gebhart/patrepeval huggingface dataset:
Introduction to Biomedical Engineering, Third Edition (2012)

The <i>Journal of Biomedical Optics</i> (JBO) is an open access journal that publishes peer-reviewed papers on the use of novel optical systems and techniques for improved health care and biomedical research.
Pep-1 as a Novel Probe for the In Situ Detection of Hyaluronan (2005)

Hyaluronan (HA) is expressed by most tissues, including skin. Localization of HA in the skin is assessed by histology with HA-binding protein (HABP) serving as the probe. Reports have suggested that HA expression in skin is altered in a number of diseases. However, interlaboratory variations in HABP staining profiles, even in normal skin, suggest a need to standardize methods and/or identify new probes. We report the staining patterns of a HA-binding peptide (termed "Pep-1") in human and mouse skin. After acetone fixation, Pep-1 stained HA in the intercellular spaces of the epidermis, whereas staining in the dermis was weak and diffuse in both human and mouse skin. HABP staining of the epidermis and dermis were comparable in human skin but failed to stain the vital epidermis of mouse skin. In human skin, Pep-1 stained the basal, spinous, and granular layers, whereas HABP failed to stain the basal layer. Precipitation of HA in situ resulted in dermal staining but weak staining in the epidermis for HABP and Pep-1. Our results may suggest that Pep-1 is sensitive to HA conformation. Furthermore, Pep-1 may represent a new probe to study HA expression in the skin.
The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms (2012)

Our results have direct implications for resource allocation and further sequencing projects. It can be extrapolated that the number of newly identified genes still significantly increases with increasing number of new sequenced genomes. Furthermore, genome analysis of multiple phototrophic strains allows us to obtain a detailed picture of metabolic diversity that can serve as a starting point for biotechnological applications and automated metabolic reconstructions.
Intercellular Signaling by Lysophosphatidate Recent Developments (1998)

Lysophosphatidate (LPA) is an intercellular phospholipid messenger with a wide range of biologic effects. The first discovered source of LPA in the human body were activated platelets, but several other sites of LPA generation are now known. The number of cellular interactions is also growing steadily and responses to the compound range wide, from induction of mitogenesis to neurite retraction. LPA acts via a specific G protein-coupled receptor, of which one or more subtypes may exist. Intracellularly, this receptor activates several heterotrimeric G proteins. LPA induces cell proliferation via the small GTP-binding proteins ras, and triggers actin-based cytoskeletal events through rho. This review describes the most relevant recent developments in our understanding of LPA signaling.
On non‐blocking switching networks (1971)

Abstract A switching network may be informally described as a collection of single‐pole, single‐throw switches arranged so as to connect a set of terminals called inputs to another set of terminals called outputs. It is non‐blocking if, given any set of connections from some of the inputs to some of the outputs, and an idle input terminal x and idle output terminal y, then it is possible to connect x to y without disturbing any of the existing connections. Denote by σ(a, b) the minimal number of switches necessary to connect a inputs to b outputs using a non‐blocking network. We are interested in studying the growth of σ(a, a) as a → ∞. Results of C. Clos show that σ(a, a) ⩽ C ae 2√log a·log 2 . We show that σ(a, a) ⩽ 8a(log 2 a) 2 .
Proinflammatory High‐Density Lipoprotein Results from Oxidized Lipid Mediators in the Pathogenesis of Both Idiopathic and Associated Types of Pulmonary Arterial Hypertension (2015)

