Relevant bibliographies by topics / Metabolic P system

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
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Academic literature on the topic 'Metabolic P system'

Author: Grafiati
Published: 11 March 2023

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Journal articles on the topic "Metabolic P system"

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Kulakovskis, Darius, and Dalius Navakauskas. "Automated Metabolic P System Placement in FPGA." Electrical, Control and Communication Engineering 10, no. 1 (July 1, 2016): 5–12. http://dx.doi.org/10.1515/ecce-2016-0001.

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Abstract An original Very High Speed Integrated Circuit Hardware Description Language (VHDL) code generation tool that can be used to automate Metabolic P (MP) system implementation in hardware such as Field Programmable Gate Arrays (FPGA) is described. Unlike P systems, MP systems use a single membrane in their computations. Nevertheless, there are many biological processes that have been successfully modeled by MP systems in software. This is the first attempt to analyze MP system hardware implementations. Two different MP systems are investigated with the purpose of verifying the developed software: the model of glucose–insulin interactions in the Intravenous Glucose Tolerance Test (IVGTT), and the Non-Photochemical Quenching process. The implemented systems’ calculation accuracy and hardware resource usage are examined. It is found that code generation tool works adequately; however, a final decision has to be done by the developer because sometimes several implementation architecture alternatives have to be considered. As an archetypical example serves the IVGTT MP systems’ 21–23 bits FPGA implementation manifesting this in the Digital Signal Processor (DSP), slice, and 4-input LUT usage.
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Kulakovskis, Darius. "APPLICATION PROSPECTS OF METABOLIC P SYSTEM / METABOLINĖS P SISTEMOS TAIKYMO GALIMYBĖS." Mokslas – Lietuvos ateitis 7, no. 3 (July 13, 2015): 285–90. http://dx.doi.org/10.3846/mla.2015.784.

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Metabolic P (MP) systems are a class of P systems and are based on metabolic process which is used by living organisms. We review for the purpose of experimental research the MP system development, implementation and modeling. To implement MP systems in dedicated hardware, some specifications need to be determined. We look into the possibility of modeling MP systems in fixed point arithmetic capable hardware and determine the minimal needed bit count for selected MP system model. A way to improve the accuracy of fixed point calculations is proposed, which includes the modification of MP grammar. This modification is done using a simple rule to multiply and divide constants in MP grammar equations. The resulting calculations have more than 250 times smaller error when compared to original calculations. When investigating the performance of MP calculations, it is determined that the time needed for all calculations to finish depends linearly on the number of modeled systems. Metabolinė P sistema yra P sistemos klasė, pagrįsta metabolinio proceso, būdingo gyviesiems organizmams, taikymu. Siekiant pasirengti įgyvendinti MP sistemas aparatine įranga, pateikiama MP sistemų kūrimo, įgyvendinimo ir modeliavimo literatūros analitinė apžvalga. Įvertinama galimybė modeliuoti MP sistemas taikant fiksuotojo kablelio aritmetiką. Imitaciniais eksperimentais nustatytas minimalus pasirinktam MP sistemos modeliui taikyti reikiamas žodžių ilgis. Pasiūlytas būdas fiksuotosios aritmetikos skaičiavimo tikslumui padidinti. Šio būdo esmė yra MP gramatikos modifikavimas pagal konstantų daugybos ir dalybos taisyklę. Skaičiavimus atliekant modifikuota sistema, paklaida esti daugiau nei 250 kartų mažesnė. Tiriant MP sistemų našumą nustatyta, kad skaičiavimo trukmė tiesiškai priklauso nuo modeliuojamų sistemų skaičiaus.
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Manca, Vincenzo, Roberto Pagliarini, and Simone Zorzan. "A photosynthetic process modelled by a metabolic P system." Natural Computing 8, no. 4 (October 17, 2008): 847–64. http://dx.doi.org/10.1007/s11047-008-9104-x.

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Pagliarini, Roberto, Giuditta Franco, and Vincenzo Manca. "An Algorithm for Initial Fluxes of Metabolic P Systems." International Journal of Computers Communications & Control 4, no. 3 (September 1, 2009): 263. http://dx.doi.org/10.15837/ijccc.2009.3.2434.

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A central issue in systems biology is the study of efficient methods inferring fluxes of biological reactions by starting from experimental data. Among the different techniques proposed in the last years, the theory of Metabolic P systems, which is based on the Log-Gain principle, proved to be helpful for deducing biologi- cal fluxes from temporal series of observed dynamics. According to this approach, the algebraic systems provided by the Log-Gain principle determine the reaction fluxes underlying a system dynamics when initial fluxes are known. Here we propose a heuristic algorithm for estimating the initial fluxes, that is tested in two case studies.
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Melanson, Edward L., Patty S. Freedson, Devra Hendelman, and Edward Debold. "Reliability and Validity of a Portable Metabolic Measurement System." Canadian Journal of Applied Physiology 21, no. 2 (April 1, 1996): 109–19. http://dx.doi.org/10.1139/h96-010.

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The purpose of this study was to assess the reliability and validity of a portable metabolic system (TEEM 100) during submaximal and maximal [Formula: see text] exercise using a computer-based metabolic system as the reference system (REF). Between repeated trials of submaximal exercise at three constant loads, differences in ventilation [Formula: see text] and oxygen consumption [Formula: see text] were 0.2 ± 4.9 L∙min−1 and 0.03 ± 0.10 L∙min−1 for REF, and 1.9 ± 0.7 L∙min−1 and 0.00 ± 0.17 L∙min−1 for TEEM 100. Pooled intraclass reliability coefficients for [Formula: see text] and [Formula: see text] calculated from the repeated submaximal trials were r =.89 and r =.94 for REF, and r =.86 and r =.94 for the TEEM 100. Respiratory exchange ratio (RER) measured by the TEEM 100 was significantly higher (p =.01) at only the lowest workload. At [Formula: see text], the TEEM 100 recorded significantly higher values for FeO2 (p =.01) and RER (p <.001). These results suggest that the TEEM 100 provides reliable and valid measurements of [Formula: see text] during submaximal and maximal exercise. Key words: oxygen consumption, indirect calorimetry, portable analysis, exercise, metabolism
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Ainegren, Mats, Kurt Jensen, and Hans Rosdahl. "Breathing resistance in automated metabolic systems is high in comparison with the Douglas Bag method and previous recommendations." Proceedings of the Institution of Mechanical Engineers, Part P: Journal of Sports Engineering and Technology 232, no. 2 (June 30, 2017): 122–30. http://dx.doi.org/10.1177/1754337117715946.

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The purpose of this study was to investigate the resistance to breathing in metabolic systems used for the distribution and measurement of pulmonary gas exchange. A mechanical lung simulator was used to standardize selected air flow rates ([Formula: see text], L/s). The delta pressure (Δ p, Pa) between the ambient air and the air inside the equipment was measured in the breathing valve’s mouthpiece adapter for four metabolic systems and four types of breathing valves. Resistance for the inspiratory and expiratory sides was calculated as RES = (Δ p/[Formula: see text]) Pa/L/s. The results for resistance showed significant ( p < 0.05) between-group variance among the tested metabolic systems, breathing valves, and between most of the completed [Formula: see text]. The lowest resistance among the metabolic systems was found for a Douglas Bag system which had approximately half of the resistance compared to the automated metabolic systems. The automated systems were found to have higher resistance even at low [Formula: see text] in comparison with previous findings and recommendations. For the hardware components, the highest resistance was found for the breathing valves, while the lowest resistance was found for the hoses. The results showed that resistance in metabolic systems can be minimized through conscious choices of system design and hardware components.
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MANCA, VINCENZO, and LUCA MARCHETTI. "LOG-GAIN STOICHIOMETRIC STEPWISE REGRESSION FOR MP SYSTEMS." International Journal of Foundations of Computer Science 22, no. 01 (January 2011): 97–106. http://dx.doi.org/10.1142/s0129054111007861.

