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1. Incubators: Building community networks and developing open educational resources to integrate bioinformatics into life science education

   https://doi.org/10.1002/bmb.21387  

   Ryder, Elizabeth F. ; Morgan, William R. ; Sierk, Michael ; Donovan, Samuel S. ; Robertson, Sabrina D. ; Orndorf, Hayley C. ; Rosenwald, Anne G. ; Triplett, Eric W. ; Dinsdale, Elizabeth ; Pauley, Mark A. ; et al ( June 2020 , Biochemistry and Molecular Biology Education)

   While it is essential for life science students to be trained in modern techniques and approaches, rapidly developing, interdisciplinary fields such as bioinformatics present distinct challenges to undergraduate educators. In particular, many educators lack training in new fields, and high‐quality teaching and learning materials may be sparse. To address this challenge with respect to bioinformatics, the Network for the Integration of Bioinformatics into Life Science Education (NIBLSE), in partnership with Quantitative Undergraduate Biology Education and Synthesis (QUBES), developed incubators, a novel collaborative process for the development of open educational resources (OER). Incubators are short‐term, online communities that refine unpublished teaching lessons into more polished and widely usable learning resources. The resulting products are published and made freely available in the NIBLSE Resource Collection, providing recognition of scholarly work by incubator participants. In addition to producing accessible, high‐quality resources, incubators also provide opportunities for faculty development. Because participants are intentionally chosen to represent a range of expertise in bioinformatics and pedagogy, incubators also build professional connections among educators with diverse backgrounds and perspectives and promote the discussion of practical issues involved in deploying a resource in the classroom. Here we describe the incubator process and provide examples of beneficial outcomes. Our experience indicates that incubators are a low cost, short‐term, flexible method for the development of OERs and professional community that could be adapted to a variety of disciplinary and pedagogical contexts.

    

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2. Multi-Scale Drivers of Immunological Variation and Consequences for Infectious Disease Dynamics

   https://doi.org/10.1093/icb/icz138  

   Becker, Daniel J. ; Downs, Cynthia J. ; Martin, Lynn B. ( July 2019 , Integrative and Comparative Biology)

   The immune system is the primary barrier to parasite infection, replication, and transmission following exposure, and variation in immunity can accordingly manifest in heterogeneity in traits that govern population-level infectious disease dynamics. While much work in ecoimmunology has focused on individual-level determinants of host immune defense (e.g., reproductive status and body condition), an ongoing challenge remains to understand the broader evolutionary and ecological contexts of this variation (e.g., phylogenetic relatedness and landscape heterogeneity) and to connect these differences into epidemiological frameworks. Ultimately, such efforts could illuminate general principles about the drivers of host defense and improve predictions and control of infectious disease. Here, we highlight recent work that synthesizes the complex drivers of immunological variation across biological scales of organization and scales these within-host differences to population-level infection outcomes. Such studies note the limitations involved in making species-level comparisons of immune phenotypes, stress the importance of spatial scale for immunology research, showcase several statistical tools for translating within-host data into epidemiological parameters, and provide theoretical frameworks for linking within- and between-host scales of infection processes. Building from these studies, we highlight several promising avenues for continued work, including the application of machine learning tools and phylogenetically controlled meta-analyses to immunology data and quantifying the joint spatial and temporal dependencies in immune defense using range expansions as model systems. We also emphasize the use of organismal traits (e.g., host tolerance, competence, and resistance) as a way to interlink various scales of analysis. Such continued collaboration and disciplinary cross-talk among ecoimmunology, disease ecology, and mathematical modeling will facilitate an improved understanding of the multi-scale drivers and consequences of variation in host defense.

