gebhart/patrepeval huggingface dataset:
Diode laser sensors for real-time control of pulsed combustion systems (1998)

A diode-laser based, closed-loop control system has been developed to nonintrusively optimize a pulsed, 50-kW dump combustor. The adaptive control system used temperature and water mole fraction measurements obtained at 10-kHz rates from the peak absorbance values of H 2 O features near 1.4 μm. In addition, measurements of CO, C 2 H 2 , and C 2 H 4 concentrations in the exhaust, determined from diode-laser absorption spectra recorded using a fast-sampling probe and a multipass absorption cell (nominal 33-m-long path), were used to evaluate the effectiveness of the control strategies. A correlation was established between the magnitude of the observed temperature oscillations and the measured CO concentration in the exhaust. Adaptive control strategies were then applied to maximize the coherence of the burning vortices in the combustion region and thus optimize the combustor performance. The closed-loop control system was able to adaptively tune the phase and amplitude of the applied forcing within 100 ms and the forcing frequency within 10 s. These results demonstrate the applicability of multiplexed diode-laser absorption sensors for rapid, continuous measurements and control of multiple flowfield parameters, including trace species concentrations, in high-temperature combustion environments.
Targeting hyaluronan (HA) in tumor stroma: Interim safety and translational evaluation of pegylated hyaluronidase (PEGPH20) in patients (pts) with advanced solid tumors—A focus on gastrointestinal malignancies. (2012)

249 Background: HA, a glycosaminoglycan in the tumor matrix, accumulates in 20-30% of solid tumors and ≥28%, ≥42% and ≥87% of colon, gastric and pancreatic ductal adenocarcinoma (PDA) tumors, respectively. Tumors that accumulate HA can develop high interstitial fluid pressure (IFP) and are resistant to chemotherapy. HA in human PDA is associated with disease progression and poor prognosis. In animal models, PEGPH20 reduced tumor-associated HA, tumor IFP and tumor growth, and increased efficacy of chemotherapy. Pharmacodynamic (PD) activity of PEGPH20 is being evaluated in Phase 1 (Ph1) trials. Methods: Two Ph1 studies in pts with advanced solid tumors refractory to prior therapy examined the safety, tolerability, PK, PD and MTD of single-agent IV PEGPH20. Dosing in Study 1 was 2x/wk and then reduced to q21d and in Study 2 is 1-2x/wk x 4wks and 1x/wk thereafter with dexamethasone pre-medication regimen. Biomarkers evaluated: Histochemistry to detect depletion of tumor HA, serum HA catabolites, Dynamic Contrast Enhanced (DCE)-MRI and FDG-PET. Results: In Study 1, the first 3 pts demonstrated musculoskeletal events (MSE; 2 pts dosed with 50 µg/kg 2x/wk, severe; 1 pt dosed with 0.5µg/kg 2x/wk, moderate) not predicted from GLP safety studies. The frequency of drug administration was reduced to q21d and the next 10 pts tolerated ≤1.5 µg/kg. In Study 2, dexamethasone pre-medication regimen was evaluated while dosing at 1-2x/wk. Nine pts were dosed ≤5.0 µg/kg. Doses ≤3.0 µg/kg administered 2x/wk were tolerated with intermittent Grade 1-2 MSE. Activity of PEGPH20 was reflected by increased HA serum catabolites. Pre- and post-dose biopsies from 2 colon pts demonstrated a 23-60% reduction in tumor HA after 4 wks of PEGPH20 dosing. DCE-MRI of PDA and FDG-PET of lung metastases increased tumor perfusion (K trans ) and decreased metabolic activity 8 and 24hrs post-PEGPH20 dose and was still apparent after 4 wks of treatment with PEGPH20. Conclusions: Ongoing Ph1 studies have shown in vivo activity of PEGPH20 through HA plasma catabolites, tumor HA depletion, DCE-MRI and FDG-PET.
Targeting Hsp90 prevents escape of breast cancer cells from tyrosine kinase inhibition (2008)

