gebhart/patrepeval huggingface dataset:
Efficient data-driven encoding of scene motion using Eccentricity (2021)

This paper presents a novel approach of representing dynamic visual scenes with static maps generated from video/image streams. Such representation allows easy visual assessment of motion in dynamic environments. These maps are 2D matrices calculated recursively, in a pixel-wise manner, that is based on the recently introduced concept of Eccentricity data analysis. Eccentricity works as a metric of a discrepancy between a particular pixel of an image and its normality model, calculated in terms of mean and variance of past readings of the same spatial region of the image. While Eccentricity maps carry temporal information about the scene, actual images do not need to be stored nor processed in batches. Rather, all the calculations are done recursively, based on a small amount of statistical information stored in memory, thus resulting in a very computationally efficient (processor- and memory-wise) method. The list of potential applications includes video-based activity recognition, intent recognition, object tracking, video description, and so on.
Majority logic synthesis (2018)

The majority function <tex>$\langle xyz\rangle$</tex> evaluates to true, if at least two of its Boolean inputs evaluate to true. The majority function has frequently been studied as a central primitive in logic synthesis applications for many decades. Knuth refers to the majority function in the last volume of his seminal The Art of Computer Programming as “probably the most important ternary operation in the entire universe.” Majority logic sythesis has recently regained signficant interest in the design automation community due to nanoemerging technologies which operate based on the majority function. In addition, majority logic synthesis has successfully been employed in CMOS-based applications such as standard cell or FPGA mapping. This tutorial gives a broad introduction into the field of majority logic synthesis. It will review fundamental results and describe recent contributions from theory, practice, and applications.
An algorithmic enquiry concerning causality (2010)

In many domains we face the problem of determining the underlying causal structure from time-course observations of a system. Whether we have neural spike trains in neuroscience, gene expression levels in systems biology, or stock price movements in finance, we want to determine why these systems behave the way they do. For this purpose we must assess which of the myriad possible causes are significant while aiming to do so with a feasible computational complexity. At the same time, there has been much work in philosophy on what it means for something to be a cause, but comparatively little attention has been paid to how we can identify these causes. Algorithmic approaches from computer science have provided the first steps in this direction, but fail to capture the complex, probabilistic and temporal nature of the relationships we seek.
This dissertation presents a novel approach to the inference of general (type-level) and singular (token-level) causes. The approach combines philosophical notions of causality with algorithmic approaches built on model checking and statistical techniques for false discovery rate control. By using a probabilistic computation tree logic to describe both cause and effect, we allow for complex relationships and explicit description of the time between cause and effect as well as the probability of this relationship being observed (e.g. “a and b until c, causing d in 10–20 time units”). Using these causal formulas and their associated probabilities, we develop a novel measure for the significance of a cause for its effect, thus allowing discovery of those that are statistically interesting, determined using the concepts of multiple hypothesis testing and false discovery control. We develop algorithms for testing these properties in time-series observations and for relating the inferred general relationships to token-level events (described as sequences of observations). Finally, we illustrate these ideas with example data from both neuroscience and finance, comparing the results to those found with other inference methods. The results demonstrate that our approach achieves superior control of false discovery rates, due to its ability to appropriately represent and infer temporal information.
Silkworm silk-based materials and devices generated using bio-nanotechnology (2018)

Silks are natural fibrous protein polymers that are spun by silkworms and spiders. Among silk variants, there has been increasing interest devoted to the silkworm silk of B. mori, due to its availability in large quantities along with its unique material properties. Silk fibroin can be extracted from the cocoons of the B. mori silkworm and combined synergistically with other biomaterials to form biopolymer composites. With the development of recombinant DNA technology, silks can also be rationally designed and synthesized via genetic control. Silk proteins can be processed in aqueous environments into various material formats including films, sponges, electrospun mats and hydrogels. The versatility and sustainability of silk-based materials provides an impressive toolbox for tailoring materials to meet specific applications via eco-friendly approaches. Historically, silkworm silk has been used by the textile industry for thousands of years due to its excellent physical properties, such as lightweight, high mechanical strength, flexibility, and luster. Recently, due to these properties, along with its biocompatibility, biodegradability and non-immunogenicity, silkworm silk has become a candidate for biomedical utility. Further, the FDA has approved silk medical devices for sutures and as a support structure during reconstructive surgery. With increasing needs for implantable and degradable devices, silkworm silk has attracted interest for electronics, photonics for implantable yet degradable medical devices, along with a broader range of utility in different device applications. This Tutorial review summarizes and highlights recent advances in the use of silk-based materials in bio-nanotechnology, with a focus on the fabrication and functionalization methods for in vitro and in vivo applications in the field of tissue engineering, degradable devices and controlled release systems.
Physical Origins of Codon Positions That Strongly Influence Cotranslational Folding: A Framework for Controlling Nascent-Protein Folding (2015)

