gebhart/patrepeval huggingface dataset:
Coinfection with recombinant vaccinia viruses expressing poliovirus P1 and P3 proteins results in polyprotein processing and formation of empty capsid structures (1991)

The assembly process of poliovirus occurs via an ordered proteolytic processing of the capsid precursor protein, P1, by the virus-encoded proteinase 3CD. To further delineate this process, we have isolated a recombinant vaccinia virus which expresses, upon infection, the poliovirus P1 capsid precursor polyprotein with an authentic carboxy terminus. Coinfection of HeLa cells with the P1-expressing vaccinia virus and with a second recombinant vaccinia virus which expresses the poliovirus proteinase 3CD resulted in the correct processing of P1 to yield the three individual capsid proteins VP0, VP3, and VP1. When extracts from coinfected cells were fractionated on sucrose density gradients, the VP0, VP3, and VP1 capsid proteins were immunoprecipitated with type 1 poliovirus antisera from fractions corresponding to a sedimentation consistent for poliovirus 75S procapsids. Examination of these fractions by electron microscopy revealed structures which lacked electron-dense cores and which corresponded in size and shape to those expected for poliovirus empty capsids. We conclude that the expression of the two poliovirus proteins P1 and 3CD in coinfected cells is sufficient for the correct processing of the capsid precursor to VP0, VP3, and VP1 as well as for the assembly of poliovirus empty capsid-like structures.
Design and Implementation of an FPGA-Based Real-Time Face Recognition System (2011)

Face recognition systems play a vital role in many applications including surveillance, biometrics and security. In this work, we present a complete real-time face recognition system consisting of a face detection, a recognition and a downsampling module using an FPGA. Our system provides an end-to-end solution for face recognition; it receives video input from a camera, detects the locations of the face(s) using the Viola-Jones algorithm, subsequently recognizes each face using the Eigenface algorithm, and outputs the results to a display. Experimental results show that our complete face recognition system operates at 45 frames per second on a Virtex-5 FPGA.
Lactate efflux is unrelated to intracellular PO2 in a working red muscle in situ (1986)

Blood flow, lactate extraction, and tissue lactate concentration were measured in an autoperfused pure red muscle (dog gracilis). Muscles were frozen in situ during steady-twitch contraction at frequencies of 1-8 Hz [10-100% of maximum O2 consumption (VO2max)]. Myoglobin saturation was determined spectrophotometrically with subcellular spatial resolution. Intracellular PO2 (Pto2) was calculated from the oxymyoglobin-dissociation curve. Tissue lactate was well correlated with VO2 but not with Pto2. Lactate efflux increased markedly above a threshold work rate near 50% VO2max. Efflux was neither linearly correlated with tissue lactate nor related to Pto2. Pto2 exceeded the minimum PO2 for maximal VO2 in each of 2,000 cells examined in muscles frozen at 1-6 Hz. A small population of anoxic cells was found in three muscles at 8 Hz, but lactate efflux from these muscles was not greater than from six other muscles at 8 Hz. Our conclusions are that 1) the concept of an anaerobic threshold does not apply to red muscle and 2) in absence of anoxia neither tissue lactate nor blood lactate can be used to impute muscle O2 availability or glycolytic rate. A mechanism by which the blood-tissue lactate gradient could support aerobic metabolism is discussed.
Catalysis and Electrocatalysis at Nanoparticle Surfaces (2003)

Illustrating developments in electrochemical nanotechnology, heterogeneous catalysis, surface science and theoretical modelling, this reference describes the manipulation, characterization, control, and application of nanoparticles for enhanced catalytic activity and selectivity. It also offers experimental and synthetic strategies in nanoscale surface science. This standard-setting work clariefies several practical methods used to control the size, shape, crystal structure, and composition of nanoparticles; simulate metal-support interactions; predict nanoparticle behavior; enhance catalytic rates in gas phases; and examine catalytic functions on wet and dry surfaces.
New Adsorbents Based on Principles of Chemical Complexation:  Monolayer-Dispersed Nickel(II) for Acetylene Separation by π-Complexation (1996)

