DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes.

Although transcriptomics data is typically used to analyze mature spliced mRNA, recent attention has focused on jointly investigating spliced and unspliced (or precursor-) mRNA, which can be used to study gene regulation and changes in gene expression production. Nonetheless, most methods for spliced/unspliced inference (such as RNA velocity tools) focus on individual samples, and rarely allow comparisons between groups of samples (e.g. healthy vs. diseased). Furthermore, this kind of inference is challenging, because spliced and unspliced mRNA abundance is characterized by a high degree of quantification uncertainty, due to the prevalence of multi-mapping reads, ie reads compatible with multiple transcripts (or genes), and/or with both their spliced and unspliced versions. Here, we present DifferentialRegulation, a Bayesian hierarchical method to discover changes between experimental conditions with respect to the relative abundance of unspliced mRNA (over the total mRNA). We model the quantification uncertainty via a latent variable approach, where reads are allocated to their gene/transcript of origin, and to the respective splice version. We designed several benchmarks where our approach shows good performance, in terms of sensitivity and error control, vs. state-of-the-art competitors. Importantly, our tool is flexible, and works with both bulk and single-cell RNA-sequencing data. DifferentialRegulation is distributed as a Bioconductor R package.

Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data.

The rapid growth of high-throughput single-cell and single-nucleus RNA-sequencing (scRNA-seq and snRNA-seq) technologies has produced a wealth of data over the past few years. The size, volume and distinctive characteristics of these data necessitate the development of new computational methods to accurately and efficiently quantify sc/snRNA-seq data into count matrices that constitute the input to downstream analyses. We introduce the alevin-fry framework for quantifying sc/snRNA-seq data. In addition to being faster and more memory frugal than other accurate quantification approaches, alevin-fry ameliorates the memory scalability and false-positive expression issues that are exhibited by other lightweight tools. We demonstrate how alevin-fry can be effectively used to quantify sc/snRNA-seq data, and also how the spliced and unspliced molecule quantification required as input for RNA velocity analyses can be seamlessly extracted from the same preprocessed data used to generate normal gene expression count matrices.

Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads.

MOTIVATION: Short-read single-cell RNA-sequencing (scRNA-seq) has been used to study cellular heterogeneity, cellular fate, and transcriptional dynamics. Modeling splicing dynamics in scRNA-seq data is challenging, with inherent difficulty in even the seemingly straightforward task of elucidating the splicing status of the molecules from which sequenced fragments are drawn. This difficulty arises, in part, from the limited read length and positional biases, which substantially reduce the specificity of the sequenced fragments. As a result, the splicing status of many reads in scRNA-seq is ambiguous because of a lack of definitive evidence. We are therefore in need of methods that can recover the splicing status of ambiguous reads which, in turn, can lead to more accuracy and confidence in downstream analyses. RESULTS: We develop Forseti, a predictive model to probabilistically assign a splicing status to scRNA-seq reads. Our model has two key components. First, we train a binding affinity model to assign a probability that a given transcriptomic site is used in fragment generation. Second, we fit a robust fragment length distribution model that generalizes well across datasets deriving from different species and tissue types. Forseti combines these two trained models to predict the splicing status of the molecule of origin of reads by scoring putative fragments that associate each alignment of sequenced reads with proximate potential priming sites. Using both simulated and experimental data, we show that our model can precisely predict the splicing status of many reads and identify the true gene origin of multi-gene mapped reads. AVAILABILITY AND IMPLEMENTATION: Forseti and the code used for producing the results are available at https://github.com/COMBINE-lab/forseti under a BSD 3-clause license.

simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fry.

SUMMARY: The alevin-fry ecosystem provides a robust and growing suite of programs for single-cell data processing. However, as new single-cell technologies are introduced, as the community continues to adjust best practices for data processing, and as the alevin-fry ecosystem itself expands and grows, it is becoming increasingly important to manage the complexity of alevin-fry's single-cell preprocessing workflows while retaining the performance and flexibility that make these tools enticing. We introduce simpleaf, a program that simplifies the processing of single-cell data using tools from the alevin-fry ecosystem, and adds new functionality and capabilities, while retaining the flexibility and performance of the underlying tools. AVAILABILITY AND IMPLEMENTATION: Simpleaf is written in Rust and released under a BSD 3-Clause license. It is freely available from its GitHub repository https://github.com/COMBINE-lab/simpleaf, and via bioconda. Documentation for simpleaf is available at https://simpleaf.readthedocs.io/en/latest/ and tutorials for simpleaf that have been developed can be accessed at https://combine-lab.github.io/alevin-fry-tutorials.

scCensus: Off-target scRNA-seq reads reveal meaningful biology.

