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Search Results: 1 - 10 of 6027 matches for " Markus Scholz "
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A Canonical Measure of Allelic Association
Markus Scholz,Dirk Hasenclever
Statistics , 2009,
Abstract: The measurement of biallelic pair-wise association called linkage disequilibrium (LD) is an important issue in order to understand the genomic architecture. A large variety of such measures of association have been proposed in the literature. We propose and justify six biometrical postulates which should be fulfilled by a canonical measure of LD. In short, LD measures are defined as a mapping of probability tables to the set of real numbers. They should be zero in case of independence and extremal if one of the entries approaches zero while the marginals are positively bounded. They should reflect the symmetry group of the tables and be invariant under certain transformations of the marginals (selection invariance). There scale should have maximum entropy relative to a calibrating symmetric distribution. None of the established measures fulfil all of these properties in general. We prove that there is a unique canonical measure of LD for each choice of a calibrating distribution. We compa- re the canonical LD measures with other candidates from the literature. We recommend the canonical measure derived from Jeffreys' non-informative prior distribution when assessing linkage disequilibrium of SNP array data. In a second part, we consider various estimators for the theoretical LD measures discussed and compare them in a simulation study.
Comparing measures of association in 2x2 probability tables
Dirk Hasenclever,Markus Scholz
Statistics , 2013,
Abstract: Measures of association play a role in selecting 2x2 tables exhibiting strong dependence in high-dimensional binary data. Several measures are in use differing on specific tables and in their dependence on the margins. We study a 2-dimensional group of margin transformations on the 3-dimensional manifold T of all 2x2 probability tables. The margin transformations allow introducing natural coordinates that identify T with the real 3-space such that the x-axis corresponds to log(sqrt(odds-ratio)) and margins vary on planes x=const. We use these coordinates to visualise and compare measures of association with respect to their dependence on the margins given the odds-ratio, their limit behaviour when cells approach zero and their weighting properties. We propose a novel measure of association in which tables with single small entries are up-weighted but those with skewed margins are down-weighted according to the relative entropy among the tables of the same odds-ratio.
fcGENE: A Versatile Tool for Processing and Transforming SNP Datasets
Nab Raj Roshyara, Markus Scholz
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0097589
Abstract: Background Modern analysis of high-dimensional SNP data requires a number of biometrical and statistical methods such as pre-processing, analysis of population structure, association analysis and genotype imputation. Software used for these purposes often rely on specific and incompatible input and output data formats. Therefore extensive data management including multiple format conversions is necessary during analyses. Methods In order to support fast and efficient management and bio-statistical quality control of high-dimensional SNP data, we developed the publically available software fcGENE using C++ object-oriented programming language. This software simplifies and automates the use of different existing analysis packages, especially during the workflow of genotype imputations and corresponding analyses. Results fcGENE transforms SNP data and imputation results into different formats required for a large variety of analysis packages such as PLINK, SNPTEST, HAPLOVIEW, EIGENSOFT, GenABEL and tools used for genotype imputation such as MaCH, IMPUTE, BEAGLE and others. Data Management tasks like merging, splitting, extracting SNP and pedigree information can be performed. fcGENE also supports a number of bio-statistical quality control processes and quality based filtering processes at SNP- and sample-wise level. The tool also generates templates of commands required to run specific software packages, especially those required for genotype imputation. We demonstrate the functionality of fcGENE by example workflows of SNP data analyses and provide a comprehensive manual of commands, options and applications. Conclusions We have developed a user-friendly open-source software fcGENE, which comprehensively supports SNP data management, quality control and analysis workflows. Download statistics and corresponding feedbacks indicate that software is highly recognised and extensively applied by the scientific community.
KMWin – A Convenient Tool for Graphical Presentation of Results from Kaplan-Meier Survival Time Analysis
Arnd Gross, Marita Ziepert, Markus Scholz
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0038960
Abstract: Background Analysis of clinical studies often necessitates multiple graphical representations of the results. Many professional software packages are available for this purpose. Most packages are either only commercially available or hard to use especially if one aims to generate or customize a huge number of similar graphical outputs. We developed a new, freely available software tool called KMWin (Kaplan-Meier for Windows) facilitating Kaplan-Meier survival time analysis. KMWin is based on the statistical software environment R and provides an easy to use graphical interface. Survival time data can be supplied as SPSS (sav), SAS export (xpt) or text file (dat), which is also a common export format of other applications such as Excel. Figures can directly be exported in any graphical file format supported by R. Results On the basis of a working example, we demonstrate how to use KMWin and present its main functions. We show how to control the interface, customize the graphical output, and analyse survival time data. A number of comparisons are performed between KMWin and SPSS regarding graphical output, statistical output, data management and development. Although the general functionality of SPSS is larger, KMWin comprises a number of features useful for survival time analysis in clinical trials and other applications. These are for example number of cases and number of cases under risk within the figure or provision of a queue system for repetitive analyses of updated data sets. Moreover, major adjustments of graphical settings can be performed easily on a single window. Conclusions We conclude that our tool is well suited and convenient for repetitive analyses of survival time data. It can be used by non-statisticians and provides often used functions as well as functions which are not supplied by standard software packages. The software is routinely applied in several clinical study groups.
