gebhart/patrepeval huggingface dataset:
Microfluidic Screening of Electrophoretic Mobility Shifts Elucidates Riboswitch Binding Function (2013)

Riboswitches are RNA sensors that change conformation upon binding small molecule metabolites, in turn modulating gene expression. Our understanding of riboswitch regulatory function would be accelerated by a high-throughput, quantitative screening tool capable of measuring riboswitch-ligand binding. We introduce a microfluidic mobility shift assay that enables precise and rapid quantitation of ligand binding and subsequent riboswitch conformational change. In 0.3% of the time required for benchtop assays (3.2 versus 1020 min), we screen and validate five candidate SAM-I riboswitches isolated from thermophilic and cryophilic bacteria. The format offers enhanced resolution of conformational change compared to slab gel formats, quantitation, and repeatability for statistical assessment of small mobility shifts, low reagent consumption, and riboswitch characterization without modification of the aptamer structure. Appreciable analytical sensitivity coupled with high-resolution separation performance allows quantitation of equilibrium dissociation constants (K(d)) for both rapidly and slowly interconverting riboswitch-ligand pairs as validated through experiments and modeling. Conformational change, triplicate mobility shift measurements, and K(d) are reported for both a known and a candidate SAM-I riboswitch with comparison to in-line probing assay results. The microfluidic mobility shift assay establishes a scalable format for the study of riboswitch-ligand binding that will advance the discovery and selection of novel riboswitches and the development of antibiotics to target bacterial riboswitches.
Chemical Studies of<i>Aloe Vera</i>Juice II: Inorganic Ingredients (1969)

(1969). Chemical Studies of Aloe Vera Juice II: Inorganic Ingredients. Quarterly Journal of Crude Drug Research: Vol. 9, No. 4, pp. 1445-1453.
Multi-Baseline Stereo Using Surface Extraction. (1996)

Abstract : Traditionally, the matching problem in stereo vision has been formulated as an ill-posed problem. However, it has been shown that the matching problem can be well-posed in scenes with no occlusions or depth discontinuities. Unfortunately most real scenes do not obey these constraints. We overcome this by finding regions within the images in which the matching problem is well-posed. That is, we find image regions in which there are no occlusions or depth discontinuities. In general, a unique set of such regions does not exist. However, we will demonstrate that in almost all cases these regions can be found efficiently. Therefore the matching problem can be well-posed in almost all cases. In order to find these corresponding regions we transform the problem from finding 2D image regions into identifying 3D surfaces. We have developed a method of 3D surface extraction which uniquely identifies correct 3D surfaces from a set of potential surfaces. In order to test the method we have built a four camera system with which we will present results from several scenes.
A high capacity metropolitan area network using lightwave transmission and time multiplexed switching (1990)

The technical feasibility of a lightwave communication system capable of providing service to thousands of subscribers within cities or large suburban areas is examined. Each subscriber in this system has available upon demand an aggregate bit rate of up to 100 Mb/s. The aggregate bit rate of the entire network is on the order of 5 Tb/s. The network topology is that of a star-on-star wherein each subscriber line terminates on one of a multitude of remote concentrators. Each high-speed link from a remote concentrator to a centrally located time-multiplexing photonic switch consists of a single-mode fiber carrying several wavelength-division multiplexed (WDM) channels. Each channel operates in a time-division multiplexed (TDM) mode at a data rate of 2 Gb/s and is powered by a multimode laser. No regeneration is required at the central switch, and at the remote concentrators, each channel is terminated by a direct-detection receiver. The approach achieves high throughput by reusing the same channels, that collectively occupy a tiny fraction of the optical band, among all interconnecting links and, with the exception of large-dimensional switch arrays, employs readily available technology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
National Surgical Quality Improvement Program (NSQIP) Risk Factors Can Be Used to Validate American Society of Anesthesiologists Physical Status Classification (ASA PS) Levels (2006)

