Cobalt Serum Level as a Biomarker of Cause-Specific Survival among Prostate Cancer Patients.

Prostate cancer is the most common cancer diagnosed in men and the second leading cause of death in male cancer patients. The WHO suggests that cobalt is involved in the carcinogenesis of prostate cancer. There are, however, no studies associating cobalt levels and prostate cancer patient survival. In this study, 261 Polish prostate cancer (n = 261) patients were recruited into a prospective cohort between 2009 and 2015. Serum cobalt levels were measured using ICP-MS after prostate cancer diagnosis and before treatment. All study participants were assigned into quartiles (QI-QIV) based on the distribution of serum cobalt levels among censored patients. Univariable and multivariable COX regression models were used to calculate hazard ratios (HRs) for each serum cobalt level quartile. We found a significant relationship between high serum cobalt levels and poor prostate cancer patient total survival (HR = 2.60; 95% CI: 1.17-5.82; p = 0.02). In relation to prostate cancer patients who died as a result of other non-cancer causes, the association with high levels of cobalt was even stronger (HR = 3.67; 95% CI: 1.03-13.00; p = 0.04). The impact of high serum cobalt levels on overall survival of prostate cancer-specific-related deaths was not statistically significant.

Correlation between Selenium and Zinc Levels and Survival among Prostate Cancer Patients.

The most prevalent type of cancer among males is prostate cancer. Survival is considered quite good, but it can be further improved when risk factors are optimized. One of these factors is micronutrients, including Se and Zn. To our knowledge, the interaction between Se and Zn and prostate cancer remains undescribed. This study aimed to investigate the optimal levels of selenium (Se) and zinc (Zn) and their impact on the survival of individuals diagnosed with prostate cancer. A total of 338 prostate cancer patients were enrolled in this study, which was conducted in Poland between 2009 and 2015. Mass spectrometry, which uses inductively coupled plasma mass, was used to assess serum element levels before treatment. The study participants were categorized into quartiles (QI-QIV) based on the distributions of Se and Zn levels observed among surviving participants. Cox regression was used to assess the association between serum Se and Zn levels and the survival of prostate cancer patients. Our results reveal the effect of combined Se and Zn levels on survival in prostate cancer patients (SeQI-ZnQI vs. SeQIV-ZnQIV; HR = 20.9). These results need further research to establish Se/Zn norms for different populations.

Coil-globule transition in two-dimensional polymer chains in an explicit solvent.

The structure of two-dimensional polymer chains in a solvent at different temperatures is still far from being fully understood. Computer simulations of high-density macromolecular systems require the use of appropriate algorithms, and therefore the simulations were carried out using the Cooperative Motion Algorithm. The polymer model studied was exactly two-dimensional, coarse-grained and based on a triangular lattice. The theta temperature and temperature of coil-to-globule transition, and critical exponents were determined. The differences between the structure of such a disk and that of a chain in a dense polymer liquid were shown.

Structure of Strongly Adsorbed Polymer Systems: A Computer Simulation Study.

The structure of very thin polymer films formed by strongly adsorbed macromolecules was studied by computer simulation. A coarse-grained model of strictly two-dimensional polymer systems was built, and its properties determined by an efficient Monte Carlo simulation algorithm. Properties of the model system were determined by means of Monte Carlo simulations with a sampling algorithm that combines Verdier-Stockmayer, pivot and reputation moves. The effects of temperature, chain length and polymer concentration on the macromolecular structure were investigated. It was shown that at low temperatures, the chain size increases with the concentration, that is, inversely with high temperatures. This behavior should be explained by the influence of inter-chain interactions.

The Influence of Constraints on Gelation in a Controlling/Living Copolymerization Process.

We developed a simple model of the copolymerization process in the formation of crosslinked macromolecular systems. A living copolymerization was carried out for free chains, in bulk and in a slit, as well as for grafted chains in a slit. In addition, polymer 2D brushes were placed in a slit with initiator molecules attached to one of the confining walls. Coarse-grained chains were embedded in the vertices of a face-centered cubic lattice with the excluded volume interactions. The simulations of the copolymerization processes were performed using the Dynamic Lattice Liquid algorithm, a version of the Monte Carlo method. The influence of the initial initiator to cross-linker ratio, slit width and grafting on the polymerization and on the gelation was examined. It was also shown that the influence of a confining slit was rather small, while the grafting of chains affected the location of the gel pint significantly.

