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1.
Nano Lett ; 2024 Apr 12.
Artigo em Inglês | MEDLINE | ID: mdl-38607288

RESUMO

Metabolites play crucial roles in cellular processes, yet their diffusion in the densely packed interiors of cells remains poorly understood, compounded by conflicting reports in existing studies. Here, we employ pulsed-gradient stimulated-echo NMR and Brownian/Stokesian dynamics simulations to elucidate the behavior of nano- and subnanometer-sized tracers in crowded environments. Using Ficoll as a crowder, we observe a linear decrease in tracer diffusivity with increasing occupied volume fraction, persisting─somewhat surprisingly─up to volume fractions of 30-40%. While simulations suggest a linear correlation between diffusivity slowdown and particle size, experimental findings hint at a more intricate relationship, possibly influenced by Ficoll's porosity. Simulations and numerical calculations of tracer diffusivity in the E. coli cytoplasm show a nonlinear yet monotonic diffusion slowdown with particle size. We discuss our results in the context of nanoviscosity and discrepancies with existing studies.

2.
Artigo em Inglês | MEDLINE | ID: mdl-38682753

RESUMO

The platelet integrin αIIbß3 undergoes long-range conformational transitions between bent and extended conformations to regulate platelet aggregation during hemostasis and thrombosis. However, how exactly αIIbß3 transitions between conformations remains largely elusive. Here, we studied how transitions across bent and extended-closed conformations of αIIbß3 integrin are regulated by effective interactions between its functional domains. We first carried out µs-long equilibrium molecular dynamics (MD) simulations of full-length αIIbß3 integrins in bent and intermediate conformations, the latter characterized by an extended headpiece and closed legs. Then, we built heterogeneous elastic network models, perturbed inter-domain interactions, and evaluated their relative contributions to the energy barriers between conformations. Results showed that integrin extension emerges from: (i) changes in interfaces between functional domains; (ii) allosteric coupling of the head and upper leg domains with flexible lower leg domains. Collectively, these results provide new insights into integrin conformational activation based on short- and long-range interactions between its functional domains and highlight the importance of the lower legs in the regulation of integrin allostery.

3.
Phys Med ; 118: 103301, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38290179

RESUMO

PURPOSE: The aim of this work is to investigate the feasibility of the Jagiellonian Positron Emission Tomography (J-PET) scanner for intra-treatment proton beam range monitoring. METHODS: The Monte Carlo simulation studies with GATE and PET image reconstruction with CASToR were performed in order to compare six J-PET scanner geometries. We simulated proton irradiation of a PMMA phantom with a Single Pencil Beam (SPB) and Spread-Out Bragg Peak (SOBP) of various ranges. The sensitivity and precision of each scanner were calculated, and considering the setup's cost-effectiveness, we indicated potentially optimal geometries for the J-PET scanner prototype dedicated to the proton beam range assessment. RESULTS: The investigations indicate that the double-layer cylindrical and triple-layer double-head configurations are the most promising for clinical application. We found that the scanner sensitivity is of the order of 10-5 coincidences per primary proton, while the precision of the range assessment for both SPB and SOBP irradiation plans was found below 1 mm. Among the scanners with the same number of detector modules, the best results are found for the triple-layer dual-head geometry. The results indicate that the double-layer cylindrical and triple-layer double-head configurations are the most promising for the clinical application, CONCLUSIONS:: We performed simulation studies demonstrating that the feasibility of the J-PET detector for PET-based proton beam therapy range monitoring is possible with reasonable sensitivity and precision enabling its pre-clinical tests in the clinical proton therapy environment. Considering the sensitivity, precision and cost-effectiveness, the double-layer cylindrical and triple-layer dual-head J-PET geometry configurations seem promising for future clinical application.


