gebhart/patrepeval huggingface dataset:
Real-time 4D signal processing and visualization using graphics processing unit on a regular nonlinear-k Fourier-domain OCT system (2010)

We realized graphics processing unit (GPU) based real-time 4D (3D+time) signal processing and visualization on a regular Fourier-domain optical coherence tomography (FD-OCT) system with a nonlinear k-space spectrometer. An ultra-high speed linear spline interpolation (LSI) method for lambda-to-k spectral re-sampling is implemented in the GPU architecture, which gives average interpolation speeds of >3,000,000 line/s for 1024-pixel OCT (1024-OCT) and >1,400,000 line/s for 2048-pixel OCT (2048-OCT). The complete FD-OCT signal processing including lambda-to-k spectral re-sampling, fast Fourier transform (FFT) and post-FFT processing have all been implemented on a GPU. The maximum complete A-scan processing speeds are investigated to be 680,000 line/s for 1024-OCT and 320,000 line/s for 2048-OCT, which correspond to 1GByte processing bandwidth. In our experiment, a 2048-pixel CMOS camera running up to 70 kHz is used as an acquisition device. Therefore the actual imaging speed is camera- limited to 128,000 line/s for 1024-OCT or 70,000 line/s for 2048-OCT. 3D Data sets are continuously acquired in real time at 1024-OCT mode, immediately processed and visualized as high as 10 volumes/second (12,500 A-scans/volume) by either en face slice extraction or ray-casting based volume rendering from 3D texture mapped in graphics memory. For standard FD-OCT systems, a GPU is the only additional hardware needed to realize this improvement and no optical modification is needed. This technique is highly cost-effective and can be easily integrated into most ultrahigh speed FD-OCT systems to overcome the 3D data processing and visualization bottlenecks.
Tiles for managing computational complexity of video encoding and decoding (2012)

In this paper, we introduce the concept of tiles. Tiles are incorporated into the current design of the High Efficiency Video Coding (HEVC) standard being developed by the Joint Collaborative Team on Video Coding (JCT-VC). In the design, tiles are introduced to support high-level parallelism and also to reduce on-chip memory requirements. This paper describes the tile concept and reports results due to the technique.
Social information filtering for music recommendation (1994)

Abstract Filters which select items for individual users based upon content suffer from several limitations. The items being filtered must be amenable to parsing by a computer. Furthermore, Content-Based Filters possess no inherent method for serendipitous exploration of the information space.
Pathogenesis of Acute Graft-Versus-Host Disease: Cytokines and Cellular Effectors (2000)

The pathogenesis of acute graft versus host disease (GVHD) is multistep process. This review considers acute GVHD in three sequential steps: conditioning regimen, donor T cell activation, and effector mechanisms. In step one, the conditioning regimen simultaneously damages and activates host tissues, amplifying antigen presentation to allogeneic donor T cells. In step two, donor T cells, activated by host alloantigens, proliferate and secrete a variety of cytokines. Type 1 cytokines (interleukin-2 and interferon-y) are critical for acute GVHD, but several regulatory mechanisms of tissue damage include inflammatory cytokines and cytolytic cellular effectors. The gastrointestinal (GI) tract is a principal target organ because damage to the GI mucosa can release inflammatory mediators such as endotoxin that amplify systemic disease. The inflammatory processes of acute GVHD can be considered as a distortion of the cellular responses to viral and bacterial infections. Cell-mediated toxicity is critical to other GVHD target organs, particularly the liver, where Fas-mediated injury predominates. The cytolytic pathways (e.g., perforin) clearly intensify acute GVHD, although they are not necessary for systemic disease in several model systems. Many of these insights come from animal models using mutant mouse strains that can clarify the role of individual proteins or cell types in the disease process. These insights should allow the testing of new classes of drugs and inhibitors in clinical bone marrow transplantation.
Highly sensitive and flexible strain sensors based on patterned ITO nanoparticle channels (2017)

