A Case Study of 15th-Century Gregorian Chant Leaves

University of Pittsburgh’s Hillman Library Special Collections Department holds 29 Gregorian chant leaves ranging from the 12th to 17th centuries from multiple locations in Western Europe. One set of six leaves, dating from the 15th century Netherlands, is particularly interesting in that many of the originally scribed neumes, and occasionally the corresponding text, were erased and replaced with newly scribed neumes and text. My goals for this project were: 1) to analyze the musical differences between the pre-edited and post-edited chants, and 2) to research the socio-cultural atmosphere of the Catholic church in 15th century Netherlands to determine what compelled the scribe to make these edits. In order to accomplish these tasks, I transcribed each of the pre-edited and post-edited versions of the chants using Sibelius notation software and subsequently analyzed the chants musically, as well as consulted multiple digital and print sources on subjects ranging from general church practices during the 15th century to specific performance practices in the Netherlands. This project is meant to serve as a case study that will augment the growing knowledge base of Gregorian chant

Hibernacula Microclimate and White-nose Syndrome Susceptibility in the Little Brown Myotis (Myotis lucifugus)

The objective of this project was to determine the relationship between hibernacula microclimate and White-nose Syndrome (WNS), an emerging infectious disease in bats. Microclimate was examined on a species scale and at the level of the individual bat to determine if there was a difference in microclimate preference between healthy and WNS-affected little brown myotis (Myotis lucifugus) and to determine the role of microclimate in disease progression. There is anecdotal evidence that colder, drier hibernacula are less affected by WNS. This was tested by placing rugged temperature and humidity dataloggers in field sites throughout the eastern USA, experimentally determining the response to microclimate differences in captive bats, and testing microclimate roosting preference. This study found that microclimate significantly differed from the entrance of a hibernaculum versus where bats traditionally roost. It also found hibernaculum temperature and sex had significant impacts on survival in WNS-affected bats. Male bats with WNS had increased survivability over WNS-affected female bats and WNS bats housed below the ideal growth range of the fungus that causes WNS, Geomyces destructans, had increased survival over those housed at warmer temperatures. The results from this study are immediately applicable to (1) predict which hibernacula are more likely to be infected next winter, (2) further our understanding of WNS, and (3) determine if direct mitigation strategies, such as altering the microclimate of mines, will be effective ways to combat the spread of the fungus

Evidence for sinusoidal phase modulation in small self-trapped filaments

Evidence is presented indicating that, in some cases at least, a sinusoidal phase modulation is responsible for the spectral broadening Observed in trapped filaments of laser (and Raman) light. This kind of modulation has been suggested recently by Cheung et al

A how-to guide for code-sharing in biology

Computational biology continues to spread into new fields, becoming more accessible to researchers trained in the wet lab who are eager to take advantage of growing datasets, falling costs, and novel assays that present new opportunities for discovery even outside of the much-discussed developments in artificial intelligence. However, guidance for implementing these techniques is much easier to find than guidance for reporting their use, leaving biologists to guess which details and files are relevant. Here, we provide a set of recommendations for sharing code, with an eye toward guiding those who are comparatively new to applying open science principles to their computational work. Additionally, we review existing literature on the topic, summarize the most common tips, and evaluate the code-sharing policies of the most influential journals in biology, which occasionally encourage code-sharing but seldom require it. Taken together, we provide a user manual for biologists who seek to follow code-sharing best practices but are unsure where to start.Comment: 19 pages, 1 figure; for supporting data see https://doi.org/10.5281/zenodo.1045994