Recent studies have identified development of resistance to tyrosine kinase inhibition (TKI) as a significant roadblock to effective treatment. One mechanism of resistance recently appreciated involves 'oncogene switching', or the re-activation of signaling pathways by one or more redundant upstream activators. In breast cancer models, ErbB TKIs such as gefitinib have been shown to lose the ability to modulate ErbB-driven signaling pathways over time, even though ErbB inhibition is maintained. Although incomplete ErbB inhibition has been proposed to underlie this phenomenon, our findings suggest that oncogene switching can also re-activate downstream signaling pathways in breast cancer cells, even when ErbB inhibition is complete. We find that ErbB TKI-induced Src activation mediates downstream signaling rebound in SKBR3 cells, and we show that combination of Src and ErbB inhibitors is more effective and longlasting than is either TKI alone. Finally, the Hsp90 inhibitor 17-AAG, by simultaneously and durably inhibiting multiple signaling activators including ErbB and Src kinases, does not permit oncogene switching and results in a more prolonged and robust inhibition of downstream signaling pathways in breast cancer cells than do individual TKIs. These data support the continued clinical evaluation of Hsp90 inhibitors in breast cancer.
Investigation of the Anti-inflammatory Activity of Acacia nilotica and Hibiscus sabdariffa (1996)

The aqueous extracts of Acacia nilotica and Hibiscus sabdariffa were tested for anti-inflammatory, analgesic and antipyretic activities in animal models. Acacia nilotica extract had an inhibitory effect on carrageenan induced paw edema and yeast-induced pyrexia in rats. It also produced a significant increase in the hot plate reaction time in mice. Hibiscus sabdariffa extract had no effect on paw edema but had an inhibitory effect on yeast induced pyrexia and a significant effect on the hot plate reaction time. Among the phytoconstituents found in both plants, flavanoids, polysaccharides and organic acids may be mainly responsible for their pharmacological activities.
Sparsity based sub-wavelength imaging with partially incoherent light via quadratic compressed sensing (2011)

We demonstrate that sub-wavelength optical images borne on partially-spatially-incoherent light can be recovered, from their far-field or from the blurred image, given the prior knowledge that the image is sparse, and only that. The reconstruction method relies on the recently demonstrated sparsity-based sub-wavelength imaging. However, for partially-spatially-incoherent light, the relation between the measurements and the image is quadratic, yielding non-convex measurement equations that do not conform to previously used techniques. Consequently, we demonstrate new algorithmic methodology, referred to as quadratic compressed sensing, which can be applied to a range of other problems involving information recovery from partial correlation measurements, including when the correlation function has local dependencies. Specifically for microscopy, this method can be readily extended to white light microscopes with the additional knowledge of the light source spectrum.
Application of fluorescence recovery after photobleaching to diffusion of a polyelectrolyte in a multilayer film (2005)

The diffusion coefficient, D, and the proportion of mobile molecules, p, is measured for a fluorescently labeled polyelectrolyte in a multilayer film using fluorescence recovery after photobleaching (FRAP). The film was composed of poly(L-lysine) (PLL) and hyaluronan (HA). The labeled polyelectrolyte (PLL(FITC)) was either deposited on top of the film or embedded within it. A circular area of diameter approximately 60 microm was bleached using a confocal laser scanning microscope. Because molecules do already diffuse during the bleaching step, the initial light intensity profile is not characteristic of a uniformly bleached circular area. A formalism is developed in which a simple mathematical representation of a measured profile serves as starting profile. This radial distribution is introduced in the equation describing the time evolution of the labeled molecule concentration under the hypothesis that the recovery results from pure, two-dimensional Brownian diffusion of the mobile molecules according to Fick's law. The analysis of a series of images taken at successive times after bleaching (up to approximately one hour) leads to estimates of D of the order of 0.2 microm(2) s(-1) for labeled molecules deposited on top of the film and a 5-fold smaller value for the molecules embedded in the film. However, p is remarkably insensitive to the position in the multilayer architecture (p approximately 0.40).
Chaos and Fractal Algorithms Applied to Signal Processing and Analysis (1993)

Modern signal processing methods strive to maximize signal to noise ratios, even in the presence of severe noise. Frequently, real world data is degraded by under sampling of intrinsic periodicities, or by sampling with unevenly spaced intervals. This results in dropout or missing data, and such data sets are particularly difficul to process using conventional methods. In many cases, one must still extract as much information as possible from a given data set, although the available discrete data is sparse or very noisy. In such cases, we have found the algorithms derived from Chaos and fractal theory to represent a viable alternative to traditional spectral analysis. The data analysis techniques discussed in this work include phase space reconstruction, Poincare projections radius of gyration exponent, artificial insymmetration patterns (AIP), Liapunov spectra, correlation techniques, R/S analysis, K-factor, fractal statistics, maximum entropy method, and wavelets.
Pim-1 Ligand-bound Structures Reveal the Mechanism of Serine/Threonine Kinase Inhibition by LY294002 (2005)

