Journal articles on the topic 'Evolutionary learning laboratory'
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McElreath, Richard, Mark Lubell, Peter J. Richerson, Timothy M. Waring, William Baum, Edward Edsten, Charles Efferson, and Brian Paciotti. "Applying evolutionary models to the laboratory study of social learning." Evolution and Human Behavior 26, no. 6 (November 2005): 483–508. http://dx.doi.org/10.1016/j.evolhumbehav.2005.04.003.
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Susilawati, Puspita Ratna. "Implementation of Web-Based Virtual Laboratory Media in Learning." TAMAN VOKASI 7, no. 2 (December 26, 2019): 122. http://dx.doi.org/10.30738/jtv.v7i2.6396.
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The integration of information and communication technology in learning through the application of virtual laboratory media can be an alternative solution to overcome the constraints of time, cost, and laboratory safety in biology labs. Virtual laboratories are very suitable to be applied to the mechanism of evolution because they involve the context of space and time, and can provide opportunities for students to learn independently and increase active student involvement in learning. These study aims are to determine the effect of the application of virtual laboratory media on the understanding of student concepts; knowing increasing students' understanding of the concept of evolutionary mechanisms, and knowing students' responses after learning with virtual laboratories.This type of research is a pre-experimental design (nondesign) with one group pretest-posttest design. The research subjects were 37 students. The media used as many as 8 web-based virtual laboratory programs (online) that can be freely accessed. Data collection techniques include tests (pretest and posttest) and questionnaires. The pretest and posttest values were analyzed by the T-test while the questionnaire data were analyzed descriptively. The application of web-based virtual laboratory media on the evolution mechanism material influences the understanding of student concepts (t arithmetic> t table then H0 is rejected and H1 is accepted) The application of these media increases students' understanding of the concept of evolutionary mechanisms. The mean value increased from pretest 23.65 to 56.08 at the posttest with an increase of 32.43. Student responses to the application of media in learning showed 91.89% of students felt helped in understanding the process of evolution while 100% of students felt helped in understanding the role of evolution in causing evolution.
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Fabian, Carole Ann. "Evolutionary Biology Digital Dissection Project, Web-Based Laboratory Learning Opportunities for Students." American Biology Teacher 66, no. 2 (February 1, 2004): 128–32. http://dx.doi.org/10.2307/4451638.
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ANIA, ANA B., and ANDREAS WAGENER. "Laboratory Federalism: The Open Method of Coordination (OMC) as an Evolutionary Learning Process." Journal of Public Economic Theory 16, no. 5 (August 15, 2014): 767–95. http://dx.doi.org/10.1111/jpet.12079.
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Kiura, Toshiro, Ockie J. H. Bosch, Nam C. Nguyen, Seiko Shirasaka, and Takashi Maeno. "Creating a New Business Through Applying the Systems-Based Evolutionary Learning Laboratory Approach." Systems Research and Behavioral Science 31, no. 6 (September 18, 2014): 696–707. http://dx.doi.org/10.1002/sres.2319.
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Owens, David C., Cindi Smith-Walters, and Angela T. Barlow. "Enhancing Motivation To Learn In A Biology Laboratory Course Through Gaming." International Journal of Designs for Learning 10, no. 1 (May 10, 2019): 53–63. http://dx.doi.org/10.14434/ijdl.v10i1.24111.
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In this design case, we describe our work to develop a gameful learning design for use in an introductory, under-graduate biology laboratory course for science majors. Our design team included three university-based mathematics and science educators and a biologist responsible for the management of curriculum and instruction in the course under study. The gameful learning design was employed during the four weeks of plant evolutionary life history in-struction. Key challenges to the design and implementation of gameful learning included the adaptation of instruction from teacher-centered to student-centered and establishing novel learning conditions in the eight laboratory sections so as to determine the value of two different elements of game design, repeat-testing and leaderboard with badges.
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Hildebrand, Terri J., Fredric R. Govedich, and Bonnie A. Bain. "Hands-On Laboratory Simulation of Evolution." American Biology Teacher 76, no. 2 (February 1, 2014): 132–36. http://dx.doi.org/10.1525/abt.2014.76.2.11.
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Evolutionary theory is the foundation of the biological sciences, yet conveying it to General Biology students often presents a challenge, especially at larger institutions where student numbers in foundation courses can exceed several hundred per lecture section. We present a pedagogically sound exercise that utilizes a series of simple and inexpensive simulations to convey the concept of evolution through mutation and natural selection. Questions after each simulation expand student comprehension; a class discussion encourages advanced thinking on mutation and speciation. A final paper requires students to synthesize their learning by summarizing selected papers on these topics. A grading rubric for the papers is included.
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Ha, Tuan M., Ockie J. H. Bosch, and Nam C. Nguyen. "Practical Contributions of the Systems-Based Evolutionary Learning Laboratory to Knowledge and Stakeholder Management." Systemic Practice and Action Research 29, no. 3 (November 2, 2015): 261–75. http://dx.doi.org/10.1007/s11213-015-9363-2.
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McElreath, Richard, Adrian V. Bell, Charles Efferson, Mark Lubell, Peter J. Richerson, and Timothy Waring. "Beyond existence and aiming outside the laboratory: estimating frequency-dependent and pay-off-biased social learning strategies." Philosophical Transactions of the Royal Society B: Biological Sciences 363, no. 1509 (September 17, 2008): 3515–28. http://dx.doi.org/10.1098/rstb.2008.0131.
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The existence of social learning has been confirmed in diverse taxa, from apes to guppies. In order to advance our understanding of the consequences of social transmission and evolution of behaviour, however, we require statistical tools that can distinguish among diverse social learning strategies. In this paper, we advance two main ideas. First, social learning is diverse, in the sense that individuals can take advantage of different kinds of information and combine them in different ways. Examining learning strategies for different information conditions illuminates the more detailed design of social learning. We construct and analyse an evolutionary model of diverse social learning heuristics, in order to generate predictions and illustrate the impact of design differences on an organism's fitness. Second, in order to eventually escape the laboratory and apply social learning models to natural behaviour, we require statistical methods that do not depend upon tight experimental control. Therefore, we examine strategic social learning in an experimental setting in which the social information itself is endogenous to the experimental group, as it is in natural settings. We develop statistical models for distinguishing among different strategic uses of social information. The experimental data strongly suggest that most participants employ a hierarchical strategy that uses both average observed pay-offs of options as well as frequency information, the same model predicted by our evolutionary analysis to dominate a wide range of conditions.
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Wilson, Christopher, and David K. Marcus. "Teaching Anatomy of the Sheep Brain: A Laboratory Exercise with PlayDoh™." Teaching of Psychology 19, no. 4 (December 1992): 223–25. http://dx.doi.org/10.1207/s15328023top1904_6.
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Undergraduates gain a three-dimensional view of the structures of the sheep brain, first by following a standard dissection procedure and then by constructing a model using PlayDoh™. Both methods demonstrate evolutionary trends in brain development. Students reported that the lab was helpful for learning about neuroanatomy, and they recommended its use in future semesters.
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Zandberg, Lies, Robert F. Lachlan, Luca Lamoni, and Ellen C. Garland. "Global cultural evolutionary model of humpback whale song." Philosophical Transactions of the Royal Society B: Biological Sciences 376, no. 1836 (September 6, 2021): 20200242. http://dx.doi.org/10.1098/rstb.2020.0242.
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Humpback whale song is an extraordinary example of vocal cultural behaviour. In northern populations, the complex songs show long-lasting traditions that slowly evolve, while in the South Pacific, periodic revolutions occur when songs are adopted from neighbouring populations and rapidly spread. In this species, vocal learning cannot be studied in the laboratory, learning is instead inferred from the songs' complexity and patterns of transmission. Here, we used individual-based cultural evolutionary simulations of the entire Southern and Northern Hemisphere humpback whale populations to formalize this process of inference. We modelled processes of song mutation and patterns of contact among populations and compared our model with patterns of song theme sharing measured in South Pacific populations. Low levels of mutation in combination with rare population interactions were sufficient to closely fit the pattern of diversity in the South Pacific, including the distinctive pattern of west-to-east revolutions. Interestingly, the same learning parameters that gave rise to revolutions in the Southern Hemisphere simulations gave rise to evolutionary patterns of cultural evolution in the Northern Hemisphere populations. Our study demonstrates how cultural evolutionary approaches can be used to make inferences about the learning processes underlying cultural transmission and how they might generate emergent population-level processes. This article is part of the theme issue ‘Vocal learning in animals and humans’.
