gebhart/patrepeval huggingface dataset:
Differentiation-induced changes in protein-tyrosine phosphatase activity and commensurate expression of CD45 in human leukemia cell lines. (1992)

Pharmacologic differentiation of the promyelocytic leukemia HL60 is associated with an increase in cellular tyrosine phosphatase activity. We asked (a) if this increase might, at least in part, be due to changes in a transmembranous protein-tyrosine phosphatase, CD45; and (b) if CD45 changes similarly in other differentiating leukemias. Differentiation of HL60, several chronic myelogenous leukemias, a monocytic leukemia (THP-1), and a monoblastoid leukemia (U-937) could be induced by phorbol ester, 1,25-dihydroxy vitamin D3, dimethyl sulfoxide, or cyclic AMP analogues. This differentiation was associated with a marked increase in (a) total cellular tyrosine phosphatase activity (2-4-fold as measured by the ability to dephosphorylate a tyrosine-phosphorylated peptide); (b) CD45-specific tyrosine phosphatase activity (2-4-fold); (c) CD45 cell surface expression by flow cytometry (2-5-fold); (d) synthesis of both exon B-dependent M(r) 205,000 and exon ABC- M(r) 185,000 CD45 proteins, as revealed by immunoprecipitation with antisera specific for CD45 isoforms. Both isoforms have enhanced electrophoretic mobility when isolated from the differentiated cells. This enhanced mobility did not appear to be due to decreased stoichiometry of CD45 phosphorylation on serine/threonine residues. Interestingly, 12-O-tetradecanoylphorbol-13-acetate transiently reduced CD45 protein-tyrosine phosphatase activity in the chronic myelogenous leukemia cell RWLeu4 without altering the CD45 amount (as measured by cell surface immunofluorescence). Modulation of CD45 tyrosine phosphatase activity (and protein levels) may play a role in differentiation or in maintaining cells in a nonproliferative state or may represent a phenotypic marker of differentiation.
ChemInform Abstract: REACTIONS WITH (+)‐Z‐3,6‐BIS(AMINOOXYMETHYL)PIPERAZINE‐2,5‐DIONE, II. SELECTIVE ELIMINATION‐ADDITION REACTIONS (1980)

Abstract Das Dimethylpiperazindion (II), Abbauprodukt von (I), reagiert mit Alkylmercaptanen oder Aziridin (IV) bei pH‐Werten unter 7 unter Monoaddition zu (III) bzw. (VI), bei pH‐Werten oberhalb 7 werden mit Mercaptanen die Derivate (VII), mit Aziridin das Bis‐Addukt (VIII) und mit Piperidin das Derivat (IX) erhalten.
The Effects of Bifidobacterium breve Administration on Campylobacter Enteritis (1987)

Abstract We studied the effects of Bifidobacterium breve on Campylobacter enteritis. Patients with Campylobacter enteritis were divided into three groups (I. Erythromycin recipients; II. B. breve recipients; III. control) and studied with regard to the duration of diarrhea and carriage of Campylobacter jejuni in the stools. Additional studies were performed to observe the effects of B. breve on fecal flora. The results showed that there were no significant differences in the duration of diarrhea among the three groups. Comparison of the duration of C. jejuni carriage in the stools was as follows: KIKIII (P&lt;0.01). Microbiological study of fecal flora demonstrated that the number of bifidobacterium was decreased in Campylobacter enteritis compared to the control, and an increase in the number of bifidobacterium could be recognized after the administration of B. breve. B. breve was useful in eradicating C. jejuni from the stools and restoring the normal intestinal flora in Campylobacter enteritis, although if was not effective in shortening the duration of diarrhea.
Hybrid organic–inorganic semiconductor-based light-emitting diodes (1997)

We demonstrate that the ability of GaN-based light-emitting diodes to emit in the short-wavelength regime makes possible “hybrid” organic–inorganic semiconductor light-emitting diodes that consist of two parts: a GaN-based electroluminescent part and an organic thin-film-based fluorescent part that absorbs the electroluminescence and fluoresces at a longer wavelength resulting in color conversion. We also show that organic films with much improved surface smoothness may be obtained by deposition at reduced temperatures.
Depressive Symptoms and Smoking Cessation After Hospitalization for Cardiovascular Disease (2008)

