Search

This study focuses on performing a multiphysics study using the ERO2.0 and UEDGE codes for two standard double null configurations for the Fusion Nuclear Science Facility: (a) 100% recycling and (b) 99% recycling. Results show that the main contributor to tungsten erosion along the divertor plates is impurities from the midplane waveguides. In addition, the standard high-recycling case (100% recycling) shows a significantly higher buildup of impurities along the divertor tiles during the startup phase, which can lead to a higher increase of energy loss in the plasma during steady-state operation. Last, for high recycling, anomalous diffusion can dominate over parallel field diffusion. The work performed in this study can be iteratively applied to a full operation scenario with additional physics such as those from neutrals, wall shaping, and additional external fields.

Graft-versus-host disease (GVHD) is one of the major complications following hematopoietic stem cell transplantation, which remains the sole curative therapy for many malignant diseases of the hematopoietic system. The immunomodulatory potential of mesenchymal stromal cells (MSCs) to treat GVHD is currently being tested in various preclinical and clinical trials. Because the results of the preclinical and clinical trials on the use of MSCs to treat GVHD have not been consistent, we analyzed the potential beneficial effects of syngeneic versus allogenic treatment, culture expansion of MSCs, and various MSC cell doses and time points of MSC transplantation in a murine GVHD model. We established the murine GVHD model based on the transplantation of umbilical cord blood-derived hematopoietic stem cells (UC-HSCs) and used this model to assess the therapeutic potential of umbilical cord blood-derived MSCs (UC-MSCs). The use of HSC and MSC populations derived from the same donor allowed us to exclude third-party cells and test the UC-HSCs and UC-MSCs in a matched setting. Moreover, we were able to compare various doses, transplantation time points, and the influence of culture expansion of MSCs on the impact of treatment. This resulted in 16 different treatment groups. The most efficient setting for treatment of UC-HSC-induced GVHD reactions was based on the simultaneous administration of 1 × 10

The carbon deposition profile on a Directional Material Probe (DMP) installed in the inboard side of the torus in the Large Helical Device (LHD) is investigated using the ERO2.0 code. The experimental result of the carbon deposition profile with short and wide shadows (lower deposition density areas) on the DMP is reasonably explained by the carbons sputtered from the carbon divertor plates installed in the inboard side. The simulation proves that the short and wide shadows are produced by carbons sputtered from the right and left divertor plate arrays, respectively. The experimental carbon deposition profile accumulated in the previous experimental campaign (FY2010) was successfully reproduced by the simulation, which provides detailed understanding of material (carbon) migration in the divertor region in the LHD.

Graft-versus-host disease (GVHD) is one of the major complications following hematopoietic stem cell transplantation, which remains the sole curative therapy for many malignant diseases of the hematopoietic system. The immunomodulatory potential of mesenchymal stromal cells (MSCs) to treat GVHD is currently being tested in various preclinical and clinical trials. Because the results of the preclinical and clinical trials on the use of MSCs to treat GVHD have not been consistent, we analyzed the potential beneficial effects of syngeneic versus allogenic treatment, culture expansion of MSCs, and various MSC cell doses and time points of MSC transplantation in a murine GVHD model. We established the murine GVHD model based on the transplantation of umbilical cord blood-derived hematopoietic stem cells (UC-HSCs) and used this model to assess the therapeutic potential of umbilical cord blood-derived MSCs (UC-MSCs). The use of HSC and MSC populations derived from the same donor allowed us to exclude third-party cells and test the UC-HSCs and UC-MSCs in a matched setting. Moreover, we were able to compare various doses, transplantation time points, and the influence of culture expansion of MSCs on the impact of treatment. This resulted in 16 different treatment groups. The most efficient setting for treatment of UC-HSC-induced GVHD reactions was based on the simultaneous administration of 1 × 106 culture-expanded, syngeneically matched UC-MSCs. This therapy effectively reduced the number of CD8+ T cells in the blood, protected the mice from weight loss, and prolonged their survival until the end of observation period. Taken together, our data show beneficial effects of (1) syngeneic over allogeneic UC-HSCs and UC-MSCs, (2) culture-expanded cells over freshly isolated primary cells, (3) simultaneous over sequential administration, and (4) high doses of UC-MSCs. The animal model of GVHD established here is now available for more detailed studies, including a comparative analysis of the efficacy of MSCs derived from alternative sources, such as adipose tissue and bone marrow.

A new analytical approximation for the electric potential profile in the presence of an oblique magnetic field and the analytical solution for the particle motion just before the impact with a plas ...

