gebhart/patrepeval huggingface dataset:
Nucleosides. 110. Synthesis and antiherpes virus activity of some 2'-fluoro-2'-deoxyarabinofuranosylpyrimidine nucleosides (1979)

A series of 5-substituted 1-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)cytosines 7a-d and their corresponding uracils 9a-d,f were prepared by condensation of 3-O-acetyl-5-O-benzoyl-2-deoxy-2-fluoro-D-arabinosyl bromide (5) with appropriately trimethylsilylated pyrimidines followed by saponification of the protected nucleosides 6 or 8. 1-(2-Deoxy-2-fluoro-beta-D-arabinofuranosyl)-5-iodocytosine (7e) was obtained by iodination of 7a. Iodination of 8a followed by removal of the protecting acyl-protecting groups afforded the 5-iodo nucleoside 9e. Several of these 2'-fluoro-substituted nucleosides completely obviated replication of herpes simplex virus type 1 (HSV-1) in monolayers of Vero cells at concentrations of 10-100 microgram/mL. The 5-iodocytosine analogue 7e was the most effective, showing 99.5% suppression of viral replication even at concentrations of 0.1 microgram/mL. The cytotoxicity of 7e to L5178Y or P815 cells in culture was minimal. A comparison of the efficacy of 7e against HSV-1 with other known nucleoside antiviral agents indicates that further in vitro and in vivo evaluation of 7e is warranted.
Interpenetrating Polymer Network (IPN): Novel Approach in DrugDelivery (2012)

al. This is an open access paper distributed under the copyright agreement with Serials Publication, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
NITRITE AND THIOSULFATE THERAPY IN CYANIDE POISONING (1952)

In 1932 Geiger<sup>1</sup>began to use methylene blue in treatment of cyanide poisoning. The antidotal action of the dye was shown by Wendel<sup>2</sup>and Hug<sup>3</sup>to be due to the formation of methemoglobin, which successfully competes with the respiratory enzyme, ferricytochrome oxidase, for cyanide ions. Subsequent reports<sup>4</sup>indicate that methylene blue is not an efficient antidote because it is a poor methemoglobin former and at the same time reverses the reaction in presence of co-enzyme.<sup>5</sup>In fact, the dye is of greater value in the treatment of methemoglobinemia<sup>6</sup>than in cyanide poisoning. Nevertheless, the trial of methylene blue stimulated a renewed search for cyanide antidotes, and led to the discovery of a more effective therapy. Independent investigations in Argentina<sup>7</sup>and the United States<sup>4a</sup>gave rise to a clear-cut conclusion that the combination of sodium nitrite and sodium thiosulfate, consecutively injected by vein,
Rapid, depth-resolved light scattering measurements using Fourier domain, angle-resolved low coherence interferometry (2004)

We present a novel angle-resolved low coherence interferometry scheme for rapid measurement of depth-resolved angular scattering distributions to enable determination of scatterer size via elastic scattering properties. Depth resolution is achieved using a superluminescent diode in a modified Mach-Zehnder interferometer with the mixed signal and reference fields dispersed by an imaging spectrograph. The spectrograph slit is located in a Fourier transform plane of the scattering sample, enabling angle-resolved measurements over a 0.21 radian range. The capabilities of the new technique are demonstrated by recording the distribution of light scattered by a sub-surface layer of polystyrene microspheres in 40 milliseconds. The data are used to determine the microsphere size with good accuracy. Future clinical application to measuring the size of cell nuclei in living epithelial tissues using backscattered light is discussed.
Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores (2008)

In genetics, many evolutionary pathways can be modeled by the ordered accumulation of permanent changes. Mixture models of mutagenetic trees have been used to describe disease progression in cancer and in HIV. In cancer, progression is modeled by the accumulation of chromosomal gains and losses in tumor cells; in HIV, the accumulation of drug resistance-associated mutations in the viral genome is known to be associated with disease progression. From such evolutionary models, genetic progression scores can be derived that assign measures for the disease state to single patients. Rtreemix is an R package for estimating mixture models of evolutionary pathways from observed cross-sectional data and for estimating associated genetic progression scores. The package also provides extended functionality for estimating confidence intervals for estimated model parameters and for evaluating the stability of the estimated evolutionary mixture models.
Peroxisome proliferator‐activated receptor γ ligands regulate neural stem cell proliferation and differentiation in vitro and in vivo (2010)