Assuntos
Terapia com Prótons , Prótons , Estudos de Viabilidade , Tomografia por Emissão de Pósitrons , Terapia com Prótons/métodos , Imagens de Fantasmas , Método de Monte Carlo
4.
J Phys Chem B ; 127(34): 7442-7448, 2023 08 31.
Artigo em Inglês | MEDLINE | ID: mdl-37591305

RESUMO

Immunoglobulin G (IgG) is the most common type of antibody found in blood and extracellular fluids and plays an essential role in our immune response. However, studies of the dynamics and reaction kinetics of IgG-antigen binding under physiological crowding conditions are scarce. Herein, we develop a coarse-grained model of IgG consisting of only six beads that we find minimal for a coarse representation of IgG's shape and a decent reproduction of its flexibility and diffusion properties measured experimentally. Using this model in Brownian dynamics simulations, we find that macromolecular crowding affects only slightly the IgG's flexibility, as described by the distribution of angles between the IgG's arms and stem. Our simulations indicate that, contrary to expectations, crowders slow down the translational diffusion of an IgG less strongly than they do for a smaller Ficoll 70, which we relate to the IgG's conformational size changes induced by crowding. We also find that crowders affect the binding kinetics by decreasing the rate of the first binding step and enhancing the second binding step.


Assuntos
Imunoglobulina G , Difusão , Ficoll , Cinética
5.
Phys Rev Lett ; 130(25): 258401, 2023 Jun 23.
Artigo em Inglês | MEDLINE | ID: mdl-37418731

RESUMO

Macromolecular crowding affects biophysical processes as diverse as diffusion, gene expression, cell growth, and senescence. Yet, there is no comprehensive understanding of how crowding affects reactions, particularly multivalent binding. Herein, we use scaled particle theory and develop a molecular simulation method to investigate the binding of monovalent to divalent biomolecules. We find that crowding can increase or reduce cooperativity-the extent to which the binding of a second molecule is enhanced after binding a first molecule-by orders of magnitude, depending on the sizes of the involved molecular complexes. Cooperativity generally increases when a divalent molecule swells and then shrinks upon binding two ligands. Our calculations also reveal that, in some cases, crowding enables binding that does not occur otherwise. As an immunological example, we consider immunoglobulin G-antigen binding and show that crowding enhances its cooperativity in bulk but reduces it when an immunoglobulin G binds antigens on a surface.


Assuntos
Simulação por Computador , Substâncias Macromoleculares/química
6.
Phys Med Biol ; 2023 Jun 09.
Artigo em Inglês | MEDLINE | ID: mdl-37295440

RESUMO

OBJECTIVE: The Jagiellonian PET (J-PET) technology, based on plastic scintillators, has been proposed as a cost effective tool for detecting range deviations during proton therapy. This study investigates the feasibility of using J-PET for range monitoring by means of a detailed Monte Carlo simulation study of 95 patients who underwent proton therapy at the Cyclotron Centre Bronowice (CCB) in Krakow, Poland. Approach: Discrepancies between prescribed and delivered treatments were artificially introduced in the simulations by means of shifts in patient positioning and in the Hounsfield unit to the relative proton stopping power calibration curve. A dual-layer, cylindrical J-PET geometry was simulated in an in-room monitoring scenario and a triple-layer, dual-head geometry in an in-beam protocol. The distribution of range shifts in reconstructed PET activity was visualised in the beam's eye view. Linear prediction models were constructed from all patients in the cohort, using the mean shift in reconstructed PET activity as a predictor of the mean proton range deviation. Main results: Maps of deviations in the range of reconstructed PET distributions showed agreement with those of deviations in dose range in most patients. The linear prediction model showed a good fit, with coefficient of determination r^2 = 0.84 (in-room) and 0.75 (in-beam). Residual standard error was below 1 mm: 0.33 mm (in-room) and 0.23 mm (in-beam). Significance: The precision of the proposed prediction models shows the sensitivity of the proposed J-PET scanners to shifts in proton range for a wide range of clinical treatment plans. Furthermore, it motivates the use of such models as a tool for predicting proton range deviations and opens up new prospects for investigations into the use of intra-treatment PET images for predicting clinical metrics that aid in the assessment of the quality of delivered treatment. .

