Publications by authors named "Marcin Sikora"

40 Publications

A Combined Analysis of Gut and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Study.

Nutrients 2021 May 15;13(5). Epub 2021 May 15.

Department of Pediatrics, Allergology and Gastroenterology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 87-100 Toruń, Poland.

The gut microbiota in patients with food allergy, and the skin microbiota in atopic dermatitis patients differ from those of healthy people. We hypothesize that relationships may exist between gut and skin microbiota in patients with allergies. The aim of this study was to determine the possible relationship between gut and skin microbiota in patients with allergies, hence simultaneous analysis of the two compartments of microbiota was performed in infants with and without allergic symptoms. Fifty-nine infants with food allergy and/or atopic dermatitis and 28 healthy children were enrolled in the study. The skin and gut microbiota were evaluated using 16S rRNA gene amplicon sequencing. No significant differences in the α-diversity of dermal or fecal microbiota were observed between allergic and non-allergic infants; however, a significant relationship was found between bacterial community structure and allergy phenotypes, especially in the fecal samples. Certain clinical conditions were associated with characteristic bacterial taxa in the skin and gut microbiota. Positive correlations were found between skin and fecal samples in the abundance of among allergic infants, and and among healthy infants. Although infants with allergies and healthy infants demonstrate microbiota with similar α-diversity, some differences in β-diversity and bacterial species abundance can be seen, which may depend on the phenotype of the allergy. For some organisms, their abundance in skin and feces samples may be correlated, and these correlations might serve as indicators of the host's allergic state.
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http://dx.doi.org/10.3390/nu13051682DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8156695PMC
May 2021

Choosing source of microorganisms and processing technology for next generation beet bioinoculant.

Sci Rep 2021 Feb 2;11(1):2829. Epub 2021 Feb 2.

Center for Modern Interdisciplinary Technologies, Nicolaus Copernicus University (NCU), Toruń, Poland.

The increase of human population and associated increasing demand for agricultural products lead to soil over-exploitation. Biofertilizers based on lyophilized plant material containing living plant growth-promoting microorganisms (PGPM) could be an alternative to conventional fertilizers that fits into sustainable agricultural technologies ideas. We aimed to: (1) assess the diversity of endophytic bacteria in sugar and sea beet roots and (2) determine the influence of osmoprotectants (trehalose and ectoine) addition during lyophilization on bacterial density, viability and salt tolerance. Microbiome diversity was assessed based on 16S rRNA amplicons sequencing, bacterial density and salt tolerance was evaluated in cultures, while bacterial viability was calculated by using fluorescence microscopy and flow cytometry. Here we show that plant genotype shapes its endophytic microbiome diversity and determines rhizosphere soil properties. Sea beet endophytic microbiome, consisting of genera characteristic for extreme environments, is more diverse and salt resistant than its crop relative. Supplementing osmoprotectants during root tissue lyophilization exerts a positive effect on bacterial community salt stress tolerance, viability and density. Trehalose improves the above-mentioned parameters more effectively than ectoine, moreover its use is economically advantageous, thus it may be used to formulate improved biofertilizers.
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http://dx.doi.org/10.1038/s41598-021-82436-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7854725PMC
February 2021

The five-analyzer point-to-point scanning crystal spectrometer at ESRF ID26.

J Synchrotron Radiat 2021 Jan 1;28(Pt 1):362-371. Epub 2021 Jan 1.

ESRF - The European Synchrotron, 71 Avenue des Martyres, 38000 Grenoble, France.

X-ray emission spectroscopy in a point-to-point focusing geometry using instruments that employ more than one analyzer crystal poses challenges with respect to mechanical design and performance. This work discusses various options for positioning the components and provides the formulas for calculating their relative placement. Ray-tracing calculations were used to determine the geometrical contributions to the energy broadening including the source volume as given by the beam footprint on the sample. The alignment of the instrument is described and examples are given for the performance.
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http://dx.doi.org/10.1107/S1600577520015416DOI Listing
January 2021

Magnetic Properties and the Electronic Structure of the GdTbCo Compound.

Materials (Basel) 2020 Dec 1;13(23). Epub 2020 Dec 1.

Institute of Physics, University of Silesia in Katowice, 75 Pułku Piechoty 1A, 41-500 Chorzów, Poland.

We report on the comprehensive experimental and theoretical studies of magnetic and electronic structural properties of the GdTbCo compound crystallization in the cubic Laves phase (C15). We present new results and compare them to those reported earlier. The magnetic study was completed with electronic structure investigations. Based on magnetic isotherms, magnetic entropy change (Δ) was determined for many values of the magnetic field change (Δ), which varied from 0.1 to 7 T. In each case, the Δ had a maximum around room temperature. The analysis of Arrott plots supplemented by a study of temperature dependency of Landau coefficients revealed that the compound undergoes a magnetic phase transition of the second type. From the () dependency, the exchange integrals between rare-earth R-R (), R-Co (), and Co-Co () atoms were evaluated within the mean-field theory approach. The electronic structure was determined using the X-ray photoelectron spectroscopy (XPS) method as well as by calculations using the density functional theory (DFT) based Full Potential Linearized Augmented Plane Waves (FP-LAPW) method. The comparison of results of ab initio calculations with the experimental data indicates that near the XPS spectrum collects excitations of electrons from Co states with different values of exchange splitting. The values of the magnetic moment on Co atoms determined from magnetic measurements, estimated from the XPS spectra, and results from ab initio calculations are quantitatively consistent.
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http://dx.doi.org/10.3390/ma13235481DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7730538PMC
December 2020

High-Entropy Perovskites as Multifunctional Metal Oxide Semiconductors: Synthesis and Characterization of (GdNdLaSmY)CoO.

ACS Appl Electron Mater 2020 Oct 18;2(10):3211-3220. Epub 2020 Sep 18.

Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, Al. Mickiewicza 30, 30059 Kraków, Poland.

