. In this paper, we present a suite of tools designed to facilitate the exploration of spatiotemporal data sets. Our system allows users to search for hotspots in both space and time, combining linked views and interactive filtering to provide users with contextual information about their data and allow the user to develop and explore their hypotheses. Statistical data models and alert detection algorithms are provided to help draw user attention to critical areas. Demographic filtering can then be further applied as hypotheses generated become fine tuned. This paper demonstrates the use of such tools on multiple geospatiotemporal data sets.
Characteristics of Reflection of Resonators Using Lamb Wave on AT-Cut Quartz (2004)

Lamb waves propagating on an AT-cut quartz substrate were studied. In this study, we propose a high-frequency resonator using a Lamb wave. A Lamb wave is excited on an extremely thin AT-cut quartz substrate which thickness is comparable to the wavelength of an elastic wave propagating on a substrate. This Lamb wave propagates at a higher phase velocity mode than surface acoustic waves. This realizes an RF resonator operable in a high frequency range in which a conventional quartz resonator hardly operates. A theoretical analysis of the reflection coefficient of a Lamb wave with a grating reflector was conducted. The analysis results and experimental results are compared and discussed in this study. A reflection coefficient which is 10 to 20 times higher than that for a Rayleigh-type surface acoustic wave is obtained.
A Parasitic Layer-Based Reconfigurable Antenna Design by Multi-Objective Optimization (2012)

A parasitic layer-based multifunctional reconfigurable antenna (MRA) design based on multi-objective genetic algorithm optimization used in conjunction with full-wave EM analysis is presented. The MRA is capable of steering its beam into three different directions <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$(\theta_{i}=-30^{\circ},0^{\circ},30^{\circ})$</tex> </formula> simultaneously with polarization reconfigurability <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">$(P_{j}={\rm Linear},\ {\rm Circular})$</tex></formula> having six different modes of operation. The MRA consists of a driven microstrip-fed patch element and a reconfigurable parasitic layer, and is designed to be compatible with IEEE-802.11 WLAN standards (5–6 GHz range). The parasitic layer is placed on top of the driven patch. The upper surface of the parasitic layer has a grid of 5 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\times$</tex> </formula> 5 electrically small rectangular-shaped metallic pixels, i.e., reconfigurable parasitic pixel surface. The EM energy from the driven patch element couples to the reconfigurable parasitic pixel surface by mutual coupling. The adjacent pixels are connected/disconnected by means of switching, thereby changing the geometry of pixel surface, which in turn changes the current distribution over the parasitic layer, results in the desired mode of operation in beam direction and polarization. A prototype of the designed MRA has been fabricated on quartz substrate. The results from simulations and measurements agree well indicating <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">$\sim$</tex></formula> 8 dB gain in all modes of operation.
Histone Deacetylase Cytoplasmic Trapping by a Novel Fluorescent HDAC Inhibitor (2011)

Inhibitors of histone deacetylases (HDAC) are an important emerging class of drugs for the treatment of cancers. HDAC inhibitors are currently under evaluation in clinical trials as single agents and as sensitizers in combinations with chemotherapies and radiation therapy. Although these drugs have important effects on cancer cell growth and functions, the mechanisms underlying HDAC inhibitor activities remain to be fully defined. By using rational drug design, compound 2, a fluorescent class II HDAC targeting inhibitor, was synthesized and observed to accumulate in the cytoplasmic compartments of treated cells, but not in the nuclei. Furthermore, immunostaining of inhibitor exposed cells for HDAC4 showed accumulation of this enzyme in the cytoplasmic compartment with concomitant increased acetylation of tubulin and nuclear histones. These observations support a mechanism by which nuclear histone acetylation is increased as a result of HDAC4 trapping and sequestration in the cytoplasm after binding to compound 2. The HDAC inhibitor offers potential as a novel theranostic agent, combining diagnostic and therapeutic properties in the same molecule.
Compact scanning laser ophthalmoscope with high-speed retinal tracker (2003)

