gebhart/patrepeval huggingface dataset:
Using spectral matching to interpret LC‐MS/MS data during RNA modification mapping (2019)

While a number of approaches have been developed to analyze liquid chromatography tandem mass spectrometry (LC-MS/MS) data obtained from modified oligonucleotides, the majority of these methods require analyzing every MS/MS spectrum de novo to sequence the oligonucleotide and place the modification. Spectral matching is an alternative approach for analyzing MS/MS data that is based on creating a library of annotated MS/MS spectra against which individual MS/MS data can be searched. Here, we have adapted the existing NIST spectral matching software to enable its use in the interpretation of MS/MS data obtained from modified oligonucleotides. In particular, we demonstrate the utility of this approach to identify specific post-transcriptionally modified nucleosides in particular transfer RNAs (tRNAs) obtained through a conventional RNA modification mapping experimental protocol. Spectral matching was found to be an efficient approach for screening for known modified tRNAs by using the experimental data as the library and previously annotated RNase T1 digestion products of tRNAs as the reference spectra. The utility of spectral matching for rapid analysis of multiple LC-MS/MS analyses was demonstrated by screening mutant strains of Streptococcus mutans to identify the enzyme(s) responsible for synthesizing the tRNA position 37 modification threonylcarbamoyladenosine (t<sup>6</sup> A).
Laser powder bed fusion of nano-CaB6 decorated 2024 aluminum alloy (2021)

The 2024 aluminum alloy (Al-Cu-Mg) is widely used in aerospace; however, due to its solidification-cracking tendency, its processability using laser powder bed fusion (LPBF) remains a critical issue. The addition of 2 wt% CaB6 nanoparticles induces a columnar-to-equiaxed transition (CET), resulting in an immediate improvement in LPBF processability. High-density (>99.5%) and crack-free specimens, with a homogeneous equiaxed microstructure and without preferred grain orientation, were obtained. The small average α-Al grain size of 0.91 ± 0.32 µm is attributed to the similar lattice constants of Al and CaB6 facilitating Al nucleation on CaB6 nanoparticles, resulting in a highly coherent Al/CaB6 interface. CaB6 nanoparticles act as heterogeneous nucleus and exert a pinning force on the grain boundaries, which reduces grain coarsening. The as-built specimens exhibit both high-yield strength (348 ± 16 MPa) and high-tensile strength (391 ± 22 MPa), combined with a high total elongation at break (12.6 ± 0.6%). The macro hardness amounts to 132 ± 4 HV5.
Parallel artefact rejection for epileptiform activity detection in routine EEG (2011)

The EEG signal is very often contaminated by electrical activity external to the brain. These artefacts make the accurate detection of epileptiform activity more difficult. A scheme developed to improve the detection of these artefacts (and hence epileptiform event detection) is introduced. A structure of parallel Support Vector Machine classifiers is assembled, one classifier tuned to perform the identification of epileptiform activity, the remainder trained for the detection of ocular and movement-related artefacts. This strategy enables an absolute reduction in false detection rate of 21.6% with the constraint of ensuring all epileptic events are recognized. Such a scheme is desirable given that sections of data which are heavily contaminated with artefact need not be excluded from analysis.
Maximal Parenteral Glucose Oxidation in Hypermetabolic Young Children: A Stable Isotope Study (1998)

Maximum glucose oxidation in severely burned children occurs at intakes approximating 5 mg.kg-1.min-1. Exogenous glucose in excess of this amount enters nonoxidative pathways and is unlikely to improve energy balance. Clinical markers such as serum glucose levels or expired respiratory quotient may not detect inefficient glucose utilization.
Postpartum Retroperitoneal Fasciitis: A Case Report and Review of Literature (2005)

