gebhart/patrepeval huggingface dataset:
Linear and nonlinear frequency shifts in acoustical resonators with varying cross sections (2001)

The frequency response of a nonlinear acoustical resonator is investigated analytically and numerically. The cross-sectional area is assumed to vary slowly but otherwise arbitrarily along the axis of the resonator, such that the Webster horn equation provides a reasonable one-dimensional model in the linear approximation. First, perturbation theory is used to derive an asymptotic formula for the natural frequencies as a function of resonator shape. The solution shows that each natural frequency can be shifted independently via appropriate spatial modulation of the resonator wall. Numerical calculations for resonators of different shapes establish the limits of the asymptotic formula. Second, the nonlinear interactions of modes in the resonator are investigated with Lagrangian mechanics. An analytical result is obtained for the amplitude-frequency response curve and nonlinear resonance frequency shift for the fundamental mode. For a resonator driven at its lowest natural frequency, it is found that whether hardening or softening behavior occurs depends primarily on whether the nonlinearly generated second-harmonic frequency is greater or less than the second natural frequency of the resonator. A fully nonlinear one-dimensional numerical code is used to verify the analytical result.
OVOL guides the epithelial-hybrid-mesenchymal transition (2015)

Metastasis involves multiple cycles of Epithelial-to-Mesenchymal Transition (EMT) and its reverse-MET. Cells can also undergo partial transitions to attain a hybrid epithelial/mesenchymal (E/M) phenotype that has maximum cellular plasticity and allows migration of Circulating Tumor Cells (CTCs) as a cluster. Hence, deciphering the molecular players helping to maintain the hybrid E/M phenotype may inform anti-metastasis strategies. Here, we devised a mechanism-based mathematical model to couple the transcription factor OVOL with the core EMT regulatory network miR-200/ZEB that acts as a three-way switch between the E, E/M and M phenotypes. We show that OVOL can modulate cellular plasticity in multiple ways - restricting EMT, driving MET, expanding the existence of the hybrid E/M phenotype and turning both EMT and MET into two-step processes. Our theoretical framework explains the differences between the observed effects of OVOL in breast and prostate cancer, and provides a platform for investigating additional signals during metastasis.
Compartmented mode workstation: prototype highlights (1990)

The primary goal of the MITRE compartmented mode workstation (CMW) project was to articulate the security requirements that workstations must meet to process highly classified intelligence data. As a basis for the validity of the requirements developed, a prototype was implemented which demonstrated that workstations could meet the requirements in an operationally useful manner while still remaining binary compatible with off-the-shelf software. The security requirements not only addressed traditional security concerns but also introduced concepts in areas such as labeling and the use of a trusted window management system. The CMW labeling paradigm is based on associating two types of security labels with objects: sensitivity levels and information labels. Sensitivity levels describe the levels at which objects must be protected. Information labels are used to prevent data overclassification and also provide a mechanism for associating with data those markings that are required for accurate data labeling, but which play no role in access control decisions. The use of a trusted window manager allows users to easily operate at multiple sensitivity levels and provides a convenient mechanism for communicating security information to users in a relatively unobtrusive manner.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Aqueous Copper-Mediated Living Polymerization: Exploiting Rapid Disproportionation of CuBr with Me6TREN (2013)

A new approach to perform single-electron transfer living radical polymerization (SET-LRP) in water is described. The key step in this process is to allow full disproportionation of CuBr/Me6TREN (TREN = tris(dimethylamino)ethyl amine to Cu(0) powder and CuBr2 in water prior to addition of both monomer and initiator. This provides an extremely powerful tool for the synthesis of functional water-soluble polymers with controlled chain length and narrow molecular weight distributions (polydispersity index approximately 1.10), including poly(N-isopropylacrylamide), N,N-dimethylacrylamide, poly(ethylene glycol) acrylate, 2-hydroxyethyl acrylate (HEA), and an acrylamido glyco monomer. The polymerizations are performed at or below ambient temperature with quantitative conversions attained in minutes. Polymers have high chain end fidelity capable of undergoing chain extensions to full conversion or multiblock copolymerization via iterative monomer addition after full conversion. Activator generated by electron transfer atom transfer radical polymerization of N-isopropylacrylamide in water was also conducted as a comparison with the SET-LRP system. This shows that the addition sequence of l-ascorbic acid is crucial in determining the onset of disproportionation, or otherwise. Finally, this robust technique was applied to polymerizations under biologically relevant conditions (PBS buffer) and a complex ethanol/water mixture (tequila).
Vector NTI, a balanced all-in-one sequence analysis suite (2004)