    

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3. Madagascar’s extraordinary biodiversity: Threats and opportunities

   https://doi.org/10.1126/science.adf1466  

   Ralimanana, Hélène ; Perrigo, Allison L. ; Smith, Rhian J. ; Borrell, James S. ; Faurby, Søren ; Rajaonah, Mamy Tiana ; Randriamboavonjy, Tianjanahary ; Vorontsova, Maria S. ; Cooke, Robert S. ; Phelps, Leanne N. ; et al ( December 2022 , Science)

   BACKGROUND Madagascar is one of the world’s foremost biodiversity hotspots. Its unique assemblage of plants, animals, and fungi—the majority of which evolved on the island and occur nowhere else—is both diverse and threatened. After human arrival, the island’s entire megafauna became extinct, and large portions of the current flora and fauna may be on track for a similar fate. Conditions for the long-term survival of many Malagasy species are not currently met because of multiple anthropogenic threats. ADVANCES We review the extinction risk and threats to biodiversity in Madagascar, using available international assessment data as well as a machine learning analysis to predict the extinction risks and threats to plant species lacking assessments. Our compilation of global International Union for Conservation of Nature (IUCN) Red List assessments shows that overexploitation alongside unsustainable agricultural practices affect 62.1 and 56.8% of vertebrate species, respectively, and each affects nearly 90% of all plant species. Other threats have a relatively minor effect today but are expected to increase in coming decades. Because only one-third (4652) of all Malagasy plant species have been formally assessed, we carried out a neural network analysis to predict the putative status and threats for 5887 unassessed species and to evaluate biases in current assessments. The percentage of plant species currently assessed as under threat is probably representative of actual numbers, except in the case of the ferns and lycophytes, where significantly more species are estimated to be threatened. We find that Madagascar is home to a disproportionately high number of Evolutionarily Distinct and Globally Endangered (EDGE) species. This further highlights the urgency for evidence-based and effective in situ and ex situ conservation. Despite these alarming statistics and trends, we find that 10.4% of Madagascar’s land area is protected and that the network of protected areas (PAs) covers at least part of the range of 97.1% of terrestrial and freshwater vertebrates with known distributions (amphibians, freshwater fishes, reptiles, birds, and mammal species combined) and 67.7% of plant species (for threatened species, the percentages are 97.7% for vertebrates and 79.6% for plants). Complementary to this, ex situ collections hold 18% of vertebrate species and 23% of plant species. Nonetheless, there are still many threatened species that do not occur within PAs and are absent from ex situ collections, including one amphibian, three mammals, and seven reptiles, as well as 559 plants and more yet to be assessed. Based on our updated vegetation map, we find that the current PA network provides good coverage of the major habitats, particularly mangroves, spiny forest, humid forest, and tapia, but subhumid forest and grassland-woodland mosaic have very low areas under protection (5.7 and 1.8% respectively). OUTLOOK Madagascar is among the world’s poorest countries, and its biodiversity is a key resource for the sustainable future and well-being of its citizens. Current threats to Madagascar’s biodiversity are deeply rooted in historical and present social contexts, including widespread inequalities. We therefore propose five opportunities for action to further conservation in a just and equitable way. First, investment in conservation and restoration must be based on evidence and effectiveness and be tailored to meet future challenges through inclusive solutions. Second, expanded biodiversity monitoring, including increased dataset production and availability, is key. Third, improving the effectiveness of existing PAs—for example through community engagement, training, and income opportunities—is more important than creating new ones. Fourth, conservation and restoration should not focus solely on the PA network but should also include the surrounding landscapes and communities. And finally, conservation actions must address the root causes of biodiversity loss, including poverty and food insecurity. In the eyes of much of the world, Madagascar’s biodiversity is a unique global asset that needs saving; in the daily lives of many of the Malagasy people, it is a rapidly diminishing source of the most basic needs for subsistence. Protecting Madagascar’s biodiversity while promoting social development for its people is a matter of the utmost urgency Visual representation of five key opportunities for conserving and restoring Madagascar’s rapidly declining biodiversity identified in this Review. The dashed lines point to representative vegetation types where these recommendations could have tangible effects, but the opportunities are applicable across Madagascar. ILLUSTRATION: INESSA VOET 

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4. Textual Ecology, Collaborative Tasks, and Genre Systems: Using PDE to Teach STEM Career Awareness/Intent

   Philip J. Piety, PhD ( January 2021 , Annual meeting program American Educational Research Association)

   null (Ed.)