A sorbent was prepared by dispersing a monolayer of Ni2+ ions (by spreading a monolayer of NiCl2·6H2O) on a high-surface-area γ-Al2O3. This sorbent showed high selectivities for acetylene (C2H2) over other hydrocarbons, by forming a weak π-complexation bond between Ni2+ and C2H2. For example, at 60 °C, the equilibrium amounts of hydrocarbons adsorbed at 1 atm were (in mmol/g) C2H2 = 1.56, C2H6 = 0.043, C2H4 = 0.061, C3H6 = 0.42, and C3H8 = 0.30. The bond energy for the Ni2+−C2H2 complex was approximately 9.3 kcal/mol, and the adsorption was reversible. The stoichiometry of the complex was Ni2+(C2H2)n where n = 1−3 at 25 °C and subatmospheric pressure. The π-complexation bond was formed by the donation of the C2H2 π-electrons to the vacant hybridized dsp2 orbitals of Ni2+ and the back-donation of electrons from the filled d (or dp-hybrid) orbitals of Ni2+ into the antibonding orbitals of C2H2. This work demonstrates that new sorbents can be designed and prepared by exploiting the weak, reversible π-complexation bonds, and, consequently, conventional separation/purification processes can be replaced by more efficient adsorption processes.
Combination Gene Therapy with CD86 and the MHC Class II Transactivator in the Control of Lung Tumor Growth (1999)

Early reports suggest that the costimulatory molecule CD86 (B7-2) has sporadic efficacy in tumor immunity, whereas changes in cancer immunity mediated by the MHC class II transactivator (CIITA) have not been extensively investigated. CIITA activates MHC class II expression in most cells; however, in the Line 1 lung carcinoma model system, CIITA activates MHC class I and well as class II. Here we show that CD86 is very effective in inducing a primary immune response against Line 1. Tumor cells expressing CD86 grew in only 50% of the mice injected with live cells, and those mice that developed tumors did so with significantly delayed kinetics. Furthermore, irradiated CD86-expressing Line 1 cells served as an effective tumor vaccine, demonstrating that CD86 is effective in inducing tumor immunity in the Line 1 system. These data suggest that if CIITA and CD86 cooperate, enhanced tumor immunity could be achieved. CIITA alone was mildly beneficial in slowing primary tumor growth but only when expressed at low levels. Clones expressing high levels of class II MHC grew as fast as or faster than parental tumor, and CIITA expression in a tumor vaccine assay lacked efficacy. When CIITA and CD86 were coexpressed, there was no cooperative immune protection from tumor growth. Cells that coexpress both genes also failed as a cancer vaccine, suggesting a negative role for CIITA in this lung carcinoma. These data suggest that human cancer vaccine trials utilizing CIITA gene therapy alone or in combination with CD86 should be approached with caution.
AZD4547: An Orally Bioavailable, Potent, and Selective Inhibitor of the Fibroblast Growth Factor Receptor Tyrosine Kinase Family (2012)

The fibroblast growth factor (FGF) signaling axis is increasingly implicated in tumorigenesis and chemoresistance. Several small-molecule FGF receptor (FGFR) kinase inhibitors are currently in clinical development; however, the predominant activity of the most advanced of these agents is against the kinase insert domain receptor (KDR), which compromises the FGFR selectivity. Here, we report the pharmacologic profile of AZD4547, a novel and selective inhibitor of the FGFR1, 2, and 3 tyrosine kinases. AZD4547 inhibited recombinant FGFR kinase activity in vitro and suppressed FGFR signaling and growth in tumor cell lines with deregulated FGFR expression. In a representative FGFR-driven human tumor xenograft model, oral administration of AZD4547 was well tolerated and resulted in potent dose-dependent antitumor activity, consistent with plasma exposure and pharmacodynamic modulation of tumor FGFR. Importantly, at efficacious doses, no evidence of anti-KDR-related effects were observed, confirming the in vivo FGFR selectivity of AZD4547. Taken together, our findings show that AZD4547 is a novel selective small-molecule inhibitor of FGFR with potent antitumor activity against FGFR-deregulated tumors in preclinical models. AZD4547 is under clinical investigation for the treatment of FGFR-dependent tumors.
Functional Characterization of Endothelin Receptors in the Bovine Retractor Penis Muscle and Penile Artery (1996)

