gebhart/patrepeval huggingface dataset:
High-Throughput Multi-Antigen Microfluidic Fluorescence Immunoassays (2006)

Here we describe the development of a high-throughput multi-antigen microfluidic fluorescence immunoassay system. A 100-chamber polydimethylsiloxane (PDMS) chip performs up to 5 tests for each of 10 samples. In this particular study system, the specificity of detection was demonstrated, and calibration curves were produced for C-reactive protein (CRP), prostate-specific antigen (PSA), ferritin, and vascular endothelial growth factor (VEGF). The measurements show sensitivity at and below clinically normal levels (with a signal-to-noise ratio >8 at as low as 10 pM antigen concentration). The chip uses 100 nL per sample for all tests. The developed system is an important step toward derivative immunoassay applications in scientific research and "point-of-care" testing in medicine.
Gas-phase separations of protease digests (1998)

A mixture of peptides from a complete tryptic digest of ubiquitin has been analyzed by ion mobility/time-of-flight mass spectrometry techniques. All components of the mixture were electrosprayed and ions were separated in the gas phase based on differences in their mobilities through helium before being dispersed into a time-of-flight mass spectrometer for mass-to-charge analysis. The data show that ions separate into families primarily according to differences in their charge states and, to a lesser extent, differences in conformation. This approach reduces spectral congestion typically associated with electrosprayed mixtures and provides charge assignments for mass-to-charge ratio data. Gas-phase separations of ions appear to provide a new physical basis for characterizing components of biological mixtures.
Criteria for Evaluation of Novel Markers of Cardiovascular Risk (2009)

There is increasing interest in utilizing novel markers of cardiovascular disease risk, and consequently, there is a need to assess the value of their use. This scientific statement reviews current concepts of risk evaluation and proposes standards for the critical appraisal of risk assessment methods. An adequate evaluation of a novel risk marker requires a sound research design, a representative at-risk population, and an adequate number of outcome events. Studies of a novel marker should report the degree to which it adds to the prognostic information provided by standard risk markers. No single statistical measure provides all the information needed to assess a novel marker, so measures of both discrimination and accuracy should be reported. The clinical value of a marker should be assessed by its effect on patient management and outcomes. In general, a novel risk marker should be evaluated in several phases, including initial proof of concept, prospective validation in independent populations, documentation of incremental information when added to standard risk markers, assessment of effects on patient management and outcomes, and ultimately, cost-effectiveness.
T cell receptor V alpha repertoire of infiltrating T cells in labial salivary glands from patients with Sjögren's syndrome. (1994)

The TCR V alpha repertoire of infiltrating T cells from the lips of 2 patients with SS was relatively restricted in individual patients, thereby suggesting the limited heterogeneity of these cells in salivary glands.
Taxus spp. Needles Contain Amounts of Taxol Comparable to the Bark of Taxus brevifolia: Analysis and Isolation (1990)

New sources for the antitumor natural product taxol [1] are needed as demands for this promising cancer chemotherapeutic agent increase. Presently, supplies of taxol for clinical studies are obtained from the bark of Taxus brevifolia, a potentially limited source. Using analytical methods, the needles and stems of six Taxus species have been examined for taxol [1] and 10-deacetylbaccatin III [5], a related compound that can be converted to taxol through a semi-synthetic route. Amounts of taxol comparable to quantities reported from the bark of T. brevifolia were found in the needles of four of the Taxus species investigated. In addition, taxol was isolated from the needles of one Taxus species. Thus, Taxus needles may provide a renewable source of this valuable compound.
Cell Breathing in Wireless LANs: Algorithms and Evaluation (2007)

Wireless LAN administrators often have to deal with the problem of sporadic client congestion in popular locations within the network. Existing approaches that relieve congestion by balancing the traffic load are encumbered by the modifications that are required to both access points and clients. We propose cell breathing, a well-known concept in cellular telephony, as a load balancing mechanism to handle client congestion in a wireless LAN. We develop power management algorithms for controlling the coverage of access points to handle dynamic changes in client workloads. We further incorporate hand-off costs and manufacturer specified power level constraints into our algorithms. Our approach does not require modification to clients or to the standard. It only changes the transmission power of beacon packets and does not change the transmission power of data packets to avoid the interactions with auto-rating. We analyze the worst-case bounds of the algorithms and show that they are either optimal or close to optimal. In addition, we evaluate our algorithms empirically using synthetic and real wireless LAN traces. Our results show that cell breathing significantly outperforms the commonly used fixed power scheme and performs at par with sophisticated load balancing schemes that require changes to both the client and access points
Gremlin, a Bone Morphogenetic Protein Antagonist, Is a Crucial Angiogenic Factor in Pituitary Adenoma (2015)