Pulmonary arterial hypertension (PAH) is characterized by abnormal elaboration of vasoactive peptides, endothelial cell dysfunction, vascular remodeling, and inflammation, which collectively contribute to its pathogenesis. We investigated the potential for high-density lipoprotein (HDL) dysfunction (i.e., proinflammatory effects) and abnormal plasma eicosanoid levels to contribute to the pathobiology of PAH and assessed ex vivo the effect of treatment with apolipoprotein A-I mimetic peptide 4F on the observed HDL dysfunction. We determined the "inflammatory indices" HII and LII for HDL and low-density lipoprotein (LDL), respectively, in subjects with idiopathic PAH (IPAH) and associated PAH (APAH) by an in vitro monocyte chemotaxis assay. The 4F was added ex vivo, and repeat LII and HII values were obtained versus a sham treatment. We further determined eicosanoid levels in plasma and HDL fractions from patients with IPAH and APAH relative to controls. The LIIs were significantly higher for IPAH and APAH patients than for controls. Incubation of plasma with 4F before isolation of LDL and HDL significantly reduced the LII values, compared with sham-treated LDL, for IPAH and APAH. The increased LII values reflected increased states of LDL oxidation and thereby increased proinflammatory effects in both cohorts. The HIIs for both PAH cohorts reflected a "dysfunctional HDL phenotype," that is, proinflammatory HDL effects. In contrast to "normal HDL function," the determined HIIs were significantly increased for the IPAH and APAH cohorts. Ex vivo 4F treatment significantly improved the HDL function versus the sham treatment. Although there was a significant "salutary effect" of 4F treatment, this did not entirely normalize the HII. Significantly increased levels for both IPAH and APAH versus controls were evident for the eicosanoids 9-HODE, 13-HODE, 5-HETE, 12-HETE, and 15-HETE, while no statistical differences were evident for comparisons of IPAH and APAH for the determined plasma eicosanoid levels in the HDL fractions. Our study has further implicated the putative role of "oxidant stress" and inflammation in the pathobiology of PAH. Our data suggest the influences on the "dysfunctional HDL phenotype" of increased oxidized fatty acids, which are paradoxically proinflammatory. We speculate that therapies that target either the "inflammatory milieu" or the "dysfunctional HDL phenotype," such as apoA-I mimetic peptides, may be valuable avenues of further research in pulmonary vascular diseases.
ChemInform Abstract: 4‐Aroyl‐1,3‐dihydro‐2H‐imidazol‐2‐ones: A New Class of Cardiotonic Agents. (1986)

Abstract Die durch Friedel‐ Crafts‐Acylierung der Dihydroimidazolone (I) mit den Pyridoylchloriden (I I) hergestellten Aroylimidazolone (III) zeigen positiv inotrope Effekte und sind blutdrucksenkend wirksam.
Generation of New Derivatives of the Antitumor Antibiotic Mithramycin by Altering the Glycosylation Pattern through Combinatorial Biosynthesis (2008)

Mithramycin is an antitumor drug produced by Streptomyces argillaceus. It consists of a tricyclic aglycone and five deoxyhexoses that form a disaccharide and a trisaccharide chain, which are important for target interaction and therefore for the antitumor activity. Using a combinatorial biosynthesis approach, we have generated nine mithramycin derivatives, seven of which are new compounds, with alterations in the glycosylation pattern. The wild-type S. argillaceus strain and the mutant S. argillaceus M7U1, which has altered D-oliose biosynthesis, were used as hosts to express various "sugar plasmids", each one directing the biosynthesis of a different deoxyhexose. The newly formed compounds were purified and characterized by MS and NMR. Compared to mithramycin, they contained different sugar substitutions in the second (D-olivose, D-mycarose, or D-boivinose instead of D-oliose) and third (D-digitoxose instead of D-mycarose) sugar units of the trisaccharide as well as in the first (D-amicetose instead of D-olivose) sugar unit of the disaccharide. All compounds showed antitumor activity against different tumor cell lines. Structure-activity relationships are discussed on the basis of the number and type of deoxyhexoses present in these mithramycin derivatives.
Simulating Individual Cow Milk Yield for Milking Parlor Simulation Models (1994)

A method of simulating individual cow milk yield per milking as a function of herd milk yield and month was formulated for milking parlor simulation models. Milk yield per milking was modeled for each month in three herd milk yield categories: 8165, 8845, and 9525 kg/yr of milk per cow. Actual individual cow DHIA test day milk weight data for three Florida dairy herds in each herd milk yield category and month were adjusted to the mean of their respective actual milk shipped per cow on test day then pooled and converted to a basis of three times per day milk yield per milking. After minor truncation, Weibull probability distributions fitted to these data sets adequately modeled milk yield per milking per cow. Analysis of simulation results for milk yield per milking per cow indicated no significant differences between actual and simulated means for any herd milk yield category or month. Simulations of monthly and yearly total herd milk yield for each herd indicated that fitted Weibull distributions also adequately modeled monthly and yearly herd milk yield characteristics and reflected seasonal herd milk yield patterns typical of Florida.
Molecular diagnostics of 15 hemophilia A patients: Characterization of eight novel mutations in the factor VIII gene, two of which result in exon skipping (1998)