Pediatric malignancies, in particular Ewing sarcoma (EwS), are characterized by low mutational load, low immunogenicity, and early metastasis. They recapitulate the embryonic immune tolerance setting and remain a challenge for established immunotherapies. These immunotherapies are not sufficient to target metastasis. Ideally, targeted therapies address gene products required for metastasis. We completed in vivo functional analyses for metastasis of 9/37 genes that we had shown to be overexpressed in EwS (Staege at al., Cancer Res 2004) and generated HLA class I restricted cytotoxic T cells against these gene products. All targets were involved in fetal development and 8/9 demonstrated functional relevance for metastasis. Allorepertoire-derived TCRs against 8/9 targets were cloned and sequenced; one target (DKK2) was nonimmunogenic. 7/8 TCRs were crossreactive, caused fratricide, or clonal TCR expansion failed (EZH2, STEAP1, PAPP-A, GPR64, ADRB3, LIPI, HOX-D1). In the tumor microenvironment we found an immunosuppressive (M0 and M2) transcriptomic signature and evidence for an immunosuppressive inflammation-associated activation of endogenous retroviral sequences. Among these most selectively expressed (n=9) and metastasis sustaining (n=8) targets, the BRICHOS chaperon domain containing antiangiogenetic bone protein chondromodulin-I (CHM1) was addressable by a non-crossreactive TCR. CHM1 is a direct downstream target of the oncogenic driver EWS-FLI1. We clinically assessed HLAA* 02:01/CHM1-specific TCR transgenic CD8+ T cells against EwS utilizing a TCR complementary determining region 3 (CDR3) recognition-sequence for the CHM1319 peptide with a Koff half-life of 113.2 ± 38.2 s. The CHM1319 motive was 130 times less homologous as compared to the 9mer ADRB3CHM1295, a crossreactive EwS target identified before. Four refractory HLA-A2+ EwS patients (pts) were treated with CHM1319-specific TCR-CDR3 transgenic T cells. Pt-derived cell lines (PDCL) were established in all cases. Pts received up to 107/kg TCR transgenic CD8+ T cells. All pts were treated with the same TCR-CDR3 recognition-sequence for CHM1. All PDCLs displayed persistent HLA-A2 expression. Transgenic T cells showed specific in vitro lysis of all PDCLs. Therapy was well tolerated and did not cause graft-versus-host disease (GvHD). Pts #1 #3 and #4 showed delayed progression, whereas pt #2, while having bone marrow (BM) involvement and accessible multifocal disease, showed partial metastatic regression associated with T-cell homing to involved lesions. In conclusion, CHM1319-TCR transgenic T cells may home to affected BM and may cause partial remission. CHM1-TCR transgenic T cells address a persistently expressed target required for metastasis, suggesting lack of immunoediting selection pressure. They proliferate in vivo without causing GvHD. This abstract is also being presented as Poster A07. Citation Format: Stefan Burdach, Guenther Richter, David Schirmer, Andreas Kirschner, Sebastian Schober, Valentina Evdokimova, Hendrik Gassmann, Elvira D’Ippolito, Maxim Barenboim, Dirk Busch, Poul Sorensen, Uwe Thiel. T-cell receptor (TCR)-based immunotherapy in pediatric malignancy: Addressing the challenge of early metastasis and low immunogenicity [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr PR05.

For arrays the placement of the single elements determines the angular resolution and the unambiguity interval. The width of the total array determines the resolution capabilities. The wider the elements are placed from each other, the more space in Fourier domain is covered by the measurement and the resolution in time domain will improve. On the other hand the density of the elements has an effect on the angular interval in which objects can be detected unambiguously. For objects within the unambiguous interval grating lobes will appear outside this area while objects outside result in grating lobes in the interval of interest. In this paper the properties of arrays regarding resolution and unambiguity interval will be discussed and methods for the suppression of ambiguous grating lobes are suggested. One approach to suppress the influence of the grating lobes lies in the evaluation of different frequency bands.

Immunotherapy can revolutionize anti-cancer therapy if specific targets are available. Recurrent somatic mutations in the exome can create highly specific neo-antigens. However, especially pediatric cancers are oligo-mutated and hardly exhibit recurrent neo-antigens. Yet, immunogenic peptides encoded by cancer-specific genes (CSGs), which are virtually not expressed in normal tissues, may enable a targeted immunotherapy of such cancers. Here, we describe an algorithm and provide a user-friendly software named RAVEN (Rich Analysis of Variable gene Expressions in Numerous tissues), which automatizes the systematic and fast identification of CSG-encoded peptides highly affine to Major Histocompatibility Complexes (MHC) starting from publicly available gene expression data. We applied RAVEN to a dataset assembled from more than 2,700 simultaneously normalized gene expression microarrays comprising 50 tumor entities, with a focus on sarcomas and pediatric cancers, and 71 normal tissue types. RAVEN performed a transcriptome-wide scan in each cancer entity for gender-specific CSGs. As a proof-of-concept we identified several established CSGs, but also many novel candidates potentially suitable for targeting multiple cancer types. The specific expression of the most promising CSGs was validated by qRT-PCR in cancer cell lines and by immunohistochemistry in a comprehensive tissue-microarray comprising 412 samples. Subsequently, RAVEN identified likely immunogenic peptides encoded by these CSGs by predicting the affinity to MHCs. Putative highly affine peptides were automatically crosschecked with the UniProt protein-database to exclude sequence identity with abundantly expressed proteins. The predicted affinity of selected peptides was validated in T2-cell peptide-binding assays in which many showed similar kinetics to a very immunogenic influenza control peptide.Collectively, we provide a comprehensive, exquisitely curated and validated catalogue of cancer-specific and highly MHC-affine peptides across 50 cancer entities. In addition, we developed an intuitive and freely available software to easily apply our algorithm to any gene expression dataset (https://github.com/JSGerke/RAVENsoftware). We anticipate that our peptide libraries and software constitute a rich resource to accelerate the development of novel immunotherapies.

Background: Chondromodulin-I (CHM1) sustains malignancy in Ewing sarcoma (ES). Refractory ES carries a dismal prognosis and patients with bone marrow (BM) metastases do not survive irrespective of therapy. We assessed HLA-A*02:01/CHM1-specific allorestricted T cell receptor (TCR) wild-type and transgenic cytotoxic (CD8+) T cells against ES. Patients and Methods: Three refractory HLA-A2+ ES patients were treated with HLA-A*02:01/peptide-specific allorepertoire-derived (i.e., allorestricted) CD8+ T cells. Patient #1 received up to 4.8 × 105/kg body weight HLA-A*02:01− allorestricted donor-derived wild-type CD8+ T cells. Patient #2 received up to 8.2 × 106/kg HLA-A*02:01− donor-derived and patient #3 up to 6 × 106/kg autologous allorestricted TCR transgenic CD8+ T cells. All patients were treated with the same TCR complementary determining region 3 allorecognition sequence for CHM1 peptide 319 (CHM1319). Results: HLA-A*02:01/CHM1319-specific allorestricted CD8+ T cells showed specific in vitro lysis of all patient-derived ES cell lines. Therapy was well tolerated and did not cause graft versus host disease (GvHD). Patients #1 and #3 showed slow progression, whereas patient #2, while having BM involvement, showed partial metastatic regression associated with T cell homing to involved lesions. CHM1319 TCR transgenic T cells could be tracked in his BM for weeks. Conclusions: CHM1319-TCR transgenic T cells home to affected BM and may cause partial disease regression. HLA-A*02:01/antigen-specific allorestricted T cells proliferate in vivo without causing GvHD.

