gebhart/patrepeval huggingface dataset:
Differential expression and prognostic significance of SOX genes in pediatric medulloblastoma and ependymoma identified by microarray analysis (2008)

The objective of this study was to identify differentially expressed and prognostically important genes in pediatric medulloblastoma and pediatric ependymoma by Affymetrix microarray analysis. Among the most discriminative genes, three members of the SOX transcription factor family were differentially expressed. Both SOX4 and SOX11 were significantly overexpressed in medulloblastoma (median, 11-fold and 5-fold, respectively) compared with ependymoma and normal cerebellum. SOX9 had greater expression in ependymoma (median, 16-fold) compared with normal cerebellum and medulloblastoma (p<0.001 for all comparisons). The differential expression of the SOX genes was confirmed at the protein level by immunohistochemical analysis. Survival analysis of the most discriminative probe sets for each subgroup showed that 35 and 13 probe sets were predictive of survival in patients with medulloblastoma and ependymoma, respectively. There was a trend toward better survival with increasing SOX4 expression in medulloblastoma. SOX9 expression was predictive for favorable outcome in ependymoma. The mRNA levels of BCAT1, a mediator of amino acid breakdown, were higher (median, 15-fold) in medulloblastoma patients with metastases compared with those without metastasized disease (p<0.01). However, the correlation between BCAT1 expression and metastatic medulloblastoma could not be confirmed at the protein level. The potential prognostic effect of the genes associated with outcome should be evaluated in ongoing studies using larger groups of patients. Furthermore, our findings support further analysis of the functional properties of the selected genes, especially SOX4 and BCAT1 for medulloblastoma and SOX9 for ependymoma, to evaluate the use of these genes as potential tumor markers, prognostic markers, and drug targets in pediatric brain tumors.
Tolerance and incorporation of a high‐dose eicosapentaenoic acid diester emulsion by patients with pancreatic cancer cachexia (2001)

Chemotherapy and radiotherapy offer little benefit to patients with advanced pancreatic cancer. Eicosapentaenoic acid (EPA) has anticancer effects both in vitro and in animal models. The dose of EPA that can be administered to cancer patients has previously been limited by the low purity of available preparations and the tolerability of large capsules. A high-purity preparation of EPA as a 20% oil-in-water diester emulsion allowed a small study of the tolerance, incorporation, and effects of EPA in high doses in five patients with advanced pancreatic cancer. Patients underwent assessment at baseline and every 4 wk thereafter. All patients managed to tolerate a dose providing 18 g EPA per day, with doses between 9 and 27 g daily being taken for at least a month. Dosage was limited by a sensation of fullness, cramping abdominal pain, steatorrhea, and nausea. All such symptoms were controlled by dose reduction or pancreatic enzyme supplements. No other adverse effects attributable to the trial agent were observed. Plasma phospholipid EPA content increased from around 1% at baseline to 10% at 4 wk and 20% at 8 wk. Incorporation of EPA into red blood cell phospholipids reached levels of around 10%. The present study has shown that a novel, high-purity, EPA diester emulsion can be tolerated at a dose providing around 18 g EPA per day with side-effects being easily controlled. The acceptibility of large doses of oral EPA should allow larger controlled clinical studies into potential anticancer effects of EPA.
Enhanced Viscoelasticity of Human Cystic Fibrotic Sputum Correlates with Increasing Microheterogeneity in Particle Transport (2003)

