HDR or SDR? A Subjective and Objective Study of Scaled and Compressed Videos.

We conducted a large-scale study of human perceptual quality judgments of High Dynamic Range (HDR) and Standard Dynamic Range (SDR) videos subjected to scaling and compression levels and viewed on three different display devices. While conventional expectations are that HDR quality is better than SDR quality, we have found subject preference of HDR versus SDR depends heavily on the display device, as well as on resolution scaling and bitrate. To study this question, we collected more than 23,000 quality ratings from 67 volunteers who watched 356 videos on OLED, QLED, and LCD televisions, and among many other findings, observed that HDR videos were often rated as lower quality than SDR videos at lower bitrates, particularly when viewed on LCD and QLED displays. Since it is of interest to be able to measure the quality of videos under these scenarios, e.g. to inform decisions regarding scaling, compression, and SDR vs HDR, we tested several well-known full-reference and no-reference video quality models on the new database. Towards advancing progress on this problem, we also developed a novel no-reference model called HDRPatchMAX, that uses a contrast-based analysis of classical and bit-depth features to predict quality more accurately than existing metrics.

Ferritinophagy induced ferroptosis in the management of cancer.

BACKGROUND: Ferroptosis, a newly form of regulated cell death (RCD), is characterized by iron dyshomeostasis and unrestricted lipid peroxidation. Emerging evidence depicts a pivotal role for ferroptosis in driving some pathological processes, especially in cancer. Triggering ferroptosis can suppress tumor growth and induce an anti-tumor immune response, denoting the therapeutic promises for targeting ferroptosis in the management of cancer. As an autophagic phenomenon, ferritinophagy is critical to induce ferroptosis by degradation of ferritin to release intracellular free iron. Recently, a great deal of effort has gone into designing and developing anti-cancer strategies based on targeting ferritinophagy to induce ferroptosis. CONCLUSION: This review delineates the regulatory mechanism of ferritinophagy firstly and summarizes the role of ferritinophagy-induced ferroptosis in cancer. Moreover, the strategies targeting ferritinophagy to induce ferroptosis are highlighted to unveil the therapeutic value of ferritinophagy as a target to manage cancer. Finally, the future research directions on how to cope with the challenges in developing ferritinophagy promoters into clinical therapeutics are discussed.

Neutrophils as potential therapeutic targets for breast cancer.

Breast cancer (BC) remains the foremost cause of cancer mortality globally, with neutrophils playing a critical role in its pathogenesis. As an essential tumor microenvironment (TME) component, neutrophils are emerging as pivotal factors in BC progression. Growing evidence has proved that neutrophils play a Janus- role in BC by polarizing into the anti-tumor (N1) or pro-tumor (N2) phenotype. Clinical trials are evaluating neutrophil-targeted therapies, including Reparixin (NCT02370238) and Tigatuzumab (NCT01307891); however, their clinical efficacy remains suboptimal. This review summarizes the evidence regarding the close relationship between neutrophils and BC, emphasizing the critical roles of neutrophils in regulating metabolic and immune pathways. Additionally, we summarize the existing therapeutic approaches that target neutrophils, highlighting the challenges, and affirming the rationale for continuing to explore neutrophils as a viable therapeutic target in BC management.

Comparison of machine learning models and CEUS LI-RADS in differentiation of hepatic carcinoma and liver metastases in patients at risk of both hepatitis and extrahepatic malignancy.

BACKGROUND: CEUS LI-RADS (Contrast Enhanced Ultrasound Liver Imaging Reporting and Data System) has good diagnostic efficacy for differentiating hepatic carcinoma (HCC) from solid malignant tumors. However, it can be problematic in patients with both chronic hepatitis B and extrahepatic primary malignancy. We explored the diagnostic performance of LI-RADS criteria and CEUS-based machine learning (ML) models in such patients. METHODS: Consecutive patients with hepatitis and HCC or liver metastasis (LM) who were included in a multicenter liver cancer database between July 2017 and January 2022 were enrolled in this study. LI-RADS and enhancement features were assessed in a training cohort, and ML models were constructed using gradient boosting, random forest, and generalized linear models. The diagnostic performance of the ML models was compared with LI-RADS in a validation cohort of patients with both chronic hepatitis and extrahepatic malignancy. RESULTS: The mild washout time was adjusted to 54 s from 60 s, increasing accuracy from 76.8 to 79.4%. Through feature screening, washout type II, rim enhancement and unclear border were identified as the top three predictor variables. Using LI-RADS to differentiate HCC from LM, the sensitivity, specificity, and AUC were 68.2%, 88.6%, and 0.784, respectively. In comparison, the random forest and generalized linear model both showed significantly higher sensitivity and accuracy than LI-RADS (0.83 vs. 0.784; all P < 0.001). CONCLUSIONS: Compared with LI-RADS, the random forest and generalized linear model had higher accuracy for differentiating HCC from LM in patients with chronic hepatitis B and extrahepatic malignancy.

