gebhart/patrepeval huggingface dataset:
The impact and control of biofouling in marine aquaculture: a review (2012)

Biofouling in marine aquaculture is a specific problem where both the target culture species and/or infrastructure are exposed to a diverse array of fouling organisms, with significant production impacts. In shellfish aquaculture the key impact is the direct fouling of stock causing physical damage, mechanical interference, biological competition and environmental modification, while infrastructure is also impacted. In contrast, the key impact in finfish aquaculture is the fouling of infrastructure which restricts water exchange, increases disease risk and causes deformation of cages and structures. Consequently, the economic costs associated with biofouling control are substantial. Conservative estimates are consistently between 5-10% of production costs (equivalent to US$ 1.5 to 3 billion yr(-1)), illustrating the need for effective mitigation methods and technologies. The control of biofouling in aquaculture is achieved through the avoidance of natural recruitment, physical removal and the use of antifoulants. However, the continued rise and expansion of the aquaculture industry and the increasingly stringent legislation for biocides in food production necessitates the development of innovative antifouling strategies. These must meet environmental, societal, and economic benchmarks while effectively preventing the settlement and growth of resilient multi-species consortia of biofouling organisms.
Optically switched erbium fiber laser using a tunable fiber-Bragg grating (2010)

The ability to tune the Bragg wavelength of a fibre-Bragg grating (FBG) in an all-fibre laser can offer added functionality such as laser wavelength tunability, polarization selectivity,1 and Q-switching.2 Compared to current techniques which rely on mechanically straining the FBG to achieve Bragg-wavelength tunability, an all-optical technique for tuning an FBG offers potentially faster switching speeds and a more robust and simple cavity. All-optical tuning of the Bragg wavelength of an FBG has been demonstrated previously by resonant optical pumping; however this technique has only been applied to passive systems for switching applications.<sup>3</sup> In this work, we have further investigated this optical-tuning process, experimentally identifying three time-scale regimes, and optimised it for application to active systems. Furthermore, we constructed an erbium all-fibre laser cavity consisting of an outputcoupler FBG and an optically-tunable, high-reflector FBG. The cavity pumping and the optical tuning of the FBG were kept independent. By repetitively tuning the high-reflector FBG on- and off-resonance with the output-coupler FBG, we actively Q-switched the erbium fibre laser at repetition rates up to 35 kHz, limited only by our diode driver. We show that grating tuning at &gt;300 kHz is possible with the existing embodiment, and discuss further potential to operate at MHz rates.
Optimizing the De-Bruijn Code of Rotary Optical Encoders Preventing From the Photocurrent Blooming (2020)

The De-Bruijn sequences could provide appropriate circular arrangements to achieve a single-track absolute rotary optical encoder in the servo motor application. One example used popularly is the maximum length sequences. High-resolution single-track encoders need a sensor array to obtain the position signal simultaneously. Nevertheless, the individual photocurrents would interference by other adjacent photocurrents, like the photocurrent blooming. The circumstances would increase the bias noise for the digital binarization. The concept in this article would try to find the optimal De-Bruijn sequences to reduce the photocurrent blooming interference intrinsically without signal process remodification. Three different types of the 9-bits codes, the adjacent De-Bruijn code, the quarter De-Bruijn codes, and the optimal De-Bruijn codes, are analyzed, manufactured, and experimented in the actual encoders. Based on the open-factor of the eye-diagram, the adjacent De-Bruijn code has 0.328 and would be the worse signal quality in De-Bruijn sequences. The quarter De-Bruijn codes have 0.386 of the open-factor with 17.7% improvement to adjacent De-Bruijn code. Finally, the optimal De-Bruijn codes have 0.436 of the open-factor with 32.9% improvement to the traditional M-code. The fact would mean the possible ability of 3-bits progress from 9-bits of adjacent De-Bruijn code to 12-bits of the optimal De-Bruijn codes under the same signal-to-noise ratio.
Surface plasmon resonator: Design, construction, and observation in the farfield (2010)