The effectiveness of image stabilization with a retinal tracker in a multifunction, compact scanning laser ophthalmoscope (TSLO) was demonstrated in initial human subject tests. The retinal tracking system uses a co confocal reflectometer with a closed-loop optical servo system to lock onto features in the fundus. The system is multifarious and modular to allow configuration for many research a clinical applications. Adult volunteers were tested without mydriasis to optimize the tracking instrumentation and to characterize imaging performance. The retinal tracking system achieves a bandwidth of greater than 1 kHz, which permits tracking at rates that greatly exceed the maximum rate of motion of the human eye. The TSLO system stabilized images to an accuracy of 0.05 deg in all test subjects during ordinary saccades with a velocity up to approximately 500 deg/s. Feature lock was maintained for minutes despite subject eye blinking. Even when nearly 1000 frames were coadded, image blur was minimal. Successful frame coaddition allowed image acquisition with decreased noise in low-light applications. The retinal tracking system significantly enhances the imaging capabilities of the scanning laser ophthalmoscope.
Roles for aluminium indium nitride insertion layers in fabrication of GaN‐based microcavities (2005)

Abstract AlInN alloys achieve an in‐plane lattice match to hexagonal GaN at an indium nitride mole fraction of ∼18%. Meanwhile Al 0.82 In 0.18 N displays a refractive index contrast of ∼7% with GaN at visible wavelengths. We illustrate the use of Al 0.82 In 0.18 N insertion layers to control layer thicknesses during homoepitaxial growth of GaN‐based microcavities, using in situ optical reflectometry. The structures discussed are 3 λ /2 microcavities incorporating distributed InGaN quantum wells tailored for emission at ∼400 nm. As‐grown samples have been characterised by techniques including cathodoluminescence spectroscopy. In addition to their role in growth monitoring, there are several post‐growth processing steps in which Al 0.82 In 0.18 N insertion layers can assist microcavity fabrication. We focus here on a demonstration of the ∼1:5 etch rate selectivity obtainable between Al 0.82 In 0.18 N and GaN in reactive ion etching. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Fast OLAP query execution in main memory on large data in a cluster (2013)

Main memory column-stores have proven to be efficient for processing analytical queries. Still, there has been little work in the context of clusters. Using only a single machine poses several restrictions: Processing power and data volume are bounded to the number of cores and main memory fitting on one tightly coupled system. To enable the processing of larger data sets, switching to a cluster becomes necessary. In this work, we explore techniques for efficient execution of analytical SQL queries on large amounts of data in a parallel database cluster while making maximal use of the available hardware. This includes precompiled query plans for efficient CPU utilization, full parallelization on single nodes and across the cluster, and efficient inter-node communication. We implement all features in a prototype for running a subset of TPC-H benchmark queries. We evaluate our implementation in a 128 node cluster running TPC-H queries with 30000 gigabyte of uncompressed data. Currently, there are no official cluster results for more than 10000 gigabyte of data, where we achieve up to one to two orders of magnitudes better performance than the current record holder.
A facile route for fabricating graphene nanoribbon array transistors using graphoepitaxy of a symmetric block copolymer (2015)

We report a facile route to form densely packed graphene nanoribbon (GNR) arrays <i>via</i> graphoepitaxial assembly of symmetric P(S-b-MMA). Since guiding channels for graphoepitaxy are the source and drain electrodes in field effect transistor (FET) geometry, we avoid laborious nanopatterning and FET device fabrication processes. By grafting a random copolymer brush on the graphene FET device, perpendicular lamellar domains are aligned normal to the electrode direction, resulting in line arrays connecting the two electrodes. Through optimization of the reactive ion etching conditions, the vertically oriented lamellar domains were transferred to the underlying graphene, leading to GNR arrays that act as conducting channels. This is a simple and efficient fabrication process using the fundamental concepts developed for the graphoepitaxial assembly of symmetric BCPs to create densely packed sub- 20 nm GNR arrays, compared to conventional fabrication process.
Enhancing Spin-Orbit Torque by Strong Interfacial Scattering From Ultrathin Insertion Layers (2019)

