gebhart/patrepeval huggingface dataset:
Exploring Bacterial Carboxylate Reductases for the Reduction of Bifunctional Carboxylic Acids (2017)

Carboxylic acid reductases (CARs) selectively reduce carboxylic acids to aldehydes using ATP and NADPH as cofactors under mild conditions. Although CARs attracts significant interest, only a few enzymes have been characterized to date, whereas the vast majority of CARs have yet to be examined. Herein the authors report that 12 bacterial CARs reduces a broad range of bifunctional carboxylic acids containing oxo-, hydroxy-, amino-, or second carboxyl groups with several enzymes showing activity toward 4-hydroxybutanoic (4-HB) and adipic acids. These CARs exhibits significant reductase activity against substrates whose second functional group is separated from the carboxylate by at least three carbons with both carboxylate groups being reduced in dicarboxylic acids. Purified CARs supplemented with cofactor regenerating systems (for ATP and NADPH), an inorganic pyrophosphatase, and an aldo-keto reductase catalyzes a high conversion (50-76%) of 4-HB to 1,4-butanediol (1,4-BDO) and adipic acid to 1,6-hexanediol (1,6-HDO). Likewise, Escherichia coli strains expressing eight different CARs efficiently reduces 4-HB to 1,4-BDO with 50-95% conversion, whereas adipic acid is reduced to a mixture of 6-hydroxyhexanoic acid (6-HHA) and 1,6-HDO. Thus, our results illustrate the broad biochemical diversity of bacterial CARs and their compatibility with other enzymes for applications in biocatalysis.
PROMO: Real‐time prospective motion correction in MRI using image‐based tracking (2009)

Artifacts caused by patient motion during scanning remain a serious problem in most MRI applications. The prospective motion correction technique attempts to address this problem at its source by keeping the measurement coordinate system fixed with respect to the patient throughout the entire scan process. In this study, a new image-based approach for prospective motion correction is described, which utilizes three orthogonal two-dimensional spiral navigator acquisitions, along with a flexible image-based tracking method based on the extended Kalman filter algorithm for online motion measurement. The spiral navigator/extended Kalman filter framework offers the advantages of image-domain tracking within patient-specific regions-of-interest and reduced sensitivity to off-resonance-induced corruption of rigid-body motion estimates. The performance of the method was tested using offline computer simulations and online in vivo head motion experiments. In vivo validation results covering a broad range of staged head motions indicate a steady-state error of less than 10% of the motion magnitude, even for large compound motions that included rotations over 15 deg. A preliminary in vivo application in three-dimensional inversion recovery spoiled gradient echo (IR-SPGR) and three-dimensional fast spin echo (FSE) sequences demonstrates the effectiveness of the spiral navigator/extended Kalman filter framework for correcting three-dimensional rigid-body head motion artifacts prospectively in high-resolution three-dimensional MRI scans.
Real-Time Monitoring of Temperature Rises of Energized Transformer Cores With Distributed Optical Fiber Sensors (2019)

Real-time temperature mapping that solves local overheating problems is important for obtaining an optimized thermal design for high-efficiency power transformers. Internal temperature monitoring of operating power transformers can also be leveraged for asset monitoring applications targeting at fault detection enabling condition-based maintenance. Transformers present a variety of challenging sensing environments such as high levels of electromagnetic interference and limited space for conventional sensors to operate. Immersion of power transformers in insulation oils for thermal management during operation and the presence of relatively large and time-varying electrical and occasional magnetic fields make sensing technologies requiring electrical wires or active power at sensing locations highly undesirable. In this work, we investigate thermal response of a standard telecom fiber instrumented on compact transformer cores by using an optical frequency-domain reflectometry scheme. Correlation between conventional temperature sensing methods and fiber-optic sensing results as well as tradeoffs between spatial resolution and temperature measurement accuracy is discussed and spatially resolved real-time monitoring of temperatures in energized transformers is experimentally demonstrated.
Serologic monitoring of a broiler breeder flock previously affected by inclusion body hepatitis and testing of the progeny for vertical transmission of fowl adenoviruses. (2007)

