gebhart/patrepeval huggingface dataset:
Platelet Reactions and Immune Processes (1971)

Summary We have studied the effect of IgG, IgA, IgM, lambda light chains, Fc fragments, heat-aggregated gammaglobulin, albumin and fibrinogen on the interaction of latex, Kaolin, celite or bentonite particles with human platelet-rich plasma. 1. Marked enhancement of platelet aggregating activity was produced by preincubating these particles with IgG at an appropriate concentration. Excess IgG abolished this platelet aggregating property. 2. Platelet aggregation could also be induced by betamethasone acetate particles. The latter and IgG-coated latex, Kaolin or bentonite particles were inhibited by chymotrypsin substrates and inhibitors. 3. Heat-aggregated IgG produced platelet aggregation in platelet-rich plasma only when adsorbed onto (Kaolin) particles. 4. Results obtained with fibrinogen-coated Kaolin suggest that the particles thus acquired a slightly increased platelet clumping activity. 5. The other proteins studied failed to enhance the platelet aggregating activity of Kaolin particles, and could even inhibit the formation of IgG-coated Kaolin particles able to readily aggregate platelets.
E‐cadherin synergistically induces hepatospecific phenotype and maturation of embryonic stem cells in conjunction with hepatotrophic factors (2005)

Since effective cell sourcing is a major challenge for the therapeutic management of liver disease and liver failure, embryonic stem (ES) cells are being widely investigated as a promising source of hepatic-like cells with their proliferative and pluripotent capacities. Cell-cell interactions are crucial in embryonic development modulating adhesive and signaling functions; specifically, the cell-cell adhesion ligand, cadherin is instrumental in gastrulation and hepatic morphogenesis. Inspired by the role of cadherins in development, we investigated the role of expression of E-cadherin in cultured murine ES cells on the induction of hepatospecific phenotype and maturation. The cadherin-expressing embryonic stem (CE-ES) cells intrinsically formed pronounced cell aggregates and cuboidal morphology whereas cadherin-deficient cadherin-expressing embryonic stem (CD-ES) cells remained more spread out and corded in morphology. Through controlled stimulation with single or combined forms of hepatotrophic growth factors; hepatocyte growth factor (HGF), dexamethasone (DEX) and oncostatin M (OSM), we investigated the progressive maturation of CE-ES cells, in relation to the control, CD-ES cells. Upon growth factor treatment, the CE-ES cells adopted a more compacted morphology, which exhibited a significant hepatocyte-like cuboidal appearance in the presence of DEX-OSM-HGF. In contrast, the CD-ES cells exhibited a mixed morphology and appeared to be more elongated in the presence of DEX-OSM-HGF. Reverse-transcriptase polymerase chain reaction was used to delineate the most differentiating condition in terms of early (alpha-fetoprotein (AFP)), mid (albumin), and late-hepatic (glucose-6-phosphatase) markers in relation to growth factor presentation for both CE-ES and CD-ES cells. We report that following the most differentiating condition of DEX-OSM-HGF stimulation, CE-ES cells expressed increased levels of albumin and glucose-6-phosphatase, whereas the CD-ES cells showed low levels of AFP and marginal levels of albumin and glucose-6-phosphatase. These trends suggest that the membrane expression of E-cadherin in ES cells can elicit a marked response to growth factor stimulation and lead to the induction of later stages of hepatocytic maturation. Thus, cadherin-engineered ES cells could be used to harness the cross-talk between the hepatotrophic and cadherin-based signaling pathways for controlled acceleration of ES hepatodifferentiation.
Segmentation in Skeletal Scintigraphy Images using Convolutional Neural Networks (2017)

