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Publications in other journals ranked by Ministry of Science and Higher Education
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Affiliation to IPPT PAN

1.Adimy M., Chekroun A., Kaźmierczak B., Traveling waves in a coupled reaction–diffusion and difference model of hematopoiesis, Journal of Differential Equations, ISSN: 0022-0396, DOI: 10.1016/j.jde.2016.12.009, Vol.262, No.7, pp.4085-4128, 2017
Adimy M., Chekroun A., Kaźmierczak B., Traveling waves in a coupled reaction–diffusion and difference model of hematopoiesis, Journal of Differential Equations, ISSN: 0022-0396, DOI: 10.1016/j.jde.2016.12.009, Vol.262, No.7, pp.4085-4128, 2017

Abstract:
The formation and development of blood cells is a very complex process, called hematopoiesis. This process involves a small population of cells called hematopoietic stem cells (HSCs). The HSCs are undifferentiated cells, located in the bone marrow before they become mature blood cells and enter the blood stream. They have a unique ability to produce either similar cells (self-renewal), or cells engaged in one of different lineages of blood cells: red blood cells, white cells and platelets (differentiation). The HSCs can be either in a proliferating or in a quiescent phase. In this paper, we distinguish between dividing cells that enter directly to the quiescent phase and dividing cells that return to the proliferating phase to divide again. We propose a mathematical model describing the dynamics of HSC population, taking into account their spatial distribution. The resulting model is a coupled reaction–diffusion equation and difference equation with delay. We study the existence of monotone traveling wave fronts and the asymptotic speed of spread.

Keywords:
Hematopoiesis, Age-structured population, Reaction–diffusion system with delay, Difference equation, Traveling wave front, Asymptotic speed of spread

2.Pierini F., Lanzi M., Nakielski P., Pawłowska S., Urbanek O., Zembrzycki K., Kowalewski T.A., Single-Material Organic Solar Cells Based on Electrospun Fullerene-Grafted Polythiophene Nanofibers, Macromolecules, ISSN: 0024-9297, DOI: 10.1021/acs.macromol.7b00857, Vol.50, No.13, pp.4972-4981, 2017
Pierini F., Lanzi M., Nakielski P., Pawłowska S., Urbanek O., Zembrzycki K., Kowalewski T.A., Single-Material Organic Solar Cells Based on Electrospun Fullerene-Grafted Polythiophene Nanofibers, Macromolecules, ISSN: 0024-9297, DOI: 10.1021/acs.macromol.7b00857, Vol.50, No.13, pp.4972-4981, 2017

Abstract:
Highly efficient single-material organic solar cells (SMOCs) based on fullerene-grafted polythiophenes were fabricated by incorporating electrospun one-dimensional (1D) nanostructures obtained from polymer chain stretching. Poly(3-alkylthiophene) chains were chemically tailored in order to reduce the side effects of charge recombination which severely affected SMOC photovoltaic performance. This enabled us to synthesize a donor–acceptor conjugated copolymer with high solubility, molecular weight, regioregularity, and fullerene content. We investigated the correlations among the active layer hierarchical structure given by the inclusion of electrospun nanofibers and the solar cell photovoltaic properties. The results indicated that SMOC efficiency can be strongly increased by optimizing the supramolecular and nanoscale structure of the active layer, while achieving the highest reported efficiency value (PCE = 5.58%). The enhanced performance may be attributed to well-packed and properly oriented polymer chains. Overall, our work demonstrates that the active material structure optimization obtained by including electrospun nanofibers plays a pivotal role in the development of efficient SMOCs and suggests an interesting perspective for the improvement of copolymer-based photovoltaic device performance using an alternative pathway.

