gebhart/patrepeval huggingface dataset:
Mesenchymal stem cell adhesion to cardiac microvascular endothelium: activators and mechanisms (2005)

Circulating stem cells home within the myocardium, probably as the first step of a tissue regeneration process. This step requires adhesion to cardiac microvascular endothelium (CMVE). In this study, we studied mechanisms of adhesion between CMVE and mesenchymal stem cells (MSCs). Adhesion was studied in vitro and in vivo. Isolated 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate-labeled rat MSCs were allowed to adhere to cultured CMVE in static and dynamic conditions. Either CMVE or MSCs were pretreated with cytokines [IL-1beta, IL-3, IL-6, stem cell factor, stromal cell-derived factor-1, or TNF-alpha, 10 ng/ml]. Control or TNF-alpha-treated MSCs were injected intracavitarily in rat hearts in vivo. In baseline in vitro conditions, the number of MSCs that adhered to CMVE was highly dependent on the flow rate of the superfusing medium but remained significant at venous and capillary shear stress amplitudes. Activation of both CMVE and MSCs with TNF-alpha or IL-1beta before adhesion concentration dependently increased adhesion of MSCs at each studied level of shear stress. Consistently, in vivo, activation of MSCs with TNF-alpha before injection significantly enhanced cardiac homing of MSCs. TNF-alpha-induced adhesion could be completely blocked by pretreating either CMVE or MSCs with anti-VCAM-1 monoclonal antibodies but not by anti-ICAM-1 antibodies. Adhesion of circulating MSCs in the heart appears to be an endothelium-dependent process and is sensitive to modulation by activators of both MSCs and endothelium. Inflammation and the expression of VCAM-1 but not ICAM-1 on both cell types have a regulatory effect on MSC homing in the heart.
Mechanically Reinforced Skin‐Electronics with Networked Nanocomposite Elastomer (2016)

Mechanically reinforced skin-electronics are presented by exploiting networked nanocomposite elastomers where high quality metal nanowires serve as conducting paths. Theoretical and experimental studies show that the established skin-electronics exhibit superior mechanical enhancements against crack and delamination phenomena. Device applications include a class of biomedical devices that offers the ability of thermotherapeutic stimulation and electrophysiological monitoring, all via the skin.
The Heart Rate Decrease Caused by Acute FTY720 Administration Is Mediated by the G Protein-Gated Potassium Channel IKACh (2005)

Sphingosine-1-phosphate (S1P) is an endogenous agonist for a family of five G protein-coupled receptors (S1P(1-5)) involved in cell proliferation, cardiovascular development and lymphocyte trafficking. The sphingolipid drug FTY720 displays structural similarity to S1P and efficacy as an immunosuppressant in models of autoimmune disease and in solid organ transplantation. While FTY720 is well-tolerated in humans, it produces a transient reduction of heart rate (HR). As S1P activates the cardiac G protein-gated potassium channel I(KACh), we speculated that the FTY720-induced HR reduction reflects I(KACh) activation. We examined FTY720 effects on atrial myocytes from wild-type and I(KACh)-deficient mice. In wild-type myocytes, the active phosphate metabolite of FTY720 (FTY720-P) induced single channel activity with conductance, open time, GTP sensitivity and rectification identical to that of I(KACh). In whole-cell recordings, FTY720-P evoked an inwardly rectifying potassium current in approximately 90% of myocytes responding to acetylcholine. Comparable channel activity was never observed in myocytes from I(KACh)-deficient mice. In wild-type mice, acute FTY720 administration produced a dose-dependent, robust HR reduction. In contrast, the HR reduction induced by FTY720 in I(KACh)-deficient mice was blunted. We conclude that the effect of acute FTY720 administration on HR is mediated primarily by I(KACh) activation.
Hydrothermal and thermal treatment of natural clinoptilolite zeolite from Bigadiç, Turkey: An experimental study (2013)