Peroxisome proliferator-activated receptor gamma (PPARγ) belongs to a family of ligand-activated nuclear receptors and its ligands are known to control many physiological and pathological situations. Its role in the central nervous system has been under intense analysis during the last years. Here we show a novel function for PPARγ in controlling stem cell expansion in the adult mammalian brain. Adult rats treated with pioglitazone, a specific ligand of PPARγ, had elevated numbers of proliferating progenitor cells in the subventricular zone and the rostral migratory stream. Electron microscopy analysis also showed important changes in the subventricular zone ultrastructure of pioglitazone-treated animals including an increased number of migratory cell chains. These results were further confirmed in vitro. Neurosphere assays revealed significant increases in the number of neurosphere forming cells from pioglitazone- and rosiglitazone (two specific ligands of PPARγ receptor)-treated cultures that exhibited enhanced capacity for cell migration and differentiation. The effects of pioglitazone were blocked by the PPARγ receptor antagonists GW9662 and T0070907, suggesting that its effects are mediated by a mechanism dependent on PPARγ activation. These results indicate for the first time that activation of PPARγ receptor directly regulates proliferation, differentiation, and migration of neural stem cells in vivo.
Coupled Fluid Flow and Geomechanics in Reservoir Study -I. Theory and Governing Equations (1995)

Abstract The purpose of this study is to examine Biot’s two-phase (fluid and rock), isothermal, linear poroelastic theory from the conventional porous fluid-flow modeling point of view. Biot’s theory and the published applications are oriented more toward rock mechanics than fluid flow. Our goal is to preserve the commonly used systematic porous fluid-flow modeling and include geomechanics as an additional module. By developing such an approach, complex reservoir situations involving geomechanical issues (e.g., naturally fractured reservoirs, stress-sensitive reservoirs) can be pursued more systematically and easily. We show how the conventional fluid-flow formulations is extended to a coupled fluid-flow-geomechanics model. Consistent interpretation of various rock compressibilities and the effective stress law are shown to be critical in achieving the coupling. The "total (or system) compressibility" commonly used in reservoir engineering is shown to be a function of boundary conditions. Under the simplest case (isotropic homogeneous material properties), the fluid pressure satisfies a fourth-order equation instead of the conventional second-order diffusion equation. Limiting cases include nondeformable, incompressible fluid and solid, and constant mean normal stress are analyzed.
High quality Ge on Si by epitaxial necking (2000)

We show that pure Ge grown selectively on SiO2/Si substrates in 100 nm holes is highly perfect at the top surface compared to conventional Ge lattice-mismatched growth on planar Si substrates. This result is achieved through a combination of interferometric lithography SiO2/Si substrate patterning and ultrahigh vacuum chemical vapor deposition Ge selective epitaxial growth. This “epitaxial necking,” in which threading dislocations are blocked at oxide sidewalls, shows promise for dislocation filtering and the fabrication of low-defect density Ge on Si. Defects at the Ge film surface only arise at the merging of epitaxial lateral overgrowth fronts from neighboring holes. These results confirm that epitaxial necking can be used to reduce threading dislocation density in lattice-mismatched systems.
Three functions of bacteriophage P1 involved in cell lysis (1996)

