gebhart/patrepeval huggingface dataset:
Isolation of plasmid DNA from cell lysates by aqueous two‐phase systems (2002)

This work presents a study of the partitioning of a plasmid vector containing the cystic fibrosis gene in polyethylene glycol (PEG)/salt (K2HPO4) aqueous two-phase systems (ATPS). The plasmid was extracted from neutralized alkaline lysates using PEG with molecular weights varying from 200 to 8000. The effects of the lysate mass loaded to the ATPS (20, 40, and 60% w/w) and of the plasmid concentration in the lysate were evaluated. The performance of the process was determined by qualitative and quantitative assays, carefully established to overcome the strong interference of impurities (protein, genomic DNA, RNA), salt, and PEG. Plasmid DNA partitioned to the top phase when PEG molecular weight was lower than 400. The bottom phase was preferred when higher PEG molecular weights were used. Aqueous two-phase systems with PEG 300, 600, and 1000 were chosen for further studies on the basis of plasmid and RNA agarose gel analysis and protein quantitation. The recovery yields were found to be proportional to the plasmid concentration in the lysate. The best yields (>67%) were obtained with PEG 1000. These systems (with 40 and 60% w/w of lysate load) were able to separate the plasmid from proteins and genomic DNA, but copartitioning of RNA with the plasmid was observed. Aqueous two-phase systems with PEG 300 concentrated both plasmid and proteins in the top phase. The best system for plasmid purification used PEG 600 with a 40% (w/w) lysate load. In this system, RNA was found mostly in the interphase, proteins were not detected in the plasmid bottom phase and genomic DNA was reduced 7.5-fold.
The Effect of Antiresorptives on Bone Quality (2011)

Antiresorptive therapy reduces risk of fracture by improving bone quality through halting removal of bone tissue and the resultant destruction of microarchitecture of bone and, perhaps to some extent, by improving the intrinsic material properties of bone tissue. Information presented here may help clinicians to improve selection of patients for antiresorptive therapy by avoiding them in cases clearly not due to excessive bone remodeling.
Independent Control of Topography for 3D Patterning of the ECM Microenvironment (2015)

Biomimetic extracellular matrix (ECM) topographies driven by the magnetic-field-directed self-assembly of ECM protein-coated magnetic beads are fabricated. This novel bottom-up method allows us to program isotropic, anisotropic, and diverse hybrid ECM patterns without changing other physicochemical properties of the scaffold material. It is demonstrated that this 3D anisotropic matrix is able to guide the dendritic protrusion of cells.
Three high molecular weight protease inhibitors of rat plasma. Isolation, characterization, and acute phase changes. (1987)

Rat blood plasma contains three high molecular weight thiol ester-containing proteinase inhibitors, alpha 1-macroglobulin (alpha 1M), alpha 1-inhibitor III (alpha 1I3), and alpha 2-macroglobulin (alpha 2M). Rat serums have been analyzed using a two-dimensional gel electrophoretic technique which optimizes recovery of high molecular weight proteins. alpha 1M, and (alpha beta)4-tetramer in native solution, separated in the second sodium dodecyl sulfate-containing electrophoretic dimension as a disulfide-linked (alpha beta)2-dimer with an approximate Mr of 360 kDa. alpha 1I3 separated in the gels as a single 190-kDa polypeptide. It is also a monomer in native solution by ultracentrifugation criteria. Native rat alpha 2M is a tetramer, but it separates in the gels as a disulfide-linked dimer with an Mr of approximately 360 kDa. The kinetics of changes in concentration of these proteins during the induction of polyarthritis was also measured by quantitative immunoelectrophoresis. In rats with adjuvant-induced polyarthritis, the concentration of alpha 1I3 dramatically decreases and alpha 2M appears and continues to increase in a biphasic manner for 2 weeks. The alpha 1M concentration remains relatively constant. All three macroglobulins were purified utilizing modern rapid chromatographic techniques, and parallel comparisons of their native physicochemical properties were carried out. The N-terminal sequence of the alpha-chain of rat alpha 1M was also shown to share sequence homology with that of alpha 2M. In agreement, Esnard et al. (Esnard, F., Gutman, N., El Moujahed, A., and Gauthier, F. (1985) FEBS Lett. 182, 125-129) recently reported that alpha 1I3 also contains a thiol ester bond, as do alpha 1M and alpha 2M, since it reacts covalently with [14C]methylamine and is cleaved autolytically at 80 degrees C. We have examined negatively stained preparations of native, trypsin-treated, and methylamine-treated human alpha 2M, rat alpha 2M, and rat alpha 1M in the electron microscope. Trypsin appears to convert globular ring-shaped native molecules to rectangular box-like structures, in agreement with the conclusions of a recent report on human alpha 2M (Tapon-Bretaudiere, J., Bros, A., Couture-Tosi, E., and Delain, E. (1985) EMBO J. 4, 85-89).
Prevalence of hydrogen peroxide-producing Lactobacillus species in normal women and women with bacterial vaginosis (1989)