The X-linked bleeding disorder hemophilia A is caused by mutations in the coagulation factor VIII gene. A high frequency of de novo mutations and the large size of this gene complicate the molecular diagnostic of hemophilia A. Characterization of mutations, however, may help identify amino acids or regions with essential functional or structural properties and thereby clarify the mechanism of pathogenesis. In the present study, we describe the identification of 15 mutations in the factor VIII gene, of which eight are novel. Among the patients with severe hemophilia A, two splice mutations (IVS5-3 and IVS19-2), a 4-bp deletion (TACA) at codon 1215, and a missense mutation G1850V have been characterized. The missense mutations G479R, R531C, V537D, N2129S and I2190N were found for five patients with a moderate course of hemophilia A disease. A silent mutation resulting in activation of a cryptic acceptor splice site within exon 11 and four other missense mutations Y114C, R1689H, R2150H (2x), M2164V have been identified for six patients with mild hemophilia A. Hum Mutat 12:301–303, 1998.© 1998 Wiley-Liss, Inc.
Corrosion resistance and behavioral characteristics of metals exposed to 70 percent by weight sulfuric acid at elevated temperatures (1994)

The development of a concentrated acid hydrolysis process may necessitate the storage, handling, and processing of concentrated solution of sulfuric acid at temperatures in excess of 70{degrees}C. Due to the corrosivity of the sulfuric acid at elevated temperatures, a series of corrosion tests was conducted to determine the corrosion performance and behavior of various construction materials using immersion and electrochemical techniques. Test results showed that among the stainless steels tested, only Carpenter 20Mo-6 performed satisfactorily up to 70{degrees}C. It passivated spontaneously and corroded at a rate less than 40 {mu}m/yr (1.6 mpy). Among numerous nickel-based alloys tested, only Hastelloy B-2 had excellent corrosion resistance up to 100{degrees}C with a corrosion rate less than 50 {mu}/yr (2 mpy), although the alloy did not passivate. Zirconium alloy Zr 702 provided excellent corrosion resistance to 100{degrees}C. The alloy passivated spontaneously, but its passive range decreased, evidently with increase in temperature. Tantalum and KBI-40 provided excellent corrosion protection at all test temperatures. The materials passivated spontaneously with a wide passive range.
Tyrosine Phosphorylation of the Integrin β3 Subunit Regulates β3 Cleavage by Calpain (2006)

Outside-in signaling of beta(3) integrins induces and requires phosphorylation at tyrosine 747 (Tyr(747)) and tyrosine 759 (Tyr(759)) of the beta(3) subunit, but the mechanism for this requirement is unclear. On the other hand, a key consequence of integrin signaling, cell spreading, is inhibited by calpain cleavage of beta(3) cytoplasmic domain. Here we show that beta(3) tyrosine phosphorylation inhibits calpain cleavage. Mutating both tyrosines to phenylalanine sensitizes beta(3) to calpain cleavage. Furthermore, phosphorylation at Tyr(747) and Tyr(759) of beta(3) in the focal adhesion sites and the leading edge of spreading platelets was differentially regulated. Selective dephosphorylation of Tyr(759) is associated with calpain cleavage at Tyr(759). Thus, one mechanism by which tyrosine phosphorylation promotes integrin signaling and cell spreading is its inhibition of calpain cleavage of the beta(3) cytoplasmic domain.
Interferometric studies of mode-locked Nd<sup>3+</sup>: Glass lasers (1975)

A general technique for measuring the electric-field vector of the ultrashort pulses from mode-locked laser systems is described. The technique is applied to perhaps the most difficult laser to analyze, the dye mode-locked Nd <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> :glass laser whose pulses change rapidly in bandwidth and amplitude, are chirped, and can occur in quite short pulse trains. The results of these measurements indicate a rather rapid change in the phases between modes, and a plot of the phase change as a function of mode frequency has been obtained.
Cerasome as an Infusible, Cell-Friendly, and Serum-Compatible Transfection Agent in a Viral Size (2006)