The effects of endothelin-1 and sarafotoxin 6c on the bovine retractor penis muscle and the bovine penile artery were studied, and a functional characterization of endothelin receptors in these tissues was performed by using the ETA-receptor antagonist BQ-123 and the ETB-receptor antagonist IRL 1038. The retractor penis muscle and the penile artery were about equipotently contracted by endothelin-1 in a concentration-dependent manner the EC50 values being 3.5 x 10(-9) M and 1.3 x 10(-9) M, respectively. In both tissues BQ-123 (10(-6) M) inhibited maximal contraction induced by endothelin-1 by about 50%. Sarafotoxin 6c substantially relaxed the retractor penis muscle, and to a lesser extent also the penile artery, whereas endothelin-1 did not relax either tissue. The sarafotoxin 6c-induced relaxation of the retractor penis muscle was totally inhibited by IRL 1038 (3 x 10(-6) M) and the nitric oxide synthase inhibitor L-NNA (10(-4) M). In both tissues L-NNA enhanced the contraction induced by endothelin-1 and lowered the threshold concentration for it. The results show that in both tissues the contraction induced by endothelin-1 was mediated primarily by ETA-receptors. The retractor penis muscle is also equipped with ETB-receptors, probably at least in part located on the inhibitory nerves, which mediate relaxation via activation of the L-arginine nitric oxide synthase pathway.
Demonstration That Mutation of the Type II Transforming Growth Factor β Receptor Inactivates Its Tumor Suppressor Activity in Replication Error-positive Colon Carcinoma Cells (1995)

Escape from negative growth regulation by transforming growth factor beta (TGF-beta) as a result of the loss of TGF-beta type II receptor (RII) expression has been found to be associated with the replication error (RER) colorectal cancer genotype, which is characteristic of hereditary nonpolyposis colorectal cancers. The RER-positive HCT 116 colon carcinoma cell line was examined for RII mutations. A 1-base deletion was found within a sequence of 10 repeating adenines (nucleotides 709-718), which resulted in a frameshift mutation. Although it is reasonable to predict that the loss of RII function would be an important determinant of malignancy, the large number of potential mutations in cells of this phenotype raises the possibility that an RII mutation may not be a key event in the tumorigenic phenotype of these cells. One way to test directly the importance of RII mutations in determining the malignant phenotype would be to restore its expression. If restoration of expression leads to diminished tumorigenicity, it would indicate that RII mutation is an important determinant of malignancy in the RER phenotype. To determine whether restoration of RII would lead to reversal of malignancy in RER colon cancers, an RII expression vector was transfected into the HCT 116 cell line. RII stable clones showed mRNA and protein expression of transfected RII. The fibronectin mRNA level was increased by exogenous TGF-beta 1 treatment in a dose-dependent manner in RII-positive clones, whereas the control cells remained insensitive. The RII transfectants showed reduced clonogenicity in both monolayer culture and soft agarose. They were growth arrested at a lower saturation density than control cells. TGF-beta 1-neutralizing antibody stimulated the proliferation of RII-transfected but not control cells, indicating that the alterations in the growth parameters of the transfected cells were due to the acquisition of autocrine-negative activity. Tumorigenicity in athymic mice was reduced and delayed in RII transfectants. These results indicate that reconstitution of TGF-beta autocrine activity by reexpression of RII can reverse malignancy in RER colon cancers, thus verifying that the malignancy of hereditary nonpolyposis colorectal cancer can be directly associated with the loss of RII expression.
Competition between dipolar and steric interactions in swallow-tailed compounds (1993)

Abstract A new class of swallow-tailed mesogen with the longitudinal dipole moment in the direction of the non-branched ‘head’ is presented. Mixtures of these compounds with ‘conventional’ swallow-tailed substances were investigated by polarization microscopy and dielectric measurements. In the mixtures, dipolar and steric interactions favour opposite arrangements of the molecules in the short range order.
Effects of 3‐5 log10 pre‐storage leucocyte depletion on red cell storage and metabolism (1994)