3.Bobrowski A., Kaźmierczak B., Kunze M., An averaging principle for fast diffusions in domains separated by semi-permeable membranes, MATHEMATICAL MODELS AND METHODS IN APPLIED SCIENCES, ISSN: 0218-2025, DOI: 10.1142/S0218202517500130, Vol.27, No.4, pp.663-706, 2017
Bobrowski A., Kaźmierczak B., Kunze M., An averaging principle for fast diffusions in domains separated by semi-permeable membranes, MATHEMATICAL MODELS AND METHODS IN APPLIED SCIENCES, ISSN: 0218-2025, DOI: 10.1142/S0218202517500130, Vol.27, No.4, pp.663-706, 2017

Abstract:
We prove an averaging principle which asserts convergence of diffusion processes on domains separated by semi-permeable membranes, when diffusion coefficients tend to infinity while the flux through the membranes remains constant. In the limit, points in each domain are lumped into a single state of a limit Markov chain. The limit chain’s intensities are proportional to the membranes’ permeability and inversely proportional to the domains’ sizes. Analytically, the limit is an example of a singular perturbation in which boundary and transmission conditions play a crucial role. This averaging principle is strongly motivated by recent signaling pathways models of mathematical biology, which are discussed toward the end of the paper.

Keywords:
Convergence of sectorial forms and of semigroups of operators, diffusion processes, boundary and transmission conditions, Freidlin–Wentzell averaging principle, singular perturbations, signaling pathways, kinase activity, intracellular calcium dynamics, neurotransmitters

4.Habibi I., Cheong R., Lipniacki T., Levchenko A., Emamian E.S., Abdi A., Computation and measurement of cell decision making errors using single cell data, PLOS COMPUTATIONAL BIOLOGY, ISSN: 1553-734X, DOI: 10.1371/journal.pcbi.1005436, Vol.13, No.4, pp.e1005436-1-17, 2017
Habibi I., Cheong R., Lipniacki T., Levchenko A., Emamian E.S., Abdi A., Computation and measurement of cell decision making errors using single cell data, PLOS COMPUTATIONAL BIOLOGY, ISSN: 1553-734X, DOI: 10.1371/journal.pcbi.1005436, Vol.13, No.4, pp.e1005436-1-17, 2017

Abstract:
In this study a new computational method is developed to quantify decision making errors in cells, caused by noise and signaling failures. Analysis of tumor necrosis factor (TNF) signaling pathway which regulates the transcription factor Nuclear Factor κB (NF-κB) using this method identifies two types of incorrect cell decisions called false alarm and miss. These two events represent, respectively, declaring a signal which is not present and missing a signal that does exist. Using single cell experimental data and the developed method, we compute false alarm and miss error probabilities in wild-type cells and provide a formulation which shows how these metrics depend on the signal transduction noise level. We also show that in the presence of abnormalities in a cell, decision making processes can be significantly affected, compared to a wild-type cell, and the method is able to model and measure such effects. In the TNF—NF-κB pathway, the method computes and reveals changes in false alarm and miss probabilities in A20-deficient cells, caused by cell’s inability to inhibit TNF-induced NF-κB response. In biological terms, a higher false alarm metric in this abnormal TNF signaling system indicates perceiving more cytokine signals which in fact do not exist at the system input, whereas a higher miss metric indicates that it is highly likely to miss signals that actually exist. Overall, this study demonstrates the ability of the developed method for modeling cell decision making errors under normal and abnormal conditions, and in the presence of transduction noise uncertainty. Compared to the previously reported pathway capacity metric, our results suggest that the introduced decision error metrics characterize signaling failures more accurately. This is mainly because while capacity is a useful metric to study information transmission in signaling pathways, it does not capture the overlap between TNF-induced noisy response curves.

Keywords:
Decision making, Radar, Probability distribution, Transcription factors, Signal processing, Signal transduction, Signaling networks, Statistical signal processing

5.Kochańczyk M., Kocieniewski P., Kozłowska E., Jaruszewicz-Błońska J., Sparta B., Pargett M., Albeck J.G., Hlavacek W.S., Lipniacki T., Relaxation oscillations and hierarchy of feedbacks in MAPK signaling, Scientific Reports, ISSN: 2045-2322, DOI: 10.1038/srep38244, Vol.7, No.38244, pp.1-15, 2017
Kochańczyk M., Kocieniewski P., Kozłowska E., Jaruszewicz-Błońska J., Sparta B., Pargett M., Albeck J.G., Hlavacek W.S., Lipniacki T., Relaxation oscillations and hierarchy of feedbacks in MAPK signaling, Scientific Reports, ISSN: 2045-2322, DOI: 10.1038/srep38244, Vol.7, No.38244, pp.1-15, 2017

