gebhart/patrepeval huggingface dataset:
MN1 overexpression induces acute myeloid leukemia in mice and predicts ATRA resistance in patients with AML (2007)

Overexpression of wild-type MN1 is a negative prognostic factor in patients with acute myeloid leukemia (AML) with normal cytogenetics. We evaluated whether MN1 plays a functional role in leukemogenesis. We demonstrate using retroviral gene transfer and bone marrow (BM) transplantation that MN1 overexpression rapidly induces lethal AML in mice. Insertional mutagenesis and chromosomal instability were ruled out as secondary aberrations. MN1 increased resistance to all-trans retinoic acid (ATRA)-induced cell-cycle arrest and differentiation by more than 3000-fold in vitro. The differentiation block could be released by fusion of a transcriptional activator (VP16) to MN1 without affecting the ability to immortalize BM cells, suggesting that MN1 blocks differentiation by transcriptional repression. We then evaluated whether MN1 expression levels in patients with AML (excluding M3-AML) correlated with resistance to ATRA treatment in elderly patients uniformly treated within treatment protocol AMLHD98-B. Strikingly, patients with low MN1 expression who received ATRA had a significantly prolonged event-free (P = .008) and overall (P = .04) survival compared with patients with either low MN1 expression and no ATRA, or high MN1 expression with or without ATRA. MN1 is a unique oncogene in hematopoiesis that both promotes proliferation/self-renewal and blocks differentiation, and may become useful as a predictive marker in AML treatment.
Semi-automatic Source Code Generation for the Hardware-Implementation of a Parallelizable and Configurable Error Correction Unit (2012)

Bose-Chaudhuri-Hocquenghem (BCH) codes are among the most used error correction codes. They are used in DVB-T receivers and are deployed for error correction in flash memories. Nowadays codes with large codeword lengths and large error correction capability are used which is a new challenge in hardware-development for the encoder and decoder. This article presents a parallel BCH error correction unit with configurable error correction capability. Furthermore, it describes how tools for source code generation can be used to support the development process.
Growth Factor-regulated Pathways in Epithelial Cell Proliferation (1990)

Investigations of the pathways regulating normal growth of epithelial cells have revealed the existence of two major growth-factor signaling cascades required for proliferation. One pathway is activated by IGF-1 or high insulin concentration. The other is triggered by EGF, TGF alpha, or members of the FGF family, including the recently discovered epithelial-cell-specific growth factor, designated keratinocyte growth factor (KGF). Its expression pattern in vivo suggests that KGF plays an important normal physiologic role as a stromal effector of epithelial cell proliferation. Oncogenes, which represent constitutively activated forms of genes critically involved in growth-factor signaling pathways, specifically abrogate the requirement for mitogens of the EGF pathway. Examples of such genes include the erbB/EGF receptor and erbB-2, which encode structurally related receptor proteins and are often amplified and/or overexpressed in epithelial malignancies. Employing reduced stringency hybridization with v-erbB as a probe, we recently identified a third member of this receptor family, designated erbB-3. cDNA cloning revealed a predicted 148-kD transmembrane polypeptide with structural features similar to those of the EGF receptor. Normal erbB-3 expression in keratinocytes and glandular epithelium suggests its physiologic role in these cell types. Moreover, markedly elevated erbB-3 mRNA levels in certain mammary tumor cell lines suggest that increased erbB-3 expression may also play a role in some human epithelial malignancies.
Small Cyclic Diammonium Cation Templated (110)-Oriented 2D Halide (X = I, Br, Cl) Perovskites with White-Light Emission (2019)

