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Bulletin of Mathematical Biology Contents, Volume 67
Bulletin of Mathematical Biology 67 (2005) I–V www.elsevier.com/locate/ybulm
Bulletin of Mathematical Biology Contents, Volume 67 Number 1 ´ , E. M ORGADO and R. G RAU , A genetic code Boolean R. S ANCHEZ structure. I. The meaning of Boolean deductions . . . . . . .
1
B. YAISH and R. M EHR , Models for the dynamics and order of immunoglobulin isotype switching . . . . . . . . . . . .
15
B. BARNES and H. S IDHU , Plant–herbivore models, where more grass means fewer grazers . . . . . . . . . . . . . . . . .
33
S.A.L.M. KOOIJMAN and L.A. S EGEL , How growth affects the fate of cellular metabolites . . . . . . . . . . . . . . . . . .
57
´ and P.K. M AINI , B. R IBBA , K. M ARRON , Z. AGUR , T. A LARC ON A mathematical model of Doxorubicin treatment efficacy for nonHodgkin’s lymphoma: investigation of the current protocol through theoretical modelling results . . . . . . . . . . . . . .
79
´ H. G OMEZ -ACEVEDO and M.Y. L I , Backward bifurcation in a model for HTLV-I infection of CD4+ T cells . . . . . . . . . . . .
101
S. TANG , Y. X IAO , L. C HEN and R.A. C HEKE , Integrated pest management models and their dynamical behaviour . . . . . .
115
H. F LORES , E. L OBATON , S. M E´ NDEZ -D IEZ , S. T LUPOVA and R. C ORTEZ , A study of bacterial flagellar bundling . . . . . .
137
¨ and Y.-K. Y U , Toward an accurate statistics M. K SCHISCHO , M. L ASSIG of gapped alignments . . . . . . . . . . . . . . . . .
169
Book review, Includes a Book by Michael Bulmer on Francis Galton: Pioneer of Heredity and Biometry . . . . . . . . . . . . .
193
D. A MBROSI , A. G AMBA and G. S ERINI , Erratum to “Cell directional persistence and chemotaxis in vascular morphogenesis” [Bull. Math. Biol. 66 (2004) 1851–1873] . . . . . . . . . . . . . . .
195
0092-8240/$30 doi:10.1016/S0092-8240(05)00070-4
II
Contents / Bulletin of Mathematical Biology 67 (2005) I–V
Number 2 P.K. M AINI , Obituary . . . . . . . . . . . . . . . . . . . K. H U , Writhe of DNA induced by a terminal twist
iii
. . . . . . . .
197
X. Z HENG , S.M. W ISE and V. C RISTINI , Nonlinear simulation of tumor necrosis, neo-vascularization and tissue invasion via an adaptive finiteelement/level-set method . . . . . . . . . . . . . . . .
211
S.J. W ILLSON , Minimum evolution using ordinary least-squares is less robust than neighbor-joining . . . . . . . . . . . . . .
261
D.C. M ISTRO , L.A.D. RODRIGUES and W.C. F ERREIRA J R ., The Africanized honey bee dispersal: a mathematical zoom . . . . .
281
S. S UN , M.F. W HEELER , M. O BEYESEKERE and C.W. PATRICK J R ., A deterministic model of growth factor-induced angiogenesis . . . .
313
R. WANG , Z. J ING and L. C HEN , Modelling periodic oscillation in gene regulatory networks by cyclic feedback systems . . . . . . . .
339
P.J. W OODROFFE , J.R. K ING , C.L. VARLEY and J. S OUTHGATE , Modelling cell signalling and differentiation in the urothelium . . .
369
Book review, Includes a Book by J.D. Murray on Mathematical Biology, vol. II
391
Number 3 V. N GUYEN , R. M ATHIAS and G.D. S MITH , A stochastic automata network descriptor for Markov chain models of instantaneously coupled intracellular Ca2+ channels . . . . . . . . . . . .
393
–Ca2+
and J. D´I AZ and G. M ART´I NEZ -M EKLER , Interaction of the IP3 MAPK signaling systems in the Xenopus blastomere: a possible frequency encoding mechanism for the control of the Xbra gene expression . . . . . . . . . . . . . . . . . . . . .
