gebhart/patrepeval huggingface dataset:
Borrelia burgdorferi contains repeated DNA sequences that are species specific and plasmid associated (1990)

Borrelia burgdorferi, the causative agent of Lyme borreliosis, contains linear and supercoiled circular (SC) plasmids. Because SC plasmids are present in multiple copies, these plasmids were examined for species-specific sequences that could serve as high-copy-number target DNAs for a diagnostic probe. Three EcoRI fragments (4.3, 4.2, and 3.5 kilobase pairs [kb]) that hybridized with multiple DNA fragments from B. burgdorferi were identified and cloned from a SC plasmid-enriched fraction. The 4.2- and 3.5-kb fragments were similar in that they hybridized with each other and with similar-sized EcoRI fragments from two unrelated strains of B. burgdorferi. The 4.3-kb fragment did not hybridize with the other two cloned sequences. Both types of sequences hybridized with most of the SC plasmids in seven B. burgdorferi isolates, whereas only a single 49-kb linear plasmid, found in two of the seven strains tested, hybridized with the cloned sequences. None of the cloned sequences hybridized with chromosomal DNA from B. burgdorferi or with total DNA or SC plasmids from Borrelia hermsii, B. turicatae, B. coriaceae, B. parkeri, or B. anserina. These data indicate that the repeated DNA sequences described in this study appear to be plasmid associated and specific to B. burgdorferi. Heteroduplexes formed from the 4.2- and 3.5-kb fragments showed that hybridizing regions in each fragment comprise a 1.8-kb conserved region that is adjacent to a 1.5-kb region that exhibits greater sequence variability. The sequence divergence seen in the variable region is likely the result of genetic drift and may mean that these regions represent closely related genes that encode functionally similar but antigenically distinct proteins.
Polarization Detection of a Fluctuating Radar Target (1983)

A mathematical framework is developed which allows a polarization description of a received radar signal for the purpose of target-clutter discrimination. Statistical models that include all changes in the polarization of an incident radar signal upon reflection are also developed for both targets and clutter. Using these models, a detector that thresholds various functions of the polarization-related parameters known as Stokes parameters is analyzed, and its performance is compared with the performance of existing detectors. Two constant false-alarm rate detection statistics are found, one of which shows an improvement in performance over the pseudocoherent detector that thresholds the sine of the relative phase between two orthogonally received electric fields.
Correlating Intrusion Events and Building Attack Scenarios Through Attack Graph Distances (2005)

We map intrusion events to known exploits in the network attack graph, and correlate the events through the corresponding attack graph distances. From this, we construct attack scenarios, and provide scores for the degree of causal correlation between their constituent events, as well as an overall relevancy score for each scenario. While intrusion event correlation and attack scenario construction have been previously studied, this is the first treatment based on association with network attack graphs. We handle missed detections through the analysis of network vulnerability dependencies, unlike previous approaches that infer hypothetical attacks. In particular, we quantify lack of knowledge through attack graph distance. We show that low-pass signal filtering of event correlation sequences improves results in the face of erroneous detections. We also show how a correlation threshold can be applied for creating strongly correlated attack scenarios. Our model is highly efficient, with attack graphs and their exploit distances being computed offline. Online event processing requires only a database lookup and a small number of arithmetic operations, making the approach feasible for real-time applications.
Selective modulation of brain network dynamics by seizure therapy in treatment-resistant depression (2018)

This study presents the first evidence for the modulation of global brain network dynamics by seizure therapy. Successful seizure therapy was shown to selectively modulate network dynamics for therapeutic efficacy.
Spatio-Temporal Cell Cycle Analysis Using 3D Level Set Segmentation of Unstained Nuclei in Line Scan Confocal Fluorescence Images (2006)

Automated analysis of live cells over extended time periods requires both novel assays and automated image analysis algorithms. Among other applications, this is necessary for studying the effect of inhibitor compounds which are designed to block the replication of cancerous cells in a high-throughput environment. Due to their toxicity, fluorescent dyes cannot be used to mark nuclei. Instead, the cell cycle itself may be marked with a fluorescent protein. This paper describes a set of image analysis methods designed to automatically segment nuclei in 2D time-lapse images. Since each nucleus is unstained, it needs to be segmented from the surrounding stained cytoplasm, and since the appearance of each cell depends on its stage in the cell cycle, standard image processing techniques cannot be used for localization. This paper addresses these challenges by segmenting the spatio-temporal volume using level sets. Experimental results show the promise of this approach
Tapped Serial Interferometric Fiber Sensor Array with Time Division Multiplexing (1988)