7.
Artigo em Inglês | MEDLINE | ID: mdl-36554267

RESUMO

BACKGROUND: In Poland, breast cancer (BC) is the most frequently diagnosed cancer in women and the second most common cause of death after lung cancer. This disease has important economic implications for patients, public payers, and the whole Polish economy. This study aimed to estimate the total National Health Fund (NHF) expenditures on the diagnosis and treatment of patients with breast cancer. In addition, the costs of productivity losses were also calculated. METHODS: Cost estimation was prepared using a top-down approach. Direct cost calculations were based on data reported by NHF for patients with the diagnosis of breast cancer. Medical care costs included the following components: screening program, oncological package, surgical treatment, hospitalization, drug program, chemotherapy, radiotherapy, and outpatient care. Indirect costs in the form of absenteeism costs were calculated based on data from Statistics Poland (gross domestic product, number of employees) and the Social Insurance Institution database (the number of sick leave days). RESULTS: Total expenditures for BC including direct costs and indirect costs amounted to EUR 305,371, EUR 332,998, and EUR 344,649, respectively in 2017, 2018, and 2019. Total healthcare costs in 2019 were EUR 4114 lower than in 2018, which resulted from the reduction in expenditure on the drug program (decrease of EUR 13,527), despite the observed increase in all remaining resources. From direct costs, the highest expense was spent on the drug program (nearly 50% of total direct costs), but this expense dropped significantly in 2019. For the remaining parameters, the costs increased year by year, of which the most expensive were surgical treatment (15%), radiotherapy (12%), and the screening program (10%). BC generated over EUR 120 thousand of social costs in 2019 and compared to 2017, there was an increase in productivity loss by 26%. CONCLUSIONS: Our results from 2017-2019 demonstrated that total expenditure for BC in Poland increased from year to year. Breast cancer generated almost EUR 345 thousand expenses in 2019, which translates into a significant burden on the public payer's budget and the society in Poland.


Assuntos
Neoplasias da Mama , Humanos , Feminino , Neoplasias da Mama/epidemiologia , Neoplasias da Mama/terapia , Polônia/epidemiologia , Efeitos Psicossociais da Doença , Custos de Cuidados de Saúde , Gastos em Saúde
8.
Phys Med Biol ; 67(24)2022 12 12.
Artigo em Inglês | MEDLINE | ID: mdl-36541512

RESUMO

Objective.Verification of delivered proton therapy treatments is essential for reaping the many benefits of the modality, with the most widely proposedin vivoverification technique being the imaging of positron emitting isotopes generated in the patient during treatment using positron emission tomography (PET). The purpose of this work is to reduce the computational resources and time required for simulation of patient activation during proton therapy using the GPU accelerated Monte Carlo code FRED, and to validate the predicted activity against the widely used Monte Carlo code GATE.Approach.We implement a continuous scoring approach for the production of positron emitting isotopes within FRED version 5.59.9. We simulate treatment plans delivered to 95 head and neck patients at Centrum Cyklotronowe Bronowice using this GPU implementation, and verify the accuracy using the Monte Carlo toolkit GATE version 9.0.Main results.We report an average reduction in computational time by a factor of 50 when using a local system with 2 GPUs as opposed to a large compute cluster utilising between 200 to 700 CPU threads, enabling simulation of patient activity within an average of 2.9 min as opposed to 146 min. All simulated plans are in good agreement across the two Monte Carlo codes. The two codes agree within a maximum of 0.95σon a voxel-by-voxel basis for the prediction of 7 different isotopes across 472 simulated fields delivered to 95 patients, with the average deviation over all fields being 6.4 × 10-3σ.Significance.The implementation of activation calculations in the GPU accelerated Monte Carlo code FRED provides fast and reliable simulation of patient activation following proton therapy, allowing for research and development of clinical applications of range verification for this treatment modality using PET to proceed at a rapid pace.


