gebhart/patrepeval huggingface dataset:
FishDrop: Estimation of reef fish population density and biomass using stereo cameras (2016)

Underwater Visual Census for fish population density and biomass measurements is the standard method for monitoring the health of a marine environment. Conducted within reef areas, it provides important documentation over time quantifying the success of reef protection and rehabilitation initiatives. The monitoring results are crucial to the formulation of strategies to improve reef resilience and increase productivity of reef fish communities. Typically this census is done by a fish expert swimming along a transect with the aid of a SCUBA. Previous attempts at incorporating videos in fish census aimed to reduce dive hours and for permanent transect records. However, subsequent manual analysis of the collected video data is tedious and time consuming. We propose a semi-automated process of performing fish census which otherwise requires high level of domain knowledge and expertise. Divers with minimal knowledge of fish can obtain high quality population and species distribution measurements using a stereo camera rig and fish video analyzer software that we have developed. Our system has two major components: a camera rig and software for fish size, density and biomass estimation. The camera rig consists of a simple stand on which one to four pairs of stereo cameras are mounted to take videos of the benthic floor for a few minutes. The collected videos are uploaded to a server which performs stereo analysis and image recognition. The software produces video clips containing estimates of fish size, density and species biodiversity and a report in csv format containing information about the individual fishes for further end user analysis.
Cathepsin S inhibitors (2004)

AbstractCysteine proteases have attracted considerable interest over the past decade. Lysosomal cysteine protease cathepsin S plays an important role in antigen presentation and matrix degradation. Interest for this enzyme has recently grown and ~ 70 patents have appeared over the last 3 years, targeting cathepsin S either solely or among other related cysteine proteases. With the rapidly growing understanding of the pharmacology of cathepsin S, a number of pharmaceutical companies have reported to be actively seeking inhibitors to treat inflammatory and autoimmune diseases. The major players in this field are Aventis Pharmaceuticals in collaboration with Celera Genomics (previously Axys pharmaceuticals), Boehringer Ingelheim and Glaxo SmithKline. These companies report compounds undergoing preclinical evaluation. Most of the disclosed inhibitors contain an electrophilic warhead, such as nitriles, activated ketones, aldehydes and β-lactams, that interacts with the catalytic cysteine thiol.Keywordsallergyantigen presentationasthmaatherosclerosisautoimmune diseasescathepsin S inhibitorchronic obstructive pulmonary disease (COPD)cysteine protease inhibitormatrix degradationrheumatoid arthritis
Comparison of the Enzymatic-Activities of Human Galactokinase Galk1 and a Related Human Galactokinase Protein GK2 (1995)

The GALK1 cDNA encoding human galactokinase was recently cloned and its cognate GALK1 gene shown to be involved in galactokinase deficient galactosemia. Previously, a separate human galactokinase cDNA, GK2, was cloned by complementation of a galactokinase deficient yeast mutant; however, the galactokinase activity of GK2 was not demonstrated in mammalian cells. To compare the relative galactokinase activity of GALK1 and GK2, their corresponding cDNAs were expressed in COS cells. Northern blot analysis indicated that both cDNAs were transcribed into mRNA transcripts of the expected size; however, only the GALK1 cDNA produced high levels of galactokinase activity. This result would suggest that GALK1 is the major enzyme for galactose metabolism while the role of GK2 remains uncertain.
Bazaar: Enabling Predictable Performance in Datacenters (2012)

The disconnect between the resource-level interface exposed by today’s cloud providers and tenant goals hurts both entities. Tenants are encumbered by having to translate their performance and cost goals into the corresponding resource requirements while providers suffer revenue loss due to uninformed resource selection by tenants. We explore this disconnect in the context of data analytics applications and present Bazaar, a system that enables predictable performance for such applications in multi-resource, multi-tenant datacenters. Bazaar allows tenants to express high-level goals and predicts the resources needed to achieve them. Since multiple resource combinations may achieve the same goal, Bazaar chooses the combination most suitable for the provider. Using large-scale simulations and deployment on a small testbed, we demonstrate that Bazaar enables a symbiotic tenant-provider relationship. Tenants achieve their performance goals. At the same time, holistic resource selection benefits providers in the form of increased goodput.
Optimal Construction of Regenerating Code Through Rate-Matching in Hostile Networks (2017)