The clinoptilolite rich zeolite from Bigadiç which was formed from alteration of volcanic glass were treated with acidic (HCl, H3BO3, H3PO4), alkaline (KOH, NaOH) solutions. Hydrothermally treated and untreated samples were heat treated at 400, 550 and 700°C. XRD, ICP-MS and N2 gas adsorption were used for physicochemical characterization of zeolites. Considering the Si/Al > 4 and Na+K/Ca+Mg < 1 ratios, zeolite sample is included to earth alkali clinoptilolite class (Heu II) which is also revealed by thermal treatments. Since zeolite structure contains low alkalies it was at collapsed 550°C. The removal of oxide elements efficiency of acids and alkalies were in the order of HCl > H3PO4 > HBO3 > KOH > NaOH. XRD analysis indicated that the structure of zeolite was not altered with acids and alkali treatments. The structure of zeolite treated with HCl and other acids started to deform at 400 and 550°C respectively. In treatment with HCl, Si/Al ratio increases with significant a decrease in K content which resulted in a decrease in the heat stability of zeolite. No change was observed in the structure and thermal stability of clinoptilolite after alkali treatments. The fact that although significant amount of Na is removed with H3BO3 acid and Na is increased with NaOH but the thermal stability remains the same indicates that Na cation is not an important parameter as much as K. HCl and H3PO4 acid treatments increased the surface area depending on the dissolution of amorphous material and H3PO4 was found to be more effective. However, the total pore size decreased due to formation of new micropores.
Degree of polarization in jointed fibers: the Lyot depolarizer (1984)

Analytic equations for the degree of polarization of the output lightwave from jointed fibers are derived taking into account the coherence time of light and polarization mode dispersion in the fibers. On the basis of the results, the depolarizing conditions and the principles of optics of the Lyot depolarizer are discussed.
Generation and Application of Type-specific Anti-Heparan Sulfate Antibodies Using Phage Display Technology (1998)

Detailed analysis of various heparan sulfate (HS) species is seriously hampered by a lack of appropriate tools, such as antibodies. We adopted phage display technology to generate anti-HS antibodies. A "single pot" semisynthetic human antibody phage display library was subjected to four rounds of selection on HS from bovine kidney using panning methodology. Three different phage clones expressing anti-HS single chain variable fragment antibodies (HS4C3, HS4D10, and HS3G8) were isolated, with an amino acid sequence of the complementarity-determining region 3 of GRRLKD (VH3 gene, DP-38), SLRMNGCGAHQ (VH3 gene, DP-42), and YYHYKVN (VH1 gene, DP-8), respectively. The antibodies react with HS and heparin, but not with DNA or other glycosaminoglycans. Kd values for HS are about 0.1 microM. The three antibodies react differently toward various HS preparations and show different staining patterns on rat kidney sections, indicating recognition of different HS molecules. This also holds for two described mouse anti-HS IgMs (JM403 and 10E4; both generated by conventional hybridoma technique) and indicates the presence of at least 5 different HS species in the kidney. O- and N-sulfation are important for binding of HS to HS4C3 and HS3G8. The three single chain antibodies, but not JM403, block a basic fibroblast growth factor binding site of HS. It is concluded that phage display technology presents a powerful technique to generate antibodies specific for HS epitopes. This is the first time this technique has been successfully applied to obtain directly antibodies to (poly)saccharides.
DNA-dependent adenosinetriphosphatase A is the eukaryotic analog of the bacteriophage T4 gene 44 protein: immunological identity of DNA replication-associated ATPases (1991)

We report the construction of three stable murine hybridomas that secrete monoclonal antibodies which recognize calf thymus DNA-dependent adenosinetriphosphatase A. All three of the antibodies react specifically with calf thymus ATPase A and the gene 44 protein from the bacteriophage T4 DNA-dependent ATPase. Each of the three anti-ATPase A antibodies appears to recognize a different epitope and none of the antibodies inhibit DNA-dependent ATP hydrolysis by ATPase A. Furthermore, one of the antibodies has been shown to react with two different preparations of HeLa cell DNA-dependent ATPases and a yeast DNA-dependent ATPase, all of which have been implicated in the enzymology of DNA replication. These findings provide strong evidence for the role of ATPase A in DNA replication. These observations lead us to conclude that, apart from the nucleotide binding sites, there are at least three epitopes common to both the bacteriophage and eukaryotic DNA-dependent ATPases that we have examined and that the different preparations of the eukaryotic ATPases contain the same DNA-dependent ATPase.
System for measuring the size of high-current density solid electron beams (2000)