Assuntos
Terapia com Prótons , Humanos , Elétrons , Prótons , Tomografia por Emissão de Pósitrons/métodos , Isótopos , Método de Monte Carlo , Imagens de Fantasmas , Planejamento da Radioterapia Assistida por Computador/métodos , Dosagem Radioterapêutica
9.
Cancers (Basel) ; 14(23)2022 Nov 23.
Artigo em Inglês | MEDLINE | ID: mdl-36497248

RESUMO

Stage IV melanoma patients develop melanoma brain metastases (MBM) in 50% of cases. Their prognosis is improving, and its understanding outside the context of clinical trials is relevant. We have retrospectively analyzed the clinical data, course of treatment, and outcomes of 531 subsequent stage IV melanoma patients with BM treated in five reference Italian and Polish melanoma centers between 2014 and 2021. Patients with MBM after 2017 had a better prognosis, with a significantly improved median of overall survival (OS) after 2017 in the worst mol-GPA prognostic groups (mol-GPA ≤ 2): a median OS >6 months and HR 0.76 vs. those treated before 2017 (CI: 0.60−0.97, p = 0.027). In our prognostic model, mol-GPA was highly predictive for survival, and symptoms without steroid use did not have prognostic significance. Local therapy significantly improved survival regardless of the year of diagnosis (treated before or after 2017), with median survival >12 months. Systemic therapy improved outcomes when it was combined with local therapy. Local surgery was associated with improved OS regardless of the timing related to treatment start (i.e., before or after 30 days from MBM diagnosis). Local and systemic treatment significantly prolong survival for the poorest mol-GPA prognosis. Use of modern treatment modalities is justified in all mol-GPA prognostic groups.

10.
Phys Med Biol ; 2022 Sep 22.
Artigo em Inglês | MEDLINE | ID: mdl-36137551

RESUMO

OBJECTIVE: This paper reports on the implementation and shows examples of the use of the ProTheRaMon framework for simulating the delivery of proton therapy treatment plans and range monitoring using positron emission tomography (PET). ProTheRaMon offers complete processing of proton therapy treatment plans, patient CT geometries, and intra-treatment PET imaging, taking into account therapy and imaging coordinate systems and activity decay during the PET imaging protocol specific to a given proton therapy facility. We present the ProTheRaMon framework and illustrate its potential use case and data processing steps for a patient treated at the Cyclotron Centre Bronowice (CCB) proton therapy center in Krakow, Poland. APPROACH: The ProTheRaMon framework is based on GATE Monte Carlo software, the CASToR reconstruction package and in-house developed Python and bash scripts. The framework consists of five separated simulation and data processing steps, that can be further optimized according to the user's needs and specific settings of a given proton therapy facility and PET scanner design. MAIN RESULTS: ProTheRaMon is presented using example data from a patient treated at CCB and the J-PET scanner to demonstrate the application of the framework for proton therapy range monitoring. The output of each simulation and data processing stage is described and visualized. SIGNIFICANCE: We demonstrate that the ProTheRaMon simulation platform is a high-performance tool, capable of running on a computational cluster and suitable for multi-parameter studies, with databases consisting of large number of patients, as well as different PET scanner geometries and settings for range monitoring in a clinical environment. Due to its modular structure, the ProTheRaMon framework can be adjusted for different proton therapy centers and/or different PET detector geometries. It is available to the community via github.

11.
Soft Matter ; 18(29): 5366-5370, 2022 Jul 27.
Artigo em Inglês | MEDLINE | ID: mdl-35833511

RESUMO

Diffusion in a macromolecularly crowded environment is essential for many intracellular processes, from metabolism and catalysis to gene transcription and translation. So far, theoretical and experimental work has focused on anomalous subdiffusion, and the effects of interactions, shapes, and composition, while the compactness or softness of macromolecules has received less attention. Herein, we use Brownian dynamics simulations to study how the softness of crowders affects macromolecular diffusion. We find that in most cases, soft crowders slow down the diffusion less effectively than hard crowders like Ficoll. For instance, at a 30% occupied volume fraction, the diffusion in Ficoll70 is about 20% slower than in soft crowders of the same size. However, our simulations indicate that elongated macromolecules, such as double-stranded DNA pieces, can diffuse comparably or even faster in hard crowders. We relate these effects to the volume excluded by soft and hard crowders to different tracers. Our results show that the softness and shape of macromolecules are crucial factors determining diffusion under crowding, relevant to diverse intracellular environments.


