gebhart/patrepeval huggingface dataset:
Electrophoretic sequencing of heparin/heparan sulfate oligosaccharides using a highly sensitive fluorescent end label (2001)

The sequencing of heparan sulfate oligosaccharides has recently become possible using Integral Glycan Sequencing, which utilizes a combination of chemical and enzymatic degradation steps followed by polyacrylamide gel electrophoresis. This technique has previously employed the fluorescent label, anthranilic acid, and has been used to sequence low nmol amounts of purified saccharides. Here, we present an improved method, which uses the alternative label, 7-aminonapthalene-1,3-disulfonic acid, the reducing agent sodium triacetoxyborohydride and optimizes the nitrous acid step in heparin/heparan sulfate degradation. These improvements increase the sensitivity at least ten-fold taking the amount of starting material required into the pmol range. We show that this label is compatible with the integral glycan sequencing methodology and demonstrate its application to the sequencing of chemically modified heparin derivatives. Advances in sequencing techniques for heparan sulfate saccharides will permit detailed structure-function studies and will in the future underpin novel proteomics-based approaches aimed at studying their diverse functional roles as protein regulators.
A pact with the devil (2006)

We study malware propagation strategies which exploit not the incompetence or naivety of users, but instead their own greed, malice and short-sightedness. We demonstrate that interactive propagation strategies, for example bribery and blackmail of computer users, are effective mechanisms for malware to survive and entrench, and present an example employing these techniques. We argue that in terms of propagation, there exists a continuum between legitimate applications and pure malware, rather than a quantised scale.
[Biophsical study of dental tissues under the effect of a local strontium application]. (1976)

Microradiographic and electronmicroscopic observations show that topical application of concentrated strontium chloride solution on an abraded dentinal surface caused the formation in the dentine of very compact superficial layer composed of fine granules and with a high degree of radiodensity. This layer not only forms a continuous deposit on the superficial zone, but also penetrates and fills the canclicules to a certain distance. A barrier is thus created, diminishing the permeability of the dentine, which would explain the desensitization of the tooth. Electron probe microanalysis and X-ray diffraction studies show that the fundamental mechanism of the formation of strontium deposits is an exchange with the calcium fo the dentinal tissue, and recrystallization in the form of strontium apatite.
Role of the sympathetic nervous system in the genesis of ventricular arrhythmia. (1990)

Activation of the sympathetic nervous system is an important factor in the genesis of ventricular arrhythmias in patients with impaired ventricular function. Such patients have an appropriate substrate that is capable of generating rhythm abnormalities, which may be related to enhanced automaticity, triggered automaticity, and reentrant mechanisms; all three mechanisms are markedly potentiated by the action of catecholamines. Additionally, the sympathetic nervous system can provoke the development of hypokalemia and ischemia (which can independently lead to the occurrence of rhythm disturbances), and catecholamines may negate the beneficial electrophysiological actions of antiarrhythmic drugs. A substantial amount of experimental data implicates the sympathetic nervous system as a potent stimulus for ventricular tachyarrhythmias and sudden cardiac death, especially in the setting of myocardial ischemia. Two important mechanisms that have been identified include 1) enhanced sympathetic outflow from the central nervous system and 2) nonuniform myocardial denervation resulting in beta-receptor up-regulation and catecholamine hypersensitivity in the infarct zone. Disruption of sympathetic neural innervation of the heart and the use of beta-blocking agents may reduce the occurrence of sudden death and improve survival in animal models of arrhythmias and in some subsets of patients, including those with the long QT syndrome, a recent myocardial infarction, and perhaps those with a cardiomyopathy. The mechanism of this beneficial effect remains to be defined.
Cutting Edge: C3d Functions as a Molecular Adjuvant in the Absence of CD21/35 Expression (2004)

