gebhart/patrepeval huggingface dataset:
DNA methylation in glioblastoma: impact on gene expression and clinical outcome (2010)

This study provides the first genome-wide integrative analysis of DNA methylation and gene expression profiles obtained from the same GBM cohort. We also present a methylome-based survival analysis for one of the largest uniformly treated GBM cohort ever studied, for more than 27,000 CpG sites. We have identified genes whose expression may be tightly regulated by epigenetic mechanisms and markers that may guide treatment decisions.
Broadband Cylindrical Acoustic Cloak for Linear Surface Waves in a Fluid (2008)

We describe the first practical realization of a cylindrical cloak for linear surface liquid waves. This structured metamaterial bends surface waves radiated by a closely located acoustic source over a finite interval of Hertz frequencies. We demonstrate theoretically its unique mechanism using homogenization theory: the cloak behaves as an effective anisotropic fluid characterized by a diagonal stress tensor in a cylindrical basis. A low azimuthal viscosity is achieved, where the fluid flows most rapidly. Numerical simulations demonstrate that the homogenized cloak behaves like the actual structured cloak. We experimentally analyze the decreased backscattering of a fluid with low viscosity and finite density (methoxynonafluorobutane) from a cylindrical rigid obstacle surrounded by the cloak when it is located a couple of wavelengths away from the acoustic source.
Improvements to the Synthesis of Psilocybin and a Facile Method for Preparing the O-Acetyl Prodrug of Psilocin (1999)

An improved procedure to accomplish the O-phosphor- ylation of 4-hydroxy-N,N-dimethyltryptamine (psilocin 5) is report- ed that utilizes reaction between the O-lithium salt of 5 and tetra-O- benzylpyrophosphate. The O-benzyl groups were removed by cata- lytic hydrogenation over palladium on carbon to afford N,N-dime- thyl-4-phosphoryloxytryptamine (psilocybin, 1). In view of difficulties encountered in the preparation of 1, it is suggested that 4-acetoxy-N,N-dimethyltryptamine (2) may be a useful alternative for pharmacological studies. The latter was obtained following cat- alytic O-debenzylation of 4-benzyloxy-N,N-dimethyltryptamine in the presence of acetic anhydride and sodium acetate.
Use of 3D Printed Bone Plate in Novel Technique to Surgically Correct Hallux Valgus Deformities (2016)

Three-dimensional (3-D) printing offers many potential advantages in designing and manufacturing plating systems for foot and ankle procedures that involve small, geometrically complex bony anatomy. Here, we describe the design and clinical use of a Ti-6Al-4V ELI bone plate (FastForward™ Bone Tether Plate, MedShape, Inc., Atlanta, GA) manufactured through 3-D printing processes. The plate protects the second metatarsal when tethering suture tape between the first and second metatarsals and is a part of a new procedure that corrects hallux valgus (bunion) deformities without relying on doing an osteotomy or fusion procedure. The surgical technique and two clinical cases describing the use of this procedure with the 3-D printed bone plate are presented within.
The role of recombinant human bone morphogenetic protein-2 in PLGA capsules at an extraskeletal site of the rat (1999)

Bone morphogenetic protein-2 (BMP-2) is a member of the transforming growth factor-beta (TGF-beta) superfamily and has strong bone-inductive activity in vivo. To examine the role of BMP-2 in an extraskeletal site of rat using a controlled release system of peptides, we encapsulated the recombinant human BMP-2 (rhBMP-2) with poly(DL-lactide-co-glycolide) (PLGA) and implanted the rhBMP-2/PLGA capsules in the subcutaneous area of rats. Upon histochemical examination, it was found that bone-inducing cells having alkaline phosphatase (ALP) activity appeared around the capsules by the suitably released rhBMP-2. In addition, the temporal histological examination showed that direct bone formation without cartilage occurred in the process of this ectopic bone induction. These data indicate that the role of rhBMP-2 in the extraskeletal site of rats is to induce the differentiation of mesenchymal cells into the osteoblasts.
Differential regulation of G protein α‐subunit GTPase activity by peptides derived from the third cytoplasmic loop of the α2‐adrenergic receptor (1995)