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Perry, Judy, Eli Meir, Jon C. Herron, Susan Maruca, and Derek Stal. "Evaluating Two Approaches to Helping College Students Understand Evolutionary Trees through Diagramming Tasks." CBE—Life Sciences Education 7, no. 2 (June 2008): 193–201. http://dx.doi.org/10.1187/cbe.07-01-0007.
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To understand evolutionary theory, students must be able to understand and use evolutionary trees and their underlying concepts. Active, hands-on curricula relevant to macroevolution can be challenging to implement across large college-level classes where textbook learning is the norm. We evaluated two approaches to helping students learn macroevolutionary topics. Treatment 1 is a laboratory for the software program EvoBeaker designed to teach students about evolutionary trees. We tested Treatment 1 among nine college-level biology classes and administered pre/posttests to assess learning gains. We then sought to determine whether the learning gains from Treatment 1 were comparable to those derived from an alternate hands-on treatment, specifically the combination of a prerecorded lecture on DVD and paper-based activity based on Goldsmith's Great Clade Race (Treatment 2). Comparisons of pre- and posttests among participants using either Treatment 1 or 2 show large learning gains on some misconceptions and skills beyond knowledge gained from reading standard textbook entries. Both treatments performed equivalently in overall learning gains, though both had areas where they performed better or worse. Furthermore, gains among students who used Treatment 1 representing a wide range of universities suggest that outcomes are potentially applicable to a variety of “real-world” biology classes.
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Aamodt, Caitlin M., Madza Farias-Virgens, and Stephanie A. White. "Birdsong as a window into language origins and evolutionary neuroscience." Philosophical Transactions of the Royal Society B: Biological Sciences 375, no. 1789 (November 18, 2019): 20190060. http://dx.doi.org/10.1098/rstb.2019.0060.
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Humans and songbirds share the key trait of vocal learning, manifested in speech and song, respectively. Striking analogies between these behaviours include that both are acquired during developmental critical periods when the brain's ability for vocal learning peaks. Both behaviours show similarities in the overall architecture of their underlying brain areas, characterized by cortico-striato-thalamic loops and direct projections from cortical neurons onto brainstem motor neurons that control the vocal organs. These neural analogies extend to the molecular level, with certain song control regions sharing convergent transcriptional profiles with speech-related regions in the human brain. This evolutionary convergence offers an unprecedented opportunity to decipher the shared neurogenetic underpinnings of vocal learning. A key strength of the songbird model is that it allows for the delineation of activity-dependent transcriptional changes in the brain that are driven by learned vocal behaviour. To capitalize on this advantage, we used previously published datasets from our laboratory that correlate gene co-expression networks to features of learned vocalization within and after critical period closure to probe the functional relevance of genes implicated in language. We interrogate specific genes and cellular processes through converging lines of evidence: human-specific evolutionary changes, intelligence-related phenotypes and relevance to vocal learning gene co-expression in songbirds. This article is part of the theme issue ‘What can animal communication teach us about human language?’
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Astuti, Wahyu Pangestuning, Murni Ramli, and Suranto Suranto. "Validity and Practicality of Sangiran Site-Based Virtual Laboratory Learning Media on Evolutionary Materials to Empower Science Literacy." Jurnal Penelitian Pendidikan IPA 8, no. 3 (July 31, 2022): 1378–84. http://dx.doi.org/10.29303/jppipa.v8i3.1672.
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The validity and practicality of the media are a condition before it can be widely piloted. This research aims to find out the validity and practicality of the Evolution Virtual Laboratory Learning Media, which was developed based on the artefacts of the Sangiran Site to empower science literacy of students. The media validity test using expert judgment involved two expert validators, and two high school biology teachers. While the media practicality test involved 20 grade 12th students. The instrument used was a validity questionnaire consisting of 9 items (material experts), 18 items (media experts), and 13 items (practitioners). Questionnaire instruments to students as many as 16 items. All questionnaires use the Likert Scale. The test results showed material experts rated 86.80%, media experts 84.6%, education practitioners 84.30%, and students by 79.00%. Based on the validity and practicality of the Sangiran Site-based Evolution virtual laboratory learning media is declared valid and practical, so it can be used for effectiveness testing.
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Whiten, Andrew. "A second inheritance system: the extension of biology through culture." Interface Focus 7, no. 5 (August 18, 2017): 20160142. http://dx.doi.org/10.1098/rsfs.2016.0142.
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By the mid-twentieth century (thus following the ‘Modern Synthesis’ in evolutionary biology), the behavioural sciences offered only the sketchy beginnings of a scientific literature documenting evidence for cultural inheritance in animals—the transmission of traditional behaviours via learning from others (social learning). By contrast, recent decades have seen a massive growth in the documentation of such cultural phenomena, driven by long-term field studies and complementary laboratory experiments. Here, I review the burgeoning scope of discoveries in this field, which increasingly suggest that this ‘second inheritance system’, built on the shoulders of the primary genetic inheritance system, occurs widely among vertebrates and possibly in invertebrates too. Its novel characteristics suggest significant implications for our understanding of evolutionary biology. I assess the extent to which this second system extends the scope of evolution, both by echoing principal properties of the primary, organic evolutionary system, and going beyond it in significant ways. This is well established in human cultural evolution; here, I address animal cultures more generally. The further major, and related, question concerns the extent to which the consequences of widespread animal cultural transmission interact with the primary, genetically based inheritance systems, shaping organic evolution.
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Nguyen, Thanh V., Ockie J. H. Bosch, and Nam C. Nguyen. "Using the Evolutionary Learning Laboratory Approach to Establish a World First Model for Integrated Governance of Haiphong, Vietnam." Systems Research and Behavioral Science 31, no. 5 (September 2014): 627–41. http://dx.doi.org/10.1002/sres.2311.
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McAuliffe, William H. B., Maxwell N. Burton-Chellew, and Michael E. McCullough. "Cooperation and Learning in Unfamiliar Situations." Current Directions in Psychological Science 28, no. 5 (June 24, 2019): 436–40. http://dx.doi.org/10.1177/0963721419848673.
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Human social life is rife with uncertainty. In any given encounter, one can wonder whether cooperation will generate future benefits. Many people appear to resolve this dilemma by initially cooperating, perhaps because (a) encounters in everyday life often have future consequences, and (b) the costs of alienating oneself from long-term social partners often outweighed the short-term benefits of acting selfishly over our evolutionary history. However, because cooperating with other people does not always advance self-interest, people might also learn to withhold cooperation in certain situations. Here, we review evidence for two ideas: that people (a) initially cooperate or not depending on the incentives that are typically available in their daily lives and (b) also learn through experience to adjust their cooperation on the basis of the incentives of unfamiliar situations. We compare these claims with the widespread view that anonymously helping strangers in laboratory settings is motivated by altruistic desires. We conclude that the evidence is more consistent with the idea that people stop cooperating in unfamiliar situations because they learn that it does not help them, either financially or through social approval.
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Babayan, Simon A., Richard J. Orton, and Daniel G. Streicker. "Predicting reservoir hosts and arthropod vectors from evolutionary signatures in RNA virus genomes." Science 362, no. 6414 (November 1, 2018): 577–80. http://dx.doi.org/10.1126/science.aap9072.
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Identifying the animal origins of RNA viruses requires years of field and laboratory studies that stall responses to emerging infectious diseases. Using large genomic and ecological datasets, we demonstrate that animal reservoirs and the existence and identity of arthropod vectors can be predicted directly from viral genome sequences via machine learning. We illustrate the ability of these models to predict the epidemiology of diverse viruses across most human-infective families of single-stranded RNA viruses, including 69 viruses with previously elusive or never-investigated reservoirs or vectors. Models such as these, which capitalize on the proliferation of low-cost genomic sequencing, can narrow the time lag between virus discovery and targeted research, surveillance, and management.
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Henrich, Joseph, and James Broesch. "On the nature of cultural transmission networks: evidence from Fijian villages for adaptive learning biases." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1567 (April 12, 2011): 1139–48. http://dx.doi.org/10.1098/rstb.2010.0323.
