Computational optical sectioning via near-field multi-slice ptychography.

We introduce a method for the computational sectioning of optically thick samples based on a combination of near-field and multi-slice ptychography. The method enables a large field-of-view 3D phase imaging of samples that is an order of magnitude thicker than the depth of field of bright-field microscopy. An axial resolution for these thick samples is maintained in the presence of multiple scattering, revealing a complex structure beyond the depth of the field limit. In this Letter, we describe the new, to the best of our knowledge, approach and demonstrate its effectiveness using a range of samples with diverse thicknesses and optical properties.

In vitro study to identify ligand-independent function of estrogen receptor-α in suppressing DNA damage-induced chondrocyte senescence.

In osteoarthritis (OA), chondrocytes undergo many pathological alternations that are linked with cellular senescence. However, the exact pathways that lead to the generation of a senescence-like phenotype in OA chondrocytes are not clear. Previously, we found that loss of estrogen receptor-α (ERα) was associated with an increased senescence level in human chondrocytes. Since DNA damage is a common cause of cellular senescence, we aimed to study the relationship among ERα levels, DNA damage, and senescence in chondrocytes. We first examined the levels of ERα, representative markers of DNA damage and senescence in normal and OA cartilage harvested from male and female human donors, as well as from male mice. The influence of DNA damage on ERα levels was studied by treating human chondrocytes with doxorubicin (DOX), which is an often-used DNA-damaging agent. Next, we tested the potential of overexpressing ERα in reducing DNA damage and senescence levels. Lastly, we explored the interaction between ERα and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathway. Results indicated that the OA chondrocytes contained DNA damage and displayed senescence features, which were accompanied by significantly reduced ERα levels. Overexpression of ERα reduced the levels of DNA damage and senescence in DOX-treated normal chondrocytes and OA chondrocytes. Moreover, DOX-induced the activation of NF-κB pathway, which was partially reversed by overexpressing ERα. Taken together, our results demonstrated the critical role of ERα in maintaining the health of chondrocytes by inhibiting DNA damage and senescence. This study also suggests that maintaining the ERα level may represent a new avenue to prevent and treat OA.

Dual Pigment Epithelium-derived Factor and Hepatocyte Growth Factor Overexpression: A New Therapy for Pulmonary Hypertension.

Pulmonary hypertension (PH) is a disease characterized by advanced pulmonary vasculature remodeling that is thought to be curable only through lung transplantation. The application of angiogenic hepatocyte growth factor (HGF) is reported to be protective in PH through its anti-vascular remodeling effect, but excessive HGF-mediated immature neovascularization is not conducive to the restoration of pulmonary perfusion because of apparent vascular leakage. As a canonical antiangiogenic molecule, pigment epithelium-derived factor (PEDF) inhibits angiogenesis and reduces vascular permeability in a variety of diseases. However, the effect of PEDF on HGF-based PH treatment remains to be determined. In this study, monocrotaline-induced PH rats and endothelial cells isolated from rat and human PH lung tissues were used. We assessed PH progression, right cardiac function, and pulmonary perfusion in HGF- and/or PEDF-treated rats with PH. Additionally, the receptor and mechanism responsible for the role of PEDF in HGF-based PH therapy were investigated. In this study, we found that HGF and PEDF jointly prevent PH development and improve right cardiac function in rats with PH. Moreover, PEDF delivery increases the pulmonary perfusion in PH lungs and inhibits immature angiogenesis and vascular endothelial (VE)-cadherin junction disintegration induced by HGF without affecting the therapeutic inhibition of pulmonary vascular remodeling by HGF. Mechanistically, PEDF targets VE growth factor receptor 2 and suppresses its phosphorylation at Y951 and Y1175 but not Y1214. Finally, VE growth factor receptor 2/VE protein tyrosine phosphatase/VE-cadherin complex formation and Akt and Erk1/2 inactivation were observed in rat and human PH lung endothelial cells. Collectively, our data indicate that PEDF additively enhances the efficacy of HGF against PH, which may provide new insights into treatment strategies for clinical PH.

