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  • 1
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    An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action [version 1; peer review: 1 approved, 1 approved with reservations] (2020)
    Details
    Publication Date: 2020-12-15
    Description: Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin.
    Language: English
    Type: article , doc-type:article
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    OPUS
  • 2
    Electronic Resource
    Electronic Resource
    Interface reactions between quaternary cobalt alloys and carbon coating in thin film disk media (2000)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 87 (2000), S. 2989-2993 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A study of interface reactions between the magnetic layer and the protective carbon coating, and the influence of these interactions on magnetic properties of rigid disk media for magnetic data storage is presented. Quaternary CoPtCrB and CoPtCrTa alloy films and protective hydrogenated or nitrogenated carbon coatings were deposited by dc magnetron sputtering onto metal hard disks (AlMg substrate/electroplated NiP layer/Cr underlayer). Core level x-ray photoelectron spectroscopy of nitrogenated carbon films on B-containing alloys showed the formation of boron nitride and small amounts of chromium nitride at the interface, and also indicated the likely presence of chromium carbide. The amount of boron nitride at the interface varied depending on substrate bias voltage and temperature during deposition of the carbon coating. From a quantitative analysis of the x-ray photoelectron spectra it was inferred that boron nitride formation was controlled by the diffusion of boron from deeper regions of the magnetic layer to the interface. Surprisingly, compared to disks using the same magnetic alloy but with a hydrogenated or pure carbon coating, no effects of these interface reactions on the magnetic properties of the disks could be detected. In contrast, for a Ta-containing alloy the same comparison revealed a drop in the coercivity of up to 200 Oe in disks with nitrogenated carbon overcoats. Strong evidence for the formation of tantalum nitride as well as small amounts of chromium nitride was found in the photoelectron spectra. Thus, while the formation of boron nitride at the interface of CoPtCrB media and protective carbon coating does not affect the magnetic properties of the disks in the range of boron and nitrogen concentrations investigated here, small changes in the chemical environment of Ta and/or Cr can lead to significant changes in the magnetic properties of the CoPtCrTa media. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.372288
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Perpendicular magnetic anisotropy and magnetic domain structure in sputtered epitaxial FePt (001) L10 films (1998)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 84 (1998), S. 5686-5692 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The magnetic domain structure and magnetization curves of chemically ordered epitaxial FePt (001) films with perpendicular magnetic anisotropy are discussed. Films were dc magnetron sputtered from a Fe50Pt50 alloy target onto Pt seeded MgO (001) at substrate temperatures of 550 °C. The thickness of the FePt layers was varied between 18 and 170 nm. Specular and grazing incidence x-ray diffraction measurements confirm the presence of the anisotropic, face centered tetragonal (L10) crystal structure. Long range chemical order parameters of up to 0.95 and small mosaic spread, similar to results reported for FePt (001) films grown by molecular beam epitaxy. For film thicknesses ≥50 nm in-plane and out-of-plane hysteresis measurements indicate large perpendicular magnetic anisotropies and at the same time low (about 10%) perpendicular remanence. Magnetic force microscopy reveals highly interconnected perpendicular stripe domain patterns. From their characteristic widths, which are strongly dependent on the film thickness, a value of the dipolar length D0∼50±5 nm is derived. Assuming an exchange constant of 10−6 erg/cm, this value is consistent with an anisotropy constant K1∼1×108 erg/cc. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.368831
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  • 4
    Electronic Resource
    Electronic Resource
    Temperature dependent chemical ordering in FePt(001) and FePt(110) films (2000)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 87 (2000), S. 6956-6958 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The growth temperature is one of the critical parameters in the formation of the chemically ordered L10 phase in FePt. To uniquely determine the influence of growth temperature, while other growth parameters remain fixed, we present the "temperature wedge method" where a calibrated temperature gradient of several hundred Kelvin is established across the substrate during co-deposition of Fe and Pt. Samples were deposited in a temperature range of 250 °C–600 °C simultaneously on MgO(001) and MgO(110) substrates. The Fe(approximate)50Pt(approximate)50 composition was verified by Rutherford backscattering. The chemical order parameter, S, at different positions along the samples, i.e., at different growth temperatures, was determined by x-ray diffraction measurements, and it was found that at all temperatures S(001)〉S(110). Perpendicular and in-plane magneto-optic Kerr hysteresis loop measurements indicate large magnetic anisotropy at the "hot ends" of the samples, corresponding to large values of S. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.372898
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  • 5
    Electronic Resource
    Electronic Resource
    Bone marrow changes in chronic myelogenous leukaemia after long-term treatment with the tyrosine kinase inhibitor STI571: an immunohistochemical study on 75 patients (2005)