Star Polymers vs. Dendrimers: Studies of the Synthesis Based on Computer Simulations.

A generic model was developed for studies of the polymerization process of regular branched macromolecules. Monte Carlo simulations were performed employing the Dynamic Lattice Liquid algorithm to study this process. A core-first methodology was used in a living polymerization of stars with up to 32 arms, and dendrimers consisted of 4-functional segments. The kinetics of the synthesis process for stars with different numbers of branches and dendrimers was compared. The size and structure of star-branched polymers and dendrimers during the synthesis were studied. The influence of the functionality of well-defined cores on the structure and on the dispersity of the system was also examined. The differences in the kinetics in the formation of both architectures, as well as changes to their structures, were described and discussed.

Synthesis of Shape-Memory Polyurethanes: Combined Experimental and Simulation Studies.

The presented research focuses on the synthesis and structure-properties relationship of poly(carbonate-urea-urethane) (PCUU) systems including investigations on shape-memory effect capability. Furthermore, we approached the topic from a broader perspective by conducting extensive analysis of the relationship between the synthesized compounds and the results of computer simulations by means of the Monte Carlo method. For the first time, by using a unique simulation tool, the dynamic lattice liquid model (DLL), all steps of multi-step synthesis of these materials were covered by the simulations. Furthermore, broad thermal, mechanical, and thermomechanical characterization of synthesized PCUUs was performed, as well as determining the shape-memory properties. PCUUs exhibited good mechanical properties with a tensile strength above 20 MPa, elongation at break around 800%, and an exhibited shape-memory effect with shape fixity and shape recovery ratios above 94% and 99%, respectively. The dynamic lattice liquid model was employed to show the products and their molar mass distribution, as well as monomer conversion or the dispersity index for individual reaction steps. The results obtained in the following manuscript allow the planning of syntheses for the PCUUs of various structures, including crosslinked and soluble systems, which can provide a broad variety of applications of these materials, as well as a better understanding of the composition-properties relationship.

Polymerization and Structure of Opposing Polymer Brushes Studied by Computer Simulations.

A model of the polymerization process during the formation of a pair of polymer brushes was designed and investigated. The obtained system consisted of two impenetrable parallel surfaces with the same number of chains grafted on both surfaces. Coarse-grained chains embedded in nodes of a face-centered cubic lattice with excluded volume interactions were obtained by a 'grafted from' procedure. The structure of synthesized macromolecular systems was also studied. Monte Carlo simulations using the dynamic lattice liquid model were employed using dedicated parallel machine ARUZ in a large size and time scale. The parameters of the polymerization process were found to be crucial for the proper structure of the brush. It was found that for high grafting densities, chains were increasingly compressed, and there is surprisingly little interpenetration of chains from opposite surfaces. It was predicted and confirmed that in a polydisperse sample, the longer chains have unique configurations consisting of a stretched stem and a coiled crown.

The structure of polymer brushes: the transition from dilute to dense systems: a computer simulation study.

Monodisperse polymer brushes were studied by means of Monte Carlo simulations. A coarse-grained model of a polymer brush was designed and the Cooperative Motion Algorithm was employed to model the polymerization process 'grafted from' and to study the structure of a brush immersed in a good solvent. The structure of brushes was determined as a function of the chain length and the grafting density. The influence of these parameters on the scaling properties of the brush was presented and discussed. A thorough analysis of the distribution of concentrations of the polymer segments and the distribution of chain free ends was also carried out. The analysis of the depth of penetration of the low molecular weight solvent into the brush area showed that the main factor determining the penetration is the grafting density. Good agreement between the simulation results and theoretical predictions is observed, especially for longer chains and higher grafting density. The origin of small quantitative differences between the simulation and theoretical results is discussed.

Dynamics of Opposing Polymer Brushes: A Computer Simulation Study.

Opposing polymer brush systems were synthesized and investigated by molecular modeling. Chains were restricted to a face-centered cubic lattice with the excluded volume interactions only. The system was confined between two parallel impenetrable walls, with the same number of chains grafted to each surface. The dynamic properties of such systems were studied by Monte Carlo simulations based on the dynamic lattice liquid model and using a highly efficient parallel machine ARUZ, which enabled the study of large systems and long timescales. The influence of the surface density and mean polymer length on the system dynamic was discussed. The self-diffusion coefficient of the solvent depended strongly on the degree of polymerization and on the polymer concentration. It was also shown that it is possible to capture changes in solvent mobility that can be attributed to the regions of different polymer densities.

