gebhart/patrepeval huggingface dataset:
A new scheme for strain typing of methicillin-resistant Staphylococcus aureus on the basis of matrix-assisted laser desorption ionization time-of-flight mass spectrometry by using machine learning approach (2018)

Methicillin-resistant Staphylococcus aureus (MRSA), one of the most important clinical pathogens, conducts an increasing number of morbidity and mortality in the world. Rapid and accurate strain typing of bacteria would facilitate epidemiological investigation and infection control in near real time. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry is a rapid and cost-effective tool for presumptive strain typing. To develop robust method for strain typing based on MALDI-TOF spectrum, machine learning (ML) is a promising algorithm for the construction of predictive model. In this study, a strategy of building templates of specific types was used to facilitate generating predictive models of methicillin-resistant Staphylococcus aureus (MRSA) strain typing through various ML methods. The strain types of the isolates were determined through multilocus sequence typing (MLST). The area under the receiver operating characteristic curve (AUC) and the predictive accuracy of the models were compared. ST5, ST59, and ST239 were the major MLST types, and ST45 was the minor type. For binary classification, the AUC values of various ML methods ranged from 0.76 to 0.99 for ST5, ST59, and ST239 types. In multiclass classification, the predictive accuracy of all generated models was more than 0.83. This study has demonstrated that ML methods can serve as a cost-effective and promising tool that provides preliminary strain typing information about major MRSA lineages on the basis of MALDI-TOF spectra.
Thick-Film Thermistor and Its Applications (1980)

The electrical properties, reliability, and several successful applications of a thick-film thermistor are described. The thick-film thermistor is composed of a semiconducting oxide, precious metal (RuO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> ), and glass. The resistivity and thermistor constant are affected to a great extent by the electrical properties of the semiconducting oxide, the particle size of RuO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> , and the characteristics of the glass. The thermal expansion coefficient of the semiconducting oxide is required to be less than 105 x 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-7</sup> K <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> in order to prevent the cracks in as-fired film. A resistivity ranging from I <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\Omega</tex> 2.cm to 10 M <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\Omega</tex> .cm together with a thermistor constant from 100 to 4500 K can be obtained by controlling these factors. These glass coated thick-film thermistors exhibit extremely high stability. An accelerated life test shows the drift rate as less than 0.02 percent/year in the resistance of a thick-film thermistor with a crystallized glass coating. A thick-film thermistor can be used widely as an accurate and stable temperature sensor and as an exact temperature compensating element in a thick-film hybrid circuit.
Replacing<scp>d</scp>-Glucosamine with Its<scp>l</scp>-Enantiomer in Glycosylated Antitumor Ether Lipids (GAELs) Retains Cytotoxic Effects against Epithelial Cancer Cells and Cancer Stem Cells (2017)

We describe metabolically inert l-glucosamine-based glycosylated antitumor ether lipids (L-GAELs) that retain the cytotoxic effects of the D-GAELs including the ability to kill BT-474 breast cancer stem cells (CSCs). When compared to adriamycin, cisplatin, and the anti-CSC agent salinomycin, L-GAELs display superior activity to kill cancer stem cells (CSCs). Mode of action studies indicate that L-GAELs like the D-GAELs kill cells via an apoptosis-independent mechanism that was not due to membranolytic effects.
Mode Dispersion Compensating Optical Transmission Line Composed of Two-Mode Optical Fibers (2012)

We fabricated mode dispersion compensating optical transmission line composed of two different kinds of two mode optical fibers with the opposite signs of mode dispersion. Its mode dispersion was successfully controlled within ±700 ps/km at C band.
Discovery of 4-Aryl-4<i>H</i>-chromenes as a New Series of Apoptosis Inducers Using a Cell- and Caspase-Based High Throughput Screening Assay. 4. Structure–Activity Relationships of <i>N</i>-Alkyl Substituted Pyrrole Fused at the 7,8-Positions (2008)