An emerging paradigm in the field of in vivo protein biophysics is that nascent-protein behavior is a type of nonequilibrium phenomenon, where translation-elongation kinetics can be more important in determining nascent-protein behavior than the thermodynamic properties of the protein. Synonymous codon substitutions, which change the translation rate at select codon positions along a transcript, have been shown to alter cotranslational protein folding, suggesting that evolution may have shaped synonymous codon usage in the genomes of organisms in part to increase the amount of folded and functional nascent protein. Here, we develop a Monte Carlo-master-equation method that allows for the control of nascent-chain folding during translation through the rational design of mRNA sequences to guide the cotranslational folding process. We test this framework using coarse-grained molecular dynamics simulations and find it provides optimal mRNA sequences to control the simulated, cotranslational folding of a protein in a user-prescribed manner. With this approach we discover that some codon positions in a transcript can have a much greater impact on nascent-protein folding than others because they tend to be positions where the nascent chain populates states that are far from equilibrium, as well as being dependent on a complex ratio of time scales. As a consequence, different cotranslational profiles of the same protein can have different critical codon positions and different numbers of synonymous mRNA sequences that encode for them. These findings explain that there is a fundamental connection between the nonequilibrium nature of cotranslational processes, nascent-protein behavior, and synonymous codon usage.
Development of squaraine dyes for photodynamic therapeutical applications: synthesis and study of electronic factors in the dye formation reaction (2007)

With a view to developing sensitizers for applications in photodynamic therapy (PDT), a series of quinaldine based squaraine dyes have been synthesized and the role of electronic factors in the dye formation have been investigated through absorption spectroscopy, product analysis and theoretical calculations. It has been observed that semisquaraine intermediates were formed as the sole products in the reaction of quinaldinium salts containing electron-donating substituents with squaric acid. However, with salts possessing electronegative and electron-withdrawing groups, the squaraine dyes were isolated in quantitative yields. The semisquaraine intermediates that have been isolated as the butyl adducts, could be converted to the squaraine dyes by reacting with the quinaldinium salts having electronegative and / or electron-withdrawing groups. These dyes exhibit absorption in the range 700-800 nm with significant molar extinction coefficients ( = 1-3 x 10 5 M -1 cm -1 ) and hence can have potential PDT applications.
Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity (2019)

Infections are a serious health concern worldwide, particularly in vulnerable populations such as the immunocompromised, elderly, and young. Advances in metagenomic sequencing availability, speed, and decreased cost offer the opportunity to supplement or even replace culture-based identification of pathogens with DNA sequence-based diagnostics. Adopting metagenomic analysis for clinical use requires that all aspects of the workflow are optimized and tested, including data analysis and computational time and resources. We tested the accuracy, sensitivity, and resource requirements of three top metagenomic taxonomic classifiers that use fast k-mer based algorithms: Centrifuge, CLARK, and KrakenUniq. Binary mixtures of bacteria showed all three reliably identified organisms down to 1% relative abundance, while only the relative abundance estimates of Centrifuge and CLARK were accurate. All three classifiers identified the organisms present in their default databases from a mock bacterial community of 20 organisms, but only Centrifuge had no false positives. In addition, Centrifuge required far less computational resources and time for analysis. Centrifuge analysis of metagenomes obtained from samples of VAP, infected DFUs, and FN showed Centrifuge identified pathogenic bacteria and one virus that were corroborated by culture or a clinical PCR assay. Importantly, in both diabetic foot ulcer patients, metagenomic sequencing identified pathogens 4-6 weeks before culture. Finally, we show that Centrifuge results were minimally affected by elimination of time-consuming read quality control and host screening steps.
Development of Recording Stacks for a Rewritable Dual-Layer Optical Disc (2002)

In this paper results are presented on the development of recording layers for a rewritable dual-layer phase-change optical disc. The disc is based on the digital video recording (DVR) system utilising a blue laser and a high numerical-aperture objective lens. With such a disc the capacity of the DVR system could be increased to about 45 GB. Various stack designs, write strategies and recording characteristics of the media are discussed. For each recording layer a design with a fairly good performance is found.
Robust interpretation in dialogue by combining confidence scores with contextual features (2006)

