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The diverse functions of WASP, the deficiency of which causes Wiskott-Aldrich syndrome (WAS), remain poorly defined. We generated three isogenic WAS models using patient induced pluripotent stem cells and genome editing. These models recapitulated WAS phenotypes and revealed that WASP deficiency causes an upregulation of numerous RNA splicing factors and widespread altered splicing. Loss of WASP binding to splicing factor gene promoters frequently leads to aberrant epigenetic activation. WASP interacts with dozens of nuclear speckle constituents and constrains SRSF2 mobility. Using an optogenetic system, we showed that WASP forms phase-separated condensates that encompasses SRSF2, nascent RNA and active Pol II. The role of WASP in gene body condensates is corroborated by ChIPseq and RIPseq. Together our data reveal that WASP is a nexus regulator of RNA splicing that controls the transcription of splicing factors epigenetically and the dynamics of the splicing machinery through liquid-liquid phase separation.

Through the generation of humanized FUS mice expressing full-length human FUS, we identify that when expressed at near endogenous murine FUS levels, both wild-type and ALS-causing and frontotemporal dementia (FTD)-causing mutations complement the essential function(s) of murine FUS. Replacement of murine FUS with mutant, but not wild-type, human FUS causes stress-mediated induction of chaperones, decreased expression of ion channels and transporters essential for synaptic function, and reduced synaptic activity without loss of nuclear FUS or its cytoplasmic aggregation. Most strikingly, accumulation of mutant human FUS is shown to activate an integrated stress response and to inhibit local, intra-axonal protein synthesis in hippocampal neurons and sciatic nerves. Collectively, our evidence demonstrates that human ALS/FTD-linked mutations in FUS induce a gain of toxicity that includes stress-mediated suppression in intra-axonal translation, synaptic dysfunction, and progressive age-dependent motor and cognitive disease without cytoplasmic aggregation, altered nuclear localization, or aberrant splicing of FUS-bound pre-mRNAs. VIDEO ABSTRACT.

Mutations in several general pre-mRNA splicing factors have been linked to myelodysplastic syndromes (MDSs) and solid tumors. These mutations have generally been assumed to cause disease by the resultant splicing defects, but different mutations appear to induce distinct splicing defects, raising the possibility that an alternative common mechanism is involved. Here we report a chain of events triggered by multiple splicing factor mutations, especially high-risk alleles in SRSF2 and U2AF1, including elevated R-loops, replication stress, and activation of the ataxia telangiectasia and Rad3-related protein (ATR)-Chk1 pathway. We further demonstrate that enhanced R-loops, opposite to the expectation from gained RNA binding with mutant SRSF2, result from impaired transcription pause release because the mutant protein loses its ability to extract the RNA polymerase II (Pol II) C-terminal domain (CTD) kinase-the positive transcription elongation factor complex (P-TEFb)-from the 7SK complex. Enhanced R-loops are linked to compromised proliferation of bone-marrow-derived blood progenitors, which can be partially rescued by RNase H overexpression, suggesting a direct contribution of augmented R-loops to the MDS phenotype.

Myelodysplastic syndromes (MDS) are heterogeneous myeloid disorders with prevalent mutations in several splicing factors, but the splicing programs linked to specific mutations or MDS in general remain to be systematically defined. We applied RASL-seq, a sensitive and cost-effective platform, to interrogate 5502 annotated splicing events in 169 samples from MDS patients or healthy individuals. We found that splicing signatures associated with normal hematopoietic lineages are largely related to cell signaling and differentiation programs, whereas MDS-linked signatures are primarily involved in cell cycle control and DNA damage responses. Despite the shared roles of affected splicing factors in the 3 splice site definition, mutations in U2AF1, SRSF2, and SF3B1 affect divergent splicing programs, and interestingly, the affected genes fall into converging cancer-related pathways. A risk score derived from 11 splicing events appears to be independently associated with an MDS prognosis and AML transformation, suggesting potential clinical relevance of altered splicing patterns in MDS.

FUS is an RNA-binding protein involved in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Cytoplasmic FUS-containing aggregates are often associated with concomitant loss of nuclear FUS Whether loss of nuclear FUS function, gain of a cytoplasmic function, or a combination of both lead to neurodegeneration remains elusive. To address this question, we generated knockin mice expressing mislocalized cytoplasmic FUS and complete FUS knockout mice. Both mouse models display similar perinatal lethality with respiratory insufficiency, reduced body weight and length, and largely similar alterations in gene expression and mRNA splicing patterns, indicating that mislocalized FUS results in loss of its normal function. However, FUS knockin mice, but not FUS knockout mice, display reduced motor neuron numbers at birth, associated with enhanced motor neuron apoptosis, which can be rescued by cell-specific CRE-mediated expression of wild-type FUS within motor neurons. Together, our findings indicate that cytoplasmic FUS mislocalization not only leads to nuclear loss of function, but also triggers motor neuron death through a toxic gain of function within motor neurons.

