21
Bibliography

24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

  • Upload
    dodung

  • View
    213

  • Download
    0

Embed Size (px)

Citation preview

Page 1: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

Bibliography

Page 2: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9

R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

164 | Bibliography

Page 3: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

Bibliography | 165

B

Bibliography

Aban N, Cinel L, Tamer L, Aktas A, and Aban M. 2005. Ischemic preconditioning reduces caspase-related intestinal apoptosis. Surgery today 35(3):228-234.

Abraham C, and Medzhitov R. 2011. Interactions between the host innate immune system and microbes in inflammatory bowel disease. Gastroenterology 140(6):1729-1737.

Adam EK, and Gunnar MR. 2001. Relationship functioning and home and work demands predict individual differences in diurnal cortisol patterns in women. Psychoneuroendocrinology 26(2):189-208.

Adam EK, Hawkley LC, Kudielka BM, and Cacioppo JT. 2006. Day-to-day dynamics of experience--cortisol associations in a population-based sample of older adults. Proc Natl Acad Sci U S A 103(45):17058-17063.

Adams JM, and Cory S. 2007. The Bcl-2 apoptotic switch in cancer development and therapy. Oncogene 26(9):1324-1337.

Alberts BAJJLMRKRPW. 1994. Molecular Biology of the Cell. New York: Garland Publishing Inc.

American Diabetes A. 2012. Standards of medical care in diabetes--2012. Diabetes Care 35 Suppl 1:S11-63.

Anagnostis P, Athyros VG, Tziomalos K, Karagiannis A, and Mikhailidis DP. 2009a. Clinical review: The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol Metab 94(8):2692-2701.

Anagnostis P, Athyros VG, Tziomalos K, Karagiannis A, and Mikhailidis DP. 2009b. The Pathogenetic Role of Cortisol in the Metabolic Syndrome: A Hypothesis. J Clin Endocrinol Metab 94(8):2692-2701.

Anderies JM, and M. A. Janssen. 2007. Robustness trade-offs in social-ecological systems. International Journal of the Commons 1(1):77-99.

Andersen V, Sonne J, Sletting S, and Prip A. 2000. The volume of the liver in patients correlates to body weight and alcohol consumption. Alcohol and alcoholism 35(5):531-532.

Ankarcrona M, Dypbukt JM, Bonfoco E, Zhivotovsky B, Orrenius S, Lipton SA, and Nicotera P. 1995. Glutamate-induced neuronal death: a succession of necrosis or apoptosis depending on mitochondrial function. Neuron 15(4):961-973.

Anvekar RA, Asciolla JJ, Missert DJ, and Chipuk JE. 2011. Born to be alive: a role for the BCL-2 family in melanoma tumor cell survival, apoptosis, and treatment. Frontiers in oncology 1(34).

Aouabdi S, Gibson GG, and Plant N. 2006. Transcriptional regulation of PXR: Identification of a PPRE within the proximal promoter responsible for fibrate-mediated transcriptional activation of PXR. Drug Metabolism and Disposition 34(1):138-144.

Arda HE, Taubert S, MacNeil LT, Conine CC, Tsuda B, Van Gilst M, Sequerra R, Doucette-Stamm L, Yamamoto KR, and Walhout AJM. 2010. Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans gene regulatory network. Molecular Systems Biology 6:367.

Arendt J. 2010. Shift work: coping with the biological clock. Occup Med (Lond) 60(1):10-20.

Ashkenazi A, and Dixit VM. 1998. Death receptors: signaling and modulation. Science 281(5381):1305-1308.

Ashkenazi IE, Reinberg AE, and Motohashi Y. 1997. Interindividual differences in the flexibility of human temporal organization: pertinence to jet lag and shiftwork. Chronobiol Int 14(2):99-113.

Bailer WWPaAJ. 2005. Quantitative Risk Assessment with Stimulus–Response Data. Analyzing environmental data: John Wiley and Sons. p 171–214.

Bailey I, Gibson GG, Plant K, Graham M, and Plant N. 2011. A PXR-Mediated Negative Feedback Loop Attenuates the Expression of CYP3A in Response to the PXR Agonist Pregnenalone-16a-Carbonitrile. PLoS One 6(2):e16703.

Page 4: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9

R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

166 | Bibliography

Baquero F, Alvarez-Ortega C, and Martinez JL. 2009. Ecology and evolution of antibiotic resistance. Environ Microbiol Rep 1(6):469-476.

Barclay JL, Husse J, Bode B, Naujokat N, Meyer-Kovac J, Schmid SM, Lehnert H, and Oster H. 2012. Circadian desynchrony promotes metabolic disruption in a mouse model of shiftwork. PLoS One 7(5):e37150.

Baynes JD, Marek H. 2014. Medical Biochemistry. Elsevier Health Sciences.

Bellivier F, Geoffroy PA, Etain B, and Scott J. 2015. Sleep- and circadian rhythm-associated pathways as therapeutic targets in bipolar disorder. Expert Opin Ther Targets 19(6):747-763.

Bernard C. 1870. Lessons on the phenomena of life common to animals and vegetables. Second lecture, the three forms of life. In: LL L, editor. Homeostasis: Origins of the Concept. Stroudsberg, PA: Dowden, Hutchinson & Ross, Inc. p 129–151.

Bertilsson G, Heidrich J, Svensson K, Asman M, Jendeberg L, Sydow-Backman M, Ohlsson R, Postlind H, Blomquist P, and Berkenstam A. 1998. Identification of a human nuclear receptor defines a new signalling pathway for CYP3A induction. Proceedings of the National Academy of Sciences USA 95(21):12208-12213.

Bieber C, Juskaitis R, Turbill C, and Ruf T. 2012. High survival during hibernation affects onset and timing of reproduction. Oecologia 169(1):155-166.

Billen LP, Kokoski CL, Lovell JF, Leber B, and Andrews DW. 2008. Bcl-XL inhibits membrane permeabilization by competing with Bax. PLoS biology 6(6):e147.

Blumberg B, Sabbagh W, Jr., Juguilon H, Bolado J, Jr., van Meter CM, Ong ES, and Evans RM. 1998. SXR, a novel steroid and xenobiotic-sensing nuclear receptor. Genes and Development 12(20):3195-3205.

Bolli R. 2007. Preconditioning: a paradigm shift in the biology of myocardial ischemia. Am J Physiol Heart Circ Physiol 292(1):H19-27.

Bombail V, Taylor K, Gibson G, and Plant N. 2004. Role of Sp1, C/EBPα, HNF3 and PXR in the basal and xenobiotic-mediated regulation of the CYP3A4 gene. Drug Metabolism and Disposition 32(5):525-535.

Bordbar A, Monk JM, King ZA, and Palsson BO. 2014. Constraint-based models predict metabolic and associated cellular functions. Nat Rev Genet 15(2):107-120.

Bouillet P, Metcalf D, Huang DC, Tarlinton DM, Kay TW, Kontgen F, Adams JM, and Strasser A. 1999. Proapoptotic Bcl-2 relative Bim required for certain apoptotic responses, leukocyte homeostasis, and to preclude autoimmunity. Science 286(5445):1735-1738.

Boveris A, and Cadenas E. 2000. Mitochondrial production of hydrogen peroxide regulation by nitric oxide and the role of ubisemiquinone. IUBMB Life 50(4-5):245-250.

Brady NR, Elmore SP, van Beek JJ, Krab K, Courtoy PJ, Hue L, and Westerhoff HV. 2004. Coordinated behavior of mitochondria in both space and time: a reactive oxygen species-activated wave of mitochondrial depolarization. Biophys J 87(3):2022-2034.

Brady NR, Hamacher-Brady A, Westerhoff HV, and Gottlieb RA. 2006. A wave of reactive oxygen species (ROS)-induced ROS release in a sea of excitable mitochondria. Antioxid Redox Signal 8(9-10):1651-1665.

Breitling R, Gilbert D, Heiner M, and Orton R. 2008. A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Brief Bioinform 9(5):404-421.

Breitschopf K, Zeiher AM, and Dimmeler S. 2000. Ubiquitin-mediated degradation of the proapoptotic active form of bid. A functional consequence on apoptosis induction. The Journal of biological chemistry 275(28):21648-21652.

Bruehl H, Wolf OT, and Convit A. 2009. A blunted cortisol awakening response and hippocampal atrophy in type 2 diabetes mellitus. Psychoneuroendocrinology 34(6):815-821.

Bruggeman FJ, Hornberg JJ, Boogerd FC, and Westerhoff HV. 2007. Introduction to systems biology. EXS 97:1-19.

Page 5: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

Bibliography | 167

B

Brunner-Ziegler S, Jilma B, Schorgenhofer C, Winkler F, Jilma-Stohlawetz P, Koppensteiner R, Quehenberger P, Seger C, Weigel G, Griesmacher A et al. . 2016. Comparison between the impact of morning and evening doses of rivaroxaban on the circadian endogenous coagulation rhythm in healthy subjects. J Thromb Haemost 14(2):316-323.

Bu HZ. 2006. A literature review of enzyme kinetic parameters for CYP3A4-mediated metabolic reactions of 113 drugs in human liver microsomes: structure-kinetics relationship assessment. Current drug metabolism 7(3):231-249.

Burrill DR, and Silver PA. 2010. Making cellular memories. Cell 140(1):13-18.

Calabrese EJ, Bachmann KA, Bailer AJ, Bolger PM, Borak J, Cai L, Cedergreen N, Cherian MG, Chiueh CC, Clarkson TW et al.. 2007. Biological stress response terminology: Integrating the concepts of adaptive response and preconditioning stress within a hormetic dose-response framework. Toxicol Appl Pharmacol 222(1):122-128.

Calabrese EJ, and Baldwin LA. 2002. Defining hormesis. Hum Exp Toxicol 21(2):91-97.

Cannon WB. 1927. Bodily changes in pain, hunger, fear and rage. New York and London: D. APPLETON AND COMPANY.

