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  1. Book ; Online: Optimising HEP parameter fits via Monte Carlo weight derivative regression

    Valassi, Andrea

    2020  

    Abstract: HEP event selection is traditionally considered a binary classification problem, involving the dichotomous categories of signal and background. In distribution fits for particle masses or couplings, however, signal events are not all equivalent, as the ... ...

    Abstract HEP event selection is traditionally considered a binary classification problem, involving the dichotomous categories of signal and background. In distribution fits for particle masses or couplings, however, signal events are not all equivalent, as the signal differential cross section has different sensitivities to the measured parameter in different regions of phase space. In this paper, I describe a mathematical framework for the evaluation and optimization of HEP parameter fits, where this sensitivity is defined on an event-by-event basis, and for MC events it is modeled in terms of their MC weight derivatives with respect to the measured parameter. Minimising the statistical error on a measurement implies the need to resolve (i.e. separate) events with different sensitivities, which ultimately represents a non-dichotomous classification problem. Since MC weight derivatives are not available for real data, the practical strategy I suggest consists in training a regressor of weight derivatives against MC events, and then using it as an optimal partitioning variable for 1-dimensional fits of data events. This CHEP2019 paper is an extension of the study presented at CHEP2018: in particular, event-by-event sensitivities allow the exact computation of the "FIP" ratio between the Fisher information obtained from an analysis and the maximum information that could possibly be obtained with an ideal detector. Using this expression, I discuss the relationship between FIP and two metrics commonly used in Meteorology (Brier score and MSE), and the importance of "sharpness" both in HEP and in that domain. I finally point out that HEP distribution fits should be optimized and evaluated using probabilistic metrics (like FIP or MSE), whereas ranking metrics (like AUC) or threshold metrics (like accuracy) are of limited relevance for these specific problems.

    Comment: 15 pages, 1 figure, submitted to CHEP2019 proceedings in EPJ Web of Conferences; revised version addressing referee's comments
    Keywords Physics - Data Analysis ; Statistics and Probability ; Computer Science - Machine Learning ; High Energy Physics - Experiment ; 62F10 ; G.3 ; I.2.6 ; J.2
    Subject code 006
    Publishing date 2020-03-28
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: Design and engineering of a simplified workflow execution for the MG5aMC event generator on GPUs and vector CPUs

    Valassi, Andrea / Roiser, Stefan / Mattelaer, Olivier / Hageboeck, Stephan

    2021  

    Abstract: Physics event generators are essential components of the data analysis software chain of high energy physics experiments, and important consumers of their CPU resources. Improving the software performance of these packages on modern hardware ... ...

    Abstract Physics event generators are essential components of the data analysis software chain of high energy physics experiments, and important consumers of their CPU resources. Improving the software performance of these packages on modern hardware architectures, such as those deployed at HPC centers, is essential in view of the upcoming HL-LHC physics programme. In this paper, we describe an ongoing activity to reengineer the Madgraph5_aMC@NLO physics event generator, primarily to port it and allow its efficient execution on GPUs, but also to modernize it and optimize its performance on vector CPUs. We describe the motivation, engineering process and software architecture design of our developments, as well as the current challenges and future directions for this project. This paper is based on our submission to vCHEP2021 in March 2021,complemented with a few preliminary results that we presented during the conference. Further details and updated results will be given in later publications.

    Comment: 17 pages, 6 figures, submitted to vCHEP2021 proceedings in EPJ Web of Conferences; minor changes to address comments from the EPJWOC reviewer
    Keywords Physics - Computational Physics ; Computer Science - Software Engineering ; High Energy Physics - Experiment ; High Energy Physics - Phenomenology
    Subject code 028
    Publishing date 2021-06-23
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Book ; Online: Integrating LHCb workflows on HPC resources

    Stagni, Federico / Valassi, Andrea / Romanovskiy, Vladimir

    status and strategies

    2020  

    Abstract: High Performance Computing (HPC) supercomputers are expected to play an increasingly important role in HEP computing in the coming years. While HPC resources are not necessarily the optimal fit for HEP workflows, computing time at HPC centers on an ... ...

