scholarly journals Bioinformatics and the Undergraduate Curriculum

2010 ◽  
Vol 9 (3) ◽  
pp. 172-174 ◽  
Author(s):  
Mark Maloney ◽  
Jeffrey Parker ◽  
Mark LeBlanc ◽  
Craig T. Woodard ◽  
Mary Glackin ◽  
...  
Keyword(s):  
Biological Sciences ◽  
Undergraduate Students ◽  
High Throughput ◽  
Undergraduate Curriculum ◽  
Colleges And Universities ◽  
Support Staff ◽  
Faculty Members ◽  
Data Generation ◽  
Rapid Rise ◽  
The Face

Recent advances involving high-throughput techniques for data generation and analysis have made familiarity with basic bioinformatics concepts and programs a necessity in the biological sciences. Undergraduate students increasingly need training in methods related to finding and retrieving information stored in vast databases. The rapid rise of bioinformatics as a new discipline has challenged many colleges and universities to keep current with their curricula, often in the face of static or dwindling resources. On the plus side, many bioinformatics modules and related databases and software programs are free and accessible online, and interdisciplinary partnerships between existing faculty members and their support staff have proved advantageous in such efforts. We present examples of strategies and methods that have been successfully used to incorporate bioinformatics content into undergraduate curricula.

scholarly journals Engaging Actively with Issues in the Responsible Conduct of Science: Lessons from International Efforts Are Relevant for Undergraduate Education in the United States

2013 ◽  
Vol 12 (4) ◽  
pp. 596-603 ◽  
Author(s):  
John D. Clements ◽  
Nancy D. Connell ◽  
Clarissa Dirks ◽  
Mohamed El-Faham ◽  
Alastair Hay ◽  
...  
Keyword(s):  
United States ◽  
Graduate Students ◽  
Learning Strategies ◽  
Undergraduate Students ◽  
National Research Council ◽  
Undergraduate Curriculum ◽  
The United States ◽  
Faculty Members ◽  
Original Research ◽  
Responsible Conduct

Numerous studies are demonstrating that engaging undergraduate students in original research can improve their achievement in the science, technology, engineering, and mathematics (STEM) fields and increase the likelihood that some of them will decide to pursue careers in these disciplines. Associated with this increased prominence of research in the undergraduate curriculum are greater expectations from funders, colleges, and universities that faculty mentors will help those students, along with their graduate students and postdoctoral fellows, develop an understanding and sense of personal and collective obligation for responsible conduct of science (RCS). This Feature describes an ongoing National Research Council (NRC) project and a recent report about educating faculty members in culturally diverse settings (Middle East/North Africa and Asia) to employ active-learning strategies to engage their students and colleagues deeply in issues related to RCS. The NRC report describes the first phase of this project, which took place in Aqaba and Amman, Jordan, in September 2012 and April 2013, respectively. Here we highlight the findings from that report and our subsequent experience with a similar interactive institute in Kuala Lumpur, Malaysia. Our work provides insights and perspectives for faculty members in the United States as they engage undergraduate and graduate students, as well as postdoctoral fellows, to help them better understand the intricacies of and connections among various components of RCS. Further, our experiences can provide insights for those who may wish to establish “train-the-trainer” programs at their home institutions.

scholarly journals Principled Decision-Making Workflow with Hierarchical Bayesian Models of High-Throughput Dose-Response Measurements

Entropy ◽  
2021 ◽  
Vol 23 (6) ◽  
pp. 727
Author(s):  
Eric J. Ma ◽  
Arkadij Kummer
Keyword(s):  
Decision Making ◽  
High Throughput ◽  
Noisy Data ◽  
Hierarchical Bayesian ◽  
Hierarchical Bayesian Models ◽  
Melting Temperatures ◽  
Hierarchical Bayesian Estimation ◽  
The Face ◽  
Point Data

We present a case study applying hierarchical Bayesian estimation on high-throughput protein melting-point data measured across the tree of life. We show that the model is able to impute reasonable melting temperatures even in the face of unreasonably noisy data. Additionally, we demonstrate how to use the variance in melting-temperature posterior-distribution estimates to enable principled decision-making in common high-throughput measurement tasks, and contrast the decision-making workflow against simple maximum-likelihood curve-fitting. We conclude with a discussion of the relative merits of each workflow.