Histopathology interpretation remains an essential, foundational method for disease diagnosis in medical practice. (1) Standard histopathology assessment is initiated through interpretation of hematoxylin and eosin--stained glass microscope slides prepared from [...], * Context.--The adoption of digital capture of pathology slides as whole slide images (WSI) for educational and research applications has proven utility. Objective.--To compare pathologists' primary diagnoses derived from WSI versus the standard microscope. Because WSIs differ in format and method of observation compared with the current standard glass slide microscopy, this study is critical to potential clinical adoption of digital pathology. Design.--The study enrolled a total of 2045 cases enriched for more difficult diagnostic categories and represented as 5849 slides were curated and provided for diagnosis by a team of 19 reading pathologists separately as WSI or as glass slides viewed by light microscope. Cases were reviewed by each pathologist in both modalities in randomized order with a minimum 31-day washout between modality reads for each case. Each diagnosis was compared with the original clinical reference diagnosis by an independent central adjudication review. Results.--The overall major discrepancy rates were 3.64% for WSI review and 3.20% for manual slide review diagnosis methods, a difference of 0.44% (95% CI, -0.15 to 1.03). The time to review a case averaged 5.20 minutes for WSI and 4.95 minutes for glass slides. There was no specific subset of diagnostic category that showed higher rates of modality-specific discrepancy, though some categories showed greater discrepancy than others in both modalities. Conclusions.--WSIs are noninferior to traditional glass slides for primary diagnosis in anatomic pathology.

RNA splicing is a major contributor to total transcriptome complexity; however, the functional role and regulation of splicing in heart failure remain poorly understood. Here, we used a total transcriptome profiling and bioinformatic analysis approach and identified a muscle-specific isoform of an RNA splicing regulator, RBFox1 (also known as A2BP1), as a prominent regulator of alternative RNA splicing during heart failure. Evaluation of developing murine and zebrafish hearts revealed that RBFox1 is induced during postnatal cardiac maturation. However, we found that RBFox1 is markedly diminished in failing human and mouse hearts. In a mouse model, RBFox1 deficiency in the heart promoted pressure overload-induced heart failure. We determined that RBFox1 is a potent regulator of RNA splicing and is required for a conserved splicing process of transcription factor MEF2 family members that yields different MEF2 isoforms with differential effects on cardiac hypertrophic gene expression. Finally, induction of RBFox1 expression in murine pressure overload models substantially attenuated cardiac hypertrophy and pathological manifestations. Together, this study identifies regulation of RNA splicing by RBFox1 as an important player in transcriptome reprogramming during heart failure that influence pathogenesis of the disease.

PSF (a.k.a. SFPQ) is a ubiquitously expressed, essential nuclear protein with important roles in DNA damage repair and RNA biogenesis. In stimulated T cells, PSF binds to and suppresses the inclusion of CD45 exon 4 in the final mRNA; however, in resting cells, TRAP150 binds PSF and prevents access to the CD45 RNA, though the mechanism for this inhibition has remained unclear. Here, we show that TRAP150 binds a region encompassing the RNA recognition motifs (RRMs) of PSF using a previously uncharacterized, 70 residue region we have termed the PSF-interacting domain (PID). TRAP150's PID directly inhibits the interaction of PSF RRMs with RNA, which is mediated through RRM2. However, interaction of PSF with TRAP150 does not appear to inhibit the dimerization of PSF with other Drosophila Behavior, Human Splicing (DBHS) proteins, which is also dependent on RRM2. Finally, we use RASL-Seq to identify ∼40 T cell splicing events sensitive to PSF knockdown, and show that for the majority of these, PSF's effect is antagonized by TRAP150. Together these data suggest a model in which TRAP150 interacts with dimeric PSF to block access of RNA to RRM2, thereby regulating the activity of PSF toward a broad set of splicing events in T cells.

Myelodysplastic syndromes (MDS) are a group of neoplasms characterized by ineffective myeloid hematopoiesis and various risks for leukemia. SRSF2, a member of the serine/arginine-rich (SR) family of splicing factors, is one of the mutation targets associated with poor survival in patients suffering from myelodysplastic syndromes. Here we report the biological function of SRSF2 in hematopoiesis by using conditional knockout mouse models. Ablation of SRSF2 in the hematopoietic lineage caused embryonic lethality, and Srsf2-deficient fetal liver cells showed significantly enhanced apoptosis and decreased levels of hematopoietic stem/progenitor cells. Induced ablation of SRSF2 in adult Mx1-Cre Srsf2(flox/flox) mice upon poly(I):poly(C) injection demonstrated a significant decrease in lineage(-) Sca(+) c-Kit(+) cells in bone marrow. To reveal the functional impact of myelodysplastic syndromes-associated mutations in SRSF2, we analyzed splicing responses on the MSD-L cell line and found that the missense mutation of proline 95 to histidine (P95H) and a P95-to-R102 in-frame 8-amino-acid deletion caused significant changes in alternative splicing. The affected genes were enriched in cancer development and apoptosis. These findings suggest that intact SRSF2 is essential for the functional integrity of the hematopoietic system and that its mutations likely contribute to development of myelodysplastic syndromes.