A predominance of Lactobacillus species in the vaginal flora is considered normal. In women with bacterial vaginosis, the prevalence and concentrations of intravaginal Gardnerella vaginalis and anaerobes are increased, whereas the prevalence of intravaginal Lactobacillus species is decreased. Because some lactobacilli are known to produce hydrogen peroxide (H2O2), which can be toxic to organisms that produce little or no H2O2-scavenging enzymes (e.g., catalase), we postulated that an absence of H2O2-producing Lactobacillus species could allow an overgrowth of catalase-negative organisms, such as those found among women with bacterial vaginosis. In this study, H2O2-producing facultative Lactobacillus species were found in the vaginas of 27 (96%) of 28 normal women and 4 (6%) of 67 women with bacterial vaginosis (P less than 0.001). Anaerobic Lactobacillus species (which do not produce hydrogen peroxide) were isolated from 24 (36%) of 67 women with bacterial vaginosis and 1 (4%) of 28 normal women (P less than 0.001). The production of H2O2 by Lactobacillus species may represent a nonspecific antimicrobial defense mechanism of the normal vaginal ecosystem.
The research that radiologists do: perspective based on a survey of the literature. (1990)

To determine the nature of radiologic research as practiced by both radiologists and nonradiologist physicians, original imaging-related reports published in the clinical literature during the first 6 months of 1989 were classified and compared. Most of the research by radiologist first authors involved technology development: invention (12%), standardization (35%), and description (32%). Original reports by nonradiologist-physician first authors involved description (28%), standardization (16%), validation (12%), assessment of other technologies (17%), and assessment of pathophysiology (19%). There were few patient outcome or cost-related articles in either category. The greatest difference between the categories was the larger number of reports by the nonradiologists that assessed pathophysiology by functional rather than morphologic criteria. The author concludes that the research performed by radiologists is primarily technology development, that assessment of pathophysiology with radiologic techniques is performed primarily by nonradiologists and is described more often in the nonradiology literature, and that academic radiology programs need to extend their research efforts to include evaluation of technology and functional assessment of disease process.
The World of Fast Moving Objects (2017)

The notion of a Fast Moving Object (FMO), i.e. an object that moves over a distance exceeding its size within the exposure time, is introduced. FMOs may, and typically do, rotate with high angular speed. FMOs are very common in sports videos, but are not rare elsewhere. In a single frame, such objects are often barely visible and appear as semitransparent streaks. A method for the detection and tracking of FMOs is proposed. The method consists of three distinct algorithms, which form an efficient localization pipeline that operates successfully in a broad range of conditions. We show that it is possible to recover the appearance of the object and its axis of rotation, despite its blurred appearance. The proposed method is evaluated on a new annotated dataset. The results show that existing trackers are inadequate for the problem of FMO localization and a new approach is required. Two applications of localization, temporal superresolution and highlighting, are presented.
Modeling and Simulation in Service-Oriented Software Development (2007)