    Abstract High Performance Computing (HPC) supercomputers are expected to play an increasingly important role in HEP computing in the coming years. While HPC resources are not necessarily the optimal fit for HEP workflows, computing time at HPC centers on an opportunistic basis has already been available to the LHC experiments for some time, and it is also possible that part of the pledged computing resources will be offered as CPU time allocations at HPC centers in the future. The integration of the experiment workflows to make the most efficient use of HPC resources is therefore essential. This paper describes the work that has been necessary to integrate LHCb workflows at a specific HPC site, the Marconi-A2 system at CINECA in Italy, where LHCb benefited from a joint PRACE (Partnership for Advanced Computing in Europe) allocation with the other Large Hadron Collider (LHC) experiments. This has required addressing two types of challenges: on the software application workloads, for optimising their performance on a many-core hardware architecture that differs significantly from those traditionally used in WLCG (Worldwide LHC Computing Grid), by reducing memory footprint using a multi-process approach; and in the distributed computing area, for submitting these workloads using more than one logical processor per job, which had never been done yet in LHCb.

    Comment: 9 pages, submitted to CHEP2019 proceedings in EPJ Web of Conferences
    Keywords Computer Science - Distributed ; Parallel ; and Cluster Computing ; High Energy Physics - Experiment ; Physics - Instrumentation and Detectors ; C.1.4 ; C.2.4 ; D.1.3 ; D.4.7 ; D.2.8
    Subject code 000
    Publishing date 2020-06-24
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article: Rhenium-188 production in hospitals, by w-188/re-188 generator, for easy use in radionuclide therapy.

    Argyrou, Maria / Valassi, Alexia / Andreou, Maria / Lyra, Maria

    International journal of molecular imaging

    2013  Volume 2013, Page(s) 290750

    Abstract: Rhenium-188 (Re-188) is a high energy β-emitting radioisotope obtained from the tungsten-188/rhenium-188 (W-188/Re-188) generator, which has shown utility for a variety of therapeutic applications in nuclear medicine, oncology, and interventional ... ...

    Abstract Rhenium-188 (Re-188) is a high energy β-emitting radioisotope obtained from the tungsten-188/rhenium-188 (W-188/Re-188) generator, which has shown utility for a variety of therapeutic applications in nuclear medicine, oncology, and interventional radiology/cardiology. Re-188 decay is accompanied by a 155 keV predominant energy γ-emission, which could be detected by γ-cameras, for imaging, biodistribution, or absorbed radiation dose studies. Its attractive physical properties and its potential low cost associated with a long-lived parent make it an interesting option for clinical use. The setup and daily use of W-188/Re-188 generator in hospital nuclear medicine departments are discussed in detail. The clinical efficacy, for several therapeutic applications, of a variety of Re-188-labeled agents is demonstrated. The high energy of the β-emission of Re-188 is particularly well suited for effective penetration in solid tumours. Its total radiation dose delivered to tissues is comparable to other radionuclides used in therapy. Furthermore, radiation safety and shielding requirements are an important subject of matter. In the case of bone metastases treatment, therapeutic ratios are presented in order to describe the efficacy of Re-188 usage.
    Language English
    Publishing date 2013-04-09
    Publishing country Egypt
    Document type Journal Article
    ZDB-ID 2595407-6
    ISSN 2090-1720 ; 2090-1712
    ISSN (online) 2090-1720
    ISSN 2090-1712
    DOI 10.1155/2013/290750
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Book ; Online: Information and treatment of unknown correlations in the combination of measurements using the BLUE method

    Valassi, Andrea / Chierici, Roberto

    2013  

    Abstract: We discuss the effect of large positive correlations in the combinations of several measurements of a single physical quantity using the Best Linear Unbiased Estimate (BLUE) method. We suggest a new approach for comparing the relative weights of the ... ...

