gebhart/patrepeval huggingface dataset:
On Chip Droplet Characterization: A Practical, High-Sensitivity Measurement of Droplet Impedance in Digital Microfluidics (2012)

We demonstrate a new approach to impedance measurement on digital microfluidics chips for the purpose of simple, sensitive, and accurate volume and liquid composition measurement. Adding only a single series resistor to existing AC droplet actuation circuits, the platform is simple to implement and has negligible effect on actuation voltage. To accurately measure the complex voltage across the resistor (and hence current through the device and droplet), the designed system is based on software-implemented lock-in amplification detection of the voltage drop across the resistor which filters out noise, enabling high-resolution and low-limit signal recovery. We observe picoliter sensitivity with linear correlation of voltage to volume extending to the microliter volumes that can be handled by digital microfluidic devices. Due to the minimal hardware, the system is robust and measurements are highly repeatable. The detection technique provides both phase and magnitude information of the real-time current flowing through the droplet for a full impedance measurement. The sensitivity and resolution of this platform enables it to distinguish between various liquids which, as demonstrated in this paper, could potentially be extended to quantify solute concentrations, liquid mixtures, and presence of analytes.
Automation of protein crystallization trials: use of a robot to deliver reagents to a novel multi-chamber vapor diffusion plate. (1989)

We report here the automation of search procedures to rapidly screen a large number of reagents and incubation conditions that lead to the formation of protein crystals. The system consists of a Biomek 1000 Automated Laboratory Workstation from Beckman Instruments under the control of a custom user-interface program developed by Cryschem. A plate composed of twenty-four vapor diffusion chambers, each with its own reservoir well and protein drop holder was designed by Cryschem to fit the Biomek table. The Cryschem software manages a large data base of incubation conditions and generates instructions for the workstation to dispense the protein, buffers, detergents, cofactors and other reagents used to promote the formation of protein crystals. The plate is manually positioned on the Biomek table and then under program control additions are automatically made to each chamber as follows: Precipitating solution is added to each reservoir well and the protein solution along with the precipitating solution and various other reagents are added to each drop holder. The plate is removed from the table and a mylar tape is applied to simultaneously seal all the chambers. The plates are placed at a controlled temperature and periodically examined for crystal formation.
A New Fuel Cell Electrocatalyst Based on Carbonized Polyacrylonitrile Foam: The Nature of Platinum‐Support Interactions (1997)

X‐ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM) have been conducted on a new fuel cell electrocatalytic material based on a highly porous carbonized polyacrylonitrile (PAN) microcellular foam with very low platinum loading (∼13 to ). TEM images of this material clearly show the existence of nanometer size platinum particles which are homogeneously distributed in the highly porous carbonized PAN matrix. An XPS study of Pt‐loaded PAN indicates that C 1s, O 1s, and N 1s peaks shift to lower binding energies, compared to virgin PAN. It was concluded that special metal‐support interaction exists, through the formation of a charge‐transfer complex between platinum and pyridine‐type nitrogen atoms of PAN support. This interaction leads to the enhancement of the catalytic activity, and the improvement of the long‐time stability of this electrocatalyst.
Kringle 5 of Plasminogen is a Novel Inhibitor of Endothelial Cell Growth (1997)

Angiostatin is a potent angiogenesis inhibitor which has been identified as an internal fragment of plasminogen that includes its first four kringle modules. We have recently demonstrated that the anti-endothelial cell proliferative activity of angiostatin is also displayed by the first three kringle structures of plasminogen and marginally so by kringle 4 (Cao, Y., Ji, R.-W., Davidson, D., Schaller, J., Marti, D., Sohndel, S., McCance, S. G., O'Reilly, M. S. , Llinás, M., and Folkman, J. (1996) J. Biol. Chem. 271, 29461-29467). We now report that the kringle 5 fragment of human plasminogen is a specific inhibitor for endothelial cell proliferation. Kringle 5 obtained as a proteolytic fragment of human plasminogen displays potent inhibitory effect on bovine capillary endothelial cells with a half-maximal concentration (ED50) of approximately 50 nM. Thus, kringle 5 would appear to be more potent than angiostatin on inhibition of basic fibroblast growth factor-stimulated capillary endothelial cell proliferation. Appropriately folded recombinant mouse kringle 5 protein, expressed in Escherichia coli, exhibits a comparable inhibitory effect as the proteolytic kringle 5 fragment. Thus, kringle 5 domain of human plasminogen is a novel endothelial inhibitor that is sufficiently potent to block the growth factor-stimulated endothelial cell growth.
Quantitation of Lysozyme Peptides Bound to Class II MHC Molecules Indicates Very Large Differences in Levels of Presentation (2001)