433
T. AWERBUCH -F RIEDLANDER , R. L EVINS and M. P REDESCU , The role of seasonality in the dynamics of deer tick populations . . . . .
467
K. B OUSHABA and M. PASCUAL , Dynamics of the ‘echo’ effect in a phytoplankton system with nitrogen fixation . . . . . . . . .
487
L.T. TAKAHASHI , N.A. M AIDANA , W.C. F ERREIRA J R ., P. P ULINO and H.M. YANG , Mathematical models for the Aedes aegypti dispersal dynamics: travelling waves by wing and wind . . . . . . . .
509
D.C. BARDOS , Probabilistic Gompertz model of irreversible growth
. .
529
S. D ITLEVSEN and A. DE G AETANO , Stochastic vs. deterministic uptake of dodecanedioic acid by isolated rat livers . . . . . . . . . .
547
Contents / Bulletin of Mathematical Biology 67 (2005) I–V
III
E.A. G AFFNEY , The mathematical modelling of adjuvant chemotherapy scheduling: incorporating the effects of protocol rest phases and pharmacokinetics . . . . . . . . . . . . . . . . . .
563
T. A ITA , S. M ORINAGA and Y. H USIMI , Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in an evolution reactor, II . . . . . . . . . . . . . . . . . . . . .
613
S. P ETROVSKII , A. M OROZOV and B.-L. L I , Regimes of biological invasion in a predator–prey system with the Allee effect . . . . .
637
Number 4 ˚ B R ANNSTR ¨ ¨ and D.J.T. S UMPTER , Coupled map lattice approximaA. OM tions for spatially explicit individual-based models of ecology . . .
663
J.H. T IEN , W.D. H AZELTON , R. S PARKS and C.M. U LRICH , A Michaelis–Menten-style model for the autocatalytic enzyme prostaglandin H synthase . . . . . . . . . . . . . . . .
683
N.L. KOMAROVA and A. S OFFER , Nonlinear waves in double-stranded DNA . . . . . . . . . . . . . . . . . . . . . . .
701
E. BAX , Checkpoint method for choice recovery in dynamic programming
719
G. M ENCONI , Sublinear growth of information in DNA sequences . . .
737
´ , R.M. G RANT, T.C. P ORCO , K.L. G ROSS and M.S. S ANCHEZ W.M. G ETZ , A decrease in drug resistance levels of the HIV epidemic can be bad news . . . . . . . . . . . . . . . . . . .
761
R.J. S MITH and L.M. WAHL , Drug resistance in an immunological model of HIV-1 infection with impulsive drug effects . . . . . . . .
783
B. BASSE , B.C. BAGULEY, E.S. M ARSHALL , G.C. WAKE and D.J.N. WALL , Modelling the flow of cytometric data obtained from unperturbed human tumour cell lines: parameter fitting and comparison . . . . . . . . . . . . . . . . . . . .
815
N.G. C OGAN , R. C ORTEZ and L. FAUCI , Modeling physiological resistance in bacterial biofilms . . . . . . . . . . . . . .
831
I. K RISHNARAJAH , A. C OOK , G. M ARION and G. G IBSON , Novel moment closure approximations in stochastic epidemics . . . . .
855
M.A. F ISHMAN and L. S TONE , Fertility assurance and breeding synchrony . . . . . . . . . . . . . . . . . . . . .
875
M. D I M ASCIO , J.K. P ERCUS , O.E. P ERCUS , M. M ARKOWITZ , D.D. H O and A.S. P ERELSON , Duration of an intermittent episode of viremia
885
IV
Contents / Bulletin of Mathematical Biology 67 (2005) I–V
Number 5 C. G ADGIL , C.H. L EE and H.G. OTHMER , A stochastic analysis of firstorder reaction networks . . . . . . . . . . . . . . . .
901
R. H INCH , A note on the asymptotic reduction of the Hodgkin–Huxley equations for nerve impulses . . . . . . . . . . . . . .
947
R.Q. G RAFTON , T. KOMPAS and D. L INDENMAYER , Marine reserves with ecological uncertainty . . . . . . . . . . . . . . . . .
957
R. T WAROCK , Mathematical models for tubular structures in the family of Papovaviridae . . . . . . . . . . . . . . . . . . .