Cannon WB. 1932. The wisdom of the body. New York,: W.W. Norton & Company. xv p., 1 l., 19-312 p. p.

Cao X, Deng X, and May WS. 2003. Cleavage of Bax to p18 Bax accelerates stress-induced apoptosis, and a cathepsin-like protease may rapidly degrade p18 Bax. Blood 102(7):2605-2614.

Carroll R, and Yellon DM. 1999. Myocardial adaptation to ischaemia--the preconditioning phenomenon. International journal of cardiology 68 Suppl 1:S93-101.

Cashman G. 2000. What causes war?: an introduction to theories of international conflict: Lexington Books. p 160–192.

Chaabane W, User SD, El-Gazzah M, Jaksik R, Sajjadi E, Rzeszowska-Wolny J, and Los MJ. 2013. Autophagy, apoptosis, mitoptosis and necrosis: interdependence between those pathways and effects on cancer. Arch Immunol Ther Exp (Warsz) 61(1):43-58.

Chaplin DD. 2003. 1. Overview of the immune response. J Allergy Clin Immunol 111(2 Suppl):S442-459.

Charmandari E, Chrousos GP, Lambrou GI, Pavlaki A, Koide H, Ng SS, and Kino T. 2011. Peripheral CLOCK regulates target-tissue glucocorticoid receptor transcriptional activity in a circadian fashion in man. PLoS One 6(9):e25612.

Chicheportiche Y, Bourdon PR, Xu H, Hsu YM, Scott H, Hession C, Garcia I, and Browning JL. 1997. TWEAK, a new secreted ligand in the tumor necrosis factor family that weakly induces apoptosis. The Journal of biological chemistry 272(51):32401-32410.

Chipuk JE, Moldoveanu T, Llambi F, Parsons MJ, and Green DR. 2010. The BCL-2 family reunion. Molecular cell 37(3):299-310.

Cinel I, Avlan D, Cinel L, Polat G, Atici S, Mavioglu I, Serinol H, Aksoyek S, and Oral U. 2003. Ischemic preconditioning reduces intestinal epithelial apoptosis in rats. Shock 19(6):588-592.

Circu ML, and Aw TY. 2010. Reactive oxygen species, cellular redox systems, and apoptosis. Free radical biology & medicine 48(6):749-762.

Conrad CD. 2008. Chronic Stress-induced Hippocampal Vulnerability: The Glucocorticoid Vulnerability Hypothesis. Rev Neurosci 19(6):395-411.

Conrad CD. 2010. A critical review of chronic stress effects on spatial learning and memory. Prog Neuro-Psychopharmacol Biol Psychiatry 34(5):742-755.

Conus S, Perozzo R, Reinheckel T, Peters C, Scapozza L, Yousefi S, and Simon HU. 2008. Caspase-8 is activated by cathepsin D initiating neutrophil apoptosis during the resolution of inflammation. J Exp Med 205(3):685-698.

Costa VV, Fagundes CT, Souza DG, and Teixeira MM. 2013. Inflammatory and innate immune responses in dengue infection: protection versus disease induction. The American journal of pathology 182(6):1950-1961.

Page 6: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9

R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

168 | Bibliography

Crofford LJ, Pillemer SR, Kalogeras KT, Cash JM, Michelson D, Kling MA, Sternberg EM, Gold PW, Chrousos GP, and Wilder RL. 1994. Hypothalamic-pituitary-adrenal axis perturbations in patients with fibromyalgia. Arthritis Rheum 37(11):1583-1592.

Cruz de Carvalho MH. 2008. Drought stress and reactive oxygen species: Production, scavenging and signaling. Plant Signal Behav 3(3):156-165.

Cutolo M. 2016. Glucocorticoids and chronotherapy in rheumatoid arthritis. RMD Open 2(1):e000203.

Czabotar PE, Westphal D, Dewson G, Ma S, Hockings C, Fairlie WD, Lee EF, Yao S, Robin AY, Smith BJ et al. . 2013. Bax crystal structures reveal how BH3 domains activate Bax and nucleate its oligomerization to induce apoptosis. Cell 152(3):519-531.

Czibik G, Wu Z, Berne GP, Tarkka M, Vaage J, Laurikka J, Jarvinen O, and Valen G. 2008. Human adaptation to ischemia by preconditioning or unstable angina: involvement of nuclear factor kappa B, but not hypoxia-inducible factor 1 alpha in the heart. European journal of cardio-thoracic surgery: official journal of the European Association for Cardio-thoracic Surgery 34(5):976-984.

Dagda RK, Cherra SJ, 3rd, Kulich SM, Tandon A, Park D, and Chu CT. 2009. Loss of PINK1 function promotes mitophagy through effects on oxidative stress and mitochondrial fission. The Journal of biological chemistry 284(20):13843-13855.

Danial NN. 2007. BCL-2 family proteins: critical checkpoints of apoptotic cell death. Clinical cancer research: an official journal of the American Association for Cancer Research 13(24):7254-7263.

Daum I, Channon S, and Canavan AG. 1989. Classical conditioning in patients with severe memory problems. J Neurol Neurosurg Psychiatry 52(1):47-51.

Daum I, Schugens MM, Breitenstein C, Topka H, and Spieker S. 1996. Classical eyeblink conditioning in Parkinson’s disease. Mov Disord 11(6):639-646.

Degli Esposti D, Sebagh M, Pham P, Reffas M, Pous C, Brenner C, Azoulay D, and Lemoine A. 2011. Ischemic preconditioning induces autophagy and limits necrosis in human recipients of fatty liver grafts, decreasing the incidence of rejection episodes. Cell Death Dis 2:e111.

Demerouti E, Geurts SA, Bakker AB, and Euwema M. 2004. The impact of shiftwork on work--home conflict, job attitudes and health. Ergonomics 47(9):987-1002.

Denecker G, Vercammen D, Steemans M, Vanden Berghe T, Brouckaert G, Van Loo G, Zhivotovsky B, Fiers W, Grooten J, Declercq W et al. . 2001. Death receptor-induced apoptotic and necrotic cell death: differential role of caspases and mitochondria. Cell Death Differ 8(8):829-840.

Desagher S, Osen-Sand A, Nichols A, Eskes R, Montessuit S, Lauper S, Maundrell K, Antonsson B, and Martinou JC. 1999. Bid-induced conformational change of Bax is responsible for mitochondrial cytochrome c release during apoptosis. The Journal of cell biology 144(5):891-901.

Deter RL, and De Duve C. 1967. Influence of glucagon, an inducer of cellular autophagy, on some physical properties of rat liver lysosomes. The Journal of cell biology 33(2):437-449.

Dirnagl U, Simon RP, and Hallenbeck JM. 2003. Ischemic tolerance and endogenous neuroprotection. Trends in neurosciences 26(5):248-254.

Dlugosz PJ, Billen LP, Annis MG, Zhu W, Zhang Z, Lin J, Leber B, and Andrews DW. 2006. Bcl-2 changes conformation to inhibit Bax oligomerization. The EMBO journal 25(11):2287-2296.

Drouhet E, Dupont B, Pelletier M, and Giroud JP. 1981. Acute non-specific inflammatory reactions and protection against experimental Candida albicans infection. Agents and actions 11(6-7):629-631.

Du H, Wolf J, Schafer B, Moldoveanu T, Chipuk JE, and Kuwana T. 2011. BH3 domains other than Bim and Bid can directly activate Bax/Bak. The Journal of biological chemistry 286(1):491-501.

Dussmann H, Rehm M, Concannon CG, Anguissola S, Wurstle M, Kacmar S, Voller P, Huber HJ, and Prehn JH. 2010. Single-cell quantification of Bax activation and mathematical modelling suggest pore formation on minimal mitochondrial Bax accumulation. Cell Death Differ 17(2):278-290.

Edelman LB, Eddy JA, and Price ND. 2010. In silico models of cancer. Wiley Interdiscip Rev Syst Biol Med 2(4):438-459.

Page 7: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

Bibliography | 169

B

Editorial N. 2016. Chow down. Nature 530(7590):254.

Edlich F, Banerjee S, Suzuki M, Cleland MM, Arnoult D, Wang C, Neutzner A, Tjandra N, and Youle RJ. 2011. Bcl-x(L) retrotranslocates Bax from the mitochondria into the cytosol. Cell 145(1):104-116.

Eguchi Y, Shimizu S, and Tsujimoto Y. 1997. Intracellular ATP levels determine cell death fate by apoptosis or necrosis. Cancer Res 57(10):1835-1840.

El-Sankary W, Bombail V, Gibson GG, and Plant N. 2002. Glucocorticoid-mediated induction of CYP3A4 is decreased by disruption of a protein: DNA interaction distinct from the pregnane X receptor response element. Drug metabolism and disposition: the biological fate of chemicals 30(9):1029-1034.

El-Sankary W, Gibson GG, Ayrton A, and Plant N. 2001. Use of a reporter gene assay to predict and rank the potency and efficacy of CYP3A4 inducers. Drug metabolism and disposition: the biological fate of chemicals 29(11):1499-1504.

El-Sankary W, Plant N, and Gibson G. 2000. Regulation of the CYP3A4 gene by hydrocortisone and xenobiotics: role of the glucocorticoid and pregnane X receptors. Drug Metabolism and Disposition 28(5):493-496.

Elmore S. 2007. Apoptosis: a review of programmed cell death. Toxicologic pathology 35(4):495-516.

Elmore SK, Betrus PA, and Burr R. 1994. Light, social zeitgebers, and the sleep-wake cycle in the entrainment of human circadian rhythms. Res Nurs Health 17(6):471-478.

Emoto C, Yamato Y, Sato Y, Ohshita H, Katoh M, Tateno C, Yokoi T, Yoshizato K, and Iwasaki K. 2008. Non-invasive method to detect induction of CYP3A4 in chimeric mice with a humanized liver. Xenobiotica 38(3):239-248.

