Although it is heavily relied on to study genetic contributors to health and disease, the current human reference genome (GRCh38) is incomplete in two major ways: firstly, it is missing large sections of heterochromatic sequence, and secondly, as a singular, linear reference genome it does not represent the full spectrum of genetic diversity that exists in the human species. In order to better understand and characterize gaps in GRCh38 and genetic diversity, we developed a method - ASLAN, an Algorithm for Sequence Location Approximation using Nuclear families - that identifies the region of origin of short reads that do not align to the GRCh38. Using unmapped reads and variant calls from whole genome sequencing (WGS) data from nuclear families, ASLAN relies on a maximum likelihood model to identify the most likely region of the genome that a subsequence belongs to, given the phasing information of family and the distribution of the subsequence in the unmapped reads. Validating ASLAN on a synthetically generated dataset, and on true reads originating from the alternative haplotypes in the decoy genome, we show that ASLAN can localize more than 90% of 100-basepair sequences with above 92% accuracy and around 1 megabase of resolution. We then run ASLAN on 100-mers from unmapped reads from WGS from over 700 families, and compare ASLAN localizations to alignment of the 100-mers to the T2T-CHM13 assembly, recently released by the Telomere-to-telomere (T2T) consortia. We find that many unmapped reads in GRCh38 originate from telomeres and centromeres that are gaps in the GRCh38 reference. We also confirm that ASLAN localizations are in high concordance with T2T-CHM13 alignments, except in the centromeres of the acrocentric chromosomes. Comparing ASLAN localizations and T2T-CHM13 alignments, we identify sequences missing from T2T-CHM13 or sequences with high divergence from their aligned region in T2T-CHM13, thus highlighting new hotspots for genetic diversity. This deposit consists of: (1) A list of non-singleton 100mers extracted from the iHART cohort from the unmapped reads (kmer_sequences.txt.zip) (2) The corresponding regions in the genome that ASLAN mapped each sequence to (GRCh38 coordinates) (ASLAN_localizations.bed) (3) The loci to which the each sequence aligned to on the CHM13-T2T assembly (CHM13-T2T coordinates) (T2T_mappings.bed)

Atlantic bluefin tuna (ABT) are large, wide-ranging pelagic predators which typically migrate between foraging regions in the North Atlantic and two principal spawning regions, the Gulf of Mexico and the Mediterranean Sea. A new spawning area has been described in the Slope Sea (SS) region off New England; however, the relationship between ABT that spawn in the SS and ABT using the principal spawning regions remains poorly understood. We used electronic tags to examine the location, temperature, and diving behavior of ABT in the SS, and identified 24 individuals that were present during the spawning season (June-August) with tag data showing temperatures and behavior consistent with spawning ABT. In general, the SS spawners had similar spatial ranges to Mediterranean-spawning ABT; however, some individuals displayed distinct behaviours that were identified first in Gulf of Mexico spawners. Using monthly spatial distributions, we estimated that the SS spawners have high exposure to fishing pressure relative to other ABT and may represent a disproportionate share of the West Atlantic catch. This analysis provides the first description of the behavior of ABT frequenting this spawning ground, creating a foundation for integrating this region into multi-stock management and, potentially, conserving an important source of genetic diversity.

This dataset includes a subset of data and all codes used in the JAMES article titled 'Recreating convection-generated gravity waves from weather radar observations via a neural network and a dynamical atmospheric model'. All files included here are compressed (*.tar.gz) NetCDF files of idealized Weather Research and Forecasting (WRF) model output at 10-minute output frequency. The run archived is that forced by a neural network trained on the Darwin and Florida runs (i.e. the DAFLNN-forced idealized WRF run) described in the paper. Additionally, all the Bramberger et al. 2020 look-up table, training data, time-averaged 3-D output of the DAFLNN-forced WRF run, the trained NNs, and all Python scripts and WRF source codes used in the paper are included in "everything_else.tar.gz". Finally, a README is contained as well, which provides further description of the contents here. Paper Abstract: Convection-generated gravity waves (CGWs) transport momentum and energy, and this momentum is a dominant driver of global features of Earth’s atmosphere’s general circulation (e.g. the quasi-biennial oscillation, the pole-to-pole mesospheric circulation). As CGWs are not generally resolved by global weather and climate models, their effects on the circulation need to be parameterized. However, quality observations of GWs are spa24 tiotemporally sparse, limiting understanding and preventing constraints on parameter izations. Convection-permitting or -resolving simulations do generate CGWs, but validation is not possible as these simulations cannot reproduce the forcing convection at correct times, locations, and intensities. Here, realistic convective diabatic heating, learned from full-physics convection-permitting Weather Research and Forecasting (WRF) simulations, is predicted from weather radar observations using neural networks and a previously developed look-up table. These heating rates are then used to force an idealized GW-resolving dynamical model. Simulated CGWs forced in this way did closely resemble those observed by the Atmospheric InfraRed Sounder in the upper stratosphere. CGW drag in these validated simulations extends 100s of kilometers away from the convective sources, highlighting errors in current gravity wave drag parameterizations due to the use of the ubiquitous single-column approx36 imation. Such validatable simulations have significant potential to be used to further basic understanding of CGWs, improve their parameterizations physically, and provide more restrictive constraints on tuning with confidence.