Regenerating code is a class of distributed storage codes that can optimally trade the bandwidth required to repair a failed node with the amount of data stored per node. There are two optimal points in the regeneration tradeoff curve: the minimum storage regeneration code and the minimum bandwidth regeneration code. However, in hostile networks where the storage nodes may be compromised, the storage capacity of the network can be significantly affected. In this paper, we propose two optimal regenerating code constructions through rate-matching to combat this kind of adversarial attacks in hostile networks. We first develop a two-layer rate-matched regenerating code construction. By matching the parameters of the full rate code and the partial rate code, we can optimize the overall storage efficiency while maintaining the corrupted node detection probability. Through comprehensive analysis, we show that the two-layer rate-matched regenerating code can achieve 70% higher storage efficiency than the universally resilient regenerating code. We then propose an optimal m-layer regenerating code construction. While the principle remains the same as the two-layer code, it is designed to optimize the total number of detectable corrupted nodes of m layers from which the errors can be corrected under the constraint of any given code efficiency. Compared with the universally resilient regenerating code with the same rate, our m-layer code can detect 50% more corrupted nodes.
Plasmonic coupling of SiO2–Ag “post-cap” nanostructures and silver film for surface enhanced Raman scattering (2011)

We demonstrate a surface enhanced Raman scattering (SERS) substrate consisting of SiO2–Ag “post-cap” nanostructures with an underlying silver film fabricated by the glancing angle deposition technique. Electromagnetic simulations predict that SERS enhancement is strongly polarization-dependent, consistent with experimental measurements. Optimized coupling between Ag cap nanoparticles and the underlying silver film can be achieved by controlling the thickness of SiO2 post sandwiched between them to significantly enhance local electric-field intensity and to increase the density of electromagnetic hot spots. A maximum SERS enhancement factor of 2.38×109 within the hot spot region is demonstrated, providing sufficient sensitivity for many important applications.
Miniaturized, 0.01 mm<sup>2</sup>, Resistor-Based Thermal Sensor With an Energy Consumption of 0.9 nJ and a Conversion Time of 80 <inline-formula> <tex-math notation="LaTeX">$\mu$ </tex-math> </inline-formula>s for Processor Applications (2018)

Thermal sensing is a key power management feature in microprocessor products and other integrated circuits. There can be as many as 40 sensors on a chip. Thus, it is important for these sensors to have a highly compact area, as well as low energy. In this paper, we report a novel resistor-based thermal sensor with an area of 0.01 mm2 in 65-nm process, an energy consumption of 0.9 nJ/conversion, and a conversion speed of 80 μs. This sensor is one of the smallest, fastest, and lowest energy sensors reported which utilize resistors as the sensing element, making it optimal for CPU applications. The sensor has a competitive resolution figure of merit of 0.02 nJ·K2, as well as a relative inaccuracy of 1.4 °C, which easily meets the accuracy requirements of these applications. The circuit architecture is based on the measurement of an RC time constant using a novel amplifier/comparator circuit, along with a dynamic bias for power savings.
Local Growth of Graphene by Ion Implantation of Carbon in a Nickel Thin Film followed by Rapid Thermal Annealing (2012)

Carbon ions were implanted in a nickel thin film. After subsequent rapid thermal annealing, they segregated on the surface, forming a graphene layer. The dependence of graphene synthesis on process conditions, including the carbon implantation dose, RTA temperature, and time, were investigated. The graphene shows quality comparable to that of the best reported CVD graphene. It was also found that local growth of graphene through local implantation requires stringent control of the process chamber conditions in order to avoid growth of graphene on unimplanted regions.
A novel phased array based on the extended resonance power dividing technique (2003)

A novel phased array based on the extended resonance power dividing technique has been presented. This phased array eliminates the need for a separate power splitter and phase shifters in a conventional phased array system. As a proof of principle, a 2 GHz extended resonance based phased array consisting of 4 microstrip patch antennas has been designed, fabricated and tested. The measured scan range was +/- 13.5 degrees with an average beamwidth of 26 degrees.
Near-field scanning optical microscopy probe fabrication using focused ion beam milling technique (2003)