In Brief Objective: The purpose of this study was to determine the relationship between the American Society of Anesthesiologists’ Physical Status (ASA PS) classifications and the other National Surgical Quality Improvement Program (NSQIP) preoperative risk factors. Background: The ASA PS has been shown to predict morbidity and mortality in surgical patients but is inconsistently applied and clinically imprecise. It is desirable to have a method for validating ASA PS classification levels. Methods: The NSQIP preoperative risk factors, including ASA PS, were recorded from a random sample of 5878 surgical patients on 6 services between October 1, 2001 and September 30, 2003 at the University of Kentucky Medical Center. Mortality, morbidity, costs, and length of stay were obtained and compared across ASA PS levels. The ability of 1) ASA PS alone, 2) the other NSQIP risk factors, and, 3) all factors combined to predict outcomes was analyzed. A model using the other NSQIP risk factors was developed to predict ASA PS. Results: ASA PS alone was a strong predictor of outcomes (P < 0.01). However, the other NSQIP risk factors were better predictors as a group. There was significant interdependence between the ASA PS and the other NSQIP risk factors. Predictions of ASA PS using the other factors showed strong agreement with the anesthesiologists’ assignments. Conclusions: The NSQIP risk factors other than ASA PS can and should be used to validate ASA PS classifications. The American Society of Anesthesiology's Physical Status Classification (ASA PS) is known to be a strong predictor of surgical outcomes. However, the ASA PS is limited because it lacks clinical precision and is inconsistently applied by different anesthesiologists. The National Surgical Quality Improvement Program tracks 60 preoperative risk factors, including the ASA PS. This study demonstrates that the other 59 risk factors are effective in predicting ASA PS and therefore can be used to validate ASA PS levels by hospital or anesthesiologist.
The effect of substrate on high-temperature annealing of GaN epilayers: Si versus sapphire (2006)

We have studied the effects of rapid thermal annealing at 1300°C on GaN epilayers grown on AlN buffered Si(111) and on sapphire substrates. After annealing, the epilayers grown on Si display visible alterations with craterlike morphology scattered over the surface. The annealed GaN∕Si layers were characterized by a range of experimental techniques: scanning electron microscopy, optical confocal imaging, energy dispersive x-ray microanalysis, Raman scattering, and cathodoluminescence. A substantial Si migration to the GaN epilayer was observed in the crater regions, where decomposition of GaN and formation of Si3N4 crystallites as well as metallic Ga droplets and Si nanocrystals have occurred. The average diameter of the Si nanocrystals was estimated from Raman scattering to be around 3nm. Such annealing effects, which are not observed in GaN grown on sapphire, are a significant issue for applications of GaN grown on Si(111) substrates when subsequent high-temperature processing is required.
Statistical Analysis of Peptide Electron Transfer Dissociation Fragmentation Mass Spectrometry (2009)

It is well established that protein sequence determination may be achieved by mass spectrometric analysis of protonated tryptic peptides subjected to collisional activation. When separated by nanoflow HPLC, a high percentage of peptides from complex mixtures of proteins can usually be identified. Recently, alternative, radical-driven fragmentation approaches of electron capture dissociation and the more common electron transfer dissociation (ETD) have been introduced and made widely available. In order to utilize these techniques in large scale proteomics studies, it is important to characterize the performance of these fragmentation processes on peptides formed by a range of enzymatic cleavages. In this study, we present a statistical analysis of the ion types that are observed from peptides produced by different enzymes and highlight the different characteristics of ETD spectra of doubly charged precursors in comparison to precursors of higher charge states.
Effects of recombinant human interleukin-3 in patients with myelodysplastic syndromes (1990)