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MP systems are a class of P systems introduced for modeling metabolic processes. Here a regression method is presented for deducing a MP system exhibiting the dynamics of an observed metabolic system. In the procedure here described the knowledge of the stoichiometry of the system is combined with the log-gain principle of MP systems and is integrated with the Least Square Estimation method and with the stepwise regression approximation.
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Singh, Arushi, Poonam Mani, Shashi Prateek, Lalita Yadav, and Eshna Gupta. "Impact of levonorgestrel intrauterine system on metabolic parameters." International Journal of Reproduction, Contraception, Obstetrics and Gynecology 8, no. 3 (February 26, 2019): 830. http://dx.doi.org/10.18203/2320-1770.ijrcog20190433.

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Background: Hormonal contraceptive is suggested to affect parameters like body mass index, body weight, blood pressure (BP), blood sugar, lipid protein, and liver function test (LFT) but effect of LNG-IUS on those parameters is still uncertain. The aim of the present study was to study the effects of LNG-IUS on the metabolic parameters.Methods: Sixty women who opted for LNG-IUS for various indications were included in the study. Lipid profile, liver function tests (LFT), glucose levels [fasting and post prandial (PP)], and hemoglobin (Hb) were tested. Bimanual genital examination and transvaginal-ultrasonography was done prior to LNG-IUS insertion. Any problems observed were recorded. The subjects were re-evaluated after 6 and 9 months on their subsequent visits. Data were analyzed using paired “t” test. P value of <0.05 was considered statistically significant.Results: Mean age of the patients was 35.5±6.79 years. Maximum number 50 (83.3%) had abnormal uterine bleeding (ovulatory dysfunction, endometrial, iatrogenic, not yet classified) [AUB (OEIN)]. Mean pictorial blood loss assessment chart (PBAC) score of patients was 164.7±56.72 and mean Hb level 11.15±1.75g/dL. LNG-IUS showed no significant adverse effects on anthropometric parameters at 6- and 9-month follow-up. Significant change was seen in total cholesterol (TC), very low-density lipoprotein (VLDL) and high density lipoproteins (HDL) values at follow-up (p<0.0001).Conclusions: In conclusion, amongst Asian population, the LNG-IUS does not have any adverse effects on metabolic parameters, TGs, LDL and blood sugar levels.
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Becker, Wolfgang, Lukas Braun, Rodrigo Suarez-Ibarrol, and Arkadiusz Miernik. "Metabolic Imaging by Simultaneous FLIM of NAD(P)H and FAD." Current Directions in Biomedical Engineering 6, no. 3 (September 1, 2020): 254–56. http://dx.doi.org/10.1515/cdbme-2020-3064.

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AbstractWe describe a metabolic imaging system based on simultaneous recording of lifetime images of NAD(P)H and FAD. The system uses one-photon excitation by ps diode lasers, scanning by galvanometer mirrors, confocal detection, and two parallel TCSPC FLIM recording channels. Two lasers, with wavelengths of 375nm and 410 nm, are multiplexed to alternatingly excite NAD(P)H and FAD. One FLIM channel detects in the emission band of NAD(P)H, the other in the emission band of FAD. For both channels, the data analysis delivers images of the amplitudes of the decay components, a1 and a2. We show that these are robust parameters to characterize the metabolic state of cells. FLIM results obtained from excised human-bladder tissue were in perfect agreement with histology.
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Pogadayev, Daniil Vladimirovich, Larisa Аnatoliyevna Miniaylo, and Svetlana Viktorovna Gridneva. "ASSESSMENT OF OXIDATIVE METABOLIC SYSTEM PARAMETERS AFTER CORRECTION WITH THE FLAVONOID DIHYDROQUERCETIN." Scientific medical Bulletin of Ugra 32, no. 2 (2022): 181–83. http://dx.doi.org/10.25017/2306-1367-2022-32-2-181-183.

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A total of 71 residents, living for more than 10 years in the Khanty-Mansiysk Autonomous Region with poor-quality water treatment and not employed in the manufacturing sector, were examined: 29 (40,8%) men and 42 (59,2%) women, average age 38,3 ± 8,9 years. The indicators of POL above the reference values, and AOZ – below the physiologically optimal values were established. After receiving for metabolic correction antioxidant drug dihydroquercetin for a month there was a statistically significant decrease in primary (GPl, p=0.025) and secondary (TBA-AP, p=0,049) of LPO products, significant 1,8-fold increase of total antioxidant activity (p<0,001), statistically significant increase of thiol status almost 1,2 times (p=0,036), decrease of COP more than 3 times (p<0,001).
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Dissertations / Theses on the topic "Metabolic P system"

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McConn, Donavon J. "Metabolic and inhibitory differences between cytochromes P450 3A4 and 3A5 /." Thesis, Connect to this title online; UW restricted, 2001. http://hdl.handle.net/1773/7980.

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Dai, Yang. "Impact of the CYP3A5 polymorphism on the metabolic disposition of calcineurin inhibitors /." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/7935.

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Dickmann, Leslie J. "Characterization of CYP2C9 residues important for conferring substrate specificity and inter-individual variability in drug metabolism /." Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/8184.

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Hutzler, James Matthew. "Factors affecting CYP2C9-mediated metabolism." Morgantown, W. Va. : [West Virginia University Libraries], 2001. http://etd.wvu.edu/templates/showETD.cfm?recnum=2204.

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Thesis (Ph. D.)--West Virginia University, 2001.
Title from document title page. Document formatted into pages; contains viii, 199 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references (p. 176-195).
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Wennerholm, Agneta. "Characteristics of cytochrome P450-catalysed drug metabolism with focus on a black Tanzanian population /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-697-9/.

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Wurden, Colleen J. "Metabolism of carbamazepine and inhibitory drug interactions /." Thesis, Connect to this title online; UW restricted, 2000. http://hdl.handle.net/1773/7977.

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Ayscue, Robyn Renee. "Computer modeling of dapsone-mediated heteroactivation of flurbiprofen metabolism by CYP2C9." Morgantown, W. Va. : [West Virginia University Libraries], 2008. https://eidr.wvu.edu/etd/documentdata.eTD?documentid=5642.

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Thesis (Ph. D.)--West Virginia University, 2008.
Title from document title page. Document formatted into pages; contains viii, 174 p. : ill. (some col.). Includes abstract. Includes bibliographical references (p. 164-174).
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O'Mahony, Brian. "Clinical and toxicological significance of the involvement of the cytocrhome p450 system in the metabolism of 3,4-methylenedioxymethamphetamine." Doctoral thesis, Universitat Pompeu Fabra, 2008. http://hdl.handle.net/10803/7209.