Assuntos
DNA , Simulação de Dinâmica Molecular , DNA/metabolismo , Difusão , Ficoll , Substâncias Macromoleculares
12.
Radiat Oncol ; 17(1): 50, 2022 Mar 09.
Artigo em Inglês | MEDLINE | ID: mdl-35264184

RESUMO

BACKGROUND: Variable relative biological effectiveness (vRBE) in proton therapy might significantly modify the prediction of RBE-weighted dose delivered to a patient during proton therapy. In this study we will present a method to quantify the biological range extension of the proton beam, which results from the application of vRBE approach in RBE-weighted dose calculation. METHODS AND MATERIALS: The treatment plans of 95 patients (brain and skull base patients) were used for RBE-weighted dose calculation with constant and the McNamara RBE model. For this purpose the Monte Carlo tool FRED was used. The RBE-weighted dose distributions were analysed using indices from dose-volume histograms. We used the volumes receiving at least 95% of the prescribed dose (V95) to estimate the biological range extension resulting from vRBE approach. RESULTS: The vRBE model shows higher median value of relative deposited dose and D95 in the planning target volume by around 1% for brain patients and 4% for skull base patients. The maximum doses in organs at risk calculated with vRBE was up to 14 Gy above dose limit. The mean biological range extension was greater than 0.4 cm. DISCUSSION: Our method of estimation of biological range extension is insensitive for dose inhomogeneities and can be easily used for different proton plans with intensity-modulated proton therapy (IMPT) optimization. Using volumes instead of dose profiles, which is the common method, is more universal. However it was tested only for IMPT plans on fields arranged around the tumor area. CONCLUSIONS: Adopting a vRBE model results in an increase in dose and an extension of the beam range, which is especially disadvantageous in cancers close to organs at risk. Our results support the need to re-optimization of proton treatment plans when considering vRBE.


Assuntos
Neoplasias Encefálicas/radioterapia , Neoplasias da Base do Crânio/radioterapia , Neoplasias Encefálicas/patologia , Feminino , Humanos , Masculino , Método de Monte Carlo , Estadiamento de Neoplasias , Órgãos em Risco , Polônia , Terapia com Prótons/métodos , Dosagem Radioterapêutica , Planejamento da Radioterapia Assistida por Computador , Eficiência Biológica Relativa , Neoplasias da Base do Crânio/patologia , Tomografia Computadorizada por Raios X
13.
Radiother Oncol ; 167: 7-13, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-34902370

RESUMO

BACKGROUND AND PURPOSE: Major differences exist among proton therapy (PT) centres regarding PT delivery in adult cancer patient. To obtain insight into current practice in Europe, we performed a survey among European PT centres. MATERIALS AND METHODS: We designed electronic questionnaires for eight tumour sites, focusing on four main topics: 1) indications and patient selection methods; 2) reimbursement; 3) on-going or planned studies, 4) annual number of patients treated with PT. RESULTS: Of 22 centres, 19 (86%) responded. In total, 4233 adult patients are currently treated across Europe annually, of which 46% consists of patients with central nervous system tumours (CNS), 15% head and neck cancer (HNC), 15% prostate, 9% breast, 5% lung, 5% gastrointestinal, 4% lymphoma, 0.3% gynaecological cancers. CNS are treated in all participating centres (n = 19) using PT, HNC in 16 centres, lymphoma in 10 centres, gastrointestinal in 10 centres, breast in 7 centres, prostate in 6 centres, lung in 6 centres, and gynaecological cancers in 3 centres. Reimbursement is provided by national health care systems for the majority of commonly treated tumour sites. Approximately 74% of centres enrol patients for prospective data registration programs. Phase II-III trials are less frequent, due to reimbursement and funding problems. Reasons for not treating certain tumour types with PT are lack of evidence (30%), reimbursement issues (29%) and/or technical limitations (20%). CONCLUSION: Across European PT centres, CNS tumours and HNC are the most frequently treated tumour types. Most centres use indication protocols. Lack of evidence for PT and reimbursement issues are the most reported reasons for not treating specific tumour types with PT.