Summary form only given. In this work we have developed a method for fabricating clean, well-defined, and highly reproducible subwavelength apertures for near-field scanning optical microscopy (NSOM) applications using a focused ion beam (FIB) milling technique. Fiber probes were produced through the use of a heating-pulling process. The pulled fiber probes were then uniformly coated all over with a 100-150 nm aluminum film in batches of 10-15 fibers with a sputtering unit usually used to metal coat specimens prior to inspection by scanning electron microscopy (SEM). The coating is smooth and exhibits no leakage or pin holes upon injection of laser light into such fiber probes.
A carboxyl-terminal propeptide is necessary for proper sorting of barley lectin to vacuoles of tobacco. (1990)

Barley lectin is synthesized as a preproprotein with a glycosylated carboxyl-terminal propeptide (CTPP) that is removed before or concomitant with deposition of the mature protein in vacuoles. Expression of a cDNA clone encoding barley lectin in transformed tobacco plants results in the correct processing, maturation, and accumulation of active barley lectin in vacuoles [Wilkins, T.A., Bednarek, S.Y., and Raikhel, N.V. (1990). Plant Cell 2, 301-313]. The glycan of the propeptide is not essential for vacuolar sorting, but may influence the rate of post-translational processing [Wilkins, T.A., Bednarek, S.Y., and Raikhel, N.V. (1990). Plant Cell 2, 301-313]. To investigate the functional role of the CTPP in processing, assembly, and sorting of barley lectin to vacuoles, a mutant barley lectin cDNA clone lacking the 15-amino acid CTPP was prepared. The CTPP deletion mutant of barley lectin was expressed in tobacco protoplasts, suspension-cultured cells, and transgenic plants. In all three systems, the wild-type barley lectin was sorted to vacuoles, whereas the mutant barley lectin was secreted to the incubation media. Therefore, we conclude that the carboxyl-terminal domain of the barley lectin proprotein is necessary for the efficient sorting of this protein to plant cell vacuoles.
Moving objects databases: issues and solutions (2002)

Consider a database that represents information about moving objects and their location. For example, for a database representing the location of taxi-cabs a typical query may be: retrieve the free cabs that are currently within 1 mile of 33 N. Michigan Ave., Chicago (to pickup a customer). In the military, moving object database applications arise in the context of the digital battlefield and in the civilian industry they arise in transportation systems. Currently, moving object database applications are being developed in an ad hoc fashion. Database management system (DBMS) technology provides a potential foundation upon which to develop these applications, however DBMSs are currently not used for this purpose. The reason is that there is a critical set of capabilities that are needed by moving object database applications and are lacking in existing DBMSs. The objective of our Databases fOr MovINg Objects (DOMINO) project is to build an envelope containing these capabilities on top of existing DBMSs. We describe the problems and our proposed solutions.
Monoamine oxidase inhibition and neuroprotection by N<sup>1</sup>‐propargylphenelzine (2001)

Abstract The ability of N 1 ‐propargylphenelzine and related N 1 ‐propargylhydrazines to inhibit monoamine oxidase‐A (MAO‐A) and ‐B (MAO‐B) and to prevent N‐(2‐chloroethyl)‐N‐ethyl‐2‐bromobenzylamine (DSP‐4)‐induced noradrenergic neurotoxicity was examined. N 1 ‐Propargylphenelzine strongly inhibited MAO‐A and MAO‐B in in vitro assays using rat brain or liver as the enzyme source. In ex vivo studies in rats, both intraperitoneal and oral administration of N 1 ‐propargylphenelzine strongly inhibited brain and liver MAO‐A and MAO‐B. The extent of ex vivo MAO inhibition and increased levels of noradrenaline and 5‐hydroxytryptamine by N 1 ‐propargylphenelzine was comparable to that of phenelzine. Unlike phenelzine, however, N 1 ‐propargylphenelzine did not elevate γ‐aminobutryic acid (GABA) concentrations in rat brain. A single intraperitoneal administration of N 1 ‐propargylphenelzine to mice, 1 week prior to sacrifice, reduced DSP‐4‐induced depletion of noradrenaline in the hippocampus. The brains of N 1 ‐propargylphenelzine‐treated mice from the DSP‐4 neurotoxicity experiments had normal MAO‐B activity, but MAO‐A was significantly inhibited; this was in contrast to animals that had received (–)‐deprenyl, who showed normal MAO‐A activity but a decrease of MAO‐B. The present results indicate that N 1 ‐propargylphenelzine may be a useful neuroprotective compound with a long‐term in vivo propensity to inhibit MAO‐A. Drug Dev. Res. 53:15–21, 2001. © 2001 Wiley‐Liss, Inc.
Genetic mapping of new DNA probes at Xq27 defines a strategy for DNA studies in the fragile X syndrome. (1991)