Knowing the abundance of peptides presented by MHC molecules is a crucial aspect for understanding T cell activation and tolerance. In this report we determined the relative abundance of four distinct peptide families after the processing of the model Ag hen egg-white lysozyme. The development of a sensitive immunochemical approach reported here made it possible to directly quantitate the abundance of these four epitopes presented by APCs, both in vitro and in vivo. We observed a wide range of presentation among these four different epitopes presented on the surface of APCs, with 250-fold differences or more between the most abundant epitope (48-63) and the least abundant epitopes. Importantly, we observe similar ratios of presentation from APCs in vitro as well as from APCs from the spleens and thymi of hen egg-white lysozyme transgenic mice. We discuss the relationship between the amount of peptide presented and their binding to I-A(k) molecules, immunogenicity, and tolerogenicity.
Alveolar Macrophages from Patients with AIDS and AIDS-related Complex Constitutively Synthesize and Release Tumor Necrosis Factor Alpha (1991)

To verify the hypothesis that alveolar macrophages (AMs) from patients infected with HIV-1 could synthesize and release TNF alpha, AMs recovered from the BAL fluid of 11 patients with seropositive HIV-1 (six with AIDS and five with ARC) were tested in vitro for their ability to destroy TNF alpha-susceptible targets. Furthermore, the presence of TNF alpha was assessed in AM-conditioned supernatants on the basis of their cytotoxic activity and by using an immunoenzymatic test and immunoblotting. Transcription of the TNF alpha gene in AMs was also studied by means of the Northern blot analysis. AMs freshly recovered from patients infected with HIV-1 exhibited high levels of cell-mediated cytotoxicity against U937 targets, and the addition of a polyclonal anti-TNF alpha antibody resulted in a significant inhibition of the target lysis. Cell-free supernatants conditioned by unstimulated AMs exerted high levels of cytotoxic activity against TNF alpha-sensitive targets, whereas duplicate, neutralization experiments performed in the presence of an anti-TNF alpha antibody proved that the observed cytotoxic activity was mostly mediated by TNF alpha. The presence of high amounts of TNF alpha in the conditioned media was confirmed by the immunoenzymatic test. In addition, the immunoblot analysis showed that the TNF alpha released by AMs has a Mr 17,000 band, identical to a standard preparation of recombinant TNF alpha. The Northern blot demonstrated that unstimulated AMs express detectable levels of mRNA transcripts for TNF alpha. Taken together, our data support the concept that AMs from patients with HIV-1 infection constitutively release TNF alpha.(ABSTRACT TRUNCATED AT 250 WORDS)
Fabrication of organic solar array for applications in microelectromechanical systems (2008)

We have developed an innovative way to fabricate organic solar arrays for application in dc power supplies for electrostatic microelectromechanical systems devices. A solar array with 20 miniature cells interconnected in series was fabricated and characterized. Photolithography was used to isolate the individual cells and output contacts of the array, whereas the thermal-vacuum deposition is employed to make the series connections of the array. With 1mm2 for single cell and a total device area of 2.2cm2, the organic solar array based on bulk heterojunction structure of π-conjugated polymers and C60 derivative [6,6]-phenyl C61 butyric acid methyl ester produced an open-circuit voltage of 7.8V and a short-circuit current of 55μA under simulated air mass (AM) 1.5 illumination with an intensity of 132mW/cm2. The procedure described here has the full potential for use in future fabrication of microarray with the size as small as 0.01mm2.
Prevention of ischemia during percutaneous transluminal coronary angioplasty by transcatheter infusion of oxygenated Fluosol DA 20 (1986)