Gremlin is an antagonist of bone morphogenetic protein (BMP) and a major driving force in skeletal modeling in the fetal stage. Several recent reports have shown that Gremlin is also involved in angiogenesis of lung cancer and diabetic retinopathy. The purpose of this study was to investigate the role of Gremlin in tumor angiogenesis in pituitary adenoma. Double fluorescence immunohistochemistry of Gremlin and CD34 was performed in pituitary adenoma tissues obtained during transsphenoidal surgery in 45 cases (7 PRLoma, 17 GHoma, 2 ACTHoma, and 2 TSHoma). Gremlin and microvascular density (MVD) were detected by double-immunofluorescence microscopy in CD34-positive vessels from tissue microarray analysis of 60 cases of pituitary adenomas (6 PRLoma, 23 GHoma, 22 NFoma, 5 ACTHoma, and 4 TSHoma). In tissue microarray analysis, MVD was significantly correlated with an increased Gremlin level (linear regression: P < 0.005, r (2) = 0.4958). In contrast, Gremlin expression showed no correlation with tumor subtype or Knosp score. The high level of expression of Gremlin in pituitary adenoma tissue with many CD34-positive vessels and the strong coherence of these regions indicate that Gremlin is associated with angiogenesis in pituitary adenoma cells.
Synthesis of C-Glycosylic Compounds Using Three-Membered Cyclic Intermediates (2000)

Numerous methods for preparation of C-glycosylic compounds (Cglycosides) have been developed. One general approach to the synthesis of these important O-glycoside analogs is based on the use of three-membered cyclic intermediates. The review is focused on the application of glycal and exo-glycal derived epoxides and episulfonium and iodonium ions for preparation of Cglycosides. Reactions of glycal epoxides with organocuprates, Grignard and organolithium reagents, allylsilane, sodio malonate, and lithium alkynyl derivatives have been shown to be convenient for stereoselective synthesis of both α- and β-C-glycosides. The unprotected C(2)-hydroxyl group in the products can be removed in two steps providing an easy excess to 2-deoxy-C-glycosides. Electrophilic addition of arylsulfenyl chloride (ArSCl) to glycals has afforded 2- (arylthio)pyranosyl chlorides. Upon the treatment with a Lewis acid, the chlorides have been converted to episulfonium-like intermediates. Reactions of the latter species with silyl enol ethers, TMSCN, allylsilanes, vinyl ethers, and heteroaromatic compounds have opened a new synthetic route to 2- (arylthio)-β-C-glycosides having a variety of functional groups in the lateral chain. The 2-arylthio group in the products can be selectively removed using Raney Ni or n-Bu3SnH/AIBN. Episulfonium ions generated from ArSCl adducts of 1-methylene sugars have reacted with O- and C-nucleophiles to afford Oketopyranosides and 1,1-dialkyl C-glycosides, respectively. Acid catalyzed and nucleophilic ring openings of spiro epoxides obtained from exo-glycals have occurred with opposite stereoselectivity. Iodoniumpromoted reactions of exo-glycals have led to O-ketopyranoside derivatives.
Towards mobile cryptography (2002)

Mobile code technology has become a driving force for recent advances in distributed systems. The concept of the mobility of executable code raises major security problems. In this paper, we deal with the protection of mobile code from possibly malicious hosts. We conceptualize the specific cryptographic problems posed by mobile code, and we are able to provide a solution for some of these problems. We present techniques to achieve "non-interactive evaluation with encrypted functions" in certain cases and give a complete solution for this problem in important instances. We further present a way in which an agent might securely perform a cryptographic primitive-digital signing-in an untrusted execution environment. Our results are based on the use of homomorphic encryption schemes and function composition techniques.
[A study on the allelic deletion and mutation of FHIT gene in human non-small cell lung cancer]. (2001)

