gebhart/patrepeval huggingface dataset:
Experimental Freezing of mid-Evolution Fluctuations with a Programmable Annealer (2016)

For randomly selected couplers and fields, the D-Wave device typically yields a highly Boltzmann like distribution [ indicating equilibration. These equilibrated data however do not contain much useful information about the dynamics which lead to equilibration. To illuminate the dynamics, special Hamiltonians can be chosen which contain large energy barriers. In this paper we generalize this approach by considering a class of Hamiltonians which map clusters of spin-like qubits into 'superspins', thereby creating an energy landscape where local minima are separated by large energy barriers. These large energy barriers allow us to observe signatures of the transverse field frozen. To study these systems, we assume that the these frozen spins are describes by the Kibble-Zurek mechanism which was originally developed to describe formation of topological defects in the early universe. It was soon realized that it also has applications in analogous superconductor systems and later realized to also be important for the transverse field Ising model . We demonstrate that these barriers block equilibration and yield a non-trivial distribution of qubit states in a regime where quantum effects are expected to be strong, suggesting that these data should contain signatures of whether the dynamics are fundamentally classical or quantum. We exhaustively study a class of 3x3 square lattice superspin Hamiltonians and compare the experimental results with those obtained by exact diagonalisation. We find that the best fit to the data occurs at finite transverse field. We further demonstrate that under the right conditions, the superspins can be relaxed to equilibrium, erasing the signature of the transverse field. These results are interesting for a number of reasons. They suggest a route to detect signatures of quantum mechanics on the device on a statistical level.
Supramolecular Amphiphiles: Spontaneous Formation of Vesicles Triggered by Formation of a Charge-Transfer Complex in a Host (2002)

A stable ternary inclusion complex comprising a host, an electron donor, and an electron acceptor with a long alkyl tail (see schematic representation) triggers the spontaneous formation of giant vesicles (see TEM image). The ternary complex behaves as a supramolecular amphiphile with a large polar head group and a single hydrophobic tail. Treatment of the complex with an oxidizing agent results in disruption of the vesicles. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2002/z19898_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
The Suv39H1 methyltransferase inhibitor chaetocin causes induction of integrated HIV-1 without producing a T cell response (2011)

Latent HIV-1 (human immunodeficiency virus-1) provirus is unaffected by current AIDS (acquired immunodeficiency syndrome) therapies. We show here that chaetocin, an SUV39H1 histone methyltransferase inhibitor, causes 25-fold induction of latent HIV-1 expression, while producing minimal toxicity and without causing T cell activation. Induction is associated with loss of histone H3 lysine 9 (H3K9) trimethylation at the long terminal repeat (LTR) promoter, and a corresponding increase in H3K9 acetylation. The effect of chaetocin is amplified synergistically in combination with histone deacetylase (HDAC) inhibitors. These results indicate that chaetocin may provide a therapy to purge cells of latent HIV-1, possibly in combination with other chromatin remodeling drugs.
Microfluidic EDGE emulsification: the importance of interface interactions on droplet formation and pressure stability (2016)

The fact that interactions of components with interfaces can influence processes is well-known; e.g. deposit accumulation on heat exchangers and membrane fouling lead to additional resistances against heat and mass transfer, respectively. In microfluidic emulsification, the situation is even more complex. Component accumulation at the liquid/liquid interface is necessary for emulsion stability, while undesired at the solid/liquid interface where it may change wettability. For successful emulsification both aspects need to be controlled, and that is investigated in this paper for o/w emulsification with microfluidic EDGE devices. These devices were characterised previously, and can be used to detect small wettability changes through e.g. the pressure stability of the device. We used various oil/emulsifier combinations (alkanes, vegetable oil, surfactants and proteins) and related droplet size and operational pressure stability to component interactions with the solid surface and liquid interface. Surfactants with a strong interaction with glass always favour emulsification, while surfactants that have week interactions with the surface can be replaced by vegetable oil that interacts strongly with glass, resulting in loss of emulsification. Our findings clearly show that an appropriate combination of construction material and emulsion components is needed to achieve successful emulsification in microfluidic EDGE devices.
Cancer Chemotherapy Using Suicide Genes (1998)

