gebhart/patrepeval huggingface dataset:
Machine Learning and Multiscale Methods in the Identification of Bivalve Larvae (2003)

This paper describes a novel application of support vec-tor machines and multiscale texture and color invariants to a problem in biological oceanography: the identifica-tion of 6 species of bivalve larvae. Our data consists of polarized color images of scallop and other bivalve larvae (between 2 and 17 days old) collected from the ocean by a shipboard optical imaging system of our design. Lar-vae of scallops, clams, and oysters are small (100 microns) with few distinguishing features when observed under stan-dard light microscopy. However, the use of polarized light with a full wave retardation plate produces a vivid color, bi-refringence pattern. The patterns display very subtle dif-ferences between species, often not discernable to human observers. We show that a soft-margin support vector ma-chine with Gaussian RBF kernel is a good discriminator on a feature set extracted from Gabor wavelet transforms and color distribution angles of each image. By constraining the Gabor center frequencies to be low, the resulting system can attain classification accuracy in excess of 90 % for ver-tically oriented images, and in excess of 80 % for randomly oriented images. 1
Design of a Compact Rat-inspired Waist Mechanism for a Biomimetic Robot (2018)

this paper, we designed a new bio-inspiredcompact waist mechanism for a robotic rat to allow a better imitation of rat movement. With the observation and analysis of animal movement recordings, we found that the dorsal spine of a rat played an important role in agile pitch and yaw movements. To mimic such agile movements, we designed a new waist mechanism inspired by the muscle-tendon actuation pattern of rat spine. The proposed mechanism consists of two sets of parallel placed linkages for driving pitch and yaw movement, respectively. Although actuated by only one DC motor, each set of the linkages was able to output $ 2-\mathrm {D}\mathrm {O}\Gamma $ movement. Consequently, the agile pitch and yaw movements were achieved in a compact space with this new rat-inspired mechanism. Compared with previously designed waist, the new one enables a wider range of movement. Remarkably, the volume and weight were decreased 50% and 67% respectively. Additionally, it similar to a rat's waist in terms of both dimension and actuation pattern.
Chemical Aerosol Flow Synthesis of Semiconductor Nanoparticles (2005)

Nanometer-sized semiconductor particles (quantum dots) have been the subject of intense research during the past decade owing to their novel electronic, catalytic, and optical properties. Fundamental properties of these nanoparticles (1-20 nm diameter) can be systematically changed simply by controlling the size of the crystals while holding their chemical composition constant. We describe here a new methodology for the continuous production of fluorescent CdS, CdSe, and CdTe nanoparticles using ultrasonically generated aerosols of high boiling point solvents. Each submicron droplet serves as a separate nanoscale chemical reactor, with reactions proceeding as the liquid droplets (which hold both reactants and surface stabilizers) are heated in a gas stream. The method is inexpensive, scalable, and allows for the synthesis of high quality nanocrystals. This chemical aerosol flow synthesis (CAFS) can be extended to the synthesis of nanostructured metals, oxides, and other materials.
Dynamic computing random access memory: A brain-inspired computing paradigm with memelements (2014)

We discuss the implementation of a novel approach to computing named memcomputing using memelements - in particular memcapacitive systems. It is shown that solid-state memcapacitive systems are ideal to implement such a concept since they support information processing and storage at the same physical location at low-energy cost. This feature can be used to perform boolean logic functions “on demand” directly in memory. In this paper, we develop the idea of a memcapacitive dynamic computing random access memory introducing a novel computing scheme based on Voltage Sense Amplifiers, and discussing some features of information storage in internal states of memcapacitive systems in the presence of leakage currents.
HUMAN NEUROGLOBIN FUNCTIONS AS A REDOX REGULATED NITRITE REDUCTASE (2011)