Amber and deletion mutants were used to assign functions in cell lysis to three late genes of bacteriophage P1. Two of these genes, lydA and lydB of the dar operon, are 330 and 444 bp in length, respectively, with the stop codon of lydA overlapping the start codon of lydB. The third, gene 17, is 558 bp in length and is located in an otherwise uncharacterized operon. A search with the predicted amino acid sequence of LydA for secondary motifs revealed a holin protein-like structure. Comparison of the deduced amino acid sequence of gene 17 with sequences of proteins in the SwissProt database revealed homologies with the proteins of the T4 lysozyme family. The sequence of lydB is novel and exhibited no known extended homology. To study the effect of gp17, LydA, and LydB in vivo, their genes were cloned in a single operon under the control of the inducible T7 promoter, resulting in plasmid pAW1440. A second plasmid, pAW1442, is identical to pAW1440 but has lydB deleted. Induction of the T7 promoter resulted in a rapid lysis of cells harboring pAW1442. In contrast, cells harboring pAW1440 revealed only a small decrease in optical density at 600 nm compared with cells harboring vector alone. The rapid lysis phenotype in the absence of active LydB suggests that this novel protein might be an antagonist of the holin LydA.
Nonrigid groupwise registration for motion estimation and compensation in compressed sensing reconstruction of breath‐hold cardiac cine MRI (2015)

Reconstruction methods based on groupwise registration show higher quality reconstructions for cardiac cine images than the pairwise counterparts tested.
Cross-Linked Bioreducible Layer-by-Layer Films for Increased Cell Adhesion and Transgene Expression (2010)

The effect of cross-linking layer-by-layer (LbL) films consisting of bioreducible poly(2-dimethylaminoethyl methacrylate) (rPDMAEMA) and DNA is examined with regard to rigidity, biodegradability, cell adhesion, and transfection activity using 1,5-diiodopentane (DIP) cross-linker. DIP chemically reacts with the tertiary amines of rPDMAEMA, altering the chemical composition of these LbL films. The result is a change in surface morphology, film swelling behavior, and film rigidity, measured with AFM and ellipsometry. It is found that the apparent Young's modulus is increased more than 4 times its original value upon cross-linking. Cross-linking mass is additionally confirmed with a quartz crystal microbalance with dissipation (QCM-D). Comprehensive analyses of these experimental values were investigated to calculate the degree of cross-linking using the rubber elasticity theory and the Flory-Rehner theory. Additionally, the Flory-Huggins parameter, chi, was calculated. Good agreement in the two methods yields a cross-linking density of approximately 0.82 mmol/cm(3). The Flory-Huggins parameter increased upon cross-linking from 1.07 to 1.2, indicating increased hydrophobicity of the network and formation of bulk water droplets within the films. In addition, the effects of cross-linking on film disassembly by 1,4-dithiothreitol (DTT) are found to be insignificant despite the alteration in film rigidity. Mouse fibroblast cells and smooth muscle cells are used to study the effect of cross-linking on cell adhesion and cell transfection activity. In vitro transfection activity up to seven days is quantified using secreted alkaline phosphatase (SEAP) DNA. Film cross-linking is found to enhance cell adhesion and prolong the duration of cellular transfection. These results contribute to the development of bioreducible polymer coatings for localized gene delivery.
Lentiviral Vectors Mediate Long-Term and High Efficiency Transgene Expression in HEK 293T cells (2015)

The results suggest that all five vectors can stably transduce 293T cells, producing long term transgene expression with different efficiencies. However, neither the insulator nor the UCOE improved the GFP expression. The vectors containing the promoter CMV or CMV (β-globin intron) generated the highest gene expressions, manifesting as more favorable candidates for recombinant protein production in HEK293T cells.
Amyloidosis (1994)