Single-cell RNA-sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity. Although scRNA-seq reads from most prevalent and popular tagged-end protocols are expected to arise from the 3' end of polyadenylated RNAs, recent studies have shown that "off-target" reads can constitute a substantial portion of the read population. In this work, we introduced scCensus, a comprehensive analysis workflow for systematically evaluating and categorizing off-target reads in scRNA-seq. We applied scCensus to seven scRNA-seq datasets. Our analysis of intergenic reads shows that these off-target reads contain information about chromatin structure and can be used to identify similar cells across modalities. Our analysis of antisense reads suggests that these reads can be used to improve gene detection and capture interesting transcriptional activities like antisense transcription. Furthermore, using splice-aware quantification, we find that spliced and unspliced reads provide distinct information about cell clusters and biomarkers, suggesting the utility of integrating signals from reads with different splicing statuses. Overall, our results suggest that off-target scRNA-seq reads contain underappreciated information about various transcriptional activities. These observations about yet-unexploited information in existing scRNA-seq data will help guide and motivate the community to improve current algorithms and analysis methods, and to develop novel approaches that utilize off-target reads to extend the reach and accuracy of single-cell data analysis pipelines.

Forseti: A mechanistic and predictive model of the splicing status of scRNA-seq reads.

Motivation: Short-read single-cell RNA-sequencing (scRNA-seq) has been used to study cellular heterogeneity, cellular fate, and transcriptional dynamics. Modeling splicing dynamics in scRNA-seq data is challenging, with inherent difficulty in even the seemingly straightforward task of elucidating the splicing status of the molecules from which sequenced fragments are drawn. This difficulty arises, in part, from the limited read length and positional biases, which substantially reduce the specificity of the sequenced fragments. As a result, the splicing status of many reads in scRNA-seq is ambiguous because of a lack of definitive evidence. We are therefore in need of methods that can recover the splicing status of ambiguous reads which, in turn, can lead to more accuracy and confidence in downstream analyses. Results: We develop Forseti, a predictive model to probabilistically assign a splicing status to scRNA-seq reads. Our model has two key components. First, we train a binding affinity model to assign a probability that a given transcriptomic site is used in fragment generation. Second, we fit a robust fragment length distribution model that generalizes well across datasets deriving from different species and tissue types. Forseti combines these two trained models to predict the splicing status of the molecule of origin of reads by scoring putative fragments that associate each alignment of sequenced reads with proximate potential priming sites. Using both simulated and experimental data, we show that our model can precisely predict the splicing status of reads and identify the true gene origin of multi-gene mapped reads. Availability: Forseti and the code used for producing the results are available at https://github.com/COMBINE-lab/forseti under a BSD 3-clause license.

simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry.

Summary: The alevin-fry ecosystem provides a robust and growing suite of programs for single-cell data processing. However, as new single-cell technologies are introduced, as the community continues to adjust best practices for data processing, and as the alevin-fry ecosystem itself expands and grows, it is becoming increasingly important to manage the complexity of alevin-fry ’s single-cell preprocessing workflows while retaining the performance and flexibility that make these tools enticing. We introduce simpleaf , a program that simplifies the processing of single-cell data using tools from the alevin-fry ecosystem, and adds new functionality and capabilities, while retaining the flexibility and performance of the underlying tools. Availability and implementation: Simpleaf is written in Rust and released under a BSD 3-Clause license. It is freely available from its GitHub repository https://github.com/COMBINE-lab/simpleaf , and via bioconda. Documentation for simpleaf is available at https://simpleaf.readthedocs.io/en/latest/ and tutorials for simpleaf are being developed that can be accessed at https://combine-lab.github.io/alevin-fry-tutorials .

Understanding and evaluating ambiguity in single-cell and single-nucleus RNA-sequencing.