In this work we have addressed the task of segmentation in skeletal scintigraphy images with deep learning models, where we research different approaches to convert convolutional neural networks designed for classification tasks to powerful pixel wise predictors. We explore different network architectures where two primary research paths have been followed. Firstly, an encoder-decoder architecture which aims to extract dense features in the first part of the network -- which works as a feature encoder -- and then up-sample these dense features to restore the original image resolution and perform pixel-wise predictions. This technique has shown great promise in other experiments of segmentation in medical images. This general architecture has been pitted against an entirely different approach, which works with expansions of the convolutional kernels, rather than sub-sampling through pooling layers, known as convolutions ``atrous'' or dilated convolutional kernels. While the atrous approach has been explored in different studies for the problem of semantic image segmentation for outdoor and indoor scenes with a large amount of classes it has yet to be tried in the medical imaging field. When compared to the encoder-decoder architecture we see that the convolutional neural networks atrous outperform the former in almost every way. We observe that the most promising atrous model generated a test error of 0.0659 on segmentations on the left scapula, which is a reduction of 50.67\% on the test error as compared to the most powerful encoder-decoder model. The atrous model also managed to reduce the amount of parameters by a factor 100 and more than halve the required training time per epoch.
Advances towards the Development of ATP‐Competitive Small‐Molecule Inhibitors of the Insulin‐Like Growth Factor Receptor (IGF‐IR) (2006)

The insulin-like growth factor receptor (IGF-IR) is a receptor tyrosine kinase that simultaneously regulates proliferation, by MAPK activation, and survival, by the PI3K/Akt pathway, of cells, indicating that IGF-IR inhibitors might possess anticancer properties. This review will focus on both cancer biology of IGF-IR and novel ATP-competitive inhibitors of IGF-IR.
An application developer's perspective on reliable multicast for distributed interactive media (2000)

In this paper we investigate which characteristics reliable multicast services should have in order to be appropriate for use by distributed interactive media applications such as shared whiteboards, networked computer games, or distributed virtual environments. We take a close look at the communication requirements of these applications and at existing approaches to realize reliable multicast. Based on this information we deduce which reliable multicast transport protocols are appropriate for the different aspects of distributed interactive media. Furthermore we discuss how the application program interface of a reliable multicast service should be designed in order to support the development of applications for distributed interactive media.
Paper Chromatography. A Laboratory Manual (1952)

Journal Article Paper Chromatography. A Laboratory Manual Get access Paper Chromatography. A Laboratory Manual . Block Richard J. LeStrange R. Zweig G. . 195 pages, illustrated. Academic Press, Inc. , 125 East 23rd Street, New York 10, N. Y. ( 1952 ). $4.50 . AIBS Bulletin, Volume 2, Issue 5, October 1952, Page 14, https://doi.org/10.1093/aibsbulletin/2.5.14-f Published: 01 October 1952
Clinical applications of urinary organic acids. Part 2. Dysbiosis markers. (2008)

Part 1 of this series focused on urinary organic acids as markers of detoxification; part 2 focuses on dysbiosis markers. Intestinal microbial growth is accompanied by the release of products of their metabolism that may be absorbed and excreted in urine. Several organic acids are known to be specific products of bacterial metabolic action on dietary polyphenols or unassimilated amino acids or carbohydrates. Associated gastrointestinal or neurological symptoms may result from irritation of the intestinal mucosa or systemic distribution of absorbed neurotoxic products. Detection of abnormally elevated levels of these products is a useful diagnostic tool for patients with gastrointestinal or toxicological symptoms. Test profiles of urinary organic acids associated with microbial overgrowth can include benzoate, hippurate, phenylacetate, phenylpropionate, cresol, hydroxybenzoate, hydroxyphenylacetate, hydroxyphenylpropionate and 3,4-dihydroxyphenylpropionate, indican, tricarballylate, D-lactate, and D-arabinitol. Effective treatments for the associated microbial overgrowths may be directed at reducing microbial populations, introducing favorable microbes, and restoring intestinal mucosal integrity.
The oxime bond formation as a useful tool for the preparation of oligonucleotide conjugates (2005)