Single-phase multicomponent perovskite-type cobalt oxide containing five cations in equiatomic amounts on the A-site, namely, (GdNdLaSmY)CoO, has been synthesized via the modified coprecipitation hydrothermal method. Using an original approach for heat treatment, which comprises quenching utilizing liquid nitrogen as a cooling medium, a single-phase ceramic with high configuration entropy, crystallizing in an orthorhombic distorted structure was obtained. It reveals the anomalous temperature dependence of the lattice expansion with two weak transitions at approx. 80 and 240 K that are assigned to gradual crossover from the low- via intermediate- to high-spin state of Co. The compound exhibits weak ferromagnetism at ≤ 10 K and signatures of antiferromagnetic correlations in the paramagnetic phase. Ab initio calculations predict a band gap Δ = 1.18 eV in the ground-state electronic structure with the dominant contribution of O_p and Co_d orbitals in the valence and conduction bands, respectively. Electronic transport measurements confirm the negative temperature coefficient of resistivity characteristic to a semiconducting material and reveal a sudden drop in activation energy at ∼ 240 K from ∼ 1 eV in the low-temperature phase to ∼ 0.3 eV at room temperature. The possibility of fine tuning of the semiconducting band gap via a subtle change in A-site stoichiometry is discussed.
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http://dx.doi.org/10.1021/acsaelm.0c00559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7660934PMC
October 2020

Selective magnetometry of superparamagnetic iron oxide nanoparticles in liquids.

Nanoscale 2020 Aug;12(31):16420-16426

AGH University of Science and Technology, Academic Centre for Materials and Nanotechnology, Al. Mickiewicza 30, 30-059 Krakow, Poland.

We show that the properties of superparamagnetic iron oxide nanoparticles suspended in liquids can be effectively studied using Magnetic Circular Dichroism in Resonant Inelastic X-ray Scattering. Analysis of the spectral shape and magnetic contrast produced by this experiment enables an assessment of the site distribution and magnetic state of metal ions in the spinel phase. The selective magnetization profile of particles as derived from the field dependence of dichroism empowers an estimation of particle size distribution. Furthermore, the new proposed methodology discriminates sizes that are below the detection limits of X-ray and light scattering probes and that are difficult to spot in TEM.
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http://dx.doi.org/10.1039/d0nr02866eDOI Listing
August 2020

Moderate intensity exercise in hypoxia increases IGF-1 bioavailability and serum irisin in individuals with type 1 diabetes.

Ther Adv Endocrinol Metab 2020 27;11:2042018820925326. Epub 2020 May 27.

School of Health Sciences, University of Salford, Salford, UK.

Aim: This study aimed to determine the effect of moderate intensity continuous exercise (Ex) and hypoxia (Hyp) on serum brain-derived neurotrophic factor (BDNF), insulin-like growth factor-1 (IGF-1) and its binding protein-3 (IGFBP-3), irisin and cytokines levels in patients with type 1 diabetes (T1D).

Methods: A total of 14 individuals with T1D (age: 28.7 ± 7.3 years) and 14 healthy adults (age: 27.1 ± 3.9 years) performed 40-min continuous Ex at moderate intensity (50% lactate threshold) on a cycle ergometer in normoxia (Nor) and Hyp (FiO = 15.1%) Biochemical factors, glucose concentrations and physiological variables were measured at rest, immediately and up to 24 h after both Ex protocols.

Results: Patients with T1D had significantly lower pre-Ex serum concentrations of BDNF ( < 0.05,  < 0.01), and total IGF-1 ( < 0.001,  < 0.05) and significantly higher irisin levels ( < 0.05,  < 0.01) in Nor and Hyp, compared with healthy subjects. Ex significantly increased in T1D group serum BDNF (in Nor only  < 0.05) and total IGF-1 levels in Nor and Hyp ( < 0.001 and  < 0.01, respectively). Immediately after Ex in Hyp, freeIGF-1 ( < 0.05) and irisin levels ( < 0.001) were significantly higher compared with the levels induced by Ex alone. Free IGF-1 and irisin serum levels remained elevated in 24 h post-Ex in Hyp. In T1D, significant blood glucose (BG) decrease was observed immediately after Ex in Hyp ( < 0.001) and in 24 h recovery ( < 0.001) compared with pre-Ex level.

Conclusion: The study results suggest that moderate intensity continuous Ex has beneficial effect on BDNF and IGF-1 levels. Ex in hypoxic conditions may be more effective in increasing availability of IGF-1. The alterations in the post-Ex irisin levels and IGF-1 system may be contributing to more effective glycaemia control in patients with T1D.
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http://dx.doi.org/10.1177/2042018820925326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7257872PMC
May 2020

Bad neighbour, good neighbour: how magnetic dipole interactions between soft and hard ferrimagnetic nanoparticles affect macroscopic magnetic properties in ferrofluids.

Nanoscale 2020 May;12(20):11222-11231

Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, CNRS, MNHN, UMR7590, 4 place Jussieu, 75052 Paris Cedex 05, France.

Fluids responding to magnetic fields (ferrofluids) offer a scene with no equivalent in nature to explore long-range magnetic dipole interactions. Here, we studied the very original class of binary ferrofluids, embedding soft and hard ferrimagnetic nanoparticles. We used a combination of X-ray magnetic spectroscopy measurements supported by multi-scale experimental techniques and Monte-Carlo simulations to unveil the origin of the emergent macroscopic magnetic properties of the binary mixture. We found that the association of soft and hard magnetic nanoparticles in the fluid has a considerable influence on their inherent magnetic properties. While the ferrofluid remains in a single phase, magnetic interactions at the nanoscale between both types of particles induce a modification of their respective coercive fields. By connecting the microscopic properties of binary ferrofluids containing small particles, our findings lay the groundwork for the manipulation of magnetic interactions between particles at the nanometer scale in magnetic liquids.
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http://dx.doi.org/10.1039/d0nr02023kDOI Listing
May 2020

Hormonal Response to Incremental and Continuous Exercise in Cyclists with Left Ventricle Hypertrophy.

J Hum Kinet 2020 Jan 31;71:155-166. Epub 2020 Jan 31.

