gebhart/patrepeval huggingface dataset:
Herpes Simplex Virus Type 1 DNA Amplified as Bacterial Artificial Chromosome in <i>Escherichia coli:</i> Rescue of Replication-Competent Virus Progeny and Packaging of Amplicon Vectors (1998)

Herpes simplex virus type 1 (HSV-1)-based amplicon vectors contain only approximately 1% of the 152-kb HSV-1 genome, and consequently, replication and packaging into virions depends on helper functions. These helper functions have been provided conventionally by a helper virus, usually a replication-defective mutant of HSV-1, or more recently, by a set of five cosmids that overlap and represent the genome of HSV-1 deleted for DNA cleavage/packaging signals (pac). In the absence of pac signals, potential HSV-1 genomes that are reconstituted from the cosmids via homologous recombination are not packageable. The resulting amplicon stocks are, therefore, virtually free of contaminating helper virus. To simplify this packing system, the HSV-1 genome was cloned and maintained stably as a single-copy, F plasmid-based bacterial artificial chromosome in E. coli. Such a plasmid containing the HSV-1 genome deleted for the pac signals (fHSV delta pac) did not generate replication-competent progeny virus on transfection into mammalian cells, but rather, it was able to support the packaging of cotransfected amplicon DNA that contained a functional pac signal. The resulting amplicon vector stocks had titers of up to 10(7) transducing units per milliliter of culture medium and efficiently transduced neural cells in the rat brain, as well as hepatocytes in the rat. The capacity of generating infectious and replication-competent HSV-1 progeny following transfection into mammalian cells was restored after insertion of a pac signal into fHSV delta pac.
First Trimester Pbmc Microrna Predicts Adverse Pregnancy Outcome (2014)

MicroRNA quantification of maternal blood cells offers the clinician a single test result that is simple to interpret and available much earlier in pregnancy than previously obtainable. In addition, it is the only early pregnancy marker, to date, that can successfully predict late pre-eclampsia. Although the studies that we report are preliminary, we hope that future research will build upon our discoveries and enhance the power of maternal cell microRNA to predict adverse pregnancy outcome in the clinic.
iSAT: The mega-fauna acoustic tracking system (2013)

The acoustic tracking module of the Integrated Satellite and Acoustic Telemetry (iSAT) system is discussed in detail. iSAT is capable of detecting the relative direction of an acoustic source by measuring the order of arrival (OOA) of the acoustic signal to each hydrophone in a triangular array. The characteristics of the hydrophones, the projector, and the target acoustic signal used for iSAT are described. Initially it is designed to study the movements of whale sharks (Rhincodon typus), but it could potentially be used to describe high resolution movements of other marine species.
Elucidating the antidepressant actions of substance P (NK1 receptor) antagonists. (2002)

Substance P (NK1 receptor) antagonists (SPAs) are currently the best validated and clinically most advanced novel approach to treating major depressive disorder (MDD), and several compounds are in advanced clinical development. Three years since the discovery of the antidepressant efficacy of MK-869 (Merck & Co Inc), the first in a new class of drugs that act by selectively blocking the actions of substance P, the principle that blocking the NK1 receptor can alleviate major depression has recently been replicated in a placebo-controlled, blinded study. SPAs are active in a range of preclinical assays that detect clinically used antidepressant drugs, but they have a pharmacological profile that is distinct from established drugs. There is preliminary evidence that substance P and NK1 receptor density may be altered in MDD, suggesting a possible link between substance P and depressive pathophysiology. Studies in animals indicate that the psychotherapeutic effects of SPAs may be mediated at least partly through stimulation of hippocampal neurogenesis, by direct blockade of NK1 receptors in the amygdala and its associated output projections, and also via interactions with monoamines. Additional studies are needed to explore these hypothesesfurther.
Continuous trip count profiling for loop optimizations in two-phase dynamic binary translators (2004)

