gebhart/patrepeval huggingface dataset:
Bayesian $k$-Space–Time Reconstruction of MR Spectroscopic Imaging for Enhanced Resolution (2010)

A k-space-time Bayesian statistical reconstruction method (K-Bayes) is proposed for the reconstruction of metabolite images of the brain from proton (1H) magnetic resonance (MR) spectroscopic imaging (MRSI) data. K-Bayes performs full spectral fitting of the data while incorporating structural (anatomical) spatial information through the prior distribution. K-Bayes provides increased spatial resolution over conventional discrete Fourier transform (DFT) based methods by incorporating structural information from higher resolution coregistered and segmented structural MR images. The structural information is incorporated via a Markov random field (MRF) model that allows for differential levels of expected smoothness in metabolite levels within homogeneous tissue regions and across tissue boundaries. By further combining the structural prior model with a k -space-time MRSI signal and noise model (for a specific set of metabolites and based on knowledge from prior spectral simulations of metabolite signals), the impact of artifacts generated by low-resolution sampling is also reduced. The posterior-mode estimates are used to define the metabolite map reconstructions, obtained via a generalized expectation-maximization algorithm. K-Bayes was tested using simulated and real MRSI datasets consisting of sets of k-space-time-series (the recorded free induction decays). The results demonstrated that K-Bayes provided qualitative and quantitative improvement over DFT methods.
The Pharmacokinetics of Omeprazole in Humans—A Study of Single Intravenous and Oral Doses (1990)

The pharmacokinetics of omeprazole, hydroxyomeprazole, omeprazolesulfone, and "remaining metabolites" have been studied in eight young healthy subjects following an acute i.v. and oral dose of 10 and 20 mg of 14C-labeled drug, respectively. The oral dose was given as a buffered solution. Two subjects exhibited essentially higher and more sustained plasma levels of omeprazole than the others. This was due to a higher bioavailability, lower clearance, and longer t1/2 of omeprazole in these two subjects. Maximum concentration (0.7-4.6 mumol/L) was reached between 10 and 25 min after oral dosing. The median bioavailability was 39% (25-117%) and the median systemic plasma clearance was 624 ml/min (range of 59-828 ml/min). The corresponding t1/2 for the i.v. dose was 35 min (16-150 min) and 39 min (14-186 min) after oral administration. The drug was rapidly distributed to extravascular sites (mean t1/2 lambda 1 = 3.0 +/- 0.8 min). Mean Vss was 0.23 +/- 0.04 L/kg. Low systemic clearance of omeprazole was associated with a decreased formation rate of hydroxyomepraxole and "remaining metabolites" while omeprazolesulfone formation seemed to be less affected. However, there was a clear-cut correlation between the t1/2 of omeprazole and of its omeprazolesulfone metabolite, indicating that the elimination of these two compounds is mediated by the same isoenzyme. The mean urinary recovery of the radioactive dose during 96 h was 78.3 +/- 2.3 and 75.7 +/- 2.6% for the i.v. and oral dose, respectively. Insignificant amounts were due to unchanged drug and omeprazolesulfone. The excretion of hydroxyomeprazole during the first 12 h varied between 4.6 to 15.5% of a given dose. The mean recovery of radioactivity in the feces was 19.3 +/- 3.1% of a given i.v. dose and 18.2 +/- 2.3% when given orally. It is concluded that omeprazole is mainly eliminated metabolically and that there is a substantial interindividual variation in the rate of formation of primary and secondary metabolites. This variation in omeprazole disposition is probably of limited clinical importance. The half-life, with a maximum of approximately 3 h, is too short to cause accumulation when the drug is administered in a once-daily regimen.
Ultrasound Images of the Tongue: A Tutorial for Assessment and Remediation of Speech Sound Errors (2017)