Head-to-head comparison of perfluorobutane contrast-enhanced US and multiparametric MRI for breast cancer: a prospective, multicenter study.

BACKGROUND: Multiparametric magnetic resonance imaging (MP-MRI) has high sensitivity for diagnosing breast cancers but cannot always be used as a routine diagnostic tool. The present study aimed to evaluate whether the diagnostic performance of perfluorobutane (PFB) contrast-enhanced ultrasound (CEUS) is similar to that of MP-MRI in breast cancer and whether combining the two methods would enhance diagnostic efficiency. PATIENTS AND METHODS: This was a head-to-head, prospective, multicenter study. Patients with breast lesions diagnosed by US as Breast Imaging Reporting and Data System (BI-RADS) categories 3, 4, and 5 underwent both PFB-CEUS and MP-MRI scans. On-site operators and three reviewers categorized the BI-RADS of all lesions on two images. Logistic-bootstrap 1000-sample analysis and cross-validation were used to construct PFB-CEUS, MP-MRI, and hybrid (PFB-CEUS + MP-MRI) models to distinguish breast lesions. RESULTS: In total, 179 women with 186 breast lesions were evaluated from 17 centers in China. The area under the receiver operating characteristic curve (AUC) for the PFB-CEUS model to diagnose breast cancer (0.89; 95% confidence interval [CI] 0.74, 0.97) was similar to that of the MP-MRI model (0.89; 95% CI 0.73, 0.97) (P = 0.85). The AUC of the hybrid model (0.92, 95% CI 0.77, 0.98) did not show a statistical advantage over the PFB-CEUS and MP-MRI models (P = 0.29 and 0.40, respectively). However, 90.3% false-positive and 66.7% false-negative results of PFB-CEUS radiologists and 90.5% false-positive and 42.8% false-negative results of MP-MRI radiologists could be corrected by the hybrid model. Three dynamic nomograms of PFB-CEUS, MP-MRI and hybrid models to diagnose breast cancer are freely available online. CONCLUSIONS: PFB-CEUS can be used in the differential diagnosis of breast cancer with comparable performance to MP-MRI and with less time consumption. Using PFB-CEUS and MP-MRI as joint diagnostics could further strengthen the diagnostic ability. Trial registration Clinicaltrials.gov; NCT04657328. Registered 26 September 2020. IRB number 2020-300 was approved in Chinese PLA General Hospital. Every patient signed a written informed consent form in each center.

An RNAi screen for secreted factors and cell-surface players in coordinating neuron and glia development in Drosophila.

The establishment of the functional nervous system requires coordinated development of neurons and glia in the embryo. Our understanding of underlying molecular and cellular mechanisms, however, remains limited. The developing Drosophila visual system is an excellent model for understanding the developmental control of the nervous system. By performing a systematic transgenic RNAi screen, we investigated the requirements of secreted proteins and cell-surface receptors for the development of photoreceptor neurons (R cells) and wrapping glia (WG) in the Drosophila visual system. From the screen, we identified seven genes whose knockdown disrupted the development of R cells and/or WG, including amalgam (ama), domeless (dome), epidermal growth factor receptor (EGFR), kuzbanian (kuz), N-Cadherin (CadN), neuroglian (nrg), and shotgun (shg). Cell-type-specific analysis revealed that ama is required in the developing eye disc for promoting cell proliferation and differentiation, which is essential for the migration of glia in the optic stalk. Our results also suggest that nrg functions in both eye disc and WG for coordinating R-cell and WG development.

Turtle interacts with borderless in regulating glial extension and axon ensheathment.