Near-field multi-slice ptychography: quantitative phase imaging of optically thick samples with visible light and X-rays.

Ptychography is a form of lens-free coherent diffractive imaging now used extensively in electron and synchrotron-based X-ray microscopy. In its near-field implementation, it offers a route to quantitative phase imaging at an accuracy and resolution competitive with holography, with the added advantages of extended field of view and blind deconvolution of the illumination beam profile from the sample image. In this paper we show how near-field ptychography can be combined with a multi-slice model, adding to this list of advantages the unique ability to recover high-resolution phase images of larger samples, whose thickness places them beyond the depth of field of alternative methods.

Efficient Communications in V2V Networks with Two-Way Lanes Based on Random Linear Network Coding.

Vehicle-to-vehicle (V2V) communication has gained significant attention in the field of intelligent transportation systems. In this paper, we focus on communication scenarios involving vehicles moving in the same and opposite directions. Specifically, we model a V2V network as a dynamic multi-source single-sink network with two-way lanes. To address rapid changes in network topology, we employ random linear network coding (RLNC), which eliminates the need for knowledge of the network topology. We begin by deriving the lower bound for the generation probability. Through simulations, we analyzed the probability distribution and cumulative probability distribution of latency under varying packet loss rates and batch sizes. Our results demonstrated that our RLNC scheme significantly reduced the communication latency, even under challenging channel conditions, when compared to the non-coding case.

ciRS-7 Enhances the Progression of Hepatocellular Carcinoma through miR-944/NOX4 Pathway.

Recently, increasing numbers of non-coding RNA have been uncovered in research. As a new class of non-coding RNA, circular RNA has been identified to be involved in various diseases including many cancers. The circular RNA ciRS-7 is reported to play critical roles in tumorigenesis. However, the role of ciRS-7 in hepatocellular carcinoma (HCC) remains unclear. In this study, we investigated the expression and function of ciRS-7 in HCC cells and cancer tissues. CCK8 was applied to detect the influence of ciRS-7 on proliferation. Wound heal assay and invasion assay were used to identify the effects on migration and invasion. Quantitative reverse transcription polymerase chain reaction (qRT-PCR), Western blot, RNA pull-down, and luciferase reporter assay were used to investigate the downstream targets of ciRS-7. The results showed that ciRS-7 was highly expressed in both hepatocellular carcinoma cells and tissues. Overexpression of ciRS-7 could promote the proliferation, migration, and invasion of HCC. Further study showed that ciRS-7 regulated the miR-944 level through acting as a microRNA sponge. q-RT-PCR, Western blot, RNA pull-down and dual luciferase activity assays showed that miR-944 targeted and regulated the expression of NOX4. Furthermore, the tumor-promoting effect of ciRS-7 could be blocked by inhibition of miR-944/NOX4. Our study demonstrated that ciRS-7 enhanced the proliferation, migration, and invasion of HCC through miR-944/NOX4 pathway. ciRS-7 could be a promising therapeutic target for HCC.

Focus on the classical and non-classical functions of EZH2: Guide the development of inhibitors and degraders.

Enhancer of zeste homologue 2 (EZH2, also known as KMT6A) is found to be a member of the histone lysine methyltransferase family. An increasing number of studies have shown that in addition to methylating histones, EZH2 plays a vital role in a variety of ways. The methylated substrates of EZH2 also include GATA4, AR/AR-related proteins, STAT3, Talin protein, and RORα. Meanwhile, EZH2 has been reported to form complexes with some proteins to perform other important biological functions as well as methylation. These complexes include: the EZH2-RelA-RelB complex, EZH2-ER-ß-catenin complex, and ß-catenin-PAF-EZH2-Mediator complex. Herein, we focus on the classical and non-classical functions of EZH2, and summarize anti-EZH2 therapeutic strategies. Finally, we highlight that understanding the physiological and pathological functions of EZH2 in specific indications can help the development of inhibitors or degraders.

Ptycho-cam: a ptychographic phase imaging add-on for optical microscopy.

