3-part lecture series given at Kwame Nkrumah University of Science and Technology about infections with Gram-negative obligate anaerobes
Because small mammals are prey species, they do not take to intensive conditions of surgery and hospitalisation very readily. Those that are handled very frequently by their owners are more bonded with humans and better surgical subjects as a result. Rodents and rabbits are particularly susceptible to the surgical complications of dehydration (blood and fluid loss), core temperature depression, hypovolaemic shock, ileus and renal and respiratory depression.
This problem illustrates how numerical theories are developed, how we might test this theory with an analog model, and how numerical models are constructed and the limitations of numerical modeling.
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The Ensembl project offers integrated genome, variation, gene regulation and comparative genomics data of mainly vertebrate genomes on an open access web browser platform.
This webinar will introduce you to the analysis of Linkage Disequilibrium (LD) between variants with Ensembl. We will look at different ways to explore and visualise LD in the Ensembl genome browser website. We will discuss the new LD Calculator tool which has been released with Ensembl 91 and show how to use it.
Who is this course for?
This webinar is aimed at individuals who wish to learn more about analysing LD with Ensembl. No prior knowledge of bioinformatics is required, but an understanding of undergraduate level genetics would be useful.
Outcomes
By the end of the webinar you will be able to:
Analyse linkage disequilibrium between variants in Ensembl
Visualise linkage disequilibrium using the Ensembl Genome Browser
A checklist used by teachers to observe and record elementary students’ analysis skills as they work on activities and projects.
A rubric in student language used by elementary students to self-assess their analysis skills.
This class analyzes complex biological processes from the molecular, cellular, extracellular, and organ levels of hierarchy. Emphasis is placed on the basic biochemical and biophysical principles that govern these processes. Examples of processes to be studied include chemotaxis, the fixation of nitrogen into organic biological molecules, growth factor and hormone mediated signaling cascades, and signaling cascades leading to cell death in response to DNA damage. In each case, the availability of a resource, or the presence of a stimulus, results in some biochemical pathways being turned on while others are turned off. The course examines the dynamic aspects of these processes and details how biochemical mechanistic themes impinge on molecular/cellular/tissue/organ-level functions. Chemical and quantitative views of the interplay of multiple pathways as biological networks are emphasized. Student work culminates in the preparation of a unique grant application in an area of biological networks.
This course focuses on computational and experimental analysis of biological systems across a hierarchy of scales, including genetic, molecular, cellular, and cell population levels. The two central themes of the course are modeling of complex dynamic systems and protein design and engineering. Topics include gene sequence analysis, molecular modeling, metabolic and gene regulation networks, signal transduction pathways and cell populations in tissues. Emphasis is placed on experimental methods, quantitative analysis, and computational modeling.
This lab activity is designed for science students in an introductory climatology course. Upon successful completion of the activity, students will have demonstrated an ability to:
Independently navigate and download climate data from online data libraries.
Work with different file types (NetCDF and CSV).
Write appropriate MATLAB code to read and manipulate climate data, and create plots (time series and maps) as instructed.
Extract meaningful information from large 3-dimensional datasets.
Understand and apply fundamental climatology concepts, such as:
Climate statistics (temporal and spatial mean and anomaly; trends; baselines)
Ice-albedo feedback resulting in disproportionate sensitivity to climate change in polar regions
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Sidewalks provide a good analog for the study of fractures when outcrops are not available. This exercise is taught as the first lab of the semester in an undergraduate structural geology course. Students learn to make systematic observations, measure the orientation and location of fractures, manipulate and analyze data, and consider some kinematic and dynamic questions regarding the origin and significance of fractures. Their experiences are also used later in the course to reinforce key concepts of brittle deformation. Done as a group project, it emphasizes the importance of group work and encourages students to propose and defend their ideas.
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This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:
"In the absence of oxygen, some prokaryotes can degrade organic matter via anaerobic digestion. This occurs in natural settings, like wetlands, and industrial ones, like wastewater treatment or biogas production. But what about viruses? Bacteriophages can impact their hosts’ community structure through selective pressure and have been used to influence microbial communities, such as through pathogen control. A recent study examined the virome of anaerobic digestion communities undergoing prophage- inducing environmental stresses. The virome was almost entirely composed of tailed bacteriophages of the order Caudovirales. Metagenome reconstruction revealed 1,092 viral genomes and 120 prokaryotic genomes, and over half of the prokaryotic genomes contained a provirus in their genomic sequence. In general, species of viruses and prokaryotes could be grouped by having similar reactions to stressors. Archaea had the most pronounced reactions to stressors and featured behaviors unique to those species..."
The rest of the transcript, along with a link to the research itself, is available on the resource itself.
An exercise to analyze trends in global oil reserves, production, and consumption.