The alteration of FHIT gene is mainly allelic loss and the frequency of allelic mutation is rare. FHIT gene alterations preferentially occur in squamous cell carcinoma patients and smokers, and FHIT gene may be a candidate molecular target of carcinogenesis in tobacco smoker. Allelic deletion of FHIT gene might be an early molecular event in smoking-related lung cancer.
File compression using variable length encodings (1972)

Withing a digital system a symbol is represented as a grouping of digits. If the length of this group is variable, rather than fixed, it is theoretically possible to achieve reductions in the total number of digits required to represent a symbol string. This paper discusses some hardware and software techniques for carrying out the encoding and decoding and gives some observations of the economies that might be achieved by their use. The final conclusions are cautiously optimistic.
Evaluation of Importance of Toll-like Receptor 4 in Acute Streptococcus pneumoniae Sinusitis in Mice (2005)

Our studies in mice suggest that stimulation of TLR4 plays a minor role in the overall response to S. pneumoniae infection of the upper airway, and stimulating this receptor before infection does not significantly enhance the immune response of immunocompetent mice to clear S. pneumoniae infection.
Novel Cdc42-binding proteins Gic1 and Gic2 control cell polarity in yeast (1997)

Cdc42p, a Rho-related GTP-binding protein, regulates cytoskeletal polarization and rearrangements in eukaryotic cells, but the effectors mediating this control remain unknown. Through the use of the complete yeast genomic sequence, we have identified two novel Cdc42p targets, Gic1p and Gic2p, which contain consensus Cdc42/Rac interactive-binding (CRIB) domains and bind specifically to Cdc42p-GTP. Gic1p and Gic2p colocalize with Cdc42p as cell polarity is established during the cell cycle and during mating in response to pheromones. Cells deleted for both GIC genes exhibit defects in actin and microtubule polarization similar to those observed in cdc42 mutants. Finally, the interaction of the Gic proteins and Cdc42p is essential, as mutations in the CRIB domain of Gic2p that eliminate Cdc42p binding disrupt Gic2p localization and function. Thus, Gic1p and Gic2p define a novel class of Cdc42p targets that are specifically required for cytoskeletal polarization in vivo.
Practical Synthesis of 3-Amino-5-tert-butylisoxazole from 4,4-Dimethyl-3-oxopentanenitrile with Hydroxylamine (1991)

A good yield of 3-amino-5-tert-butylisoxazole (3) was obtained regioselectively from a reaction of 4,4-dimethyl-3-oxopentanenitrile (1) with hydroxylamine in the aqueous solution of which was adjusted to weak basic, followed by treatment of the resulting 4,4-dimethyl-3-oxopentaneamidoxime (2) with hydrochloric acid
Plasma generation and plasma sources (2000)

This paper reviews the most commonly used methods for the generation of plasmas with special emphasis on non-thermal, low-temperature plasmas for technological applications. We also discuss various technical realizations of plasma sources for selected applications. This paper is further limited to the discussion of plasma generation methods that employ electric fields. The various plasmas described include dc glow discharges, either operated continuously (CW) or pulsed, capacitively and inductively coupled rf discharges, helicon discharges, and microwave discharges. Various examples of technical realizations of plasmas in closed structures (cavities), in open structures (surfatron, planar plasma source), and in magnetic fields (electron cyclotron resonance sources) are discussed in detail. Finally, we mention dielectric barrier discharges as convenient sources of non-thermal plasmas at high pressures (up to atmospheric pressure) and beam-produced plasmas. It is the main objective of this paper to give an overview of the wide range of diverse plasma generation methods and plasma sources and highlight the broad spectrum of plasma properties which, in turn, lead to a wide range of diverse technological and technical applications.
A Multicenter Analysis of Percutaneous Discectomy (1990)