Neuroglobin (Ngb) is a highly conserved hemoprotein of uncertain physiological function that evolved from a common ancestor to hemoglobin and myoglobin. Ngb shows a six‐coordinate heme iron with proximal and distal histidines in the heme pocket directly bound to the heme iron however coordination of the sixth ligand is reversible. Deoxygenated human neuroglobin reacts with nitrite to form nitric oxide (NO). This reaction is regulated by redox sensitive surface thiols, cysteine 55 and 46, which regulate the open probability of heme pocket, nitrite binding and NO formation. Replacement of the distal histidine by leucine (H64L) leads to a stable five‐coordinated geometry; the Ngb H64L mutant reduces nitrite to NO approximately 2000‐times faster than the wild type, while mutation of either C55 or C46 to alanine stabilizes the six‐coordinate structure and slows the reaction. Using lentivirus expression systems we show that the nitrite‐reductase activity of Ngb inhibits cellular respiration via NO binding to cytochrome c oxidase and confirm that the six‐to‐five coordinate status of Ngb regulates intracellular hypoxic NO signaling pathways. These studies suggest that Ngb may function as a physiological oxidative stress sensor and a post‐translationally redox regulated nitrite reductase, that generates NO under six‐to‐five coordinate heme pocket control.
Novel wavelength-resonant optoelectronic structure and its application to surface-emitting semiconductor lasers (1988)

An optimised design for optoelectronic devices which depends on the interaction between an electromagnetic standing wave and the carrier population is described. The structure consists of quantum well layers spaced at one half the wavelength of a selected optical transition in quantum wells. This spatial periodicity allows the amplifying or absorbing medium (quantum wells) to coincide with the peaks of the standing wave optical field in the Fabry-Pérot cavity. In such a periodic medium, the gain or absorption for the selected wavelength is enhanced by a factor of two compared to a uniform medium. This concept was applied to fabricate a surface-emitting semiconductor laser in the GaAs/AlGaAs system. Lasing was achieved with the shortest gain medium length (320 nm) ever reported.
Piecewise Sliding-Mode Control for Sludge Bulking Under Multiple Operating Conditions (2022)

The phenomenon of sludge bulking, which can be classified as slight or serious abnormal operating conditions according to sludge volume index (SVI), is a widespread problem in wastewater treatment process. In this article, a piecewise sliding-mode control (PSMC) strategy is developed to overcome the adverse effects and furthermore improve the operating performance for wastewater treatment process under different operating conditions of sludge bulking. First, a soft sensing model of SVI based on fuzzy neural network is established. Then, it can online determine the state of sludge and whether sludge bulking has occurred. Second, in view of the specific operating condition of sludge, a piecewise sliding-mode controller is designed. Then, the sludge bulking can be eliminated by regulating the concentration of dissolved oxygen and nitrate nitrogen. Third, the boundary condition of PSMC is evaluated. Then, the stability of the control system is proved on the basis of ensuring the boundary condition of PSMC. Finally, the performance of PSMC is verified in the benchmark simulation platform. The results further demonstrate the effectiveness of the proposed control method.
An Adaptable, Portable Microarray Reader for Biodetection (2009)

We have developed an inexpensive portable microarray reader that can be applied to standard microscope slide-based arrays and other array formats printed on chemically modified surfaces. Measuring only 19 cm in length, the imaging device is portable and may be applicable to both triage and clinical settings. For multiplexing and adaptability purposes, it can be modified to work with multiple excitation/emission wavelengths. Our device is shown to be comparable to a commercial laser scanner when detecting both streptavidin-biotin and antibody interactions. This paper presents the development and characterization of a handheld microarray imager and directly compares it with a commercial scanner.
Screening of a<i>Planococcus</i>bacterium producing a cold‐adapted protease and its application in low‐salt fish sauce fermentation (2020)

A strain of bacteria isolated from a traditional fermented shrimp paste showed high protease activity at low-temperature (15°C). The strain was identified as Planococcus maritimus and named Planococcus maritimus XJ2. P. maritimus XJ2 grows well in a low-temperature, low-salt, and alkaline environment. The protease produced by P. maritimus XJ2 exhibited the highest enzyme activity at 40°C, pH 9.0 and showed salt tolerance. The amino acid nitrogen content of low-salt fish sauce inoculated with P. maritimus XJ2 was 1.28 ± 0.04 g/100 ml, which was significantly higher than that of the control without P. maritimus XJ2 (0.89 ± 0.02 g/100 ml, p < .01). The amounts of key desirable volatiles, such as alcohols, ketones, acids, esters, and pyrazine were higher in P. maritimus XJ2 than in the control (p < .05). P. maritimus XJ2 could be used as a starter culture for low-salt fish sauce incubated at 21°C. Practical applications The bacteria identified in this study has a good capacity to ferment the fish for good quality of fish sauce. A new method for the rapid fermentation of low-salt fish sauce and the improvement of its flavor by using Planococcus maritimus XJ2 is established. The procedure can help people to produce fish sauce in a shorter time, which will promote the development of fish sauce industry. Therefore, the starter and the method have good practical application in fish sauce produce.
Comparison of VRX CT scanners geometries (2001)