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La 3,4-metilenodioximetanfetamina (MDMA, éxtasis) es una anfetamina sustituida de consumo frecuente y abusivo. La enzima principal que participa en el metabolismo de fase I de la MDMA, la isoforma 2D6 (CYP2D6) del citocromo P450, resulta también inhibida por la MDMA. Además, ésta es a la vez metabolizada por otras isoformas de CYP, por ejemplo la CYP1A2. La contribución de esta enzima y los posibles cambios en su actividad tras una administración de MDMA nunca han sido estudiados in-vivo. En consecuencia, se realizó un ensayo clínico donde los marcadores, dextrometorfano y cafeína se administraron tras una dosis oral de MDMA. En base a la farmacocinética de ambos marcadores se evaluaron posibles cambios en la actividad de las enzimas. En base al ratio metabólico urinario de dextrometorfano i dextrorfano (MR) se calculó la vida-media de degradación de CYP2D6. Tras una dosis de MDMA, el Cmax i AUC del dextrometorfano aumentó aproximadamente 10 veces con la correspondiente disminución en los parámetros farmacocineticos de dextrorfano. Se aumentó el MR casi 100 veces después de una dosis de MDMA, con un 67% de los sujetos superando la antimoda de 0.3 para la asignación del fenotipo de metabolizador lento de CYP2D6. La actividad de CYP2D6 se recuperó después de 10 días con una vida media de degradación de CYP2D6 de 46.6 h. La farmacocinética de la cafeína y sus metabolitos no fue afectada por la MDMA. Se debería avisar los consumidores de MDMA de las consecuencias de tal inhibición. A pesar de que hay muchas evidencias en animales sugiriendo que el MDMA es una neurotoxina serotonergica, todavía hay mucho debate sobre cuál es la causa de estos cambios cerebrales a largo plazo. La investigación apunta a la producción excesiva de especies reactivos de oxigeno (ROS) en el cerebro después de la administración de MDMA. La MDMA induce hipertermia, la liberación excesiva de dopamina cerebral y lleva a la desregulación energética del metabolismo. Conjuntamente, el metabolismo de MDMA produce un catecol reactivo, cuyos productos causan neurotoxicidad serotonergica en ratas. Cualquiera de los factores anteriores podrían ser la causa de la excesiva producción de ROS y los consecuentes cambios serotonergicos. A tenor de estas hipótesis, se investigó si diferentes temperaturas corporales afectarían el metabolismo de MDMA. Se administró MDMA a ratas a tres temperaturas ambientales distintas con el fin de prevenir o exacerbar la hipertermia inducida por MDMA. Se determinaron las concentraciones plasmáticas de MDMA y sus metabolitos principales durante las 6 h posteriores a la administración de la droga. Después de siete días, se sacrificaron los animales y se determinaron las cantidades de índoles cerebral. La administración de MDMA a 15ºC bloqueó la respuesta hipertermica y la disminución a largo plazo de 5-HT encontrada en ratas administradas a 21.5 ºC. A 15ºC, las concentraciones plasmáticas de MDMA aumentaron significativamente mientras que las concentraciones de sus metabolitos disminuyeron en comparación con ratas administradas a 21.5ºC. En contraste, la hipertermia y las deficiencias de indoles fueron exacerbadas en ratas tratadas a 30ºC. Se observó que las concentraciones plasmáticas de metabolitos de MDMA aumentaron significativamente en estos animales. La depleción a largo plazo de 5-HT no estuvo potenciada por la perfusión intrastriatal de MDMA después de una dosis sistémica de MDMA. Además, la interferencia del metabolismo de MDMA con la administración del inhibidor de catecol-o-metiltransferasa, entacapona, potenció la neurotoxicidad de MDMA, indicando que los metabolitos que son sustratos para este enzima podrían contribuir a la neurotoxicidad. Estos resultados tienen implicaciones tanto con el papel de la temperatura en el mecanismo del desarrollo de la neurotoxicidad del MDMA como en el abuso en humanos donde la hipertermia esta asociado con casos de toxicidad aguda. Se ha sugerido también que la causa de la depleción de 5-HT por MDMA es debido a un aumento de niveles de tirosina en el cerebro, cuyo hidroxilación no enzimática conduce a la formación de radicales libres derivados de la dopamina. En consecuencia, se propuso que el metabolismo de MDMA en compuestos pro-oxidantes fuera el paso limitante del proceso. En una serie de experimentos se encontraron niveles más altos de hipertermia aguda, concentraciones plasmáticas de tirosina, MDMA y sus metabolitos después de una dosis toxica de MDMA (15 mg/kg i.p.) versus una dosis no-toxica (7.5 mg/kg i.p.). La administración de una dosis no-toxica de MDMA (7.5 mg/kg i.p.) en conjunto con L-tirosina (0.2 mmol/kg i.p.) produció un aumento similar de niveles de tirosina en el suero con los niveles encontrados tras una dosis toxica de MDMA, sin embargo, los niveles de 5-HT cerebral permanecieron en niveles normales. Una dosis no-toxica de MDMA en combinación con una dosis alta de tirosina (0.5 mmol/kg i.p.) causó depleciones a largo plazo en ratas administradas a 21.5ºC pero no a 15ºC, condiciones conocidas por disminuir el metabolismo de MDMA. Al mismo tiempo, la perfusión estriatal de MDMA en combinación con tirosina (0.5 mmol/kg i.p.) en ratas hipertermicas no causaron depleciones de 5-HT. En contraste, se observaron reducciones significativas en 5-HT cerebral tras la administración de una dosis no-toxica de MDMA en ratas en condiciones de hipertermia en combinación con entacapona o acivisina, compuestos capaces de interferir con el metabolismo de MDMA o aumentar la disponibilidad de sus metabolitos en el cerebro, respectivamente. En conjunto estos datos indican que a pesar de que la tirosina y la hipertermia pueden contribuir a la neurotoxicidad inducida por la MDMA, el metabolismo de la droga parece ser el paso limitante.
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Ufer, Mike. "The in-vitro and in-vivo metabolism of the oral anticoagulant phenprocoumon as influenced by genetic polymorphisms of cytochrome P4502C9 /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7140-172-5/.

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Kabulski, Jarod L. "Development of Au-immobilized P450 platform for exploring the effect of oligomer formation on P450-mediated metabolism for In vitro to In vivo drug metabolism predictions." Morgantown, W. Va. : [West Virginia University Libraries], 2010. http://hdl.handle.net/10450/10892.

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Thesis (Ph. D.)--West Virginia University, 2010.
Title from document title page. Document formatted into pages; contains xiv, 180 p. : ill. (some col.). Includes abstract. Includes bibliographical references.
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Books on the topic "Metabolic P system"

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1935-, Bock K. W., ed. Hepatic metabolism and disposition of endo- and xenobiotics: Proceedings of the 57th Falk Symposium held in Freiburg-im-Breisgau, Germany, October 8-10, 1990. Dordrecht: Kluwer Academic Publishers, 1991.

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Ahlström, Marie. Cytochrome P450, metabolism and inhibition: Computational and experimental studies. Göteborg: Göteborg University, 2007.

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Cozza, Kelly L. Quick guide to the Cytochrome P450 system: Overview of drug interaction principles. Washington, DC: American Psychiatric Pub., 2002.

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S, Lee Jae, Obach R. Scott, and Fisher Michael B, eds. Drug metabolizing enzymes: Cytochrome P450 and other enzymes in drug discovery and development. Lausanne, Switzerland: FontisMedia SA, 2003.

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Cozza, Kelly L. Concise guide to the cytochrome P450 system: Drug interaction principles for medical practice. Washington, DC: American Psychiatric Pub., 2001.

