gebhart/patrepeval huggingface dataset:
Fast and efficient implementation of Convolutional Neural Networks on FPGA (2017)

State-of-the-art CNN models for Image recognition use deep networks with small filters instead of shallow networks with large filters, because the former requires fewer weights. In the light of above trend, we present a fast and efficient FPGA based convolution engine to accelerate CNN models over small filters. The convolution engine implements Winograd minimal filtering algorithm to reduce the number of multiplications by 38% to 55% for state-of-the-art CNNs. We exploit the parallelism of the Winograd convolution engine to scale the overall performance. We show that our overall design sustains the peak throughput of the convolution engines. We propose a novel data layout to reduce the required memory bandwidth of our design by half. One noteworthy feature of our Winograd convolution engine is that it hides the computation latency of the pooling layer. As a case study we implement VGG16 CNN model and compare it with previous approaches. Compared with the state-of-the-art reduced precision VGG16 implementation, our implementation achieves 1.2× improvement in throughput by using 3× less multipliers and 2× less on-chip memory without impacting the classification accuracy. The improvements in throughput per multiplier and throughput per unit on-chip memory are 3.7× and 2.47× respectively, compared with the state-of-the-art design.
The Major Cell Populations of the Mouse Retina (1998)

We report a quantitative analysis of the major populations of cells present in the retina of the C57 mouse. Rod and cone photoreceptors were counted using differential interference contrast microscopy in retinal whole mounts. Horizontal, bipolar, amacrine, and Müller cells were identified in serial section electron micrographs assembled into serial montages. Ganglion cells and displaced amacrine cells were counted by subtracting the number of axons in the optic nerve, learned from electron microscopy, from the total neurons of the ganglion cell layer. The results provide a base of reference for future work on genetically altered animals and put into perspective certain recent studies. Comparable data are now available for the retinas of the rabbit and the monkey. With the exception of the monkey fovea, the inner nuclear layers of the three species contain populations of cells that are, overall, quite similar. This contradicts the previous belief that the retinas of lower mammals are "amacrine-dominated", and therefore more complex, than those of higher mammals.
Randomized Switched Antenna Array FMCW Radar for Automotive Applications (2014)

Frequency-modulated continuous-wave (FMCW) methods and switched antenna arrays (SAAs) are very attractive for application in automotive radar because of their low hardware complexity. In traditional SAA radar, the receiving antenna array elements are successively switched according to their natural spatial order [referred to as sequential SAAs (SSAAs)]. For radars using both SSAA and FMCW methods, the phase difference caused by the target azimuth and time delay will be difficult to distinguish, thus resulting in delay-space coupling, which may lead to degradation of the road target observation. In this paper, randomized SAA (RSAA) FMCW radar is proposed. The new radar scheme has high delay/space resolution for target location detection and character extraction, and can also solve the coupling problem. The signal model of RSAA FMCW radar is derived and compared with that of SSAA radar. The influence of the antenna-array switching mode on the radar performance is also analyzed. A conventional zero-padding algorithm and a new clustering FOCUSS algorithm are both introduced for the signal processing of the new radar scheme. The numerical results illustrate the performance of RSAA FMCW radar in high-resolution target imaging and delay-space decoupling.
Gene Reactivation in Erythrocytes: Nuclear Transplantation in Oocytes and Eggs of <i>Rana</i> (1983)

Adult erythrocyte nuclei of Rana, transplanted and incubated in the cytoplasm of maturing oocytes, direct matured oocytes to form swimming tadpoles. These results demonstrate that nuclei of noncycling and terminally differentiated erythrocytes contain the genes to specify tadpole development, and conditioning these nuclei in the cytoplasm of oocytes leads to a widespread reactivation of dormant genes.
Poly(dimethylsiloxane) coatings for controlled drug release. III. Drug release profiles and swelling properties of the free‐standing films (2005)

