gebhart/patrepeval huggingface dataset:
Choice of DNA extraction protocols from Gram negative and positive bacteria and directly from the soil (2015)

DNA extraction is a fundamentally important step for the implementation of genotypic techniques in microbial identification, and the use of such techniques has become essential for the analysis of soil microbial diversity. Considering culture independent methodologies, it is still necessary to ensure that DNA is extracted in appropriate amounts and that extracted DNA is inhibitor-free. This study aimed at selecting a single protocol suitable for the extraction of total DNA from Gram positive and negative bacteria isolated from different sources, as well as a protocol for the direct extraction of DNA from soil. Four experimental protocols and a commercial kit were tested for the extraction of total DNA from isolated bacteria. Among the protocols, the detergent + salt + thermal incubation method (based on Harju et al., 2004) was considered the most promising because it produced satisfactory yields of DNA, with adequate quality for all isolates studied, especially Staphylococcus aureus, without the need to use enzymes and glass beads which can make the extraction process more expensive. Three experimental protocols and the commercial kit were tested for the direct extraction of DNA from soil. Regarding PCR amplification, the amount of total DNA extracted is less limiting than its quality. Thus, commercial kit PowerMax™ Soil DNA Isolation (MoBio) offered more promising results, because although this provided low yields of DNA, it was sufficient for polymerase chain reaction (PCR) amplification. Key words: Genotypic characterization, bacterial diversity, polymerase chain reaction (PCR), agroforestry system, organic farming.
Aspartate and glutamate mediate excitatory synaptic transmission in area CA1 of the hippocampus (1993)

We examined whether L-aspartate (ASP) and L-glutamate (GLU) both function as endogenous neurotransmitters in area CA1 of the rat hippocampus. Radioligand displacement experiments using 3H-DL-alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (3H-AMPA) to label AMPA/kainate receptors and 3H-cis-4-phosphonomethyl-2-piperidine carboxylic acid (3H-CGS-19755) to label NMDA receptors confirmed that GLU (Ki approximately 500 nM) but not ASP (Ki > 1 mM) has high affinity for AMPA/kainate receptors whereas GLU (Ki approximately 250 nM) and ASP (Ki approximately 1.3 microM) both have high affinity for NMDA receptors. Elevating extracellular potassium concentration (50 mM, 1 min) evoked the calcium-dependent release of both ASP (approximately 50% increase) and GLU (approximately 200% increase) from hippocampal slices and from minislices of area CA1. Reducing extracellular glucose concentration (0.2 mM) reduced GLU release, enhanced ASP release, and reduced AMPA/kainate receptor-mediated responses more than NMDA receptor-mediated responses (to 7% and 34% of control, respectively). Fiber volleys, antidromic population spikes, membrane potential, input resistance, and ATP content all were not affected by glucose reduction. Unlike low glucose, the inhibitory neuromodulator adenosine (5 microM), which reduces ASP and GLU release to a similar extent, reduced AMPA/kainate and NMDA receptor-mediated population EPSPs similarly (to 11% and 12% of control, respectively). AMPA/kainate and NMDA receptor-mediated population EPSPs were also similarly reduced by 0.4 microM TTX (to 32% and 22% of control, respectively) and similarly enhanced by 10 microM 4-aminopyridine (to 206% and 248% of control, respectively). Finally, NMDA receptor-mediated EPSCs measured by whole-cell recording decayed faster in low glucose (73 msec vs 54 msec) but not in adenosine (73 msec vs 78 msec). Together, these results confirm that ASP and GLU are both involved in excitatory synaptic transmission at the Schaffer collateral-commissural terminals in area CA1 of the rat hippocampus.
Vibration Reed Electrometer for Accurate Measurement of Electrical Currents Below 10 pA (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We have developed a home-built vibrating reed (VR) electrometer. The heart of the meter is a VR capacitor, which excels in a stable and low input leakage current of only 8 aA with a 2 aA noise for a 1 h measurement. This paper demonstrates that this makes the instrument ideal for the characterization of subtle charge effects in, for example, connectors and cables. The exceptional sensitivity of the electrometer is proven in a measurement of the leakage resistance of an air gap capacitor which results in a value of <formula formulatype="inline"><tex>$R_{\rm leak} = (8.8 \pm 0.3)\cdot 10^{17}\ \Omega$</tex></formula>, obtained at a test voltage of only 10 V. Calibration of the system with both a picoampere and a picocoulomb generator shows that the instrument has an accuracy of 15 parts in <formula formulatype="inline"><tex>$10^{6}\, (k = 1)$</tex></formula> at a current of 1 pA. As far as we are aware, this is the best uncertainty for a room temperature electrometer published so far. </para>
Efficacy of Novel Therapeutics in Psoriatic Arthritis: A Network Meta-analysis of Randomised Controlled Trials (2018)