Institute of Sport Sciences, Academy of Physical Education, Katowice, Poland.

The aim of this study was to assess the effects of incremental and continuous exercise on the concentration of insulin-like growth factor-1 (IGF-1), growth hormone (GH), testosterone (T), and cortisol (C), as well as to investigate whether increased cardiac dimensions in cyclists were related to changes in these hormones and cardiac biomarkers. The study included 30 elite cyclists divided into two groups, i.e., athletes with left ventricle hypertrophy (a LVH group), and a control group (CG) without LVH. The study protocol included performance of a standard incremental exercise (IncEx) test to measure athletes' maximum power (Pmax), maximum oxygen uptake (VO2max), and lactate threshold (LAT). The IncEx test results were then used to determine the intensity of the continuous exercise (ConEx) test which was performed after the 1-week washout period. Cyclists with LVH and without LVH did not differ in resting hormone concentrations and cardiac biomarkers levels. There was a significant effect of exercise on serum IGF-1 levels (p < 0.05) in the LVH group and a combined effect of the type of exercise and LVH on IGF-1 (p < 0.05). Cyclists with LVH demonstrated higher post exercise T levels recorded in response to exercise compared to the CG (p < 0.01). Significantly higher serum T levels were observed in response to ConEx compared to IncEx in the LVH group and the CG (p < 0.05 and p < 0.05, respectively). In the LVH group, a significant positive correlation between the post-exercise T/C ratio and left ventricular mass index was observed (r = 0.98, p < 0.01). There were no effects of heart hypertrophy on cardiac standard biomarkers. Incremental and continuous exercise caused a marked increase in steroid hormone concentrations and moderate strengthening of insulin growth factors effects. Regular incremental exercise seems to induce beneficial cardiac adaptations via significant increases in the concentration of anabolic factors compared to the same training mode yet with constant exercise intensity.
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http://dx.doi.org/10.2478/hukin-2019-0120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7052704PMC
January 2020

Cobalt-platinum nanomotors for local gas generation.

Nanotechnology 2020 Feb 1;31(7):07LT01. Epub 2019 Nov 1.

Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, A. Mickiewicza 30, 30-059 Krakow, Poland.

Bimetallic Co-Pt nanorods exhibit an enhanced capacity for the production of gas from liquid-phase chemicals. Based on the systematic structural and magnetic characterization we discuss potential applications of these hybrid nanostructures for localized fuel generation in microdevices. Experimental proof of the feasibility for controlling the rate of catalytic reaction via external magnetic stimuli is shown. This unique functionality makes these hybrids promising candidates for optimizing the energy conversion rate in microfluidics fuel cells.
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http://dx.doi.org/10.1088/1361-6528/ab53bdDOI Listing
February 2020

Comparison of the Effectiveness of High-Intensity Interval Training in Hypoxia and Normoxia in Healthy Male Volunteers: A Pilot Study.

Biomed Res Int 2019 22;2019:7315714. Epub 2019 Sep 22.

Department of Neuroscience and Imaging, Dipartimento, University di Madonna delle Piane, Via dei Vestini 31, 66100 Chieti, Italy.

Aims: The study investigated the effect of high-intensity interval training in hypoxia and normoxia on serum concentrations of proangiogenic factors, nitric oxide, and inflammatory responses in healthy male volunteers.

Methods: Twelve physically active male subjects completed a high-intensity interval training (HIIT) in normoxia (NorTr) and in normobaric hypoxia (HypTr) (FiO = 15.2%). The effects of HIIT in hypoxia and normoxia on maximal oxygen uptake, hypoxia-inducible factor-1-alpha, vascular endothelial growth factor, nitric oxide, and cytokines were analyzed.

Results: HIIT in hypoxia significantly increases maximal oxygen uptake (=0.01) levels compared to pretraining levels. Serum hypoxia-inducible factor-1 (=0.01) and nitric oxide levels (=0.05), vascular endothelial growth factor (=0.04), and transforming growth factor- (=0.01) levels were increased in response to exercise test after hypoxic training. There was no effect of training conditions for serum baseline angiogenic factors and cytokines ( > 0.05) with higher HIF-1 and NO levels after hypoxic training compared to normoxic training ( = 9.1; < 0.01 and  = 5.7; < 0.05, respectively).

Conclusions: High-intensity interval training in hypoxia seems to induce beneficial adaptations to exercise mediated via a significant increase in the serum concentrations of proangiogenic factors and serum nitric oxide levels compared to the same training regimen in normoxia.
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http://dx.doi.org/10.1155/2019/7315714DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6778879PMC
March 2020

Gradient of zinc content in core-shell zinc ferrite nanoparticles - precise study on composition and magnetic properties.

Phys Chem Chem Phys 2019 Nov 16;21(42):23473-23484. Epub 2019 Oct 16.

AGH University of Science and Technology, Academic Centre for Materials and Nanotechnology, al. A. Mickiewicza 30, 30-059 Krakow, Poland.

A broad spectrum of applications of magnetic nanoparticles leads to the need for the precise tuning of their magnetic properties. In this study, a series of magnetite and zinc-ferrite nanoparticles were successfully prepared by modified high-temperature synthesis in a controlled gas atmosphere. Nanoparticles with different zinc to iron ratios and pure FeO were obtained. The structure of the nanoparticles was studied by transmission electron microscopy and Mössbauer spectroscopy. These revealed the single domain character of the nanoparticles and the influence of the synthesis temperature and zinc to iron ratio on their shape and size. Chemical structure was characterized by inductively coupled plasma optical emission spectroscopy, energy dispersive X-ray spectroscopy and thermogravimetric analysis. X-ray photoelectron spectroscopy coupled with an argon gas cluster ion beam (Ar-GCIB) allowed the study of subsequent layers of the nanoparticles without altering their chemical structure. This revealed the presence of a carbon layer on all nanoparticles consisting of capping agents used in the synthesis and revealed the core-shell character of the zinc ferrite particles. In addition, different types of zinc infusions in the nanoparticle structure were observed when using different Zn/Fe ratios. Finally, magnetic studies performed by means of vibrating sample magnetometry proved the superparamagnetic behavior of all the samples.
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http://dx.doi.org/10.1039/c9cp03591eDOI Listing
November 2019

Magnetic Contrast at Spin-Flip Excitations: An Advanced X-Ray Spectroscopy Tool to Study Magnetic-Ordering.