Eskes R, Desagher S, Antonsson B, and Martinou JC. 2000. Bid induces the oligomerization and insertion of Bax into the outer mitochondrial membrane. Mol Cell Biol 20(3):929-935.

Esposti DD, Domart MC, Sebagh M, Harper F, Pierron G, Brenner C, and Lemoine A. 2010. Autophagy is induced by ischemic preconditioning in human livers formerly treated by chemotherapy to limit necrosis. Autophagy 6(1):172-174.

Fabre B, Grosman H, Mazza O, Nolazco C, Machulsky NF, Mesch V, Schreier L, Gidron Y, and Berg G. 2013. Relationship between cortisol, life events and metabolic syndrome in men. Stress 16(1):16-23.

Faircloth ME, Redwood SR, and Marber MS. 2004. Ischaemic preconditioning and myocardial adaptation to serial intracoronary balloon inflation: cut from the same cloth? Heart 90(4):358-360.

Fisher CP, Plant NJ, Moore JB, and Kierzek AM. 2013. QSSPN: Dynamic Simulation of Molecular Interaction Networks Describing Gene Regulation, Signalling and Whole-Cell Metabolism in Human Cells. Bioinformatics 29(24):3181-3190.

Flack JE, 3rd, Kimura Y, Engelman RM, Rousou JA, Iyengar J, Jones R, and Das DK. 1991. Preconditioning the heart by repeated stunning improves myocardial salvage. Circulation 84(5 Suppl):III369-374.

Fleischman FD, K. Boenning, G. A. Garcia-Lopez, S. Mincey, M. Schmitt-Harsh, K. Daedlow, M. Lopez, X. Basurto, B. Fischer, and E. Ostrom. 2010. Disturbance, response, and persistence in self-organized forested communities: analysis of robustness and resilience in five communities in southern Indiana. Ecology and Society 15(4):

Fletcher JI, Meusburger S, Hawkins CJ, Riglar DT, Lee EF, Fairlie WD, Huang DC, and Adams JM. 2008. Apoptosis is triggered when prosurvival Bcl-2 proteins cannot restrain Bax. Proc Natl Acad Sci U S A 105(47):18081-18087.

Francis GA, Fayard E, Picard F, and Auwerx J. 2003. Nuclear receptors and the control of metabolism. Annual Review of Physiology 65:261-311.

Garcia-Saez AJ, Ries J, Orzaez M, Perez-Paya E, and Schwille P. 2009. Membrane promotes tBID interaction with BCL(XL). Nat Struct Mol Biol 16(11):1178-1185.

Page 8: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9

R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

170 | Bibliography

Garcia MC, de Souza A, Bella GP, Grassi-Kassisse DM, Tacla AP, and Spadari-Bratfisch RC. 2008. Salivary cortisol levels in Brazilian citizens of distinct socioeconomic and cultural levels. Ann N Y Acad Sci 1148:504-508.

Garmizo G, and Frauens BJ. 2008. Corneal copper deposition secondary to oral contraceptives. Optometry and vision science: official publication of the American Academy of Optometry 85(9):E802-807.

Gavathiotis E, Reyna DE, Davis ML, Bird GH, and Walensky LD. 2010. BH3-triggered structural reorganization drives the activation of proapoptotic BAX. Molecular cell 40(3):481-492.

Gavrila A, Peng CK, Chan JL, Mietus JE, Goldberger AL, and Mantzoros CS. 2003. Diurnal and ultradian dynamics of serum adiponectin in healthy men: comparison with leptin, circulating soluble leptin receptor, and cortisol patterns. J Clin Endocrinol Metab 88(6):2838-2843.

Ged C, Rouillon JM, Pichard L, Combalbert J, Bressot N, Bories P, Michel H, Beaune P, and Maurel P. 1989. The increase in urinary excretion of 6 beta-hydroxycortisol as a marker of human hepatic cytochrome P450IIIA induction. British journal of clinical pharmacology 28(4):373-387.

Geenen S, Taylor PN, Snoep JL, Wilson ID, Kenna JG, and Westerhoff HV. 2012. Systems biology tools for toxicology. Arch Toxicol 86(8):1251-1271.

Gibbs JE, and Ray DW. 2013. The role of the circadian clock in rheumatoid arthritis. Arthritis Res Ther 15(1):205.

Gibson GG, Phillips A, Aouabdi S, Plant K, and Plant N. 2006. Transcriptional regulation of the human pregnane-X receptor. Drug Metabolism Reviews 38(1-2):31-49.

Gille C, Bolling C, Hoppe A, Bulik S, Hoffmann S, Hubner K, Karlstadt A, Ganeshan R, Konig M, Rother K et al. . 2010. HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Mol Syst Biol 6:411.

Glick D, Barth S, and Macleod KF. 2010. Autophagy: cellular and molecular mechanisms. The Journal of pathology 221(1):3-12.

Goldstein JC, Waterhouse NJ, Juin P, Evan GI, and Green DR. 2000. The coordinate release of cytochrome c during apoptosis is rapid, complete and kinetically invariant. Nat Cell Biol 2(3):156-162.

Golier JA, Schmeidler J, Legge J, and Yehuda R. 2007. Twenty-four hour plasma cortisol and adrenocorticotropic hormone in Gulf War Veterans: Relationships to posttraumatic stress disorder and health symptoms. Biol Psychiatry 62(10):1175-1178.

Goligorsky MS. 2001. The concept of cellular “fight-or-flight” reaction to stress. American Journal of Physiology - Renal Physiology 280(4):F551-561.

Gordo I, and Campos PR. 2013. Evolution of clonal populations approaching a fitness peak. Biol Lett 9(1):20120239.

Graber DA. 2001. Processing politics: learning from television in the Internet age. Chicago: University of Chicago Press. xiii, 231 p. p.

Gross A, Jockel J, Wei MC, and Korsmeyer SJ. 1998. Enforced dimerization of BAX results in its translocation, mitochondrial dysfunction and apoptosis. The EMBO journal 17(14):3878-3885.

Gross A, McDonnell JM, and Korsmeyer SJ. 1999. BCL-2 family members and the mitochondria in apoptosis. Genes & development 13(15):1899-1911.

Hamacher-Brady A, Brady NR, and Gottlieb RA. 2006. Enhancing macroautophagy protects against ischemia/reperfusion injury in cardiac myocytes. The Journal of biological chemistry 281(40):29776-29787.

Hamilton RF, and Herwig HH. 2003. The origins of World War I. Cambridge; New York: Cambridge University Press. xiii, 537 p. p.

Handschin C, Blattler S, Roth A, Looser R, Oscarson M, Kaufmann MR, Podvinec M, Gnerre C, and Meyer UA. 2004. The evolution of drug-activated nuclear receptors: one ancestral gene diverged into two xenosensor genes in mammals. Nuclear Receptors 2(1):7.

Page 9: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

Bibliography | 171

B

Handschin C, and Meyer UA. 2005. Regulatory network of lipid-sensing nuclear receptors: roles for CAR, PXR, LXR, and FXR. Archives of Biochemistry and Biophysics 433(2):387-396.

Hargrove JL. 1993. Microcomputer-assisted kinetic modeling of mammalian gene expression. FASEB journal: official publication of the Federation of American Societies for Experimental Biology 7(12):1163-1170.

Harrington HA, Ho KL, Ghosh S, and Tung KC. 2008. Construction and analysis of a modular model of caspase activation in apoptosis. Theor Biol Med Model 5:26.

Hartley TA, Knox SS, Fekedulegn D, Barbosa-Leiker C, Violanti JM, Andrew ME, and Burchfiel CM. 2012a. Association between depressive symptoms and metabolic syndrome in police officers: results from two cross-sectional studies. Journal of environmental and public health 2012:861219.

Hartley TA, Knox SS, Fekedulegn D, Barbosa-Leiker C, Violanti JM, Andrew ME, and Burchfiel CM. 2012b. Association between depressive symptoms and metabolic syndrome in police officers: results from two cross-sectional studies. J Environ Public Health 2012:861219.

He C, and Levine B. 2010. The Beclin 1 interactome. Current opinion in cell biology 22(2):140-149.

He F, Murabito E, and Westerhoff HV. 2016. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering. J R Soc Interface 13(117).

Heckmann M, Wudy SA, Haack D, and Pohlandt F. 1999. Reference range for serum cortisol in well preterm infants. Arch Dis Child Fetal Neonatal Ed 81(3):F171-174.

Helm B, Ben-Shlomo R, Sheriff MJ, Hut RA, Foster R, Barnes BM, and Dominoni D. 2013. Annual rhythms that underlie phenology: biological time-keeping meets environmental change. Proc Biol Sci 280(1765):20130016.

Henley DE, and Lightman SL. 2014. Cardio-metabolic consequences of glucocorticoid replacement: relevance of ultradian signalling. Clin Endocrinol (Oxf) 80(5):621-628.

Hennig J, Kieferdorf P, Moritz C, Huwe S, and Netter P. 1998. Changes in cortisol secretion during shiftwork: implications for tolerance to shiftwork? Ergonomics 41(5):610-621.

Hess S. 2013. From the Arab Spring to the Chinese Winter: The institutional sources of authoritarian vulnerability and resilience in Egypt, Tunisia, and China. International Political Science Review 34(3):254-272.

Heusch G, and Schulz R. 1997. Endogenous protective mechanisms in myocardial ischemia: hibernation and ischemic preconditioning. The American journal of cardiology 80(3A):26A-33A.

Heyman GM, Grisanzio KA, and Liang V. 2016. Introducing a Method for Calculating the Allocation of Attention in a Cognitive “Two-Armed Bandit” Procedure: Probability Matching Gives Way to Maximizing. Front Psychol 7:223.

