gebhart/patrepeval huggingface dataset:
Precision spectroscopy with femtosecond light pulses (2000)

Summary form only given. The reciprocal relationship between time and frequency implies that a single short laser pulse has a broad spectrum. A pulse circulating inside a laser cavity or the periodic pulse train if a mode-locked laser, however, can be described as a coherent superposition of discrete laser modes. This frequency-domain comb of modes is now providing an elegant and universal solution to the long challenging problem of how to measure the frequency of light. In a Kerr-lens mode-locked Ti:sapphire laser, each mode is injection locked by modulation sidebands of the other modes via a nonlinear refractive index. Any mode must follow this collective dictate and oscillate in precise lock-step, or it will suffer high round trip losses in a properly designed cavity. We have demonstrated experimentally that the teeth of such a frequency comb are precisely equally spaced to within a few parts in 10/sup 18/, and that their spacing is exactly given by the pulse repetition rate.
A robust approach to IMRT optimization (2006)

Managing uncertainty is a major challenge in radiation therapy treatment planning, including uncertainty induced by intrafraction motion, which is particularly important for tumours in the thorax and abdomen. Common methods to account for motion are to introduce a margin or to convolve the static dose distribution with a motion probability density function. Unlike previous work in this area, our development does not assume that the patient breathes according to a fixed distribution, nor is the patient required to breathe the same way throughout the treatment. Despite this generality, we create a robust optimization framework starting from the convolution method that is robust to fluctuations in breathing motion, yet spares healthy tissue better than a margin solution. We describe how to generate the data for our model using breathing motion data and we test our model on a computer phantom using data from real patients. In our numerical results, the robust solution delivers approximately 38% less dose to the healthy tissue than the margin solution, while providing the same level of protection against breathing uncertainty.
Crystal structure of 3-(adamantan-1-yl)-1-(4-bromophenyl)urea, C<sub>17</sub>H<sub>21</sub>BrN<sub>2</sub>O (2016)

Abstract C 17 H 21 BrN 2 O, orthorhombic, Pna 2 1 (no. 33), a = 9.2558(12) Å, b = 13.0186(17) Å, c = 13.4684(18) Å, V = 1622.9(4) Å 3 , Z = 4, R gt ( F ) = 0.0471, wR ref ( F 2 ) = 0.1059, T = 100 K.
Association of revascularisation with low mortality in non-ST elevation acute coronary syndrome, a report from GUSTO IV-ACS (2004)

Revascularisation within 30 days is associated with an improved prognosis in ACS without ST-segment elevation. The relative high mortality in medically treated patients may be related in part to patient selection, but warrants further studies to improve outcome of these patients.
Increased metal-insulator transition temperatures in epitaxial thin films of V2O3 prepared in reduced oxygen environments (2011)

Thin films of V2O3 were grown epitaxially on c-plane sapphire substrates by oxygen plasma-assisted thermal evaporation. Reducing the amount of oxygen supplied during growth led to a nearly 50 K increase in V2O3’s metal-insulator transition temperature to a temperature as high as 184 K. By systematically varying the oxygen pressure the transition temperature monotonically increased, which was accompanied by a concomitant increase in the room-temperature resistivity. These trends are consistent with a continuous change in the stoichiometry of V2O3.
GATA2 facilitates steroid receptor coactivator recruitment to the androgen receptor complex (2014)