The fragile X syndrome is the most common cause of familial mental retardation and is characterized by a fragile site at the end of the long arm of the X chromosome. The unusual genetics and cytogenetics of this X-linked condition make genetic counseling difficult. DNA studies were of limited value in genetic counseling, because the nearest polymorphic DNA loci had recombination fractions of 12% or more with the fragile X mutation, FRAXA. Five polymorphic loci have recently been described in this region of the X chromosome. The positions of these loci in relation to FRAXA were defined in a genetic linkage study of 112 affected families. The five loci--DXS369, DXS297, DXS296, IDS, and DXS304--had recombination fractions of 4% or less with FRAXA. The closest locus, DXS296, was distal to FRAXA and had a recombination fraction of 2%. The polymorphisms at these loci can be detected in DNA enzymatically digested with a limited number of restriction endonucleases. A strategy for DNA studies which is based on three restriction endonucleases and on five probes will detect one or more of these polymorphisms in 94% of women. This strategy greatly increases the utility of DNA studies in providing genetic advice to families with the fragile X syndrome.
Highly Permeable Oligo(ethylene oxide)‐<i>co</i>‐poly(dimethylsiloxane) Membranes for Carbon Dioxide Separation (2017)

Abstract A series of cross‐linked, freestanding oligo(ethylene oxide)‐ co ‐(polydimethylsiloxane‐norbornene) membranes with varied composition is synthesized via in situ ring‐opening metathesis polymerization. These membranes show remarkably high CO 2 permeabilities (3400 Barrer) and their separation performance approaches the Robeson upper bound. The excellent permeability of these copolymer membranes provides great potential for real‐world applications where enormous volumes of gases must be separated. The gas transport properties of these films are found to be directly proportional to oligo(ethylene oxide) content incorporation, which stems from the increased solubility selectivity change within the copolymer matrix. This work provides a systematic study of how gas separation performance in rubbery membranes can be enhanced by tuning the CO 2 ‐philicity of their constituent monomeric subunits.
<i>Lactobacillus plantarum</i>-derived Extracellular Vesicles Protect Atopic Dermatitis Induced by<i>Staphylococcus aureus</i>-derived Extracellular Vesicles (2018)

The microbial environment is an important factor that contributes to the pathogenesis of atopic dermatitis (AD). Recently, it was revealed that not only bacteria itself but also extracellular vesicles (EVs) secreted from bacteria affect the allergic inflammation process. However, almost all research carried out so far was related to local microorganisms, not the systemic microbial distribution. We aimed to compare the bacterial EV composition between AD patients and healthy subjects and to experimentally find out the beneficial effect of some bacterial EV composition. Methods: Twenty-seven AD patients and 6 healthy control subjects were enrolled. After urine and serum were obtained, EVs were prepared from samples. Metagenomic analysis of 16s ribosomal DNA extracted from the EVs was performed, and bacteria showing the greatest difference between controls and patients were identified. In vitro and in vivo therapeutic effects of significant bacterial EV were evaluated with keratinocytes and with Staphylococcus aureus-induced mouse AD models, respectively. Results: The proportions of Lactococcus, Leuconostoc and Lactobacillus EVs were significantly higher and those of Alicyclobacillus and Propionibacterium were lower in the control group than in the AD patient group. Therefore, lactic acid bacteria were considered to be important ones that contribute to the difference between the patient and control groups. In vitro, interleukin (IL)-6 from keratinocytes and macrophages decreased and cell viability was restored with Lactobacillus plantarum-derived EV treatment prior to S. aureus EV treatment.
Lesion contrast and detection using sonoelastographic shear velocity imaging: preliminary results (2007)