973
J.R. S TIRLING , M.S. Z AKYNTHINAKI and B. S ALTIN , A model of oxygen uptake kinetics in response to exercise: Including a means of calculating oxygen demand/deficit/debt . . . . . . . . . . .
989
R. S ANCHEZ and R. G RAU , A genetic code Boolean structure. II. The genetic information system as a Boolean information system . . .
1017
´ , I.M. M EYER and B. NAGY , Moments of the Boltzmann I. M IKL OS distribution for RNA secondary structures . . . . . . . . . .
1031
J.A. S TEWART-C OX , N.F. B RITTON and M. M OGIE , Pollen limitation or mate search need not induce an Allee effect . . . . . . . . .
1049
M. FAN , Y. K UANG and Z. F ENG , Cats protecting birds revisited
. . .
1081
C. B OWMAN , A.B. G UMEL , P. VAN DEN D RIESSCHE , J. W U and H. Z HU , A mathematical model for assessing control strategies against West Nile virus . . . . . . . . . . . . . . . . . . . . .
1107
´ , E. M ARC E´ L. G IUGGIOLI , G. A BRAMSON , V.M. K ENKRE , G. S UZ AN and T.L. YATES , Diffusion and home range parameters from rodent population measurements in Panama . . . . . . . . . . . .
1135
D.C. M ISTRO , L.A.D. RODRIGUES and W.C. F ERREIRA J R ., Corrigendum to “The Africanized honey bee dispersal: a mathematical zoom” [Bull. Math. Biol. 67 (2005) 281–312] . . . . . . . . . . .
1151
B. BASSE , B.C. BAGULEY, E.S. M ARSHALL , G.C. WAKE and D.J.N. WALL , Erratum to “Modelling the flow cytometric data obtained from unperturbed human tumour cell lines: parameter fitting and comparison” [Bull. Math. Biol. 67 (2005) 815–830] . . . . .
1153
K. H U , Erratum to “Writhe of DNA induced by a terminal twist” [Bull. Math. Biol. 67 (2005) 197–209] . . . . . . . . . . . . .
1155
Contents / Bulletin of Mathematical Biology 67 (2005) I–V
V
Number 6 G.
˜ -H IROSE and C RUZ -PACHECO , L. E STEVA , J.A. M ONTA NO C. VARGAS , Modelling the dynamics of West Nile Virus . . . .
1157
J.K. P ERCUS , Small population effects in stochastic population dynamics
1173
´ , J. M IE¸ KISZ and M. Z ABOROWSKI , Stochastic stability in D. K AMI NSKI three-player games . . . . . . . . . . . . . . . . . .
1195
D. X U , J. C URTIS , Z. F ENG and D.J. M INCHELLA , On the role of schistosome mating structure in the maintenance of drug resistant strains . . . . . . . . . . . . . . . . . . . . . .
1207
L.E. J ONES and A.S. P ERELSON , Opportunistic infection as a cause of transient viremia in chronically infected HIV patients under treatment with HAART . . . . . . . . . . . . . . . . . . . .
1227
M. KOENIGSBERGER , R. S AUSER and J.-J. M EISTER , Emergent properties of electrically coupled smooth muscle cells . . . . . .
1253
J.A. S TEWART-C OX , N.F. B RITTON and M. M OGIE , Space mediates coexistence of females and hermaphrodites . . . . . . . . .
1273
R.A. R EYMENT , The statistical analysis of multivariate serological frequency data . . . . . . . . . . . . . . . . . . .
1303
S.J. S NEDECOR , Dynamic treatment model to examine the association between phenotypic drug resistance and duration of HIV viral suppression . . . . . . . . . . . . . . . . . . . .
1315
J.-H. H E , The allometry of leaf form in early plant ontogeny . . . . .
1333
H. YOSHIDA , T. YOKOMORI and A. S UYAMA , A simple classification of the volvocine algae by formal languages . . . . . . . . . .
1339
H. G OODARZI , H.S. NAJAFABADI , H.A. N EJAD and N. T ORABI , The impact of including tRNA content on the optimality of the genetic code . . . . . . . . . . . . . . . . . . . . . . .
1355
Contents of Volume 67 Index to Volume 67
. . . . . . . . . . . . . . . . . .