Synthetic oligonucleotides are attracting considerable interest as potential therapeutic agents for the selective inhibition of gene expression. The attainment of effective cellular delivery however remains a problem. The conjugation of oligonucleotides to cell penetrating peptides is one of the most promising alternatives, that is being currently investigated to improve the uptake efficiency of oligonucleotides. The synthesis of peptide–oligonucleotide conjugates (POC) is however still a problem. Work from our laboratory has attempted to address the problem of POC synthesis by using the chemoselective oxime bond formation. Herein, we present an account of the work accomplished in our laboratory in the recent past, concerning the conjugation of various reporters to oligonucleotides. .
A Graph-Space Optimal Transport Approach for Full Waveform Inversion (2018)

Summary The use of optimal transport distances has been recently promoted to mitigate cycle skipping issues in full waveform inversion. This distance is convex with respect to shifted patterns between compared data. This is the reason why it has attracted interest for full waveform inversion as the convexity with respect to time shifts can be seen as a proxy for the convexity with respect to wave velocities. The main difficulty for the application of optimal transport to seismic data is related to their non positivity: the optimal transport theory is developed for the comparison of positive quantities. We present a review of the strategies proposed to overcome this issue, and explain their limitations. They are either not adapted for the comparison of realistic data, or lose the convexity property. On this basis, we propose a novel approach based on a graph space interpretation of the seismic traces. Synthetic and observed traces are seen as point clouds in a 2D space (the graph space), which are compared using a 2D optimal transport technique. This strategy overcomes the positivity issue while preserving the convexity property. An application of this strategy on the Marmousi 2 model illustrates its interest for mitigating cycle skipping.
[Application of X-ray diffraction to the analysis of traditional Chinese medicine]. (1999)

This technique may have broad prospects for pharmaceutical analysis.
Investigation of Silicon Nanowire Gate-All-Around Junctionless Transistors Built on a Bulk Substrate (2013)

A silicon nanowire (Si-NW) with a gate-all-around (GAA) structure is implemented on a bulk wafer for a junctionless (JL) field-effect transistor (FET). A suspended Si-NW from the bulk-Si is realized using a deep reactive ion etching (RIE) process. The RIE process is iteratively applied to make multiply stacked Si-NWs, which can increase the on-state current when amplified with the number of iterations or enable integration of 3-D stacked Flash memory. The fabricated JL FETs exhibit excellent electrostatic control with the aid of the GAA and junction-free structure. The influence on device characteristics according to the channel dimensions and additional doping at the source and drain extension are studied for various geometric structures of the Si-NW.
GALLIUM ARSENIDE EPITAXIAL FILM GROWTH (1963)

Abstract : Oxygen was shown to be a major factor in the formation of surface imperfections previously observed. The source of the oxygen in the system was traced to a fault in the palladium furnace. Analyses of commercial hydrochloric acid samples from several sources have been made showing that impurities up to 0.3% (volume) are frequently present. Doping with sulfur in the form of sulfur monochloride yields maximum donor concentrations of 3.7 x 10 to the 18th power/cubic cm. Attempts to achieve higher doping levels with tellurium were not successful. Non-destructive techniques for the measurement of carrier concentration are presented covering the range 10 to the 15th power to 10 to the 19th power for n-type material. Evidence is presented to show that the layers have doping gradients near the interface. Details are given of the procedure for surface preparation, including the etch composition, rotation speed, etchrate and final rinsing and drying of the wafer. An evaluation of the growth rates is also given.
Embedding Equality Constraints of Optimization Problems into a Quantum Annealer (2019)

Quantum annealers such as D-Wave machines are designed to propose solutions for quadratic unconstrained binary optimization (QUBO) problems by mapping them onto the quantum processing unit, which tries to find a solution by measuring the parameters of a minimum-energy state of the quantum system. While many NP-hard problems can be easily formulated as binary quadratic optimization problems, such formulations almost always contain one or more constraints, which are not allowed in a QUBO. Embedding such constraints as quadratic penalties is the standard approach for addressing this issue, but it has drawbacks such as the introduction of large coefficients and using too many additional qubits. In this paper, we propose an alternative approach for implementing constraints based on a combinatorial design and solving mixed-integer linear programming (MILP) problems in order to find better embeddings of constraints of the type ∑ x i = k for binary variables x i. Our approach is scalable to any number of variables and uses a linear number of ancillary variables for a fixed k.
Structure-tunable synthesis of titanate nanotube thin films via a simple hydrothermal process (2007)