Abstract:
We formulated a computational model for a MAPK signaling cascade downstream of the EGF receptor to investigate how interlinked positive and negative feedback loops process EGF signals into ERK pulses of constant amplitude but dose-dependent duration and frequency. A positive feedback loop involving RAS and SOS, which leads to bistability and allows for switch-like responses to inputs, is nested within a negative feedback loop that encompasses RAS and RAF, MEK, and ERK that inhibits SOS via phosphorylation. This negative feedback, operating on a longer time scale, changes switch-like behavior into oscillations having a period of 1 hour or longer. Two auxiliary negative feedback loops, from ERK to MEK and RAF, placed downstream of the positive feedback, shape the temporal ERK activity profile but are dispensable for oscillations. Thus, the positive feedback introduces a hierarchy among negative feedback loops, such that the effect of a negative feedback depends on its position with respect to the positive feedback loop. Furthermore, a combination of the fast positive feedback involving slow-diffusing membrane components with slower negative feedbacks involving faster diffusing cytoplasmic components leads to local excitation/global inhibition dynamics, which allows the MAPK cascade to transmit paracrine EGF signals into spatially non-uniform ERK activity pulses.

Keywords:
MAPK signaling, Oscillations, Mathematical modelling

6.Varga A., Ehrenreiter K., Aschenbrenner B., Kocieniewski P., Kochańczyk M., Lipniacki T., Baccarini M., RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα, Science Signaling, ISSN: 1945-0877, DOI: 10.1126/scisignal.aai8482, Vol.10, No.469, pp.eaai8482-1-11, 2017
Varga A., Ehrenreiter K., Aschenbrenner B., Kocieniewski P., Kochańczyk M., Lipniacki T., Baccarini M., RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα, Science Signaling, ISSN: 1945-0877, DOI: 10.1126/scisignal.aai8482, Vol.10, No.469, pp.eaai8482-1-11, 2017

Abstract:
Downstream of growth factor receptors and of the guanine triphosphatase (GTPase) RAS, heterodimers of the serine/threonine kinases BRAF and RAF1 are critical upstream kinases and activators of the mitogen-activated protein kinase (MAPK) module containing the mitogen-activated and extracellular signal–regulated kinase kinase (MEK) and their targets, the extracellular signal–regulated kinase (ERK) family. Either direct or scaffold protein–mediated interactions among the components of the ERK module (the MAPKKKs BRAF and RAF1, MEK, and ERK) facilitate signal transmission. RAF1 also has essential functions in the control of tumorigenesis and migration that are mediated through its interaction with the kinase ROKα, an effector of the GTPase RHO and regulator of cytoskeletal rearrangements. We combined mutational and kinetic analysis with mathematical modeling to show that the interaction of RAF1 with ROKα is coordinated with the role of RAF1 in the ERK pathway. We found that the phosphorylated form of RAF1 that interacted with and inhibited ROKα was generated during the interaction of RAF1 with the ERK module. This mechanism adds plasticity to the ERK pathway, enabling signal diversification at the level of both ERK and RAF. Furthermore, by connecting ERK activation with the regulation of ROKα and cytoskeletal rearrangements by RAF1, this mechanism has the potential to precisely coordinate the proper timing of proliferation with changes in cell shape, adhesion, or motility.

Keywords:
MAPK pathway, kinase RAF, protein isoform, phosphorylation, mathematical modeling

7.Piechocka I.K., Kurniawan N.A., Grimbergen J., Koopman J., Koenderink G.H., Recombinant fibrinogen reveals the differential roles of α- and γ-chain cross-linking and molecular heterogeneity in fibrin clot strain-stiffening, Journal of Thrombosis and Haemostasis, ISSN: 1538-7933, DOI: 10.1111/jth.13650, Vol.15, No.5, pp.938-949, 2017
Piechocka I.K., Kurniawan N.A., Grimbergen J., Koopman J., Koenderink G.H., Recombinant fibrinogen reveals the differential roles of α- and γ-chain cross-linking and molecular heterogeneity in fibrin clot strain-stiffening, Journal of Thrombosis and Haemostasis, ISSN: 1538-7933, DOI: 10.1111/jth.13650, Vol.15, No.5, pp.938-949, 2017

