Immune cell landscapes are associated with high-grade serous ovarian cancer survival.

High-grade serous ovarian cancer (HGSOC) is an aggressive disease known to develop resistance to chemotherapy. We investigated the prognostic significance of tumor cell states and potential mechanisms underlying chemotherapy resistance in HGSOC. Transcriptome deconvolution was performed to address cellular heterogeneity. Kaplan-Meier survival curves were plotted to illustrate the outcomes of patients with varying cellular abundances. The association between gene expression and chemotherapy response was tested. After adjusting for surgery status and grading, several cell states exhibited a significant correlation with patient survival. Cell states can organize into carcinoma ecotypes (CE). CE9 and CE10 were proinflammatory, characterized by higher immunoreactivity, and were associated with favorable survival outcomes. Ratios of cell states and ecotypes had better prognostic abilities than a single cell state or ecotype. A total of 1265 differentially expressed genes were identified between samples with high and low levels of C9 or CE10. These genes were partitioned into three co-expressed modules, which were associated with tumor cells and immune cells. Pogz was identified to be linked with immune cell genes and the chemotherapy response of paclitaxel. Collectively, the survival of HGSOC patients is correlated with specific cell states and ecotypes.

Immunologic insights in recurrent spontaneous abortion: Molecular mechanisms and therapeutic interventions.

Recurrent spontaneous abortion refers to the occurrence of two or more spontaneous abortions before or during the early stages of pregnancy. The immune system plays a crucial role in the maintenance of pregnancy and embryo implantation. Various immune cells, cytokines, and immune regulatory pathways are involved in the complex immune balance required for a stable pregnancy. Studies suggest that immune abnormalities may be associated with some recurrent spontaneous abortion cases, particularly those involving the dysregulation of immune cell function, autoimmune responses, and placental immunity. In terms of treatment, interventions targeting immune mechanisms are crucial. Various therapeutic approaches, including immunomodulatory drugs, immunoadsorption therapies, and immunocellular therapies, are continually being researched and developed. These approaches aim to restore the immune balance, enhance the success rate of pregnancies, and provide more effective treatment options for patients with recurrent spontaneous abortion.

Effectiveness of nanomaterials and their counterparts in improving rice growth and yield under arsenic contamination.

Arsenic (As) pollution in rice (Oryza sativa L.), a staple food for over 3.5 billion people, is a global problem. Mixed effects of Zn, Cu, and Si amendments on plant growth and yield, including in the presence of As pollution have been reported in previous studies. To better investigate the effectiveness of these amendments on rice growth, yield, and As accumulation, we conducted a rice greenhouse experiment with 11 treatments, including control pots with and without As contamination and pots with amendments of ZnO, CuO, and SiO2 nanoparticles (ZnO NPs, CuO NPs, and SiO2 NPs), their ionic counterparts (ZnSO4, CuSO4, and Na2SiO3), and bulk particles (ZnO BPs, CuO BPs, and SiO2 BPs). Compared with the background soil, the treatment of adding As decreased rice plant height, panicle number, and grain yield by 16.5%, 50%, and 85.7%, respectively, but significantly increased the As accumulation in milled rice grains by 3.2 times. Under As contamination, the application of Zn amendments increased rice grain yield by 4.6-7.3 times; among the three Zn amendments, ZnSO4 performed best by fully recovering grain yield to the background level and significantly reducing grain AsIII/total As ratio by 46.9%. Under As contamination, the application of Cu amendments increased grain yield by 3.8-5.6 times; all three Cu amendments significantly reduced grain AsIII/total As ratio by 20.2-65.6%. The results reveal that Zn and Cu amendments could promote rice yield and prevent As accumulation in rice grains under As contamination. Despite the observed reduction in As toxicity by the tested NPs, they do not offer more advantages over their ionic counterparts and bulk particles in promoting rice growth under As contamination. Future field research using a broader range of rice varieties, investigating various As concentrations, and encompassing diverse climate conditions will be necessary to validate our findings in achieving more extensive understanding of effective management of arsenic contaminated rice field.

Therapeutic efficacy of drilling drainage combined with intraoperative middle meningeal artery occlusion in the management of chronic subdural hematoma: a clinical study.