Near field ptychography uses diffraction data collected at large Fresnel numbers, together with iterative reconstruction algorithms, to realize quantitative phase imaging of transmissive samples. It delivers excellent phase sensitivity with a wide field of view from a simple optical system using a relatively small number of measured diffraction patterns. In this paper, we develop an add-on to a standard optical microscope that implements near-field ptychography. The add-on is self-contained and attaches to the microscope camera port, requiring no modification to the microscope itself. Unlike conventional ptychography, it does not involve sample translation, making it more suitable for delicate samples or samples in liquid.

Identification of Important Factors Causing Developmental Arrest in Cloned Pig Embryos by Embryo Biopsy Combined with Microproteomics.

The technique of pig cloning holds great promise for the livestock industry, life science, and biomedicine. However, the prenatal death rate of cloned pig embryos is extremely high, resulting in a very low cloning efficiency. This limits the development and application of pig cloning. In this study, we utilized embryo biopsy combined with microproteomics to identify potential factors causing the developmental arrest in cloned pig embryos. We verified the roles of two potential regulators, PDCD6 and PLK1, in cloned pig embryo development. We found that siRNA-mediated knockdown of PDCD6 reduced mRNA and protein expression levels of the pro-apoptotic gene, CASP3, in cloned pig embryos. PDCD6 knockdown also increased the cleavage rate and blastocyst rate of cloned porcine embryos. Overexpression of PLK1 via mRNA microinjection also improved the cleavage rate of cloned pig embryos. This study provided a new strategy to identify key factors responsible for the developmental defects in cloned pig embryos. It also helped establish new methods to improve pig cloning efficiency, specifically by correcting the expression pattern of PDCD6 and PLK1 in cloned pig embryos.

Integrating ecosystem services modeling into effectiveness assessment of national protected areas in a typical arid region in China.

Protected areas (PAs) are essential for biodiversity conservation and for the delivery of ecosystem services (ESs). However, little is known about their effectiveness in providing ESs and contribution to species richness, especially in arid regions. Effectiveness evaluation is fundamental to understanding the extent of management enhancement required to fulfill conservation targets. In this study, we analyzed the supply of six ESs (water yield, nutrient retention, soil retention, sand fixation, carbon storage, and biodiversity richness) by landscapes in China's arid region of Xinjiang Uygur Autonomous Region (hereafter Xinjiang). The aim was to identify distribution of ESs hotspots and the extent of hotspots located within or outside national PAs. The results showed significant spatial heterogeneity and coverage differences in six types of ESs hotspots. Hotspots coverage of six ESs on average accounted for 10.45 % of the total area, distributed mainly in mountains and oases covered by vegetation and wetlands. Among these ESs hotspots, over 50 % fell within PAs. This suggested that although PAs delivered moderately well outcomes in preserving ESs and biodiversity in Xinjiang, conservation gaps needed to be addressed. Our study also revealed substantial differences in ESs supplied by different PAs, and serious deficiency existed in some PAs in protecting either biodiversity or key ESs outlined in their conservation objectives. Our study illustrated the priority areas for future conservation expansion and stressed the urgent shift toward broadening the goals of PAs from a dominant focus to ones that encompass multiple ESs for human well-being.

MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq.

BACKGROUND: Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) is a popular sequencing method for studying RNA modifications and, in particular, for N6-methyladenosine (m6A), the most abundant RNA methylation modification found in various species. The detection of enriched regions is a main challenge of MeRIP-Seq analysis, however current tools either require a long time or do not fully utilize features of RNA sequencing such as strand information which could cause ambiguous calling. On the other hand, with more attention on the treatment experiments of MeRIP-Seq, biologists need intuitive evaluation on the treatment effect from comparison. Therefore, efficient and user-friendly software that can solve these tasks must be developed. RESULTS: We developed a software named "model-based analysis and inference of MeRIP-Seq (MoAIMS)" to detect enriched regions of MeRIP-Seq and infer signal proportion based on a mixture negative-binomial model. MoAIMS is designed for transcriptome immunoprecipitation sequencing experiments; therefore, it is compatible with different RNA sequencing protocols. MoAIMS offers excellent processing speed and competitive performance when compared with other tools. When MoAIMS is applied to studies of m6A, the detected enriched regions contain known biological features of m6A. Furthermore, signal proportion inferred from MoAIMS for m6A treatment datasets (perturbation of m6A methyltransferases) showed a decreasing trend that is consistent with experimental observations, suggesting that the signal proportion can be used as an intuitive indicator of treatment effect. CONCLUSIONS: MoAIMS is efficient and easy-to-use software implemented in R. MoAIMS can not only detect enriched regions of MeRIP-Seq efficiently but also provide intuitive evaluation on treatment effect for MeRIP-Seq treatment datasets.

