gebhart/patrepeval huggingface dataset:
Quantifying streambed deposition and scour from stream and hyporheic water temperature time series (2013)

[1] We propose a new method based on temperature time series of surface and streambed pore waters to monitor local changes in streambed surface elevations at a nominally daily time scale. The proposed method uses the naturally occurring daily temperature signal changes in amplitude and phase between stream water and the water flowing within the streambed sediment. Application of the method in a fine-bedded stream predicts the timing and magnitude of a prescribed sequence of scour and deposition. This provides a new, effective, easy to use, and economic methodology to monitor the temporal evolution of erosion and depositional patterns in rivers.
Network-Attack-Resilient Intrusion-Tolerant SCADA for the Power Grid (2018)

As key components of the power grid infrastructure, Supervisory Control and Data Acquisition (SCADA) systems are likely to be targeted by nation-state-level attackers willing to invest considerable resources to disrupt the power grid. We present Spire, the first intrusion-tolerant SCADA system that is resilient to both system-level compromises and sophisticated network-level attacks and compromises. We develop a novel architecture that distributes the SCADA system management across three or more active sites to ensure continuous availability in the presence of simultaneous intrusions and network attacks. A wide-area deployment of Spire, using two control centers and two data centers spanning 250 miles, delivered nearly 99.999% of all SCADA updates initiated over a 30-hour period within 100ms. This demonstrates that Spire can meet the latency requirements of SCADA for the power grid.
Explosive Nanocrystalline Porous Silicon and Its Use in Atomic Emission Spectroscopy (2002)

A material serving as both matrix and excitation source for atomic emission spectroscopy (AES) is presented in this article. Freshly etched porous silicon is doped with gadolinium nitrate to form an explosive solid, to be loaded with analyte and ignited by coil discharge (see Figure and also front cover for flash upon ignition). With Gd not emitting in the visible region, undisturbed AES spectra of several metals could be recorded.
Repeatable use assessment of silicon carbide as permanent susceptor bed in ex situ microwave remediation of petroleum-impacted soils (2021)

Efficiency of microwave-enabled ex situ soil remediation can be improved by dielectric susceptors. Cost, and environmental burden of these susceptors can be minimized if they are used repeatedly in a permanent bed set-up. In this study, carbon nanofibers, activated carbon, magnetite, and silicon carbide were tested at the lab scale for repeated use in permanent microwave-induced thermal soil remediation. Despite their superior ability to convert microwaves into heat, carbon nanofibers experienced electrokinesis and activated carbon partially combusted in the microwave cavity, which complicates their pragmatic use in remediation applications. Magnetite was also able to convert microwaves into heat effectively and it was relatively more stable; however, repeated heating/and cooling cycles changed its physicochemical properties, which was attributed to oxidation of iron oxides at the air-soil interface. Silicon carbide, on the other hand, was an efficient heating agent and was stable during repeatable heating and cooling cycles. Through 25 heating/cooling cycles, an average peak temperature of 329 ± 55 °C was achieved for a 29 cm3 sample and analysis of dielectric properties after every 10th and 25th cycle indicated that there were no significant losses in thermal conductivity or permittivity of the material. Subsequent remediation experiments with silicon carbide demonstrated that between 89 and 97 % of the total petroleum hydrocarbons were removed from soil including a marked fraction of heavy hydrocarbons when 20.2 kJ g−1 of microwave energy was introduced. In addition, post-treatment experiments demonstrated that soil conditions were capable of supporting seed germination indicating that some conditions of soil were recovered after microwave remediation.
Magnetic resonance coronary angiography. (1993)