Pim-1 is an oncogene-encoded serine/threonine kinase primarily expressed in hematopoietic and germ cell lines. Pim-1 kinase was originally identified in Maloney murine leukemia virus-induced T-cell lymphomas and is associated with multiple cellular functions such as proliferation, survival, differentiation, apoptosis, and tumorigenesis (Wang, Z., Bhattacharya, N., Weaver, M., Petersen, K., Meyer, M., Gapter, L., and Magnuson, N. S. (2001) J. Vet. Sci. 2, 167-179). The crystal structures of Pim-1 complexed with staurosporine and adenosine were determined. Although a typical two-domain serine/threonine protein kinase fold is observed, the inter-domain hinge region is unusual in both sequence and conformation; a two-residue insertion causes the hinge to bulge away from the ATP-binding pocket, and a proline residue in the hinge removes a conserved main chain hydrogen bond donor. Without this hydrogen bond, van der Waals interactions with the hinge serve to position the ligand. The hinge region of Pim-1 resembles that of phosphatidylinositol 3-kinase more closely than it does other protein kinases. Although the phosphatidylinositol 3-kinase inhibitor LY294002 also inhibits Pim-1, the structure of the LY294002.Pim-1 complex reveals a new binding mode that may be general for Ser/Thr kinases.
Localization of vasa protein to the Drosophila pole plasm is independent of its RNA-binding and helicase activities (1994)

The Drosophila gene vasa encodes a DEAD-box protein, which is localized during early oogenesis to the perinuclear region of the nurse cells and later to the pole plasm at the posterior end of the oocyte. Posterior localization of vasa protein depends upon the functions of four genes: capu, spir, osk and stau. We have found that localization of vasa to the perinuclear nuage is abolished in most vas alleles, but is unaffected by mutations in four genes required upstream for its pole plasm localization. Thus localization of vasa to the nuage particles is independent of the pole plasm assembly pathway. Furthermore, electron-dense nuage particles are less abundant in the cytoplasm of nurse cells from vas mutants that fail to exhibit perinuclear localization, suggesting that the formation of the nuage depends upon vas function. Eight of nine vas point mutations cause codon substitutions in a region conserved among DEAD-box genes. The proteins from two mutant alleles that retain the capacity to localize to the posterior pole of the oocyte, vasO14 and vasO11, are both severely reduced in RNA-binding and -unwinding activity as compared to the wild-type protein on a variety of RNA substrates including in vitro synthesized pole plasm RNAs. Initial recruitment of vasa to the pole plasm must consequently depend upon protein-protein interactions but, once localized, vasa must bind to RNA to mediate germ cell formation.
Expression and regulation of the atrial natriuretic factor encoding gene during development and disease (2005)

The endocrine function of the heart was shown by the identification of a potent inhibitor of renal tubular NaCl reabsorbtion, atrial natriuretic peptide/factor (ANP), in atrial extracts. Since then, Nppa, the gene encoding ANP, has become an important tool for molecular and developmental biologists. Expression of Nppa is an early and specific marker for the differentiating working myocardium of the atria and ventricles of the developing heart. Around the time of birth, ventricular Nppa expression is down-regulated, to be reactivated in response to a variety of cardiovascular disorders. Many aspects of the regulatory pathways that control Nppa gene expression during cardiac development or disease have been revealed. However, several fundamental issues remain to be resolved. Particularly, the regulatory mechanisms underlying the ventricular Nppa expression in the embryonic heart and the reactivation in the failing ventricle remain unclear. Here we review current knowledge on the transcriptional regulation of the Nppa gene.
Interfacial metal and antibody recognition (2005)

