gebhart/patrepeval huggingface dataset:
Regulation of Macrophage-Derived Fibroblast Growth Factor Release by Arachidonate Metabolites (1987)

The macrophage is a source of many mediators with direct and indirect fibrogenic potential. In this study, release of macrophage-derived fibroblast growth factor (MDGF) activity by murine peritoneal macrophages is examined with regard to its regulation by arachidonate metabolites. Upon stimulation with 10 micrograms/ml lipopolysaccharide (LPS), resident peritoneal macrophages from CBA/J mice released MDGF activity into media rapidly, reaching maximal levels in approximately 1 h. Lysates of these stimulated cells also revealed significantly increased cell-associated MDGF activity, composing 45% of the total assayable activity. This activity, as assayed by radioactive thymidine incorporation by primary cultures of rat lung fibroblasts, was separable from interleukin-1 (IL-1) activity by reverse phase high performance liquid chromatography (HPLC). Furthermore, purified murine IL-1 had no MDGF activity in this assay system. This stimulated MDGF release was enhanced by the cyclooxygenase inhibitors indomethacin, ibuprofen, and aspirin at micromolar concentrations, but inhibited in a dose-dependent manner by prostaglandin E2 (PGE2). On the other hand, nordihydroguaiaretic acid (NDGA), a lipoxygenase inhibitor was inhibitory at 0.1 and 0.4 microM but not at 2.5 microM. Zymosan-stimulated macrophages also markedly increased MDGF release, albeit with a different time course which was characterized by a delay of approximately 7 h before peak levels were attained. Such stimulation, which is known to cause increased lipoxygenase activity, was also inhibited by 0.5 microM NDGA. In contrast, the lipoxygenase pathway products leukotrienes B4 (LTB4) and C4 (LTC4) stimulated MDGF release in a dose-dependent (10(-10)-10(-8) M) manner, with LTC4 being more potent on a per unit dose basis. Stimulation by LTC4 was inhibited by the putative leukotriene receptor antagonist, FPL55712, while LTD4 and LTE4 did not stimulate MDGF release, thus suggesting the mediation of this effect by specific LTC4 receptors. These data suggest also that products of the cyclooxygenase and lipoxygenase pathways are potentially important both as exogenous (ie, derived from cells other than the macrophage itself) and auto- or self-regulators of macrophage MDGF release. This, in turn, implies that cyclooxygenase products are antifibrogenic and important in maintaining or returning to the quiescent or normal state, whereas the lipoxygenase products are profibrogenic and important in induction of fibrosis or wound-healing and tissue repair. Any alteration in the balance between these two pathways may result in either a desirable or a harmful outcome.
The growth of endothelium from human corneal rims in tissue culture. (1984)

The authors report the successful in vitro growth of human corneal endothelium derived from 12 of 31 corneal-scleral rims obtained following corneal transplantation. The average age of donors whose endothelium grew was 17.6 +/- 3.2 years. The average interval between death and culturing was 51.5 +/- 10.1 hr. The cells migrated from the explants within 3-7 days and were characterized by a flattened, polygonal shape with a centrally located nucleus. Cell growth exhibited a doubling time of 72-96 hr in the second and third tissue culture passages. A reduced growth rate was observed by cell lines maintained in vitro for over 6 months. Fibroblast growth factor, epidermal growth factor, and endothelial cell growth supplement all exerted a positive influence on cell proliferation. Corneal-scleral rims can be a valuable source of endothelial cells for corneal research.
N-(2-chloroethyl)-N-nitrosourea tethered to lexitropsin induces minor groove lesions at the p53 cDNA that are more cytotoxic than mutagenic. (1999)