Moderate to severe depressive symptoms during hospitalization for acute CVD are independently associated with rapid relapse to smoking after discharge and lower rates of smoking cessation at long-term follow-up. The relationship was mediated in part by the stronger nicotine withdrawal symptoms experienced by smokers with higher depressive symptoms.
A hybrid adaptation protocol for TCP-friendly layered multicast and its optimal rate allocation (2003)

Layered transmission has been proposed as a solution to video multicast over the Internet. Existing protocols usually perform adaptation at the receiver and use static rate allocation techniques at the sender. As a result, significant mismatches between the fixed transmission rates and the heterogeneous and dynamic rate requirements for the receivers can occur. We show that such mismatches can be minimized by employing dynamic layer rate allocation at the sender by taking advantage of the recent development in layered video coding. Specifically, we study the optimization criteria for layer rate allocation, and propose a metric, called fairness index, which fairly reflects the degree of a receiver's satisfaction. We then formulate this into an optimization problem with the objective of maximizing the expected fairness index, and derive an efficient and scalable algorithm to solve it. We further demonstrate that such sender rate adaptation can be seamlessly integrated into an end-to-end adaptation protocol called HALM (hybrid adaptation layered multicast). This protocol is designed for the current best-effort Internet and is TCP-friendly. Its control overhead is also kept at a low level. Simulation results show that HALM improves the degree of fairness for receivers with heterogeneous bandwidth requirements, and interacts with TCP flows substantially better than static allocation based protocols. In addition, increasing the number of layers in HALM always leads to a higher degree of fairness and 3 to 5 layers are usually sufficient. However, this is not true for the static allocation based protocols.
THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER SINGLE-STRANDED DNA APTAMER (1993)

The structure of a complex between human alpha-thrombin and a GGTTGGTGTGGTTGG 15-nucleotide consensus sequence has been solved by x-ray crystallography and refined at 2.9-A resolution to an R value of 0.159. As in solution, in the complex the single-stranded DNA folds into a structure with two G-quartets. The DNA is sandwiched between two different positively charged regions of two symmetry-related thrombin molecules in the crystal structure making ionic and hydrophobic interactions. One region is the fibrinogen recognition exosite and the other, the putative heparin binding site. The lack of inhibition of fibrinogen clotting and platelet activation by the DNA 15-mer with the Arg75-->Glu mutant of thrombin is consistent with the several salt bridges of the DNA in the fibrinogen exosite. The association of DNA with the heparin site of a neighboring molecule appears to simply compensate residual charge. Differences in the 15-mer loop conformations between the complex and NMR solution structures can be attributed to conformational changes upon thrombin binding. Although G-quadruplexes are favored in the presence of monovalent cations, there is no evidence of the latter in the thrombin complex.
NMR solution structure of a parallel LNA quadruplex (2004)

The solution structure of a locked nucleic acid (LNA) quadruplex, formed by the oligomer d(TGGGT), containing only conformationally restricted LNA residues is reported. NMR and CD spectroscopy, as well as molecular dynamics and mechanic calculations, has been used to characterize the complex. The molecule adopts a parallel stranded conformation with a 4-fold rotational symmetry, showing a right-handed helicity and the guanine residues in an almost planar conformation with three well-dened G-tetrads. The thermal stability of Q-LNA has been found to be comparable with that of [r(UGGGU)] 4 , while a T m increment of 20 o C with respect to the corresponding DNA quadruplex structure [d(TGGGT)] 4 has been observed. The structural features of the LNA quadruplex reported here may open new perspectives for the biological application of LNAs as novel versatile tools to design aptamer or catalyst oligonucleotides.
Fetal Cells and Fetal DNA in Maternal Blood (2001)

