gebhart/patrepeval huggingface dataset:
Synergistic interaction between 17‐AAG and phosphatidylinositol 3‐kinase inhibition in human malignant glioma cells (2005)

The phosphatidylinositol 3'-kinase (PI3K)/Akt pathway is often constitutively activated in malignant glioma cells, in many cases as a result of mutation of phosphatase and tensin homologue deleted on chromosome ten (PTEN), an endogenous inhibitor of Akt, which renders tumor cells resistant to cytotoxic insults, including those related to anticancer drugs. Pharmacological inhibition of this pathway may potentially restore or augment the effectiveness of conventional chemotherapy or other signaling-targeted agents. Because the heat shock protein (HSP) is involved in the conformational maturation of a number of signaling proteins critical to the proliferation of malignant glioma cells, we hypothesized that the combination of the PI3K inhibitor LY294002 and the HSP90 inhibitor 17-allyl-aminogeldanamycin (17-AAG) would promote glioma cytotoxicity by decreasing both the activation status and levels of Akt, as well as downregulating the levels of other relevant signaling effectors. We, therefore, examined the effects of LY294002 and 17-AAG, alone and in combination, on signal transduction and apoptosis in a series of malignant glioma cell lines. Simultaneous exposure to these inhibitors significantly induced cell death, and irreversibly inhibited proliferative activity and colony forming ability of the glioma cell lines. Quantitative analysis revealed that enhancement by LY294002 of 17-AAG-induced cytotoxicity was synergistic, leading to a pronounced increase in active caspase-3 and poly (adenosine diphosphate-ribose) polymerase (PARP) cleavage together with the release of cytochrome c and apoptosis inducing factor (AIF). No significant growth inhibition or caspase activation was seen in control cells. The enhanced cytotoxicity of this combination was associated with diminished Akt activation and a significant downregulation of epidermal growth factor receptor (EGFR), Raf-1, and mitogen activated protein kinase. Combination of 17-AAG and LY294002 did not modify phospho-JNK/SPK and phospho-p38. Cells exposed to 17-AAG and LY294002 displayed a significant reduction in cell-cycle regulatory proteins, such as retinoblastoma (Rb), cyclin dependent kinase (CDK)4, CDK6, cyclin D1, and cyclin D3. Taken together, these findings suggest that the PI3K/Akt pathway plays a critical role in regulating the apoptotic response to 17-AAG and that targeting this pathway could provide a potent strategy to treat patients with malignant gliomas.
A Simple Orthogonal Approach to Poly(phenylenevinylene) Dendrimers (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA Simple Orthogonal Approach to Poly(phenylenevinylene) DendrimersShirshendu K. Deb, Todd M. Maddux, and Luping YuView Author Information Department of Chemistry and The James Frank Institute The University of Chicago 5735 South Ellis Avenue, Chicago, Illinois 60637 Cite this: J. Am. Chem. Soc. 1997, 119, 38, 9079–9080Publication Date (Web):September 24, 1997Publication History Received2 June 1997Published online24 September 1997Published inissue 1 September 1997https://pubs.acs.org/doi/10.1021/ja971790ohttps://doi.org/10.1021/ja971790orapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views753Altmetric-Citations145LEARN 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 InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Aromatic compounds,Dendrons,Fluorescence,Materials,Molecules Get e-Alerts
Inactivation of YME1, a member of the ftsH-SEC18-PAS1-CDC48 family of putative ATPase-encoding genes, causes increased escape of DNA from mitochondria in Saccharomyces cerevisiae. (1993)

The yeast nuclear gene YME1 was one of six genes recently identified in a screen for mutations that elevate the rate at which DNA escapes from mitochondria and migrates to the nucleus. yme1 mutations, including a deletion, cause four known recessive phenotypes: an elevation in the rate at which copies of TRP1 and ARS1, integrated into the mitochondrial genome, escape to the nucleus; a heat-sensitive respiratory-growth defect; a cold-sensitive growth defect on rich glucose medium; and synthetic lethality in rho- (cytoplasmic petite) cells. The cloned YME1 gene complements all of these phenotypes. The gene product, Yme1p, is immunologically detectable as an 82-kDa protein present in mitochondria. Yme1p is a member of a family of homologous putative ATPases, including Sec18p, Pas1p, Cdc48p, TBP-1, and the FtsH protein. Yme1p is most similar to the Escherichia coli FtsH protein, an essential protein involved in septum formation during cell division. This observation suggests the hypothesis that Yme1p may play a role in mitochondrial fusion and/or division.
Production of Recombinant Proteins in thelon-Deficient BL21(DE3) Strain ofEscherichia coliin the Absence of the DnaK Chaperone (2009)