The effect of peptides homologous to segments of a G protein-coupled receptor on the GTPase activity of recombinant Go alpha (rGo alpha) and Gs alpha (rGs alpha) has been tested. These peptides contain overlapping sequences spanning from amino acid 212 of the putative fifth transmembrane domain to amino acid 229 of the third cytoplasmic loop of the alpha 2 adrenergic receptor. Interestingly, two peptides (comprising residues 212-227 and 214-227) strongly inhibit the basal GTPase activity of both rGo alpha and rGs alpha. Instead, a C-terminally extended peptide (residues 216-229) stimulates rGo alpha but slightly inhibits rGs alpha. Circular dichroism spectroscopy of the peptides reveals that an a helical structure is more easily inducible in the inhibitory ones. These findings constitute an example of peptides representing cytoplasmic receptor sequences that differentially modulate the GTPase activity of recombinant G protein alpha-subunits.
Stabilized single-frequency stimulated Brillouin fiber ring laser (1981)

The detailed behavior of the cw stimulated Brillouin fiber laser has been studied by using a narrow-linewidth cw pump argon laser at 5145 A and an 83-m fiber ring cavity. By stabilizing the fiber cavity, we achieved stable single-frequency Brillouin-laser output with a linewidth determined primarily by the 100-kHz modulation used in the feedback system. Lasing threshold for the 4.5-microm-core fiber used was observed at a pump power of 77 mW, and the maximum Brillouin output was 13 mW for a pump of 320 mW. The Brillouin gain medium was shown to exhibit homogeneouslike behavior.
Interaction between cyclin-dependent kinases and human papillomavirus replication-initiation protein E1 is required for efficient viral replication (1999)

We have identified the human papillomavirus (HPV) DNA replication initiation protein E1 as a tight-binding substrate of cyclin E/cyclin-dependent kinase (Cdk) complexes by using expression cloning. E1, a DNA helicase, collaborates with the HPV E2 protein in ori-dependent replication. E1 formed complexes with cyclin E in insect and mammalian cells, independent of Cdks and E2. Additional cyclins, including A-, B-, and F-type (but not D-type), interacted with the E1/E2 complex, and A- and E-type cyclin kinases were capable of phosphorylating E1 and E2 in vitro. Association with cyclins and efficient phosphorylation of E1 required the presence of a cyclin interaction motif (the RXL motif). E1 lacking the RXL motif displayed defects in E2-dependent HPV ori replication in vivo. Consistent with a role for Cdk-mediated phosphorylation in E1 function, an E1 protein lacking all four candidate Cdk phosphorylation sites still associated with E2 and cyclin E but was impaired in HPV replication in vitro and in vivo. Our data reveal a link between cyclin/Cdk function and activation of HPV DNA replication through targeting of Cdk complexes to the E1 replication-initiation protein and suggest a functional role for E1 phosphorylation by Cdks. The use of cyclin-binding RXL motifs is now emerging as a major mechanism by which cyclins are targeted to key substrates.
Estrogen Receptor β-Selective Transcriptional Activity and Recruitment of Coregulators by Phytoestrogens (2001)

Estrogens used in hormone replacement therapy regimens may increase the risk of developing breast cancer. Paradoxically, high consumption of plant-derived phytoestrogens, particularly soybean isoflavones, is associated with a low incidence of breast cancer. To explore the molecular basis for these potential different clinical outcomes, we investigated whether soybean isoflavones elicit distinct transcriptional actions from estrogens. Our results demonstrate that the estrogen 17beta-estradiol effectively triggers the transcriptional activation and repression pathways with both estrogen receptors (ERs) ERalpha and ERbeta. In contrast, soybean isoflavones (genistein, daidzein, and biochanin A) are ERbeta-selective agonists of transcriptional repression and activation at physiological levels. The molecular mechanism for ERbeta selectivity by isoflavones involves their capacity to create an activation function-2 surface of ERbeta that has a greater affinity for coregulators than ERalpha. Phytoestrogens may act as natural selective estrogen receptor modulators that elicit distinct clinical effects from estrogens used for hormone replacement by selectively recruiting coregulatory proteins to ERbeta that trigger transcriptional pathways.
Regulatory macrophages: Setting the Threshold for Therapy (2011)