Effectiveness of cytopenia prophylaxis for different filgrastim and pegfilgrastim schedules in a chemotherapy mouse model
Markus Scholz, Manuela Ackermann, Frank Emmrich, Markus Loeffler, Manja Kamprad
Biologics: Targets and Therapy , 2009, DOI: http://dx.doi.org/10.2147/BTT.S4426
Abstract: tiveness of cytopenia prophylaxis for different filgrastim and pegfilgrastim schedules in a chemotherapy mouse model Original Research (4703) Total Article Views Authors: Markus Scholz, Manuela Ackermann, Frank Emmrich, Markus Loeffler, Manja Kamprad Published Date December 2008 Volume 2009:3 Pages 27 - 37 DOI: http://dx.doi.org/10.2147/BTT.S4426 Markus Scholz1, Manuela Ackermann2, Frank Emmrich2, Markus Loeffler1, Manja Kamprad2 1Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16–18, 04107 Leipzig, Germany; 2Institute for Clinical Immunology and Transfusion Medicine, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany Objectives: Recombinant human granulocyte colony-stimulating factor (rhG-CSF) is widely used to treat neutropenia during cytotoxic chemotherapy. The optimal scheduling of rhG-CSF is unknown and can hardly be tested in clinical studies due to numerous therapy parameters affecting outcome (chemotherapeutic regimen, rhG-CSF schedules, individual covariables). Motivated by biomathematical model simulations, we aim to investigate different rhG-CSF schedules in a preclinical chemotherapy mouse model. Methods: The time course of hematotoxicity was studied in CD-1 mice after cyclophosphamide (CP) administration. Filgrastim was applied concomitantly in a 2 × 3-factorial design of two dosing options (2 × 20 μg and 4 × 10 μg) and three timing options (directly, one, and two days after CP). Alternatively, a single dose of 40 μg pegfilgrastim was applied at the three timing options. The resulting cytopenia was compared among the schedules. Results: Dosing and timing had a significant influence on the effectiveness of filgrastim schedules whereas for pegfilgrastim the timing effect was irrelevant. The best filgrastim and pegfilgrastim schedules exhibited equivalent toxicity. Monocytes dynamics performed analogously to granulocytes. All schedules showed roughly the same lymphotoxicity. Conclusion: We conclude that effectiveness of filgrastim application depends heavily on its scheduling during chemotherapy. There is an optimum of timing. Dose splitting is better than concentrated applications. Effectiveness of pegfilgrastim is less dependent on timing.
Effectiveness of cytopenia prophylaxis for different filgrastim and pegfilgrastim schedules in a chemotherapy mouse model
Markus Scholz,Manuela Ackermann,Frank Emmrich,Markus Loeffler
Biologics: Targets and Therapy , 2008,
Abstract: Markus Scholz1, Manuela Ackermann2, Frank Emmrich2, Markus Loeffler1, Manja Kamprad21Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16–18, 04107 Leipzig, Germany; 2Institute for Clinical Immunology and Transfusion Medicine, University of Leipzig, Johannisallee 30, 04103 Leipzig, GermanyObjectives: Recombinant human granulocyte colony-stimulating factor (rhG-CSF) is widely used to treat neutropenia during cytotoxic chemotherapy. The optimal scheduling of rhG-CSF is unknown and can hardly be tested in clinical studies due to numerous therapy parameters affecting outcome (chemotherapeutic regimen, rhG-CSF schedules, individual covariables). Motivated by biomathematical model simulations, we aim to investigate different rhG-CSF schedules in a preclinical chemotherapy mouse model.Methods: The time course of hematotoxicity was studied in CD-1 mice after cyclophosphamide (CP) administration. Filgrastim was applied concomitantly in a 2 × 3-factorial design of two dosing options (2 × 20 μg and 4 × 10 μg) and three timing options (directly, one, and two days after CP). Alternatively, a single dose of 40 μg pegfilgrastim was applied at the three timing options. The resulting cytopenia was compared among the schedules.Results: Dosing and timing had a significant influence on the effectiveness of filgrastim schedules whereas for pegfilgrastim the timing effect was irrelevant. The best filgrastim and pegfilgrastim schedules exhibited equivalent toxicity. Monocytes dynamics performed analogously to granulocytes. All schedules showed roughly the same lymphotoxicity.Conclusion: We conclude that effectiveness of filgrastim application depends heavily on its scheduling during chemotherapy. There is an optimum of timing. Dose splitting is better than concentrated applications. Effectiveness of pegfilgrastim is less dependent on timing.Keywords: rhG-CSF, chemotherapy toxicity, mice, cyclophosphamide, cytopenia, neutropenia
A Biomathematical Model of Human Erythropoiesis under Erythropoietin and Chemotherapy Administration
Sibylle Schirm, Christoph Engel, Markus Loeffler, Markus Scholz
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0065630