Recently, a new modification has been proposed by Hjörleifsson and Sullivan et al. to the model used to classify the splicing status of reads (as spliced (mature), unspliced (nascent), or ambiguous) in single-cell and single-nucleus RNA-seq data. Here, we evaluate both the theoretical basis and practical implementation of the proposed method. The proposed method is highly-conservative, and therefore, unlikely to mischaracterize reads as spliced (mature) or unspliced (nascent) when they are not. However, we find that it leaves a large fraction of reads classified as ambiguous, and, in practice, allocates these ambiguous reads in an all-or-nothing manner, and differently between single-cell and single-nucleus RNA-seq data. Further, as implemented in practice, the ambiguous classification is implicit and based on the index against which the reads are mapped, which leads to several drawbacks compared to methods that consider both spliced (mature) and unspliced (nascent) mapping targets simultaneously - for example, the ability to use confidently assigned reads to rescue ambiguous reads based on shared UMIs and gene targets. Nonetheless, we show that these conservative assignment rules can be obtained directly in existing approaches simply by altering the set of targets that are indexed. To this end, we introduce the spliceu reference and show that its use with alevin-fry recapitulates the more conservative proposed classification. We also observe that, on experimental data, and under the proposed allocation rules for ambiguous UMIs, the difference between the proposed classification scheme and existing conventions appears much smaller than previously reported. We demonstrate the use of the new piscem index for mapping simultaneously against spliced (mature) and unspliced (nascent) targets, allowing classification against the full nascent and mature transcriptome in human or mouse in <3GB of memory. Finally, we discuss the potential of incorporating probabilistic evidence into the inference of splicing status, and suggest that it may provide benefits beyond what can be obtained from discrete classification of UMIs as splicing-ambiguous.

Static analysis of elastic cable structures under mechanical load using discrete catenary theory.

In this paper, the nonlinear mechanical response of elastic cable structures under mechanical load is studied based on the discrete catenary theory. A cable net is discretized into multiple nodes and edges in our numerical approach, which is followed by an analytical formulation of the elastic energy and the associated Hessian matrix to realize the dynamic simulation. A fully implicit framework is proposed based on the discrete differential geometry (DDG) theory. The equilibrium configuration of a target object is derived by adding damping force into the system, known as the dynamic relaxation method. The mechanical response of a single suspended cable is investigated and compared with the analytical solution for cross-validation. A more intricate scenario is further discussed in detail, where a structure consisting of multiple slender cables is connected through joints. Utilizing the robustness and efficiency of our discrete numerical framework, a systematic parameter sweep is performed to quantify the force displacement relationships of nets with the different number of cables and different directions of fibers. Finally, an empirical scaling law is provided to account for the rigidity of elastic cable net in terms of its geometric properties, material characteristics, component numbers, and cable orientations. Our results would provide new insight in revealing the connections between flexible structures and tensegrity structures, and could motivate innovative designs in both mechanical and civil engineered equipment.

DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes.

Motivation: Although transcriptomics data is typically used to analyse mature spliced mRNA, recent attention has focused on jointly investigating spliced and unspliced (or precursor-) mRNA, which can be used to study gene regulation and changes in gene expression production. Nonetheless, most methods for spliced/unspliced inference (such as RNA velocity tools) focus on individual samples, and rarely allow comparisons between groups of samples (e.g., healthy vs. diseased). Furthermore, this kind of inference is challenging, because spliced and unspliced mRNA abundance is characterized by a high degree of quantification uncertainty, due to the prevalence of multi-mapping reads, i.e., reads compatible with multiple transcripts (or genes), and/or with both their spliced and unspliced versions. Results: Here, we present DifferentialRegulation, a Bayesian hierarchical method to discover changes between experimental conditions with respect to the relative abundance of unspliced mRNA (over the total mRNA). We model the quantification uncertainty via a latent variable approach, where reads are allocated to their gene/transcript of origin, and to the respective splice version. We designed several benchmarks where our approach shows good performance, in terms of sensitivity and error control, versus state-of-the-art competitors. Importantly, our tool is flexible, and works with both bulk and single-cell RNA-sequencing data. Availability and implementation: DifferentialRegulation is distributed as a Bioconductor R package.

