cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Supplementary material from Assessing model mismatch and model selection in a Bayesian uncertainty quantification analysis of a fluid-dynamics model of pulmonary blood circulation
Creators: name: Paun, L. Mihaela
name: Colebank, Mitchel J.
name: Olufsen, Mette S.
name: Hill, Nicholas A.
name: Husmeier, Dirk
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Biophysics
subject: Computational Biology
subject: 10202 Biological Mathematics
subject: FOS: Mathematics

description: The Supplementary material accompanying the paper
Optimizing Optical And Digital Resolution For Brightfield Whole Slide Scanning
Creators: name: Isola, J.
name: Ylinen, O.
name: Tolonen, T.
name: Tolonen, P.
Publisher: name: Diagnostic Pathology
Year: 2016

description: Introduction/ Background
Whole slide imaging lacks standards for defining image resolution. Scanner vendors usually describe the image resolution according to the microscope objectives “20X” or “40X”. This has caused confusion, since scanning with a 20X objective lens may mean spatial resolution 0.25 to 0.5 microns per pixel, due to variable pixel size of the camera sensor and/or use of a magnifying relay lens.
Aims
Our aim was to compare image quality obtained by two digital cameras (with pixel sizes 5.5um and 3.1um conbined with 10X, 20X, and 40X Plan Apo objective lenses.
Methods
As for image quality readouts we used standardized resolution charts, Peak-Signal-To-Noise Ratio, and evaluation by three pathologists who ranked the images by their “visually lossless quality”, when displayed with a 4K computer monitor. Lossless JPEG2000 was used as a reference.
Results
The differences in scanned image quality were significant. The image quality achieved with a CCD camera with 3.1 um pixels was superior in all tests. It was noteworthy that the camera with 3.1 um pixels (Lumenera 1265R) gave visually as good diagnostic image quality with 10X lens (0.31 um/pixel) as did the 5.5 um pixel camera (Lumenera LT425) with 20X lens (0.28 um/pixel). This gives a significant speed advantage in scanning of standard H&E slides, because the scanner needs to capture only one 10X field instead of four 20X fields. In higher resolution scanning tasks, such as cytology and in situ hybridization, we found 3.1 um pixel Lumenera 1265R camera and Plan-Apo 20X lens to give diagnostically satisfactory scanning results. We anticipate that in the future scanners will be equipped with cameras having small pixel size sensors (typically 2-3microns). This matches with the optical resolution of Plan-Apo objective lenses. Compared to current scanners, significant image quality and/or scanning speed improvement can be gained by upgrading the camera.
description: Diagnostic Pathology, Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
Hematoxylin Counterstain To Simplify Whole Slide Scanning Of Immunofluorescence Stains
Creators: name: Isola, J.
name: Tolonen, T.
name: Tolonen, P.
name: Ylinen, O.
Publisher: name: Diagnostic Pathology
Year: 2016

description: Introduction/ Background
Whole slide scanning of immunofluorescence (IF) stained slides is a well-recognized need, because fluorescence signal fading makes slides non-archivable. Technically scanning of IF has remained difficult, because tissue finding and autofocus operations are slow and prone to errors under epifluorescence illumination.
Aims
To simplify and to make IF scans more reliable, we started to look for counterstains that are compatible with IF and that can be scanned under brightfield illumination first.
Methods
Of the many alternative counterstains tested, light hematoxylin (H) proved the best counterstain for IF (with or without DAPI). Hematoxylin staining allowed the scanner (OIT Turboscanner) to perform rapid and accurate tissue finding and to define autofocus points, yet it did not increase background autofluorescence or decrease true fluorescence signal during subsequent scanning of IF under epifluorescence illumination. By using Cy2 (green) and Cy3 (orange) as secondary antibody fluorochromes (Jackson Immunotech), we were able to use standard xylene-based DPX mounting medium without observing significant fluorescence signal fading.
Results
As a result, IF scans of H counterstained slides could not be distinguished from those stained without hematoxylin counterstaining. As a bonus, the two scans (IF and H) could be viewed on the viewer screen side-by-side, or by gradually blending the two layers with each other. Both viewing modes were found useful in diagnostic dermatopathology when analyzing e.g. blistering skin lesions. A brightfield-IF scanning combination was also found useful in double immunostains, where cellular co-localization makes use of two precipitating (chromogenic) markers unreliable. The peroxidase IHC-hematoxylin-IF stain was exemplified with Ki-67 and pan-cytokeratin in breast cancer samples. The brightfield WSI of Ki-67 with H counterstain is an easily evaluable chromogenic DAB stain, but the image analysis software (ImmunoRatio2, embedded in the WSI viewer) utilizes the hidden pan-cytokeratin IF to create a cancer mask to exclude counting of non-epithelial stromal and lymphoid cells in the Ki-67 labeling index counting. Together these results demonstrate that a minor modification in the staining protocol (using hematoxylin instead of or in parallel to DAPI as counterstain) provides a significant help for whole slide scanning of immunofluorescence stains. Some scanners may need to be re-programmed to allow scanning of brightfield and epifluorescence automatically in sequence.
description: Diagnostic Pathology, Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
Optical Properties of Manganese Doped Wide Band Gap ZnS and ZnO
Creators: name: Godlewski, M.
name: Wojcik-Glodowska, A.
name: Guziewicz, E.
name: Yatsunenko, S.
name: Zakrzewski, A.
name: Dumont, Y.
name: Chikoidze, E.
name: Phillips, M. R.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Optical properties of ZnMnO layers grown at low temperature by Atomic Layer Deposition and Metalorganic Vapor Phase Epitaxy are discussed and compared to results obtained for ZnMnS samples. Present results suggest a double valence of Mn ions in ZnO lattice. Strong absorption, with onset at about 2.1 eV, is tentatively related to Mn 2+ to 3+ photoionization. Mechanism of emission deactivation in ZnMnO is discussed and is explained by the processes following the assumed Mn 2+ to 3+ recharging.
description: 17 pages, 4 figures, 32 references
Microanatomical Analysis And Quantification Of Plasma Cell Niche Interactions In The Bone Marrow
Creators: name: Hauser-Hankeln, A.
name: Zehentmeier, S.
name: Cseresnyes, Z.
name: Holzwarth, K.
name: Stefanowski, J.
name: Reismann, D.
name: Niesner, R.
name: Radbruch, A.
Publisher: name: Diagnostic Pathology
Year: 2016