Recently, Service-Oriented Architecture (SOA) has received significant attention. SOA simulation can play an important role in SOA software development as it can be used to verify the SOA application models and to demonstrate runtime and collaborative behaviors of the SOA applications. SOA simulation differs from traditional simulation as it emphasizes on reusability, collaborative behaviors, and its unique model-driven development. This paper focuses on these issues and illustrates how these can be achieved.
Generating a fault-tolerant global clock using high-speed control signals for the MetaNet architecture (1994)

Describes a new technique, based on exchanging control signals between neighboring nodes, for constructing a stable and fault-tolerant global clock in a distributed system with an arbitrary topology. It is shown that it is possible to construct a global clock reference with a time step that is much smaller than the propagation delay over the network's links. The synchronization algorithm ensures that the global clock "tick" has a stable periodicity, and therefore, it is possible to tolerate failures of links and clocks that operate faster and/or slower than nominally specified, as well as hard failures. The approach taken is to generate a global clock from the ensemble of the local transmission clocks and not to directly synchronize these high-speed clocks. The steady-state algorithm, which generates the global clock, is executed in hardware by the network interface of each node. At the network interface, it is possible to measure accurately the propagation delay between neighboring nodes with a small error or uncertainty and thereby to achieve global synchronization that is proportional to these error measurements. It is shown that the local clock drift (or rate uncertainty) has only a secondary effect on the maximum global clock rate. The synchronization algorithm can tolerate any physical failure. It will continue to operate correctly on any connected segment of the network, i.e., it can tolerate any number of link and node failures, as long as the network remains connected.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Adaptive rate control for High Efficiency Video Coding (2012)

A frame level adaptive rate control scheme for the emerging High Efficiency Video Coding (HEVC) standard is proposed in this paper, where both rate model and distortion model are provided. For rate modeling, a new rate model is proposed based on the weighted complexity estimation of the previously encoded frames. For distortion modeling, the distortion is modeled as an exponential function of the sum of absolute transformed difference (SATD) and the quantization parameter of the current frame. Moreover, a quality smoothing method based on the distortion model is proposed to reduce the quality fluctuation. The proposed rate control algorithm is implemented into HM5.0. The proposed scheme can control the bitrate accurately with smoothing quality, and the coding gain compared with state-of-the-art technique is up to 0.64dB for LB HE & LB LC, 0.33dB, 0.31dB, 0.42dB, 0.44dB for LP HE, LP LC, RA HE and RA LC respectively.
Detection and treatment of atherosclerosis using nanoparticles (2016)

Atherosclerosis is the key pathogenesis of cardiovascular disease, which is a silent killer and a leading cause of death in the United States. Atherosclerosis starts with the adhesion of inflammatory monocytes on the activated endothelial cells in response to inflammatory stimuli. These monocytes can further migrate into the intimal layer of the blood vessel where they differentiate into macrophages, which take up oxidized low-density lipoproteins and release inflammatory factors to amplify the local inflammatory response. After accumulation of cholesterol, the lipid-laden macrophages are transformed into foam cells, the hallmark of the early stage of atherosclerosis. Foam cells can die from apoptosis or necrosis, and the intracellular lipid is deposed in the artery wall forming lesions. The angiogenesis for nurturing cells is enhanced during lesion development. Proteases released from macrophages, foam cells, and other cells degrade the fibrous cap of the lesion, resulting in rupture of the lesion and subsequent thrombus formation. Thrombi can block blood circulation, which represents a major cause of acute heart events and stroke. There are generally no symptoms in the early stages of atherosclerosis. Current detection techniques cannot easily, safely, and effectively detect the lesions in the early stages, nor can they characterize the lesion features such as the vulnerability. While the available therapeutic modalities cannot target specific molecules, cells, and processes in the lesions, nanoparticles appear to have a promising potential in improving atherosclerosis detection and treatment via targeting the intimal macrophages, foam cells, endothelial cells, angiogenesis, proteolysis, apoptosis, and thrombosis. Indeed, many nanoparticles have been developed in improving blood lipid profile and decreasing inflammatory response for enhancing therapeutic efficacy of drugs and decreasing their side effects. WIREs Nanomed Nanobiotechnol 2017, 9:e1412. doi: 10.1002/wnan.1412 For further resources related to this article, please visit the WIREs website.
Characterization of a Focal Plane Camera Fitted to a Mattauch−Herzog Geometry Mass Spectrograph. 1. Use with a Glow-Discharge Source (2002)