We report a new architecture for multiplexed interferometric fiber-optic sensors based on time-division addressing. Intrinsic crosstalk of the system is analysed and compared to experimental results obtained using a three element network.
Thin, X-ray-Transparent Windows for Imaging Applications with a Pneumatically Pressurized Enclosure (2007)

We have developed a novel thin, x‐ray‐transparent window system for environmental chambers involving pneumatic pressures above 10 bar. The windows allow for x‐ray access to fuel sprays injected into a pressurized chamber that mimics realistic internal combustion engine cylinder operating conditions. The design of the window system and its experimental test results are presented in this paper, as well as its further development for in situ x‐ray imaging applications in a high‐pressure and high‐temperature environment.
A nickel containing polyoxometalate water oxidation catalyst (2012)

A new pentanickel silicotungstate complex, K(10)H(2)[Ni(5)(OH)(6)(OH(2))(3)(Si(2)W(18)O(66))]·34H(2)O (KH-), has been synthesized and characterized by X-ray crystallography and several other methods. Dynamic light scattering, kinetics and other experiments confirm that in the presence of [Ru(bpy)(3)](2+) (the photosensitizer for light-driven water oxidations) and [Ru(bpy)(3)](3+) (the oxidant in the dark water oxidations) exists in an equilibrium between solution (soluble) and a [Ru(bpy)(3)](n+)- complex (minimally soluble) form. This new pentanickel polyoxometalate catalyzes efficient water oxidation in both the dark and on irradiation with 455 nm LED light with 1.0 mM [Ru(bpy)(3)](2+) photosensitizer and 5.0 mM Na(2)S(2)O(8), sacrificial electron acceptor. Four lines of evidence indicate that in this solution [symbol:see text] Ru(bpy)(3)](n+)- complex equilibrium remains molecular and does not decompose to nickel hydroxide particles.
Bistable States of Quantum Dot Array Junctions for High-Density Memory (2009)

We demonstrate that two-dimensional (2D) arrays of coupled quantum dots (QDs) with six-fold degenerate p orbitals can display bistable states, suitable for application in high-density memory device with low power consumption. Due to the inter-dot coupling of $p_x$ and $p_y$ orbitals in these QD arrays, two dimensional conduction bands can be formed in the x-y plane, while the $p_z$ orbitals remain localized in the x-y plane such that the inter-dot coupling between them can be neglected. We model such systems by taking into account the on-site repulsive interactions between electrons in $p_z$ orbitals and the coupling of the localized $p_z$ orbitals with the 2D conduction bands formed by $p_x$ and $p_y$ orbitals. The Green's function method within an extended Anderson model is used to calculate the tunneling current through the QDs. We find that bistable tunneling current can exist for such systems due to the interplay of the on-site Coulomb interactions (U) between the $p_z$ orbitals and the delocalized nature of conduction band states derived from the hybridization of $p_x$ / $p_y$ orbitals. This bistable current is not sensitive to the detailed band structure of the two dimensional band, but depends critically on the strength of $U$ and the ratio of the left and right tunneling rates. The behavior of the electrical bistability can be sustained when the 2D QD array reduces to a one-dimensional QD array, indicating the feasibility for high-density packing of these bistable nanoscale structures.
Improved Germline Transmission in Chicken Chimeras Produced by Transplantation of Gonadal Primordial Germ Cells into Recipient Embryos1 (2003)