We have studied the behavior of surface plasmons (SPs) in valley like structures [Schroter et al., Ultramicroscopy 68, 223 (1997)] and found that SPs traveling in both directions in such a cavity yield interference patterns in the farfield, which can be measured as specular and retroreflection. We have studied and designed the structures using finite element method in addition to a heuristic model, fabricated the devices using photolithography and experimentally verified the operation of the resonators, by observing the interference patterns of the specular and retroreflection in the farfield. We have found that the experimental results agree with the simulations, and explained the discrepancies. These structures can be useful in the study of the propagation length of SPs via observation in the farfield of the specular and the retroreflected light in laser industry and could be miniaturized to yield small biosensors.
Crystal structure of enterotoxigenic Escherichia coli colonization factor CS6 reveals a novel type of functional assembly (2012)

Coli surface antigen 6 (CS6) is a widely expressed enterotoxigenic Escherichia coli (ETEC) colonization factor that mediates bacterial attachment to the small intestinal epithelium. CS6 is a polymer of two protein subunits CssA and CssB, which are secreted and assembled on the cell surface via the CssC/CssD chaperone usher (CU) pathway. Here, we present an atomic resolution model for the structure of CS6 based on the results of X-ray crystallographic, spectroscopic and biochemical studies, and suggest a mechanism for CS6-mediated adhesion. We show that the CssA and CssB subunits are assembled alternately in linear fibres by the principle of donor strand complementation. This type of fibre assembly is novel for CU assembled adhesins. We also show that both subunits in the fibre bind to receptors on epithelial cells, and that CssB, but not CssA, specifically recognizes the extracellular matrix protein fibronectin. Taken together, structural and functional results suggest that CS6 is an adhesive organelle of a novel type, a hetero-polyadhesin that is capable of polyvalent attachment to different receptors.
Speaker Diarization Using EHMM and CLR (2012)

To solve the problem of speaker information deficiency affecting accuracy of segmentation in the conventional speaker diarization system,this paper proposes the method of multistage speaker segmentation and clustering algorithm based on EHMM and CLR.On the basis of traditional algorithm,we develop a resegmentation and reclustering scheme which combine with unsupervised segmentation algorithm based on GLR distance measure and a hierachical clustering algorithm based on BIC.Test on the national institute of standards and technology(NIST) RT′03S corpus,by comparing the conventional one,more than 41% of relative diarization error is reduced.
Structure and Function of the Rubella Virus Proteins (1985)

Rubella virus strain HPV-77 contains three structural polypeptides. The nucleocapsid is constructed with the C polypeptide chain, which has a molecular weight of 30,000. The envelope proteins are constructed with two glycopolypeptides; the E1 glycopolypeptide has a molecular weight of 63,000, and the E2 glycopolypeptide has a molecular weight of 45,000-48,000. The nucleocapsid capsomere is approximately 6.2S, has a molecular weight of 130,000, and consists of two disulfide-linked dimers of the C polypeptide. The E1 and E2 glycopolypeptides are associated, but the size and structure of the spike protein have not been determined. Strain-specific antigens were detected within the E2 glycopolypeptide in all of the strains tested. In chronologic serum samples, the titers of antibody to the E2 and C polypeptides were the first to decline. Hybridomas were produced that exhibited hemagglutination-inhibiting and neutralizing activities; however, these functions did not always correlate. Both the hemagglutination-inhibiting and neutralizing antibodies reacted with the E1 glycopolypeptide.
Dietary polyunsaturated fatty acids and regulation of gene transcription (2002)