Hoeck W, Rusconi S, and Groner B. 1989. Down-regulation and phosphorylation of glucocorticoid receptors in cultured cells. Investigations with a monospecific antiserum against a bacterially expressed receptor fragment. The Journal of biological chemistry 264(24):14396-14402.

Hoekstra PJ, Anderson GM, Troost PW, Kallenberg CG, and Minderaa RB. 2007. Plasma kynurenine and related measures in tic disorder patients. Eur Child Adolesc Psychiatry 16 Suppl 1:71-77.

Hofmeyr JH, and Cornish-Bowden A. 1996. Co-response analysis: a new experimental strategy for metabolic control analysis. J Theor Biol 182(3):371-380.

Holland PC. 2008. Cognitive versus stimulus-response theories of learning. Learn Behav 36(3):227-241.

Hood L, and Tian Q. 2012. Systems approaches to biology and disease enable translational systems medicine. Genomics Proteomics Bioinformatics 10(4):181-185.

Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, and Kummer U. 2006. COPASI — a COmplex PAthway SImulator. Bioinformatics 22:3067-3074.

Hornberg JJ, Bruggeman FJ, Bakker BM, and Westerhoff HV. 2007. Metabolic control analysis to identify optimal drug targets. Prog Drug Res 64:171, 173-189.

Page 10: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9

R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

172 | Bibliography

Hornberg JJ, Bruggeman FJ, Westerhoff HV, and Lankelma J. 2006. Cancer: a Systems Biology disease. Biosystems 83(2-3):81-90.

Howells CC, Baumann WT, Samuels DC, and Finkielstein CV. 2011. The Bcl-2-associated death promoter (BAD) lowers the threshold at which the Bcl-2-interacting domain death agonist (BID) triggers mitochondria disintegration. J Theor Biol 271(1):114-123.

Hsu YT, Wolter KG, and Youle RJ. 1997. Cytosol-to-membrane redistribution of Bax and Bcl-X(L) during apoptosis. Proc Natl Acad Sci U S A 94(8):3668-3672.

Hsu YT, and Youle RJ. 1998. Bax in murine thymus is a soluble monomeric protein that displays differential detergent-induced conformations. The Journal of biological chemistry 273(17):10777-10783.

Hu J, Zhang Z, Shen WJ, and Azhar S. 2010. Cellular cholesterol delivery, intracellular processing and utilization for biosynthesis of steroid hormones. Nutr Metab (Lond) 7:47.

Hua F, Cornejo MG, Cardone MH, Stokes CL, and Lauffenburger DA. 2005. Effects of Bcl-2 levels on Fas signaling-induced caspase-3 activation: molecular genetic tests of computational model predictions. J Immunol 175(2):985-995.

Huang PL. 2009. A comprehensive definition for metabolic syndrome. Dis Model Mech 2(5-6):231-237.

Huihai Wu AvK, Vytautas Leoncikas, Wataru Mori, Nilgun Sahin, Albert Gevorgyan, Catherine Linley, Marek Grabowski, Ahmad A Mannan, Nicholas Stoy, Hans V Westerhoff, Johnjoe McFadden, Nicholas J Plant & Andrzej M Kierzek. 2016. MUFINS: multi-formalism interaction network simulator. npj Systems Biology and Applications 2.

Huizenga N, De Herder WW, Koper JW, de Lange P, van der Lely AJ, Brinkmann AO, de Jong FH, and Lamberts SWJ. 2000. Decreased ligand affinity rather than glucocorticoid receptor down-regulation in patients with endogenous Cushing’s syndrome. European Journal of Endocrinology 142(5):472-476.

Hviid L, Barfod L, and Fowkes FJ. 2015. Trying to remember: immunological B cell memory to malaria. Trends Parasitol 31(3):89-94.

Iliodromitis EK, Kremastinos DT, Katritsis DG, Papadopoulos CC, and Hearse DJ. 1997. Multiple cycles of preconditioning cause loss of protection in open-chest rabbits. J Mol Cell Cardiol 29(3):915-920.

Iliodromitis EK, Lazou A, and Kremastinos DT. 2007. Ischemic preconditioning: protection against myocardial necrosis and apoptosis. Vascular health and risk management 3(5):629-637.

Iliodromitis EK, Papadopoulos C, Paraskevaidis IA, Kyriakides ZS, Flessa C, and Kremastinos DT. 1996. Protection from preconditioning can be reinstated at various reperfusion intervals. Cardiovasc Drugs Ther 10(3):341-346.

Jafari Roodbandi A, Choobineh A, and Daneshvar S. 2015. Relationship between circadian rhythm amplitude and stability with sleep quality and sleepiness among shift nurses and health care workers. Int J Occup Saf Ergon 21(3):312-317.

Jain HV, and Meyer-Hermann M. 2011. The molecular basis of synergism between carboplatin and ABT-737 therapy targeting ovarian carcinomas. Cancer Res 71(3):705-715.

Jain M, Nilsson R, Sharma S, Madhusudhan N, Kitami T, Souza AL, Kafri R, Kirschner MW, Clish CB, and Mootha VK. 2012. Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation. Science 336(6084):1040-1044.

James FO, Cermakian N, and Boivin DB. 2007. Circadian rhythms of melatonin, cortisol, and clock gene expression during simulated night shift work. Sleep 30(11):1427-1436.

Janeway C. 2001. Immunobiology: the immune system in health and disease. London, New York, NY, US: Current Biology Publications; Garland Pub. xix, 635 p. p.

Jangamreddy JR, and Los MJ. 2012. Mitoptosis, a novel mitochondrial death mechanism leading predominantly to activation of autophagy. Hepat Mon 12(8):e6159.

Page 11: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

Bibliography | 173

B

Jeggo P, Defais TM, Samson L, and Schendel P. 1977. An adaptive response of E. coli to low levels of alkylating agent: comparison with previously characterised DNA repair pathways. Mol Gen Genet 157(1):1-9.

Jensen-Dahm C, Werner MU, Jensen TS, Ballegaard M, Andersen BB, Hogh P, and Waldemar G. 2015. Discrepancy between stimulus response and tolerance of pain in Alzheimer disease. Neurology 84(15):1575-1581.

Jin JY, DuBois DC, Almon RR, and Jusko WJ. 2004. Receptor/gene-mediated pharmacodynamic effects of methylprednisolone on phosphoenolpyruvate carboxykinase regulation in rat liver. The Journal of pharmacology and experimental therapeutics 309(1):328-339.

Johnston JD. 2014. Physiological responses to food intake throughout the day. Nutr Res Rev 27(1):107-118.

Kadenbach B. 1969. A quantitative study of the biosynthesis of cytochrome c. Eur J Biochem 10(2):312-317.

Kang R, Zeh HJ, Lotze MT, and Tang D. 2011. The Beclin 1 network regulates autophagy and apoptosis. Cell Death Differ 18(4):571-580.

Kihara A, Kabeya Y, Ohsumi Y, and Yoshimori T. 2001. Beclin-phosphatidylinositol 3-kinase complex functions at the trans-Golgi network. EMBO reports 2(4):330-335.

Kino T. 2012. Circadian rhythms of glucocorticoid hormone actions in target tissues: potential clinical implications. Sci Signal 5(244):pt4.

Kino T, and Chrousos GP. 2011. Acetylation-mediated epigenetic regulation of glucocorticoid receptor activity: Circadian rhythm-associated alterations of glucocorticoid actions in target tissues. Molecular and Cellular Endocrinology 336(1-2):23-30.

Kirschbaum C, Prussner JC, Stone AA, Federenko I, Gaab J, Lintz D, Schommer N, and Hellhammer DH. 1995. Persistent high cortisol responses to repeated psychological stress in a subpopulation of healthy-men. Psychosom Med 57(5):468-474.

Kischkel FC, Hellbardt S, Behrmann I, Germer M, Pawlita M, Krammer PH, and Peter ME. 1995. Cytotoxicity-dependent APO-1 (Fas/CD95)-associated proteins form a death-inducing signaling complex (DISC) with the receptor. The EMBO journal 14(22):5579-5588.

Kitano H. 2004. Biological robustness. Nature Reviews Genetics 5(11):826-837.

Kliewer SA, Moore JT, Wade L, Staudinger JL, Watson MA, Jones SA, McKee DD, Oliver BB, Willson TM, Zetterstrom RH et al. . 1998. An orphan nuclear receptor activated by pregnanes defines a novel steroid signaling pathway. Cell 92(1):73-82.

Koefoed S, Otten MF, Koebmann BJ, Bruggeman FJ, Bakker BM, Snoep JL, Krab K, van Spanning RJM, van Verseveld HW, Jensen PR et al. . 2002. A turbo engine with automatic transmission? How to many chemicomotion to the subtleties and robustness of life. Biochimica Et Biophysica Acta-Bioenergetics 1555(1-3):75-82.

Kolodkin A, Boogerd FC, Plant N, Bruggeman FJ, Goncharuk V, Lunshof J, Moreno-Sanchez R, Yilmaz N, Bakker BM, Snoep JL et al. . 2012. Emergence of the silicon human and network targeting drugs. Eur J Pharm Sci 46(4):190-197.

Kolodkin A, Sahin N, Phillips A, Hood SR, Bruggeman FJ, Westerhoff HV, and Plant N. 2013a. Optimization of stress response through the nuclear receptor-mediated cortisol signalling network. Nature communications 4:1792.

Kolodkin A, Simeonidis E, and Westerhoff HV. 2013b. Computing life: Add logos to biology and bios to physics. Prog Biophys Mol Biol 111(2-3):69-74.

Kolodkin AN, Bruggeman FJ, Plant N, Mone MJ, Bakker BM, Campbell MJ, van Leeuwen JPTM, Carlberg C, Snoep JL, and Westerhoff HV. 2010. Design principles of nuclear receptor signaling: how complex networking improves signal transduction. Molecular Systems Biology 6:446.

Korkmaz A, Topal T, Tan DX, and Reiter RJ. 2009. Role of melatonin in metabolic regulation. Rev Endocr Metab Disord 10(4):261-270.

