gebhart/patrepeval huggingface dataset:
Hydrophobic and Hydrophilic Interactions of Ionic Liquids and Polymers in Solid Polymer Gel Electrolytes (2007)

Poly(ethylene oxide), PEO, or poly(vinylidenefluoride-co-hexafluoropropene), PVdF-HFP, and the ionic liquids 1-n-propyl-2,3-dimethylimidazolium tetrafluoroborate and 1-n-propyl-2,3-dimethylimidazolium hexafluorophosphate with and without Li salt were used to prepare solid polymer gel electrolytes. Experimentation indicates that for the PEO films, the 20 and polymer gels exhibited the highest ionic conductivity, although the film is fragile and exhibits poor mechanical properties. Therefore, the composition of all gels studied is polymer and ionic liquid. For all systems, addition of the lithium salts results in approximately a 33% drop in ionic conductivity. Results indicate that for the formation of polymer gel electrolytes, selection of a nonpolar polymer paired with a hydrophobic electrolyte results in greater ionic conductivity and reversibility in the intercalation of Li ion into graphite. These results are interpreted in terms of the type of solid solution formed between the hydrophobic and hydrophilic polymers and the ionic liquids.
Online Nonnegative Matrix Factorization With Robust Stochastic Approximation (2012)

Nonnegative matrix factorization (NMF) has become a popular dimension-reduction method and has been widely applied to image processing and pattern recognition problems. However, conventional NMF learning methods require the entire dataset to reside in the memory and thus cannot be applied to large-scale or streaming datasets. In this paper, we propose an efficient online RSA-NMF algorithm (OR-NMF) that learns NMF in an incremental fashion and thus solves this problem. In particular, OR-NMF receives one sample or a chunk of samples per step and updates the bases via robust stochastic approximation. Benefitting from the smartly chosen learning rate and averaging technique, OR-NMF converges at the rate of in each update of the bases. Furthermore, we prove that OR-NMF almost surely converges to a local optimal solution by using the quasi-martingale. By using a buffering strategy, we keep both the time and space complexities of one step of the OR-NMF constant and make OR-NMF suitable for large-scale or streaming datasets. Preliminary experimental results on real-world datasets show that OR-NMF outperforms the existing online NMF (ONMF) algorithms in terms of efficiency. Experimental results of face recognition and image annotation on public datasets confirm the effectiveness of OR-NMF compared with the existing ONMF algorithms.
Image segmentation of trabecular spongiosa by visual inspection of the gradient magnitude (2006)

Recent advances in physical models of skeletal dosimetry utilize high-resolution 3-dimensional microscopic computed tomography images of trabecular spongiosa. These images are coupled to radiation transport codes to assess energy deposition within active bone marrow and trabecular endosteum. These transport codes rely primarily on the segmentation of the spongiosa images into bone and marrow voxels. Image thresholding has been the segmentation of choice for bone sample images because of its extreme simplicity. However, the ability of the segmentation to reproduce the physical boundary between bone and marrow depends on the selection of the threshold value. Statistical models, as well as visual inspection of the image, have been employed extensively to determine the correct threshold. Both techniques are affected by partial volume effect and can provide unexpected results if performed without care. In this study, we propose a new technique to threshold trabecular spongiosa images based on visual inspection of the image gradient magnitude. We first show that the gradient magnitude of the image reaches a maximum along a surface that remains almost independent of partial volume effect and that is a good representation of the physical boundary between bone and marrow. A computer program was then developed to allow a user to compare the position of the iso-surface produced by a threshold with the gradient magnitude. The threshold that produces the iso-surface that best coincides with the maximum gradient is chosen. The technique was finally tested with a set of images of a true bone sample with different resolutions, as well as with three images of a cube of Duocell aluminium foam of known mass and density. Both tests demonstrate the ability of the gradient magnitude technique to retrieve sample volumes or media volume fractions with 1% accuracy at 30 µm voxel size.
Fc receptor inside‐out signaling and possible impact on antibody therapy (2015)