Assuntos
Neoplasias do Sistema Nervoso Central , Neoplasias Gastrointestinais , Neoplasias de Cabeça e Pescoço , Terapia com Prótons , Adulto , Europa (Continente) , Humanos , Masculino , Estudos Prospectivos
14.
Radiother Oncol ; 163: 143-149, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34461183

RESUMO

PURPOSE: We investigated the relationship between RBE-weighted dose (DRBE) calculated with constant (cRBE) and variable RBE (vRBE), dose-averaged linear energy transfer (LETd) and the risk of radiographic changes in skull base patients treated with protons. METHODS: Clinical treatment plans of 45 patients were recalculated with Monte Carlo tool FRED. Radiographic changes (i.e. edema and/or necrosis) were identified by MRI. Dosimetric parameters for cRBE and vRBE were computed. Biological margin extension and voxel-based analysis were employed looking for association of DRBE(vRBE) and LETd with brain edema and/or necrosis. RESULTS: When using vRBE, Dmax in the brain was above the highest dose limits for 38% of patients, while such limit was never exceeded assuming cRBE. Similar values of Dmax were observed in necrotic regions, brain and temporal lobes. Most of the brain necrosis was in proximity to the PTV. The voxel-based analysis did not show evidence of an association with high LETd values. CONCLUSIONS: When looking at standard dosimetric parameters, the higher dose associated with vRBE seems to be responsible for an enhanced risk of radiographic changes. However, as revealed by a voxel-based analysis, the large inter-patient variability hinders the identification of a clear effect for high LETd.


Assuntos
Terapia com Prótons , Neoplasias da Base do Crânio , Encéfalo/diagnóstico por imagem , Humanos , Método de Monte Carlo , Necrose/etiologia , Terapia com Prótons/efeitos adversos , Planejamento da Radioterapia Assistida por Computador , Eficiência Biológica Relativa , Neoplasias da Base do Crânio/diagnóstico por imagem , Neoplasias da Base do Crânio/radioterapia
15.
Phys Chem Chem Phys ; 23(15): 9065-9069, 2021 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-33885078

RESUMO

We study how crowding affects the activity and catalysis-enhanced diffusion of enzymes and passive tracers by employing a fluctuating-dumbbell model of conformation-changing enzymes. Our Brownian dynamics simulations reveal that the diffusion of enzymes depends qualitatively on the type of crowding. If only enzymes are present in the system, the catalysis-induced enhancement of the enzyme diffusion - somewhat counter-intuitively - increases with crowding, while it decreases if crowding is due to inert particles. For the tracers, the diffusion enhancement increases with increasing the enzyme concentration. We also show how the enzyme activity is reduced by crowding and propose a simple expression to describe this reduction. Our results highlight subtle effects at play concerning enzymatic activity and macromolecular transport in crowded systems, such as, e.g., the interior of living cells.


Assuntos
Enzimas/química , Biocatálise , Difusão , Simulação de Dinâmica Molecular , Conformação Proteica
16.
Cells ; 10(2)2021 02 10.
Artigo em Inglês | MEDLINE | ID: mdl-33578676

RESUMO

BACKGROUND: Due to the rarity of osteosarcoma and limited indications for radiotherapy (RT), data on RT for this tumor are scarce. This study aimed to investigate the utilization of RT for osteosarcomas in the recent 20 years and to identify factors related to patients' response to radiation. METHODS: We performed a retrospective analysis of patients irradiated for osteosarcoma treatment. We planned to assess differences in the utilization of RT between the periods of 2000-2010 and 2011-2020, identify the risk factors associated with local progression (LP), determine whether RT-related parameters are associated with LP, and calculate patients' survival. RESULTS: A total of 126 patients with osteosarcoma who received 181 RT treatments were identified. We found a difference in RT techniques between RT performed in the years 2000-2010 and that performed in the years 2011-2020. LP was observed after 37 (20.4%) RT treatments. Intent of RT, distant metastases, and concomitant systemic treatment affected the risk of LP. Five-year overall survival was 33% (95% confidence interval (26%-43%)). CONCLUSIONS: RT for osteosarcoma treatment has evolved from simple two-dimensional palliative irradiation into more conformal RT applied for new indications including oligometastatic and oligoprogressive disease. RT may be a valuable treatment modality for selected patients with osteosarcoma.