A technique called Variable-Resolution X-ray (VRX) detection greatly increases the spatial resolution in computed tomography (CT) and digital radiography (DR) as the field size decreases. The technique is based on a principle called `projective compression' that allows both the resolution element and the sampling distance of a CT detector to scale with the subject or field size. For very large (40 - 50 cm) field sizes, resolution exceeding 2 cy/mm is possible and for very small fields, microscopy is attainable with resolution exceeding 100 cy/mm. This paper compares the benefits obtainable with two different VRX detector geometries: the single-arm geometry and the dual-arm geometry. The analysis is based on Monte Carlo simulations and direct calculations. The results of this study indicate that the dual-arm system appears to have more advantages than the single-arm technique.
Joint order identification and estimation of the discrete relaxation spectrum for ground penetrating radars (2016)

This paper suggests a novel procedure to jointly identify the order of a GPR discrete relaxation spectrum and estimate its parameters (relaxation frequencies and their strengths). These quantities are important for interpreting the contents of the subsurface layers. The suggested method turns the estimator into a nonlinear control system that can convert an initial guess of the number and parameters of the relaxation modes into the correct one. Blindly identifying the number of relaxation modes and estimating their values and strengths is guaranteed if the number of assumed modes is higher than the number of actual modes. The procedure is hardware-friendly and exhibit high resistance to noise.
Enzymatic Neutralization of the Chemical Warfare Agent VX: Evolution of Phosphotriesterase for Phosphorothiolate Hydrolysis (2013)

The V-type nerve agents (VX and VR) are among the most toxic substances known. The high toxicity and environmental persistence of VX make the development of novel decontamination methods particularly important. The enzyme phosphotriesterase (PTE) is capable of hydrolyzing VX but with an enzymatic efficiency more than 5 orders of magnitude lower than with its best substrate, paraoxon. PTE has previously proven amenable to directed evolution for the improvement of catalytic activity against selected compounds through the manipulation of active-site residues. Here, a series of sequential two-site mutational libraries encompassing 12 active-site residues of PTE was created. The libraries were screened for catalytic activity against a new VX analogue, DEVX, which contains the same thiolate leaving group of VX coupled to a diethoxyphosphate core rather than the ethoxymethylphosphonate core of VX. The evolved catalytic activity with DEVX was enhanced 26-fold relative to wild-type PTE. Further improvements were facilitated by targeted error-prone PCR mutagenesis of loop-7, and additional PTE variants were identified with up to a 78-fold increase in the rate of DEVX hydrolysis. The best mutant hydrolyzed the racemic nerve agent VX with a value of kcat/Km = 7 × 10(4) M(-1) s(-1), a 230-fold improvement relative to wild-type PTE. The highest turnover number achieved by the mutants created for this investigation was 137 s(-1), an enhancement of 152-fold relative to wild-type PTE. The stereoselectivity for the hydrolysis of the two enantiomers of VX was relatively low. These engineered mutants of PTE are the best catalysts ever reported for the hydrolysis of nerve agent VX.
A Rapid Pathway Toward a Superb Gene Delivery System: Programming Structural and Functional Diversity into a Supramolecular Nanoparticle Library (2010)