Is noninvasive, risk-free prenatal diagnosis of fetal genetic characteristics still a fantasy, or will it soon become reality? The current status of both the leading European research groups as well as the NIH-funded NIFTY study are reported here, indicating that certain fetal genetic traits can now be examined efficiently in a noninvasive manner.
Efficacy and safety of telaprevir in patients with genotype 1 hepatitis C infection (2011)

Chronic hepatitis C infection represents a significant and growing health problem worldwide. Patients with genotype 1 hepatitis C respond poorly to the current standard of care, pegylated interferon and ribavirin, which is frequently associated with unpleasant side effects. Consequently new agents with improved efficacy and tolerability are needed. The efficacy and safety of the direct-acting antiviral agent telaprevir in the treatment of genotype 1 hepatitis C infection have been demonstrated in a number of clinical trials. The addition of telaprevir to standard therapy considerably improves response rates and allows response-guided shortening of treatment duration in a substantial number of treatment-naïve patients. Side effects associated with telaprevir therapy include rash, anaemia, gastrointestinal disturbance and anorectal discomfort. Telaprevir-resistant variants have been identified in patients who have failed telaprevir-containing therapy, and whether selection of these variants will compromise future therapeutic options is currently unknown. The efficacy and safety of telaprevir in the treatment of the most challenging patients, including those with recurrent hepatitis C following liver transplantation and those co-infected with HIV, remains to be established.
Dose-Dependent Effects of Glyburide on Insulin Secretion and Glucose Uptake in Humans (1991)

The data suggest that glyburide (and probably other sulfonylureas), operates within a narrow range of plasma concentrations (50-200 nM), which can be achieved with very low doses of the drug. It remains to be shown whether the threshold of maximal effect also in clinical practice is achieved with lower sulfonylurea doses than that currently used.
Plants for Stormwater Pollution Removal: Greenhouse Research and Field-Study at Green Meadows Subdivision Logan, UT (2012)

Much of the stormwater protection in Cache Valley is done with respect to prevention of TSS contamination during construction activities. Preventing contamination of stormwater from construction activities is critical, but stormwater can still be highly polluted
Waste disposal—An attractive strategy for cancer therapy (2017)

Targeted therapies for cancer are typically small molecules or monoclonal antibodies that act by inhibiting the activity of specific proteins that drive tumor growth. Although many of these drugs are effective in cancer patients, the response is often not durable because tumor cells develop resistance to the drugs. Another limitation of this strategy is that not all oncogenic driver proteins are "druggable" enzymes or receptors with activities that can be inhibited. Here we describe an alternative approach to targeted therapy that is based on co-opting the cellular quality-control machinery-the ubiquitin-proteasome system-to remove specific cancer-causing proteins from the cell. We first discuss examples of existing cancer drugs that work by degrading specific proteins and then review recent progress in the rational design and preclinical testing of small molecules that induce selective degradation of specific target proteins.
Aging-induced type I interferon response at the choroid plexus negatively affects brain function (2014)

Aging-associated cognitive decline is affected by factors produced inside and outside the brain. By using multiorgan genome-wide analysis of aged mice, we found that the choroid plexus, an interface between the brain and the circulation, shows a type I interferon (IFN-I)-dependent gene expression profile that was also found in aged human brains. In aged mice, this response was induced by brain-derived signals, present in the cerebrospinal fluid. Blocking IFN-I signaling within the aged brain partially restored cognitive function and hippocampal neurogenesis and reestablished IFN-II-dependent choroid plexus activity, which is lost in aging. Our data identify a chronic aging-induced IFN-I signature, often associated with antiviral response, at the brain's choroid plexus and demonstrate its negative influence on brain function, thereby suggesting a target for ameliorating cognitive decline in aging.
DNABII proteins play a central role in UPEC biofilm structure (2015)

