gebhart/patrepeval huggingface dataset:
Serum Protease Changes in Spontaneously Hypertensive Rats: Contrast with Those in Essential Hypertension in Man. (1991)

Our previous report suggested that increased serum angiotensin-converting enzyme (ACE) activity plays a central part in the pathogenesis of essential hypertension in man. In the present study, we investigated whether such findings can be seen in spontaneously hypertensive rats (SHR). The results suggested that serum carboxypeptidase N and kallikrein, rather than ACE, plays a central part in this experimental model. The ACE activity was decreased rather than increased in spontaneously hypertensive rat when compared with that in Wistar-Kyoto rats.
Heterogeneous catalysis for production of value-added chemicals from biomass (2009)

Almost everything around us is in some way a product of controlled chemical processes. That is either chemical processes conducted in Nature or chemical processes conducted in the chemical industry. In the most developed parts of the World, it is in fact products from the chemical industry that comp...
Ideal phonon-scattering-limited mobility in inversion channels of 4H-SiC(0001) MOSFETs with ultralow net doping concentrations (2019)

The phonon-limited mobility in 4H-silicon carbide (SiC) inversion channels was precisely evaluated by employing ultralow net doping concentrations. The measured mobility in the inversion channels of these samples was comparable to the electron mobility in bulk 4H-SiC, and the temperature dependence indicated that the mobility can be ascribed to phonon-scattering-limited mobility. The strong dependence of the mobility on the net doping concentration cannot be explained by Coulomb scattering by dopant impurities. This indicates the existence of scattering origins at the SiO2/SiC interface. Comparison of dry oxidized samples and samples subjected to postoxidation annealing in nitric oxide revealed that the scattering origins were not attributable to trapped electrons at the SiO2/SiC interface states, although the nature of the scattering origins remains unclear.
Abstract 1425: A multi-enzyme DNA repair mix improves library quality and sequencing accuracy in FFPE tumor samples (2018)

Abstract Next-generation sequencing (NGS) methods are used extensively to profile mutations present in diseased human tissues. These genomic approaches hold great promise for personalized medicine but sequencing accuracy is essential for proper patient diagnosis and determining a treatment plan. A common source of DNA for genomic profiling is formalin-fixed, paraffin-embedded (FFPE) tissue samples obtained from patient biopsy. FFPE DNA poses important challenges for preparing NGS libraries including low input amounts and poor DNA quality, resulting from extensive fixation- and storage-induced DNA damage. Additionally, these damage-induced sequencing artifacts raise the background level of mutations, making it difficult to discern true, low frequency, disease-causing variants from noise. We previously showed that a major fraction of somatic mutations described in publicly available datasets are due to such sequencing artifacts (Chen et al., Science 2017). Furthermore, we showed that enzymatic repair of DNA before library preparation improves the library quality and reduces background noise. We developed a second-generation DNA repair enzyme mix (V2) that efficiently repairs the most prevalent damage types found in FFPE DNA and further improves the quality and yield of NGS libraries. Additionally, we tested the efficacy of the V2 repair mix in improving sequencing accuracy for FFPE DNA samples obtained from different cancer tissues. We performed target enrichment on a panel of 151 cancer genes, deep sequenced, and performed variant analysis. For a subset of variants, we further validated our results using a droplet digital PCR (ddPCR) assay. Both methods showed that the V2 repair mix did not alter the overall frequency of variants identified, thus it did not introduce bias, but significantly improved the sequencing accuracy by reducing the number of false variant calls. Therefore, enzymatic repair is a critical first step in preparing FFPE DNA sequencing libraries, allowing more sensitive and robust detection of low frequency, disease variants. Citation Format: Pingfang Liu, Margaret Heider, Chen Song, Lixin Chen, Laurence Ettwiller, Lauren Higgins, Eileen Dimalanta, Theodore Davis, Thomas Evans. A multi-enzyme DNA repair mix improves library quality and sequencing accuracy in FFPE tumor samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1425.
Evaluation strategies for top-k queries over memory-resident inverted indexes (2011)