BACKGROUND: The bone holes in the skull during surgical drainage were accurately located at the site of the MMA. The MMA was severed, and the hematoma was removed intraoperatively; furthermore, surgical drainage removed the pathogenic factors of CSDH. This study aimed to describe and compare the results of the new treatment with those of traditional surgical drainage, and to investigate the relevance of this approach. METHODS: From December 2021 to June 2023, 72 patients were randomly assigned to the observation group and the control group. The control group was treated with traditional surgical drainage, while the observation group was treated with DSA imaging to accurately locate the bone holes drilled in the skull on the MMA trunk before traditional surgical drainage. The MMA trunk was severed during the surgical drainage of the hematoma. The recurrence rate, time of indwelling drainage tube, complications, mRS, and other indicators of the two groups were compared, and the changes of cytokine components and imaging characteristics of the patients were collected and analyzed. RESULTS: Overall, 27 patients with 29-side hematoma in the observation group and 45 patients with 48-side hematoma in the control group were included in the study. The recurrence rate was 0/29 in the observation group and 4/48 in the control group, indicating that the recurrence rate in the observation group was lower than in the control group (P = .048). The mean indwelling time of the drainage tube in the observation group was 2.04 ± 0.61 days, and that in the control group was 2.48 ± 0.61 days. The indwelling time of the drainage tube in the observation group was shorter than in the control group (P = .003). No surgical complications were observed in the observation group or the control group. The differences in mRS scores before and after operation between the observation group and the control group were statistically significant (P < .001). The concentrations of cytokine IL6/IL8/IL10/VEGF in the hematoma fluid of the observation and control groups were significantly higher than those in venous blood (P < .001). After intraoperative irrigation and drainage, the concentrations of cytokines (IL6/IL8/IL10/VEGF) in the subdural hematoma fluid were significantly lower than they were preoperatively. In the observation group, the number of MMA on the hematoma side (11/29) before STA development was higher than that on the non-hematoma side (1/25), and the difference was statistically significant (P = .003). CONCLUSION: In patients with CSDH, accurately locating the MMA during surgical trepanation and drainage, severing the MMA during drainage, and properly draining the hematoma, can reduce the recurrence rate and retention time of drainage tubes, thereby significantly improving the postoperative mRS Score without increasing surgical complications.

Development and Validation of an In-Hospital Mortality Prediction Model for Patients with Acute Exacerbation of Chronic Obstructive Pulmonary Disease.

Purpose: Patients with chronic obstructive pulmonary disease (COPD) often face unknown risks during acute exacerbation of the disease (AECOPD), which could potentially result in mortality. This study aimed to develop and validate a nomogram model for predicting the risk of in-hospital mortality in AECOPD patients. Patients and Methods: Clinical data of patients hospitalized at The Second People's Hospital of Wuhu City for AECOPD between January 2013 and December 2022 were retrospectively collected. Variables underwent selection through LASSO regression and multivariable logistic regression to develop a nomogram model. The model's predictive performance was assessed using the concordance index, calibration curve, and decision curve analysis (DCA), with internal validation conducted using the bootstrap method. Results: A total of 1224 patients were included in this study, with 98 (8%) deaths occurring during hospitalization. LASSO regression identified 11 variables, used to construct model A. Further multivariable logistic regression was conducted to select variables with P < 0.05 to establish model B. model B was selected as the final model based on discrimination, calibration, and clinical utility, encompassing variables including acute respiratory failure, lung cancer, heart rate, hemoglobin, absolute neutrophil count, serum albumin, blood urea nitrogen, and serum chloride. The nomogram model achieved a concordance index of 0.858. Internal validation of the model was conducted using the bootstrap method with 500 repetitions, resulting in a concordance index of 0.851 (95% CI: 0.805, 0.893). The calibration curve demonstrated a good fit, with a Hosmer-Lemeshow goodness-of-fit test P-value of 0.520. Moreover, DCA findings suggested patient benefit within a threshold probability range of 0.02 to 0.73, with a maximum net benefit of 0.07. Conclusion: The model constructed in this study has good predictive performance, which helps clinical doctors identify patients at high risk of death early.

Superconductivity in Freestanding Infinite-Layer Nickelate Membranes.