The androgen receptor (AR) is a key driver of prostate cancer (PC), even in the state of castration-resistant PC (CRPC) and frequently even after treatment with second-line hormonal therapies such as abiraterone and enzalutamide. The persistence of AR activity via both ligand-dependent and ligand-independent mechanisms (including constitutively active AR splice variants) highlights the unmet need for alternative approaches to block AR signaling in CRPC. We investigated the transcription factor GATA-binding protein 2 (GATA2) as a regulator of AR signaling and an actionable therapeutic target in PC. We demonstrate that GATA2 directly promotes expression of both full-length and splice-variant AR, resulting in a strong positive correlation between GATA2 and AR expression in both PC cell lines and patient specimens. Conversely, GATA2 expression is repressed by androgen and AR, suggesting a negative feedback regulatory loop that, upon androgen deprivation, derepresses GATA2 to contribute to AR overexpression in CRPC. Simultaneously, GATA2 is necessary for optimal transcriptional activity of both full-length and splice-variant AR. GATA2 colocalizes with AR and Forkhead box protein A1 on chromatin to enhance recruitment of steroid receptor coactivators and formation of the transcriptional holocomplex. In agreement with these important functions, high GATA2 expression and transcriptional activity predicted worse clinical outcome in PC patients. A GATA2 small molecule inhibitor suppressed the expression and transcriptional function of both full-length and splice-variant AR and exerted potent anticancer activity against PC cell lines. We propose pharmacological inhibition of GATA2 as a first-in-field approach to target AR expression and function and improve outcomes in CRPC.
gDLS*: Generalized Pose-and-Scale Estimation Given Scale and Gravity Priors (2020)

Many real-world applications in augmented reality (AR), 3D mapping, and robotics require both fast and accurate estimation of camera poses and scales from multiple images captured by multiple cameras or a single moving camera. Achieving high speed and maintaining high accuracy in a pose-and-scale estimator are often conflicting goals. To simultaneously achieve both, we exploit a priori knowledge about the solution space. We present gDLS*, a generalized-camera-model pose-and-scale estimator that utilizes rotation and scale priors. gDLS* allows an application to flexibly weigh the contribution of each prior, which is important since priors often come from noisy sensors. Compared to state-of-the-art generalized-pose-and-scale estimators (e.g., gDLS), our experiments on both synthetic and real data consistently demonstrate that gDLS* accelerates the estimation process and improves scale and pose accuracy.
Histidine Orientation Modulates the Structure and Dynamics of a <i>de Novo</i> Metalloenzyme Active Site (2015)

The ultrafast dynamics of a de novo metalloenzyme active site is monitored using two-dimensional infrared spectroscopy. The homotrimer of parallel, coiled coil α-helices contains a His3-Cu(I) metal site where CO is bound and serves as a vibrational probe of the hydrophobic interior of the self-assembled complex. The ultrafast spectral dynamics of Cu-CO reveals unprecedented ultrafast (2 ps) nonequilibrium structural rearrangements launched by vibrational excitation of CO. This initial rapid phase is followed by much slower ∼40 ps vibrational relaxation typical of metal-CO vibrations in natural proteins. To identify the hidden coupled coordinate, small molecule analogues and the full peptide were studied by QM and QM/MM calculations, respectively. The calculations show that variation of the histidines' dihedral angles in coordinating Cu controls the coupling between the CO stretch and the Cu-C-O bending coordinates. Analysis of different optimized structures with significantly different electrostatic field magnitudes at the CO ligand site indicates that the origin of the stretch-bend coupling is not directly due to through-space electrostatics. Instead, the large, ∼3.6 D dipole moments of the histidine side chains effectively transduce the electrostatic environment to the local metal coordination orientation. The sensitivity of the first coordination sphere to the protein electrostatics and its role in altering the potential energy surface of the bound ligands suggests that long-range electrostatics can be leveraged to fine-tune function through enzyme design.
Array model interpolation and subband iterative adaptive filters applied to beamforming-based acoustic echo cancellation (2016)

In this paper, an evolutionary exposition is given in regard to the enhancing strategies for acoustic echo cancellers (AECs). A fixed beamformer (FBF) is utilized to focus on the near-end speaker while suppressing the echo from the far end. In reality, the array steering vector could differ considerably from the ideal freefield plane wave model. Therefore, an experimental procedure is developed to interpolate a practical array model from the measured frequency responses. Subband (SB) filtering with polyphase implementation is exploited to accelerate the cancellation process. Generalized sidelobe canceller (GSC) composed of an FBF and an adaptive blocking module is combined with AEC to maximize cancellation performance. Another enhancement is an internal iteration (IIT) procedure that enables efficient convergence in the adaptive SB filters within a sample time. Objective tests in terms of echo return loss enhancement (ERLE), perceptual evaluation of speech quality (PESQ), word recognition rate for automatic speech recognition (ASR), and subjective listening tests are conducted to validate the proposed AEC approaches. The results show that the GSC-SB-AEC-IIT approach has attained the highest ERLE without speech quality degradation, even in double-talk scenarios.
Quantitative Cryo-TEM Reveals New Structural Details of Doxil-Like PEGylated Liposomal Doxorubicin Formulation (2021)