Vector NTI is a well-balanced desktop application integrated for molecular sequence analysis and biological data management. It has a centralised database and five application modules: Vector NTI, AlignX, BioAnnotator, ContigExpress and GenomBench. In this review, the features and functions available in this software are examined. These include database management, primer design, virtual cloning, alignments, sequence assembly, 3D molecular viewer and internet tools. Some problems encountered when using this software are also discussed. It is hoped that this review will introduce this software to more molecular biologists so they can make better-informed decisions when choosing computational tools to facilitate their everyday laboratory work. This tool can save time and enhance analysis but it requires some learning on the user's part and there are some issues that need to be addressed by the developer.
Structure and evolution of mammalian VH families (1990)

Antibodies are encoded by a limited number of germline gene segments that undergo somatic diversification through rearrangement and mutation. Because these mutation processes are efficient, it is widely believed that there is little environmental selection pressure for the maintenance of specific antibody gene sequences. We have performed pairwise comparisons of known germline (as opposed to somatically generated) antibody VH elements with the hope of identifying conserved structural features common to sets of VH gene segments. These studies reveal that VH families arose prior to the mammalian radiation and have since been conserved, that this conservation appears to reflect selection at the level of protein sequence, and that the conserved regions are discretely localized on a solvent-exposed face of the heavy chain, at some distance from the antibody combining site. A family-specific region was also identified within the recombinase recognition sequences. Our results provide a context for theories that address the physiological significance of variations in VH family utilization during the development of the immune repertoire.
Azodioxides Activated by Electron Acceptors in Geminal or Vicinal Position (1998)

Twenty-two nitroso compounds with cyano, acyloxy, or carbonyl groups in geminal position were prepared, eight of them for the first time. In the solid state these compounds dimerize to colorless azodioxides. Exceptions are the 4-nitrobenzoyloxynitroso compounds 7b, f, and g which form bright blue crystals. In vitro (Born test, collagen) considerable antiplatelet activity was observed in each class of compounds. Azodioxides with cyano groups in geminal position (3a, b) were most active (IC50 approximately 10 microM) suggesting the importance of strong electron withdrawing groups in geminal position to the azodioxide partial structure. When administered orally to rats (60 mg/kg) all compounds inhibited the thrombus formation in mesenteric arterioles and venules. The acetyloxy derivatives 5d and 5e were most active (18-21% inhibition in arterioles and 11-15% inhibition in venules). In aqueous media at 37 degrees C the cyanonitroso compound 3b and the benzoyloxynitroso compound 7a decomposed to nitric oxide and its reduced form nitrosohydrogen. This suggests that the above pharmacological effects are mediated by a NO dependent mechanism.
High-performance InP-based enhancement-mode HEMTs using non-alloyed ohmic contacts and Pt-based buried-gate technologies (1996)