Fc receptors (FcR) are expressed on immune cells and bind to the Fc tail of antibodies. This interaction is essential for FcR-mediated signaling and triggering of cellular effector functions. FcR activation is tightly regulated to prevent immune responses by non-antigen bound antibodies or in the absence of 'danger signals'. FcR activity may be modulated at the plasma membrane via cross-talk with integrins. In addition, cytokines at the site of infection/inflammation can increase FcR avidity, a process referred to as inside-out signaling. This regulatory mechanism has been described for FcγRI (CD64), FcγRIIa (CD32a), and FcαRI (CD89) and is also well-known for integrins. Key cellular events during inside-out signaling are (de)phosphorylation, clustering, cytoskeleton rearrangements, and conformational changes. The latter can be studied with antibodies that specifically recognize epitopes exposed by the active (high affinity) or inactive (low affinity) state of the FcR. These antibodies are important tools to investigate the role of FcR activation in disease settings. Research on FcR has gained momentum with the rise of monoclonal antibodies (mAb) entering the clinic for the treatment of cancer and other diseases. The clinical outcome of mAb therapy may be improved by increasing FcR avidity by cytokine stimulation.
Polarized secretion of IL-6 and IL-8 by human retinal pigment epithelial cells (1998)

A number of cell types situated along interfaces of various tissues and organs such as the peritoneum and the intestine have been shown to secrete inflammatory cytokines in a polarized fashion. Retinal pigment epithelial (RPE) cells are positioned at the interface between the vascularized choroid and the avascular retina, forming part of the blood-retina barrier. These cells are potent producers of inflammatory cytokines and are therefore considered to play an important role in the pathogenesis of ocular inflammation. Whether cytokine secretion by these cells also follows a vectorial pattern is not yet known, and was therefore the subject of this study. Monolayers of human RPE cells (primary cultures and the ARPE-19 cell line) cultured on transwell filters were stimulated to produce IL-6 and IL-8 by adding IL-1beta (100 U/ml) to either the upper or the lower compartment. After stimulation, the human RPE cell lines showed polarized secretion of IL-6 and IL-8 towards the basal side, irrespective of the side of stimulation. The ARPE- 19 cell line also secreted IL-6 and IL-8 in a polarized fashion towards the basal side after basal stimulation; polarized secretion was, however, not apparent after apical stimulation. The observation that human RPE cells secrete IL-6 and IL-8 in a polarized fashion towards the choroid may represent a mechanism to prevent damage to the adjacent fragile retinal tissue.
Nerve growth factor promotes human hemopoietic colony growth and differentiation. (1988)

Nerve growth factor (NGF) is a neurotropic polypeptide necessary for the survival and growth of some central neurons, as well as sensory afferent and sympathetic neurons. Much is now known of the structural and functional characteristics of NGF, whose gene has recently been cloned. Since it is synthesized in largest amounts by the male mouse submandibular gland, its role exclusively in nerve growth is questionable. NGF also causes histamine release from rat peritoneal mast cells in vitro, and we have shown elsewhere that it causes significant, dose-dependent, generalized mast cell proliferation in the rat in vivo when administered neonatally. Our experiments now indicate that NGF causes a significant stimulation of granulocyte colonies grown from human peripheral blood in standard hemopoietic methylcellulose assays. Further, NGF appears to act in a relatively selective fashion to induce the differentiation of eosinophils and basophils/mast cells. Depletion experiments show that the NGF effect may be T-cell dependent and that NGF augments the colony-stimulating effect of supernatants from the leukemic T-cell (Mo) line. The hemopoietic activity of NGF is blocked by polyclonal and monoclonal antibodies to NGF. We conclude that NGF may indirectly act as a local growth factor in tissues other than those of the nervous system by causing T cells to synthesize or secrete molecules with colony-stimulating activity. In view of the synthesis of NGF in tissue injury, the involvement of basophils/mast cells and eosinophils in allergic and other inflammatory processes, and the association of mast cells with fibrosis and tissue repair, we postulate that NGF plays an important biological role in a variety of repair processes.
Cigarette smoking is associated with dose-related and potentially reversible impairment of endothelium-dependent dilation in healthy young adults. (1993)