The unique ligation properties of metal ions are widely exploited by proteins, with approximately one-third of all proteins estimated to be metalloproteins. Although antibodies use various mechanisms for recognition, to our knowledge, none has ever been characterized that uses an interfacial metal. We previously described a family of CD4-reactive antibodies, the archetype being Q425. CD4:Q425 engagement does not interfere with CD4:HIV-1 gp120 envelope glycoprotein binding, but it blocks subsequent steps required for viral entry. Here, we use surface-plasmon resonance to show that Q425 requires calcium for recognition of CD4. Specifically, Q425 binding of calcium resulted in a 55,000-fold enhancement in affinity for CD4. X-ray crystallographic analyses of Q425 in the presence of Ca(2+), Ba(2+), or EDTA revealed an exposed metal-binding site, partially coordinated by five atoms contributed from four antibody complementarity-determining regions. The results suggest that Q425 recognition of CD4 involves direct ligation of antigen by the Q425-held calcium, with calcium binding each ligating atom of CD4 with approximately 1.5 kcal/mol of binding energy. This energetic contribution, which is greater than that from a typical protein atom, demonstrates how interfacial metal ligation can play a unique role in antigen recognition.
Purified cytochrome b from human granulocyte plasma membrane is comprised of two polypeptides with relative molecular weights of 91,000 and 22,000. (1987)

A new method has been developed for purification of cytochrome b from stimulated human granulocytes offering the advantage of high yields from practical quantities of whole blood. Polymorphonuclear leukocytes were treated with diisopropylfluorophosphate, degranulated and disrupted by nitrogen cavitation. Membranes enriched in cytochrome b were prepared by differential centrifugation. Complete solubilization of the cytochrome from the membranes was achieved in octylglucoside after a 1-M salt wash. Wheat germ agglutinin-conjugated Sepharose 4B specifically bound the solubilized cytochrome b and afforded a threefold purification. Eluate from the immobilized wheat germ agglutinin was further enriched by chromatography on immobilized heparin. The final 260-fold purification of the b-type cytochrome with a 20-30% yield was achieved by velocity sedimentation in sucrose density gradients. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of the purified preparation revealed two polypeptides of Mr 91,000 and Mr 22,000. Treatment of the 125I-labeled, purified preparation with peptide:N-glycosidase F, which removes N-linked sugars, decreased relative molecular weight of the larger species to approximately 50,000, whereas beta-elimination, which removes O-linked sugars, had little or no effect on the mobility of the Mr-91,000 polypeptide. Neither of the deglycosylation conditions had any effect on electrophoretic mobility of the Mr-22,000 polypeptide. Disuccinimidyl suberate cross-linked the two polypeptides to a new Mr of 120,000-135,000 by SDS-PAGE. Antibody raised to the purified preparation immunoprecipitated spectral activity and, on Western blots, bound to the Mr-22,000 polypeptide but not the Mr-91,000 polypeptide. Western blot analysis of granulocytes from patients with X-linked chronic granulomatous disease revealed a complete absence of the Mr-22,000 polypeptide. These results (a) suggest that the two polypeptides are in close association and are part of the cytochrome b, (b) provide explanation for the molecular weight discrepancies previously reported for the protein, and (c) further support the involvement of the cytochrome in superoxide production in human neutrophils.
High Prevalence of Human Papillomavirus in Prostate Tissues (1991)

Specific human papillomavirus (HPV) types are associated with benign and malignant lesions of the anogenital region including the prostate gland. Using polymerase chain reaction (PCR) amplification of type-specific HPV sequences, we have assessed the prevalence of HPV DNA in prostate tissue from 88 individuals. Amplified sequences specific for HPV 16 were found in 34 of 56 benign prostatic hyperplasias and in 14 of 27 prostatic carcinomas. In contrast, HPV 18 was identified in only three benign hyperplasias and one carcinoma, all of which also contained HPV 16 DNA. Four of five normal prostates obtained at autopsy had no detectable HPV infection; one contained HPV 16 sequences. No significant difference in the prevalence of HPV DNA is observed between patients with benign disease and those with evidence of malignancy when fragments of surgical material are analyzed. Surgical method (transurethral resection or suprapubic prostatectomy) had no effect on the frequency of HPV detection. The prevalence of HPV DNA in the small number of normal prostates analyzed was not significantly different from that in the surgical samples. The presence of HPV in prostate tissues suggests a possible reservoir for sexual transmission of types with oncogenic potential. A role for the virus in the etiology of prostatic neoplasia remains to be demonstrated.
High-refractive-index polymer coatings for optoelectronics applications (2004)