Data used in manuscript: Spatial and interannual variability of Antarctic sea ice algal habitat, 2004–2019

Though the Soviet Union fell decades ago, the red specter of communism still looms large over parts of the world, including Colombia. In this thesis, I explore the anticommunist rhetoric in Colombia through the discourse of two former presidents who lived in two very different realities. I compare the discourse of Laureano Gómez with that of Álvaro Uribe Vélez, using a speech titled “El Basilisco” as a case study of Gómez’s discourse and various tweets published by Uribe between 2016 and 2018 as examples of his discourse. I argue that while communism was a “real” threat during Gómez’s time and within his rhetoric, for Uribe, his anticommunist discourse function less as an expression of a real threat and more as a tool that leverages the history and context of Colombia and to a certain extent Venezuela. I place the discourse of both men firmly within the general context that shaped their time, meaning that I explore various events that occurred during the 20th century in Colombia, paying particular attention to the position of Marxism within Colombian society. Furthermore, I also briefly discuss the implications of the evolution of communication from the present day in comparison to the 1940s and 50s. I also engage with various literature across multiple fields such as history, communication, and political science.

Manuscripts of early music works and skecthes. Greece, 1982 to 1984. Documents the artist's transition from music theory student to aspiring composer influenced by Mozart and, especially, Beethoven.

Video recordings of unrehearsed performances of original piano works by Ilias Chrissochoidis. Stanford University, August-September 2022.

Video recordings of unrehearsed performances of repertory piano works by Ilias Chrissochoidis. Stanford University, August-September 2022.

The purpose of this LEGO DNA Sequencer is to provide a complete blueprint for an open source DIY tool that can be used to explain the complex DNA sequencing operation with a colorful easy to understand model.

Geometry is the math of the 3D world. It is a significant portion of the math curriculum in formal education. The most common learning trajectory of elementary geometry initiates from establishing familiarity with names of shapes as well as distinguishing 2D and 3D shapes, and gradually progresses into more complex geometric forms and theorems. However, the structured nature of formal education teaching and assessments has often resulted in a problem: students may find success in these school assessments yet still be unable to apply their knowledge to authentic activities of a specific practice. The recent rise of Maker Education, as a result of the Maker Movement, has provided opportunities for extending geometry learning from formal education to create more ‘authentic’ learning experiences. Maker Education utilizes problem-based, project-based, hands-on learning. Our solution, Maker Maths, will situate geometry learning in making processes to enhance the authenticity of learning as students experience legitimate application of their knowledge. The three key features of Maker Maths - Take-Apart, Tool Making, and Maker Activities - provide a scaffolded educational experience that guides learners to identify, investigate, and apply geometry to the making process. The ultimate goal of Maker Maths is to create a learning ecosystem that guides learners to understand and apply geometry through making.

Service work is messy, particularly when working with marginalized communities. It requires navigating complex power dynamics, stakeholder relationships, and much more. However, novices with the best intentions, eager to help, often do not recognize this challenge. This especially applies to service-learning programs where students learn through a service project involving a ‘developing’ community. Students often have a design-for-charity mindset, characterized by the desire to “help” communities without equitably engaging them as opposed to a design-for-justice mindset, characterized by deep community involvement. Though experiences in service work can help students transition from a design-for-charity to a design-for-justice mindset, their inexperience can lead their projects to be ineffective or even harmful to communities as they struggle to find their footing. Muddy Waters is a story-based approach to instilling a design-for-justice mindset in students engaged in service work. Through an interactive fiction story of a student entering their first service project and discussion activities, students vicariously experience a similar learning journey as a traditional service project within a simulated environment. Muddy Waters helps students recognize the “muddiness” of service work and provides stepping stones for them to engage communities equitably and effectively.

Nuclear magnetic resonance and direct push hydraulic conductivity data for four wells in central Wisconsin. Details on the two sites where these data were acquired can be found in Kendrick et al (2020), https://doi.org/10.1111/gwat.13014.

Background: Although farm workers are integral to the agricultural industry, they are systematically excluded from health and social resources. Such exclusion has created economic, social, and health disparities (Anthony et al., 2008; Liebman et al., 2021; Ramos A. K, 2018). Objectives: This study aims to explore farmworkers’ experiences related to health pre and post COVID, and to understand social disparities in their lives while narrating their priorities and concerns. Political and economic factors contributing to the unmet social and health needs of farmworkers are discussed. Methods: This qualitative study was conducted in full partnership with a farmworker community organization on the San Mateo coast. Testimonios and semi-structured interview questions were developed with input from farmworker advocates and farmworkers. Transcripts were coded and analyzed using an inductive approach. Results: Four core themes regarding the community’s lived experiences and needs emerged: (a) Racialization and Dehumanization; (b) Social Welfare and Basic Needs; (c) Cultural Wealth and Community Agency (d) Violence and Trauma. Conclusion: Findings yield implications for the impact of this methodology and of community organizations on improving farmworker lives and to center lived experiences to inform program development and policy priorities to aid farm workers and bridge social and health outcome gaps.