We demonstrate a highly sensitive and flexible bending strain sensor using tin-doped indium oxide (ITO) nanoparticles (NPs) assembled in line patterns on flexible substrates. By utilizing transparent ITO NPs without any surface modifications, we could produce strain sensors with adjustable gauge factors and optical transparency. We were able to control the dimensional and electrical properties of the sensors, such as channel height and resistance, by controlling the NP assembly speed. Furthermore, we were able to generate controlled gauge factor with values ranging from 18 to 157, which are higher than previous cases using metallic Cr NPs and Au NPs. The alignment of the ITO NPs in parallel lines resulted in low crosstalk between the transverse and longitudinal bending directions. Finally, our sensor showed high optical transmittance, up to ∼93% at 500 nm wavelength, which is desirable for flexible electronic applications.
Characterization of the Secreted Form of Endothelial-Cell-Specific Molecule 1 by Specific Monoclonal Antibodies (2000)

Endothelial-cell-specific molecule 1 (ESM-1) is a recently identified endothelial cell molecule. As ESM-1 mRNA is preferentially expressed in human lung and kidney tissues, and as ESM-1 mRNA expression is regulated by inflammatory cytokines, ESM-1 is thought to play a role in the vascular contribution to organ-specific inflammation. In order to define its behavior, mouse anti-ESM-1 monoclonal antibodies were developed, and three distinct epitopes were mapped, which allowed development of a specific ELISA assay, immunohistological staining and immunoblot analysis. Here, we demonstrate that ESM-1 is present in cell lysates of human endothelial cells (human umbilical vein endothelial cells) with an apparent molecular weight of 20 kD. In contrast, the secreted form of ESM-1 is shifted to an apparent molecular weight of 50 kD, indicating that the secreted form of ESM-1 is posttranslationally modified. By ELISA, we show that the secretion of ESM-1 is significantly enhanced in the presence of TNFalpha. In contrast, the spontaneous as well as TNFalpha-induced secretion of ESM-1 is strongly inhibited by IFNgamma. Moreover, ESM-1 was detected in the serum of healthy subjects at an average concentration of 1.08 ng/ml, and we demonstrated that the serum level of ESM-1 is dramatically increased in patients presenting a septic shock. Analysis of ESM-1 expression in normal human tissues by immunohistochemistry showed that ESM-1 is localized in the vascular network, but also in the bronchial and renal epithelia. Our results demonstrate that ESM-1 is mainly expressed in the vascular endothelium both in vitro and in vivo, but also by different epithelia. ESM-1 may represent a new marker of endothelial cell activation, and may have a functional role in endothelium-dependent pathological disorders.
Analysis of Food and Drug Administration–Approved Anticancer Agents in the NCI60 Panel of Human Tumor Cell Lines (2010)

Since the early 1990s the Developmental Therapeutics Program of the National Cancer Institute (NCI) has utilized a panel of 60 human tumor cell lines (NCI60) representing 9 tissue types to screen for potential new anticancer agents. To date, about 100,000 compounds and 50,000 natural product extracts have been screened. Early in this program it was discovered that the pattern of growth inhibition in these cell lines was similar for compounds of similar mechanism. The development of the COMPARE algorithm provided a means by which investigators, starting with a compound of interest, could identify other compounds whose pattern of growth inhibition was similar. With extensive molecular characterization of these cell lines, COMPARE and other user-defined algorithms have been used to link patterns of molecular expression and drug sensitivity. We describe here the results of screening current Food and Drug Administration (FDA)-approved anticancer agents in the NCI60 screen, with an emphasis on those agents that target signal transduction. We analyzed results from agents with mechanisms of action presumed to be similar; we also carried out a hierarchical clustering of all of these agents. The addition of data from recently approved anticancer agents will increase the utility of the NCI60 databases to the cancer research community. These data are freely accessible to the public on the DTP website (http://dtp.cancer.gov/). The FDA-approved anticancer agents are themselves available from the NCI as a plated set of compounds for research use.
Induction of Immunoreactive Somatomedin C in Human Serum by Growth Hormone: Dose-Response Relationships and Effect on Chromatographic Profiles* (1980)