Many different N-chloroethyl-N-nitrosourea (CENU) derivatives have been synthesized in an attempt to minimize carcinogenic activity while favoring antineoplastic activity. CENU derivatives linked to the dipeptide lexitropsin (lex) showed significant changes in groove- and sequence-selective DNA alkylation inducing thermolabile N3-alkyladenines (N3-Alkyl-As) at lex equilibrium binding sites. CENU-lex sequence specificity for DNA alkylation was determined using 32P-end-labeled restriction fragments of the p53 cDNA. The adducted sites were converted into single-strand breaks by sequential heating at neutral pH and exposure to piperidine. To establish the mutagenic and lethal properties of CENU-lex-specific lesions, a yeast expression vector harboring a human wild-type p53 cDNA was treated in vitro with CENU-lex and transfected into a yeast strain containing the ADE2 gene regulated by a p53-responsive promoter. p53 mutants were isolated from independent ade- transformants. The results revealed that: (a) CENU-lex preferentially induces N3-Alkyl-A at specific lex equilibrium binding sites, the formations of which are strongly inhibited by distamycin; (b) reactivity toward Gs is still present, albeit to a lesser extent when compared to N-(2-chloroethyl)-N-cyclohexyl-N-nitrosourea and to CENU; (c) 91% of the 49 CENU-lex p53 mutations (45 of 49) were bp substitutions, 29 of which were GC-->AT transitions, mainly at 5' purine G sites; (d) all AT-targeted mutations but one were AT-->TA transversions; (e) the distribution of the CENU-lex mutations along the p53 cDNA was not random, with position 273 (codon 91), where only GC-->AT transitions were observed, being a real (n = 3, P < 0.0002) CENU-lex mutation hot spot; and (f) a shift in DNA alkylation sites between lesion spectra induced by CENU-lex and N-(2-chloroethyl-N-cyclohexyl-N-nitrosourea was associated with an increased lethality and a decreased mutagenicity, whereas no dramatic change in mutational specificity was observed. Hence, it is tempting to conclude that, in this experimental system, N3-Alkyl-A is more lethal than mutagenic, whereas O6-alkylguanine is a common premutational lesion formed at non-lex binding sites. These results suggest that CENU derivatives with virtually absolute specificity for A residues would make targeting of lethal, nonmutagenic lesions at A+T-rich regions possible, and this may represent a new strategy for the development of new chemotherapeutic agents with a higher therapeutic index.
Effect of noise suppression on quality of 2C OBC image (2004)

Two component ocean bottom cable (2C OBC) data are often affected by substantial noise. The noise is probably caused by shear wave energy registered on the vertical geophone. It exhibits random properties in common shot domain but coherent properties in common receiver domain. This phenomenon is observed in most OBC surveys worldwide, and the noise level can be very substantial. Typically, there is a substantial move out difference between the noise and the signal, i.e., reflected PP waves, allowing use of velocity filtering for noise suppression. Velocity of sound in water can be used as a quite universal parameter for normal moveout (NMO) correction before the velocity filtering. The NMO correction substantially simplifies design of the velocity filter. Efficiency of the proposed approach is illustrated using real 2C OBC data.
Mass spectrometry of glycans (2013)

Powerful new strategies based on mass spectrometry are revolutionizing the structural analysis and profiling of glycans and glycoconjugates. We survey here the major biosynthetic pathways that underlie the biological diversity in glycobiology, with emphasis on glycoproteins, and the approaches that can be used to address the resulting heterogeneity. Included among these are derivatizations, on- and off-line chromatography, electrospray and matrix-assisted laser desorption/ionization, and a variety of dissociation methods, the recently introduced electron-based techniques being of particular interest.
Fiber-Optic Cavity Ring Down Using an Added-Signal for Curvature Sensing (2015)

This letter presents a fiber-optic cavity ring down (CRD) configuration using an added-signal for curvature sensing. An optical time-domain reflectometer was used to send impulses down into the fiber loop cavity, inside of which a long period grating was placed to act as a sensing device. The added-signal was obtained by the sum of several conventional CRD impulses, thus providing an improvement on the curvature sensitivity when compared with the conventional CRD signal processing. A linear response to applied curvature in the range of 2.2-3.6 m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> was observed, and a sensitivity of 15.3 μs/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> was obtained. This result was found to be 20-fold the one obtained for the conventional CRD signal processing. The added-signal increases the optical power but increases as well the ring-down time due to the sum of the several loops that light travels inside the ring. A ring-down time response of 43.3 μs was attained (versus $23.7μs for the conventional CRD signal processing).
Synthetic as compared with natural vitamin E is preferentially excreted as α‐CEHC in human urine: studies using deuterated α‐tocopheryl acetates (1998)

