A Bioinformatics Module for Use in an Introductory Biology Laboratory

Since biomedical science has become increasingly data-intensive, acquisition of computational and quantitative skills by science students has become more important. For non-science students, an introduction to biomedical databases and their applications promotes the development of a scientifically literate population. Because typical college introductory biology laboratories do not include experiences of this type, we present a bioinformatics module that can easily be included in a 90-minute session of a biology course for both majors and non-majors. Students completing this computational, inquiry-based module observed the value of computer-assisted analysis. The module gave students an understanding of how to read files in a biological database (GenBank) and how to use a software tool (BLAST) to mine the database.

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FDG PET/CT in cancer therapy monitoring

Nuklearmedizin ◽

10.3413/nukmed-0314-10-05 ◽

2011 ◽

Vol 50 (02) ◽

pp. 83-92 ◽

Cited By ~ 2

Author(s):

S. Renisch ◽

R. Opfer ◽

T. Derlin ◽

R. Buchert ◽

I. C. Carlsen ◽

...

Keyword(s):

Quantitative Analysis ◽

Cancer Therapy ◽

Fdg Pet ◽

Visual Analysis ◽

Therapy Monitoring ◽

Software Tool ◽

Computer Assisted ◽

Pet Ct ◽

Fdg Pet Ct ◽

Assisted Analysis

SummaryObjectives: We developed and tested a software tool for computer-assisted analysis of FDG-PET/CT in cancer therapy monitoring. The tool provides automatic semi-quantitative analysis of a baseline scan together with up to two follow-up scans (standardized uptake values, glycolytic volume). The tool also supports visual analysis by local spatial registration which allows display of tumor lesions with the same orientation in all scans. The tool’s stability and accuracy was tested at typical everyday image quality. Patients, methods: Ten unselected cancer patients in whom three FDG PET/CT scans had been performed were included. A total of 18 lesions were analyzed. Results: Automatic lesion tracking worked properly in all lesions but one. In this lesion local coregistration had to be adjusted manually tuwhich, however, is easily performed with the tool. Semi-automatic lesion segmentation and fully automatic semi-quantitative analysis worked properly in all cases. Computer-assisted analysis was significantly less time consuming than manual analysis. Conclusions: The novel software tool appears useful for analysis of FDGPET/ CT in cancer therapy monitoring in clinical routine patient care.

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Integrating Active Learning & Quantitative Skills into Undergraduate Introductory Biology Curricula

The American Biology Teacher ◽

10.1525/abt.2011.73.8.6 ◽

2011 ◽

Vol 73 (8) ◽

pp. 454-461 ◽

Cited By ~ 7

Author(s):

Jessica Goldstein ◽

Dan F. B. Flynn

Keyword(s):

Data Analysis ◽

Statistical Analysis ◽

Quantitative Data ◽

Thinking Skills ◽

Introductory Biology ◽

Quantitative Skills ◽

Quantitative Data Analysis ◽

Testing Data ◽

Core Components ◽

Biology Laboratory

Analytical and quantitative thinking skills are core components of science but can be challenging to teach in introductory biology courses. To address this issue, modest curriculum modifications, including methods of hypothesis testing, data collection, and statistical analysis, were introduced into existing exercises in an introductory biology laboratory course. After completing the updated course, students demonstrated improved ability to understand and interpret statistical analyses. Furthermore, students were more likely to understand that hypothesis development and quantitative data analysis are important parts of biology. This study indicates that small changes to laboratory curricula can effect important changes in student learning and attitudes.

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Computer-Assisted Analysis of Multi-Color Confocal Microscopic Datasets: Automated Light Microscopic Discrimination of Synaptic Relationships

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100163885 ◽

1996 ◽

Vol 54 ◽

pp. 284-285

Author(s):

M Wessendorf ◽

A Beuning ◽

D Cameron ◽

J Williams ◽

C Knox

Keyword(s):

Nerve Fibers ◽

Confocal Scanning Laser Microscopy ◽

Computer Assisted ◽

Nerve Terminals ◽

Neuronal Somata ◽

Scanning Laser Microscopy ◽

Confocal Scanning ◽

Entire Cell ◽

Confocal Scanning Laser ◽

Assisted Analysis

Multi-color confocal scanning-laser microscopy (CSLM) allows examination of the relationships between neuronal somata and the nerve fibers surrounding them at sub-micron resolution in x,y, and z. Given these properties, it should be possible to use multi-color CSLM to identify relationships that might be synapses and eliminate those that are clearly too distant to be synapses. In previous studies of this type, pairs of images (e.g., red and green images for tissue stained with rhodamine and fluorescein) have been merged and examined for nerve terminals that appose a stained cell (see, for instance, Mason et al.). The above method suffers from two disadvantages, though. First, although it is possible to recognize appositions in which the varicosity abuts the cell in the x or y axes, it is more difficult to recognize them if the apposition is oriented at all in the z-axis—e.g., if the varicosity lies above or below the neuron rather than next to it. Second, using this method to identify potential appositions over an entire cell is time-consuming and tedious.