Abstract Previous reports in this series have described the preparation of stable poly(dimethylsiloxane) (PDMS) latices suitable for spray‐coating of drug tablets, as well as the mechanism of associated crosslinking reactions in PDMS emulsions. In the present investigation, in vitro evaluations were performed to study the effects of the amount of channeling agents, the addition of colloidal silica, and the pH of the dissolution media used. The study involved hydrochlorothiazide (as a marker drug) released from compressed tablets, which had been spray coated using PDMS latices with various polyethylene glycol (PEG) loadings as channeling agents. The dissolution results showed that coated tablets containing up to 25% (w/w dps) PEG could have constant release rates. Higher amounts of PEG resulted in nonlinear release patterns. The addition of colloidal silica decreased the rates of drug release. The pH of dissolution media affected the structures of the exposed PDMS films. Swelling tests were carried out to determine water uptake. Scanning electron microscopy and density measurements showed that the films obtained after soaking in higher‐pH media were more condensed, with corresponding changes in drug‐release rates. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 96: 494–501, 2005
Human physiologically based pharmacokinetic model for propofol (2005)

BACKGROUND: Propofol is widely used for both short-term anesthesia and long-term sedation. It has unusual pharmacokinetics because of its high lipid solubility. The standard approach to describing the pharmacokinetics is by a multi-compartmental model. This paper presents the first detailed human physiologically based pharmacokinetic (PBPK) model for propofol. METHODS: PKQuest, a freely distributed software routine http://www.pkquest.com, was used for all the calculations. The "standard human" PBPK parameters developed in previous applications is used. It is assumed that the blood and tissue binding is determined by simple partition into the tissue lipid, which is characterized by two previously determined set of parameters: 1) the value of the propofol oil/water partition coefficient; 2) the lipid fraction in the blood and tissues. The model was fit to the individual experimental data of Schnider et. al., Anesthesiology, 1998; 88:1170 in which an initial bolus dose was followed 60 minutes later by a one hour constant infusion. RESULTS: The PBPK model provides a good description of the experimental data over a large range of input dosage, subject age and fat fraction. Only one adjustable parameter (the liver clearance) is required to describe the constant infusion phase for each individual subject. In order to fit the bolus injection phase, for 10 or the 24 subjects it was necessary to assume that a fraction of the bolus dose was sequestered and then slowly released from the lungs (characterized by two additional parameters). The average weighted residual error (WRE) of the PBPK model fit to the both the bolus and infusion phases was 15%; similar to the WRE for just the constant infusion phase obtained by Schnider et. al. using a 6-parameter NONMEM compartmental model. CONCLUSION: A PBPK model using standard human parameters and a simple description of tissue binding provides a good description of human propofol kinetics. The major advantage of a PBPK model is that it can be used to predict the changes in kinetics produced by variations in physiological parameters. As one example, the model simulation of the changes in pharmacokinetics for morbidly obese subjects is discussed.
Dietary Control of Ganglioside Expression in Mammalian Tissues (2019)

Gangliosides are series of glycosphingolipids containing sialic acids in the oligosaccharide portion in mammalian cells. Gangliosides are a component of cellular membranes and play roles in modulating membrane function and the activity of membrane proteins. Abnormal expression and metabolism of gangliosides lead to the onset of several conditions in humans, such as neurologic diseases, diabetes, and cancer. A number of studies have been carried out to date to investigate the role of gangliosides in these diseases, and the effect of diet on tissue expression of gangliosides has recently become a topic of interest in this field. As gangliosides are degraded in the intestinal tract, ingested food-derived gangliosides are not directly absorbed into tissues in vivo, but the degradation products can be absorbed and affect ganglioside expression in the tissues. Recent studies have also shown that the expression of gangliosides in tissue cells can be indirectly induced by controlling the expression of ganglioside metabolism-related genes via the diet. These results indicate that dietary control can regulate the expression levels of gangliosides in tissues, which is expected to play a role in preventing and treating ganglioside-related diseases. This review introduces recent studies on the effect of diet on the expression of gangliosides in tissues, with a focus on our findings.
Effects of Altering Dietary Cation-Anion Difference on Calcium and Energy Metabolism in Peripartum Cows (2000)