Despite the availability of numerous noninvasive tests to identify those with inducible myocardial ischemia, 20% of conventional contrast angiograms demonstrate no significant coronary artery stenoses. Magnetic resonance (MR) imaging is ideally suited for evaluation of the heart, and has already been shown to be highly accurate for the depiction and assessment of cardiac chamber size, ventricular function, and valvular insufficiency. Using conventional spin-echo and gradient-echo techniques, investigators have previously been able to characterize coronary artery bypass grafts as "patent" or "occluded," but visualization of large segments of the native coronary vessels was unsuccessful due to artifacts related to cardiac and respiratory motion. Recently, several new "fast imaging" breath-hold techniques, including k-space segmentation and spiral imaging, have shown great promise for both visualizing the native coronary arteries, assessing vessel patency, and quantifying coronary blood flow. Echo planar MR coronary angiography also appears to be feasible. Further software and hardware improvements are needed, but MR may soon prove to be the premier cardiac imaging technique by providing a comprehensive cardiac evaluation for those with suspected coronary artery disease, including information previously unobtainable by any other noninvasive test.
Preclinical potential of TRAIL-death receptor agonist for the treatment of human prostate cancer (2007)

C242 Clinical trials on TRAIL and death receptor (TRAIL-R1 and TRAIL-R2) agonist antibodies are being carried out through out the world. Until today, there are no small organic molecules that bind to TRAIL-death receptors, and induce apoptosis mainly in cancer cells. Through molecular and biological approaches, we have identified a novel death receptor agonist (small molecular weight organic compound). Death receptor agonist termed as “DRA11” inhibited cell viability and colony formation, and induced apoptosis in androgen-dependent (LNCaP) and -independent (PC-3) human prostate cancer cell lines, but had no effect on human normal prostate epithelial cells and hepatocytes. The combination of DRA11 with TRAIL had an additive effect on apoptosis of prostate cancer cells. DRA11 recruited FADD and activated caspase-8, and thus formed active TRAIL-DISC (death-inducing signaling complex) similar to that of TRAIL. DRA11 inhibited the growth of PC-3 and LNCaP xenografts in nude mice. In vivo, DRA11 inhibited tumor cells proliferation (Ki67 staining) and induced caspase-3 activity and apoptosis (TUNEL staining). Our data suggest, for the first time, that DRA11 is a specific activator of death receptor pathway of apoptosis, and can be used to treat human prostate cancer. Clinical trials are needed to demonstrate its clinical utility for prostate cancer.
US pioneers ‘high speed’ tiny tungsten (2006)

An innovative plasma processing technique has been developed, bringing a new dimension to manufacturing tungsten nano powders. Refractory metal-based nanomaterials can now be produced more quickly and more effectively using newly developed techniques, according to US scientists.
High-Bandwidth Pulsed Microactuators for High-Speed Flow Control (2010)

A systematic study on the design, development, and characterization of high-momentum, high-bandwidth microactuators for high-speed flow control is described in this paper. Beginning with building-block experiments, multiple resonant flow phenomena are used in the actuator design to arrive at an actuator configuration that provides the desired flow properties. The first-generation actuator design consists of an underexpanded source jet incident upon a cavity. The lower surface of this cavity contains micronozzles through which the unsteady microjets (400 μm) issue. Results show that microjets produced by this actuator have a high mean momentum (300―400 m/s) and a significant unsteady component (20―30% of the mean). Experiments were conducted over a large range of parameters in terms of cavity length, source jet nozzle pressure ratio, and impingement distance. The results unequivocally demonstrate the ability to vary the frequency and the amplitude of the mean and unsteady momentum of microjets issuing from this actuator. By varying the dimensions of the actuator by few hundred microns and/or source jet pressure by roughly 1 atm, one is able to vary the frequency rather precisely over a range of 5―20 kHz. A correlation based on Strouhal number and jet column length is suggested for the design of actuators. Actuators in the frequency range of a few to well over 50 kHz have been designed and characterized. It is believed that the frequency range may be extended down to O(100 Hz) and up to O(100 kHz) using this actuator approach.
PPR (2007)

Bit errors occur in wireless communication when interference or noise overcomes the coded and modulated transmission. Current wireless protocols may use forward error correction (FEC) to correct some small number of bit errors, but generally retransmit the whole packet if the FEC is insufficient. We observe that current wireless mesh network protocols retransmit a number of packets and that most of these retransmissions end up sending bits that have already been received multiple times, wasting network capacity. To overcome this inefficiency, we develop, implement, and evaluate a partial packet recovery (PPR) system.
Detection of air in sensing lines from standing wave frequencies (1987)