A measurement system is described for determining the size of a high-current density solid electron beam from a Pierce-type electron gun. The apparatus incorporates ten graphite apertures and two graphite tubes mounted at 30/spl deg/ intervals on an off-axis drum that is rotated by a stepper motor. The graphite apertures are used to make localized beam-edge current-interception measurements at ten discrete locations at 1-cm intervals along the length of the beam. The graphite tubes can be used either to produce an integrated edge-current profile over an 11.4-cm length of the beam, or to measure the net current outside of two specific diameters centered on the beam axis. The active aperture or tube and its position with respect to the beam axis are determined by the orientation of the drum, which is read out using an absolute shaft encoder. This permits the position of each aperture or tube to be determined to an accuracy of 60 /spl mu/m.
Three-dimensional Video Generation for Realistic Broadcasting Services (2008)

In this paper, we propose a new scheme to generate multi-view video-plus-depth using a hybrid camera system, which is composed of one depth camera and multiple video cameras. In order to create the threedimensional (3-D) video, we first calculate the initial disparity for each view by projecting depth camera data onto each video camera using 3-D image warping. Then, a stereo matching algorithm is applyed to estimate the final disparity from the initial disparity in each view. Finally, we convert the final disparity into depth information in each frame to generate a multi-view depth map. Experimental results show that the proposed hybrid camera system not only provides high-qualtiy depth information for 3-D realistic broadcasting services, but also minimizes inherent problems of the conventional depth camera system.
Cyclooxygenase-2-derived prostaglandin D2is an early anti-inflammatory signal in experimental colitis (2000)

The ability of nonsteroidal anti-inflammatory drugs and cyclooxygenase-2 inhibitors to exacerbate inflammatory bowel disease suggests that prostaglandins are important anti-inflammatory mediators in this context. Prostaglandin D(2) has been suggested to exert anti-inflammatory effects. We investigated the possibility that prostaglandin D(2) derived from cyclooxygenase-2 plays an important role in downregulating colonic inflammation in rats. Colitis was induced by intracolonic administration of trinitrobenzene sulfonic acid. At various times thereafter (from 1 h to 7 days), colonic prostaglandin synthesis and myeloperoxidase activity (index of granulocyte infiltration) were measured. Prostaglandin D(2) synthesis was elevated >4-fold above controls within 1-3 h of induction of colitis, preceding significant granulocyte infiltration. Treatment with a selective cyclooxygenase-2 inhibitor abolished the increase in prostaglandin D(2) synthesis and caused a doubling of granulocyte infiltration. Colonic granulocyte infiltration was significantly reduced by administration of prostaglandin D(2) or a DP receptor agonist (BW-245C). These results demonstrate that induction of colitis results in a rapid increase in prostaglandin D(2) synthesis via cyclooxygenase-2. Prostaglandin D(2) downregulates granulocyte infiltration into the colonic mucosa, probably through the DP receptor.
Spectroscopic intravascular photoacoustic imaging to differentiate atherosclerotic plaques (2008)

The potential of intravascular photoacoustic (IVPA) imaging to detect atherosclerosis was previously demonstrated using a 532 nm nanosecond pulsed laser and an intravascular ultrasound (IVUS) imaging catheter. However, to differentiate vulnerable plaques, the composition of plaques needs to be imaged. Therefore, we introduce a multi-wavelength photoacoustic imaging method to distinguish various types of plaques. Multi-spectral IVPA imaging of ex vivo samples of normal and atherosclerotic rabbit aorta was performed at several wavelengths within 680-900 nm range. The spectral variation of photoacoustic response was extracted and a spectroscopic analysis was performed. The results of our preliminary study suggest that the spectroscopic intravascular photoacoustic imaging technique can be used to differentiate fibrous and lipid components of the atherosclerotic plaques.
Toward Understanding the Structural Basis of Cyclin-Dependent Kinase 6 Specific Inhibition (2006)