Molecular transport in systems containing binding obstacles.

We studied the movement of particles in crowded environments by means of extensive Monte Carlo simulations. The dynamic lattice liquid model was employed for this purpose. It is based on the cooperative movement concept and allows the study of systems at high densities. The cooperative model of molecular transport is assumed: the motion of all moving particles is highly correlated. The model is supposed to mimic lateral motion in a membrane and therefore the system is two-dimensional with moving objects and traps placed on a triangular lattice. In our study the interaction (binding) of traps with moving particles was assumed. The conditions in which subdiffusive motion appeared in the system were analysed. The influence of the strength of binding on the dynamic percolation threshold was also shown. The differences in the dynamics compared to systems with impenetrable obstacles and with systems without correlation in motion were presented and discussed. It was shown that in the case of correlated motion the influence of deep traps is similar to that of impenetrable obstacles. If the traps are shallow a recovery to normal diffusion was observed for longer time periods.

Motion in a crowded environment: the influence of obstacles' size and shape and model of transport.

Simulations of motion in a complex crowded environment were performed. We employed the dynamic lattice liquid model, which was based on the cooperative movement concept. This algorithm is capable of working at very high densities, and the motion of all objects was highly correlated. The so-called motion of a single agent, where the motion of molecules is considered as a random walk without any correlation with other moving objects, was also calculated as the state of reference. Immobilized chains embedded in a two-dimensional triangular lattice modeled the crowded environment. The dynamic behavior of movable objects was studied and the influence of the structure of the matrix of obstacles on the molecular transport was discussed. It was shown that the type of transport has an impact on the dynamics of the system. The appearance and properties of subdiffusive motion were analyzed and referred to the structure of polymer systems.

Universal scaling behavior of polymer chains at the percolation threshold.

Two-dimensional macromolecular systems were studied by means of Monte Carlo simulations employing the Cooperative Motion Algorithm. The influence of chain length and internal architecture on the location of the percolation thresholds was shown. A universal behavior of chain size at these thresholds was presented.

Diffusion of small particles in polymer films.

The motion of small probe molecules in a two-dimensional system containing frozen polymer chains was studied by means of Monte Carlo simulations. The model macromolecules were coarse-grained and restricted to vertices of a triangular lattice. The cooperative motion algorithm was used to generate representative configurations of macromolecular systems of different polymer concentrations. The remaining unoccupied lattice sites of the system were filled with small molecules. The structure of the polymer film, especially near the percolation threshold, was determined. The dynamic lattice liquid algorithm was then employed for studies of the dynamics of small objects in the polymer matrix. The influence of chain length and polymer concentration on the mobility and the character of motion of small molecules were studied. Short- and long-time dynamic behaviors of solvent molecules were also described. Conditions of anomalous diffusions' appearance in such systems are discussed. The influence of the structure of the matrix of obstacles on the molecular transport was discussed.

Monte Carlo studies of two-dimensional polymer-solvent systems.

The static properties of two-dimensional athermal polymer solutions were studied by performing Monte Carlo lattice simulations using the cooperative motion algorithm (CMA) and taking into account the presence of explicit solvent molecules. The simulations were performed for a wide range of polymer chain lengths N (16-1024) and concentrations φ (0.0156-1). The results obtained for short chains (N < 256) were in good agreement with those given by previous simulations. For the longest chains (512 or 1024 beads), some unexpected behavior was observed in the dilute and semidilute regimes. A pronounced change in the concentration dependence of chain size and shape was observed below a certain critical concentration (0.6 for the longest chains under consideration, consisting of 1024 beads). Longer chains became more extended below this concentration. The behavior of the single-chain structure factor confirmed these changes in the fractal dimension of the chain as a function of the concentration. The observed phenomena are related to the excluded volume of solvent molecules, which causes the chain statistics to be modified in the vicinity of other chains; this effect is important in strictly 2D systems. Graphical abstract Extended long chains at moderate density with solvent molecules inside coils.

Simulation of Molecular Transport in Systems Containing Mobile Obstacles.