Selected Personnel Policies for Faculty Members: An Empirical Analysis

1986 ◽  
Vol 15 (3) ◽  
pp. 345-350 ◽  
Author(s):  
John R. Tanner
Keyword(s):  
Performance Appraisal ◽  
Empirical Analysis ◽  
Colleges And Universities ◽  
Faculty Members ◽  
University Faculty ◽  
Job Evaluation ◽  
Evaluation Systems ◽  
Policies And Procedures ◽  
Personnel Policies ◽  
Made In

There are few who would disagree with the fact that sound personnel policies are important to any organization. This would include personnel policies and procedures for university faculty members as well as members of other organizations. This study was designed to analyze any change which had occurred in faculty personnel policies in selected southeastern and midwestern universities from 1972–73. Significant improvements were made in the areas of performance appraisal procedures, promotion systems, the use of position descriptions, and job evaluation systems. This is an encouraging trend in colleges and universities, and one that will hopefully continue to improve.

DNA-Directed Patterning for Versatile Validation and Characterization of a Lipid-Based Nanoparticle Model of SARS-CoV-2

2021 ◽  
Author(s):  
Molly Kozminsky ◽  
Thomas Carey ◽  
Lydia L. Sohn
Keyword(s):  
High Throughput ◽  
Glass Substrate ◽  
Rapid Development ◽  
Neutralizing Antibody ◽  
S Protein ◽  
Biological Relevance ◽  
The Face ◽  
Great Control ◽  
Tetraspanin Cd63

Lipid-based nanoparticles have risen to the forefront of the COVID-19 pandemic—from encapsulation of vaccine components to modeling the virus, itself. Their rapid development in the face of the volatile nature of the pandemic requires high-throughput, highly flexible methods for characterization. DNA-directed patterning is a versatile method to immobilize and segregate lipid-based nanoparticles for subsequent analysis. DNA-directed patterning selectively conjugates oligonucleotides onto a glass substrate and then hybridizes them to complementary oligonucleotides tagged to the liposomes, thereby patterning them with great control and precision. The power of this method is demonstrated by characterizing a novel recapitulative lipid-based nanoparticle model of SARS-CoV-2 —S-liposomes— which present the SARS-CoV-2 spike (S) protein on their surfaces. Patterning of a mixture of S-liposomes and liposomes that display the tetraspanin CD63 into discrete regions of a substrate is used to show that ACE2 specifically binds to S-liposomes. Importantly, DNA-directed patterning of S-liposomes is used to verify the performance of a commercially available neutralizing antibody against the S protein. Ultimately, the introduction of S-liposomes to ACE2-expressing cells demonstrates the biological relevance of DNA-directed patterning. Overall, DNA-directed patterning enables a wide variety of custom assays for the characterization of any lipid-based nanoparticle.

Whose History?: The Americas and Music Curricula in the United States

2021 ◽  
Vol 15 (4) ◽  
pp. 457-460
Author(s):  
M. Leslie Santana
Keyword(s):  
Graduate Students ◽  
Undergraduate Students ◽  
Curriculum Reform ◽  
Undergraduate Curriculum ◽  
The United States ◽  
Concert Music ◽  
Music Department ◽  
Theoretical Approaches ◽  
Western European ◽  
Teaching Music

One moment from the much-discussed 2017 curriculum reform in the Music Department at Harvard University has stuck with me and transformed the way I approach teaching music in higher education. In one of the meetings leading up to the revision, graduate students in the department led an activity in which attendees—who included undergraduate students, graduate students, and faculty alike—got into small groups and discussed the relative merits of three hypothetical models for the new undergraduate curriculum. Each of the models involved decentering to some extent the existing curriculum's emphasis on the history of Western European music and dominant music theoretical approaches to it. After a short while, we all gathered back together and one person from each group shared a bit about what had transpired. From the circle of desks nearest the door, an undergraduate student rose to speak and expressed enthusiasm for a broadening of curricular coverages. But, they said, their group also had some reservations about jettisoning the overall focus on Western European concert music altogether. “We still need to learn about our history,” they said, while a faculty member nodded behind them.