Current biochemical characterizations of cystic fibrosis (CF) sputum do not address the high degree of microheterogeneity in the rheological properties of the mucosal matrix and only provide bulk-average particle diffusion coefficients. The viscoelasticity of CF sputum greatly reduces the diffusion rates of colloidal particles, limiting the effectiveness of gene delivery to underlying lung cells. We determine diffusion coefficients of hundreds of individual amine-modified and carboxylated polystyrene particles (diameter 100-500 nm) embedded in human CF sputum with 5 nm and 33 ms of spatiotemporal resolution. High resolution multiple particle tracking is used to calculate the effective viscoelastic properties of CF sputum at the micron scale, which we relate to its macroscopic viscoelasticity. CF sputum microviscosity, as probed by 100- and 200-nm particles, is an order of magnitude lower than its macroviscosity, suggesting that nanoparticles dispersed in CF sputum are transported primarily through lower viscosity pores within a highly elastic matrix. Multiple particle tracking provides a non-destructive, highly sensitive method to quantify the high heterogeneity of the mucus pore network. The mean diffusion coefficient becomes dominated by relatively few but fast-moving particles as particle size is reduced from 500 to 100 nm. Neutrally charged particles with a diameter <200 nm undergo more rapid transport in CF sputum than charged particles. Treatment with recombinant human DNase (Pulmozyme) reduces macroviscoelastic properties of CF sputum by up to 50% and dramatically narrows the distribution of individual particle diffusion rates but surprisingly does not significantly alter the ensemble-average particle diffusion rate.
A Human STX cDNA Confers Polysialic Acid Expression in Mammalian Cells (1995)

Polysialic acid, or PSA, is a term used to refer to linear homopolymers of alpha(2,8)-sialic acid residues displayed at the surface of some mammalian cells. PSA is typically linked to the neural cell adhesion molecule N-CAM, where it can modulate the homotypic adhesive properties of this polypeptide. PSA expression is developmentally regulated, presumably through mechanisms involving regulated expression of sialyltransferases involved in PSA biosynthesis. Several different sialytransferase sequences have been implicated in PSA expression, although the precise roles of these enzymes in this context remain unclear. One such sequence, termed STX, maintains approximately 59% amino acid sequence identity with another sialyltransferase (PST-1, from hamster; PST, human) that is known to participate in PSA expression. While a murine STX fusion protein can catalyze the synthesis of a single alpha(2,8)-sialic acid linkage in vitro, the ability of STX to participate in PSA expression in vivo has not been demonstrated. We show here that STX transcripts are present in a PSA-positive, N-CAM-positive human small cell carcinoma line (NCI-H69/F3), but are absent in a variant of this line (NCI-H69/E2) selected to be PSA-negative and N-CAM-positive. To functionally confirm this correlation, we have cloned a human cDNA encoding the human STX sequence, and show, by transfection studies, that human STX can restore PSA expression when expressed in the PSA-negative, N-CAM-positive small cell carcinoma variant. We furthermore show that STX can confer PSA expression when expressed in a PSA-negative, N-CAM-positive murine cell line (NIH-3T3 cells), or when expressed in PSA-negative, N-CAM-negative COS-7 cells. These observations imply that STX, like PST-1/PST, can determine PSA expression in vivo. When considered together with the correlation between STX expression and PSA expression in vivo in the brain, these results suggest a regulatory role for STX in PSA expression in the developing central nervous system and small cell lung carcinoma.
Cyclodextrins in eye drop formulations: enhanced topical delivery of corticosteroids to the eye (2002)

Cyclodextrins are cylindrical oligosaccharides with a lipophilic central cavity and hydrophilic outer surface. They can form water-soluble complexes with lipophilic drugs, which 'hide' in the cavity. Cyclodextrins can be used to form aqueous eye drop solutions with lipophilic drugs, such as steroids and some carbonic anhydrase inhibitors. The cyclodextrins increase the water solubility of the drug, enhance drug absorption into the eye, improve aqueous stability and reduce local irritation. Cyclodextrins are useful excipients in eye drop formulations of various drugs, including steroids of any kind, carbonic anhydrase inhibitors, pilocarpine, cyclosporins, etc. Their use in ophthalmology has already begun and is likely to expand the selection of drugs available as eye drops. In this paper we review the properties of cyclodextrins and their application in eye drop formulations, of which their use in the formulation of dexamethasone eye drops is an example. Cyclodextrins have been used to formulate eye drops containing corticosteroids, such as dexamethasone, with levels of concentration and ocular absorption which, according to human and animal studies, are many times those seen with presently available formulations. Cyclodextrin-based dexamethasone eye drops are well tolerated in the eye and seem to provide a higher degree of bioavailability and clinical efficiency than the steroid eye drop formulations presently available. Such formulations offer the possibility of once per day application of corticosteroid eye drops after eye surgery, and more intensive topical steroid treatment in severe inflammation. While cyclodextrins have been known for more than a century, their use in ophthalmology is just starting. Cyclodextrins are useful excipients in eye drop formulations for a variety of lipophilic drugs. They will facilitate eye drop formulations for drugs that otherwise might not be available for topical use, while improving absorption and stability and decreasing local irritation.
Morphometry of human coronary capillaries during normal growth and the effect of age in left ventricular pressure-overload hypertrophy. (1992)