Heart failure is characterized by the transition from an initial compensatory response to decompensation, which can be partially mimicked by transverse aortic constriction (TAC) in rodent models. Numerous signaling molecules have been shown to be part of the compensatory program, but relatively little is known about the transition to decompensation that leads to heart failure. Here, we show that TAC potently decreases the RBFox2 protein in the mouse heart, and cardiac ablation of this critical splicing regulator generates many phenotypes resembling those associated with decompensation in the failing heart. Global analysis reveals that RBFox2 regulates splicing of many genes implicated in heart function and disease. A subset of these genes undergoes developmental regulation during postnatal heart remodeling, which is reversed in TAC-treated and RBFox2 knockout mice. These findings suggest that RBFox2 may be a critical stress sensor during pressure overload-induced heart failure.

The U2AF heterodimer has been well studied for its role in defining functional 3' splice sites in pre-mRNA splicing, but many fundamental questions still remain unaddressed regarding the function of U2AF in mammalian genomes. Through genome-wide analysis of U2AF-RNA interactions, we report that U2AF has the capacity to directly define ~88% of functional 3' splice sites in the human genome, but numerous U2AF binding events also occur in intronic locations. Mechanistic dissection reveals that upstream intronic binding events interfere with the immediate downstream 3' splice site associated either with the alternative exon, to cause exon skipping, or with the competing constitutive exon, to induce exon inclusion. We further demonstrate partial functional impairment with leukemia-associated mutations in U2AF35, but not U2AF65, in regulated splicing. These findings reveal the genomic function and regulatory mechanism of U2AF in both normal and disease states.

Objective To analyze the incidence trends and spatiotemporal distribution characteristics of dengue fever in China based on the data from the China Disease Control Information System and the "National Statutory Infectious Disease Epidemic Overview" published by the National Health Commission of the People's Republic of China, and to provide a scientific basis for the prevention and control of dengue fever epidemics. Methods The incidence rates and monthly case numbers of dengue fever in China from 2015 to 2023 were collected. Provinces were classified according to the severity of the epidemic and the distribution status of the Aedes vector. The incidence trends, seasonal distribution, and spatial aggregation of dengue fever in China were statistically analyzed. Results The top five provinces with the highest average annual incidence rates from 2015 to 2023 were Yunnan (6.16/100 000), Guangdong (1.70/100 000), Hainan (1.13/100 000), Fujian (1.13/100 000), and Chongqing (0.74/100 000). The average annual incidence rate of dengue fever in China increased by 70.79% from 2015 to 2019 (AAPC=70.79, P=0.045). In Class I regions, the incidence of Guangxi and Hainan showed a linear regression trend, with average annual increases of 844.73% (AAPC=844.73, P=0.021) and 516.51% (AAPC=516.51, P=0.013), respectively. In Class II regions, except for Shanghai, the incidence of other provinces showed a linear regression trend, with Jiangxi having the highest average annual increase of 610.16% (AAPC=610.16, P=0.021), followed by Chongqing at 345.12% (AAPC=345.12, P=0.038). In Class III regions, the incidence of Hebei, Shanxi, and Liaoning had a linear regression trend, with average annual increases of 80.67% (AAPC=80.67, P=0.028), 202.31% (AAPC=202.31, P=0.001), and 70.19% (AAPC=70.19, P=0.031), respectively. The epidemic of dengue fever showed no obvious seasonality in 2021, strict seasonality in 2022, and strong seasonality in the rest of the years. The epidemic peak days were mostly concentrated in the middle and late September to early October of each year, and the epidemic peak periods were mainly concentrated in August-early November. From 2015 to 2018, the incidence rate had no spatial aggregation nationwide, and the incidence rate in 2019 had spatial aggregation nationwide. In 2015-2019 and 2023, there were no high-low gathering areas in the country, and high-high gathering areas appeared in 2018 (Fujian, Hainan) and 2019 (Guangxi). Conclusions The situation of dengue fever prevention and control in China is grim. High-risk epidemic areas of dengue fever will no longer be limited to Class I provinces, and the risk of expansion to Class II provinces is increasing. [ABSTRACT FROM AUTHOR]

Expanded hexanucleotide repeats in the chromosome 9 open reading frame 72 (C9orf72) gene are the most common genetic cause of ALS and frontotemporal degeneration (FTD). Here, we identify nuclear RNA foci containing the hexanucleotide expansion (GGGGCC) in patient cells, including white blood cells, fibroblasts, glia, and multiple neuronal cell types (spinal motor, cortical, hippocampal, and cerebellar neurons). RNA foci are not present in sporadic ALS, familial ALS/FTD caused by other mutations (SOD1, TDP-43, or tau), Parkinson disease, or nonneurological controls. Antisense oligonucleotides (ASOs) are identified that reduce GGGGCC-containing nuclear foci without altering overall C9orf72 RNA levels. By contrast, siRNAs fail to reduce nuclear RNA foci despite marked reduction in overall C9orf72 RNAs. Sustained ASO-mediated lowering of C9orf72 RNAs throughout the CNS of mice is demonstrated to be well tolerated, producing no behavioral or pathological features characteristic of ALS/FTD and only limited RNA expression alterations. Genome-wide RNA profiling identifies an RNA signature in fibroblasts from patients with C9orf72 expansion. ASOs targeting sense strand repeat-containing RNAs do not correct this signature, a failure that may be explained, at least in part, by discovery of abundant RNA foci with C9orf72 repeats transcribed in the antisense (GGCCCC) direction, which are not affected by sense strand-targeting ASOs. Taken together, these findings support a therapeutic approach by ASO administration to reduce hexanucleotide repeat-containing RNAs and raise the potential importance of targeting expanded RNAs transcribed in both directions.