Comparison of a computer simulation program and a traditional laboratory practical class for teaching the principles of intestinal absorption.

1994 ◽  
Vol 267 (6) ◽  
pp. S95 ◽  
Author(s):  
D G Dewhurst ◽  
J Hardcastle ◽  
P T Hardcastle ◽  
E Stuart
Keyword(s):  
Undergraduate Students ◽  
Epithelial Transport ◽  
Undergraduate Curriculum ◽  
Computer Assisted ◽  
Knowledge Gain ◽  
Student Centered ◽  
Student Centered Learning ◽  
Before And After ◽  
Resource Requirements ◽  
Approach Working

Here we describe an evaluation of the effectiveness, compared with a traditional laboratory, of an interactive computer-assisted learning (CAL) program, which simulates a series of experiments performed using isolated, everted sacs of rat small intestine. The program is aimed at undergraduate students of physiology and is designed to offer an alternative student-centered learning approach to the traditional laboratory-based practical class. The evaluative study compared two groups of second-year undergraduate students studying a module on epithelial transport: one group worked independently using the CAL program and associated learning materials, and the other group followed a conventional practical class approach, working in the laboratory under supervision. Knowledge gain of each group was measured by means of a test consisting of a range of question types (e.g., short-answer factual, calculation, interpretation) given to students before and after the module. Student attitude to both approaches was assessed by questionnaire, and the resource requirements were also compared. It was found that the knowledge gain of both groups of students was the same, that students had a positive attitude toward using CAL programs of this type, and that the cost of the conventional laboratory-based approach was five times greater. The potential for integrating CAL programs into the undergraduate curriculum is discussed.

scholarly journals Prevalence of Psychoactive Substance Use Among Undergraduate Students at Chirunga College, Malawi.

2019 ◽  
Vol 8 ◽  
pp. 53-68
Author(s):  
John Kuyokwa ◽  
Symon Ernest Chiziwa ◽  
Nertha Semphere
Keyword(s):  
Undergraduate Students ◽  
Theory Of Planned Behaviour ◽  
Qualitative Data ◽  
Higher Learning ◽  
Data Generation ◽  
Psychoactive Substance ◽  
Psychoactive Substances ◽  
Research Methodologies ◽  
Quantitative And Qualitative Research ◽  
Quantitative Data Analysis

The purpose of this study was to determine the prevalence of use of psychoactive substances among undergraduate students at Chirunga College in Malawi.  The study was guided by Ajzen’s Theory of Planned Behaviour. Mixed research methodologies were used, in which both quantitative and qualitative research methodologies were employed in data generation and analysis. SPSSv20 and Excel were used in quantitative data analysis and qualitative data was analyzed thematically. The study involved 147 participants and the findings revealed that (34%) of students used psychoactive substances. It recommends that undergraduate students who use psychoactive substances like any other user of these substances, require help. Accordingly, as an institution of higher learning, Chirunga College has to take the necessary steps to address this problem; including introducing counselling and psychotherapy services at the institution

scholarly journals SpiderSeqR: an R package for crawling the web of high-throughput multi-omic data repositories for data-sets and annotation

2020 ◽  
Author(s):  
Anna M. Sozanska ◽  
Charles Fletcher ◽  
Dóra Bihary ◽  
Shamith A. Samarajiwa
Keyword(s):  
High Throughput ◽  
R Package ◽  
Data Reuse ◽  
Massively Parallel ◽  
Data Sets ◽  
Similar Data ◽  
Data Generation ◽  
Data Repositories ◽  
Public Data ◽  
Omic Data