The observation of superconductivity in infinite-layer nickelates has attracted significant attention due to its potential as a new platform for exploring high-Tc superconductivity. However, thus far, superconductivity has only been observed in epitaxial thin films, which limits the manipulation capabilities and modulation methods compared to two-dimensional exfoliated materials. Given the exceptionally giant strain tunability and stacking capability of freestanding membranes, separating superconducting nickelates from the as-grown substrate is a novel way to engineer the superconductivity and uncover the underlying physics. Herein, this work reports the synthesis of the superconducting freestanding La0.8Sr0.2NiO2 membranes ( T c zero = 10.6 K ${T}_{\mathrm{c}}^{\mathrm{zero}}\ =\ 10.6\ \mathrm{K}$ ), emphasizing the crucial roles of the interface engineering in the precursor phase film growth and the quick transfer process in achieving superconductivity. This work offers a new versatile platform for investigating superconductivity in nickelates, such as the pairing symmetry via constructing Josephson tunneling junctions and higher Tc values via high-pressure experiments.

Spatially distinct epithelial and mesenchymal cell subsets along progressive lineage restriction in the branching embryonic mammary gland.

How cells coordinate morphogenetic cues and fate specification during development remains a fundamental question in organogenesis. The mammary gland arises from multipotent stem cells (MaSCs), which are progressively replaced by unipotent progenitors by birth. However, the lack of specific markers for early fate specification has prevented the delineation of the features and spatial localization of MaSC-derived lineage-committed progenitors. Here, using single-cell RNA sequencing from E13.5 to birth, we produced an atlas of matched mouse mammary epithelium and mesenchyme and reconstructed the differentiation trajectories of MaSCs toward basal and luminal fate. We show that murine MaSCs exhibit lineage commitment just prior to the first sprouting events of mammary branching morphogenesis at E15.5. We identify early molecular markers for committed and multipotent MaSCs and define their spatial distribution within the developing tissue. Furthermore, we show that the mammary embryonic mesenchyme is composed of two spatially restricted cell populations, and that dermal mesenchyme-produced FGF10 is essential for embryonic mammary branching morphogenesis. Altogether, our data elucidate the spatiotemporal signals underlying lineage specification of multipotent MaSCs, and uncover the signals from mesenchymal cells that guide mammary branching morphogenesis.

In Situ Preparation of Superconducting Infinite-Layer Nickelate Thin Films with Atomically Flat Surface.

Since their discovery, the infinite-layer nickelates have been regarded as an appealing system for gaining deeper insights into high-temperature superconductivity (HTSC). However, the synthesis of superconducting samples has been proven to be challenging. Here, an ultrahigh vacuum (UHV) in situ ${\mathrm{\text{in situ}}}$ reduction method is developed using atomic hydrogen as a reducing agent and is applied in the lanthanum nickelate system. The reduction parameters, including the reduction temperature (TR) and hydrogen pressure (PH), are systematically explored. It is found that the reduction window for achieving superconducting transition is quite wide, reaching nearly 80°C in TR and three orders of magnitude in PH when the reduction time is set to 30 min. And there exists an optimal PH for achieving the highest Tc if both TR and reduction time are fixed. More prominently, as confirmed by atomic force microscopy and scanning transmission electron microscopy, the atomically flat surface can be preserved during the in situ ${\mathrm{\text{in situ}}}$ reduction process, providing advantages over the ex situ ${\mathrm{\text{ex situ}}}$ CaH2 method for surface-sensitive experiments.

NLRX1: a key regulator in mitochondrial respiration and colorectal cancer progression.