    Abstract We discuss the effect of large positive correlations in the combinations of several measurements of a single physical quantity using the Best Linear Unbiased Estimate (BLUE) method. We suggest a new approach for comparing the relative weights of the different measurements in their contributions to the combined knowledge about the unknown parameter, using the well-established concept of Fisher information. We argue, in particular, that one We discuss the effect of large positive correlations in the combinations of several measurements of a single physical quantity using the Best Linear Unbiased Estimate (BLUE) method. We suggest a new approach for comparing the relative weights of the different measurements in their contributions to the combined knowledge about the unknown parameter, using the well-established concept of Fisher information. We argue, in particular, that one contribution to information comes from the collective interplay of the measurements through their correlations and that this contribution cannot be attributed to any of the individual measurements alone. We show that negative coefficients in the BLUE weighted average invariably indicate the presence of a regime of high correlations, where the effect of further increasing some of these correlations is that of reducing the error on the combined estimate. In these regimes, we stress that assuming fully correlated systematic uncertainties is not a truly conservative choice, and that the correlations provided as input to BLUE combinations need to be assessed with extreme care instead. In situations where the precise evaluation of these correlations is impractical, or even impossible, we provide tools to help experimental physicists perform more conservative combinations.
    Keywords Physics - Data Analysis ; Statistics and Probability ; High Energy Physics - Experiment
    Subject code 612
    Publishing date 2013-07-15
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: DNA profiling, telomere analysis and antioxidant properties as tools for monitoring ex situ seed longevity.

    Donà, M / Balestrazzi, A / Mondoni, A / Rossi, G / Ventura, L / Buttafava, A / Macovei, A / Sabatini, M E / Valassi, A / Carbonera, D

    Annals of botany

    2013  Volume 111, Issue 5, Page(s) 987–998

    Abstract: Background and aims: The germination test currently represents the most used method to assess seed viability in germplasm banks, despite the difficulties caused by the occurrence of seed dormancy. Furthermore, seed longevity can vary considerably across ...

    Abstract Background and aims: The germination test currently represents the most used method to assess seed viability in germplasm banks, despite the difficulties caused by the occurrence of seed dormancy. Furthermore, seed longevity can vary considerably across species and populations from different environments, and studies related to the eco-physiological processes underlying such variations are still limited in their depth. The aim of the present work was the identification of reliable molecular markers that might help in monitoring seed deterioration.
    Methods: Dry seeds were subjected to artificial ageing and collected at different time points for molecular/biochemical analyses. DNA damage was measured using the RAPD (random amplified polymorphic DNA) approach while the seed antioxidant profile was obtained using both the DPPH (1,1-diphenyl, 2-picrylhydrazyl) assay and the Folin-Ciocalteu reagent method. Electron paramagnetic resonance (EPR) provided profiles of free radicals. Quantitative real-time polymerase chain reaction (QRT-PCR) was used to assess the expression profiles of the antioxidant genes MT2 (type 2 metallothionein) and SOD (superoxide dismutase). A modified QRT-PCR protocol was used to determine telomere length.
    Key results: The RAPD profiles highlighted different capacities of the two Silene species to overcome DNA damage induced by artificial ageing. The antioxidant profiles of dry and rehydrated seeds revealed that the high-altitude taxon Silene acaulis was characterized by a lower antioxidant specific activity. Significant upregulation of the MT2 and SOD genes was observed only in the rehydrated seeds of the low-altitude species. Rehydration resulted in telomere lengthening in both Silene species.
    Conclusions: Different seed viability markers have been selected for plant species showing inherent variation of seed longevity. RAPD analysis, quantification of redox activity of non-enzymatic antioxidant compounds and gene expression profiling provide deeper insights to study seed viability during storage. Telomere lengthening is a promising tool to discriminate between short- and long-lived species.
    MeSH term(s) Altitude ; Antioxidants/metabolism ; DNA Fingerprinting/methods ; DNA Primers/metabolism ; Electron Spin Resonance Spectroscopy ; Free Radical Scavengers/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Germination/genetics ; Phenols/metabolism ; Phylogeny ; Plant Extracts/metabolism ; Random Amplified Polymorphic DNA Technique ; Reactive Oxygen Species/metabolism ; Seeds/genetics ; Seeds/growth & development ; Silene/genetics ; Silene/growth & development ; Telomere/metabolism ; Telomere Homeostasis/genetics
    Chemical Substances Antioxidants ; DNA Primers ; Free Radical Scavengers ; Phenols ; Plant Extracts ; Reactive Oxygen Species
    Language English
    Publishing date 2013-03-26
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1461328-1
    ISSN 1095-8290 ; 0305-7364
    ISSN (online) 1095-8290
    ISSN 0305-7364
    DOI 10.1093/aob/mct058
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Pollen grain preservation at low temperatures in valuable commercial rose cultivars