ERO is a Monte-Carlo code for modeling plasma-wall interaction and 3D plasma impurity transport for applications in fusion research. The code has undergone a significant upgrade (ERO2.0) which allows increasing the simulation volume in order to cover the entire plasma edge of a fusion device, allowing a more self-consistent treatment of impurity transport and comparison with a larger number and variety of experimental diagnostics. In this contribution, the physics-relevant technical innovations of the new code version are described and discussed. The new capabilities of the code are demonstrated by modeling of beryllium (Be) erosion of the main wall during JET limiter discharges. Results for erosion patterns along the limiter surfaces and global Be transport including incident particle distributions are presented. A novel synthetic diagnostic, which mimics experimental wide-angle 2D camera images, is presented and used for validating various aspects of the code, including erosion, magnetic shadowing, non-local impurity transport, and light emission simulation. EURATOM 633053

A set of quartz crystal microbalances (QMB) was used at JET with full carbon wall to monitor mass erosion/ deposition rates in the remote areas of the divertor. After introduction of the ITER-like wall (ILW) in JET with beryllium main wall and tungsten divertor, strong reduction of the material deposition and accompanied fuel retention was observed. Therefore the existing QMB electronics have been modified to improve the accuracy of frequency measurements by a factor of ten down to 0.1 Hz which corresponds to 1.4 ng cm(-2). The averaged deposition rates of 1.2-3 ng cm(-2) s(-1) and erosion rates of 5.6-8.1 ng cm(-2) s(-1) were observed in the inner divertor of JET-ILW with the inner strike point positions close to the bottom edge of vertical tile 3 and at the horizontal tile 4 respectively. The erosion with averaged rates of approximate to 2.1 ng cm(-2) s(-1) and approximate to 120 ng cm(-2) s(-1) were observed in the outer divertor for the outer strike point positions at tile 5 and tile 6 respectively. (C) 2017 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license. For complete list of authors see http://dx.doi.org/10.1016/j.nme.2017.03.007

Since 2011 the JET tokamak has been operated with a metal ITER-like wall (JET-ILW) including castellated beryllium limiters and lamellae-type bulk tungsten tiles in the divertor. This has allowed for a large scale test of castellated plasma-facing components (PFC). Procedures for sectioning the limiters into single blocks of castellation have been developed. This facilitated morphology studies of morphology of surfaces inside the grooves for limiters after experimental campaigns 2011–2012 and 2013–2014. The deposition in the 0.4–0.5mm wide grooves of the castellation is ‘shallow’. It reaches 1–2mm into the 12mm deep gap. Deuterium concentrations are small (mostly below 1 × 1018 cm−2 ). The estimated total amount of deuterium in all the castellated limiters does not exceed the inventory of the plasma-facing surfaces (PFS) of the limiters. There are only traces of Ni, Cr and Fe deposited in the castellation gaps. The same applies to the carbon content. Also low deposition of D, Be and C has been measured on the sides of the bulk tungsten lamellae pieces. Modelling clearly reflects: (a) a sharp decrease in the measured deposition profiles and (b) an increase in deposition with the gap width. Both experimental and modelling data give a strong indication and information to ITER that narrow gaps in the castellated PFC are essential. X-ray diffraction on PFS has clearly shown two distinct composition patterns: Be with an admixture of Be–W intermetallic compounds (e.g. Be22W) in the deposition zone, whilst only pure Be has been detected in the erosion zone. The lack of compound formation in the erosion zone indicates that no distinct changes in the thermo-mechanical properties of the Be PFC might be expected. EURATOM 633053 Swedish Research Council (VR) 2015–04844

Pregnancy-associated plasma protein-A (PAPPA), also known as pappalysin, is a member of the insulin-like growth factor (IGF) family. PAPPA acts as a protease, cleaving IGF inhibitors, i.e., IGF binding proteins (IGFBPs), thereby setting free IGFs. The insulin/IGF-axis is involved in cancer in general and in Ewing sarcoma (ES) in particular. ES is a highly malignant bone tumor characterized by early metastatic spread. PAPPA is associated with various cancers. It is overexpressed and required for proliferation in ES. PAPPA also stimulates normal bone growth. We isolated HLA-A*02:01+/peptide-restricted T cells from A*02:01− healthy donors directed against PAPPA, generated by priming with A*02:01+ PAPPA peptide loaded dendritic cells. After TCR identification, retrovirally TCR transduced CD8+ T cells were assessed for their in vitro specificity and in vivo efficacy in human ES bearing Rag2−/−γc−/− mice. Engraftment in mice and tumor infiltration of TCR transgenic T cells in the mice was evaluated. The TCR transgenic T cell clone PAPPA-2G6 demonstrated specific reactivity toward HLA-A*02:01+/PAPPA+ ES cell lines. We furthermore detected circulating TCR transgenic T cells in the blood in Rag2−/−γc−/− mice and in vivo engraftment in bone marrow. Tumor growth in mice with xenografted ES was significantly reduced after treatment with PAPPA-2G6 TCR transgenic T cells in contrast to controls. Tumors of treated mice revealed tumor-infiltrating PAPPA-2G6 TCR transgenic T cells. In summary, we demonstrate that PAPPA is a first-rate target for TCR-based immunotherapy of ES.

During the recent decade, coherent MIMO radar systems have been examined intensively. Although well proven conventional modulation schemes can be applied to coherent MIMO radars, such as linear frequency modulation (LFM), the system implementation, and therefore also the modulation, usually underlies errors such as non-linearities, phase noise etc. Nevertheless, the academic world in turn has developed methods for calibration, correction and error prediction against corrupted radar signal modulation. One of these methods is the so-called resampling method which had been developed for correction of linear frequency modulation. However, the convolution operation in coherent MIMO radars with collocated antennas incorporates another grade of complexity. This paper sketches the efforts needed, as well as results, for the resampling method applied to coherent MIMO radars with respect to maintenance of coherency between single MIMO channels.