In the avian species, germline chimera production could be possible by transfer of donor germ cells into the blood vessel of recipient embryos. This study was conducted to establish an efficient transfer system of chicken gonadal primordial germ cells (gPGCs) for producing the chimeras having a high capacity of germline transmission. Gonadal PGCs retrieved from 5.5-day-old embryos (stage 28) of Korean Ogol chicken (KOC with i/i gene) were transferred into the dorsal aorta of 2.5-day-old embryos (stage 17) of White Leghorn chicken (WL with I/I gene). Prospective evaluations of whether culture duration (0, 5, or 10 days) and subsequent Ficoll separation of gPGCs before transfer affected chimera production and germline transmission in the chimeras were made while retrospective analysis was conducted for examining the effect of chimera sexuality. A testcross analysis by artificial insemination of presumptive chimeras with adult KOC was performed for evaluating each treatment effect. First, comparison was made for evaluating whether experimental treatments could improve chimera production, but none of the treatments were significantly (P = 0.6831) influenced (5.1%-14.4%). Second, it was determined whether each treatment could enhance germline transmission in produced chimeras. More (P < 0.0001) progenies with black feathers (i/i) were produced in the germline chimeras derived from the transfer of 10-day-cultured gPGCs than from the transfer of 0- or 5-day-cultured gPGCs (0.6%-7.8% vs. 10.7%-49.7%). Ficoll separation was negatively affected (P < 0.0001), whereas there was no effect in chimera sexuality (P = 0.6011). In conclusion, improved germline transmission of more than a 45% transmission rate was found in chicken chimeras produced by transfer of 10-day-cultured gPGCs being separated without Ficoll treatment.
Use of a Multiple-Enzyme/Multiple-Reagent Assay System To Quantify Activity Levels in Samples Containing Mixtures of Matrix Metalloproteinases (2004)

Matrix metalloproteinases (MMPs) are a family of enzymes that are up-regulated in many diseases, including osteoarthritis (OA) and rheumatoid arthritis (RA). Here we report on a novel technique that can be used to simultaneously measure activity levels for a panel of enzymes, such as the MMPs. The technique, termed the multiple-enzyme/multiple-reagent assay system (MEMRAS), relies on the use of reagents such as substrates with varying selectivity profiles against a group of enzymes. When reaction rates are measured by following a change in fluorescence with time, for mixtures of enzymes, an equation with unknown concentrations for each activity is generated for each reagent used. Simultaneously solving the set of equations leads to a solution for the unknown concentrations. We have applied this mathematical technique to measure activity levels for mixtures of MMPs such as collagenase 3 and gelatinase A. In addition, because we were most interested in determining collagenase 3 levels as a potential biological marker for OA, we developed highly selective substrates for this enzyme by using results found in previous bacteriophage substrate-mapping experiments. Some of the best substrates tested have specific activities for collagenase 3 that are 37,000-, 17,000-, 90-, and 200-fold selective over stromelysin 1, collagenase 1, and gelatinases A and B, respectively.
Energy expenditure estimation in beta-blocker-medicated cardiac patients by combining heart rate and body movement data (2016)

Our results show that combining HR and body movement data improves the accuracy of energy expenditure prediction models in cardiac patients, similar to methods that have been developed for healthy subjects. The proposed methodology does not require individual calibration and is based on the data that are available in clinical practice.
Weighted nearest valid motion vector averaging for spatial motion vector recovery in wireless HD video transmission using H.264 over WLANs (2013)

High definition (HD) video is the standard of choice for today's video demands. HD video is characterized by high data rates, but it can be compressed using H.264 and transmitted over 802.11 wireless networks. However, such networks are prone to packet losses, which result in degraded perceptual video quality. It is thus important to perform error concealment. Spatial motion vector recovery is a key error concealment technique. This paper proposes a new spatial motion vector recovery technique called Weighted Nearest Valid Motion Vector Averaging (WNVMVA), which uses properly decoded motion vectors to estimate lost ones.
Carbonate melt regeneration for efficient capture of SO2 from coal combustion (2013)