In our continuing effort to discover and develop apoptosis inducing 4-aryl-4H-chromenes as novel anticancer agents, we explored the structure-activity relationship (SAR) of alkyl substituted pyrrole fused at the 7,8-positions. A methyl group substituted at the nitrogen in the 7-position of the pyrrole ring led to a series of potent apoptosis inducers with potency in the low nanomolar range. These compounds were also found to be low nanomolar or subnanomolar inhibitors of cell growth, and they inhibited tubulin polymerization, indicating that methylation of the 7-position nitrogen does not change the mechanism of action of these chromenes. Compound 2d was identified as a highly potent apoptosis inducer with an EC50 value of 2 nM and a highly potent inhibitor of cell growth with a GI50 value of 0.3 nM in T47D cells.
Capacitive-type counter of nanoparticles in air (2010)

A capacitive-type counter of nanoparticles in air, based on measurement of the capacitance of a capacitor with a variable dielectric part, has been developed. The method is suitable for detection of aerosols in a wide concentration range, regardless of shape or chemical composition. The method is demonstrated experimentally and verified by numerical simulations. The counter allows for construction of a simple, portable, and cheap nanoparticle detector for air quality control.
Exploration of Sodium Metal Fluorosulphate Electrodes and Their Derivatives: Low Temperature Synthesis and Characterization (2010)

Abstract not Available.
Single-View Dressed Human Modeling via Morphable Template (2014)

We introduce a morph able template for dressed human modeling, called Morph able Dressed Human (MDH) template. The template is obtained by learning basic functions from two common types of clothes (long shirts and trousers) and defining a deform-combine manipulation. Our MDH template is parametric, spans variation in both clothes and body/pose, and can generate various dressed human shapes. The template can be morphed to perform dressed human modeling from just a single image through shape fitting and deformation/texture transfer. We demonstrate the effectiveness of our MDH template in single-view dressed human estimation and garment transfer.
CHIRAL LIGANDS: SYNTHESIS AND CHARACTERIZATION OF CARBOHYDRATE DERIVATIVES OF SEVEN- AND EIGHT-MEMBERED CYCLIC PHOSPHITES (1994)

Abstract The synthesis and characterization of carbohydrate derivatives of the dibenzo[d,f][1,3,2]dioxaphosphepin and dibenzo[d,g][1,3,2]dioxaphosphocin ring system is described. Key Words: Dibenzo[d,f][1,3,2]dioxaphosphepindibenzo[d,g][1,3,2]dioxaphosphocincarbohydrate derivativestereoaxischiral ligand
Synthesis and antitumor activity of sugar-ring hydroxyl analogs of daunorubicin (1979)

Daunorubicin analogues in which the natural amino sugar, daunosamine, is replaced by neutral 2,6-dideoxy-hexopyranosyl residues have been prepared in high yields. Glycosidation of 3,4-di-O-acetyl-2,6-dideoxy-alpha-L-lyxo-hexopyranosyl chloride (13) with daunomycinone under Koenigs-Knorr conditions yielded exclusively the protected alpha-anomeric product 4, which was converted into the free glycoside 5. In contrast, the 1-chloro-D-ribo isomer 19, bearing p-nitrobenzoyl groups for hydroxyl-group protection, furnished a 5:3 mixture of the alpha (6) and beta (7) glycosides. Separation and individual deprotection afforded the target compounds 8 (from 6) and 9 (from 7). Whereas all of the D-ribo analogues (6--9) are inactive as antitumor agents in vivo against P388 lymphocytic leukemia in mice, the protected L-lyxo glycoside 4 (T/C 186) and also the free glycoside 5 (T/C 183) are highly effective in this test system; 5 is also active (T/C 146) in vivo against murine B16 melanocarcinoma.
Comparison of Classic and Molecular Approaches for the Identification of Untypeable Enteroviruses (2000)