This paper covers coherent MIMO radar systems with collocated antennas combined with minimum redundancy principles. The fundament of the first are virtual arrays which can be considered as discrete convolution of transmitter and receiver distributions. This technique can be connected to sparse arrays regarding minimum redundancy (MR) aspects. However, MR setups are usually suited for so-called uncorrelated signal scenarios, whereas coherent MIMO radar setups provide correlated or coherent signal outputs. The standard angular signal processing of MR arrays would become corrupted in coherent signal case. The spatial smoothing algorithm can provide a possible solution for this conflict by lateral shifts. However, the pure amount of required shifts would make the idea of sparse arrays obsolete. Therefore, the spatial smoothing algorithm was adapted in order to find also sparse lateral shift positions. The solution could again be found by means of minimum redundancy. This paper presents simulation results which were generated during design and implementation of radar sensors.

Rotating collectors and quartz microbalances (QMBs) are used in JET to provide time-dependent measurements of erosion and deposition. Rotation of collector discs behind apertures allows recording of the long term evolution of deposition. QMBs measure mass change via the frequency deviations of vibrating quartz crystals. These diagnostics are used to investigate erosion/deposition during JET-C carbon operation and JET-ILW (ITER-like wall) beryllium/ tungsten operation. A simple geometrical model utilising experimental data is used to model the time-dependent collector deposition profiles, demonstrating good qualitative agreement with experimental results. Overall, the JET-ILW collector deposition is reduced by an order of magnitude relative to JET-C, with beryllium replacing carbon as the dominant deposit. However, contrary to JET-C, in JET-ILW there is more deposition on the outer collector than the inner. This reversal of deposition asymmetry is investigated using an analysis of QMB data and is attributed to the different chemical properties of carbon and beryllium. EURATOM 633053

// Andreas Kirschner 1 , Melanie Thiede 1 , Franziska Blaeschke 1, 2 , Gunther H.S. Richter 1 , Julia S. Gerke 3 , Michaela C. Baldauf 3 , Thomas G.P. Grunewald 3, 4, 5 , Dirk H. Busch 6 , Stefan Burdach 1, * , Uwe Thiel 1, * 1 Laboratory for Functional Genomics and Transplantation Biology, Departments of Pediatrics and Children’s Cancer Research Center, Klinikum rechts der Isar, Technische Universitat Munchen, Munich, Germany 2 Laboratory for Immunotherapy, Dr. von Hauner Children’s Hospital, Medical center of the LMU Munich, Munich, Germany 3 Laboratory for Pediatric Sarcoma Biology, Institute of Pathology of the LMU Munich, Munich, Germany 4 German Cancer Consortium (DKTK), Heidelberg, Germany 5 German Cancer Research Center (DKFZ), Heidelberg, Germany 6 Institute for Medical Microbiology, Immunology and Hygiene, Technische Universitat Munchen, Munich, Germany * Share senior authorship Correspondence to: Andreas Kirschner, email: andi.kirschner@tum.de Keywords: fratricide, CD107a, TCR transgenic T cells, cross reactivity, amino-acid exchange scan Received: April 18, 2016 Accepted: May 30, 2016 Published: July 18, 2016 ABSTRACT Aim: Autologous as well as allogeneic CD8 + T cells transduced with tumor antigen specific T cell receptors (TCR) may cause significant tumor lysis upon adoptive transfer. Besides unpredictable life-threatening off-target effects, these TCRs may unexpectedly commit fratricide. We hypothesized lysosome-associated membrane glycoprotein 1 (LAMP1, CD107a) to be a marker for fratricide in TCR transgenic CD8 + T cells. Methods: We identified HLA-A*02:01/peptide-restricted T cells directed against ADRB3 295 . After TCR identification, we generated HLA-A*02:01/peptide restricted TCR transgenic T cells by retroviral transduction and tested T cell expansion rates as well as A*02:01/peptide recognition and ES killing in ELISpot and xCELLigence assays. Expansion arrest was analyzed via Annexin and CD107a staining. Results were compared to CHM1 319 -TCR transgenic T cells. Results: Beta-3-adrenergic receptor (ADRB3) as well as chondromodulin-1 (CHM1) are over-expressed in Ewing Sarcoma (ES) but not on T cells. TCR transgenic T cells demonstrated HLA-A*02:01/ADRB3 295 mediated ES recognition and killing in ELISpot and xCELLigence assays. 24h after TCR transduction, CD107a expression correlated with low expansion rates due to apoptosis of ADRB3 specific T cells in contrast to CHM1 specific transgenic T cells. Amino-acid exchange scans clearly indicated the cross-reactive potential of HLA-A*02:01/ADRB3 295 - and HLA-A*02:01/CHM1 319 -TCR transgenic T cells. Comparison of peptide motive binding affinities revealed extended fratricide among ADRB3 295 specific TCR transgenic T cells in contrast to CHM1 319 . Conclusion: Amino-acid exchange scans alone predict TCR cross-reactivity with little specificity and thus require additional assessment of potentially cross-reactive HLA-A*02:01 binding candidates. CD107a positivity is a marker for fratricide of CD8 + TCR transgenic T cells.

The endochondral bone protein Chondromodulin-I (CHM1) provides oncogene addiction in Ewing sarcoma (ES). We pre-clinically tested the targetability of CHM1 by TCR transgenic, allo-restricted, peptide specific T cells to treat ES. We previously generated allo-restricted wildtype CD8+ T cells directed against the ES specific antigen CHM1319 causing specific responses against ES. However, utilization of these cells in current therapy protocols is hampered due to high complexity in production, relatively low cell numbers, and rapid T cell exhaustion. In order to provide off-the-shelf products in the future, we successfully generated HLA-A*02:01-restricted T cell receptor (TCR) transgenic T cells directed against CHM1319 by retroviral transduction. After short-term expansion a 100% purified CHM1319-TCR-transgenic T cell population expressed a CD62L+/CD45RO and CD62L+/CD45RA+ phenotype. These cells displayed specific in vitro IFNg and granzyme B release in co-culture with HLA-A*02:01+ ES cell lines expressing CHM1. When co-injected with ES cells in Rag2−/−ɣc−/− mice, CHM1-specific TCR-transgenic T cells significantly inhibited the formation of lung and liver metastases in contrast to control mice. Lungs and livers of representative mice displayed CD8+ T cell infiltration in the presence (control group treated with unspecific T cells) and in the absence (study group) of metastatic disease, respectively. Furthermore, mice receiving unspecific T cells showed signs of graft-versus-host-disease in contrast to all mice, receiving CHM1319-TCR-transgenic T cells. CHM1319 specific TCR-transgenic T cells were successfully generated causing anti-ES responses in vitro and in vivo. In the future, CHM1319-TCR-transgenic T cells may control minimal residual disease rendering donor lymphocyte infusions more efficacious and less toxic.

