gebhart/patrepeval huggingface dataset:
Aberration control by high NA focusing in transparent media (2017)

High numerical aperture (NA) focusing of light in transparent media is important in microscopy, various techniques of optical data storage and laser microprocessing. By high NA focusing through a flat bounding surface of a medium there appears positive spherical aberration reducing light energy concentration and lowering physical resolution. The deeper is focusing and higher NA, the stronger is aberration and light scattering. By laser material processing the spherical aberration results in uncontrolled energy distribution along optical axis that makes inherently complex physical processes of laser radiation interaction with material even more complex and less predictable. To control the spherical aberration induced by internal high NA focusing it is suggested to apply specially designed aplanatic objective of patent pending optical design. The objective provides full compensation of spherical aberration for diffraction limited on-axis and off-axis high NA focusing at wide range of depths, for example from 0 to 2 mm in fused silica for NA0.8 without immersion. By setting movable components in optimum for particular depth reciprocal positions it is possible to provide not only full aberration compensation but also under- and over-compensation, thus providing control of energy distribution along optical axis at arbitrary depth and achieving special material processing effects. The paper describes design features of this optical approach as well as comparative results of spot size calculations and corresponding microphotographs of processed areas in fused silica by laser radiation focusing at various depths using NA0.8 objectives with and without compensation of aberrations.
Single-shot ptychography (2015)

Ptychography is a particularly powerful coherent diffraction imaging technique. In ptychography, a localized beam that illuminates the object is scanned in a step-wise fashion, resulting in an array of partially overlapping probing spots on the object. The intensity diffraction pattern from each spot is recorded separately. Then, a complex-valued image is computationally constructed from the set of measured diffraction patterns. Ptychography is based on scanning, hence it results with a long overall acquisition time, in the order of a second or more. Also, the scanning limited resolution, vibration stability, drift, and dynamic range weaken the performances of ptychographic microscopes. We propose and analyze single-shot ptychography, where tens or hundreds of quasi-localized, partially overlapping beams illuminate the object simultaneously. Various schemes for single-shot ptychography, in both the transmission and reflection modes, with coherent and partially coherent illumination and for single-shot Fourier ptychography are proposed. Experimentally, we demonstrate single-shot ptychography with a 180 ms exposure time (limited by the CCD minimal acquisition time) using a sub-milliwatt diode laser that simultaneously illuminates the object with 49 partially overlapping beams. Single-shot ptychography, which combines the celebrated power of ptychography with (ultra)fast imaging, will surely open up new opportunities in microscopy.
An Iterative Approach to Locating Simple Devices in an Ad-hoc Network (2002)

This paper considers the problems associated with location determination in wireless ad-hoc networks. It presents a simple algorithm allowing a distributed set of devices to independently determine their location given only the distances between themselves and neighbouring devices if some devices in the network (location aware devices) have external location information (such as GPS or being at a known fixed location). The algorithm allows each device to make a guess of location that it then communicates to all neighbouring devices. Depending on the information received from neighbours each device may then modify its guess. In this way, over time, the network as a whole is able to identify a set of positions that satisfies all the available distance data. The algorithm is shown to be resistant to errors in measuring the distances between devices.
CCF: Fast and scalable connected component computation in MapReduce (2014)

Finding connected components in a graph is a well-known problem in a wide variety of application areas such as social network analysis, data mining, image processing, and etc. In this paper, we present an efficient and scalable approach in MapReduce to find all the connected components in a given graph. We compare our approach with the state-of-the-art on a real-world graph. We also demonstrate the viability of our approach on a massive graph with ~6B nodes and ~92B edges on an 80-node hadoop cluster. To the best of our knowledge, this is the largest graph publicly used in such an experiment.
Automated inverse optimization facilitates lower doses to normal tissue in pancreatic stereotactic body radiotherapy (2018)