Macrophages exhibit remarkable plasticity and can change their phenotype in response to different environmental cues. They can become activated to kill intracellular microbes or they can assume regulatory properties to modulate immune responses. Regulatory macrophages are fundamentally different from classically activated, and we propose from non-classically activated macrophages; they arise in response to different stimuli and perform different physiological functions. They are likely to express unique biochemical markers that could be exploited to identify and potentially target these macrophage subsets in tissue. Furthermore, inducers of regulatory macrophages may have the potential to be used as anti-inflammatory therapeutics. Therefore, a better understanding of the various macrophage phenotypes may pave the way for new therapies that are directed at modulating macrophage functions or manipulating individual macrophage subsets.
A mutant epidermal growth factor receptor with defective protein tyrosine kinase is unable to stimulate proto-oncogene expression and DNA synthesis. (1987)

Cultured NIH-3T3 cells devoid of endogenous epidermal growth factor (EGF) receptors were transfected with cDNA expression constructs encoding either normal human EGF receptor or a receptor mutated in vitro at Lys-721, a residue that is thought to function as part of the ATP-binding site of the kinase domain. Unlike the wild-type EGF-receptor expressed in these cells, which exhibited EGF-dependent protein tyrosine kinase activity, the mutant receptor lacked protein tyrosine kinase activity and was unable to undergo autophosphorylation and to phosphorylate exogenous substrates. Despite this deficiency, the mutant receptor was normally expressed on the cell surface, and it exhibited both high- and low-affinity binding sites. The addition of EGF to cells expressing wild-type receptors caused the stimulation of various responses, including enhanced expression of proto-oncogenes c-fos and c-myc, morphological changes, and stimulation of DNA synthesis. However, in cells expressing mutant receptors, EGF was unable to stimulate these responses, suggesting that the tyrosine kinase activity is essential for EGF receptor signal transduction.
The discovery and use of HLA-associated epitopes as drugs. (1997)

MHC receptors "display" peptide fragments to T cells. These peptides are predominantly derived from proteins expressed within or ingested by the presenting cell. Since empty MHC molecules are highly unstable, peptide ligands are bound prior to MHC surface expression and the ensuing t1/2 off rates are often on the order of days. It is the remarkable stability of MHC/peptide complexes, which provide us an opportunity to purify MHC molecules from infected, transfected, or antigen pulsed cells and subsequently identify the naturally processed peptides being presented. On the other hand, the stability of MHC/peptide complexes substantially reduces the potency of parenterally administered peptides in vivo. Using serial immuno-affinity chromatography and mass spectrometry, naturally processed peptides can be identified. When these peptides are then encoded into nucleic acid and delivered parenterally, they are highly immunogenic. Application of these techniques to induce vigorous CTL responses will be discussed.
Induction of Tolerance in Mice by Uricase and Monomethoxypolyethylene Glycol-Modified Uricase (1984)

The ability to induce tolerance to uricase by the administration of native uricase, and uricase modified by the covalent attachment of monomethoxypolyethylene glycol (PEG) was examined. Uricase, and uricase with PEG attached to 35% (PEG-uricase 35%) and 70% (PEG-uricase 70%) of available amino groups were found to induce tolerance in mice not previously sensitized to uricase. There was a dampening of the IgG, IgE and IgM antibody response to uricase which persisted even after a second sensitizing dose of uricase was administered to these animals. PEG-uricases were found to have little or no immunogenicity when injected into mice and a reduced immunogenicity and antigenicity when tested in rabbits. Native uricase, however, was found to be immunogenic and antigenic in mice and rabbits. Mice sensitized to native uricase were injected with uricase, PEG-uricase 35% or 70% to induce tolerance. After a second sensitizing injection of uricase, circulating levels of IgE, IgG and IgM were measured. All three enzymes induced tolerance in the IgE class of antibody but there was no significant change in the hemagglutinating antibody levels of the mice. Mice injected with 1 mg of uricase died from anaphylaxis. PEG-uricase 35% was found to induce the most effective tolerance in both unsensitized and sensitized mice.
A practical global distortion correction method for an image intensifier based x‐ray fluoroscopy system (2008)