   The paper discusses the use of Productive Disciplinary Engagement (PDE) for a curricular project that features a technology-based alternate reality game (ARG) with the objective of teaching undergraduate students about the collaborative nature of STEM careers. Much of the PDE research uses PDE as either a design-principle or as an analytics lens. This project does both. Most of this extant research focuses on spoken discourse to teach disciplinary knowledge. This project uses workplace documentary texts that are embedded within a semester-long undergraduate course designed to teach students collaboration skills using the context of natural disasters. A range of texts are used in this design from didactic to disciplinary. Students learn about professional work through educational renditions of professional cultural historical activity systems. This paper focuses on design decisions and illustrates some ways that workplace documents can be used in education. 

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5. Understanding the Professional Formation of Engineers through the Lens of Design Thinking: Unpacking theWicked Problem of Diversity and Inclusion

   Zoltowski, Carla B. ; Buzzanell, Patrice M. ; Brightman, Andrew O. ; Torres, David ; Eddington, Sean M. ( June 2017 , ASEE annual conference & exposition proceedings)

   Three broad issues have been identified in the professional formation of engineers: 1) the gap between what students learn in universities and what they practice upon graduation; 2) the limiting perception that engineering is solely technical, math, and theory oriented; and 3) the lack of diversity (representation of a wide range of people) and lack of inclusion (incorporation of different perspectives, values, and ways of thinking and being in engineering) in many engineering programs. These are not new challenges in engineering education, rather they are persistent and difficult to change. There have been countless calls to recruit and retain women and underrepresented minority group members into engineering careers and numerous strategies proposed to improve diversity, inclusion, and retention, as well as to calls to examine socio-technical integration in engineering cultures and education for professional formation. Despite the changes in some disciplinary profiles in engineering and the curricular reforms within engineering education, there still has not been the deep transformation needed to integrate inclusionary processes and thinking into professional formation. In part, the reason is that diversity and inclusion are still framed as simply “numbers problems” to be solved. What is needed instead is an approach that understands and explores diversity and inclusion as interrelated with the epistemological (what do engineers need to know) and ontological (what does it mean to be an engineer) underpinnings of engineering. These issues are highly complex, interconnected, and not amenable to simple solutions, that is, they are “wicked” problems. They require design thinking. Thus our NSF-funded Research in the Formation of Engineers (RFE) study utilizes a design thinking approach and research activities to explore foundational understandings of formation and diversity and inclusion in engineering while addressing the three project objectives: 1) Better prepare engineers for today’s workforce; 2) Broaden understandings of engineering practice as both social and technical; and 3) Create and sustain more diverse and inclusionary engineering programs. The project is organized around the three phases of the design process (inspiration, ideation, and implementation), and embedded within the design process is a longitudinal, multiphase, mixed-methods study. Although the goal is to eventually study these objectives on a broader scale, we begin with a smaller context: the School of Electrical and Computer Engineering (ECE) and the Weldon School of Biomedical Engineering (BME) at Purdue University. These schools share similarities with some common coursework and faculty, but also provide contrasts as BME’s undergraduate population, on average for recent semesters, has been 44-46% female, where ECE has been 13-14% female. Although BME has slightly more underrepresented minority students (7-8% versus 5%), approximately 60% of BME students are white, versus 40% for ECE. It is important to note that Purdue’s School of ECE offers B.S. degrees in Electrical Engineering (EE) and Computer Engineering (CmpE), which reflect unique disciplinary cultures. Additionally, the schools differ significantly on undergraduate enrollment. The BME enrollment was 278, whereas ECE’s enrollment was 675 in EE and 541 in CmpE1. In this paper we describe the background literature and the research design, including the study contexts, target subject populations, and procedures for quantitative and qualitative data collection and analysis. In addition, we present the data collected during the first phase of the research project. In our poster, we will present preliminary analysis of the first phase data. 

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