Dietary polyunsaturated fatty acids (PUFAs) are a source of energy and structural components for cells. PUFAs also have dramatic effects on gene expression by regulating the activity or abundance of four families of transcription factor, including peroxisome proliferator activated receptor (PPAR) (alpha, beta and gamma), liver X receptors (LXRs) (alpha and beta), hepatic nuclear factor-4 (HNF-4)alpha and sterol regulatory element binding proteins (SREBPs) 1 and 2. These transcription factors play a major role in hepatic carbohydrate, fatty acid, triglyceride, cholesterol and bile acid metabolism. Non-esterified fatty acids or fatty acid metabolites bind to and regulate the activity of PPARs, LXRs and HNF-4. In contrast, PUFAs regulate the nuclear abundance of SREBPs by controlling the proteolytic processing of SREBP precursors, or regulating transcription of the SREBP-1c gene or turnover of mRNA(SREBP-1c). The n3 and n6 PUFAs are feed-forward activators of PPARs, while these same fatty acids are feedback inhibitors of LXRs and SREBPs. Saturated fatty acyl coenzyme A thioesters activate HNF-4 alpha, while coenzyme A thioesters of PUFAs antagonize HNF-4 alpha action. Understanding how fatty acids regulate the activity and abundance of these and other transcription factors will likely provide insight into the development of novel therapeutic strategies for better management of whole body lipid and cholesterol metabolism.
Interspecies cathelicidin comparison reveals divergence in antimicrobial activity, TLR modulation, chemokine induction and regulation of phagocytosis (2017)

Cathelicidins are short cationic peptides initially described as antimicrobial peptides, which can also modulate the immune system. Because most findings have been described in the context of human LL-37 or murine CRAMP, or have been investigated under varying conditions, it is unclear which functions are cathelicidin specific and which functions are general cathelicidin properties. This study compares 12 cathelicidins from 6 species under standardized conditions to better understand the conservation of cathelicidin functions. Most tested cathelicidins had strong antimicrobial activity against E. coli and/or MRSA. Interestingly, while more physiological culture conditions limit the antimicrobial activity of almost all cathelicidins against E. coli, activity against MRSA is enhanced. Seven out of 12 cathelicidins were able to neutralize LPS and another 7 cathelicidins were able to neutralize LTA; however, there was no correlation found with LPS neutralization. In contrast, only 4 cathelicidins enhanced DNA-induced TLR9 activation. In conclusion, these results provide new insight in the functional differences of cathelicidins both within and between species. In addition, these results underline the importance not to generalize cathelicidin functions and indicates that caution should be taken in extrapolating results from LL-37- or CRAMP-related studies to other animal settings.
Spectral differential imaging using kernel phase with CHARIS/SCExAO: technique performance and current limitation (2022)

Kernel phase interferometry (KPI) is a data processing technique that allows for the detection of assymetries arising from companions of disks in high-Strehl AO-corrected images, close to or beyond the limit of traditional approaches. We show that this technique can be applied to the CHARIS IFS (with SCExAO), by recovering a known binary HD 44927 with CHARIS’s high resolution K-band mode. Currently, KPI is limited by residual systematic errors in the kernel phases. We show that these errors can be mitigated during calibration, by taking advantage of the information available in adjacent wavelength bands. This spectral differential imaging (SDI) calibration method is a promising avenue towards achieving photon noise limited kernel phase observations.
Structural Performance of Steel-Concrete-Steel Sandwich Composite Structures (2010)

This paper investigates the structural performance of steel-concrete-steel (SCS) sandwich structures comprising a lightweight concrete core sandwiched in between two steel plates. Different types of mechanical shear connectors such as stud shear connectors and Bi-Steel bar connectors are reviewed and their uses in SCS sandwich construction are discussed. Special J-hook connectors are developed and their uses are not restricted by the concrete core thickness. Direct shear (push-out test) and tension tests have been carried out on J-hook connectors to investigate their performance in transferring shear and tension forces between steel and concrete. The structural performance of SCS sandwich beams and slabs with J-hook connectors subjected to static and dynamic loads is also investigated and test results show that SCS sandwich structures with the J-hook connectors are capable of resisting impact with less degree of damage in comparison with the sandwich structures with overlapping stud shear connectors. The plastic capacity of the sandwich beams and slabs can be predicted with reasonable accuracy using the plastic analysis described in this paper.
Identification of the human cytochrome P450, P450RAI-2, which is predominantly expressed in the adult cerebellum and is responsible for all-trans-retinoic acid metabolism (2000)