The increasing number of clinical cases of inclusion body hepatitis (IBH) associated with fowl adenoviruses (FAdVs) is a growing concern in different parts of the world, including Canada. After an outbreak of IBH in a 10-d-old pullet broiler breeder flock, we serologically monitored the flock from 8 to 46 wk of age, using the agar gel precipitation test (AGPT) offered by diagnostic laboratories and an FAdV group-specific enzyme-linked immunosorbemt assay (ELISA) developed earlier. In addition, we tested 1-d-old progeny for possible vertical transmission of FAdV when the breeder flock approached the peak of egg production by performing virus isolation and polymerase chain reaction (PCR) procedures on target organs. As in previous studies comparing the 2 tests, ELISA was more sensitive than AGPT. With ELISA, a few birds had weakly positive results at 8 wk of age, and all the birds had strongly positive results from 12 wk of age until the end of the study. This group-specific ELISA is therefore a sensitive and practical way to monitor FAdV antibodies in commercial flocks. None of the 1-d-old chicks tested were positive by PCR, nor was FAdV isolated from the same tissues, indicating an absence of transmission of infectious virus to the progeny. The lack of virus production and transmission could be due to the presence of high antibody titers in the layers.
Novel PAPR Reduction Algorithms for OFDM Signals (2022)

This paper proposes two efficient peak-to-average power ratio (PAPR) reduction algorithms for OFDM signals based on the principle of tone reservation. The first algorithm is performed in the time domain, whereas the second algorithm is a new clipping-and-filtering method. Both algorithms consist of two stages. The first stage, which is done off-line, precomputes a set of canceling signals based on the settings of the OFDM system. In particular, these signals are constructed to cancel signals at different levels of maximum instantaneous power that are above a predefined threshold. The second stage, which is online and iterative, reduces the signal peaks using modified versions of the canceling signals constructed in the first stage. When the reserved tones are distributed among the data tones, analysis and simulation results obtained with Data Over Cable Service Interface Specifications (DOCSIS) parameters show that the proposed algorithms achieve slightly better PAPR reduction performance and with significantly lower complexity when compared to the conventional algorithms.
The search for the cystic fibrosis gene (1989)

This article reviews progress made to date in the attempt to find the gene causing cystic fibrosis (CF). The search has been focused on a region of the human genome containing no more than 10 genes and has been accomplished in two steps. First, linkage analysis was used to localize the gene to the q31 band of chromosome 7. Subsequently, molecular cloning methods were employed to isolate DNA segments estimated to be within 400,000 base pairs of the CF gene. The current challenge in the research is to find the genes located in this interval and to then prove that one of them is the CF gene. The approaches by which this will be accomplished are discussed.
CARES: Completely Automated Robust Edge Snapper for carotid ultrasound IMT measurement on a multi-institutional database of 300 images: a two stage system combining an intensity-based feature approach with first order absolute moments (2011)

The carotid intima-media thickness (IMT) is the most used marker for the progression of atherosclerosis and onset of the cardiovascular diseases. Computer-aided measurements improve accuracy, but usually require user interaction. In this paper we characterized a new and completely automated technique for carotid segmentation and IMT measurement based on the merits of two previously developed techniques. We used an integrated approach of intelligent image feature extraction and line fitting for automatically locating the carotid artery in the image frame, followed by wall interfaces extraction based on Gaussian edge operator. We called our system - CARES. We validated the CARES on a multi-institutional database of 300 carotid ultrasound images. IMT measurement bias was 0.032 ± 0.141 mm, better than other automated techniques and comparable to that of user-driven methodologies. Our novel approach of CARES processed 96% of the images leading to the figure of merit to be 95.7%. CARES ensured complete automation and high accuracy in IMT measurement; hence it could be a suitable clinical tool for processing of large datasets in multicenter studies involving atherosclerosis.pre-
Analysis of a 3-D System Function Measured for Magnetic Particle Imaging (2012)