In the Tennessee Valley Authority's (TVA's) nuclear and fossil plants, liquid-filled sensing lines are used extensively to transmit pressure from various process lines to electronic pressure transmitters. Because air can affect pressure transmission, TVA's engineering laboratory has been working to develop an instrument for detecting air in sensing lines. The presence of air can be detected by comparing measurements of the standing pressure wave frequencies for a sensing line with reference measurements taken when the line contains no air. Air in a sensing line shifts standing wave frequencies from their values with no air and can provide internal spring-like boundaries for surge oscillations. Standing pressure waves are elastic waves propagating through water in pipes. Characteristics to every piping system is an infinite number of natural, resonant frequencies at which standing waves can oscillate. Surge oscillation in sensing lines refers to harmonic oscillations of water columns acting as rigid masses. Both active and passive techniques have been tested. In either technique, air is indicated if standing wave frequencies are shifted relative to their values with no air or if a new surge oscillation frequency is detected. In both techniques, pressure fluctuations are measured with a hydrophone. Fourier transform techniques decompose themore » pressure signal into its various frequency components. The peaks in the frequency spectrum represent the standing wave and surge oscillation frequencies.« less
Novel bistable liquid crystal displays based on grating alignment (2000)

The ability of surface relief gratings to align liquid crystals has been known for many years. Renewed interest has recently been stimulated through the invention of novel devices in which the grating gives the additional benefit of bistability. This allows complex images to be retained without constant updating, and without the need for Thin Film Transistors at each pixel. Two types of bistable liquid crystal have been demonstrated: azimuthal bistability using bi-gratings, and zenithal bistability using gratings that give surface alignment to the liquid crystal director parallel to the local surface normal. The latter type is called ZBD and gives exceptional performance compared to all other bistable display technologies. This is because the nematic liquid crystal has different tilts in the direction of the applied field, allowing latching times of better than 40 microseconds (at 30 V) and switching thresholds below 10 V. The orientation of the liquid crystal is not required to change at the surface when switching between the two states and so there are no problems with image sticking. Also, the bistability is surface induced, which makes the states exceptionally tolerant to mechanical stress. An 83 by 90 pixel display is demonstrated, illustrating the potential of this exciting new technology.
Redesign of a Plugged β-Barrel Membrane Protein (2010)

The redesign of biological nanopores is focused on bacterial outer membrane proteins and pore-forming toxins, because their robust β-barrel structure makes them the best choice for developing stochastic biosensing elements. Using membrane protein engineering and single-channel electrical recordings, we explored the ferric hydroxamate uptake component A (FhuA), a monomeric 22-stranded β-barrel protein from the outer membrane of Escherichia coli. FhuA has a luminal cross-section of 3.1 × 4.4 nm and is filled by a globular N-terminal cork domain. Various redesigned FhuA proteins were investigated, including single, double, and multiple deletions of the large extracellular loops and the cork domain. We identified four large extracellular loops that partially occlude the lumen when the cork domain is removed. The newly engineered protein, FhuAΔC/Δ4L, was the result of a removal of almost one-third of the total number of amino acids of the wild-type FhuA (WT-FhuA) protein. This extensive protein engineering encompassed the entire cork domain and four extracellular loops. Remarkably, FhuAΔC/Δ4L forms a functional open pore in planar lipid bilayers, with a measured unitary conductance of ∼4.8 nanosiemens, which is much greater than the values recorded previously with other engineered FhuA protein channels. There are numerous advantages and prospects of using such an engineered outer membrane protein not only in fundamental studies of membrane protein folding and design, and the mechanisms of ion conductance and gating, but also in more applicative areas of stochastic single-molecule sensing of proteins and nucleic acids.
<title>Time varying halftoning</title> (1999)

For displays with limited color capability, color halftoning is often used to induce the illusion of more color levels than the device can truly render. In such cases, the pattern created by the halftone technique can be visible due to the limited geometrical resolution of the display device. Unlike printing, the halftone pixels of the display devices are still visible and the patterns created on display devices can be easily detected. When animated images are played and the frame rates are played in a mode that uses a limited number of colors and halftoning techniques, the patterns are very visible because they are perceived as a reference system fix to the playing window, while the image content is moving. In this paper we propose a halftone technique that varies the halftone pattern in time such that the pattern visibility is reduced. This conducts to a higher quality of the displayed image, especially noticeable for dynamic images. The technique enables the use of display devices (or displaying modes) with limited color capability for higher quality images.
A novel semiconductor pixel device and system for X-ray and gamma ray imaging (2002)

