gebhart/patrepeval huggingface dataset:
Analysis of aromatic catabolic pathways in <b><i>Pseudomonas putida</i></b> KT 2440 using a combined proteomic approach: 2‐DE/MS and cleavable isotope‐coded affinity tag analysis (2006)

Proteomic analysis of Pseudomonas putida KT2440 cultured in monocyclic aromatic compounds was performed using 2-DE/MS and cleavable isotope-coded affinity tag (ICAT) to determine whether proteins involved in aromatic compound degradation pathways were altered as predicted by genomic analysis (Jiménez et al., Environ Microbiol. 2002, 4, 824-841). Eighty unique proteins were identified by 2-DE/MS or MS/MS analysis from P. putida KT2440 cultured in the presence of six different organic compounds. Benzoate dioxygenase (BenA, BenD) and catechol 1,2-dioxygenase (CatA) were induced by benzoate. Protocatechuate 3,4-dixoygenase (PcaGH) was induced by p-hydroxybenzoate and vanilline. beta-Ketoadipyl CoA thiolase (PcaF) and 3-oxoadipate enol-lactone hydrolase (PcaD) were induced by benzoate, p-hydroxybenzoate and vanilline, suggesting that benzoate, p-hydroxybenzoate and vanilline were degraded by different dioxygenases and then converged in the same beta-ketoadipate degradation pathway. An additional 110 proteins, including 19 proteins from 2-DE analysis, were identified by cleavable ICAT analysis for benzoate-induced proteomes, which complemented the 2-DE results. Phenylethylamine exposure induced beta-ketoacyl CoA thiolase (PhaD) and ring-opening enzyme (PhaL), both enzymes of the phenylacetate (pha) biodegradation pathway. Phenylalanine induced 4-hydroxyphenyl-pyruvate dioxygenase (Hpd) and homogentisate 1,2-dioxygenase (HmgA), key enzymes in the homogentisate degradation pathway. Alkyl hydroperoxide reductase (AphC) was induced under all aromatic compounds conditions. These results suggest that proteome analysis complements and supports predictive information obtained by genomic sequence analysis.
Contributions to the Optimal Use of Human Blood (1983)

Investigations were performed concerning the elimination of the risk of hepatitis B transmission of potentially infectious plasma derivatives by the addition of a low dose of hepatitis B immunoglobulin (HBIg). To this end, clotting factor VIII concentrate, prothrombin complex, Cl esterase inhibitor concentrate, plasminogen and antithrombin III were prepared from plasma strongly positive for hepatitis B surface antigen (HBsAg). To one half of every preparation, HBIg was added up to a final concentration of 0.4 IU anti-HBs/ml (test preparations), the other half was not treated (control preparations). Furthermore, to 10^-3 diluted infectious reference plasma (Bureau of Biologies, FDA, USA), an overdose HBIg was added to a final concentration of about 0.4 IU anti-HBs/ml. 6 chimpanzees, injected either with the control plasma derivatives or with the untreated infectious reference plasma, were infected with hepatitis B virus, whereas 5 chimpanzees, injected either with the test plasma derivatives or the infectious reference plasma to which the HBIg had been added, did not show any evidence of hepatitis B infection during the follow-up of 1 year. Addition of a low dose of HBIg to potentially infectious plasma derivatives appears to be a reliable measure to eliminate the hepatitis B transmission and is preferred to other methods for labile plasma derivatives.
Active high resolution time delay estimation for large BT signals (1991)