To eliminate unavoidable contamination of purified recombinant proteins by DnaK, we present a unique approach employing a BL21(DE3) DeltadnaK strain of Escherichia coli. Selected representative purified proteins remained soluble, correctly assembled, and active. This finding establishes DnaK dispensability for protein production in BL21(DE3), which is void of Lon protease, key to eliminating unfolded proteins.
Limited proteolysis of γII‐crystallin from calf eye lens (1990)

Gamma II-crystallin from calf eye lens consists of two homologous domains, connected by a six-residue linker peptide. In order to study the intrinsic properties of the domains and their mutual stabilization, limited proteolysis was applied. Optimum conditions providing a homogeneous 10-kDa fragment at high yield were pepsin cleavage in 0.1 M NaCl/HCl pH 2.0, in the presence of 3.0 M urea. Determination of the N-terminus and the C-terminal sequence showed that cleavage occurred at the Phe88-Arg89 peptide bond, giving rise to the complete N-terminal domain including the connecting hexapeptide. The C-terminal part of the polypeptide chain is cleaved to small fragments. Comparing the spectral properties of the isolated N-terminal domain and intact gamma II-crystallin proved the structure of the fragment to be closely similar to that of the native domain. Small differences in absorbance, fluorescence emission and circular dichroism point to alterations caused by the increase in surface area as a consequence of domain separation. The resistance of the 10-kDa fragment toward thermal and alkaline denaturation, as well as unfolding in the presence of urea or guanidine . HCl is decreased, due to the lack of domain interactions stabilizing the intact protein. Unfolding/folding kinetics of the 10-kDa fragment coincide with the second phase of the bimodal transition of intact gamma II-crystallin, in agreement with independent sequential folding and modular assembly of the domains within the native molecule.
Low-molecular-weight proteins as carriers for renal drug targeting. Preparation of drug-protein conjugates and drug-spacer derivatives and their catabolism in renal cortex homogenates and lysosomal lysates (1992)

Low molecular weight proteins (LMWPs) are known to be reabsorbed and catabolized primarily by the proximal tubular cells of the kidneys. As such, LMWPs might serve as drug carriers that release drugs site-specifically in the kidney. We tested this concept in vitro by coupling different drugs to the LMWP lysozyme both directly (amide bond) and via different spacers: oligopeptides (amide bond), (poly-)alpha-hydroxy acids (ester bond), and a pH sensitive cis-aconityl spacer (amide bond). The capability of the kidney to release the parent drug from such drug-spacer derivatives and drug-LMWP conjugates by enzymatic or chemical hydrolysis of the bond was tested by incubation experiments in renal cortex homogenates and lysosomal lysates. Directly coupled conjugates of terminal carboxyl group containing drugs and lysozyme were catabolized to single amino acids, but did not result in release of the parent drug. The amide bond between the drug and the final amino acid (lysine) appeared to be stable in the incubation milieu. Different oligopeptide spacers coupled to the drugs showed similar results: the oligopeptide itself was cleaved but the amide bond between the drug and different single amino acids remained untouched. Only amide bonds of derivatives of carboxylic drugs with peptide structures themselves were cleaved. Some of the directly coupled conjugates of terminal amino drugs and oligopeptides showed clear release of the parent drug whereas others were stable. Terminal amino drugs were rapidly released from an acid-sensitive cis-aconityl spacer. Terminal carboxyl group containing drugs were enzymatically released from their glycolic and lactic ester spacers at different rates. These kinds of drugs were also released as parent drug from LMWP conjugates with ester spacers like L-lactic acid. Increasing spacer length by intercalating a tetra(L-lactic acid) molecular between the drug and the protein further increased the extent and rate of drug release, indicating increased accessibility of the bond to the enzymes. Terminal amino group containing drugs were rapidly generated as parent drug from LMWP conjugates using an acid-sensitive spacer. In addition the conjugates were found to be adequately stable in plasma, considering their rapid clearance from the bloodstream. It is concluded that LMWPs may indeed be of use as carriers for specific renal delivery of drugs, since renal cortex homogenates and lysosomal lysates are able to catabolize the protein and generate the parent drug from drug-LMWP conjugates bearing suitable spacers. The option of enzymatic release is limited by the narrow specificity of the lysosomal enzymes.(ABSTRACT TRUNCATED AT 400 WORDS)
Automated single-cell manipulation and sorting by light trapping (1987)