Top-k retrieval over main-memory inverted indexes is at the core of many modern applications: from large scale web search and advertising platforms, to text extenders and content management systems. In these systems, queries are evaluated using two major families of algorithms: document-at-a-time (DAAT) and term-at-a-time (TAAT). DAAT and TAAT algorithms have been studied extensively in the research literature, but mostly in disk-based settings. In this paper, we present an analysis and comparison of several DAAT and TAAT algorithms used in Yahoo!'s production platform for online advertising. The low-latency requirements of online advertising systems mandate memory-resident indexes. We compare the performance of several query evaluation algorithms using two real-world ad selection datasets and query workloads. We show how some adaptations of the original algorithms for main memory setting have yielded significant performance improvement, reducing running time and cost of serving by 60% in some cases. In these results both the original and the adapted algorithms have been evaluated over memory-resident indexes, so the improvements are algorithmic and not due to the fact that the experiments used main memory indexes.
Modelling of Radical Reactions at Platinum Deposits in Polymer Electrolyte Membranes (2015)

Hydroxyl radicals are the leading cause of chemical degradation observed in polymer electrolyte membranes (PEM). Recent experimental studies have shown that Pt nano-deposits in the PEM (PITM), which originate from Pt dissolution in the catalyst layer, could play a dual role in radical-initiated membrane degradation [1]. Surface reactions at Pt particles could facilitate the formation as well as the scavenging of radicals. The net effect of Pt surface processes on the radical balance depends on the local equilibrium conditions around the Pt nano-deposits, specifically, their equivalent local electrode potential [2]. In this presentation, we will first discuss the potential distribution at PITM as a function of externally controlled thermodynamic conditions. Thereafter, we will present a Density Functional Theory investigation of the surface reactions at the Pt(111)|water interface that involve O 2 , H 2 O, H 2 O 2 and OH radical species. We calculate the effective rates of radical production at PITM by incorporating the local conditions obtained in the above steps. The results are compared to experimental measurements of fluoride emission under varying pressure settings in Pt impregnated PEMs. References: [1] M. P. Rodgers et al., J. Electrochem. Soc. 160 (10) F1123-F1128 (2013) [2] M. J. Eslamibidgoli et al., J. Phys. Chem. C. Submitted.
Design, Synthesis, and Properties of New Biodegradable Aromatic/Aliphatic Liquid Crystalline Copolyesters (2003)

Liquid crystalline copolyesters of high molecular weight were obtained by polycondensation of aromatic diols, diacyl dichlorides, oligolactides, and poly(ethylene glycol)s. Hydrophilicity of the copolyesters was controlled by the content of ethyleneoxy moieties as verified by contact angle measurements. Copolyesters with ethyleneoxy moieties showed significant enhancement of degradability under physiological conditions in comparison to copolyester without ethyleneoxy moieties, which makes these copolyesters promising materials for bone tissue engineering as also verified by hardness testing and mechanical testing.
SELECTIVE INHIBITION OF IL-2 GENE EXPRESSION BY IL-2 ANTISENSE OLIGONUCLEOTIDES BLOCKS HEART ALLOGRAFT REJECTION1 (2001)

Selective inhibition of IL-2 mRNA in vivo inhibits T-cell function and extends allograft survival.
Crystallographic insights into DNA minor groove recognition by drugs (1997)

This review surveys the crystal structures between minor groove drugs and oligonucleotides, of which over thirty have now been determined. The various factors that are involved in the observed A/T sequence selectivity of these drugs are examined in structural terms. The roles of, in particular, hydrogen-bond recognition and sequence-dependent groove width, are assessed, and as a consequence the minor groove drugs have been classified into two categories, dependent on the relative roles played by these two factors in sequence recognition. Implications for the recognition of non-A/T sequences are discussed. © 1997 John Wiley & Sons, Inc. Biopoly 44: 105–121, 1997
Detonation Nanodiamond and Onion‐Like‐Carbon‐Embedded Polyaniline for Supercapacitors (2010)