In vivo odorant input induces distinct synaptic plasticity of GABAergic synapses in developing zebrafish olfactory bulb.

In the first station of central odor processing, the main olfactory bulb, signal processing is regulated by synaptic interactions between glutamatergic and GABAergic inputs of the mitral cells (MCs), the major projection neurons. Our previous study has found that repetitive postsynaptic spiking within a critical time window after presynaptic activation by natural odorant stimulation results in persistent enhancement of glutamatergic inputs of MCs in larval zebrafish. Here we observed a long-term depression of GABAergic synapses induced by the same protocol. This long-term depression was mediated by presynaptic NMDA receptors (NMDARs). Further dissecting GABAergic neurotransmission revealed that the STDP-induction protocol induced persistent modification in recurrent and lateral inhibition with opposite directions and distinct requirements on NMDARs. Thus, at the plasticity level, different types of GABAergic inhibition may utilize different mechanisms to cooperate or compete with excitatory inputs to optimize patterns of olfactory bulb output.

Increased number of intratumoral IL-17+ cells, a harbinger of the adverse prognosis of triple-negative breast cancer.

INTRODUCTION: Triple negative breast cancer (TNBC) is an aggressive cancer subtype and lack of effective targeted therapies. It has been recently reported that Interleukin 17 (IL-17), a family of cytokines secreted in tumor microenvironment, affects tumor progression through a variety of molecular pathways. Its role in TNBC is so far still poorly explored. MATERIALS AND METHODS: We employed immunohistochemistry to evaluate the distribution of IL-17+ cells in TNBC with no special type features (TNBC-NST), their association with tumor microangiogenesis, as well as their impact on prognosis of the patients. RESULTS: In comparison to medullary carcinoma with triple-negative molecular features (TNBC-MC), we found a significant increase in IL-17+ cell infiltrates in intratumoral stroma and extratumoral stroma of TNBC-NST. Similarly, stromal cells with co-expression of CD4 and IL-17 were noted in intratumoral and extratumoral stroma in both TNBC-NST and TNBC-MC. In addition, intratumoral IL-17+ cells were positively associated with tumor cell expression of vascular endothelial growth factor A (VEGFA) and with intratumoral tumor microvascular density (MVD). Multivariate analysis identified that intratumoral IL-17+ cells (P = 0.018), MVD (P = 0.039), and TNM stage (P = 0.002) were independent prognostic factors for predicting poor PFS. CONCLUSION: The study indicates that IL-17 is overexpressed in intratumoral stromal cells of TNBC-NST. The overexpression of IL-17 might engage in active tumor microangiogenesis through its signal transduction pathways resulting in increased tumor secretion of VEGFA, and then promote tumor progression. IL-17 might serve as a potential new target for individualized therapy to TNBC-NST patients by development of specific antibodies. Additional study is deemed to further explore the role of IL-17+ stromal cells in breast cancer.

Impact of patient comfort on diagnostic image quality during PET/MR exam: A quantitative survey study for clinical workflow management.