This study was performed to evaluate a group of patients undergoing percutaneous discectomy. All patients had a single level unilateral L4-5 or L5-S1 disc herniation documented on either computer tomographic (CT) scan, myelogram, and/or magnetic resonance imaging (MRI). Average follow-up after percutaneous discectomy was 16.8 months (range, 2-46 months). The average hospitalization time was 1.7 days (range, 1-5 days). Only 21 patients (55%) were able to return to work after the procedure. Thirteen patients ultimately underwent surgical discectomy for continued symptoms after the procedure. The additional 4 patients did not undergo surgical discectomy and never returned to work. Of those 25 percutaneous discectomy patients who did not undergo surgical discectomy, there was significantly more pain, residual weakness, and numbness compared with the patients undergoing surgical discectomy. The results of this study clearly indicate that percutaneous discectomy does not appear to be as predictable or successful a treatment modality as surgical discectomy.
Rendering high dynamic range images (2000)

In this paper, we review several algorithms that have been proposed to transform a high dynamic range image into a reduced dynamic range image that matches the general appearance of the original. We organize these algorithms into two categories: tone reproduction curves (TRCs) and tone reproduction operators (TROs). TRCs operate pointwise on the image data, making the algorithms simple and efficient. TROs use the spatial structure of the image data and attempt to preserve local image contrast.
A model of the stimulation of a nerve fiber by electromagnetic induction (1990)

A model is presented to explain the physics of nerve stimulation by electromagnetic induction. Maxwell's equations predict the induced electric field distribution that is produced when a capacitor is discharged through a stimulating coil. A nonlinear Hodgkin-Huxley cable model describes the response of the nerve fiber to this induced electric field. Once the coil's position, orientation, and shape are given and the resistance, capacitance, and initial voltage of the stimulating circuit are specified, this model predicts the resulting transmembrane potential of the fiber as a function of distance and time. It is shown that the nerve fiber is stimulated by the gradient of the component of the induced electric field that is parallel to the fiber, which hyperpolarizes or depolarizes the membrane and may stimulate an action potential. Finally, it predicts complicated dynamics such as action potential annihilation and dispersion.
Large-scale purification and characterization of the Escherichia coli rep gene product (1989)

We report a procedure for the large-scale purification of the Escherichia coli Rep protein, a helicase that is involved in the replication of the E. coli chromosome as well as a number of single-stranded bacteriophages. The procedure starts with E. coli cells harboring an overproducing plasmid, pRepO, in which the E. coli rep gene is under transcriptional control of the inducible lambda PL promoter (Colasanti, J., and Denhardt, D. T. (1987) Mol. Gen. Genet. 209, 382-390). The purification procedure results in greater than 98% pure Rep protein, which is free of contaminating nuclease activity, with yields of 40-50 mg of Rep protein/50 g of induced MZ-1/pRepO cells. We also show that cell death occurs upon inducing such a large overproduction of the E. coli Rep protein in MZ-1/pRepO. The Rep protein purified by this procedure has high specific single-stranded DNA-dependent ATPase activity, as well as helicase activity, with an apparent 3' to 5' directionality. The extinction coefficient of purified E. coli Rep protein is epsilon 280 = 1.16 +/- 0.04 ml mg-1 cm-1 (8.47 +/- 0.28 X 10(4) M-1 cm-1) in 10 mM Tris (pH 7.5), 20% (v/v) glycerol, 0.10 M NaCl at 25 degrees C. The solubility properties of the purified Rep protein have been examined as a function of glycerol, NaCl, MgCl2, ATP, and ADP concentrations at 25 and 37 degrees C (pH 7.5). Rep protein solubility decreases significantly with decreasing concentrations of glycerol and monovalent salt and increasing temperature; however, the presence of 1.5 mM ATP or ADP or MgCl2 at low NaCl concentrations increases the solubility. At 4 degrees C, in the presence of 20% glycerol and greater than or equal to 50 mM NaCl, the free Rep protein exists as a stable monomer under all conditions examined (+/- ATP and +/- MgCl2). The single-stranded DNA-dependent ATPase activity decreases with increasing glycerol concentration, such that in 25% (v/v) glycerol it has approximately 40% of its activity as compared to solutions that contain no glycerol. The dependence of the single-stranded DNA-dependent ATPase activity on salt concentration for a series of monovalent salts indicates the presence of both cation and anion effects, with decreasing activity in the order glutamate greater than acetate greater than chloride. The ability to obtain highly purified E. coli Rep protein in large quantities with relative ease will greatly facilitate physical characterizations of the protein and its interactions with DNA.
Binding of Antithrombin III and Thrombin to Immobilized Heparin under Flow Conditions (1996)