Most dynamic binary translators use a two-phase approach to identify and optimize frequently executed code dynamically. In the profiling phase, blocks of code are interpreted or translated without optimization to collect execution frequency information for the blocks. In the optimization phase, frequently executed blocks are grouped into regions and advanced optimizations are applied on them. This approach implicitly assumes that the initial execution of each block is representative of the block throughout its lifetime. In particular, loop optimizations may use the block frequency information to determine loop trip counts to guide their optimizations. If the trip count information is incorrect, however, a loop may be improperly optimized, and program performance suffers. In this paper we show that the initial profile is inadequate at predicting loop trip count information for several integer programs. We propose and evaluate efficient algorithms to continuously profile for trip count. Our results show that accurate trip count information may be obtained with very low overhead (about 0.5%). This enables advanced loop optimizations in dynamic binary translators.
Humoral-Phagocyte Axis of Immune Defense in Burn Patients (1982)

Both serum opsonic capacity and granulocyte oxygenation activity were measured in 35 burn patients during their course of therapy. The microbicidal action of granulocytes is effected via the metabolic generation of oxygenating agents; introduction of chemoluminigenic substrates, such as luminol or dimethyl biacridinium dinitrate, allows ultrasensitive measurement of phagocyte oxygenation activity. Serum opsonic capacity can also be assayed by measuring the rate of activation of phagocyte oxygenation activity. Alterations in granulocyte oxygenation activity were observed in individuals patients in temporal association with changes in clinical condition, and sepsis was associated with a marked decrease in activity. An initial depression in opsonic capacity was noted at the time of admission of patients with major burns, more than 40% total body surface. Thereafter, depression of opsonic capacity was temporally associated with sepsis in individual patients. Chemoluminigenic probing provides a rapid, sensitive, and objective method for assessing the status of the humoral-phagocyte axis, and as a clinical laboratory technique is particularly applicable for monitoring patient populations in which sepsis is prevalent.
Dynamically reconfigurable vision with high performance CMOS active pixel sensors (APS) (2003)

A high-performance computational imager based on integration of CMOS active pixel imager array with on-chip signal processing and control via a new column-parallel architecture is presented. Unlike CCDs and other CMOS imagers, the sensor is capable of providing simultaneous image data from three flexible, partially overlapping, dynamically reconfigurable regions of interest (ROIs) with different spatial resolution over a large field-of-view (FOV) to achieve data-efficient operation with high update rates. The power dissipation depends upon reconfiguration modes, but is small even in the worst case. Unlike conventional computational imagers, the integration of processing circuitry does not trade with radiometric accuracy, nor does it impose any limit to scaling the imager size to larger format and smaller pixels. By eliminating the need for mechanical pointing through floating-fovea support, the dynamically reconfigurable vision sensor (DSRVS) enables a low-power staring vision system. By maximizing system throughput through intelligent data reduction and through real-time programmability, it meets the diverse and conflicting requirements of search, identify and track vision-modes, and represents an efficient platform for high-bandwidth automatic target acquisition and tracking.
Expression of two [Fe]‐hydrogenases in <i>Chlamydomonas reinhardtii</i> under anaerobic conditions (2003)

We have isolated and characterized a second [Fe]-hydrogenase gene from the green alga, Chlamydomonas reinhardtii. The HydA2 gene encodes a protein of 505 amino acids that is 74% similar and 68% identical to the known HydA1 hydrogenase from C. reinhardtii. HydA2 contains all the conserved residues and motifs found in the catalytic core of the family of [Fe]-hydrogenases. We demonstrate that both the HydA1 and the HydA2 transcripts are expressed upon anaerobic induction, achieved either by neutral gas purging or by sulfur deprivation of the cultures. Furthermore, the expression levels of both transcripts are regulated (in some cases differently) by incubation conditions, such as the length of anaerobiosis, the readdition of O2, the presence of acetate, and/or the absence of nutrients such as sulfate during growth. Antibodies specific for HydA2 recognized a protein of about 49 kDa in extracts from anaerobically induced C. reinhardtii cells, strongly suggesting that HydA2 encodes for an expressed protein. Homology-based 3D modeling of the HydA2 hydrogenase shows that its catalytic site models well to the known structure of Clostridium pasteurianum CpI, including the H2-gas channel. The major differences between HydA1, HydA2 and CpI are the absence of the N-terminal Fe-S centers and the existence of extra sequences in the algal enzymes. To our knowledge, this work represents the first systematic study of expression of two algal [Fe]-hydrogenases in the same organism.
Rational Molecular Design of Complementary Self‐Assembling Peptide Hydrogels (2012)