Cigarette smoking is associated with dose-related and potentially reversible impairment of endothelium-dependent arterial dilation in asymptomatic young adults, consistent with endothelial dysfunction.
Efficient formation of influenza virus-like particles: dependence on the expression levels of viral proteins. (1999)

It has previously been demonstrated in this laboratory that an influenza virus-like chloramphenicol acetyltransferase (CAT) RNA could be expressed in COS-1 cells that synthesized all ten influenza A virus-encoded proteins from recombinant plasmids. It was also shown that supernatant fluids harvested from these cultures contained virus-like particles (VLPs) that could deliver an enclosed CAT RNA to MDCK cells. Here, it is shown that the levels of expression of the reporter gene in the COS-1 and/or MDCK cells can be altered drastically by modifying the concentrations of the recombinant plasmids transfected in the COS-1 cells. Thus, it was observed that overexpression of NS2 reduced CAT expression in COS-1 cells, whereas overexpression of M2 and NS1 proteins dramatically decreased transmission of the CAT RNA to the MDCK cultures. These results are discussed with reference to the roles of these proteins during virus replication. From these experiments, a ratio of transfected plasmids was found that increased the efficiency of the previously described system by 50-100-fold. Under these optimized conditions, it was demonstrated that VLPs can be formed in the absence of neuraminidase expression and that these VLPs remained aggregated to each other and to cell membranes. Moreover, it is shown that CAT RNA transmission was dependent on specific interactions of the ribonucleoprotein complex with other viral structural polypeptides. These data demonstrate the usefulness of this encapsidation-packaging system for the study of different aspects of the influenza virus life-cycle.
Addition Polymerization of Cyclopentene with Nickel and Palladium Catalysts (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTAddition Polymerization of Cyclopentene with Nickel and Palladium CatalystsStephan J. McLain, Jerald Feldman, Elizabeth F. McCord, Kenncorwin H. Gardner, Mark F. Teasley, E. Bryan Coughlin, K. Jeff Sweetman, Lynda K. Johnson, and Maurice BrookhartView Author Information DuPont Central Research & Development, DuPont Experimental Station, P.O. Box 80328, Wilmington, Delaware 19880-0328 Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290 Cite this: Macromolecules 1998, 31, 19, 6705–6707Publication Date (Web):September 1, 1998Publication History Received6 November 1997Published online1 September 1998Published inissue 1 September 1998https://doi.org/10.1021/ma971639zCopyright © 1998 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1491Altmetric-Citations95LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (88 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Catalysts,Oligomers,Palladium,Polymerization,Polymers Get e-Alerts
Antimalarial immunity in Saimiri monkeys. Immunization with surface components of asexual blood stages. (1984)

Plasmodium falciparum polypeptides of 200 and 140 K mol wt exposed at the surface of merozoites and/or schizonts were purified by affinity chromatography and by electroelution from sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Monkeys were separated into three groups of four and immunized either with one of the two polypeptides or with saline (control). After intravenous challenge with 2.5 X 10(7) P. falciparum asexual blood stages, two monkeys of the control group had to be treated and two recovered spontaneously after peak parasitemia of 9 and 11%. The four monkeys immunized with the 140 K polypeptide recovered without treatment after peak parasitemia between 1.5 and 4.5%. Monkeys immunized with the 200 K polypeptide had similar peak parasitemia except one monkey who suffered from a large skin excoriation and who recovered spontaneously after a peak parasitemia of 11%. Prechallenge sera of the immunized monkeys reacted only with the polypeptide used for immunization except for one serum of the 140 K group, which precipitated an additional polypeptide of 39 K, and a polypeptide of 31 K weakly precipitated by the four sera of monkeys immunized with the 200 K polypeptide. The relatedness between the 200 and 140 K polypeptides was investigated using tryptic digestion and reverse phase chromatography. No clear analogy was found between the two polypeptides, which suggests that immunization with either of two independent surface components of P. falciparum asexual blood stages is able to induce at least a partial protective immunity in immunized hosts.
Application of Genetic Algorithms to Combinatorial Synthesis:  A Computational Approach to Lead Identification and Lead Optimization, (1996)