Abstract The detonation nanodiamond is a versatile low‐cost nanomaterial with tunable properties and surface chemistry. In this work, it is shown how the application of nanodiamond (ND) can greatly increase the performance of electrochemically active polymers, such as polyaniline (PANI). Symmetric supercapacitors containing PANI‐ND nanocomposite electrodes with 3–28 wt% ND show dramatically improved cycle stability and higher capacitance retention at fast sweep rate than pure PANI electrodes. Contrary to other PANI‐carbon nanocomposites, specific capacitance of the selected PANI electrodes with embedded ND increases after 10 000 galvanostatic cycles and reaches 640 F g −1 , when measured in a symmetric two‐electrode configuration with 1 M H 2 SO 4 electrolyte. The demonstrated specific capacitance is 3–4 times higher than that of the activated carbons and more than 15 times higher than that of ND and onion‐like carbon (OLC).
Enhanced tissue development in autologous tissue-engineered heart valves using a customised bioreactor conditioning system (2008)

Our group has previously demonstrated the synthesis of completely autologous fibrin-based heart valves using the principles of tissue engineering. The present approach aims to guide more mature tissue development in fibrin-based valves based on in vitro conditioning in a customised bioreactor system.
Convergence of the Huber Regression M-Estimate in the Presence of Dense Outliers (2014)

We consider the problem of estimating a deterministic unknown vector which depends linearly on <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$n$</tex> </formula> noisy measurements, additionally contaminated with (possibly unbounded) additive outliers. The measurement matrix of the model (i.e., the matrix involved in the linear transformation of the sought vector) is assumed known, and comprised of standard Gaussian i.i.d. entries. The outlier variables are assumed independent of the measurement matrix, deterministic or random with possibly unknown distribution. Under these assumptions we provide a simple proof that the minimizer of the Huber penalty function of the residuals converges to the true parameter vector with a <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\sqrt n $</tex> </formula> -rate, even when outliers are dense, in the sense that there is a constant linear fraction of contaminated measurements which can be arbitrarily close to one. The constants influencing the rate of convergence are shown to explicitly depend on the outlier contamination level.
Completion Time Minimization in NOMA Systems: Learning for Combinatorial Optimization (2021)

In this letter, we study a completion-time minimization problem by jointly optimizing time slots (TSs) and power allocation for time-critical non-orthogonal multiple access (NOMA) systems. The original problem is non-linear/non-convex with discrete variables, leading to high computational complexity in conventional iterative methods. Towards an efficient solution, we train deep neural networks to perform fast and high-accuracy predictions to tackle the difficult combinatorial parts, i.e., determining the minimum consumed TSs and user-TS allocation. Based on the learning-based predictions, we develop a low-complexity post-process procedure to provide feasible power allocation. The numerical results demonstrate promising improvements of the proposed scheme compared to other baseline schemes in terms of computational efficiency, approximating optimum, and feasibility guarantee.
Study on Hinsberg Thiophene Synthesis of 4,8-Dihydro-4,8-ethanobenzo[1,2-c;4,5-c’]dithiophene (2013)

The Hinsberg thiophene synthesis using 4,5,6,7-tetrahydro-4,7ethanothiophene-5,6-dione and diethyl thiodiglycolate afforded a mixture of diethyl 4,8-dihydro-4,8-ethanobenzo[1,2-c;4,5-c']dithiophene-1,3-dicarboxylate and its dihydrate, although the yields were low.The latter dihydrate was converted to the former dithiophene in a good yield by the treatment with Ac 2 O and DMAP.
Scaling of ferroelectric and piezoelectric properties in Pt/SrBi2Ta2O9/Pt thin films (1999)

Scaling of the ferroelectric and piezoelectric properties in Pt/SrBi2Ta2O9/Pt thin films was studied. Focused ion beam milling was used to fabricate submicron devices (1×1, 0.5×0.5, 0.25×0.25, 0.09×0.09, and 0.07×0.07 μm2) and scanning force microscopy was used to examine their piezoelectric response. It was found that capacitors as small as 0.09×0.09 μm2 exhibit good piezoelectric/ferroelectric properties and that submicron (0.25×0.25 μm2) capacitors show resistance to bipolar fatigue with up to at least 109 cycles. The results were compared with similar capacitor structures milled in the Pb1.0(Nb0.04Zr0.28Ti0.68)O3 system where structures as small as 0.07×0.07 μm2 were analyzed.
Lagrangian wrench distribution for cooperating robotic mechanisms (2002)