description: Introduction
Long-lived plasma cells (PCs), responsible for the production of long-term antibody titers, have been shown to survive in the bone marrow for months to years in the absence of antigen. They are supported by a special microenvironment, the PC survival niche. Various cell types have been reported to contribute to this niche by providing survival factors, e.g. CXCL12-producing reticular stromal cells. Additionally, hematopoietic cells have been shown to mediate PC survival in vivo, amongst them megakaryocytes and eosinophils, but the spatiotemporal dynamics of the various niche components in the tissue remain elusive.
Aims
The aim of our work is to analyze the cellular and molecular composition of plasma cell survival niches in the bone marrow in situ.
Methods
In order to unambiguously quantify the localization of PCs, we are analyzing bone marrow cryosections and whole mounts for PCs, stromal cells, vasculature and accessory niche cells. Additionally, we have developed a computer modeling approach which allows us to distinguish random co-localization from non-random cell positioning.

Using these approaches, we have previously shown that PCs directly contact reticular stromal cells in a non-random fashion, while 30% of PCs are found in 10 µm vicinity to eosinophils, which represent only transient contributors to the niche. We have now analyzed PC localization in relation to mineralized bone, bone marrow vasculature and hematopoietic cell types in 3 dimensions and found that PC niches are situated at large distance to sinusoids.
Results
Semi-automated 3D analyses of whole mounts allow for a comprehensive and unbiased quantification of PC localization and their possible interactions with accessory niche cells in the bone marrow. We show that the survival niche for long-lived PCs is located distant from sinusoidal blood vessels, in contrast to what has been reported for the hematopoietic stem cell niche. We are now testing ways to mobilize PCs from their niches, which should result in shifted PC localization - from vessel-distant to peri-sinusoidal spaces. We are further exploring ways to perform multiplexed histological analysis using multi-epitope ligand cartography (MELC) in the bone marrow in order to further characterize the plasma cell niche.
description: Diagnostic Pathology, Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
Condensate Fraction in Neutron Matter
Creators: name: Salasnich, Luca
Publisher: name: arXiv
Year: 2011
Subjects: subject: Nuclear Theory (nucl-th)
subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We study the Bose-Einstein condensation of fermionic pairs in the uniform neutron matter by using the concept of the off-diagonal long-range order of the two-body density matrix of the system. We derive explicit formulas for the condensate density $ρ_c$ and the condensate fraction $ρ_c/ρ$ in terms of the scaled pairing energy gap $Δ/ε_F$, where $ε_F$ is the Fermi energy. We calculate the condensate fraction $ρ_c/ρ$ as a function of the density $ρ$ by using previously obtained results for the pairing gap $Δ$. We find the maximum condensate fraction $(ρ_c/ρ)_{max}= 0.42$ at the density $ρ=5.3\cdot 10^{-4}$ fm$^{-3}$, which corresponds to the Fermi wave number $k_F= 0.25$ fm$^{-1}$.
description: 4 pages, 3 figures, to be published in Phys. Rev. C
Cosmic string evolution with a conserved charge
Creators: name: Oliveira, M. F.
name: Avgoustidis, A.
name: Martins, C. J. A. P.
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Cosmic strings with degrees of freedom beyond the standard Abrikosov-Nielsen-Olesen or Nambu-Goto strings are ubiquitous in field theory as well as in models with extra dimensions, such as string theoretic brane inflation scenarios. Here we carry out an analytic study of a simplified version of one such cosmic string model. Specifically, we extend the velocity-dependent one-scale (VOS) string evolution model to the case where there is a conserved microscopic charge on the string worldsheet. We find that whether the standard scale-invariant evolution of the network is preserved or destroyed due to the presence of the charge will crucially depend on the amount of damping and energy losses experienced by the network. This suggests, among other things, that results derived in Minkowski space (field theory) simulations may not extend to the case of an expanding universe.
description: 12 pages, 4 figures; submitted to Phys. Rev. D
The philosopher's teahouse : implementing critical pedagogy in multicultural ESL academic preparation classes
Creators: name: Royal, Wendy Ann
Publisher: name: University of British Columbia
Year: 2010