We present a case of a postpartum female with iliopsoas fasciitis in the puerperium. Two days after a spontaneous vaginal delivery at 38 weeks without any complications, the patient complained of pain in the left thigh and hip, associated with a temperature of 38 degrees C. Consequently, she could not walk 4 days after delivery and her body temperature had increased to 39 degrees C. Extreme left flank pain and tenderness in the left pelvic wall were prominent, whereas the tenderness in the pelvis was moderate. Magnetic resonance imaging led us to diagnose iliopsoas fasciitis. This was complicated by sepsis but improved after a protracted antibiotic treatment without any surgical intervention. A literature review revealed that serious complications, including sepsis or permanent functional disturbance, could arise although retroperitoneal fasciitis and/or abscesses are very rare after vaginal delivery. Iliopsoas fasciitis could be considered when patients complain of extreme pain in the pelvic wall, sacroiliac joint region, or thigh-symptoms that are uncommon in uncomplicated endometritis.
Language Camp Guidelines (1974)

Maurice W. Conner and Barbara Ludwig Language camps are becoming increasingly popular as a way to generate interest and to increase enrollments in FLs. As a chapter project, members of Nebraska AATG decided in the spring of 1971 to establish a German camp for junior and senior high-school students from the state.2 Patterned after the successful language camps which are sponsored by Concordia College, Moorhead, Minnesota, our camp was planned and shaped during a series of meetings in 1972 and 1973. In an effort to keep the cost of the camp low, an ESEA Title III Mini-Grant was secured through the Nebraska Department of Education, and the counselors agreed to serve without salary. The camp was held from August 12-17, 1973, at the 4-H facilities located in the Nebraska National Forest near Halsey, Nebraska.
Copper‐Catalysed Domino Silylative Aldol Reaction Leading to Stereocontrolled Chiral Quaternary Carbons (2010)

Asymmetric aldol reaction: A domino silylation–aldol reaction between enoyloxazolidinones and various aldehydes has been developed (see scheme). The process catalysed by a copper complex in the presence of a borosilane led to high diastereoselectivities. Yields between 59 and 90 % and d.r. values between 78:22 to 95:5 were obtained. When methacryloyloxazolidinones were used, a controlled chiral quaternary carbon was generated. BPin=4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl.
Kaon Weak Matrix Elements in 2+1 flavor DWF QCD (2008)

$K \to π$ and $K \to 0$ weak matrix elements of $ΔS = 1$ operators have been measured in 2+1 flavor domain wall fermion (DWF) QCD on (3 fm)$^3$ lattices with $a^{-1} = 1.73(3)$ GeV. As is well known, using these matrix elements and chiral perturbation theory allows a determination of the $K \to ππ$ matrix elements that enter in the quantitative value for the $ΔI = 1/2$ rule and $ε^\prime/ε$. Two light dynamical sea quark masses have been used, along with six valence quark masses, with the lightest valence quark mass $\approx 1/10$ the physical strange quark mass. We report our results for lattice matrix elements in the $SU(3)_L \times SU(3)_R$ (27,1), (8,1), and (8,8) representations, paying particular attention to the statistical errors achieved after measurements on 75 configurations. We also report on our calculation of the non-perturbative renormalization coefficients for these $ΔS=1$ weak operators, using the Rome-Southampton method.
Ocular Blood Flow Measurement Methodologies and Clinical Application (2012)

Abstract The sections in this article are Background and Significance Blood flow Methodologies Color Doppler Imaging Laser Doppler Flowmetry and Scanning Laser Flowmetry Retinal Vessel Analyzer Ocular Pulse Amplitude and Pulsatile Ocular Blood Flow Laser Speckle Method (Laser Speckle Flowgraphy) Digital Scanning Laser Ophthalmoscope Angiography Doppler Optical Coherence Tomography Retinal Oximetry Newly Developed Techniques Relationship Between Blood Flow and Visual Function Relationship Between Blood Flow and Optic Nerve Structure
Type 1-programmed dendritic cells drive antigen-specific latency reversal and immune elimination of persistent HIV-1 (2019)

Inclusion of virus-associated MHC class II 'helper' antigens in MDC1-based HIV-1 immunotherapies could serve both as a targeted means to safely unmask antigen-specific CD4<sup>+</sup> T cells harboring HIV-1, and to support CTL responses that can effectively target the MDC1-exposed HIV-1 cellular reservoir as a functional cure strategy. FUND: This study was supported by the NIH-NAID grants R21-AI131763, U01-AI35041, UM1-AI126603, and T32-AI065380.
SUMOylation Pathway in Trypanosoma cruzi: Functional Characterization and Proteomic Analysis of Target Proteins (2011)

