Radar Micro-Doppler Signature Generation Based on Time-Domain Digital Coding Metasurface.

Micro-Doppler effect is a vital feature of a target that reflects its oscillatory motions apart from bulk motion and provides an important evidence for target recognition with radars. However, establishing the micro-Doppler database poses a great challenge, since plenty of experiments are required to get the micro-Doppler signatures of different targets for the purpose of analyses and interpretations with radars, which are dramatically limited by high cost and time-consuming. Aiming to overcome these limits, a low-cost and powerful simulation platform of the micro-Doppler effects is proposed based on time-domain digital coding metasurface (TDCM). Owing to the outstanding capabilities of TDCM in generating and manipulating nonlinear harmonics during wave-matter interactions, it enables to supply rich and high-precision electromagnetic signals with multiple micro-Doppler frequencies to describe the micro-motions of different objects, which are especially favored for the training of artificial intelligence algorithms in automatic target recognition and benefit a host of applications like imaging and biosensing.

Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells.

The genome is organized in functional compartments and structural domains at the sub-megabase scale. How within these domains interactions between numerous cis-acting enhancers and promoters regulate transcription remains an open question. Here, we determined chromatin folding and composition over several hundred kb around estrogen-responsive genes in human breast cancer cell lines after hormone stimulation. Modeling of 5C data at 1.8 kb resolution was combined with quantitative 3D analysis of multicolor FISH measurements at 100 nm resolution and integrated with ChIP-seq data on transcription factor binding and histone modifications. We found that rapid estradiol induction of the progesterone gene expression occurs in the context of preexisting, cell type-specific chromosomal architectures encompassing the 90 kb progesterone gene coding region and an enhancer-spiked 5' 300 kb upstream genomic region. In response to estradiol, interactions between estrogen receptor α (ERα) bound regulatory elements are reinforced. Whereas initial enhancer-gene contacts coincide with RNA Pol 2 binding and transcription initiation, sustained hormone stimulation promotes ERα accumulation creating a regulatory hub stimulating transcript synthesis. In addition to implications for estrogen receptor signaling, we uncover that preestablished chromatin architectures efficiently regulate gene expression upon stimulation without the need for de novo extensive rewiring of long-range chromatin interactions.

Comparing Three Methods of Selecting Training Samples in Supervised Classification of Multispectral Remote Sensing Images.

Selecting training samples is crucial in remote sensing image classification. In this paper, we selected three images-Sentinel-2, GF-1, and Landsat 8-and employed three methods for selecting training samples: grouping selection, entropy-based selection, and direct selection. We then used the selected training samples to train three supervised classification models-random forest (RF), support-vector machine (SVM), and k-nearest neighbor (KNN)-and evaluated the classification results of the three images. According to the experimental results, the three classification models performed similarly. Compared with the entropy-based method, the grouping selection method achieved higher classification accuracy using fewer samples. In addition, the grouping selection method outperformed the direct selection method with the same number of samples. Therefore, the grouping selection method performed the best. When using the grouping selection method, the image classification accuracy increased with the increase in the number of samples within a certain sample size range.

Protein arginine methyltransferase 5 (Prmt5) localizes to chromatin loop anchors and modulates expression of genes at TAD boundaries during early adipogenesis.

Protein arginine methyltransferase 5 (Prmt5) is an essential regulator of embryonic development and adult progenitor cell functions. Prmt5 expression is mis-regulated in many cancers, and the development of Prmt5 inhibitors as cancer therapeutics is an active area of research. Prmt5 functions via effects on gene expression, splicing, DNA repair, and other critical cellular processes. We examined whether Prmt5 functions broadly as a genome-wide regulator of gene transcription and higher-order chromatin interactions during the initial stages of adipogenesis using ChIP-Seq, RNA-seq, and Hi-C using 3T3-L1 cells, a frequently utilized model for adipogenesis. We observed robust genome-wide Prmt5 chromatin-binding at the onset of differentiation. Prmt5 localized to transcriptionally active genomic regions, acting as both a positive and a negative regulator. A subset of Prmt5 binding sites co-localized with mediators of chromatin organization at chromatin loop anchors. Prmt5 knockdown decreased insulation strength at the boundaries of topologically associating domains (TADs) adjacent to sites with Prmt5 and CTCF co-localization. Genes overlapping such weakened TAD boundaries showed transcriptional dysregulation. This study identifies Prmt5 as a broad regulator of gene expression, including regulation of early adipogenic factors, and reveals an unappreciated requirement for Prmt5 in maintaining strong insulation at TAD boundaries and overall chromatin organization.