Rational molecular design of self- assembling peptide-based materials that spontaneously form self-supporting hydrogels shows potential in many healthcare applications. Binary peptides based on complementary charged sequences are developed, and the use of biophysical analysis and cell-based studies highlights that the charged interactions can influence the properties of peptide materials and ultimately affect biomaterial applications.
<sup>31</sup>P Spectroscopic localization using pinwheel NMR excitation pulses (1991)

Spectroscopic imaging with a one-dimensional phase-encoding gradient and surface-coil reception relies on the restricted range of sensitivity of the surface coil to provide localization in the dimensions transverse to the coil axis and consequently suffers from relatively poor localization in these dimensions. A two-dimensional (2D) cylindrically selective excitation pulse with a large spectral bandwidth is presented here to remedy this problem. The gradient waveforms are derived from multiple spirals in k space which form an overall pinwheel pattern, resulting in a pulse which is much shorter than the equivalent single-spiral trajectory. Nonuniform traversal of the spirals further reduces the pulse width under conditions of gradient slew-rate limitations, yielding overall gains in bandwidth of up to about 30 compared with the equivalent single-spiral trajectory traversed at constant angular rate. The accompanying rf waveform is obtained by weighted 2D Fourier transformation of the desired sensitivity profile. A new weighting factor is introduced into the rf waveform to compensate for nonuniform sampling of k space by the pinwheel near the origin. This factor is independent of the weighting used to account for the rate of traversal of the trajectory and is applicable to 2D pulse design in general. Pulse sequences employing pinwheel excitation in conjunction with either phase-encoding or slice-selective inversion are used to produce multiple-voxel and single-voxel localization in a human heart and a phantom. Pinwheel pulses may be used to advantage on moieties with long spin-lattice relaxation times and short transverse relaxation times and are therefore ideal for applications in phosphorus (31P) NMR.
Radar-based Target Tracking Method: Application to Real Road (2005)

<div class="htmlview paragraph">Principle of the target tracking method for the Adaptive Cruise Control (ACC) system, which is applicable to non-uniform or transient condition, had been proposed by one of the authors. This method does not need any other information rather than that from the radar and host vehicle. Here the method is modified to meet more complex traffic scenarios and then applied to data measured on real highway. The modified method is based on the phase chart between the lateral component of the relative velocity and azimuth of a preceding vehicle. From the trace on the chart, the behavior of a preceding vehicle is judged and the discrimination between the lane change and curve-entry/exit can be made. The method can deal with the lane-change of a preceding vehicle on the curve as well as on the straight lane. And it is applied to more than <i>20</i> data including several road/vehicle conditions: road is straight, or turns right or left; vehicles are motorbikes, sedans and trucks. The algorithm could identify a target vehicle during the lane change and curve-entry/exit successfully. The trace of the data on the chart was found to be similar to what is expected in the analysis.</div>
A Ku-band variable power divider for reconfigurable satellite antennas (1993)