Colorectal cancer (CRC) is a prevalent and aggressive malignancy with high mortality rates and significant risks to human well-being. Population-wide screening for tumor suppressor genes and oncogenes shows promise for reducing the incidence and fatality of CRC. Recent studies have suggested that NLRX1, an innate immunity suppressor, may play a role in regulating chronic inflammation and tumorigenesis. However, further investigation is needed to understand the specific role of NLRX1 in CRC. To evaluate the impact of NLRX1 on migration, invasion, and metastasis, two human colon cancer cell lines were studied in vitro. Additionally, a knockout mouse tumor-bearing model was used to validate the inhibitory effect of NLRX1 on tumor emergence and progression. The Seahorse XF96 technology was employed to assess mitochondrial function and glycolysis in colorectal cancer cells overexpressing NLRX1. Moreover, public databases were consulted to analyze gene and protein expression levels of NLRX1. Finally, the results were validated using a series of CRC patient samples. Our findings demonstrate that downregulation of NLRX1 enhances proliferation, colony formation, and tumor-forming capacity in HCT116 and LoVo cells. Conversely, overexpression of NLRX1 negatively impacts basal respiration and mitochondrial ATP-linked respiration in both cell lines, resulting in a notable decrease in maximal respiration during the standard mitochondrial stress test. Furthermore, analysis of data from the TCGA database reveals a significant reduction in NLRX1 expression in colon and rectal cancer tissues compared to normal tissues. This result was validated using clinical samples, where immunohistochemistry staining and western blotting demonstrated a notable reduction in NLRX1 protein levels in CRC compared to adjacent normal tissues. The decreased expression of NLRX1 may serve as a significant prognostic indicator and diagnostic biomarker for CRC patients.

Identification, pathogenicity and molecular characterization of a novel fowl adenovirus 8b strain.

Since 2012, there has been a noticeable upward trend in the global incidence of inclusion body hepatitis (IBH) cases, leading to substantial economic losses in the poultry industry. In response to this trend, the current study aimed to investigate the phylogenetic information, genetic mutations, and pathogenicity of the highly pathogenic fowl adenovirus (FAdV) strain HN1472, which was isolated from liver samples obtained from a laying flock affected by IBH. This investigation was carried out using 1-day-old specific pathogen-free (SPF) chickens. Recombination and phylogenetic analyses confirmed that HN1472 is a recombinant strain derived from FAdV-8a and FAdV-8b, and exhibited significant genetic divergence in the hexon, fiber, and ORF19 genes. Notably, the phylogenetic analysis identified recombination events in these regions. Furthermore, animal experiments revealed that HN1472 is a highly pathogenic isolate, causing 80% mortality and manifesting clinical signs of IBH in SPF chickens. Furthermore, the recombinant FAdV serotype 8b (FAdV-8b) was found to be widely distributed in various tissues, with a higher concentration in the livers and gizzard tissue at 3 d postchallenge (dpc). Collectively, these findings contribute to our current understanding of the factors influencing the pathogenicity and genetic diversity of FAdV serotype 8b (FAdV-8b) in China.

SMEK1 ablation promotes glucose uptake and improves obesity-related metabolic dysfunction via AMPK signaling pathway.

Obesity has become a major risk of global public health. SMEK1 is also known as a regulatory subunit of protein phosphatase 4 (PP4). Both PP4 and SMEK1 have been clarified in many metabolic functions, including the regulation of hepatic gluconeogenesis and glucose transporter gene expression in yeast. Whether SMEK1 participates in obesity and the broader metabolic role in mammals is unknown. Thus, we investigated the function of SMEK1 in white adipose tissue and glucose uptake. GWAS/GEPIA/GEO database was used to analyze the correlation between SMEK1 and metabolic phenotypes/lipid metabolism-related genes/obesity. Smek1 KO mice were generated to identify the role of SMEK1 in obesity and glucose homeostasis. Cell culture and differentiation of stromal-vascular fractions (SVFs) and 3T3-L1 were used to determine the mechanism. 2-NBDG was used to measure the glucose uptake. Compound C was used to confirm the role of AMPK. We elucidated that SMEK1 was correlated with obesity and adipogenesis. Smek1 deletion enhanced adipogenesis in both SVFs and 3T3-L1. Smek1 KO protected mice from obesity and had protective effects on metabolic disorders, including insulin resistance and inflammation. Smek1 KO mice had lower levels of fasting serum glucose. We found that SMEK1 ablation promoted glucose uptake by increasing p-AMPKα(T172) and the transcription of Glut4 when the effect on AMPK-regulated glucose uptake was due to the PP4 catalytic subunits (PPP4C). Our findings reveal a novel role of SMEK1 in obesity and glucose homeostasis, providing a potential new therapeutic target for obesity and metabolic dysfunction.NEW & NOTEWORTHY Our study clarified the relationship between SMEK1 and obesity for the first time and validated the conclusion in multiple ways by combining available data from public databases, human samples, and animal models. In addition, we clarified the role of SMEK1 in glucose uptake, providing an in-depth interpretation for the study of its function in glucose metabolism.