Catheter balloon inflation performed during percutaneous transluminal coronary angioplasty (PTCA) results in temporary interruption of coronary blood flow and subsequent myocardial ischemia. This produces transient but profound regional left ventricular dysfunction. In an effort to mitigate this inflation-related dysfunction, oxygenated Fluosol DA 20%, a perfluorochemical oxygen transport fluid, was infused distal to the balloon through the central lumen of the dilating catheter during balloon inflation. Regional wall motion during PTCA was assessed by simultaneous continuous two-dimensional echocardiography and was quantified by computer analysis. During control inflations accompanied by no intracoronary infusion or by transcatheter infusion of Ringer's lactate solution or nonoxygenated Fluosol DA 20%, there was profound regional left ventricular dysfunction with a greater than 90% decrease in regional contraction. In contrast, regional contraction during transcatheter infusion of oxygenated Fluosol DA 2...
Regulation of Gene Expression by Ethylene in Wild-Type and rin Tomato (Lycopersicon esculentum) Fruit (1988)

Levels of ethylene biosynthesis and ethylene-inducible gene expression in wild-type tomato (Lycopersicon esculentum) fruit and in nonripening fruit from the tomato mutant rin (ripening inhibitor) were compared in order to investigate the mechanism of ethylene action. Whereas wild-type tomato fruit dramatically increase the rate of ethylene biosynthesis at the onset of ripening, rin fruit constitutively produce ethylene at a low basal level. We have compared the mRNA levels and transcription rates of four cloned ethylene-inducible genes (JE Lincoln, S Cordes, E Read, RL Fischer 1987 Proc Natl Acad Sci USA 84: 2793-2797) during wild-type and rin fruit development. In wild-type fruit, both mRNA levels and transcription rates of these genes increase. The effect of the rin mutation on gene expression is different for each ethylene-inducible gene. In one case expression is completely suppressed, while in other instances it is either partially inhibited or relatively unaffected by the mutation. The mRNA levels of each of these genes in response to exogenous ethylene in rin fruit was also measured. The mRNAs for all four genes accumulate to similar levels in both ethylene treated rin and ethylene treated wild-type fruit. These results are discussed with regard to the response of plants to ethylene hormone at the level of gene expression.
Mechanism of hydrolysis of O-nitrophenyl-beta-galactoside in Staphylococcus aureus and its significance for theories of sugar transport. (1967)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Discrimination of Human Lung Neoplasm from Normal Lung by Two Target Genes (2004)

Simple tools for discrimination of lung tissues can be useful in a fast machine-aided diagnosis, for example, by tumor-specific microarrays. We demonstrate that an easy ratio technique, based on the expression levels of only two genes differentially expressed in lung tumor and normal lung samples, allows discrimination of normal and neoplastic lung with a sensitivity of 100% and specificity of 90.5%. DNA microarray analysis of 99 lung tumor samples and 15 normal lung tissues revealed that receptor for advanced glycation end products (RAGE) mRNA is reduced fourfold (p = 7.8 x 10(-11)) and cyclin-B2 mRNA is upregulated twofold (p = 5.9 x 10(-18)) in lung carcinoma compared with normal lung. The microarray-calculated expression ratio of RAGE to cyclin-B2 was used in polymerase chain reaction analysis of 84 independent blinded samples to discriminate tumor and corresponding normal lung tissues. In 94.7% of the samples this quotient correctly distinguished non-small cell lung cancer from normal lung tissue, suggesting the RAGE/cyclin-B2 quotient as a potential means for diagnosis of lung cancer.
Isolation of Membranes from Tissue Culture Cells (2003)

The isolation of membranes from cultured mammalian cells poses a number of problems. First and foremost is the problem of homogenization, which is particularly difficult with suspension culture cells, as opposed to those that grow as an adherent monolayer. The choice of subcellular fractionation procedure depends on the results of the homogenization. For a review of the problems associated with the isolation of plasma membranes from tissue culture cells, see Graham (1).
Fluorescence Single-Molecule Counting Assays for High-Sensitivity Detection of Cytokines and Chemokines (2007)

A recent focus in clinical immunodiagnostics is to improve sensitivity of assays for rare circulating protein biomarkers. The ability to detect low concentrations of certain biomarkers translates to diagnosis of disease at an earlier stage, which can positively impact prognosis and disease management (1)(2)(3). In research (for example in the discovery and development of new biomarkers), targeted assays for individual proteins are often required before multiplexing strategies are developed. Cross-reactivity of antibodies often compromises assay sensitivity in multiplexed immunoassays(4). Ultrasensitive individual assays consume only small sample volumes, a characteristic that can be advantageous in the case of scarce archival clinical samples.