Two-dimensional (2D) halide perovskites exhibit excellent potential for optoelectronics because of their outstanding physical properties and structural diversity. White-light emission is one property of 2D perovskites that originates from self-trapped excitons (STE) in the highly distorted structures. The so-called (110)-oriented 2D perovskites are generally distorted and believed to be good candidates for white-light emitting devices. Here, we report (110)-oriented 2D perovskites, C4N2H12PbX4 (X = I, Br, Cl), templated by the small cyclic diammonium cation, 3-aminopyrrolidinium (3APr). Structural characterization by single-crystal X-ray diffraction reveals that the distortion of the inorganic part of the structures is influenced by the stereochemical conformation of the cation between the perovskite layers. The experimental bandgaps follow the trend I < Br < Cl (2.56 eV, 3.29 eV, 3.85 eV, respectively). Density functional theory calculations reveal a weak but significant electronic band dispersion along the stacking axis, suggesting a non-negligible interlayer electronic coupling caused by the short proximity of adjacent inorganic layers. The high level of distortion results in the emergence of white-light emission, rarely seen in iodide perovskites, as well as the bromide and chloride isostructural analogues, which provides perfect platform to compare the broad emission mechanism for all three halides. The bromide and chloride perovskites show longer lifetimes and higher color rendering index (CRI) (83 and 85), relevant to solid-state lighting. Temperature-dependent PL measurements confirm that the broad emission comes from different STE mechanism for different halides, with the peak broadening persisting even at low temperature for the chloride compound.
Simultaneous update iterative algorithm for variance reduction on random coincidences in PET (2007)

The use of the ordinary Poisson iterative reconstruction algorithm in PET requires the estimation of expected random coincidences. In a clinical environment, random coincidences are often acquired with a delayed coincidence technique, and expected randoms are estimated through variance reduction (VR) of measured delayed coincidences. While numerous analytical methods exist for reducing the variance of measured random coincidences, iterative methods have the advantage of being easily adapted to any acquisition geometry and of allowing the estimation of the singles rate at the crystal level, when the number of crystals is relatively small. In this paper we present a VR algorithm with a simultaneous update, which is derived by using surrogate functions. A monotonic algorithm is designed for data in line-of- response projection or list mode formats. The updated equation requires the knowledge of a fan sum of random data; therefore, the algorithm is extremely fast. The algorithm derivation provides a theoretical basis for a more heuristic simultaneous update algorithm, which was used in our previous work with list mode data. Measured data from a Siemens TruePoint clinical scanner were used to validate the algorithm.
Improving Laser Cutting Quality for Two-Dimensional Contoured Paths (1998)

Quality improvements in laser cutting of mild steel have been achieved by a newly developed model-based optimization strategy and its application to one-dimensional cut has been reported early. The specific aims of this paper are to assure quality of cut when cornering and generating small diameter holes. Such routines encompass a large proportion of all features processed on laser cutting systems, and therefore their successful production is significant. Currently, extensive trial-and-error based experimentation is needed in order to improve quality for these routines. Thus model-based optimization has the benefit of reducing this time-exhaustive step whilst leading to an optimal solution. Nonlinear power adaptation profiles are generated via the optimization strategy in order to stabilize cutting front temperatures. Uniform temperatures produce better quality by reducing (i) kerf widening effects, (ii) heat-affected zone extents, and (iii) workpiece self-burning effects. Experimental results are presented, and it is demonstrated that such process manipulation can produce significant quality improvements. In addition, predicted heat-affected zones correlate closely to those actually obtained. The process manipulation is successfully implemented in an industrial laser cutting system under laboratory condition.
Slide: Streaming and Load-Adaptive Periodicity Estimation (2006)

We introduce a CPU-adaptive algorithm for spectrum estimation on streaming data. Our approach combines a fast and intelligent load-shedding scheme with a closed form incremental spectrum computation, which adapts gracefully to the available computational resources.
Simulating Recordings from Intrafascicular Electrodes to Facilitate Decoding Algorithm Development (2013)

While decoded peripheral neural activity recorded by a longitudinal intrafascicular electrode (LIFE) from amputees can be used to control a single degree-of-freedom (DOF) robot arm, recording and decoding of signals from multiple LIFEs for multi-DOF motor control has not yet been achieved. We developed a tool to facilitate the development of online decoding algorithms for this task. The tool translates motor intent signals to simulated neural recordings from many LIFEs. Motor intent signals drive a pool of simulated motor neurons with various spike shapes, recruitment characteristics, and firing rate properties. Each LIFE records a weighted sum of a subset of simulated motor neuron activity patterns. Furthermore, we show by using simulated data sets that simple decoding schemes such as spike counting is a 'good' estimator of motor intents.
Germanium oxynitride (GeOxNy) as a back interface passivation layer for Germanium-on-insulator substrates (2008)