A common strategy for many recent migrants is the clustering around a particular locale with other co-ethnic members as a way to make living in their new environment much more palatable. This includes the formation of certain ethnic enclaves, common in many urban centers that include Chinatowns, Little Mexicos, or Little Italys, that serve as a necessary cultural hub that provides information on resources like housing, job opportunities, or support networks for other arriving co-ethnic migrants. In some cases, migrants even cluster around a particular profession that often become synonymous with said groups. In my thesis, I focus on Mexican Ice-Cream street vendors, colloquially known as Paleteros, in order to better understand the history of recent Mexican immigration and the social conditions by which these migrants choose street food vending, an otherwise highly visible profession. I play close attention to the inception, growth, and proliferation of the Ice-Cream street vending business by interviewing both street vendors and ice-cream street vending business owners located throughout the San Francisco Bay Area. In doing so, the ensuing thesis strives to add to the growing literature on studies pertaining to small, informal businesses that are largely operated by Latinx immigrants as well as examining the historical and social conditions that promulgated an otherwise understudied topic

This is the final report for the Learning Design and Technology project Re-Ignite, a card game developed to address teacher retention. Through needfinding and co-designing prototypes with educators, Re-Ignite is built on a solid foundation. There is evidence from extensive user testing that Re-Ignite engages educators in meaningful conversations. The ultimate goal of Re-Ignite is to increase educator belonging and agency, helping to keep teachers engaged and sustained in their profession.

Differences in the prevalence and burden of depression among women have been extensively documented, proving stable across culture, age, and time. Towards characterizing sexual dimorphism in the proteomics of depression, this investigation evaluated the serum levels of over 7,500 analytes on the SomaLogic SomaScan proteomic assay in 75 moderately to severely depressed patients enriched for endogenomorphic symptoms and 78 healthy controls. Combining differential expression and pathway enrichment analyses, the distribution of sex-dependent protein expression in depressed males and females was compared, and significantly sex-dependent proteins are explored. Differential protein expression results are used to inform the development of classifiers distinguishing between depressed patients and healthy controls. An equal number of differentially expressed proteins were found between males and females, with males displaying more proteins with increased expression in cases versus controls and the opposite observed among females. The immune system was the only overrepresented pathway among the proteins with significant sex-dependent expression in depression. Individual examination of immune-identified proteins highlighted multiple proteins not previously associated with depression. Together, these proteins exhibited bidirectional support for alterations of immune and inflammatory protein expression between males and females. Results from classifier development showed that leveraging differentially expressed proteins resulted in improved classifier performance. These findings have implications for research on therapeutic targets in depression and classifier development. Future investigations should elaborate on these findings through studies with larger sample sizes of phenotypically diverse cohorts.

In any learning experience, learners must receive feedback in order to address misconceptions, adjust understanding, and make progress towards a learning goal. Teachers know this fact, yet many constraints make the feedback process difficult. For one, delivering meaningful and personalized feedback is time-intensive; teachers often spend their weekends working on feedback only to find that their students no longer care. Secondly, existing classroom tools focusing on feedback tend to elicit surface-level knowledge, such as what students can recognize or recall, meaning that teachers do not receive the needed insight into what their students can do with knowledge. In this sense, the feedback challenge is also a formative assessment issue, as it is the daily cycle of feedback that teachers and students struggle with the most. Teachers need better methods of capturing deep student comprehension in order to make teaching adjustments, and students need immediate, personalized feedback to move their learning forward. Our solution, Short Answer, meets this need in middle and high school classrooms by leveraging peer feedback and comparative judgment. Students construct answers, compare peer responses, and provide feedback. The comparative judgment process serves as a jumping off point for rich class discussion, enabling students to become stronger self-evaluators and deepen their understanding of material, while teachers receive the insight they need on their students’ comprehension. Initial learner studies indicate that teachers see the value of peer feedback in their formative assessment practice, and early feedback lays the groundwork for improving the student learning experience.

The study is divided not into chapters but into areas of questions. The first area offers a structural analysis of the Prologue which supports La Musica's claims about the power of music; the second one challenges the traditional view of Orfeo as representing a consistent statement about that power; the third, is devoted to a refutation (the first as far as I know) of McClary's reading of the opera. The study concludes with a discussion of the so-called "problem" of the opera's two finales. M.Mus. (Historical Musicology) thesis, King's College London, 1995.