The development of single-molecule detection approaches has provided new opportunities for improving immunoassay sensitivity and miniaturization (5). Fluorescence confocal microscopy with laser-induced excitation enables single-molecule detection in extremely small interrogation zones (on the order of femtoliters). By reducing interrogation zones to these dimensions and carefully tuning the timescales of the data acquisition and molecular flow rates, background interference is decreased and individual molecules are readily recorded as discrete fluorescence bursts above background(6). Counting these bursts, or molecular events, by applying fluorescence thresholds on the basis of the internally derived background noise generates experimental data whose precision is dictated by counting statistics. Hence, sample read times can be adjusted to achieve a desired counting precision. The combination of small interrogation volumes and short sample read times can also lead to rapid analysis.

Despite the advantages of single-molecule detection and the development of single-molecule detection instruments, adaptation of this technology to quantification of serum or plasma analytes has only scarcely been reported in the literature [for example, (7)]. Building on our previous work(8), we constructed single-molecule immunoassays (SMIAs) that use immune capture of analytes on microparticles, tagging with biotinylated antibodies, and quantification of fluorophore-labeled …
Network management issues in internetworks based on hybrid fiber-coax cable plants (2002)

The trend in commercial cable television networks is to build the physical layer of the network using a hybrid of optical fiber and coaxial cable. These networks provide a high bandwidth medium on which a data communications network can be overlaid. This paper addresses some of the network management issues relating to the use of such a network for data communications.
The effect of attenuated vaccinia virus AS strain on multiple myeloma; a case report. (1987)

The case of a 67-year-old male with IgA multiple myeloma successfully treated with AS strain of vaccinia virus is reported. The intravenous injection of this virus strain caused a definite decrease in the levels of monoclonal IgA from 1,309 mg/dl in the early stage of the treatment to 432 mg/dl on the 96th day of the regime. NK cell activity rose from 20.0% on the 10th day to 33% on the 106th day of the treatment. No adverse effects were observed throughout the entire course of the treatment. These results strongly suggest that AS strain vaccinia virus is a most promising and safe agent for the treatment of human malignancy. The possible mechanism of the beneficial effects of this virus strain is also briefly discussed.
Social-mobile applications (2005)

Mobile communications devices and applications are primarily designed to increase efficiency and productivity for professionals on the go. However, users invariably appropriate such technology to meet their social needs as well. For many people, particularly younger users, BlackBerry devices, Hiptops, and other handhelds primarily have a social function. A few small companies are beginning to exploit the growing demand for social-mobile applications, also known as mobile social-software services. One of the most popular MoSoSos applications is dodgeball, a New York-based social-mobile network. Dodgeball users also can broadcast messages, or "shout," to those in their network.
Use of the GTPγS ([35S]GTPγS and Eu‐GTPγS) binding assay for analysis of ligand potency and efficacy at G protein‐coupled receptors (2010)

This article is part of a themed section on Analytical Receptor Pharmacology in Drug Discovery. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2010.161.issue-6
Colonoscopy simulation (2007)