Abstract Myelodysplastic syndromes (MDS) are a group of neoplasms that are ineffective in generating multiple lineages of myeloid cells and have various risks to progress to acute myeloid leukemia. Recent genome-wide sequencing studies reveal that mutations in genes of splicing factors are commonly associated with MDS. However, the importance of these splicing factors in hematopoiesis has been unclear and the causal effect of their mutations on MDS development remains to be determined. One of these newly identified genes is SRSF2, and its mutations have been linked to poor survival among MDS patients. Interestingly, most of SRSF2 mutations occur at proline 95 and the majority of these mutations change this proline to histidine (P95H). Given that SRSF2 is a well-characterized splicing factor involved in both constitutive and regulated splicing, we hypothesize that SRSF2 plays an important role in normal hematopoiesis and the SRSF2 mutations induce specific changes in alternative splicing that favor disease progression. We first examined the role of SRSF2 in hematopoiesis by generating Srsf2 null mutation in mouse blood cells via crossing conditional Srsf2 knockout mice (Srsf2f/f) with blood cell-specific Cre transgenic mice (Vav-Cre). The mutant mice produced significantly fewer definitive blood cells (10% of wild type controls), exhibited increased apoptosis in the remaining blood cells, and died during embryonic development. Importantly, we detected no hematopoietic stem/progenitor cells (lineage-/cKit+) in E14 fetal livers of Vav-Cre/Srsf2f/f mice. These results indicate that SRSF2 is essential for hematopoiesis during embryonic development. We next examined the role of SRSF2 in adult hematopoiesis by injecting polyIC into mice that carry a polyIC inducible Cre expression unit. Unexpectedly, after multiple polyIC treatments, the Srsf2f/f mice stayed alive during several months of observation. Time course genotyping analyses of polyIC treated mice revealed an increased rate of incomplete Srsf2 deletion in peripheral blood cells. These observations suggest that Srsf2 ablation did not cause immediate cell lethality in differentiated blood cells, but the gene is indispensable for the function of blood stem/progenitor cells. Since mutations of splicing factors are generally heterozygous in MDS patients, we also examined mice with Srsf2+/- blood cells. No obvious defect of hematopoiesis was observed under normal conditions or in response to stress with 5-FU treatment and sublethal irradiation. To gain molecular insight into the splicing activity of MDS-associated mutant forms of SRSF2, we performed large-scale alternative splicing surveys by using RNA-mediated oligonucleotide annealing, selection, and ligation coupled with next-generation sequencing (RASL-seq) previously developed in our lab, which offers a robust and cost-effective platform for splicing profiling. Compared to vector transduction controls, we found that overexpression of both wild type and P95H SRSF2 induced many, but distinct changes in alternative splicing in lineage-negative bone marrow cells, and importantly, we noted several changes in genes with known roles in hematopoietic malignancies that were uniquely induced by the mutant SRSF2. To further link the mutations to altered splicing in MDS patients, we also applied RASL-seq to a large number of MDS patient samples with or without mutations in SRSF2 or other splicing regulators. The data revealed a specific set of alternative splicing events that are commonly linked to MDS with splicing factor mutations. These findings strongly suggest that many of these mutations in splicing regulators are gain-of-function mutations that are causal to MDS. In conclusion, we report that SRSF2 plays an essential role in hematopoietic stem/progenitor cells and that the MDS-associated mutations in SRSF2 have a dominant effect on RNA alternative splicing. These findings provide functional information and molecular basis of SRSF2 and its MDS-related mutations in hematopoiesis and related clinical disorders. Disclosures: No relevant conflicts of interest to declare.