High performance InP-based InAlAs/InGaAs enhancement-mode HEMT's are demonstrated using two improved approaches to device structure design and fabrication, i.e., nonalloyed ohmic contacts and Pt-based buried-gate technologies, to reduce the source resistance (R/sub S/). With specially designed cap layer structures, nonalloyed ohmic contacts to the device channel were obtained providing contact resistance as low as 0.067 /spl Omega//spl middot/mm. Furthermore, in device fabrication, a Pt-based buried-gate approach is used in which depletion-mode HEMTs are first intentionally fabricated, and then, the Pt-based gate metal is annealed at 250/spl deg/C, causing the Pt-InAlAs reaction to take place under the gate electrode so that Pt sinks into InAlAs and depletes the channel. As a result, the depletion-mode HEMTs are changed to enhancement-mode, while the channel region between the source and gate electrodes remain undepleted, and therefore, the small R/sub S/ of 0.2 /spl Omega//spl middot/mm can be maintained. Excellent maximum transconductance of 1170 mS/mm was obtained for a 0.5-/spl mu/m-gate device. A maximum current-gain cutoff frequency f/sub T/ of 41.2 GHz and maximum unilateral power-gain cutoff frequency f/sub max/ of 61 GHz were demonstrated for a 0.6-/spl mu/m-gate enhancement-mode HEMT.
The glomerular mesangial cell: an expanding role for a specialized pericyte (1987)

The mesangial cell occupies a central position in the renal glomerulus. It has characteristics of a modified smooth muscle cell, but is also capable of a number of other functions. Among these are generation of prostaglandins (PGs) and mediators of inflammation; production and breakdown of basement membrane and other biomatrix material; synthesis of cytokines; and uptake of macromolecules, including immune complexes. In terms of its smooth muscle activity, the mesangial cell contracts or relaxes in response to a number of vasoactive agents. This ability allows the cells to modify glomerular filtration locally. The cellular mechanism of action of many agents influencing mesangial cells involves activation of phospholipase C for phosphatidylinositol 4,5-bisphosphate. This results in generation of inositol trisphosphate and release of intracellular calcium. Mesangial cell relaxation can be mediated by enhanced cAMP or cGMP generation. Many vasoactive substances also stimulate PG production by mesangial cells. This involves activation of both phospholipase C and A2, the latter being responsible for the release of arachidonic acid. Mesangial cells are also capable of endocytosis of macromolecules, including immune complexes. This is initiated by binding to a specific receptor, resulting in formation of PG, platelet-activating factor, and reactive oxygen species. Mesangial cells can generate interleukin 1 and platelet-derived growth factor and respond to these in an autocrine manner. Thus, the mesangial cell not only can control glomerular filtration, but may also be involved in the response to local injury, including cell proliferation and basement membrane remodeling.
Thrombospondin and other possible related matrix proteins in malignant and benign breast disease. An immunohistochemical study. (1992)

Thrombospondin (TSP), which plays an important hemostatic role, is a 450-kd cytoadhesive protein present in the alpha granules of platelets. In vitro experiments using cultured malignant cells suggest that it may help to mediate malignant cell attachment to extracellular matrix and may be important in cancer invasiveness. The authors studied a group of malignant and benign breast tissues for the expression of TSP and provide evidence that TSP may have a role in tumor invasiveness. Using immunohistochemical techniques, the authors found in 48 fresh specimens of breast carcinoma that TSP stained strongly in the desmoplastic stroma or at the basement membrane associated with the malignant ductal epithelium. Tumor cells abutting these tissues revealed cytoplasmic staining for TSP. Stronger TSP staining was seen in the poorly differentiated tumors. These findings were compared with those of normal and benign breast tissue, which showed no TSP staining apart from reactivity in the large distended cysts of fibrocystic disease and faint staining in the stroma of fibroadenomas. Staining for integrin was positive in lymphocytes of both malignant and benign breast disease and equivocally also in the stromal cells of the breast cancer tissue. Immunoreactivity to TSP in tissues was also compared with that of fibronectin, laminin, and collagen type I, III, and IV. The overall findings suggest that thrombospondin may have a role in the tumor biology of invasiveness.
Nitric Oxide in Hypertension: Relationship With Renal Injury and Left Ventricular Hypertrophy (1998)