    Oxford, UK : Blackwell Science Ltd
    Histopathology 46 (2005), S. 0 
    Details
    ISSN: 1365-2559
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: Aims:  To carry out an immunohistochemical study on bone marrow (BM) biopsy specimens in 75 patients with chronic myelogenous leukaemia (CML) on long-term STI571 therapy.Methods and results:  Sequential BM specimens taken at intervals of 21 ± 6 months were investigated by enzyme- and immunohistochemistry including proliferating cell nuclear antigen and apoptosis. Evaluation was performed either by semiquantitative scoring or by morphometry (CD61+ megakaryopoiesis). In 41 patients with chronic phase CML, treatment resulted in a significant decrease in cellularity and neutrophil granulopoiesis contrasting with an accumulation of erythroid precursor cells. Morphometry showed a reduction of abnormal micromegakaryocytes consistent with normalization. Regression of myelofibrosis was identified in eight of 15 patients, whereas progression occurred in 17 patients; mostly in those with acceleration and blastic crisis. The increased post-treatment incidence of reactive lymphoid nodules was remarkable. Myeloblasts, CD34+ progenitors and immature myelomonocytic cells initially decreased, but recurred in 14 patients who later developed a relapse. STI571 exerted an inhibitory effect on cell proliferation associated with enhanced apoptosis in responding patients.Conclusion:  Long-term treatment with STI571 exerts pronounced changes on BM histopathology that not only involve haematopoiesis and stromal constituents, but also proliferation and apoptosis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2559.2005.02119.x
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  • 6
    Electronic Resource
    Electronic Resource
    Proliferating cell nuclear antigen expression by erythroid precursors in normal bone marrow, in reactive lesions and in polycythaemia rubra vera (1993)
    Oxford, UK : Blackwell Publishing Ltd
    Histopathology 22 (1993), S. 0 
    Details
    ISSN: 1365-2559
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: Using a sequential double-imunostaining technique, a morphometric analysis was performed on routinely processed bone marrow trephines from 20 patients with secondary (reactive) polycythaemia and 28 patients with polycythaemia rubra vera to determine the proliferation capacity of erythropoiesis. Monoclonal antibodies PC10—anti-proliferating cell nuclear antigen (PCNA)—and Ret40f—anti-glycophorin C—were employed. For comparison with the PCNA-labelling index, in a pilot study, Ki-67 was additionally used on frozen-section material. In comparison with normal bone marrow (15 patients) morphometric and statistical evaluation revealed a numerical increase in erythroid precursors (pro-, erythro- and normoblasts) in secondary polycythaemia and to a pronounced degree in polycythaemia rubra vera. In comparison with secondary polycythaemia and the control group, in polycythaemia rubra vera there was a significant enhancement of proliferation according to PCNA-staining reactivity in all haematopoietic cell elements and particularly in the erythroid series. Evaluation of PCNA v. Ki-67 immunostaining disclosed only a slight difference, which could be mainly attributed to various modalities of antigen expression during the cell cycle. Our findings are in keeping with in vitro studies on cultured erythroid progenitor cells and, in problematic cases, may present a valuable aid in differentiation between reactive lesions and polycythaemia rubra vera.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2559.1993.tb00156.x
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  • 7
    Electronic Resource
    Electronic Resource
    Immunological importance of the second gut segment of carp. (1989)
    Oxford, UK : Blackwell Publishing Ltd
    Journal of fish biology 35 (1989), S. 0 
    Details
    ISSN: 1095-8649
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Lymphocytes, plasma cells, granulocytes (three to four types), macrophages and monocyte-like cells were ultrastructurally distinguished in the intestinal mucosa of carp. Neutrophilic granulocytes and lymphoid cells were present in and under the epithelium throughout the gut. In contrast to macrophages which dominated in the epithelium of the second segment, basophilic and eosinophilic granulocytes (and their intermediates) were mainly found in the connective tissue of the first segment. Applying monoclonal antibodies against serum immunoglobulin (Ig) in an immunogold technique, only a minority of lymphoid cells appeared to be Ig-immunoreactive at their external membrane, suggesting the presence of many more T than B cells in the intestinal mucosa. Except for cells which resembled immature plasma cells, plasma cells did not show, or hardly showed, Ig at their surface. In contrast with the head kidney, plasma cells with an Ig-immunoreactive cytoplasm were scarce in the intestinal mucosa. As mucosa plasma cells were regularly found with the electron microscope, they possibly contain another class of Ig. Macrophages and monocyte-like cells were also found to be Ig-immunoreactive, suggesting the presence of immune complexes at their external membrane. The immunological significance of B- and T-like lymphocytes next to immune complex-binding and antigen-presenting macrophages in the second gut segment is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1095-8649.1989.tb02966.x
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    Paper (German National Licenses)
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  • 8
    Electronic Resource
    Electronic Resource
    Characterization of carp thrombocytes with specific monoclonal antibodies (1996)
    Oxford, UK : Blackwell Publishing Ltd
    Journal of fish biology 49 (1996), S. 0 
    Details
    ISSN: 1095-8649