Nutritional control regulates symbiont proliferation and life history in coral-dinoflagellate symbiosis.

BACKGROUND: The coral-Symbiodiniaceae symbiosis is fundamental for the coral reef ecosystem. Corals provide various inorganic nutrients to their algal symbionts in exchange for the photosynthates to meet their metabolic demands. When becoming symbionts, Symbiodiniaceae cells show a reduced proliferation rate and a different life history. While it is generally believed that the animal hosts play critical roles in regulating these processes, far less is known about the molecular underpinnings that allow the corals to induce the changes in their symbionts. RESULTS: We tested symbiont cell proliferation and life stage changes in vitro in response to different nutrient-limiting conditions to determine the key nutrients and to compare the respective symbiont transcriptomic profiles to cells in hospite. We then examined the effects of nutrient repletion on symbiont proliferation in coral hosts and quantified life stage transitions in vitro using time-lapse confocal imaging. Here, we show that symbionts in hospite share gene expression and pathway activation profiles with free-living cells under nitrogen-limited conditions, strongly suggesting that symbiont proliferation in symbiosis is limited by nitrogen availability. CONCLUSIONS: We demonstrate that nitrogen limitation not only suppresses cell proliferation but also life stage transition to maintain symbionts in the immobile coccoid stage. Nutrient repletion experiments in corals further confirmed that nitrogen availability is the major factor limiting symbiont density in hospite. Our study emphasizes the importance of nitrogen in coral-algae interactions and, more importantly, sheds light on the crucial role of nitrogen in symbiont life history regulation.

Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation.

The levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10x Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia)-an established ecological model for studying the phenotypic effects of natural and artificial selection-and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is among the highest reported for a fish, or any vertebrate (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ∼23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.

Selective Phosphoranation of Unactivated Alkynes with Phosphonium Cation To Achieve Isoquinoline Synthesis.

We herein develop a selective phosphoranation of alkynes with phosphonium cation, which directs a concise approach to isoquinolines from unactivated alkyne and nitrile feedstocks in a single step. Mechanistic studies suggest that the annulation reaction is initiated by the unprecedented phosphoranation of alkynes, thus representing a unique reaction pattern of phosphonium salts and distinguishing it from existing protocols that largely rely on the utilization of highly functionalized imines/oximes and/or highly polarized alkynes.

Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum.

Dinoflagellates are main primary producers in the oceans, the cause of algal blooms and endosymbionts of marine invertebrates. Much remains to be understood about their biology, including their peculiar crystalline chromosomes. We assembled 94 chromosome-scale scaffolds of the genome of the coral endosymbiont Symbiodinium microadriaticum and analyzed their organization. Genes are enriched towards the ends of chromosomes and are arranged in alternating unidirectional blocks. Some chromosomes are enriched for genes involved in specific biological processes. The chromosomes fold as linear rods and each is composed of a series of structural domains separated by boundaries. Domain boundaries are positioned at sites where transcription of two gene blocks converges and disappear when cells are treated with chemicals that block transcription, indicating correlations between gene orientation, transcription and chromosome folding. The description of the genetic and spatial organization of the S. microadriaticum genome provides a foundation for deeper exploration of the extraordinary biology of dinoflagellates and their chromosomes.

Trans-illumination intestine projection imaging of intestinal motility in mice.