Amyloidosis is a heterogeneous group of disorders characterized by extracellular deposition of abnormal protein fibrils which are derived from different proteins in different forms of the disease. Asymptomatic amyloid deposition in a variety of tissues is a universal accompaniment of ageing, and clinical amyloidosis is not rare. Intracerebral and cerebrovascular beta-protein amyloid deposits are a hallmark of the pathology of both sporadic and familial Alzheimer's disease, beta 2-microglobulin-derived amyloid is a common complication of long term haemodialysis, and islet amyloid polypeptide is the fibril protein in the universal islet amyloidosis of type II diabetes mellitus. New fibril proteins have lately been identified in hereditary amyloidosis, including variants of gelsolin, apolipoprotein AI, lysozyme and fibrinogen. The development of radiolabelled serum amyloid P component (SAP) scintigraphy has allowed amyloid to be diagnosed non-invasively in vivo for the first time, provided unique insight into the distribution and size of amyloid deposits, and yielded novel information on the natural history and the effects of treatment. Amyloid deposits are in a state of dynamic turnover and can regress if new fibril formation is halted. The recent elucidation of the three dimensional structure of human SAP may enable the design of specific therapeutic agents.
ErbB-3 Predicts Survival in Ovarian Cancer (2006)

HER3 may represent a new prognostic factor in primary epithelial ovarian cancer. Pending validation, exploration of therapeutic strategies to block HER3 could be warranted.
Hybrid organic–inorganic materials: a land of multidisciplinarity (1996)

Organic-inorganic hybrids appear as a creative alternative for obtaining new materials with unusual features. This is related to their diphasic structures, leading to multifunctional materials. The low-temperature processes which are used to synthesize such structures provide a wide versatility in the design of the compounds. The potentiality of the chemistry is to play on the structure of these mixtures and dissociate the various contributions in tailoring both phases and controlling the interfaces. In this paper, a review of some chemistry pathways to hybrid materials is presented. The nature of the bonds between organic and inorganic phases is used to divide them in two major families: class I corresponds to materials with weak interphase bonding, while class II corresponds to materials where both phases are chemically grafted. Applications of these materials in the fields of optics, iono-electronics, mechanics, biology and others are expected. Some applications are reviewed, with respect to the versatility of the synthetic procedure. Most of the properties of these new high-technology materials are dependent on their structural and chemical composition as well as on the dynamical properties inside the blends.
Molecular mechanisms of development of the gastrointestinal tract (2000)

The gut offers a complex but rich organ system to study visceral pattern formation. The gut is an early evolutionary advance. Data supports that the molecular controls of gut pattern formation are be conserved across species. The gut develops in a stereotyped manner in many different species, by using a basic mechanism of development, the epithelial-mesenchymal interaction. Signaling between the endoderm and mesoderm is essential for normal gut development. The signaling molecules involved are just being described and include factors known to be critical in embryonic development of other systems. The gut has four major patterned axes: anterior-posterior (AP), dorsal-ventral (DV), left-right (LR), and radial (RAD). The molecular pathways used to control pattern in each of these axes are the subject of this review. Major advances in the understanding of AP and LR axis formation in the gut have been described within the past few years. RAD and DV axes are now hot topics for investigation. Despite advances in these areas of gut development, basic events remain poorly understood. Discovery of specific factors that control gut pattern formation may provide a template for the study of pattern formation in other visceral/organ systems.
A Machine Learning Approach to Twitter User Classification (2021)

This paper addresses the task of user classification in social media, with an application to Twitter. We automatically infer the values of user attributes such as political orientation or ethnicity by leveraging observable information such as the user behavior, network structure and the linguistic content of the user’s Twitter feed. We employ a machine learning approach which relies on a comprehensive set of features derived from such user information. We report encouraging experimental results on 3 tasks with different characteristics: political affiliation detection, ethnicity identification and detecting affinity for a particular business. Finally, our analysis shows that rich linguistic features prove consistently valuable across the 3 tasks and show great promise for additional user classification needs.
Histological Findings Compared with Magnetic Resonance and Ultrasonographic Imaging in Irreversible Postmastectomy Lymphedema: A Case Study (2009)