X-ray images acquired on systems with image intensifiers (II) exhibit characteristic distortion which is due to both external and internal factors. The distortion is dependent on the orientation of the II, a fact particularly relevant to II's mounted on C arms which have several degrees of freedom of motion. Previous descriptions of distortion correction strategies have relied on a dense sampling of the C-arm orientation space, and as such have been limited mostly to a single arc of the primary angle, alpha. We present a new method which smooths the trajectories of the segmented vertices of the grid phantom as a function of a prior to solving the two-dimensional warping problem. It also shows that the same residual errors of distortion correction could be achieved without fitting the trajectories of the grid vertices, but instead applying the previously described global method of distortion correction, followed by directly smoothing the values of the polynomial coefficients as functions of the C-arm orientation parameters. When this technique was applied to a series of test images at arbitrary alpha, the root-mean-square (RMS) residual error was 0.22 pixels. The new method was extended to three degrees of freedom of the C-arm motion: the primary angle, alpha; the secondary angle, beta; and the source-to-intensifier distance, lambda. Only 75 images were used to characterize the distortion for the following ranges: alpha, +/- 45 degrees (Deltaalpha = 22.5 degrees); beta, +/- 36 degrees (Deltabeta = 18 degrees); lambda, 98-118 cm (Deltalambda = 10 cm). When evaluated on a series of test images acquired at arbitrary (alpha, beta, lambda), the RMS residual error was 0.33 pixels. This method is targeted at applications such as guidance of catheter-based interventions and treatment planning for brachytherapy, which require distortion-corrected images over a large range of C-arm orientations.
Fresh and cultured buccal cells as a source of mRNA and protein for molecular analysis (2004)

We developed a method for obtaining viable buccal cells from mouthwash samples for use as a source of mRNA and protein. Immunofluorescent analysis showed that most cells were derived from nonkeratinized parabasal epithelia, with a minor proportion of proliferative cells. Gene expression was detected in buccal cells using reverse transcription PCR, Western blot analysis, and immunofluorescence. Using a keratinocyte-specific medium, buccal cells could be cultured on Matrigel-coated permeable filters for up to 2 weeks while maintaining the expression of some epithelial-specific markers, including cytokeratin 13, cytokeratin 10, transferrin receptor, and beta-integrin. The basal marker cytokeratin 14 and Ki67, an indicator of cellular proliferation, were detected in a few cells. We show that buccal cells can be obtained from a noninvasive procedure for use as a source of material for biochemical analyses. A population of the buccal cells can be maintained in culture for up to 2 weeks using keratinocyte-specific medium in combination with extracellular matrix.
A software-defined communications baseband design (2003)

Software-defined radios offer a programmable and dynamically reconfigurable method of reusing hardware to implement the physical layer processing of multiple communications systems. An SDR can dynamically change protocols and update communications systems over the air as a service provider allows. In this article we discuss a baseband solution for an SDR system and describe a 2 Mb/s WCDMA design with GSM/GPRS and 802.11b capability that executes all physical layer processing completely in software. We describe the WCDMA communications protocols with a focus on latency reduction and unique implementation techniques. We also describe the underlying technology that enables software execution. Our solution is programmed in C and executed on a multithreaded processor in real time.
Differential Activation of Mitogenic Signaling Pathways in Aortic Smooth Muscle Cells Deficient in Superoxide Dismutase Isoforms (2005)

Our results suggest that SOD1 and SOD2 regulate SMC quiescence by suppressing divergent mitogenic signaling pathways, and dysregulation of these enzymes under pathophysiological conditions may lead to SMC hyperplasia and hypertrophy.
Dose intensification of daunorubicin and cytarabine during treatment of adult acute lymphoblastic leukemia (2012)

Intensive systemic, oral, and intrathecal methotrexate dosing permitted the omission of CNS irradiation in adult patients with ALL. This intensive approach using higher doses of daunorubicin and cytarabine failed to result in an overall improvement in DFS or OS compared with historic CALGB studies. Future therapeutic strategies for adults with ALL should be tailored to specific age and molecular genetic subsets.
Initial testing (stage 1) of the BH3 mimetic ABT‐263 by the pediatric preclinical testing program (2007)