    Giovannini, A / Macovei, A / Dona, M / Valassi, A / Caser, M / Mansuino, A / Ghione, G. G / Carbonera, D / Scariot, V / Balestrazzi, A

    Acta horticulturae. 2015 Jan. 25, , no. 1064

    2015  

    Abstract: Modern rose cultivars require hand pollination for rose hip production and collection of seeds. Breeding programs are often focused on the quality of rose pollen, which is genotype dependent and it is affected by the conditions used for its conservation. ...

    Abstract Modern rose cultivars require hand pollination for rose hip production and collection of seeds. Breeding programs are often focused on the quality of rose pollen, which is genotype dependent and it is affected by the conditions used for its conservation. In this study in vitro pollen germination and shelf life of six commercial rose cultivars were evaluated under different storage conditions in order to establish preservation procedures. Flowers of Rosa ‘Alba’, ‘Anastasia’, ‘Encanto’, ‘Marvelle’, ‘Swan’ and ‘Touch of Class’ were collected from plants cultivated in the NIRP International greenhouses. Anthers were removed from flowers and dried on Petri dishes for 24 h (T = 24°C). Then, they were placed into polyethylene tubes in the freezer (T = -20°C) and in the deep freezer (T= -80°C). Pollen germination was measured soon after 24 h from flower collection and after 44, 134, and 190 days of storage, respectively. The pollen grains were spread on a culture medium containing agar (0.7%), sucrose (15%), calcium chloride (152 mg L-1) and boric acid (40 mg L-1). Our results confirmed that the viable level in fresh pollen varied among cultivars and also that pollen preservation at low temperatures is cultivar dependent.
    Keywords Rosa ; agar ; anthers ; boric acid ; breeding ; calcium chloride ; cultivars ; culture media ; flowers ; genotype ; greenhouses ; in vitro studies ; pollen ; pollen germination ; pollination ; polyethylene ; rose hips ; seeds ; shelf life ; storage conditions ; sucrose ; temperature
    Language English
    Dates of publication 2015-0125
    Size p. 63-66.
    Publishing place International Society for Horticultural Science.
    Document type Article
    Note Paper presented at the VI International Symposium on Rose Research and Cultivation held August 25-30, 2013 Hannover (Germany)
    ISSN 0567-7572
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: Copper-mediated genotoxic stress is attenuated by the overexpression of the DNA repair gene MtTdp2α (tyrosyl-DNA phosphodiesterase 2) in Medicago truncatula plants.

    Faè, Matteo / Balestrazzi, Alma / Confalonieri, Massimo / Donà, Mattia / Macovei, Anca / Valassi, Alberto / Giraffa, Giorgio / Carbonera, Daniela

    Plant cell reports

    2014  Volume 33, Issue 7, Page(s) 1071–1080

    Abstract: Key message: Our study highlights the use of the DNA repair gene MtTdp2α as a tool for improving the plant response to heavy metal stress. Tyrosyl-DNA phosphodiesterase 2 (Tdp2), involved in the removal of DNA topoisomerase II-mediated DNA damage and ... ...