Physical and chemical assisted physical sputtering were characterised by the Be I and Be II line and BeD band emission in the observation chord measuring the sightline integrated emission in front of the inner beryllium limiter at the torus midplane. The 3D local transport and plasma-surface interaction Monte-Carlo modelling (ERO code [18]) is a key for the interpretation of the observations in the vicinity of the shaped solid Be limiter. The plasma parameter variation (density scan) in limiter regime has provided a useful material for the simulation benchmark. The improved background plasma parameters input, the new analytical expression for particle tracking in the sheath region and implementation of the BeD release into ERO has helped to clarify some deviations between modelling and experiments encountered in the previous studies [4,5]. Reproducing the observations provides additional confidence in our 'ERO-min' fit for the physical sputtering yields for the plasma-wetted areas based on simulated data. For complete list of authors see http://dx.doi.org/10.1016/j.nme.2016.08.013

Background: Chondromodulin-I (CHM1) sustains malignancy in Ewing sarcoma (ES). Refractory ES carries a dismal prognosis and patients with bone-marrow (BM) metastases do not survive irrespective of therapy. We assessed HLA-A*02:01/CHM1 specific allorestricted T-cell receptor (TCR) wild-type and transgenic cytotoxic (CD8+) T cells against ES. Patients and Methods: Three refractory HLA-A2+ ES patients were treated with HLA-A*02:01/peptide specific allorepertoire-derived (i.e., allorestricted) CD8+ T cells. Patient #1 received up to 4.8 x 105/kg body weight HLA-A*02:0 allorestricted donor-derived wild type CD8+ T cells. Patient #2 received up to 8.2 x 106/kg HLA-A*02:01 donor-derived and patient #3 up to 6 x 106/kg autologous allorestricted TCR transgenic CD8+ T cells. All patients were treated with the same TCR complementary determining region 3 allorecognition sequence for CHM1 peptide 319 (CHM1319). Findings: HLA-A*02:01/CHM1319 specific allorestricted CD8+ T cells showed specific in vitro lysis of all patient-derived ES cell lines. Therapy was well tolerated and did not cause graft-versus-host disease (GVHD). Patients #1 and #3 showed slow progression, whereas patient #2, while having BM involvement, showed partial metastatic regression associated with T-cell homing to involved lesions. CHM1319 TCR transgenic T cells could be tracked in his BM for weeks. Interpretation: HLA-A*02:01/antigen specific allorestricted T cells proliferate in vivo without causing GVHD. CHM1319 TCR transgenic T cells home to affected BM and are associated with partial disease regression. Funding: Wilhelm Sander-Stiftung (2006.109.1), Else Kröner-Stiftung (GR & SB; P31/08//A123/07), BMBF (GR, UT and SB, TranSarNet 01GM1104B; SB, PROVABES 01KT1311) and Cura Placida Children's Cancer Research Foundation. PHS is funded by the Excellenzinitiative at TUM/CCC Munich. Citation Format: Uwe Thiel, Sebastian J. Schober, Ingo Einspieler, Andreas Kirschner, David Schirmer, Katja Gall, Oxana Schmidt, Thomas G. P. Grunewald, Poul H. Sorensen, Guenther H. S. Richter, Irene Teichert von Luettichau, Dirk H. Busch, Stefan Burdach. Ewing sarcoma regression without GVHD by allo-MHC/CHM1 specific T cells [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr B38.

This article reports on the principles of evaluation and the experimental re- sults obtained by a mm-wave FMCW MIMO radar system with a sparse aperture con- figuration and an additional receive antenna for the application of the phase monopulse principle. While ranging information is obtained by standard FMCW techniques the 2D system capability stems from the generated virtual array. The azimuth information is evaluated by exploiting the characteristics of the signal covariance matrix. Supplemen- tary information about elevation can be obtained from the originating monopulse virtual array. A new evaluation method which can handle the occurring phase ambiguities and allows to correct for the system-inherent coupling between elevation and azimuth, is pre- sented. Laboratory experiments confirm suitability and accuracy of the approach.

We propose a machine-learning approach to sequence-based prediction of protein crystallizability in which we exploit subtle differences between proteins whose structures were solved by X-ray analysis [or by both X-ray and nuclear magnetic resonance (NMR) spectroscopy] and those proteins whose structures were solved by NMR spectroscopy alone. Because the NMR technique is usually applied on relatively small proteins, sequence length distributions of the X-ray and NMR datasets were adjusted to avoid predictions biased by protein size. As feature space for classification, we used frequencies of mono-, di-, and tripeptides represented by the original 20-letter amino acid alphabet as well as by several reduced alphabets in which amino acids were grouped by their physicochemical and structural properties. The classification algorithm was constructed as a two-layered structure in which the output of primary support vector machine classifiers operating on peptide frequencies was combined by a second-level Naive Bayes classifier. Due to the application of metamethods for cost sensitivity, our method is able to handle real datasets with unbalanced class representation. An overall prediction accuracy of 67% [65% on the positive (crystallizable) and 69% on the negative (noncrystallizable) class] was achieved in a 10-fold cross-validation experiment, indicating that the proposed algorithm may be a valuable tool for more efficient target selection in structural genomics. A Web server for protein crystallizability prediction called SECRET is available at http://webclu.bio.wzw.tum.de:8080/secret. Proteins 2006. © 2005 Wiley-Liss, Inc.