Eine algebraische Spezifikation des Software-Produkts INTAKT

A worked example of a complete specification and abstract implementation of a sizable software system is given in terms of a predecessor of the software specification language ASPIK. The specified software system INTAKT has been developed by Siemens AG (München). INTAKT is an interactive system for analyzing and upgrading programs written in a variety of programming languages. This paper only provides a specification and abstract implementation for part of the analysis support in INTAKT. The remainder is specified in a companion paper by W. Schrupp and J. Tamme. (Int. Bericht 84/83)Ein ausgearbeitetes Beispiel einer vollständigen Spezifikation und abstrakten Implementierung eines unfangreichen Softwaresystems wird angegeben, das in einem Vorläufer der Softwarespezifikationssprache ASPIK beschrieben ist. Das spezifizierte Softwaresystem INTAKT wurde bei der Siemens AG (München) entwickelt. INTAKT ist ein Dialogsystem zur Analyse und Aufbereitung von Programmen verschiedener Programmiersprachen. Diese Arbeit beschreibt Spezifikation und abstrakte Implementierung eines Teils der Analyseunterstützung in INTAKT. Der restliche Teil ist spezifiziert in der Arbeit von W. Schrupp und J. Tamme. (Int. Bericht 84/83

Examining Graduate Student Perspectives and Use of Web Resources and Tools for Academic Support

This mixed methods study was conducted to examine University of Central Florida (UCF) graduate student use and perceptions of usefulness of Web resources and tools that may support academic work, research, and academic goals. The frameworks of Connectivism and Personal Learning Networks (PLN) were used as a foundation to support the importance of Web resources and tools in relation to student learning, academic support, and progression. Qualitative and quantitative data was collected from active UCF graduate students using an electronic survey, with 998 participants completing the survey. Data analysis was conducted using an ANOVA one-way test to compare program mode types and the frequency of use with Web resources and tools. Participants that reported enrollment in face-to-face programs identified a higher frequency of use for Web resources and tools than participants in online programs. File-sharing tools and telecommunications applications were reported as used most frequently among the resources and tools identified on the survey, and these were also found as Web resources and tools perceived as the most useful. The examination of qualitative data showed that Zoom and Google Docs were reported most often by the participants as beneficial for use, which is consistent with the frequency of use and perceptions of usefulness data. The qualitative data also showed that participants are using the Web resources and tools the most to support course work, but they are also using these tools and resources for collaboration, research support, and cloud support. Further research would need to be conducted to help understand the factors that may contribute to the statistical difference from these groups. Overall, the reported data supports that the graduate student study participants were using several collaborative tools regularly and they were also identified as useful in support of academic course work, research, and academic goals. Further research could help to provide additional understanding related to the factors behind reported usage frequency and how Web resources and tools are identified for use

The biophysical nature of cells: Potential cell behaviours revealed by analytical and computational studies of cell surface mechanics

Background The biophysical characteristics of cells determine their shape in isolation and when packed within tissues. Cells can form regular or irregular epithelial structures, round up and form clusters, or deform and attach to substrates. The acquired shape of cells and tissues is a consequence of (i) internal cytoskeletal processes, such as actin polymerisation and cortical myosin contraction, (ii) adhesion molecules within the cell membrane that interact with substrates and neighbouring cells, and (iii) processes that regulate cell volume. Although these processes seem relatively simple, when combined they unleash a rich variety of cellular behaviour that is not readily understandable outside a theoretical framework. Methods We perform a mathematical analysis of a commonly used class of model formalisms that describe cell surface mechanics using an energy-based approach. Predictions are then confirmed through comparison with the computational outcomes of a Vertex model and 2D and 3D simulations of the Cellular Potts model. Results The analytical study reveals the complete possible spectrum of single cell behaviour and tissue packing in both 2D and 3D, by taking the typical core elements of cell surface mechanics into account: adhesion, cortical tension and volume conservation. We show that from an energy-based description, forces and tensions can be derived, as well as the prediction of cell behaviour and tissue packing, providing an intuitive and biologically relevant mapping between modelling parameters and experiments. Conclusions The quantitative cellular behaviours and biological insights agree between the analytical study and the diverse computational model formalisms, including the Cellular Potts model. This illustrates the generality of energy-based approaches for cell surface mechanics and highlights how meaningful and quantitative comparisons between models can be established. Moreover, the mathematical analysis reveals direct links between known biophysical properties and specific parameter settings within the Cellular Potts model