SUMOylation is a relevant protein post-translational modification in eukaryotes. The C terminus of proteolytically activated small ubiquitin-like modifier (SUMO) is covalently linked to a lysine residue of the target protein by an isopeptide bond, through a mechanism that includes an E1-activating enzyme, an E2-conjugating enzyme, and transfer to the target, sometimes with the assistance of a ligase. The modification is reversed by a protease, also responsible for SUMO maturation. A number of proteins have been identified as SUMO targets, participating in the regulation of cell cycle progression, transcription, translation, ubiquitination, and DNA repair. In this study, we report that orthologous genes corresponding to the SUMOylation pathway are present in the etiological agent of Chagas disease, Trypanosoma cruzi. Furthermore, the SUMOylation system is functionally active in this protozoan parasite, having the requirements for SUMO maturation and conjugation. Immunofluorescence analysis showed that T. cruzi SUMO (TcSUMO) is predominantly found in the nucleus. To identify SUMOylation targets and get an insight into their physiological roles we generated transfectant T. cruzi epimastigote lines expressing a double-tagged T. cruzi SUMO, and SUMOylated proteins were enriched by tandem affinity chromatography. By two-dimensional liquid chromatography-mass spectrometry a total of 236 proteins with diverse biological functions were identified as potential T. cruzi SUMO targets. Of these, metacaspase-3 was biochemically validated as a bona fide SUMOylation substrate. Proteomic studies in other organisms have reported that orthologs of putative T. cruzi SUMOylated proteins are similarly modified, indicating conserved functions for protein SUMOylation in this early divergent eukaryote.
Crystal structure and thermal expansion of α-quartz SiO2 at low temperatures (1982)

The crystal structure of α-SiO2 (low quartz) has been refined at 296, 78, and 13 K from time-of-flight neutron powder diffraction data. The major effect of temperature from 296 to 78 K is a nearly rigid body rotation of the SiO4 tetrahedra. Below 78 K, tetrahedral rotation is substantially reduced giving rise to a much smaller thermal expansion. A comparison of the volume dependence of the Si-O-Si angle, the rotation angle for SiO4 tetrahedra and the c/a ratio suggests that the mechanism for expansion may be changing from tetrahedral rotation to tetrahedral distortion at the lowest temperatures. The inverse linear relation between the mean Si-O bond distance and −sec(Si-O-Si) which has been observed for silica minerals at both ambient and high-temperature conditions appears to be consistent with the structural variations that occur at low temperatures.
Airborne Particulate Matter and Mortality: Timescale Effects in Four US Cities (2003)

While time-series studies have consistently provided evidence for an effect of particulate air pollution on mortality, uncertainty remains as to the extent of the life-shortening implied by those associations. In this paper, the authors estimate the association between air pollution and mortality using different timescales of variation in the air pollution time series to gain further insight into this question. The authors' method is based on a Fourier decomposition of air pollution time series into a set of independent exposure variables, each representing a different timescale. The authors then use this set of variables as predictors in a Poisson regression model to estimate a separate relative rate of mortality for each exposure timescale. The method is applied to a database containing information on daily mortality, particulate air pollution, and weather in four US cities (Pittsburgh, Pennsylvania; Minneapolis, Minnesota; Seattle, Washington; and Chicago, Illinois) from the period 1987-1994. The authors found larger relative rates of mortality associated with particulate air pollution at longer timescale variations (14 days-2 months) than at shorter timescales (1-4 days). These analyses provide additional evidence that associations between particle indexes and mortality do not imply only an advance in the timing of death by a few days for frail individuals.
Microeconomic Theory: An Integrated Approach (2002)