BACKGROUND: PET/MR is transferring from a powerful scientific research tool to an imaging modality in clinical routine practice. Whole body PET/MR screening usually takes 30-50 minutes to finish, during which a few factors might induce patient discomfort and further cause degraded image quality. The aim of this report is to investigate the patients' perception of the imaging procedure and its correlation with image quality. METHODS: One hundred and twenty patients (63 males and 57 females, average age = 51.3 years, range 22-70 years) who had been diagnosed with cancer or had previous history of cancer were recruited and scanned with a simultaneous PET/MR system. A questionnaire was given to all patients retrospectively after the PET/MR scan, which has nine questions to assess patients' feeling of the scan on a Likert scale scoring system (1-5, 1 as most satisfied). All PET/MR images were also visually examined by two experts independently to evaluate the quality of the images. Six body locations were assessed and each location was evaluated also with a Likert scale scoring system (1-5, 5 as the best quality). Mann-Whitney U-test was used for statistical analysis to check if there is significant correlation between image quality and patient perceptions. RESULTS: With a total of 120 patients, 118 questionnaires were filled and returned for analysis. The patients' characteristics were summarized in Table 4. The statistics of the patients' perception in the questionnaire were illustrated in Tables 5-7. Statistical significant correlations were found between MR image quality and patients' characteristics/perception. CONCLUSION: Our results show that PET/MR scanning is generally safe and comfortable for most of the patients. Statistical analysis does not support the hypothesis that bad patient's perception leads to degraded image quality.

DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning.

BACKGROUND: N6-methyladensine (m6A) is a common and abundant RNA methylation modification found in various species. As a type of post-transcriptional methylation, m6A plays an important role in diverse RNA activities such as alternative splicing, an interplay with microRNAs and translation efficiency. Although existing tools can predict m6A at single-base resolution, it is still challenging to extract the biological information surrounding m6A sites. RESULTS: We implemented a deep learning framework, named DeepM6ASeq, to predict m6A-containing sequences and characterize surrounding biological features based on miCLIP-Seq data, which detects m6A sites at single-base resolution. DeepM6ASeq showed better performance as compared to other machine learning classifiers. Moreover, an independent test on m6A-Seq data, which identifies m6A-containing genomic regions, revealed that our model is competitive in predicting m6A-containing sequences. The learned motifs from DeepM6ASeq correspond to known m6A readers. Notably, DeepM6ASeq also identifies a newly recognized m6A reader: FMR1. Besides, we found that a saliency map in the deep learning model could be utilized to visualize locations of m6A sites. CONCULSION: We developed a deep-learning-based framework to predict and characterize m6A-containing sequences and hope to help investigators to gain more insights for m6A research. The source code is available at https://github.com/rreybeyb/DeepM6ASeq .

Aldosterone modulates thiazide-sensitive sodium chloride cotransporter abundance via DUSP6-mediated ERK1/2 signaling pathway.

Thiazide-sensitive sodium chloride cotransporter (NCC) plays an important role in maintaining blood pressure. Aldosterone is known to modulate NCC abundance. Previous studies reported that dietary salts modulated NCC abundance through either WNK4 [with no lysine (k) kinase 4]-SPAK (Ste20-related proline alanine-rich kinase) or WNK4-extracellular signal-regulated kinase-1 and -2 (ERK1/2) signaling pathways. To exclude the influence of SPAK signaling pathway on the role of the aldosterone-mediated ERK1/2 pathway in NCC regulation, we investigated the effects of dietary salt changes and aldosterone on NCC abundance in SPAK knockout (KO) mice. We found that in SPAK KO mice low-salt diet significantly increased total NCC abundance while reducing ERK1/2 phosphorylation, whereas high-salt diet decreased total NCC while increasing ERK1/2 phosphorylation. Importantly, exogenous aldosterone administration increased total NCC abundance in SPAK KO mice while increasing DUSP6 expression, an ERK1/2-specific phosphatase, and led to decreasing ERK1/2 phosphorylation without changing the ratio of phospho-T53-NCC/total NCC. In mouse distal convoluted tubule (mDCT) cells, aldosterone increased DUSP6 expression while reducing ERK1/2 phosphorylation. DUSP6 Knockdown increased ERK1/2 phosphorylation while reducing total NCC expression. Inhibition of DUSP6 by (E)-2-benzylidene-3-(cyclohexylamino)-2,3-dihydro-1H-inden-1-one increased ERK1/2 phosphorylation and reversed the aldosterone-mediated increments of NCC partly by increasing NCC ubiquitination. Therefore, these data suggest that aldosterone modulates NCC abundance via altering NCC ubiquitination through a DUSP6-dependent ERK1/2 signal pathway in SPAK KO mice and part of the effects of dietary salt changes may be mediated by aldosterone in the DCTs.