Pressure-overload left ventricular hypertrophy in children demonstrates proportional capillary angiogenesis, whereas in adults, hypertrophy appears to be associated with failure of compensatory angiogenesis.
Transforming growth factor beta 1 stimulates the production of basic fibroblast growth factor binding proteoglycans in Balb/c3T3 cells. (1992)

Basic fibroblast growth factor (bFGF) binds to cell surface receptors and to heparin sulfate proteoglycans. Heparan sulfate binding may limit bFGF degradation and be an obligatory step for bFGF cell interaction. Transforming growth factor-beta 1 (TGF-beta 1) is a potent regulator of proteoglycan production and composition. The possibility that TGF-beta 1 synergistically regulates bFGF activity by altering bFGF-proteoglycan interactions was investigated. TGF-beta 1 increased 125I-bFGF binding to the extracellular matrix (ECM) of Balb/c3T3 cells 2-4-fold by increasing the number of bFGF binding sites. Increased bFGF binding correlated with a 2-5-fold increase in the production of sulfated proteoglycans, including heparan sulfate proteoglycans. TGF-beta 1 selectively stimulated production of high molecular mass proteoglycans (190-300 kDa) in conditioned medium and stimulated all proteoglycans in ECM. 125I-bFGF bound to TGF-beta 1 induced proteoglycans immobilized onto cationic nylon filters. Furthermore, ECM isolated from TGF-beta 1-treated cells incorporated more mitogenically active bFGF than native ECM. The mitogenic potential of the ECM was significantly reduced by treatment with heparinase. These results suggest that the ability of TGF-beta 1 to stimulate binding of bFGF to ECM, increase ECM heparan sulfate proteoglycan, and potentiate the mitogenic activity of bFGF are linked. Thus one aspect of TGF-beta 1/bFGF synergy may involve modulation of the ECM.
Efficient Computation of Absolute Pose for Gravity-Aware Augmented Reality (2015)

We propose a novel formulation for determining the absolute pose of a single or multi-camera system given a known vertical direction. The vertical direction may be easily obtained by detecting the vertical vanishing points with computer vision techniques, or with the aid of IMU sensor measurements from a smartphone. Our solver is general and able to compute absolute camera pose from two 2D-3D correspondences for single or multi-camera systems. We run several synthetic experiments that demonstrate our algorithm's improved robustness to image and IMU noise compared to the current state of the art. Additionally, we run an image localization experiment that demonstrates the accuracy of our algorithm in real-world scenarios. Finally, we show that our algorithm provides increased performance for real-time model-based tracking compared to solvers that do not utilize the vertical direction and show our algorithm in use with an augmented reality application running on a Google Tango tablet.
Ultrasound modulates ion channel currents (2016)