I. PRELIMINARIES. 1. Review of Basic Calculus Techniques. 2. Unconstrained and Constrained Optimization of Multivariate Functions. II. THEORY OF THE CONSUMER. 3. Utility Theory. 3AW. Uncertainty, Risk, and Expected Utility. (Can be viewed at www.prenhall.com/mathis.) 4. Consumer Optimization. 5. Individual Demand Functions and Related Topics. 6. Market Demand Curves. 7. Demand-Related Elasticities. III. THEORY OF THE FIRM. 8. Production in the Short Run. 9. Production in the Long Run. 10. Long-Run Optimization for the Firm. 11. Costs of Production in the Long Run. 12. Costs of Production in the Short Run. IV. MARKET STRUCTURES. 13. Perfect Competition in the Short Run. 14. Perfect Competition in the Long Run. 15. Monopoly. 16. Additional Topics Related to Monopoly. 17. Oligopoly. 18. Applications of Game Theory to Oligopolistic Firm Behavior. 19. Monopolistic Competition. V. INPUT MARKETS. 20. Demand for Labor. 21. Supply of Labor. 22. Capital Markets. VI. GENERAL EQUILIBRIUM ANALYSIS. 23. General Equilibrium Analysis in an Exchange Economy. 24. General Equilibrium Analysis in an Economy with Production and Exchange. Glossary.
Isolation, purification and characterization ofTrichothecinol-A produced by endophytic fungusTrichothecium sp. and its antifungal, anticancerand antimetastatic activities (2014)

Background: A total of 30 endophytic fungi (AAP-PS 1–30) were isolated from the medicinal herb Phyllanthus
amarus and screened for the production of Trichothecinol-A. Out of all the endophytic strains screened for
Trichothecinol-A production, the culture filtrate of AAP-PS-1 extracted with ethyl acetate yielded Trichothecinol-A
extracellularly in appreciable amounts. Trichothecinol-A was purified, quantified and completely characterized by
different standard chromatographic and spectroscopic techniques including reverse phase HPLC, 1D and 2D
NMR spectroscopy, etc. The compound was tested for antifungal activity against filamentous fungi and yeast,
apoptotic activity against B16F10 cells, anticancer activity against MDA-MB-231, HeLa and B16F10 cells as well as
antimetastatic activity against MDA-MB-231 cell line.
Results: The endophyte producing Trichothecinol-A was identified as Trichothecium sp. by morphological, cultural
and molecular methods. RP-HPLC analyses performed on a Waters model using a C18 symmetry pack column with
a flow rate of 0.5 ml/min and the eluting compounds were detected by a dual mode wavelength detector set at
220 nm and 240 nm. The 1D (1H, 13C) and 2D NMR (COSY, NOESY, TOCSY, DEPT, 13C–1H HMBC, 13C–1H HSQC),
ESI-MS, HRMS, IR and UV–vis show conclusively that the isolated compound was Trichothecinol–A. One liter of
Trichothecium sp. yielded 4.37 mg of Trichothecinol-A. Trichothecinol-A exhibited antifungal activity against
Cryptococcus albidus (NCIM 3372) up to 20 μg/ml. Cytotoxicity studies indicate that Trichothecinol-A causes 50%
cell death at 500nM concentration in HeLa and B16F10 cells and induces apoptosis in later. Inhibition of wound
migration assay performed on MDA-MB-231 cells reveals that 500nM of Trichothecinol-A was able to inhibit wound
migration by 50% indicating its remarkable antimetastatic property.
Conclusion: The compound Trichothecinol-A has previously been isolated from Trichothecium roseum and
characterized by various standard techniques. Anti-cancer studies conducted on Trichothecinol-A showed that it
significantly inhibits cancer cell migration and can thus be developed as a new class of anti-metastatic drug. Here,
we for the first time report the anti-metastatic as well as anti-fungal activity exhibited by Trichothecinol-A isolated
by us from the endophytic fungus Trichothecium sp. of medicinal plant Phyllanthus amarus. Trichothecinol-A also
exhibited apoptotic activity.
Complexity Analysis on Flattened PDEVS Simulations (2021)

Discrete Event Systems Specification (DEVS) is a well-known formalism to develop models using the discrete event approach. One advantage of DEVS is a clear separation between the modeling and simulation activities. The user only needs to develop models and general algorithms exist in the literature to execute simulations. DEVS was enhanced to handle better simultaneous events in the PDEVS formalism. To execute PDEVS simulations, a well-know and widely accepted algorithm was introduced: the PDEVS simulation protocol. However, since its creation, the protocol has evolved, and several versions have been proposed and implemented. In this work we propose and analytical approach to fully define and analyze this protocol. We divide the protocol into steps and sub-steps and for each of them we present a computer complexity analysis based on two key factors of the protocol&#x0027;s execution: the messages the components interchange and the computations the components execute.
VR Resolver Voltage Detection Analysis Based on Core Form. (2002)