Introduction: Novel therapeutic agents demonstrated superior efficacy over placebo in psoriatic arthritis (PsA) patients. However, there is no direct comparison between different novel therapeutic agents. Therefore, we compared the efficacy of these therapeutic agents by network meta-analysis.
Elastic maps and nets for approximating principal manifolds and their application to microarray data visualization (2012)

Summary. Principal manifolds are defined as lines or surfaces passing through “the middle ” of data distribution. Linear principal manifolds (Principal Components Analysis) are routinely used for dimension reduction, noise filtering and data visualization. Recently, methods for constructing non-linear principal manifolds were proposed, including our elastic maps approach which is based on a physical analogy with elastic membranes. We have developed a general geometric framework for constructing “principal objects ” of various dimensions and topologies with the simplest quadratic form of the smoothness penalty which allows very effective parallel implementations. Our approach is implemented in three programming languages (C++, Java and Delphi) with two graphical user interfaces (VidaExpert and ViMiDa applications). In this paper we overview the method of elastic maps and present in detail one of its major applications: the visualization of microarray data in bioinformatics. We show that the method of elastic maps outperforms linear PCA in terms of data approximation, representation of between-point distance structure, preservation of local point neighborhood and representing point classes in low-dimensional spaces. Key words: elastic maps, principal manifolds, elastic functional, data analysis, data visualization, surface modeling 1
High Responsivity, Large-Area Graphene/MoS<sub>2</sub> Flexible Photodetectors (2016)

We present flexible photodetectors (PDs) for visible wavelengths fabricated by stacking centimeter-scale chemical vapor deposited (CVD) single layer graphene (SLG) and single layer CVD MoS2, both wet transferred onto a flexible polyethylene terephthalate substrate. The operation mechanism relies on injection of photoexcited electrons from MoS2 to the SLG channel. The external responsivity is 45.5A/W and the internal 570A/W at 642 nm. This is at least 2 orders of magnitude higher than bulk-semiconductor flexible membranes. The photoconductive gain is up to 4 × 10(5). The photocurrent is in the 0.1-100 μA range. The devices are semitransparent, with 8% absorptance at 642 nm, and are stable upon bending to a curvature of 1.4 cm. These capabilities and the low-voltage operation (<1 V) make them attractive for wearable applications.
Theory of Unipole Acoustic Logging Tools and their Relevance to Dipole and Quadrupole Tools for Slow Formations (2011)

Abstract A simplistic mathematical model has been developed to study a unipole acoustic logging tool. The model allows us to quantitatively relate a unipole tool response to monopole, dipole, and quadrupole tool responses, and vice versa. The interconnections between the different forms of excitation and reception provide some useful insights into the acoustic tool physics. The model is confirmed by numerical simulations. The unipole flexural wave sensitivity to shear slowness has been carefully studied. Numerical modeling and slowness-time-coherence analysis show that unipole, dipole, and quadrupole appear to have similar sensitivity to the shear slowness of a slow formation. The dispersion results suggest that a unipole flexural wave cannot be dispersion corrected based on any standard wave mode such as a dipole mode. Instead, the dispersion effect needs to be corrected by considering the mode-mixing nature. The look-up table approach used for this study represents the first step in the development. The unipole sensitivity to azimuthal shear anisotropy is studied. Substantial sensitivity is observed from the modeled responses in an azimuthally anisotropic medium. The same is true for a simplistic dipole tool. A conceptual quadrupole tool in the same formation shows reduced variation in waveforms with the rotation angle. Dispersion correction of the unipole flexural waves from the anisotropic formations is attempted by treating the formation as being isotropic. Corrections of the slow shear waves are less satisfactory. Interesting relations among unipole, dipole, and quadrupole also are revealed from a large-borehole scenario. The models confirm that in a large borehole with excessive tool eccentricity, both dipole and quadrupole responses may approach that of a unipole tool as some of the dipole and quadrupole excitation and reception sectors lose their proximity to the borehole wall. The modeling also shows that the dispersion effect in a unipole wave will be dependent on tool standoff, implying the necessity of standoff measurement for accurate dispersion corrections.
Twenty-Four Hour Ambulatory Simultaneous Impedance and pH Monitoring: A Multicenter Report of Normal Values From 60 Healthy Volunteers (2004)