We are presenting clinical images (objects, mammography phantoms, dental phantoms, dead animals) and data from a novel X-ray imaging device and system. The device comprises a pixel semiconductor detector flip-chip joined to an ASIC circuit. CdZnTe and Si pixel detectors with dimensions of the order of 1 cm/sup 2/ have been implemented with a pixel pitch of 35 /spl mu/m. Individual detectors comprise, therefore, tens of thousands of pixels. A novel ASIC accumulates charge created from directly absorbed X-rays impinging on the detector. Each circuit on the ASIC, corresponding to a detector pixel, is capable of accumulating thousands of X-rays in the energy spectrum from a few to hundreds of keV with high efficiency (CdZnTe). Image (X-ray) accumulation times are user controlled and range from just a few to hundreds of ms. Image frame updates are also user controlled and can be provided as fast as every 20 ms, thus offering the possibility of real time imaging. The total thickness of an individual imaging the including the mounting support does not exceed 4 mm. Individual imaging tiles are combined in a mosaic providing an imaging system with any desired shape and useful active area. The mosaic allows for cost effective replacement of individual tiles. A scanning system, allows for elimination, in the final image, of any inactive space between the imaging tiles without use of software interpolation techniques. The Si version of our system has an MTF of 20% at 14 1p/mm and the CdZnTe version an MTF of 15% at 10 1p/mm. Our digital imaging devices and systems are intended for use in X-ray and gamma-ray imaging for medical diagnosis in a variety of applications ranging from conventional projection X-ray imaging and mammography to fluoroscopy and CT scanning. Similarly, the technology is intended for use in non destructive testing, product quality control and real time on-line monitoring. The advantages over existing X-ray digital imaging modalities (such as digital imaging plates, scintillating screens coupled to CCDs etc.) include compactness, direct X-ray conversion to an immediate real time digital display, exquisite image resolution, dose reduction and large continuous imaging areas. Our measurements and images confirm that this new digital imaging system compares favourably to photoluminescence.
P1‐273: Development of Alzheimer AFFITOPE vaccines ‐ from concept to clinical testing (2009)

Based on the notion that cerebral accumulation of Aβ is central to the AD pathogenesis and endowed with the knowledge that emerged during clinical testing of the first AD vaccine, AN1792, we designed a new generation of Alzheimer vaccines. Rather than relying on full-length Aβ or fragments thereof, AFFITOPE vaccines use short peptides, mimicking parts of the native Aβ sequence, as their antigenic component. The technology created to identify these peptides, termed AFFITOPE-technology, concurrently provides the basis for the multi-component safety concept realized in AFFITOPE vaccines. First, as they are non-self, AFFITOPES don't need to break tolerance typically established against self proteins. This allows us to use aluminium hydroxide, the agent first approved as immunological adjuvant for human use and, thus, exhibiting an excellent safety profile. Second, AFFITOPES employed in Alzheimer vaccines are only 6 amino acids in length, which precludes the activation of Aβ-specific autoreactive T cells. Third, and above all, the AFFITOPE technology allows for controlling the specificity of the vaccine-induced antibody response focusing it exclusively on Aβ and preventing crossreactivity with APP. In a program based on two AFFITOPES of the N-terminus of Aβ (AD 01 and AD02), this approach was taken all the way from concept to clinical application. Preclinical testing established the validity of the AFFITOPE concept. Based on these data, two phase I trials designed to primarily assess potential immunotoxicity of the first two AFFiRiS Alzheimer vaccine' candidates were initiated. To this end, patients (n=24 / trial) exhibiting mild to moderate AD, received 4 vaccinations of a single dose of either vaccine at 4-week intervals. Patients are closely monitored for safety, the primary study objective, up to 2 months after the last immunization. In addition, information on the immunological and clinical activity of the two vaccines is gathered. Clinical data obtained so far support the safety concept inherent to AFFITOPE Alzheimer vaccines. In conclusion, AFFiRiS develops a new generation of Alzheimer vaccines. First clinical results support its safety features. Further clinical testing will focus on the vaccines' effects on the pathology underlying AD and their clinical activity.
Amino acid sequence of alpha-amylase from Bacillus amyloliquefaciens deduced from the nucleotide sequence of the cloned gene. (1983)