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Computer Assisted Analysis and Modelling of Structured Problems

10.21236/ada222991 ◽

1990 ◽

Author(s):

E. Hadjiconstantinou ◽

G. Mitra

Keyword(s):

Computer Assisted ◽

Structured Problems ◽

Assisted Analysis

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Darwin Puzzled? A Computer-assisted Analysis of Language in the Origin of Species

Topoi ◽

10.1007/s11245-021-09744-3 ◽

2021 ◽

Author(s):

Bárbara Jiménez-Pazos

Keyword(s):

Computer Assisted ◽

Origin Of Species ◽

Assisted Analysis

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Syllabification of the Divine Comedy

Journal on Computing and Cultural Heritage ◽

10.1145/3459011 ◽

2021 ◽

Vol 14 (3) ◽

pp. 1-26

Author(s):

Andrea Asperti ◽

Stefano Dal Bianco

Keyword(s):

Text Processing ◽

Solution Space ◽

Generative Models ◽

Divine Comedy ◽

Point Of View ◽

Computer Assisted ◽

Wide Range ◽

The Divine Comedy ◽

Left And Right ◽

Assisted Analysis

We provide a syllabification algorithm for the Divine Comedy using techniques from probabilistic and constraint programming. We particularly focus on the synalephe , addressed in terms of the "propensity" of a word to take part in a synalephe with adjacent words. We jointly provide an online vocabulary containing, for each word, information about its syllabification, the location of the tonic accent, and the aforementioned synalephe propensity, on the left and right sides. The algorithm is intrinsically nondeterministic, producing different possible syllabifications for each verse, with different likelihoods; metric constraints relative to accents on the 10th, 4th, and 6th syllables are used to further reduce the solution space. The most likely syllabification is hence returned as output. We believe that this work could be a major milestone for a lot of different investigations. From the point of view of digital humanities it opens new perspectives on computer-assisted analysis of digital sources, comprising automated detection of anomalous and problematic cases, metric clustering of verses and their categorization, or more foundational investigations addressing, e.g., the phonetic roles of consonants and vowels. From the point of view of text processing and deep learning, information about syllabification and the location of accents opens a wide range of exciting perspectives, from the possibility of automatic learning syllabification of words and verses to the improvement of generative models, aware of metric issues, and more respectful of the expected musicality.

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Chiming In: A Computer-Assisted Analysis of Popular Musicians’ Political Engagement on Twitter

Social Media + Society ◽

10.1177/20563051211019013 ◽

2021 ◽

Vol 7 (2) ◽

pp. 205630512110190

Author(s):

Josephine Lukito ◽

Luis Loya ◽

Carlos Dávalos ◽

Jianing Li ◽

Chau Tong ◽

...

Keyword(s):

Case Studies ◽

Hip Hop ◽

Political Engagement ◽

Future Research ◽

Computer Assisted ◽

Christian Music ◽

Political Issues ◽

Qualitative Case Studies ◽

Systematic Examination ◽

Assisted Analysis

While music as an artistic form is well studied, the individuals behind the art receive relatively less attention. In this article, we provide evidence of celebrity advocacy with a systematic examination of musicians’ political engagement on Twitter. This study estimates the extent to which musicians use Twitter for political purposes, with particular attention to whether such engagement varies across music genres. Through a computational-assisted analysis of 2,286,434 tweets, we group 881 musicians into three categories of political engagement on Twitter: not engaged (comprising the majority of artists), circumstantial engagement, and active political engagement. We examine the latter categories in detail with two qualitative case studies. The findings indicate that musicians from different genres have distinct patterns of political engagement. The Christian music genre shows the most engagement as a whole, especially in philanthropy. On the contrary, the most active accounts are rock and hip-hop artists, some of whom discuss political issues and call for mobilization. We conclude with suggestions for future research.

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