Following the recently reported trapping of biological particles by finely focused laser beams, we report on the automated micromanipulation of cells and other microscopic particles by purely optical means as well as on a newly observed interaction between particles in the trapping beam. A simple instrument is described which allows single cells to be positioned with high accuracy, transported over several millimeters, and automatically sorted on the basis of their optical properties. These operations are performed inside a small enclosed chamber without mechanical contact or significant fluid flow. Potential applications of this technique in experimental cell biology are discussed.
Intraoperative Brain Shift and Deformation: A Quantitative Analysis of Cortical Displacement in 28 Cases (1998)

These data suggest that loss of spatial registration with preoperative images is gravity-dominated and of sufficient extent that attention to errors resulting from misregistration during the course of surgery is warranted.
A volumetric stereo matching method: application to image-based modeling (2003)

We formulate stereo matching as an extremal surface extraction problem. This is made possible by embedding the disparity surface inside a volume where the surface is composed of voxels with locally maximal similarity values. This formulation naturally implements the coherence principle, and allows us to incorporate most known global constraints. Time efficiency is achieved by executing the algorithm in a coarse-to-fine fashion, and only populating the full volume at the coarsest level. To make the system more practical, we present a rectification algorithm based on the fundamental matrix, avoiding full camera calibration. We present results on standard stereo pairs, and on our own data set. The results are qualitatively evaluated in terms of both the generated disparity maps and the 3-D models.
Effect of Hydroxymethylglutaryl Coenzyme A Reductase Inhibitors on the Progression of Calcific Aortic Stenosis (2001)

Statin-treated patients, despite a higher risk profile for progression, had reduced aortic stenosis progression compared with those not treated with a statin. These data provide justification for a prospective randomized trial to substantiate whether statin therapy slows the progression of aortic stenosis.
16-fs, 1-μJ ultraviolet pulses generated by third-harmonic conversion in air (1996)

We describe a simple method for generating sub-20-fs ultraviolet light pulses with useful average powers, using a kilohertz Ti:sapphire laser system. By focusing a 22-fs, 1-mJ laser pulse in air, we obtain ultraviolet pulses with an energy of 1 microJ and at a wavelength of 266 nm and with an average power of 1 mW. The pulse duration of the ultraviolet pulses was measured to be 16 fs with frequency-resolved optical gating.
Characterization of the primary immunity region of the Escherichia coli linear plasmid prophage N15 (1996)

N15 is the only bacteriophage of Escherichia coli known to lysogenize as a linear plasmid. Clear-plaque mutations lie in at least two regions of the 46-kb genome. We have cloned, sequenced, and characterized the primary immunity region, immB. This region contains a gene, cB, whose product shows homology to lambdoid phage repressors. The cB3 mutation confers thermoinducibility on N15 lysogens, consistent with CB being the primary repressor of N15. Downstream of cB lies the locus of N15 plasmid replication. Upstream of cB lies an operon predicted to encode two products: one homologous to the late repressor of P22 (Cro), the other homologous to the late antiterminator of phi 82 (Q). The Q-like protein is essential for phage development. We show that CB protein regulates the expression of genes that flank the cB gene by binding to DNA at symmetric 16-bp sites. Three sites are clustered upstream of cB and overlap a predicted promoter of the cro and Q-like genes as well as two predicted promoters of cB itself. Two sites downstream of cB overlap a predicted promoter of a plasmid replication gene, repA, consistent with the higher copy number of the mutant, N15cB3. The leader region of repA contains terminators in both orientations and a putative promoter. The organization of these regulatory elements suggests that N15 plasmid replication is controlled not only by CB but also by an antisense RNA and by a balance between termination and antitermination.
MEMS technology for timing and frequency control (2006)