Two different high-resolution time-delay estimation (HRTDE) methods, a temporal method and a frequency method, specially adapted to large bandwidth duration (BT) product time-resolvent signals, are described. The performance gain of these methods is shown to be about four times better in comparison with the classical time-delay resolution methods. The frequency HRTDE method is applied to real data obtained from an ocean acoustic experiment. Although classic methods cannot distinguish close signal components, the method presented yields estimates of the delay differences and the attenuation associated with each propagation path.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Molecular Design and Synthesis of 3-Oxocyclohexyl Methacrylate for ArF and KrF Excimer Laser Resist (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular Design and Synthesis of 3-Oxocyclohexyl Methacrylate for ArF and KrF Excimer Laser ResistKoji Nozaki, Yuko Kaimoto, Makoto Takahashi, Satoshi Takechi, and Naomichi AbeCite this: Chem. Mater. 1994, 6, 9, 1492–1498Publication Date (Print):September 1, 1994Publication History Published online1 May 2002Published inissue 1 September 1994https://pubs.acs.org/doi/10.1021/cm00045a004https://doi.org/10.1021/cm00045a004research-articleACS PublicationsRequest reuse permissionsArticle Views228Altmetric-Citations27LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
First-Order Transverse Phonon Deformation Potentials of Tetragonal Perovskites (2008)

A theoretical formalism is put forward with the aim of describing the softening of first-order transverse optical phonons in a strained tetragonal perovskitic lattice. On the basis of the dynamical equation for nondegenerate polar modes, the influence of oblique phonons could be first described by assuming a prevalence of short-range interatomic forces; then, the softening effect arising from external stress could be explicitly expressed as a function of orientation of the crystallographic texture. As a further step in the adopted formalism, the microstructure of a perovskitic polycrystal has been ideally modeled as an ensemble of mesocrystals, whose individual crystallographic directions corresponded to an average orientation over the unit volume of the probe. An experimental confirmation of the theoretical formalism is concurrently carried out, and phonon deformation potentials (PDP) have been directly measured for the first-order transverse phonon of a tetragonal PbZrTiO3 perovskite lattice.
Real time data transmission over GSM voice channel for secure voice & data applications (2004)

This paper describes a real time prototype implementation of a system, which enables secure voice and data communication over the GSM voice channel. The security of GSM is not guaranteed especially over the core network. The proposed system modulates digital data, which may be encrypted onto speech-like waveforms. The modulated waveform is then transmitted over the GSM voice channel, which can be demodulated and decrypted at the receiver. The real time prototype system has been tested on GSM-to-GSM voice calls, and a proprietary speech codec is used on the real time data channel to produce communication quality speech. A demonstration will be provided at the presentation. (4 pages)
Fibromodulin-Deficiency Alters Temporospatial Expression Patterns of Transforming Growth Factor-β Ligands and Receptors during Adult Mouse Skin Wound Healing (2014)

Fibromodulin (FMOD) is a small leucine-rich proteoglycan required for scarless fetal cutaneous wound repair. Interestingly, increased FMOD levels have been correlated with decreased transforming growth factor (TGF)-β1 expression in multiple fetal and adult rodent models. Our previous studies demonstrated that FMOD-deficiency in adult animals results in delayed wound closure and increased scar size accompanied by loose package collagen fiber networks with increased fibril diameter. In addition, we found that FMOD modulates in vitro expression and activities of TGF-β ligands in an isoform-specific manner. In this study, temporospatial expression profiles of TGF-β ligands and receptors in FMOD-null and wild-type (WT) mice were compared by immunohistochemical staining and quantitative reverse transcriptase-polymerase chain reaction using a full-thickness, primary intention wound closure model. During the inflammatory stage, elevated inflammatory infiltration accompanied by increased type I TGF-β receptor levels in individual inflammatory cells was observed in FMOD-null wounds. This increased inflammation was correlated with accelerated epithelial migration during the proliferative stage. On the other hand, significantly more robust expression of TGF-β3 and TGF-β receptors in FMOD-null wounds during the proliferative stage was associated with delayed dermal cell migration and proliferation, which led to postponed granulation tissue formation and wound closure and increased scar size. Compared with WT controls, expression of TGF-β ligands and receptors by FMOD-null dermal cells was markedly reduced during the remodeling stage, which may have contributed to the declined collagen synthesis capability and unordinary collagen architecture. Taken together, this study demonstrates that a single missing gene, FMOD, leads to conspicuous alternations in TGF-β ligand and receptor expression at all stages of wound repair in various cell types. Therefore, FMOD critically coordinates temporospatial distribution of TGF-β ligands and receptors in vivo, suggesting that FMOD modulates TGF-β bioactivity in a complex way beyond simple physical binding to promote proper wound healing.
A primer of diffusion problems (1989)