Automated inverse optimization holds great potential for personalization and tailoring of radiotherapy to particular patient anatomies. It can be utilized for normal tissue sparing or for an isotoxic dose escalation.
A Real-Time Energy-Optimal Trajectory Generation Method for a Servomotor System (2014)

This paper considers real-time energy-optimal trajectory generation for a servomotor system that performs a single-axis point-to-point positioning task for a fixed time interval. The servomotor system is subject to acceleration and speed constraints. The trajectory generation is formulated as a linear-constrained optimal control problem (LCOCP), and the Pontryagin's maximum principle is applied to derive necessary optimality conditions. Instead of solving multipoint boundary value problems directly, this paper proposes a novel real-time algorithm based on two realizations: solving the LCOCP is equivalent to determining an optimal time interval of the speed-constrained arc and solving a specific acceleration-constrained optimal control problem (ACOCP), and solving an ACOCP is equivalent to determining optimal switch times of acceleration-constrained arcs and solving a specific two-point boundary value problem (TBVP). The proposed algorithm constructs sequences of time intervals, ACOCPs, switch times, and TBVPs, such that all sequences converge to their counterparts of an optimal solution of the LCOCP. Numerical simulation verifies that the proposed algorithm is capable of generating energy-optimal trajectories in real time. Experiments validate that the use of energy-optimal trajectories as references in a servomotor system does not compromise tracking performance but leads to considerable less energy consumption.
Isolation and Characterization of Two Cryptic Plasmids in the Ammonia-Oxidizing Bacterium <i>Nitrosomonas</i> sp. Strain ENI-11 (1999)

Two plasmids were discovered in the ammonia-oxidizing bacterium Nitrosomonas sp. strain ENI-11, which was isolated from activated sludge. The plasmids, designated pAYS and pAYL, were relatively small, being approximately 1.9 kb long. They were cryptic plasmids, having no detectable plasmid-linked antibiotic resistance or heavy metal resistance markers. The complete nucleotide sequences of pAYS and pAYL were determined, and their physical maps were constructed. There existed two major open reading frames, ORF1 in pAYS and ORF2 in pAYL, each of which was more than 500 bp long. The predicted product of ORF2 was 28% identical to part of the replication protein of a Bacillus plasmid, pBAA1. However, no significant similarity to any known protein sequences was detected with the predicted product of ORF1. pAYS and pAYL had a highly homologous region, designated HHR, of 262 bp. The overall identity was 98% between the two nucleotide sequences. Interestingly, HHR-homologous sequences were also detected in the genomes of ENI-11 and the plasmidless strain Nitrosomonas europaea IFO14298. Deletion analysis of pAYS and pAYL indicated that HHR, together with either ORF1 or ORF2, was essential for plasmid maintenance in ENI-11. To our knowledge, pAYS and pAYL are the first plasmids found in the ammonia-oxidizing autotrophic bacteria.
Nanoscale patterning in high resolution HSQ photoresist by interferometric lithography with tabletop extreme ultraviolet lasers (2007)

Arrays of nanodots and nanoholes were patterned with a highly coherent tabletop 46.9nm laser on high resolution hydrogen silsesquioxane photoresist using multiple exposure interferometric lithography. The authors observed for λ=46.9nm radiation a penetration depth in excess of 150nm. This laser-based extreme ultraviolet interferometric setup allows printing of 0.5×0.5mm2 areas with different nanoscale patterns using a compact tabletop system and exposure times of tens of seconds.
Modeling the mechanics of tissue-engineered human heart valve leaflets (2005)

Mathematical models can provide valuable information to assess and evaluate the mechanical behavior of tissue-engineered constructs. In this study, a structurally based model is applied to describe and analyze the mechanics of tissue-engineered human heart valve leaflets. The results from two orthogonal uniaxial tensile tests are used to determine the model parameters of the constructs after two, three and four weeks of culturing. Subsequently, finite element analyses are performed to simulate the mechanical response of the engineered leaflets to a pressure load. The stresses in the leaflets induced by the pressure load increase monotonically with culture time due to a decrease in the construct's thickness. The strains, on the other hand, eventually decrease as a result of an increase in the elastic modulus. Compared to native porcine leaflets, the mechanical response of the engineered tissues after four weeks of culturing is more linear, stiffer and less anisotropic. (c) 2006 Elsevier Ltd. All rights reserved.
Vector Doppler ultrasound for the detection of internal bleeding (2004)