An overview on the use of microelectromechanical systems (MEMS) technologies for timing and frequency control is presented. In particular, micromechanical RF filters and reference oscillators based on recently demonstrated vibrating on-chip micromechanical resonators with Q's >10,000 at 1.5 GHz, are described as an attractive solution to the increasing count of RF components (e.g., filters) expected to be needed by future multi-band wireless devices. With Q's this high in on-chip abundance, such devices might also enable a paradigm-shift in the design of timing and frequency control functions, where the advantages of high-Q are emphasized, rather than suppressed (e.g., due to size and cost reasons), resulting in enhanced robustness and power savings. With even more aggressive 3D MEMS technologies, even higher on-chip Q's have been achieved via chip-scale atomic physics packages, which so far have achieved Q's >10/sup 7/ using atomic cells measuring only 10 mm/sup 3/ in volume, consuming just 5 mW of power, all while still allowing Allan deviations down to 10/sup -11/ at one hour.
The expression of the soluble isoform of hFlt3 ligand by recombinant vaccinia virus enhances immunogenicity of the vector (2009)

Recombinant vaccinia viruses (rVACV) expressing various tumor-associated antigens have been shown to elicit anti-tumor effect in numerous experimental models and clinical trials. We tested the hypotheses that rVACV expressing biologically active fms-like tyrosine kinase 3 ligand (Flt3L) would show higher immunogenicity than control viruses expressing only model antigen and that coexpression of Flt3L would influence anti-tumor activity of rVACV in the preventive and therapeutic arrangements of the in vivo experiment. To answer these questions, we took advantage of the well-described model of transplanted tumor cells expressing HPV16 E6 and E7 oncoproteins. To determine the effects of hFlt3L on the induction of anti-tumor immunity, we generated live vaccinia viruses that express human Flt3L regulated by the early H5 or strong synthetic E/L promoter together with fusion protein SigE7LAMP, which is a highly immunogenic form of HPV E7 oncoprotein. We tested Flt3L production in vitro and in vivo. Despite higher expression of Flt3L from the synthetic E/L promoter in vitro, the P13-E/L-FL-SigE7LAMP induced lower levels of Flt3L in the serum of mice than P13-H5-FL-SigE7LAMP. The Flt3L expression under the strong early VACV H5 promoter is able to inhibit expansion of CD11b+Gr-1+ myeloid suppressor cells (MSC) and increase the amount of CD11b+ CD11c+ dendritic cells in the spleen of mice immunized with vaccinia virus. Determination of viral DNA isolated from the ovaries of infected animals did not reveal differences in replication between rVACVs in this organ. Coexpression of Flt3L by replication-competent virus P13-FL-SigE7LAMP induced enhancement of the cellular immune response against HPV16 E7 and VACV E3 proteins as well as increased anti-tumor efficacy in both the protective and therapeutic immunization schemes. On the other hand, the short-time Flt3L coexpression by MVA-H5-FL-SigE7LAMP was not sufficient to enhance anti-tumor effect of immunization.
Atomic: A High-Speed Local Communication Architecture (1994)

ATOMIC is an inexpensive high-speed LAN built by USC/ISI. It is based upon Mosaic technology developed for fine-grain, message-passing, massively paraIiel computation. Each Mosaic processor is capable of routing variable length packets, while providing added value through simultaneous computing and buffering. ATOMIC adds a general routing capability to the native Mosaic wormhole routing through store-and-forward and path concatenation. ATOMIC aggregate bandwidth scales as the number of nodes increases, and it has a small interface cost. Each ATOMIC channel has a data carrying capacity of 480 Mb/s. A prototype ATOMIC LAN has been constructed along with host interfaces and software that provides full TCP/IP compatibility. Using ATOMIC, 1500-byte packets have been exchanged between hosts at an aggregate transfer rate of more than 1 Gb/s. Other tests have demonstrated throughput of 5.25 million packets per second over a single Mosaic channel. The architecture is flexible both in topology and functionality. This paper describes the architecture and performance of ATOMIC.
tRNA-mediated transcription antitermination in vitro : Codon–anticodon pairing independent of the ribosome (2002)