Members of the family Picornaviridae are the most common viruses infecting humans, and species in several genera also infect a wide variety of other mammals. Picornaviruses have traditionally been classified by antigenic type, based on a serum neutralization assay. However, this method is time-consuming and labor-intensive, is sensitive to virus aggregation and antigenic variation, and requires a large number of antisera to identify all serotypes, even when antiserum pools are used. We developed generic reverse transcription (RT)-PCR primers that will amplify all human enterovirus serotypes, as well as many rhinoviruses and other picornaviruses, and used RT-PCR amplification of the VP1 gene and amplicon sequencing to identify enteroviruses that were refractory to typing by neutralization with pooled antisera. Enterovirus serotypes determined by sequencing were confirmed by neutralization with monospecific antisera. Of 55 isolates tested, 49 were of known enterovirus serotypes, two were rhinoviruses, and four were clearly picornaviruses but did not match any known picornavirus sequence. All four untyped picornaviruses were closely related to one another in sequence, suggesting that they are of the same serotype. RT-PCR, coupled with amplicon sequencing, is a simple and rapid method for the typing and classification of picornaviruses and may lead to the identification of many new picornavirus serotypes.
Isomeric Tuning Yields Bright and Targetable Red Ca<sup>2+</sup> Indicators (2019)

Targeting small-molecule fluorescent indicators using genetically encoded protein tags yields new hybrid sensors for biological imaging. Optimization of such systems requires redesign of the synthetic indicator to allow cell-specific targeting without compromising the photophysical properties or cellular performance of the small-molecule probe. We developed a bright and sensitive Ca2+ indicator by systematically exploring the relative configuration of dye and chelator, which can be targeted using the HaloTag self-labeling tag system. Our “isomeric tuning” approach is generalizable, yielding a far-red targetable indicator to visualize Ca2+ fluxes in the primary cilium.
Adaptive critic design based dynamic optimal power flow controller for a smart grid (2011)

An adaptive critic design (ACD) based dynamic optimal power flow control (DOPFC) is proposed in this paper as a solution to the smart grid operation in a high short-term uncertainty and variability environment. With the increasing penetration of intermittent renewable generation, power system stability and security need to be ensured dynamically as the system operating condition continuously changes. The proposed DOPFC dynamically tracks the power system optimal operating point by continuously adjusting the steady-state set points from the traditional OPF algorithms. The ACD technique, specifically the dual heuristic dynamic programming (DHP), is used to provide nonlinear optimal control, where the control objective is formulated explicitly to incorporate system operation economy, stability and security considerations. A 12 bus test power system is used to demonstrate the development and effectiveness of the proposed ACD-based DOPFC using recurrent neural networks.
Uncertainty aware query execution time prediction (2014)

Predicting query execution time is a fundamental issue underlying many database management tasks. Existing predictors rely on information such as cardinality estimates and system performance constants that are difficult to know exactly. As a result, accurate prediction still remains elusive for many queries. However, existing predictors provide a single, point estimate of the true execution time, but fail to characterize the uncertainty in the prediction. In this paper, we take a first step towards providing uncertainty information along with query execution time predictions. We use the query optimizer's cost model to represent the query execution time as a function of the selectivities of operators in the query plan as well as the constants that describe the cost of CPU and I/O operations in the system. By treating these quantities as random variables rather than constants, we show that with low overhead we can infer the distribution of likely prediction errors. We further show that the estimated prediction errors by our proposed techniques are strongly correlated with the actual prediction errors.
Erratum: “Increased Polarization Ratio on Semipolar (1122) InGaN/GaN Light-Emitting Diodes with Increasing Indium Composition” (2009)

Optical properties of InGaN/GaN light-emitting diode (LED) samples prepared on the (1122) surface of bulk GaN were investigated. Four samples were prepared with increasing indium concentrations. The LEDs emitted at 527, 531, 556, and 568 nm at 20 mA dc. Their optical polarization ratios were measured and the samples with higher In showed a higher ratio than the shorter wavelength ones. A polarization ratio of 0.65 was measured for the longest wavelength sample. This suggests that the more In incorporated into the quantum well layers leads to an increase in the splitting of the valence subband levels.
5-(Diethoxyphosphoryl)-5-methyl-1-pyrroline N-oxide: A New Efficient Phosphorylated Nitrone for the in Vitro and in Vivo Spin Trapping of Oxygen-Centered Radicals (1995)