A vector Doppler (VD) ultrasound system has four advantages over color-flow Doppler (CFD) in identifying internal bleeding: (1) measures instantaneous velocity more accurately, (2) measures flows perpendicular to the transmitter, (3) distinguishes between flows at different depths, and (4) detects the 3-D direction of the flow. A real-time vector Doppler system has been built and tested in vitro. The system consists of one focused transmitting/receiving transducer (10 mm diameter, 50 mm curvature, 5 MHz frequency) and four receiver transducers (5 mm diameter, flat discs, 5 MHz frequency). The signals are passed through analog filters and preamplifiers and then digitized at 20 MHz to obtain a Doppler signal. A digital signal processing algorithm is implemented to calculate flow direction from a combination of the five received signals as well as remove error from systematic phase shifts inherent in the instrumentation. The software was also designed to decrease the time it takes a user to locate arterial flow vessels. The system was tested using two flow phantoms: a moving string to verify accuracy and precision of the velocity, and cornstarch flowing through a tube to simulate blood flow. For both phantoms, device accuracy was tested over a range of angles and velocities.
Controlled-phase gate by dynamic coupling of photons to a two-level emitter (2022)

Abstract We propose an architecture for achieving high-fidelity deterministic quantum logic gates on dual-rail encoded photonic qubits by letting photons interact with a two-level emitter (TLE) inside an optical cavity. The photon wave packets that define the qubit are preserved after the interaction due to a quantum control process that actively loads and unloads the photons from the cavity and dynamically alters their effective coupling to the TLE. The controls rely on nonlinear wave mixing between cavity modes enhanced by strong externally modulated electromagnetic fields or on AC Stark shifts of the TLE transition energy. We numerically investigate the effect of imperfections in terms of loss and dephasing of the TLE as well as control field miscalibration. Our results suggest that III-V quantum dots in GaAs membranes is a promising platform for photonic quantum information processing.
Tunable High-Order Multi-Band Bandpass Filters Using Transversal Multi-Resonant Cells (2020)

This paper reports on the design of tunable high-order multi-band bandpass filters (BPFs). The proposed concept lays its foundations on series-cascaded multi-band stages, each of them shaped by two identical transversal multi-resonant cells. The transfer function characteristics of each band are tuned by a pair of resonators in each cell that control the center frequency, bandwidth (BW), and mode of operation—bandpass or all-reject—. The overall BPF exhibits a multi-band transfer function with 1-to-N bands that can be independently tuned in terms of frequency, BW, and number. The operating principles of this multi-passband filter concept are demonstrated through simulated examples of a quad-band BPF and the measurement of a tri-band microstrip prototype.
Fine structure of the human galactokinase GALK1 gene. (1996)

Defects in the human GALK1 gene result in galactokinase deficiency and cataract formation. We have isolated this gene and established its structural organization. The gene contains 8 exons and spans approximately 7.3 kb of genomic DNA. The GALK1 promoter was localized and found to have many features in common with other housekeeping genes, including high GC content, several copies of the binding site for the Sp1 transcription factor, and the absence of TATA-box and CCAAT-box motifs typically present in eukaryotic Pol II promoters. Analysis by 5'-RACE PCR indicates that the GALK1 mRNA is heterogeneous at the 5' terminus, with transcription sites occurring at many locations between 21 and 61 bp upstream of the ATG start site of the coding region. In vitro translation experiments of the GALK1 cDNA indicate that the protein is cytosolic and not associated with the endoplasmic reticulum membrane.
Determining Reservoir Connectivity in Producing Fields – Examples from Eastern Canada and the Gulf of Mexico (2007)