Complement component C3 covalently attaches to Ags following activation, where the C3d cleavage fragment can function as a molecular adjuvant to augment humoral immune responses. C3d is proposed to exert its adjuvant-like activities by targeting Ags to the C3d receptor (CD21/35) expressed by B cells and follicular dendritic cells. To directly assess the importance of CD21/35 in mediating the immunostimulatory effects of C3d, CD21/35-deficient (CD21/35(-/-)) mice were immunized with streptavidin (SA), SA-C3dg tetramers, recombinant HIV gp120 (gp120), or gp120 fused with linear multimers of C3d. Remarkably, SA- and gp120-specific Ab responses were significantly augmented in CD21/35(-/-) mice when these Ags were complexed with C3d in comparison to Ag alone. In fact, primary and secondary Ab responses and Ab-forming cell responses of CD21/35(-/-) mice approached those of wild-type mice immunized with SA-C3dg and gp120-C3d. Thus, C3d can function as a molecular adjuvant in the absence of CD21/35 expression.
Light-assisted direct-write of 3D functional biomaterials (2013)

Light-assisted 3D direct-printing of biomaterials and cellular-scaffolds has the potential to develop novel lab-on-a-chip devices (LOCs) for a variety of biomedical applications, from drug discovery and diagnostic testing to in vitro tissue engineering and regeneration. Direct-writing describes a broad family of fabrication methods that typically employ computer-controlled translational stages to manufacture structures at multi-length scales. This review focuses on light-assisted direct-write fabrication for generating 3D functional scaffolds with precise micro- and nano-architecture, using both synthetic as well as naturally derived biomaterials. Two bioprinting approaches are discussed in detail - projection printing and laser-based systems - where each method is capable of modulating multiple scaffold parameters, such as 3D architecture, mechanical properties (e.g. stiffness), Poisson's ratio, chemical gradients, biological cell distributions, and porosity. The light-assisted direct-writing techniques described in this review provide the reader with alternative approaches to fabricate 3D biomaterials for utility in LOCs.
Palmitic Acid Is a Novel CD4 Fusion Inhibitor That Blocks HIV Entry and Infection (2009)

The high rate of HIV-1 mutation and the frequent sexual transmission highlight the need for novel therapeutic modalities with broad activity against both CXCR4 (X4) and CCR5 (R5)-tropic viruses. We investigated a large number of natural products, and from Sargassum fusiforme we isolated and identified palmitic acid (PA) as a natural small bioactive molecule with activity against HIV-1 infection. Treatment with 100 microM PA inhibited both X4 and R5 independent infection in the T cell line up to 70%. Treatment with 22 microM PA inhibited X4 infection in primary peripheral blood lymphocytes (PBL) up to 95% and 100 microM PA inhibited R5 infection in primary macrophages by over 90%. Inhibition of infection was concentration dependent, and cell viability for all treatments tested remained above 80%, similar to treatment with 10(-6)M nucleoside analogue 2', 3'-dideoxycytidine (ddC). Micromolar PA concentrations also inhibited cell-to-cell fusion and specific virus-to-cell fusion up to 62%. PA treatment did not result in internalization of the cell surface CD4 receptor or lipid raft disruption, and it did not inhibit intracellular virus replication. PA directly inhibited gp120-CD4 complex formation in a dose-dependent manner. We used fluorescence spectroscopy to determine that PA binds to the CD4 receptor with K(d) approximately 1.5 +/- 0.2 microM, and we used one-dimensional saturation transfer difference NMR (STD-NMR) to determined that the PA binding epitope for CD4 consists of the hydrophobic methyl and methelene groups located away from the PA carboxyl terminal, which blocks efficient gp120-CD4 attachment. These findings introduce a novel class of antiviral compound that binds directly to the CD4 receptor, blocking HIV-1 entry and infection. Understanding the structure-affinity relationship (SAR) between PA and CD4 should lead to the development of PA analogs with greater potency against HIV-1 entry.
Optimization of Steam Explosion to Enhance Hemicellulose Recovery and Enzymatic Hydrolysis of Cellulose in Softwoods (1999)