description: This study investigates how students understand and experience critical pedagogy in four culturally diverse ESL classes in Northwest University, located in a multicultural metropolis in Canada. I conducted the study in my own classes, simultaneously examining my practice and its impact on my students since teachers’ and students’ identities are entwined. Through dialogue and negotiations among teacher and students, critical language pedagogy provides an innovative approach to teaching English language skills that enables students to challenge inequality, since language is a powerful tool, often used to control, persuade or exclude. I chose a critical ethnographic case study as the most appropriate methodology for uncovering the multiple ways ESL students make meaning of a pedagogical process that has to date received little practical guidance. My study, which took place over one academic year, offers an introspective and detailed portrait of the pitfalls, practicalities and possibilities of such an approach, from the perspectives of the students and pedagogue themselves. An analysis of the classroom interactions, assignments and private interviews, reveals that students considered the pedagogy meaningful because it not only taught them practical language skills, but also connected their lives to the sociopolitical, alerted them to their rights and prepared them to become active, engaged and equal participants in their new society. My research contradicts the stereotype of the submissive, uncritical ESL student through numerous examples which illustrate how students exhibited multifaceted, agentive subjectivities, both within and outside the classroom. My findings show that a critical pedagogy enabled some of the students to identify and challenge unfair situations in their everyday lives in Canada. In addition, they reflected on and sometimes rejected their own internalized hegemonic cultural practices, and even encouraged others to consider different perspectives, thereby claiming and asserting redefined self-determined identities. One student articulated her dream of establishing a teahouse in China that reflected our critical classroom. And so I chose the Philosopher’s Teahouse as a metaphor for my classroom – a place where students discuss among equals the controversial issues of the day, learn new multicultural perspectives and in the process provoke changes in themselves.
On Providing Downlink Services in Collocated Spectrum-Sharing Macro and Femto Networks
Creators: name: Chu, Xiaoli
name: Wu, Yuhua
name: López-Pérez, David
name: Tao, Xiaofeng
Publisher: name: arXiv
Year: 2012
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences

description: Femtocells have been considered by the wireless industry as a cost-effective solution not only to improve indoor service providing, but also to unload traffic from already overburdened macro networks. Due to spectrum availability and network infrastructure considerations, a macro network may have to share spectrum with overlaid femtocells. In spectrum-sharing macro and femto networks, inter-cell interference caused by different transmission powers of macrocell base stations (MBS) and femtocell access points (FAP), in conjunction with potentially densely deployed femtocells, may create dead spots where reliable services cannot be guaranteed to either macro or femto users. In this paper, based on a thorough analysis of downlink (DL) outage probabilities (OP) of collocated spectrum-sharing orthogonal frequency division multiple access (OFDMA) based macro and femto networks, we devise a decentralized strategy for an FAP to self-regulate its transmission power level and usage of radio resources depending on its distance from the closest MBS. Simulation results show that the derived closed-form lower bounds of DL OPs are tight, and the proposed decentralized femtocell self-regulation strategy is able to guarantee reliable DL services in targeted macro and femto service areas while providing superior spatial reuse, for even a large number of spectrum-sharing femtocells deployed per cell site.
Continuous Transition between Antiferromagnetic Insulator and Paramagnetic Metal in the Pyrochlore Iridate Eu2Ir2O7
Creators: name: Ishikawa, Jun J.
name: O'Farrell, Eoin C. T.
name: Nakatsuji, Satoru
Publisher: name: arXiv
Year: 2012
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Our single crystal study of the magneto-thermal and transport properties of the pyrochlore iridate Eu2Ir2O7 reveals a continuous phase transition from a paramagnetic metal to an antiferromagnetic insulator for a sample with stoichiometry within ~1% resolution. The insulating phase has strong proximity to an antiferromagnetic semimetal, which is stabilized by several % level of the off-stoichiometry. Our observations suggest that in addition to electronic correlation and spin-orbit coupling the magnetic order is essential for opening the charge gap.
description: 6 pages, 6 figures
JUSTNORTH EU Integrated Arctic Policy Analysis Report and Recommendations. Key Challenge 4: Social Integration of Extractive Activities
Creators: name: JUSTNORTH
Publisher: name: Zenodo
Year: 2023
Subjects: Arctic economies, Economic development, Sustainable development, Values