Sulfur emission in the form of SO2 in flue gas is the most serious pollutant associated with coal combustion. Calcium carbonate sulfur scrubbing, the process most commonly in use today, is costly, produces a large amount of waste and leaves a considerable amount of SO2 in the gas. The carbonate eutectic method for removing SO2 from flue gas at 450–650 °C was initially proposed in the 1970's but despite its great efficiency could not be used due to the complexity of the carbonate melt regeneration stage. We propose a simple way to remove sulfur from the carbonate eutectic melt by purging it with CO. In contrast to expectation, this reaction leads to the reduction of sulfate to carbonyl sulfide gas that leaves the melt, rather than to sulfide ions that remain in the melt. The experiments conducted show that nearly complete sulfur removal from the melt is possible at 550 °C and that the reaction rate is sufficiently high for a large scale process. The proposed modifications provide solutions to two critical issues: (i) at 550 °C there is no problem of corrosion because a reaction cell of stainless steel with high chromium content is stable with respect to the carbonate eutectic melt at that temperature and (ii) removal of sulfur in the form of COS, rather than H2S, provides considerable freedom in choosing the final product: either sulfuric acid or elemental sulfur. In addition, we verified that fly ash does not dissolve in the carbonate eutectic melt and therefore will not interfere with SO2 removal. One can foresee that the carbonate melt-based SO2 removal technique may become a practical and viable method for limiting sulfur emission to the atmosphere.
Lysophosphatidylserine analogues differentially activate three LysoPS receptors (2014)

Lysophosphatidylserine (1-oleoyl-2 R-lysophosphatidylserine, LysoPS) has been shown to have lipid mediator-like actions such as stimulation of mast cell degranulation and suppression of T lymphocyte proliferation, although the mechanisms of LysoPS actions have been elusive. Recently, three G protein-coupled receptors (LPS1/GPR34, LPS2/P2Y10 and LPS3/GPR174) were found to react specifically with LysoPS, raising the possibility that LysoPS serves as a lipid mediator that exerts its role through these receptors. Previously, we chemically synthesized a number of LysoPS analogues and evaluated them as agonists for mast-cell degranulation. Here, we used a transforming growth factor-α (TGFα) shedding assay to see if these LysoPS analogues activated the three LysoPS receptors. Modification of the serine moiety significantly reduced the ability of the analogues to activate the three LysoPS receptors, whereas modification of other parts resulted in loss of activity in receptor-specific manner. We found that introduction of methyl group to serine moiety (1-oleoyl-lysophosphatidylallothreonine) and removal of sn-2 hydroxyl group (1-oleoyl-2-deoxy-LysoPS) resulted in reduction of reactivity with LPS1 and LPS3, respectively. Accordingly, we synthesized a LysoPS analogue with the two modifications (1-oleoyl-2-deoxy-lysophosphatidylallothreonine) and found it to be an LPS2-selective agonist. These pharmacological tools will definitely help to identify the biological roles of these LysoPS receptors.
Synthesis and properties of novel phosphorus-containing hardener for epoxy resins (2000)

A novel phosphorus-containing curing agent, 2-(6-oxid-6H-dibenz〈c,e〉〈1,2〉oxa-phosphorin-6-yl) phenol formaldehyde novolac [OD-PN], was prepared from phenol formaldehyde novolac resin (PN) and a reactive 2-(6-oxid-6H-dibenz〈c,e〉〈1,2〉oxa-phosphorin-6-yl)chloride (ODC) while ODC was synthesized through reaction between o-phenylphenol and phosphoryl trichloride. The compound (OD-PN) was used as a reactive flame-retardant in o-cresol formaldehyde novolac epoxy resin (CNE) for electronic application. Owing to the rigid structure of ODC and pendant P group, the resulted phosphorus containing epoxy resin exhibited better flame retardancy, higher glass transition temperature, and thermal stability than the noncyclic P-containing curing agent or the bromine containing flame-retardant epoxy resin. UL 94-VO rating could be achieved with a phosphorus content of as low as 1.21% (comparable to bromine content of 6%) in the cured resin, and no fumes and toxic gas emission were observed. The relationship between the structure and flammability for both phosphorus containing curing agents OD-PN and TP-PN (triphenyl phosphate-phenol formaldehyde novolac reaction product) are also examined. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 78: 1636–1644, 2000
Targeting Glioma Stem Cells by Functional Inhibition of a Prosurvival OncomiR-138 in Malignant Gliomas (2012)

