Sensei: how many samples to tell a change in cell type abundance?

Cellular heterogeneity underlies cancer evolution and metastasis. Advances in single-cell technologies such as single-cell RNA sequencing and mass cytometry have enabled interrogation of cell type-specific expression profiles and abundance across heterogeneous cancer samples obtained from clinical trials and preclinical studies. However, challenges remain in determining sample sizes needed for ascertaining changes in cell type abundances in a controlled study. To address this statistical challenge, we have developed a new approach, named Sensei, to determine the number of samples and the number of cells that are required to ascertain such changes between two groups of samples in single-cell studies. Sensei expands the t-test and models the cell abundances using a beta-binomial distribution. We evaluate the mathematical accuracy of Sensei and provide practical guidelines on over 20 cell types in over 30 cancer types based on knowledge acquired from the cancer cell atlas (TCGA) and prior single-cell studies. We provide a web application to enable user-friendly study design via https://kchen-lab.github.io/sensei/table_beta.html.

Sensei: How Many Samples to Tell Evolution in Single-Cell Studies?

Cellular heterogeneity underlies cancer evolution and metastasis. Advances in single-cell technologies such as single-cell RNA sequencing and mass cytometry have enabled interrogation of cell type-specific expression profiles and abundance across heterogeneous cancer samples obtained from clinical trials and preclinical studies. However, challenges remain in determining sample sizes needed for ascertaining changes in cell type abundances in a controlled study. To address this statistical challenge, we have developed a new approach, named Sensei, to determine the number of samples and the number of cells that are required to ascertain such changes between two groups of samples in single-cell studies. Sensei expands the t-test and models the cell abundances using a beta-binomial distribution. We evaluate the mathematical accuracy of Sensei and provide practical guidelines on over 20 cell types in over 30 cancer types based on knowledge acquired from the cancer cell atlas (TCGA) and prior single-cell studies. We provide a web application to enable user-friendly study design via https://kchen-lab.github.io/sensei/table_beta.html.

Axiomatic and Dynamic Processes for a Symmetric Allocation Rule

It has recently become imperative to analyze relevant issues to improve the efficiency of resource allocation by means of different perspectives and ways of thinking. There exist numerous decisive factors, such as changes in forms of allocation, reactive behavior, and the interaction and functional effectiveness of strategies, that need to be complied. In contrast to expert meetings, rules of thumb, or other existing concepts, this article aims to offer a different and efficient resource allocation approach by applying game-theoretical methods to resource-allocation situations. Our major investigative procedures are as follows: (1) after comparing our method with pre-existing allocation rules from pre-existing allocation rules, a symmetric allocation rule is proposed that considers both units and their energy grades; (2) based on the properties of grade completeness, criterion for models, unmixed equality symmetry, grade synchronization, and consistency, some axiomatic outcomes are used to examine the mathematical accuracy and the applied rationality of this symmetric allocation rule; (3) based on a symmetrical revising function, a dynamic process is applied to show that this symmetric allocation rule can be reached by units that start from an arbitrary grade completeness situation; and (4) these axiomatic and dynamic results and related meanings are applied to show that this symmetric allocation rule can present an optimal alternative guide for resource-allocation processes. Related applications, comparisons, and statements are also offered throughout this article.

APPLICATION OF UAV OBLIQUE PHOTOGRAPHY IN REAL SCENE 3D MODELING

Aiming at the phenomenon that the traditional measurement methods cannot complete large-scale measurement in a short time, and the image quality obtained by remote sensing in cloudy and rainy areas is difficult to meet the demand, this paper puts forward the idea of using UAV tilt photography to build three-dimensional modeling of urban real scene. The UAV tilt photography technology is used to collect the image data of about 200 km2 in Wuzhishan City. By laying a small number of ground image control points, the aerial triangulation is used to establish the connection, and the three-dimensional modeling of the collected data is carried out. Through the field verification to verify the attribute information of ground objects, the accuracy is verified by using CORS system field coordinate collection. The results show that the ground property and mathematical accuracy of UAV tilt photography model meet the requirements, and can be effectively used in real 3D modeling.

Effects of Using Virtual Manipulatives for Students With Disabilities: Three-Level Multilevel Modeling for Single-Case Data

We synthesized studies published since 2000 that assessed the effects of using virtual manipulatives to increase the mathematical accuracy of students with disabilities. We extracted a total of 1,796 raw data points from 114 cases across 35 single-case studies. By applying three-level multilevel modeling, we analyzed both immediate effects and trends during the intervention phase as well as moderation effects related to student characteristics (case level) and intervention features (study level). Both the average immediate effect and trend during the intervention were statistically significant. The average immediate effect varied significantly by student grade, disability type, developer, device, type of virtual manipulative, and visual model embedded in virtual manipulatives. Neither student characteristics nor intervention feature–related moderators significantly influenced the average trend during the use of virtual manipulatives.

Theory Driven Modeling as the Core of Software Development

Some experts opine that software is built in a primitive way. The role of modeling as a treatment for the weakness of software engineering became more important when the principles of Model Driven Architecture (MDA) appeared. Its main advantage is architectural separation of concerns. It showed the necessity of modeling and opened the way for software development to become an engineering discipline. However, this principle does not demonstrate its whole potential power in practice because of lack of mathematical accuracy in the very initial steps of software development. The sufficiency of modeling in software development is still disputable. The authors believe that software development in general (and modeling in particular) based on mathematical formalism in all of its stages and together with the implemented principle of architectural separation of concerns can become an important part of software engineering in its real sense. They propose the formalism by topological modeling of system functioning as the first step towards engineering.