Pregnancy-associated plasma protein-A (PAPPA), also known as pappalysin, is a member of the insulin like growth factor (IGF) family. PAPPA acts as a protease, cleaving IGF inhibitors, i.e. IGF binding proteins (IGFBPs), thereby releasing IGFs from IGFBPs. The insulin/IGF-axis is involved in cancer in general and in Ewing sarcoma (ES) in particular. ES is a highly malignant bone tumor characterized by early metastatic spread. PAPPA stimulates normal bone growth, and is also associated with various cancers. In particular, PAPPA is overexpressed and required for proliferation in ES. We isolated HLA-A*02:01+/peptide restricted T cells from A*02:01- healthy donors directed against PAPPA, generated by priming with A*02:01+ PAPPA peptide-loaded dendritic cells. After T cell receptor (TCR) identification, retrovirally TCR transduced CD8+ T cells were assessed for their in vitro specificity and in vivo efficacy in human ES bearing Rag2-/-γc-/- mice. Engraftment in mice and tumor infiltration of TCR transgenic T cells in the mice was evaluated. The TCR transgenic T cell clone PAPPA-2G6 demonstrated specific reactivity towards HLA-A*02:01+/PAPPA+ ES cell lines. We furthermore detected circulating TCR transgenic T cells in the blood in Rag2-/-γc-/- mice and in vivo engraftment of the in bone marrow. Tumor growth in mice with xenografted ES was significantly reduced after treatment with PAPPA-2G6 TCR transgenic T cells compared to controls, and tumors from treated mice revealed tumor infiltrating PAPPA-2G6 TCR transgenic T cells. In summary, we demonstrate that PAPPA is a promising target for TCR based immunotherapy of ES. We demonstrate that TCR transgenic T cells recognize this target, home to the tumor, and causes tumor regression in a preclinical mouse model. Citation Format: Uwe Thiel, Andreas Kirschner, Melanie Thiede, Thomas GP Grünewald, Rebeca Alba Rubio, Günther Richter, Thomas Kirchner, Dirk Busch, Poul Sorensen, Stefan Burdach. Pappalysin-1 is a suitable target for T cell receptor transgenic T cells to kill Ewing sarcoma in vivo and in vitro [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 692. doi:10.1158/1538-7445.AM2017-692

Background: Chondromodulin-I (CHM1) sustains malignancy in Ewing sarcoma (ES). Refractory ES carries a dismal prognosis and patients with bone marrow (BM) metastases do not survive irrespective of therapy. We assessed HLA-A*02:01/ CHM1 specific allorestricted T cell receptor (TCR) wildtype and transgenic cytotoxic (CD8+) T cells against ES. Patients and Methods: Three refractory HLA-A2+ ES patients were treated with HLA-A*02:01/peptide specific allorepertoire-derived (i.e. allorestricted) CD8+ T cells. Patient #1 received up to 4.8x105/kg body weight HLA-A*02:01- allorestricted donor derived wild type CD8+ T cells. Patient #2 received up to 8.2x106/kg HLA-A*02:01- donor derived and patient #3 up to 6x106/kg autologous allorestricted TCR transgenic CD8+ T cells. All patients were treated with the same TCR complementary determining region 3 allorecognition sequence for CHM1319. Results: HLA-A*02:01/CHM1319 specific allorestricted CD8+ T cells showed specific in vitro lysis of all patient-derived ES cell lines. Therapy was well tolerated and did not cause graft versus host disease (GVHD). Patients #1 and #3 showed slow progression, whereas patient #2, while having BM involvement, showed partial metastatic regression associated with T cell homing to involved lesions. CHM1319 TCR transgenic T cells could be tracked in his BM for weeks. Conclusions: CHM1319-TCR transgenic T cells home to affected BM and may cause partial disease regression. HLA-A*02:01/antigen specific allorestricted T cells proliferate in vivo without causing GVHD. Citation Format: Uwe Thiel, Sebastian Schober, ingo Einspieler, Andreas Kirschner, David Schirmer, Thomas Grünewald, Irene Teichert-von Lüttichau, Guenther Richter, Poul Sorensen, Stefan Burdach. Ewing Sarcoma regression by Allo-MHC/Chm1 specific T cells without GVHD [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3757. doi:10.1158/1538-7445.AM2017-3757

Pregnancy-associated plasma protein-A (PAPPA), also known as pappalysin, is a member of the insulin-like growth factor (IGF) family. PAPPA acts as a protease, cleaving IGF inhibitors, i.e., IGF binding proteins (IGFBPs), thereby setting free IGFs. The insulin/IGF-axis is involved in cancer in general and in Ewing sarcoma (ES) in particular. ES is a highly malignant bone tumor characterized by early metastatic spread. PAPPA is associated with various cancers. It is overexpressed and required for proliferation in ES. PAPPA also stimulates normal bone growth. We isolated HLA-A*02:01+/peptide-restricted T cells from A*02:01− healthy donors directed against PAPPA, generated by priming with A*02:01+ PAPPA peptide loaded dendritic cells. After TCR identification, retrovirally TCR transduced CD8+ T cells were assessed for their in vitro specificity and in vivo efficacy in human ES bearing Rag2−/−γc−/− mice. Engraftment in mice and tumor infiltration of TCR transgenic T cells in the mice was evaluated. The TCR transgenic T cell clone PAPPA-2G6 demonstrated specific reactivity toward HLA-A*02:01+/PAPPA+ ES cell lines. We furthermore detected circulating TCR transgenic T cells in the blood in Rag2−/−γc−/− mice and in vivo engraftment in bone marrow. Tumor growth in mice with xenografted ES was significantly reduced after treatment with PAPPA-2G6 TCR transgenic T cells in contrast to controls. Tumors of treated mice revealed tumor-infiltrating PAPPA-2G6 TCR transgenic T cells. In summary, we demonstrate that PAPPA is a first-rate target for TCR-based immunotherapy of ES.

For a multiple input multiple output (MIMO) radar system that uses a frequency modulated continuous wave (FMCW) signal and time domain multiplexing (TDM), different effects occur in the presence of relative motion between radar system and target. These effects have an influence on the correct position detection of the targets. Therefore, two different modulation schemes are analyzed that have the ability to overcome the issues of movement and estimate the correct target location and velocity.