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Unlike other animals, humans are heavily dependent on cumulative bodies of culturally learned information. Selective processes operating on this socially learned information can produce complex, functionally integrated, behavioural repertoires—cultural adaptations. To understand such non-genetic adaptations, evolutionary theorists propose that (i) natural selection has favoured the emergence of psychological biases for learning from those individuals most likely to possess adaptive information, and (ii) when these psychological learning biases operate in populations, over generations, they can generate cultural adaptations. Many laboratory experiments now provide evidence for these psychological biases. Here, we bridge from the laboratory to the field by examining if and how these biases emerge in a small-scale society. Data from three cultural domains—fishing, growing yams and using medicinal plants—show that Fijian villagers (ages 10 and up) are biased to learn from others perceived as more successful/knowledgeable, both within and across domains (prestige effects). We also find biases for sex and age, as well as proximity effects. These selective and centralized oblique transmission networks set up the conditions for adaptive cultural evolution.
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Akbar, F., A. Ghosh, S. Young, S. Akhter, Z. Ahmad Dar, V. Ansari, M. V. Ascencio, et al. "Vertex finding in neutrino-nucleus interaction: a model architecture comparison." Journal of Instrumentation 17, no. 08 (August 1, 2022): T08013. http://dx.doi.org/10.1088/1748-0221/17/08/t08013.
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Abstract We compare different neural network architectures for machine learning algorithms designed to identify the neutrino interaction vertex position in the MINERvA detector. The architectures developed and optimized by hand are compared with the architectures developed in an automated way using the package “Multi-node Evolutionary Neural Networks for Deep Learning” (MENNDL), developed at Oak Ridge National Laboratory. While the domain-expert hand-tuned network was the best performer, the differences were negligible and the auto-generated networks performed as well. There is always a trade-off between human, and computer resources for network optimization and this work suggests that automated optimization, assuming resources are available, provides a compelling way to save significant expert time.
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Amini, Azizah Nur, and Hanafi Eko Darono. "PERANCANGAN SISTEM VIRTUAL LABORATORY PRAKTIKUM RESPIRASI KELAS INSEKTA PADA SMA NEGERI 98 JAKARTA." INTI Nusa Mandiri 15, no. 1 (August 2, 2020): 65–72. http://dx.doi.org/10.33480/inti.v15i1.1408.
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Dalam dunia pendidikan, e-learning dan virtual laboratorium menjadi bentuk penyesuaian terhadap perkembangan sistem informasi yang ada. SMA Negeri 98 Jakarta membutuhkan adanya suatu sistem informasi yang dapat menunjang kegiatan belajar mengajar. Untuk itulah penulis membangun perancangan sistem virtual lab di SMA Negeri 98 Jakarta khususnya pada mata pelajaran biologi praktikum respincarasi kelas insekta. Pada saat ini, SMA Negeri 98 Jakarta masih terkendala dalam penggunaan ruang laboratorium, dimana hanya ada satu ruangan dan tidak adanya laboran yang mengatur jadwal penggunaan ruang laboratorium. Selain itu, siswa juga dinilai masih kurang memahami cara kerja dan penggunaan alat praktikum. Pembuatan rancangan sistem virtual laboratory sebagai solusi yang terbaik ini menggunakan metode penelitian dan pengembangan sistem evolutionary prototype dimana tahapan ini melalui analisa kebutuhan user, pembuatan, penyesuaian dan penggunaan prototype. Hasil pembuatan perancangan sistem ini bertujuan untuk menjadi bahan referensi SMA Negeri 98 Jakarta untuk membuat sistem virtual laboratory agar kegiatan praktikum dapat berjalan dengan efisien dan efektif.
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Davidson, Gabrielle L., Amy C. Cooke, Crystal N. Johnson, and John L. Quinn. "The gut microbiome as a driver of individual variation in cognition and functional behaviour." Philosophical Transactions of the Royal Society B: Biological Sciences 373, no. 1756 (August 13, 2018): 20170286. http://dx.doi.org/10.1098/rstb.2017.0286.
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Research into proximate and ultimate mechanisms of individual cognitive variation in animal populations is a rapidly growing field that incorporates physiological, behavioural and evolutionary investigations. Recent studies in humans and laboratory animals have shown that the enteric microbial community plays a central role in brain function and development. The ‘gut–brain axis’ represents a multi-directional signalling system that encompasses neurological, immunological and hormonal pathways. In particular it is tightly linked with the hypothalamic–pituitary–adrenal axis (HPA), a system that regulates stress hormone release and influences brain development and function. Experimental examination of the microbiome through manipulation of diet, infection, stress and exercise, suggests direct effects on cognition, including learning and memory. However, our understanding of these processes in natural populations is extremely limited. Here, we outline how recent advances in predominantly laboratory-based microbiome research can be applied to understanding individual differences in cognition. Experimental manipulation of the microbiome across natal and adult environments will help to unravel the interplay between cognitive variation and the gut microbial community. Focus on individual variation in the gut microbiome and cognition in natural populations will reveal new insight into the environmental and evolutionary constraints that drive individual cognitive variation. This article is part of the theme issue ‘Causes and consequences of individual differences in cognitive abilities’.
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Plum, Karissa, Jason Tarkington, and Rebecca A. Zufall. "Experimental Evolution in Tetrahymena." Microorganisms 10, no. 2 (February 11, 2022): 414. http://dx.doi.org/10.3390/microorganisms10020414.
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Experimental evolution has provided novel insight into a wide array of biological processes. Species in the genus Tetrahymena are proving to be a highly useful system for studying a range of questions using experimental evolution. Their unusual genomic architecture, diversity of life history traits, importance as both predator and prey, and amenability to laboratory culture allow them to be studied in a variety of contexts. In this paper, we review what we are learning from experimental evolution with Tetrahymena about mutation, adaptation, and eco-evolutionary dynamics. We predict that future experimental evolution studies using Tetrahyemena will continue to shed new light on these processes.
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Hanauer, David I., Mark J. Graham, Laura Betancur, Aiyana Bobrownicki, Steven G. Cresawn, Rebecca A. Garlena, Deborah Jacobs-Sera, et al. "An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning." Proceedings of the National Academy of Sciences 114, no. 51 (December 5, 2017): 13531–36. http://dx.doi.org/10.1073/pnas.1718188115.
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Engaging undergraduate students in scientific research promises substantial benefits, but it is not accessible to all students and is rarely implemented early in college education, when it will have the greatest impact. An inclusive Research Education Community (iREC) provides a centralized scientific and administrative infrastructure enabling engagement of large numbers of students at different types of institutions. The Science Education Alliance–Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) is an iREC that promotes engagement and continued involvement in science among beginning undergraduate students. The SEA-PHAGES students show strong gains correlated with persistence relative to those in traditional laboratory courses regardless of academic, ethnic, gender, and socioeconomic profiles. This persistent involvement in science is reflected in key measures, including project ownership, scientific community values, science identity, and scientific networking.
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Everson, Kathryn, and Link Olson. "Integrating Phylogenetics and Morphology to Study Diversification and Species Limits in Madagascar’s Tenrecs (Tenrecidae)." Biodiversity Information Science and Standards 2 (May 21, 2018): e25936. http://dx.doi.org/10.3897/biss.2.25936.
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Madagascar is one of the world’s hottest biodiversity hotspots and a natural laboratory for evolutionary research. Tenrecs (Tenrecidae; 32 currently recognized species) – small placental mammals endemic to Madagascar – colonized the island >35 million years ago and have evolved a stunning range of behaviors and morphologies, including heterothermic species; species with hedgehog-like spines; and fossorial, aquatic, and scansorial ecotypes. In 2016, we produced the first taxonomically complete phylogeny of tenrecs, which has served as a framework for studying morphological evolution, phylogeography, and species limits. Most recently, we have built on this phylogeny to incorporate an enormous database of genetic, morphometric, and geographic data from >800 vouchered tenrec specimens. These data have revealed interesting and unexpected aspects of their evolutionary history, including decoupled diversification of the cranium and postcranium. Using a machine learning approach, we have also uncovered numerous new, cryptic species in the family Tenrecidae. As phylogenetic and phenotypic data become more readily available through online repositories, we expect that the same approaches can be applied to other taxonomic groups, providing unprecented resolution of the tree of life.