Cyclin-dependent kinases (CDKs) are key players in cell cycle control, and genetic alterations of CDKs and their regulators have been linked to a variety of cancers. Hence, CDKs are obvious targets for therapeutic intervention in various proliferative diseases, including cancer. To date, drug design efforts have mostly focused on CDK2 because methods for crystallization of its inhibitor complexes have been well established. CDK4 and CDK6, however, may be at least as important as enzymes for cell cycle regulation and could provide alternative treatment options. We describe here two complex structures of human CDK6 with a very specific kinase inhibitor, PD0332991, which is based on a pyrido[2,3-d]pyrimidin-7-one scaffold, and with the less specific aminopurvalanol inhibitor. Analysis of the structures suggests that relatively small conformational differences between CDK2 and CDK6 in the hinge region are contributing to the inhibitor specificity by inducing changes in the inhibitor orientation that lead to sterical clashes in CDK2 but not CDK6. These complex structures provide valuable insights for the future development of CDK-specific inhibitors.
Learning Hierarchical Partially Observable Markov Decision Process Models for Robot Navigation (2001)

Abstract | We propose and investigate a general frame-work for hierarchical modeling of partially observable envi-ronments, such as oÆce buildings, using Hierarchical Hid-den Markov Models (HHMMs). Our main goal is to ex-plore hierarchical modeling as a basis for designing more eÆcient methods for model construction and useage. As a case study we focus on indoor robot navigation and show how this framework can be used to learn a hierarchy of mod-els of the environment at dierent levels of spatial abstrac-tion. We introduce the idea of model reuse that can be used to combine already learned models into a larger model. We describe an extension of the HHMM model to includes ac-tions, which we call hierarchical POMDPs, and describe a modi ed hierarchical Baum-Welch algorithm to learn these models. We train dierent families of hierarchical models for a simulated and a real world corridor environment and compare them with the standard \\\n at &amp;quot; representation of the same environment. We show that the hierarchical POMDP approach, combined with model reuse, allows learning hier-archical models that t the data better and train faster than at models. I.
Suppression of HIV-specific T cell activity by lymph node CD25+regulatory T cells from HIV-infected individuals (2007)

CD25(+) CD4(+) FoxP3(+) regulatory T (Treg) cells isolated from the peripheral blood of asymptomatic HIV-infected individuals have been demonstrated to significantly suppress HIV-specific immune responses in vitro. CD25(+) Treg cell suppressor activity in the peripheral blood seems to diminish with progression of HIV disease, and it has been suggested that loss of Treg cells contributes to aberrant immune activation and disease progression. However, phenotypic studies suggest that Treg cells may migrate to, and be maintained or even expanded in, tissue sites of HIV replication. Currently, it is not known whether tissue-associated Treg cells maintain suppressive activity in the context of HIV infection, particularly in individuals with advanced disease. The present study demonstrates that CD25(+) Treg cells isolated from lymph nodes and peripheral blood of HIV(+) subjects, even those with high viral loads and/or low CD4(+) T cell counts, maintain potent suppressive activity against HIV-specific cytolytic T cell function. This activity was better in lymph node as compared with peripheral blood, particularly in patients with high levels of plasma viremia. In addition, the expression of certain CD25(+) Treg-associated markers on CD4(+) T cells isolated from lymph nodes differed significantly from those on CD4(+) T cell subsets isolated from the peripheral blood. These data suggest that CD25(+) Treg cell-mediated suppression of HIV-specific responses continues throughout the course of HIV disease and, because of their particularly potent suppression of HIV-specific CTL activity in lymphoid tissue, may considerably impact the ability to control HIV replication in vivo.
Changing the Enzymatic Activity of T7 Endonuclease by Mutations at the β-Bridge Site:  Alteration of Substrate Specificity Profile and Metal Ion Requirements by Mutation Distant from the Catalytic Domain (2004)

