Structural variations (SVs) or copy number variations (CNVs) greatly impact the functions of the genes encoded in the genome and are responsible for diverse human diseases. Although a number of ...existing SV detection algorithms can detect many types of SVs using whole genome sequencing (WGS) data, no single algorithm can call every type of SVs with high precision and high recall.
We comprehensively evaluate the performance of 69 existing SV detection algorithms using multiple simulated and real WGS datasets. The results highlight a subset of algorithms that accurately call SVs depending on specific types and size ranges of the SVs and that accurately determine breakpoints, sizes, and genotypes of the SVs. We enumerate potential good algorithms for each SV category, among which GRIDSS, Lumpy, SVseq2, SoftSV, Manta, and Wham are better algorithms in deletion or duplication categories. To improve the accuracy of SV calling, we systematically evaluate the accuracy of overlapping calls between possible combinations of algorithms for every type and size range of SVs. The results demonstrate that both the precision and recall for overlapping calls vary depending on the combinations of specific algorithms rather than the combinations of methods used in the algorithms.
These results suggest that careful selection of the algorithms for each type and size range of SVs is required for accurate calling of SVs. The selection of specific pairs of algorithms for overlapping calls promises to effectively improve the SV detection accuracy.
The helicity-orbital coupling is an intriguing feature of magnetic skyrmions in frustrated magnets. Here we explore the skyrmion dynamics in a frustrated magnet based on the J
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classical ...Heisenberg model explicitly by including the dipole-dipole interaction. The skyrmion energy acquires a helicity dependence due to the dipole-dipole interaction, resulting in the current-induced translational motion with a fixed helicity. The lowest-energy states are the degenerate Bloch-type states, which can be used for building the binary memory. By increasing the driving current, the helicity locking-unlocking transition occurs, where the translational motion changes to the rotational motion. Furthermore, we demonstrate that two skyrmions can spontaneously form a bound state. The separation of the bound state forced by a driving current is also studied. In addition, we show the annihilation of a pair of skyrmion and antiskyrmion. Our results reveal the distinctive frustrated skyrmions may enable viable applications in topological magnetism.
•Genetic abnormality for autism spectrum disorder (ASD) is overviewed.•Genomic abnormality for ASD including copy number variation is summarized.•Genome-wide association and linkage studies for ASD ...are summarized.•Next generation sequencing studies for ASD are reviewed.•The convergent biological pathways for ASD are proposed.
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with a strong genetic component. The past decade has witnessed tremendous progress in the genetic studies of ASD. In this article, we review the accumulating literatures on the monogenic forms of ASD and chromosomal abnormalities associated with ASD, the genome-wide linkage and association studies, the copy number variation (CNV) and the next generation sequencing (NGS) studies. With more than hundreds of mutations being implicated, the convergent biological pathways are emerging and the genetic landscape of ASD becomes clearer. The genetic studies provide a solid basis for future translational study for better diagnoses, intervention and treatment of ASD.
A magnetic bimeron is a topologically nontrivial spin texture carrying an integer topological charge, which can be regarded as the counterpart of the skyrmion in easy-plane magnets. The controllable ...creation and manipulation of bimerons are crucial for practical applications based on topological spin textures. Here, we analytically and numerically study the dynamics of an antiferromagnetic bimeron driven by a spin current. Numerical simulations demonstrate that the spin current can create an isolated bimeron in the antiferromagnetic thin film via the dampinglike spin torque. The spin current can also effectively drive the antiferromagnetic bimeron without a transverse drift. The steady motion of an antiferromagnetic bimeron is analytically derived and is in good agreement with the simulation results. Also, we find that the alternating-current-induced motion of the antiferromagnetic bimeron can be described by the Duffing equation due to the presence of the nonlinear boundary-induced force. The associated chaotic behavior of the bimeron is analyzed in terms of the Lyapunov exponents. Our results demonstrate the inertial dynamics of an antiferromagnetic bimeron, and may provide useful guidelines for building future bimeron-based spintronic devices.
Video transformers achieve superior performance in video recognition. Despite the recent advances in video transformers, they still require substantial computation and memory resources. To cater for ...the computation efficiency, a kernel‐based video transformer is proposed, including: (1) a new formulation of the video transformer via the kernel learning is presented to better understand the individual components of it; (2) a lightweight Kernel‐based spatial–temporal multi‐head self‐attention block is explored to learn the compact joint spatial–temporal video feature; (3) an adaptive‐score position embedding method is conducted to promote the flexibility of video transformer. Experimental results on several action recognition datasets demonstrate the effectiveness of the proposed method. Only pretrained on ImageNet‐1K, the method achieves the preferable balance between computation and accuracy, while requiring 7×$\times$ fewer parameters and 13×$\times$ fewer floating point operations than other comparable methods.