Alanine-based cationic lipid 1 having a (EtO)3SiCH2CH2CH2 group on the quaternized ammonium nitrogen forms a liposome which self-rigidifies via in situ sol-gel processes (Si-OEt + H2O --> Si-OH + EtOH followed by 2Si-OH --> Si-O-Si + H2O) on the surface. The resulting cerasome (partially ceramic- or silica-coated liposome) (60-70 nm) retains the integrity of such in the complexation with lucifarase-encoding plasmid DNA pGL3. The resultant pGL3 complex of infusible or monomeric cerasome in a viral size ( approximately 70 nm) exhibits a remarkable transfection performance toward HeLa and HepG2 cells with a 102-3-fold higher efficiency (relative to that of the nonsilylated reference lipid 2), minimized cytotoxicity, and serum compatibility. Reference lipid 2, i.e., alanine-based lipid having a simple quaternized ammonium headgroup, forms liposome (60-70 nm) which is less self-confined and more mobile undergoes DNA-induced fusion to give endocytosis-irrelevant and more toxic bigger (100-300 nm) particles. The silicon strategy thus provides a simple and widely applicable tool to overcome general problems associated with current technology of artificial gene delivery.
Path Planning of Data Mules in Sensor Networks (2011)

We study the problem of planning the motion of “data mules” for collecting the data from stationary sensor nodes in wireless sensor networks. Use of data mules significantly reduces energy consumption at sensor nodes compared to commonly used multihop forwarding approaches, but has a drawback in that it increases the latency of data delivery. Optimizing the motion of data mules, including path and speed, is critical for improving the data delivery latency and making the data mule approach more useful in practice. In this article, we focus on the path selection problem: finding the optimal path of data mules so that the data delivery latency can be minimized. We formulate the path selection problem as a graph problem that is capable of expressing the benefit from larger communication range. The problem is NP-hard and we present approximation algorithms for both single-data mule case and multiple-data mules case. We further consider the case in which we have only partial knowledge of communication range, where we design semionline algorithms that improve the offline plan using online knowledge at runtime. Simulation experiments on Matlab and ns2 demonstrate that our offline and semionline algorithms produce significantly shorter path lengths and data delivery latency compared to previously proposed methods, suggesting that controlled mobility can be exploited much more effectively.
Simulation of anisotropic wave propagation based upon a spectral element method (2000)

Abstract We introduce a numerical approach for modeling elastic wave propagation in 2-D and 3-D fully anisotropic media based upon a spectral element method. The technique solves a weak formulation of the wave equation, which is discretized using a high-order polynomial representation on a finite element mesh. For isotropic media, the spectral element method is known for its high degree of accuracy, its ability to handle complex model geometries, and its low computational cost. We show that the method can be extended to fully anisotropic media. The mass matrix obtained is diagonal by construction, which leads to a very efficient fully explicit solver. We demonstrate the accuracy of the method by comparing it against a known analytical solution for a 2-D transversely isotropic test case, and by comparing its predictions against those based upon a finite difference method for a 2-D heterogeneous, anisotropic medium. We show its generality and its flexibility by modeling wave propagation in a 3-D transversely isotropic medium with a symmetry axis tilted relative to the axes of the grid.
Coherent-mode propagation in spatially band-limited wave fields (1986)

Some new results are established regarding a recently developed coherent-mode representation of steady-state sources and fields of any state of coherence. It is shown that when a planar source is spatially band limited in the sense that its cross-spectral density function contains only spatial frequencies smaller than the corresponding wave number, the mode representation has some very simple and useful properties. Some potential applications of the results are mentioned.
Simultaneous all-optical packet-header replacement and wavelength shifting for a dynamically-reconfigurable WDM network (1995)

We experimentally demonstrate a method of simultaneous all-optical header replacement and wavelength shifting. These functions, important in a dynamically-reconfigurable WDM network, are realized by using cross-gain compression in a semiconductor optical amplifier, and by using three-level modulation of a probe laser only when the header bits require changing. We simultaneously replace the 8-bit header of a 1-Gb/s packet and wavelength-shift the entire packet by 19 nm. A receiver sensitivity of -27 dBm at 10/sup -9/ BER is measured when using a 416-bit NRZ data packet. Our approach requires no guard bits and allows both the header and data to be at the same bit rate and wavelength.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
GLP-1 treatment reduces endogenous insulin resistance via activation of central GLP-1 receptors in mice fed a high-fat diet (2010)