This paper describes the development of a GeOxNy surface passivation of germanium, which is mandatory for microelectronics germanium-on-insulator (GeOI) substrate fabrication. Indeed, germanium surface reactivity in ambient atmosphere requires the development of Ge surface passivation in order to provide an electrically acceptable interface between the active layer and the buried oxide (BOX) of GeOI substrates. In this paper, GeOI substrates with a passivation interlayer between the Ge film and the BOX were fabricated using the Smart Cut™ technology. Plasma treatments produced a germanium oxynitride (GeOxNy) passivation interlayer with a nitrogen concentration up to 40% and thickness of 3nm. Electrical activity in such GeOI active layer was investigated with pseudo-metal-oxide-semiconductor field effect transistor measurements. Electron mobility reaches a value of 670cm2V−1s−1, notably higher than those typically reported on nonpassivated GeOI structures.
Synthesis, Crystal Structure, and Molecular Modeling of a Layered Manganese(II) Phosphate:  Mn<sub>3</sub>(PO<sub>4</sub>)<sub>4</sub>·2(H<sub>3</sub>NCH<sub>2</sub>CH<sub>2</sub>)<sub>3</sub>N·6(H<sub>2</sub>O) (2004)

A novel layered manganese(II) phosphate, Mn3(PO4)4·2(H3NCH2CH2)3N·6(H2O), has been synthesized solvothermally using tris(2-aminoethyl)amine (TREN) as a template. The structure was solved ab initio using X-ray powder diffraction data and confirmed by molecular modeling. The compound was further characterized by SEM, IR spectroscopy, photoluminescence, and elemental and thermal analysis. The compound crystallizes in the trigonal space group P3̄c1 with a = 8.8706(4) Å, c = 26.158(2) Å, and V = 1782.6(2) Å3. The structure consists of layers of corner sharing Mn(II)O4 and PO4 tetrahedra forming infinite [Mn3(PO4)4]6- macroanions with 4.6 net topology, sandwiched by layers of TREN and water molecules. The protonated TREN molecules provide charge balancing for the inorganic sheets; the interlayer stability is accomplished mainly by a network of hydrogen bonds between water molecules and the inorganic macroanions. This hybrid organic/inorganic layered material can be reversibly dehydrated.
Advanced Glycation End Products Predict Loss of Renal Function and Correlate With Lesions of Diabetic Kidney Disease in American Indians With Type 2 Diabetes (2016)

We examined associations of advanced glycation end products (AGEs) with renal function loss (RFL) and its structural determinants in American Indians with type 2 diabetes. Data were from a 6-year clinical trial that assessed renoprotective efficacy of losartan. Participants remained under observation after the trial concluded. Glomerular filtration rate (GFR) was measured annually. Kidney biopsies were performed at the end of the trial. Five AGEs were measured in serum collected at enrollment and at kidney biopsy. RFL was defined as ≥40% decline of measured GFR from baseline. Of 168 participants (mean baseline age 41 years, HbA<sub>1c</sub> 9.2%, GFR 164 mL/min, and albumin-to-creatinine ratio 31 mg/g), 104 reached the RFL end point during median follow-up of 8.0 years. After multivariable adjustment, each doubling of carboxyethyl lysine (hazard ratio [HR] 1.60 [95% CI 1.08-2.37]) or methylglyoxal hydroimidazolone (HR 1.30 [95% CI 1.02-1.65]) concentration was associated with RFL. Carboxyethyl lysine, carboxymethyl lysine, and methylglyoxal hydroimidazolone correlated positively with cortical interstitial fractional volume (partial r = 0.23, P = 0.03; partial r = 0.25, P = 0.02; and partial r = 0.31, P = 0.003, respectively). Glyoxyl hydroimidazolone and methylglyoxal hydroimidazolone correlated negatively with total filtration surface per glomerulus (partial r = -0.26, P = 0.01; and partial r = -0.21, P = 0.046, respectively). AGEs improve prediction of RFL and its major structural correlates.
2-D mesh geometry and motion compression for efficient object-based video representation (2002)