A genetic algorithms (GA) based strategy is described for the identification or optimization of active leads. This approach does not require the synthesis and evaluation of huge libraries. Instead it involves iterative generations of smaller sample sets, which are assayed, and the “experimentally” determined biological response is used as an input for GA to rapidly find better leads. The GA described here has been applied to the identification of potent and selective stromelysin substrates from a combinatorial-based population of 206 or 64 000 000 possible hexapeptides. Using GA, we have synthesized less then 300 unique immobilized peptides in a total of five generations to achieve this end. The results show that each successive generation provided better and unique substrates. An additional strategy of utilizing the knowledge gained in each generation in a spin-off SAR activity is described here. Sequences from the first generations were evaluated for stromelysin and collagenase activity to identify stromelysin-selective substrates. GlyProSerThr-TyrThr with Tyr as the P1‘ residue is such an example. A number of peptides replacing Tyr with unusual monomers were synthesized and evaluated as stromelysin substrates. This led to the identification of Ser(OBn) as the best and most selective P1‘ residue for stromelysin.
Correlated increases of tumour necrosis factor-alpha, interleukin-6 and granulocyte monocyte-colony stimulating factor levels in suction blister fluids and sera of psoriatic patients relationships with disease severity (1994)

Tumour necrosis factor-alpha (TNF-alpha), interleukin-6 (IL-6) and granulocyte monocyte-colony stimulating factor (GM-CSF) were measured in serum and involved and uninvolved skin blister fluids of 20 psoriatic patients and 10 healthy subjects, by enzyme immunoassay. TNF-alpha and IL-6 were always detectable in involved skin blister fluids, while GM-CSF was detected only in 45% of these samples. TNF-alpha, IL-6 and GM-CSF were detected in 95, 100 and 10% of uninvolved skin blister fluid samples, respectively. TNF-alpha and IL-6 were found in 50 and 30% of control blister fluids, while GM-CSF was never detected. In serum, TNF-alpha was detected in 75% of patients and in 70% of controls; IL-6 in 45% of patients and in no controls; and GM-CSF in 35% of patients and in 20% of the controls. The median TNF-alpha and IL-6 levels in involved skin were statistically higher than those of both uninvolved and control skin blister fluids. TNF-alpha and IL-6 levels in blister fluids obtained from both involved and uninvolved skin were higher than those of the patients' sera. GM-CSF, when present in involved skin blister fluids, showed correlated levels with the other cytokines (TNF-alpha: R = 0.85, P = 0.004; IL-6: R = 0.72, P = 0.03). TNF-alpha was highly correlated with IL-6 (R = 0.78, P < 0.00001) in involved skin blister fluids. TNF-alpha and IL-6 levels of involved skin blister fluids showed significant correlations with the psoriasis area and severity index scores in the patients, suggesting a direct relationship between these cytokines and the clinical manifestations of the disease. Moreover, the TNF-alpha levels were particularly related to the erythema scores in the patients, further supporting evidence of their role in the pathogenesis of the disease.
Mononucleotide and dinucleotide frequencies, and codon usage in poliovirion RNA (1981)

The polio type 1 (Mahoney) RNA sequence (1) has been analyzed in terms of the distribution of its mononucleotides, dinucleotides and trinucleotides (codons). The distribution of adenosine in the sequence is nonuniform, being lower at the 5' end and higher at the 3' end. The dinucleotide CG is relatively rare and the dinucleotides UG and CA are relatively more common than expected. Codon usage is decidedly nonrandom. Codons containing CG are avoided and those ending in adenosine are favored. The asymmetric use of mononucleotides, dinucleotides and codons in polio RNA is unexplained at the present time although the lowered CG frequency may be the result of a DNA origin for polio RNA.
The Lumiere Project: Bayesian User Modeling for Inferring the Goals and Needs of Software Users (2013)