Proper recognition between axons and glial processes is required for the establishment of axon ensheathment in the developing nervous system. Recent studies have begun to reveal molecular events underlying developmental control of axon-glia recognition. In our previous work, we showed that the transmembrane protein Borderless (Bdl) is specifically expressed in wrapping glia (WG), and is required for the extension of glial processes and the ensheathment of photoreceptor axons in the developing Drosophila visual system. The exact mechanism by which Bdl mediates axon-glia recognition, however, remains unknown. Here, we present evidence showing that Bdl interacts with the Ig transmembrane protein Turtle (Tutl). Tutl is specifically expressed in photoreceptor axons. Loss of tutl in photoreceptors, like loss of bdl in WG, disrupts glial extension and axon ensheatment. Epistasis analysis shows that Tutl interacts genetically with Bdl. Tutl interacts with Bdl in trans in cultured cells. We propose that Tutl interacts with Bdl in mediating axon-glia recognition for WG extension and axon ensheathment.

Borderless regulates glial extension and axon ensheathment.

Ensheathment of axons by glial processes is essential for normal brain function. While considerable progress has been made to define molecular and cellular mechanisms underlying the maintenance of axon ensheathment, less is known about molecular details of early events for the wrapping of axons by glial processes in the developing nervous system. In this study, we investigate the role of the transmembrane protein Borderless (Bdl) in the developing Drosophila visual system. Bdl belongs to the immunoglobulin (Ig) superfamily, and its in vivo function is unknown. We show that Bdl is expressed in wrapping glia (WG) in the developing eye disc. Cell-type-specific transgene rescue and knockdown indicate that Bdl is specifically required in WG for the extension of glial processes along photoreceptor axons in the optic lobe, and axon ensheathment. Our results identify Bdl as a novel glia-specific cell-surface recognition molecule in regulating glial extension and axon ensheathment.

Methods for TALEN-Mediated Genomic Manipulations in Drosophila.

TALEN (transcription activator-like effector nuclease) is a powerful tool for gene disruption and other genomic modifications. In the past 3 years or so, it has attracted eyes from every corner of the biological world, due to its characteristics of simplicity, high efficiency, low toxicity, and applicability across almost all species. In our lab, we first reported the TALEN-mediated gene disruption in Drosophila, and recently employed this technique in precisely modifying the Drosophila genome, such as in vivo tagging and gene correction. Here, we describe in detail the protocols and experiences in TALEN-mediated genomic modifications to share with the Drosophilists all over the world.

TALEN-mediated Drosophila genome editing: protocols and applications.

TALEs (transcription activator-like effectors) are a family of natural transcriptional activators originally isolated from the plant pathogen of Xanthomonas spp. The DNA binding motif of TALEs can be re-designed in such way that they bind specific DNA sequences other than their original targets. Fusion of customized TALEs with an endonuclease, Fok I, generates artificial enzymes that are targeted to specific DNA sites for cutting, allowing gene specific modification of both animal and plant genomes. Previously, we reported the use of TALEN (transcription activator-like effector nuclease) for the highly specific and efficient modification of the two Drosophila loci yellow and CG9797. Here, we describe a detailed protocol for TALEN-mediated genomic modification in Drosophila, with the aim of providing a practical bench guide for the Drosophila research community.

Various applications of TALEN- and CRISPR/Cas9-mediated homologous recombination to modify the Drosophila genome.

Modifying the genomes of many organisms is becoming as easy as manipulating DNA in test tubes, which is made possible by two recently developed techniques based on either the customizable DNA binding protein, TALEN, or the CRISPR/Cas9 system. Here, we describe a series of efficient applications derived from these two technologies, in combination with various homologous donor DNA plasmids, to manipulate the Drosophila genome: (1) to precisely generate genomic deletions; (2) to make genomic replacement of a DNA fragment at single nucleotide resolution; and (3) to generate precise insertions to tag target proteins for tracing their endogenous expressions. For more convenient genomic manipulations, we established an easy-to-screen platform by knocking in a white marker through homologous recombination. Further, we provided a strategy to remove the unwanted duplications generated during the "ends-in" recombination process. Our results also indicate that TALEN and CRISPR/Cas9 had comparable efficiency in mediating genomic modifications through HDR (homology-directed repair); either TALEN or the CRISPR/Cas9 system could efficiently mediate in vivo replacement of DNA fragments of up to 5 kb in Drosophila, providing an ideal genetic tool for functional annotations of the Drosophila genome.

Visual circuit assembly requires fine tuning of the novel Ig transmembrane protein Borderless.