5-(Diethoxyphosphoryl)-5-methyl-1-pyrroline N-oxide (DEPMPO, 2), a new spin trap, has been synthesized via a two-step synthetic route, and its ability to spin trap oxy radicals in biological milieu has been addressed. The in vitro spin trapping of hydroxyl and superoxide radicals was investigated in a phosphate buffer 0.1 M, and the hyperfine coupling constants of the spin adducts were determined. The rates of spin trapping of hydroxyl and superoxide radicals with 2 were found to be close to those reported for 5,5-dimethyl-1-pyrroline N-oxide (DMPO). However, the DEPMPO-superoxide spin adduct was shown to be significantly more persistent (15 times at pH 7) than the DMPO--superoxide spin adduct. Using 2 as a spin trap, the production of superoxide has been clearly characterized during the reperfusion of ischemic isolated rat hearts.
The Magnetic Stability of Spin-Dependent Tunneling Devices (1998)

The tunneling resistance between two ferromagnetic metal layers that are separated by a thin insulator depends on the relative orientation of the magnetization M of each layer. In a memory device, independent switching of the magnetically soft layer is achieved by making the other layer either exchange-biased or magnetically hard. The repeated reversal of M of the soft layer by field cycling can demagnetize the other magnetically hard layer and thus erase the tunnel junction9s memory. The M of exchange-biased structures was stable at least to 107cycles, whereas in hard structures, M generally decayed logarithmically with the number of field cycles. The decay was very sensitive to the thickness of the hard layer and the composition of the soft layer. However, no decay was observed when the moment reversal was accomplished by coherent rotation, establishing that demagnetization results from the formation and motion of domain walls in the soft layer during field cycling.
<i>cKit</i> <sup>+</sup> cardiac progenitors of neural crest origin (2015)

The degree to which cKit-expressing progenitors generate cardiomyocytes in the heart is controversial. Genetic fate-mapping studies suggest minimal contribution; however, whether or not minimal contribution reflects minimal cardiomyogenic capacity is unclear because the embryonic origin and role in cardiogenesis of these progenitors remain elusive. Using high-resolution genetic fate-mapping approaches with cKit(CreERT2/+) and Wnt1::Flpe mouse lines, we show that cKit delineates cardiac neural crest progenitors (CNC(kit)). CNC(kit) possess full cardiomyogenic capacity and contribute to all CNC derivatives, including cardiac conduction system cells. Furthermore, by modeling cardiogenesis in cKit(CreERT2)-induced pluripotent stem cells, we show that, paradoxically, the cardiogenic fate of CNC(kit) is regulated by bone morphogenetic protein antagonism, a signaling pathway activated transiently during establishment of the cardiac crescent, and extinguished from the heart before CNC invasion. Together, these findings elucidate the origin of cKit(+) cardiac progenitors and suggest that a nonpermissive cardiac milieu, rather than minimal cardiomyogenic capacity, controls the degree of CNC(kit) contribution to myocardium.
Amorphous alloys as soft magnetic materials II (1976)

A year ago C. D. Graham Jr. [1] reviewed the behavior and applications of ferromagnetic glasses. This paper will discuss the progress made since that time by a number of investigators in various laboratories. Substantial effort has been directed towards the study of the dynamic properties of these alloys. The dynamic properties examined include the complex permeability and the coercive force as a function of frequency, the rapid flux reversal time as a function of applied field, and the damping associated with domain wall motion. Essentially all of the dynamic properties can be understood by considering the ferromagnetic glasses to be just soft magnetic materials with a resistivity about three times that of permalloy. The details of the domain structure in the two materials differ, but not in a substantial or fundamental way. Because the glassy alloys are in general not isotropic, their domain structure in determined by a local anisotropy which arises due to strain or ’’pair ordering’’.
Therapeutic efficacy of cerium oxide nanoparticles in treatment of sepsis induced renal failure (LB608) (2014)