Nano-drugs based on nanoparticles (NP) or on nano-assemblies as carriers of the active pharmaceutical ingredient (API) are often expected to perform better compared to conventional dosage forms. Maximum realization of this potential though requires optimization of multiple physico-chemical, including structural and morphological, parameters. Meaningful distributions of these parameters derived from sufficient populations of individual NPs rather than ensemble distributions are desirable for this task, provided that relevant high-resolution data is available. In this study we demonstrate powerful capabilities of the up-to-date cryogenic transmission electron-microscopy (cryo-TEM) as well as correlations with other techniques abundant in the nano-research milieu. We explored Doxil<sup>®</sup>-like (an anticancer drug and the first FDA-approved nano-drug) (75-100 nm) PEGylated liposomes encapsulating single doxorubicin-sulfate nano-rod-crystals (PLD). These crystals induce liposome sphere-to-ellipsoid deformation. Doxil<sup>®</sup> was characterized by a multitude of physicochemical methods. We demonstrate, that accompanied by advanced image-analysis means, cryo-TEM can successfully enable the determination of multiple structural parameters of such complex liposomal nano-drugs with an added value of statistically-sound distributions. The latter could not be achieved by most other physicochemical approaches. It seems that cryo-TEM is capable of quantitative description of individual liposome morphological features, including meaningful distributions of all structural elements, with averages that correlate with other physical methods. Here it is demonstrated that such quantitative cryo-TEM analysis is a powerful tool in determining what is the optimal drug to lipid ratio in PLD, which is found to be the drug to lipid ratio existing in Doxil<sup>®</sup>.
Super-resolution in Phase Space (2015)

This work considers the problem of super-resolution. The goal is to resolve a Dirac distribution from knowledge of its discrete, low-pass, Fourier measurements. Classically, such problems have been dealt with parameter estimation methods. Recently, it has been shown that convex-optimization based formulations facilitate a continuous time solution to the super-resolution problem. Here we treat super-resolution from low-pass measurements in Phase Space. The Phase Space transformation parametrically generalizes a number of well known unitary mappings such as the Fractional Fourier, Fresnel, Laplace and Fourier transforms. Consequently, our work provides a general super-resolution strategy which is backward compatible with the usual Fourier domain result. We consider low-pass measurements of Dirac distributions in Phase Space and show that the super-resolution problem can be cast as Total Variation minimization. Remarkably, even though are setting is quite general, the bounds on the minimum separation distance of Dirac distributions is comparable to existing methods.
Enteropathogenicity of purified Clostridium perfringens enterotoxin in the pig (1985)

In an assay procedure, purified Clostridium perfringens enterotoxin induced the accumulation of fluid in the ileal loop of the axenic pig. The smallest amount of enterotoxin causing a positive response was 25 micrograms (1:32 titer by counterimmunoelectrophoresis [CIEP] ), and 100 micrograms (1:128 CIEP titer) caused a marked response. Possibly, diarrhea in pigs with 1:32 CIEP titer or more of enterotoxin in the feces may be associated with enterotoxigenic C perfringens.
Visualizing Surface Aberration Contributions in Freeform Systems (2015)

We present a method to calculate and visualize individual surface aberrations within freeform systems. The method is verified for rotational-symmetric systems, where a comparison to Aldis calculus is possible, and then extended to freeform systems.
Structural Characteristics Predict the Stability of HIV (2011)

This chapter contains sections titled: Introduction Results Discussion Materials and Methods Circular Dichroism HPLC CD4 Binding Assay Differential Scanning Calorimetric Analysis of Proteins Hydrodynamic Radius Measurement Surface Plasmon Resonance Assay References
Elemental Microanalysis of Bacillus Anthracis Spores from the Amerithrax Case. (2009)