This paper assesses lesion contrast and detection using sonoelastographic shear velocity imaging. Shear wave interference patterns, termed crawling waves, for a two phase medium were simulated assuming plane wave conditions. Shear velocity estimates were computed using a spatial autocorrelation algorithm that operates in the direction of shear wave propagation for a given kernel size. Contrast was determined by analyzing shear velocity estimate transition between mediums. Experimental results were obtained using heterogeneous phantoms with spherical inclusions (5 or 10 mm in diameter) characterized by elevated shear velocities. Two vibration sources were applied to opposing phantom edges and scanned (orthogonal to shear wave propagation) with an ultrasound scanner equipped for sonoelastography. Demodulated data was saved and transferred to an external computer for processing shear velocity images. Simulation results demonstrate shear velocity transition between contrasting mediums is governed by both estimator kernel size and source vibration frequency. Experimental results from phantoms further indicates that decreasing estimator kernel size produces corresponding decrease in shear velocity estimate transition between background and inclusion material albeit with an increase in estimator noise. Overall, results demonstrate the ability to generate high contrast shear velocity images using sonoelastographic techniques and detect millimeter-sized lesions.
Direct interaction between causative genes of DYT1 and DYT6 primary dystonia (2010)

Primary dystonia is a movement disorder characterized by sustained muscle contractions and in which dystonia is the only or predominant clinical feature. TOR1A(DYT1) and the transcription factor THAP1(DYT6) are the only genes identified thus far for primary dystonia. Using electromobility shift assays and chromatin immunoprecipitation (ChIP) quantitative polymerase chain reaction (qPCR), we demonstrate a physical interaction between THAP1 and the TOR1A promoter that is abolished by pathophysiologic mutations. Our findings provide the first evidence that causative genes for primary dystonia intersect in a common pathway and raise the possibility of developing novel therapies targeting this pathway.
Sensitivity encoding as a means of enhancing the SNR efficiency in steady‐state MRI (2004)

Sensitivity encoding (SENSE) with a receiver coil array is typically used as a means of reducing the scan time in MRI. The speed benefit usually comes at some expense in terms of the signal-to-noise ratio (SNR) efficiency, which has been notorious as the main downside of SENSE and parallel MRI in general. In this work it is shown that in steady-state gradient-echo imaging the parallel approach may as well be used to increase the SNR efficiency. The basic idea is to balance reduced phase encoding by increasing the repetition time. In this fashion both the acquisition duty cycle and the steady-state magnetization can be enhanced, resulting in considerable net gains in SNR yield. It is argued that the reduction factor in parallel imaging is essentially an additional degree of freedom in optimizing the SNR. The optimal SENSE factor depends on scan, tissue, and hardware parameters, assuming values up to 3.0 and higher. The achievable SNR benefit also depends on the spoiling regime and is most pronounced for RF-spoiled techniques. The proposed mechanism is demonstrated by simulations and phantom experiments, as well as by contrast-enhanced angiography in vivo, achieving an approximate doubling of the SNR efficiency.
Cooperation diversity through coding (2003)

We propose a new user cooperation scheme for wireless communications in which we combine cooperation with existing channel coding methods. Simulation results show a significant improvement in the BER for both users, even when the channel between them is poor, or when they have significantly different channel qualities to the base station.
Hot-carrier-induced off-state current leakage in submicrometer PMOSFET devices (1994)

Hot-carrier-induced off-state leakage (HCIOL) currents were successfully used as a new monitor in characterizing device reliability. HCIOL current increases drastically with reducing channel length, but the stress bias only affects the onset time of HCIOL current. For buried-channel PMOSFET's, only the HCIOL currents at the reverse measurement configuration were dominant. However, in surface-channel devices, HCIOL currents at both forward and reverse configurations became important. An empirical HCIOL current model was developed to quantify device lifetime as a function of channel length and stress voltage. Estimated lifetime results indicated that HCIOL current will impose a major limit on device reliability especially for deep-submicrometer technology and low power applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>