Retinoids, particularly all-trans-retinoic acid (RA), are potent regulators of cell differentiation, cell proliferation, and apoptosis. The role of all-trans-RA during development and in the maintenance of adult tissues has been well established. The control of all-trans-RA levels in cells and tissues is regulated by the balance between its biosynthesis and its catabolism to inactive metabolites. The cytochrome P450 enzyme P450RAI (herein renamed P450RAI-1) is partially responsible for this inactivation of all-trans-RA. In this report, we describe the identification, molecular cloning, and characterization of a second related enzyme, P450RAI-2, which is also involved in the specific inactivation of all-trans-RA. Transiently transfected P450RAI-2 can convert all-trans-RA to more polar metabolites including 4-oxo-, 4-OH-, and 18-OH-all-trans-RA. Competition experiments with other retinoids suggest that all-trans-RA is the preferred substrate. The high level of expression of P450RAI-2, particularly in the cerebellum and pons of human adult brain, suggests a unique role for this enzyme in the protection of specific tissues from exposure to retinoids.
Control of DNA Hybridization with Photocleavable Adducts¶ (2005)

Abstract Previous reports have shown that 1-(4,5-dimethoxy-2-nitrophenyl)ethyl ester (DMNPE) adducts coupled to DNA plasmids block transcription in vitro and in vivo until removed with light. In this report, we explore the use of DMNPE to control DNA hybridization. We found that DMNPE-caged oligonucleotides have changed spectrophotometric and electrophoretic properties that can be restored with light exposure. Caged oligonucleotides have slower electrophoretic mobility than noncaged oligonucleotides and caged oligonucleotides exposed to light. Effects of caging on hybridization were assessed in a fluorescence-based assay using a 20mer caged DNA oligonucleotide complementary to a 30mer molecular beacon. Fluorescence results indicate that hybridization is reduced and subsequently restored by light. Subsequent gel shift assays confirmed these results. Hybridization activity of caged oligonucleotides with an average of 14–16 DMNPE adducts per oligonucleotide was 14% of noncaged control oligonucleotides and after 365 nm photolysis, increased to nearly 80% of controls. Spectrophotometric characterization of caged oligonucleotides exposed to light and then filtered to remove the released DMNPE adducts indicates two to four attached cage groups remaining following photoactivation. These results suggest that this light-based technology can be used as a tool for the spatial and temporal regulation of hybridization-based DNA bioactivity.
A New Family of Ultralow Loss Reversible Phase‐Change Materials for Photonic Integrated Circuits: Sb2S3 and Sb2Se3 (2020)

Abstract Phase‐change materials (PCMs) are seeing tremendous interest for their use in reconfigurable photonic devices; however, the most common PCMs exhibit a large absorption loss in one or both states. Here, Sb 2 S 3 and Sb 2 Se 3 are demonstrated as a class of low loss, reversible alternatives to the standard commercially available chalcogenide PCMs. A contrast of refractive index of Δ n = 0.60 for Sb 2 S 3 and Δ n = 0.77 for Sb 2 Se 3 is reported, while maintaining very low losses ( k &lt; 10 −5 ) in the telecommunications C‐band at 1550 nm. With a stronger absorption in the visible spectrum, Sb 2 Se 3 allows for reversible optical switching using conventional visible wavelength lasers. Here, a stable switching endurance of better than 4000 cycles is demonstrated. To deal with the essentially zero intrinsic absorption losses, a new figure of merit (FOM) is introduced taking into account the measured waveguide losses when integrating these materials onto a standard silicon photonics platform. The FOM of 29 rad phase shift per dB of loss for Sb 2 Se 3 outperforms Ge 2 Sb 2 Te 5 by two orders of magnitude and paves the way for on‐chip programmable phase control. These truly low‐loss switchable materials open up new directions in programmable integrated photonic circuits, switchable metasurfaces, and nanophotonic devices.
Estimation of heterozygosity for single-probe multilocus DNA fingerprints. (1992)