In this paper, we investigate the movement of molecules in crowded environments with obstacles undergoing Brownian motion by means of extensive Monte Carlo simulations. Our investigations were performed using the dynamic lattice liquid model, which was based on the cooperative movement concept and allowed to mimic systems at high densities where the motion of all elements (obstacles as well as moving particles) were highly correlated. The crowded environments are modeled on a two-dimensional triangular lattice containing obstacles (particles whose mobility was significantly reduced) moving by a Brownian motion. The subdiffusive motion of both elements in the system was analyzed. It was shown that the percolation transition does not exist in such systems in spite of the cooperative character of the particles' motion. The reduction of the obstacle mobility leads to the longer caging of liquid particles by mobile obstacles.

The structure of adsorbed cyclic chains.

In order to determine the structure of polymer films formed of cyclic chains (rings) we developed and studied a simple coarse-grained model. Our main goal was to check how the percolation and jamming thresholds in such a system were related to the thresholds obtained for linear flexible chains system, i.e., how the geometry of objects influenced both thresholds. All atomic details were suppressed and polymers were represented as a sequence of identical beads and the chains were embedded to a square lattice (a strictly 2D model). The system was athermal and the excluded volume was the only potential introduced. A random sequential adsorption algorithm was chosen to determine the properties of a polymer monolayer. It was shown that the percolation threshold of cyclic chains was considerably higher than those of linear flexible chains while the jamming thresholds for both chain architectures are very similar. The shape of adsorbed cyclic chains was found to be more prolate when compared to average single chain.

The variant allele of the rs188140481 polymorphism confers a moderate increase in the risk of prostate cancer in Polish men.

A number of single nucleotide polymorphisms (SNPs) in the human genome have been associated with increased risk of prostate cancer. Recently, a single SNP in the region of chromosome 8q24 (rs188140481) has been associated with a three-fold increased risk of prostate cancer in Europe and North America. To establish whether rs188140481 is associated with the risk of prostate cancer in Poland, we genotyped 3467 men with prostate cancer and 1958 controls. The A allele of rs188140481 was detected in 44 of 3467 (1.3%) men with prostate cancer and in seven of 1958 (0.4%) controls (odds ratio=3.6; 95% confidence interval 1.6-7.9; P=0.0006). The allele was present in eight of 390 (2.1%) men with familial prostate cancer (odds ratio=5.8; 95% confidence interval 2.1-16.2; P=0.001). A positive family history of cancers at sites other than the prostate was observed in 27% of men who carried the rs188140481 risk allele and in 44% of noncarriers (P=0.04). No cancer at a site other than the prostate was more common in first-degree or second-degree relatives of carriers of the rs188140481 risk allele than relatives of noncarriers. The rs188140481 polymorphism in the 8q24 region confers a moderate increase in the risk of prostate cancer in Polish men. The SNP does not appear to be associated with susceptibility to cancers of other types.

Common variants of xeroderma pigmentosum genes and prostate cancer risk.

The genetic basis of prostate cancer (PC) is complex and appears to involve multiple susceptibility genes. A number of studies have evaluated a possible correlation between several NER gene polymorphisms and PC risk, but most of them evaluated only single SNPs among XP genes and the results remain inconsistent. Out of 94 SNPs located in seven XP genes (XPA-XPG) a total of 15 SNPs were assayed in 720 unselected patients with PC and compared to 1121 healthy adults. An increased risk of disease was associated with the XPD SNP, rs1799793 (Asp312Asn) AG genotype (OR=2.60; p<0.001) and with the AA genotype (OR=531; p<0.0001) compared to the control population. Haplotype analysis of XPD revealed one protective haplotype and four associated with an increased disease risk, which showed that the A allele (XPD rs1799793) appeared to drive the main effect on promoting prostate cancer risk. Polymorphism in XPD gene appears to be associated with the risk of prostate cancer.

Simulation of diffusion in a crowded environment.

We performed extensive and systematic simulation studies of two-dimensional fluid motion in a complex crowded environment. In contrast to other studies we focused on cooperative phenomena that occurred if the motion of particles takes place in a dense crowded system, which can be considered as a crude model of a cellular membrane. Our main goal was to answer the following question: how do the fluid molecules move in an environment with a complex structure, taking into account the fact that motions of fluid molecules are highly correlated. The dynamic lattice liquid (DLL) model, which can work at the highest fluid density, was employed. Within the frame of the DLL model we considered cooperative motion of fluid particles in an environment that contained static obstacles. The dynamic properties of the system as a function of the concentration of obstacles were studied. The subdiffusive motion of particles was found in the crowded system. The influence of hydrodynamics on the motion was investigated via analysis of the displacement in closed cooperative loops. The simulation and the analysis emphasize the influence of the movement correlation between moving particles and obstacles.