Abstract not provided.
FPGA Implementation of Wave Digital Filters with Multiple exp-based Nonlinearities (2021)

In this paper, an FPGA implementation of a Diode Clipper circuit as an application of Wave Digital Filters with multiple exp-based nonlinearities is presented. Therefore, an efficient look-up table design in combination with an iterative approach, namely Newtons’s and Halley’s method is proposed for real-time evaluation of the Lambert function. A sequential and a concurrent version of the circuit were implemented, for each of which FPGA resource utilization and a rule for latency depending on the iteration steps required were determined. It is shown that although Halley’s method generally converges faster, the overall latency is the same for Newton’s method while achieving same accuracy and being more resource-saving.
Nickel Sulfide Freestanding Holey Films as Air-Breathing Electrodes for Flexible Zn–Air Batteries (2018)

In this work, a combination of bottom-up electrochemical deposition and top-down electrochemical etching strategies followed by a subsequent sulfuration treatment was employed to rationally synthesize a nickel sulfide (NiS <sub>x</sub>) freestanding holey film (FHF). Owing to the holey structure along with the optimal electrochemically active surface area and active sites, the as-prepared NiS <sub>x</sub> FHF showed an impressive bifunctional electrocatalytic performance toward both oxygen evolution and reduction reactions. The holey and freestanding features provide the NiS <sub>x</sub> FHF with promising characteristics to be used as an ideal air-breathing cathode in flexible Zn-air batteries (ZABs). As a proof-of-concept, the rationally designed NiS <sub>x</sub> FHF achieved remarkable rechargeability and flexibility in a ZAB configuration.
Magnetic Domain Wall Manipulation Using MFM Probe (2007)

Magnetic force microscopy (MFM) has been applied to permalloy multistep-semicircular wires containing nearly-free magnetic domain walls (DWs). In this study, we investigated the effect of stray-magnetic fields from the probes in the MFM measurement using low-, medium-, and high-moment probes, which are coated by 12 nm-, 24 nm-, and 72 nm-thick CoPtCr films, respectively. By using the low-moment probe, the DW signal was clearly observed at the side of the wires, which is consistent with a micromagnetic simulation. By using the high and medium moment probes, in contrast, we observed complete and incomplete DW manipulations, respectively. These manipulation signals were found to be maximized immediately above the wire. These phenomena were analyzed by calculating the stray fields from the MFM probes. We also discussed the possibility of the controllable DW manipulation in terms of the stray fields and the MFM scanning sequences.
A <i>let-7</i> microRNA-Binding Site Polymorphism in <i>KRAS</i> Predicts Improved Outcome in Patients with Metastatic Colorectal Cancer Treated with Salvage Cetuximab/Panitumumab Monotherapy (2014)

LCS6-variant patients with metastatic colorectal cancer have an excellent response to anti-EGFR mAb monotherapy, without any benefit from the addition of chemotherapy. These findings further confirm the importance of this mutation as a biomarker of anti-EGFR mAb response in patients with metastatic colorectal cancer, and warrant further prospective confirmation.
Müller's Muscle–Conjunctival Resection for Correction of Upper Eyelid Ptosis (2007)

Müller's muscle-conjunctival resection is effective for ptosis correction in patients with good levator muscle function; good eyelid symmetry is achieved in most patients. Phenylephrine testing underestimated the ptosis correction achieved with MMCR by 40%. The relationship between MMCR and ptosis correction is complex.
Corpus Callosum Partitioning Schemes and Their Effect on Callosal Morphometry (2006)