Alpha-CEHC (2,5,7,8-tetramethyl-2(2'-carboxyethyl)-6-hydroxychroman) is a urinary vitamin E metabolite with a truncated phytyl tail. To test whether natural and synthetic vitamin E are similarly converted to alpha-CEHC, 6 humans consumed 150 mg each RRR-alpha-[5-(C2H3)]- and all rac-alpha-[5,7(C2H3)2]-tocopheryl acetates (d3RRR-alpha- and d6all rac-alpha-tocopheryl acetates, respectively). Plasma was collected at 0, 6, 12 and 24 h; urine (24 h) at 0, 1, 2, 3, 4 and 8 days. Following dosing, plasma was enriched with d3RRR-alpha-tocopherol, while urine was enriched with alpha-CEHC derived from d6all rac-alpha-tocopherol. Thus, synthetic compared with natural vitamin E is preferentially metabolized to alpha-CEHC and excreted.
Two different IL-13 receptor chains are expressed in normal human skin fibroblasts, and IL-4 and IL-13 mediate signal transduction through a common pathway (1998)

IL-13 and IL-4, pleiotropic immune regulatory cytokines, have been shown to mediate similar prominent effects in human fibroblast cell lines. However, molecular mechanisms for their redundant effects are not known. Here, we have investigated the structure of IL-13 receptors (IL-13R) and molecular mechanisms of signal transduction through IL-13 and IL-4 receptors in non-transformed normal skin fibroblast cell lines. We demonstrate that high-affinity IL-13R is expressed in normal skin fibroblast cell lines. Upon [125I]1L-13 cross-linking, a approximately 60-70 kDa band was observed in sk559 and sk574 fibroblast cell lines. By RT-PCR analysis, mRNA for IL-13R alpha, IL-13R alpha' and IL-4Rbeta chains were expressed; however, the IL-2Rgamma chain, shown to participate and modulate IL-4 and IL-13 binding, was not expressed in any of the cell lines examined. The Janus kinase (JAK)2 and Tyk2 were phosphorylated in response to IL-4 or IL-13 in sk559 and sk574 cell lines. JAK1 was also phosphorylated in one of two cell lines while JAK3 was present but not phosphorylated in any of the cell lines studied. A signal transduction and activator of transcription (STAT)6 was also activated in response to both IL. An insulin receptor substrate (IRS)-1 was constitutively phosphorylated and its phosphorylation level was augmented in response to both IL. These results suggest that the mechanism of signal transduction through IL-13 and IL-4 receptors in human fibroblast cell lines is similar, and this may, at least in part, be responsible for the redundant effects of these two cytokines. In addition, JAK2 tyrosine kinase instead of JAK3 appears to play a major role in IL-4- and IL-13-induced signal transduction in human fibroblasts.
Identification of the satA gene encoding a streptogramin A acetyltransferase in Enterococcus faecium BM4145 (1993)

Enterococcus faecium BM4145, a clinical isolate from urine, was resistant to streptogramin group A antibiotics by inactivation. The strain harbored a plasmid containing a gene, satA, responsible for this resistance; this gene was cloned and sequenced. It encoded SatA, a protein deduced to be 23,634 Da in mass and homologous with a new family of chloramphenicol acetyltransferases described in Agrobacterium tumefaciens, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. The similarity of SatA to other acetyltransferases, LacA (thiogalactoside acetyltransferase) and CysE (serine acetyltransferase) from E. coli, and to two putative acetyltransferases, NodL from Rhizobium leguminosarum and Urf1 from E. coli, was also observed in a region considered to be the enzyme's active site. Acetylation experiments indicated that acetyl coenzyme A was necessary for SatA activity and that a single acetylated derivative of pristinamycin IIA was produced. Other members of the streptogramin A group such as virginiamycin M and RP54476 were also substrates for the enzyme. We conclude that resistance to the streptogramin A group of antibiotics in E. faecium BM4145 is due to acetylation by an enzyme related to the novel chloramphenicol acetyltransferase family.
Context-based connectivity and characterization of Wireless Mesh Networks: Simulation study (2010)