Diagnostic ultrasound imaging has been a common tool in medical practice for several decades. It provides a safe and effective method for imaging structures internal to the body. There has been a recent increase in the use of ultrasound technology to visualize the shape and movements of the tongue during speech, both in typical speakers and in clinical populations. Ultrasound imaging of speech has greatly expanded our understanding of how sounds articulated with the tongue (lingual sounds) are produced. Such information can be particularly valuable for speech-language pathologists. Among other advantages, ultrasound images can be used during speech therapy to provide (1) illustrative models of typical (i.e. "correct") tongue configurations for speech sounds, and (2) a source of insight into the articulatory nature of deviant productions. The images can also be used as an additional source of feedback for clinical populations learning to distinguish their better productions from their incorrect productions, en route to establishing more effective articulatory habits. Ultrasound feedback is increasingly used by scientists and clinicians as both the expertise of the users increases and as the expense of the equipment declines. In this tutorial, procedures are presented for collecting ultrasound images of the tongue in a clinical context. We illustrate these procedures in an extended example featuring one common error sound, American English /r/. Images of correct and distorted /r/ are used to demonstrate (1) how to interpret ultrasound images, (2) how to assess tongue shape during production of speech sounds, (3), how to categorize tongue shape errors, and (4), how to provide visual feedback to elicit a more appropriate and functional tongue shape. We present a sample protocol for using real-time ultrasound images of the tongue for visual feedback to remediate speech sound errors. Additionally, example data are shown to illustrate outcomes with the procedure.
An XOR-based erasure-resilient coding scheme (1995)

The influence of the lack of the gravity force on contractile properties of the slow-twitch soleus (SOL) and the fast-twitch extensor digitorum longus (EDL) muscles was investigated in 3 week or 6-month-old rats suspended by their tail. In both groups suspension hypokinesia (SH) lasting 3 weeks or longer leads to a marked decrease of the mass and of the mean cross-sectional area of the SOL. The SOL of suspended animals shows decreased contraction and half-relaxation times and a lower tension of the single twitch, a decreased maximum tetanic force output, an increased fusion frequency and a decreased tetanus-half-rise time. The force developed per unit cross-sectional area and the twitch-tetanus ratio are unchanged. The atrophy and the changes in contractile properties are more pronounced in young developing rats than in adult ones. The SOL of suspended young rats does not develop into a slow-twitch muscle and shows a posttetanic potentiation and a cooling potentiation of the single twitch, properties observed in fast-twitch muscles only. In comparison to controls SH has no influence on the wet weight, mean cross-sectional area, and contractile properties of the EDL of young or adult rats. The data presented here and supported by histochemical and biochemical results demonstrates the importance of the gravity force for slow-twitch muscles especially during development.
Perspectives of γδ T Cells in Tumor Immunology (2007)

Subsets of human gammadelta T cells recognize tumor cell-expressed ligands that are not seen by the T-cell receptor of conventional alphabeta T cells. Vdelta1 T cells recognize MHC class I chain-related molecules A and B and UL-16-binding proteins expressed at variable levels on epithelial tumor cells and some leukemias and lymphomas. In addition, therapeutically used aminobisphosphonates and synthetic phosphoantigens activate Vdelta2 T cells, the dominant subset of gammadelta T cells in human peripheral blood that display strong cytotoxicity towards various epithelial tumors. Intentional activation of gammadelta T cells in vivo and/or adoptive cell therapy with in vitro expanded gammadelta T cells holds considerable promise as a novel immunotherapy in certain types of cancer.
Design, Preparation, and Applications of Fiber-Optic Chemical Sensors for Continuous Monitoring (1989)

Fiber optic sensors now exist to measure a variety of analytes. When used for in situ and in vivo applications, the sensor reagents must be attached directly to the optical fiber tip. This paper describes technology for covalently attaching indicator reagents to the fiber sensing tip. The method serves to increase the fiber surface area and results in an amplified signal. The individual processing steps of the technique are described, as are the preparation of sensors measuring pH, CO2, and penicillin. New indicator systems based on energy transfer are also described. A physiological pH sensor based on energy transfer from a pH insensitive fluorophore to a pH sensitive absorber was prepared successfully. Finally, a sensor based on irreversible reagents are described. This sensor utilizes a polymeric release system to deliver fresh reagent over a long period of time.
Ubiquitin-dependent Destruction of Topoisomerase I Is Stimulated by the Antitumor Drug Camptothecin (1997)