Suicide gene therapy is a unique form of drug delivery system that allows for negative selection of malignant cells using a prodrug approach. Malignant cells are transduced with a gene encoding an enzyme that can metabolize an otherwise nontoxic prodrug into a toxic metabolite. The prototype of this system is the herpes simplex virus thymidine kinase gene (HSV-tk). Suicide genes may be introduced into tumor cells either by viral vectors or nonviral methods. Current work is underway to fine tune both the delivery systems and optimize the efficacy of the production of the toxic metabolites. Suicide gene therapy is an exciting strategy currently in clinical trial in the treatment of a number of tumors.
TheJAK2V617Ftyrosine kinase mutation in myelofibrosis with myeloid metaplasia: lineage specificity and clinical correlates (2005)

An association between an activating JAK2 mutation (JAK2(V617F)) and BCR/ABL-negative myeloproliferative disorders was recently reported in multiple simultaneous publications. In the current study, mutation analysis for JAK2(V617F) was performed in peripheral blood mononuclear cells (PBMC) from 157 patients with myelofibrosis with myeloid metaplasia (MMM) including 117 with agnogenic (AMM), 22 with postpolycythaemic (PPMM), and 18 with post-thrombocythaemic (PTMM) myeloid metaplasia. The detection rate for JAK2(V617F) was significantly higher in PPMM (91%; homozygous in 18%) compared with either AMM (45.3%; homozygous in 2.6%) or PTMM (38.9%; homozygous in 11.1%). Concomitant analysis in granulocytes (n=57) and CD34(+) cells (n=25) disclosed a higher incidence of homozygous JAK2(V617F) mutation but the overall mutation rate was similar to that obtained from PBMC. JAK2(V617F) was not detected in DNA derived from T cells (n=19). In AMM, the presence of JAK2(V617F) was associated with an older age at diagnosis and a history of thrombosis or pruritus. Multivariate analysis identified only age and the Dupriez prognostic score as independent prognostic factors; JAK2(V617F) had no prognostic significance. In conclusion, JAK2(V617F) is a myeloid lineage-specific event, its incidence in MMM is significantly higher with an antecedent history of polycythaemia vera (PV), and its presence in AMM does not affect prognosis but is associated with PV-characteristic clinical features.
Analytical method for localizing a fluorescent inclusion in a turbid medium (2007)

We describe a novel method for localizing a fluorescent inclusion in a homogeneous turbid medium through the use of time-resolved techniques. Based on the calculation of the mean time of the fluorescence curves, the method does not require a priori knowledge of either the fluorescence lifetime or the mean time of the instrument response function since it adopts a differential processing approach. Theoretical expressions were validated and experiments for assessing the accuracy of localization were carried out on liquid optical phantoms with a small fluorescent inclusion. The illumination and detection optical fibers were immersed in the medium to achieve infinite medium geometry as required by the model used. The experimental setup consisted of a time-correlated single-photon counting system. Submillimeter accuracy was achieved for the localization of the inclusion.
Dysregulation of Adipose Glutathione Peroxidase 3 in Obesity Contributes to Local and Systemic Oxidative Stress (2008)

Glutathione peroxidase 3 (GPx3) accounts for the major antioxidant activity in the plasma. Here, we demonstrate that down-regulation of GPx3 in the plasma of obese subjects is associated with adipose GPx3 dysregulation, resulting from the increase of inflammatory signals and oxidative stress. Although GPx3 was abundantly expressed in kidney, lung, and adipose tissue, we observed that GPx3 expression was reduced selectively in the adipose tissue of several obese animal models as decreasing plasma GPx3 level. Adipose GPx3 expression was greatly suppressed by prooxidative conditions such as high levels of TNFalpha and hypoxia. In contrast, the antioxidant N-acetyl cysteine and the antidiabetic drug rosiglitazone increased adipose GPx3 expression in obese and diabetic db/db mice. Moreover, GPx3 overexpression in adipocytes improved high glucose-induced insulin resistance and attenuated inflammatory gene expression whereas GPx3 neutralization in adipocytes promoted expression of proinflammatory genes. Taken together, these data suggest that suppression of GPx3 expression in the adipose tissue of obese subjects might constitute a vicious cycle to expand local reactive oxygen species accumulation in adipose tissue potentially into systemic oxidative stress and obesity-related metabolic complications.
Structure and Function of Procollagen C-Proteinase (mTolloid) Domains Determined by Protease Digestion, Circular Dichroism, Binding to Procollagen Type I, and Computer Modeling (2000)