Abstract:
Essentials Fibrinogen circulates in human plasma as a complex mixture of heterogeneous molecular variants. We measured strain-stiffening of recombinantly produced fibrinogen upon clotting. Factor XIII and molecular heterogeneity alter clot elasticity at the protofibril and fiber level. This highlights the hitherto unknown role of molecular composition in fibrin clot mechanics.

Keywords:
blood coagulation, elasticity, fibrin, polymers, rheology, turbidimetry

8.Urbanek O., Sajkiewicz P., Pierini F., The effect of polarity in the electrospinning process on PCL/chitosan nanofibres' structure, properties and efficiency of surface modification, POLYMER, ISSN: 0032-3861, DOI: 10.1016/j.polymer.2017.07.064, Vol.124, pp.168-175, 2017
Urbanek O., Sajkiewicz P., Pierini F., The effect of polarity in the electrospinning process on PCL/chitosan nanofibres' structure, properties and efficiency of surface modification, POLYMER, ISSN: 0032-3861, DOI: 10.1016/j.polymer.2017.07.064, Vol.124, pp.168-175, 2017

Abstract:
The aim of this research was to study the effect of charge polarity applied to the spinning nozzle on the structure and properties of polycaprolactone/chitosan (PCL/CHT) blends, in particular the efficiency of further surface modification by chondroitin sulphate (CS). The observed differences in the morphology and properties of fibres formed at different polarities were interpreted in terms of molecular interactions occurring in the system. FTIR results indicate stronger PCL-chitosan interactions at negative polarity, resulting in lower PCL crystallinity and crystal size distribution determined by DSC, as well as lower wettability. The charge polarity influences PCL/CHT fibre morphology and tailors some of their properties, e.g. wettability, mechanical properties and the efficiency of surface modification. Better efficiency of CS attachment was observed at negative polarity using atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS) is most probably related to higher chitosan content at the fibres' surface being attracted by the negative external potential.

Keywords:
Polycaprolactone/chitosan nanofibres, Charge potential effect in electrospinning, Polycaprolactone-chitosan interactions

9.Urbanek O., Sajkiewicz P., Pierini F., Czerkies M., Kołbuk D., Structure and properties of polycaprolactone/chitosan nonwovens tailored by solvent systems, Biomedical Materials, ISSN: 1748-6041, DOI: 10.1088/1748-605X/aa5647, Vol.12, No.1, pp.015020-1-12, 2017
Urbanek O., Sajkiewicz P., Pierini F., Czerkies M., Kołbuk D., Structure and properties of polycaprolactone/chitosan nonwovens tailored by solvent systems, Biomedical Materials, ISSN: 1748-6041, DOI: 10.1088/1748-605X/aa5647, Vol.12, No.1, pp.015020-1-12, 2017

Abstract:
Electrospinning of chitosan blends is a reasonable idea to prepare fibre mats for biomedical applications. Synthetic and natural components provide, for example, appropriate mechanical strength and biocompatibility, respectively. However, solvent characteristics and the polyelectrolyte nature of chitosan influence the spinnability of these blends. In order to compare the effect of solvent on polycaprolactone/chitosan fibres, two types of the most commonly used solvent systems were chosen, namely 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) and acetic acid (AA)/formic acid (FA). Results obtained by various experimental methods clearly indicated the effect of the solvent system on the structure and properties of electrospun polycaprolactone/chitosan fibres. Viscosity measurements confirmed different polymer–solvent interactions. Various molecular interactions resulting in different macromolecular conformations of chitosan influenced its spinnability and properties. HFIP enabled fibres to be obtained whose average diameter was less than 250 nm while maintaining the brittle and hydrophilic character of the nonwoven, typical for the chitosan component. Spectroscopy studies revealed the formation of chitosan salts in the case of the AA/FA solvent system. Chitosan salts visibly influenced the structure and properties of the prepared fibre mats. The use of AA/FA caused a reduction of Young's modulus and wettability of the proposed blends. It was confirmed that wettability, mechanical properties and the antibacterial effect of polycaprolactone/chitosan fibres may be tailored by selecting an appropriate solvent system. The MTT cell proliferation assay revealed an increase of cytotoxicity to mouse fibroblasts in the case of 25% w/w of chitosan in electrospun nonwovens.