Topoisomerase I (TOP1) relaxes superhelical DNA through a breakage/rejoining reaction in which the active site tyrosine links covalently to a 3' phosphate at the break site as a transient intermediate. The antitumor drug camptothecin (CPT) and its analogs inhibit the rejoining step of the breakage/rejoining reaction, which traps the enzyme in covalent linkage with DNA (the cleavable complex). Little is known about the fate of cellular TOP1 trapped in the cleavable complex. We have analyzed TOP1 in mammalian cell lines treated with CPT. When CPT-treated cells were lysed with either SDS or alkali and analyzed by Western blotting, greater than 90% of the TOP1 was linked to DNA. Nuclease treatment of the cell lysate to remove the covalently linked DNA from TOP1 revealed a distinct ladder of higher molecular weight bands having properties indicative of multi-ubiquitin (Ub) conjugates of TOP1. Approximately 5-10% of TOP1 was present as these conjugates within minutes of CPT treatment. Consistent with ubiquitination, TOP1 was not modified in ts85 cells at the restrictive temperature for its thermolabile ubiquitin-activating enzyme (E1). Because conjugation with ubiquitin can mark proteins for destruction by the 26S proteasome, we analyzed TOP1 protein levels during prolonged CPT treatment. TOP1 protein levels were reduced to about 25% during CPT treatments of 2-4 h resulting from increased destruction, with the half-life dropping from 10-16 h down to 1-2 h. The destruction of TOP1, like the formation of Ub-TOP1 conjugates, was not observed in ts85 cells at the restrictive temperature. The destruction of TOP1 was also prevented in cells treated with MG-132 and lactacystin, specific inhibitors of the 26S proteasome. Finally, the multi-Ub conjugates of TOP1 were observed whether or not aphidicolin was included in cotreatment with CPT, indicating that replication fork activity was not involved in making TOP1 a substrate for ubiquitination. These results demonstrate that independent of DNA replication, the TOP1 cleavable complex is ubiquitinated and destroyed in cells treated with antitumor drugs that block the religation step of the TOP1 reaction.
Experiments with lithium limiter on T-11M tokamak and applications of the lithium capillary-pore system in future fusion reactor devices (2006)

The paper is an overview of recent results of Li limiter testing in T-11M tokamak. The lithium limiter is based on the capillary-pore system (CPS) concept. The Li erosion process and deuterium (D 2 ) and helium (He) sorption by Li first wall were investigated. The ability of capillary forces to confine the liquid Li in the CPS limiter during disruption was demonstrated. The idea of combined lithium limiter with thin (0.6 mm) CPS coating as a solution of the heat removal problem was realized. As a result the quasi steady-state tokamak regime with duration up to 0.3 s and clean ( Z eff = 1) deuterium plasma has been achieved. The temporal evolution of the lithium surface temperature during discharge was measured by a IR radiometer and then was recalculated to the surface power load. For the estimation of the Li limiter erosion the Li neutral and ions spectral line emission were observed. The increase in lithium erosion as a result of limiter heating was discovered. The radial distribution of plasma column radiation measurements showed up to 90% of the total radiation losses in a relatively thin (5 cm) boundary layer and only 10% in a plasma centre during discharges with high Li influx. Oscillations of Li emission and saw-tooth-like oscillations of the limiter surface temperature have been detected in discharge regimes with highest Li limiter temperature (&gt;600 °C). A version of Li CPS first wall of DEMO reactor and Li CPS limiter experiment in the International Thermonuclear Energy Reactor are suggested.
Molecular Characterization of Preintegration Latency in Human Immunodeficiency Virus Type 1 Infection (2002)

Most current evidence suggests that the infection of resting CD4(+) T cells by human immunodeficiency virus type 1 (HIV-1) is not productive due to partial or complete blocks in the viral life cycle at steps prior to integration of the viral genome into the host cell chromosome. However, stimulation of an infected resting T cell by antigen, cytokines, or microenvironmental factors can overcome these blocks and allow for the production of progeny virions. In this study, we sought to understand the structure and fate of the virus in unstimulated resting CD4(+) T cells. Using a novel linker-mediated PCR assay designed to detect and characterize linear unintegrated forms of the HIV-1 genome, we demonstrate that reverse transcription can proceed to completion following the infection of resting T cells, generating the substrate for the retroviral integration reaction. However, reverse transcription in resting T cells is far slower than in activated T cells, requiring 2 to 3 days to complete. The delay in completing reverse transcription may make the viral DNA genome more susceptible to competing decay processes. To explore the relationship between the formation of the linear viral genome and the stability of the preintegration state, we employed a recombinant HIV-1 virus expressing the enhanced green fluorescent protein to measure the rate at which HIV-1 decays in the preintegration state. Our results demonstrate that the preintegration state is labile and decays rapidly (half-life = 1 day) following the entry of HIV-1 into a resting T cell, with significant decay occurring during the slow process of reverse transcription.
State of Stress and Critical Thickness of Strained Small-Area SiGe Layers (1999)