AbstractMore than three decades ago, the microarray revolution brought about high-throughput data generation capability to biology and medicine. Subsequently, the emergence of massively parallel sequencing technologies led to many big-data initiatives such as the human genome project and the encyclopedia of DNA elements (ENCODE) project. These, in combination with cheaper, faster massively parallel DNA sequencing capabilities, have democratised multi-omic (genomic, transcriptomic, translatomic and epigenomic) data generation leading to a data deluge in bio-medicine. While some of these data-sets are trapped in inaccessible silos, the vast majority of these data-sets are stored in public data resources and controlled access data repositories, enabling their wider use (or misuse). Currently, most peer reviewed publications require the deposition of the data-set associated with a study under consideration in one of these public data repositories. However, clunky and difficult to use interfaces, subpar or incomplete annotation prevent discovering, searching and filtering of these multi-omic data and hinder their re-purposing in other use cases. In addition, the proliferation of multitude of different data repositories, with partially redundant storage of similar data are yet another obstacle to their continued usefulness. Similarly, interfaces where annotation is spread across multiple web pages, use of accession identifiers with ambiguous and multiple interpretations and lack of good curation make these data-sets difficult to use. We have produced SpiderSeqR, an R package, whose main features include the integration between NCBI GEO and SRA databases, enabling an integrated unified search of SRA and GEO data-sets and associated annotations, conversion between database accessions, as well as convenient filtering of results and saving past queries for future use. All of the above features aim to promote data reuse to facilitate making new discoveries and maximising the potential of existing data-sets.Availabilityhttps://github.com/ss-lab-cancerunit/SpiderSeqR

scholarly journals Sexual Violence on Religious Campuses

2017 ◽  
Vol 47 (2) ◽  
pp. 1-21 ◽  
Author(s):  
James R. Vanderwoerd ◽  
Albert Cheng
Keyword(s):  
Sexual Violence ◽  
Undergraduate Students ◽  
Colleges And Universities ◽  
Christian Colleges ◽  
Full Time ◽  
Exploratory Investigation ◽  
Part Time ◽  
Religious Colleges ◽  
Public Colleges And Universities ◽  
Unwanted Sexual Contact

Religious colleges and universities make up a substantial segment of the higher education landscape in North America, but the incidence of sexual violence on these campuses remains understudied. This study estimates the incidence of sexual violence on independent Christian campuses using a sample of part-time and full-time undergraduate students (N = 668) from eight private Christian colleges in Ontario, Canada. Using two widely used measures of sexual violence enabled comparisons with studies of self-reported incidents at secular and public colleges and universities. The findings show that 18% of women at religious colleges reported experiencing unwanted sexual contact within the past year, compared to studies of self-reported rates on secular campuses ranging from 21.4% to 31.4%. Exploratory investigation of factors related to victimization suggests that religious colleges may provide a “moral community” that could reduce the risk of sexual violence.  

scholarly journals The Principle of Continuous Biological Information Flow as the Fundamental Foundation for the Biological Sciences. Implications for Ageing Research

2021 ◽  
Author(s):  
Xavi Marsellach
Keyword(s):  
Biological Sciences ◽  
Biological Information ◽  
Biological Knowledge ◽  
Phenotypic Characteristics ◽  
Apparent Contradiction ◽  
Current State ◽  
The Face ◽  
Unique Definition ◽  
Definition Of ◽  
Flow Of Information

The current state of biological knowledge contains an unresolved paradox: life as a continuity in the face of the phenomena of ageing. In this manuscript I propose a theoretical framework that offers a solution for this apparent contradiction. The framework proposed is based on a rethinking of what ageing is at a molecular level, as well as on a rethinking of the mechanisms in charge of the flow of information from one generation to the following ones. I propose an information-based conception of ageing instead of the widely accepted damage-based conception of ageing and propose a full recovery of the chromosome theory of inheritance to describe the intergenerational flow of information. Altogether the proposed framework allows a precise and unique definition of what life is: a continuous flow of biological information. The proposed framework also implies that ageing is merely a consequence of the way in which epigenetically-coded phenotypic characteristics are passed from one generation to the next ones.

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