In spite of the increasing application of DNA fingerprinting to natural populations and to the genetic identification of humans, explicit methods for estimation of basic population genetic parameters from DNA fingerprinting data have not been developed. Contributing to this omission is the inability to determine, for multilocus fingerprinting probes, relatively important genetic information, such as the number of loci, the number of alleles, and the distribution of these alleles into specific loci. One of the most useful genetic parameters that could be derived from such data would be the average heterozygosity, which has traditionally been employed to measure the level of genetic variation within populations and to compare genetic variation among different loci. We derive here explicit formulas for both the estimation of average heterozygosity at multiple hypervariable loci and a maximum value for this estimate. These estimates are based upon the DNA restriction-pattern matrices that are typical for fingerprinting studies of humans and natural populations. For several empirical data sets from our laboratory, estimates of average and maximal heterozygosity are shown to be relatively close to each other. Furthermore, variances of these statistics based on simulation studies are relatively small. These observations, as well as consideration of the effect of missing alleles and alternate numbers of loci, suggest that the average heterozygosity can be accurately estimated using phenotypic DNA fingerprint patterns, because this parameter is relatively insensitive to the lack of certain genetic information.
Plasma-Enhanced, Hypersonic Performance Enabled by MHD Power Extraction (2005)

This paper reviews work underway on the development of new technologies that will enhance the performance of hypersonic vehicles through plasma-related processes and the utilization of MHD to provide the large power levels that are required to drive these processes. Three technologies are discussed for plasma-enhanced hypersonic performance. These include: (1) the use of off-body plasmas for drag reduction, steering, and enhanced inlet performance; (2) the use of surface or near-surface plasmas for mitigating local heating and controlling separation; and (3) the use of electron beam and plasma processes for controlling combustion for enhanced performance inside the engine and for local heat addition applications in other regions of the flow path. For realistic scale vehicles, the energies required for these applications exceed the present capability of on-board auxiliary power units, and, therefore, will require power to be generated directly from the hypersonic air passing over the vehicle or through the engine. In the high Mach number regime characteristic of re-entry vehicles, there is sufficient heating of the air to allow MHD power extraction using equilibrium ionization of alkali vapor seed material. By replacing a portion of the vehicle surface with a hollow core truss structure containing an embedded magnet coil, hundreds of kilowatts of power can be extracted during re-entry and used for vehicle control or other applications. At lower Mach numbers, MHD power extraction can be done downstream of the engine, then the temperature of the exhaust can be high enough to allow conductivity to be achieved with alkali seeding. This MHD generated power extracted from the flow aft of the engine can be used for plasma control upstream of the engine as well as for engine performance enhancement. Some aspects of this reverse energy bypass concept are analyzed in the paper, including plasma heating of the inlet flow that would allow elimination of the isolator, snowplow surface arcs for boundary layer and separation control, and electron beam and microwaves for initiation and control of combustion.
The Effect of Offset Correction and Cursor on Mid-Air Pointing in Real and Virtual Environments (2018)

Pointing at remote objects to direct others' attention is a fundamental human ability. Previous work explored methods for remote pointing to select targets. Absolute pointing techniques that cast a ray from the user to a target are affected by humans' limited pointing accuracy. Recent work suggests that accuracy can be improved by compensating systematic offsets between targets a user aims at and rays cast from the user to the target. In this paper, we investigate mid-air pointing in the real world and virtual reality. Through a pointing study, we model the offsets to improve pointing accuracy and show that being in a virtual environment affects how users point at targets. In the second study, we validate the developed model and analyze the effect of compensating systematic offsets. We show that the provided model can significantly improve pointing accuracy when no cursor is provided. We further show that a cursor improves pointing accuracy but also increases the selection time.
Overview of Space Transportation and Propulsion at NASA (2003)

Topics considered include: 1. Scientific discovery: The search for the life beyond Earth. Understanding our Planet. Understanding our Universe. Exploration of the Planets and beyond. 2. The ultimate high ground for national security: Intelligence, communications, rapid response, GPS. 3. Space-based commerce: Communications and Earth observing.