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Ha, Tuan M., Ockie J. H. Bosch, and Nam C. Nguyen. "Establishing an Evolutionary Learning Laboratory for Improving the Quality of Life of Vietnamese Women in Small-scale Agriculture: Part II - Systemic Interventions." Systems Research and Behavioral Science 33, no. 3 (July 15, 2015): 341–59. http://dx.doi.org/10.1002/sres.2349.
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Ha, Tuan M., Ockie J. H. Bosch, and Nam C. Nguyen. "Establishing an Evolutionary Learning Laboratory for Improving the Quality of Life of Vietnamese Women in Small-scale Agriculture: Part I-The Current Situation." Systems Research and Behavioral Science 33, no. 4 (July 14, 2015): 532–43. http://dx.doi.org/10.1002/sres.2346.
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LaDage, Lara D. "Factors That Modulate Neurogenesis: A Top-Down Approach." Brain, Behavior and Evolution 87, no. 3 (2016): 184–90. http://dx.doi.org/10.1159/000446906.
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Although hippocampal neurogenesis in the adult brain has been conserved across the vertebrate lineage, laboratory studies have primarily examined this phenomenon in rodent models. This approach has been successful in elucidating important factors and mechanisms that can modulate rates of hippocampal neurogenesis, including hormones, environmental complexity, learning and memory, motor stimulation, and stress. However, recent studies have found that neurobiological research on neurogenesis in rodents may not easily translate to, or explain, neurogenesis patterns in nonrodent systems, particularly in species examined in the field. This review examines some of the evolutionary and ecological variables that may also modulate neurogenesis patterns. This ‘top-down' and more naturalistic approach, which incorporates ecology and natural history, particularly of nonmodel species, may allow for a more comprehensive understanding of the functional significance of neurogenesis.
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Sandaruwan, Pahalage Dhanushka, and Champi Thusangi Wannige. "An improved deep learning model for hierarchical classification of protein families." PLOS ONE 16, no. 10 (October 20, 2021): e0258625. http://dx.doi.org/10.1371/journal.pone.0258625.
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Although genes carry information, proteins are the main role player in providing all the functionalities of a living organism. Massive amounts of different proteins involve in every function that occurs in a cell. These amino acid sequences can be hierarchically classified into a set of families and subfamilies depending on their evolutionary relatedness and similarities in their structure or function. Protein characterization to identify protein structure and function is done accurately using laboratory experiments. With the rapidly increasing huge amount of novel protein sequences, these experiments have become difficult to carry out since they are expensive, time-consuming, and laborious. Therefore, many computational classification methods are introduced to classify proteins and predict their functional properties. With the progress of the performance of the computational techniques, deep learning plays a key role in many areas. Novel deep learning models such as DeepFam, ProtCNN have been presented to classify proteins into their families recently. However, these deep learning models have been used to carry out the non-hierarchical classification of proteins. In this research, we propose a deep learning neural network model named DeepHiFam with high accuracy to classify proteins hierarchically into different levels simultaneously. The model achieved an accuracy of 98.38% for protein family classification and more than 80% accuracy for the classification of protein subfamilies and sub-subfamilies. Further, DeepHiFam performed well in the non-hierarchical classification of protein families and achieved an accuracy of 98.62% and 96.14% for the popular Pfam dataset and COG dataset respectively.
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Cummings, Molly E. "Looking for sexual selection in the female brain." Philosophical Transactions of the Royal Society B: Biological Sciences 367, no. 1600 (August 19, 2012): 2348–56. http://dx.doi.org/10.1098/rstb.2012.0105.
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Female mate choice behaviour has significant evolutionary consequences, yet its mechanistic origins are not fully understood. Recent studies of female sensory systems have made great strides in identifying internal mechanisms governing female preferences. Only recently, however, have we begun to identify the dynamic genomic response associated with mate choice behaviour. Poeciliids provide a powerful comparative system to examine genomic responses governing mate choice and female preference behaviour, given the great range of mating systems: from female mate choice taxa with ornamental courting males to species lacking male ornamentation and exhibiting only male coercion. Furthermore, they exhibit laboratory-tractable preference responses without sexual contact that are decoupled from reproductive state, allowing investigators to isolate mechanisms in the brain without physiological confounds. Early investigations with poeciliid species ( Xiphophorus nigrensis and Gambusia affinis ) have identified putative candidate genes associated with female preference response and highlight a possible genomic pathway underlying female social interactions with males linked functionally with synaptic plasticity and learning processes. This network is positively correlated with female preference behaviour in the female mate choice species, but appears inhibited in the male coercive species. This behavioural genomics approach provides opportunity to elucidate the fundamental building blocks, and evolutionary dynamics, of sexual selection.
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Kelley, Patricia H., and Christy C. Visaggi. "Learning Paleontology Through Doing: Integrating an Authentic Research Project into an Invertebrate Paleontology Course." Paleontological Society Special Publications 12 (2012): 181–98. http://dx.doi.org/10.1017/s247526220000931x.
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We implemented an authentic research experience as part of the invertebrate paleontology course at University of North Carolina Wilmington to promote student learning objectives related to understanding course content, critical thinking, problem solving, and oral and written communication. This semester-long research project, worth 20% of the course grade, is incorporated into the laboratory component of the course, and employs best practices of active and collaborative learning. Students work as teams to develop and test paleoecological and/or evolutionary hypotheses using field-collected or archived bulk samples. Following sample processing, specimen identification, and data collecting and analysis, students write a research paper using the format of a professional paper, with individually and team-written parts, and present their results orally. After completion, one or more abstracts based on the results are submitted to a professional meeting. Typically, several students attend the meeting and present the posters. This approach allows students to experience authentic research from conception to dissemination. Since 2003, the course has been offered seven times, resulting in 13 published and presented abstracts. Over half the students remained involved in paleontology following the course by presenting the work or taking additional courses or independent study, demonstrating that the experience was received positively. This approach provides a model for other instructors, as the research project can be adapted to a variety of geological settings and topics. Successes and challenges in implementing such a project are discussed.
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Dávila, Nállarett, Edweslley Moura, Leonardo M. Versieux, Fernanda Antunes Carvalho, and Alice Calvente. "Urban Forest Fragments as a Living Laboratory for Teaching Botany: An Example from Federal University of Rio Grande do Norte, Brazil." Systematic Botany 46, no. 1 (March 29, 2021): 6–17. http://dx.doi.org/10.1600/036364421x16128061189378.
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Abstract—“Plant blindness” is affecting humans’ relationships with plants, which has negative consequences for both science and conservation. It is, therefore, important to find new ways to promote societal interest in botany and plants. One possibility is encouraging the use of informal settings to promote curiosity and provide education to students. Forest fragments can be regarded as open air labs for teaching botany, especially on university campuses. We aimed to formally document the angiosperm diversity in the Mata dos Saguis (MS), a fragment of Atlantic forest under restoration belonging to the central campus of the Federal University of Rio Grande do Norte (UFRN), Brazil. We recorded 140 species, 113 genera in 52 families, and 24 orders of angiosperms. The MS has nearly 10% of the species and one third of all the families occurring in the entire state of Rio Grande do Norte, representing the main evolutionary groups of angiosperms, and we also recorded two new species occurrences for the state. Here we provide a checklist of the MS, a location that has been used as an open-air laboratory by many UFRN undergraduate courses in biosciences. We also share examples that can be replicated in other institutions and discuss the process of learning systematic botany in floristically rich countries by means of alternative and hands-on experiences.
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Fitch, W. Tecumseh. "On the Biology and Evolution of Music." Music Perception 24, no. 1 (September 1, 2006): 85–88. http://dx.doi.org/10.1525/mp.2006.24.1.85.
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I suggest that the question of whether music is an adaptation has been overemphasized in recent discussions of the biology and evolution of music, because the subtleties of this question combine with our poor fossil record for musical abilities of extinct hominids to render many of the key facts necessary to answer it empirically inaccessible, for now and perhaps forever. Thus the “adaptation question” seems a poor choice as a defining issue for the new but rapidly growing field of biomusicology. This field will be better served if we treat this and similar evolutionary questions as “intuition pumps” to help generate testable hypotheses that spur further experimental work on living animals (in both laboratory and field) and humans. In addition to work on music perception, studies of production in animals such as songbirds and humpback whales will play an important role. Finally, I suggest that the distinction between culture and biology made by many in the field creates a false dichotomy: like birdsong learning, human musical ability is better treated as an “instinct to learn” with biological and cultural aspects intimately intertwined.