Keywords:
chitosan, electrospinning, PCL/chitosan fibres, solvent system, chitosan salts

10.Martincuks A., Andryka K., Küster A., Schmitz-Van de Leur H., Komorowski M., Müller-Newen G., Nuclear translocation of STAT3 and NF-κB are independent of each other but NF-κB supports expression and activation of STAT3, Cellular Signalling, ISSN: 0898-6568, DOI: 10.1016/j.cellsig.2017.01.006, Vol.32, pp.36-47, 2017
Martincuks A., Andryka K., Küster A., Schmitz-Van de Leur H., Komorowski M., Müller-Newen G., Nuclear translocation of STAT3 and NF-κB are independent of each other but NF-κB supports expression and activation of STAT3, Cellular Signalling, ISSN: 0898-6568, DOI: 10.1016/j.cellsig.2017.01.006, Vol.32, pp.36-47, 2017

Abstract:
NF-κB and STAT3 are essential transcription factors in immunity and act at the interface of the transition from chronic inflammation to cancer. Different functional crosstalks between NF-κB and STAT3 have been recently described arguing for a direct interaction of both proteins. During a systematic analysis of NF-κB/STAT3 crosstalk we observed that appearance of the subcellular distribution of NF-κB and STAT3 in immunofluorescence heavily depends on the fixation procedure. Therefore, we established an optimized fixation protocol for the reliable simultaneous analysis of the subcellular distributions of both transcription factors. Using this protocol we found that cytokine-induced nuclear accumulation of NF-κB or STAT3 did not alter the subcellular distribution of the other transcription factor. Both knockout and overexpression of STAT3 does not have any major effect on canonical TNFα-NF-κB signalling in MEF or HeLa cells. Similarly, knockout of p65 did not alter nuclear accumulation of STAT3 in response to IL-6. However, p65 expression correlates with elevated total cellular levels of STAT3 and STAT1 and supports activation of these transcription factors. Our findings in MEF cells argue against a direct physical interaction of free cellular NF-κB and STAT3 but point to more intricate functional interactions.

Keywords:
STAT3, NF-κB, Signal transduction, Nuclear translocation, Crosstalk

11.Pierini F., Lanzi M., Nakielski P., Kowalewski T.A., Electrospun Polyaniline-Based Composite Nanofibers: Tuning the Electrical Conductivity by Tailoring the Structure of Thiol-Protected Metal Nanoparticles, Journal of Nanomaterials, ISSN: 1687-4110, DOI: 10.1155/2017/6142140, Vol.2017, pp.1-10, 2017
Pierini F., Lanzi M., Nakielski P., Kowalewski T.A., Electrospun Polyaniline-Based Composite Nanofibers: Tuning the Electrical Conductivity by Tailoring the Structure of Thiol-Protected Metal Nanoparticles, Journal of Nanomaterials, ISSN: 1687-4110, DOI: 10.1155/2017/6142140, Vol.2017, pp.1-10, 2017

Abstract:
Composite nanofibers made of a polyaniline-based polymer blend and different thiol-capped metal nanoparticles were prepared using ex situ synthesis and electrospinning technique. The effects of the nanoparticle composition and chemical structure on the electrical properties of the nanocomposites were investigated. This study confirmed that Brust’s procedure is an effective method for the synthesis of sub-10 nm silver, gold, and silver-gold alloy nanoparticles protected with different types of thiols. Electron microscopy results demonstrated that electrospinning is a valuable technique for the production of composite nanofibers with similar morphology and revealed that nanofillers are well-dispersed into the polymer matrix. X-ray diffraction tests proved the lack of a significant influence of the nanoparticle chemical structure on the polyaniline chain arrangement. However, the introduction of conductive nanofillers in the polymer matrix influences the charge transport noticeably improving electrical conductivity. The enhancement of electrical properties is mediated by the nanoparticle capping layer structure. The metal nanoparticle core composition is a key parameter, which exerted a significant influence on the conductivity of the nanocomposites. These results prove that the proposed method can be used to tune the electrical properties of nanocomposites.