Uncharged tRNA acts as the effector for transcription antitermination of genes in the T box family in Bacillus subtilis and other Gram-positive bacteria. Genetic studies suggested that expression of these genes is induced by stabilization of an antiterminator element in the leader RNA of each target gene by the cognate uncharged tRNA. The specificity of the tRNA response is dependent on a single codon in the leader, which was postulated to pair with the anticodon of the corresponding tRNA. It was not known whether the leader RNA–tRNA interaction requires additional factors. We show here that tRNA-dependent antitermination occurs in vitro in a purified transcription system, in the absence of ribosomes or accessory factors, demonstrating that the RNA–RNA interaction is sufficient to control gene expression by antitermination. The tRNA response exhibits similar specificity in vivo and in vitro , and the antitermination reaction in vitro is independent of NusA and functions with either B. subtilis or Escherichia coli RNA polymerase.
Cloning of another human serotonin receptor (5-HT1F): a fifth 5-HT1 receptor subtype coupled to the inhibition of adenylate cyclase. (1993)

An intronless gene encoding an additional human serotonin (5-HT) 5-HT1-like receptor subtype was isolated from a human genomic library with probes obtained from degenerate PCR primers used to amplify 5-HT-receptor-specific sequences. The highest degree of homology was found with the 5-HT1E subtype (70%) and the 5-HT1D alpha (63%) and 5-HT1D beta (60%) receptors. RNA for this gene was detected in the human brain but was not detected in kidney, liver, spleen, heart, pancreas, and testes. High-affinity (Kd = 9.2 nM) 3H-labeled 5-HT binding was detected. Competition studies revealed the following rank order of potencies for serotonergic ligands: 5-HT > sumatriptan >> 5-carboxyamidotryptamine > 8-hydroxy-2(di-1-propylamino)tetralin > spiperone. 5-HT produced a dose-dependent inhibition of forskolin-stimulated cAMP accumulation (EC50 = 7.9 nM) in transfected cells. These properties distinguish this receptor from any previously characterized and establish a fifth 5-HT1-like receptor subtype (5-HT1F) coupled to the inhibition of adenylate cyclase.
The Characterization of Starch and Its Components. Part 3. The Technique of Semi‐Micro, Differential, Potentiometric, Iodine Titration, and the Factors Affecting It (1971)

Abstract An improved apparatus for the semi‐micro, differential, potentiometric titration of starch and its components with iodine is described. The necessary experimental manipulations are given in detail. The factors affecting the measurement — the amount of dimethylsulphoxide present, the buffer concentration, the method of dissolving the starch, the defatting procedure used on the starch, and the temperature of measurement — are critically examined. The new technique results in values of iodine binding capacity for starches which are 5‐ 15% higher than previous measurements. The significance of this finding is discussed.
A Graph Theoretic Approach for Modeling Mobile Robot Team Formations (2002)

Abstract This paper addresses a new approach for modeling and control of multiple teams of mobile robots navigating in a terrain with obstacles, while maintaining a desired formation and changing formations when required. We model each team as a triple, ( g , r , ℋ︁ ), consisting of a group element, g ∈ SE (2), that describes the gross position of the lead robot, a set of shape variables, r , that describe the relative positions of robots, and a control graph, ℋ︁, that describes the behaviors of the robots in the formation. We assume that all the robots are equipped with the appropriate sensors to detect and avoid other robots and obstacles in the environment. Our framework enables the representation and enumeration of possible control graphs, and the coordination of transitions between any two control graphs. Further, we describe an algorithm that allows each team of robots to move between any two formations, while avoiding obstacles. As the number of robots increases, the number of possible control graphs increases. However, because the control computations are decentralized, the algorithms scale with the number of robots. We present examples to illustrate the control graphs and the algorithm for transitioning between them in the presence and absence of sensor noise. © 2002 Wiley Periodicals, Inc.