Our objective was to determine the effects of varying dietary cation-anion differences (DCAD: meq[(Na + K) - (Cl + S)]/100 g of dry matter) in prepartum diets on Ca, energy, and endocrine status prepartum and postpartum. Holstein cows (n = 21) and heifers (n = 34) were fed diets with varying amounts of CaCl2, CaSO4, and MgSO4 to achieve a DCAD of +15 (control), 0, or -15 meq/100 g of dry matter for the last 24 d before expected calving. Dietary Ca concentration was increased (by CaCO3 supplementation) with decreasing DCAD. Plasma ionized Ca concentrations prepartum and at calving in both cows and heifers increased with reduced DCAD in the diet. At calving, plasma ionized Ca concentration was 3.67, 3.85, and 4.35 for cows and 4.44, 4.57, and 4.62 mg/dl for heifers fed diets containing +15, 0, and -15 DCAD, respectively. All heifers had normal concentrations of plasma ionized Ca (>4 mg/dl) at calving. Also at calving, plasma concentrations ofparathyroid hormone and calcitriol were less in cows and heifers fed diets containing reduced DCAD, but the plasma concentration of hydroxyproline was not affected by diet. Prepartum dry matter intake, energy balance, and body weight gains were lower and concentration of liver triglyceride was higher for heifers but not cows fed the -15 DCAD diet. Also, nonesterified fatty acids the last week prepartum were positively correlated with liver triglyceride for heifers but not cows. Feeding of anionic salts plus CaCO3 to reduce DCAD to -15 and increase Ca in prepartum diets prevents hypocalcemia at calving in cows, but decreases prepartum dry matter intake and increases the concentration of liver triglyceride in heifers. That heifers maintained calcium homeostasis at calving regardless of diet but ate less when fed the -15 DCAD diet suggests that they should not be fed anionic salts before calving.
Injury‐induced apoptosis of neurons in adult brain is mediated by p53‐dependent and p53‐independent pathways and requires bax (2001)

The mechanisms of injury-induced apoptosis of neurons within the CNS are not understood. We used a model of cortical injury in rat and mouse to induce retrograde neuronal apoptosis in thalamus. In this animal model, unilateral ablation of the occipital cortex causes unequivocal apoptosis of corticopetal projection neurons in the dorsal lateral geniculate nucleus (LGN) by 7 days postlesion. We tested the hypothesis that p53 and Bax regulate this retrograde neuronal apoptosis. We found, by using immunocytochemistry, that p53 accumulates in nuclei of neurons destined to undergo apoptosis. By immunoblotting, p53 levels increase ( approximately 150% of control) in nuclear-enriched fractions of the ipsilateral LGN by 5 days after occipital cortex ablation. p53 is functionally activated in nuclear fractions of the ipsilateral LGN at 5 days postlesion, as shown by DNA binding assay (approximately fourfold increase) and by immunodetection of phosphorylated p53. The levels of procaspase-3 increase at 4 days postlesion, and caspase-3 is activated prominently at 5 days postlesion. To identify whether neuronal apoptosis in the adult brain is dependent on p53 and Bax, cortical ablations were done on p53 and bax null mice. Neuronal apoptosis in the dorsal LGN is significantly attenuated (approximately 34%) in p53(-/-) mice. In lesioned p53(+/+) mice, Bax immunostaining is enhanced in the ipsilateral dorsal LGN and Bax immunoreactivity accumulates at perinuclear locations in dorsal LGN neurons. The enhancement and redistribution of Bax immunostaining is attenuated in lesioned p53(-/-) mice. Neuronal apoptosis in the dorsal LGN is blocked completely in bax(-/-) mice. We conclude that neuronal apoptosis in the adult thalamus after cortical injury requires Bax and is modulated by p53.
Enhancement of Aptamer Microarray Sensitivity through Spacer Optimization and Avidity Effect (2009)

This work aims for ultrasensitive detection of target proteins in complex biological matrixes based on aptamer microarrays. Two extensively studied aptamers (HTQ and HTDQ) that bind distinct epitopes of thrombin are chosen for the microarray study. Although HTQ and HTDQ have nanomolar to subnanomolar affinities, it is found that either aptamer when applied directly has difficulty in detecting a few nanomoles per liter thrombin in the presence of a 10- or 100-fold (w/w) excess of serum total protein (STP). By investigating dodecyl (12-carbon) and oligodeoxythymidine (oligo(dT)) spacers, we observe both spacers enhance the microarray signal response, but oligo(dT) is strikingly better than dodecyl. Moreover, we discover that a microarray spot coprinted with the two distinct aptamers (HTQ and HTDQ) functions like a bivalent molecular construct and exhibits an avidity effect. With the synergy of oligo(dT) spacers and the avidity effect, detection of picomolar-range thrombin in the presence of either 10% unlabeled serum or a 10,000-fold excess of labeled serum total protein is achieved. It corresponds to a 100-1000-fold sensitivity enhancement as compared to using an individual aptamer without a spacer.
Combustion Synthesis of Aluminum Nitride Particles and Whiskers (1999)