description: Key Recommendations:
(R1) Lead the further development of a Social License to Operate framework for extractive activities in the European Arctic
(R2) Develop or promote the development of regulations on localisation effects and requirements
(R3) Develop a EU commonly accepted definition of CSR as well as legal requirements and implementation mechanisms following existing international guidelines
(R4) Influence and guide technical standards and best practices in the Arctic energy production sectors
Generalization of Hasimoto's transformation
Creators: name: Molitor, Mathieu
Publisher: name: arXiv
Year: 2012
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 76B47, 53Z05

description: In this paper, we generalize the famous Hasimoto's transformation by showing that the dynamics of a closed unidimensional vortex filament embedded in a three-dimensional manifold of constant curvature gives rise under Hasimoto's transformation to the non-linear Schrodinger equation. We also give a natural interpretation of the function ψintroduced by Hasimoto in terms of moving frames associated to a natural complex bundle over the filament.
Optimal Image Data Compression For Whole Slide Images
Creators: name: Isola, J.
Publisher: name: Diagnostic Pathology
Year: 2016

description: Introduction/ Background
Whole slide scanning is rapidly entering routine pathology laboratories. Modern scanners enable digitization of tens or even hundreds of thousands slides each year. If all WSI images are stored permanently, hundreds of terabytes image files need to be stored. It is essential to use image storage methods that preserve the scan image quality, but also keep storage costs in a reasonable level.
Aims
Today all WSIs are stored with lossy compression methods using a variety of different file formats. At the practical level it is important to find an image file format, which results in small-sized image files but retaining image quality as “visually lossless”.
Methods
In this study we compared file formats ofHamamatsu, Aperio, and 3D-Histech scanners to standard JPEG2000 and to JPEG2000 specially optimized for brightfield histology WSIs. As for image quality readout we used standardized resolution charts, and evaluation by three pathologists who ranked the images by their visual quality, when displayed on a 4K computer monitor.
Results
Differences in WSI file sizes of scanned images deemed “visually lossless” were significant. If we set Hamamatsu Nanozoomer .NDPI file size (using its default “jpeg80 quality”) as 100%, the size of a “visually lossless” JPEG2000 file was only 15-20% of that. Comparisons to Aperio and 3D-Histech files (.svs and .mrxs at their default settings) yielded similar results. A further optimization of JPEG2000 was done by treating empty slide area as uniform white-grey surface, which could be maximally compressed. Using this algorithm, JPEG2000 file sizes were only half, or even smaller, of original JPEG2000. Variation was due to the proportion of empty slide area on the scan. We anticipate that wavelet-based image compression methods, such as JPEG2000, have a significant advantage in saving storage costs of scanned whole slide image. In routine pathology laboratories applying WSI technology widely to their histology material, absolute cost savings can be substantial.
description: Diagnostic Pathology, Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
Anatomic Pathology Structured Report Under FHIR
Creators: name: Schrader, T.
name: Libramm, J.
Publisher: name: Diagnostic Pathology
Year: 2016

description: Introduction/ Background
The last version of profile for the structured report of IHE was created 2011(IHE). Many discussions took place to improve and adapt the model of described document models for clinical practice. The working group developed xxx templates to cover e.g. the main tumor locations and the requirements of various organizations about tumor documentation (e.g. CAP, national societies of pathology). The complexity of a Structured Report Document based on IHE and HL7 CDA structured increased. Up to now no German software vendor supports these templates directly. Another strategy was suggested by the German Working Group: the IHE should provide generic models usable for the other do- mains in pathology. But the general problem of missing implementation was not solved. The development of Fast Health Interoperability Resource (FHIR) began in 2012 and started a fascinating movement to prioritize the implementation over the theoretical correctness. The resources, documentation and examples are completely open and available under http://wiki.hl7. org/?title=FHIR .
Aims
In a first approach we started to “translate” the structured pathology report based on the requirements of the technical framework. The aim was to analyze the usage of FHIR resources for the Anatomic Pathology Structured Report, simplify the document structure and increase the flexibility of document handling.
Methods
At first a complete report was created based on the CDA-XML-structure and model of the IHE Anatomic Pathology Working Group. The data based on a real, but anonymous case (many thanks to Prof. Haroske, Dresden, Germany). If possible each segment of CDA report was mapped to FHIR resources. The FHIR report consisting of different internal and external document fragments (resources) was evaluated by a public available FHIR communication server (http://spark.furore. com/fhir) to validate and verify this document.
Results
A first FHIR based structured report was created and validated against a public available FHIR server (http:// spark.furore.com/fhir). FHIR allows to create different document structures for any type of document: a document only with inside resources or a document with inside and outside (linked) resources. Our example consists of resources embedded in the main document file and linked resources. The FHIR document allows a great flexibility related to the document resources as well as data files. It is possible FHIR documents as XML, JSON (JavaScript Object Notation) or RDF (Resource Description Framework). Due to these various possibilities FHIR documents can be used in a web based application context easily.
description: Diagnostic Pathology, Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
Color Calibration In Digital Pathology: The Clinical Impact Of A Novel Test Object
Creators: name: Clarke, E.
name: Revie, C.
name: Brettle, D.
name: Wilson, R.
name: Mello-Thoms, C.
name: Treanor, D.
Publisher: name: Diagnostic Pathology
Year: 2016

description: Introduction/ Background
Guidance from the Food and Drug Administration has recommended color standardization for whole slide imaging, as with all other digital systems. However there is known, unresolved and substantial variation in color between digital slide scanners. To address this issue, we created a novel color calibration test object which uniquely utilizes histochemical stains and a tissue-like substrate, affording accurate internal calibration of WSIs.
Aims
We aimed to evaluate the clinical application of the novel test object.