Procollagen C-proteinase-2 (pCP-2, mTld) is derived from the longest splicing variant of the gene encoding bone morphogenetic protein 1 (BMP-1). The variants have identical amino terminal signal peptides, prodomains and astacin-like protease domains. However, they differ in the length of their carboxy terminal part, which in pCP-2 has the composition CUB1, CUB2, EGF-like1, CUB3, EGF-like2, CUB4, CUB5, and C-tail. In the shorter form, pCP-1 (i.e., BMP-1), the sequence ends after the CUB3-domain. Using a combination of mutagenesis and structural approaches, we have investigated the structure and function of subfragments of pCP-2. The full-length latent recombinant enzyme and its N-terminally truncated form lacking the prodomain were tested for their enzymic activity. The intact protein showed only partial processing of procollagen type I, whereas the truncated form expressed enzymic activity indistinguishable from its native counterpart purified from chick embryo tendons. These results clearly demonstrated that the prodomain is required for the latency of the enzyme but not for its correct folding. Limited proteolysis of the recombinant protein with alpha-chymotrypsin produced four discrete fragments revealing the location of cleavage sites between the repetitive CUB/EGF domains. The results provide evidence that the CUB sequences form independently folded modules that are stabilized by two pairs of internal disulfide bridges. The modules are linked to each other by more flexible, hinge-like peptides. Solid-phase binding assays with isolated CUB domains and immobilized procollagen type I demonstrated that the first three but not the last two CUB domains specifically bound to the substrate. To define putative sites for CUB-CUB or CUB-substrate interactions, we generated molecular models for pCP-2 CUB domains. The models were obtained using as a template the structure of CUB domain in zona pellucida adhesion protein PSP-I/PSP-II from porcine sperm. The predicted conformations for homology models were, subsequently, confirmed by circular dichroism spectroscopy of polypeptide domains isolated following limited proteolysis with alpha-chymotrypsin.
Robust segmentation of intraretinal layers in the normal human fovea using a novel statistical model based on texture and shape analysis (2010)

A novel statistical model based on texture and shape for fully automatic intraretinal layer segmentation of normal retinal tomograms obtained by a commercial 800nm optical coherence tomography (OCT) system is developed. While existing algorithms often fail dramatically due to strong speckle noise, non-optimal imaging conditions, shadows and other artefacts, the novel algorithm’s accuracy only slowly deteriorates when progressively increasing segmentation task difficulty. Evaluation against a large set of manual segmentations shows unprecedented robustness, even in the presence of additional strong speckle noise, with dynamic range tested down to 12dB, enabling segmentation of almost all intraretinal layers in cases previously inaccessible to the existing algorithms. For the first time, an error measure is computed from a large, representative manually segmented data set (466 B-scans from 17 eyes, segmented twice by different operators) and compared to the automatic segmentation with a difference of only 2.6% against the inter-observer variability.
Miniaturized magnetoelastic tags using frame-suspended hexagonal resonators (2014)

Magnetoelastic tags - also referred to as acousto-magnetic or magnetomechanical tags - are used in wireless detection systems that electromagnetically query the resonant response of the tags. This paper presents miniaturized magnetoelastic tags using hexagonal resonators with an overall size of about ø1.3 mm × 27 μm and a resonant frequency as high as 2.13 MHz. The tags are 100X smaller than typical commercial tags. A unique feature is the frame-suspension, which results in ≈75X improvement in signal amplitude compared to that of non-suspended disc tags with similar size and frequency. This paper also demonstrates that the signal amplitude can be boosted by utilizing signal superposition of an ensemble of tags.
The role of the ninth and tenth type III domains of human fibronectin in cell adhesion (1994)