A combination of Douglas fir heartwood and sapwood chips were steam pretreated under three conditions as measured by the Severity Factor (log R°), which incorporated the time, temperature/pressure of pretreatment. By adjusting the steam pretreatment conditions, it was hoped to recover the majority of the hemicellulose component as monomers in the water-soluble stream, while providing a cellulosic-rich, water-insoluble fraction that could be readily hydrolyzed by cellulases. These three conditions were chosen to represent either high hemicellulose sugar recovery (low severity [L], log R° = 3.08), high-enzyme hydrolyzability of the cellulosic component (high severity [H], log R° = 4.21), and a compromise between the two conditions (medium severity [M], log R° = 3.45). The medium-severity pretreatment conditions (195°C, 4.5 min, 4.5% SO2. logR° = 3.45) gave the best compromise in terms of relatively high hemicellulose recovery after stream pretreatment and the subsequent efficiency of enzymatic hydrolysis of the water-insoluble cellulosic fraction. The percent recovery of the original hemicellulose in the water-soluble fraction dropped significantly when the severity was increased (L-76.8%, M-64.7%, and H-37.5%). However, the ease of enzymatic hydrolysis of the cellulose-rich, water-insoluble fraction increased with increasing severity (L-24%, M-86.6%, and H-97.9%). Although more severe pretreatment conditions provided optimum hydrolysis of the cellulosic component, less severe conditions resulted in better recovery of the combined hemicellulose and cellulosic components.
Induction of granulomatous experimental autoimmune thyroiditis in mice with in vitro activated effector T cells and anti-IFN-γ antibody (1992)

Experimental autoimmune thyroiditis (EAT) can be induced in mice after the transfer of mouse thyroglobulin (MTg)-sensitized donor spleen cells that have been activated in vitro with MTg. CD4+ T cells are required for the transfer of EAT in this model. Because CD4+ T cells produce various lymphokines, such as IFN-gamma, that may be involved in the activation or regulation of the immune response to MTg and the development of EAT, the present study was undertaken to determine whether a neutralizing mAb to IFN-gamma could modulate the induction or expression of EAT. The anti-IFN-gamma mAb XMG-1.2 had no effect on sensitization of donor cells. However, addition of XMG-1.2 mAb during in vitro activation of MTg-primed spleen cells resulted in more severe EAT in recipient mice. The thyroid lesions in recipients of cells cultured with MTg and XMG-1.2 mAb also exhibited granulomatous changes, which differed qualitatively from the predominantly lymphocytic cell infiltrates in recipients of cells cultured with MTg alone. Recipients of MTg-activated spleen cells also developed severe granulomatous EAT when they were given injections of XMG-1.2 mAb. The effects of XMG-1.2 could be neutralized by IFN-gamma. Recipients of cells cultured in the presence of XMG-1.2 mAb had augmented autoantibody responses, although there were no apparent differences in the IgG subclass distribution of the anti-MTg autoantibody responses. These studies suggest that neutralization of endogenous IFN-gamma results in increased activity of cells capable of inducing granulomatous EAT in mice.
HAL: A High-Speed Logic Simulation Machine (1985)

The architecture of a very-high-speed logic simulation machine (HAL), which can simulate up to one-half million gates and 2M-byte memory chips at a 5 ms clock speed, is described. This machine makes it possible to debug the total system-CPU, main memory, cache memory and control storage-before the actual machine is fabricated. HAL employs parallel and pipeline processing, and event-driven, block-level logic simulation. The prototype system for a 32-processor system has been constructed and is now in use as a tool for large mainframe computer development. HAL is more than a thousand times faster than existing software logic simulators.
Dielectrophoretic Concentration and Separation of Live and Dead Bacteria in an Array of Insulators (2004)