Combining impedance and pH monitoring improves the detection and characterization of GER. This study characterizes the frequency, duration, and extent of reflux in health and provides normal values for 24-h Imp-pH for future comparison with GERD patients.
Grain Boundary Josephson Junctions Using Y-Ba-Cu-O Films Operative at 77 K (1987)

Grain boundary Josephson junctions were fabricated from superconducting oxide Y-Ba-Cu-O films. The junctions were made by a chemical wet etching technique with phosphoric acid (H 3 PO 4 ) solution. Typical dimensions of the junctions were a width of 4 µm and a length of 20 µm. The junctions showed the so-called bridge-type Josephson effect. Shapiro steps were observed in the I - V curves at a temperature as high as 77 K.
Separate versus Simultaneous Saccharification and Fermentation of Two‐Step Steam Pretreated Softwood for Ethanol Production (2005)

Abstract In two previous studies, optimal conditions were identified for two‐step steam pretreatment of SO2‐ and H2SO4‐impregnated softwood. In the present study the yield of sugar and ethanol was determined in a process development unit where pretreatment was performed in a 10‐L reactor and simultaneous saccharification and fermentation (SSF) or enzymatic hydrolysis (EH) were performed in 30‐L reactors. The study showed that a steam pretreatment reactor should be larger than 2 L to yield acceptable results. Two pretreatment combinations were studied. In the H2SO4 case, the first pretreatment step was at 180°C for 10 min with 0.5% H2SO4 and the second step at 210°C for 2 min with 1% H2SO4. In the SO2 case, first step was at 190°C for 2 min followed by a second step at 210°C for 5 min. The concentration of SO2 was 3% in both steps. EH and SSF were performed on the whole slurry after the second pretreatment step to determine the yield of sugars and ethanol. The liquid after the first pretreatment step was also analyzed and fermented. When SSF and EH were performed at the same dry matter content and enzymatic activity, the ethanol yield in SSF exceeded the yield obtained with EH in both pretreatment cases, even when 100% yield in the fermentation step was assumed. Thus SSF is a better process if yield is the main priority. Comparison of the yields with the two acid catalysts showed higher yields with SO2 in both SSF and EH. The overall ethanol yield following SSF of SO2‐impregnated and pretreated wood reached 81% of the theoretical, that is, 357 liters per metric ton of dry raw material.
Molecular Dynamics Simulations of Helium Permeation in Polyimides with a Bulky Dianhydride and a Fluorinated Diamine (2007)

Abstract Fully‐atomistic molecular dynamics (MD) simulations have been carried out to model helium transport through four different glassy polyimides. While the polymer matrices had been pre‐validated, specific parameters and combination rules were used here in order to describe helium‐helium and helium‐polymer interactions. Gas permeabilities are in very good agreement with experimental evidence. Two ways to decrease chain cohesion and improve gas transport were considered – the replacement of an ODPA by a bulky BCDA dianhydride, and the substitution of a site on an ODA diamine by a CF 3 . The fluorinated polyimide appears to be the most promising material with more heterogeneity in the void‐space distribution, the highest model permeability and fewer constraints from an experimental point of view. magnified image
Aerodynamic Performance of a Vibrating Piezoelectric Blade Under Varied Operational and Confinement States (2017)

