gebhart/patrepeval huggingface dataset:
A rapid and specific radioimmunoassay for methotrexate. (1975)

A sensitive and precise radioimmunoassay for methotrexate has been developed using antibody induced in rabbits, tritium-labeled methotrexate, and a nitrocellulose membrane separation technique. Antibody specificity was characterized by comparing the effectiveness of various related compounds to displace labeled methotrexate from the antibody-binding site. Assay of serum samples from persons receiving the drug was rapid and easy to perform. In a pharmacokinetic study of methotrexate, corresponding results were obtained when measurements were made by either enzymic assay or by radioimmunoassay. Drug concentrations could also be monitored in the cerebrospinal fluid and urine of patients on high-dose methotrexate therapy followed by citrovorum factor rescue. The system measured a little as 0.1 to 1 pmole of methotrexate, depending upon the antiserum used, and naturally occurring folates did not interfere with these determinations.
Water assisted atomic layer deposition of yttrium oxide using tris(<i>N</i>,<i>N</i>′-diisopropyl-2-dimethylamido-guanidinato) yttrium(<scp>iii</scp>): process development, film characterization and functional properties (2018)

We report a new atomic layer deposition (ALD) process for yttrium oxide (Y<sub>2</sub>O<sub>3</sub>) thin films using tris(<i>N</i>,<i>N'</i>-diisopropyl-2-dimethylamido-guanidinato) yttrium(iii) [Y(DPDMG)<sub>3</sub>] which possesses an optimal reactivity towards water that enabled the growth of high quality thin films. Saturative behavior of the precursor and a constant growth rate of 1.1 Å per cycle confirm the characteristic self-limiting ALD growth in a temperature range from 175 °C to 250 °C. The polycrystalline films in the cubic phase are uniform and smooth with a root mean squared (RMS) roughness of 0.55 nm, while the O/Y ratio of 2.0 reveal oxygen rich layers with low carbon contaminations of around 2 at%. Optical properties determined <i>via</i> UV/Vis measurements revealed the direct optical band gap of 5.56 eV. The valuable intrinsic properties such as a high dielectric constant make Y<sub>2</sub>O<sub>3</sub> a promising candidate in microelectronic applications. Thus the electrical characteristics of the ALD grown layers embedded in a metal insulator semiconductor (MIS) capacitor structure were determined which resulted in a dielectric permittivity of 11, low leakage current density (≈10<sup>-7</sup> A cm<sup>-2</sup> at 2 MV cm<sup>-1</sup>) and high electrical breakdown fields (4.0-7.5 MV cm<sup>-1</sup>). These promising results demonstrate the potential of the new and simple Y<sub>2</sub>O<sub>3</sub> ALD process for gate oxide applications.
Rhodamine 800 as a Probe of Energization of Cells and Tissues in the Near-Infrared Region: A Study with Isolated Rat Liver Mitochondria and Hepatocytes (1997)

To examine the feasibility of optical monitoring of cellular energy states with tissue-transparent near-infrared (NIR) light, the absorption and fluorescence characteristics of Rhodamine 800 in isolated rat liver mitochondria and hepatocytes were investigated. When the dye was incubated with isolated mitochondria, a large red shift of the absorption spectra and quenching of the fluorescence intensity were observed. The absorbance difference at 730 minus 685 nm, or at 730 minus 800 nm, and the fluorescence intensity measured at 692 nm varied linearly with the mitochondrial membrane potential. The spectral changes observed could be explained in terms of the potential-dependent uptake of the dye from the buffer solution into the mitochondrial matrix. The respiration control ratio and oxygen consumption rate were not affected by the addition of Rhodamine 800 at concentrations lower than 5 microM, which was the concentration range mostly employed throughout the present study. In a suspension of hepatocytes, the red shift and fluorescence quenching of Rhodamine 800 characteristic of energized mitochondria were also observed, and these changed to those of the buffer solution with the addition of an uncoupler under normoxia. At the early stage of anoxia, within about 5 min, when cytochrome oxidase was completely reduced, hepatocytes were concluded to be in the fully energized state, since the optical characteristics of Rhodamine 800 were the same as those of energized mitochondria. On the basis of these in vitro data, Rhodamine 800 is concluded to be a possible NIR-active contrast agent, that can be used to monitor the energy states of living tissues, in addition to the tissue oxygenation states, by the use of near-infrared spectrophotometry (NIRS) without harmful effects.
Superficial Bladder Cancer: Progression and Recurrence (1983)