Functional intestinal imaging holds importance for the diagnosis and evaluation of treatment of gastrointestinal diseases. Currently, preclinical imaging of intestinal motility in animal models is performed either invasively with excised intestines or noninvasively under anesthesia, and cannot reveal intestinal dynamics in the awake condition. Capitalizing on near-infrared optics and a high-absorbing contrast agent, we report the Trans-illumination Intestine Projection (TIP) imaging system for free-moving mice. After a complete system evaluation, we performed in vivo studies, and obtained peristalsis and segmentation motor patterns of free-moving mice. We show the in vivo typical segmentation motor pattern, that was previously shown in ex vivo studies to be controlled by intestinal pacemaker cells. We also show the effects of anesthesia on motor patterns, highlighting the possibility to study the role of the extrinsic nervous system in controlling motor patterns, which requires unanesthetized live animals. Combining with light-field technologies, we further demonstrated 3D imaging of intestine in vivo (3D-TIP). Importantly, the added depth information allows us to extract intestines located away from the abdominal wall, and to quantify intestinal motor patterns along different directions. The TIP system should open up avenues for functional imaging of the GI tract in conscious animals in natural physiological states.

The parameter optimization of lasers' energy ratio of the double-pulse laser induced breakdown spectrometry for heavy metal elements in the soil.

Laser-induced breakdown spectroscopy (LIBS) is a rapid, no-sample preparation, remote detection method that has been applied widely in the area of heavy metal detection in the soil. However, the promotion of LIBS is limited by its disadvantages, such as low precision analysis, a high detection limit, and so on. In recent years, many studies have been conducted to improve the LIBS spectral intensity. The double-pulse LIBS (DP-LIBS) is a representative technology in this area. Most of the research work focuses on the analytical methods of DP-LIBS, including the spatial configuration, the inter-pulse time, and the effect of signal enhancement of the DP-LIBS. However, there are few reports about the effect of the energy proportion of the two lasers and the contribution of different laser energies on the signal enhancement, and the inter-pulse time under the conditions of different laser energies. Moreover, DP-LIBS is mostly evaluated by the enhancement factor of the spectral signal, and there are few reports on the quantitative analysis of double-pulse LIBS. This study, which mainly detects Cu, Ni, and Pb in the soil, focuses on the contribution of the signal enhancement by adjusting the energy ratio of the two lasers and the best inter-pulse time under the conditions of different laser energies. Then, quantitative analysis of spectral signals obtained by single-pulse LIBS (SP-LIBS) and DP-LIBS are performed based on the random forest (RF) model. The results demonstrate that DP-LIBS shows better analytical performance than SP-LIBS, the coefficients of determination (R2) of the test have great improvement, the root-mean-squared error (RMSE) is much decreased and the relative error is much improved. Thus, this study shows that DP-LIBS is an effective method for the quantitative analysis of heavy metals in the soil.

3D finger vein biometric authentication with photoacoustic tomography.

Biometric authentication is the recognition of human identity via unique anatomical features. The development of novel methods parallels widespread application by consumer devices, law enforcement, and access control. In particular, methods based on finger veins, as compared to face and fingerprints, obviate privacy concerns and degradation due to wear, age, and obscuration. However, they are two-dimensional (2D) and are fundamentally limited by conventional imaging and tissue-light scattering. In this work, for the first time, to the best of our knowledge, we demonstrate a method of three-dimensional (3D) finger vein biometric authentication based on photoacoustic tomography. Using a compact photoacoustic tomography setup and a novel recognition algorithm, the advantages of 3D are demonstrated via biometric authentication of index finger vessels with false acceptance, false rejection, and equal error rates <1.23%, <9.27%, and <0.13%, respectively, when comparing one finger, a false acceptance rateimprovement>10× when comparing multiple fingers, and <0.7% when rotating fingers ±30.

Perfluoropolyether Nanoemulsion Encapsulating Chlorin e6 for Sonodynamic and Photodynamic Therapy of Hypoxic Tumor.

Sonodynamic therapy (SDT) has emerged as an important modality for cancer treatment. SDT utilizes ultrasound excitation, which overcomes the limitations of light penetration in deep tumors, as encountered by photodynamic therapy (PDT) which uses optical excitations. A comparative study of these modalities using the same sensitizer drug can provide an assessment of their effects. However, the efficiency of SDT and PDT is low in a hypoxic tumor environment, which limits their applications. In this study, we report a hierarchical nanoformulation which contains a Food and Drug Administration (FDA) approved sensitizer chlorin, e6, and a uniquely stable high loading capacity oxygen carrier, perfluoropolyether. This oxygen carrier possesses no measurable cytotoxicity. It delivers oxygen to overcome hypoxia, and at the same time, boosts the efficiency of both SDT and PDT. Moreover, we comparatively analyzed the efficiency of SDT and PDT for tumor treatment throughout the depth of the tissue. Our study demonstrates that the strengths of PDT and SDT could be combined into a single multifunctional nanoplatform, which works well in the hypoxia environment and overcomes the limitations of each modality. The combination of deep tissue penetration by ultrasound and high spatial activation by light for selective treatment of single cells will significantly enhance the scope for therapeutic applications.