Most chronic and recurrent bacterial infections involve a biofilm component, the foundation of which is the extracellular polymeric substance (EPS). Extracellular DNA (eDNA) is a conserved and key component of the EPS of pathogenic biofilms. The DNABII protein family includes integration host factor (IHF) and histone-like protein (HU); both are present in the extracellular milieu. We have shown previously that the DNABII proteins are often found in association with eDNA and are critical for the structural integrity of bacterial communities that utilize eDNA as a matrix component. Here, we demonstrate that uropathogenic Escherichia coli (UPEC) strain UTI89 incorporates eDNA within its biofilm matrix and that the DNABII proteins are not only important for biofilm growth, but are limiting; exogenous addition of these proteins promotes biofilm formation that is dependent on eDNA. In addition, we show that both subunits of IHF, yet only one subunit of HU (HupB), are critical for UPEC biofilm development. We discuss the roles of these proteins in context of the UPEC EPS.
Analysis of serum granulysin in patients with hematopoietic stem‐cell transplantation: Its usefulness as a marker of graft‐versus‐host reaction (2006)

Granulysin is a newly identified CTL/NK cell-related cytotoxic protein, which is secreted in both constitutive and Ca-dependent manner. To evaluate its significance in stem-cell transplantation (SCT), serum granulysin was measured by newly established ELISA method in 26 patients undergoing SCT (21 allogeneic and 5 autologous). In the allogeneic SCT, granulysin was transiently increased in 3 weeks, which was not observed in autologous SCT. In acute GVHD, serum granulysin was markedly increased and correlated with the severity of GVHD. Elevation of granulysin was not necessarily associated with increase of sIL2R or IFN-gamma. In vitro, allospecific T cells released granulysin in an allo-specific manner, and it was correlated with allo-specific cytotoxic activity. These results indicate that increased release of granulysin presents alloreactivity and serum granulysin is useful as a marker of GVHD in SCT.
Trans Complementation of Variant Cre Proteins for Defects in Cleavage and Synapsis (2000)

The Cre recombinase is a member of the integrase family of conservative site-specific recombinases. These proteins share five conserved catalytic residues, one of which is a tyrosine that acts as the nucleophile to attack the scissile phosphodiester bond in the DNA target. Recombination by the Cre recombinase takes place in a supramolecular structure called a synapse that consists of four molecules of Cre bound to two DNA target sequences called lox sites. The synapse is held together by an intricate network of protein-protein interactions. They bend the two sites into square planar structure that resembles a Holliday intermediate. We have studied three mutant Cre proteins that appear to have defects in synapsis (Cre A36V, Cre T41F, and Cre G314R). We found that they were unable to carry out strand cleavage but that cleavage occurred if they were mixed with a cleavage-defective Cre protein that lacks the catalytic nucleophilic tyrosine residue. The three variant proteins could also be complemented for the formation of a novel structure ("complexV"), which may be a cleaved synaptic intermediate. We suggest that these three mutant proteins have a defect in DNA bending and discuss the relationship between bending, synapsis, and cleavage.
Transformation in Bacillus subtilis: purification and partial characterization of a membrane-bound DNA-binding protein (1983)

In DNA binding-deficient mutants of Bacillus subtilis a competence-specific protein with a subunit molecular weight of 18,000 was absent. The native protein containing this subunit was purified from B. subtilis membranes by chromatography on hydroxyapatite, DEAE-cellulose, and Sephacryl S-200. This protein appeared to be complexed with a second protein of slightly lower molecular weight (17,000) and a different isoelectric point. The native protein complex (apparent molecular weight, 75,000) contained approximately equal amounts of the two polypeptides and showed a strong DNA-binding activity. Incubation of the complex with plasmid and bacteriophage DNA revealed nuclease activity, specifically directed toward double-stranded DNA. Predominantly single-stranded nicks and a limited number of double-stranded breaks were introduced in the presence of Mg2+ ions. In the presence of Mn2+ ions the complex produced low-molecular-weight breakdown products from the DNA.
Synergy of cefotaxime and fosfomycin against penicillin-resistant pneumococci (1993)

The killing kinetics of cefotaxime and fosfomycin, alone and in combination, against seven clinical isolates of penicillin-resistant pneumococci were studied. The antibiotics were tested at 1 x, 2 x and 4 x the MIC for each individual isolate. The results showed a synergic interaction of the two antibiotics for three of the seven strains. This strategy may be useful clinically.
A yeast genetic system for selecting small molecule inhibitors of protein–protein interactions in nanodroplets (1997)