VR resolvers were developed as angle sensors for the motors of hybrid electric vehicles. Because the angle error of the resolver affects motor efficiency, the angle accuracy of the resolver must be improved. Results of investigations up to now showed the major cause of angle error of the resolver to be determined by imbalance of induced voltages on the coils caused by uneven distribution of magnetic flux around the coils. We, therefore, searched for a shape core that makes the distribution of magnetic flux more even around the coils. Finally we found that a thicker core stack, a smaller minimum air gap between the rotor and stator, and wider tooth tips of the core are effective for reducing the angle error.
Oxygen Radicals and Neuropsychiatric Illness (1991)

Free radicals are reactive chemical species with an unpaired electron that are produced through a variety of physiologic and pathologic processes. Free radicals have been implicated in a variety of neuropsychiatric conditions, many of which are marked by the gradual development of psychopathologic symptoms and movement disorder. There is evidence that radical-induced damage may be important in Parkinson's disease, tardive dyskinesia, metal intoxication syndromes, and Down's syndrome, and possibly also in schizophrenia, Huntington's disease, and Alzheimer's disease. Although some of this evidence is highly speculative, it may offer an avenue for further understanding and treatment of these conditions.
Force allocation in a large-scale distributed active surface (2003)

This paper investigates the problem of closed-loop control of a small number of parameters by allocating actuation in a system with many binary degrees of freedom, using an actual large-scale air-jet table as an example. In this system, the desired force and torque are produced by a large number of spatially distributed binary air jets directing individual forces on an object. Various algorithms for solving the force allocation problem-determining the appropriate valve states in this hyper-redundant system-are investigated. The algorithms range from discrete optimal search to continuous constrained optimization to a hybrid hierarchical approach that can be distributed. The latter consists of using the continuous optimal solutions to recursively break the large optimization problems into smaller problems that can be solved using optimal search methods or precomputed lookup tables. A tradeoff between computation time and allocation error was found. The optimal algorithms yield low errors but the time is exponential in the number of actuators, while the continuous solutions execute quickly but yield larger errors. The hybrid hierarchical optimal algorithms give the best compromise between these conflicting goals, and their applicability spans the full range of degrees of freedom from a few to many thousands. These hierarchical algorithms are useful in many such highly redundant systems.
Establishing Reachset Conformance for the Formal Analysis of Analog Circuits (2020)

We present the first work on the automated generation of reachset conformant models for analog circuits. Our approach applies reachset conformant synthesis to add nondeterminism to piecewise-linear circuit models so that they enclose all recorded behaviors of the real system. To achieve this, we present a novel technique to compute the required nondeterminism for the piecewise-linear models. The effectiveness of our approach is demonstrated on a real analog circuit. Since the resulting models enclose all measurements, they can be used for formal verification.
Excited state mixed valence in a dual‐bridged three‐chromophore system (2012)

The optical and resonance Raman spectra of the 2,2′: 6′,2″:6″,6‐trioxytriphenyl‐amine cation are measured and interpreted. This molecule contains two simultaneous types of coupling between three chromophores and two types of bridging atoms. The first and conventional coupling involves a single nitrogen bridge that couples all three aryl groups. The second is provided by the three oxygen atoms, each of which bridges two adjacent aryl groups. There are two bands in the visible region of the optical absorption spectrum; their assignment and the interpretation of the contributing orbitals and electronic states are described in terms of the neighboring orbital model that explains the effects of the two types of coupling. The bonding changes that take place in the excited electronic states are probed by resonance Raman spectroscopy intensities and analyzed using the time‐dependent theory of resonance Raman spectroscopy. The optical absorption spectrum was fit using the measured vibrational frequencies and excited state distortions. The distortions correlate well with the bonding changes predicted by the neighboring orbital model. The resonance Raman data and neighboring orbital model analysis reveal that the two optical absorption bands correspond to charge transfers from aryl groups with different nodal structures in their pi orbitals. Copyright © 2012 John Wiley &amp; Sons, Ltd.