Magnetic particle imaging (MPI) is a new tomographic imaging approach that can quantitatively map magnetic nanoparticle distributions in vivo. It is capable of volumetric real-time imaging at particle concentrations low enough to enable clinical applications. For image reconstruction in 3-D MPI, a system function (SF) is used, which describes the relation between the acquired MPI signal and the spatial origin of the signal. The SF depends on the instrumental configuration, the applied field sequence, and the magnetic particle characteristics. Its properties reflect the quality of the spatial encoding process. This work presents a detailed analysis of a measured SF to give experimental evidence that 3-D MPI encodes information using a set of 3-D spatial patterns or basis functions that is stored in the SF. This resembles filling 3-D k-space in magnetic resonance imaging, but is faster since all information is gathered simultaneously over a broad acquisition bandwidth. A frequency domain analysis shows that the finest structures that can be encoded with the presented SF are as small as 0.6 mm. SF simulations are performed to demonstrate that larger particle cores extend the set of basis functions towards higher resolution and that the experimentally observed spatial patterns require the existence of particles with core sizes of about 30 nm in the calibration sample. A simple formula is presented that qualitatively describes the basis functions to be expected at a certain frequency.
Abstract 09: HDL That Contains Apolipoprotein C-III is Not Inversely Associated with Risk of Coronary Events: The Multi-Ethnic Study of Atherosclerosis (2015)

Background: Apolipoprotein A-I (apoA-I), the major protein component of high density lipoprotein (HDL), is inversely associated with risk of coronary heart disease (CHD). However, the cardioprotective benefits of HDL levels remain controversial. HDL is comprised of a heterogeneous group of lipoproteins, and subtypes of HDL could have different cardioprotective potential. Apolipoprotein C-III (apoC-III) is a small pro-inflammatory protein that resides on the surface of some lipoproteins. In case-control studies of mostly white participants, the presence or absence of apoC-III defines lipoprotein subtypes that show differential associations with CHD risk. Methods and Results: We used a novel in-house combo ELISA to measure the concentration of total apoC-III, apoA-I with and without apoC-III in 5668 white, black, Hispanic and Chinese members of the Multi-Ethnic Study of Atherosclerosis without known cardiovascular disease from the baseline visit in 2000-2002. A total of 386 incident CHD events occurred by 2...
Orthonormal Polynomials in Wavefront Analysis: Analytical Solution (2006)

This paper derives closed-form orthonormal polynomials over noncircular apertures using the Gram-Schmidt orthogonalization process. Isometric plots, interferograms, and point-spread functions are illustrated. Their use in wavefront analysis is discussed.
Critical overcurrent turn-off close to IGBT current saturation (2015)

A failure mechanism in the edge termination of a 1200V IGBT during overcurrent turn-off is studied with simulations and verified by experiments. The position of the destruction in the experiment can be correlated to the formation of a critical filament in the simulation. The destruction mechanism is investigated in detail. It is only observed if the IGBT enters its current saturation regime. I.e., the IGBT survives a turn-off from the same current level for an increased gate voltage. It is shown that an IGBT provided with a properly-designed High Dynamic Ruggedness (HDR) edge termination structure [1] is no longer susceptible to the destruction mechanism.
GnRH antagonists in the treatment of gynecological and breast cancers. (2003)

Approximately 80% of human ovarian and endometrial cancers and 50% of breast cancers express GnRH and its receptor as part of an autocrine regulatory system. After binding of its ligand the tumor GnRH receptor couples to G-protein alphai and activates a variety of intracellular signaling mechanisms. (1) Through activation of a protein tyrosine phosphatase, autophosphorylation of growth factor receptors is reverted leading to an inhibition of mitogenic signaling and reduced cell proliferation. (2) Through activation of nuclear factor kappa B antiapoptotic mechanisms are induced protecting tumor cells from apoptosis induced, for example, by doxorubicin. (3) Through activation of the Jun kinase pathway AP-1 is induced, leading to cell cycle arrest in the G0/G1 phase. It seems reasonable to speculate that this system enables the tumor cell to reduce proliferation and to activate repair mechanisms while being protected simultaneously from apoptosis. Interestingly, GnRH antagonists show the same activity in this system as agonists, indicating that the dichotomy GnRH agonist-GnRH antagonist defined in the pituitary gonadotrope is not valid for the tumor GnRH system. Recently, a second type of GnRH receptor, specific for GnRH-II, has been identified in ovarian and endometrial cancers, which transmits significantly stronger antiproliferative effects than the GnRH-I receptor. GnRH antagonists have agonistic effects on this type II receptor. In animal models of human cancers, GnRH antagonists had stronger antitumor effects than GnRH agonists. Therefore, we performed a phase II clinical trial with the GnRH antagonist, cetrorelix (10 mg/day), in patients with ovarian or mullerian carcinoma refractory to platinum chemotherapy. Of 17 evaluable patients treated with cetrorelix, 3 obtained a partial remission (18%) which lasted for 2 to 6 months. Furthermore, 6 patients experienced disease stabilization (35%) for up to 1 year. In this very refractory patient population (median number of prior chemotherapies = 3) these results are quite remarkable when compared with palliative chemotherapy. In addition, cytotoxic GnRH analogs have been developed, where for example doxorubicin was covalently coupled to GnRH analogs. These compounds have superior antitumor effects in cancers expressing GnRH receptors as compared with native doxorubicin and allow for a targeted cytotoxic chemotherapy of gynecologic and breast cancers.
A ρ<i>c</i> hydrophone (1986)