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Emel, Arinç, Schenkman John B, Hodgson Ernest 1932-, and NATO Advanced Study Institute on Molecular Aspects of Drug Metabolizing Enzymes (1993 : Kus̜adası, Turkey), eds. Molecular aspects of oxidative drug metabolizing enzymes: Their significance in environmental toxicology, chemical carcinogenesis, and health. Berlin: Springer-Verlag, 1995.

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B, Matchar David, United States. Agency for Healthcare Research and Quality., and Duke University Evidence-based Practice Center., eds. Testing for cytochrome P450 polymorphisms in adults with non-psychotic depression treated with selective serotonin reuptake inhibitors (SSRIs). Rockville, MD: Agency for Healthcare Research and Quality, 2007.

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(Editor), Karl-Walter Bock, W. Gerok (Editor), and S. Matern (Editor), eds. Hepatic Metabolism and Disposition of Endo- and Xenobiotics (Falk Symposium). Springer, 1991.

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Drug Metabolism Enzymes. Marcel Dekker, 2003.

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Neil B., M.d. Sandson. Drug Interactions Casebook: The Cytochrome P450 System and Beyond. American Psychiatric Publishing, 2003.

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Book chapters on the topic "Metabolic P system"

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Castellini, Alberto, Vincenzo Manca, and Yasuhiro Suzuki. "Metabolic P System Flux Regulation by Artificial Neural Networks." In Membrane Computing, 196–209. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-11467-0_15.

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Lombardo, Rosario, and Vincenzo Manca. "Arithmetical Metabolic P Systems." In Lecture Notes in Computer Science, 284–94. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-21344-1_30.

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Karp, Frank, and Rodney Croteau. "Hydroxylation of (-)-β-Pinene and (-)-α-Pinene by a Cytochrome P-450 System from Hyssop (Hyssopus Officinalis)." In Secondary-Metabolite Biosynthesis and Metabolism, 253–60. Boston, MA: Springer US, 1992. http://dx.doi.org/10.1007/978-1-4615-3012-1_17.

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Manca, Vincenzo. "Log-gain Principles for Metabolic P Systems." In Algorithmic Bioprocesses, 585–605. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-540-88869-7_28.

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Castellini, Alberto, and Vincenzo Manca. "MetaPlab: A Computational Framework for Metabolic P Systems." In Membrane Computing, 157–68. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-540-95885-7_12.

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Ermakova, Inna, Alexey Leontievsky, Alexey Sviridov, Tatyana Shushkova, and Dmitriy Epiktetov. "Catabolism of organophosphonates: biochemistry, physiology and interactions of degrading bacteria in the environment." In ORGANOPHOSPHORUS NEUROTOXINS, 253–87. ru: Publishing Center RIOR, 2020. http://dx.doi.org/10.29039/42_253-287.

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The major contribution of microorganisms in metabolism of natural and synthetic phosphonates, the biochemical bases of these processes and possible interactions between degrading bacteria in natural and anthropogenic ecosystems are presented in the light of the recent data on significant role of reduced phosphorus compounds in the biosphere. Special emphasis is placed on C-P lyase and phosphonatase which are pivotal enzyme systems for catabolism of both natural and synthetic phosphonates. Modern data on structure, diversity, regulation and physiological role of both enzymes are reviewed and discussed.
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Dahl, Alan R. "The Effect of Cytochrome P-450-Dependent Metabolism and Other Enzyme Activities on Olfaction." In Molecular Neurobiology of the Olfactory System, 51–70. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4613-0989-5_3.

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Barrett, M., N. Polge, R. Baerg, L. Bradshaw, and C. Poneleit. "Role of Cytochrome P-450s in Herbicide Metabolism and Selectivity and Multiple Herbicide Metabolizing Cytochrome P-450 Activities in Maize." In Regulation of Enzymatic Systems Detoxifying Xenobiotics in Plants, 35–50. Dordrecht: Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-015-8927-7_4.

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Brđanović, Damir. "Effect of Poly-phosphate Limitation on the Anaerobic Metabolism of Bio-P Bacteria." In Modeling Biological Phosphorus Removal in Activated Sludge Systems, 195–205. London: CRC Press, 2021. http://dx.doi.org/10.1201/9780429332234-8.

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Chen, Bohang. "A Historico-Logical Re-assessment of Hans Driesch’s Vitalism." In History, Philosophy and Theory of the Life Sciences, 49–65. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-12604-8_4.

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AbstractToday vitalism is widely dismissed as a metaphysical heresy. For instance, Brigandt and Love (Reductionism in biology. In: Zalta EN (ed) The stanford encyclopedia of philosophy, 2017) claimed that “the denial of physicalism by vitalism, the doctrine that biological systems are governed by forces that are not physico-chemical, is largely of historical interest” (p. 3). Perhaps the most “infamous” vitalist is the German biologist Hans Driesch. However, Driesch (In Rádl E (ed) Actes du Huitième Congrès International de Philosophie a Prague 2–7 septembre 1934. Comité d’Organisation du Congrès, Prague, pp 10–30, 1936) himself very explicitly stated that his vitalism is “neither ‘mysticism’[…]nor ‘metaphysics’” (p. 27). So, in order to address the mismatch between the present conception of vitalism and his own, I seek to offer a historico-logical re-assessment of Driesch’s vitalism. From the historical point of view, I show that Driesch had provided long ignored theoretical reflections on the nature of entelechy (the central concept in his vitalism), especially those in relation to evolution and physics. From the logical point of view, following logical empiricists (Phillipp Frank and Rudolf Carnap), I indicate that Driesch’s vitalism should be rejected due to its lack of vital laws, at least with respect to current biology; it is an unestablished theory rather than a metaphysical heresy. Ironically, some current theoretical biologists have proposed similar theories (or principles and laws) of life, even though they (incoherently) reject Driesch’s vitalism. In the end, I briefly conclude that the failure of vitalism actually alludes to the fact that even today we understand very little about the nature of life (I mean, the pure concept/phenomenon of life!) (While I cannot elaborate here, it is of extremely importance not to conflate knowledge about the pure concept/phenomenon of life and knowledge about objects predicatable of life (Ben-Naim, manuscript, p. 281). For instance, it is common among philosophers of biology today to cite elementary knowledge in a particular biological discipline as offering a better understanding of life. Yet their promise fails to be delivered. At best, they are merely relying on knowledge about objects predicatable of life (in most cases, merely knowledge about complex organizations of matter: about heredity, reproduction, development, metabolism, etc); but such knowledge has not been shown of any relevance to the pure concept/phenomenon of life).
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Conference papers on the topic "Metabolic P system"

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Kulakovskis, Darius, Tomyslav Sledevic, Aurimas Gedminas, and Dalius Navakauskas. "Alternative implementations of metabolic P system in FPGA." In 2016 IEEE 4th Workshop on Advances in Information, Electronic and Electrical Engineering (AIEEE). IEEE, 2016. http://dx.doi.org/10.1109/aieee.2016.7821816.

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Kulakovskis, Darius, and Dalius Navakauskas. "Automation of metabolic P system implementation in FPGA: A case study." In 2015 IEEE 3rd Workshop on Advances in Information, Electronic and Electrical Engineering (AIEEE). IEEE, 2015. http://dx.doi.org/10.1109/aieee.2015.7367289.

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Marchetti, Luca, Vincenzo Manca, and Ivan Zelinka. "On the inference of deterministic chaos: Evolutionary algorithm and metabolic P system approaches." In 2014 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2014. http://dx.doi.org/10.1109/cec.2014.6900434.