The performance of many solid-state devices including emissive displays, optical sensors, integrated optical circuits, and light-emitting diodes can be improved by applying a transparent high refractive index coating (&ge; 1.65) onto the light-emitting or light-sensing portion of the device. Ideally, the coating should combine the excellent durability and easy deposition of a spin-applied polymer coating with the high refractive index and optical clarity of a vacuum deposited metal oxide coating such as titanium dioxide or zirconium oxide. While some success has been achieved in combining these very dissimilar materials to form transparent hybrid coating systems, for example, using sol-gel or nanoparticle dispersion techniques, the resulting coating systems often require complicated manufacturing schemes and have limited storage stability and reliability. We have demonstrated two new approaches to development of high refractive index polymer coatings. In the first approach, an organometallic polymer and a conventional organic polymer are combined to form a compatible coating. When cured at elevated temperatures, the organometallic polymer decomposes to form a highly dispersed metal oxide phase that imparts high index properties to the final hybrid coating. The new coatings are transparent and have refractive indices ranging from 1.6 to as high as 1.9 depending on the metal oxide content. The second approach utilizes our discovery that polyimide materials possess naturally high refractive indices in comparison to most polymer materials. Through careful molecular design, we have developed a new class of polyimide materials having refractive indices ranging from 1.60 to 1.78 at visible wavelengths and exhibiting excellent optical clarity. The new polyimides can be spin-applied to a layer thickness of more than 10 microns in a single coating step and form thermally stable films with good mechanical strength and adhesion to device substrates.
Synthesis and Characterization of Thickness-Aligned Carbon Nanotube−Polymer Composite Films (2005)

To optimize the properties of carbon nanotube−polymer composites, it is important to control nanotube dispersion and alignment. One way to achieve such control is by growing homogeneous, well-aligned arrays of carbon nanotubes using chemical vapor deposition and infiltrating polymer or monomer into the arrays, followed by in situ polymerization. In this paper, pre-aligned multiwalled carbon nanotube arrays were infiltrated with methyl methacrylate (MMA) and the MMA was polymerized. The resulting composite films have well-dispersed, aligned nanotubes. Using the Washburn technique, it was found that the infiltration of monomers into aligned nanotube arrays is largely driven by the wetting of liquids against the nanotube walls and the low viscosity of liquids. Once polymerized, the PMMA had higher thermal stability. This synthesis process is adaptable to various polymers. It is possible to combine conventional micro-patterning techniques with infiltration process for achieving selective infiltration of polymer across nanotube arrays. Thus, the present synthesis strategy has tremendous implications toward building some of the novel architectures with nanotubes and polymers, having unique properties.
Identification and primary sequence of an unspliced human urokinase poly(A)+ RNA. (1984)

Human urokinase cDNA clones have been identified from a cDNA library prepared from total RNA of human fibroblasts transformed by simian virus 40 [Okayama, H. & Berg, P. (1983) Mol. Cell. Biol. 3, 280-289]. Synthetic oligonucleotides, corresponding to urokinase protein sequence, were used as probes. The cloned cDNA covers most of the coding sequence and the entire 3' untranslated region. The nucleotide sequence of one of the clones identifies this as a copy of a partially spliced polyadenylylated precursor to urokinase mRNA. The introns separate functionally different domains of the enzyme. Human urokinase mRNA has been identified by RNA blot and its size was estimated at 2500 nucleotides.
In-Cell Polymerase Chain Reaction: Strategy and Diagnostic Applications (2006)

In situ polymerase chain reaction (PCR) refers to the amplification of specific nucleic acid sequences and subsequent visualization of the PCR products in tissue sections. When PCR is performed in fixed cells in suspension the term in-cell PCR is normally applied instead. For example, in-cell PCR has been used for intracellular detection of specific viruses. Furthermore, in mixtures of cells in suspension with different genotypes, in-cell PCR may be used for intracellular detection of DNA or mRNA sequences specific for one of the genotypes/population of cells. An in-cell PCR method is described that makes it possible to genotype a specific gene of interest derived from one individual in a mixture of cells from two individuals. This new method is based on in-cell PCR and dependent upon the presence of a well characterized and specific DNA sequence or polymorphism, which has to be present only in the cells from the individual being genotyped for the gene sequence of interest. The in-cell PCR method might find diagnostic applications in detection of intracellular pathogenic sequences in subgroups of cells and in noninvasive prenatal genetic diagnoses with the use of the few fetal cells circulating in maternal blood.