The induction of somatomedin C (SM-C) was evaluated in 30 hypopituitary patients and in normal subjects using a sensitive, specific RIA for SM-C. Two hypopituitary patients each received an iv bolus of 0.1 U human GH (hGH)⁄kg BW, followed by continuous infusion of 0.01 U hGH⁄kg-h for 12 h. The earliest rise in SM-C was detectable between 6-8 h. In response to the im administration of hGH, hypopituitary patients demonstrated a delay of 8 h before the rise in SM-C, a peak response between 16-28 h, and a fall nearly to basal levels by 48 h. The delay in the serum SM-C response to the administration of hGH suggests that SM is not stored in a readily releasable form and that the effect of GH on SM production may be through the stimulation of de novo synthesis. Graded doses of hGH in a sequence of 0.1, 0.2, 0.4, and 0.8 U/kg (im) elicited a stairstep pattern of SM-C response. When the sequence of administration of these doses was altered, however, it was apparent that the magnitude of the SM-C response was determined less by the dose of hGH employed than by the prior experience of the patient with hGH. When two identical doses of hGH were administered at 48-h intervals, the response to the second dose was uniformly greater than that to the first. Two of 28 hypopituitary children receiving hGH therapy failed to raise their SM-C levels out of the hypopituitary range and 6 other responses were subnormal. These noninducers were undernourished and had normal growth rates in spite of persistently low SM-C levels. Sephadex G-200 chromatography of the serum from 2 of these patients revealed neither an elevation in [125Ι]SM-C binding in the large 150,000 (150 K) mol wt region nor a significant increase in endogenous SM-C activity after hGH. This contrasts with the pattern seen in most hypopituitary patients in whom hGH causes a marked increase in endogenous activity in the 150 K region as well as the emergence of [125I]- SM-C binding in this region. From these results, it is concluded that the 150 K SM-binding complex is GH dependent and is a major determinant of the immunoreactive SM-C measured in native serum.
Half-width and peak-intensity measurement of a rocking curve obtained from silicon on sapphire using soft x-ray beams (1977)

The crystalline quality of a silicon film on a sapphire substrate (SOS) is investigated by measuring both a half-width and a peak intensity of a rocking curve using a double-crystal arrangement. Contrary to conventional techniques, it is confirmed that an asymmetric diffraction technique using a soft x-ray beam (TiKα1) enables the sampling of only a surface layer within 0.12 μm. The improved technique is successfully applied to SOS wafers. As a result, the half-width is found to correlate with both a fault density and a Hall mobility. On the other hand, the intensity has a correlation with an interstitial Al content in the film which is introduced by autodoping during growth.
Osteoblast-Derived Factors Induce Androgen-Independent Proliferation and Expression of Prostate-Specific Antigen in Human Prostate Cancer Cells (2004)

Osteoblasts secrete factors, such as IL-6, that cause androgen-independent induction of PSA gene expression and proliferation of prostate cancer cells by a mechanism that partially relies on the AR. Identifying such molecular mechanisms may lead to improved clinical management of metastatic prostate cancer.
Stoichiometric and temporal requirements of Oct4, Sox2, Klf4, and c-Myc expression for efficient human iPSC induction and differentiation (2009)

Human-induced pluripotent stem cells (hiPSCs) are generated from somatic cells by ectopic expression of the 4 reprogramming factors (RFs) Oct-4, Sox2, Klf4, and c-Myc. To better define the stoichiometric requirements and dynamic expression patterns required for successful hiPSC induction, we generated 4 bicistronic lentiviral vectors encoding the 4 RFs co-expressed with discernable fluorescent proteins. Using this system, we define the optimal stoichiometry of RF expression to be highly sensitive to Oct4 dosage, and we demonstrate the impact that variations in the relative ratios of RF expression exert on the efficiency of hiPSC induction. Monitoring of expression of each individual RF in single cells during the course of reprogramming revealed that vector silencing follows acquisition of pluripotent cell markers. Pronounced lentiviral vector silencing was a characteristic of successfully reprogrammed hiPSC clones, but lack of complete silencing did not hinder hiPSC induction, maintenance, or directed differentiation. The vector system described here presents a powerful tool for mechanistic studies of reprogramming and the optimization of hiPSC generation.
The effect of large openings on cavity amplification at ultrasonic frequencies (2002)