Objectives included: 1. Whether calibration made WSIs appear closer in color to the glass slide counterpart;

2. Whether pathologists prefer calibrated WSIs; and, 3. Whether calibration affected diagnostic confidence.
Methods
Six pathology cases that present known difficulties when viewed using a digital microscope were selected and WSIs were generated. These WSIs were calibrated using a color ICC profile created using spectral measurements from the test object. Twelve pathologists, blinded to intervention, compared calibrated and uncalibrated versions of each WSI on a medical-grade monitor. The display was color calibrated using a colorimeter which accounted for ambient lighting. Three, subjective responses were recorded on 7-point Likert scales.
Results
Calibrated WSIs were closer in appearance to the microscope in 40 of 72 trials, (56%) and were preferred in 46 of 72 trials (64%). Calibration improved diagnostic confidence (median 6.00 vs. 5.00, p=0.001). Diagnostic confidence with the calibrated slides was correlated with preference for color calibration (r=0.499; p<0.001).
description: Diagnostic Pathology, Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
Spin superfluidity and spin-orbit gauge symmetry fixing
Creators: name: Berche, Bertrand
name: Medina, Ernesto
name: López, Alexander
Publisher: name: arXiv
Year: 2012
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The Hamiltonian describing 2D electron gas, in a spin-orbit active medium, can be cast into a consistent non-Abelian gauge field theory leading to a proper definition of the spin current. The generally advocated gauge symmetric version of the theory results in current densities that are gauge covariant, a fact that poses severe concerns on their physical nature. We show that in fact the problem demands gauge fixing, leaving no room to ambiguity in the definition of physical spin currents. Gauge fixing also allows for polarized edge excitations not present in the gauge symmetric case. The scenario here is analogous to that of superconductivity gauge theory. We develop a variational formulation that accounts for the constraints between U(1) physical fields and SU(2) gauge fields and show that gauge fixing renders a physical matter and radiation currents and derive the particular consequences for the Rashba SO interaction.
description: to appear in EPL
Triple-gap superconductivity of MgB2 - (La,Sr)MnO3 composite. Which of the gaps is proximity induced?
Creators: name: Krivoruchko, V. N.
name: Tarenkov, V. Yu.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: Interplay of superconductivity and magnetism in a composite prepared of the ferromagnetic half-metallic La_0.67Sr_0.33MnO (LSMO) nanoparticles and the conventional s-wave superconductor MgB_2 has been studied. A few principal effects have been found in bulk samples. With an onset of the MgB_2 superconductivity, a spectacular drop of the sample resistance has been detected and superconductivity has been observed at temperature up to 20K. Point-contact (PC) spectroscopy has been used to measure directly the superconducting energy coupling. For small voltage, an excess current and doubling of the PC's normal state conductance have been found. Conductance peaks corresponding to three energy gaps are clearly observed. Two of these gaps we identified as enhanced Δ_π and Δ_σ gaps originating from the MgB_2; the third gap Δ_{tr} is more than three times larger than the largest MgB_2 gap. The experimental results provide unambiguous evidences for a new type of proximity effect which follows the phase coherency scenario of proximity induced superconductivity. Specifically, at low temperature, the p-wave spin-triplet condensate with pairing energy Δ_{tr} is essentially sustained in LSMO but is incapable to display long-range supercurrent response because of a phase-disordering state. The proximity coupling to MgB_2 restores the long-range phase coherency of the triplet superconducting state, which, in turn, enhances superconducting state of the MgB_2.
description: 10 pages, 6 figures
Typing, Grading, Staging - The Ultimate Goals Of Pathology Reports Modelled In HL7V3/CDA
Creators: name: Haroske, Gunter
name: Oemig, F.
Publisher: name: Diagnostic Pathology
Year: 2016