Fibronectins (FN) contain sites, in addition to the cell recognition site RGD in the tenth type III domain (FIII10), that are required for adhesive activity. The role of FIII10 and the adjacent FIII9 was analysed in functional cell adhesion assays recombinant FIII domains in which the domain boundaries were strictly conserved. FIII9 had no adhesive activity. FIII10, and FIII9 plus FIII10 had less activity than FN, whereas the activity of FIII9-10 was similar to FN. We conclude that FIII9 acts synergistically with FIII10 in cell adhesion, and that this synergy is dependent upon the structural integrity of the FIII9-10 pair of domains.
Role of Neurotrophin Receptor TrkB in the Maturation of Rod Photoreceptors and Establishment of Synaptic Transmission to the Inner Retina (1999)

Brain-derived neurotrophic factor (BDNF) acts through TrkB, a receptor with kinase activity, and mitigates light-induced apoptosis in adult mouse rod photoreceptors. To determine whether TrkB signaling is necessary for rod development and function, we examined the retinas of mice lacking all isoforms of the TrkB receptor. Rod migration and differentiation occur in the mutant retina, but proceed at slower rates than in wild-type mice. In postnatal day 16 (P16) mutants, rod outer segment dimensions and rhodopsin content are comparable with those of photoreceptors in P12 wild type (WT). Quantitative analyses of the photoreceptor component in the electroretinogram (ERG) indicate that the gain and kinetics of the rod phototransduction signal in dark-adapted P16 mutant and P12 WT retinas are similar. In contrast to P12 WT, however, the ERG in mutant mice entirely lacks a b-wave, indicating a failure of signal transmission in the retinal rod pathway. In the inner retina of mutant mice, although cells appear anatomically and immunohistochemically normal, they fail to respond to prolonged stroboscopic illumination with the normal expression of c-fos. Absence of the b-wave and failure of c-fos expression, in view of anatomically normal inner retinal cells, suggest that lack of TrkB signaling causes a defect in synaptic signaling between rods and inner retinal cells. Retinal pigment epithelial cells and cells in the inner retina, including Müller, amacrine, and retinal ganglion cells, express the TrkB receptor, but rod photoreceptors do not. Moreover, inner retinal cells respond to exogenous BDNF with c-fos expression and extracellular signal-regulated kinase phosphorylation. Thus, interactions of rods with TrkB-expressing cells must be required for normal rod development.
Comparison of Low-Dose Isotretinoin with Beta Carotene to Prevent Oral Carcinogenesis (1993)

When preceded by high-dose induction therapy, low-dose isotretinoin therapy was significantly more active against leukoplakia than beta carotene and was easily tolerated.
Controlled Release of Biologically Active Agents (1987)

Principles of Membrane Diffusion Diffusion- Controlled Systems Biodegradable Systems Osmotic and Mechnical Devices Materials Used in Controlled Release Devices Device Preparation and Evaluation Applications The Future Index.
The vertebrate adhesive junction proteins beta-catenin and plakoglobin and the Drosophila segment polarity gene armadillo form a multigene family with similar properties. (1992)

Three proteins identified by quite different criteria in three different systems, the Drosophila segment polarity gene armadillo, the human desmosomal protein plakoglobin, and the Xenopus E-cadherin-associated protein beta-catenin, share amino acid sequence similarity. These findings raise questions about the relationship among the three molecules and their roles in different cell-cell adhesive junctions. We have found that antibodies against the Drosophila segment polarity gene armadillo cross react with a conserved vertebrate protein. This protein is membrane associated, probably via its interaction with a cadherin-like molecule. This cross-reacting protein is the cadherin-associated protein beta-catenin. Using anti-armadillo and antiplakoglobin antibodies, it was shown that beta-catenin and plakoglobin are distinct molecules, which can coexist in the same cell type. Plakoglobin interacts with the desmosomal glycoprotein desmoglein I, and weakly with E-cadherin. Although beta-catenin interacts tightly with E-cadherin, it does not seem to be associated with either desmoglein I or with isolated desmosomes. Anti-armadillo antibodies have been further used to determine the intracellular localization of beta-catenin, and to examine its tissue distribution. The implications of these results for the structure and function of different cell-cell adhesive junctions are discussed.
Rigor or Rigor Mortis? Rational Choice and Security Studies (1999)