ABT-263 demonstrated in vitro activity against a range of cell lines, with the ALL cell lines showing the greatest sensitivity. ABT-263 demonstrated limited single agent in vivo activity against the PPTP's solid tumor panels but showed significant activity against xenografts in the ALL panel.
Two components of cardiac delayed rectifier K+ current. Differential sensitivity to block by class III antiarrhythmic agents. (1990)

An envelope of tails test was used to show that the delayed rectifier K+ current (IK) of guinea pig ventricular myocytes results from the activation of two outward K+ currents. One current was specifically blocked by the benzenesulfonamide antiarrhythmic agent, E-4031 (IC50 = 397 nM). The drug-sensitive current, "IKr" exhibits prominent rectification and activates very rapidly relative to the slowly activating drug-insensitive current, "IKs." IKs was characterized by a delayed onset of activation that occurs over a voltage range typical of the classically described cardiac IK. Fully activated IKs, measured as tail current after 7.5-s test pulses, was 11.4 times larger than the fully activated IKr. IKr was also blocked by d-sotalol (100 microM), a less potent benzenesulfonamide Class III antiarrhythmic agent. The activation curve of IKr had a steep slope (+7.5 mV) and a negative half-point (-21.5 mV) relative to the activation curve of IKs (slope = +12.7 mV, half-point = +15.7 mV). The reversal potential (Erev) of IKr (-93 mV) was similar to EK (-94 mV for [K+]o = 4 mM), whereas Erev of IKs was -77 mV. The time constants for activation and deactivation of IKr made up a bell-shaped function of membrane potential, peaking between -30 and -40 mV (170 ms). The slope conductance of the linear portion of the fully activated IKr-V relation was 22.5 S/F. Inward rectification of this relation occurred at potentials greater than -50 mV, resulting in a voltage-dependent decrease in peak IKr at test potentials greater than 0 mV. Peak IKr at 0 mV averaged 0.8 pA/pF (n = 21). Although the magnitude of IKr was small relative to fully activated IKs, the two currents were of similar magnitude when measured during a relatively short pulse protocol (225 ms) at membrane potentials (-20 to +20 mV) typical of the plateau phase of cardiac action potentials.
Dual Action-Based Approaches to Antibacterial Agents (2007)

This review collates and analyses recent work done on dual action approaches to tackling the mounting health problem of resistance by human pathogenic bacteria to antibacterial agents. In particular the areas reviewed include the use of two drugs in combination, dual action prodrugs, and dual action drugs (or hybrid drugs).
The Development and Function of Regulatory B Cells Expressing IL-10 (B10 Cells) Requires Antigen Receptor Diversity and TLR Signals (2009)

Autoimmunity and inflammation are controlled in part by regulatory B cells, including a recently identified IL-10-competent CD1d(high)CD5(+) B cell subset termed B10 cells that represents 1-3% of adult mouse spleen B cells. In this study, pathways that influence B10 cell generation and IL-10 production were identified and compared with previously described regulatory B cells. IL-10-competent B cells were predominantly CD1d(high)CD5(+) in adult spleen and were the prevalent source of IL-10, but not other cytokines. B10 cell development and/or maturation in vivo required Ag receptor diversity and intact signaling pathways, but not T cells, gut-associated flora, or environmental pathogens. Spleen B10 cell frequencies were significantly expanded in aged mice and mice predisposed to autoimmunity, but were significantly decreased in mouse strains that are susceptible to exogenous autoantigen-induced autoimmunity. LPS, PMA, plus ionomycin stimulation in vitro for 5 h induced B10 cells to express cytoplasmic IL-10. However, prolonged LPS or CD40 stimulation (48 h) induced additional adult spleen CD1d(high)CD5(+) B cells to express IL-10 following PMA plus ionomycin stimulation. Prolonged LPS or CD40 stimulation of newborn spleen and adult blood or lymph node CD1d(low) and/or CD5(-) B cells also induced cytoplasmic IL-10 competence in rare B cells, with CD40 ligation uniformly inducing CD5 expression. IL-10 secretion was induced by LPS signaling through MyD88-dependent pathways, but not following CD40 ligation. LPS stimulation also induced rapid B10 cell clonal expansion when compared with other spleen B cells. Thereby, both adaptive and innate signals regulate B10 cell development, maturation, CD5 expression, and competence for IL-10 production.