Page 12: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9

R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

174 | Bibliography

Kubli DA, and Gustafsson AB. 2012. Mitochondria and mitophagy: the yin and yang of cell death control. Circulation research 111(9):1208-1221.

Kuwana T, Bouchier-Hayes L, Chipuk JE, Bonzon C, Sullivan BA, Green DR, and Newmeyer DD. 2005. BH3 domains of BH3-only proteins differentially regulate Bax-mediated mitochondrial membrane permeabilization both directly and indirectly. Molecular cell 17(4):525-535.

Langley LL. 1973. Homeostasis: origins of the concept. Stroudsburg, Pa.,: Dowden. xi, 362 p. p.

Le Novere N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B et al. . 2006. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Research 34:D689-D691.

Lebailly B, Boitard C, and Rogner UC. 2015. Circadian rhythm-related genes: implication in autoimmunity and type 1 diabetes. Diabetes Obes Metab 17 Suppl 1:134-138.

Leber B, Lin J, and Andrews DW. 2007. Embedded together: the life and death consequences of interaction of the Bcl-2 family with membranes. Apoptosis 12(5):897-911.

Leber B, Lin J, and Andrews DW. 2010. Still embedded together binding to membranes regulates Bcl-2 protein interactions. Oncogene 29(38):5221-5230.

Lee JA, and Gao FB. 2008. Regulation of Abeta pathology by beclin 1: a protective role for autophagy? J Clin Invest 118(6):2015-2018.

Legewie S, Herzel H, Westerhoff HV, and Bluthgen N. 2008. Recurrent design patterns in the feedback regulation of the mammalian signalling network. Mol Syst Biol 4:190.

Leibenluft E, and Suppes T. 1999. Treating bipolar illness: focus on treatment algorithms and management of the sleep-wake cycle. Am J Psychiatry 156(12):1976-1981.

Leist M, Gantner F, Bohlinger I, Tiegs G, Germann PG, and Wendel A. 1995. Tumor necrosis factor-induced hepatocyte apoptosis precedes liver failure in experimental murine shock models. The American journal of pathology 146(5):1220-1234.

Leist M, Gantner F, Kunstle G, Bohlinger I, Tiegs G, Bluethmann H, and Wendel A. 1996. The 55-kD tumor necrosis factor receptor and CD95 independently signal murine hepatocyte apoptosis and subsequent liver failure. Mol Med 2(1):109-124.

Leist M, Single B, Castoldi AF, Kuhnle S, and Nicotera P. 1997. Intracellular adenosine triphosphate (ATP) concentration: a switch in the decision between apoptosis and necrosis. J Exp Med 185(8):1481-1486.

Leloup JC, and Goldbeter A. 2003. Toward a detailed computational model for the mammalian circadian clock. Proc Natl Acad Sci U S A 100(12):7051-7056.

Levi F, Okyar A, Dulong S, Innominato PF, and Clairambault J. 2010. Circadian timing in cancer treatments. Annual review of pharmacology and toxicology 50:377-421.

Lewis JG, Bagley CJ, Elder PA, Bachmann AW, and Torpy DJ. 2005. Plasma free cortisol fraction reflects levels of functioning corticosteroid-binding globulin. Clin Chim Acta 359(1-2):189-194.

Li GC, Vasquez JA, Gallagher KP, and Lucchesi BR. 1990. Myocardial protection with preconditioning. Circulation 82(2):609-619.

Li H, Zhu H, Xu CJ, and Yuan J. 1998. Cleavage of BID by caspase 8 mediates the mitochondrial damage in the Fas pathway of apoptosis. Cell 94(4):491-501.

Lin EJ, Symes CW, Townsend-Nicholson A, Klugmann M, Klugmann CB, Lehnert K, Fong D, Young D, and During MJ. 2014. An Immunological Approach to Increase the Brain’s Resilience to Insults. ISRN neuroscience 2014:103213.

Lin WY, Chang YC, Ho CJ, and Huang CC. 2013. Ischemic preconditioning reduces neurovascular damage after hypoxia-ischemia via the cellular inhibitor of apoptosis 1 in neonatal brain. Stroke; a journal of cerebral circulation 44(1):162-169.

Page 13: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

Bibliography | 175

B

Lipsky NG, and Pedersen PL. 1981. Mitochondrial turnover in animal cells. Half-lives of mitochondria and mitochondrial subfractions of rat liver based on [14C]bicarbonate incorporation. The Journal of biological chemistry 256(16):8652-8657.

Liu GS, Thornton J, Van Winkle DM, Stanley AW, Olsson RA, and Downey JM. 1991. Protection against infarction afforded by preconditioning is mediated by A1 adenosine receptors in rabbit heart. Circulation 84(1):350-356.

Liu X, Dai S, Zhu Y, Marrack P, and Kappler JW. 2003. The structure of a Bcl-xL/Bim fragment complex: implications for Bim function. Immunity 19(3):341-352.

Liu X, Kim CN, Yang J, Jemmerson R, and Wang X. 1996. Induction of apoptotic program in cell-free extracts: requirement for dATP and cytochrome c. Cell 86(1):147-157.

Liu Y, and Downey JM. 1992. Ischemic preconditioning protects against infarction in rat heart. Am J Physiol 263(4 Pt 2):H1107-1112.

Locksley RM, Killeen N, and Lenardo MJ. 2001. The TNF and TNF receptor superfamilies: integrating mammalian biology. Cell 104(4):487-501.

Long JE, Drayson MT, Taylor AE, Toellner KM, Lord JM, and Phillips AC. 2016. Morning vaccination enhances antibody response over afternoon vaccination: A cluster-randomised trial. Vaccine 34(24):2679-2685.

Lorsch JR, and Herschlag D. 1999. Kinetic dissection of fundamental processes of eukaryotic translation initiation in vitro. The EMBO journal 18(23):6705-6717.

Lovell JF, Billen LP, Bindner S, Shamas-Din A, Fradin C, Leber B, and Andrews DW. 2008. Membrane binding by tBid initiates an ordered series of events culminating in membrane permeabilization by Bax. Cell 135(6):1074-1084.

Lu YY, Chen TS, Wang XP, and Li L. 2010. Single-cell analysis of dihydroartemisinin-induced apoptosis through reactive oxygen species-mediated caspase-8 activation and mitochondrial pathway in ASTC-a-1 cells using fluorescence imaging techniques. J Biomed Opt 15(4):046028.

Luke NS, DeVito MJ, Shah I, and El-Masri HA. 2010. Development of a quantitative model of pregnane X receptor (PXR) mediated xenobiotic metabolizing enzyme induction. Bulletin of mathematical biology 72(7):1799-1819.

Luo S, and Rubinsztein DC. 2010. Apoptosis blocks Beclin 1-dependent autophagosome synthesis: an effect rescued by Bcl-xL. Cell Death Differ 17(2):268-277.

Ma PTS, Yamamoto T, Goldstein JL, and Brown MS. 1986. Increased mRNA for low density lipoprotein receptor in livers of rabbits treated with 17α-ethinylestrαdiol. Proceedings of the National Academy of Sciences USA 83:792-796.

MacHale SM, Cavanagh JT, Bennie J, Carroll S, Goodwin GM, and Lawrie SM. 1998. Diurnal variation of adrenocortical activity in chronic fatigue syndrome. Neuropsychobiology 38(4):213-217.

Madan A, Graham RA, Carroll KM, Mudra DR, Burton LA, Krueger LA, Downey AD, Czerwinski M, Forster J, Ribadeneira MD et al. . 2003. Effects of prototypical microsomal enzyme inducers on cytochrome P450 expression in cultured human hepatocytes. Drug Metabolism and Disposition 31(4):421-431.

Maes M, Calabrese J, and Meltzer HY. 1994. The relevance of the in- versus outpatient status for studies on HPA-axis in depression: spontaneous hypercortisolism is a feature of major depressed inpatients and not of major depression per se. Prog Neuropsychopharmacol Biol Psychiatry 18(3):503-517.

Maiuri MC, Le Toumelin G, Criollo A, Rain JC, Gautier F, Juin P, Tasdemir E, Pierron G, Troulinaki K, Tavernarakis N et al. . 2007. Functional and physical interaction between Bcl-X(L) and a BH3-like domain in Beclin-1. The EMBO journal 26(10):2527-2539.

Manary MJ, Muglia LJ, Vogt SK, and Yarasheski KE. 2006. Cortisol and its action on the glucocorticoid receptor in malnutrition and acute infection. Metabolism 55(4):550-554.

Manzella N, Bracci M, Strafella E, Staffolani S, Ciarapica V, Copertaro A, Rapisarda V, Ledda C, Amati M, Valentino M et al. . 2015. Circadian Modulation of 8-Oxoguanine DNA Damage Repair. Sci Rep 5:13752.

Page 14: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9

R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

176 | Bibliography

Marani M, Tenev T, Hancock D, Downward J, and Lemoine NR. 2002. Identification of novel isoforms of the BH3 domain protein Bim which directly activate Bax to trigger apoptosis. Mol Cell Biol 22(11):3577-3589.

Marissal-Arvy N, Mormede P, and Sarrieau A. 1999. Strain differences in corticosteroid receptor efficiencies and regulation in Brown Norway and Fischer 344 rats. Journal of neuroendocrinology 11(4):267-273.

Martinez JL, and Baquero F. 2014. Emergence and spread of antibiotic resistance: setting a parameter space. Ups J Med Sci 119(2):68-77.

Martinou JC, and Youle RJ. 2011. Mitochondria in apoptosis: Bcl-2 family members and mitochondrial dynamics. Developmental cell 21(1):92-101.

Martiny K, Refsgaard E, Lund V, Lunde M, Thougaard B, Lindberg L, and Bech P. 2015. Maintained superiority of chronotherapeutics vs. exercise in a 20-week randomized follow-up trial in major depression. Acta Psychiatr Scand 131(6):446-457.