ACS Appl Mater Interfaces 2019 Oct 20;11(39):36213-36220. Epub 2019 Sep 20.

Debye Institute for Nanomaterials Science , Utrecht University , Universiteitsweg 99 , 3584 CA Utrecht , The Netherlands.

The determination of the local orientation and magnitude of the magnetization in spin textures plays a pivotal role in understanding and harnessing magnetic properties for technological applications. Here, we show that by employing the polarization dependence of resonant inelastic X-ray scattering (RIXS), we can directly probe the spin ordering with chemical and site selectivity. Applied on the prototypical ferrimagnetic mixed-valence system, magnetite ([Fe][Fe,Fe]O), we can distinguish spin-flip excitations at the A and B antiferromagnetically coupled Fe sublattices and quantify the exchange field. Furthermore, it is possible to determine the orbital contribution to the magnetic moment from detailed angular dependence measurements. RIXS dichroism measurements performed at spin-flip excitations with nanometer spatial resolution will offer a powerful mapping contrast suitable for the characterization of magnetic ordering at interfaces and engineered spin textures.
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http://dx.doi.org/10.1021/acsami.9b10196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6778912PMC
October 2019

Room-Temperature Ferromagnetism in InSb-Mn Nanowires.

Nano Lett 2019 10 9;19(10):7144-7148. Epub 2019 Sep 9.

Academic Centre for Materials and Nanotechnology , AGH University of Science and Technology , A. Mickiewicza 30 , 30-059 Krakow , Poland.

The successful synthesis of one-dimensional nanostructures of a narrow band gap semiconductor, exhibiting a ferromagnetic response at room temperature, is reported. High-quality nanowires of InSb-Mn have been produced by template-assisted pulse electrodeposition. Detailed structural and spectroscopic characterizations revealed good crystallinity, a narrow size distribution of the nanostructures, and the ability to control the Mn doping level. The dominating magnetic response at a cryogenic temperature evolves with an increasing Mn concentration from paramagnetic through antiferromagnetic to ferromagnetic. A robust ferromagnetic response of InSb nanowires doped with 2.5% at. of Mn is retained up to a Curie temperature of nearly 500 K.
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http://dx.doi.org/10.1021/acs.nanolett.9b02690DOI Listing
October 2019

Validation of Microsatellite Instability Detection Using a Comprehensive Plasma-Based Genotyping Panel.

Clin Cancer Res 2019 12 4;25(23):7035-7045. Epub 2019 Aug 4.

The University of Texas MD Anderson Cancer Center, Houston, Texas.

Purpose: To analytically and clinically validate microsatellite instability (MSI) detection using cell-free DNA (cfDNA) sequencing.

Experimental Design: Pan-cancer MSI detection using Guardant360 was analytically validated according to established guidelines and clinically validated using 1,145 cfDNA samples for which tissue MSI status based on standard-of-care tissue testing was available. The landscape of cfDNA-based MSI across solid tumor types was investigated in a cohort of 28,459 clinical plasma samples. Clinical outcomes for 16 patients with cfDNA MSI-H gastric cancer treated with immunotherapy were evaluated.

Results: cfDNA MSI evaluation was shown to have high specificity, precision, and sensitivity, with a limit of detection of 0.1% tumor content. In evaluable patients, cfDNA testing accurately detected 87% (71/82) of tissue MSI-H and 99.5% of tissue microsatellite stable (863/867) for an overall accuracy of 98.4% (934/949) and a positive predictive value of 95% (71/75). Concordance of cfDNA MSI with tissue PCR and next-generation sequencing was significantly higher than IHC. Prevalence of cfDNA MSI for major cancer types was consistent with those reported for tissue. Finally, robust clinical activity of immunotherapy treatment was seen in patients with advanced gastric cancer positive for MSI by cfDNA, with 63% (10/16) of patients achieving complete or partial remission with sustained clinical benefit.

Conclusions: cfDNA-based MSI detection using Guardant360 is highly concordant with tissue-based testing, enabling highly accurate detection of MSI status concurrent with comprehensive genomic profiling and expanding access to immunotherapy for patients with advanced cancer for whom current testing practices are inadequate..
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http://dx.doi.org/10.1158/1078-0432.CCR-19-1324DOI Listing
December 2019

One-Step Synthesis of Long Term Stable Superparamagnetic Colloid of Zinc Ferrite Nanorods in Water.

Materials (Basel) 2019 Mar 29;12(7). Epub 2019 Mar 29.

Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, al. A. Mickiewicza 30, 30-059 Krakow, Poland.

Synthesis of spinel zinc ferrite ultrafine needle-like particles that exhibit exceptional stability in aqueous dispersion (without any surfactants) and superparamagnetic response is reported. Comprehensive structural and magnetic characterization of the particles is performed using X-ray and electron diffraction, small angle X-ray scattering, transmission electron microscopy, dynamic light scattering, vibrating sample magnetometry, Mössbauer spectroscopy and high-resolution X-ray spectroscopy. It reveals nearly stoichiometric ZnFe₂O₄ nanorods with mixed spinel structure and unimodal size distribution of mean length of 20 nm and diameter of 5 nm. Measurements performed in aqueous and dried form shows that particles' properties are significantly changed as a result of drying.
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http://dx.doi.org/10.3390/ma12071048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6480960PMC
March 2019

A Hybrid System for Magnetic Hyperthermia and Drug Delivery: SPION Functionalized by Curcumin Conjugate.

Materials (Basel) 2018 Nov 27;11(12). Epub 2018 Nov 27.

Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland.