We present an approach in equilibrium theory for strain relief in small-area heteroepitaxial SiGe/Si structures, which includes surface and film-edge induced relaxation effects. With a view to computer simulation, the state of stress and shear components on the slip planes of strained mesa-like SiGe/Si systems are treated here in a simple analytical form in terms of strain and stress components, valid in linear elasticity. The two-dimensional analysis yields a complete description of the state of plane stress of small-area structural elements in a consistent manner. The present system of equations is generally sufficient to quantitatively determine the lowered stress components of stable, metastable, and plastically deformed finite strained layers. It is shown that there is a significant decrease in heteroepitaxial film stress as a function of material and size characteristics of the SiGe/Si system that allows one to increase substantially the critical layer thickness for loss of coherency for a given Ge content. The equilibrium theory proposed here provides guidance for computer simulation to configure stable small-area SiGe deposits for the development of technologies in which stress problems must be alleviated. A complete input deck for stress simulation including a run is given. The developed physics and computer simulation can be used for the design of small-geometry heterojunction bipolar transistors and SiGe channel MOSFETs, and for estimation of stress-related problems in sub-micron size devices.
The growing reality of virtual reality (1995)

Journal Article The growing reality of virtual reality: A darling of the entertainment world breaks into science research and public education Get access Jane Ellen Stevens Jane Ellen Stevens Search for other works by this author on: Oxford Academic Google Scholar BioScience, Volume 45, Issue 7, July/August 1995, Pages 435–439, https://doi.org/10.2307/1312785 Published: 01 August 1995
AIDS-associated anorexia. (1995)

The pathogenesis of AIDS-associated anorexia involves any one or a combination of several factors, including malnutrition and nutrient abnormalities, gastrointestinal dysfunction, metabolic dysfunctions, neuropsychiatric disturbances, economic and sociocultural factors, and anorexigenic medications. Appropriate management of anorexia is multidisciplinary, involving pharmacologic assessment, neuropsychiatric evaluation, and appetite stimulants. Two pharmacologic agents, the cannabinoid dronabinol (Marinol) and the synthetic progesterone megestrol acetate (Megace), are approved by the FDA for use as appetite stimulants. Corticosteroid replacement is approved to reverse anorexia and weight loss associated with adrenal insufficiency. The use of androgen replacement or growth hormone in the treatment of anorexia and weight loss is currently investigational but shows promise. Dronabinol has been studied in a double-blind appetite stimulation study run in 18 centers. The six-week study focused on appetite stimulation and weight gain as end points in patients with AIDS-related weight loss. Results are summarized, and considerations that must be addressed by the administering clinician are presented.
Interleukin-1β, Interleukin-5, Interleukin-6, Interleukin-8, and Tumor Necrosis Factor-α in Chronic Sinusitis: Response to Systemic Corticosteroids (2000)

Recently, the role of various cytokines in the pathogenesis of chronic rhinosinusitis has come under investigation. Various studies have reported increased levels of interleukin-3, interleukin-4, interleukin-5, interleukin-13, and granulocyte macrophage-colony stimulating factor in the sinonasal mucosa of patients with chronic rhinosinusitis. The present study investigated the levels of pro-inflammatory cytokines, including interleukin-1 beta (IL-1 beta), interleukin-5 (IL-5), interleukin-6 (IL-6) interleukin-8 (IL-8), and tumor necrosis factor-alpha (TNF-alpha), in the sinonasal mucosa of patients with chronic rhinosinusitis, and evaluated the response of these cytokines to oral corticosteroids. Chronic rhinosinusitis subjects (n = 15) and control subjects (n = 9) underwent nasal endoscopy and biopsy of the sinonasal mucosa. Chronic rhinosinusitis subjects were subsequently treated with a 10-day tapering dose of prednisone followed by a second sinonasal endoscopic exam and biopsy. Mucosal biopsy specimens were immunostained for IL-1 beta, IL-5, IL-6, IL-8, and TNF-a. In chronic rhinosinusitis subjects, mucosal levels of IL-1 beta, IL-6, IL-8, and TNF-alpha were significantly elevated when compared with control subjects, and levels of IL-5 demonstrated a strong trend toward elevation. In posttreatment chronic rhinosinusitis subjects, levels of IL-6 were significantly decreased when compared with pretreatment levels, and TNF-alpha levels demonstrated a significant trend toward reduction. These findings support the hypothesis that the inflammatory response in chronic rhinosinusitis is associated with elevated levels of pro-inflammatory cytokines, and suggest that oral corticosteroids may exert a beneficial effect by significantly reducing the levels of IL-6 and TNF-alpha.
Glycoengineering of Therapeutic Glycoproteins:  In Vitro Galactosylation and Sialylation of Glycoproteins with Terminal N-Acetylglucosamine and Galactose Residues (2001)