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Monoclonal antibodies (WCL6) specific for carp Cyprinus carpio thrombocytes were produced by immunizing mice with membrane lysates of IgM-negative peripheral blood leucocytes (PBL) and selected on the negative reaction with B cells. WCL6 was reactive with a membrane molecule of approximately 90 kDa and to a lesser extent with molecules of approximately 95 and 110 kDa. In general, between 30 and 40% of PBL were WCL6+ and appeared to be round to spindle-shaped cells. Immunohistochemical analysis of cryo-sections showed much higher numbers of WCL6+ cells in the spleen than in the pronephros, intestine and thymus. Flow cytometric analysis of cell suspensions isolated from these organs only revealed WCL6+ cells (4–10%) in the spleen. Electron microscopy of immunogold-stained WCL6+ PBL showed round but also some spindle-shaped cells with canalicular and granular structures, and a more irregular and electron-dense nucleus than found in lymphocytes. WCL6+ cells with electrondense pyknotic nuclei (without a clear nuclear envelope) were found also and their frequency increased with the length of the isolation and staining procedure used. In the spleen, several differentiation steps of WCL6+ cells were found and hence the spleen seems to be the thrombopoietic organ in carp. Thrombocytes from blood could be activated with collagen; the collagen-activated cells showed a higher side (90°) scatter by flow cytometric analysis and finally considerable cell death.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1095-8649.1996.tb00047.x
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  • 9
    Electronic Resource
    Electronic Resource
    Bone marrow histopathology following cytoreductive therapy in chronic idiopathic myelofibrosis (2003)
    Oxford, UK : Blackwell Science Ltd
    Histopathology 43 (2003), S. 0 
    Details
    ISSN: 1365-2559
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: Aims:  To analyse systematically therapy-induced lesions of haematopoiesis in chronic idiopathic myelofibrosis (IMF).Methods and results:  A total of 759 sequential bone marrow (BM) biopsies (median interval 32 months) were performed in 261 patients with IMF. Besides a control group (symptomatic treatment), monotherapies included busulfan, hydroxyurea and interferon. In all therapy groups hypoplasia of varying degree was a frequent finding and often accompanied by a patchy distribution of haematopoiesis. Most conspicuous was gelatinous oedema showing a tendency to develop discrete reticulin fibrosis (scleroedema). Minimal to moderate maturation defects of megakaryopoiesis and erythroid precursors occurred, but overt myelodysplastic features were most prominent following hydroxyurea and busulfan therapy. Acceleration and blastic crisis were characterized by the appearance of immature and CD34+ progenitor cells. Concerning the dynamics of fibrosis, no differences were observed between controls and the various therapy groups. In 143 patients (55%) without or with little reticulin at onset, an increase in myelofibrosis was detectable that progressed to overt collagen fibrosis.Conclusions:  Therapy-related bone marrow lesions in IMF comprise a strikingly variable spectrum that may include aplasia with scleroedema and a patchy distribution of myelodysplastic haematopoiesis associated with progressive myelofibrosis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2559.2003.01732.x
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  • 10
    Electronic Resource
    Electronic Resource
    Immunoreactivity of cytokeratins (CK7, CK20) and mucin peptide core antigens (MUC1, MUC2, MUC5AC) in adenocarcinomas, normal and metaplastic tissues of the distal oesophagus, oesophago–gastric junction and proximal stomach (2003)
    Oxford, UK : Blackwell Science Ltd
    Histopathology 43 (2003), S. 0 
    Details
    ISSN: 1365-2559
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: Aims:  Adenocarcinomas of the distal oesophagus and especially the oesophago–gastric junction have shown an increasing incidence during the last decade. Definition of subgroups according to different sites of development, histogenesis or aetiology may prove to be valuable for clinical diagnosis and treatment. Previous studies have shown differences in cytokeratin patterns between Barrett's metaplasia of the oesophagus and intestinal metaplasia in the stomach. The aim of our study was to investigate whether the expression of certain cytokeratins (CK7, CK20) and mucins (MUC1, MUC2, MUC5AC) exhibit clear-cut patterns, thus allowing a subclassification of adenocarcinomas of the oesophago–gastric junction. The possibility of a relationship between antigen expression and the presence or absence of Barrett's metaplastic epithelium was also studied.Methods and results:  CK7, CK20, MUC1, MUC2 and MUC5AC were visualized in six adenocarcinomas of the distal oesophagus, 29 adenocarcinomas of the oesophago–gastric junction and eight adenocarcinomas of the proximal stomach. CK7, CK20 and MUC1 were strongly expressed in the great majority of all neoplasms under study, whereas MUC2 and MUC5AC were absent or only faintly detectable. CK20 exhibited a significantly stronger expression in poorly differentiated tumours (G3) and MUC1 immunoreactivity correlated with tubular and papillary versus signet-ring cell histopathology. Other statistically significant correlations between antigens and histopathological features (pTNM stage, grading, histopathological subtype, presence/absence of Barrett's epithelium) were not observed.Conclusions:  According to our results, most adenocarcinomas of the oesophago–gastric junction show a CK7+, CK20+, MUC1+ phenotype irrespective of the presence or absence of Barrett's epithelium. The immunohistochemical data suggest a similar histogenesis of these tumours.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2559.2003.01680.x
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