In a phase I-II study, nine patients with myelodysplastic syndromes and concomitant severe transfusion-dependent cytopenias were treated with recombinant human interleukin-3 (rhIL-3) to improve hematopoietic function. Doses of rhIL-3 ranged from 250 micrograms/m2 to 500 micrograms/m2 and were given as daily subcutaneous bolus injections for 15 days. Blood leucocyte counts increased 1.3- to 3.6-fold in all nine patients, including neutrophils, eosinophils, lymphocytes, basophils, and monocytes. The mean absolute neutrophil counts increased from 1,350/microL (range, 150 to 2,420) to 2,660/microL (range, 300 to 9,380) (P less than .05) immediately after the end of rhIL-3 therapy and to a maximum count of 4,096/microL (range, 350 to 10,820) (P less than .01). Platelet responses were seen in two of four profoundly thrombocytopenic patients, resulting in discontinuation of platelet transfusion. The requirements for red blood cell transfusion temporarily improved in one patient. Stimulation of plasma cells was evident by a significant increase in serum IgM and IgA levels. Mild side effects (fever, headache, local erythema, and bone pain) were observed in some patients, while transient thrombocytopenia developed in two patients. Disease progression with an increase in blast cells was seen in one patient. These results suggest that rhIL-3 is effective in stimulating hematopoiesis of all lineages in patients with myelodysplastic syndromes and may produce at least short-term hematologic improvement.
Scarless Genome Editing of Human Pluripotent Stem Cells via Transient Puromycin Selection (2018)

Genome-edited human pluripotent stem cells (hPSCs) have broad applications in disease modeling, drug discovery, and regenerative medicine. We present and characterize a robust method for rapid, scarless introduction or correction of disease-associated variants in hPSCs using CRISPR/Cas9. Utilizing non-integrated plasmid vectors that express a puromycin N-acetyl-transferase (PAC) gene, whose expression and translation is linked to that of Cas9, we transiently select for cells based on their early levels of Cas9 protein. Under optimized conditions, co-delivery with single-stranded donor DNA enabled isolation of clonal cell populations containing both heterozygous and homozygous precise genome edits in as little as 2 weeks without requiring cell sorting or high-throughput sequencing. Edited cells isolated using this method did not contain any detectable off-target mutations and displayed expected functional phenotypes after directed differentiation. We apply the approach to a variety of genomic loci in five hPSC lines cultured using both feeder and feeder-free conditions.
Discrimination of Sinus Rhythm, Atrial Flutter, and Atrial Fibrillation Using Bipolar Endocardial Signals (1998)

The investigated algorithm provides discrimination of NSR, AFL, and AF with high sensitivity and specificity. Incorporation of this algorithm in an implantable automated antitachycardia device may lead to adequate differential therapy in patients suffering from spontaneous episodes of AF and AFL.
Recombinant human bone morphogenetic protein-2 induces osteoblastic differentiation in W-20-17 stromal cells. (1992)

To better understand the in vivo bone-inductive properties of recombinant human (rh) BMP-2, we examined the ability of the protein to alter the phenotype of a bone marrow stromal cell line. W-20-17. rhBMP-2 increased alkaline phosphatase activity in W-20-17 cells in a dose-responsive manner in the absence of an effect on proliferation. The induction of alkaline phosphatase activity was not apparent until 12 h after rhBMP-2 treatment had begun and was effectively eliminated by cotreatment with cycloheximide, suggesting a requirement for protein synthesis. Continued treatment of W-20-17 cells with rhBMP-2 for 8 days resulted in a significant increase, compared to control cultures, in the production of cellular cAMP in response to a PTH challenge. In addition, 4-day treatment with rhBMP-2 induced osteocalcin levels in W-20-17 cells. These results indicate that rhBMP-2 induces the expression of several markers associated with the osteoblast phenotype in W-20-17 cells and raises the possibility that BMP-2 may be involved in the differentiation of osteoblasts from progenitor cells resident in bone marrow.
Polysaccharide derivatives as useful chiral stationary phases in high-performance liquid chromatography (2007)

Abstract The chromatographic separation of enantiomers using chiral stationary phases (CSPs) has significantly advanced. The esters and carbamates of polysaccharides coated on silica gel have been extensively studied and widely used as CSPs for high-performance liquid chromatography (HPLC). In order to overcome the strict solvent limitation on these coated CSPs, the preparation of a new generation of CSPs consisting of immobilized polysaccharide derivatives has become increasingly important. The universal solvent compatibility of the new CSPs provides flexibility in both analytical and preparative chromatographies.
On the design, robustness, implementation and use of quasi-linear feedback compensators (2004)