The Lumiere Project centers on harnessing probability and utility to provide assistance to computer software users. We review work on Bayesian user models that can be employed to infer a users needs by considering a user's background, actions, and queries. Several problems were tackled in Lumiere research, including (1) the construction of Bayesian models for reasoning about the time-varying goals of computer users from their observed actions and queries, (2) gaining access to a stream of events from software applications, (3) developing a language for transforming system events into observational variables represented in Bayesian user models, (4) developing persistent profiles to capture changes in a user expertise, and (5) the development of an overall architecture for an intelligent user interface. Lumiere prototypes served as the basis for the Office Assistant in the Microsoft Office '97 suite of productivity applications.
Anti-CD38 Antibody Therapy: Windows of Opportunity Yielded by the Functional Characteristics of the Target Molecule (2013)

In vivo use of monoclonal antibodies (mAbs) has become a mainstay of routine clinical practice in the treatment of various human diseases. A number of molecules can serve as targets, according to the condition being treated. Now entering human clinical trials, CD38 molecule is a particularly attractive target because of its peculiar pattern of expression and its twin role as receptor and ectoenzyme. This review provides a range of analytical perspectives on the current progress in and challenges to anti-CD38 mAb therapy. We present a synopsis of the evidence available on CD38, particularly in myeloma and chronic lymphocytic leukemia (CLL). Our aim is to make the data from basic science helpful and accessible to a diverse clinical audience and, at the same time, to improve its potential for in vivo use. The topics covered include tissue distribution and signal implementation by mAb ligation and the possibility of increasing cell density on target cells by exploiting information about the molecule's regulation in combination with drugs approved for in vivo use. Also analyzed is the behavior of CD38 as an enzyme: CD38 is a component of a pathway leading to the production of adenosine in the tumor microenvironment, thus inducing local anergy. Consequently, not only might CD38 be a prime target for mAb-mediated therapy, but its functional block may contribute to general improvement in cancer immunotherapy and outcomes.
Inhibition of tumorigenesis by a cytosine–DNA, methyltransferase, antisense oligodeoxynucleotide (1997)

This paper tests the hypothesis that cytosine DNA methyltransferase (DNA MeTase) is a candidate target for anticancer therapy. Several observations have suggested recently that hyperactivation of DNA MeTase plays a critical role in initiation and progression of cancer and that its up-regulation is a component of the Ras oncogenic signaling pathway. We show that a phosphorothioate-modified, antisense oligodeoxynucleotide directed against the DNA MeTase mRNA reduces the level of DNA MeTase mRNA, inhibits DNA MeTase activity, and inhibits anchorage independent growth of Y1 adrenocortical carcinoma cells ex vivo in a dose-dependent manner. Injection of DNA MeTase antisense oligodeoxynucleotides i.p. inhibits the growth of Y1 tumors in syngeneic LAF1 mice, reduces the level of DNA MeTase, and induces demethylation of the adrenocortical-specific gene C21 and its expression in tumors in vivo. These results support the hypothesis that an increase in DNA MeTase activity is critical for tumorigenesis and is reversible by pharmacological inhibition of DNA MeTase.
CU-2010—A Novel Small Molecule Protease Inhibitor with Antifibrinolytic and Anticoagulant Properties (2008)

These findings suggest that CU-2010 has similar antifibrinolytic potency compared to aprotinin, is more potent than tranexamic acid, and possesses some anticoagulant effects.
Microwave Synthesis of CdSe and CdTe Nanocrystals in Nonabsorbing Alkanes (2008)

Controlling nanomaterial growth via the "specific microwave effect" can be achieved by selective heating of the chalcogenide precursor. The high polarizability of the precursor allows instantaneous activation and subsequent nucleation leading to the synthesis of CdSe and CdTe in nonmicrowave absorbing alkane solvents. Regardless of the desired size, narrow dispersity nanocrystals can be isolated in less than 3 min with high quantum efficiencies and elliptical morphologies. The reaction does not require a high temperature injection step, and the alkane solvent can be easily removed. In addition, batch-to-batch variance in size is 4.2 +/- 0.14 nm for 10 repeat experimental runs. The use of a stopped-flow reactor allows near continuous automation of the process leading to potential industrial benefits.