I
. . . . . . . . . . . . . . . . . . .
VII
Bulletin of Mathematical Biology Contents, Volume 67 Number 1 ´ , E. M ORGADO and R. G RAU , A genetic code Boolean R. S ANCHEZ structure. I. The meaning of Boolean deductions . . . . . . .
1
B. YAISH and R. M EHR , Models for the dynamics and order of immunoglobulin isotype switching . . . . . . . . . . . .
15
B. BARNES and H. S IDHU , Plant–herbivore models, where more grass means fewer grazers . . . . . . . . . . . . . . . . .
33
S.A.L.M. KOOIJMAN and L.A. S EGEL , How growth affects the fate of cellular metabolites . . . . . . . . . . . . . . . . . .
57
´ and P.K. M AINI , B. R IBBA , K. M ARRON , Z. AGUR , T. A LARC ON A mathematical model of Doxorubicin treatment efficacy for nonHodgkin’s lymphoma: investigation of the current protocol through theoretical modelling results . . . . . . . . . . . . . .
79
´ H. G OMEZ -ACEVEDO and M.Y. L I , Backward bifurcation in a model for HTLV-I infection of CD4+ T cells . . . . . . . . . . . .
101
S. TANG , Y. X IAO , L. C HEN and R.A. C HEKE , Integrated pest management models and their dynamical behaviour . . . . . .
115
H. F LORES , E. L OBATON , S. M E´ NDEZ -D IEZ , S. T LUPOVA and R. C ORTEZ , A study of bacterial flagellar bundling . . . . . .
137
¨ and Y.-K. Y U , Toward an accurate statistics M. K SCHISCHO , M. L ASSIG of gapped alignments . . . . . . . . . . . . . . . . .
169
Book review, Includes a Book by Michael Bulmer on Francis Galton: Pioneer of Heredity and Biometry . . . . . . . . . . . . .
193
D. A MBROSI , A. G AMBA and G. S ERINI , Erratum to “Cell directional persistence and chemotaxis in vascular morphogenesis” [Bull. Math. Biol. 66 (2004) 1851–1873] . . . . . . . . . . . . . . .
195
0092-8240/$30 doi:10.1016/S0092-8240(05)00070-4
II
Contents / Bulletin of Mathematical Biology 67 (2005) I–V
Number 2 P.K. M AINI , Obituary . . . . . . . . . . . . . . . . . . . K. H U , Writhe of DNA induced by a terminal twist
iii
. . . . . . . .
197
X. Z HENG , S.M. W ISE and V. C RISTINI , Nonlinear simulation of tumor necrosis, neo-vascularization and tissue invasion via an adaptive finiteelement/level-set method . . . . . . . . . . . . . . . .
211
S.J. W ILLSON , Minimum evolution using ordinary least-squares is less robust than neighbor-joining . . . . . . . . . . . . . .
261
D.C. M ISTRO , L.A.D. RODRIGUES and W.C. F ERREIRA J R ., The Africanized honey bee dispersal: a mathematical zoom . . . . .
281
S. S UN , M.F. W HEELER , M. O BEYESEKERE and C.W. PATRICK J R ., A deterministic model of growth factor-induced angiogenesis . . . .
313
R. WANG , Z. J ING and L. C HEN , Modelling periodic oscillation in gene regulatory networks by cyclic feedback systems . . . . . . . .
339
P.J. W OODROFFE , J.R. K ING , C.L. VARLEY and J. S OUTHGATE , Modelling cell signalling and differentiation in the urothelium . . .
369
Book review, Includes a Book by J.D. Murray on Mathematical Biology, vol. II
391
Number 3 V. N GUYEN , R. M ATHIAS and G.D. S MITH , A stochastic automata network descriptor for Markov chain models of instantaneously coupled intracellular Ca2+ channels . . . . . . . . . . . .
393
–Ca2+
and J. D´I AZ and G. M ART´I NEZ -M EKLER , Interaction of the IP3 MAPK signaling systems in the Xenopus blastomere: a possible frequency encoding mechanism for the control of the Xbra gene expression . . . . . . . . . . . . . . . . . . . . .
433
T. AWERBUCH -F RIEDLANDER , R. L EVINS and M. P REDESCU , The role of seasonality in the dynamics of deer tick populations . . . . .