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Marcus, A. J., L. B. Safier, H. L. Ullman, N. Islam, M. J. Broekman, and C. V. Schacky. "NEW EICOSANOIDS FORMED DURING PLATELET-NEUTROPHIL INTERACTIONS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644626.

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In physiologic and pathologic processes such as hemostasis, thrombosis and inflammation, multiple cell types are brought into close proximity - thereby increasing the possibility of metabolic interactions in the microenvironment. Activated platelets synthesize12-hydroxyeicosatetraenoic acid (12-HETE) in the presence or absence of aspirin. During a cell-cell interaction, platelet 12-HETE is metabolized by a cytochrome P-450 enzyme system in unstimulated neutrophils to 12.20-dihydroxyeicosatetraenoic acid (12,20-DiHETE). Recently, we observed time-dependent formation of a new eicosanoid following exposure of neutrophils to 12-HETE. This compound is more polar than the parent eicosanoid 12,20-DiHETE (reversed-phase HPLC). Incubation of purified 12,20-DiHETE with neutrophils resulted in a progressive decrease in the 12,20-DiHETE with increasing formation of the polar metabolite. In the absence of neutrophils, 12.20-DiHETE was quantitatively unchanged. The new metabolite of 12.20-DiHETE has been tentatively identified as 12-hydroxyeicosatetraen-l,20-dioic acid. The UV absorption maximum of the new compound is 237 nm which is identical to that of 12-HETE and 12,20-DiHETE. 20-hydroxy-LTB4 is the omega-hydroxylated derivative of the pro-inflammatory eicosanoid LTB4. When added to neutrophils 15 sec prior to 12,20-DiHETE, equimolar concentrations of 20-hydroxy-LTB4 (2.8uM) inhibited formation of the new metabolite by 28%. A concentration of 8uM 20-hydroxy-LTB4 inhibited the reaction by 49%. These results indicate that the neutrophil enzyme system responsible for conversion of 20-hydroxy-LTB4 to 20-carboxy-LTB4 may also be involved in further metabolism of-12,20-DiHETE. Neutrophil homogenization resulted in loss of the capacity to transform 12.20-DiHETE to the new metabolite despite pretreatment with DFP and addition of NADPH. Our data provide further evidence for the occurrence of transcellular metabolic events during thrombosis and the inflammatory response.
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Norris, James A., Anthony P. Marsh, Kevin P. Granata, and Shane D. Ross. "Positive Feedback in Powered Exoskeletons: Improved Metabolic Efficiency at the Cost of Reduced Stability?" In ASME 2007 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2007. http://dx.doi.org/10.1115/detc2007-35657.

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A broad objective of many lower extremity exoskeletons is to allow the wearer to expend less of their own energy for locomotion. Existing exoskeleton control algorithms are based on positive feedback. Forces are generated to augment movement initiated by the wearer. Positive feedback, however, can have destabilizing effects in dynamic systems. In fact, stability in these lower extremity exoskeletons is achieved by relying on the wearer’s neuromuscular system. Relying on the wearer to maintain stability may increase metabolic demand, which is counter productive to increasing efficiency. Thus, the goal of this study was to measure how a simple form of positive feedback that augments ankle push-off power affects both metabolic efficiency and dynamic walking stability. We developed a pair of powered ankle-foot orthoses (PAFOs) similar in design to Ferris, et al. (J. Appl. Biomech. 21, 189–197, 2005). Nine young healthy adults (23.3±1.6 years) walked on a treadmill in the PAFOs under two conditions: (1) with and (2) without push-off power assistance. Metabolic energy expenditure was calculated using indirect calorimetry. Walking stability was quantified using techniques for studying stability of dynamic system trajectories. The maximum Lyapunov exponent for assessing local dynamic stability, and the maximum Floquet multiplier magnitude for assessing orbital stability were calculated from foot and shank kinematics for each condition. Greater Lyapunov exponents and Floquet multipliers indicate decreased stability. Walking with mechanically generated push-off power increased metabolic efficiency (2.58±0.39 to 2.97±0.38, p&lt;0.01), did not affect local dynamic stability (0.14±0.02 to 0.14±0.02, p = 0.77), but decreased orbital dynamic stability (0.43±0.03 to 0.48±0.06, p = 0.05). This study provides evidence that positive feedback can negatively affect stability. Further investigations into understanding stability of movement will be necessary for the design of controllers for powered lower extremity exoskeletons.
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Manca, Vincenzo, and Luca Marchetti. "XML Representation of Metabolic P Systems." In 2009 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2009. http://dx.doi.org/10.1109/cec.2009.4983336.

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Obradović, Darija, Milica Radan, Marija Popović-Nikolić, Slavica Oljačić, and Katarina Nikolić. "THE MOLECULAR BASIS OF DRUG-PLASMA PROTEIN INTERACTION FOR CNS ACTIVE COMPOUNDS." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.375o.

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The human serum albumin (HSA) is well known for its extraordinary binding capacity for both endogenous and exogenous compounds, including a wide range of drugs. The goal of our investigation was to evaluate the distribution process for 15 CNS active compounds. The drug-plasma protein interaction was evaluated under simulative physiological conditions on the HSA-based stationary phase by using the mixture of Sørensen phosphate buffer (pH 7.40) and acetonitrile modifier as a mobile phase (84:16 v/v). The retention parameters (k) were used to approximate the % of protein-binding by calculating the P(%) values. The results obtained through this study demonstrated that the constitutional properties (e.g. number of total bonds, atoms, carbon atoms) and lipophilicity have a strong positive impact on the HSA-binding affinity. The coefficient of diffusion has a negative impact, while the atoms and sites available for the CYP450 oxidation showed the most significant correlation (r = 0.92). This study provides a basis for further in vitro chromatographical investigations of drug-HSA interaction for CNS active compounds. The correlation between obtained retention data and the availability to enzymes oxidation indicates the application of the tested system in the assessment of the metabolic degradation profile of CNS related drugs.
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Iles, Tinen L., Timothy G. Laske, David L. Garshelis, Lars Mattison, Brian Lee, Val Eisele, Erik Gaasedelen, and Paul A. Iaizzo. "Medtronic Reveal LINQ™ Devices Provide Better Understanding of Hibernation Physiology in the American Black Bear (Ursus Americanus)." In 2017 Design of Medical Devices Conference. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/dmd2017-3498.