Establishment of synaptic connections in the neuropils of the developing nervous system requires the coordination of specific neurite-neurite interactions (i.e., axon-axon, dendrite-dendrite and axon-dendrite interactions). The molecular mechanisms underlying coordination of neurite-neurite interactions for circuit assembly are incompletely understood. In this report, we identify a novel Ig superfamily transmembrane protein that we named Borderless (Bdl), as a novel regulator of neurite-neurite interactions in Drosophila. Bdl induces homotypic cell-cell adhesion in vitro and mediates neurite-neurite interactions in the developing visual system. Bdl interacts physically and genetically with the Ig transmembrane protein Turtle, a key regulator of axonal tiling. Our results also show that the receptor tyrosine phosphatase leukocyte common antigen-related protein (LAR) negatively regulates Bdl to control synaptic-layer selection. We propose that precise regulation of Bdl action coordinates neurite-neurite interactions for circuit formation in Drosophila.

Efficient and specific modifications of the Drosophila genome by means of an easy TALEN strategy.

Technology development has always been one of the forces driving breakthroughs in biomedical research. Since the time of Thomas Morgan, Drosophilists have, step by step, developed powerful genetic tools for manipulating and functionally dissecting the Drosophila genome, but room for improving these technologies and developing new techniques is still large, especially today as biologists start to study systematically the functional genomics of different model organisms, including humans, in a high-throughput manner. Here, we report, for the first time in Drosophila, a rapid, easy, and highly specific method for modifying the Drosophila genome at a very high efficiency by means of an improved transcription activator-like effector nuclease (TALEN) strategy. We took advantage of the very recently developed "unit assembly" strategy to assemble two pairs of specific TALENs designed to modify the yellow gene (on the sex chromosome) and a novel autosomal gene. The mRNAs of TALENs were subsequently injected into Drosophila embryos. From 31.2% of the injected F(0) fertile flies, we detected inheritable modification involving the yellow gene. The entire process from construction of specific TALENs to detection of inheritable modifications can be accomplished within one month. The potential applications of this TALEN-mediated genome modification method in Drosophila are discussed.

Drosophila RecQ5 is required for efficient SSA repair and suppression of LOH in vivo.

RecQ5 in mammalian cells has been suggested to suppress inappropriate homologous recombination. However, the specific pathway(s) in which it is involved and the underlining mechanism(s) remain poorly understood. We took advantage of genetic tools in Drosophila to investigate how Drosophila RecQ5 (dRecQ5) functions in vivo in homologous recombination-mediated double strand break (DSB) repair. We generated null alleles of dRecQ5 using the targeted recombination technique. The mutant animals are homozygous viable, but with growth retardation during development. The mutants are sensitive to both exogenous DSB-inducing treatment, such as gamma-irradiation, and endogenously induced double strand breaks (DSBs) by I-Sce I endonuclease. In the absence of dRecQ5, single strand annealing (SSA)-mediated DSB repair is compromised with compensatory increases in either inter-homologous gene conversion, or non-homologous end joining (NHEJ) when inter-chromosomal homologous sequence is unavailable. Loss of function of dRecQ5 also leads to genome instability in loss of heterozygosity (LOH) assays. Together, our data demonstrate that dRecQ5 functions in SSA-mediated DSB repair to achieve its full efficiency and in suppression of LOH in Drosophila.

CAF-1 is essential for Drosophila development and involved in the maintenance of epigenetic memory.

DNA synthesis during S-phase and upon DNA repair is accompanied by chromatin assembly. The chromatin assembly factor CAF-1 has been biochemically well-characterized to deposit histones onto newly synthesized DNA. To gain insights into the in vivo functions of CAF-1 in Drosophila, we generated null mutants of the largest subunit of dCAF-1, dCAF-1-p180. We show that, unlike CAF-1 mutant yeast, dCAF-1-p180 mutant flies are hemizygous lethal. Removal of maternal dCAF-1-p180 activity by germline clones blocks oogenesis. Tissue-specific deletion of dCAF-1-p180 in the eye primordia disrupts eye development. In addition, reduction of dCAF-1-p180 activity suppresses gene silencing at heterochromatin and antagonizes Polycomb-mediated cell fate determination. Furthermore, heterozygous dCAF-1-p180 mutant flies display an increased sensitivity to gamma-irradiation and a reduced efficiency in recombinational double strand break (DSB) repair. Our experiments also show that human hCAF-1-p150 can rescue the dCAF-1-p180 mutant flies, demonstrating a functional conservation of eukaryotic CAF-1 activities in vivo. Together, our results establish that dCAF-1-p180 is an essential gene for Drosophila development and further underscore the importance of dCAF-1 in regulating gene expression and DNA repair in vivo.