Methods for object-based compression and composition of natural and synthetic video content are currently emerging in standards such as MPEG-4 and VRML. This paper describes novel techniques for compression of 2-D triangular mesh geometry and motion, enabling efficient representation and manipulation of video content. Specifically, mesh geometry is compressed by predictive coding of mesh node locations. Mesh node motion vectors are compressed by predictive techniques as well. Preliminary results show that the mesh data can be coded at a fraction of the bits used to code a typical video object.
Influence of organ pathology on the electrical parameters in organ projection areas of the skin. (2006)

Pathology of an internal organ causes significant rectification of electrical currents (diode phenomenon) in related skin areas--organ projection areas (OPAs), once the resistance 'breakthrough effect' has been induced in the skin. Also, the impedance of the diseased organ's projection areas is increased. The aim of this double-blind study was to confirm these phenomena statistically using a broad spectrum of measuring parameters. Skin impedance vs. measurement frequency, skin impedance vs. applied voltage, and skin resistance vs. voltage were evaluated at 335 auricular OPAs related to the healthy internal organs and 203 auricular OPAs related to the diseased organs. These measurements confirmed that the skin electrical characteristics of specific locations are dependent on the health state of the corresponding internal organs. It was found that the impedance of OPAs corresponding to the healthy internal organs equals 185 +/- 291 komega at 10 Hz and decreases to 64 +/- 49 komega at 10 kHz; and that the impedance of OPAs related to the diseased organs equals 7.5 +/- 2.2 Momega at 10 Hz and 99 +/- 50 komega at 10 kHz. The disparity of the impedances between the healthy and diseased organs related OPAs is greater at higher potentials. The skin resistance, when measured with a negatively polarized point electrode, undergoes a rapid resistance decrease of approximately two orders of magnitude, if the applied current is sufficient. After this reversible 'breakthrough effect' is obtained the skin exhibits rectification. The degree of rectification is low for OPAs related to the healthy organs. For OPAs related to the diseased organs, the resistance measured with a positive polarisation of measuring electrode could be five times greater than the resistance measured at the same voltage with the same but negatively polarised electrode. The disparity between the resistance measured with a negatively and with a positively polarised electrode at OPAs related to the diseased organs was greater at higher measurement voltages. The influence of organ pathology on the electrical parameters of related OPAs does not depend on the kind of internal organ and is not affected by the etiology of pathology. The degree of rectification or difference in impedance is proportional to the extent of the pathological process within the related organ.
Capturing and Executing Behavioral Requirements: The Play-In/Play-Out Approach, (2001)

A powerful methodology for specifying scenario-based requirements of reactive systems is described, in which the behavior is \\played in &quot; directly from the system&apos;s GUI or some abstract version thereof, and can then be \\played out&quot;. The approach is supported and illustrated by a tool, which we call the play-engine. As the requirements are played in, the play-engine automatically generates a formal version in the language of live sequence charts (LSCs). As they are played out, it causes the application to react according to the uni-versal (\\must&quot;) parts of the specication; the existential (\\may&quot;) parts can be monitored to check their successful completion. Play-in is a user-friendly high-level way of specify-ing behavior and play-out is a rather surprising way of working with a fully operational system directly from its requirements. The ideas appear to be relevant to many stages of system development, including requirements engineering, specication, testing, analysis and implementation.
Space-Based Multifunction Radar Systems: Future Tool for Civilian and Military Surveillance, (1986)

Abstract : Space-based surveillance systems, including primary radar (SBR) and secondary surveillance radar (SBSR) are of interest for both the Air Traffic Control and the Air Defence. This paper surveys the relevant state of the art, architectures considers surveillance system with special reference to the European scenario and closes with remarks pointing toward areas of future work.
Potential anticancer agents. IV. Constituents of Jacaranda caucana Pittier (Bignoniaceae). (1977)

