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  1. Abstract Background

    Structural variation (SV), which ranges from 50 bp to$$\sim$$ 3 Mb in size, is an important type of genetic variations. Deletion is a type of SV in which a part of a chromosome or a sequence of DNA is lost during DNA replication. Three types of signals, including discordant read-pairs, reads depth and split reads, are commonly used for SV detection from high-throughput sequence data. Many tools have been developed for detecting SVs by using one or multiple of these signals.


    In this paper, we develop a new method called EigenDel for detecting the germline submicroscopic genomic deletions. EigenDel first takes advantage of discordant read-pairs and clipped reads to get initial deletion candidates, and then it clusters similar candidates by using unsupervised learning methods. After that, EigenDel uses a carefully designed approach for calling true deletions from each cluster. We conduct various experiments to evaluate the performance of EigenDel on low coverage sequence data.


    Our results show that EigenDel outperforms other major methods in terms of improving capability of balancing accuracy and sensitivity as well as reducing bias. EigenDel can be downloaded from

  2. Free, publicly-accessible full text available February 1, 2024
  3. Abstract

    Roll vortices are a series of large-scale turbulent eddies that nearly align with the mean wind direction and prevail in the hurricane boundary layer. In this study, the one-way nested WRF-LES model simulation results from Li et al. (J Atmos Sci 78(6):1847–1867,, 2021) are used to examine the structure and generation mechanism of roll vortices and associated coherent turbulence in the hurricane boundary layer during the landfall of Hurricane Harvey from 00 UTC 25 to 18 UTC 27 August 2017. Results indicate that roll vortices prevail in the hurricane boundary layer. The intense roll vortices and associated large turbulent eddies above them (at a height of ~ 200 to 3000 m) accumulate within a hurricane radius of 20–40 km. Their intensity is proportional to hurricane intensity during the simulation period. Before and during hurricane landfall, strong inflow convergence leads to horizontal advection of roll vortices throughout the entire hurricane boundary layer. Combined with the strong wind shear, the strongest roll vortices and associated large turbulent eddies are generated near the eyewall with suitable thermodynamic (Richardson number at around − 0.2 to 0.2) and dynamic conditions (strong negative inflow wind shear). After landfall, the decayed inflow weakens the inflow convergence and quickly reducesmore »the strong roll vortices and associated large turbulent eddies. Diagnosis of vertical turbulent kinetic energy indicates that atmospheric pressure perturbation, caused by horizontal convergence, transfers the horizontal component of turbulence to the vertical component with a mean wavelength of about 1 km. The buoyancy term is weak and negative, and the large turbulent eddies are suppressed.

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  4. Free, publicly-accessible full text available January 6, 2024
  5. Free, publicly-accessible full text available December 26, 2023
  6. Abstract During development, neural progenitors are temporally patterned to sequentially generate a variety of neural types. In Drosophila neural progenitors called neuroblasts, temporal patterning is regulated by cascades of Temporal Transcription Factors (TTFs). However, known TTFs were mostly identified through candidate approaches and may not be complete. In addition, many fundamental questions remain concerning the TTF cascade initiation, progression, and termination. In this work, we use single-cell RNA sequencing of Drosophila medulla neuroblasts of all ages to identify a list of previously unknown TTFs, and experimentally characterize their roles in temporal patterning and neuronal specification. Our study reveals a comprehensive temporal gene network that patterns medulla neuroblasts from start to end. Furthermore, the speed of the cascade progression is regulated by Lola transcription factors expressed in all medulla neuroblasts. Our comprehensive study of the medulla neuroblast temporal cascade illustrates mechanisms that may be conserved in the temporal patterning of neural progenitors.
    Free, publicly-accessible full text available December 1, 2023
  7. Context. Solar observations of carbon monoxide (CO) indicate the existence of lower-temperature gas in the lower solar chromosphere. We present an observation of pores, and quiet-Sun, and network magnetic field regions with CO 4.66 μm lines by the Cryogenic Infrared Spectrograph (CYRA) at Big Bear Solar Observatory. Aims. We used the strong CO lines at around 4.66 μm to understand the properties of the thermal structures of lower solar atmosphere in different solar features with various magnetic field strengths. Methods. Different observations with different instruments were included: CO 4.66 μm imaging spectroscopy by CYRA, Atmospheric Imaging Assembly (AIA) 1700 Å images, Helioseismic and Magnetic Imager (HMI) continuum images, line-of-sight (LOS) magnetograms, and vector magnetograms. The data from 3D radiation magnetohydrodynamic (MHD) simulation with the Bifrost code are also employed for the first time to be compared with the observation. We used the Rybicki-Hummer (RH) code to synthesize the CO line profiles in the network regions. Results. The CO 3-2 R14 line center intensity changes to be either enhanced or diminished with increasing magnetic field strength, which should be caused by different heating effects in magnetic flux tubes with different sizes. We find several “cold bubbles” in the CO 3-2 R14more »line center intensity images, which can be classified into two types. One type is located in the quiet-Sun regions without magnetic fields. The other type, which has rarely been reported in the past, is near or surrounded by magnetic fields. Notably, some are located at the edge of the magnetic network. The two kinds of cold bubbles and the relationship between cold bubble intensities and network magnetic field strength are both reproduced by the 3D MHD simulation with the Bifrost and RH codes. The simulation also shows that there is a cold plasma blob near the network magnetic fields, causing the observed cold bubbles seen in the CO 3-2 R14 line center image. Conclusions. Our observation and simulation illustrate that the magnetic field plays a vital role in the generation of some CO cold bubbles.« less
    Free, publicly-accessible full text available January 1, 2024
  8. Abstract

    How many species are there on Earth and to what groups do these species belong? These fundamental questions span systematics, ecology, and evolutionary biology. Yet, recent estimates of overall global biodiversity have ranged wildly, from the low millions to the trillions. Insects are a pivotal group for these estimates. Insects make up roughly half of currently described extant species (across all groups), with ~1 million described species. Insect diversity is also crucial because many other taxa have species that may be unique to each insect host species, including bacteria, apicomplexan protists, microsporidian fungi, nematodes, and mites. Several projections of total insect diversity (described and undescribed) have converged on ~6 million species. However, these projections have not incorporated the morphologically cryptic species revealed by molecular data. Here, we estimate the extent of cryptic insect diversity. We perform a systematic review of studies that used explicit species-delimitation methods with multilocus data. We estimate that each morphology-based insect species contains (on average) 3.1 cryptic species. We then use these estimates to project the overall number of species on Earth and their distribution among major groups. Our estimates suggest that overall global biodiversity may range from 563 million to 2.2 billion species. [Biodiversity;more »cryptic species; insects; species delimitation; species richness.]

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  9. Abstract

    Electrical modulation of magnetic states in single-phase multiferroic materials, using domain-wall magnetoelectric (ME) coupling, can be enhanced substantially by controlling the population density of the ferroelectric (FE) domain walls during polarization switching. In this work, we investigate the domain-wall ME coupling in multiferroic h-YbFeO3thin films, in which the FE domain walls induce clamped antiferromagnetic (AFM) domain walls with reduced magnetization magnitude. Simulation according to the phenomenological theory indicates that the domain-wall ME effect is dramatically enhanced when the separation between the FE domain walls shrinks below the characteristic width of the clamped AFM domain walls during the ferroelectric switching. Experimentally, we show that while the magnetization magnitude remains same for both the positive and the negative saturation polarization states, there is evidence of magnetization reduction at the coercive voltages. These results suggest that the domain-wall ME effect is viable for electrical control of magnetization.

  10. Free, publicly-accessible full text available October 1, 2023