    Abstract Key message: Our study highlights the use of the DNA repair gene MtTdp2α as a tool for improving the plant response to heavy metal stress. Tyrosyl-DNA phosphodiesterase 2 (Tdp2), involved in the removal of DNA topoisomerase II-mediated DNA damage and cell proliferation/differentiation signalling in animal cells, is still poorly characterised in plants. The Medicago truncatula lines Tdp2α-13c and Tdp2α-28 overexpressing the MtTdp2α gene and control (CTRL) line were exposed to 0.2 mM CuCl2. The DNA diffusion assay revealed a significant reduction in the percentage of necrosis caused by copper in the aerial parts of the Tdp2α-13c and Tdp2α-28 plants while neutral single cell gel electrophoresis highlighted a significant decrease in double strand breaks (DSBs), compared to CTRL. In the copper-treated Tdp2α-13c and Tdp2α-28 lines there was up-regulation (up to 4.0-fold) of genes encoding the α and β isoforms of Tyrosyl-DNA phosphodiesterase 1, indicating the requirement for Tdp1 function in the response to heavy metals. As for DSB sensing, the MtMRE11, MtRAD50 and MtNBS1 genes were also significantly up-regulated (up to 2.3-fold) in the MtTdp2α-overexpressing plants grown under physiological conditions, compared to CTRL line, and then further stimulated in response to copper. The basal antioxidant machinery was always activated in all the tested lines, as indicated by the concomitant up-regulation of MtcytSOD and MtcpSOD genes (cytosolic and chloroplastic Superoxide Dismutase), and MtMT2 (type 2 metallothionein) gene. The role of MtTdp2α gene in enhancing the plant response to genotoxic injury under heavy metal stress is discussed.
    MeSH term(s) Antioxidants/metabolism ; Cell Death/drug effects ; Cell Survival/drug effects ; Chlorophyll/metabolism ; Copper/toxicity ; DNA Breaks, Double-Stranded/drug effects ; DNA Damage/drug effects ; DNA Damage/genetics ; DNA Repair/genetics ; Gene Expression Regulation, Plant ; Medicago truncatula/cytology ; Medicago truncatula/drug effects ; Medicago truncatula/genetics ; Metals, Heavy/toxicity ; Phosphoric Diester Hydrolases/genetics ; Phosphoric Diester Hydrolases/metabolism ; Superoxide Dismutase/genetics ; Superoxide Dismutase/metabolism
    Chemical Substances Antioxidants ; Metals, Heavy ; Chlorophyll (1406-65-1) ; Copper (789U1901C5) ; Superoxide Dismutase (EC 1.15.1.1) ; Phosphoric Diester Hydrolases (EC 3.1.4.-) ; tyrosyl-DNA phosphodiesterase (EC 3.1.4.-) ; cupric chloride (S2QG84156O)
    Language English
    Publishing date 2014-03-18
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 8397-5
    ISSN 1432-203X ; 0721-085X ; 0721-7714
    ISSN (online) 1432-203X
    ISSN 0721-085X ; 0721-7714
    DOI 10.1007/s00299-014-1595-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Book ; Online: Using HEP experiment workflows for the benchmarking and accounting of WLCG computing resources

    Valassi, Andrea / Alef, Manfred / Barbet, Jean-Michel / Datskova, Olga / De Maria, Riccardo / Medeiros, Miguel Fontes / Giordano, Domenico / Grigoras, Costin / Hollowell, Christopher / Javurkova, Martina / Khristenko, Viktor / Lange, David / Michelotto, Michele / Rinaldi, Lorenzo / Sciabà, Andrea / Van Der Laan, Cas

    2020  

    Abstract: Benchmarking of CPU resources in WLCG has been based on the HEP-SPEC06 (HS06) suite for over a decade. It has recently become clear that HS06, which is based on real applications from non-HEP domains, no longer describes typical HEP workloads. The aim of ...

    Abstract Benchmarking of CPU resources in WLCG has been based on the HEP-SPEC06 (HS06) suite for over a decade. It has recently become clear that HS06, which is based on real applications from non-HEP domains, no longer describes typical HEP workloads. The aim of the HEP-Benchmarks project is to develop a new benchmark suite for WLCG compute resources, based on real applications from the LHC experiments. By construction, these new benchmarks are thus guaranteed to have a score highly correlated to the throughputs of HEP applications, and a CPU usage pattern similar to theirs. Linux containers and the CernVM-FS filesystem are the two main technologies enabling this approach, which had been considered impossible in the past. In this paper, we review the motivation, implementation and outlook of the new benchmark suite.