Maximizing recovery from oil and gas fields requires an understanding of the initial distribution of fluid contacts that may vary between segments of the field. It also requires an understanding of which geologic elements affect connections between wells as the field is produced. We have developed a technique, Reservoir Connectivity Analysis (RCA), for rigorously defining differences in fluid contact elevation and relating these contact differences to geologic elements with the goal of identifying pre-production, reservoir compartments. This technique has been applied to more than a dozen ExxonMobil fields in depositional environments ranging from aeolian to deepwater and in structures that range from simple folds to complexly folded and faulted structures. Some of these studies have led to successful predictions of contacts in previously undrilled compartments of mature fields. In other cases, we have found that as the field is produced these geologic features affect production by limiting drainage area and pressure support. In addition to geologic features that control contact elevation over geologic timescales, we have observed other features that may be transmissible over geologic time, but that affect connectivity as the field is produced.
An analysis of the effects of frequency crossing in the resonant scattering of thermal phonons (1975)

An analysis has been made of the change in thermal conductivity that occurs when the frequencies of two resonant phonon-scattering processes become equal, a situation which is termed a frequency crossing. The analysis is applicable when the effective width of the scattering processes is small compared with the spectral width of the thermal phonons. The frequency-crossing effect, which is an incoherent effect, is due to the non-linear relation between the strength of the scattering and the thermal conductivity, and can give rise to sharp changes in conductivity. Brief consideration is also given to analogous effects which are expected to occur in heat pulse work. A method is suggested for producing an amplitude-modulated component of narrow spectral width from a heat current, which might have application as a 'monochromatic' phonon source.
General data-path organization of a MAC unit for VLSI implementation of DSP processors (2002)

This paper describes the data-path and VLSI implementation of a 32/spl times/32 bit signed/unsigned multiply accumulate (MAC) unit. In this design we have solved the problem of dealing with signed and unsigned numbers simultaneously, using the modified Booth algorithm. This MAC unit can perform 32/spl times/32, 32/spl times/16, and two 16/spl times/16 multiplications, on signed/unsigned operands with a throughput of 2,1, and 1 cycle, respectively. The Booth encoding technique reduces the number of partial products (PP) by half. Further increase in speed is achieved by using the Three Dimensional reduction Method (TDM) to add the partial products. Special circuitry has been designed to accommodate sign/unsigned operands and to deal with sign extension. The modified Booth algorithm coupled with TDM and sign correction circuitry results in a multiplier, with a delay (partial product addition) equivalent to 6 XOR gates. The MAC unit has been modeled in VHDL, and it implements an algorithm which makes this data path organization fast and efficient in silicon.
The new wave: time to bring EEG to the emergency department (2011)

Emergency electroencephalography (EEG) is indicated in the diagnosis and management of non-convulsive status epilepticus (NCSE) underlying an alteration in the level of consciousness. NCSE is a frequent, treatable, and under-diagnosed entity that can result in neurological injury. This justifies the need for EEG availability in the emergency department (ED). There is now emerging evidence for the potential benefits of EEG monitoring in various acute conditions commonly encountered in the ED, including convulsive status after treatment, breakthrough seizures in chronic epilepsy patients who are otherwise controlled, acute head trauma, and pseudo seizures. However, attempts to allow for routine EEG monitoring in the ED face numerous obstacles. The main hurdles to an optimized use of EEG in the ED are lack of space, the high cost of EEG machines, difficulty of finding time, as well as the expertise needed to apply electrodes, use the machines, and interpret the recordings. We reviewed the necessity for EEGs in the ED, and to meet the need, we envision a product that is comprised of an inexpensive single-use kit used to wirelessly collect and send EEG data to a local and/or remote neurologist and obtain an interpretation for managing an ED patient.
Purification to Apparent Homogeneity and Properties of Pig Kidneyl-Fucose Kinase (1998)