In this study, titanium metal acts as the titanium source to prepare oriented titanate nanotube thin film. The effects of preparation parameters, such as reaction temperature, duration and post-treatment conditions, on the film morphology and stability have been examined. A general formation mechanism for oriented titanate nanotube thin film is proposed on the basis of detailed observations of the products using two-dimensional surface SEM studies and TEM images. The overall formation of titanate nanotubes can be summarized as a sequence of four steps: (a) titanium dissolution and alkali titanate hydrogel formation; (b) alkali titanate hydrogel dissolution, increased TiO32−, TiO2(OH)22− or TinO2n+m2m− concentration and layered Na2Ti3O7 formation; (c) layered Na2Ti3O7 growth; (d) nanotube formation via Na2Ti3O7 splitting and the multilayer scrolling process. The Na2Ti3O7 lamellar structures split between the (010) planes into nanosheets.
Chorioamnionitis as a Risk Factor for Cerebral Palsy (2000)

Our meta-analysis indicates that chorioamnionitis is a risk factor for both cerebral palsy and cPVL. JAMA. 2000;284:1417-1424.
Identification of Mycobacterium kansasii by DNA hybridization (1991)

A DNA probe specific for Mycobacterium kansasii was obtained from a plasmid clone library of EcoRI-digested genomic DNA. The probe specifically identified culture-confirmed isolates of M. kansasii and isolates in cultures of environmental water samples. In an attempt to distinguish between isolates of M. kansasii, we used two methods to demonstrate restriction fragment length polymorphisms in the genomic DNA. Both of these methods failed to detect any differences between the isolates. These isolates included the type strain TMC 1201, environmental isolates, and clinical isolates from Australia and the Solomon Islands. This result suggests that the genome of M. kansasii is highly conserved and that genetic divergence within this species in insignificant.
Epigenetic Modifications in Hepatic Stellate Cells Contribute to Liver Fibrosis (2012)

Liver fibrosis represents the final common pathway of virtually all types of chronic liver diseases, and it has been a major public health concern. Many genes have been demonstrated to be involved in the pathogenesis of liver fibrosis, while the mechanisms underlying gene regulation still needs further research. On the other hand, hepatic stellate cells (HSCs) are quiescent cells in the perisinusoidal space in liver. HSCs facilitate hepatocytes interactions via releasing soluble inflammatory factors and producing extracellular matrix. HSCs can be activated in response to liver injury, and they differentiate to myofibroblasts, which greatly contribute to the fibrogenesis process. Various epigenetic procedures, including DNA methylation, histone modification and formation of particular chromatin structure, play crucial roles in the gene transcriptional expression in HSCs, regulating various vital processes. For instance, epigenetic modulation on the peroxisome proliferator-activated receptor gamma (PPAR-γ) gene promoter accounts for HSC differentiation through interacting pathways. Aberrant expression of a series of histones and chemokines in activated HSCs can aggravate inflammation and oxidative stress, which in turn promotes differentiation of HSCs to myofibroblasts and enhances the whole fibrogenesis process. Degradation of extracellular matrix is also regulated through epigenetic modulation on matrix associated enzymes. Moreover, fibrosis-related epigenetic modifications in the parental generation may be inherited to their offspring. In this review, we firstly summarize the vital epigenetic modifications of fibrosis-related genes in HSCs, and highlight specific nucleic acid sequences and structures in gene promoters as important action sites, which may provide indicators for liver fibrosis diagnosis in the future.
An intronic polymorphic domain often associated with susceptibility to affective disorders has allele dependent differential enhancer activity in embryonic stem cells (1999)