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The American black bear (Ursus americanus) has been called a metabolic marvel6. In northern Minnesota, where we have conducted long-term physiological and ecological studies of this species, bears may remain in their winter dens for 6 months or more without eating, drinking, urinating or defecating and yet lose very little muscle mass2. We also found that hibernating black bears elicit asystolic events of over 30 seconds and experience an exaggerated respiratory sinus arrhythmia2. In this previous work we employed Medtronic Reveal® XT devices that required us to visit the den and temporarily extract the bear (under anesthesia) to download the stored data.4 Here we describe Medtronic’s latest generation of Insertable Cardiac Monitor (ICM), the Reveal LINQ™, which enables continuous transmission of data via a relay station from the den site3. Black bear hibernation physiology remains of high interest because of the multiple potential applications to human medicine. ICMs have been used for nearly two decades by clinicians as a critical diagnostic tool to assess the nature of cardiac arrhythmias in humans. Such devices are primarily implanted subcutaneously to record electrocardiograms. The device size, battery life and transmission capabilities have evolved in recent years. The first devices were relatively large and a programmer was needed to retrieve information during each clinical (or in our case, den visit). These devices were programmed to capture cardiac incidents such as asystolic events, arrhythmias and tachycardias and apply algorithms that ensure proper data collection: e.g. ectopy rejection and p-wave presence algorithms. The new generation Reveal LINQ was made to telemetrically transmit heart data from human patients, but we needed to develop a system to enable transmission from bear dens, which are remote (cannot easily be checked and adjusted) and are subject to extreme winter weather conditions. Besides the advantage of these devices transmitting data automatically, they are considerably smaller and thus less prone to rejection by the extraordinary immune system of the hibernating bear1.
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Nilsson, T., O. Johnson, and F. Lithner. "MOLECULAR MARKERS OF ENDOTHELIAL CELL DYSFUNCTION: OBSERVATIONS ON EXTRINSIC FIBRINOLYSIS IN SURVIVORS OF MYOCARDIAL INFARCTION AND IN TYPE-1 DIABETES MELLITUS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643102.

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We have studied the extrinsic fibrinolytic system in survivors, below 70 years, from myocardial infarction (AMI) treated in Umeci during 1983; in 43 type-1 diabetics; and in controls. Elderly controls underwent chest x-ray, ECG, EEG, brain CT scan to verify their health. Tissue plasminogen activator (tPA) activity was measured with a fibrin-stimulated rate assay, before and after a 10 min venous occlusion test (VO), tPA antigen (Ag) with an ELISA, and plasminogen activator inhibitor (PAI) by incubating samples with purified tPA and measuring remaining tPA with a polylysine-stimulated rate assay.In the diabetics, PAI and tPA:Ag were similar to the controls. tPA:Ag correlated with age (r=0.6). Diabetics had much higher specific activity of tPA (61,300 vs 21,900), and had also much higher tPA activity after VO (2.2 vs 1.2 U/ml). The tPA activities after VO correlated well with HbA1c (r=0.39). A significant effect of smoking was disclosed. Smoking diabetics had higher PAI and tPA antigen but also lower specific activity of tPA (60,600 vs 115,700 U/mg). Ex-smokers were very similar to smokers, not to the non-smokers. Retinopathy, nephropathy, or hypertension didn’t appear to affect fibrinolysis independently.In the AMI survivors (sampled 3 months after discharge from hospital), PAI was 6-fold higher than in elderly controls (p less than 0.0001). tPA activity after VO was much higher (3.2 vs 1.2 U/ml), as was tPA:Ag. tPA specific activity was lower. Among AMI patients with PAI over 10 U/ml, PAI correlated with triglycerides (r=0.4) and negatively with age (r=™0.4): these relations were not seen in the patients with PAI less than 10. The effects of smoking seen in diabetics were not observed among the AMI patients, von Willebrand factor was not increased among AMI nor diabetic patients, except for those with retinopathy.The results suggest that the tPA/PAI system is a more sensitive indicator than vWF of endothelial cell dysfunction. It relates to effects of age, atherosclerotic vascular disease, and among diabetics also to degree of metabolic control and to tobacco smoking habits.
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Hauptman, J. G., H. I. Hassouna, J. A. Penner, T. G. Bell, and T. E. Emerson. "ANTITHROMBIN-III SUPPLEMENTATION ATTENUATES DISSEMINATED INTRAVASCULAR COAGULATION IN THEE.COLI ENDOTOXEMIC DOG MODEL." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644890.

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We reported previously that disseminated intravascular coagulation (DIC) occurs early during E. coli endotoxemia in the rat, before the development of serious cardiovascular, metabolic or biochemical abnormalities, and that pretreatment with large doses of purified human antithrombin-III (AT-III; 250 U/kg) markedly attenuates DIC and increases survival (PC0.05). The present study was an extension ofan earlier one in which pretreatment of dogs with a low dose ofhuman AT-III (50 U/kg) provided borderline protection against DIC during endotoxemia. In the present study, mongrel dogs were anesthetized with sodium pentobarbital, continuously monitored over a 21 hour protocol and given full fluid support. Twenty-three dogs were given iv infusions of E. coli endotoxin (0.5mg/kg) at times zero and 15 hours. Of these, seven received iv infusions of purified human AT-III (250 U/kg) 30 minutes prior to endotoxin; 16 received no AT-III and served as controls. Comparing the AT-III treated with the control group, there was significantimprovement in the activated partial thromboplastin time and prothrombin time (P<0.05). Also, fibrinogenand fibrin degradation products were improved significantly in the AT-III treated group (P<0.05). Platelet counts decreased in both groups and there was no between group difference (P>0.05). There was no s i gni fi cant between group differences in other parameters (e.g. hemodynamic, acid-base, metabolic). These data are in agreement with earlier studies in the endotoxemic rat which show that ore occurs early in endotoxemia, that DIC occurs before the development of serious abnormalities in other systems and that AT-III supplementation significantly attenuates OIC. This study supports the hypothes1s that AT-III supplementation is efficacious in conditions of impending OIC such as gram-negative endotoxemia/septicemia.
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Reports on the topic "Metabolic P system"

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Sionov, Edward, Nancy Keller, and Shiri Barad-Kotler. Mechanisms governing the global regulation of mycotoxin production and pathogenicity by Penicillium expansum in postharvest fruits. United States Department of Agriculture, January 2017. http://dx.doi.org/10.32747/2017.7604292.bard.

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The original objectives of the study, as defined in the approved proposal, are: To characterize the relationship of CreA and LaeA in regulation of P T production To understand how PacC modulates P. expansumpathogenicity on apples To examine if other secondary metabolites are involved in virulence or P. expansumfitness To identify the signaling pathways leading to PAT synthesis Penicilliumexpansum, the causal agent of blue mould rot, is a critical health concern because of the production of the mycotoxinpatulin (PAT) in colonized apple fruit tissue. Although PAT is produced by many Penicilliumspecies, the factors activating its biosynthesis were not clear. This research focused on host and fungal mechanisms of activation of LaeA (the global regulator of secondary metabolism), PacC (the global pH modulator) and CreA (the global carbon catabolite regulator) on PAT synthesis with intention to establish P. expansumas the model system for understanding mycotoxin synthesis in fruits. The overall goal of this proposal is to identify critical host and pathogen factors that mechanistically modulate P. expansumgenes and pathways to control activation of PAT production and virulence in host. Several fungal factors have been correlated with disease development in apples, including the production of PAT, acidification of apple tissue by the fungus, sugar content and the global regulator of secondary metabolism and development, LaeA. An increase in sucrose molarity in the culture medium from 15 to 175 mM negatively regulated laeAexpression and PAT accumulation, but, conversely, increased creAexpression, leading to the hypothesis that CreA could be involved in P. expansumPAT biosynthesis and virulence, possibly through the negative regulation of LaeA. We found evidence for CreAtranscriptional regulation of laeA, but this was not correlated with PAT production either in vitro or in vivo, thus suggesting that CreA regulation of PAT is independent of LaeA. Our finding that sucrose, a key ingredient of apple fruit, regulates PAT synthesis, probably through suppression of laeAexpression, suggests a potential interaction between CreA and LaeA, which may offer control therapies for future study. We have also identified that in addition to PAT gene cluster, CreA regulates other secondary metabolite clusters, including citrinin, andrastin, roquefortine and communesins, during pathogenesis or during normal fungal growth. Following creation of P. expansumpacCknockout strain, we investigated the involvement of the global pH regulator PacC in fungal pathogenicity. We demonstrated that disruption of the pH signaling transcription factor PacC significantly decreased the virulence of P. expansumon deciduous fruits. This phenotype is associated with an impairment in fungal growth, decreased accumulation of gluconic acid and reduced synthesis of pectolytic enzymes. We showed that glucose oxidase- encoding gene, which is essential for gluconic acid production and acidification during fruit colonization, was significantly down regulated in the ΔPepacCmutant, suggesting that gox is PacC- responsive gene. We have provided evidence that deletion of goxgene in P. expansumled to a reduction in virulence toward apple fruits, further indicating that GOX is a virulence factor of P. expansum, and its expression is regulated by PacC. It is also clear from the present data that PacC in P. expansumis a key factor for the biosynthesis of secondary metabolites, such as PAT. On the basis of RNA-sequencing (RNA-seq) analysis and physiological experimentation, the P. expansumΔlaeA, ΔcreAand ΔpacCmutants were unable to successfully colonize apples for a multitude of potential mechanisms including, on the pathogen side, a decreased ability to produce proteolytic enzymes and to acidify the environment and impaired carbon/nitrogen metabolism and, on the host side, an increase in the oxidative defence pathways. Our study defines these global regulatory factors and their downstream signalling pathways as promising targets for the development of strategies to fight against this post-harvest pathogen.
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Alfano, James, Isaac Barash, Thomas Clemente, Paul E. Staswick, Guido Sessa, and Shulamit Manulis. Elucidating the Functions of Type III Effectors from Necrogenic and Tumorigenic Bacterial Pathogens. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7592638.bard.