Spin-orbit torques (SOTs) show promise in efficiently driving magnetic memory, logic, and oscillators. However, low-resistivity spin Hall metals (including Pt, which has the highest intrinsic spin Hall conductivity yet known) are usually inefficient in generating SOTs. The authors demonstrate that enhancing interfacial scattering by inserting ultrathin layers within a spin Hall metal with intrinsic or side-jump mechanisms can significantly enhance the spin Hall ratio and dampinglike SOT efficiency. Inserting submonolayer Hf into Pt doubles the intrinsic spin Hall effect, and yields a very low critical switching current of 73 $\ensuremath{\mu}$A in memory devices.
Innovative peritoneal dialysis: flow-thru and dialysate regeneration. (1999)

As the peritoneal dialysis (PD) patient's residual renal function declines, the dialysis dose must be increased. However, the options for increasing the dose are limited to increasing the number of exchanges and/or the volume of each exchange. A review of the literature indicates that the dialysis dose can be significantly increased by flow-through PD, wherein the dialysate flows continuously into the peritoneal cavity through one catheter and out another and/or by regenerating the spent dialysate, thereby, significantly increasing the dialysate flow rate. Flow-thru PD has been used with and without dialysate regeneration. Regeneration has been used with standard inflow/outflow PD. In nearly all cases, substantially increased clearances over standard PD were obtained with reported urea and creatinine clearances as high as 58 and 48 ml/min, respectively. Applying flow-thru to the PD patient would require two catheters or a dual lumen catheter, and to obtain optimum clearances, the dialysate should be pumped through the peritoneal cavity at a high flow rate. Regenerating the dialysate allows high dialysate flow rates while reducing the total amount of dialysate required. For the continuous ambulatory peritoneal dialysis (CAPD) patient, the unit would have to be wearable; whereas for the patient on automated PD, flow-thru and/or regeneration PD could be incorporated into the equipment. With sorbent regeneration, the protein in the spent PD could be purified and returned to the patient thereby minimizing protein loss, increasing ultrafiltration, and enhancing the removal of protein-bound metabolic toxins.
Application of digital imaging in tooth whitening randomized controlled trials. (2007)

In the in vitro study, shade tab yellowness (b*) ranged from 9.0-18.6, lightness (L*) ranged from 63.4-76.2, and redness (a*) ranged from 0.9-3.6. Overall daily means differed by 0.08 units or less, and intra-class correlations for the image pairs were 0.998 for L*, 0.996 for a* and 0.998 for b*. In the in vivo assessment, the 14 volunteers exhibited considerable range in tooth color. Yellowness (b*) ranged from 13.5-21.3, lightness (L*) ranged from 69.2-78.0, and redness (a*) ranged from 5.2-8.8. Clinical measurement of mean tooth color from digital images was highly reproducible across visits. Intra-class correlations for the image pairs were 0.989 for b*, 0.970 for L* and 0.979 for a*.
Optimal Verification of Operations on Dynamic Sets. (2010)

We study the design of protocols for set-operation verification, namely the problem of cryptographically checking the correctness of outsourced set operations performed by an untrusted server over a dynamic collection of sets that are owned (and updated) by a trusted source. We present new authenticated data structures that allow any entity to publicly verify a proof attesting the correctness of primitive set operations such as intersection, union, subset and set difference. Based on a novel extension of the security properties of bilinear-map accumulators as well as on a primitive called accumulation tree, our protocols achieve optimal verification and proof complexity (i.e., only proportional to the size of the query parameters and the answer), as well as optimal update complexity (i.e., constant), while incurring no extra asymptotic space overhead. The proof construction is also efficient, adding a logarithmic overhead to the computation of the answer of a set-operation query. In contrast, existing schemes entail high com-munication and verification costs or high storage costs. Applications of interest include efficient verification of keyword search and database queries. The security of our protocols is based on the bilinear q-strong Diffie-Hellman assumption.
Measurement of Central Aortic Pulse Pressure: Noninvasive Brachial Cuff-Based Estimation by a Transfer Function Vs. a Novel Pulse Wave Analysis Method (2012)

Large random and systematic errors are introduced into the PP-C estimates when PP-C is calculated as the difference between the estimated central SBP and central or cuff DBP. The accuracy can be improved substantially with the novel PWA approach.