Cancer is among the leading causes of death worldwide, thus there is a constant demand for new solutions, which may increase the effectiveness of anti-cancer therapies. We have designed and successfully obtained a novel, bifunctional, hybrid system composed of colloidally stabilized superparamagnetic iron oxide nanoparticles (SPION) and curcumin containing water-soluble conjugate with potential application in anticancer hyperthermia and as nanocarriers of curcumin. The obtained nanoparticulate system was thoroughly studied in respect to the size, morphology, surface charge, magnetic properties as well as some biological functions. The results revealed that the obtained nanoparticles, ca. 50 nm in diameter, were the agglomerates of primary particles with the magnetic, iron oxide cores of ca. 13 nm, separated by a thin layer of the applied cationic derivative of chitosan. These agglomerates were further coated with a thin layer of the sodium alginate conjugate of curcumin and the presence of both polymers was confirmed using thermogravimetry. The system was also proven to be applicable in magnetic hyperthermia induced by the oscillating magnetic field. A high specific absorption rate (SAR) of 280 [W/g] was registered. The nanoparticles were shown to be effectively uptaken by model cells. They were found also to be nontoxic in the therapeutically relevant concentration in in vitro studies. The obtained results indicate the high application potential of the new hybrid system in combination of magnetic hyperthermia with delivery of curcumin active agent.
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http://dx.doi.org/10.3390/ma11122388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317039PMC
November 2018

Statistical motion modelling for robust evaluation of clinically delivered accumulated dose distributions after curative radiotherapy of locally advanced prostate cancer.

Radiother Oncol 2018 08 22;128(2):327-335. Epub 2018 Jun 22.

Department of Oncology and Medical Physics, Haukeland University Hospital, Bergen, Norway; Department of Physics and Technology, University of Bergen, Norway.

Background And Purpose: Planned doses are used as surrogate for the actually delivered dose in radiotherapy. We have estimated the delivered dose in a dose-escalation trial of locally advanced prostate cancer by statistical dose-accumulation and by DVH-summation, and compared to planned dose.

Materials And Method: Prescribed dose-escalation to the prostate was 67.5 Gy/25fr., corresponding to 81GyEQD2 assuming α/β = 1.5. The 21 patients had three targets (i.e. CTV67.5 + 2 mm, CTV60 + 5 mm, CTV50 + 10 mm) irradiated by a simultaneous-integrated-boost technique. Analysis was based on 213 CT scans and 5-years of follow-up. For statistical dose-accumulation, we modelled 10000 possible treatment courses based on planned dose and deformation-vector-fields from contour-based registration. For DVH-summation we recalculated dose on repeat-CTs and estimated median D98%/EUD. Groups with/without disease recurrence were compared.

Results: Discrepancies between planned and accumulated dose were mostly seen for CTV67.5, where under-dosage was found at different locations in the prostate in 12/21 patients. Delivered dose-escalation (D98%) was on average 73.9GyEQD2 (range: 68.3-78.7GyEQD2). No significant difference in accumulated-D98% was found in patients with (n = 8) and without (n = 13) recurrence (p > 0.05). Average D98%/EUD with statistical dose-accumulation vs DVH-summation was significantly different in CTV60, CTV50, rectum and bladder but not in CTV67.5.

Conclusion: The planned dose escalation was not received by more than half-of-the patients. Robustness of the prostate target (CTV67.5) should therefore be better prioritized in these patients given the low toxicity profile. Estimates of delivered dose were less conservative for dose-accumulation due to interaction of random organ motion with the dose matrix.
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http://dx.doi.org/10.1016/j.radonc.2018.06.004DOI Listing
August 2018

Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition.

Microb Ecol 2019 Jan 30;77(1):56-75. Epub 2018 May 30.

Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland.

Plant litter decomposition is a process enabling biogeochemical cycles closing in ecosystems, and decomposition in forests constitutes the largest part of this process taking place in terrestrial biomes. Microbial communities during litter decomposition were studied mainly with low-throughput techniques not allowing detailed insight, particularly into coniferous litter, as it is more difficult to obtain high quality DNA required for analyses. Motivated by these problems, we analyzed archaeal, bacterial, and eukaryotic communities at three decomposition stages: fresh, 3- and 8-month-old litter by 16/18S rDNA pyrosequencing, aiming at detailed insight into early stages of pine litter decomposition. Archaea were absent from our libraries. Bacterial and eukaryotic diversity was greatest in 8-month-old litter and the same applied to bacterial and fungal rDNA content. Community structure was different at various stages of decomposition, and phyllospheric organisms (bacteria: Acetobacteraceae and Pseudomonadaceae members, fungi: Lophodermium, Phoma) were replaced by communities with metabolic capabilities adapted to the particular stage of decomposition. Sphingomonadaceae and Xanthomonadaceae and fungal genera Sistotrema, Ceuthospora, and Athelia were characteristic for 3-month-old samples, while 8-month-old ones were characterized by Bradyrhizobiaceae and nematodes (Plectus). We suggest that bacterial and eukaryotic decomposer communities change at different stages of pine litter decomposition in a way similar to that in broadleaf litter. Interactions between bacteria and eukaryotes appear to be one of the key drivers of microbial community structure.
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http://dx.doi.org/10.1007/s00248-018-1209-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318262PMC
January 2019

Validation of a Plasma-Based Comprehensive Cancer Genotyping Assay Utilizing Orthogonal Tissue- and Plasma-Based Methodologies.

Clin Cancer Res 2018 08 24;24(15):3539-3549. Epub 2018 Apr 24.

Guardant Health, Redwood City, California.