Nanoparticles are regarded as promising transfection reagents for effective and safe delivery of nucleic acids into a specific type of cells or tissues providing an alternative manipulation/therapy strategy to viral gene delivery. However, the current process of searching novel delivery materials is limited due to conventional low-throughput and time-consuming multistep synthetic approaches. Additionally, conventional approaches are frequently accompanied with unpredictability and continual optimization refinements, impeding flexible generation of material diversity creating a major obstacle to achieving high transfection performance. Here we have demonstrated a rapid developmental pathway toward highly efficient gene delivery systems by leveraging the powers of a supramolecular synthetic approach and a custom-designed digital microreactor. Using the digital microreactor, broad structural/functional diversity can be programmed into a library of DNA-encapsulated supramolecular nanoparticles (DNA⊂SNPs) by systematically altering the mixing ratios of molecular building blocks and a DNA plasmid. In vitro transfection studies with DNA⊂SNPs library identified the DNA⊂SNPs with the highest gene transfection efficiency, which can be attributed to cooperative effects of structures and surface chemistry of DNA⊂SNPs. We envision such a rapid developmental pathway can be adopted for generating nanoparticle-based vectors for delivery of a variety of loads.
Dual-etalon frequency-comb cavity ringdown spectrometer (2012)

We have demonstrated a spectroscopic technique for simultaneously obtaining broad spectral bandwidth and high frequency resolution absorption measurements, with 5 μs temporal resolution, continuously for tens of microseconds in an apparatus with no active stabilization. The technique utilizes two passive air-gap etalons to imprint two frequency comb patterns onto a single pulsed light source. The air-gap etalons also serve as cavity ringdown cells increasing the sensitivity of the absorption spectroscopy by increasing the interrogation path length. Here, we demonstrate the operation of the spectrometer utilizing a ~0.15 cm(-1) bandwidth pulsed dye laser and two nearly identical 300 MHz free-spectral range confocal air-gap etalons each with a finesse of ~1 × 10(5), to investigate the (1,1,3) overtone of water and the R(7) transition of the O(2) b(1)Σ(g)(+)←X(3)Σ(g)(-) (2,0) band with high spectral resolution.
Near Maximum-Likelihood Sequential-Search Decoding Algorithms for Binary Convolutional Codes (2008)

In this work, the maximum-likelihood sequential-search decoding algorithm proposed in [17] is revisited. By replacing the conventional Fano metric with one that is derived based on the Wagner rule, the sequential-search decoding in [17] guarantees the maximum-likelihood (ML) performance, and was therefore named the maximum-likelihood sequential decoding algorithm (MLSDA). It was then concluded by simulations that when the MLSDA is operated over the convolutional code trellis, its software computational complexity is in general considerably smaller than that of the Viterbi algorithm. A common problem on sequential-type decoding is that at the signal-to-noise ratio (SNR) below the one corresponding to the cut off rate, the average decoding complexity and the required stack size grow rapidly with the information length [25]. This problem, to some extent, prevents the practical use of sequential-type decoding from codes with long information sequence. In order to alleviate the problem in the MLSDA, we propose to directly eliminate the top path whose end node is ∆-trellis-level prior to the farthest one among all nodes that have been expanded thus far by the sequential search, which we termed the early elimination. We then analyze the early-elimination window that results in negligible performance degradation for the MLSDA. Our asymptotic-based analytical result indicates that the required early elimination window for negligible performance degradation is around three times (resp. 2.2-fold) of the constraint length for rate one-half convolutional codes under additive white Gaussian (resp. binary symmetric) channel. For rate one-third convolutional codes, the required early-elimination window reduces to two times (resp. 1.2-fold) of the constraint length for the same channel. The theoretical level thresholds almost coincide with the simulation results. As a consequence of small early elimination window required for near maximum-likelihood performance, the MLSDA with early elimination modification iv rules out considerable computational burdens, as well as memory requirement, by directly eliminating a big number of the top paths. This makes the MLSDA with early elimination suitable for applications that dictate a low-complexity software implementation with near maximum-likelihood performance. The upper bounds of decoding complexity of both the MLSDAs with and without early elimination are subsequently derived by utilizing the Berry-Esseen inequality. Both the upper bound and the simulated complexity indicate that the average decoding complexity per output bit for the MLSDA with early elimination is almost irrelevant to the memory order, as well as the message length, for medium to high SNRs.
Vesicular Stomatitis Virus G-Pseudotyped Lentivirus Vectors Mediate Efficient Apical Transduction of Polarized Quiescent Primary Alveolar Epithelial Cells (2001)

