gebhart/patrepeval huggingface dataset:
Characterization of Visible Dyes for Four-Decay Fluorescence Detection in DNA Sequencing (1997)

Dyes of several classes were investigated as candidates for use in a multiplex, four-decay fluorescence detection scheme for DNA sequencing. The dyes include nitrobenzofuran dyes, rhodamine dyes, fluorescein dyes, cyanine dyes, Nile Red, and BODIPY dyes. Based on the results of fluorescence spectral and lifetime studies, an initial set of four dyes was selected for further study: NBD-aminohexanoic acid (NBD-HA, r = 1.1 ns), tetramethyl-rhodamine, methyl ester (r = 2.2 ns), rhodamine green (r = 4.3 ns), and BODIPY 505/515 (r = 5.9 ns). Limits of lifetime detection of the four dyes were investigated, and lifetime resolution was demonstrated for mixtures of the free dyes in batch solution. Lifetime of dye-labeled DNA primers also were determined in batch solution and detected on-the-fly in capillary electrophoresis (CE). Conjugation of the dyes to DNA improved the resolution of their individual lifetimes in mixtures in batch measurements. When attached to the primer, tetramethyl-rhodamine exhibited biexponential decay with a dominant lifetime of 3.8 ns, making it unsuitable for four-decay sequencing. Contact with the CE gel lengthened the lifetime of NBD-HA-labeled primer from 1.3 to 2.1 ns but did not affect the lifetimes of the other dyes. Lifetime detectability of labeled primers at individual points along an electrophoretic peak in the attomole range.
Field-portable quantitative lensless microscopy based on translated speckle illumination and sub-sampled ptychographic phase retrieval (2019)

We report a compact, cost-effective, and field-portable lensless imaging platform for quantitative microscopy. In this platform, the object is placed on top of an image sensor chip without using a lens. We use a low-cost galvo scanner to rapidly scan an unknown laser speckle pattern on the object. To address the positioning repeatability and accuracy issues, we directly recover the positional shifts of the speckle pattern based on the phase correlation of the captured images. To bypass the resolution limit set by the imager pixel size, we employ a sub-sampled ptychographic phase retrieval process to recover the complex object. We validate our approach using a resolution target, phase target, and biological sample. Our results show that accurate, high-quality complex images can be obtained from a lensless dataset with as few as ∼10 images. We also demonstrate the reported approach to achieve a 6.4-mm by 4.6-mm field of view and a half-pitch resolution of 1 μm. The reported approach may provide a quantitative lensless imaging strategy for addressing point-of-care-, global-health-, and telemedicine-related challenges.
Near-Field Effects in Spatial Coherence of Thermal Sources (1999)

We present an exact calculation of the cross-spectral density tensor of the near field thermally emitted into free space by an opaque planar surface. The approach, based on fluctuational electrodynamics and the fluctuation-dissipation theorem, yields novel near-field correlation properties. We show that the spatial coherence length of the field close to the surface at a given wavelength $\ensuremath{\lambda}$ may be much smaller than the well-known $\ensuremath{\lambda}/2$ of blackbody radiation. We also show that a long-range correlation may exist, when resonant surface waves, such as surface-plasmon or surface-phonon polaritons, are excited. These results should have important consequences in the study of coherence in thermal emission and in the modeling of nanometer scale radiative transfer.
Adenoviral gene transfer of endothelial nitric-oxide synthase (eNOS) partially restores normal pulmonary arterial pressure in eNOS-deficient mice (2002)