Space-time waveform-encoding (STWE) synthetic aperture radar (SAR) has great potential to improve the performance of the future spaceborne SAR system. With the aim of solving the problem of overlapped echoes, one effective approach involves the use of digital beamforming (DBF) in elevation combined with the null-steering techniques. However, the traditional real-time echo separation scheme with single-null-steering techniques occupies huge digital resources. In this letter, a novel real-time echo separation processing scheme in intermediate frequency domain is proposed to overcome the disadvantage of the conventional scheme. Based on the 2-D simulation results, the proposed scheme has the same accuracy of separating the overlapped echoes as the traditional scheme. The detailed analysis of the system complexity indicates that the proposed scheme can greatly reduce the resource occupation. Moreover, the effectiveness of the proposed scheme is further verified and demonstrated by the experimental results on the X-band 16-channel DBF-SAR system. [ABSTRACT FROM AUTHOR]

Space-time waveform-encoding (STWE)-synthetic aperture radar (SAR) is an effective way to accomplish high-resolution and wide-swath (HRWS) imaging. By designing the specific signal transmit mode, the echoes from several subswaths are received within a single receiving window and overlap each other in STWE-SAR. In order to separate the overlapped echoes, the linear-constrained minimum variance (LCMV) beamformer, a single-null beamformer, is typically used. However, the LCMV beamformer has a very narrow and unstable notch depth, which is not sufficient to accurately separate the overlapped echoes with large signal energy differences between subswaths. The issue of signal energy differences in STWE-SAR is first raised in this paper. Moreover, a novel echo separation scheme based on a second-order cone programming (SOCP) beamformer is proposed. The beam pattern generated by the SOCP beamformer allows flexible adjustment of the notch width and depth, which effectively improves the quality of separation results compared to the LCMV beamformer. The simulation results illustrate that the scheme can greatly enhance the performance of echo separation. Furthermore, the experimental results based on the X-band STWE-SAR airborne system not only demonstrate the scheme's effectiveness but also indicate that it holds great promise for future STWE-SAR missions. [ABSTRACT FROM AUTHOR]

To achieve high-resolution and wide-swath (HRWS) imaging, a space-time waveform-encoding (STWE) spaceborne synthetic aperture radar (SAR) system is adopted. In rugged terrain, the beam-pointing mismatch problem will appear when the traditional digital beamforming (DBF) technique is used to separate the received echoes. This problem leads to decreasing the received echo's gain, deteriorating the quality of the image product and making the interpretation of SAR image difficult. To address this problem, an advanced echo separation scheme for STWE spaceborne SAR based on the DBF and blind source separation (BSS) is put forward in this paper. In the scheme, the echoes are transmitted within the adjacent pulse repetition intervals to simulate multiple beams, and the scattered echoes are received by the sixteen-channel antennas in elevation simultaneously. In post-processing, a detailed flow is adopted. In the method, the DBF is firstly performed on received echoes. Due to the error caused by terrain undulation, the degree of echo separation is not enough. Then, the BSS is performed on the multiple echoes obtained after the DBF processing. Finally, the highly separated echo signal can be obtained. In this scheme, there is no need to perform the direction of arrival (DOA) estimation before the DBF processing, which saves valuable computing resources. In addition, to verify the proposed scheme, point target and distributed target simulations based on the 16-channel data of an elevation X-band DBF-SAR system are carried out. The results of point targets indicate that the residual echo caused by rough terrain can be reduced by more than 14 dB using the proposed scheme. The proposed scheme can be directly implemented into existing SAR systems; thus, it does not increase the complexity of the system design. The scheme has the potential to be applied to future spaceborne SAR missions. [ABSTRACT FROM AUTHOR]

Digital beamforming (DBF) with scan-on-receive (SCORE) technique in elevation is a powerful technique that enables a spaceborne synthetic aperture radar (SAR) to achieve high-resolution wide swath (HRWS) imaging. In the spaceborne DBF-SAR system, sampling signals from each channel are weighted by weights generated by a digital signal processing system in real-time. However, the contradiction between the shortage of spaceborne hardware resources and resource demand of the multichannel real-time signal processing increases the difficulty of system design. In order to solve this problem, a novel weight generator and an improved intermediate frequency (IF) DBF real-time processing architecture are proposed in this article. By taking advantage of the special properties of the SCORE algorithm, the proposed weight generator calculates weights using a linear polynomial algorithm. The simulation result shows that a low-order approximation can achieve high performance. The proposed generator can correct multichannel amplitude and phase error at a low cost on hardware resources. The effectiveness of the proposed method is verified by experiments with a raw data processing instance of an X-band 16 channels DBF-SAR. [ABSTRACT FROM AUTHOR]

The displaced phase center antennas in azimuth and digital beamforming (DBF) in elevation are two state-of-the-art techniques for achieving high-resolution wide swath (HRWS) imaging in the multichannel synthetic aperture radar (SAR) systems. However, due to the atmospheric turbulence, airborne HRWS-SARs inevitably suffer trajectory disturbances, which will consequently defocus the SAR image. Although various motion compensation (MoCo) methods have been proposed, they are mostly designed for the traditional single-channel SAR and, therefore, ignore the channel-dependent posture error. The posture motion error will introduce residual motion and time-variant channel errors, which not only defocuses the image but also causes azimuth ambiguity and degrades the SNR improvement of the final images of the azimuth multichannel and DBF-SAR, respectively. To solve these problems, a novel MoCo scheme for 2-D multichannel SAR systems is proposed. The posture error is described and calculated in matrix form through the use of quaternions. Then, the posture error is transformed into the translational motion error for each receiving channel and is subsequently compensated precisely. To address the residual aperture-variant motion error, a modified aperture-dependent MoCo is integrated into the proposed scheme. Simulations and airborne experiments, including processing the data of a C-band SAR system with four azimuth channels and an X-band DBF-SAR system with 16 elevation channels, have been implemented to validate the effectiveness of the proposed MoCo scheme. [ABSTRACT FROM AUTHOR]