Monotropein Alleviates Ovalbumin-Induced Asthma in Mouse Model by Inhibiting AKT/NF-κB Pathway.

INTRODUCTION: Clinical management of asthma remains as a prevalent challenge. Monotropein (MON) is a naturally occurring cyclic enol ether terpene glycoside with medical application potential. This study aims to evaluate the potential therapeutic effects of MON in the mouse model of chronic asthma. METHODS: An ovalbumin (OVA)-induced asthmatic mouse model was established to evaluate the therapeutic effect of MON at different doses (20, 40, and 80 mg/kg). The potential involvement of protein kinase B (AKT)/nuclear factor kappa B (NF-κB) pathway in the effect of MON was investigated by the administration of an AKT activator SC79. Histological changes in pulmonary tissues were examined by hematoxylin and eosin staining. The profiles of inflammatory cytokines (interleukin [IL]-4, IL-5, IL-13, and tumor necrosis factor [TNF]-α) in bronchoalveolar lavage fluid (BALF), and OVA-specific IgE in blood samples were analyzed by enzyme-linked immunosorbent assay (ELISA). The oxidative stress in the lung tissues was determined by measuring malondialdehyde level. The phosphorylation activation of AKT and NF-κB was examined by immunoblotting in the lung tissues. RESULTS: MON treatment suppressed the infiltration of inflammatory cells in the airways of OVA-induced asthma mice and reduced the thickness of the bronchial wall and smooth muscle layer in a dose-dependent manner. MON treatment also reduced the levels of OVA-specific IgE in serum and cytokines in BALF in asthma-induced mice, and attenuated the oxidative stress in the lung tissues. OVA induced the phosphorylation of AKT and NF-κB proteins in the lung tissues of asthmatic mice, which was significantly suppressed by MON treatment. The co-administration of AKT activator SC79 impaired the therapeutic effect of MON on asthma-induced mice. CONCLUSION: Our data demonstrated the potential therapeutic effect of MON on asthmatic mouse model, suggesting that MON attenuated the inflammatory and oxidative damages in ling tissues by dampening the AKT/NF-κB signaling pathway.

Utilization of Nitrogen-Doped Graphene Quantum Dots to Neutralize ROS and Modulate Intracellular Antioxidant Pathways to Improve Dry Eye Disease Therapy.

Purpose: Patients afflicted with dry eye disease (DED) experience significant discomfort. The underlying cause of DED is the excessive accumulation of ROS on the ocular surface. Here, we investigated the nitrogen doped-graphene quantum dots (NGQDs), known for their ROS-scavenging capabilities, as a treatment for DED. Methods: NGQDs were prepared by using citric acid and urea as precursors through hydrothermal method. The antioxidant abilities of NGQDs were evaluated through: scavenging the ROS both extracellular and intracellular, regulating the nuclear factor-erythroid 2-related factor (Nrf2) antioxidant pathway of human corneal epithelial cells (HCECs) and their transcription of inflammation related genes. Furthermore, NGQDs were modified by Arg-Gly-Asp-Ser (RGDS) peptides to obtain RGDS@NGQDs. In vivo, both the NGQDs and RGDS@NGQDs were suspended in 0.1% Pluronic F127 (w/v) and delivered as eye drops in the scopolamine hydrobromide-induced DED mouse model. Preclinical efficacy was compared to the healthy and DPBS treated DED mice. Results: These NGQDs demonstrated pronounced antioxidant properties, efficiently neutralizing free radicals and activating the intracellular Nrf2 pathway. In vitro studies revealed that treatment of H2O2-exposed HCECs with NGQDs induced a preservation in cell viability. Additionally, there was a reduction in the transcription of inflammation-associated genes. To prolong the corneal residence time of NGQDs, they were further modified with RGDS peptides and suspended in 0.1% Pluronic F127 (w/v) to create RGDS@NGQDs F127 eye drops. RGDS@NGQDs exhibited superior intracellular antioxidant activity even at low concentrations (10 µg/mL). Subsequent in vivo studies revealed that RGDS@NGQDs F127 eye drops notably mitigated the symptoms of DED mouse model, primarily by reducing ocular ROS levels. Conclusion: Our findings underscore the enhanced antioxidant benefits achieved by modifying GQDs through nitrogen doping and RGDS peptide tethering. Importantly, in a mouse model, our novel eye drops formulation effectively ameliorated DED symptoms, thereby representing a novel therapeutic pathway for DED management.