Coherent multiple-input multiple-output (MIMO) radar systems with co-located antennas, form monostatic vir- tual arrays by discrete convolution of a bistatic setup of transmitters and receivers. Thereby, a trade-off between maximum array dimension, element spacing and hardware efforts exists. In terms of estimating the direction of arrival, the covariance matrix of the array element signals plays an important role. Here, minimum redundancy arrays aim at a hardware reduction with signal reconstruction by exploiting the Toeplitz characteristics of the covariance matrix. However, the discrete spatial convolution complicates the finding of an optimal antenna setup with minimum redundancy. Combinatorial effort is the consequence. This paper presents a possible simplified algorithm in order to find MIMO array setups of maximum dimension with minimum redundancy.

Coherent multiple-input multiple-output (MIMO) radar systems with co-located antennas, form monostatic virtual arrays by discrete convolution of a bistatic setup of transmitters and receivers. Thereby, a trade-off between maximum array dimension, element spacing and hardware efforts exists. In terms of estimating the direction of arrival, the covariance matrix of the array element signals plays an important role. Here, minimum redundancy arrays aim at a hardware reduction with signal reconstruction by exploiting the Toeplitz characteristics of the covariance matrix. However, the discrete spatial convolution complicates the finding of an optimal antenna setup with minimum redundancy. Combinatorial effort is the consequence. This paper presents a possible simplified algorithm in order to find MIMO array setups of maximum dimension with minimum redundancy.

A coherent multiple input multiple output (MIMO) radar system that uses the principles of a frequency modulated continuous wave (FMCW) radar and a time domain multiplexing technique can use a special modulation scheme to enable the unambiguous location estimation as well as a velocity estimation and compensation in a short measurement time [1]. To use this modulation scheme a special calibration procedure is needed. This strategy shall be displayed here.

The European Defence Agency (EDA) engages countermeasures against Improvised Explosive Devices (IEDs) by funding several scientific programs on threat awareness, countermeasures IEDs or land-mine detection, in which this work is only one of numerous projects. The program, denoted as Surveillance in an urban environment using mobile sensors (SUM), covers the idea of equipping one or more vehicles of a patrol or a convoy with a set of sensors exploiting different physical principles in order to gain detailed insights of the road situation ahead. In order to give an added value to a conventional visual camera system, measurement data from an infra-red (IR) camera, a radiometer and a millimetre-wave radar are fused with data from an optical image and are displayed on a human-machine-interface (HMI) which shall assist the vehicle’s co-driver to identify suspect objects or persons on or next to the road without forcing the vehicle to stop its cruise. This paper shall especially cover the role of the millimetre-wave radar sensor and its different operational modes. Measurement results are discussed. It is possible to alter the antenna mechanically which gives two choices for a field of view and angular resolution trade-off. Furthermore a synthetic aperture radar mode is possible and has been tested successfully. MIMO radar principles like orthogonal signal design were exploited tofrom a virtual array by 4 transmitters and 4 receivers. In joint evaluation, it was possible to detect e.g. grenade shells under cardboard boxes or covered metal barrels which were invisible for optical or infra-red detection.

This paper covers the implementation of a near-range FMCW radar within a joint European scientific program for force protection from IEDs or landmines. The radar is one of four sensors whose data are fused and evaluated to provide a threat classification of suspicious objects or persons on or nearby the road ahead of a patrol or transport vehicle. A fully functionally low-cost demonstrator system has been implemented and succesfully tested. Results are given.

Millimeter-wave (mmW) sensorics are an interesting option for several short range applications like the imaging of persons or the monitoring of indoor environments. Due to the small antenna dimensions, compact sensor setups can be realised. This paper will discuss different setups for mmW-sensors based on the principle of a frequency-modulated continuous wave radar with respect to system architecture, calibration concepts, resulting sensor capabilities and imaging results.

This paper covers the role of a millimetre-wave (mmw) radar sensor within a European scientific program with the aim of preventing security or supply patrols from harms caused by improvised explosive devices (IEDs), land-mines etc. in hostile conflict zones. In order to give an added value to a conventional visual camera system, measurement data from an infra-red (IR) camera, a visual camera, a radiometer and a millimetre-wave radar are fused and displayed on a human-machine-interface (HMI) which shall assist the vehicle's co-driver to identify suspect objects or persons on or next to the road without forcing the vehicle to stop its cruise. Within an international consortium, a complete demonstration system with the afore mentioned sensors, as well as a data fusion engine were designed, constructed, mounted on a military patrol truck and successfully tested for different objects in different scenarios. Furthermore, this paper introduces the applied radar modes in more detail and gives measurement results. (6 pages)

BackgroundWe have previously reported that human recombinant granzyme B (grB) mediates apoptosis in membrane heat shock protein 70 (Hsp70)-positive tumor cells in a perforin-independent manner.Methodology/principal findingsOptical imaging of uptake kinetics revealed co-localization of grB with recycling endosomes (Rab9/11) as early as 5 min after internalization, with late endosomes (Rab7) after 30 min, and the lysosomal compartment (LAMP1/2) after 60 to 120 min. Active caspase-3-mediated apoptosis was induced in mouse CT26 monolayer cells and 3D tumor spheroids, but not in normal mouse endothelial cells. Granzyme B selectively reduced the proportion of membrane Hsp70-positive cells in CT26 tumor spheroids. Consecutive i.v. injections of recombinant human grB into mice bearing membrane Hsp70-positive CT26 tumors resulted in significant tumor suppression, and a detailed inspection of normal mouse organs revealed that the administration of anti-tumoral concentrations of grB elicited no clinicopathological changes.Conclusions/significanceThese findings support the future clinical evaluation of human grB as a potential adjuvant therapeutic agent, especially for treating immunosuppressed patients that bear membrane Hsp70-positive tumors.

Helix-helix contacts are an important feature of alpha-helical membrane proteins as they define their characteristic helix bundle structure. No bioinformatics approaches for the prediction of pairwise residue contacts in membrane proteins have existed until recently. In this chapter we describe novel contact prediction methods based on residue coevolution and machine learning techniques specifically geared towards membrane proteins. While contact prediction accuracies are limited to ~10% using co-evolving residues alone, machine learning methods are able to improve these accuracies significantly to more than 25% by using available membrane protein structures as a training dataset and incorporating membrane protein specific sequence features into the prediction process. Importantly, predicted residue contacts allow for identification of interacting transmembrane helices with high accuracy. As different membrane protein structures can be distinguished by their specific pattern of helix interactions, predicted residue contacts may not only serve as structural constraints in modeling experiments, but also constitute valuable information for structural classification of membrane proteins with unknown structure.