It has been shown that mice deficient in the gene coding for endothelial nitric-oxide synthase (eNOS) have increased pulmonary arterial pressure and pulmonary vascular resistance. In the present study, the effect of transfer to the lung of an adenoviral vector encoding the eNOS gene (AdCMVeNOS) on pulmonary arterial pressure and pulmonary vascular resistance was investigated in eNOS-deficient mice. One day after intratracheal administration of AdCMVeNOS to eNOS(-/-) mice, there was an increase in eNOS protein, cGMP levels, and calcium-dependent conversion of l-arginine to l-citrulline in the lung. The increase in eNOS protein and activity in eNOS(-/-) mice was associated with a reduction in mean pulmonary arterial pressure and pulmonary vascular resistance when compared with values in eNOS-deficient mice treated with vehicle or a control adenoviral vector coding for beta-galactosidase, AdCMVbetagal. These data suggest that in vivo gene transfer of eNOS to the lung in eNOS(-/-) mice can increase eNOS staining, eNOS protein, calcium-dependent NOS activity, and cGMP levels and partially restore pulmonary arterial pressure and pulmonary vascular resistance to near levels measured in eNOS(+/+) mice. Thus, the major finding in this study is that in vivo gene transfer of eNOS to the lung in large part corrects a genetic deficiency resulting from eNOS deletion and may be a useful therapeutic intervention for the treatment of pulmonary hypertensive disorders in which eNOS activity is reduced.
Chronic, Intermittent Microdoses of the Psychedelic <i>N</i> , <i>N</i> -Dimethyltryptamine (DMT) Produce Positive Effects on Mood and Anxiety in Rodents (2019)

Drugs capable of ameliorating symptoms of depression and anxiety while also improving cognitive function and sociability are highly desirable. Anecdotal reports have suggested that serotonergic psychedelics administered in low doses on a chronic, intermittent schedule, so-called "microdosing", might produce beneficial effects on mood, anxiety, cognition, and social interaction. Here, we test this hypothesis by subjecting male and female Sprague Dawley rats to behavioral testing following the chronic, intermittent administration of low doses of the psychedelic <i>N</i>,<i>N</i>-dimethyltryptamine (DMT). The behavioral and cellular effects of this dosing regimen were distinct from those induced following a single high dose of the drug. We found that chronic, intermittent, low doses of DMT produced an antidepressant-like phenotype and enhanced fear extinction learning without impacting working memory or social interaction. Additionally, male rats treated with DMT on this schedule gained a significant amount of body weight during the course of the study. Taken together, our results suggest that psychedelic microdosing may alleviate symptoms of mood and anxiety disorders, though the potential hazards of this practice warrant further investigation.
Preparation and Characterization of Ranitidine-HC1 Crystals (1994)

Four crystalline and one noncrystalline form of RANITIDINE-HC1 were prepared and characterized by means of X-Ray powder diffraction, Thermal analysis (D.T.A. & T.G.A.), Polarising microscopy, Scanning electron microscopy, Infra red spectrophotometry and Ultra violet spectrophotometry. All the four crystalline forms were solvates or pseudopolymorphs. Stability determination of various forms under different conditions exhibited FORM II as most stable and all other forms convert to FORM II during storage. Humidity, Temperature and Compression force affected the polymorphic stability of various forms. Transition temperatures of different forms were determined using Equilibrium solubility method.
Network Dimensioning under Scheduled and Random Lightpath Demands in All-Optical WDM Networks (2007)

In WDM optical networks connection requests can be classified into three different types: Permanent Lightpath Demands (PLDs), Scheduled Lightpath Demands (SLDs), and Random Lightpath Demands (RLDs). These three types of traffic demands are considered for network planning, network engineering and traffic engineering respectively. In this paper we investigate the Routing and Wavelength Assignment (RWA) problem in all-optical WDM networks operating under the wavelength continuity constraint by jointly considering PLDs, SLDs and RLDs. We aim to model a realistic situation where an operator wishes to employ its optical network initially designed for PLDs and/or SLDs to offer on the fly lightpath provisioning. To the best of our knowledge, our global approach has not already been investigated in the literature. According to the considered timescale, various types of optimization tools are used. Numerous numerical results are presented and discussed to outline the benefits of such a global perspective.
Aeration Pathways in Soybean Root Nodules (1973)

Soybean root nodule tissues contain many interconnected gas-filled intercellular spaces. They have been studied, in fresh and embedded tissue during the development and functional life of the nodules, by light and electron microscopy.
Sleep in patients with disorders of consciousness characterized by means of machine learning (2018)