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Many phytopathogenic bacteria use a type III protein secretion system (T3SS) to inject type III effectors into plant cells. In the experiments supported by this one-year feasibility study we investigated type III effector function in plants by using two contrasting bacterial pathogens: Pseudomonas syringae pv. tomato, a necrotrophic pathogen and Pantoea agglomerans, a tumorigenic pathogen. The objectives are listed below along with our major conclusions, achievements, and implications for science and agriculture. Objective 1: Compare Pseudomonas syringae and Pantoea agglomerans type III effectors in established assays to test the extent that they can suppress innate immunity and incite tumorigenesis. We tested P. agglomerans type III effectors in several innate immunity suppression assays and in several instances these effectors were capable of suppressing plant immunity, outputs that are suppressed by P. syringae effectors. Interestingly, several P. syringae effectors were able to complement gall production to a P. agglomerans pthGmutant. These results suggest that even though the disease symptoms of these pathogens are dramatically different, their type III effectors may function similarly. Objective 2: Construct P. syringae mutants in different combinations of type III-related DNA clusters to reduce type III effector redundancy. To determine their involvement in pathogenicity we constructed mutants that lack individual and multiple type III-related DNA clusters using a Flprecombinase-mediated mutagenesis strategy. The majority of single effector mutants in DC3000 have weak pathogenicity phenotypes most likely due to functional redundancy of effectors. Supporting this idea, Poly-DNAcluster deletion mutants were more significantly reduced in their ability to cause disease. Because these mutants have less functional redundancy of type III effectors, they should help identify P. syringae and P. agglomerans effectors that contribute more significantly to virulence. Objective 3: Determine the extent that P. syringae and P. agglomerans type III effectors alter hormone levels in plants. Inhibition of auxin polar transport by 2,3,5-triiodobenzoic acid (TIBA) completely prevented gall formation by P. agglomerans pv. gypsophilae in gypsophila cuttings. This result supported the hypothesis that auxin and presumably cytokinins of plant origin, rather than the IAA and cytokinins secreted by the pathogen, are mandatory for gall formation. Transgenic tobacco with pthGshowed various phenotypic traits that suggest manipulation of auxin metabolism. Moreover, the auxin levels in pthGtransgenic tobacco lines was 2-4 times higher than the control plants. External addition of auxin or cytokinins could modify the gall size in gypsophila cuttings inoculated with pthGmutant (PagMx27), but not with other type III effectors. We are currently determining hormone levels in transgenic plants expressing different type III effectors. Objective 4: Determine whether the P. agglomerans effectors HsvG/B act as transcriptional activators in plants. The P. agglomerans type III effectors HsvG and HsvB localize to the nucleus of host and nonhost plants and act as transcription activators in yeast. Three sites of adjacent arginine and lysine in HsvG and HsvB were suspected to act as Nuclear localization signals (NLS) domains. A nuclear import assay indicated two of the three putative NLS domains were functional NLSs in yeast. These were shown to be active in plants by fusing HsvG and HsvB to YFP. localization to the nucleus was dependent on these NLS domains. These achievements indicate that our research plan is feasible and suggest that type III effectors suppress innate immunity and modulate plant hormones. This information has the potential to be exploited to improve disease resistance in agricultural crops.
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Rezaie, Shogofa, Fedra Vanhuyse, Karin André, and Maryna Henrysson. Governing the circular economy: how urban policymakers can accelerate the agenda. Stockholm Environment Institute, September 2022. http://dx.doi.org/10.51414/sei2022.027.

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We believe the climate crisis will be resolved in cities. Today, while cities occupy only 2% of the Earth's surface, 57% of the world's population lives in cities, and by 2050, it will jump to 68% (UN, 2018). Currently, cities consume over 75% of natural resources, accumulate 50% of the global waste and emit up to 80% of greenhouse gases (Ellen MacArthur Foundation, 2017). Cities generate 70% of the global gross domestic product and are significant drivers of economic growth (UN-Habitat III, 2016). At the same time, cities sit on the frontline of natural disasters such as floods, storms and droughts (De Sherbinin et al., 2007; Major et al., 2011; Rockström et al., 2021). One of the sustainability pathways to reduce the environmental consequences of the current extract-make-dispose model (or the "linear economy") is a circular economy (CE) model. A CE is defined as "an economic system that is based on business models which replace the 'end-of-life' concept with reducing, alternatively reusing, recycling and recovering materials in production/distribution and consumption processes" (Kirchherr et al., 2017, p. 224). By redesigning production processes and thereby extending the lifespan of goods and materials, researchers suggest that CE approaches reduce waste and increase employment and resource security while sustaining business competitiveness (Korhonen et al., 2018; Niskanen et al., 2020; Stahel, 2012; Winans et al., 2017). Organizations such as the Ellen MacArthur Foundation and Circle Economy help steer businesses toward CE strategies. The CE is also a political priority in countries and municipalities globally. For instance, the CE Action Plan, launched by the European Commission in 2015 and reconfirmed in 2020, is a central pillar of the European Green Deal (European Commission, 2015, 2020). Additionally, more governments are implementing national CE strategies in China (Ellen MacArthur Foundation, 2018), Colombia (Government of the Republic of Colombia, 2019), Finland (Sitra, 2016), Sweden (Government Offices of Sweden, 2020) and the US (Metabolic, 2018, 2019), to name a few. Meanwhile, more cities worldwide are adopting CE models to achieve more resource-efficient urban management systems, thereby advancing their environmental ambitions (Petit-Boix & Leipold, 2018; Turcu & Gillie, 2020; Vanhuyse, Haddaway, et al., 2021). Cities with CE ambitions include, Amsterdam, Barcelona, Paris, Toronto, Peterborough (England) and Umeå (Sweden) (OECD, 2020a). In Europe, over 60 cities signed the European Circular Cities Declaration (2020) to harmonize the transition towards a CE in the region. In this policy brief, we provide insights into common challenges local governments face in implementing their CE plans and suggest recommendations for overcoming these. It aims to answer the question: How can the CE agenda be governed in cities? It is based on the results of the Urban Circularity Assessment Framework (UCAF) project, building on findings from 25 interviews, focus group discussions and workshops held with different stakeholder groups in Umeå, as well as research on Stockholm's urban circularity potential, including findings from 11 expert interviews (Rezaie, 2021). Our findings were complemented by the Circular Economy Lab project (Rezaie et al., 2022) and experiences from working with municipal governments in Sweden, Belgium, France and the UK, on CE and environmental and social sustainability.
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Prusky, Dov, Nancy P. Keller, and Amir Sherman. global regulation of mycotoxin accumulation during pathogenicity of Penicillium expansum in postharvest fruits. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7600012.bard.