We investigated the use of lentivirus vectors for gene transfer to quiescent alveolar epithelial cells. Primary rat alveolar epithelial cells (AEC) grown on plastic or as polarized monolayers on tissue culture-treated polycarbonate semipermeable supports were transduced with a replication-defective human immunodeficiency virus-based lentivirus vector pseudotyped with the vesicular stomatitis virus G (VSV-G) protein and encoding an enhanced green fluorescent protein reporter gene. Transduction efficiency, evaluated by confocal microscopy and quantified by fluorescence-activated cell sorting, was dependent on the dose of vector, ranging from 4% at a multiplicity of infection (MOI) of 0.1 to 99% at an MOI of 50 for AEC grown on plastic. At a comparable titer and MOI, transduction of these cells by a similarly pseudotyped murine leukemia virus vector was approximately 30-fold less than by the lentivirus vector. Importantly, comparison of lentivirus-mediated gene transfer from the apical or basolateral surface of confluent AEC monolayers (R(t) > 2 kOmega. cm(2); MOI = 10) revealed efficient transduction only when VSV-G-pseudotyped lentivirus was applied apically. Furthermore, treatment with EGTA to increase access to the basolateral surface did not increase transduction of apically applied virus, indicating that transduction was primarily via the apical membrane domain. In contrast, differentiated tracheal epithelial cells were transduced by apically applied lentivirus only in the presence of EGTA and at a much lower overall efficiency (approximately 15-fold) than was observed for AEC. Efficient transduction of AEC from the apical cell surface supports the feasibility of using VSV-G-pseudotyped lentivirus vectors for gene transfer to the alveolar epithelium and suggests that differences exist between upper and lower airways in the polarity of available receptors for the VSV-G protein.
Thermal atomic layer deposition of rhenium nitride and rhenium metal thin films using methyltrioxorhenium (2021)

The growth of rhenium nitride and rhenium metal thin films is presented using atomic layer deposition (ALD) with the precursors methyltrioxorhenium and 1,1-dimethylhydrazine. Saturative, self-limiting growth was determined at 340 °C for pulse times of ≥4.0 s for methyltrioxorhenium and ≥0.1 s for 1,1-dimethylhydrazine. An ALD window was observed from 340 to 350 °C with a growth rate of about 0.60 Å per cycle. Films grown at 340 °C revealed a root mean square surface roughness of 2.7 nm for a 70 nm thick film and possessed a composition of ReN<sub>0.14</sub> with low O and C content of 1.6 and 2.6 at%, respectively. Enhanced nucleation on <i>in situ</i> grown TiN, relative to thermal SiO<sub>2</sub>, enabled a conformality of 98% on high aspect ratio trenched structures. Subjecting the ReN<sub>0.14</sub> thin films to thermal or chemical and thermal treatments reduced the nitrogen content to ≤1.6 at%, yielding a film purity of about 96 at% rhenium and resistivities as low as 51 μΩ cm. The Re metal film thicknesses on the trenched structures remained intact during the post-deposition annealing treatments and the films did not delaminate from the substrate surfaces.
A bit planes predictive-transform source coder illustrated with SAR imagery (2006)

In this paper it is found that the outstanding memory space compression achieved with predictive-transform (PT) source coding is not affected by its integration with a very fast and simple bit planes methodology that operates on the quantized coefficient errors emanating from the 'lossy' PT source encoder section. It is shown, in particular, that the technique outperforms wavelets based JPEG2000 by more than 5 dBs when it compresses by a factor of 8,192 a test synthetic aperture radar (SAR) image used in knowledge-aided airborne moving target indicator (AMTI) radar.
Multi-scale tunable filter covering a frequency range of 6.5:1 (2008)

A multi-scale filter topology is proposed in the form of a switched comb-line structure loaded by varactors. This topology is capable of implementing a tunable frequency response with consistent performance over very large tuning ranges. Two prototype filters of orders two and four have been fabricated in a coplanar geometry. The filters are tunable in a 6.5:1 frequency range.