description: Introduction/ Background
Clinicians want pathologists to provide their reports fast, understandable, and useable for clinical decision making. Reports without a concise diagnostic conclusion in terms of typing, grading and staging of a disease are of low value. Therefore Anatomic Pathology Structured Reports (APSR) should have those keystones also reflected.
Aims
Instead to define very long lists with specific TNM-formulas, grading values, and tumor classifications information models have been developed which allow a flexible use in the diagnostic reporting approach and a compact programming.
Methods
Exemplarily for any diagnostic conclusion a model for TNM- as well as ICD-O-classification of malignant tumors for HL7 reporting to cancer registries in Germany was modified and completed with codes and value sets by means of Art-Decor. Additionally, an assessment score model was developed applicable for a wide variety of grading systems used in neoplastic as well as non-neoplastic diseases. ART-DECOR is a toolkit allowing for maintaining information models designated to data exchange facilitating communication standards.
Results
An information model for TNM as well as ICD-O-classification of malignant tumors for reporting to cancer registries in Germany supporting the required data set was developed and filled with appropriate codes and value sets by means of ART-DECOR. The IHE APSR Trial implementation with its templates and value sets was mirrored in ART-DECOR and completed by templates for TNM-, ICD-O-3 and Assessment-Scores, based on the German HL7 Oncology Reporting requirements. A model based approach for structured reporting of complex problems is the preferred approach instead of exhaustive lists of permutated single values.

Conclusion:
The developed templates are to be used as entries in the Diagnostic Conclusion section of IHE APSR allowing for a structured data exchange so that automatic clinical decision support is maximized.
description: Diagnostic Pathology, Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
Applying Software-Based Side-Channels to Hardware Vulnerabilities
Creators: name: Kwong, Andrew
Publisher: name: My University
Year: 2023
Subjects: subject: computer security
subject: hardware security
subject: side channels
subject: applied cryptography
subject: rowhammer
subject: Computer Science
subject: Engineering

description: The discrepancy between the abstract model used to reason about the security of computer systems and their actual hardware implementation has led to a myriad of security issues. Security researchers have demonstrated how to use shared microarchitectural components, speculative execution attacks, and even hardware based memory integrity attacks to extract sensitive information across nearly all hardware backed security domains. These "side-channel" attacks have violated boundaries necessary for the isolation and security of virtual machines, browser tabs, kernel memory, and even Trusted Execution Environments, making it clear that side-channels present a formidable challenge to safely multiplexing hardware. This thesis explores these side-channel attacks at the intersection of software, hardware, and applied cryptography. By leveraging shared microarchitectural components, memory integrity vulnerabilities, and even physical effects, this thesis demonstrates new classes of attacks in which software-level attackers abuse vulnerabilities present in hardware. More specifically, this thesis investigates the threat of side-channels to secure execution environments (e.g. Intel's SGX), cryptographic schemes (both standardized by NIST and candidates for future post quantum crypto schemes), web browsers, micro architectural systems, and hardware, such as memory modules and storage devices. By surveying the landscape of potential side-channel threats and discovering new classes of attacks, this thesis contributes novel insights into adversarial capabilities and how to develop effective mitigations. Thus, the works contained in this thesis aim to serve as stepping stones towards securing the next generation of computers against these side-channel attacks in a principled manner.
A Geometric Method to Investigate Prolongation Structures for Differential Systems With Applications to Integrable Systems
Creators: name: Bracken, Paul
Publisher: name: arXiv
Year: 2011
Subjects: subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 35A30, 32A25, 35C05

description: A type of prolongation structure for several general systems is discussed. They are based on a set of one-forms in which the underlying structure group of the integrability condition corresponds to the Lie-algebra of SL (2,R), O(3), or SU(3). Each will be considered in turn and the latter two systems represent larger 3by3 cases. This geometric approach is applied to all three of these systems to obatin prolongation structures explicitly. In both 3by3 cases the prolongation structure is reduced to the situation of three smaller 2by2 problems. Many types of conservation laws can be obtained at different stages of the development, and at the end, a single result is developed to show how this can be done.
description: 16
Pathologies and complicities : high school and the identities of disaffected South Asian "Brown boys"
Creators: name: Sayani, Anish
Publisher: name: University of British Columbia
Year: 2010

description: This study is a response to a growing disquietude in many schools in the Lower Mainland of British Columbia that there is “something wrong” with South Asian boys. During the past twenty years, approximately 100 South Asian young men have been killed as a result of criminal violence (Ministry Report, 2006), with these murder numbers steadily increasing each month. Reports from think-tanks and informal conversations and surveys with teachers and administrators in schools with high populations of South Asian students all support disturbing levels of academic failure and disaffection. Since there are no reliable data or very few published studies about the school experiences and achievement of South Asian students, educators do not understand the magnitude of this problem. Using a three-dimensional narrative methodology (Clandinin & Connelly, 2000), this study, therefore, investigated how the schooling experiences of disaffected South Asian male students may exacerbate or alleviate the problem of disaffection. Specifically, it sought to understand South Asian male students' school experiences (including experiences of inclusion, marginalization, disaffection, success, and failure); and how educators and educational leaders understand and relate to their South Asian students. Eight months of ethnographic fieldwork at a mid-size secondary school in a Vancouver suburb and sixty-one interviews conducted with students, educators, and educational leaders generated several key findings. The study showed that the educators and educational leaders at this school pathologized the lived experiences of the “Brown boys”; engaged in deficit theorizing discourses and practices; failed to mobilize the identities of the “Brown boys” in the classrooms; and excluded the “Brown boys” and community members from authorizing their perspectives to inform disciplinary and other school practice-shaping decisions. This study also showed that the Brown boys were complicit in the pathologizing of their own identities, which among other detrimental effects, exacerbated their disaffection at school. Through narratives and first hand voices of the participants, this study attempts to provide all educators and educational leaders new ways to understand the schooling experiences of disaffected South Asian male students and possibly even to mitigate the schooling factors that may exacerbate the disaffection of all minoritized students.
The Effects Of Digital Workflow Support And Workflow Control For The Performance Of Routine Pathology
Creators: name: Haroske, Gunter
name: Mörz, M.
Publisher: name: Diagnostic Pathology
Year: 2016