Glucagon-like peptide-1 (GLP-1) improves insulin sensitivity in humans and rodents. It is currently unknown to what extent the (metabolic) effects of GLP-1 treatment are mediated by central GLP-1 receptors. We studied the impact of central GLP-1 receptor (GLP-1R) antagonism on the metabolic effects of peripheral GLP-1 administration in mice. High-fat-fed insulin-resistant C57Bl/6 mice were treated with continuous subcutaneous infusion of GLP-1 or saline (PBS) for 2 wk, whereas the GLP-1R antagonist exendin-9 (EX-9) and cerebrospinal fluid (CSF) were simultaneously infused in the left lateral cerebral ventricle (icv). Glucose and glycerol turnover were determined during a hyperinsulinemic euglycemic clamp. VLDL-triglyceride (VLDL-TG) production was determined in hyperinsulinemic conditions. Our data show that the rate of glucose infusion necessary to maintain euglycemia was significantly increased by GLP-1. Simultaneous icv infusion of EX-9 diminished this effect by 62%. The capacities of insulin to stimulate glucose disposal and inhibit glucose production were reinforced by GLP-1. Simultaneous icv infusion of EX-9 significantly diminished the latter effect. Central GLP-1R antagonism alone did not affect glucose metabolism. Also, GLP-1 treatment reinforced the inhibitory action of insulin on VLDL-TG production. In conclusion, peripheral administration of GLP-1 reinforces the ability of insulin to suppress endogenous glucose and VLDL-TG production (but not lipolysis) and boosts its capacity to stimulate glucose disposal in high-fat-fed C57Bl/6 mice. Activation of central GLP-1Rs contributes substantially to the inhibition of endogenous glucose production by GLP-1 treatment in this animal model.
Electron–Lattice Coupling in Armchair Graphene Nanoribbons (2012)

We report the effects of electron-lattice coupling on the charge density distribution study of armchair graphene nanoribbons (GNRs). Here, we perform a theoretical investigation explaining the unexpected electronic density states observed experimentally. By means of a tight-binding approach with electron-lattice coupling, we obtained the same characteristic pattern of charge density along the C-C bonds suggested by both scanning tunneling and transmission electron microscopic measurements. Our results suggest electronic localized states whose sizes are dependent on the GNR width. We also show that our model rescues the quasi-particle charge-transport mechanism in GNRs. The remarkable agreement with experimental evidence allows us to conclude that our model could be, in many aspects, a fundamental tool when it comes to the phenomenological understanding of the charge behavior in this kind of system.
Antibody Modified Gold Nanoparticles for Fast and Selective, Colorimetric T7 Bacteriophage Detection (2014)

Herein, we report a colorimetric immunosensor for T7 bacteriophage based on gold nanoparticles modified with covalently bonded anti-T7 antibodies. The new immunosensor allows for a fast, simple, and selective detection of T7 virus. T7 virions form immunological complexes with the antibody modified gold nanoparticles which causes them to aggregate. The aggregation can be observed with the naked eye as a color change from red to purple, as well as with a UV-vis spectrophotometer. The aggregate formation was confirmed with SEM imaging. Sensor selectivity against the M13 bacteriophage was demonstrated. The limit of detection (LOD) is 1.08 × 10(10) PFU/mL (18 pM) T7. The new method was compared with a traditional plaque test. In contrast to biological tests the colorimetric method allows for detection of all T7 phages, not only those biologically active. This includes phage ghosts and fragments of virions. T7 virus has been chosen as a model organism for adenoviruses. The described method has several advantages over the traditional ones. It is much faster than a standard plaque test. It is more robust since no bacteria-virus interactions are utilized in the detection process. Since antibodies are available for a large variety of pathogenic viruses, the described concept is very flexible and can be adapted to detect many different viruses, not only bacteriophages. Contrary to the classical immunoassays, it is a one-step detection method, and no additional amplification, e.g., enzymatic, is needed to read the result.