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Background to the topic- Penicilliumas a postharvest pathogen and producer of the mycotoxin PAT. Penicilliumspp. are destructive phytopathogens, capable of causing decay in many deciduous fruits, during postharvest handling and storage; and the resulting losses can amount to 10% of the stored produce and the accumulation of large amounts of the mycotoxinpatulin. The overall goal of this proposal is to identify critical host and pathogen factors that modulate P. expansummycotoxin genes and pathways which are required for PAT production and virulence. Our preliminary results indicated that gluconic acid are strongly affecting patulin accumulation during colonization. P. expansumacidifies apple fruit tissue during colonization in part through secretion of gluconic acid (GLA). Several publications suggested that GLA accumulation is an essential factor in P. expansumpathogenicity. Furthermore, down regulation of GOX2 significantly reduced PAT accumulation and pathogenicity. PAT is a polyketide and its biosynthesis pathway includes a 15-gene cluster. LaeA is a global regulator of mycotoxin synthesis. It is now known that patulin synthesis might be subjected to LaeA and sometimes by environmental sensing global regulatory factors including the carbon catabolite repressor CreA as well as the pH regulator factor PacC and nitrogen regulator AreA. The mechanisms by which LaeA regulates patulin synthesis was not fully known and was part of our work. Furthermore, the regulatory system that controls gene expression in accordance with ambient pH was also included in our work. PacC protein is in an inactive conformation and is unable to bind to the promoter sites of the target genes; however, under alkaline growth conditions activated PacC acts as both an activator of alkaline-expressed genes and a repressor of acid-expressed genes. The aims of the project- This project aims to provide new insights on the roles of LaeA and PacC and their signaling pathways that lead to GLA and PAT biosynthesis and pathogenicity on the host. Specifically, our specific aims were: i) To elucidate the mechanism of pH-controlled regulation of GLA and PAT, and their contribution to pathogenesis of P. expansum. We are interested to understanding how pH and/or GLA impact/s under PacC regulation affect PAT production and pathogenesis. ii) To characterize the role of LaeA, the global regulator of mycotoxin production, and its effect on PAT and PacC activity. iii) To identify the signaling pathways leading to GLA and PAT synthesis. Using state- of-the-art RNAseq technologies, we will interrogate the transcriptomes of laeAand pacCmutants, to identify the common signaling pathways regulating synthesis of both GLA and PAT. Major conclusions, solutions, achievements- In our first Aim our results demonstrated that ammonia secreted at the leading edge of the fungal colony induced transcript activation of the global pH modulator PacC and PAT accumulation in the presence of GLA. We assessed these parameters by: (i) direct exogenous treatment of P. expansumgrowing on solid medium; (ii) direct exogenous treatment on colonized apple tissue; (iii) growth under self-ammonia production conditions with limited carbon; and (iv) analysis of the transcriptional response to ammonia of the PAT biosynthesis cluster. Ammonia induced PAT accumulation concurrently with the transcript activation of pacCand PAT biosynthesis cluster genes, indicating the regulatory effect of ammonia on pacCtranscript expression under acidic conditions. Transcriptomic analysis of pH regulated processes showed that important genes and BARD Report - Project 4773 Page 2 of 10 functionalities of P. expansumwere controlled by environmental pH. The differential expression patterns of genes belonging to the same gene family suggest that genes were selectively activated according to their optimal environmental conditions to enable the fungus to cope with varying conditions and to make optimal use of available enzymes. Concerning the second and third Aims, we demonstrated that LaeA regulates several secondary metabolite genes, including the PAT gene cluster and concomitant PAT synthesis invitro. Virulence studies of ΔlaeAmutants of two geographically distant P. expansumisolates (Pe-21 from Israel and Pe-T01 from China) showed differential reduction in disease severity in freshly harvested fruit ranging from no reduction for Ch-Pe-T01 strains in immature fruit to 15–25% reduction for both strains in mature fruit, with the ΔlaeAstrains of Is-Pe-21 always showing a greater loss in virulence. Results suggest the importance of LaeA regulation of PAT and other secondary metabolites on pathogenicity. Our work also characterized for the first time the role of sucrose, a key nutritional factor present in apple fruit, as a negative regulator of laeAexpression and consequent PAT production in vitro. This is the first report of sugar regulation of laeAexpression, suggesting that its expression may be subject to catabolite repression by CreA. Some, but not all of the 54 secondary metabolite backbone genes in the P. expansumgenome, including the PAT polyketide backbone gene, were found to be regulated by LaeA. Together, these findings enable for the first time a straight analysis of a host factor that potentially activates laeAand subsequent PAT synthesis.
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5

Aly, Radi, and John I. Yoder. Development of resistant crop plants to parasitic weeds based on trans-specific gene silencing. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598146.bard.

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Abstract:
Broomrapes (Orobanche/Phelipanchespp.) are holo parasitic plants that subsist on the roots of a variety of agricultural crops and cause severe losses to the yield quality and quantity. Effective methods for controlling parasitic weeds are scarce, with only a few known cases of genetic resistance. In the current study, we proposed an improved strategy for the control of parasitic weeds based on trans-specific gene-silencing of three parasite genes at once. We used two strategies to express dsRNA containing selected sequences of three Phelipancheaegyptiacagenes PaACS, PaM6PR and PaPrx1 (pma): transient expression using Tobacco rattle virus (TRV:pma) as a virus-induced gene-silencing (VIGS) vector and stable expression in transgenic tomato Solanumlycopersicum(Mill.) plants harboring a hairpin construct (pBINPLUS35:pma). siRNA-mediated transgene-silencing (20–24 nt) was detected in the host plants. Our results demonstrate that the quantities of PaACSand PaM6PR transcripts from P. aegyptiacatubercles grown on transgenic tomato or on Tobacco rattle virus-infected Nicotianabenthamianaplants were significantly reduced. However, only partial reductions in the quantity of PaPrx1 transcripts were observed in the parasite tubercles grown on tomato and on N. benthamianaplants. Concomitant with the suppression of the target genes, there were significant decreases in the number and weight of the parasite tubercles that grew on the host plants, in both the transient and the stable experimental systems. The results of the work carried out using both strategies point to the movement of mobile exogenous siRNA from the host to the parasite, leading to the impaired expression of essential parasite target genes. In light of the importance of parasitic weeds to world agriculture and the difficulty of obtaining resistance by conventional methods, we assume that genetic resistance based on the silencing of key metabolic genes in the parasite is now feasible. BARD Report - Project4622 Page 2 of 60
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