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Ferrari, Maud C. O., Brian D. Wisenden, and Douglas P. Chivers. "Chemical ecology of predator–prey interactions in aquatic ecosystems: a review and prospectusThe present review is one in the special series of reviews on animal–plant interactions." Canadian Journal of Zoology 88, no. 7 (July 2010): 698–724. http://dx.doi.org/10.1139/z10-029.
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The interaction between predator and prey is an evolutionary arms race, for which early detection by either party is often the key to success. In aquatic ecosystems, olfaction is an essential source of information for many prey and predators and a number of cues have been shown to play a key role in trait-mediated indirect interactions in aquatic communities. Here, we review the nature and role of predator kairomones, chemical alarm cues, disturbance cues, and diet cues on the behaviour, morphology, life history, and survival of aquatic prey, focusing primarily on the discoveries from the last decade. Many advances in the field have been accomplished: testing the survival value of those chemicals, providing field validation of laboratory results, understanding the extent to which chemically mediated learning may benefit the prey, understanding the role of these chemicals in mediating morphological and life-history adaptations, and most importantly, the selection pressures leading to the evolution of chemical alarm cues. Although considerable advances have been made, several key questions remain, the most urgent of which is to understand the chemistry behind these interactions.
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Benbrahim, Houssam, Hanaâ Hachimi, and Aouatif Amine. "Deep Convolutional Neural Network with TensorFlow and Keras to Classify Skin Cancer Images." Scalable Computing: Practice and Experience 21, no. 3 (August 1, 2020): 379–90. http://dx.doi.org/10.12694/scpe.v21i3.1725.
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Skin cancer is a dangerous disease causing a high proportion of deaths around the world. Any diagnosis of cancer begins with a careful clinical examination, followed by a blood test and medical imaging examinations. Medical imaging is today one of the main tools for diagnosing cancers. It allows us to obtain precise images, internal organs and thus to visualize the possible tumours that they present. These images provide information on the location, size and evolutionary stage of tumour lesions. Automatic classification of skin tumours using images is an important task that can help doctors, laboratory technologists, and researchers to make the best decisions. This work has developed a classification model of skin tumours in images using Deep Learning with a Convolutional Neural Network based on TensorFlow and Keras model. This architecture is tested in the HAM10000 dataset consists of 10,015 dermatoscopic images. The results of the classification of the experiment show that the accuracy was achieved by our model, which is in order of 94.06% in the validation set and 93.93% in the test set.
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Honess, P., M.-A. Stanley-Griffiths, S. Narainapoulle, S. Naiken, and T. Andrianjazalahatra. "Selective breeding of primates for use in research: consequences and challenges." Animal Welfare 19, S1 (May 2010): 57–65. http://dx.doi.org/10.1017/s0962728600002244.
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AbstractPrimates are bred in captivity for a number of purposes, from zoo-based captive breeding programmes for conservation to breeding for biomedical research. In each case, breeding animals that are fit for purpose, either as viable candidates for reintroduction or as valid research models, has presented challenges and resulted in steep learning curves. The breeding of animals for biomedical research has become increasingly focused on the production of animals that are less stressed by captive (specifically laboratory) environments. This is because elevated, particularly chronic, stress responses can result in altered physiological, neurological and behavioural states that have the potential to compromise the validity of scientific results. Selective breeding in captivity to, for example, maximise production, select for docile temperament or specific genotypes for biomedical research, is likely to be counter to natural selective pressures for evolutionary fitness. Given that many natural selective pressures active in the wild are absent in captivity, this paper reviews the selective breeding of primates (especially Old World monkeys) in captivity, its potential negative effects, and options that exist for ameliorating these negative effects.
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Chen, Jong-Chen. "Continual Learning for Addressing Optimization Problems with a Snake-Like Robot Controlled by a Self-Organizing Model." Applied Sciences 10, no. 14 (July 15, 2020): 4848. http://dx.doi.org/10.3390/app10144848.
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We have entered a new era, “Industry 4.0”, that sees the overall industry marching toward an epoch of man–machine symbiosis and intelligent production. The developers of so-called “intelligent” systems must attempt to seriously take into account all possible situations that might occur in the real world, to minimize unexpected errors. By contrast, biological systems possess comparatively better “adaptability” than man-made machines, as they possess a self-organizing learning that plays an indispensable role. The objective of this study was to apply a malleable learning system to the movement control of a snake-like robot, to investigate issues related to self-organizing dynamics. An artificial neuromolecular (ANM) system previously developed in our laboratory was used to control the movements of an eight-joint snake-like robot (called Snaky). The neuromolecular model is a multilevel neural network that abstracts biological structure–function relationships into the system’s structure, in particular into its intraneuronal structure. With this feature, the system possesses structure richness in generating a broad range of dynamics that allows it to learn how to complete the assigned tasks in a self-organizing manner. The activation and rotation angle of each motor are dependent on the firing activity of neurons that control the motor. An evolutionary learning algorithm is used to train the system to complete the assigned tasks. The key issues addressed include the self-organizing learning capability of the ANM system in a physical environment. The experimental results show that Snaky was capable of learning in a continuous manner. We also examined how the ANM system controlled the angle of each of Snaky’s joints, to complete each assigned task. The result might provide us with another dimension of information on how to design the movement of a snake-like robot.
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Greggor, Alison Linda. "A functional paradigm for evaluating culture: An example with cetaceans." Current Zoology 58, no. 2 (April 1, 2012): 271–86. http://dx.doi.org/10.1093/czoolo/58.2.271.
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Abstract Nonhuman culture was first considered in nonhuman primates because they are genetically similar to humans. However, evolution is not progressive and therefore many species may occupy niches that favor socially transmitted, group specific behavior. Not surprisingly, evidence for culture has accrued in several taxonomic groups, including cetaceans. If culture is an adaptation, it is imperative we understand the factors that favor its formation. Understanding the evolutionary origin of culture will allow for a wider range of species to be studied, including those that are difficult to test in the laboratory. I propose a broad-based functional paradigm for evaluating nonhuman culture; based on the idea that while not all cultural behaviors may garner fitness benefits to the individual, the ecological and social environments in which cultural behaviors evolved must have favored the physical attributes and social learning capabilities that allow for cultural formation. Specifically this framework emphasizes the relationships between social learning, ecology, social systems, and biology in relation to culture. I illustrate the utility of the functional paradigm with evidence from the ceteacean group, while setting the stage for a stringent species by species analysis. By means of contextualizing culture, the Functional Paradigm can evaluate a species’ potential to exhibit culture and can investigate potentially cultural behaviors [Current Zoology 58 (2): 271–286, 2012].
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Sulikowski, Danielle, and Darren Burke. "From the lab to the world: The paradigmatic assumption and the functional cognition of avian foraging." Current Zoology 61, no. 2 (April 1, 2015): 328–40. http://dx.doi.org/10.1093/czoolo/61.2.328.
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Abstract Mechanisms of animal learning and memory were traditionally studied without reference to niche-specific functional considerations. More recently, ecological demands have informed such investigations, most notably with respect to foraging in birds. In parallel, behavioural ecologists, primarily concerned with functional optimization, have begun to consider the role of mechanistic factors, including cognition, to explain apparent deviations from optimal predictions. In the present paper we discuss the application of laboratory-based constructs and paradigms of cognition to the real-world challenges faced by avian foragers. We argue that such applications have been handicapped by what we term the ‘paradigmatic assumption’ – the assumption that a given laboratory paradigm maps well enough onto a congruent cognitive mechanism (or cognitive ability) to justify conflation of the two. We present evidence against the paradigmatic assumption and suggest that to achieve a profitable integration between function and mechanism, with respect to animal cognition, a new conceptualization of cognitive mechanisms functional cognition – is required. This new conceptualization should define cognitive mechanisms based on the informational properties of the animal’s environment and the adaptive challenges faced. Cognitive mechanisms must be examined in settings that mimic the important aspects of the natural environment, using customized tasks designed to probe defined aspects of the mechanisms’ operation. We suggest that this approach will facilitate investigations of the functional and evolutionary relevance of cognitive mechanisms, as well as the patterns of divergence, convergence and specialization of cognitive mechanisms within and between species.