Insulator-based (electrodeless) dielectrophoresis (iDEP) is an innovative approach in which the nonuniform electric field needed to drive DEP is produced by insulators, avoiding problems associated with the use of electrodes. Live and dead Escherichia coli were concentrated and selectively released by applying stepped DC voltages across a microchannel containing an array of insulating posts etched in glass. The only electrodes present were two platinum wires placed in the inlet and outlet reservoirs, producing mean electric fields of up to 200 V/mm across the insulators. The cells were labeled with Syto 9 and propidium iodide and imaged through a fluorescent microscope. Cell trapping and release were controlled by modifying the relative responses of electrokinesis and DEP by adjusting the magnitude of the applied voltage. Dead cells were observed to have significantly lower dielectrophoretic mobility than live cells, whereas the electrokinetic mobilities of live and dead cells were indistinguishable. The locations of the bands of differentially trapped cells were consistent with predictions. In addition, cells were selectively trapped and concentrated against backgrounds of 1- and 0.2-microm carboxylate-modified polystyrene particles. This first application of iDEP for simultaneous live/dead bacteria separation and concentration illustrates its potential as a front-end method for bacterial analysis.
Nickel induced crystallization of amorphous silicon thin films (1998)

Nickel (Ni) induced crystallization of amorphous silicon (a-Si) has been studied by selective deposition of Ni on a-Si thin films. The a-Si under and near the Ni-covered regions was found to be crystallized after heat treatment at 500 °C from 1 to 90 h. Micro-Auger electron spectroscopy revealed that a large amount of Ni stayed in the region under the original Ni coverage, but no Ni was detected either in the crystallized region next to the Ni coverage or in the amorphous region beyond the front of the laterally crystallized Si. X-ray photoelectron spectroscopy revealed a nonuniform Ni distribution through the depth of the crystallized film under the original Ni coverage. In particular, a Ni concentration peak was found to exist at the interface of the crystallized Si and the buried oxide. It was found that a layer of 5-nm-thick Ni could effectively induce lateral crystallization of over 100 μm of a-Si, but the lateral crystallization rate was found to decrease upon extended heat treatment. Transmission electron microscopy analysis showed that the crystallized film under the Ni coverage was composed of randomly oriented fine grains, while that outside the Ni coverage was mainly composed of large (110)-oriented grains. A unified mechanism is proposed to explain the Ni induced crystallization of a-Si and possible reasons for the reduction in the lateral crystallization rate are discussed.
Developmentally regulated expression of vascular smooth muscle myosin heavy chain isoforms (1989)

Two types of smooth muscle myosin heavy chain (MHC) isoforms, SM1 and SM2, were recently identified to have different carboxyl termini (Nagai, R., Kuro-o, M., Babij, P., and Periasamy, M. (1989) J. Biol. Chem. 264, 9734-9737). SM1 and SM2 are considered to be generated from a single gene through alternative RNA splicing. In this study we investigated expression of vascular MHC isoforms during development in rabbits at the mRNA, protein, and histological levels. In adults, all smooth muscle cells reacted with both anti-SM1 and anti-SM2 antibodies on immunofluorescence, suggesting the coexpression of SM1 and SM2 in a single cell. In fetal and perinatal rabbits, however, only anti-SM1 antibody consistently reacted with smooth muscles. Reactivity with anti-SM2 antibody was negative in the fetal and neonatal blood vessels and gradually increased during 30 days after birth. These developmental changes in SM1 and SM2 expression at the histological level coincided with mRNA expression of each MHC isoform as determined by S1 nuclease mapping, indicating that expression of SM1 and SM2 is controlled at the level of RNA splicing. However, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of myosin from fetal and perinatal aortas revealed the presence of large amount of SM2. Interestingly, fetal SM2 did not cross-react with our anti-SM2 antibody on immunoblotting. We conclude that expression of SM1 and SM2 are differentially regulated during development and that a third type of MHC isoform may exist in embryonic and perinatal vascular smooth muscles.
Noninvasive genomic detection of melanoma (2011)

These results demonstrate that EGIR-harvested specimens can be used to detect melanoma accurately by means of a 17-gene genomic biomarker.
Channel and interference mitigation in the MUOS base-to-user link (2008)

The mobile user objective system (MUOS) will provide global communication for the U.S. government using WCDMA technology. The base-to-user (B2U) physical link is subject to imperfections consisting of multi-path channel effects, multiple high-powered non-MUOS in-band interferers, and competing MUOS WCDMA signals (multiple access interference (MAI)). Various techniques are developed to mitigate the effects of these channel imperfections. This paper analyzes the effects on signal-to-noise ratio (SNR) caused by multi-path channel propagation, undesired interference within the B2U spectrum, and MAI.
Hormonal Changes and Catabolic/Anabolic Imbalance in Chronic Heart Failure and Their Importance for Cardiac Cachexia (1997)