This paper investigates the aerodynamic performance of a piezoelectrically actuated cantilever blade operating in the first mode of vibration. Bulk air-moving capability and local velocity field features have been experimentally measured for different operational conditions and blade confinement states. A testing facility has been developed to determine the pressure-flow rate characteristics of a vibrating blade and simultaneously conduct particle image velocimetry. Under high system resistance, similar to that found in densely packed electronics, flow reversal occurs at the blade outlet region analogous to stall. This is accompanied by increased local unsteadiness in the airflow being emitted. Local turbulence intensity increases by 50% between maximum flow rate and maximum efficiency operating points. The introduction of confinement around a vibrating blade reduces bulk air-moving capability significantly, with pressure rise and volumetric flow rate measured as low as 20% of what can be achieved for an unconfined blade. However, there is an accompanying change in spatial velocity distribution, which focuses the flow normal to the outlet. This has potentially beneficial uses for targeted electronics cooling applications. The findings identify the relationship between local and bulk airflow characteristics that ultimately provides information about the sensitivity of this type of air-moving device in practical installations.
Once Daily Pregabalin Eye Drops for Management of Glaucoma (2019)

Elevated intraocular pressure (IOP) is the most significant risk factor contributing to visual field loss in glaucoma. Unfortunately, the deficiencies associated with current therapies have resulted in reduced efficacy, several daily dosings, and poor patient compliance. Previously, we identified the calcium voltage-gated channel auxiliary subunit alpha2delta 1 gene (<i>Cacna2d1</i>) as a modulator of IOP and demonstrated that pregabalin, a drug with high affinity and selectivity for CACNA2D1, lowered IOP in a dose-dependent manner. Unfortunately, IOP returned to baseline at 6 h after dosing. In the current study, we develop a once daily topical pregabalin-loaded multiple water-in-oil-in-water microemulsion formulation to improve drug efficacy. We characterize our formulations using multiple <i>in vitro</i> and <i>in vivo</i> evaluations. Our lead formulation provides continuous release of pregabalin for up to 24 h. Because of its miniscule droplet size (<20 nm), our microemulsion has a transparent appearance and should not blur vision. It is also stable at one month of storage at temperatures ranging from 5 to 40 °C. Our formulation is nontoxic, as illustrated by a cell toxicity study and slit-lamp biomicroscopic exams. CACNA2D1 is highly expressed in both the ciliary body and the trabecular meshwork, where it functions to modulate IOP. A single drop of our lead pregabalin formulation reduces IOP by greater than 40%, which does not return to baseline until >30 h post-application. Although there were no significant differences in the amplitude of IOP reduction between the formulations we tested, a significant difference was clearly observed in their duration of action. Our multilayered microemulsion is a promising carrier that sustains the release and prolongs the duration of action of pregabalin, a proposed glaucoma therapeutic.
Fully-Automated Volumetric MRI with Normative Ranges: Translation to Clinical Practice (2009)

Neurodegenerative disorders, such as Alzheimer’s disease (AD), are associated with characteristic patterns of neuropathological spread in the brain. Disease progression is usually accompanied by regional atrophy that can be detected noninvasively using structural magnetic resonance imaging (MRI). A wealth of data has demonstrated the value of quantitative measurements of regional atrophy in AD, suggesting that volumetric MRI (vMRI) may be a useful clinical tool. vMRI provides biological evidence of neurodegenerative disease in patients with cognitive impairment. However, several hurdles impede implementation of vMRI in clinical practice. These include a lack of standardized MRI acquisition protocols, spatial distortions in MRI data, labor-intensive vMRI methods susceptible to interoperator variability, a lack of normative ranges for volume measures, and difficulty integrating vMRI in clinical workflow. Advances in vMRI have resulted from multi-institutional studies of brain imaging, such as the Alzheimer’s Disease Neuroimaging Initiative (ADNI), and help address these challenges. New, fully-automated measures of brain structure volumes coupled with large, multi-center studies using standardized MRI protocols now allow the development of age-adjusted normative ranges for vMRI. Such advances are critical for providing physicians a framework for assessing the pattern and degree of regional atrophy in a patient's brain and applying vMRI in clinical practice.
Techniques for Foundry Identification (2014)

Foundry identification is essential for many tasks including intellectual property protection, trust, and preventing counterfeiting. In this paper, we introduce statistical techniques for foundry detection, specifically for identifying from which foundry a particular chip originates from. The key idea is to consider the distributions of channel lengths and threshold voltages after employing a variant of SAT that extracts these two metrics. We apply Kolmogorov-Smirnov and other statistical tests for comparing the two empirical distributions. Finally, we study the effects of sample size and measurement error on the correct identification rate and establish an interval of confidence using resubstitution techniques.
High selectivity varactor-tuned MMIC bandpass filter using lossless active resonators (2002)