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Santamaría-Buitrago, Frey Alfonso, Javier Antonio Ballesteros-Ricaurte, and Ángela María González-Amarillo. "Ecosystem for the deployment and management of virtual laboratories based on the standard IMS LTI." Revista Facultad de Ingeniería 28, no. 53 (October 2, 2019): 79–99. http://dx.doi.org/10.19053/01211129.v28.n53.2019.10148.
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The advancement of information and communication technologies occurs due to the evolutionary capacity of computer equipment as well as the existence of increasingly sophisticated tools and applications. Virtual laboratories, a flexible tool which allows to design, simulate, model and test through experimentation real-life processes, are an example. Virtual laboratories have a great impact on engineering as they improve accessibility to experiments, facilitating the development of strategies in the field of education; they include interactive ways to observe, illustrate, demonstrate and investigate, aside from support system users in the elaboration and exchange of results. For this reason, the experience reflected in this article highlights the design and implementation of an ecosystem for the deployment and management of virtual laboratories, based on the IMS Learning Tools Interoperability standard. In this process, the methods and technologies applicable to the development of virtual laboratories are characterized with an instructional model for experimental environments that identifies the scope of the procedure and the technical criteria, taking into account LabManager, WebLabDeusto and LMS Sakai, and finally the installation and configuration of the cloud platform and the laboratory prototype that responds to the proposed ecosystem.
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Domjan, Michael, Brian Cusato, and Ronald Villarreal. "Pavlovian feed-forward mechanisms in the control of social behavior." Behavioral and Brain Sciences 23, no. 2 (April 2000): 235–49. http://dx.doi.org/10.1017/s0140525x00002430.
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The conceptual and investigative tools for the analysis of social behavior can be expanded by integrating biological theory, control systems theory, and Pavlovian conditioning. Biological theory has focused on the costs and benefits of social behavior from ecological and evolutionary perspectives. In contrast, control systems theory is concerned with how machines achieve a particular goal or purpose. The accurate operation of a system often requires feed-forward mechanisms that adjust system performance in anticipation of future inputs. Pavlovian conditioning is ideally suited to subserve this function in behavioral systems. Pavlovian mechanisms have been demonstrated in various aspects of sexual behavior, maternal lactation, and infant suckling. Pavlovian conditioning of agonistic behavior has been also reported, and Pavlovian processes may likewise be involved in social play and social grooming. Several further lines of evidence indicate that Pavlovian conditioning can increase the efficiency and effectiveness of social interactions, thereby improving their cost/benefit ratio. We extend Pavlovian concepts beyond the traditional domain of discrete secretory and other physiological reflexes to complex real-world behavioral interactions and apply abstract laboratory analyses of the mechanisms of associative learning to the daily challenges animals face as they interact with one another in their natural environments.
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Riley, Noah G., Carlos C. Goller, Zakiya H. Leggett, Danica M. Lewis, Karen Ciccone, and Robert R. Dunn. "Catalyzing rapid discovery of gold-precipitating bacterial lineages with university students." PeerJ 8 (April 14, 2020): e8925. http://dx.doi.org/10.7717/peerj.8925.
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Intriguing and potentially commercially useful microorganisms are found in our surroundings and new tools allow us to learn about their genetic potential and evolutionary history. Engaging students from different disciplines and courses in the search for microbes requires an exciting project with innovative but straightforward procedures and goals. Here we describe an interdisciplinary program to engage students from different courses in the sampling, identification and analysis of the DNA sequences of a unique yet common microbe, Delftia spp. A campus-wide challenge was created to identify the prevalence of this genus, able to precipitate gold, involving introductory level environmental and life science courses, upper-level advanced laboratory modules taken by undergraduate students (juniors and seniors), graduate students and staff from the campus. The number of participants involved allowed for extensive sampling while undergraduate researchers and students in lab-based courses participated in the sample processing and analyses, helping contextualize and solidify their learning of the molecular biology techniques. The results were shared at each step through publicly accessible websites and workshops. This model allows for the rapid discovery of Delftia presence and prevalence and is adaptable to different campuses and experimental questions.
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Staub, Nancy L., Marianne Poxleitner, Amanda Braley, Helen Smith-Flores, Christine M. Pribbenow, Leslie Jaworski, David Lopatto, and Kirk R. Anders. "Scaling Up: Adapting a Phage-Hunting Course to Increase Participation of First-Year Students in Research." CBE—Life Sciences Education 15, no. 2 (June 2016): ar13. http://dx.doi.org/10.1187/cbe.15-10-0211.
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Authentic research experiences are valuable components of effective undergraduate education. Research experiences during the first years of college are especially critical to increase persistence in science, technology, engineering, and mathematics fields. The Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) model provides a high-impact research experience to first-year students but is usually available to a limited number of students, and its implementation is costly in faculty time and laboratory space. To offer a research experience to all students taking introductory biology at Gonzaga University (n = 350/yr), we modified the traditional two-semester SEA-PHAGES course by streamlining the first-semester Phage Discovery lab and integrating the second SEA-PHAGES semester into other courses in the biology curriculum. Because most students in the introductory course are not biology majors, the Phage Discovery semester may be their only encounter with research. To discover whether students benefit from the first semester alone, we assessed the effects of the one-semester Phage Discovery course on students’ understanding of course content. Specifically, students showed improvement in knowledge of bacteriophages, lab math skills, and understanding experimental design and interpretation. They also reported learning gains and benefits comparable with other course-based research experiences. Responses to open-ended questions suggest that students experienced this course as a true undergraduate research experience.
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THOMSON, VICKI, ANDREW WIEWEL, ALDO CHINEN, IBNU MARYANTO, M. H. SINAGA, RIC HOW, KEN APLIN, and HITOSHI SUZUKI. "A perspective for resolving the systematics of Rattus, the vertebrates with the most influence on human welfare." Zootaxa 4459, no. 3 (August 15, 2018): 431. http://dx.doi.org/10.11646/zootaxa.4459.3.2.
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The murid rodent genus Rattus Fischer 1803 contains several species that are responsible for massive loss of crops and food, extinction of other species and the spread of zoonotic diseases to humans, as well as a laboratory species used to answer important questions in physiology, immunology, pharmacology, toxicology, nutrition, behaviour and learning. Despite the well-known significant impacts of Rattus, a definitive evolutionary based systematic framework for the genus is not yet available. The past 75 years have seen more dramatic changes in membership of Rattus than in almost any other genus of mammals. In fact, the Rattus genus has been a receptacle for any generalised Old World murine that lacked morphological specialisation and at one point, has included more than 560 species and/or subspecies, spread across Eurasia, Africa and the Australo-Papuan region. The dissolution of Rattus is ongoing as many of its constituent species and many genera of Rattini remain unsampled in any molecular study. To address this sampling limitation, we sequenced the mitochondrial cytochrome b (cytb) gene and examined phylogenetic relationships using both Bayesian and Maximum Likelihood algorithms for an expanded set of taxa within Rattus and among closely related genera. Here we place previously unsampled taxa in a phylogenetic context for the first time, including R. burrus, R. hoogerwerfi, R. lugens, and R. mindorensis within the Asian Rattus group, R. facetus within the Australo-Papuan Rattus radiation, and the undescribed ‘Bisa Rat’ described by Flannery as sister to the recently described genus Halmaheramys. We also present an exploratory foray into the wider topic of Rattus phylogenetics and propose that a reorganisation of the Rattus genus should require that it be a monophyletic group, include at least the type species R. norvegicus and R. rattus (plus their close allies); and exclude the Bandicota/Nesokia clade and other such specialised genera.
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Pravosudov, Vladimir V., and Tom V. Smulders. "Integrating ecology, psychology and neurobiology within a food-hoarding paradigm." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1542 (March 27, 2010): 859–67. http://dx.doi.org/10.1098/rstb.2009.0216.