L-Fucokinase was purified to apparent homogeneity from pig kidney cytosol. The molecular mass of the enzyme on a gel filtration column was 440 kDa, whereas on SDS gels a single protein band of 110 kDa was observed. This 110-kDa protein was labeled in a concentration-dependent manner by azido-[32P]ATP, and labeling was inhibited by cold ATP. The 110-kDa protein was subjected to endo-Lys-C digestion, and several peptides were sequenced. These showed very little similarity to other known protein sequences. The enzyme phosphorylated L-fucose using ATP to form beta-L-fucose-1-P. Of many sugars tested, the only other sugar phosphorylated by the purified enzyme was D-arabinose, at about 10% the rate of L-fucose. Many of the properties of the enzyme were determined and are described in this paper. This enzyme is part of a salvage pathway for reutilization of L-fucose and is also a valuable biochemical tool to prepare activated L-fucose derivatives for fucosylation reactions.
Temporal Similarity Analysis of Remote Photoplethysmography for Fast 3D Mask Face Presentation Attack Detection (2020)

To tackle the 3D mask face presentation attack, remote Photoplethysmography (rPPG), a biomedical technique that can detect heartbeat signal remotely, is employed as an intrinsic liveness cue. Although existing rPPG-based methods exhibit encouraging results, they require long observation time (10-12 seconds) to identify the heartbeat information, which limits their employment in real applications such as smartphone unlock and e-payment. To shorten the observation time (within 1-second) while keeping the performance, we propose a fast rPPG-based 3D mask presentation attack detection (PAD) method by analyzing the similarity of local facial rPPG signals in the time domain. In particular, a set of temporal similarity features of facial and background local rPPG signals are designed and fused to adapt the real world variations based on rPPG shape and phase properties. For better evaluation under practical variations, we build the HKBU-MARsV2+ dataset that includes 16 masks from 2 types and 6 lighting conditions. Finally, extensive experiments are conducted on 11092 shortterm video slots from 4 datasets with a large number of real- world variations, in terms of mask type, lighting condition, camera, resolution of face region, and compression setting. Results show that the proposed TSrPPG outperforms the state-of-the-art competitors dramatically on discriminabil- ity and generalizability. To our best knowledge, this is the first work that addresses the length of observation time issue of rPPG-based 3D mask PAD.
Multiplicity assignments for algebraic soft-decoding of reed-solomon codes (2003)

A soft-decision decoding algorithm for Reed- Solomon codes was recently proposed in (2). This algorithm converts probabilities observed at the channel output into algebraic interpolation conditions, specified in terms of a multiplicity matrix M. Koetter-Vardy (2) show that the probability of decoding failure is given by h{SM 5 A(M)}, where SM is a random variable and A(M) is a known func- tion of M. They then compute the multiplicity matrix M that maximizes the eqected value of SM. Here, we attempt to directly minimize the overall probability of decoding fail- ure PT{SM < A(M)}. First, we recast this optimization problem into a geometrical framework. Using this frame- work, we derive a simple modification to the KV algorithm which results in a provably better multiplicity assignment. Alternatively, we approximate the distribution of SM by a Gaussian distribution, and develop an iterative algorithm to minimize Pr{sM 5 A(M)} under this approximation. This leads to coding gains of about 0.20dB for RS codes of length 255 and up to 0.75dB for RS codes of length 15, as compared to the Koetter-Vardy algorithm.
Tackling the Provenance Challenge one layer at a time (2007)

Abstract VisTrails is a new workflow and provenance management system that provides support for scientific data exploration and visualization. Whereas workflows have been traditionally used to automate repetitive tasks, for applications that are exploratory in nature, change is the norm. VisTrails uses a new change‐based provenance mechanism, which was designed to handle rapidly evolving workflows. It uniformly and automatically captures provenance information for data products and for the evolution of the workflows used to generate these products. In this paper, we describe how the VisTrails provenance data are organized in layers and present a first approach for querying this data that we developed to tackle the Provenance Challenge queries. Copyright © 2007 John Wiley & Sons, Ltd.