We present an approach to dialogue management and interpretation that evaluates and selects amongst candidate dialogue moves based on features at multiple levels. Multiple interpretation methods can be combined, multiple speech recognition and parsing hypotheses tested, and multiple candidate dialogue moves considered to choose the highest scoring hypothesis overall. We integrate hypotheses generated from shallow slot-filling methods and from relatively deep parsing, using pragmatic information. We show that this gives more robust performance than using either approach alone, allowing n-best list reordering to correct errors in speech recognition or parsing. Index Terms: dialogue management, robust interpretation
Five new cytotoxic T cell epitopes identified within Epstein-Barr virus nuclear antigen 3 (1994)

Epstein-Barr virus (EBV) CD8+ cytotoxic T lymphocyte (CTL) epitopes are currently being considered for inclusion into subunit vaccines. Here we describe the characterization of five new CTL epitopes within EBV nuclear antigen 3 (EBNA3), confirming EBNA3 as a major target for CTL recognition.
The effect of patterned susceptor on the thickness uniformity of rapid thermal oxides (1999)

A temperature compensation concept suitable for rapid thermal processing (RTP) with a nonuniform wafer temperature distribution is proposed in this work. Concentric Si rings with different diameters are placed on planar quartz or Si susceptors and are regarded as patterned susceptors for temperature compensation. We put monitor wafers on the patterned susceptor and see the effect of the patterned susceptor on the oxide thickness uniformity of the monitor wafers. The Si rings work as radiation barriers when placed on the quartz susceptor, but as heat conduction media when placed on the Si susceptor. By properly arranging the Si rings on the planar susceptors, the monitor wafers' oxide thickness uniformity can be improved.
Real-Time Onboard Global Nonlinear Aerodynamic Modeling from Flight Data (2016)

Flight test and modeling techniques were developed to accurately identify global nonlinear aerodynamic models onboard an aircraft. The techniques were developed and demonstrated during piloted flight testing of an Aermacchi MB-326M Impala jet aircraft. Advanced piloting techniques and nonlinear modeling techniques based on fuzzy logic and multivariate orthogonal function methods were implemented with efficient onboard calculations and flight operations to achieve real-time maneuver monitoring and analysis, and near-real-time global nonlinear aerodynamic modeling and prediction validation testing in flight. Results demonstrated that global nonlinear aerodynamic models for a large portion of the flight envelope were identified rapidly and accurately using piloted flight test maneuvers during a single flight, with the final identified and validated models available before the aircraft landed.
Effects of systematic phase errors on phase only correlation (1994)

The performance of phase-only optical correlators is usually reduced if the filter-plane phase differs from that prescribed for the classical matched filter. Current spatial light modulators, which frequently produce less than 2π phase modulation, and interface circuits, which quantize or incorrectly amplify signals placed on the spatial light modulator, both can produce systematic phase errors. We examine these effects using a model of correlation-peak amplitude as a function of phase error. The correlation peak is reasonably approximated as the product of an average of unity-amplitude error phasors multiplied by the average amplitude across the filter plane. The trends predicted by this new model compare favorably with computer simulations that use gray-scale images.
Embedded Microjets for Thermal Management of High Power-Density Electronic Devices (2018)

With current trends toward increased power in smaller devices and packages, the search continues for high-performance thermal management solutions for MOSFETs, high-electron mobility transistors, and other power electronics. Microjet impingement cooling has been shown to produce high heat transfer capabilities for electronics cooling. In this paper, microjets based on well-studied geometries were embedded within the substrate of a heat-producing device, removing several layers of thermal resistance typically found in advanced packages. In contrast with competing liquid cooling solutions that use expensive materials and processes, industry-standard silicon microfabrication techniques were used to build a low-cost microjet cooler. Numerical analysis of the embedded microjet device showed average heat transfer coefficients greater than 250 kW/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> · K and low peak temperature rises in high power-density devices. Using an innovative micro-Raman thermography technique, experimental measurements with a 1-μm spatial resolution were taken, supporting the numerically predicted heat transfer coefficients on a device with a heat flux of over 5 kW/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and a temperature rise of 46 °C. As devices continue to become miniaturized, both low-cost embedded microjet cooling technology and micro-Raman thermography may play a vital role in the design, operation and evaluation of advanced high power-density electronics.
Self‐calibrated interpolation of non‐Cartesian data with GRAPPA in parallel imaging (2019)

The proposed SING reconstruction enables significant improvement of acquisition efficiency for calibration data, while matching the reconstruction performance of TT-GRAPPA.
The <i>Pseudomonas syringae</i> Hrp pathogenicity island has a tripartite mosaic structure composed of a cluster of type III secretion genes bounded by exchangeable effector and conserved effector loci that contribute to parasitic fitness and pathogenicity in plants (2000)