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Many animals regularly hoard food for future use, which appears to be an important adaptation to a seasonally and/or unpredictably changing environment. This food-hoarding paradigm is an excellent example of a natural system that has broadly influenced both theoretical and empirical work in the field of biology. The food-hoarding paradigm has played a major role in the conceptual framework of numerous fields from ecology (e.g. plant–animal interactions) and evolution (e.g. the coevolution of caching, spatial memory and the hippocampus) to psychology (e.g. memory and cognition) and neurobiology (e.g. neurogenesis and the neurobiology of learning and memory). Many food-hoarding animals retrieve caches by using spatial memory. This memory-based behavioural system has the inherent advantage of being tractable for study in both the field and laboratory and has been shaped by natural selection, which produces variation with strong fitness consequences in a variety of taxa. Thus, food hoarding is an excellent model for a highly integrative approach to understanding numerous questions across a variety of disciplines. Recently, there has been a surge of interest in the complexity of animal cognition such as future planning and episodic-like-memory as well as in the relationship between memory, the environment and the brain. In addition, new breakthroughs in neurobiology have enhanced our ability to address the mechanisms underlying these behaviours. Consequently, the field is necessarily becoming more integrative by assessing behavioural questions in the context of natural ecological systems and by addressing mechanisms through neurobiology and psychology, but, importantly, within an evolutionary and ecological framework. In this issue, we aim to bring together a series of papers providing a modern synthesis of ecology, psychology, physiology and neurobiology and identifying new directions and developments in the use of food-hoarding animals as a model system.
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Kluska, J., H. Van Winckel, Q. Coppée, G. M. Oomen, K. Dsilva, D. Kamath, V. Bujarrabal, and M. Min. "A population of transition disks around evolved stars: Fingerprints of planets." Astronomy & Astrophysics 658 (February 2022): A36. http://dx.doi.org/10.1051/0004-6361/202141690.
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Context. Post-asymptotic giant branch (post-AGB) binaries are surrounded by massive disks of gas and dust that are similar to the protoplanetary disks that are known to surround young stars. Aims. We assembled a catalog of all known Galactic post-AGB binaries featuring disks. We explore the correlations between the different observables with the aim of learning more about potential disk-binary interactions. Methods. We compiled spectral energy distributions of 85 Galactic post-AGB binary systems. We built a color-color diagram to differentiate between the different disk morphologies traced by the characteristics of the infrared excess. We categorized the different disk types and searched for correlations with other observational characteristics of these systems. Results. Between 8 and 12% of our targets are surrounded by transition disks, that is, disks having no or low near-infrared excess. We find a strong link between these transition disks and the depletion of refractory elements seen on the surface of the post-AGB star. We interpret this correlation as evidence of the presence of a mechanism that stimulates the dust and gas separation within the disk and that also produces the transition disk structure. We propose that such a mechanism is likely to be due to a giant planet carving a hole in the disk, effectively trapping the dust in the outer disk parts. We propose two disk evolutionary scenarios, depending on the actual presence of such a giant planet in the disk. Conclusions. We advocate that giant planets can successfully explain the correlation between the transition disks and the depletion of refractory materials observed in post-AGB binaries. If the planetary scenario is confirmed, disks around post-AGB binaries could be a unique laboratory for testing planet-disk interactions and their influence on the late evolution of binary stars. The question of whether such planets are first- or second-generation bodies also remains to be considered. We argue that these disks are ideal for studying planet formation scenarios in an unprecedented parameter space.
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SAMOILENKO, Oleksandr, Oleksandr STAVYTSKYI, Olena ZAKREVSKA, and Tetiana DANYLCHENKO. "Approaches to the study disciplines of the information technologies' cycle in the economy." Economics. Finances. Law 9, no. - (September 2, 2022): 28–31. http://dx.doi.org/10.37634/efp.2022.9.6.
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Introduction. The paper analyzes the works of scientists on the development of competences in the researched disciplines of the information technology cycle. The distribution of competencies according to different methodologies is shown. The classification of competencies is described. The technological toolkit of a single informational and educational environment has been studied. The concept of accumulation of competences is highlighted. The purpose of thr paper is to investigate the implementation' methodology of the competence approach to the study of the information technology' cycle disciplines Results. The paper presents the main software products. The author's vision of solving the problem of information technology development in universities is presented. The competency-based approach is determined by the pan-European trend of building educational programs of higher education - Tuning and its use in the educational process of Ukraine. The study of general competencies was one of the most important tasks of the implementation of the Tuning project in the educational process. Obtaining the planned results of the educational process is facilitated by the effective organization of independent work of the discipline "Internet technology" with the use of a single informational and educational environment. In such conditions, the approach to evaluation changes. The usual setting of grades for the discipline turns into tying grades to individual competencies that the student must acquire in the process of learning. The assessment for each work becomes multi-component. It has been established that the technological toolkit of a single informational and educational environment is an effective means of assessing the level of competence formation of higher education seekers. To use it, you need to create a "Competence Repository". Conclusions. Summarizing, we can draw the following conclusions. Thus, mastering the content of the disciplines of the cycle of information technologies by students of higher education in the conditions of a single informational and educational environment allows to speed up the process of obtaining and consolidating information, simplifying its perception, mastering a large amount of educational material in a fairly short period of time. Most higher education students are happy to learn new technologies with the help of their devices, develop intellectual abilities and try to increase their level of use of Internet technologies. And teachers get the opportunity to shape the development trajectories of each student; fundamentally new opportunities for the organization of research, project activities and adaptation of educational material to real life; fundamentally new opportunities for knowledge transfer: video lectures, webinars, video broadcasts, integrated practical classes, cooperative laboratory work; online communication. Therefore, the combination of face-to-face and remote forms of education is the next evolutionary step towards providing the educational process with the properties of adaptability, flexibility, openness and mobility.
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Knisbacher, Binyamin A., Ziao Lin, Cynthia K. Hahn, Ferran Nadeu, Martí Duran-Ferrer, Kristen E. Stevenson, Eugen Tausch, et al. "The CLL-1100 Project: Towards Complete Genomic Characterization and Improved Prognostics for CLL." Blood 136, Supplement 1 (November 5, 2020): 3–4. http://dx.doi.org/10.1182/blood-2020-140987.