Despite rapidly increasing numbers of available 3D structures, membrane proteins still account for less than 1% of all structures in the Protein Data Bank. Recent high-resolution structures indicate a clearly broader structural diversity of membrane proteins than initially anticipated, motivating the development of reliable structure prediction methods specifically tailored for this class of molecules. One important prediction target capturing all major aspects of a protein's 3D structure is its contact map. Our analysis shows that computational methods trained to predict residue contacts in globular proteins perform poorly when applied to membrane proteins. We have recently published a method to identify interacting alpha-helices in membrane proteins based on the analysis of coevolving residues in predicted transmembrane regions. Here, we present a substantially improved algorithm for the same problem, which uses a newly developed neural network approach to predict helix-helix contacts. In addition to the input features commonly used for contact prediction of soluble proteins, such as windowed residue profiles and residue distance in the sequence, our network also incorporates features that apply to membrane proteins only, such as residue position within the transmembrane segment and its orientation toward the lipophilic environment. The obtained neural network can predict contacts between residues in transmembrane segments with nearly 26% accuracy. It is therefore the first published contact predictor developed specifically for membrane proteins performing with equal accuracy to state-of-the-art contact predictors available for soluble proteins. The predicted helix-helix contacts were employed in a second step to identify interacting helices. For our dataset consisting of 62 membrane proteins of solved structure, we gained an accuracy of 78.1%. Because the reliable prediction of helix interaction patterns is an important step in the classification and prediction of membrane protein folds, our method will be a helpful tool in compiling a structural census of membrane proteins.

Background We have recently released a comprehensive, manually curated database of mammalian protein complexes called CORUM. Combining CORUM with other resources, we assembled a dataset of over 2700 mammalian complexes. The availability of a rich information resource allows us to search for organizational properties concerning these complexes. Results As the complexity of a protein complex in terms of the number of unique subunits increases, we observed that the number of such complexes and the mean non-synonymous to synonymous substitution ratio of associated genes tend to decrease. Similarly, as the number of different complexes a given protein participates in increases, the number of such proteins and the substitution ratio of the associated gene also tends to decrease. These observations provide evidence relating natural selection and the organization of mammalian complexes. We also observed greater homogeneity in terms of predicted protein isoelectric points, secondary structure and substitution ratio in annotated versus randomly generated complexes. A large proportion of the protein content and interactions in the complexes could be predicted from known binary protein-protein and domain-domain interactions. In particular, we found that large proteins interact preferentially with much smaller proteins. Conclusion We observed similar trends in yeast and other data. Our results support the existence of conserved relations associated with the mammalian protein complexes.

Prediction of β-turns from amino acid sequences has long been recognized as an important problem in structural bioinformatics due to their frequent occurrence as well as their structural and functional significance. Because various structural features of proteins are intercorrelated, secondary structure information has been often employed as an additional input for machine learning algorithms while predicting β-turns. Here we present a novel bidirectional Elman-type recurrent neural network with multiple output layers (MOLEBRNN) capable of predicting multiple mutually dependent structural motifs and demonstrate its efficiency in recognizing three aspects of protein structure: β-turns, β-turn types, and secondary structure. The advantage of our method compared to other predictors is that it does not require any external input except for sequence profiles because interdependencies between different structural features are taken into account implicitly during the learning process. In a sevenfold cross-validation experiment on a standard test dataset our method exhibits the total prediction accuracy of 77.9% and the Mathew's Correlation Coefficient of 0.45, the highest performance reported so far. It also outperforms other known methods in delineating individual turn types. We demonstrate how simultaneous prediction of multiple targets influences prediction performance on single targets. The MOLEBRNN presented here is a generic method applicable in a variety of research fields where multiple mutually depending target classes need to be predicted. Availability: http://webclu.bio.wzw.tum.de/predator-web/ .

JET is used as a test bed for ITER, to investigate beryllium migration which connects the lifetime of first-wall components under erosion with tokamak safety, in relation to long-term fuel retention. The (i) limiter and the (ii) divertor configurations have been studied in JET-ILW (JET with a Be first wall and W divertor), and compared with those for the former JET-C (JET with carbon-based plasma-facing components (PFCs)). (i) For the limiter configuration, the Be gross erosion at the contact point was determined in situ by spectroscopy as between 4% (E-in = 35 eV) and more than 100%, caused by Be self-sputtering (E-in = 200 eV). Chemically assisted physical sputtering via BeD release has been identified to contribute to the effective Be sputtering yield, i.e. at E-in = 75 eV, erosion was enhanced by about 1/3 with respect to the bare physical sputtering case. An effective gross yield of 10% is on average representative for limiter plasma conditions, whereas a factor of 2 difference between the gross erosion and net erosion, determined by post-mortem analysis, was found. The primary impurity source in the limiter configuration in JET-ILW is only 25% higher (in weight) than that for the JET-C case. The main fraction of eroded Be stays within the main chamber. (ii) For the divertor configuration, neutral Be and BeD from physically and chemically assisted physical sputtering by charge exchange neutrals and residual ion flux at the recessed wall enter the plasma, ionize and are transported by scrape-off layer flows towards the inner divertor where significant net deposition takes place. The amount of Be eroded at the first wall (21 g) and the Be amount deposited in the inner divertor (28 g) are in fair agreement, though the balancing is as yet incomplete due to the limited analysis of PFCs. The primary impurity source in the JET-ILW is a factor of 5.3 less in comparison with that for JET-C, resulting in lower divertor material deposition, by more than one order of magnitude. Within the divertor, Be performs far fewer re-erosion and transport steps than C due to an energetic threshold for Be sputtering, and inhibits as a result of this the transport to the divertor floor and the pump duct entrance. The target plates in the JET-ILW inner divertor represent at the strike line a permanent net erosion zone, in contrast to the net deposition zone in JET-C with thick carbon deposits on the CFC (carbon-fibre composite) plates. The Be migration identified is consistent with the observed low long-term fuel retention and dust production with the JET-ILW. EURATOM 633053