To analytically and clinically validate a circulating cell-free tumor DNA sequencing test for comprehensive tumor genotyping and demonstrate its clinical feasibility. Analytic validation was conducted according to established principles and guidelines. Blood-to-blood clinical validation comprised blinded external comparison with clinical droplet digital PCR across 222 consecutive biomarker-positive clinical samples. Blood-to-tissue clinical validation comprised comparison of digital sequencing calls to those documented in the medical record of 543 consecutive lung cancer patients. Clinical experience was reported from 10,593 consecutive clinical samples. Digital sequencing technology enabled variant detection down to 0.02% to 0.04% allelic fraction/2.12 copies with ≤0.3%/2.24-2.76 copies 95% limits of detection while maintaining high specificity [prevalence-adjusted positive predictive values (PPV) >98%]. Clinical validation using orthogonal plasma- and tissue-based clinical genotyping across >750 patients demonstrated high accuracy and specificity [positive percent agreement (PPAs) and negative percent agreement (NPAs) >99% and PPVs 92%-100%]. Clinical use in 10,593 advanced adult solid tumor patients demonstrated high feasibility (>99.6% technical success rate) and clinical sensitivity (85.9%), with high potential actionability (16.7% with FDA-approved on-label treatment options; 72.0% with treatment or trial recommendations), particularly in non-small cell lung cancer, where 34.5% of patient samples comprised a directly targetable standard-of-care biomarker. High concordance with orthogonal clinical plasma- and tissue-based genotyping methods supports the clinical accuracy of digital sequencing across all four types of targetable genomic alterations. Digital sequencing's clinical applicability is further supported by high rates of technical success and biomarker target discovery. .
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http://dx.doi.org/10.1158/1078-0432.CCR-17-3831DOI Listing
August 2018

Association between Val158Met and polymorphisms and depressive symptoms in the obese population.

Neuropsychiatr Dis Treat 2017 18;13:2221-2229. Epub 2017 Aug 18.

Department of Clinical Neuropsychology, Nicolaus Copernicus University in Toruń, Collegium Medicum in Bydgoszcz, Bydgoszcz.

Objectives: Depressive symptoms are common among patients with obesity. Abnormalities in dopamine signaling involved in the reward circuit may ensue excessive consumption of food, resulting in obesity and leading to neuropsychiatric disorders such as depression. This study sought to investigate the association of polymorphisms in the genes encoding and with the intensity of depressive symptoms in obese subjects.

Participants And Methods: Prevalence and severity of depressive symptoms were assessed in a group of 364 obese patients using the Beck Depression Inventory (BDI) and the Hamilton Depression Rating Scale (HDRS). Genetic polymorphisms in and were evaluated in peripheral blood samples.

Results: The results indicated an association between alleles and depressive symptoms, as well as severity of obesity. Subjects homozygous for the nine-repeat allele scored higher in BDI (=0.022) and HDRS (=0.00001), suggesting higher intensity of depression in both sexes. This allele was also associated with the highest body mass index (BMI; =0.001). Carriers of the Val158Met allele of scored higher on both depression scales (BDI, =0.0005; HRDS, =0.002) and had the highest BMI values.

Conclusion: Polymorphisms in the and genes are associated with a greater intensity of depressive symptoms in the obese population.
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http://dx.doi.org/10.2147/NDT.S138565DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5571853PMC
August 2017

Molecular phylogeny of Miltogramminae (Diptera: Sarcophagidae): Implications for classification, systematics and evolution of larval feeding strategies.

Mol Phylogenet Evol 2017 11 11;116:49-60. Epub 2017 Jul 11.

Chair of Ecology and Biogeography, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland.

Miltogramminae is one of the phylogenetically most poorly studied taxa of the species-rich family Sarcophagidae (Diptera). Most species are kleptoparasites in nests of solitary aculeate wasps and bees, although parasitoids and saprophagous species are also known, and the ancestral miltogrammine life habit remains unsettled. Here, we present for the first time a comprehensive phylogenetic tree consisting of 58 representatives of Miltogramminae, reconstructed using sequence data from three mitochondrial (COI, cytB, ND4) and one nuclear (Ef-1α) genes. Our phylogenetic hypothesis suggests that: (1) Miltogramminae are sister to Paramacronychiinae, (2) Miltogramminae can be divided into the "lower miltogrammines" containing two clades of mainly saprophages and a clade of "higher miltogrammines" with mainly kleptoparasitic species, (3) only three genera turn out to be non-monophyletic: Miltogramma, Senotainia and Pterella and (4) the genus Sarcotachina, which traditionally has been considered as belonging to the Paramacronychiinae, is placed in one of the clades of "lower miltogrammines". Ancestral state reconstruction of larval feeding strategy and five larval characters reveals that the ancestor of Miltogramminae was likely a saprophage retaining plesiomorphic oral ridges and a cephaloskeleton with sclerotized dorsal bridge. Synapomorphies like large pseudocephalic sensory organs and well-developed cuticular sculpture suggest that the ancestral first instar larva actively searched for a buried food supply.
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http://dx.doi.org/10.1016/j.ympev.2017.07.001DOI Listing
November 2017

X-ray magnetic circular dichroism measured at the Fe K-edge with a reduced intrinsic broadening: x-ray absorption spectroscopy versus resonant inelastic x-ray scattering measurements.

J Phys Condens Matter 2016 12 26;28(50):505202. Epub 2016 Oct 26.

Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités, UMR CNRS 7590, UPMC Univ Paris 06, Muséum National d'Histoire Naturelle, IRD UMR206, 4 Place Jussieu, F-75005 Paris, France.

X-ray magnetic circular dichroism is measured at the Fe K pre-edge in yttrium iron garnet using two different procedures that allow reducing the intrinsic broadening due to the 1s corehole lifetime. First, deconvolution of XMCD data measured in total fluorescence yield (TFY) with an extremely high signal-to-noise ratio enables a factor of 2.4 to be gained in the XMCD intensity. Ligand field multiplet calculations performed with different values of intrinsic broadening show that deconvolving such high quality XMCD data is similar to reducing the lifetime broadening from a 1s corehole to a 2p corehole. Second, MCD is measured by resonant inelastic x-ray scattering spectroscopy as a function of incident energy and emission energy. Selection of a fixed emission energy, instead of using the TFY, allows enhancing the MCD intensity up to a factor of  ∼4.7. However, this significantly changes the spectral shape of the XMCD signal, which cannot be interpreted any more as an absorption spectrum.
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http://dx.doi.org/10.1088/0953-8984/28/50/505202DOI Listing
December 2016

Pushing up the magnetisation values for iron oxide nanoparticles via zinc doping: X-ray studies on the particle's sub-nano structure of different synthesis routes.