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Although chronic lymphocytic leukemia (CLL) has been consistently at the forefront of genomic discovery, complete characterization of its genomic landscape has been limited by sample size and cohort diversity. To address this challenge, we assembled and generated new genomic data from CLL samples from ~1100 patients ('CLL-1100'). In total, we analyzed 984 whole-exome sequences (WES), 177 whole-genome sequences (WGS), RNA-sequencing of 717 cases, and 758 methylome profiles. With our large dataset, we had increased sensitivity to detect candidate drivers even with frequency less than 1%. By applying MutSig2CV to the WES data, we identified 89 putative cancer driver genes (q<0.1), 46 of which were novel. New candidate driver genes highlighted cellular pathways including metabolism (e.g. GPS2, CHKB, CD36) and protein synthesis/stability (e.g. RPS16, EEF1A1,USP8), thus expanding our knowledge of the processes contributing to CLL leukemogenesis. Analysis of somatic copy number alterations (CNAs) using GISTIC2 confirmed both high frequency and rarely reported arm-level events, as well as identified 6 novel focal amplifications and 54 deletions (35 new). Many of these genomic regions primarily contained known CLL drivers but also novel drivers found based on somatic single nucleotide variants (e.g. DDX5), providing further evidence that these likely contribute to pathogenesis. Thus, by approximately doubling the previously reported number of driver genes in CLL, we are able to assign a putative driving event to >92% of CLL samples within the cohort. The gain in power was most evident in our characterization of the two major molecular subtypes of CLL, those with mutated (M-CLL) or unmutated (U-CLL) IGHV. Separate WES analyses of 513 M-CLLs and 459 U-CLLs revealed numerous differences between these two subtypes: (i) Mutation analysis revealed 24 and 59 candidate driver genes in M-CLL and U-CLL, respectively (q<0.1). Only a minority of genes were significant in both subgroups (n=13; e.g. TP53, SF3B1, NOTCH1), while most were significant in either M-CLL (n=11; e.g. MYD88, KLHL6, ITPKB) or U-CLL (n=46; e.g. XPO1, BCOR, KRAS). Moreover, IGHV subtype-specific analyses enabled further sensitivity to identify 13 novel putative drivers that were not identified in the pan-CLL analysis (e.g. DIS3 in M-CLL; CHKA in U-CLL); (ii) We found 37 and 46 putative focal CNA drivers specific to M-CLL and U-CLL; (iii) By evaluating mutation clustering in 3-D protein structures (using CLUMPS), we identified additional drivers enriched in M-CLL (e.g. DICER1) or U-CLL (e.g. RPS23, RAF1, MAP2K2) (q<0.1); and finally (iv) inference of timing and order of mutation acquisition (by PhylogicNDT) also revealed distinct evolutionary trajectories between subtypes. Altogether, these results highlight the divergent genomic landscape of the IGHV subtypes. To further understand disease biology and to develop improved prognostic models for this heterogeneous disease, we performed transcriptomic analysis of 610 treatment-naive CLLs after correction for known and inferred covariates (e.g. PEER factors). We identified 8 expression clusters (ECs) that represent subgroups of U-CLL (n=2), M-CLL (n=5) or an intermediate methylation epigenetic subtype (n=1). The ECs were distinguishable based on association (q<0.1) with genomic drivers (e.g. tri(12), SF3B1, XPO1), biological processes (e.g. B-cell differentiation, TNF-𝜶 signaling, oxphos, migration, metabolism) and EC-defining marker genes (e.g. LPL, CTLA4, HCK, BCL7A, TOX2). Multivariable analysis including clinical features and IGHV subtype, revealed distinct outcomes, demonstrating their prognostic potential (OS p=0.013). Of note, ~10% of M-CLLs had U-CLL-like expression profiles and vice-versa. The known difference in clinical outcome between the IGHV subtypes was not observed within these non-canonical cases (OS log-rank p>0.05; p<0.01 for reduced OS difference in comparison to canonical M-CLL vs. U-CLL). Finally, we used machine-learning to robustly classify new samples into these ECs to demonstrate the potential for future clinical utility. Altogether, the CLL-1100 cohort facilitates novel genomic discovery with multiomic insights and cross-validation, showing the distinct molecular spectrum of a diverse patient population. This sets the stage for the development of comprehensive and more precise genome-based prognostic tools. Disclosures Nadeu: Janssen: Honoraria. Tausch:AbbVie: Consultancy, Honoraria, Research Funding; Roche: Consultancy, Honoraria, Research Funding; Janssen-Cilag: Consultancy, Honoraria, Research Funding. Wiestner:Pharmacyclics LLC, an AbbVie Company, Acerta, Merck, Nurix, Verastem, and Genmab: Research Funding; NIH: Patents & Royalties: NIH. Burger:AstraZeneca: Consultancy; Gilead Sciences: Consultancy, Research Funding; Janssen Pharmaceuticals: Consultancy, Speakers Bureau; Beigene: Research Funding, Speakers Bureau; Pharmacyclics, an AbbVie company: Consultancy, Research Funding, Speakers Bureau; TG Therapeutics: Research Funding, Speakers Bureau. Kipps:Ascerta/AstraZeneca, Celgene, Genentech/F. Hoffmann-La Roche, Gilead, Janssen, Loxo Oncology, Octernal Therapeutics, Pharmacyclics/AbbVie, TG Therapeutics, VelosBio, and Verastem: Membership on an entity's Board of Directors or advisory committees; Pharmacyclics/ AbbVie, Breast Cancer Research Foundation, MD Anderson Cancer Center, Oncternal Therapeutics, Inc., Specialized Center of Research (SCOR) - The Leukemia and Lymphoma Society (LLS), California Institute for Regenerative Medicine (CIRM): Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Oncternal Therapeutics, Inc.: Other: Cirmtuzumab was developed by Thomas J. Kipps in the Thomas J. Kipps laboratory and licensed by the University of California to Oncternal Therapeutics, Inc., which provided stock options and research funding to the Thomas J. Kipps laboratory, Research Funding; Genentech/Roche: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; VelosBio: Research Funding; Celgene: Honoraria, Research Funding; Gilead: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Brown:Gilead, Loxo, Sun, Verastem: Research Funding; Abbvie, Acerta, AstraZeneca, Beigene, Invectys, Juno/Celgene, Kite, Morphosys, Novartis, Octapharma, Pharmacyclics, Sunesis, TG Therapeutics, Verastem: Consultancy; Janssen, Teva: Speakers Bureau. Neuberg:Celgene: Research Funding; Pharmacyclics: Research Funding; Madrigak Pharmaceuticals: Current equity holder in publicly-traded company. Stilgenbauer:Pharmacyclics: Consultancy, Honoraria, Other, Research Funding; Novartis: Consultancy, Honoraria, Other, Research Funding; Mundipharma: Consultancy, Honoraria, Other, Research Funding; Janssen-Cilag: Consultancy, Honoraria, Other: travel support, Research Funding; GlaxoSmithKline: Consultancy, Honoraria, Other: travel support, Research Funding; Gilead: Consultancy, Honoraria, Other: travel support, Research Funding; Genzyme: Consultancy, Honoraria, Other: travel support, Research Funding; Genentech: Consultancy, Honoraria, Other: travel support, Research Funding; F. Hoffmann-LaRoche: Consultancy, Honoraria, Other: travel support, Research Funding; Celgene: Consultancy, Honoraria, Other: travel support, Research Funding; Boehringer-Ingelheim: Consultancy, Honoraria, Other: travel support, Research Funding; Amgen: Consultancy, Honoraria, Other: travel support, Research Funding; AbbVie: Consultancy, Honoraria, Other: travel support, Research Funding. Wu:BionTech: Current equity holder in publicly-traded company; Pharmacyclics: Research Funding. Campo:NIH: Consultancy, Other: Co-inventor on a patent related to the MCL35 assay filed at the National Institutes of Health, United States of America.. Getz:Broad Institute: Patents & Royalties: MuTect, ABSOLUTE, MutSig, MSMuTect, MSMutSig, POLYSOLVER and TensorQTL; Pharmacyclics: Research Funding; IBM: Research Funding; Scorpion Therapeutics: Consultancy, Current equity holder in publicly-traded company, Other: Founder.
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Maeda, Tomoya, Junichiro Iwasawa, Hazuki Kotani, Natsue Sakata, Masako Kawada, Takaaki Horinouchi, Aki Sakai, Kumi Tanabe, and Chikara Furusawa. "High-throughput laboratory evolution reveals evolutionary constraints in Escherichia coli." Nature Communications 11, no. 1 (November 24, 2020). http://dx.doi.org/10.1038/s41467-020-19713-w.
Full textAbstract:
AbstractUnderstanding the constraints that shape the evolution of antibiotic resistance is critical for predicting and controlling drug resistance. Despite its importance, however, a systematic investigation of evolutionary constraints is lacking. Here, we perform a high-throughput laboratory evolution of Escherichia coli under the addition of 95 antibacterial chemicals and quantified the transcriptome, resistance, and genomic profiles for the evolved strains. Utilizing machine learning techniques, we analyze the phenotype–genotype data and identified low dimensional phenotypic states among the evolved strains. Further analysis reveals the underlying biological processes responsible for these distinct states, leading to the identification of trade-off relationships associated with drug resistance. We also report a decelerated evolution of β-lactam resistance, a phenomenon experienced by certain strains under various stresses resulting in higher acquired resistance to β-lactams compared to strains directly selected by β-lactams. These findings bridge the genotypic, gene expression, and drug resistance gap, while contributing to a better understanding of evolutionary constraints for antibiotic resistance.
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Konno, Naoki, and Wataru Iwasaki. "Machine learning enables prediction of metabolic system evolution in bacteria." Science Advances 9, no. 2 (January 13, 2023). http://dx.doi.org/10.1126/sciadv.adc9130.
Full textAbstract:
Evolution prediction is a long-standing goal in evolutionary biology, with potential impacts on strategic pathogen control, genome engineering, and synthetic biology. While laboratory evolution studies have shown the predictability of short-term and sequence-level evolution, that of long-term and system-level evolution has not been systematically examined. Here, we show that the gene content evolution of metabolic systems is generally predictable by applying ancestral gene content reconstruction and machine learning techniques to ~3000 bacterial genomes. Our framework, Evodictor, successfully predicted gene gain and loss evolution at the branches of the reference phylogenetic tree, suggesting that evolutionary pressures and constraints on metabolic systems are universally shared. Investigation of pathway architectures and meta-analysis of metagenomic datasets confirmed that these evolutionary patterns have physiological and ecological bases as functional dependencies among metabolic reactions and bacterial habitat changes. Last, pan-genomic analysis of intraspecies gene content variations proved that even “ongoing” evolution in extant bacterial species is predictable in our framework.