A novel planar version of the classical variable power divider (VPD) comprising two hybrids and two variable phase shifters is described. A significantly improved variable phase shifter, based on a 3 dB hybrid terminated by two sliding non-contacting moveable short circuits, is used in this VPD. The differential phase spreading of such a phase shifter has been reduced to less than one-sixth of the typical transmission line dispersion by compensating short terminations. The device has been modelled by an accurate full wave analysis software available at Alenia Spazio. The measured performance on a breadboard model is flat over a 16% bandwidth and significantly improved with respect to the classical solution. Planar integration, wideband performance, medium-high power handling capabilities and low loss are some of the key features of this VPD which is presently undertaking a space qualification process. >
Mutations in <i>DSTYK</i> and Dominant Urinary Tract Malformations (2013)

We detected independent DSTYK mutations in 2.3% of patients with congenital abnormalities of the kidney or urinary tract, a finding that suggests that DSTYK is a major determinant of human urinary tract development, downstream of FGF signaling. (Funded by the National Institutes of Health and others.).
Synthesis, Structure−Activity Relationship, and Mode-of-Action Studies of Antimalarial Reversed Chloroquine Compounds (2010)

We have previously shown that a "reversed chloroquine (RCQ)" molecule, composed of a chloroquine-like moiety and a resistance reversal-like moiety, can overcome chloroquine resistance in P. falciparum ( Burgess , S. J. ; Selzer , A. ; Kelly , J. X. ; Smilkstein , M. J. ; Riscoe , M. K. ; Peyton , D. H. J. Med. Chem. 2006 , 49 , 5623 . Andrews , S. ; Burgess , S. J. ; Skaalrud , D. ; Kelly , J. X. ; Peyton , D. H. J. Med. Chem. 2010 , 53 , 916 ). Here, we present an investigation into the structure-activity relationship of the RCQ structures, resulting in an orally active molecule with good in vitro and in vivo antimalarial activity. We also present evidence of the mode of action, indicating that the RCQ molecules inhibit hemozoin formation in the parasite's digestive vacuole in a manner similar to that of chloroquine.
Mapping of the α-1,6-fucosyltransferase gene, FUT8, to human chromosome 14q24.3 (1999)

Alpha-1,6-Fucosyltransferase (alpha1,6FucT) is involved in the biosynthesis of asparagine-linked glycoprotein oligosaccharides. In this study, we isolated a genomic clone for the human alpha1,6FucT gene (FUT8) and mapped it by fluorescence in situ hybridization to chromosome 14q24.3. This study suggests a distinct localization of FUT8 from genes for other human fucosyltransferases reported to date.
Photonic analog-to-digital conversion based on oversampling techniques (2000)

A novel photonic approach to analog-to-digital (A/D) conversion based on temporal and spatial oversampling techniques in conjunction with a smart pixel hardware implementation of a neural algorithm is described. In this approach, the input signal is first sampled at a rate higher than that required by the Nyquist criterion and then presented spatially as the input to the 2D error diffusion neural network consisting of M X N pixels. The neural network processes the input oversampled analog image and produces an M X N pixel binary output image which is an optimum representation of the input analog signal. Upon convergence, the neural network minimizes an energy function representing the frequency-weighted squared error between the input analog image and the output halftoned image. Decimation and low-pass filtering techniques, common to oversampling A/D converters, digitally sum and average the M X N pixel output binary image using high-speed digital electronic circuitry. By employing a 2D smart pixel neural approach to oversampling A/D conversion, each pixel constitutes a simple oversampling modulator thereby producing a distributed A/D architecture. Spectral noise shaping across the array diffuses quantization error thereby improving the signal-to-noise ratio performance. Here, each quantizer within the network is embedded in a fully- connected, distributed mesh feedback loop which spectrally shapes the overall quantization noise significantly reducing the effects of component mismatch typically associated with parallel or channelized A/D approaches. The 2D neural array provides higher aggregate bit rates which can extend the useful bandwidth of oversampling converters.
EPITAXIAL DESIGN AND PERFORMANCE OF <font>AlGaInP</font> RED (650–690 <font>nm</font>) VCSELs (1994)