A new, in-line high-efficiency 3-5 log10 leucodepletion filter system (Leukotrap RC system) was used to investigate the effect of pre-storage white cell removal on the quality of AS-3 red cell concentrates stored for 42 d at 4 degrees C. Median residual white cell content was 4 x 10(5) when filtration was performed at 22 degrees C within 8 h of phlebotomy (n = 20) and 3.2 x 10(4) when filtration was performed at 4 degrees C 12-24 h after phlebotomy (n = 24). None exceeded 1 x 10(6) WBC per red cell product. Filtration was rapid (median 28 min), and red cell loss averaged (mean +/- 1 SD) 6.4 +/- 0.7%. In a paired study design, post-transfusion recoveries of 42 d stored red cells in the filtered units averaged 84 +/- 6% v 82 +/- 8% for unfiltered units (P < 0.05) and post-storage haemolysis. ATP, osmotic fragility, K+ and pH were significantly (P < 0.05) better in the filtered units. Reduced glycolytic activity was also observed in the filtered units, and there was a correlation between osmotic fragility, glucose consumption, and lactate produced in standard units that was not present in leucodepleted units. In conclusion, this study suggests that leucodepletion of AS-3 red cell concentrates prior to storage results in better maintenance of the integrity of the red cell membrane with reduced glycolytic activity. There was a modest improvement in post-infusion viability sufficient to offset the filtration-induced loss and to result in an equivalent red cell product.
Calcitonin gene‐related peptide (CGRP) modulates nociceptive trigeminovascular transmission in the cat (2004)

Calcitonin gene-related peptide (CGRP) is released into the cranial circulation of humans during acute migraine. To determine whether CGRP is involved in neurotransmission in craniovascular nociceptive pathways, we microiontophoresed onto neurons in the trigeminocervical complex and intravenously administered the CGRP receptor antagonists alpha-CGRP-(8-37) and BIBN4096BS. Cats were anaesthetised with alpha-chloralose, and using halothane during surgical preparation. A craniotomy and C1/C2 laminectomy allowed access to the superior sagittal sinus (SSS) and recording site. Recordings of activity in the trigeminocervical complex evoked by electrical stimulation of the SSS were made. Multibarrelled micropipettes incorporating a recording electrode were used for microiontophoresis of test substances. Cells recorded received wide dynamic range (WDR) or nociceptive specific (NS) input from cutaneous receptive fields on the face or forepaws. Cell firing was increased to 25-30 Hz by microiontophoresis of L-glutamate (n = 43 cells). Microiontophoresis of alpha-CGRP excited seven of 17 tested neurons. BIBN4096BS inhibited the majority of units (26 of 38 cells) activated by l-glutamate, demonstrating a non-presynaptic site of action for CGRP. alpha-CGRP-(8-37) inhibited a similar proportion of units (five of nine cells). Intravenous BIBN4096BS resulted in a dose-dependent inhibition of trigeminocervical SSS-evoked activity (ED50 31 microg kg(-1)). The maximal effect observed within 30 min of administration. The data suggest that there are non-presynaptic CGRP receptors in the trigeminocervical complex that can be inhibited by CGRP receptor blockade and that a CGRP receptor antagonist would be effective in the acute treatment of migraine and cluster headache.
Phospholipase Cγ Binds α1β1Integrin and Modulates α1β1 Integrin-specific Adhesion (2002)

Integrin adhesion receptors have been implicated in bidirectional signal transduction. The dynamic regulation of integrin affinity and avidity as well as post-ligand effects involved in outside-in signaling depends on the interaction of integrins with cytoskeletal and signaling proteins. In this study, we attempted to identify cytoplasmic binding partners of alpha(1)beta(1) integrin. We were able to show that cell adhesion to alpha(1)beta(1)-specific substrates results in the association of phospholipase Cgamma (PLCgamma) with the alpha(1)beta(1) integrin independent of PLCgamma tyrosine phosphorylation. Using peptide-binding assays, the membrane proximal sequences within the alpha(1)beta(1) integrin subunits were identified as binding sites for PLCgamma. In particular, the conserved sequence of beta(1) subunit binds the enzyme very efficiently. Because purified PLCgamma also binds the integrin peptides, binding seems to be direct. Inhibition of PLC by leads to reduced cell adhesion on alpha(1)beta(1)-specific substrates. Cells lacking the conserved domain of the alpha(1) subunit fail to respond to the PLC inhibition, indicating that this domain is necessary for PLC-dependent adhesion modulation of alpha(1)beta(1) integrin.
Continuous contact simulation for smooth surfaces (2003)