PEDF attenuates hypoxia-induced apoptosis and necrosis in H9c2 cells by inhibiting p53 mitochondrial translocation via PEDF-R.

Pigment epithelial-derived factor (PEDF) is a multifunctional secreted glycoprotein, which could protect against hypoxia-induced cell death related to its anti-oxidative effect in cultured cardiomyocytes. However, the pathway mediating this cytoprotective process has not been fully established. Here we confirmed that PEDF bound to pigment epithelial-derived factor receptor (PEDF-R) expressed on the membrane of H9c2 cells. Under hypoxic condition, PEDF increased the ratio of MDM2:p53, so as to inhibited p53 mitochondrial translocation via PEDF-R. As a result, mitochondrial outer membrane permeabilization (MOMP) and mitochondrial permeability transition pore (MPTP) opening were inhibited, meanwhile cleaved caspase-3, PARP and the release of HMGB1 were reduced. Accordingly, apoptosis and necrosis were attenuated simultaneously. We conclude that PEDF-R mediates PEDF attenuates hypoxia-induced apoptosis and necrosis in H9c2 cells by inhibiting p53 mitochondrial translocation.

PEDF improves cardiac function in rats with acute myocardial infarction via inhibiting vascular permeability and cardiomyocyte apoptosis.

Pigment epithelium-derived factor (PEDF) is a pleiotropic gene with anti-inflammatory, antioxidant and anti-angiogenic properties. However, recent reports about the effects of PEDF on cardiomyocytes are controversial, and it is not known whether and how PEDF acts to inhibit hypoxic or ischemic endothelial injury in the heart. In the present study, adult Sprague-Dawley rat models of acute myocardial infarction (AMI) were surgically established. PEDF-small interfering RNA (siRNA)-lentivirus (PEDF-RNAi-LV) or PEDF-LV was delivered into the myocardium along the infarct border to knockdown or overexpress PEDF, respectively. Vascular permeability, cardiomyocyte apoptosis, myocardial infarct size and animal cardiac function were analyzed. We also evaluated PEDF's effect on the suppression of the endothelial permeability and cardiomyocyte apoptosis under hypoxia in vitro. The results indicated that PEDF significantly suppressed the vascular permeability and inhibited hypoxia-induced endothelial permeability through PPARγ-dependent tight junction (TJ) production. PEDF protected cardiomyocytes against ischemia or hypoxia-induced cell apoptosis both in vivo and in vitro via preventing the activation of caspase-3. We also found that PEDF significantly reduced myocardial infarct size and enhanced cardiac function in rats with AMI. These data suggest that PEDF could protect cardiac function from ischemic injury, at least by means of reducing vascular permeability, cardiomyocyte apoptosis and myocardial infarct size.

PfgPDI: Pocket feature-enabled graph neural network for protein-drug interaction prediction.

Biomolecular interaction recognition between ligands and proteins is an essential task, which largely enhances the safety and efficacy in drug discovery and development stage. Studying the interaction between proteins and ligands can improve the understanding of disease pathogenesis and lead to more effective drug targets. Additionally, it can aid in determining drug parameters, ensuring proper absorption, distribution, and metabolism within the body. Due to incomplete feature representation or the model's inadequate adaptation to protein-ligand complexes, the existing methodologies suffer from suboptimal predictive accuracy. To address these pitfalls, in this study, we designed a new deep learning method based on transformer and GCN. We first utilized the transformer network to grasp crucial information of the original protein sequences within the smile sequences and connected them to prevent falling into a local optimum. Furthermore, a series of dilation convolutions are performed to obtain the pocket features and smile features, subsequently subjected to graphical convolution to optimize the connections. The combined representations are fed into the proposed model for classification prediction. Experiments conducted on various protein-ligand binding prediction methods prove the effectiveness of our proposed method. It is expected that the PfgPDI can contribute to drug prediction and accelerate the development of new drugs, while also serving as a valuable partner for drug testing and Research and Development engineers.