Therapeutic glycoproteins produced in different host cells by recombinant DNA technology often contain terminal GlcNAc and Gal residues. Such glycoproteins clear rapidly from the serum as a consequence of binding to the mannose receptor and/or the asialoglycoprotein receptor in the liver. To increase the serum half-life of these glycoproteins, we carried out in vitro glycosylation experiments using TNFR-IgG, an immunoadhesin molecule, as a model therapeutic glycoprotein. TNFR-IgG is a disulfide-linked dimer of a polypeptide composed of the extracellular portion of the human type 1 (p55) tumor necrosis factor receptor (TNFR) fused to the hinge and Fc regions of the human IgG(1) heavy chain. This bivalent antibody-like molecule contains four N-glycosylation sites per polypeptide, three in the receptor portion and one in the Fc. The heterogeneous N-linked oligosaccharides of TNFR-IgG contain sialic acid (Sia), Gal, and GlcNAc as terminal sugar residues. To increase the level of terminal sialylation, we regalactosylated and/or resialylated TNFR-IgG using beta-1,4-galactosyltransferase (beta1,4GT) and/or alpha-2,3-sialyltransferase (alpha2,3ST). Treatment of TNFR-IgG with beta1,4GT and UDP-Gal, in the presence of MnCl(2), followed by MALDI-TOF-MS analysis of PNGase F-released N-glycans showed that the number of oligosaccharides with terminal GlcNAc residues was significantly decreased with a concomitant increase in the number of terminal Gal residues. Similar treatment of TNFR-IgG with alpha2,3ST and CMP-sialic acid (CMP-Sia), in the presence of MnCl(2), produced a molecule with an approximately 11% increase in the level of terminal sialylation but still contained oligosaccharides with terminal GlcNAc residues. When TNFR-IgG was treated with a combination of beta1,4GT and alpha2,3ST (either in a single step or in a stepwise fashion), the level of terminal sialylation was increased by approximately 20-23%. These results suggest that in vitro galactosylation and sialylation of therapeutic glycoproteins with terminal GlcNAc and Gal residues can be achieved in a single step, and the results are similar to those for the stepwise reaction. This type of in vitro glycosylation is applicable to other glycoproteins containing terminal GlcNAc and Gal residues and could prove to be useful in increasing the serum half-life of therapeutic glycoproteins.
Evaluation of [−2] proPSA and Prostate Health Index (phi) for the detection of prostate cancer: a systematic review and meta-analysis (2012)

The usefulness of %[-2] proPSA and Prostate Health Index (phi) in the detection of prostate cancer are currently unknown. It has been suggested that these tests can distinguish prostate cancer from benign prostatic diseases better than PSA or %fPSA. We performed a systematic review and meta-analysis of the available scientific evidence to evaluate the clinical usefulness of %[-2] proPSA and phi. Relevant published papers were identified by searching computerized bibliographic systems. Data on sensitivity and specificity were extracted from 12 studies: 10 studies about %[-2] proPSA (3928 patients in total, including 1762 with confirmed prostate cancer) and eight studies about phi (2919 patients in total, including 1515 with confirmed prostate cancer). The sensitivity for the detection of prostate cancer was 90% for %[-2] proPSA and phi, while the pooled specificity was 32.5% (95% CI 30.6-34.5) and 31.6% (95% CI 29.2-34.0) for %[-2] proPSA and phi, respectively. The measurement of %[-2] proPSA improves the accuracy of prostate cancer detection in comparison with PSA or %fPSA, particularly in the group of patients with PSA between 2 μg/L and 10 μg/L. Similar results were obtained measuring phi. Using these tests, it is possible to reduce the number of unnecessary biopsies, maintaining a high cancer detection rate. Published results also showed that %[-2] proPSA and phi are related to the aggressiveness of the tumor.