Effective colonoscopic screening for polyps with optical or virtual means requires adequate visualization of the entire colon surface. The purpose of this study is to investigate by simulation the degree of colon surface coverage during a routine optical colonoscopy (OC). To simulate OC, a generic wide angle and fisheye camera model is used to calibrate the fisheye lens of an Olympus endoscope with a field of view of 140 degrees. Then, the colonoscopy procedure is simulated using volume rendering fly-through along the hugging corner path in the retrograde direction. This shortest path is computed using the segmented and cleansed colon CT datasets. A large number of virtual fisheye cameras are placed along the shortest path to simulate the OC. At each camera position, a discrete volumetric ray-casting method is used to determine which triangles can be seen from the camera. Then, the percentage of the covered colon surface of the OC simulation is computed. Surface coverage at this point may serve as a rough estimate of readily visualized mucosa in a standard OC examination. We also compute the percentage of the covered colon surface for the virtual colonoscopy (VC) by placing virtual pinhole cameras on the central path of the colon and flying in only the antegrade direction as well as flying in both antegrade and retrograde directions. Our simulation study reveals that about 23% of the colon surface is missed in the standard OC examination and about 9% of the colon surface is missed in the VC examination when navigating in both directions.
Tracking Antigen-Specific CD8 T Lymphocytes in the Lungs of Mice Vaccinated with the Mtb72F Polyprotein (2005)

This study used a major histocompatibility complex class I tetramer reagent to track antigen-specific CD8 T cells in the lungs of mice immunized with the tuberculosis vaccine candidate Mtb72F. The results show that CD8 T cells recognizing an immunodominant Mtb32-specific epitope could be detected in significant numbers over the course of infection in mice exposed to low-dose aerosol challenge with Mycobacterium tuberculosis and that prior vaccination substantially increased the numbers of these cells early in the lungs. The effector phenotype of the cells was shown by the demonstration that many secreted gamma interferon, but very few contained granzyme B. As the course of the infection progressed, many activated CD8 T cells down-regulated expression of CD45RB and upregulated expression of the interleukin-7 receptor alpha chain, indicating a transition of these cells to a state of memory. These data support the hypothesis that M. tuberculosis-specific CD8 T cells can be targeted by vaccination with the Mtb72F polyprotein.
Mutations in the SHR5 Gene of Saccharomyces cerevisiae Suppress Ras Function and Block Membrane Attachment and Palmitoylation of Ras Proteins (1995)

We have identified a gene, SHR5, in a screen for extragenic suppressors of the hyperactive RAS2Val-19 mutation in the budding yeast Saccharomyces cerevisiae. SHR5 was cloned, sequenced, and found to encode a 23-kDa protein not significantly homologous to other proteins in the current data bases. Genetic evidence arguing that Shr5 operates at the level of Ras is presented. We tested whether SHR5, like previously isolated suppressors of hyperactivated RAS2, acts by affecting the membrane attachment and/or posttranslational modification of Ras proteins. We found that less Ras protein is attached to the membrane in shr5 mutants than in wild-type cells and that the Ras proteins are markedly underpalmitoylated, suggesting that Shr5 is involved in palmitoylation of Ras proteins. However, shr5null mutants exhibit normal palmitoyltransferase activity measured in vitro. Further, shr5null mutations attenuate Ras function in cells containing mutant Ras2 proteins that are not palmitoylated or farnesylated. We conclude that SHR5 encodes a protein that participates in the membrane localization of Ras but also interacts in vivo with completely unprocessed and cytosolic Ras proteins.
The Campylobacter jejuni Porin Trimers Pack into Different Lattice Types when Reconstituted in the Presence of Lipid (1997)

Purified major outer membrane protein of Campylobacter jejuni exhibited different classes of molecules by SDS/PAGE and immunoblotting. A high-molecular-mass product (120-140 kDa) was observed under mild conditions of solubilization, a folded monomeric form of 35 kDa was seen when treated at high SDS concentrations and finally, a single band around 45 kDa occurred when the sample was heated to 96 degrees C [Bolla, J. M., Loret, E., Zalewski. M. & Pages, J. M. (1995) J. Bacteriol. 177, 4266-4271]. The high-molecular-mass product was reconstituted into two-dimensional crystals in the presence of phospholipids and Mg2+. The C. jejuni porin required different conditions for successful reconstitution into two-dimensional crystals than the Escherichia coli porin OmpF. Electron microscopy and digital image processing of negatively stained specimens revealed a rectangular lattice with a unit cells size of a = 8.9 nm, b = 14.9 nm, an oblique lattice with a = 8.9 nm, b = 30.1 nm, gamma = 98 degrees, and a trigonal lattice with a = b = 9.6 nm. Projection maps were calculated to a resolution of 2 nm, and exhibited a trimeric protein with three stain-filled indentations.