467
K. B OUSHABA and M. PASCUAL , Dynamics of the ‘echo’ effect in a phytoplankton system with nitrogen fixation . . . . . . . . .
487
L.T. TAKAHASHI , N.A. M AIDANA , W.C. F ERREIRA J R ., P. P ULINO and H.M. YANG , Mathematical models for the Aedes aegypti dispersal dynamics: travelling waves by wing and wind . . . . . . . .
509
D.C. BARDOS , Probabilistic Gompertz model of irreversible growth
. .
529
S. D ITLEVSEN and A. DE G AETANO , Stochastic vs. deterministic uptake of dodecanedioic acid by isolated rat livers . . . . . . . . . .
547
Contents / Bulletin of Mathematical Biology 67 (2005) I–V
III
E.A. G AFFNEY , The mathematical modelling of adjuvant chemotherapy scheduling: incorporating the effects of protocol rest phases and pharmacokinetics . . . . . . . . . . . . . . . . . .
563
T. A ITA , S. M ORINAGA and Y. H USIMI , Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in an evolution reactor, II . . . . . . . . . . . . . . . . . . . . .
613
S. P ETROVSKII , A. M OROZOV and B.-L. L I , Regimes of biological invasion in a predator–prey system with the Allee effect . . . . .
637
Number 4 ˚ B R ANNSTR ¨ ¨ and D.J.T. S UMPTER , Coupled map lattice approximaA. OM tions for spatially explicit individual-based models of ecology . . .
663
J.H. T IEN , W.D. H AZELTON , R. S PARKS and C.M. U LRICH , A Michaelis–Menten-style model for the autocatalytic enzyme prostaglandin H synthase . . . . . . . . . . . . . . . .
683
N.L. KOMAROVA and A. S OFFER , Nonlinear waves in double-stranded DNA . . . . . . . . . . . . . . . . . . . . . . .
701
E. BAX , Checkpoint method for choice recovery in dynamic programming
719
G. M ENCONI , Sublinear growth of information in DNA sequences . . .
737
´ , R.M. G RANT, T.C. P ORCO , K.L. G ROSS and M.S. S ANCHEZ W.M. G ETZ , A decrease in drug resistance levels of the HIV epidemic can be bad news . . . . . . . . . . . . . . . . . . .
761
R.J. S MITH and L.M. WAHL , Drug resistance in an immunological model of HIV-1 infection with impulsive drug effects . . . . . . . .
783
B. BASSE , B.C. BAGULEY, E.S. M ARSHALL , G.C. WAKE and D.J.N. WALL , Modelling the flow of cytometric data obtained from unperturbed human tumour cell lines: parameter fitting and comparison . . . . . . . . . . . . . . . . . . . .
815
N.G. C OGAN , R. C ORTEZ and L. FAUCI , Modeling physiological resistance in bacterial biofilms . . . . . . . . . . . . . .
831
I. K RISHNARAJAH , A. C OOK , G. M ARION and G. G IBSON , Novel moment closure approximations in stochastic epidemics . . . . .
855
M.A. F ISHMAN and L. S TONE , Fertility assurance and breeding synchrony . . . . . . . . . . . . . . . . . . . . .
875
M. D I M ASCIO , J.K. P ERCUS , O.E. P ERCUS , M. M ARKOWITZ , D.D. H O and A.S. P ERELSON , Duration of an intermittent episode of viremia
885
IV
Contents / Bulletin of Mathematical Biology 67 (2005) I–V
Number 5 C. G ADGIL , C.H. L EE and H.G. OTHMER , A stochastic analysis of firstorder reaction networks . . . . . . . . . . . . . . . .
901
R. H INCH , A note on the asymptotic reduction of the Hodgkin–Huxley equations for nerve impulses . . . . . . . . . . . . . .
947
R.Q. G RAFTON , T. KOMPAS and D. L INDENMAYER , Marine reserves with ecological uncertainty . . . . . . . . . . . . . . . . .
957
R. T WAROCK , Mathematical models for tubular structures in the family of Papovaviridae . . . . . . . . . . . . . . . . . . .