Assuntos
Osteossarcoma/radioterapia , Adolescente , Adulto , Criança , Estudos de Coortes , Feminino , Humanos , Masculino , Análise Multivariada , Osteossarcoma/patologia , Modelos de Riscos Proporcionais , Análise de Sobrevida , Adulto Jovem
17.
J Phys Chem B ; 124(35): 7537-7543, 2020 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-32790396

RESUMO

A significant fraction of the cell volume is occupied by various proteins, polysaccharides, nucleic acids, etc., which considerably reduces the mobility of macromolecules. Theoretical and experimental work so far have mainly focused on the dependence of the mobility on the occupied volume, while the effect of a macromolecular shape received less attention. Herein, using fluorescence correlation spectroscopy (FCS) and Brownian dynamics (BD) simulations, we report on a dramatic slowdown of tracer diffusion by cylindrically shaped double-stranded (ds) DNAs (16 nm in length). We find, for instance, that the translational diffusion coefficient of a streptavidin tracer is reduced by about 60% for a volume fraction of dsDNA as low as just 5%. For comparison, for a spherical crowder (Ficoll70) the slowdown is only 10% at the same volume fraction and 60% reduction occurs at a volume fraction as high as 35%. BD simulations reveal that this reduction can be attributed to a larger volume excluded to a tracer by dsDNA particles, as compared with spherical Ficoll70 at the same volume fraction, and to the differences in the tracer-crowder attractive interactions. In addition, we find using BD simulations that rotational diffusion of dsDNA is less affected by the crowder shape than its translational motion. Our results show that diffusion in crowded systems is determined not merely by the occupied volume fraction, but that the shape and interactions can determine diffusion, which is relevant to the diverse intracellular environments inside living cells.


Assuntos
Simulação de Dinâmica Molecular , Proteínas , DNA , Difusão , Substâncias Macromoleculares
18.
Acta Oncol ; 58(12): 1720-1730, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31393203

RESUMO

Background and purpose: A collaborative network between proton therapy (PT) centres in Trento in Italy, Poland, Austria, Czech Republic and Sweden (IPACS) was founded to implement trials and harmonize PT. This is the first report of IPACS with the aim to show the level of harmonization that can be achieved for proton therapy planning of head and neck (sino-nasal) cancer.Methods: CT-data sets of five patients were included. During several face-to-face and online meetings, a common treatment planning protocol was developed. Each centre used its own treatment planning system (TPS) and planning approach with some restrictions specified in the treatment planning protocol. In addition, volumetric modulated arc therapy (VMAT) photon plans were created.Results: For CTV1, the average Dmedian was 59.3 ± 2.4 Gy(RBE) for protons and 58.8 ± 2.0 Gy(RBE) for VMAT (aim was 56 Gy(RBE)). For CTV2, the average Dmedian was 71.2 ± 1.0 Gy(RBE) for protons and 70.6 ± 0.4 Gy(RBE) for VMAT (aim was 70 Gy(RBE)). The average D2% for the spinal cord was 25.1 ± 8.5 Gy(RBE) for protons and 47.6 ± 1.4 Gy(RBE) for VMAT. The average D2% for chiasm was 46.5 ± 4.4 Gy(RBE) for protons and 50.8 ± 1.4 Gy(RBE) for VMAT, respectively. Robust evaluation was performed and showed the least robust plans for plans with a low number of beams.Discussion: In conclusion, several influences on harmonization were identified: adherence/interpretation to/of the protocol, available technology, experience in treatment planning and use of different beam arrangements. In future, all OARs that should be included in the optimization need to be specified in order to further harmonize treatment planning.