Progress in addressing critical epitaxial design issues associated with AlGaInP -based visible (red) vertical-cavity surface-emitting laser (VCSEL) diodes is reviewed, with emphasis on those issues that differentiate red VCSELs from conventional AlGaAs -based near-IR VCSELs. Key issues include epitaxial growth techniques for red VCSELs, the unique properties of AlGaInP alloys and heterostructures, design and growth of visible distributed Bragg reflectors, and integration of AlGaInP and AlGaAs hetero-structures into the hybrid VCSEL device structure. The performance characteristics of AlGaInP/AlGaAs red VCSEL diodes are overviewed in the context of the epitaxial design.
<title>Tissue optics and dosimetry for photodynamic cancer therapy in the esophagus</title> (1994)

For safe light dosimetry in photodynamic therapy (PDT) in organs like the oesophagus, the knowledge of the space irradiance distribution in tissue is especially important. In order to obtain this distribution we are studying two methods which are being evaluated in a clinical environment. The first method is non invasive and is based on the measurement of optical tissue parameters. For this measurement, several types of optical probe have been developed. The second method is invasive and measures light in situ by means of an optical fiber probe with a fluorescent tip. Together with these measuring techniques and results we present some simple notions of light dosimetry which can be used to improve the safety and the efficacy of the clinical PDT.
Plasma characteristics and element analysis of steels from a nuclear power plant based on fiber-optic laser-induced breakdown spectroscopy (2018)

Abstract The laser-produced plasma and laser-induced breakdown spectroscopy (LIBS) of two steels from a nuclear power plant, including the Z3CN20-09M steel used for the main reactor coolant pipes, and the 16MND5 steel used for nuclear reactor pressure vessels. These were investigated based on a fiber-optic LIBS system. Under the same input laser energy, the laser-produced plasma from the Z3CN20-09M steel had a weaker emission intensity compared to the 16MND5 steel, probably due to a greater content of Cr. Thus, plasma from the Z3CN20-09M steel had a larger kinetic energy and induced a faster expansion shockwave in air. Calibrations of the fiber-optic LIBS system by the means of internal standardization, support vector regression and random forest regression were set up. For the Cr element, as a major element in Z3CN20-09M (19.33wt.%), it was determined with the relative error controlled under 3.5%; as a trace element (0.11wt.%) in 16MND5 it was measured with the best root-mean-square error of prediction as 0.032wt.%, and the Mn content (1.19–1.51wt.%) in both steels was measured with the relative error around 10%.
What are exosomes and how can they be used in multiple sclerosis therapy? (2014)

Current treatment options for multiple sclerosis are limited and consist of immunosuppressors or agents to prevent immune infiltration of the brain. These therapies have potentially harmful side effects and do little to promote myelin repair. Instead, we suggest using exosomes, naturally occurring small vesicles that exert influence through the delivery of mRNA, microRNA and protein. Dendritic cells can be cultured from bone marrow and stimulated to release exosomes. When administered to the brain, these exosomes significantly increase myelination and improve remyelination following injury by prompting preoligodendrocytes to differentiate into myelin producing cells. Additionally, they are non-toxic and can easily cross the blood-brain barrier and, thus, have great potential as a therapeutic.
Improving limited-view photoacoustic tomography with an acoustic reflector (2013)

The versatility and real-time imaging capability of commercial linear array transducers make them widely used in clinical ultrasound and photoacoustic imaging. However, they often suffer from limited detection view. For instance, acoustic waves traveling at a grazing angle to the transducer surface are difficult to detect. In this letter, we propose a simple and easy approach to ameliorate this problem by using a 45-deg acoustic reflector. The reflector forms a virtual array that is perpendicular to the physical array, thereby doubling the detection coverage. The improvement in image quality in photoacoustic tomography was demonstrated through a hair phantom, a leaf skeleton phantom, and an ex vivo mouse ear experiment.