Variable computed tomography appearances of COVID-19.

The coronavirus disease 2019 (COVID-19) is typically diagnosed by specific assays that detect viral nucleic acid from the upper respiratory tract; however, this may miss infections involving only the lower airways. Computed tomography (CT) has been described as a diagnostic modality in the COVID-19 diagnosis and treatment plan. We present a case series with virologically confirmed COVID-19 pneumonia. Variable CT features were observed: consolidation with ground-glass opacities, ground-glass opacities with subpleural reticular bands, and an anterior-posterior gradient of lung abnormalities resembling that of acute respiratory distress syndrome. Evolution of CT findings was observed in one patient, where there was interval resolution of bilateral lung consolidation with development of bronchiolectasis and subpleural fibrotic bands. While sensitive for detecting lung parenchymal abnormalities in COVID-19 pneumonia, the use of CT for initial diagnosis is discouraged and should be reserved for specific clinical indications. Interpretation of chest CT findings should be correlated with duration of symptoms to better determine the disease stage and aid in patient management.

SPEN integrates transcriptional and epigenetic control of X-inactivation.

Xist represents a paradigm for the function of long non-coding RNA in epigenetic regulation, although how it mediates X-chromosome inactivation (XCI) remains largely unexplained. Several proteins that bind to Xist RNA have recently been identified, including the transcriptional repressor SPEN1-3, the loss of which has been associated with deficient XCI at multiple loci2-6. Here we show in mice that SPEN is a key orchestrator of XCI in vivo and we elucidate its mechanism of action. We show that SPEN is essential for initiating gene silencing on the X chromosome in preimplantation mouse embryos and in embryonic stem cells. SPEN is dispensable for maintenance of XCI in neural progenitors, although it significantly decreases the expression of genes that escape XCI. We show that SPEN is immediately recruited to the X chromosome upon the upregulation of Xist, and is targeted to enhancers and promoters of active genes. SPEN rapidly disengages from chromatin upon gene silencing, suggesting that active transcription is required to tether SPEN to chromatin. We define the SPOC domain as a major effector of the gene-silencing function of SPEN, and show that tethering SPOC to Xist RNA is sufficient to mediate gene silencing. We identify the protein partners of SPOC, including NCoR/SMRT, the m6A RNA methylation machinery, the NuRD complex, RNA polymerase II and factors involved in the regulation of transcription initiation and elongation. We propose that SPEN acts as a molecular integrator for the initiation of XCI, bridging Xist RNA with the transcription machinery-as well as with nucleosome remodellers and histone deacetylases-at active enhancers and promoters.

Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts.

A major challenge in biology is to understand how complex gene expression patterns are encoded in the genome. While transcriptional enhancers have been studied extensively, few transcriptional silencers have been identified, and they remain poorly understood. Here, we used a novel strategy to screen hundreds of sequences for tissue-specific silencer activity in whole Drosophila embryos. Almost all of the transcriptional silencers that we identified were also active enhancers in other cellular contexts. These elements are bound by more transcription factors than non-silencers. A subset of these silencers forms long-range contacts with promoters. Deletion of a silencer caused derepression of its target gene. Our results challenge the common practice of treating enhancers and silencers as separate classes of regulatory elements and suggest the possibility that thousands or more bifunctional CRMs remain to be discovered in Drosophila and 104-105 in humans.