Abstract: Anaemia is a common haematologic side effect of dose-dense multi-cycle cytotoxic polychemotherapy requiring erythrocyte transfusions or erythropoietin (EPO) administration. To simulate the effectiveness of different EPO application schedules, we performed both modelling of erythropoiesis under chemotherapy and pharmacokinetic and dynamic modelling of EPO applications in the framework of a single comprehensive biomathematical model. For this purpose, a cell kinetic model of bone marrow erythropoiesis was developed that is based on a set of differential compartment equations describing proliferation and maturation of erythropoietic cell stages. The system is regulated by several feedback loops comprising those mediated by EPO. We added a model of EPO absorption after injection at different sites and a pharmacokinetic model of EPO derivatives to account for the effects of external EPO applications. Chemotherapy is modelled by a transient depletion of bone marrow cell stages. Unknown model parameters were determined by fitting the predictions of the model to data sets of circulating erythrocytes, haemoglobin, haematocrit, percentage of reticulocytes or EPO serum concentrations derived from the literature or cooperating clinical study groups. Parameter fittings resulted in a good agreement of model and data. Depending on site of injection and derivative (Alfa, Beta, Delta, Darbepoetin), nine groups of EPO applications were distinguished differing in either absorption kinetics or pharmacokinetics. Finally, eight different chemotherapy protocols were modelled. The model was validated on the basis of scenarios not used for parameter fitting. Simulations were performed to analyze the impact of EPO applications on the risk of anaemia during chemotherapy. We conclude that we established a model of erythropoiesis under chemotherapy that explains a large set of time series data under EPO and chemotherapy applications. It allows predictions regarding yet untested EPO schedules. Prospective clinical studies are needed to validate model predictions and to explore the feasibility and effectiveness of the proposed schedules.
Pharmacokinetic and -dynamic modelling of G-CSF derivatives in humans
Scholz Markus,Schirm Sibylle,Wetzler Marcus,Engel Christoph
Theoretical Biology and Medical Modelling , 2012, DOI: 10.1186/1742-4682-9-32
Abstract: Background The human granulocyte colony-stimulating factor (G-CSF) is routinely applied to support recovery of granulopoiesis during the course of cytotoxic chemotherapies. However, optimal use of the drug is largely unknown. We showed in the past that a biomathematical compartment model of human granulopoiesis can be used to make clinically relevant predictions regarding new, yet untested chemotherapy regimen. In the present paper, we aim to extend this model by a detailed pharmacokinetic and -dynamic modelling of two commonly used G-CSF derivatives Filgrastim and Pegfilgrastim. Results Model equations are based on our physiological understanding of the drugs which are delayed absorption of G-CSF when applied to the subcutaneous tissue, dose-dependent bioavailability, unspecific first order elimination, specific elimination in dependence on granulocyte counts and reversible protein binding. Pharmacokinetic differences between Filgrastim and Pegfilgrastim were modelled as different parameter sets. Our former cell-kinetic model of granulopoiesis was essentially preserved, except for a few additional assumptions and simplifications. We assumed a delayed action of G-CSF on the bone marrow, a delayed action of chemotherapy and differences between Filgrastim and Pegfilgrastim with respect to stimulation potency of the bone marrow. Additionally, we incorporated a model of combined action of Pegfilgrastim and Filgrastim or endogenous G-CSF which interact via concurrent receptor binding. Unknown pharmacokinetic or cell-kinetic parameters were determined by fitting the predictions of the model to available datasets of G-CSF applications, chemotherapy applications or combinations of it. Data were either extracted from the literature or were received from cooperating clinical study groups. Model predictions fitted well to both, datasets used for parameter estimation and validation scenarios as well. A unique set of parameters was identified which is valid for all scenarios considered. Differences in pharmacokinetic parameter estimates between Filgrastim and Pegfilgrastim were biologically plausible throughout. Conclusion We conclude that we established a comprehensive biomathematical model to explain the dynamics of granulopoiesis under chemotherapy and applications of two different G-CSF derivatives. We aim to apply the model to a large variety of chemotherapy regimen in the future in order to optimize corresponding G-CSF schedules or to individualize G-CSF treatment according to the granulotoxic risk of a patient.