The tumors in 249 patients presenting initially with stages Ta and T1 bladder cancer were analyzed for tumor progression and recurrence. Only transurethral resection and/or fulguration was used before the first recurrence. Patients who received intravesical chemotherapy after the first tumor recurrence were excluded from an analysis of progression. Progression according to stages Ta and T1, and grades I, II and III was 4, 30, 2, 11 and 45 per cent, respectively. All differences were statistically significant. Progression also correlated with nontumor dysplasia and size. High tumor grade, lamina propria invasion, atypia elsewhere in the bladder, positive urinary cytology, tumor multiplicity and large tumors were associated with shorter intervals free of disease.
Vehicle-to-Vehicle Real-Time Relative Positioning Using 5.9 GHz DSRC Media (2013)

Vehicular accidents are one of the deadliest safety hazards and accordingly an immense concern of individuals and governments. Although, a wide range of active autonomous safety systems, such as advanced driving assistance and lane keeping support, are introduced to facilitate safer driving experience, these stand-alone systems have limited capabilities in providing safety. Therefore, cooperative vehicular systems were proposed to fulfill more safety requirements. Most of cooperative vehicle-to-vehicle safety applications require relative positioning accuracy of decimeter with an update rate of at least 10 Hz. These requirements cannot be met via direct navigation or differential positioning techniques. This paper studies a cooperative vehicle platform that aims to facilitate real-time relative positioning (RRP) among adjacent vehicles. The developed system is capable of exchanging both GPS position solutions and raw observations using RTCM-104 format over vehicular dedicated short range communication (DSRC) links. Real-time kinematic (RTK) positioning technique is integrated into the system to enable RRP to be served as an embedded real-time warning system. The 5.9 GHz DSRC technology is adopted as the communication channel among road-side units (RSUs) and on-board units (OBUs) to distribute GPS corrections data received from a nearby reference station via the Internet using cellular technologies, by means of RSUs, as well as to exchange the vehicular real-time GPS raw observation data. Ultimately, each receiving vehicle calculates relative positions of its neighbors to attain a RRP map. A series of real-world data collection experiments was conducted to explore the synergies of both DSRC and positioning systems. The results demonstrate a significant enhancement in precision and availability of relative positioning at mobile vehicles.
Building realistic structure models to train convolutional neural networks for seismic structural interpretation (2019)

ABSTRACT Seismic structural interpretation involves highlighting and extracting faults and horizons that are apparent as geometric features in a seismic image. Although seismic image processing methods have been proposed to automate fault and horizon interpretation, each of which today still requires significant human effort. We improve automatic structural interpretation in seismic images by using convolutional neural networks (CNNs) that recently have shown excellent performances in detecting and extracting useful image features and objects. The main limitation of applying CNNs in seismic interpretation is the preparation of many training data sets and especially the corresponding geologic labels. Manually labeling geologic features in a seismic image is highly time-consuming and subjective, which often results in incompletely or inaccurately labeled training images. To solve this problem, we have developed a workflow to automatically build diverse structure models with realistic folding and faulting features. In this workflow, with some assumptions about typical folding and faulting patterns, we simulate structural features in a 3D model by using a set of parameters. By randomly choosing the parameters from some predefined ranges, we are able to automatically generate numerous structure models with realistic and diverse structural features. Based on these structure models with known structural information, we further automatically create numerous synthetic seismic images and the corresponding ground truth of structural labels to train CNNs for structural interpretation in field seismic images. Accurate results of structural interpretation in multiple field seismic images indicate that our workflow simulates realistic and generalized structure models from which the CNNs effectively learn to recognize real structures in field images.
The Effect of Small Cations on the Positive Electrospray Responses of Proteins at Low pH (2003)