Arthroscopic repair of partial articular supraspinatus tendon avulsion lesions by conversion to full-thickness tears through a small incision / 中华创伤杂志(英文版)

PURPOSE@#To assess the clinical efficacy of converting partial articular supraspinatus tendon avulsion (PASTA) lesions to full-thickness tears through a small local incision of the bursal-side supraspinatus tendon followed by repair.@*METHODS@#We retrospectively analyzed 41 patients with Ellman grade 3 PASTA lesions and an average age of (54.7 ± 11.4) years from March 2013 to July 2017. Patients without regular conservative treatment and concomitant with other shoulder pathologies or previous shoulder surgery were excluded from the study. The tears were confirmed via arthroscopy, and a polydioxanone suture was placed to indicate the position of each tear. A small incision of approximately 6 mm was made using a plasma scalpel on the bursal-side supraspinatus tendon around the positioned suture to convert the partial tear into a full-thickness tear. The torn rotator cuff was sutured through the full thickness using a suture passer after inserting a 4.5-mm double-loaded suture anchor. Data were analyzed using a paired Student's t-test with statistical significance defined as p <0.05.@*RESULTS@#At the final follow-up of 2 years, the pain-free shoulder joint range of motion and visual analog scale score were significantly improved compared to those before surgery (p < 0.001). The postoperative American Shoulder and Elbow Surgeons shoulder score was (90.6 ± 6.2), which was significantly higher than the preoperative score of (47.9 ± 8.3) (p < 0.001). The University of California at Los Angeles shoulder rating scale score increased from (14.7 ± 4.1) prior to surgery to (32.6 ± 3.4) points after surgery (p < 0.001). No patient had joint stiffness.@*CONCLUSION@#This modified tear completion repair, by conversion to full-thickness tears through a small incision, has less damage to the supraspinatus tendon on the side of the bursa compared to traditional tear completion repair in the treatment of PASTA lesions. This surgical method is a simple and effective treatment that can effectively alleviate pain and improve shoulder joint function.

Variable computed tomography appearances of COVID-19

The coronavirus disease 2019 (COVID-19) is typically diagnosed by specific assays that detect viral nucleic acid from the upper respiratory tract; however, this may miss infections involving only the lower airways. Computed tomography (CT) has been described as a diagnostic modality in the COVID-19 diagnosis and treatment plan. We present a case series with virologically confirmed COVID-19 pneumonia. Variable CT features were observed: consolidation with ground-glass opacities, ground-glass opacities with subpleural reticular bands, and an anterior-posterior gradient of lung abnormalities resembling that of acute respiratory distress syndrome. Evolution of CT findings was observed in one patient, where there was interval resolution of bilateral lung consolidation with development of bronchiolectasis and subpleural fibrotic bands. While sensitive for detecting lung parenchymal abnormalities in COVID-19 pneumonia, the use of CT for initial diagnosis is discouraged and should be reserved for specific clinical indications. Interpretation of chest CT findings should be correlated with duration of symptoms to better determine the disease stage and aid in patient management.

A portable three-dimensional photoacoustic tomography system for imaging of chronic foot ulcers.

BACKGROUND: Chronic leg ulcers affect approximately 6.5 million Americans and the disorder is associated with a range of serious complications. Since many chronic ulcers have underlying vascular insufficiency, accurate assessment of tissue perfusion is critical to treatment planning and post-surgical monitoring. However, existing clinical tests fail to meet this need in practice due to their low sensitivity or accuracy. METHODS: In this paper, we introduce a portable photoacoustic tomography (PAT) system for wound assessment. Since hemoglobin serves as the major endogenous contrast at near-infrared wavelengths, PAT provides label-free, three-dimensional (3D) imaging of hemoglobin distribution, which is closely related to blood perfusion. The proposed system consists of a 128-element linear transducer array, a data acquisition (DAQ) system, and a pulsed Nd:YAG laser source, all mounted on a portable cart for easy clinical testing. RESULTS: We validated our system through both phantom and human imaging studies. The phantom imaging results indicate that the system's spatial resolution ranges from 0.5 mm along the axial direction to 1.3 mm along the elevational direction. The healthy volunteer result shows clear foot vasculature, indicating good perfusion. The preliminary patient imaging results agree very well with the clinical test, demonstrating that PAT has a high potential for assessing the circulation around the wound. CONCLUSIONS: We believe that our technique will be a valuable tool for assessing tissue perfusion and guiding wound treatment in vascular clinics.