Hypertension is accompanied by architectural changes in the kidney, heart, and vessels that are often maladaptive and can eventually contribute to end-organ disease such as renal failure, heart failure, and coronary disease. Nitric oxide, an endogenous vasodilator and antithrombotic agent synthesized in the endothelium by a constitutive nitric oxide synthase, inhibits growth-related responses to injury in vascular cells. Specifically, in the presence of hypertension, nitric oxide may work in the kidney by inhibiting both mesangial cell hypertrophy and hyperplasia as well as synthesis of extracellular matrix and in the heart and systemic vessels by modulating smooth muscle cell hypertrophy and hyperplasia. The effects of nitric oxide are antagonistic of the effects of angiotensin II. Shear stress and cyclic strain, physical forces known to operate in hypertension, are accompanied by increases in endothelial nitric oxide synthase expression, nitric oxide synthase protein, and nitric oxide synthase activity in endothelial cells. Experimental studies using genetic models of hypertension show a variation in hypertension-modulated vascular nitric oxide synthase activity in different strains of rats. These studies suggest that upregulation of vascular nitric oxide synthase activity is a homeostatic adaptation to increased hemodynamic workload in hypertension and that this may help prevent end-organ damage. If these findings apply to humans, differences in end-organ disease seen in patients with similar degrees of hypertension may be due in part to genetic differences in vascular nitric oxide synthase activity in response to hypertension.
A time-multiplexed switched-capacitor circuit for neural network applications (2003)

A time-multiplexed switched-capacitor computational block with some neural network characteristics is under development. The goal of this work is not to model biological neuron qualities exactly but rather to emulate their primary characteristics to the extent necessary to solve some types of problems not suited to digital processing. The circuit operation and limitations on its performance are described. The circuit is intended to serve as a coprocessor to a digital microprocessor. Circuit functionality has been demonstrated with breadboarded circuit, and the circuit is currently being integrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Inhibition of HIV-1 Integration by Mono- & Bifunctionalized Triple Helix Forming Oligonucleotides (1999)

HIV-1 DNA integration is carried out by integrase, a viral protein which binds to specific sequences located on both extremities of the HIV-1 DNA LTR. Inhibition of integration was observed with submicromolar concentrations of mono- or bifunctionalized 11-mer oligonucleotide-intercalators, which were designed to form an alternate strand triple helix with the U5 LTR end containing two adjacent purine tracts on opposite strands 5'-GGAAAATCTCT-3'/3'-CCTTTTAGAGA-5'.
The Role of Allergy and Nonspecific Airway Hyperresponsiveness in the Pathogenesis of Chronic Obstructive Pulmonary Disease (1989)

Although the information that has been reviewed leaves many questions unanswered, some conclusions can be drawn from available data. (1) Smoking appears to increase the risk of sensitization to certain inhaled antigens encountered in the workplace; however, there is no definite evidence that smoking increases the frequency or intensity of allergy to common aeroallergens in the general population. On average, smokers have higher serum total IgE concentrations and blood eosinophil counts than do nonsmokers, but the mechanisms underlying these alterations are not clear. Analysis of these relationships is complicated by observations suggesting that atopic persons are less likely to become and to remain regular cigarette smokers. (2) Long-term cigarette smoking may be associated with increased nonspecific airway responsiveness, although the magnitude of this effect is relatively small when one adjusts for prechallenge level of pulmonary function. This effect of smoking may be more pronounced in atopic persons. (3) Atopy, as assessed by skin testing and serum IgE concentrations, is associated with asthma, nonspecific airway hyperresponsiveness, and reduced pulmonary function level in population data. However, there is no clear evidence that atopy is a risk factor for irreversible airflow obstruction in persons without asthma. Population data do not indicate how much of the reduction in pulmonary function associated with atopy and asthma is potentially reversible. (4) Blood eosinophil count appears inversely related to the level of pulmonary function and directly related to the rate of decline of pulmonary function among nonsmokers. Reports vary concerning whether the relationship of eosinophil count to level of pulmonary function remains after excluding subjects with diagnosed asthma. This relationship may be determined largely by a clinically distinguishable subset of nonsmokers with "asthmatic bronchitis." Presumably, these observations reflect an adverse impact of eosinophilic inflammation in the airways or lung parenchyma. It is not clear whether this represents an allergic response because skin-test reactivity to common aeroallergens and serum total IgE concentration do not show similar relationships to reduced level and rapid decline of pulmonary function. (5) Among smokers, nonspecific airway hyperresponsiveness appears to be associated with an accelerated longitudinal decline of pulmonary function, although most studies indicating this association are limited by either a retrospective design or lack of adjustment for prechallenge level of pulmonary function.(ABSTRACT TRUNCATED AT 400 WORDS)
Bitter stimuli induce Ca2+ signaling and CCK release in enteroendocrine STC-1 cells: role of L-type voltage-sensitive Ca2+ channels (2006)