In the Earth observation mission of the synthetic aperture radar (SAR), wide swath can be used to complete global monitoring in a short time and high resolution can provide rich detailed information about the feature space and prominent structure and texture. However, the traditional single-channel classical SAR system cannot meet high-resolution and wide-swath (HRWS) imaging demand due to the constraint of minimum antenna area. Fortunately, this fundamental limitation can be overcome by using multiple receive subapertures in combination with advanced digital beamforming (DBF) technique. DBF in elevation can provide high gain and better system performance and has recently gained much attention in the field of SAR imaging. This article presents a 16-channel in elevation airborne X-band DBF-SAR system with 500-MHz bandwidth, characterized by high speed data acquisition and storage, as a test bed to provide the technical reserves and support for a future spaceborne DBF-SAR system in China. The hardware configuration of this system is designed according to a realistic flight mission. To verify the feasibility and operability of this advanced 16-channel DBF-SAR system, an outfield airborne flight experiment was successfully conducted in eastern Guangdong Province in November 2019. Meanwhile, considering the inevitable channel mismatch from airborne system, a precise strategy as well as the underlying signal processing is proposed to process the experiment data. In addition to the channel mismatch due to the topographic height, the Scan-On-Receive (SCORE) pattern loss (SPL) is also an inherent factor, which will deteriorate the output SNR in final SAR images. Therefore, this article also implements a quantitative assessment of SPL combined with the practical flight parameters and the real airborne data. Finally, the corresponding processing results are presented and analyzed in detail. The practical SNR improvement of 11.23 dB emphasize that DBF technology can significantly improve the quality of SAR images and will make an essential contribution to next generation of HRWS technology for environment monitoring. [ABSTRACT FROM AUTHOR]

Digital beamforming (DBF) is an effective method for improving the signal-to-noise ratio (SNR) in synthetic aperture radar (SAR) images. However, further enhancing the SNR in DBF-SAR is limited by the antenna size and the expensive system cost. To address this problem, in this letter we implement a hybrid strip-map/spotlight mode for DBF. By utilizing the proposed processing method, DBF is adapted for hybrid strip-map/spotlight mode data. Furthermore, the additional synthetic aperture acquired from the hybrid strip-map/spotlight mode is employed to implement multilook processing for further enhancing the SNR of DBF-SAR images. The proposed processing method was verified by an airborne X-band 16-channel DBF-SAR system. The results confirmed that a remarkable additional SNR improvement in DBF-SAR images can be obtained using the proposed method without increasing system complexity. [ABSTRACT FROM AUTHOR]

The software of artificial organ is more and more complex, but it lacks real-time operating system to manage and schedule its resources. In this paper, we propose a lightweight real-time operating system (RTOS) Cyborgan OS based on the SmartOSEK OS. Cyborgan OS optimizes and improves it from the code size, context switch, low power consumption, and partial dynamic update, making it suitable for the artificial organ control system. Finally, we use the heart blood pump model to analyze the task allocation and execution sequence as well as the code size of the whole program. In this application, the maximum space occupied by the code is only 15 kB, which is suitable for most microcontrollers. [ABSTRACT FROM AUTHOR]

The ability to modulate the production of the wild-type transcript in cells bearing the splice-altering familial dysautonomia ( FD) causing mutation in the IKBKAP gene prompted a study of the impact of a panel of pharmaceuticals on the splicing of this transcript, which revealed the ability of the cardiac glycoside digoxin to increase the production of the wild-type, exon-20-containing, IKBKAP-encoded transcript and the full-length IκB-kinase-complex-associated protein in FD-derived cells. Characterization of the cis elements and trans factors involved in the digoxin-mediated effect on splicing reveals that this response is dependent on an SRSF3 binding site(s) located in the intron 5′ of the alternatively spliced exon and that digoxin mediates its effect by suppressing the level of the SRSF3 protein. Characterization of the digoxin-mediated effect on the RNA splicing process was facilitated by the identification of several RNA splicing events in which digoxin treatment mediates the enhanced inclusion of exonic sequence. Moreover, we demonstrate the ability of digoxin to impact the splicing process in neuronal cells, a cell type profoundly impacted by FD. This study represents the first demonstration that digoxin possesses splice-altering capabilities that are capable of reversing the impact of the FD-causing mutation. These findings support the clinical evaluation of the impact of digoxin on the FD patient population. [ABSTRACT FROM AUTHOR]