description: Introduction/ Background
Although the scanning technology for microscopic slides has been known for more than 15 years, its practical use in daily routine is still on the very beginning. Fast and reliable scanners enabled their increasing use in teaching, but not yet in consultation and primary diagnostics. So far the scanning is not handled as a process in the pathology laboratory by most of the pathology systems, leading to an interrupted workflow with delays and additional expenses. The requirement profiles for slide scanners can only be formulated with respect to their workflow integration.
Aims
The effects of different degrees of workflow digitalization have been studied as to analyze the sources of possible benefits of digital pathology as well as to identify the bottlenecks and inconsistencies in the workflow control in a routine pathology laboratory. The adherence to existing IHE Technical Frameworks has been evaluated, too.
Methods
Performance statistics of routine pathology were evaluated in different phases of digital workflow control over more than 10 years in a medium-sized institute of pathology.

Three phases were defined:
• Uncontrolled, but digitally supported workflow with digital dictation, digital macrophotography, digital microphotograpy at few pathology Workstations, and a “classic” pathology software system;
• Digital workflow control including digital dictation and digital photography;
• In a pilot study at the end of the evaluation period the additional benefits of slide scanning were estimated.
Results
In the period between 2006 and 2015 a decrease of turnaround-time of roughly 40% was seen. Alone the effects of a (sub)total digital workflow control contributed about half of that effect. The implementation of slide-scanning did not add further acceleration so far, but enabled some additional functionality for improving quantitative reporting. This was achieved without an explicit commitment of the pathology software to standards in workflow control and with still leaving a few laboratory processes out of the control. Milestones and key elements of workflow management are reported in detail.

Conclusion:
All processes both in the laboratory and in the diagnostics have to be checked (and changed, if necessary) for being fit in a streamlined pathology workflow. The implementation of scanners into the routine diagnostics will enforce those essential developments leading to increased productivity and quality.
description: Diagnostic Pathology, Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
Observational Constraints of Modified Chaplygin Gas in Loop Quantum Cosmology
Creators: name: Chakraborty, Shuvendu
name: Debnath, Ujjal
name: Ranjit, Chayan
Publisher: name: arXiv
Year: 2012
Subjects: subject: General Physics (physics.gen-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We have considered the FRW universe in loop quantum cosmology (LQC) model filled with the dark matter (perfect fluid with negligible pressure) and the modified Chaplygin gas (MCG) type dark energy. We present the Hubble parameter in terms of the observable parameters $Ω_{m0}$, $Ω_{x0}$ and $H_{0}$ with the redshift $z$ and the other parameters like $A$, $B$, $C$ and $α$. From Stern data set (12 points), we have obtained the bounds of the arbitrary parameters by minimizing the $χ^{2}$ test. The best-fit values of the parameters are obtained by 66%, 90% and 99% confidence levels. Next due to joint analysis with BAO and CMB observations, we have also obtained the bounds of the parameters ($B,C$) by fixing some other parameters $α$ and $A$. From the best fit of distance modulus $μ(z)$ for our theoretical MCG model in LQC, we concluded that our model is in agreement with the union2 sample data.
description: 14 pages, 10 figures, Accepted in EPJC. arXiv admin note: text overlap with arXiv:astro-ph/0311622 by other authors
A magnetar-like event from LS I +61 303 and its nature as a gamma-ray binary
Creators: name: Torres, Diego F.
name: Rea, Nanda
name: Esposito, Paolo
name: Li, Jian
name: Chen, Yupeng
name: Zhang, Shu
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We report on the Swift-BAT detection of a short burst from the direction of the TeV binary LS I +61 303, resembling those generally labelled as magnetar-like. We show that it is likely that the short burst was indeed originating from LS I +61 303 (although we cannot totally exclude the improbable presence of a far-away line-of-sight magnetar) and that it is a different phenomena with respect to the previously-observed ks-long flares from this system. Accepting as a hypothesis that LS I +61 303 is the first magnetar detected in a binary system, we study which are the implications. We find that a magnetar-composed LS I +61 303-system would most likely be (i.e., for usual magnetar parameters and mass-loss rate) subject to a flip-flop behavior, from a rotational powered regime (in apastron) to a propeller regime (in periastron) along each of the LS I +61 303, eccentric orbital motion. We prove that whereas near apastron an inter-wind shock can lead to the normally observed LS I +61 303behavior, with TeV emission, the periastron propeller is expected to efficiently accelerate particles only to sub-TeV energies. This flip-flop scenario would explain the system's behavior where a recurrent TeV emission was seen appearing near apastron only, the anti-correlation of GeV and TeV emission, and the long-term TeV variability (which seems correlated to LS I +61 303's super-orbital period), including the appearance of a low TeV-state. Finally, we qualitatively put the multi-wavelength phenomenology in context of our proposed model, and make some predictions for further testing.
description: The Astrophysical Journal, in press
Superfield description of 10D SYM theory with magnetized extra dimensions
Creators: name: Abe, Hiroyuki
name: Kobayashi, Tatsuo
name: Ohki, Hiroshi
name: Sumita, Keigo
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We present a four-dimensional (4D) ${\cal N}=1$ superfield description of supersymmetric Yang-Mills (SYM) theory in ten-dimensional (10D) spacetime with certain magnetic fluxes in compactified extra dimensions preserving partial ${\cal N}=1$ supersymmetry out of full ${\cal N}=4$. We derive a 4D effective action in ${\cal N}=1$ superspace directly from the 10D superfield action via dimensional reduction, and identify its dependence on dilaton and geometric moduli superfields. A concrete model for three generations of quark and lepton superfields are also shown. Our formulation would be useful for building various phenomenological models based on magnetized SYM theories or D-branes.
description: 19pages, no figures
Efficient mm-Wave and THz Circuits and Systems
Creators: name: Khalifa, Zainulabideen
Publisher: name: My University
Year: 2023
Subjects: subject: mm-Wave and THz Circuits
subject: Super-Harmonic Self-Injection Locking
subject: Injection-locking
subject: parametric process
subject: Travelling-Wave amplifier
subject: Electrical Engineering
subject: Engineering