We previously demonstrated the expression of bitter taste receptors of the type 2 family (T2R) and the alpha-subunits of the G protein gustducin (Galpha(gust)) in the rodent gastrointestinal (GI) tract and in GI endocrine cells. In this study, we characterized mechanisms of Ca(2+) fluxes induced by two distinct T2R ligands: denatonium benzoate (DB) and phenylthiocarbamide (PTC), in mouse enteroendocrine cell line STC-1. Both DB and PTC induced a marked increase in intracellular [Ca(2+)] ([Ca(2+)](i)) in a dose- and time-dependent manner. Chelating extracellular Ca(2+) with EGTA blocked the increase in [Ca(2+)](i) induced by either DB or PTC but, in contrast, did not prevent the effect induced by bombesin. Thapsigargin blocked the transient increase in [Ca(2+)](i) induced by bombesin, but did not attenuate the [Ca(2+)](i) increase elicited by DB or PTC. These results indicate that Ca(2+) influx mediates the increase in [Ca(2+)](i) induced by DB and PTC in STC-1 cells. Preincubation with the L-type voltage-sensitive Ca(2+) channel (L-type VSCC) blockers nitrendipine or diltiazem for 30 min inhibited the increase in [Ca(2+)](i) elicited by DB or PTC. Furthermore, exposure to the L-type VSCCs opener BAY K 8644 potentiated the increase in [Ca(2+)](i) induced by DB and PTC. Stimulation with DB also induced a marked increase in the release of cholecystokinin from STC-1 cells, an effect also abrogated by prior exposure to EGTA or L-type VSCC blockers. Collectively, our results demonstrate that bitter tastants increase [Ca(2+)](i) and cholecystokinin release through Ca(2+) influx mediated by the opening of L-type VSCCs in enteroendocrine STC-1 cells.
Thinning methodologies-a comprehensive survey (1992)

A comprehensive survey of thinning methodologies is presented. A wide range of thinning algorithms, including iterative deletion of pixels and nonpixel-based methods, is covered. Skeletonization algorithms based on medial axis and other distance transforms are not considered. An overview of the iterative thinning process and the pixel-deletion criteria needed to preserve the connectivity of the image pattern is given first. Thinning algorithms are then considered in terms of these criteria and their modes of operation. Nonpixel-based methods that usually produce a center line of the pattern directly in one pass without examining all the individual pixels are discussed. The algorithms are considered in great detail and scope, and the relationships among them are explored.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Scanning Tunneling Microscopy Manipulation of Native Substrate Atoms: A New Way to Obtain Registry Information on Foreign Adsorbates (1996)

We demonstrate successful lateral manipulation of host atoms on Cu(211): In a controlled manner we are able to release Cu atoms from upper terraces, move them on the lower terrace to form dimers and trimers, and adhere them to the terrace edge again. We apply this novel ability to deduce information on adsorption sites of foreign species: By bringing Cu atoms close to CO molecules, we determine the location of the adsorbate. The sites of ${\mathrm{C}}_{2}{\mathrm{H}}_{4}$ and Pb are then found via coadsorption with CO.