Marwan W, Rohr C, and Heiner M. 2012. Petri Nets in Snoopy: A Unifying Framework for the Graphical Display, Computational Modelling, and Simulation of Bacterial Regulatory Networks. In: VanHelden J, Toussaint A, and Thieffry D, editors. Bacterial Molecular Networks: Methods and Protocols. p 409-437.

Masson MJ, Collins LA, Carpenter LD, Graf ML, Ryan PM, Bourdi M, and Pohl LR. 2010. Pathologic role of stressed-induced glucocorticoids in drug-induced liver injury in mice. Biochem Biophys Res Commun 397(3):453-458.

Masuyama H, Inoshita H, Hiramatsu Y, and Kudo T. 2002. Ligands have various potential effects on the degradation of pregnane X receptor by proteasome. Endocrinology 143(1):55-61.

Maulik N, Engelman RM, Rousou JA, Flack JE, 3rd, Deaton D, and Das DK. 1999. Ischemic preconditioning reduces apoptosis by upregulating anti-death gene Bcl-2. Circulation 100(19 Suppl):II369-375.

Maury E, Ramsey KM, and Bass J. 2010. Circadian rhythms and metabolic syndrome: from experimental genetics to human disease. Circulation research 106(3):447-462.

Michael Bell KD, Mark Smith, John Hallenbeck. 2002. Ischemic tolerance in the brain: models and mechanisms. In: K.B. Storey JMS, editor. Sensing, signaling and cell adaptation Amsterdam, The Netherlands: Elsevier Science B.V. p 1-12.

Miwa S, Lawless C, and von Zglinicki T. 2008. Mitochondrial turnover in liver is fast in vivo and is accelerated by dietary restriction: application of a simple dynamic model. Aging Cell 7(6):920-923.

Mizushima N, Levine B, Cuervo AM, and Klionsky DJ. 2008. Autophagy fights disease through cellular self-digestion. Nature 451(7182):1069-1075.

Mola PW, Farah IO, Kariuki TM, Nyindo M, Blanton RE, and King CL. 1999. Cytokine control of the granulomatous response in Schistosoma mansoni-infected baboons: role of exposure and treatment. Infect Immun 67(12):6565-6571.

Moreno-Risueno MA, and Benfey PN. 2011. Time-based patterning in development: The role of oscillating gene expression. Transcription 2(3):124-129.

Munck A, Guyre PM, and Holbrook NJ. 1984. Physiological functions of glucocorticoids in stress and their relation to pharmacological actions. Endocr Rev 5(1):25-44.

Murry CE, Jennings RB, and Reimer KA. 1986. Preconditioning with ischemia: a delay of lethal cell injury in ischemic myocardium. Circulation 74(5):1124-1136.

Nader N, Chrousos GP, and Kino T. 2009. Circadian rhythm transcription factor CLOCK regulates the transcriptional activity of the glucocorticoid receptor by acetylating its hinge region lysine cluster: potential physiological implications. Faseb Journal 23(5):1572-1583.

Neeck G, Federlin K, Graef V, Rusch D, and Schmidt KL. 1990. Adrenal secretion of cortisol in patients with rheumatoid arthritis. J Rheumatol 17(1):24-29.

Page 15: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

Bibliography | 177

B

Nikoletopoulou V, Markaki M, Palikaras K, and Tavernarakis N. 2013. Crosstalk between apoptosis, necrosis and autophagy. Biochim Biophys Acta 1833(12):3448-3459.

Norbury CJ, and Hickson ID. 2001. Cellular responses to DNA damage. Annual review of pharmacology and toxicology 41:367-401.

Noreault TL, Kostrubsky VE, Wood SG, Nichols RC, Strom SC, Trask HW, Wrighton SA, Evans RM, Jacobs JM, Sinclair PR et al. . 2005. Arsenite decreases CYP3A4 and RXRalpha in primary human hepatocytes. Drug metabolism and disposition: the biological fate of chemicals 33(7):993-1003.

O’Connor L, Strasser A, O’Reilly LA, Hausmann G, Adams JM, Cory S, and Huang DC. 1998. Bim: a novel member of the Bcl-2 family that promotes apoptosis. The EMBO journal 17(2):384-395.

Oakley RH, and Cidlowski JA. 1993. Homologous down regulation of the glucocorticoid receptor: The molecular machinery. Critical Reviews in Eukaryotic Gene Expression 3(2):63-88.

Oberstein A, Jeffrey PD, and Shi Y. 2007. Crystal structure of the Bcl-XL-Beclin 1 peptide complex: Beclin 1 is a novel BH3-only protein. The Journal of biological chemistry 282(17):13123-13132.

Ogilvie LA, Wierling C, Kessler T, Lehrach H, and Lange BM. 2015. Predictive Modeling of Drug Treatment in the Area of Personalized Medicine. Cancer Inform 14(Suppl 4):95-103.

Oike H, Oishi K, and Kobori M. 2014. Nutrients, Clock Genes, and Chrononutrition. Curr Nutr Rep 3:204-212.

Oike H, Sakurai M, Ippoushi K, and Kobori M. 2015. Time-fixed feeding prevents obesity induced by chronic advances of light/dark cycles in mouse models of jet-lag/shift work. Biochem Biophys Res Commun 465(3):556-561.

Ola MS, Nawaz M, and Ahsan H. 2011. Role of Bcl-2 family proteins and caspases in the regulation of apoptosis. Molecular and cellular biochemistry 351(1-2):41-58.

Onuki R, Nagasaki A, Kawasaki H, Baba T, Uyeda TQ, and Taira K. 2002. Confirmation by FRET in individual living cells of the absence of significant amyloid beta -mediated caspase 8 activation. Proc Natl Acad Sci U S A 99(23):14716-14721.

Orias M, and Correa-Rotter R. 2011. Chronotherapy in hypertension: a pill at night makes things right? J Am Soc Nephrol 22(12):2152-2155.

Orth JD, Thiele I, and Palsson BO. 2010. What is flux balance analysis? Nat Biotechnol 28(3):245-248.

Pan D, Kocherginsky M, and Conzen SD. 2011. Activation of the Glucocorticoid Receptor Is Associated with Poor Prognosis in Estrogen Receptor-Negative Breast Cancer. Cancer Research 71(20):6360-6370.

Pascussi J-M, Drocourt L, Fabre J-M, Maurel P, and Vilarem M-J. 2000. Dexamethasone induces pregnane X receptor and retinoid X receptor-α expression in human hepatocytes: Synergistic increase of CYP3A4 induction by pregnane X receptor. Molecular Pharmacology 58:361-372.

Pattingre S, Tassa A, Qu X, Garuti R, Liang XH, Mizushima N, Packer M, Schneider MD, and Levine B. 2005. Bcl-2 antiapoptotic proteins inhibit Beclin 1-dependent autophagy. Cell 122(6):927-939.

Pavlatou MG, Vickers KC, Varma S, Malek R, Sampson M, Remaley AT, Gold PW, Skarulis MC, and Kino T. 2013. Circulating cortisol-associated signature of glucocorticoid-related gene expression in subcutaneous fat of obese subjects. Obesity (Silver Spring) 21(5):960-967.

Pavlov IP. Psychopathology and psychiatry; selected works. Moskow: Foreign Languages Pub. House. 542 p. p.

Pavlov IP. 1955. Selected works. Moscow,: Foreign Languages Pub. House. 653 p. p.

Pavlov IP, Gantt WH, and Fol’bort GV. 1928. Lectures on conditioned reflexes. New York,: International publishers.

Peter ME, and Krammer PH. 1998. Mechanisms of CD95 (APO-1/Fas)-mediated apoptosis. Current opinion in immunology 10(5):545-551.

Page 16: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9

R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

178 | Bibliography

Phillips A, Hood SR, Gibson GG, and Plant NJ. 2005. Impact of transcription factor profile and chromatin conformation on human hepatocyte CYP3A gene expression. Drug metabolism and disposition: the biological fate of chemicals 33(2):233-242.

Plant N. 2007. The human cytochrome P450 3A sub-family: transcriptional regulation, inter-individual variation and interaction networks. Biochimica et Biophysica Acta-General Subjects 1770(3):478-488.

Plant N, and Aouabdi S. 2009. Nuclear receptors: the controlling force in drug metabolism of the liver? Xenobiotica 39(8):597-605.

Polman JAE, Welten JE, Bosch DS, de Jonge RT, Balog J, van der Maarel SM, de Kloet ER, and Datson NA. 2012. A genome-wide signature of glucocorticoid receptor binding in neuronal PC12 cells. BMC Neurosci 13:118.

Proskuryakov SY, Konoplyannikov AG, and Gabai VL. 2003. Necrosis: a specific form of programmed cell death? Exp Cell Res 283(1):1-16.

Pruessner JC, Hellhammer DH, and Kirschbaum C. 1999. Burnout, perceived stress, and cortisol responses to awakening. Psychosom Med 61(2):197-204.

Psychogios N, Hau DD, Peng J, Guo AC, Mandal R, Bouatra S, Sinelnikov I, Krishnamurthy R, Eisner R, Gautam B et al. . 2011. The human serum metabolome. PLoS One 6(2):e16957.

Pujols L, Mullol J, Roca-Ferrer J, Torrego A, Xaubet A, Cidlowski JA, and Picado C. 2002. Expression of glucocorticoid receptor alpha- and beta-isoforms in human cells and tissues. American journal of physiology Cell physiology 283(4):C1324-1331.

Puthalakath H, Huang DC, O’Reilly LA, King SM, and Strasser A. 1999. The proapoptotic activity of the Bcl-2 family member Bim is regulated by interaction with the dynein motor complex. Molecular cell 3(3):287-296.

Quinton-Tulloch MJ, Bruggeman FJ, Snoep JL, and Westerhoff HV. 2013. Trade-off of dynamic fragility but not of robustness in metabolic pathways in silico. FEBS J 280(1):160-173.