A systematic method for analysis of cooperating robotic mechanisms is investigated using constrained optimization. The wrench distribution problem is formulated as a quadratic optimization problem with a linear constraint. This leads to the definition of the Lagrangian screw, which is shown to be an important geometrical tool for analysis. The geometrical meaning of the distributed wrench field is explained in terms of the Lagrangian screw. Examples show that several previous investigations in the literature may be included as special cases.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Laboratory astrophysics experiments in X-ray transfer physics relevant to cosmic accretion-powered sources. (1988)

L'interprétation des observations spectroscopiques des rayons cosmics X à basse énergie nécessite un grand progrès dans nos connaissances en physique atomique et processus radiatifs, notamment pour la catégorie des systèmes qui tirent leur énergie de l'accrétion comme les variables cataclysmiques, les binaires X et les noyaux actifs de galaxies. Pour de telles sources, on obtient des raies spectrales à courte longueur d'onde qui sont formées lors du transfert d'une radiation X d'une source centrale énergétique vers un milieu extérieur plus froid. Le gas responsable de l'émission est photoionisé et les populations des différents niveaux sont gouvernées principalement par les cascades de recombination et la photoexcitation, les collisions ne jouant qu'un rôle négligeable. De tels processus peuvent être assez complexes et plusieurs incertitudes demeurent. Nous développons une nouvelle approche de ce problème à l'aide de spectres résolus en temps de plasmas excités par des lasers. Les expériences que nous menons actuellement incluent la mesure : (a) des sections efficaces de photoabsorption dans les couches internes et externes pour des ions intermédiaires d'éléments abondants, et (b) des processus de fluorescences résultant de la coïncidence de longueurs d'onde de transitions résonnantes pour des ions différents. En relation avec ce programme, nous avons développé un nouveau spectromètre à réseau à réflexion couplé à une "streak" camera qui fournit des spectres haute résolution dans les domaines rayons X à basse énergie et UV extrême, au niveau subnanoseconde Nous décrivons notre appareillage et quelques résultats prelinaires.
Identification of OFDM signals under multipath fading channels (2012)

Modulation identification is an important part of wireless communications systems e.g., blind receivers can benefit from the methods that can identify the modulation of the received signals without a priori information. Moreover, distinction of OFDM systems from single carrier systems is highly important for adaptive receiver design algorithms. OFDM signals exhibit Gaussian characteristics in time domain in contrast with the single carrier signals. However, when the wireless communications considered, Gaussianity of the received samples is affected from the channel impairments along with the frequency, phase offsets and sampling mismatch. In this paper, we analyzed how the time-domain Gaussianity of fourth order cumulants of OFDM signals is affected under these conditions. A general chi-square constant false alarm rate Gaussianity test which employs estimates of cumulants and their covariances is adapted to the specific case of OFDM signals. A parametric simulation analysis which investigates the performance of the proposed method by the changes in the parameters such as signal to noise ratio, number of symbols, and modulation order is provided. The performance of proposed method is compared with moment based tests as well.
Heterogeneous Clearance of Antithymocyte Globulin after CD34+-Selected Allogeneic Hematopoietic Progenitor Cell Transplantation (2005)