The plant pathogenic bacterium Pseudomonas syringae is divided into pathovars differing in host specificity, with P. syringae pv. syringae (Psy) and P. syringae pv. tomato (Pto) representing particularly divergent pathovars. P. syringae hrp/hrc genes encode a type III protein secretion system that appears to translocate Avr and Hop effector proteins into plant cells. DNA sequence analysis of the hrp/hrc regions in Psy 61, Psy B728a, and Pto DC3000 has revealed a Hrp pathogenicity island (Pai) with a tripartite mosaic structure. The hrp/hrc gene cluster is conserved in all three strains and is flanked by a unique exchangeable effector locus (EEL) and a conserved effector locus (CEL). The EELs begin 3 nt downstream of the stop codon of hrpK and end, after 2.5-7.3 kb of dissimilar intervening DNA with tRNA(Leu)-queA-tgt sequences that are also found in Pseudomonas aeruginosa but without linkage to any Hrp Pai sequences. The EELs encode diverse putative effectors, including HopPsyA (HrmA) in Psy 61 and proteins similar to AvrPphE and the AvrB/AvrC/AvrPphC and AvrBsT/AvrRxv/YopJ protein families in Psy B728a. The EELs also contain mobile genetic element sequences and have a G + C content significantly lower than the rest of the Hrp Pai or the P. syringae genome. The CEL carries at least seven ORFs that are conserved between Psy B728a and Pto DC3000. Deletion of the Pto DC3000 EEL slightly reduces bacterial growth in tomato, whereas deletion of a large portion of the CEL strongly reduces growth and abolishes pathogenicity in tomato.
On Practical Inter-Carrier Interference Cancellation Techniques (2011)

For Orthogonal Frequency Division Multiplex (OFDM)-based wireless communication systems, mobile receivers could suffer significant performance degradation due to intercarrier interference (ICI). ICI cancellation becomes necessary to achieve good detection. We proposed a novel iterative decision-directed ICI cancellation technique (IDDICI) and its low-complexity implementation (LC-IDDICI), and showed its performance by simulation. In this paper, we first present a theoretical analysis to obtain the achievable performance of an OFDM receiver using IDDICI. Next, we show analytically that the "sub-optimal" LC-IDDICI actually provides better ICI cancellation than the original IDDICI. Finally, the LC-IDDICI is compared to two other published ICI cancellation techniques, which are also standard conformable. The comparison shows that the LC-IDDICI requires the lowest complexity while providing comparable performance.
An atmospheric pressure glow discharge optical emission source for the direct sampling of liquid media (2001)

A liquid sampling–atmospheric pressure glow discharge (LS-APGD) optical emission spectroscopy source is described. This device utilizes an electrolytic solution containing the analyte specimen as one of the discharge electrodes. The passage of an electrical current (either electrons or positive ions) across the solution/gas phase interface causes local heating and the volatilization of the analyte species. Collisions in the negative glow region of the plasma result in optical emission, which is characteristic of the analyte elements. Operation of this device with the analyte solution acting as either the cathode or anode is demonstrated. Typical discharge conditions include currents of 80 mA, potentials of up to 1000 V, with the i-V characteristics exhibiting ‘abnormal’ glow discharge behavior. The analyte-containing electrolyte solution is not limited to hydronium ions, as other salts (e.g., Li+ and Na+) also provide sufficient conductivity to sustain the discharge. Spatial maps of analyte emission and spectral background provide insights into the basic operation mechanism of the discharge. The use of a coaxial gas flow around the stainless-steel capillary outlet permits stable plasma operation at low liquid flow rates (0.1–0.3 mL min−1) where pulsation present in the liquid delivery system makes the discharge itself quite unstable. Analytical response curves for Hg, Mg, Na and Pb are demonstrated to have good linearity, with preliminary limits of detection determined to be in the range of 1.1–2.0 ppm (≈10 ng) for 5 µL sample volumes.
Feasibility studies for the Sonic Sensor System for noninvasive temperature measurement in the food processing industry (1991)

Feasibility studies for development of the Sonic Sensor System to measure temperature in the interior of particulates during food processing are described. The method involves tomography-based acquisition and interpretation of speed of sound data. The method is found to be feasible, and representative engineering problems and other technical issues are identified. A two-step approach to concept commercialization, involving replacement of the present puncture-and-thermometer method is conventional batch processing and development of a device to use in continuous aseptic processing, is proposed. A conservative estimate of immediate energy savings, just for food processing, is 0.01 quad/y. Potential follow-on applications are discussed.