April 01 1999 Rigor or Rigor Mortis? Rational Choice and Security Studies Stephen M. Walt Stephen M. Walt Stephen M. Walt is Professor of Political Science and Master of the Social Science Collegiate Division at the University of Chicago. He will join the faculty of the John F. Kennedy School of Government at Harvard University in July 1999. Search for other works by this author on: This Site Google Scholar Author and Article Information Stephen M. Walt Stephen M. Walt is Professor of Political Science and Master of the Social Science Collegiate Division at the University of Chicago. He will join the faculty of the John F. Kennedy School of Government at Harvard University in July 1999. Online Issn: 1531-4804 Print Issn: 0162-2889 © 1999 by the President and Fellows of Harvard College and the Massachusetts Institute of Technology.1999 International Security (1999) 23 (4): 5–48. https://doi.org/10.1162/isec.23.4.5 Cite Icon Cite Permissions Share Icon Share Facebook Twitter LinkedIn MailTo Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Search Site Citation Stephen M. Walt; Rigor or Rigor Mortis? Rational Choice and Security Studies. International Security 1999; 23 (4): 5–48. doi: https://doi.org/10.1162/isec.23.4.5 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsInternational Security Search Advanced Search This content is only available as a PDF. © 1999 by the President and Fellows of Harvard College and the Massachusetts Institute of Technology.1999 Article PDF first page preview Close Modal You do not currently have access to this content.
Peptide and beta 2-microglobulin regulation of cell surface MHC class I conformation and expression (1992)

We have examined the roles of peptide and beta 2-microglobulin (beta 2m) in regulating the conformation and expression level of class I molecules on the cell surface. Using a cell line synthesizing H-2Dd H chain and mouse beta 2m but defective in endogenous peptide loading, we demonstrate the ability of either exogenous peptide or beta 2m alone to increase surface H-2Dd expression at both 25 degrees C and 37 degrees C. Peptide and beta 2m show marked synergy in their abilities to increase surface class I expression, with minimal increases promoted by peptide in the absence of free beta 2m. Low temperature-induced molecules have indistinguishable rates of loss of beta 2m and alpha 1/alpha 2 domain conformational epitopes during culture at 37 degrees C. However, the rate of alpha 3 epitope loss is much slower, indicating a minimum of two steps in class I loss from the cell surface: 1) loss of beta 2m binding to H chain and unfolding of the alpha 1/alpha 2 region; then 2) denaturation, degradation, or internalization of the free H chains possessing alpha 3 epitopes. These data show for the first time that free H chains survive for a finite time on the membrane in a form capable of refolding into alpha 1/alpha 2 epitope positive molecules upon addition of beta 2m and peptide. This refolding in the presence of beta 2m and peptide can explain the reported requirement for both components in sensitizing cells for class I-dependent CTL lysis. It also indicates that such conformational changes in class I molecules are not strictly dependent on either newly synthesized H chains or on intracellular chaperons. The study of H chain-peptide-beta 2m interaction on the cell surface may be relevant to understanding intracellular peptide loading events.
The Transporter Classification Database: recent advances (2008)

The Transporter Classification Database (TCDB), freely accessible at http://www.tcdb.org, is a relational database containing sequence, structural, functional and evolutionary information about transport systems from a variety of living organisms, based on the International Union of Biochemistry and Molecular Biology-approved transporter classification (TC) system. It is a curated repository for factual information compiled largely from published references. It uses a functional/phylogenetic system of classification, and currently encompasses about 5000 representative transporters and putative transporters in more than 500 families. We here describe novel software designed to support and extend the usefulness of TCDB. Our recent efforts render it more user friendly, incorporate machine learning to input novel data in a semiautomatic fashion, and allow analyses that are more accurate and less time consuming. The availability of these tools has resulted in recognition of distant phylogenetic relationships and tremendous expansion of the information available to TCDB users.