@article {1513, title = {Dynamic trade-offs in granulocyte colony-stimulating factor (G-CSF) administration during chemotherapy}, journal = {System Dynamics Review}, volume = {36}, year = {2021}, pages = {397{\textendash}446}, abstract = {

Chemotherapeutic treatment of cancer comes with side effects on the immune system, such as Chemotherapy-Induced Neutropenia (CIN). A recombinant form of Granulocyte Colony-Stimulating Factor (G-CSF) has been used to alleviate CIN. This is a challenging task due to the feedback complexity of the hematological system. A System Dynamics model is constructed to study this system and to derive practical insights for the management of CIN. Stimulation of neutrophil production via G-CSF is observed to propose crucial trade-offs. On one hand, production by stem cells and mobilization from bone marrow should be stimulated to compensate for the impairment caused by chemotherapy. On the other hand, it is important to avoid overstimulation, which reduces the regenerative capacity, as well as draining the much-needed bone-marrow reservoir. Our analysis supports the intuition that the response to G-CSF administration is conditional to patient characteristics, and {\textquotedblleft}one for all{\textquotedblright} treatment protocols are impractical. {\textcopyright} 2021 System Dynamics Society.

}, issn = {10991727}, doi = {10.1002/sdr.1671}, author = {{\.I}rsoy, Orkun and G{\"u}z, {\c S}anser and Akan, Naz Beril and G{\"o}nen{\c c} Y{\"u}cel} } @article {1425, title = {Decentralized decomposition algorithms for peer-to-peer linear optimization}, journal = {RAIRO-Oper. Res.}, volume = {54}, year = {2020}, pages = {1835-1861}, doi = {10.1051/ro/2019097}, url = {https://doi.org/10.1051/ro/2019097}, author = {Aydin, M. Asli and Z C Ta{\c s}k{\i}n} } @article {1431, title = {A decomposition approach to solve the selective graph coloring problem in some perfect graph families}, journal = {Networks}, volume = {73}, year = {2019}, pages = {145-169}, abstract = {

Graph coloring is the problem of assigning a minimum number of colors to all vertices of a graph such that no two adjacent vertices receive the same color. The selective graph coloring problem is a generalization of the standard graph coloring problem; given a graph with a partition of its vertex set into clusters, the objective is to choose exactly one vertex per cluster so that, among all possible selections, the number of colors necessary to color the vertices in the selection is minimum. This study focuses on a decomposition based exact solution framework for selective coloring in some perfect graph families: in particular, permutation, generalized split, and chordal graphs where the selective coloring problem is known to be NP-hard. Our method combines integer programming techniques and combinatorial algorithms for the graph classes of interest. We test our method on graphs with different sizes and densities, present computational results and compare them with solving an integer programming formulation of the problem by CPLEX, and a state-of-the art algorithm from the literature. Our computational experiments indicate that our decomposition approach significantly improves solution performance in low-density graphs, and regardless of edge-density in the class of chordal graphs.

}, keywords = {chordal graphs, decomposition algorithm, generalized split graphs, integer programming, partition coloring, permutation graphs, selective graph coloring}, doi = {https://doi.org/10.1002/net.21850}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/net.21850}, author = {{\c S}eker, Oylum and Ekim, Tinaz and Z C Ta{\c s}k{\i}n} } @article {1432, title = {The determination of optimal treatment plans for Volumetric Modulated Arc Therapy (VMAT)}, journal = {European Journal of Operational Research}, volume = {272}, year = {2019}, pages = {372-388}, abstract = {