Cachexia is more closely associated with hormonal changes in CHF than conventional measures of the severity of CHF. This study suggests that the syndrome of heart failure progresses to cardiac cachexia if the normal metabolic balance between catabolism and anabolism is altered.
Complications Following Injection of Soft-Tissue Fillers (2013)

Although soft-tissue fillers are a popular choice for minimally invasive rejuvenation of the face, physicians should be aware of the serious potential adverse effects, recognize their presentations, and have appropriate treatments readily available.
Caustic Spray for Sewer Crown Corrosion Control (1993)

A novel method to control sewer crown corrosion which involves spray application of a caustic solution to the sewer crown is described. Corrosion control using this concept is based on raising the sewer crown pH, thereby, neutralizing the sulfuric acid formed by the Thiobacillus thiooxidans, inactivating and possibly destroying these bacteria, and limiting the formation of new colonies. An experimental system to apply the caustic solution was designed, built, and put into operation in June 1989. Currently, the Districts continue to use this system for both research and control of sulfide corrosion in selected sewers. A description of the caustic spray process is provided.
Discrete-time modeling of transition noise dominant channels and study of detection performance (1991)

Discrete-time modeling of transition-noise-dominant channels is considered which facilitates performance analysis of various sample-data detection schemes. Based on the proposed channel description method in the presence of transition noise, expressions for signal-to-total-noise-power ratios associated with a few selected detection schemes are derived. Under the assumption of a Lorentzian step response and perfect equalization, a comparison is made among different detectors based on the signal-to-noise ratio figure-of-merit evaluated as a function of linear density.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Superconducting Quantum Node for Entanglement and Storage of Microwave Radiation (2015)

Superconducting circuits and microwave signals are good candidates to realize quantum networks, which are the backbone of quantum computers. We have realized a quantum node based on a 3D microwave superconducting cavity parametrically coupled to a transmission line by a Josephson ring modulator. We first demonstrate the time-controlled capture, storage, and retrieval of an optimally shaped propagating microwave field, with an efficiency as high as 80%. We then demonstrate a second essential ability, which is the time-controlled generation of an entangled state distributed between the node and a microwave channel.
Multi-level regulation and metabolic scaling (2005)

Metabolic control analysis has revealed that flux through pathways is the consequence of system properties, i.e. shared control by multiple steps, as well as the kinetic effects of various pathways and processes over each other. This implies that the allometric scaling of flux rates must be understood in terms of properties that pertain to the regulation of flux rates. In contrast, proponents of models considering the scaling of branching or fractal-like systems suggest that supply rates determine metabolic rates. Therefore, the allometric scaling of supply alone provides a sufficient explanation for the allometric scaling of metabolism. Examination of empirical data from the literature of comparative physiology reveals that basal metabolic rates (BMR) are driven by rates of energy expenditure within internal organs and that the allometric scaling of BMR can be understood in terms of the scaling of the masses and metabolic rates of internal organs. Organ metabolic rates represent the sum of tissue metabolic rates while, within tissues, cellular metabolic rates are the outcome of shared regulation by multiple processes. Maximal metabolic rates (MMR, measured as maximum rates of O2 consumption, VO2max) during exercise also scale allometrically, are also subject to control by multiple processes, but are due mainly to O2 consumption by locomotory muscles. Thus, analyses of the scaling of MMR must consider the scaling of both muscle mass and muscle energy expenditure. Consistent with the principle of symmorphosis, allometry in capacities for supply (the outcome of physical design constraints) is observed to be roughly matched by allometry in capacities for demand (i.e. for energy expenditure). However, physiological rates most often fall far below maximum capacities and are subject to multi-step regulation. Thus, mechanistic explanations for the scaling of BMR and MMR must consider the manner in which capacities are matched and how rates are regulated at multiple levels of biological organization.