Solutions consisting of protein and small molecule mixtures have been subjected to electrospray ionization to study the influence of small molecule/cation components at high concentrations on the electrospray responses of proteins. Emphasis was placed on solutions consisting of equal parts methanol and water and containing 1 vol % acetic acid. The results, therefore, are relevant to low pH solutions with significant organic content, a commonly used set of conditions in electrospray ionization mass spectrometry that tends to denature proteins. A variety of small cations/molecules were selected to sample a range of chemical characteristics. For example, sodium and cesium cations were studied to represent metal ions, tetrabutylammonium and tetramethylammonium cations were studied to represent quaternary ammonium compounds with different surface activities, and octadecylamine and glycine were studied to represent species that compete for protons but have different surface activities. A methodology for measuring relative ion suppression efficiencies was developed and applied for protein ions derived from bovine cytochrome c. The form of the small cation (i.e., metal ion, quaternary ammonium ion, or protonated molecule) did not appear to be a factor in determining the efficiency with which protein ion signals were suppressed. The extent to which ions are expected to concentrate on the surface, however, was the major factor in determining the ion suppression efficiency. Itwas found that the ion suppression efficiency of the most surface active species in this study was comparable to that of a protein on another protein after normalization by charge. These results are particularly relevant to the development of mixture analysis strategies based on ionization and tandem mass spectrometry applied to mixtures of whole proteins.
UML to XML-Schema transformation: a case study in managing alternative model transformations in MDA (2003)

In a Model Driven Architecture (MDA) software development process, models are
repeatedly transformed to other models in order to finally achieve a set of models with enough details to implement a system. Generally, there are multiple ways to transform one model into another model. Alternative target models differ in their quality properties and the selection of a particular model is determined on the basis of specific requirements. Software engineers must be able to identify, compare and select the appropriate transformations within the given set of requirements. The current transformation languages used for describing and executing model transformations only provide means to specify the transformations but do not help to identify and select from the alternative transformations. In this paper we propose a process and a set of techniques for constructing a transformation space for a given transformation problem. The process uses a source model, its meta-model and the meta-model of the target as input and generates a transformation space. Every element in that space represents a transformation that produces a result that is an instance of the target meta-model. The requirements that must be fulfilled by the result are captured and represented in a quality model. We explain our approach using an illustrative example for transforming a platform independent model expressed in UML into platform specific models that represent XML schemas. A particular quality model of extensibility is presented in the paper.
Hierarchical Memory System With STT-MRAM and SRAM to Support Transfer and Real-Time Reinforcement Learning in Autonomous Drones (2019)

This article presents a transfer learning (TL) followed by reinforcement learning (RL) algorithm mapped onto a hierarchical embedded memory system to meet the stringent power budgets of autonomous drones. The power reduction is achieved by 1. TL on meta-environments followed by online RL only on the last few layers of a deep convolutional neural network (CNN) instead of end-to-end (E2E) RL and 2. Mapping of the algorithm onto a memory hierarchy where the pretrained weights of all the conv layers and the first few fully connected (FC) layers are stored in dense, low standby leakage Spin Transfer Torque (STT) RAM eNVM arrays and the weights of the last few FC layers are stored in the on-die SRAM. This memory hierarchy enables real-time RL as the drone explores unknown territories and the system only reads the weights from eNVM (that are slow and power hungry to write otherwise) for inference and uses the on-die SRAM for low latency training through both write and read of the weights of the last few layers. The proposed system is extensively simulated on a virtual environment and dissipates 83.5% lower energy per image frame as well as 79.4% lower latency as compared to E2E RL without any loss of accuracy. The speed of the drone is improved by a factor of 3× due to higher frame rates as well.
The Simplified<i>P</i><sub>3</sub>Approximation (2000)