A quasi-linear feedback compensator is one in which its poles depend in an appropriate way on its gain. The reason for introducing this new concept was the desire to remove the limitation to performance imposed by a plant with more than one pole in excess of its zeros. In this article it is shown that this objective is realized for plants with zeros in the left half of the complex plane. The consequences are surprising. In time domain it is possible to track arbitrarily fast a class of reference inputs despite a large class of disturbances and uncertainty in plant parameters. The response is non-oscillatory for high enough compensator gains, which is explained by the automatic adaptation of the closed loop poles to stability and stability margins for such gains. And in frequency domain the phase margin tends to 90° while the gain margin and crossover frequency become unlimited. Technically the design procedure of quasi-linear compensators presented here is based on our theoretical result concerning the asymptotic behaviour of the roots of certain polynomials in a complex variable which depend also on a large positive parameter. We also show how to implement such quasi-linear compensators in practical feedback control schemes, and their use at lower gains which is the case of most industrial applications.
Routing Algorithm of Wireless Sensor Network for Building Automation System (2009)

Wireless Sensor Network (WSN) has been very popular in unattended surveillance systems recently. For Applying WSN into Building Automation system (BAS), a novel hierarchial network structure and static routing algorithm which eliminates the scalability limitation of Zigbee are proposed in this paper. The static routing algorithm relying on the hierarchial network address reduces the computational complexity to a great extent and has a real-time performance which satisfies urgent applications well.
<i>When Time Breaks Down: The Three-Dimensional Dynamics of Electrochemical Waves and Cardiac Arrhythmias</i> (1988)

The Description for this book, When Time Breaks Down: The Three-Dimensional Dynamics of Electrochemical Waves and Cardiac Arrhythmias, will be forthcoming.
Correlation between electron trap density and hydrogen concentration in ultrathin rapidly reoxidized nitrided oxides (1988)

Ultrathin nitrided oxides (8 nm) were reoxidized for the first time by lamp-heated rapid thermal annealing in dry oxygen at 900–1150 °C for 15–200 s. Extensive measurements of hydrogen concentration [H] using secondary ion mass spectroscopy were performed. Electron trapping was monitored by flatband voltage shift ΔVfb under high-field stress. Both [H] and the ΔVfb decrease monotonically as reoxidation proceeds in the present experimental conditions. We have found for the first time that the ΔVfb is correlated with the [H] by a single proportional relation regardless of the fabrication condition. This fact gives evidence that the electron traps in the (reoxidized) nitrided-oxide system originate from hydrogen-containing species.
A Difference Method of the Gravity Center with Double Pilots for the MC CDMA System (2000)

A carrier recovery method of the power spectrum center difference adapting to the mobile channel of the MC CDMA system with serious Doppler shift using double pilots is presented. In the transmitter, two pilots of equal frequency distance to the carrier with one putting on the left position and the other on the right position of the carrier frequency are used. Even if a continuous sine wave is transmitted, the power spectrum is expanded to a Doppler band in the receiver owing to the multi path transmission and the Doppler shift. The pilot spectrum is made to pass through two narrow band filters which are transformed to the base band with local carrier wave in the receiver. The frequency difference between the local carrier and the transmitter carrier is obtained when the difference of the gravity centers of the two pilot spectra is computed.
The Molecular Basis for the Broad Substrate Specificity of Human Sulfotransferase 1A1 (2011)

Cytosolic sulfotransferases (SULTs) are mammalian enzymes that detoxify a wide variety of chemicals through the addition of a sulfate group. Despite extensive research, the molecular basis for the broad specificity of SULTs is still not understood. Here, structural, protein engineering and kinetic approaches were employed to obtain deep understanding of the molecular basis for the broad specificity, catalytic activity and substrate inhibition of SULT1A1. We have determined five new structures of SULT1A1 in complex with different acceptors, and utilized a directed evolution approach to generate SULT1A1 mutants with enhanced thermostability and increased catalytic activity. We found that active site plasticity enables binding of different acceptors and identified dramatic structural changes in the SULT1A1 active site leading to the binding of a second acceptor molecule in a conserved yet non-productive manner. Our combined approach highlights the dominant role of SULT1A1 structural flexibility in controlling the specificity and activity of this enzyme.
A Disposable, Coated Wire Heparin Sensor (1994)