The frequency diverse array (FDA) technique is a novel scheme for high resolution wide swath synthetic aperture radar (SAR) imaging, which employs a frequency increment across the array elements. This introduces a range-angle-dependence to the transmission steering vector, which is exploited for range ambiguity resolution in strip-map SAR. Generally in spotlight mode, scatterers dispersively distributed in azimuth have different Doppler histories, in which the range ambiguity resolution for strip-map SAR fails. To extend the flexibility of FDA, in this paper a novel FDA imaging scheme for spotlight mode SAR is proposed. Exploiting the property of the same illuminated period of all scatterers in spotlight mode, the proposed scheme is carried out entirely in the azimuth time domain, which allows for higher processing efficiency and real-time implementations. Still, excessive Doppler history differences among scatterers deteriorate the scheme performance for azimuth-edge scatterers. Aiming at this situation, a residual angle phase compensation in time domain is considered for the cases of a large azimuth beam width, improving the applicability of the proposed scheme. Compared with existing methods, the proposed spotlight FDA-SAR offers the possibility of achieving simultaneously high azimuth resolution and wide swath performance with high efficiency. Simulations and analyses are performed to demonstrate the effectiveness of the proposed spotlight FDA-SAR scheme. [ABSTRACT FROM AUTHOR]

Space–time waveform-encoding (STWE) SAR can receive echoes from multiple sub-swaths simultaneously with a single receive window. The echoes overlap each other in the time domain. To separate the echoes from different directions, traditional schemes adapt single-null steering techniques for digital receive beam patterns. However, the problems of spaceborne DBF-SAR, in practice, such as null extension loss, terrain undulation, elevation angle of arrival extension, and spaceborne antenna beam control, make the conventional scheme unable to effectively separate the echoes from different sub-swaths, which overlap each other in the time domain.A novel multi-null constrained echo separation scheme is proposed to overcome the shortcomings of the conventional scheme. The proposed algorithm can flexibly adjust the width of the notch to track the time-varying pulse extension angle with less resource consumption. Moreover, the hardware implementation details of the corresponding real-time processing architecture are discussed. The two-dimensional simulation results indicate that the proposed scheme can effectively improve the performance of echo separation. The effectiveness of the proposed method is verified by raw data processing instance of an X-band 16-channel DBF-SAR airborne system. [ABSTRACT FROM AUTHOR]

The RNA-binding protein FUS/TLS, mutation in which is causative of the fatal motor neuron disease ALS, is demonstrated to directly bind to the U1-snRNP and SMN complexes. ALS-causative mutations in FUS/TLS are shown to abnormally enhance their interaction with SMN and dysregulate its function, including loss of Gems and altered levels of small nuclear RNAs (snRNAs). The same mutants are found to have reduced association with U1-snRNP. Correspondingly, global RNA analysis reveals a mutant-dependent loss of splicing activity, with ALS-linked mutants failing to reverse changes caused by loss of wild-type FUS/TLS. Furthermore, a common FUS/TLS mutant-associated RNA splicing signature is identified in ALS patient fibroblasts. Taken together, these studies establish potentially converging disease mechanisms in ALS and spinal muscular atrophy, with ALS-causative mutants acquiring properties representing both gain (dysregulation of SMN) and loss (reduced RNA processing mediated by U1-snRNP) of function.

Due to the atmospheric turbulence, the motion trajectory of airborne very high resolution (VHR) synthetic aperture radars (SARs) is inevitably affected, which introduces range-variant range cell migration (RCM) and aperture-dependent azimuth phase error (APE). Both types of errors consequently result in defocused images, as residual range- and aperture-dependent motion errors are significant in VHR-SAR images. Nevertheless, little work has been devoted to the range-variant RCM auto-correction and aperture-dependent APE auto-correction. In this paper, a precise motion compensation (MoCo) scheme for airborne VHR-SAR is studied. In the proposed scheme, the motion error is obtained from inertial measurement unit and SAR data, and compensated for with respect to both range and aperture. The proposed MoCo scheme compensates for the motion error without space-invariant approximation. Simulations and experimental data from an airborne 3.6 GHz bandwidth SAR are employed to demonstrate the validity and effectiveness of the proposed MoCo scheme. [ABSTRACT FROM AUTHOR]

HnRNP L is a ubiquitous splicing-regulatory protein that is critical for the development and function of mammalian T cells. Previous work has identified a few targets of hnRNP L-dependent alternative splicing in T cells and has described transcriptome-wide association of hnRNP L with RNA. However, a comprehensive analysis of the impact of hnRNP L on mRNA expression remains lacking. Here we use next-generation sequencing to identify transcriptome changes upon depletion of hnRNP L in a model T-cell line. We demonstrate that hnRNP L primarily regulates cassette-type alternative splicing, with minimal impact of hnRNP L depletion on transcript abundance, intron retention, or other modes of alternative splicing. Strikingly, we find that binding of hnRNP L within or flanking an exon largely correlates with exon repression by hnRNP L. In contrast, exons that are enhanced by hnRNP L generally lack proximal hnRNP L binding. Notably, these hnRNP L-enhanced exons share sequence and context features that correlate with poor nucleosome positioning, suggesting that hnRNP may enhance inclusion of a subset of exons via a cotranscriptional or epigenetic mechanism. Our data demonstrate that hnRNP L controls inclusion of a broad spectrum of alternative cassette exons in T cells and suggest both direct RNA regulation as well as indirect mechanisms sensitive to the epigenetic landscape., (© 2015 Cole et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)