Malignant gliomas are the most aggressive forms of brain tumors, associated with high rates of morbidity and mortality. Recurrence and tumorigenesis are attributed to a subpopulation of tumor-initiating glioma stem cells (GSCs) that are intrinsically resistant to therapy. Initiation and progression of gliomas have been linked to alterations in microRNA expression. Here, we report the identification of microRNA-138 (miR-138) as a molecular signature of GSCs and demonstrate a vital role for miR-138 in promoting growth and survival of bona fide tumor-initiating cells with self-renewal potential. Sequence-specific functional inhibition of miR-138 prevents tumorsphere formation in vitro and impedes tumorigenesis in vivo. We delineate the components of the miR-138 regulatory network by loss-of-function analysis to identify specific regulators of apoptosis. Finally, the higher expression of miR-138 in GSCs compared to non-neoplastic tissue and association with tumor recurrence and survival highlights the clinical significance of miR-138 as a prognostic biomarker and a therapeutic target for treatment of malignant gliomas.
Novel magnetic-field sensor using carrier-domain rotation: operation and practical performance (1976)

A magnetic field applied to a circular p-n-p-n structure causes rotation of a carrier domain, the localised region where bipolar-transistor action occurs. A theoretical explanation is given of device operation, including the dependence of rotation frequency on flux density. Experimental results are given for a prototype device.
Validation and Application of Cavity-Enhanced, Near-Infrared Tunable Diode Laser Absorption Spectrometry for Measurements of Methane Carbon Isotopes at Ambient Concentrations (2013)

Methane is an effective greenhouse gas but has a short residence time in the atmosphere, and therefore, reductions in emissions can alleviate its greenhouse gas warming effect within a decadal time frame. Continuous and high temporal resolution measurements of methane concentrations and carbon isotopic ratios (δ(13)CH4) can inform on mechanisms of formation, provide constraints on emissions sources, and guide future mitigation efforts. We describe the development, validation, and deployment of a cavity-enhanced, near-infrared tunable diode laser absorption spectrometry system capable of quantifying δ(13)CH4 at ambient methane concentrations. Laboratory validation and testing show that the instrument is capable of operating over a wide dynamic range of methane concentration and provides a measurement precision for δ(13)CH4 of better than ± 0.5 ‰ (1σ) over 1000 s of data averaging at ambient methane concentrations. The analyzer is accurate to better than ± 0.5 ‰, as demonstrated by measurements of characterized methane/air samples with minimal dependence (<1 ‰) of measured carbon isotope ratio on methane concentration. Deployment of the instrument at a marsh over multiple days demonstrated how methane fluxes varied by an order of magnitude over 2 day deployment periods, and showed a 17 ‰ variability in δ(13)CH4 of the emitted methane during the growing season.
Imaging surface roughness with continuous-wave ultrasound reflectometry. (2008)

Measurement of surface roughness irregularities is an important indicator of product quality for many nondestructive testing industries. Many techniques exist; however, because of their qualitative, time-consuming and direct-contact modes, it is of some importance to work out new experimental methods and efficient tools for quantitative estimation of surface roughness. Continuous-wave ultrasound reflectometry (CWUR) is presented here as a novel nondestructive modality for imaging and measuring surface roughness in a noncontact mode. In CWUR, voltage variations due to phase shifts in the reflected ultrasound waves are recorded and processed to form an image of surface roughness. An acrylic test block with surface irregularities ranging from 4.22 to 19.05 μm as measured by a coordinate measuring machine (CMM) is scanned by an ultrasound transducer having a diameter of 45 mm, a focal distance of 70 mm, and a central frequency of 3 MHz. It is shown that CWUR technique gives very good agreement with the results obtained through CMM inasmuch as the maximum average percent error is around 11.5%.
Microfabrication and Packaging Issues in the Development of a Planar Silicon Loop Heat Pipe, Using Si02 Fiber Wicks (2006)

The focus of this work is the physical development and performance of an infinitely expandable planar non-standard MEMS loop heat pipe, targeted for electronic cooling. The composition is principally semiconductor grade silicon, with some glass components, requiring neither internal pumps nor external power, except the waste heat which causes its operation. In as much as modern microelectronics is of a planar configuration, the cooling device surfaces (unlike the classical cylindrical heat pipe) should ideally also be planar. Here the authors report such a compatible planar heat pipe, infinitely expandable in surface area, using inexpensive batch processing and glass (silicon dioxide) fiber as the wick. Preliminary results have demonstrated 42 and 65 W/Cm2 in closed and open loop configurations, respectively. These power dissipating levels greatly exceed that required for most emerging CPU's and other electronics.