The development of an ion-selective electrode heparin sensor consisting of a specially formulated polymer membrane doped with tridodecylmethylammonium chloride as the heparin complexing agent was recently reported. Because of the simple nature of the membrane technology used, the authors envisioned that the sensor could be configured as a disposable single-use device for rapid clinical or bedside measurement of heparin in a small, discrete sample. To explore this possibility, an inexpensive, disposable heparin sensor was created by dip-coating a copper wire with the specially formulated heparin-sensing polymeric membrane. Coated wire heparin sensors with a broad range of membrane thicknesses, prepared by repeatedly dipping the wire in the membrane solution for various times, were examined. Data show that increasing the membrane thickness of the sensor to a certain degree (more than 10 microns) enhanced the sensor's potentiometric response to heparin, although the time required to achieve 90% of the steady-state potential change was also prolonged. In addition, increasing membrane thickness also magnified the stirring effect on the sensor's response. In undiluted plasma samples, the coated-wire sensor with an optimized membrane thickness yielded a significant (5 to 30 mV) and reproducible response to heparin in a clinically relevant concentration range (0.5 to 12 units/ml, respectively). The clinical utility of the coated wire heparin sensor was shown using the sensor during protamine titration of heparinized plasma to assess the titration end-point. Preliminary results showed that the titration end-points determined by the heparin sensor strongly correlated with those determined by the activated partial thromboplastin time clotting assay. The overall time requirement to complete the titration process using a set of prefabricated coated wire heparin sensors, however, was less than 3 minutes. Further titration studies using undiluted clinical whole blood samples are in progress.
New insights in the relation between electron trap generation and the statistical properties of oxide breakdown (1998)

In this paper it is demonstrated in a wide stress field range that breakdown in thin oxide layers occurs as soon as a critical density of neutral electron traps in the oxide is reached. It is proven that this corresponds to a critical hole fluence, since a unique relationship between electron trap generation and hole fluence is found independent of stress field and oxide thickness. In this way literature models relating breakdown to hole fluence or to trap generation are linked. A new model for intrinsic breakdown, based on a percolation concept, is proposed. It is shown that this model can explain the experimentally observed statistical features of the breakdown distribution, such as the increasing spread of the Q/sub BD/-distribution for ultrathin oxides. An important consequence of this large spread is the strong area dependence of the Q/sub BD/ for ultrathin oxides.
Codoping method for the fabrication of low-resistivity wide band-gap semiconductors in p-type GaN, p-type AlN and n-type diamond: prediction versus experiment (2001)

We review our new valence control method of a co-doping for the fabrication of low-resistivity p-type GaN, p-type AlN and n-type diamond. The co-doping method is proposed based upon ab initio electronic structure calculation in order to solve the uni-polarity and the compensation problems in the wide band-gap semiconductors. In the co-doping method, we dope both the acceptors and donors at the same time by forming the meta-stable acceptor-donor-acceptor complexes for the p-type or donor-acceptor-donor complexes for the n-type under thermal non-equilibrium crystal growth conditions. We propose the following co-doping method to fabricate the low-resistivity wide band-gap semiconductors; p-type GaN: [Si + 2 Mg (or Be)], [H + 2 Mg (or Be)], [O + 2 Mg (or Be)], p-type AlN: [O + 2 C] and n-type diamond: [B + 2 N], [H + S], [H + 2 P]. We compare our prediction of the co-doping method with the recent successful experiments to fabricate the low-resistivity p-type GaN, p-type AlN and n-type diamond. We show that the co-doping method is the efficient and universal doping method by which to avoid carrier compensation with an increase of the solubility of the dopant, to increase the activation rate by decreasing the ionization energy of acceptors and donors, and to increase the mobility of the carrier.