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Comparative planetary geology requires understanding how geological processes are affected by changes in physical environment-each planet and moon provides an opportunity to refine our understanding of how physical geological processes operate. Volcanism is a great example of a major geological process highly susceptible to such variations. Students performing this exercise will constrain how "Amboy Crater" would look if the same eruption happened on the Moon and Mars. Part 1 of the exercise asks small groups to assess either the yield strength of the Amboy flows or the time required for the flow to travel a given distance. After discussion of the results, Part 2 asks students to characterize the dimensions of the same flow, if emplaced on Mars or the Moon (changing only gravitational acceleration), and the time required for it to form; they are asked to predict the outcome in advance. Part 3 uses "Erupt" freeware by Ken Wohletz to explore how gravity changes will affect cinder cone geometry; the model is tested first to see if it correctly predicts an Amboy-like geometry, and afterwards students are asked to brainstorm what other factors should also be modified to improve the accuracy of the simulation, and how these changes would be expected to affect the geomorphological outcome. Finally, Part 4 asks students to use simple ballistic equations, implemented via an online Applet (Stromboli), to constrain the launch angle and starting velocity for the eruption that formed Amboy Crater (modifications are supposedly underway to permit this applet to run with different values of gravitational acceleration and air resistance).
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Analytic epidemiological studies aim to investigate and identify factors associated with the presence of disease within populations, through the investigation of factors which may vary between individual members of these populations. Details on study designs appropriate for these investigations are given elsewhere. Conceptually, this involves investigating the disease experience amongst different 'groups' of animals within an overall population, distinguished according to the factor(s) of interest. These factors can be classified as one of the components of the 'epidemiological triad' of Host, Agent and Environment, many of which are closely interrelated with each other.
The activity is divided into seven parts, as follows:
Part A: students access an online data set of historic global temperature anomalies and use the webpage to answer questions about the source and presentation of the data.
Part B: students copy the data into an Excel spreadsheet and organize it so that it is easy for them to use and for others to follow.
Part C: students graph their data, explore the use of trend lines, and use a linear regression line to predict future temperatures.
Part D: students access an online data set of historic temperature anomalies within their latitude zone, analyze this data, and compare their results to those from Part C.
Part E: students access an online data set of historic temperatures for their state, analyze this data, and compare their results to those from Parts C and D.
Part F: students choose two original questions related to climate variability and use these or other data sets to address their questions.
Part G: students evaluate the statistical significance of their linear regression lines and interpret their results in the context of climate variability
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During a lab period, students go out in the field to an area that contains at least 2 fault/fracture sets. Students measure orientations of faults and make observations about the relationship between different fault sets. After the field trip, the students compile their field data, plot it on a stereonet and write-up a brief report. In this report students will use their field observations and stereonet patterns to determine whether faults are related or unrelated to each other.
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In preparation for this lab activity, students have read the textbook material on Waves (Garrison, 6th ed., Oceanography), and attended a lecture on the same topic. In class, students will access Coastal Data Information Program (CDIP) data published by the Ocean Engineering Research Group, Center for Coastal Studies, Scripps Institute of Oceanography. Students will compile specific real-time wave and sea surface temperature data sets as specified in the lab assignment. This requires students to generate and interpret multiple graphs from the available data, set-up their own system of data acquisition, and interpret the wave height and sea surface data in the context of the local physical oceanographic parameters.
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Reflection questions are offered at two levels:
1. District and school level, for system-wide reflection, appropriate for district
administrators, building principals, department chairs, content lea ders, coaches
2. Teacher level, appropriate for individual teachers in considering their
data/information
This quarter-long project forms the basis of a third-year course for majors and nonmajors at the University of Washington, Bothell called Science Methods and Practice. Students use databases to identify novel research questions, and extract data to test their hypotheses. They frame the question with primary literature, address the questions with inferential statistics, and discuss the results with more primary literature. The product is a scientific paper; each step of the process is scaffolded and evaluated. Given time limitations, we avoid devoting time to data collection; instead, we sharpen
students' ability to make sense of a large body of quantitative data, a situation they may rarely have encountered.
We treat statistics with a strictly conceptual, pragmatic, and abbreviated approach; i.e., we ask students to know which basic test to choose to assess a linear relationship vs. a difference between two means. We stress the need for a normal distribution
in order to use these tests, and how to interpret the results; we leave the rest for stats courses, and we do not teach the mathematics. This approach proves beneficial even to those who have already had a statistics course, because it is often the first time
they make decisions about applying statistics to their own research questions.
We incorporate peer review and collaborative work throughout the quarter. We form collaborative groups around the research questions they ask, enabling them to share primary literature they find, and preparing them well to review each other's writing. We encourage them to cite each other's work. They write formal peer reviews of each other's papers, and they submit their final paper with a letter-to-the-editor highlighting how their research has addressed previous feedback.
A major advantage of this course is that an instructor can easily modify it to suit any area of expertise. Students have worked with data about how a snail's morphology changes in response to its environment (Price, 2012), how students understand genetic drift (Price et al. 2014), maximum body size in the fossil record (Payne et al. 2008), range shifts (Ettinger et al. 2011), and urban crop pollination (Waters and Clifford 2014).
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College-level adaptation of a chapter in the Earth Exploration Toolbook. Examine satellite images of atmospheric ozone in the Southern Hemisphere to study changes in concentration over a time.
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