The success of radiation therapy depends on the ability to deliver the proper amount of radiation to cancerous cells while protecting healthy tissues. As a natural consequence, any new treatment technology improves quality standards concerning primarily this issue. Similar to the widely used Intensity Modulated Radiation Therapy (IMRT), the radiation resource is outside of the patient{\textquoteright}s body and the beam is shaped by a multi-leaf collimator mounted on the linear accelerator{\textquoteright}s head during the state-of-the-art Volumetric Modulated Arc Therapy (VMAT) as well. However, unlike IMRT, the gantry of the accelerator may rotate along one or more arcs and deliver radiation continuously. This property makes VMAT powerful in obtaining high conformal plans in terms of dose distribution; but the apertures are interdependent and optimal treatment planning problem cannot be decomposed into simpler independent subproblems as a consequence. In this work, we consider optimal treatment planning problem for VMAT. First, we formulate a mixed-integer linear program minimizing total radiation dose intensity subject to clinical requirements embedded within the constraints. Then, we develop efficient solution procedures combining Benders decomposition with certain acceleration strategies. We investigate their performance on a large set of test instances obtained from an anonymous real prostate cancer data.

}, keywords = {algorithms, Benders decomposition, integer programming, Radiation therapy, VMAT}, issn = {0377-2217}, doi = {https://doi.org/10.1016/j.ejor.2018.06.023}, url = {https://www.sciencedirect.com/science/article/pii/S0377221718305514}, author = {P{\i}nar Dursun and Z C Ta{\c s}k{\i}n and I. Kuban Altinel} } @article {1443, title = {Determining the most vulnerable components in a transportation network}, journal = {Sigma}, volume = {9}, year = {2018}, pages = {371{\textendash}382}, author = {K{\"u}{\c c}{\"u}kayd{\i}n, Hande and Necati Aras} } @article {1164, title = {Designing distribution systems with reverse flows}, journal = {Journal of Remanufacturing}, volume = {7}, year = {2017}, pages = {113{\textendash}137}, author = {Tombu{\c s}, Ay{\c s}e Cilac{\i} and Necati Aras and Verter, Vedat} } @conference {mutallip2014desired, title = {Desired Supply Line Value Calculation for Multi-Supplier Systems}, booktitle = {The 32nd International System Dynamics Conference, Delft, Netherlands}, year = {2014}, publisher = {System Dynamics Society (http://www.systemdynamics.org/conferences/2014/index.html)}, organization = {System Dynamics Society (http://www.systemdynamics.org/conferences/2014/index.html)}, author = {Mutallip, Ahmet and Yasarcan, Hakan} } @conference {feichtinger2014distributional, title = {A Distributional Approach to Generalized Stochastic Processes on Locally Compact Abelian Groups}, year = {2014}, pages = {423{\textendash}446}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, author = {Feichtinger, HG and Wolfgang H{\"o}rmann} } @article {BodurEtAl2013, title = {Decomposition Algorithms for Solving the Minimum Weight Maximal Matching Problem}, journal = {Networks}, volume = {62}, number = {4}, year = {2013}, pages = {273{\textendash}287}, doi = {http://dx.doi.org/10.1002/net.21516}, author = {Merve Bodur and Ekim, Tinaz and Z C Ta{\c s}k{\i}n} } @article {barlas2011demand, title = {Demand forecasting and sharing strategies to reduce fluctuations and the bullwhip effect in supply chains}, journal = {Journal of the Operational Research Society}, volume = {62}, number = {3}, year = {2011}, pages = {458{\textendash}473}, publisher = {Nature Publishing Group}, author = {Yaman Barlas and Baris Gunduz} } @article {becsikcci2011different, title = {Different resource management policies in multi-mode resource constrained multi-project scheduling}, year = {2011}, publisher = {Institute of Electrical and Electronics Engineers, Inc.