Phys Chem Chem Phys 2016 Sep;18(36):25221-25229

Fraunhofer Institute for Silicate Research ISC, Neunerplatz 2, 97082 Wuerzburg, Germany. and Department of Chemical Technology of Materials Synthesis, University of Wuerzburg, Roentgenring 11, 97070 Wuerzburg, Germany.

The maximum magnetisation (saturation magnetisation) obtainable for iron oxide nanoparticles can be increased by doping the nanocrystals with non-magnetic elements such as zinc. Herein, we closely study how only slightly different synthesis approaches towards such doped nanoparticles strongly influence the resulting sub-nano/atomic structure. We compare two co-precipitation approaches, where we only vary the base (NaOH versus NH), and a thermal decomposition route. These methods are the most commonly applied ones for synthesising doped iron oxide nanoparticles. The measurable magnetisation change upon zinc doping is about the same for all systems. However, the sub-nano structure, which we studied with Mössbauer and X-ray absorption near edge spectroscopy, differs tremendously. We found evidence that a much more complex picture has to be drawn regarding what happens upon Zn doping compared to what textbooks tell us about the mechanism. Our work demonstrates that it is crucial to study the obtained structures very precisely when "playing" with the atomic order in iron oxide nanocrystals.
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http://dx.doi.org/10.1039/c6cp04221jDOI Listing
September 2016

Single Nucleotide Polymorphism Discovery in Bovine Pituitary Gland Using RNA-Seq Technology.

PLoS One 2016 8;11(9):e0161370. Epub 2016 Sep 8.

Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America.

Examination of bovine pituitary gland transcriptome by strand-specific RNA-seq allows detection of putative single nucleotide polymorphisms (SNPs) within potential candidate genes (CGs) or QTLs regions as well as to understand the genomics variations that contribute to economic trait. Here we report a breed-specific model to successfully perform the detection of SNPs in the pituitary gland of young growing bulls representing Polish Holstein-Friesian (HF), Polish Red, and Hereford breeds at three developmental ages viz., six months, nine months, and twelve months. A total of 18 bovine pituitary gland polyA transcriptome libraries were prepared and sequenced using the Illumina NextSeq 500 platform. Sequenced FastQ databases of all 18 young bulls were submitted to NCBI-SRA database with NCBI-SRA accession numbers SRS1296732. For the investigated young bulls, a total of 113,882,3098 raw paired-end reads with a length of 156 bases were obtained, resulting in an approximately 63 million paired-end reads per library. Breed-wise, a total of 515.38, 215.39, and 408.04 million paired-end reads were obtained for Polish HF, Polish Red, and Hereford breeds, respectively. Burrows-Wheeler Aligner (BWA) read alignments showed 93.04%, 94.39%, and 83.46% of the mapped sequencing reads were properly paired to the Polish HF, Polish Red, and Hereford breeds, respectively. Constructed breed-specific SNP-db of three cattle breeds yielded at 13,775,885 SNPs. On an average 765,326 breed-specific SNPs per young bull were identified. Using two stringent filtering parameters, i.e., a minimum 10 SNP reads per base with an accuracy ≥ 90% and a minimum 10 SNP reads per base with an accuracy = 100%, SNP-db records were trimmed to construct a highly reliable SNP-db. This resulted in a reduction of 95,7% and 96,4% cut-off mark of constructed raw SNP-db. Finally, SNP discoveries using RNA-Seq data were validated by KASP™ SNP genotyping assay. The comprehensive QTLs/CGs analysis of 76 QTLs/CGs with RNA-seq data identified KCNIP4, CCSER1, DPP6, MAP3K5 and GHR CGs with highest SNPs hit loci in all three breeds and developmental ages. However, CAST CG with more than 100 SNPs hits were observed only in Polish HF and Hereford breeds.These findings are important for identification and construction of novel tissue specific SNP-db and breed specific SNP-db dataset by screening of putative SNPs according to QTL db and candidate genes for bovine growth and reproduction traits, one can develop genomic selection strategies for growth and reproductive traits.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161370PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015895PMC
August 2017

The polymorphisms in serotonin-related genes (5-HT₂A and SERT) and the prevalence of depressive symptoms in obese patients.

Neurosci Lett 2015 Jan 5;586:31-5. Epub 2014 Dec 5.

Collegium Medicum of Nicolaus Copernicus University, Department of Clinical Neuropsychology, Bydgoszcz, Poland.

As overweight and obesity are a growing problem in industrialized societies, they become a main focus of many studies. The aim of this study was to determine whether there is an association between the occurrence of polymorphisms in serotonin-related genes and the prevalence of depressive symptoms in obese patients. Two polymorphisms were tested: a 44-bp insertion/deletion in the serotonin transporter (SERT) gene and a single-nucleotide variation (1438G/A) in the serotonin 2A receptor (5-HT2A) gene. The study involved 180 patients (41 men; 139 women) previously diagnosed as obese. All patients were subjected to clinical, biochemical, and neuropsychological evaluation and genotyping. Amplification of the gene fragments was obtained by the polymerase chain reaction (PCR) method. Products of the genotyping were separated via electrophoresis. The intensity of depressive symptoms was measured using the Beck Depression Inventory (BDI) and Hamilton Depression Scale (HAM-D). Clinically relevant depressive symptoms were diagnosed in 39% of subjects. The lowest intensities of depressive symptoms were ascertained in the group with the least advanced obesity, but this trend was statistically insignificant. Small differences were observed in obesity indicators among three groups of patients with various genotypes of the SERT gene, but these differences were also statistically insignificant. Furthermore, in the context of the intensity of depressive symptoms, no significant associations were observed in these two groups. Furthermore, no statistically significant differences were observed among specific obesity parameters and intensity of depressive symptoms as a function of the 5-HT2A gene polymorphism. To conclude, depressive symptoms were prevalent in obese participants: 39% of subjects experienced symptoms of clinical relevance. However, no significant associations were observed between 5-HT2A and SERT gene polymorphisms and depressive symptoms in this study group.
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http://dx.doi.org/10.1016/j.neulet.2014.12.012DOI Listing
January 2015

Direct evidence for an interdiffused intermediate layer in bi-magnetic core-shell nanoparticles.