12.Lanzi M., Salatelli E., Di-Nicola F.P., Zuppiroli L., Pierini F., A new photocrosslinkable oligothiophene for organic solar cells with enhanced stability, MATERIALS CHEMISTRY AND PHYSICS, ISSN: 0254-0584, DOI: 10.1016/j.matchemphys.2016.10.034, Vol.186, pp.98-107, 2017
Lanzi M., Salatelli E., Di-Nicola F.P., Zuppiroli L., Pierini F., A new photocrosslinkable oligothiophene for organic solar cells with enhanced stability, MATERIALS CHEMISTRY AND PHYSICS, ISSN: 0254-0584, DOI: 10.1016/j.matchemphys.2016.10.034, Vol.186, pp.98-107, 2017

Abstract:
A novel thiophenic tetramer containing a cinnamate group in the side chain with a functionalization degree of 50% is reported. The tetramer was obtained by means of a simple and straightforward procedure involving the functionalization of a p-methoxyphenoxy substituted thiophenic precursor, which led to a soluble product with a good yield. The oligomer was fully characterized from a structural and chemical point of view and employed for the fabrication of small molecule organic solar cells exploiting the bulk heterojunction (BHJ) architecture. The presence of an UV-light sensitive group in the tetramer allowed the photocrosslinking of tetramer/PCBM blends, giving high values of photocurrent and conversion efficiency for the exposed samples. Moreover, the UV-treated devices showed improved stability, even upon heating for three days at 130 °C, thus confirming that photocrosslinking can strongly reduce phase segregation under severe operational conditions.

Keywords:
Electronic materials, Polymers, Fullerenes, Nanostructures, Electrical characterization, Semiconductors

13.Białecki S., Kaźmierczak B., Nowicka D., Tsai J.-C., Regularity of solutions to a reaction–diffusion equation on the sphere: the Legendre series approach, MATHEMATICAL METHODS IN THE APPLIED SCIENCES, ISSN: 0170-4214, DOI: 10.1002/mma.4390, pp.1-21, 2017
Białecki S., Kaźmierczak B., Nowicka D., Tsai J.-C., Regularity of solutions to a reaction–diffusion equation on the sphere: the Legendre series approach, MATHEMATICAL METHODS IN THE APPLIED SCIENCES, ISSN: 0170-4214, DOI: 10.1002/mma.4390, pp.1-21, 2017

Abstract:
In the paper, we study some ‘a priori’ properties of mild solutions to a single reaction–diffusion equation with discontinuous nonlinear reaction term on the two-dimensional sphere close to its poles. This equation is the counterpart of the well-studied bistable reaction–diffusion equation on the Euclidean plane. The investigation of this equation on the sphere is mainly motivated by the phenomenon of the fertilization of oocytes or recent studies of wave propagation in a model of immune cells activation, in which the cell is modeled by a ball. Because of the discontinuous nature of reaction kinetics, the standard theory cannot guarantee the solution existence and its smoothness properties. Moreover, the singular nature of the diffusion operator near the north/south poles makes the analysis more involved. Unlike the case in the Euclidean plane, the (axially symmetric) Green's function for the heat operator on the sphere can only be represented by an infinite series of the Legendre polynomials. Our approach is to consider a formal series in Legendre polynomials obtained by assuming that the mild solution exists. We show that the solution to the equation subject to the Neumann boundary condition is C1 smooth in the spatial variable up to the north/south poles and Hölder continuous with respect to the time variable. Our results provide also a sort of ‘a priori’ estimates, which can be used in the existence proofs of mild solutions, for example, by means of the iterative methods.

Keywords:
discontinuous reaction term, stationary fronts, sphere