Aluminum nitride (AlN) was produced via the combustion synthesis of loosely packed aluminum powder (pore fraction of ∼0.8) in a graphite reactor that was lined with permeable carbon felt. Almost‐complete conversion was achieved with a forced flow of nitrogen for beds 50‐150 mm deep (mass of 200‐650 g). The product was in the form of a loosely aggregated bed, with regions of distinct morphology, and had a predominantly whisker morphology. Some control over the microstructure was possible by changing the processing parameters. The addition of 5% of ammonia to the nitrogen resulted in a uniform production of whiskers, whereas a 50% solid‐phase dilution with AlN favored the production of particles.
Design of a new squaring function for the Viterbi algorithm (1994)

An approximate squaring method has been developed for the Viterbi algorithm that is faster and more area efficient than conventional exact squaring methods and table look-up. Using Monte-Carlo simulations, it is shown here that the performance of the Viterbi algorithm is not degraded using this approximation. The circuit performance is verified by implementing a 7-b approximate squaring function in a 2-/spl mu/m CMOS process. It operates at a maximum speed of 20 MHz, consumes 95 pW/Hz of power, and occupies an active area of 380 /spl mu/m/spl times/650 /spl mu/m.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Dephosphorylation of Photosystem II Reaction Center Proteins in Plant Photosynthetic Membranes as an Immediate Response to Abrupt Elevation of Temperature (2000)

Kinetic studies of protein dephosphorylation in photosynthetic thylakoid membranes revealed specifically accelerated dephosphorylation of photosystem II (PSII) core proteins at elevated temperatures. Raising the temperature from 22 degrees C to 42 degrees C resulted in a more than 10-fold increase in the dephosphorylation rates of the PSII reaction center proteins D1 and D2 and of the chlorophyll a binding protein CP43 in isolated spinach (Spinacia oleracea) thylakoids. In contrast the dephosphorylation rates of the light harvesting protein complex and the 9-kD protein of the PSII (PsbH) were accelerated only 2- to 3-fold. The use of a phospho-threonine antibody to measure in vivo phosphorylation levels in spinach leaves revealed a more than 20-fold acceleration in D1, D2, and CP43 dephosphorylation induced by abrupt elevation of temperature, but no increase in light harvesting protein complex dephosphorylation. This rapid dephosphorylation is catalyzed by a PSII-specific, intrinsic membrane protein phosphatase. Phosphatase assays, using intact thylakoids, solubilized membranes, and the isolated enzyme, revealed that the temperature-induced lateral migration of PSII to the stroma-exposed thylakoids only partially contributed to the rapid increase in the dephosphorylation rate. Significant activation of the phosphatase coincided with the temperature-induced release of TLP40 from the membrane into thylakoid lumen. TLP40 is a peptidyl-prolyl cis-trans isomerase, which acts as a regulatory subunit of the membrane phosphatase. Thus dissociation of TLP40 caused by an abrupt elevation in temperature and activation of the membrane protein phosphatase are suggested to trigger accelerated repair of photodamaged PSII and to operate as possible early signals initiating other heat shock responses in chloroplasts.
Wrist-mounted smartphone-based navigation device for visually impaired people using ultrasonic sensing (2016)

This paper presents a wrist-mounted wearable device for helping visually impaired people to avoid obstacles and to enable them to move around more efficiently than when using only a white cane. The device is designed to be worn on the wrist of the user and is connected to the user's smartphone. The detection algorithm is based on the information acquired from an ultrasonic sensor on the wristband and the accelerometer in the smartphone. The device has two detection modes; the ground level detection mode, and the above ground level detection mode. The ground level detection mode is used to detect obstacles (both bumps and holes) on the ground based on the distance data from the ultrasonic sensor together with the angle data of the user's arm from the accelerometer. The above ground level detection mode uses solely the information from the ultrasonic sensor. When an obstacle is found, the device alerts the user with both audio and haptic tactile feedback via the smartphone. Experimental results tested on blindfolded sighted individuals show that using the device with a white cane increases efficiency in avoiding obstacles. The results also show that the device is easy to learn.
High Spectral Efficiency 400 Gb/s Transmission Using PDM Time-Domain Hybrid 32–64 QAM and Training-Assisted Carrier Recovery (2013)