Sleep has been proposed to indicate preserved residual brain functioning in patients suffering from disorders of consciousness (DOC) after awakening from coma. However, a reliable characterization of sleep patterns in this clinical population continues to be challenging given severely altered brain oscillations, frequent and extended artifacts in clinical recordings and the absence of established staging criteria. In the present study, we try to address these issues and investigate the usefulness of a multivariate machine learning technique based on permutation entropy, a complexity measure. Specifically, we used long-term polysomnography (PSG), along with video recordings in day and night periods in a sample of 23 DOC; 12 patients were diagnosed as Unresponsive Wakefulness Syndrome (UWS) and 11 were diagnosed as Minimally Conscious State (MCS). Eight hour PSG recordings of healthy sleepers (N = 26) were additionally used for training and setting parameters of supervised and unsupervised model, respectively. In DOC, the supervised classification (wake, N1, N2, N3 or REM) was validated using simultaneous videos which identified periods with prolonged eye opening or eye closure.The supervised classification revealed that out of the 23 subjects, 11 patients (5 MCS and 6 UWS) yielded highly accurate classification with an average F1-score of 0.87 representing high overlap between the classifier predicting sleep (i.e. one of the 4 sleep stages) and closed eyes. Furthermore, the unsupervised approach revealed a more complex pattern of sleep-wake stages during the night period in the MCS group, as evidenced by the presence of several distinct clusters. In contrast, in UWS patients no such clustering was found. Altogether, we present a novel data-driven method, based on machine learning that can be used to gain new and unambiguous insights into sleep organization and residual brain functioning of patients with DOC.
Classification of voiceband data signals (1990)

The viability of a voiceband signal classification technique which can service as a front-end for digital signal interpolation is demonstrated. The technique uses second-order statistical parameters of the complex envelope of the input signal. The input signal is assumed to be in mu -law PCM (pulse code modulation) form. For observation windows of at least 128 ms, it is shown that this method correctly classifies the input baud (e.g. 2400, 1600, 1200, 600 and 300 symbols/s) and modulation type (e.g. QAM, PSK, and FSK). This information allows the determination of the bit rate of most voiceband data signals. Coupled with a digital signal interpolator and variable rate coding, an increased compression ratio on long-haul digital trunks can be achieved.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Geodesy by radio interferometry: The application of Kalman Filtering to the analysis of very long baseline interferometry data (1990)

We discuss the application of Kalman filtering techniques to the analysis of very long baseline interferometry (VLBI) data. The VLBI observables are geometrically related to the geodetic and astrometric parameters which can be determined from them. However, contributions to the observables from the clocks at, and the atmospheres above, the VLBI sites must be accounted for if reliable estimates of geodetic and astrometric parameters are to be obtained. Here an implementation of a Kaiman filter to account for stochastic behavior on those parameters which vary during the course of a VLBI experiment is discussed. Both the nature of the stochastic processes which should be used in the model for the VLBI data and the implementation of the Kaiman filter estimator are considered. From the results obtained, we conclude that the Kaiman filter is appropriate for analyzing VLBI data. The choice of stochastic model does not unduly affect the estimates of the geodetic parameters and the quality of these estimates is higher than that for conventional weighted least squares estimators.
Conformational Equilibrium in Alanine-Rich Peptides Probed by Reversible Stretching Simulations (2006)

Reversible stretching of the alanine-rich peptide 3K (Proc. Natl. Acad. Sci. USA 1989, 86, 5286-5290) and its analogue MW (Nature 1992, 359, 653-655) is examined using molecular dynamics simulations in explicit water. In both cases, sampling of the extension pathway is obtained on the 10 ns time scale by applying an adaptive biasing force. The free energy profile reveals a single minimum associated with a contiguous alpha-helix. Short 3(10)-helical motifs are observed in folded as well as extended conformations, in accordance with their proposed role as folding intermediates. The native 3(10)-helical content of both peptides is found, however, to be no higher than a few percent. Difficulties in both the definition and the detection of secondary structure motifs, most notably in relation to bifurcated hydrogen bonds, are proposed to account for the discrepancy between 3(10)-helical propensities reported by several authors, based on experimental and computational results.
Transcriptional Regulatory Elements Within the First Intron of Bruton's Tyrosine Kinase (1998)