We have isolated by molecular cloning the gene coding for the alpha-amylase (1,4-alpha-D-glucan glucanohydrolase, EC 3.2.1.1.) from Bacillus amyloliquefaciens and determined its complete nucleotide sequence. The gene cloned in the plasmid pUB110 using Bacillus subtilis as a host, was contained in a 2.3-kilobase insert. Starting from an ATG initiator codon, an open reading frame comprising a total of 514 amino acids (1542 base pairs) was found within the cloned DNA fragment. The gene region encoding the COOH terminus of alpha-amylase was located by direct COOH-terminal analysis of the purified exoenzyme. The NH2-terminal portion of the gene encodes a 31 amino acid-long signal peptide (Palva, L., Pettersson, R. F., Kalkkinen, N., Lehtovaara, P., Sarvas, M., Söderlund, H., Takkinen, K., and Kääriäinen, L. (1981) Gene 15, 43-51). Since the signal peptide is correctly cleaved in the new host, as shown here by direct NH2-terminal sequence analysis, the exoamylase consists of 483 amino acid residues, corresponding to a molecular weight of 54,778. The reading frame used to deduce the amino acid sequence was found to be correct by comparison with partial amino acid sequence data published previously (Detera, S. D., and Friedberg, F. (1979) Int. J. Peptide Protein Res. 14, 364-372; Chung, H., and Friedberg, F. (1980) Biochem. J. 185, 387-395). Several differences between the sequence presented here and the partial ones published previously, however, were found. The nucleotide sequences both 5' and 3' to the alpha-amylase gene revealed palindromic structures including a stretch of six T-residues, suggesting transcription termination signals on both sides of the gene. Thus, it appears that alpha-amylase is translated from a monocistronic mRNA.
HIV hijacks cholesterol transporter ABCA1 to get access to cellular cholesterol (2009)

Cholesterol plays an important role in the HIV life cycle, and cholesterol depletion impairs both production and infectivity of HIV virions. Such dependence on cholesterol suggests that HIV may have evolved mechanisms to ensure access to cellular cholesterol during viral assembly. Recently, we demonstrated that HIV-1, via its protein Nef, inhibits activity of the cellular cholesterol transporter ABCA1 and impairs reverse cholesterol transport (RCT) from infected cells. In this study, we examined interaction between Nef and ABCA1 and investigated the role of ABCA1 in cholesterol delivery to nascent HIV virions. ABCA1 is a 12-transmembrane domain protein, and co-immunoprecipitation analysis using Nef and various fragments of ABCA1 identified multiple sites of interaction. Importantly, Nef was found to interact with the 46-aminoacid carboxyl-terminal domain of ABCA1, which was previously implicated in RCT. Mutation of leucines to alanines in positions 2230, 2233 and 2235 impaired interaction of this C-terminal domain of ABCA1 with Nef. When these mutations were introduced in the full-length ABCA1, such mutant protein was able to support RCT but lost sensitivity to Nef. To further characterize the role of ABCA1 inhibition in HIV biology, we analyzed cholesterol content of lipid rafts and HIV virions produced in cells expressing or not ABCA1. This analysis demonstrated that ABCA1 expression significantly reduced lipid raft cholesterol content, resulting in a corresponding reduction of virus-associated cholesterol and viral infectivity. This result is consistent with ABCA1-mediated redirection of cholesterol from lipid rafts (sites of HIV assembly) to non-raft regions of the plasma membrane (physiological localization of ABCA1). Intriguingly, Nef expression induced re-localization of ABCA1 to lipid rafts, suggesting that HIV hijacks the ABCA1 pathway to deliver cholesterol to the sites of HIV assembly.