Cellular processes are mediated by complex networks of molecular interactions. Dissection of their role most commonly is achieved by using genetic mutations that alter, for example, protein-protein interactions. Small molecules that accomplish the same result would provide a powerful complement to the genetic approach, but it generally is believed that such molecules are rare. There are several natural products, however, that illustrate the feasibility of this approach. Split-pool synthesis now provides a simple mechanical means to prepare vast numbers of complex, even natural product-like, molecules individually attached to cell-sized polymer beads. Here, we describe a genetic system compatible with split-pool synthesis that allows the detection of cell-permeable, small molecule inhibitors of protein-protein interactions in 100- to 200-nl cell culture droplets, prepared by a recently described technique that arrays large numbers of such droplets. These "nanodroplets" contain defined media, cells, and one or more beads containing approximately 100 pmol of a photoreleasable small molecule and a controlled number of cells. The engineered Saccharomyces cerevisiae cells used in this study express two interacting proteins after induction with galactose whose interaction results in cell death in the presence of 5-fluoroorotic acid (inducible reverse two-hybrid assay). Disruption of the interaction by a small molecule allows growth, and the small molecule can be introduced into the system hours before induction of the toxic interaction. We demonstrate that the interaction between the activin receptor R1 and the immunophilin protein FKBP12 can be disrupted by the small molecule FK506 at nanomolar concentrations in nanodroplets. This system should provide a general method for selecting cell-permeable ligands that can be used to study the relevance of protein-protein interactions in living cells or organisms.
MapNet: An Allocentric Spatial Memory for Mapping Environments (2018)

Autonomous agents need to reason about the world beyond their instantaneous sensory input. Integrating information over time, however, requires switching from an egocentric representation of a scene to an allocentric one, expressed in the world reference frame. It must also be possible to update the representation dynamically, which requires localizing and registering the sensor with respect to the world reference. In this paper, we develop a differentiable module that satisfies such requirements, while being robust, efficient, and suitable for integration in end-to-end deep networks. The module contains an allocentric spatial memory that can be accessed associatively by feeding to it the current sensory input, resulting in localization, and then updated using an LSTM or similar mechanism. We formulate efficient localization and registration of sensory information as a dual pair of convolution/deconvolution operators in memory space. The map itself is a 2.5D representation of an environment storing information that a deep neural network module learns to distill from RGBD input. The result is a map that contains multi-task information, different from classical approaches to mapping such as structure-from-motion. We present results using synthetic mazes, a dataset of hours of recorded gameplay of the classic game Doom, and the very recent Active Vision Dataset of real images captured from a robot.
Bidentate Chelate Compounds. III. Metal Complexes of Some Pyridyl-Imidazole Derivatives (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBidentate Chelate Compounds. III. Metal Complexes of Some Pyridyl-Imidazole DerivativesBarry Chiswell, Francis Lions, and Benjamin S. MorrisCite this: Inorg. Chem. 1964, 3, 1, 110–114Publication Date (Print):January 1, 1964Publication History Published online1 May 2002Published inissue 1 January 1964https://doi.org/10.1021/ic50011a023RIGHTS & PERMISSIONSArticle Views1271Altmetric-Citations117LEARN 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 PDF (606 KB) Get e-Alerts Get e-Alerts
A Stochastic Approximation Technique for Generating Maximum Likelihood Parameter Estimates (1987)

This paper shows how stochastic approximation (SA) can be used to construct maximum likelihood estimates of system parameters. The procedure described here relies on a derivative approximation other than the usual finite-difference approximation associated with a Kiefer-Wolfowitz SA procedure. This alternative derivative approximation requires fewer, by a factor equal to the dimension of the parameter vector being estimated, computations than the standard finite-difference approximation. Numerical evidence presented in the paper indicates that this SA procedure is, relative to a Kiefer-Wolfowitz procedure, most efficient when considering large-scale systems.