Dynamics simulation of smooth surfaced rigid bodies in contact is a critical problem in physically based animation and interactive virtual environments. We describe a technique that uses reduced coordinates to evolve a single continuous contact between smooth piecewise parametric surfaces. The incorporation of friction into our algorithm is straightforward. The dynamics equations, although slightly more complex due to the reduced coordinate formulation, can be integrated easily using explicit integrators without the need for constraint stabilization. Reduced coordinates confine integration errors to the constraint manifold, thereby permitting a wide choice of step sizes with visually acceptable results. We demonstrate these results using Loop Subdivision surfaces with parametric evaluation.
A fluorescent probe designed for studying protein conformational change (2005)

The usefulness of fluorescence in studying protein motions derives from its sensitivity, kinetic resolution, and compatibility with both live cells and physiological assays. Recent advances in microscopy and membrane protein purification have permitted the observation of fluorescence changes that accompany the functional transitions of complex eukaryotic membrane proteins. These techniques rely on probes that can clearly report the environmental changes of specific residues, but most commonly available side-chain-reactive probes are not well suited for this purpose. Here, we introduce a red Cys-reactive probe, aminophenoxazone maleimide (APM), designed with improved chemical and spectral properties for reporting protein conformational change. APM is compact, uncharged, and has a short linker between probe and protein, all of which ensure that it can closely track the motions of the side chain to which it is attached. It undergoes large polarity-dependent changes in Stokes shift, as well as large bathochromic shifts in both excitation maximum (from 521 nm in toluene to 598 nm in water) and emission maximum (580 nm to 633 nm). These polarity-dependent spectral changes offer a potentially simple means of relating fluorescence to local structure and motion, although they are partially offset by some complicating factors in APM fluorescence. We find that, like a rhodamine maleimide, APM senses the conformational changes underlying voltage sensing in the Shaker potassium channel, and it is superior at a site that shows limited reactivity to the rhodamine. The spectral characteristics of APM can also report subtle differences between aqueous positions in purified preparations of the β 2 adrenergic receptor.
Cloud computing networking: challenges and opportunities for innovations (2013)

Cloud computing materializes the vision of utility computing. Tenants can benefit from on-demand provisioning of compute, storage, and networking resources according to a pay-per-use business model. Tenants have only limited visibility and control over network resources. The owners of cloud computing facilities are also facing challenges in various aspects of providing and efficiently managing IaaS facilities. In this work we present the networking issues in IaaS and federation challenges that are currently addressed with existing technologies. We also present innovative software-defined networking proposals, which are applied to some of the challenges and could be used in future deployments as efficient solutions.
Sustainable Biofuels Redux (2008)

Science-based policy is essential for guiding an environmentally sustainable approach to cellulosic biofuels.
The size-dependent phonon frequency of semiconductor nanocrystals (2004)

A model, without adjustable parameters, describing the size-dependent phonon frequency of semiconductor nanocrystals is established based on the size-dependent force constant and thus the size-dependent bond length and bond energy of nanocrystals. This model shows frequency shifts as the size of the crystals decreases. Our predictions agree with the results of experiments for the blue shift of TiO2 nanoparticles, Si and InP quantum dots. The model will be useful for understanding the origins of the phonon behaviour of nanocrystals and the effect of the thermodynamic parameters on the phonon frequency.
Securing Cloud from DDOS Attacks Using Intrusion Detection System in Virtual Machine (2010)

Innovation is necessary to ride the inevitable tide of change. The buzzword of 2009 seems to be "cloud computing" which is a futuristic platform to provides dynamic resource pools, virtualization, and high availability and enables the sharing, selection and aggregation of geographically distributed heterogeneous resources for solving large-scale problems in science and engineering. But with this ever developing cloud concept, problems are arising from this ¿golden solution¿ in the enterprise arena. Preventing intruders from attacking the cloud infrastructure is the only realistic thing the staff, management and planners can foresee. Regardless of company size or volume and magnitude of the cloud, this paper explains how maneuver IT virtualization strategy could be used in responding to a denial of service attack. After picking up a grossly abnormal spike in inbound traffic, targeted applications could be immediately transferred to virtual machines hosted in another data center. We're not reinventing the wheel. We have lots of technology and standardized solutions we can already use to engineer into the stack. We are just introducing them in the way least expected.