Assuntos
Neoplasias de Cabeça e Pescoço/radioterapia , Cooperação Internacional , Órgãos em Risco , Terapia com Prótons/métodos , Planejamento da Radioterapia Assistida por Computador/métodos , Tronco Encefálico/efeitos da radiação , Cóclea/efeitos da radiação , Europa (Continente) , Neoplasias de Cabeça e Pescoço/diagnóstico por imagem , Humanos , Laringe/efeitos da radiação , Neoplasias Nasais/diagnóstico por imagem , Neoplasias Nasais/radioterapia , Nervo Óptico/efeitos da radiação , Órgãos em Risco/efeitos da radiação , Neoplasias dos Seios Paranasais/diagnóstico por imagem , Neoplasias dos Seios Paranasais/radioterapia , Glândula Parótida/efeitos da radiação , Fótons/uso terapêutico , Radioterapia de Intensidade Modulada/métodos , Tomografia Computadorizada por Raios X , Carga Tumoral
19.
J Radiat Oncol ; 7(1): 77-84, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29576860

RESUMO

OBJECTIVE: The purpose of this study was to evaluate the clinical outcome of preoperative short-course radiotherapy for rectal cancer patients. METHODS: The study group comprised 210 patients with pathologically proven resectable rectal cancer. Between 2001 and 2013, they were treated preoperatively with short-course radiotherapy (25 Gy delivered in five fractions), followed by total mesorectal excision. Adjuvant 5-fluorouracil-based chemotherapy was administered at the discretion of the treating physician, depending on the pathological stage. RESULTS: After a median follow-up of 57 months, the following 5-year survival rates were observed: overall survival-66.4%, disease-free survival-67.2%, locoregional relapse-free survival-91.7%, and distant metastases-free survival-71.5%. The local failure was observed in 15 patients. Ten patients (4.8%) achieved pathologic complete response. The multivariate analysis demonstrated the regional lymph node involvement to be statistically significant for unfavorable outcomes in terms of all estimated survival rates. Lymphovascular invasion was found to be a strong predictor of survival (HR = 1.68; 95% CI 1.29-3.55) and treatment failure (HR = 1.54; 95% CI 1.08-3.34). The presence of positive surgical circumferential margin was related to six times higher risk of locoregional recurrence. Early and late severe treatment-induced toxicity was reported in 1 and 7.6% patients, respectively. CONCLUSIONS: Preoperative short-course radiotherapy followed by total mesorectal excision and adjuvant chemotherapy allows to achieve excellent local control and favorable survival rates. The treatment-induced toxicity is acceptable.

20.
Hematol Oncol ; 35(3): 317-322, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-26450521

RESUMO

Extramedullary solitary plasmacytoma (EMP) is a rare type of malignancy. This paper presents a retrospective review of the experience with EMP at the Krakow Oncology Center. Records of 17 patients with head and neck EMP, treated with definitive radiotherapy between 1976 and 2009, were analyzed. The total tumour dose ranged from 45 to 70 Gy (median 56 Gy). In four patients with partial response after radiotherapy, adjuvant melphalan-based chemotherapy was applied. The median follow-up period was 8.6 years. The treatment was well tolerated. The estimated 10-year overall survival, disease-free survival, and multiple myeloma-free survival were 68.4%, 49.3%, and 55%, respectively. The 10-year local control rate was 90.9%. No in-field local recurrence was observed. During the follow-up, progression into multiple myeloma was observed in five patients, with a mean time to conversion of 24 months. The only factor adversely affecting overall survival on univariate analysis was the age >56 years, whereas a complete tumour regression after radiotherapy was associated with a significant improvement in both disease-free survival and multiple myeloma-free survival. Despite the high effectiveness of local radiotherapy, there is still a significant treatment failure risk due to the EMP conversion into generalized disease. An attempt to identify prognostic factors may facilitate selection of patients with a high risk of progression to multiple myeloma. Copyright © 2015 John Wiley & Sons, Ltd.


Assuntos
Plasmocitoma/mortalidade , Plasmocitoma/radioterapia , Adulto , Idoso , Biomarcadores Tumorais , Fracionamento da Dose de Radiação , Feminino , Humanos , Estimativa de Kaplan-Meier , Masculino , Pessoa de Meia-Idade , Metástase Neoplásica , Estadiamento de Neoplasias , Plasmocitoma/diagnóstico , Prognóstico , Dosagem Radioterapêutica , Estudos Retrospectivos , Resultado do Tratamento
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