Using conceptual metaphor and functional grammar to explore how language used in physics affects student learning

This paper introduces a theory about the role of language in learning physics. The theory is developed in the context of physics students' and physicists' talking and writing about the subject of quantum mechanics. We found that physicists' language encodes different varieties of analogical models through the use of grammar and conceptual metaphor. We hypothesize that students categorize concepts into ontological categories based on the grammatical structure of physicists' language. We also hypothesize that students over-extend and misapply conceptual metaphors in physicists' speech and writing. Using our theory, we will show how, in some cases, we can explain student difficulties in quantum mechanics as difficulties with language.Comment: Accepted for publication in Phys. Rev. ST:PE

Researching and Designing for the Orchestration of Learning in the CSCL Classroom

Designing tools for teachers to orchestrate computer supported collaborative learning activities in their classrooms requires that attention be paid to the range of roles and activities a teacher must take throughout the process. Drawing on the Implementing Collaborative Learning in the Classroom framework proposed by Kaendler, Wiedmann, Rummel and Spada (2014), the contributors to this symposium will speak to the way their designs address the various parts of this framework, allowing us to draw conclusions about what has been successful for different parts of this process, and identifying future directions for development and research

Strange Messages: Chemical and Thermal Freeze-out in Nuclear Collisions

Thermal models are commonly used to interpret heavy-ion data on particle yields and spectra and to extract the conditions of chemical and thermal freeze-out in heavy-ion collisions. I discuss the usefulness and limitations of such thermal model analyses and review the experimental and theoretical evidence for thermalization in nuclear collisions. The crucial role of correlating strangeness production data with single particle spectra and two-particle correlation measurements is pointed out. A consistent dynamical picture for the heavy-ion data from the CERN SPS involves an initial prehadronic stage with deconfined color and with an appreciable isotropic pressure component. This requires an early onset of thermalization.Comment: 15 pages, 2 figures, talk given at Strange Quark Matter '98, Padova, Italy, 20-24 July 1998, to be published in J. Phys. G 25; final version with updated reference

Chemical equilibration of strangeness

Thermal models are very useful in the understanding of particle production in general and especially in the case of strangeness. We summarize the assumptions which go into a thermal model calculation and which differ in the application of various groups. We compare the different results to each other. Using our own calculation we discuss the validity of the thermal model and the amount of strangeness equilibration at CERN-SPS energies. Finally the implications of the thermal analysis on the reaction dynamics are discussed.Comment: 23 pages, LaTeX (figures included); Talk given at the Int. Symposium on Strangeness in Quark Matter 1997, Santorini (Greece), April 199

Quantum radiation in external background fields

A canonical formalism is presented which allows for investigations of quantum radiation induced by localized, smooth disturbances of classical background fields by means of a perturbation theory approach. For massless, non-selfinteracting quantum fields at zero temperature we demonstrate that the low-energy part of the spectrum of created particles exhibits a non-thermal character. Applied to QED in varying dielectrics the response theory approach facilitates to study two distinct processes contributing to the production of photons: the squeezing effect due to space-time varying properties of the medium and of the velocity effect due to its motion. The generalization of this approach to finite temperatures as well as the relation to sonoluminescence is indicated.Comment: 20 page

PRIDE: Quality control in a proteomics data repository

The PRoteomics IDEntifications (PRIDE) database is a large public proteomics data repository, containing over 270 million mass spectra (by November 2011). PRIDE is an archival database, providing the proteomics data supporting specific scientific publications in a computationally accessible manner. While PRIDE faces rapid increases in data deposition size as well as number of depositions, the major challenge is to ensure a high quality of data depositions in the context of highly diverse proteomics work flows and data representations. Here, we describe the PRIDE curation pipeline and its practical application in quality control of complex data depositions

Histological assessment of paxgene tissue fixation and stabilization reagents

Within SPIDIA, an EC FP7 project aimed to improve pre analytic procedures, the PAXgene Tissue System (PAXgene), was designed to improve tissue quality for parallel molecular and morphological analysis. Within the SPIDIA project promising results were found in both genomic and proteomic experiments with PAXgene-fixed and paraffin embedded tissue derived biomolecules. But, for this technology to be accepted for use in both clinical and basic research, it is essential that its adequacy for preserving morphology and antigenicity is validated relative to formalin fixation. It is our aim to assess the suitability of PAXgene tissue fixation for (immuno)histological methods. Normal human tissue specimens (n = 70) were collected and divided into equal parts for fixation either with formalin or PAXgene. Sections of the obtained paraffin-embedded tissue were cut and stained. Morphological aspects of PAXgene-fixed tissue were described and also scored relative to formalin-fixed tissue. Performance of PAXgene-fixed tissue in immunohistochemical and in situ hybridization assays was also assessed relative to the corresponding formalin-fixed tissues. Morphology of PAXgene-fixed paraffin embedded tissue was well preserved and deemed adequate for diagnostics in most cases. Some antigens in PAXgene-fixed and paraffin embedded sections were detectable without the need for antigen retrieval, while others were detected using standard, formalin fixation based, immunohistochemistry protocols. Comparable results were obtained with in situ hybridization and histochemical stains. Basically all assessed histological techniques were found to be applicable to PAXgene-fixed and paraffin embedded tissue. In general results obtained with PAXgene-fixed tissue are comparable to those of formalin-fixed tissue. Compromises made in morphology can be called minor compared to the advantages in the molecular pathology possibilities

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types