Defects in the gene for Bruton's tyrosine kinase (Btk) result in the disorder X-linked agammaglobulinemia (XLA). Whereas XLA is characterized by a profound defect in B-cell development, Btk is expressed in both the B lymphocyte and myeloid cell lineages. We evaluated a patient with XLA who had reduced amounts of Btk transcript but no abnormalities in his coding sequence. A single base-pair substitution in the first intron of Btk was identified in this patient, suggesting that this region may contain regulatory elements. Using reporter constructs we identified two transcriptional control elements in the first 500 bp of intron 1. A strong positive regulator, active in both pre-B cells and B cells, was identified within the first 43 bp of the intron. Gel-shift assays identified two Sp1 binding sites within this element. The patient's mutation results in an altered binding specificity of the proximal Sp1 binding site. A negative regulator, active in pre-B cells only, was located between base pairs 281 and 491 of the intron. These findings indicate that regulation of Btk transcription is complex and may involve several transcriptional regulatory factors at the different stages of B-cell differentiation.
Structure of V<sub>2</sub>O<sub>5</sub>·<i>n</i>H<sub>2</sub>O Xerogel Solved by the Atomic Pair Distribution Function Technique (2002)

A long-standing issue regarding the local and long-range structure of V(2)O(5)*nH(2)O xerogel has been successfully addressed. The full three-dimensional structure of the lamellar turbostratic V(2)O(5)*nH(2)O xerogel was determined by the atomic pair distribution function technique. We show that on the atomic scale the slabs of the xerogel can be described well as almost perfect pairs (i.e., bilayers) of single V(2)O(5) layers made of square pyramidal VO(5) units. These slabs are separated by water molecules and stack along the z-axis of a monoclinic unit cell (space group C2/m) with parameters a = 11.722(3) A, b = 3.570(3) A, c = 11.520(3) A, and beta = 88.65 degrees. The stacking sequence shows signatures of turbostratic disorder and a structural coherence limited to 50 A.
150 Mbit/s Cmos Led-driver And Pin-receiver Ic For Optical Communication. (1992)

An integrated full CMOS driver has tieen realized with a modulation current of 60 mA at a maximum bit rate of 150 Mbit/s. A CMOS receiver has been developed which can amplify PIN modulation currents less than 10 pA at the same bit rate of 150 Mbit/s. Both circuits are integrated on one chip, showing the possibility of integrating a ratio between detecting and driving currents of almost four orders of magnitude in CMOS technology. The circuit has been developed in a 0.8 pm digital CMOS process.
Central nervous system mechanisms of pain in fibromyalgia and other musculoskeletal disorders: behavioral and psychologic treatment approaches (2002)

Pain is one of the most important and challenging consequences of musculoskeletal disorders. This article examines the role of central nervous system structures in the physiology of pain. It also describes the neuromatrix, a construct that provides a framework for understanding the interaction between physiologic mechanisms and psychosocial factors in the development and maintenance of chronic pain. This construct suggests that behavioral and psychologic interventions may alter the pain experience primarily through their effects on emotional states and cognitive processes. The literature on cognitive-behavioral interventions for patients with rheumatoid arthritis and osteoarthritis indicates that they are well-established treatments for these disorders. However, the efficacy of these interventions for patients with fibromyalgia has not been established. It is anticipated that the development of valid measures of readiness for behavioral change may allow investigators to identify the patients with musculoskeletal disorders who are most likely to benefit from cognitive-behavioral intervention.
FP-map-an approach to the functional pipelining of embedded programs (2002)