Wireless Mesh Networks (WMNs) are promising networks to enable personalized access over wireless environments. On the other hand, network virtualization brings well-known advantages, such as, flexible, programmable, and isolated management of network resources. Therefore, we propose a multi-virtual architecture for WMNs to deal with the huge heterogeneity of context requirements of mesh clients, e.g., cost or security preferences, mobility patterns, and applications' Quality-of-Service (QoS) requirements. In this approach, a WMN is split into a different number of Virtual Networks (VNs), each one specific to a set of context features. Among several challenges raised by this context-aware approach, this paper focus on the mapping of different requirements of users into appropriate VNs' topologies and assigned resources. Moreover, it defines local and global control mechanisms to discover, extend, and update the VNs that best fit users' and services' requirements. The specified mechanisms are the base support for a distributed and scalable control of the architecture. The simulation results show the potential of network virtualization to enable the context-based characterization of WMN communications. Moreover, the proposed control mechanisms present acceptable delays, even in the presence of mobility of mesh clients.
Allogeneic Stem Cell Transplantation for Solid Tumors: Which Way Forward? (2007)

Abstract The patients presenting with metastatic solid tumors remains with poor prognosis. Despite advances in treatment and better understanding of the biological pathway during the past two decades, outcome remains often very poor. On the other hand, allogeneic stem cell transplantation has been established as a potent antitumoral immunotherapy in various hematological malignancies. Preliminary results confirm that graft versus tumor effect does exist. The main challenge is now to transform this biological and clinical effect into a real clinical benefit in term of curability and survival.
Media eyepliances (2005)

This paper discusses the use of eye contact sensing for focus selection operations in remote controlled media appliances. Focus selection with remote controls tends to be cumbersome as selection buttons place the remote in a device-specific modality. We addressed this issue with the design of Media EyePliances, home theatre appliances augmented with a digital eye contact sensor. An appliance is selected as the focus of remote commands by looking at its sensor. A central server subsequently routes all commands provided by remote, keyboard or voice input to the focus EyePliance. We discuss a calibration-free digital eye contact sensing technique that allows Media EyePliances to determine the user's point of gaze.
Identification of Critical Determinants for Autoinhibition in the Pseudosubstrate Region of Type Iα cAMP-dependent Protein Kinase (1997)

The consensus substrate site for cAMP-dependent protein kinase (PKA) is Arg-Arg-Xaa-Ser(P)-Xaa and the autoinhibitory domain of the PKA type I alpha regulatory subunit (RI subunit) contains a similar sequence, Arg92-Arg-Arg-Arg-Gly-Ala-Ile-Ser-Ala-Glu. The italicized amino acids form a putative pseudosubstrate site (Ser is replaced with Ala), which together with adjacent residues could competitively inhibit substrate phosphorylation by the PKA catalytic subunit (C subunit). The present studies determine the contributions of Arg92-95, Ile98, and Glu101 to inhibitory potency. Amino-terminal truncation of RI subunit through Arg92 (delta1-92) or Arg93 (delta1-93) had no detectable effect on inhibition of C subunit. Truncation through Arg94 (delta1-94), or point mutation of Arg95 within truncated mutants (delta1-93.R95A or delta1-92.R95A), caused a dramatic reduction in inhibitory potency. Truncation through Arg95 (delta1-95) had a greater effect than did replacement or deletion of Arg94 or Arg95 alone. Using full-length RI subunit, the inhibitory potency was reduced by replacing Ile98 with Ala, Gly, or Gln, but not by replacing it with Val. The inhibitory potency of RI subunit was unchanged when Glu101 was replaced with Ala or Gln. It is concluded that Arg94, Arg95 and, to a lesser extent, Ile98 are vital constituents of PKA autoinhibition by type I alpha R subunit.
Partial Convolution Based Multimodal Autoencoder for Art Investigation. (2019)

Autoencoders have been widely used in applications with limited annotations to extract features in an unsupervised manner, pre-processing the data to be used in machine learning models. This is especially helpful in image processing for art investigation where annotated data is scarce and difficult to collect. We introduce a structural similarity index based loss function to train the autoencoder for image data. By extending the recently developed partial convolution to partial deconvolution, we construct a fully partial convolutional autoencoder (FP-CAE) and adapt it to multimodal data, typically utilized in art investigation. Experimental results on images of the Ghent Altarpieceshow that our method significantly suppresses edge artifacts and improves the overall reconstruction performance. The proposed FP-CAE can be used for data preprocessing in craquelure detection and other art investigation tasks in future studies.
Reject option for VQ-based Bayesian classification (2002)