The chemical immobilization of heparin onto polymeric materials through hydrophilic spacer groups was performed to improve the hemocompatibility of blood-contacting devices. Significant data have been gathered attesting to the biological activity of immobilized heparin in static in vitro studies (clotting times) and dynamic in vivo studies (thrombus formation). However, few studies have been performed to investigate the binding kinetics of spacer-immobilized heparin under flow (shear stress) with antithrombin III (ATIII) and thrombin. To help elucidate this binding mechanism, a mathematical model was developed which parallels experiments to measure protein binding and dissociation at the heparin immobilized surface under flow conditions. Heparinized tubing was prepared by chemically immobilizing a high-ATIII-affinity fraction of heparin onto the surface of poly(ethylene)-oxide grafted, poly(styrene-co-p-aminostyrene)-coated polyethylene tubing. ATIII was first bound onto the immobilized heparin, followed by the introduction of thrombin to interact with ATIII. The concentration of thrombin-ATIII complex (TAT) flowing from the tubing was determined, and the dissociation rate constants (kD) of TAT from immobilized heparin were calculated as a function of flow rate. The results indicate that the dissociation rate constant of TAT varied with flow rate, especially low flow rates, high flow rates, and turbulent flow. As the TAT complex dissociates from immobilized heparin, this "recovered" heparin is available for subsequent binding of more ATIII and thrombin. These in vitro mathematical results may help support mechanisms and hypotheses generated for the biological activity of spacer-immobilized heparin observed during long-term in vivo and ex vivo experiments.
Mesoporous Thin Films of “Molecular Squares” as Sensors for Volatile Organic Compounds (2000)

Mesoporous thin films of rhenium-based “molecular squares”, [Re(CO)3Cl(L)]4 (L = pyrazine, 4,4‘- bipyridine), have been utilized as sensors for volatile organic compounds (VOCs). The sensing was conducted using a quartz crystal microbalance with the target compounds present in the gas phase at concentrations ranging from 0.05 to 1 mM. Quartz crystal microbalance studies with these materials allowed for distinction between the following VOCs: (1) small aromatic versus aliphatic molecules of almost identical size and volatility and (2) an array of benzene molecules derivatized with electron donating/withdrawing substituents. The experiments suggest that the mesoporous host materials interact with VOC guest molecules through both van der Waals and weak charge-transfer interactions. In addition, size selectivity is shown by exposure of the molecular squares to cyclic ethers of differing size.
Coating Nanomagnetic Particles for Biomedical Applications (2011)

Magnetic particles with dimensions ranging from the nanometer to the micrometer scales are being used in an increasing number of medical applications, since the mid-1970s. The most important properties of magnetic particles for clinical diagnostics and medical therapies are clearly nontoxicity, biocompatiblilty, injectability, and high-level accumulation in the target tissue or specific organ, being strictly and spatially confined to the planned region of the internal body The unique feature of NMPs to be guided by an external magnetic field has been used in magnetic resonance imaging (MRI), tissue repair, hyperthermia, drug delivery, and in cell separation For these biomedical applications, magnetic particles exhibiting superparamagnetic behavior at room temperature are preferred because they do not retain any magnetism after removal of the magnetic field. For NMPs, this behavior can be explained by their extraordinarily reduced sizes (Mrup et al., 1976; The magnetization relaxation depends on KV/kT At a certain reduced size (volume), KV becomes comparable to the thermal energy kT. As a result, the magnetization of the particle fluctuates rapidly from one direction to another due to the thermal agitation, leaving no net magnetic moment. At this magnetic stage, the particle is said to be superparamagnetic Fig. This shows that a particle can be magnetized under an external magnetic field (H), reaching a maximum moment (M) when the field is strong enough. However, there is no remnant magnetic moment, i.e. without an external magnetic field, the net moment of the particle is randomized to zero. Therefore, these superparamagnetic nanoparticles are very useful for biomedical applications as they are not subject to strong magnetic interactions in the dispersion and are readily stabilized in physiological conditions (