Parental Involvement in Minnesota Online Schools

Abstract The purpose of this study was to determine the existence of parental involvement practices and successes or difficulties experienced with those practices–as reported by directors–in selected Minnesota online schools. The study was undertaken because, in a review of the research and related literature, it was clear that the resources and knowledge to implement quality parental involvement practices existed, but this may not have meant they were being implemented. Student achievement in Minnesota Online Schools appeared lower than traditional schools. However, no studies existed that documented the parental involvement practices that were in place or the successes and difficulties experienced with parental involvement in Minnesota’s Online Schools. The study utilized Epstein’s (1995; Epstein et al., 2008) framework of six types of involvement to classify and examine collected data. The study was designed as a comparative case study, which examined a total of seven online school sites in Minnesota that served students in grades K-12. Data was collected through the use of case study and interview protocols, and included document collection and examination. The study was designed and conducted with a joint researcher to form a case study team. Some of the study findings included; the prevalence of Communication and Learning at Home parental involvement types–taken from Epstein’s (1995; Epstein et al., 2008) framework, numerous newly documented practices and also common shared practices–such as required numbers of teacher-parent contacts and conferences, and reported successful involvement practices for online schools–such as in person meetings or orientation sessions, as well as reported difficulties. Notably, a major difficulty across the study’s school sites was revealed in the area of county truancy support. Recommendations for future research and current practice are made in the final chapter of the study

Using genotype abundance to improve phylogenetic inference

Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in phylogenetic inference. In this paper, we synthesize a stochastic process model with standard sequence-based phylogenetic optimality, and show that tree estimation is substantially improved by doing so. Our method is validated with extensive simulations and an experimental single-cell lineage tracing study of germinal center B cell receptor affinity maturation

Mean-field interacting multi-type birth-death processes with a view to applications in phylodynamics

Multi-type birth-death processes underlie approaches for inferring evolutionary dynamics from phylogenetic trees across biological scales, ranging from deep-time species macroevolution to rapid viral evolution and somatic cellular proliferation. A limitation of current phylogenetic birth-death models is that they require restrictive linearity assumptions that yield tractable likelihoods, but that also preclude interactions between individuals. Many fundamental evolutionary processes -- such as environmental carrying capacity or frequency-dependent selection -- entail interactions, and may strongly influence the dynamics in some systems. Here, we introduce a multi-type birth-death process in mean-field interaction with an ensemble of replicas of the focal process. We prove that, under quite general conditions, the ensemble's stochastically evolving interaction field converges to a deterministic trajectory in the limit of an infinite ensemble. In this limit, the replicas effectively decouple, and self-consistent interactions appear as nonlinearities in the infinitesimal generator of the focal process. We investigate a special case that is amenable to calculations in the context of a phylogenetic birth-death model, and is rich enough to model both carrying capacity and frequency-dependent selection.Comment: 30 pages, 1 figur

Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph

In many situations, it would be useful to know not just the best phylogenetic tree for a given data set, but the collection of high-quality trees. This goal is typically addressed using Bayesian techniques, however, current Bayesian methods do not scale to large data sets. Furthermore, for large data sets with relatively low signal one cannot even store every good tree individually, especially when the trees are required to be bifurcating. In this paper, we develop a novel object called the "history subpartition directed acyclic graph" (or "history sDAG" for short) that compactly represents an ensemble of trees with labels (e.g. ancestral sequences) mapped onto the internal nodes. The history sDAG can be built efficiently and can also be efficiently trimmed to only represent maximally parsimonious trees. We show that the history sDAG allows us to find many additional equally parsimonious trees, extending combinatorially beyond the ensemble used to construct it. We argue that this object could be useful as the "skeleton" of a more complete uncertainty quantification.Comment: To appear in JM

Stress-Energy Tensor for the Massless Spin 1/2 Field in Static Black Hole Spacetimes