973
J.R. S TIRLING , M.S. Z AKYNTHINAKI and B. S ALTIN , A model of oxygen uptake kinetics in response to exercise: Including a means of calculating oxygen demand/deficit/debt . . . . . . . . . . .
989
R. S ANCHEZ and R. G RAU , A genetic code Boolean structure. II. The genetic information system as a Boolean information system . . .
1017
´ , I.M. M EYER and B. NAGY , Moments of the Boltzmann I. M IKL OS distribution for RNA secondary structures . . . . . . . . . .
1031
J.A. S TEWART-C OX , N.F. B RITTON and M. M OGIE , Pollen limitation or mate search need not induce an Allee effect . . . . . . . . .
1049
M. FAN , Y. K UANG and Z. F ENG , Cats protecting birds revisited
. . .
1081
C. B OWMAN , A.B. G UMEL , P. VAN DEN D RIESSCHE , J. W U and H. Z HU , A mathematical model for assessing control strategies against West Nile virus . . . . . . . . . . . . . . . . . . . . .
1107
´ , E. M ARC E´ L. G IUGGIOLI , G. A BRAMSON , V.M. K ENKRE , G. S UZ AN and T.L. YATES , Diffusion and home range parameters from rodent population measurements in Panama . . . . . . . . . . . .
1135
D.C. M ISTRO , L.A.D. RODRIGUES and W.C. F ERREIRA J R ., Corrigendum to “The Africanized honey bee dispersal: a mathematical zoom” [Bull. Math. Biol. 67 (2005) 281–312] . . . . . . . . . . .
1151
B. BASSE , B.C. BAGULEY, E.S. M ARSHALL , G.C. WAKE and D.J.N. WALL , Erratum to “Modelling the flow cytometric data obtained from unperturbed human tumour cell lines: parameter fitting and comparison” [Bull. Math. Biol. 67 (2005) 815–830] . . . . .
1153
K. H U , Erratum to “Writhe of DNA induced by a terminal twist” [Bull. Math. Biol. 67 (2005) 197–209] . . . . . . . . . . . . .
1155
Contents / Bulletin of Mathematical Biology 67 (2005) I–V
V
Number 6 G.
˜ -H IROSE and C RUZ -PACHECO , L. E STEVA , J.A. M ONTA NO C. VARGAS , Modelling the dynamics of West Nile Virus . . . .
1157
J.K. P ERCUS , Small population effects in stochastic population dynamics
1173
´ , J. M IE¸ KISZ and M. Z ABOROWSKI , Stochastic stability in D. K AMI NSKI three-player games . . . . . . . . . . . . . . . . . .
1195
D. X U , J. C URTIS , Z. F ENG and D.J. M INCHELLA , On the role of schistosome mating structure in the maintenance of drug resistant strains . . . . . . . . . . . . . . . . . . . . . .
1207
L.E. J ONES and A.S. P ERELSON , Opportunistic infection as a cause of transient viremia in chronically infected HIV patients under treatment with HAART . . . . . . . . . . . . . . . . . . . .
1227
M. KOENIGSBERGER , R. S AUSER and J.-J. M EISTER , Emergent properties of electrically coupled smooth muscle cells . . . . . .
1253
J.A. S TEWART-C OX , N.F. B RITTON and M. M OGIE , Space mediates coexistence of females and hermaphrodites . . . . . . . . .
1273
R.A. R EYMENT , The statistical analysis of multivariate serological frequency data . . . . . . . . . . . . . . . . . . .
1303
S.J. S NEDECOR , Dynamic treatment model to examine the association between phenotypic drug resistance and duration of HIV viral suppression . . . . . . . . . . . . . . . . . . . .
1315
J.-H. H E , The allometry of leaf form in early plant ontogeny . . . . .
1333
H. YOSHIDA , T. YOKOMORI and A. S UYAMA , A simple classification of the volvocine algae by formal languages . . . . . . . . . .
1339
H. G OODARZI , H.S. NAJAFABADI , H.A. N EJAD and N. T ORABI , The impact of including tRNA content on the optimality of the genetic code . . . . . . . . . . . . . . . . . . . . . . .
1355
Contents of Volume 67 Index to Volume 67
. . . . . . . . . . . . . . . . . .
I
. . . . . . . . . . . . . . . . . . .
VII