Postmastectomy edema is a current complication after axillary lymph node dissection in cases of breast cancer treatment. Staging is important in order to select those patients who can benefit from complex physical therapy (CPT). Different imaging techniques can be used to evaluate the edema. Ultrasonography (US) is a harmless, cheap, and easily applicable technique to visualize the dermal and subcutaneous tissue, but interpretation of the obtained images is not always evident. The aim of this study was to compare ultrasound images of irreversible edema with tissue histology, magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS). Ultrasonographic images of the edematous dermis show an homogeneous hypoechogenic dermal layer that appears on tissue histology to be less compact, due to the excess of fluid in the interstitium separating the collagen fibres and making it more transparent on light microscopy. MRI of the dermis gives a hyperintense signal, indicating the presence of fluid. In the subcutis, increase of the adipose tissue could be observed on US, MRI, and tissue histology. In the case of lymphedema, the area and perimeter of fat cells is significantly (p < 0.05) increased. Hypoechogenic areas near the muscle fascia are registered on US corresponding with epifascial fluid on MRI, and hyperechogenic branches are embedded within the adipose tissue, on tissue histology seen as large fibrotic septa enclosing adipose cells. MRI has a honeycomb picture corresponding with fluid bound to fibrosis.
Formaldehyde stabilization facilitates lignin monomer production during biomass depolymerization (2016)

Practical, high-yield lignin depolymerization methods could greatly increase biorefinery productivity and profitability. However, development of these methods is limited by the presence of interunit carbon-carbon bonds within native lignin, and further by formation of such linkages during lignin extraction. We report that adding formaldehyde during biomass pretreatment produces a soluble lignin fraction that can be converted to guaiacyl and syringyl monomers at near theoretical yields during subsequent hydrogenolysis (47 mole % of Klason lignin for beech and 78 mole % for a high-syringyl transgenic poplar). These yields were three to seven times those obtained without formaldehyde, which prevented lignin condensation by forming 1,3-dioxane structures with lignin side-chain hydroxyl groups. By depolymerizing cellulose, hemicelluloses, and lignin separately, monomer yields were between 76 and 90 mole % for these three major biomass fractions.
The structure of secondary education in developing countries (1996)

This report describes the recent history of the size and structure of secondary education in developing World Bank countries. Enrollment and organizational data about secondary schooling in about 100 World Bank countries have been collected from several sources. The data reach back to 1960, a period before some of the largest recent growth in education among these countries, and extends until 1990. This thirty year period has witnessed growth in primary education in almost all countries of the world, including the least developed. For example, among the countries studied in this report, on average over 85 percent of eligible children were enrolled in primary school. This educational expansion has prepared large cohorts of students for available secondary education opportunities. The period between 1960 and 1990 represents for many World Bank countries a shift from primary to secondary expansion. It is thus the crucial period to study educational subsector development among developing countries. Before the results section of this report, there is a brief description of data sources and analysis techniques. Then the results are broken down into three main sections of size of secondary enrollments, structure of secondary schooling, and selected relationships among them. In each section, historical trends, gender, and regional variations and other related topics are examined.
Interaction between Ebola Virus Glycoprotein and Host Toll-Like Receptor 4 Leads to Induction of Proinflammatory Cytokines and SOCS1 (2009)

Ebola virus initially targets monocytes and macrophages, which can lead to the release of proinflammatory cytokines and chemokines. These inflammatory cytokines are thought to contribute to the development of circulatory shock seen in fatal Ebola virus infections. Here we report that host Toll-like receptor 4 (TLR4) is a sensor for Ebola virus glycoprotein (GP) on virus-like particles (VLPs) and that resultant TLR4 signaling pathways lead to the production of proinflammatory cytokines and suppressor of cytokine signaling 1 (SOCS1) in a human monocytic cell line and in HEK293-TLR4/MD2 cells stably expressing the TLR4/MD2 complex. Ebola virus GP was found to interact with TLR4 by immunoprecipitation/Western blot analyses, and Ebola virus GP on VLPs was able to stimulate expression of NF-kappaB in a TLR4-dependent manner. Interestingly, we found that budding of Ebola virus VLPs was more pronounced in TLR4-stimulated cells than in unstimulated control cells. In sum, these findings identify the host innate immune protein TLR4 as a sensor for Ebola virus GP which may play an important role in the immunopathogenesis of Ebola virus infection.