Antithymocyte globulins (ATG) are purified, concentrated preparations of polyclonal immunoglobulin G from hyperimmune serum of horses or rabbits immunized with human thymus lymphocytes. Both the horse and the rabbit products induce immunosuppression as a result of lymphocyte depletion and immune modulation. The exact mechanism of action is unknown but may include T-cell clearance from the circulation and modulation of T-cell activation, homing, and cytotoxic activities. Both horse and rabbit ATG include multiple antibodies against T-cell surface antigens and have been used extensively in allogeneic hematopoietic progenitor cell transplantation (HPCT) for the treatment and prevention of graft-versus-host disease or graft rejection. To quantify the active ATG after HPCT, we developed a flow-based assay to measure residual ATG capable of binding to lymphocytes. In contrast to prior assays that measure total rabbit or horse immunoglobulin, this assay quantitates only the antibody capable of binding to lymphocytes, which presumably reflects the functionally active fraction of the xenoantiserum. Thirty patients with hematologic malignancies underwent T cell-depleted HPCT and had ATG levels assayed during the peritransplantation period. The time required for ATG levels to decay to background was quite variable (mean, 46 days; range, 14-91 days), although most patients demonstrated a rapid early clearance followed by a slower decline. The actual mean half-life was 6.8 days (range, 2.4-14.0 days). The persistence of ATG for months after administration has significant implications for the pace of immune reconstitution after transplantation and is a potentially confounding variable in any study that involves early administration of donor lymphocyte infusions or other cellular transfer. These findings indicate that ATG levels should be explicitly measured in studies that involve early donor lymphocyte administration so that proper conclusions regarding dose, safety, and efficacy can be reached.
Deep Neural Network Model of Hearing-Impaired Speech-in-Noise Perception (2020)

Many individuals struggle to understand speech in listening scenarios that include reverberation and background noise. An individual's ability to understand speech arises from a combination of peripheral auditory function, central auditory function, and general cognitive abilities. The interaction of these factors complicates the prescription of treatment or therapy to improve hearing function. Damage to the auditory periphery can be studied in animals; however, this method alone is not enough to understand the impact of hearing loss on speech perception. Computational auditory models bridge the gap between animal studies and human speech perception. Perturbations to the modeled auditory systems can permit mechanism-based investigations into observed human behavior. In this study, we propose a computational model that accounts for the complex interactions between different hearing damage mechanisms and simulates human speech-in-noise perception. The model performs a digit classification task as a human would, with only acoustic sound pressure as input. Thus, we can use the model's performance as a proxy for human performance. This two-stage model consists of a biophysical cochlear-nerve spike generator followed by a deep neural network (DNN) classifier. We hypothesize that sudden damage to the periphery affects speech perception and that central nervous system adaptation over time may compensate for peripheral hearing damage. Our model achieved human-like performance across signal-to-noise ratios (SNRs) under normal-hearing (NH) cochlear settings, achieving 50% digit recognition accuracy at -20.7 dB SNR. Results were comparable to eight NH participants on the same task who achieved 50% behavioral performance at -22 dB SNR. We also simulated medial olivocochlear reflex (MOCR) and auditory nerve fiber (ANF) loss, which worsened digit-recognition accuracy at lower SNRs compared to higher SNRs. Our simulated performance following ANF loss is consistent with the hypothesis that cochlear synaptopathy impacts communication in background noise more so than in quiet. Following the insult of various cochlear degradations, we implemented extreme and conservative adaptation through the DNN. At the lowest SNRs (<0 dB), both adapted models were unable to fully recover NH performance, even with hundreds of thousands of training samples. This implies a limit on performance recovery following peripheral damage in our human-inspired DNN architecture.
Inverse modelling of an aneurysm's stiffness using surrogate-based optimization of a three-dimensional ﬂuid-structure interaction simulation (2011)

Characterization of the mechanical properties of arterial tissues is highly relevant, both as a direct diagnostic tool as well indirectly to provide material parameters for patientspecific computer simulations. This is especially true in the context of (aortic) aneurysms. In this work, we apply an inverse modelling approach to a model accounting for an aneurysm and the distal part of the circulation. The stiffness of the aneurysm itself and of the rest of the arterial system are modelled using two independent stiffness parameters. For given values of these parameters, the position of the arterial wall as a function of time is calculated using a forward simulation which takes the fluid-structure interaction (FSI) between the blood flow and the arterial wall into account. Using this forward simulation, the correct values of the stiffness parameters are obtained by minimizing a cost function, which is defined as the difference between the forward simulation and a measurement (in this case synthetic data from a simulation). The minimization is performed by means of surrogate-based optimization using a Kriging model combined with the expected improvement infill criterion. Results for a three-dimensional fluid-structure interaction model of the aneurysm show that the stiffness parameters converge to the correct values.