Because traditional piezoelectric materials have much higher acoustic impedances than water, most hydrophones are ‘‘hard’’ compared to the surrounding water medium. This hardness causes internal and external reflections that manifest themselves as resonance and diffraction effects, respectively. Even nonvoided polyvinylidene fluoride (PVDF), a piezoelectric polymer, has a characteristic acoustic impedance, ρoco, about 2.7 times that of water. With the advent of voided PVDF, however, it is possible to match water’s impedance as closely as desired. Using ρc window material and ρc PVDF, we have constructed a ρc hydrophone whose response is essentially free of resonance and diffraction effects.
A statistical study of magnetic tunnel junctions for high-density spin torque transfer-MRAM (STT-MRAM) (2008)

We have demonstrated a robust magnetic tunnel junction (MTJ) with a resistance-area product RA=8 Ω—μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> that simultaneously satisfies the statistical requirements of high tunneling magnetoresistance TMR ≫ 15σ(R <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</inf> ), write threshold spread σ(Vw)/≪Vw≫ ≪7.1%, breakdown-to-write voltage margin over 0.5V, read-induced disturbance rate below 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−9</sup> , and sufficient write endurance, and is free of unwanted write-induced magnetic reversal. The statistics suggest that a 64Mb chip at the 90-nm node is feasible.
Chip-integrated plasmonic flat optics for mid-infrared full-Stokes polarization detection (2019)

Flat optics presents a new path to control the phase, amplitude, and polarization state of light with ultracompact devices. Here we demonstrate chip-integrated metasurface devices for polarization detection of mid-infrared light with arbitrary polarization states. Six high-performance microscale linear and circular polarization filters based on vertically stacked plasmonic metasurfaces (with total thickness <600  nm) are integrated on the same chip to obtain all four Stokes parameters of light with high accuracy. The device designs can be tailored to operate at any wavelength in the mid-infrared spectral region and are feasible for on-chip integration with mid-infrared (mid-IR) photodetectors and imager arrays. Our work will enable on-chip mid-IR polarimeters and polarimetric imaging systems, which are highly desirable for many applications, such as clinical diagnosis, target detection, and space exploration.
The soud of light: Towards ocean acoustic sensing with an optical breakdown transducer (2019)

When a high-power laser is focused to a small spot in a fluid, nonlinear interactions at the focus can excite a plasma that evolves and glows according to the properties of the breakdown medium. This phenomenon—optical breakdown—is commonly used for underwater chemical measurements in a technique called Laser-Induced Breakdown Spectroscopy (LIBS). However, LIBS generally operates at short ranges and only leverages the optical emission of the plasma for sensing. If instead, the laser systems were tuned to amplify the mechanical effects of optical breakdown, then it could be deployed as a versatile source for broadband acoustic sensing. The optical breakdown acoustic source is simultaneously compact (mm-scale), loud (MPa peak pressures), ultra-broadband (10 kHz–4 MHz), and geometrically reconfigurable. Here, I will describe the physics governing optical breakdown transduction and then show how can this be tuned to enable new single-vehicle sensing strategies in the ocean.
Ionene elastomers from polytetramethylene oxide diamines and reactive dihalides. I. Effect of dihalide structure on polymerization and thermal reversibility (1989)