Vibration Characteristics of a Laminated Composite Double-Cylindrical Shell System Coupled with a Variable Number of Annular Plates.

A vibration characteristic analysis model of a laminated composite double cylindrical shell system (LCDCSS) coupled with several annular plates under general boundary conditions is established. Artificial springs are used to simulate the coupling relationship between substructures to ensure the continuity of displacement both at ends of the shells and coupling boundaries. The variable number of annular plates can be distributed unevenly and coupled elastically. Displacement functions of LCDCSS are expressed with improved Fourier series. Based on the principle of energy, obtain the unknown coefficients of the displacement components by using the Rayleigh-Ritz method. The convergence and effectiveness of the proposed method are verified by comparing with the results with literature and FEM, and then carried out parametric investigation to study the free and steady-state response vibration characteristics of LCDCSS. Rapid prediction of free vibration and response vibration of a double-layer cylindrical shell system with various structures and scales is realized by exploiting the model, and some new results of double-layer cylindrical shell system are explored, which can provide reference for further research.

Research on Improving NVH Performance of Automobile Side Door Glass in Use Based on 6 Sigma Method.

Automobile side door glass squeaks and rattles during use. This abnormal noise can make the driver and occupants irritable and reduce the comfort of the automobile. This reduces the sales of this automobile. This paper analyzes and determines the cause of squeak and rattle during the lifting and lowering process of the side door glass of an automobile. The noise is due to four reasons. One is that the distance between the inner waterproof belt and the automobile side door glass of the automobile is unreasonable, causing excessive friction between the automobile side door glass and the inner waterproof belt during the automobile side door glass up and down movement. Other factors affecting squeak and rattle may be the distance between the automobile side door sheet metal and the automobile side door glass, the thickness of the automobile side door glass and the characteristics of the inner waterproof belt. The first two dimensions are analyzed using the 6 sigma method, and the structure of the inner waterproof belt is improved and the flocking position is adjusted. The squeak and rattle phenomenon is explained using the implicit dynamic analysis method ABAQUS, and the compression load deflection after the installation of the inner waterproof belt is 3-9 N/100 mm. This research completely solves the squeak and rattle problem caused by the up and down movement of the side door glass of the automobile. This research has significance for solving practical engineering problems.

Free Vibration Analysis of Closed Moderately Thick Cross-Ply Composite Laminated Cylindrical Shell with Arbitrary Boundary Conditions.

A semi-analytic method is adopted to analyze the free vibration characteristics of the moderately thick composite laminated cylindrical shell with arbitrary classical and elastic boundary conditions. By Hamilton's principle and first-order shear deformation theory, the governing equation of the composite shell can be established. The displacement variables are transformed into the wave function forms to ensure the correctness of the governing equation. Based on the kinetic relationship between the displacement variables and force resultants, the final equation associated with arbitrary boundary conditions is established. The dichotomy method is conducted to calculate the natural frequencies of the composite shell. For verifying the correctness of the present method, the results by the present method are compared with those in the pieces of literatures with various boundary conditions. Furthermore, some numerical examples are calculated to investigate the effect of several parameters on the composite shell, such as length to radius ratios, thickness to radius ratios and elastic restrained constants.

Wave Based Method for Free Vibration Analysis of Cross-Ply Composite Laminated Shallow Shells with General Boundary Conditions.

In this paper, a semi-analytical method is adopted to analyze the free vibration characteristics of composite laminated shallow shells under general boundary conditions. Combining two kinds of shell theory, that is, first-order shear deformation shell theory (FSDT) and classical shell theory (CST), to describe the dynamic relationship between the displacement resultants and force vectors, the theoretical formulations are established. According to the presented work, the displacement and transverse rotational variables are transformed into wave function forms to satisfy the theoretical formulation. Related to diverse boundary conditions, the total matrix of the composite shallow shell can be established. Searching the determinant of the total matrix using the dichotomy method, the natural frequency of composite laminated shallow shells is obtained. Through several classical numerical examples, it is proven that the results calculated by the presented method are more accurate and reliable. Furthermore, to discuss the effect of geometric parameters and material constants on the natural frequencies of composite laminated shallow shells, some numerical examples are calculated to analyze. Also, the influence of boundary elastic restrained stiffness is discussed.