<p>Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) was used to analyze a series of synthetic organic ions bearing fixed multiple charges. Despite the multiple intrinsic charges, only singly charged ions were recorded in each case. In addition to the pseudo-molecular ions formed by counterion adduction, deprotonation and electron capture, a number of fragment ions were also observed. Charge splitting by fragmentation was found to be a viable route for charge reduction leading to the formation of the observed singly charged fragment ions. Unlike multivalent metal ions, organic ions can rearrange and/or fragment during charge reduction. This fragmentation process will evidently complicate the interpretation of the MALDI MS spectrum. Because MALDI MS is usually considered as a soft ionization technique, the fragment ion peaks can easily be erroneously interpreted as impurities. Therefore, the awareness and understanding of the underlying MALDI-induced fragmentation pathways is essential for a proper interpretation of the corresponding mass spectra. Due to the fragment ions generated during charge reduction, special care should be taken in the MALDI MS analysis of multiply charged ions. In this work, the possible mechanisms by which the organic ions bearing fixed multiple charges fragment are investigated. With an improved understanding of the fragmentation mechanisms, MALDI TOF MS should still be a useful technique for the characterization of organic ions with fixed multiple charges.</p>
Broadband optical interferometric tomography with computational adaptive optics using ‘guide stars’ (2012)

We present a method to utilize ‘guide stars’ within a sample, as in hardware-based adaptive optics, in order to correct aberrations using computational adaptive optics. Interferometric synthetic aperture microscopy (ISAM), a computed imaging technique to overcome the depth-of-field limitations in optical coherence tomography/microscopy (OCT/OCM), is utilized to correct defocus and reveal local high-scattering regions that can serve as potential guide stars. The correction of pupil aberrations using Zernike polynomials can be applied pre- or post-ISAM in order to improve resolution and signal-to-noise ratio of these guide stars. Aberrations of the effective pupil function can then be determined through subsequent windowing and Fourier transforming of a guide star signal. Computational adaptive optics based on guide stars is demonstrated in a phantom consisting of sub-resolution scatterers, with work underway to extend this method to biological tissues.
Hadamard Coded Modulation: An Alternative to OFDM for Optical Wireless Communications (2014)

Orthogonal frequency division multiplexing (OFDM) is a modulation technique susceptible to source, channel and amplifier nonlinearities because of its high peak-to-average ratio (PAPR). The distortion gets worse by increasing the average power of the OFDM signals since larger portion of the signals are affected by nonlinearity. In this paper we introduce Hadamard coded modulation (HCM) that uses the fast Walsh-Hadamard transform (FWHT) to modulate data as an alternative technique to OFDM in direct-detection wireless optical systems. This technique is shown to have a better performance for high average optical power scenarios because of its small PAPR, and can be used instead of OFDM in two scenarios: 1) in optical systems that require high average optical powers such as visible light communications (VLC), and 2) in optical wireless systems unconstrained by average power, for which HCM achieves lower bit error rate (BER) compared to OFDM. The power efficiency of HCM can be improved by removing a part of the signal's DC bias without losing any information. In this way, the amplitude of the transmitted signal is decreased and the signals become less susceptible to nonlinearity. Interleaving can be applied on HCM to make the resulting signals resistent against inter-symbol interference (ISI) effects in dispersive channels by uniformly distributing the interference over all symbols.
Radiation damping of an arbitrarily shaped bubble (2015)

Large encapsulated bubbles have recently been used for abating low-frequency anthropogenic underwater noise [J. Acoust. Soc. Am. 135, 1700–1708 (2014)]. The use of encapsulation allows for the possibility of bubbles that are significantly nonspherical in their equilibrium state. Strasberg [J. Acoust. Soc. Am. 25, 536–537 (1953)] investigated the resonance frequency of an ideal bubble with arbitrary shape and found that the dependence of resonance frequency on the shape of the bubble reduced to a well-known problem in electrostatics. The present work extends that analysis to include the effects of radiation damping on the oscillation of a bubble, and does so by including a loss term due to Ilinskii and Zabolotskaya [J. Acoust. Soc. Am. 92, 2837–2841 (1992)] in the volume-frame dynamical equation for the bubble. An expression is given for the amplitude of the acoustic field scattered from the bubble, and it is shown that radiation damping scales as resonance frequency cubed for arbitrarily shaped bubbles having the same volume. Comparisons are made with previous work on scattering from spherical and prolate spheroidal bubbles, and various new bubble shapes are considered. [Work supported by AdBm Technologies, the ARL:UT McKinney Fellowship in Acoustics and ONR.]