The simplified P3 (SP3) approximation to the multigroup neutron transport equation in arbitrary geometries is derived using a variational analysis. This derivation yields the SP3 equations along with material interface and Marshak-like boundary conditions. The multigroup SP3 approximation is reformulated as a system of within-group problems that can be solved iteratively. An “explicit” iterative algorithm for solving the within-group problem is described, Fourier analyzed, and shown to be more efficient than the traditional FLIP implicit algorithm. Numerical results compare diffusion (P1), simplified P2 (SP2), and simplified P3 calculations of a mixed-oxide (MOX) fuel benchmark problem to a reference transport calculation. The SP3 approximation can eliminate much of the inaccuracy in the diffusion and SP2 calculations of MOX fuel problems.
Nasal and Oral Flow-Volume Loops in Normal Subjects and Patients with Obstructive Sleep Apnea (1990)

Because flow-volume loops (FVLs) are clinically useful in evaluating upper airway (UA) obstruction and the fact that patency of the nasopharyngeal ventilatory pathway is important to the prevention of obstructive sleep apnea (OSA), the present study examined the role of nasal compared with oral FVLs in evaluating patients with OSA. Fourteen obese male patients 56 +/- 3 yr of age with a mean apnea plus hypopnea index (AHI) of 51 +/- 9/h were studied along with 14 nonobese, healthy, age- and sex-matched control subjects whose mean AHI was 6 +/- 1/h. Nasal and oral FVLs obtained in the normal subjects indicated the nose behaved like a variable resistor, with flow limitation during inspiration but not during expiration. In the patient group, flow limitation was observed during expiration as well as inspiration indicating nondistensibility of the nasopharyngeal ventilatory pathway in the patients compared to the control subjects. A change in body position from upright to supine in the OSA group was associated with small reductions in expiratory but not inspiratory flow rates. The area under the nasal supine flow-volume loop (FVLANaSup) was found to be highly correlated with awake resting PaO2 (r = 0.80) and PaCO2 (r = -0.83) in the patient group. In addition, multiple linear regression analysis revealed that PaO2 and the area under the nasal FVLs independently contributed to the prediction of AHI with a multiple R of 0.89. These results suggest that limitations to ventilation via the nasopharynx may significantly influence both gas exchange and the frequency of sleep-disordered breathing in patients with OSA.(ABSTRACT TRUNCATED AT 250 WORDS)
Further Development of Traditional Chinese Medicine and Medication (2007)

As a experimental medicine,traditional Chinese medicine and its medication(TCM) still left mach mysteries for explanation and acceptation,which did not do much to influenceits existenceand its medical function.However,that is not the excuse that we neglect the future development of it.The author analysesthe advantages of TCM,the better time and future of combination of west medicine and TCM,and the necessityand the urgencyof modernization of TCM.
Ultra-Wideband Millimeter-Wave Dielectric Characteristics of Freshly Excised Normal and Malignant Human Skin Tissues (2017)

Millimeter waves have recently gained attention for the evaluation of skin lesions and the detection of skin tumors. Such evaluations heavily rely on the dielectric contrasts existing between normal and malignant skin tissues at millimeter-wave frequencies. However, current studies on the dielectric properties of normal and diseased skin tissues at these frequencies are limited and inconsistent. In this study, a comprehensive dielectric spectroscopy study is conducted for the first time to characterize the ultra-wideband dielectric properties of freshly excised normal and malignant skin tissues obtained from skin cancer patients having undergone Mohs micrographic surgeries at Hackensack University Medical Center. Measurements are conducted using a precision slim-form open-ended coaxial probe in conjunction with a millimeter-wave vector network analyzer over the frequency range of 0.5-50 GHz. A one-pole Cole-Cole model is fitted to the complex permittivity dataset of each sample. Statistically considerable contrasts are observed between the dielectric properties of malignant and normal skin tissues over the ultra-wideband millimeter-wave frequency range considered.
Microtransport induced by ultrasonic Lamb waves (1991)