    Comment: 9 pages, submitted to CHEP2019 proceedings in EPJ Web of Conferences; revised version addressing referee's comments
    Keywords Computer Science - Performance ; High Energy Physics - Experiment ; Physics - Instrumentation and Detectors ; K.6.2 ; D.2.8
    Subject code 020
    Publishing date 2020-04-03
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: DNA profiling, telomere analysis and antioxidant properties as tools for monitoring ex situ seed longevity

    Donà, M / Balestrazzi, A / Mondoni, A / Rossi, G / Ventura, L / Buttafava, A / Macovei, A / Sabatini, M. E / Valassi, A / Carbonera, D

    Annals of botany. 2013 May, v. 111, no. 5

    2013  

    Abstract: Background and AimsThe germination test currently represents the most used method to assess seed viability in germplasm banks, despite the difficulties caused by the occurrence of seed dormancy. Furthermore, seed longevity can vary considerably across ... ...

    Abstract Background and AimsThe germination test currently represents the most used method to assess seed viability in germplasm banks, despite the difficulties caused by the occurrence of seed dormancy. Furthermore, seed longevity can vary considerably across species and populations from different environments, and studies related to the eco-physiological processes underlying such variations are still limited in their depth. The aim of the present work was the identification of reliable molecular markers that might help in monitoring seed deterioration.MethodsDry seeds were subjected to artificial ageing and collected at different time points for molecular/biochemical analyses. DNA damage was measured using the RAPD (random amplified polymorphic DNA) approach while the seed antioxidant profile was obtained using both the DPPH (1,1-diphenyl, 2-picrylhydrazyl) assay and the Folin–Ciocalteu reagent method. Electron paramagnetic resonance (EPR) provided profiles of free radicals. Quantitative real-time polymerase chain reaction (QRT-PCR) was used to assess the expression profiles of the antioxidant genes MT2 (type 2 metallothionein) and SOD (superoxide dismutase). A modified QRT-PCR protocol was used to determine telomere length.Key ResultsThe RAPD profiles highlighted different capacities of the two Silene species to overcome DNA damage induced by artificial ageing. The antioxidant profiles of dry and rehydrated seeds revealed that the high-altitude taxon Silene acaulis was characterized by a lower antioxidant specific activity. Significant upregulation of the MT2 and SOD genes was observed only in the rehydrated seeds of the low-altitude species. Rehydration resulted in telomere lengthening in both Silene species.ConclusionsDifferent seed viability markers have been selected for plant species showing inherent variation of seed longevity. RAPD analysis, quantification of redox activity of non-enzymatic antioxidant compounds and gene expression profiling provide deeper insights to study seed viability during storage. Telomere lengthening is a promising tool to discriminate between short- and long-lived species.
    Keywords DNA ; DNA damage ; DNA fingerprinting ; Silene ; antioxidant activity ; antioxidants ; ecophysiology ; electron paramagnetic resonance spectroscopy ; free radicals ; gene expression ; gene expression regulation ; genes ; genetic markers ; germination ; germplasm ; longevity ; metallothionein ; monitoring ; quantitative polymerase chain reaction ; random amplified polymorphic DNA technique ; rehydration ; seed dormancy ; seeds ; superoxide dismutase ; telomeres ; viability
    Language English
    Dates of publication 2013-05
    Size p. 987-998.
    Publishing place Oxford University Press
    Document type Article
    ZDB-ID 1461328-1
    ISSN 1095-8290 ; 0305-7364 ; 0003-4754
    ISSN (online) 1095-8290
    ISSN 0305-7364 ; 0003-4754
    DOI 10.1093/aob/mct058
    Database NAL-Catalogue (AGRICOLA)

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