Severe sepsis is a complex disease of multifactorial etiology that is characterized by systemic inflammation which can rapidly progress to multi‐organ dysfunction and death. Although most of the deaths due to sepsis are related to the release of inflammatory mediators, treatments to date have largely centered on the administration of antibiotics, i.v. fluids, NSAIDS, and vasopressors. Studies have shown that the release of inflammatory mediators is mediated, at least in part, through the generation of reactive oxygen species (ROS). Other work has shown that cerium oxide (CeO 2 ) nanoparticles can function to scavenge ROS and that these particles exhibit anti‐bacterial activity. On the basis of these data, we hypothesized a CeO 2 nanoparticle based treatment strategy would diminish sepsis‐induced mortality, sepsis‐associated inflammation and that these improvements would be associated with improved renal function. Male Sprague Dawley rats were subjected to polymicrobial sepsis and treated with 0.5mg/kg of CeO 2 nanoparticles intravenously. Our preliminary data suggests that the CeO 2 nanoparticle intervention improved animal survivability and promoted the restoration of core body temperature. Changes in survivability and thermoregulation were associated with an attenuation in the sepsis‐induced release of β2 microglobulin, cystatin, gluthatione‐s transferase alpha, gluthatione‐s transferase mu, kidney injury molecule‐1, osteopontin and a reduction in serum total ROS. Histological analysis demonstrated that CeO 2 nanoparticles decreased sepsis‐induced proximal tubular dilatation and loss of brush border. Taken together, these data suggest that CeO 2 nanoparticle based interventions may exhibit potential for the treatment of sepsis‐induced renal failure and death. Grant Funding Source : This work was supported in part from DOE grant (DE‐PS02‐09ER‐01 to E.R.B)
Practical Cross-Section Imaging of External Tendons to Reveal Grout Deficiencies Relative to Strand Pattern (2020)

External post-tensioned tendons in concrete segmental bridges have had strand corrosion failures due to grouting deficiencies such as voids or bleed water. Nondestructive assessment of the grout condition is thus often needed, preferably by a cross-section imaging method. Here, a magnetic sensing approach to image the position of the steel strand bundle is combined with an electric impedance method to evaluate the condition of the grout space. Both are embodied in a device that images the tendon’s cross section. The magnetic sensor travels around the circumference of the tendon and measures the force of attraction to the steel strands from which an image of the strand pattern inside the tendon is created. Simultaneously, a traveling plate rotates around the tendon, and variations of the electric impedance between the plate and strands identify grout deficiencies. The impedance and strand position data create a complete color-coded image of the tendon cross-section flagging grout deficiencies. The approach was validated by experiments with tendon specimens with known deficiencies and under field conditions. The method is rapid, economical, easy to replicate, with a small and safe device not requiring specialized operator training.
Evidence for cellular uptake of recombinant hepatitis C virus non‐enveloped capsid‐like particles (2007)

Although the hepatitis C virus (HCV) is an enveloped virus, naked nucleocapsids have been reported in the serum of infected patients, and most recently novel HCV subgenomes with deletions of the envelope proteins have been identified. However the significance of these findings remains unclear. In this study, we used the baculovirus expression system to generate recombinant HCV capsid-like particles, and investigated their possible interactions with cells. We show that expression of HCV core in insect cells can sufficiently direct the formation of capsid-like particles in the absence of the HCV envelope glycoproteins and of the 5' untranslated region. By confocal microscopy analysis, we provide evidence that the naked capsid-like particles could be uptaken by human hepatoma cells. Moreover, our findings suggest that they have the potential to produce cell-signaling effects.
Airborne temperature survey maps of heat flow anomalies for exploration geology (1982)

Airborne temperature surveys were used to depict the small surface temperature differences related to heat flow anomalies. Zones with conductive heat flow differences of 45 +- 16 ..mu..cal/cm/sup 2/(s) had predawn surface temperature differences of 1.4 +- 0.3/sup 0/C. Airborne temperature surveys were coordinated with field temperature surveys at Long Valley, California, the site of a known geothermal resource area. The airborne temperature surveys recorded redundant, predawn temperatures at two wavelengths and at two elevations. Overall temperature corrections were determined by calibrating dry soil surface temperatures with thermistor probes. The probes measured air and soil temperatures within 2 cm of the surface, every twenty minutes, during the survey overflights.
Transgenic Microalgae With Increased Production Of At Least One Omega-3 Long Chain Polyunsaturated Fatty Acid (Patent US 2018/0312888 A1) (2018)

The invention relates to genetically modified organisms with enhanced production of omega-3 long chain polyunsaturated fatty acids.