Video transformers have achieved superior performance in video recognition. Despite the recent advances in video transformers, they still requires substantial computation and memory resources. To cater for the computation efficiency, the kernel learning is utilized to reformulate video transformer, and propose a novel lightweight kernel‐based video transformer.
Perpendicular magnetization and precise control over the magnetic easy axis in magnetic thin film is necessary for a variety of applications, particularly in magnetic recording media. A strong (111) ...orientation is successfully achieved in the CoFe2O4 (CFO) thin film at relatively low substrate temperature of 100 °C, whereas the (311)-preferred randomly oriented CFO is prepared at room temperature by the DC magnetron sputtering technique. The oxygen-deficient porous CFO film after post-annealing gives rise to compressive strain perpendicular to the film surface, which induces large perpendicular coercivity. We observe the coercivity of 11.3 kOe in the 40-nm CFO thin film, which is the highest perpendicular coercivity ever achieved on an amorphous SiO2/Si substrate. The present approach can guide the systematic tuning of the magnetic easy axis and coercivity in the desired direction with respect to crystal orientation in the nanoscale regime. Importantly, this can be achieved on virtually any type of substrate.
Multiple studies have established associations between human gut bacteria and host physiology, but determining the molecular mechanisms underlying these associations has been challenging1-3. ...Akkermansia muciniphila has been robustly associated with positive systemic effects on host metabolism, favourable outcomes to checkpoint blockade in cancer immunotherapy and homeostatic immunity4-7. Here we report the identification of a lipid from A. muciniphila's cell membrane that recapitulates the immunomodulatory activity of A. muciniphila in cell-based assays8. The isolated immunogen, a diacyl phosphatidylethanolamine with two branched chains (a15:0-i15:0 PE), was characterized through both spectroscopic analysis and chemical synthesis. The immunogenic activity of a15:0-i15:0 PE has a highly restricted structure-activity relationship, and its immune signalling requires an unexpected toll-like receptor TLR2-TLR1 heterodimer9,10. Certain features of the phospholipid's activity are worth noting: it is significantly less potent than known natural and synthetic TLR2 agonists; it preferentially induces some inflammatory cytokines but not others; and, at low doses (1% of EC50) it resets activation thresholds and responses for immune signalling. Identifying both the molecule and an equipotent synthetic analogue, its non-canonical TLR2-TLR1 signalling pathway, its immunomodulatory selectivity and its low-dose immunoregulatory effects provide a molecular mechanism for a model of A. muciniphila's ability to set immunological tone and its varied roles in health and disease.
Digital data, generated by corporate and individual users, is growing day by day due to a vast range of digital applications. Magnetic hard disk drives (HDDs) currently fulfill the demand for storage ...space, required by this data growth. Although flash memory devices are replacing HDDs in applications like mobile phones, laptops, and desktops, HDDs cover the majority of digital data stored in the cloud and servers. Since the capacity growth of HDDs is slowing down, it is essential to look for a potential alternative. One such alternative is domain wall (DW) memory, where magnetic domains in the form of two-dimensional or three-dimensional wires are used to store the information. DW memory (DWM) devices should satisfy the four basic operations, such as writing (nucleating domains or inserting DWs in memory element), storing (stabilizing DWs), shifting (moving DWs), and reading (reading magnetization direction). An external magnetic field or spin-transfer torque can be used to write the information. Spin–orbit torque or electric field may be used for shifting the DWs. The information can be read using tunneling magnetoresistance. The domains may be stored along the tracks using artificial pinning potentials. The absence of moving parts makes the DWM consume less power as compared to HDDs, and be more robust. The potential to stack many layers to store information in three dimensions makes them potentially a large storage capacity device. In addition to memory, DW devices also offer a route for making synaptic devices for neuromorphic computing.
Despite these potential advantages of DWM, significant advances in research are needed before DWM could become commercially viable. One of the major challenges associated with DWM is DW dynamics. Many problems, such as controlled DW motion, the stability of domains, reducing the dimensions of the DW devices are still to be addressed. Artificial pinning sites fabricated through either geometrical or non-geometrical methods have been proposed for controlling DW motion. This review paper presents a survey of the investigations carried out so far and the future perspective of such devices.
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