It is sometimes desired to exploit acoustic amplification in a cavity that is not entirely enclosed. Because of the presence of openings in the cavity, acoustic energy will leave the cavity and degrade the degree of amplification. The extent of this problem is unknown when the size of the openings becomes large relative to a wavelength. The present paper describes a quantitative estimation of the effect of large openings on the amplification performance of an acoustic cavity. Air was assumed to be the working medium. The amplification taking place in a rigid-walled rectangular channel excited by a transducer flush-mounted in one wall was compared to the amplification that would take place in a bounded rectangular resonator excited by the same transducer. It was found, for frequencies in the range 25 kHz-1 MHz, that source ka's greater than 37 and 42 were required in order for the collimation of the transducer beam to overcome the leakage of acoustic energy through the openings for one- and two-half wavelength resonances, respectively. Experimental measurements conducted over source ka's ranging from 6.5 to 26.1, resulted in quality factors 8%-18% lower than theoretically predicted values for one-, two-, and three-half wavelength resonances.
Resolution of racemic gossypol (1985)

Z. D. Kai, S. Y. Kang, M. J. Ke, Z. Jin and H. Liang, J. Chem. Soc., Chem. Commun., 1985, 168 DOI: 10.1039/C39850000168
Articular cartilage preservation and storage (1979)

Articular cartilage slice explants were stored under various conditions, including freezing-thawing at various rates by using dimethyl sulfoxide (DMSO) as a cryoprotective agent, incubating in standard tissue culture medium (MEM Eagle:NCTC 135:15% fetal calf serum) in 5% CO2 and air at 4 degrees, 21 degrees, and 37 degrees C, and incubating in standard tissue culture medium containing 200 micrograms/ml alpha-tocopherol (vitamin E) at 37 degrees C after first ascertaining a dose-response curve of vitamin E. Results indicated that articular cartilage slice explants did not survive freezing or storage at 4 degrees and 21 degrees C as measured by 35S uptake. When stored at 37 degrees C in standard tissue culture in 5% CO2 and air, the slice explants remained viable for up to 60 days. The addition of alpha-tocopherol to the medium resulted in significantly less release of previously incorporated 35Sin stored cartilage slices and significantly less reduction of the amount of hexosamine present in the stored explants. alpha-Tocopherol in the medium also preserved safranin O staining. Thus, the application of tissue culture techniques to the storage of articular cartilage made it possible to preserve cartilage slice explants in a viable, biochemically "normal" state.
Key Elements of Clinical Physician Leadership at an Academic Medical Center (2011)

Physician leadership exists in clinical settings. This study highlights the elements essential to that leadership. Understanding the physician attributes and behaviors that result in effective leadership and teamwork can lay the groundwork for more formal leadership education for physicians-in-training.
Solvent Compatibility of Poly(dimethylsiloxane)-Based Microfluidic Devices (2003)

This paper describes the compatibility of poly(dimethylsiloxane) (PDMS) with organic solvents; this compatibility is important in considering the potential of PDMS-based microfluidic devices in a number of applications, including that of microreactors for organic reactions. We considered three aspects of compatibility: the swelling of PDMS in a solvent, the partitioning of solutes between a solvent and PDMS, and the dissolution of PDMS oligomers in a solvent. Of these three parameters that determine the compatibility of PDMS with a solvent, the swelling of PDMS had the greatest influence. Experimental measurements of swelling were correlated with the solubility parameter, delta (cal(1/2) cm(-3/2)), which is based on the cohesive energy densities, c (cal/cm(3)), of the materials. Solvents that swelled PDMS the least included water, nitromethane, dimethyl sulfoxide, ethylene glycol, perfluorotributylamine, perfluorodecalin, acetonitrile, and propylene carbonate; solvents that swelled PDMS the most were diisopropylamine, triethylamine, pentane, and xylenes. Highly swelling solvents were useful for extracting contaminants from bulk PDMS and for changing the surface properties of PDMS. The feasibility of performing organic reactions in PDMS was demonstrated by performing a Diels-Alder reaction in a microchannel.
Neurotrophins promote revascularization by local recruitment of TrkB+ endothelial cells and systemic mobilization of hematopoietic progenitors (2005)