Sensei: How many samples to tell evolution in single-cell studies?

1AbstractCellular heterogeneity underlies cancer evolution and metastasis. Advances in single-cell technologies such as single-cell RNA sequencing and mass cytometry have enabled interrogation of cell type-specific expression profiles and abundance across heterogeneous cancer samples obtained from clinical trials and preclinical studies. However, challenges remain in determining sample sizes needed for ascertaining changes in cell type abundances in a controlled study. To address this statistical challenge, we have developed a new approach, named Sensei, to determine the number of samples and the number of cells that are required to ascertain such changes between two groups of samples in single-cell studies. Sensei expands the t-test and models the cell abundances using a beta-binomial distribution. We evaluate the mathematical accuracy of Sensei and provide practical guidelines on over 20 cell types in over 30 cancer types based on knowledge acquired from the cancer cell atlas (TCGA) and prior single-cell studies. We provide a web application to enable user-friendly study design via https://kchen-lab.github.io/sensei/table_beta.html.

The Development of BasinVis: Lessons learned from an open-source collaboration of geoscience and computer science

<p>Geoscience is a highly interdisciplinary field of study, drawing upon conclusions from physics, chemistry and many other academic disciplines. Over the course of the last decades, computer science has become an integral component of geoscientific research. This coincides with the rising popularity of the open-source movement, which helped to develop better tools for collaboration on complex software projects across physical distances and academic boundaries.</p><p>However, while the technical frameworks supporting interdisciplinary work between geoscience and computer science exist, there are still several hurdles one must take in order to achieve successful collaborations. This work summarizes the lessons learned from the development of BasinVis from the perspective of a computer science collaborator. BasinVis is a modular open-source application that aims to allow geoscientists to analyze and visualize sedimentary basins in a comprehensive workflow. A particular development goal was to introduce the advances of 2D and 3D visualization techniques to the quantitative analysis of the stratigraphic setting and subsidence of sedimentary basins based on well data and/or stratigraphic profiles.</p><p>Development of BasinVis started in 2013 with its first release as a MATLAB GUI application in 2016. Apart from functionality, one of the major problems to solve in this period was the alignment of research goals and methodology, which may diverge greatly between geoscience and computer science. Examples of this would be to clarify the scientific terminologies of each fields early on and to clearly establish the expected results of the application in terms of mathematical accuracy and uncertainty (a concept that may catch computer scientists off guard).</p>

Application of Different Standard Error Estimates in Reliable Change Methods

Objective This study attempted to clarify the applicability of standard error (SE) terms in clinical research when examining the impact of short-term practice effects on cognitive performance via reliable change methodology. Method This study compared McSweeney’s SE of the estimate (SEest) to Crawford and Howell’s SE for prediction of the regression (SEpred) using a developmental sample of 167 participants with either normal cognition or mild cognitive impairment (MCI) assessed twice over 1 week. One-week practice effects in older adults: Tools for assessing cognitive change. Using these SEs, previously published standardized regression-based (SRB) reliable change prediction equations were then applied to an independent sample of 143 participants with MCI. Results This clinical developmental sample yielded nearly identical SE values (e.g., 3.697 vs. 3.719 for HVLT-R Total Recall SEest and SEpred, respectively), and the resultant SRB-based discrepancy z scores were comparable and strongly correlated (r = 1.0, p < .001). Consequently, observed follow-up scores for our sample with MCI were consistently below expectation compared to predictions based on Duff’s SRB algorithms. Conclusions These results appear to replicate and extend previous work showing that the calculation of the SEest and SEpred from a clinical sample of cognitively intact and MCI participants yields similar values and can be incorporated into SRB reliable change statistics with comparable results. As a result, neuropsychologists utilizing reliable change methods in research investigation (or clinical practice) should carefully balance mathematical accuracy and ease of use, among other factors, when determining which SE metric to use.

On Four New Methods of Analytical Calculation of Rocket Trajectories

The calculation of rocket trajectories is most often performed using purely numerical methods that account for all relevant parameters and provide the required results. There is a complementary need for analytical methods that make more explicit the effect of the various rocket and atmospheric parameters of the trajectory and can be used as test cases with unlimited accuracy. The available analytical methods take into account (i) variable rocket mass due to propellant consumption. The present paper includes four new analytical methods taking into account besides (i) also (ii) nonlinear aerodynamic forces proportional to the square of the velocity and (iii) exponential dependence of the mass density with altitude for an isothermal atmospheric layer. The four new methods can be used in “hybrid analytical-numerical” approach in which: (i) the atmosphere is divided into isothermal rather than homogeneous layers for greater physical fidelity; and (ii) in each layer, an exact analytical solution of the equations of motion with greater mathematical accuracy than a numerical approximation is used. This should allow a more accurate calculation of rocket trajectories while discretizing the atmosphere into a smaller number of layers. The paper therefore concentrates on four analytical methods of calculation of rocket trajectories in an isothermal atmospheric layers using new exact solutions of the equations of motion beyond those currently available in the literature. The four methods are developed first for the simpler case of a vertical climb and will be subsequently extended to the practically more relevant case of a gravity turn.