A Mattauch-Herzog geometry mass spectrograph (MHMS) has been equipped with a novel array detector, the focal plane camera (FPC). The FPC consists of an array of gold Faraday cups, each coupled to its own integrator, with interrogation of the integrators performed by a multiplexer. The initial coupling of this instrument with a pin-type glow discharge source has provided limits of detection in the single to hundreds of nanograms per gram regime; isotope ratio accuracy and precision better than 5% error and 0.2% RSD, respectively; and a linear dynamic range of at least 6 orders of magnitude. A current weakness of the FPC is its pixel size, which limits both sensitivity and baseline resolution (to R = 130). The minimum data acquisition time for multiple images at present is 1 ms/image, with a dead time of 3.2 ms between images, which will limit the ability of the FPC to monitor extremely short transient signals.
Impacts of multiprocessing on GTD-5 EAX call processing and related operating system software and data base (1982)

Taking full advantage of the flexibility provided by GTD-5 EAX architecture, while meeting system performance goals, presented a significant challenge to the design of call processing software and related operating system and data base. These challenges were also opportunities to design a flexible and easily expandable system based on building blocks of functional processor types. 2 references.
Hydro-Political Hyperbole: Examining Incentives for Overemphasizing the Risks of Water Wars (2011)

Predictions of inevitable and imminent wars over scarce water are routinely made by prominent political figures, academics, journalists, and non-governmental organizations (NGOs). These statements continue to occur despite both a questionable theoretical foundation and little empirical evidence to support them. This study demonstrates that several sets of actors—policymakers, academics, journalists, and NGO activists—each have different incentives to stress and even exaggerate the probability of war over water. This confluence of incentives has likely contributed to an overemphasis in public discourse of the likelihood of water wars.
Age-Related Changes in 1/<i>f</i>Neural Electrophysiological Noise (2015)

Aging is associated with performance decrements across multiple cognitive domains. The neural noise hypothesis, a dominant view of the basis of this decline, posits that aging is accompanied by an increase in spontaneous, noisy baseline neural activity. Here we analyze data from two different groups of human subjects: intracranial electrocorticography from 15 participants over a 38 year age range (15-53 years) and scalp EEG data from healthy younger (20-30 years) and older (60-70 years) adults to test the neural noise hypothesis from a 1/f noise perspective. Many natural phenomena, including electrophysiology, are characterized by 1/f noise. The defining characteristic of 1/f is that the power of the signal frequency content decreases rapidly as a function of the frequency (f) itself. The slope of this decay, the noise exponent (χ), is often <-1 for electrophysiological data and has been shown to approach white noise (defined as χ = 0) with increasing task difficulty. We observed, in both electrophysiological datasets, that aging is associated with a flatter (more noisy) 1/f power spectral density, even at rest, and that visual cortical 1/f noise statistically mediates age-related impairments in visual working memory. These results provide electrophysiological support for the neural noise hypothesis of aging. Significance statement: Understanding the neurobiological origins of age-related cognitive decline is of critical scientific, medical, and public health importance, especially considering the rapid aging of the world's population. We find, in two separate human studies, that 1/f electrophysiological noise increases with aging. In addition, we observe that this age-related 1/f noise statistically mediates age-related working memory decline. These results significantly add to this understanding and contextualize a long-standing problem in cognition by encapsulating age-related cognitive decline within a neurocomputational model of 1/f noise-induced deficits in neural communication.
Sigma Profile Database for Predicting Solid Solubility in Pure and Mixed Solvent Mixtures for Organic Pharmacological Compounds with COSMO-Based Thermodynamic Methods (2008)