Abstract The reaction of α,ω‐bis(dimethylamino) polytetramethylene oxide with various dihalides provided a series of elastomeric ionenes. The influence of dihalide structure on the reaction was studied and a number of substituents were found which dramatically increased the rate of polymerization and ultimate molecular weights achieved. These ionene elastomers were thermoplastic and it was shown that in some cases this result was due at least in part to a depolymerization reaction via a dequaternization of the ammonium links. Again, structural features in the dihalide were important not only for the reverse reaction, but for the repolymerization to high molecular weight elastomer as well. An uncharged “analogue” was also prepared to address the feature of microphase separation and compared with the above ionene materials.
Inhibition of NOTCH1 Signaling Reverses Glucocorticoid Resistance in T-ALL. (2007)

Abstract Gamma-secretase inhibitors (GSIs), which block the activation of the NOTCH1 receptor, are currently being tested in the treatment of T-cell lymphoblastic leukemias (T-ALL) with activating mutations in the NOTCH1 gene. However, inhibition of NOTCH1 signaling induces only a delayed cytostatic antileukemic effect with little or no apoptosis and GSI treatment is associated with severe gastrointestinal toxicity, which limits the clinical application of these molecularly targeted drugs. Here we show that combination therapy with GSIs plus glucocorticoids reverses glucocorticoid resistance and is highly effective against T-ALL. Inhibition of NOTCH1 signaling with CompE, a highly active GSI, in combination with dexamethasone, induced apoptotic cell death in glucocorticoid-resistant T-ALL cell lines. The synergistic antileukemic effect of GSIs and glucocorticoids was effectively rescued by forced expression of ICN1, an intracellular form of NOTCH1 that does not require gamma-secretase processing; or by treatment with the glucocorticoid receptor antagonist RU486. Reversal of glucocorticoid resistance by CompE treatment was mediated by transcriptional upregulation of BIM, a BH3-only proapototic factor previously involved in glucocorticoid induced cell death. Thus, shRNA knock down of BIM effectively impaired the ability of CompE plus dexamethasone to induce programmed cell death in leukemic lymphoblasts. Using a mouse xenograft model of glucocorticoid-resistant T-ALL we demonstrated that the combination of DBZ, a GSI with well established activity in vivo, and dexamethasone is highly effective against glucocorticoid resistant T-ALL in vivo. All animals treated with DBZ plus dexamethasone showed complete clearance of leukemic lymphoblasts and improved survival, while mice treated with vehicle or dexamethasone alone died because of disease progression (P&lt;0.05). In these studies, treatment with DBZ alone was associated with accelerated mortality because of severe intestinal toxicity characterized by goblet cell metaplasia in the small intestine. Surprisingly, mice treated with DBZ plus dexamethasone were protected clinically and histologically from GSI-induced intestinal toxicity. Pharmacokinetic analysis demonstrated that the interaction of dexamethasone and DBZ in the gut was not mediated by increased DBZ metabolism induced by dexamethasone. Molecular characterization of GSI induced gut toxicity demonstrated transcriptional upregulation of Klf4, a critical regulator of goblet cell differentiation, in the intestines of animals treated with DBZ. Klf4 regulation downstream of NOTCH signaling is mediated by HES1, a transcriptional repressor regulated by NOTCH. Importantly, dexamethasone treatment blocked the upregulation Klf4 induced by GSI treatment in vivo, suggesting that modulation of Klf4 expression may mediate the enteroprotective effects of glucocorticoids against GSI-induced toxicity. Overall, these results support a role for the combination of glucocorticoids plus GSIs in the treatment of glucocorticoid resistant T-ALL.
Measuring Trench Structures For Microelectronics With Model-Based Infrared Reflectometry (2007)

We provide an overview of state‐of‐the‐art metrology of periodic trench structures based on infrared reflectance spectroscopy, focusing on measuring dimensional parameters of trench arrays in silicon. The presentation outlines classes of trench metrology problems for which infrared optical measurement is advantageous versus visible/UV techniques, such as measuring very high aspect ratio trenches used to form dynamic random access memory capacitors. We discuss modeling approaches and compare effective medium models with rigorous coupled wave analysis calculations. The discussion is illustrated by infrared reflectance spectra from both model and real‐life examples of trench structures.