Nanoscale 2014 Oct;6(20):11911-20

Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités, UMR CNRS 7590, UPMC Univ Paris 06, Muséum National d'Histoire Naturelle, IRD UMR 206, 4 Place Jussieu, F-75005 Paris, France.

Core-shell nanoparticles attract continuously growing interest due to their numerous applications, which are driven by the possibility of tuning their functionalities by adjusting structural and morphological parameters. However, despite the critical role interdiffused interfaces may have in the properties, these are usually only estimated in indirect ways. Here we directly evidence the existence of a 1.1 nm thick (Fe,Mn)3O4 interdiffused intermediate shell in nominally γ-Fe2O3-Mn3O4 core-shell nanoparticles using resonant inelastic X-ray scattering spectroscopy combined with magnetic circular dichroism (RIXS-MCD). This recently developed magneto-spectroscopic probe exploits the unique advantages of hard X-rays (i.e., chemical selectivity, bulk sensitivity, and low self-absorption at the K pre-edge) and can be advantageously combined with transmission electron microscopy and electron energy loss spectroscopy to quantitatively elucidate the buried internal structure of complex objects. The detailed information on the structure of the nanoparticles allows understanding the influence of the interface quality on the magnetic properties.
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http://dx.doi.org/10.1039/c4nr02886dDOI Listing
October 2014

Magnetic manipulation of molecules on a non-magnetic catalytic surface.

Nanoscale 2013 Sep;5(18):8462-5

Paul Scherrer Institute (PSI), 5232 Villigen-PSI, Switzerland.

Non-magnetic Pt catalysts, supported on carbon coated magnetic Co nanoparticles, changed catalytic performance in the presence of an external magnetic field. This behavior relates to an electronic change of Pt induced by a localized magnetic field, which modifies the CO adsorption geometry. In situ resonant inelastic X-ray scattering (RIXS) experiments and theory reveal the change of atop CO adsorption geometry on the Pt catalyst to bridged geometry under an external magnetic field. This observation opens the possibility of catalytic control by means of an external magnetic field.
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http://dx.doi.org/10.1039/c3nr02237dDOI Listing
September 2013

Correlations between polymorphisms in genes coding elements of dopaminergic pathways and body mass index in overweight and obese women.

Endokrynol Pol 2013 ;64(2):101-7

Nicolaus Copernicus University Biotechnology Department, Toruń, Poland.

Introduction: Dopamine is considered to be crucial for food craving and intake, drug abuse and electrical brain stimulation. Increased levels of dopamine occur after energy intake in the dorsal striatum. In the ventral tagmental area, dopamine is responsible for motivation. There is a natural synaptic dopamine level, and as a result its activity is controlled by density of receptors, amount of released neurotransmitter, and defectiveness of re-uptake by specific transporters. In our study, we wanted to investigate if there is a correlation between mean BMI values and VNTR polymorphisms in SLC6A3 (rs28363170) and DRD4 genes.

Material And Methods: Chosen gene fragments were amplified using polymerase chain reaction on the DNA template obtained from 506 women. The products of the reaction were electrophoresed and visualised in 3% agarose gel. The genotyping data was analysed with Kruskal-Wallis tests (p 〈 0.05).

Results: In the case of SLC6A3, statistically significant differences in mean BMI were found in the group of obese women (p 〈 0.05) but not for the whole population of women with normal weight or with overweight (p 〉 0.05). The mean BMI was higher for the SS genotype than for combined LL and LS genotypes. The difference in mean BMI values for variants of DRD4 was significant for the whole studied population and in the obese group (p 〉 0.05), and the higher value was correlated with the presence of a variant with seven or more repeats of 48 bp motif.

Conclusions: When the two analysed polymorphisms were combined, the spread between the mean BMI values became greater than for single genes. This suggests that the effect on body mass of these two polymorphisms may combine and cause hypo-functionality of the dopaminergic reward system.
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January 2014

Validation of a virtual source model for Monte Carlo dose calculations of a flattening filter free linac.

Med Phys 2012 Jun;39(6):3262-9

Hall-Edwards Radiotherapy Research Group, University Hospital Birmingham NHS Foundation Trust, United Kingdom, B15 2TH.

Purpose: A linac delivering intensity-modulated radiotherapy (IMRT) can benefit from a flattening filter free (FFF) design which offers higher dose rates and reduced accelerator head scatter than for conventional (flattened) delivery. This reduction in scatter simplifies beam modeling, and combining a Monte Carlo dose engine with a FFF accelerator could potentially increase dose calculation accuracy. The objective of this work was to model a FFF machine using an adapted version of a previously published virtual source model (VSM) for Monte Carlo calculations and to verify its accuracy.

Methods: An Elekta Synergy linear accelerator operating at 6 MV has been modified to enable irradiation both with and without the flattening filter (FF). The VSM has been incorporated into a commercially available treatment planning system (Monaco™ v 3.1) as VSM 1.6. Dosimetric data were measured to commission the treatment planning system (TPS) and the VSM adapted to account for the lack of angular differential absorption and general beam hardening. The model was then tested using standard water phantom measurements and also by creating IMRT plans for a range of clinical cases.

Results: The results show that the VSM implementation handles the FFF beams very well, with an uncertainty between measurement and calculation of <1% which is comparable to conventional flattened beams. All IMRT beams passed standard quality assurance tests with >95% of all points passing gamma analysis (γ < 1) using a 3%/3 mm tolerance.

Conclusions: The virtual source model for flattened beams was successfully adapted to a flattening filter free beam production. Water phantom and patient specific QA measurements show excellent results, and comparisons of IMRT plans generated in conventional and FFF mode are underway to assess dosimetric uncertainties and possible improvements in dose calculation and delivery.
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http://dx.doi.org/10.1118/1.4709601DOI Listing
June 2012
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