A comparison of transcranial Doppler with near infrared spectroscopy and indocyanine green during hemorrhagic shock: a prospective experimental study
Berthold Bein, Patrick Meybohm, Erol Cavus, Peter H Tonner, Markus Steinfath, Jens Scholz, Volker Doerges
Critical Care , 2005, DOI: 10.1186/cc3980
Abstract: After approval from the Animal Investigational Committee, 20 healthy pigs underwent a simulated penetrating liver trauma. Following hemodynamic decompensation, all animals received a hypertonic-isooncotic hydroxyethyl starch solution and either arginine vasopressin or norepinephrine, and bleeding was subsequently controlled. ICG passage through the brain was monitored by near infrared spectroscopy. BFI was calculated by dividing maximal ICG absorption change by rise time. Mean blood flow velocity (FVmean) of the right middle cerebral artery was recorded by TCD. FVmean and BFI were assessed at baseline (BL), at hemodynamic decompensation, and repeatedly after control of bleeding.At hemodynamic decompensation, cerebral perfusion pressure (CPP), FVmean and BFI dropped compared to BL (mean ± standard deviation; CPP 16 ± 5 mmHg versus 70 ± 16 mmHg; FVmean 4 ± 5 cm·s-1 versus 28 ± 9 cm·s-1; BFI 0.008 ± 0.004 versus 0.02 ± 0.006; p < 0.001). After pharmacological intervention and control of bleeding, FVmean and BFI increased close to baseline values (FVmean 23 ± 9 cm·s-1; BFI 0.02 ± 0.01), respectively. FVmean and BFI were significantly correlated (r = 0.62, p < 0.0001).FVmean and BFI both reflected the large variations in cerebral perfusion during hemorrhage and after resuscitation and were significantly correlated. BFI is a promising tool to monitor cerebral hemodynamics at the bedside.Reliable monitoring of cerebral oxygenation is an issue of paramount importance in anesthesia and critical care, since an impaired balance of oxygen demand and supply puts viable brain tissue at risk of ischemia [1]. Cerebral oxygenation is, among other influencing factors, highly dependent on cerebral blood flow (CBF). Despite its clinical relevance, a reliable and suitable method for measuring CBF rapidly, repeatedly and non-invasively at the bedside is currently still lacking. Perfusion magnetic resonance and computed tomographic imaging, though offering a very high spatial resolution,
Evidence for neuroprotective properties of human umbilical cord blood cells after neuronal hypoxia in vitro
Susann Hau, Doreen M Reich, Markus Scholz, Wilfried Naumann, Frank Emmrich, Manja Kamprad, Johannes Boltze
BMC Neuroscience , 2008, DOI: 10.1186/1471-2202-9-30
Abstract: Hypoxic cultivation of neurons initially induced a rate of 26% ± 13% of apoptosis. Hypoxia also caused an enhanced expression of Caspase-3 and cleaved poly(ADP-ribose) polymerase (PARP). Necrosis was only detected in low amounts. Within the next three days rate of apoptosis in untreated hypoxic cultures cumulated to 85% ± 11% (p ≤ 0.001). Specific cytokine (VEGF) patterns also suggest anti-apoptotic strategies of neuronal cells. Remarkably, the administration of MNC showed a noticeable reduction of apoptosis rates to levels of normoxic control cultures (7% ± 3%; p ≤ 0.001). In parallel, clustering of administered MNC next to axons and somata of neuronal cells was observed. Furthermore, MNC caused a pronounced increase of chemokines (CCL5; CCL3 and CXCL10).We established an in vitro model of neuronal hypoxia that affords the possibility to investigate both, apoptotic neuronal cell death and neuroprotective therapies. Here we employed the therapeutic model to study neuroprotective properties of HUCB cells.We hypothesize that the neuroprotective effect of MNC was due to anti-apoptotic mechanisms related to direct cell-cell contacts with injured neuronal cells and distinct changes in neuroprotective, inflammatory cytokines as well as to the upregulation of chemokines within the co-cultures.Acute ischemic stroke is characterised by the immediate depletion of oxygen and glucose in brain tissue. A residual cerebral blood flow (CBF) of ≤ 6 cm3 × 100 g-1 × min-1 representing severe ischemia is associated with a nearly total loss of energy on vulnerable neurons. Ischemia therefore rapidly culminates in the formation of a necrotic core [1]. In the penumbra, mild ischemia (CBF 11–20 cm3 × 100 g-1 × min-1) leads to the activation of complex neurochemical cascades of cell death, mainly apoptosis. In principle these apoptotic cascades are reversible and form an important aspect of the penumbra concept, which is the major target of therapeutic interventions [2,3]. Recent findings i
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