description: Millimeter-wave and Terahertz circuits are gaining more attraction in communication and sensing applications. This is mainly due to the advancement in IC fabrication technology which allows for higher values for $f_{max}$ and thus higher operating frequencies. Nevertheless, operating near that limit is very challenging because of the low activity of the transistors and high losses in passives due to skin effect. This will require the use of larger transistors and more power consumption. Unfortunately, increasing the size of the transistor will limit the operating frequency. Harmonics generated from the non-linearity will leak part of the energy if not used. This is applicable to oscillators and amplifiers as well. Multistages are needed due to the low gain in amplifiers which when properly conditioned for high activity, act as resonators limiting the bandwidth. This work addresses these limitations by applying several techniques to oscillators and amplifiers. The first technique uses super-harmonic self-injection locking in oscillators to utilize the unused harmonics enhancing the performance at the fundamental frequency. More than 10dB improvement in phase noise was measured for an oscillator with fundamental frequency extraction at 105GHz and another with harmonic extraction at 210GHz. An application of this dynamics between the oscillator and its harmonics is IQ generation. Two IQ oscillators have been designed, one at 105GHz and another at 220GHz where the 2$^{nd}$ harmonic is above $f_{max}$ of the technology. The second technique uses the properties of periodic structures to allow for multiple cascading of amplifiers with no limit on the number of stages and thus enables the use of minimum-size transistors. The circuit can amplify up to the unity-current gain frequency $f_T$. The amplifier designed has the highest gain at 260GHz and it has been constructed using 200 transistors.
The Einstein-Hilbert Action Horizons and Connections with Thermodynamics
Creators: name: Bracken, Paul
Publisher: name: arXiv
Year: 2011
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 0.40.Cv, 04.20.Fy, 04.60.Bc

description: It is shown that the Einstein-Hilbert action can be constructed by minimizing free energy. The entropy used to determine the free energy is determined on the horizon of a black hole. Some further considerations with regard to generalizations of these ideas to other situations of physical importance are presented as well.
description: 13
THE ECONOMY - WIDE IMPACT OF CONTINENTAL FREE TRADE AREA (CFTA) ON ETHIOPIA: A RECURSIVE DYNAMIC COMPUTABLE GENERAL EQUILIBRIUM APPROACH
Creators: name: BEGIDU HAILEMESKEL
Publisher: name: Zenodo
Year: 2016

description: This study examines the economy wide impact of CFTA on Ethiopia. The analysis is made based

on Ethiopian social accounting matrix (SAM) of 2009/10 constructed by EDRI. The study has

utilized a recursive dynamic CGE model. The model is simulated for an import tariff reduction

on different sectors using three different scenarios. The scenarios involve joining CFTA at one

time, in 2016, or through phases, a 25% tariff removal each year from 2016-2019. Another

scenario involves excluding strategic sectors from the CFTA.

The impact of CFTA result shows, Government revenue also decreases as tariff revenue is an

important source of revenue for the Ethiopian government. GDP and trade balance are, however,

positively affected. The increase in GDP might be associated to the increase in disaggregated

production