Transcranial focused ultrasound (US) has been demonstrated to stimulate neurons in animals and humans, but the mechanism of this effect is unknown. It has been hypothesized that US, a mechanical stimulus, may mediate cellular discharge by activating mechanosensitive ion channels embedded within cellular membranes. To test this hypothesis, we expressed potassium and sodium mechanosensitive ion channels (channels of the two-pore-domain potassium family (K2P) including TREK-1, TREK-2, TRAAK; NaV1.5) in the Xenopus oocyte system. Focused US (10 MHz, 0.3-4.9 W/cm(2)) modulated the currents flowing through the ion channels on average by up to 23%, depending on channel and stimulus intensity. The effects were reversible upon repeated stimulation and were abolished when a channel blocker (ranolazine to block NaV1.5, BaCl2 to block K2P channels) was applied to the solution. These data reveal at the single cell level that focused US modulates the activity of specific ion channels to mediate transmembrane currents. These findings open doors to investigations of the effects of US on ion channels expressed in neurons, retinal cells, or cardiac cells, which may lead to important medical applications. The findings may also pave the way to the development of sonogenetics: a non-invasive, US-based analogue of optogenetics.
Quantum-Transport Study on the Impact of Channel Length and Cross Sections on Variability Induced by Random Discrete Dopants in Narrow Gate-All-Around Silicon Nanowire Transistors (2011)

In this paper, we review and extend recent work on the effect of random discrete dopants on the statistical variability in gate-all-around silicon nanowire transistors. The electron transport is described using the nonequilibrium Green's function formalism. Full 3-D real-space and coupled-mode-space repre sentations are used. Two different cross sections (i.e., 2.2 × 2.2 and 4.2 × 4.2 nm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) and two different channel lengths (i.e., 6 and 12 nm) have been considered. The resistivity associated with discrete dopants can be estimated from the averaged current-voltage characteristics. The threshold-voltage variability and the sub threshold-slope variability are reduced greatly in the transistors with longer channel length. Both are smaller at equivalent channel lengths in the 2.2 × 2.2 nm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> device due to better electrostatic integrity. At the same time, the ON-state-current variability associated with the varying resistance of the access regions is virtually independent of the channel length. However, it is reduced greatly in the 4.2 × 4.2 nm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> transistor due to a fourfold increase in the number of dopants in the access regions and corresponding self-averaging effects. Finally, we present results for the smallest transistor combining two sources of variability (i.e., discrete random dopants and surface roughness) and phonon scattering.
Memories of winter: vernalization and the competence to flower (2000)

ABSTRACT The promotion of flowering in response to a prolonged exposure to cold temperatures (i.e. winter) is a useful adaptation for plant species that flower in the spring. This promotion is known as vernalization and results in a permanent memory of cold exposure. While the physiology of vernalization has been extensively studied in many species, the molecular mechanism of vernalization remains largely unknown. Recent studies, however, have revealed some of the molecular events that create the requirement for vernalization. In Arabidopsis, naturally occurring late‐flowering ecotypes and plants containing late‐flowering mutations in the autonomous floral‐promotion pathway are relatively late flowering unless cold treated. The vernalization requirement of these late‐flowering ecotypes and autonomous‐pathway mutants is largely created by an upregulation of the floral inhibitor FLOWERING LOCUS C (FLC) . After cold treatment, as imbibed seeds or young seedlings, FLC transcript levels are downregulated and remain low for the remainder of the plant's life, but return to high levels in the next generation. Plants containing a constitutively expressed 35S:FLC construct remain late flowering after cold treatment, indicating that FLC levels must be downregulated for vernalization to be effective. Thus the epigenetic downregulation of FLC appears to be a major target of the vernalization pathway and provides a molecular marker of the vernalized state.
Investigation of a Sequential Three-Dimensional Process for Back-Illuminated CMOS Image Sensors With Miniaturized Pixels (2009)

A new 3-D CMOS image sensor architecture is presented as a potential candidate for submicrometer pixels. To overcome the scaling challenge related to miniaturized pixel design rules, far beyond traditional 3-D stacking alignment capabilities, a sequential construction is applied. This paper gives a technical overview of this 3-D scheme and validates a part of its building blocks. As a consequence of a sequential process, the thermal budget is limited to ensure bottom device immunity. Subsequently, high-quality SOI film transfer above the first layer by direct bonding and etch back is demonstrated. Finally, the low-temperature processing of HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /TiN fully depleted silicon-on-insulator readout transistors is detailed and evaluated from a low frequency noise point of view.
In vivo Quantitative characterization of trabecular bone by NMR (1991)