We report the successful transmission of ten 494.85 Gbit/s DWDM signals on the standard 50 GHz ITU-T grid over 32 × 100 km of ultra-large-area (ULA) fiber. A net spectral efficiency (SE) of 8.25 b/s/Hz was achieved, after excluding the 20% soft-decision forward-error-correction (FEC) overhead. Such a result was accomplished by the use of a recently proposed polarization-division-multiplexed (PDM) time-domain hybrid 32-64 quadrature-amplitude-modulation (QAM) format, along with improved carrier frequency and phase recovery algorithms. It is shown that time-domain hybrid QAM provides a new degree of design freedom to optimize the transmission performance by fine tuning the SE of the modulation format for a specific channel bandwidth and FEC redundancy requirement. In terms of carrier recovery, we demonstrate that 1) hardware efficient estimation and tracking of the frequency offset between the signal and local-oscillator (LO) can be achieved by using a new feedback-based method, and 2) a training-assisted two-stage phase estimation algorithm effectively mitigates cyclic phase slipping problems. This new phase recovery algorithm not only improves the receiver sensitivity by eliminating the need for differential coding and decoding, but also enables an additional equalization stage following the phase recovery. We have shown that the introduction of this additional equalization stage (with larger number of taps) helps reduce the implementation penalty. This paper also presents the first experimental study of the impact of inphase (I) and quadrature (Q) correlation for a high-order QAM. It is shown that an adaptive equalizer could exploit the correlation between I and Q signal components to artificially boost the performance by up to 0.7 dB for a PDM time-domain hybrid 32-64 QAM signal when the equalizer length is significantly longer than I/Q de-correlation delay.
The Contribution of Exon-Skipping Events on Chromosome 22 to Protein Coding Diversity (2001)

Completion of the human genome sequence provides evidence for a gene count with lower bound 30,000-40,000. Significant protein complexity may derive in part from multiple transcript isoforms. Recent EST based studies have revealed that alternate transcription, including alternative splicing, polyadenylation and transcription start sites, occurs within at least 30-40% of human genes. Transcript form surveys have yet to integrate the genomic context, expression, frequency, and contribution to protein diversity of isoform variation. We determine here the degree to which protein coding diversity may be influenced by alternate expression of transcripts by exhaustive manual confirmation of genome sequence annotation, and comparison to available transcript data to accurately associate skipped exon isoforms with genomic sequence. Relative expression levels of transcripts are estimated from EST database representation. The rigorous in silico method accurately identifies exon skipping using verified genome sequence. 545 genes have been studied in this first hand-curated assessment of exon skipping on chromosome 22. Combining manual assessment with software screening of exon boundaries provides a highly accurate and internally consistent indication of skipping frequency. 57 of 62 exon skipping events occur in the protein coding regions of 52 genes. A single gene, (FBXO7) expresses an exon repetition. 59% of highly represented multi-exon genes are likely to express exon-skipped isoforms in ratios that vary from 1:1 to 1:>100. The proportion of all transcripts corresponding to multi-exon genes that exhibit an exon skip is estimated to be 5%.
Nature of interfaces and oxidation processes in Ge+-implanted Si (1989)

We have studied the nature of the interfaces between silicon dioxide and germanium-rich layer (SiO2/GexSi1−x) in Ge+-ion implanted and oxidized Si (100) samples. A series of implants were used to study the interfacial roughness as a function of implant dose. Oxidations were carried out at temperatures both above and below the viscous flow point of silicon dioxide (SiO2). In each case, the SiO2/GexSi1−x interface was found to be sharper on an atomic scale compared to the oxide/silicon (SiO2/Si) interface in virgin Si formed after similar oxidation treatments. An enhancement in oxidation was found for the implanted samples over the virgin silicon samples. This enhancement was greater for oxidation carried out at 900 °C for 30 min compared to that at 1000 °C for 20 min. At the higher implant doses, predominantly 60° misfit dislocations were observed at the GexSi1−x/Si interface. The mechanism of oxidation leading to these phenomena is discussed in detail.