}, author = {Be{\c s}ikci, Umut and {\"U}mit Bilge and Ulusoy, G{\"u}nd{\"u}z} } @article {kuccukaydin2011discrete, title = {A discrete competitive facility location model with variable attractiveness}, journal = {Journal of the Operational Research Society}, volume = {62}, number = {9}, year = {2011}, pages = {1726{\textendash}1741}, publisher = {Nature Publishing Group}, author = {K{\"u}{\c c}{\"u}kayd{\i}n, H and Necati Aras and I. Kuban Altinel} } @article {aras2010designing, title = {Designing the reverse logistics network}, journal = {Closed-loop supply chains: new developments to improve the sustainability of business practices. Auerbach Publications}, year = {2010}, pages = {67{\textendash}97}, author = {Necati Aras and Boyaci, Tamer and Verter, Vedat and Ferguson, M and Souza, GC} } @conference {herdem2010dynamics, title = {Dynamics of Glucose-Insulin Regulation: Insulin Injection Regime for Patients with Diabetes Type 1}, booktitle = {The 28th International System Dynamics Conference, Seoul, Korea}, year = {2010}, publisher = {System Dynamics Society (http://www.systemdynamics.org/conferences/2010/index.htm)}, organization = {System Dynamics Society (http://www.systemdynamics.org/conferences/2010/index.htm)}, author = {Herdem, Canan and Yasarcan, Hakan} } @article {Yucel2010, title = {Dynamics of the North{\textendash}South welfare gap and global sustainability}, journal = {Technological Forecasting and Social Change}, volume = {77}, number = {4}, year = {2010}, pages = {594{\textendash}614}, publisher = {Elsevier Inc.}, keywords = {north, south welfare gap}, issn = {00401625}, doi = {10.1016/j.techfore.2009.11.004}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0040162509001887}, author = {G{\"o}nen{\c c} Y{\"u}cel and Yaman Barlas} } @article {aksen2009design, title = {Design and analysis of government subsidized collection systems for incentive-dependent returns}, journal = {International Journal of Production Economics}, volume = {119}, number = {2}, year = {2009}, pages = {308{\textendash}327}, publisher = {Elsevier}, author = {Aksen, Deniz and Necati Aras and Karaarslan, Ay{\c s}e G{\"o}n{\"u}l} } @article {4756751, title = {{Discrete approximation heuristics for the capacitated continuous location-allocation problem with probabilistic customer locations}}, journal = {Computers \& Operations Research}, volume = {36}, year = {2009}, pages = {2139{\textendash}2148}, doi = {10.1016/j.cor.2008.08.003}, author = {Engin Durmaz and Necati Aras and I. Kuban Altinel} } @proceedings {nisa4, title = {A Dynamic Simulation Model of Academic Publications and Citations}, journal = {26th International Conference of the System Dynamics Society}, year = {2008}, author = {K{\"u}{\c c}{\"u}k, B. and Nisa {\"O}nsel and B. Eskici} } @article {2526247, title = {{The design of optimum component test plans for system reliability}}, journal = {Computational Statistics \& Data Analysis}, volume = {50}, year = {2006}, pages = {3099{\textendash}3112}, doi = {10.1016/j.csda.2005.06.015}, author = {Orhan Feyzioglu and I. Kuban Altinel and S{\"u}leyman {\"O}zekici} } @article {48044444, title = {{Dynamic component testing of a series system with redundant subsystems}}, journal = {Iie Transactions}, volume = {33}, year = {2001}, pages = {1093{\textendash}1108}, doi = {10.1023/A:1010922720237}, author = {I. Kuban Altinel and S{\"u}leyman {\"O}zekici} } @article {1654599, title = {{Discrete vector quantization for arbitrary distance function estimation}}, journal = {IEEE Transactions on Systems, Man, and Cybernetics}, volume = {28}, year = {1998}, pages = {496{\textendash}510}, doi = {10.1109/3477.704289}, author = {John Oommen and I. Kuban Altinel and Necati Aras} } @article {26063414, title = {{A dynamic model for component testing}}, journal = {Naval Research Logistics}, volume = {44}, year = {1997}, pages = {187{\textendash}197}, doi = {10.1002/(SICI)1520-6750(199703)44:2<187::AID-NAV3>3.0.CO;2-5}, author = {I. Kuban Altinel} } @book {eksioglu1996determining, title = {Determining the optimum grip span and modeling work/rest cycles for intermittent gripping tasks}, year = {1996}, author = {Mahmut Ek{\c s}io{\u g}lu} } @article {14442391, title = {{The design of optimum component test plans in the demonstration of system reliability}}, journal = {European Journal of Operational Research}, volume = {78}, year = {1994}, pages = {318{\textendash}333}, doi = {10.1016/0377-2217(94)90043-4}, author = {I. Kuban Altinel} }