Partial table of contents: THE DIFFUSION EQUATION. Isotropic One-dimensional Random Walk. Elementary Properties of the Diffusion Equation. Higher Dimensions and Coordinate Systems. STEADY STATE EXAMPLES. The Steady State is Not the Equilibrium State. The Thermal Oxidation of Silicon. The Precipitation of Spherical Particles. DIFFUSION UNDER EXTERNAL FORCES. One-dimensional Anisotropic Random Walk. Diffusivity and Mobility Coefficients. An Introduction to Double-layers. SIMPLE TIME-DEPENDENT EXAMPLES. The Gaussian and One of Its Relatives. Two Applications of Error Functions to One-dimensional Phases. Crystal Growth under Conditions of Constant Cooling Rate. AN INTRODUCTION TO SIMILARITY. Boltzmann's Transformation. Boltzmann's Transformation and Variable Diffusivity. Analytic Solutions for Variable Diffusivity. A USER'S GUIDE TO THE LAPLACE TRANSFORM. Elementary Properties and Further Examples. The Convolution Theorem. A Few Words on Asymptotics. FURTHER TIME-DEPENDENT EXAMPLES. Laser Processing. Thermally Stimulated Diffusion. Application to the Numerical Solution for Nonlinear Surface Conditions. Appendix A: Random Walks in Higher Dimensions. Appendix B: The Phase Rule and Some of Its Consequences. Appendix C: Moments of Distributions and Asymptotic Behavior. Index.
Cardiac matrix metalloproteinase-2 expression independently induces marked ventricular remodeling and systolic dysfunction (2006)

Although enhanced cardiac matrix metalloproteinase (MMP)-2 synthesis has been associated with ventricular remodeling and failure, whether MMP-2 expression is a direct mediator of this process is unknown. We generated transgenic mice expressing active MMP-2 driven by the alpha-myosin heavy chain promoter. At 4 mo MMP-2 transgenic hearts demonstrated expression of the MMP-2 transgene, myocyte hypertrophy, breakdown of Z-band registration, lysis of myofilaments, disruption of sarcomere and mitochondrial architecture, and cardiac fibroblast proliferation. Hearts from 8-mo-old transgenic mice displayed extensive myocyte disorganization and dropout with replacement fibrosis and perivascular fibrosis. Older transgenic mice also exhibited a massive increase in cardiac MMP-2 expression, representing recruitment of endogenous MMP-2 synthesis, with associated expression of MMP-9 and membrane type 1 MMP. Increases in diastolic [control (C) 33 +/- 3 vs. MMP 51 +/- 12 microl; P = 0.003] and systolic (C 7 +/- 2 vs. MMP 28 +/- 14 microl; P = 0.003) left ventricular (LV) volumes and relatively preserved stroke volume (C 26 +/- 4 vs. MMP 23 +/- 3 microl; P = 0.16) resulted in markedly decreased LV ejection fraction (C 78 +/- 7% vs. MMP 48 +/- 16%; P = 0.0006). Markedly impaired systolic function in the MMP transgenic mice was demonstrated in the reduced preload-adjusted maximal power (C 240 +/- 84 vs. MMP 78 +/- 49 mW/microl(2); P = 0.0003) and decreased end-systolic pressure-volume relation (C 7.5 +/- 1.5 vs. MMP 4.7 +/- 2.0; P = 0.016). Expression of active MMP-2 is sufficient to induce severe ventricular remodeling and systolic dysfunction in the absence of superimposed injury.
Diazotization of Weakly Basic and Insoluble Amines. The Use of Pyridine, Quinoline and Isoquinoline as Solvents for the Amines (1936)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiazotization of Weakly Basic and Insoluble Amines. The Use of Pyridine, Quinoline and Isoquinoline as Solvents for the AminesClara deMilt and Gertrude van ZandtCite this: J. Am. Chem. Soc. 1936, 58, 10, 2044–2046Publication Date (Print):October 1, 1936Publication History Published online1 May 2002Published inissue 1 October 1936https://pubs.acs.org/doi/10.1021/ja01301a064https://doi.org/10.1021/ja01301a064research-articleACS PublicationsRequest reuse permissionsArticle Views332Altmetric-Citations9LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A distributed globally convergent algorithm for fair, queue-length-based congestion control (2003)