In trabecular bone the NMR linewidth is found to be governed by the magnetic field inhomogeneity arising from the difference in magnetic permeability between bone and marrow. T2* was measured in vivo in the distal femur by interferometry and localized spectroscopy. Both methods showed T2* to be inversely related to trabecular plate density.
Developmental changes in embryonic and extra-embryonic insulin-like growth factor-I tissue concentrations in the turkey embryo (1997)

The ontogeny of insulin-like growth factor-I (IGF-I) embryonic and extra-embryonic tissue concentrations were determined in the developing turkey embryo. At 2-d intervals, starting on Day 6 of incubation, individual tissues (n = 8 for each stage of incubation) were removed, weighed, pulverized, and extracted in 1 M acetic acid for IGF-I determination. Amniotic and allantoic fluid were collected starting on Day 8, serum on Day 12, and analyzed for IGF-I levels. Serum IGF-I levels were the lowest on Days 12 and 28 of incubation (5.9 and 9.5 ng/mL), respectively, and the highest on Day 20 (16.2 ng/mL). Allantoic and amniotic fluid IGF-I concentrations were essentially unchanged during incubation. Extra-embryonic tissue IGF-I levels increased in both the yolk sac and chorioallantoic membranes as incubation advanced with concentrations being 8- to 10-fold greater in the chorioallantois. Embryo tissue IGF-I concentrations varied greatly with regard to tissue and stage of development. Brain IGF-I levels were the highest on Day 8 and lowest on Day 26 (423 vs 35 pg/mg protein, respectively). Tissue IGF-I pattern in the heart mirrored that of brain. Liver IGF-I was low (< 40 pg/mg protein) from Day 10 to 20 and undetectable on Days 22 to 28. Muscle IGF-I levels were similar in the final days of development to those observed in early incubation. Bone IGF-I levels were highest in mid-incubation and lowest on Day 26. Peptide levels in the gastrointestinal tract (GI) tract and gizzard were dissimilar in that IGF-I was elevated in the GI tract in early incubation and declined with advancing incubation, whereas gizzard IGF-I levels peaked in late incubation. It is apparent that tissue synthesis of IGF-I is differentially regulated within a given tissue and stage of incubation during embryogenesis in the turkey embryo.
Asymptomatic Intracorneal Graphite Deposits following Graphite Pencil Injury (2012)

Reports of graphite pencil lead injuries to the eye are rare. Although graphite is considered to remain inert in the eye, it has been known to cause severe inflammation and damage to ocular structures. We report a case of a 12-year-old girl with intracorneal graphite foreign bodies following a graphite pencil injury.
Anterior electrophysiological asymmetries, emotion, and depression: Conceptual and methodological conundrums (1998)

Two reports in the last issue of this journal attempted to replicate aspects of our previous studies on anterior electroencephalogram (EEG) asymmetry, affective style, and depression. In this commentary, an overview is provided of our model of anterior asymmetries, affective style, and psychopathology. Emphasis is placed on conceptualizing the prefrontal and anterior temporal activation patterns within a circuit that includes cortical and subcortical structures. The causal status of individual differences in asymmetric activation in the production of affective style and psychopathology is considered. Major emphasis is placed on EEG methods, particularly the need for multiple assessments to obtain estimates of asymmetric activation that better reflect an individual's true score. Issues specific to each of the two articles are also considered. Each of the articles has more consistency with our previously published data than the authors themselves suggest. Recommendations are made for future research to resolve some of the outstanding issues.
Modulation of antitumor immune responses by hematopoietic cytokines (2003)

Immune-modulating cytokines may be used alone or in combination with other treatments to help restore immune function, improve response to tumor-associated antigens, and reduce the toxic effects of standard antitumor therapies. The evolving understanding of how dendritic cells regulate immune responses and promising results from published studies of immune-enhancing cytokines in the treatment of patients with malignant disease support the conduct of randomized clinical trials to confirm the clinical benefit of these immunotherapeutic strategies.