Ramakrishnan R, DuBois DC, Almon RR, Pyszczynski NA, and Jusko WJ. 2002. Fifth-generation model for corticosteroid pharmacodynamics: application to steady-state receptor down-regulation and enzyme induction patterns during seven-day continuous infusion of methylprednisolone in rats. Journal of pharmacokinetics and pharmacodynamics 29(1):1-24.

Rehman S, Day PJ, Bayat A, and Westerhoff HV. 2012. Understanding Dupuytren’s Disease Using Systems Biology: A Move Away from Reductionism. Front Physiol 3:316.

Reul JM, and de Kloet ER. 1985. Two receptor systems for corticosterone in rat brain: microdistribution and differential occupation. Endocrinology 117(6):2505-2511.

Rhen T, and Cidlowski JA. 2005. Antiinflammatory action of glucocorticoids - New mechanisms for old drugs. New England Journal of Medicine 353(16):1711-1723.

Richard P, Bakker BM, Teusink B, Van Dam K, and Westerhoff HV. 1996. Acetaldehyde mediates the synchronization of sustained glycolytic oscillations in populations of yeast cells. Eur J Biochem 235(1-2):238-241.

Riddick G, and Macara IG. 2007. The adapter importin-alpha provides flexible control of nuclear import at the expense of efficiency. Mol Syst Biol 3:118.

Rigaud G, Roux J, Pictet R, and Grange T. 1991. In vivo footprinting of rat TAT gene - Dynamic interplay between the glucocorticoid receptor and a liver-specific factor. Cell 67(5):977-986.

Risberg A, Sjoquist M, Wedenberg K, and Larsson A. 2016. Elevated glucose levels in early puerperium, and association with high cortisol levels during parturition. Scand J Clin Lab Invest 76(4):309-312.

Roberts AD, Wessely S, Chalder T, Papadopoulos A, and Cleare AJ. 2004. Salivary cortisol response to awakening in chronic fatigue syndrome. Br J Psychiatry 184:136-141.

Robles MS, Cox J, and Mann M. 2014. In-Vivo Quantitative Proteomics Reveals a Key Contribution of Post-Transcriptional Mechanisms to the Circadian Regulation of Liver Metabolism. Plos Genetics 10(1).

Page 17: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

Bibliography | 179

B

Roy MJ, Vom A, Czabotar PE, and Lessene G. 2013. Cell death and the mitochondria: therapeutic targeting of the BCL-2 family-driven pathway. British journal of pharmacology.

Ruebenbauer A. 2007. Simulation of the neural response to the odour stimulus. J Theor Biol 248(2):311-316.

Ruger M, and Scheer FA. 2009. Effects of circadian disruption on the cardiometabolic system. Rev Endocr Metab Disord 10(4):245-260.

Rundlett KL, and Armstrong DW. 1996. Examination of the origin, variation, and proper use of expressions for the estimation of association constants by capillary electrophoresis. J Chromatogr A 721(1):173-186.

Rybakova KN, Bruggeman FJ, Tomaszewska A, Mone MJ, Carlberg C, and Westerhoff HV. 2015. Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism. PLoS Comput Biol 11(4):e1004236.

Sacan A, Ekins S, and Kortagere S. 2012. Applications and limitations of in silico models in drug discovery. Methods Mol Biol 910:87-124.

Saito M, Korsmeyer SJ, and Schlesinger PH. 2000. BAX-dependent transport of cytochrome c reconstituted in pure liposomes. Nat Cell Biol 2(8):553-555.

Samarasinghe AE, Woolard SN, Boyd KL, Hoselton SA, Schuh JM, and McCullers JA. 2014. The immune profile associated with acute allergic asthma accelerates clearance of influenza virus. Immunology and cell biology 92(5):449-459.

Savvidis C, and Koutsilieris M. 2012. Circadian rhythm disruption in cancer biology. Mol Med 18:1249-1260.

Schellenberg B, Wang P, Keeble JA, Rodriguez-Enriquez R, Walker S, Owens TW, Foster F, Tanianis-Hughes J, Brennan K, Streuli CH et al. . 2013. Bax exists in a dynamic equilibrium between the cytosol and mitochondria to control apoptotic priming. Molecular cell 49(5):959-971.

Schlotz W, Hellhammer J, Schulz P, and Stone AA. 2004. Perceived work overload and chronic worrying predict weekend-weekday differences in the cortisol awakening response. Psychosom Med 66(2):207-214.

Schott RJ, Rohmann S, Braun ER, and Schaper W. 1990. Ischemic preconditioning reduces infarct size in swine myocardium. Circulation research 66(4):1133-1142.

Scott KA, Melhorn SJ, and Sakai RR. 2012. Effects of Chronic Social Stress on Obesity. Curr Obes Rep 1(1):16-25.

Sedlak TW, Oltvai ZN, Yang E, Wang K, Boise LH, Thompson CB, and Korsmeyer SJ. 1995. Multiple Bcl-2 family members demonstrate selective dimerizations with Bax. Proc Natl Acad Sci U S A 92(17):7834-7838.

Seldin MM, Byerly MS, Petersen PS, Swanson R, Balkema-Buschmann A, Groschup MH, and Wong GW. 2014. Seasonal oscillation of liver-derived hibernation protein complex in the central nervous system of non-hibernating mammals. J Exp Biol 217(Pt 15):2667-2679.

Shamas-Din A, Bindner S, Zhu W, Zaltsman Y, Campbell C, Gross A, Leber B, Andrews DW, and Fradin C. 2013a. tBid undergoes multiple conformational changes at the membrane required for Bax activation. The Journal of biological chemistry 288(30):22111-22127.

Shamas-Din A, Kale J, Leber B, and Andrews DW. 2013b. Mechanisms of action of Bcl-2 family proteins. Cold Spring Harb Perspect Biol 5(4):a008714.

Shamas-Din A, Satsoura D, Khan O, Zhu W, Leber B, Fradin C, and Andrews DW. 2014. Multiple partners can kiss-and-run: Bax transfers between multiple membranes and permeabilizes those primed by tBid. Cell Death Dis 5:e1277.

Sher L. 2004. Daily hassles, cortisol, and the pathogenesis of depression. Med Hypotheses 62(2):198-202.

Page 18: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9

R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

180 | Bibliography

Shi S, Yang W, Tu X, Chen C, and Wang C. 2013. Ischemic preconditioning reduces ischemic brain injury by suppressing nuclear factor kappa B expression and neuronal apoptosis. Neural regeneration research 8(7):633-638.

Shimizu S, Eguchi Y, Kamiike W, Itoh Y, Hasegawa J, Yamabe K, Otsuki Y, Matsuda H, and Tsujimoto Y. 1996. Induction of apoptosis as well as necrosis by hypoxia and predominant prevention of apoptosis by Bcl-2 and Bcl-XL. Cancer Res 56(9):2161-2166.

Shivakumar S, Kurylowicz M, Hirmiz N, Manan Y, Friaa O, Shamas-Din A, Masoudian P, Leber B, Andrews DW, and Fradin C. 2014. The proapoptotic protein tBid forms both superficially bound and membrane-inserted oligomers. Biophys J 106(10):2085-2095.

Shively CA, Register TC, and Clarkson TB. 2009a. Social Stress, Visceral Obesity, and Coronary Artery Atherosclerosis: Product of a Primate Adaptation. Am J Primatol 71(9):742-751.

Shively CA, Register TC, and Clarkson TB. 2009b. Social stress, visceral obesity, and coronary artery atherosclerosis: product of a primate adaptation. Am J Primatol 71(9):742-751.

Sinha S, and Levine B. 2008. The autophagy effector Beclin 1: a novel BH3-only protein. Oncogene 27 Suppl 1:S137-148.

Skulachev VP. 2000. Mitochondria in the programmed death phenomena; a principle of biology: “it is better to die than to be wrong”. IUBMB Life 49(5):365-373.

Smyth JM, Ockenfels MC, Gorin AA, Catley D, Porter LS, Kirschbaum C, Hellhammer DH, and Stone AA. 1997. Individual differences in the diurnal cycle of cortisol. Psychoneuroendocrinology 22(2):89-105.

Snoep JL, Green K, Eicher J, Palm DC, Penkler G, du Toit F, Walters N, Burger R, Westerhoff HV, and van Niekerk DD. 2015. Quantitative analysis of drug effects at the whole-body level: a case study for glucose metabolism in malaria patients. Biochem Soc Trans 43(6):1157-1163.

Sohlenius-Sternbeck AK. 2006. Determination of the hepatocellularity number for human, dog, rabbit, rat and mouse livers from protein concentration measurements. Toxicol In Vitro 20(8):1582-1586.

Southam CM, Ehrlich, J. 1943. Effects of extracts of western red cedar heartwood on certain wood-decaying fungi in culture. Phytopathology(33):517-524.

Spence KW. 1950. Cognitive versus stimulus-response theories of learning. Psychol Rev 57(3):159-172.

Starr C, and Taggart R. 1989. Biology: the unity and diversity of life. Belmont, Calif.: Wadsworth Pub. Co. xx, 834 p. p.

Steptoe A, and Wardle J. 2005. Positive affect and biological function in everyday life. Neurobiol Aging 26 Suppl 1:108-112.

Stranges PM, Drew AM, Rafferty P, Shuster JE, and Brooks AD. 2015. Treatment of hypertension with chronotherapy: is it time of drug administration? Ann Pharmacother 49(3):323-334.

Street A, Cuddihy L, Best D, Wilks D, Geladas D, and Chew S. 1997. Rostering: placing the nurse in the picture. Contemp Nurse 6(3-4):145-151.

Sullivan PJ, Sweeney KJ, Hirpara KM, Malone CB, Curtin W, and Kerin MJ. 2009. Cyclical ischaemic preconditioning modulates the adaptive immune response in human limb ischaemia-reperfusion injury. Br J Surg 96(4):381-390.