A novel MMIC varactor-tuned bandpass filter technique using lossless active resonators has been demonstrated. The resonator has a simple topology and uses only one FET, and yet can produce high values of negative resistance to compensate for losses in the filter. A monolithic three-resonator lumped-element/active filter design has been realised with a chip area of 3/spl times/2 mm/sup 2/. The filter has a 120 MHz 3 dB bandwidth centred on 2.3 GHz, has 0 dB insertion loss with only /spl plusmn/0.1 dB ripple in the pass-band, and gives up to 100 dB of stop-band attenuation at low frequencies, and over 50 dB of rejection up to 6 GHz.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Overexpression of Proteasome β5 Assembled Subunit Increases the Amount of Proteasome and Confers Ameliorated Response to Oxidative Stress and Higher Survival Rates (2005)

The proteasome is the major cellular proteolytic machinery responsible for the degradation of both normal and damaged proteins. Proteasomes play a fundamental role in retaining cellular homeostasis. Alterations of proteasome function have been recorded in various biological phenomena including aging. We have recently shown that the decrease in proteasome activity in senescent human fibroblasts relates to the down-regulation of beta-type subunits. In this study we have followed our preliminary observation by developing and further characterizing a number of different human cell lines overexpressing the beta5 subunit. Stable overexpression of the beta5 subunit in WI38/T and HL60 cells resulted in elevated levels of other beta-type subunits and increased levels of all three proteasome activities. Immunoprecipitation experiments have shown increased levels of assembled proteasomes in stable clones. Analysis by gel filtration has revealed that the recorded higher level of proteasome assembly is directly linked to the efficient integration of "free" (not integrated) alpha-type subunits identified to accumulate in vector-transfected cells. In support we have also found low proteasome maturation protein levels in beta5 transfectants, thus revealing an increased rate/level of proteasome assembly in these cells as opposed to vector-transfected cells. Functional studies have shown that beta5-overexpressing cell lines confer enhanced survival following treatment with various oxidants. Moreover, we demonstrate that this increased rate of survival is due to higher degradation rates following oxidative stress. Finally, because oxidation is considered to be a major factor that contributes to aging and senescence, we have overexpressed the beta5 subunit in primary IMR90 human fibroblasts and observed a delay of senescence by 4-5 population doublings. In summary, these data demonstrate the phenotypic effects following genetic up-regulation of the proteasome and provide insights toward a better understanding of proteasome regulation.
Boundaries, Near-Field Optics, and Near-Field Imaging (2003)

Chapter 2 deals with evanescent waves, which are the basis of diffraction-unlimited optical microscopes whose power of resolution is far shorter than a wavelength of light.
Functional Test Generation Based on Combined Random and Deterministic Search Methods (2007)

The aim of this paper is to explore some features of the functional test generation problem, and on the basis of the gained experience, to propose a practical method for functional test generation. In the paper presented analysis of random search methods and adjacent stimuli generation allowed formulating a practical method for generating functional tests. This method incorporates the analyzed termination conditions of generation, exploits the advantages of random and deterministic search, as well as the feature that the sets of the selected input stimuli can be merged easily in order to obtain a better set of test patterns.
Fast and efficient synthesis of <sup>14</sup>C labelled benzonitriles and their corresponding acids (2009)

Abstract 14 C‐Anthranilic acid has been prepared in a fast and efficient way in a two‐step reaction in 82% overall radiochemical yield. Thus, 2‐iodoaniline was transformed into 2‐amino‐[7‐ 14 C]‐benzonitrile using a palladium catalyzed cyanation with zinc 14 C‐cyanide. Subsequent basic hydrolysis of the cyano group afforded [7‐ 14 C]‐anthranilic acid. The method was successfully applied to a benzophenone scaffold, 4‐iodophenol and 4‐iodobenzoic acid producing the corresponding carboxylic acids in good to excellent radiochemical yields (62–82%) and with high specific activity (1.94–1.98 GBq/mmol). Copyright © 2009 John Wiley & Sons, Ltd.