We present an easy-to-implement explicit rate congestion control algorithm for connection-oriented data networks. The algorithm is adaptive to changing network conditions, robust to network delays, and is decentralized. Further, it achieves max-min fairness and queue length stability under finite buffer length and minimum rate constraints. The proof of global convergence of the algorithm involves stability analysis of discrete-time linear systems with saturation.
Friction on ice: stick and slip (2012)

Faraday made investigations into behaviour of ice and snow. He was ahead of his time. Our paper briefly describes the current state of knowledge in ice friction and adhesion and its historical development. Important aspects of these phenomena in engineering, winter sports and the natural environment are considered. We report new results for static and dynamic friction of a metal (steel) and a polymer (PMMA) on ice over a range of temperatures (-3 to -13 degrees C), and interpret the behaviour by considering processes that operate at the interface and in the bulk of the materials. Clearly the chemical and thermomechanical properties of steel, PMMA and ice differ. The thermomechanical properties of ice itself also vary within the temperature range examined. We find higher static friction with increasing time, and a curious difference in the behaviour of the metal and polymer with temperature. We explain the results by considering the materials' stiffness, plastic deformation and creep, the ductile/brittle transition in ice, thermal properties, physicochemical properties of the surfaces and the real area of contact.
Computational‐fluid‐dynamics (CFD) analysis of mixing and gas–liquid mass transfer in shake flasks (2004)

CFD (computational fluid dynamics) techniques were used to predict mixing and gas-liquid mass transfer in a 250 ml shake flask operating over a range of shaking frequencies between 100 and 300 rev./min, shaking diameters between 20 and 60 mm, and fill volumes between 25 and 100 ml. Interfacial area, a, volumetric mass-transfer coeffcient, kLa, and the power input per unit volume, epsilonv, of the liquid were predicted to be 300<a<800 m2 . m(-3), 10<kLa<100 h(-1) and 40<epsilonv<600 W . m(-3) respectively. These values are significantly different from the reported range for laboratory and pilot-scale bioreactors used in the fermentation of bacterial and fungal micro-organisms (100<a<300 m2 . m(-3), 100<kLa<400 h(-1) and 1000<epsilonv<3000 W . m(-3)). Our analysis showed that, at the highest shaking frequency and amplitude of operation, the specific power input in the shake flask was much lower than in laboratory bioreactors. Bacterial and fungal micro-organisms require dissolved oxygen concentrations typically in the range 50-250 mmol of O2 . h(-1) . litre(-1), corresponding to volumetric mass-transfer coefficients, kLa, in the range of 250-400 h(-1). Poor mixing and dissolved-oxygen limitation in shake flasks may limit their use in process design and media optimization in fermentation. In contrast, mammalian cells have relatively low demand for oxygen and consequently require a lower specific power input, this being typically between 1 and 10 W . m(-3), allowing efficient operation in shake flasks. Experimental data presented as part of the present study showed that mammalian cell growth in shake flasks was essentially independent of the specific power input, the maximum specific cell growth rate being 0.056 h(-1). The corresponding maximum oxygen-uptake rate was 0.74 mmol of O2 . h(-1) . litre(-1) for a viable cell count of 1.3 x 10(6) cells . ml(-1). These values are comparable with reported values for laboratory and pilotscale bioreactors. This analysis suggests that growth of mammalian cells in shake flasks (and hence in laboratory bioreactors) is not limited by the gas-liquid mass-transfer rate. In mammalian cell cultures, the requirement for good mixing is driven by other considerations, including the need for good cell suspension and reduction in heterogeneity, for example, in pH, temperature, nutrient concentration, osmolality and lactate/glucose ratio.
Returnable GPS Sonde (1998)