Variable number tandem repeats (VNTR) within non-coding regions of a number of genes have been correlated with susceptibility to various disease states. In particular, a VNTR polymorphism of a 16 or 17 bp element within intron 2 of the human serotonin transporter gene has been correlated with a predisposition to affective disorders. We have demonstrated that this region will support differential levels of reporter gene expression in differentiating embryonic stem cells, this being dependent on the presence of 10 or 12 copies of the repeat. The VNTR domain can therefore act as a transcriptional regulator, a property which potentially contributes to disease susceptibility.
Least-squares array processing for signals of unknown form (1965)

Statistical methods are applied to the estimation of the velocity, arrival-angle and waveform of a signal appearing in an array of sensors in the presence of random noise. The signal is assumed to be a plane wave propagating through a linear, homogeneous, non-dispersive medium so that it is the same in each sensor except for a time delay due to its finite velocity. A novel formulation is introduced which requires no assumptions concerning the signal waveform but permits its estimation along with the vector of time delays per unit distance. The method is appropriate for applications such as seismology and passive sonar in which the signal waveform is unknown, yet cannot be realistically represented as a stationary random process (as is required, for example, by Wiener filtering theory).A least-squares procedure is described which does not depend on any assumptions regarding the noise. This simple criterion is found to imply time-shift and sum processing which is related to other techniques previously employed. For known noise statistics the mean-square response of the processor to the noise is calculated and the covariance matrix of the estimates is approximated for the high signal-to-noise ratio case. The resulting array pattern is evaluated in terms of the signal spectrum and the array geometry. The results are compared with a more elaborate maximumlikelihood approach based on stationary Gaussian noise with a known spectral density matrix.
P-323 (2012)

Hart, Jaime E; Feskanich, Diane; Puett, Robin C; Yanosky, Jeff D; Laden, Francine Author Information
Inflammatory cytokines induce synthesis and secretion of <i>gro</i> protein and a neutrophil chemotactic factor but not β2-microglobulin in human synovial cells and fibroblasts (1989)

Exposure of human synovial cells and fibroblasts in monolayer culture to interleukin 1 results in prominent secretion of proteins with Mr values of 6000 and 7000. By N-terminal sequence analysis, the Mr-6000 protein is identified as the protein encoded by a recently described gro mRNA. The Mr-7000 protein is identical to a neutrophil chemotactic factor released from monocytes. Stimulation of normal human fibroblasts with tumour necrosis factor alpha also results in expression and secretion of these two proteins. In addition to these cytokine-induced proteins, we have identified beta 2-microglobulin as an Mr-8000 protein constitutively secreted by synovial cells.
Strained Metallocenophanes and Related Organometallic Rings Containing π‐Hydrocarbon Ligands and Transition‐Metal Centers (2007)

The structures, bonding, and ring-opening reactions of strained cyclic carbon-based molecules form a key component of standard textbooks. In contrast, the study of strained organometallic molecules containing transition metals is a much more recent development. A wealth of recent research has revealed fascinating nuances in terms of structure, bonding, and reactivity. Building on initial work on strained ferrocenophanes, a broad range of strained organometallic rings composed of a variety of different metals, pi-hydrocarbon ligands, and bridging elements has now been developed. Such strained species can potentially undergo ring-opening reactions to functionalize surfaces and ring-opening polymerization to form easily processed metallopolymers with properties determined by the presence of the metal and spacer. This Review summarizes the current state of knowledge on the preparation, structural characterization, electronic structure, and reactivity of strained organometallic rings with pi-hydrocarbon ligands and d-block metals.
<i>Eimeria tenella</i>: <i>in vitro</i> development in irradiated bovine kidney cells (1984)

The initial infection and first-generation development of Eimeria tenella was quantified using a cloned MDBK (Madin-Darby Bovine Kidney) cell line, irradiated with gamma radiation prior to infection, as the host cell. Irradiated cell cultures were found to be more susceptible to infection and had a greater capacity to support parasite development than non-irradiated cultures. It was suggested that the larger proportion of cells in the G2 phase of the cell cycle, the larger individual cell size and the inhibition of cell division in the irradiated cultures were all factors contributing to the increased susceptibility to infection and capacity to support parasite growth and development. The application of this technique (host cell irradiation) to the cultivation of other intracellular, protozoan parasites is discussed.