Early effective intervention can significantly reduce all-cause mortality in prediabetic patients: a systematic review and meta-analysis based on high-quality clinical studies.

Background: Reducing the occurrence of diabetes is considered a primary criterion for evaluating the effectiveness of interventions for prediabetes. There is existing evidence that early lifestyle-based interventions can significantly decrease the incidence of diabetes. However, whether effective interventions can reduce long-term outcomes in patients, including all-cause mortality, cardiovascular risks, and the occurrence of microvascular complications, which are the most concerning issues for both patients and clinicians, remains a subject of inconsistent research findings. And there is no direct evidence to answer whether effective intervention has long-term benefits for prediabetic patients. Therefore, we conducted a systematic review and meta-analysis to assess the relationship between early effective intervention and macrovascular and microvascular complications in prediabetic patients. Methods: PubMed, Embase, and Cochrane Central Register of Controlled Trials were searched for the randomized controlled trials of lifestyle or/and drugs intervention in prediabetes from inception to 2023.9.15. Two investigators independently reviewed the included studies and extracted relevant data. Random or fixed effects model meta-analysis to derive overall relative risk (RR) with 95% CI for all-cause mortality, cardiovascular events, and microvascular complications. Results: As of September 15, 2023, a total of 7 effective intervention studies were included, comprising 26 articles out of 25,671 articles. These studies involved 26,389 patients with a total follow-up duration of 178,038.6 person-years. The results indicate that effective intervention can significantly reduce all-cause mortality in prediabetic patients without a history of cardiovascular disease by 17% (RR 0.83, 95% CI 0.70-0.98). Additionally, effective intervention reduced the incidence of retinopathy by 38% (RR 0.62, 95% CI 0.70-0.98). Furthermore, the study results suggest that women and younger individuals have lower all-cause mortality and cardiovascular mortality. Subsequently, we conducted an in-depth analysis of patients without a history of cardiovascular disease. The results revealed that prediabetic patients with a 10-year cardiovascular risk >10% experienced more significant benefits in terms of all-cause mortality (P=0.01). When comparing the results of all-cause mortality and cardiovascular mortality from the Da Qing Diabetes Prevention Outcome Study longitudinally, it was evident that the duration of follow-up is a key factor influencing long-term benefits. In other words, the beneficial effects become more pronounced as the intervention duration reaches a certain threshold. Conclusion: Early effective intervention, which significantly reduces the incidence of diabetes, can effectively lower all-cause mortality in prediabetic patients without a history of cardiovascular disease (especially those with a 10-year cardiovascular risk >10%), with women and younger individuals benefiting more significantly. Additionally, the duration of follow-up is a key factor influencing outcomes. The conclusions of this study can provide evidence-based guidance for the clinical treatment of prediabetic patients to prevent cardiovascular and microvascular complications. Systematic review registration: https://www.crd.york.ac.uk/prospero, identifier CRD42020160985.

Parallelism and non-parallelism in diabetic nephropathy and diabetic retinopathy.

Diabetic nephropathy (DN) and diabetic retinopathy (DR), as microvascular complications of diabetes mellitus, are currently the leading causes of end-stage renal disease (ESRD) and blindness, respectively, in the adult working population, and they are major public health problems with social and economic burdens. The parallelism between the two in the process of occurrence and development manifests in the high overlap of disease-causing risk factors and pathogenesis, high rates of comorbidity, mutually predictive effects, and partial concordance in the clinical use of medications. However, since the two organs, the eye and the kidney, have their unique internal environment and physiological processes, each with specific influencing molecules, and the target organs have non-parallelism due to different pathological changes and responses to various influencing factors, this article provides an overview of the parallelism and non-parallelism between DN and DR to further recognize the commonalities and differences between the two diseases and provide references for early diagnosis, clinical guidance on the use of medication, and the development of new drugs.