Phage-encoded resolvase T7 endonuclease I is a structure-specific endonuclease. The enzyme acts on a broad spectrum of substrates with a variety of DNA structures. The enzyme is a dimer with two separated catalytic domains connected by an elongated beta-sheet bridge. The activities of enzymes with mutations in the beta-bridge segment were studied. Mutations that did not affect catalytic domain folding and function but did alter the relative positions of these domains retained catalytic activity but with altered specificity and metal ion dependence. Our results suggest that the enzyme recognizes its substrates by DNA conformation exclusion and offer a simple explanation for the broad substrate specificity of phage resolvase.
Experimental Determination of Quantum Dot Size Distributions, Ligand Packing Densities, and Bioconjugation Using Analytical Ultracentrifugation (2008)

Analytical ultracentrifugation (AUC) was used to characterize the size distribution and surface chemistry of quantum dots (QDs). AUC was found to be highly sensitive to nanocrystal size, resolving nanocrystal sizes that differ by a single lattice plane. Sedimentation velocity data were used to calculate the ligand packing density at the crystal surface for different sized nanocrystals. Dihydrolipoic acid poly(ethylene glycol) was found to bind between 66 and 60% of the surface cadmium atoms for CdSe nanocrystals in the 1.54-2.59 nm radius size regime. The surface ligand chemistry was found to affect QD sedimentation, with larger ligands decreasing the sedimentation rate through an increase in particle volume and increase in frictional coefficient. Finally, AUC was used to detect and analyze protein association to QDs. Addition of bovine serum albumin (BSA) to the QD sample resulted in a reduced sedimentation rate, which may be attributed to an associated frictional drag. We calculated that one to two BSA molecules bind per QD with an associated frictional ratio of 1.2.
Parallel dip-pen nanolithography with arrays of individually addressable cantilevers (2004)

In dip-pen nanolithography (DPN), nanoscale chemical patterns are created by directly transferring chemical molecules from the tip of an atomic force microscope probe to a surface. We report the development of a thermally actuated probe array for DPN applications. The array consists of ten thermal bimorph actuated probes, each 300 μm long, with a lateral spacing of 100 μm. The probes are actuated by passing dc current through a heater embedded in the probe base. The array is demonstrated by using it to simultaneously write ten different octadecanethiol patterns on a gold surface.
Activation and overexpression of centrosome kinase BTAK/Aurora-A in human ovarian cancer. (2003)

Previous studies have demonstrated amplification of the centrosome serine/threonine kinase BTAK/Aurora-A in 10-25% of ovarian cancers. However, alterations of BTAK/Aurora-A at kinase and protein levels and its role in ovarian cancer progression have not been well documented. In this study, we examined the kinase activity and protein levels of BTAK/Aurora-A in 92 patients with primary ovarian tumors. In vitro kinase analyses revealed elevated BTAK/Aurora-A kinase activity in 44 cases (48%). Increased BTAK/Aurora-A protein levels were detected in 52 (57%) specimens. High protein levels of BTAK/Aurora-A correlated well with elevated kinase activity. Activation and overexpression of BTAK/Aurora-A were more frequently detected in early stage/low-grade ovarian tumors, although there was no statistic significance at the kinase level between early stage/low-grade and late stage/high-grade tumors. Moreover, BTAK/Aurora-A was preferentially expressed in noninvasive tumors, as revealed by immunohistochemical staining, suggesting that alterations of BTAK/Aurora-A could be an early event in human ovarian oncogenesis. To our knowledge, this is the first demonstration of recurrent activation and overexpression of BTAK/Aurora-A in human ovarian cancer, which may play a critical role in development of this malignancy.
CMOS passive pixel image design techniques (2002)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2002.
Laboratory evaluation of a microangioscope for potential percutaneous cerebrovascular applications. (2001)

A laboratory-based study of the physical and performance characteristics of a new 0.25-mm-thin microangioscope was performed. The microangioscope tested was compatible with currently available microcatheters, but its tip was considerably stiff and of limited radiopacity. Poor image quality and difficult image interpretation were further drawbacks. Intensive efforts are directed at addressing current limitations and testing further innovations that could pave the way for future performance in neurovascular endoscopy.