Practice shows that increasing the amount of instruction level parallelism offered by an architecture (like adding instruction slots to VLIW instructions) does not necessarily lead to significant performance gains. Instead, high hardware costs and inefficient use of this hardware may occur. Mapping embedded applications onto multiprocessor systems forms a very interesting extension to ILP. We propose a functional pipelining approach to the mapping of embedded programs written in ANSI C onto a pipeline of application specific processors. Our novel functional pipelining algorithm has low computational complexity and was especially developed to form the parallelization engine of a (semi) automatic system for multiprocessor embedded system design. The paper explains the proposed algorithm and demonstrates its applicability.
[The diagnosis and treatment of nipple discharge in 253 cases]. (1998)

Among 253 cases of nipple discharge, 96 cases of them were diagnosed as intracanalicular papilloma(37.9%), 73 cases as cystic disease of breast(28.9%), 41 cases as mammary duct ectasia (16.2%), 35 cases as breast cancer(13.8%) and 8 cases as acute suppurative mastitis(3.2%). The masses beneath areolar region were smaller those outside areola. Finding of cancer cells or suspicious cancer cells through cytologic examination of nipple discharge smear and breast mass puncture usually had important significance. In addition, near infrared ray scanning shows high rate of correct diagnosis; estimation of carcinoembryonic autigen(CEA) in nipple discharge is beneficial to the early diagnosis of malignant diseases.
Transition noise spectral measurements in thin film media (1994)

Noise in thin film media is concentrated at the transition center and must be characterized by a nonstationary autocorrelation function. The noise voltage spectrum is determined by the frequency response of this correlation function beyond the standard head field terms. In this work, the use of spectral measurement to determine the nonstationary noise is illustrated. Noise spectra of thin film media are experimentally studied in detail for various thin film disks using both inductive and MR heads. The results compare extremely well to the analytical expression of the spectrum derived utilizing a good approximation for the correlation function of the magnetization fluctuations. Both transition length and medium noise cross-track correlation width were determined from the measured spectra. The measured transition lengths agree with signal analysis, and the noise cross-track correlation widths range from 15 to 71 nm. Lowering the flying height reduces the transition widths, and the cross-track correlation width remains unchanged.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Ectopic Bone Induction in Recombinant Human Bone Morphogenetic Protein-2(rhBMP-2) Combined with Biphasic Calcium Phosphate(BCP). (1996)

The purpose of this study was to investigate the efficacy of BCP granules combined with rhBMP-2 for ectopic bone formation in rats. BCP granules were used as a carrier for rhBMP-2. The rhBMP-2 was adsorbed to BCP granules under the reduction of pressure. Twenty Wistar rats were used for this experiment and were divided into 4 groups according to the concentration (0,2,10,50 micrograms/700 microliters) of rhBMP-2 implanted in each rat. The BMP and BCP complex was implanted under the dorsal skin of the rats. Three weeks after the implantation, the rats were sacrificed. The experimental sites were immediately dissected and histological sections were prepared. In the 50 micrograms group, new bone formation was observed in all rats, while bone tissue was not found in the 2 micrograms and 0 microgram groups. These results indicated that BCP combined with rhBMP-2 could effectively induce ectopic bone formation. It was suggested that BCP granules alone could be applicable as a carrier for rhBMP-2 in order to induce new bone formation.
The Effect of 5-Aminolevulinic Acid on Cytochrome P450-Mediated Prodrug Activation (2015)

Of late, numerous prodrugs are widely used for therapy. The hemeprotein cytochrome P450 (CYP) catalyzes the activation of prodrugs to form active metabolites. Therefore, the activation of CYP function might allow the use of lower doses of prodrugs and decrease toxicity. We hypothesized that the addition of 5-aminolevulinic acid (ALA), a precursor in the porphyrin biosynthetic pathway, enhances the synthesis of heme, leading to the up-regulation of CYP activity. To test this hypothesis, we treated a human gastric cancer cell line with ALA and determined the effect on CYP-dependent prodrug activation. For this purpose, we focused on the anticancer prodrug tegafur, which is converted to its active metabolite 5-fluorouracil (5-FU) mainly by CYP2A6. We show here that ALA increased CYP2A6-dependent tegafur activation, suggesting that ALA elevated CYP activity and potentiated the activation of the prodrug.