This note is intended to discuss the returnable Global Positioning System (GPS) sonde (RGS). RGS, adopting the shape of an aircraft, is 700–1000 g in weight. RGS is carried up into the air by a balloon and continuously transmits atmospheric temperature, humidity, and wind data to the ground. As soon as the balloon bursts or stops rising, RGS will get detached from it and glide back, under the guidance of GPS data and the control of CPU, to the ground station or the preset recovering spot. The flight and the landing are completely autonomous. Since the returned RGS can be repeatedly used, the cost of air sounding could be reasonably reduced.
A Method for Representing Data Items of Unlimited Length in a Computer Memory (1981)

In this paper, a recursive data structure is defined which permits a data item of-unlimited length to be represented in a computer memory. The encoded data are a linear string of symbols which contains a specification of the length of the data item and the data item itself. In a single forward scan of the encoded data string, the length of the data item can be determined and the data item located and/or extracted.
The Effect of Soybean Protein on Bone Loss in a Rat Model of Postmenopausal Osteoporosis. (1998)

This study was designed to investigate the modulatory effect of dietary soybean protein on the skeleton of an ovariectomized rat model with postmenopausal osteoporosis. Thirty-two female Sprague-Dawley rats were weight matched and divided into the following four experimental groups: Soy group, ovariectomized and fed soy protein diet; Estrogen group, ovariectomized, fed casein diet and injected with estrogen; Casein group, ovariectomized and fed casein diet; and Sham group, sham-operated and fed casein diet. The diets and estrogen were started two weeks after surgery, and continued for four weeks. Rats in the Sham, Soy and Estrogen groups had significantly higher (p<0.05) femur and tibia ash content than those in the Casein group. Accordingly, the calcium content of the tibia and femur were also significantly higher (p<0.05) in the Soy, Estrogen and Sham groups as compared to the Casein group. Serum total and bone-type alkaline phosphatase levels were both significantly lower (p<0.05) in the Estrogen and Sham groups in relation to the Soy and Casein groups. This study demonstrated that a 22% soybean protein diet could be just as effective as daily estrogen administration in suppressing bone loss due to ovariectomy. However, unlike estrogen, soy protein diet did not have any uterotrophic effect and did not decrease the markers of bone turnover measured, suggesting a possible difference in the mechanism of action.
Minimization of Inertia-Induced Forces in Spherical Four-Bar Mechanisms. Part 1: The General Spherical Four-Bar Linkage (1983)

Computer-aided design procedures have been developed for the optimum mass distribution of the links of high-speed spherical four-bar linkages. The analysis, which includes a quadratic-programming technique, allows an optimum trade-off between shaking forces, shaking moments, bearing reactions, and input-torque fluctuation. The results are illustrated in the case of a Hooke joint and a wobble-plate linkage.
Tensile and Compressive Properties of the Medial Rabbit Meniscus (2005)

Quantification of the material properties of the meniscus is of paramount importance, creating a 'gold-standard' reference for future tissue engineering research. The purpose of this study was to determine the compressive and circumferential tensile properties in the rabbit meniscus. Creep and recovery indentation experiments were performed on the meniscus using a creep indentation apparatus and analysed via a finite element optimization method to determine the compressive material properties at six topographical locations. Tensile properties of samples taken circumferentially from the rabbit meniscus were also examined. Results show that the femoral side of the anterior portion exhibits the highest aggregate modulus (510 +/- 100 kPa) and shear modulus (240 +/- 40 kPa), while the lowest aggregate modulus (120 +/- 30 kPa) and shear modulus (60 +/- 20 kPa) were found on the femoral side of the posterior location. Values of 156.6 +/- 48.9 MPa for Young's modulus and of 21.6 +/- 7.0 MPa for the ultimate tensile strength of were found from the tensile samples, which are similar to the values found in other animal models. These baseline values of material properties will be of help in future tissue engineering efforts.