The neurotrophin brain-derived neurotrophic factor (BDNF) is required for the maintenance of cardiac vessel wall stability during embryonic development through direct angiogenic actions on endothelial cells expressing the tropomysin receptor kinase B (TrkB). However, the role of BDNF and a related neurotrophin ligand, neurotrophin-4 (NT-4), in the regulation of revascularization of the adult tissues is unknown. To study the potential angiogenic capacity of BDNF in mediating the neovascularization of ischemic and non-ischemic adult mouse tissues, we utilized a hindlimb ischemia and a subcutaneous Matrigel model. Recruitment of endothelial cells and promotion of channel formation within the Matrigel plug by BDNF and NT-4 was comparable to that induced by VEGF-A. The introduction of BDNF into non-ischemic ears or ischemic limbs induced neoangiogenesis, with a 2-fold increase in the capillary density. Remarkably, treatment with BDNF progressively increased blood flow in the ischemic limb over 21 days, similar to treatment with VEGF-A. The mechanism by which BDNF enhances capillary formation is mediated in part through local activation of the TrkB receptor and also by recruitment of Sca-1+CD11b+ pro-angiogenic hematopoietic cells. BDNF induces a potent direct chemokinetic action on subsets of marrow-derived Sca-1+ hematopoietic cells co-expressing TrkB. These studies suggest that local regional delivery of BDNF may provide a novel mechanism for inducing neoangiogenesis through both direct actions on local TrkB-expressing endothelial cells in skeletal muscle and recruitment of specific subsets of TrkB+ bone marrow-derived hematopoietic cells to provide peri-endothelial support for the newly formed vessels.
A Modular DNA Carrier Protein Based on the Structure of Diphtheria Toxin Mediates Target Cell-specific Gene Delivery (1998)

Modular fusion proteins that combine distinct functions required for cell type-specific uptake and intracellular delivery of DNA present an attractive approach for the development of self-assembling vectors for targeted gene delivery. Here, we describe a novel DNA carrier protein termed GD5 that mimics the structure of the bacterial diphtheria toxin (DT) and facilitates target cell-specific gene transfer via receptor-mediated endocytosis. GD5 carries at the N terminus the DNA-binding domain of the yeast transcription factor Gal4, which is connected to a C-terminal antibody fragment specific for the tumor-associated ErbB2 antigen via an internal DT translocation domain as an endosome escape activity. Bacterially expressed GD5 protein specifically bound to ErbB2-expressing cells and formed protein-DNA complexes with a luciferase reporter gene construct. These complexes, after compensation of excess negative charge with poly-L-lysine, served as a specific transfection vector for ErbB2-expressing cells. Inhibitors of endosomal acidification drastically reduced GD5-mediated transfection, indicating that the DT translocation domain of GD5, similar to the parental toxin, is strictly dependent on the transit through an acidic environment. Our results suggest that fusion proteins that employ the natural endosome escape mechanism of bacterial toxins might aid in the development of efficient nonviral vectors for applications in gene therapy.
Structure and biological activities of a heparin-derived hexasaccharide with high affinity for basic fibroblast growth factor. (1993)

We demonstrated previously that heparin-derived hexasaccharides are the smallest fragments of the polysaccharide with comparable basic fibroblast growth factor (bFGF)-modulating activity in vitro (Ishihara, M., Tyrrell, D.J., Stauber, G.B., Brown, S., Cousens, L., and Stack, R.J. (1993) J. Biol. Chem. 268, 4675-4683. In this report, a specific hexasaccharide having high affinity for recombinant human bFGF was isolated and its structure deduced by analysis of its reduced disaccharide products after treatment with nitrous acid at pH 1.5, and by 1H NMR spectroscopy. The hexasaccharide has the structure [IdoA(2-OSO3)alpha 1-4GlcNSO3(6-OSO3)alpha 1-4]2IdoA(2-OSO3)alpha 1-4 AManR(6-OSO3). The hexasaccharide effectively inhibits the binding of syndecan-transfected RO-12 UC cells to bFGF-coated wells (Ishihara, M., Tyrrell, D.J., Kiefer, M.C., Barr, P.J., and Swiedler, S.J. (1992) Anal. Biochem. 202, 310-315), prevents the binding of 125I-bFGF to confluent monolayers of adrenocortical endothelial (ACE) cells, and inhibits the bFGF-dependent proliferation of ACE cells. Unlike the heparin from which it was derived, however, the hexasaccharide cannot promote the binding of 125I-bFGF to a recombinant high affinity bFGF receptor (flg) or restore the bFGF-dependent proliferative response to ACE cells grown in the presence of 5 mM sodium chlorate. Collectively, these data indicate that a hexasaccharide can be as effective as heparin as an antagonist of bFGF-mediated cell mitogenesis.