We have developed a reject option for VQ-based supervised Bayesian classification to improve classification accuracy by sieving out patterns that are classified with a low confidence value. A small codebook extracted from a learning vector quantizer (LVQ) is used to estimate the class-conditional densities of the feature vector. We adapt the two commonly used rejection criteria, outlier rejection and ambiguity rejection, for the VQ-based Bayesian classifiers. Using three high-level image classification problems, we demonstrate how local rejection criteria can improve the error vs. reject characteristics of our classifier over a global rejection method.
A memory of errors in sensorimotor learning (2014)

The current view of motor learning suggests that when we revisit a task, the brain recalls the motor commands it previously learned. In this view, motor memory is a memory of motor commands, acquired through trial-and-error and reinforcement. Here we show that the brain controls how much it is willing to learn from the current error through a principled mechanism that depends on the history of past errors. This suggests that the brain stores a previously unknown form of memory, a memory of errors. A mathematical formulation of this idea provides insights into a host of puzzling experimental data, including savings and meta-learning, demonstrating that when we are better at a motor task, it is partly because the brain recognizes the errors it experienced before.
A network model for the aperture coupled microstrip patch (1993)

Abstract A network model for an aperture coupled microstrip patch is developed. The derivation of the topology of the network model is based on electromagnetic arguments. The values of the components in the network model are found by optimization using input reflection coefficient data computed from a method of moments model. The topology of the network model is described together with a procedure for the determination of the values of its components. After the determination of the values of the components, the network model can be used in a CAD program for a large range of mechanical dimensions, without the need of additional method of moments calculations. © 1993 John Wiley & Sons, Inc.
Astrocyte survival and HSP70 heat shock protein induction following heat shock and acidosis (1996)

Although severe acidosis is an important mediator of brain infarction, recent evidence suggests that mild acidosis may protect ischemic cells. The HSP70 heat shock protein is induced by acidosis in cultured cells and in ischemic brain and protects cells against many types of injury. Therefore, this study determined whether induction of heat shock proteins protects cultured astrocytes against acidosis. Brief exposure of cultured cortical astrocytes to acid (pH 5.2 for 40 min) or heat shock (45°C for 40 min) markedly induced hsp70 mRNA and HSP70 protein. HSP70 protein was detected with the C92 monoclonal antibody (Welch and Suhan: J Cell Biol 103:2035, 1986), which has been shown to recognize the protein product of the full-length rat hsp70 cDNA (Longo et al: J Neurosci Res 36:325, 1993). Heat shock of the cultured cortical astrocytes completely protected the astrocytes from an otherwise lethal heat exposure 24 h later (45°C for 4 h). In contrast, heat pretreatment sensitized the astrocytes to injury from acidosis 24 h later. Acid pretreatment, which markedly induced the HSP70 protein without producing astrocytic cell death, similarly sensitized the cells to injury from acidosis 24 h later (60% survival following pH 5.2 for 3 h versus 90% survival in controls; P < 0.0001). Surprisingly, heat shock pretreatment protected astrocytes against exposure to acid 48 h later (P < 0.05, 1.5–3 h), whereas acid pretreatment had no effect on astrocyte survival 48 h later. Since heat shock did not protect against acidosis at 24 h when HSP70 induction was maximal but did protect at 48 h when HSP70 was markedly diminished, the protective effect of heat shock at 48 h may be related to stress proteins present at 48 h. It is concluded that induction of HSP70 and other heat shock proteins by heat shock protects astrocytes against subsequent lethal heat shock. However, heat shock and acid treatment increase the vulnerability of astrocytes to acidosis 24 h later in spite of the induction of HSP70 heat shock proteins. The finding that heat shock protected astrocytes against acidosis 2 days later may suggest that delayed induction of stress proteins partially protects the astrocytes against damage produced by high concentrations of hydrogen ions. © 1996 Wiley-Liss, Inc.
Competition Between Stimulated Brillouin and Rayleigh Scattering in Absorbing Media (1971)

Rayleigh scattering is the dominating stimulated scattering process when the absorption coefficient of the medium exceeds a critical value ${\ensuremath{\alpha}}_{\mathrm{cr}}$. It is found that the transient gain of Rayleigh scattering is important for the competition with stimulated Brillouin scattering. The initial slope- not the peak power- of the incident laser pulse determines the value of ${\ensuremath{\alpha}}_{\mathrm{cr}}$. Our findings are in full agreement with theoretical investigations.