Alternative splicing is prevalent among genes encoding signaling molecules; however, the functional consequence of differential isoform expression remains largely unknown. Here we demonstrate that, in response to T-cell activation, the Jun kinase (JNK) kinase MAP kinase kinase 7 (MKK7) is alternatively spliced to favor an isoform that lacks exon 2. This isoform restores a JNK-docking site within MKK7 that is disrupted in the larger isoform. Consistently, we show that skipping of MKK7 exon 2 enhances JNK pathway activity, as indicated by c-Jun phosphorylation and up-regulation of TNF-α. Moreover, this splicing event is itself dependent on JNK signaling. Thus, MKK7 alternative splicing represents a positive feedback loop through which JNK promotes its own signaling. We further show that repression of MKK7 exon 2 is dependent on the presence of flanking sequences and the JNK-induced expression of the RNA-binding protein CELF2, which binds to these regulatory elements. Finally, we found that ∼25% of T-cell receptor-mediated alternative splicing events are dependent on JNK signaling. Strikingly, these JNK-dependent events are also significantly enriched for responsiveness to CELF2. Together, our data demonstrate a widespread role for the JNK-CELF2 axis in controlling splicing during T-cell activation, including a specific role in propagating JNK signaling., (© 2015 Martinez et al.; Published by Cold Spring Harbor Laboratory Press.)

The alternative splicing of human genes is dependent on SR proteins, a family of essential splicing factors whose name derives from a signature C-terminal domain rich in arginine-serine dipeptide repeats (RS domains). Although the SRPKs (SR-specific protein kinases) phosphorylate these repeats, RS domains also contain prolines with flanking serines that are phosphorylated by a second family of protein kinases known as the CLKs (Cdc2-like kinases). The role of specific serine-proline phosphorylation within the RS domain has been difficult to assign since CLKs also phosphorylate arginine-serine dipeptides and, thus, display overlapping residue specificities with the SRPKs. In the present study, we address the effects of discrete serine-proline phosphorylation on the conformation and cellular function of the SR protein SRSF1 (SR protein splicing factor 1). Using chemical tagging and dephosphorylation experiments, we show that modification of serine-proline dipeptides broadly amplifies the conformational ensemble of SRSF1. The induction of these new structural forms triggers SRSF1 mobilization in the nucleus and alters its binding mechanism to an exonic splicing enhancer in precursor mRNA. These physical events correlate with changes in the alternative splicing of over 100 human genes based on a global splicing assay. Overall, these studies draw a direct causal relationship between a specific type of chemical modification in an SR protein and the regulation of alternative gene splicing programmes., Competing Interests: Author Contributions Malik Keshwani, Brandon Aubol, Chen-Ting Ma, and Jinsong Qui performed all the experiments in the study. Xiang-Dong Fu, Patricia Jennings, and Laurent Fattet participated in discussions and helped with data analysis. Joseph Adams and Malik Keshwani planned the experiments and wrote the paper.

Alternative splicing modulates expression of most human genes. The kinetic model of cotranscriptional splicing suggests that slow elongation expands and that fast elongation compresses the "window of opportunity" for recognition of upstream splice sites, thereby increasing or decreasing inclusion of alternative exons. We tested the model using RNA polymerase II mutants that change average elongation rates genome-wide. Slow and fast elongation affected constitutive and alternative splicing, frequently altering exon inclusion and intron retention in ways not predicted by the model. Cassette exons included by slow and excluded by fast elongation (type I) have weaker splice sites, shorter flanking introns, and distinct sequence motifs relative to "slow-excluded" and "fast-included" exons (type II). Many rate-sensitive exons are misspliced in tumors. Unexpectedly, slow and fast elongation often both increased or both decreased inclusion of a particular exon or retained intron. These results suggest that an optimal rate of transcriptional elongation is required for normal cotranscriptional pre-mRNA splicing., (© 2014 Fong et al.; Published by Cold Spring Harbor Laboratory Press.)

Large-scale, quantitative analysis of gene expression can be accomplished by microarray or RNA-seq analysis. While these methods are applicable to genome-wide analysis, it is often desirable to quantify expression of a more limited set of genes in hundreds, thousands, or even tens of thousands of biological samples. For example, some studies may require monitoring a sizable panel of key genes under many different experimental conditions, during development, or following treatment with a large library of small molecules, for which current genome-wide methods are either inefficient or cost-prohibitive. This unit presents a method that permits quantitative profiling of several hundred selected genes in a large number of samples by coupling RNA-mediated oligonucleotide Annealing, Selection, and Ligation with Next-Gen sequencing (RASL-seq). The method even allows direct analysis of RNA levels in cell lysates and is also adaptable to full automation, making it ideal for large-scale analysis of multiple biological pathways or regulatory gene networks in the context of systematic genetic or chemical genetic perturbations., (© 2012 by John Wiley & Sons, Inc.)