We have observed pumping of water induced by 4.7 MHz ultrasonic Lamb waves traveling in a 4-μm-thick composite membrane of silicon nitride and piezoelectric zinc oxide. The observed pumping speed is proportional to the square of the wave amplitude; the speed was 100 μm/s for a rf drive voltage of 8 V and a 6.5 nm wave amplitude. A nonlinear model based on acoustic streaming theory predicts velocities in good agreement with experiment.
Scalusamides A−C, New Pyrrolidine Alkaloids from the Marine-Derived Fungus <i>Penicillium c</i><i>itrinum</i> (2005)

Three new pyrrolidine alkaloids, scalusamides A-C (1-3), were isolated from the cultured broth of the fungus Penicillium citrinum, which was separated from the gastrointestine of a marine fish, and the structures were elucidated by spectroscopic data. The absolute stereochemistry of C-2 in the pyrrolidine unit was determined by HPLC analysis of a Marfey's derivative of the hydrolysate of 1, while that of 2 and 3 was assigned by comparison of spectroscopic data of 3 and reductive products of 1 and 2. On the other hand, each of 1-3 was found to be a mixture of epimers at C-7. Scalusamide A (1) exhibited antifungal and antibacterial activities.
Characterization of engineering surfaces by grazing-incidence X-ray reflectivity (1993)

This paper covers the principles and practice of grazing-incidence reflectometry and its application to the characterization of surfaces and very thin surface layers of single or polycrystalline materials. It is shown that film thicknesses may be accurately measured in the range from monolayers up to about a micrometre, that roughness parameters from zero to about 2 nm may be deduced, and that the diffuse reflectivity is sensitive to the distribution and correlation length of the surface structure. Applications to semiconductor and magnetic multilayers are demonstrated, and the use of the method for study of interfaces and conformal roughening is considered.
Regulation cascade of flagellar expression in Gram-negative bacteria (2003)

Flagellar motility helps bacteria to reach the most favourable environments and to successfully compete with other micro-organisms. These complex organelles also play an important role in adhesion to substrates, biofilm formation and virulence process. In addition, because their synthesis and functioning are very expensive for the cell (about 2% of biosynthetic energy expenditure in Escherichia coli) and may induce a strong immune response in the host organism, the expression of flagellar genes is highly regulated by environmental conditions. In the past few years, many data have been published about the regulation of motility in polarly and laterally flagellated bacteria. However, the mechanism of motility control by environmental factors and by some regulatory proteins remains largely unknown. In this respect, recent experimental data suggest that the master regulatory protein-encoding genes at the first level of the cascade are the main target for many environmental factors. This mechanism might require DNA topology alterations of their regulatory regions. Finally, despite some differences the polar and lateral flagellar cascades share many functional similarities, including a similar hierarchical organisation of flagellar systems. The remarkable parallelism in the functional organisation of flagellar systems suggests an evolutionary conservation of regulatory mechanisms in Gram-negative bacteria.
Learning Deep Representations for Graph Clustering (2014)

Recently deep learning has been successfully adopted in many applications such as speech recognition and image classification. In this work, we explore the possibility of employing deep learning in graph clustering. We propose a simple method, which first learns a nonlinear embedding of the original graph by stacked autoencoder, and then runs $k$-means algorithm on the embedding to obtain the clustering result. We show that this simple method has solid theoretical foundation, due to the similarity between autoencoder and spectral clustering in terms of what they actually optimize. Then, we demonstrate that the proposed method is more efficient and flexible than spectral clustering. First, the computational complexity of autoencoder is much lower than spectral clustering: the former can be linear to the number of nodes in a sparse graph while the latter is super quadratic due to eigenvalue decomposition. Second, when additional sparsity constraint is imposed, we can simply employ the sparse autoencoder developed in the literature of deep learning; however, it is non-straightforward to implement a sparse spectral method. The experimental results on various graph datasets show that the proposed method significantly outperforms conventional spectral clustering which clearly indicates the effectiveness of deep learning in graph clustering.