Thermodynamic methods based on COSMO (COnductor-like Screening MOdels), such as COSMO-RS (Real Solvent) and COSMO-SAC (Segment Activity Coefficient), represent significant and recent developments of solvation thermodynamics and computational quantum mechanics. These are a priori prediction methods based on molecular structures and a few parameters that are fixed for all of the compounds. They require no experimental data and rely on sigma profiles specific to each molecule as their only input. A sigma profile is the probability distribution of a molecular surface segment having a specific charge density. Generating sigma profiles by quantum mechanical calculations represents the most time-consuming and computationally expensive aspect of using COSMO-based methods. This article presents a free, web-based VT-2006 Solute Sigma Profile Database for large, pharmaceutical-related solutes, to supplement the published VT-2005 Sigma Profile Database for solvents and small molecules (www.design.che.vt.edu). Together, these databases contain sigma profiles for 1645 unique compounds, enabling the users to predict binary and multicomponent vapor−liquid equilibrium (VLE) and solid−liquid equilibrium (SLE), as well as other thermodynamic properties. We validate the VT-2006 Solute Sigma Profile Database by solid solubility predictions in pure solvents for 2434 literature solubility values, which include 194 solutes, 160 solvents, and 1356 solute−solvent pairs. We also compare solubility predictions for mixed solvents to literature values for 39 systems. By comparison with experimental data, we find a root-mean-squared error (RMSE) of 0.7419 between experimental and predicted solute mole fractions (xsol) on a log10 (xsol) scale for solubilities in pure solvents. This article also presents examples investigating the effects of conformational isomerism on solubility predictions of small, medium-sized, and large drug molecules. To provide better understanding of accuracy, we compare a priori COSMO-SAC solubility predictions, which use molecule-specific sigma profiles, to those by the non-random two-liquid segment activity coefficient (NRTL-SAC) model, which uses regressed molecule-specific parameters, for 17 solutes and 258 experimental solubility values. We find that NRTL-SAC, which contains regressed parameters based on experimental data, is a more accurate method for predicting SLE behavior than the COSMO-SAC model for many of the systems studied. Finally, this article presents a set of guidelines for applying the COSMO-SAC model for solubility predictions for new drug molecules when no experimental data are available.
Sensor placement for on-orbit modal identification and correlation of large space structures (1991)

A method is presented for the selection of a set of sensor locations from a larger candidate set for the purpose of on-orbit identification and correlation of Large Space Structures. The method ranks the candidate sensor locations according to their contribution to the linear independence of the target modal partitions. In an iterative maner, the locations which do not contribute significantly are removed. The final sensor configuration tends to maximize determinant of the corresponding Fisher Information Matrix.
Error Detection of Data Conversion in Flash ADC using Code Width Based Technique (2019)

The high integration density of the complex electronic system requires the multi-functional testing facility to ensure the accuracy of the circuit function. In addition, the wide population of submicron technologies results in the persistent requirements of high precision analog and mixed-signal (AMS) circuits. In the complex, high-density circuits, observing the correctness of output are limited due to the limitations of input and output pins which develop the AMS circuit test as very difficult and expensive. A digital built-in self-test (BIST) scheme has been presented in this paper for testing an analog to digital converter (ADC) in the time domain. The testing scheme consists of the linear analog ramp generator, ADC as a circuit under test, output response analyzer and a BIST controller. Bootstrap linear ramp generator is used to generate the linear analog ramp signal which is applied to ADC to develop the digital word sequence for testing. Among various types of ADCs, here a Flash ADC has used since it is fastest and accurate in digital conversion. A Flash ADC has been designed with the seven-bit resolution and tested using the proposed digital BIST scheme. The ADC comprises a sample-hold circuit, 2N -1 comparator, XOR gates, and encoder block. The output response analyzer verifies the digital output sequence to validate the static test parameters of ADC called monotonicity, missing codes, DNL, and INL error. The BIST controller generates the control signals to control the test sequence. The complete test sequence of ADC BIST has simulated in Tanner EDA with TSMC 0.18um technology. ORA is used to analyze the presence of monotonicity, missing codes, DNL and INL error in the ADC output.