The stress-energy tensor for the massless spin 1/2 field is numerically computed outside and on the event horizons of both charged and uncharged static non-rotating black holes, corresponding to the Schwarzschild, Reissner-Nordstrom and extreme Reissner-Nordstr\"om solutions of Einstein's equations. The field is assumed to be in a thermal state at the black hole temperature. Comparison is made between the numerical results and previous analytic approximations for the stress-energy tensor in these spacetimes. For the Schwarzschild (charge zero) solution, it is shown that the stress-energy differs even in sign from the analytic approximation. For the Reissner-Nordstrom and extreme Reissner-Nordstrom solutions, divergences predicted by the analytic approximations are shown not to exist.Comment: 5 pages, 4 figures, additional discussio

Increased mutation and gene conversion within human segmental duplications

Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data1,2. Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared the pattern of SNVs between unique and duplicated regions3,4. We find that human SNVs are elevated 60% in SDs compared to unique regions and estimate that at least 23% of this increase is due to interlocus gene conversion (IGC) with up to 4.3 megabase pairs of SD sequence converted on average per human haplotype. We develop a genome-wide map of IGC donors and acceptors, including 498 acceptor and 454 donor hotspots affecting the exons of about 800 protein-coding genes. These include 171 genes that have ‘relocated’ on average 1.61 megabase pairs in a subset of human haplotypes. Using a coalescent framework, we show that SD regions are slightly evolutionarily older when compared to unique sequences, probably owing to IGC. SNVs in SDs, however, show a distinct mutational spectrum: a 27.1% increase in transversions that convert cytosine to guanine or the reverse across all triplet contexts and a 7.6% reduction in the frequency of CpG-associated mutations when compared to unique DNA. We reason that these distinct mutational properties help to maintain an overall higher GC content of SD DNA compared to that of unique DNA, probably driven by GC-biased conversion between paralogous sequences5,6.We thank T. Brown for help in editing this manuscript, P. Green for valuable suggestions, and R. Seroussi and his staff for their generous donation of time and resources. This work was supported in part by grants from the US National Institutes of Health (NIH 5R01HG002385, 5U01HG010971 and 1U01HG010973 to E.E.E.; K99HG011041 to P.H.; and F31AI150163 to W.S.D.). W.S.D. was supported in part by a Fellowship in Understanding Dynamic and Multi-scale Systems from the James S. McDonnell Foundation. E.E.E. is an investigator of the Howard Hughes Medical Institute (HHMI). This article is subject to HHMI’s Open Access to Publications policy. HHMI laboratory heads have previously granted a nonexclusive CC BY 4.0 licence to the public and a sublicensable licence to HHMI in their research articles. Pursuant to those licences, the author-accepted manuscript of this article can be made freely available under a CC BY 4.0 licence immediately on publication.Peer Reviewed"Article signat per 19 autors/es: Mitchell R. Vollger, Philip C. Dishuck, William T. Harvey, William S. DeWitt, Xavi Guitart, Michael E. Goldberg, Allison N. Rozanski, Julian Lucas, Mobin Asri, Human Pangenome Reference Consortium, Katherine M. Munson, Alexandra P. Lewis, Kendra Hoekzema, Glennis A. Logsdon, David Porubsky, Benedict Paten, Kelley Harris, PingHsun Hsieh & Evan E. Eichler"Postprint (published version

Theoretical Feasibility of Vasodilator-enhanced Local Tumor Heating

Normal arterioles, in contrast to the abnormal microvasculature of many solid tumors, provide a target for selective drug action that can enhance local heat treatment of the tumors. Measurements of tissue blood flow with radioactive microspheres and estimates of changes in blood flow with thermal clearance methods revealed that vasodilator drugs either decreased or did not alter blood flow in hamster melanoma, rat hepatoma, and canine transmissible venereal tumor, while increasing perfusion in adjacent normal tissues 2 to 4-fold. Solutions of the bio-heat transfer equation, which take into account such selective effects of vasodilators on blood flow in normal tissues, clearly demonstrate improved selective heating for spheroidal tumors over 2 cm in diameter. In the presence of vasodilator drug effect, steady-state center tumor temperatures of 45-50°C can be achieved by increased power input, while surrounding normal tissues remain below 42°C