C. Ryberg, M. B. Stegmann, K. Sjostrand, E. Rostrup, F. Fazekas, F. Barkhof, G. Waldemar Dept. of Neurology, Memory Disorders Research Unit, Copenhagen, Denmark, Technical University of Denmark, Informatics and Mathematical Modelling, Kongens Lyngby, Denmark, Copenhagen University Hospital, Danish Reseach center for Magnetic Resonance, Copenhagen, Denmark, Dept. of Neurology, Medical University, Graz, Austria, Dept. of Radiology and Image Analysis Center, VU Medical Center, Amsterdam, Netherlands Introduction The Corpus Callosum (CC) is the main fiber tract connecting the two hemispheres in the brain. It functions to communicate e.g. cognitive and learned information between the hemispheres. The lack of evident landmarks that delimit anatomical and functionally distinct callosal regions has spawned several geometric partitioning schemes to subdivide the CC into regions where the fiber topography is expected to be different. These regions might be affected differently in development of disease and their structural parameters (such as size and shape) might correlate with cognitive and functional tests that evaluate different channels of interhemispheric communication. The aim of this work was to investigate the statistical impact of six common partitioning schemes for regional analysis of CC. We hypothesize that conflicts among different CC studies may partially arise from hidden methodological differences.
Semiautomatic sequence‐specific assignment of proteins based on the tertiary structure—The program <i>st2nmr</i> (2001)

The sequence-specific assignment of resonances is still the most time-consuming procedure that is necessary as the first step in high-resolution NMR studies of proteins. In many cases a reliable three-dimensional (3D) structure of the protein is available, for example, from X-ray spectroscopy or homology modeling. Here we introduce the st2nmr program that uses the 3D structure and Nuclear Overhauser Effect spectroscopy (NOESY) peak list(s) to evaluate and optimize trial sequence-specific assignments of spin systems derived from correlation spectra to residues of the protein. A distance-dependent target function that scores trial assignments based on the presence of expected NOESY crosspeaks is optimized in a Monte Carlo fashion. The performance of the program st2nmr is tested on real NMR data of an alpha-helical (cytochrome c) and beta-sheet (lipocalin) protein using homology models and/or X-ray structures; it succeeded in completely reproducing the correct sequence-specific assignments in most cases using 2D and/or 15N/13C Nuclear Overhauser Effect (NOE) data. Additionally to amino acid residues the program can also handle ligands that are bound to the protein, such as heme, and can be used as a complementary tool to fully automated assignment procedures.
Dependence of Cure Parameters on Pdlc Films Prepared by Electron Beam and Ultraviolet Curing (1999)

Abstract One basic method for the preparation of Polymer Dispersed Liquid Crystal (PDLC) films is the formation of microdroplets of liquid crystals (LCs) in a polymer matrix by a phase separation process. This can be achieved by radiation-initiated polymerization of a mixture including polymer precursors and LCs. The PDLC films used in this study were prepared by two different methods: Electron Beam (EB) or Ultraviolet (UV) curing. The electro-optical properties of the obtained PDLC-films based on a selected representative composition were investigated as a function of the chosen radiation. The transmission versus voltage curves exhibit a good reproducibility and a strong dependence on the curing conditions for samples prepared in the same experimental conditions. The evaluation of the electro-optical behavior indicates remarkable differences between EB- and UV-cured samples. The results are discussed in terms of off-/on-state transmission values and threshold voltage.
Lithographic process optimization using process capability analysis (2003)

A capable process fulfills many requirements on e.g. depth of focus, exposure latitude, and mask error factor. This makes a full optimization complicated. Traditionally only a few parameters are included in the optimization routine, such as the focus-dose process window, while other parameters like the (NA,&sigma; ) illumination conditions are fixed at a specified value. In this paper we present an analytical model for describing the effect of variations in dose, focus and mask CD. We optimize the overall CD distribution, both the target value and the CD variation, taking the statistical variations of focus, dose and mask line width variations into account. The improved CD control is measured quantitatively, using the well-known process capability index (<i>C<sub>pk</sub></i>). The results are compared to traditional optimization schemes and brute force Monte Carlo simulations. Process latitudes can be better optimized while calculating the OPC curve. This is achieved by tuning the mask corrections to the process variations and simultaneously optimizing the global mask bias. Furthermore, the optimization method enables a trade off between mask error and process control. Simulated aerial image data is used to determine the optimum mask bias and illumination condition for different levels of process variation, including mask CD variation. The effect of optimizing the global mask bias is calculated. Finally, the results will be compared to experimental data for a number of illumination settings.