Takacs-Vellai K, Vellai T, Puoti A, Passannante M, Wicky C, Streit A, Kovacs AL, and Muller F. 2005. Inactivation of the autophagy gene bec-1 triggers apoptotic cell death in C. elegans. Curr Biol 15(16):1513-1517.

Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD et al. . 2013. A community-driven global reconstruction of human metabolism. Nat Biotechnol 31(5):419-425.

Tomai F, Crea F, Chiariello L, and Gioffre PA. 1999. Ischemic preconditioning in humans: models, mediators, and clinical relevance. Circulation 100(5):559-563.

Page 19: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

Bibliography | 181

B

Turbill C, Bieber C, and Ruf T. 2011. Hibernation is associated with increased survival and the evolution of slow life histories among mammals. Proc Biol Sci 278(1723):3355-3363.

Ueda K, Fujiki K, Shirahige K, Gomez-Sanchez CE, Fujita T, Nangaku M, and Nagase M. 2014. Genome-wide analysis of murine renal distal convoluted tubular cells for the target genes of mineralocorticoid receptor. Biochem Biophys Res Commun 445(1):132-137.

Ugazio G, Koch RR, and Recknagel RO. 1972. Mechanism of protection against carbon tetrachloride by prior carbon tetrachloride administration. Exp Mol Pathol 16(3):281-285.

Uhal BD, Ramos, C., Joshi, I., Bifero, A., Pardo, A. & Selman, M. 1998. Cell size, cell cycle, and alpha-smooth muscle actin expression by primary human lung fibroblasts. The American journal of physiology 275(L998-L1005).

van Steensel B, Brink M, van der Meulen K, van Binnendijk EP, Wansink DG, de Jong L, de Kloet ER, and van Driel R. 1995. Localization of the glucocorticoid receptor in discrete clusters in the cell nucleus. Journal of cell science 108 ( Pt 9):3003-3011.

Vogel SW, Bijlenga D, Tanke M, Bron TI, van der Heijden KB, Swaab H, Beekman AT, and Kooij JJ. 2015. Circadian rhythm disruption as a link between Attention-Deficit/Hyperactivity Disorder and obesity? J Psychosom Res 79(5):443-450.

Volkert MR. 1988. Adaptive response of Escherichia coli to alkylation damage. Environ Mol Mutagen 11(2):241-255.

Wada T, Gao J, and Xie W. 2009. PXR and CAR in energy metabolism. Trends in Endocrinology and Metabolism 20(6):273-279.

Walker EF, Bonsall R, and Walder DJ. 2002. Plasma hormones and catecholamine metabolites in monozygotic twins discordant for psychosis. Neuropsychiatry Neuropsychol Behav Neurol 15(1):10-17.

Wang Y, Liao M, Hoe N, Acharya P, Deng C, Krutchinsky AN, and Correia MA. 2009. A role for protein phosphorylation in cytochrome P450 3A4 ubiquitin-dependent proteasomal degradation. The Journal of biological chemistry 284(9):5671-5684.

Watkins PB, Wrighton SA, Schuetz EG, Maurel P, and Guzelian PS. 1986. Macrolide antibiotics inhibit the degradation of the glucocorticoid-responsive cytochrome P-450p in rat hepatocytes in vivo and in primary monolayer culture. The Journal of biological chemistry 261(14):6264-6271.

Wee KB, Yio WK, Surana U, and Chiam KH. 2012. Transcription factor oscillations induce differential gene expressions. Biophys J 102(11):2413-2423.

Wei MC, Zong WX, Cheng EH, Lindsten T, Panoutsakopoulou V, Ross AJ, Roth KA, MacGregor GR, Thompson CB, and Korsmeyer SJ. 2001. Proapoptotic BAX and BAK: a requisite gateway to mitochondrial dysfunction and death. Science 292(5517):727-730.

Weitzman ED, Fukushima D, Nogeire C, Roffwarg H, Gallagher TF, and Hellman L. 1971. Twenty-four hour pattern of the episodic secretion of cortisol in normal subjects. J Clin Endocrinol Metab 33(1):14-22.

West AC, and Bechtold DA. 2015. The cost of circadian desynchrony: Evidence, insights and open questions. Bioessays 37(7):777-788.

West S. 2001. Circadian rhythm, shiftwork and you! Collegian 8(4):14-21.

Westerhoff HV. 2007. Mathematical and theoretical biology for systems biology, and then ... vice versa. Journal of mathematical biology 54(1):147-150.

Westerhoff HV, Kolodkin A, Conradie R, Wilkinson SJ, Bruggeman FJ, Krab K, van Schuppen JH, Hardin H, Bakker BM, Mone MJ et al. . 2009. Systems biology towards life in silico: mathematics of the control of living cells. Journal of mathematical biology 58(1-2):7-34.

Westerhoff HV, Mosekilde E, Noe CR, and Clemensen AM. 2008. Integrating systems approaches into pharmaceutical sciences. Eur J Pharm Sci 35(1-2):1-4.

Page 20: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell

R1R2R3R4R5R6R7R8R9

R10R11R12R13R14R15R16R17R18R19R20R21R22R23R24R25R26R27R28R29R30R31R32R33R34R35R36R37R38R39

182 | Bibliography

Westphal D, Dewson G, Czabotar PE, and Kluck RM. 2011. Molecular biology of Bax and Bak activation and action. Biochim Biophys Acta 1813(4):521-531.

Wirawan E, Vande Walle L, Kersse K, Cornelis S, Claerhout S, Vanoverberghe I, Roelandt R, De Rycke R, Verspurten J, Declercq W et al. . 2010. Caspase-mediated cleavage of Beclin-1 inactivates Beclin-1-induced autophagy and enhances apoptosis by promoting the release of proapoptotic factors from mitochondria. Cell Death Dis 1:e18.

Withanage GS, Wigley P, Kaiser P, Mastroeni P, Brooks H, Powers C, Beal R, Barrow P, Maskell D, and McConnell I. 2005. Cytokine and chemokine responses associated with clearance of a primary Salmonella enterica serovar Typhimurium infection in the chicken and in protective immunity to rechallenge. Infect Immun 73(8):5173-5182.

Wolf OT, Schommer NC, Hellhammer DH, McEwen BS, and Kirschbaum C. 2001. The relationship between stress induced cortisol levels and memory differs between men and women. Psychoneuroendocrinology 26(7):711-720.

Wust S, Federenko I, Hellhammer DH, and Kirschbaum C. 2000. Genetic factors, perceived chronic stress, and the free cortisol response to awakening. Psychoneuroendocrinology 25(7):707-720.

Xue L, Fletcher GC, and Tolkovsky AM. 2001. Mitochondria are selectively eliminated from eukaryotic cells after blockade of caspases during apoptosis. Curr Biol 11(5):361-365.

Yamamoto M, and Matsui N. 1978. [Effects of changes of body temperature on serum cortisol fractions (author’s transl)]. Nihon Naibunpi Gakkai Zasshi 54(3):187-202.

Yan WJ, Dong HL, and Xiong LZ. 2013. The protective roles of autophagy in ischemic preconditioning. Acta pharmacologica Sinica 34(5):636-643.

Yang J, Liu X, Bhalla K, Kim CN, Ibrado AM, Cai J, Peng TI, Jones DP, and Wang X. 1997. Prevention of apoptosis by Bcl-2: release of cytochrome c from mitochondria blocked. Science 275(5303):1129-1132.

Yao Y, Bobkov AA, Plesniak LA, and Marassi FM. 2009. Mapping the interaction of pro-apoptotic tBID with pro-survival BCL-XL. Biochemistry 48(36):8704-8711.

Yethon JA, Epand RF, Leber B, Epand RM, and Andrews DW. 2003. Interaction with a membrane surface triggers a reversible conformational change in Bax normally associated with induction of apoptosis. The Journal of biological chemistry 278(49):48935-48941.

Youle RJ, and Strasser A. 2008. The BCL-2 protein family: opposing activities that mediate cell death. Nat Rev Mol Cell Biol 9(1):47-59.

Zha J, Weiler S, Oh KJ, Wei MC, and Korsmeyer SJ. 2000. Posttranslational N-myristoylation of BID as a molecular switch for targeting mitochondria and apoptosis. Science 290(5497):1761-1765.

Zhang H, Bosch-Marce M, Shimoda LA, Tan YS, Baek JH, Wesley JB, Gonzalez FJ, and Semenza GL. 2008. Mitochondrial autophagy is an HIF-1-dependent adaptive metabolic response to hypoxia. The Journal of biological chemistry 283(16):10892-10903.

Zhang J, and Bowden GT. 2007. Targeting Bcl-X(L) for prevention and therapy of skin cancer. Mol Carcinog 46(8):665-670.

Zhou L, and Chang DC. 2008. Dynamics and structure of the Bax-Bak complex responsible for releasing mitochondrial proteins during apoptosis. Journal of cell science 121(Pt 13):2186-2196.

Zhu Y, Massen S, Terenzio M, Lang V, Chen-Lindner S, Eils R, Novak I, Dikic I, Hamacher-Brady A, and Brady NR. 2013. Modulation of serines 17 and 24 in the LC3-interacting region of Bnip3 determines pro-survival mitophagy versus apoptosis. The Journal of biological chemistry 288(2):1099-1113.

Ziegelhoffer A, Vrbjar N, Styk J, Breier A, Dzurba A, and Ravingerova T. 1995. Adaptation of the heart to ischemia by preconditioning: effects on energy equilibrium, properties of sarcolemmal ATPases and release of cardioprotective proteins. Molecular and cellular biochemistry 147(1-2):129-137.

Page 21: 24001 Nilgun ID55 - research.vu.nl Bibliography.pdf · The pathogenetic role of cortisol in the metabolic syndrome: a hypothesis. J Clin Endocrinol ... Billen LP, Kokoski CL, Lovell