Phylogenetic Relationships of Malvatheca (Bombacoideae and Malvoideae; Malvaceae sensu lato) as Inferred from Plastid DNA Sequences

Previous molecular phylogenetic analyses have revealed that elements of the former families Malvaceae sensu stricto and Bombacaceae together form a well-supported clade that has been named Malvatheca. Within Malvatheca, two major lineages have been observed; one, Bombacoideae, corresponds approximately to the palmate-leaved Bombacaceae, and the other, Malvoideae, includes the traditional Malvaceae (the mallows or Eumalvoideae). However, the composition of these two groups and their relationships to other elements of Malvatheca remain a source of uncertainty. Sequence data from two plastid regions, ndhF and trnK/matK, from 34 exemplars of Malvatheca and six outgroups were analyzed. Parsimony, likelihood, and Bayesian analyses of the sequence data provided a well-resolved phylogeny except that relationships among five lineages at the base of Malvatheca are poorly resolved. Nonetheless, a 6-bp insertion in matK suggests that Fremontodendreae is sister to the remainder of Malvatheca. Our results suggest that the Malvoideae originated in the Neotropics and that a mangrove taxon dispersed across the Pacific from South America to Australasia and later radiated out of Australasia to give rise to the ca. 1,700 living species of Eumalvoideae. Local clock analyses imply that the plastid genome underwent accelerated molecular evolution coincident with the dispersal out of the Americas and again with the radiation into the three major clades of Eumalvoideae

Digital Astronaut Project Biomechanical Models: Biomechanical Modeling of Squat, Single-Leg Squat and Heel Raise Exercises on the Hybrid Ultimate Lifting Kit (HULK)

The NASA Digital Astronaut Project (DAP) implements well-vetted computational models to predict and assess spaceflight health and performance risks, and to enhance countermeasure development. The DAP Musculoskeletal Modeling effort is developing computational models to inform exercise countermeasure development and to predict physical performance capabilities after a length of time in space. For example, integrated exercise device-biomechanical models can determine localized loading, which will be used as input to muscle and bone adaptation models to estimate the effectiveness of the exercise countermeasure. In addition, simulations of mission tasks can be used to estimate the astronaut's ability to perform the task after exposure to microgravity and after using various exercise countermeasures. The software package OpenSim (Stanford University, Palo Alto, CA) (Ref. 1) is being used to create the DAP biomechanical models and its built-in muscle model is the starting point for the DAP muscle model. During Exploration missions, such as those to asteroids and Mars, astronauts will be exposed to reduced gravity for extended periods. Therefore, the crew must have access to exercise countermeasures that can maintain their musculoskeletal and aerobic health. Exploration vehicles may have very limited volume and power available to accommodate such capabilities, even more so than the International Space Station (ISS). The exercise devices flown on Exploration missions must be designed to provide sufficient load during the performance of various resistance and aerobic/anaerobic exercises while meeting potential additional requirements of limited mass, volume and power. Given that it is not practical to manufacture and test (ground, analog and/or flight) all candidate devices, nor is it always possible to obtain data such as localized muscle and bone loading empirically, computational modeling can estimate the localized loading during various exercise modalities performed on a given device to help formulate exercise prescriptions and other operational considerations. With this in mind, NASA's Digital Astronaut Project (DAP) is supporting the Advanced Exercise Concepts (AEC) Project, Exercise Physiology and Countermeasures (ExPC) laboratory and NSBRI-funded researchers by developing and implementing well-validated computational models of exercises with advanced exercise device concepts. This report focuses specifically on lower-body resistance exercises performed with the Hybrid Ultimate Lifting Kit (HULK) device as a deliverable to the AEC Project