Extracting, filtering and simulating cellular barcodes using CellBarcode tools.

Identifying true DNA cellular barcodes among polymerase chain reaction and sequencing errors is challenging. Current tools are restricted in the diversity of barcode types supported or the analysis strategies implemented. As such, there is a need for more versatile and efficient tools for barcode extraction, as well as for tools to investigate which factors impact barcode detection and which filtering strategies to best apply. Here we introduce the package CellBarcode and its barcode simulation kit, CellBarcodeSim, that allows efficient and versatile barcode extraction and filtering for a range of barcode types from bulk or single-cell sequencing data using a variety of filtering strategies. Using the barcode simulation kit and biological data, we explore the technical and biological factors influencing barcode identification and provide a decision tree on how to optimize barcode identification for different barcode settings. We believe that CellBarcode and CellBarcodeSim have the capability to enhance the reproducibility and interpretation of barcode results across studies.

Tropomyosin1 isoforms underlie epithelial to mesenchymal plasticity, metastatic dissemination, and resistance to chemotherapy in high-grade serous ovarian cancer.

Phenotypic plasticity, defined as the ability of individual cells with stable genotypes to exert different phenotypes upon exposure to specific environmental cues, represent the quintessential hallmark of the cancer cell en route from the primary lesion to distant organ sites where metastatic colonization will occur. Phenotypic plasticity is driven by a broad spectrum of epigenetic mechanisms that allow for the reversibility of epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions (EMT/MET). By taking advantage of the co-existence of epithelial and quasi-mesenchymal cells within immortalized cancer cell lines, we have analyzed the role of EMT-related gene isoforms in the regulation of epithelial mesenchymal plasticity (EMP) in high grade serous ovarian cancer. When compared with colon cancer, a distinct spectrum of downstream targets characterizes quasi-mesenchymal ovarian cancer cells, likely to reflect the different modalities of metastasis formation between these two types of malignancy, i.e. hematogenous in colon and transcoelomic in ovarian cancer. Moreover, upstream RNA-binding proteins differentially expressed between epithelial and quasi-mesenchymal subpopulations of ovarian cancer cells were identified that underlie differential regulation of EMT-related isoforms. In particular, the up- and down-regulation of RBM24 and ESRP1, respectively, represent a main regulator of EMT in ovarian cancer cells. To validate the functional and clinical relevance of our approach, we selected and functionally analyzed the Tropomyosin 1 gene (TPM1), encoding for a protein that specifies the functional characteristics of individual actin filaments in contractile cells, among the ovarian-specific downstream AS targets. The low-molecular weight Tpm1.8/9 isoforms are specifically expressed in patient-derived ascites and promote invasion through activation of EMT and Wnt signaling, together with a broad spectrum of inflammation-related pathways. Moreover, Tpm1.8/9 expression confers resistance to taxane- and platinum-based chemotherapy. Small molecule inhibitors that target the Tpm1 isoforms support targeting Tpm1.8/9 as therapeutic targets for the development of future tailor-made clinical interventions.

CUL4B mutations impair human cortical neurogenesis through PP2A-dependent inhibition of AKT and ERK.

Mutation in CUL4B gene is one of the most common causes for X-linked intellectual disability (XLID). CUL4B is the scaffold protein in CUL4B-RING ubiquitin ligase (CRL4B) complex. While the roles of CUL4B in cancer progression and some developmental processes like adipogenesis, osteogenesis, and spermatogenesis have been studied, the mechanisms underlying the neurological disorders in patients with CUL4B mutations are poorly understood. Here, using 2D neuronal culture and cerebral organoids generated from the patient-derived induced pluripotent stem cells and their isogenic controls, we demonstrate that CUL4B is required to prevent premature cell cycle exit and precocious neuronal differentiation of neural progenitor cells. Moreover, loss-of-function mutations of CUL4B lead to increased synapse formation and enhanced neuronal excitability. Mechanistically, CRL4B complex represses transcription of PPP2R2B and PPP2R2C genes, which encode two isoforms of the regulatory subunit of protein phosphatase 2 A (PP2A) complex, through catalyzing monoubiquitination of H2AK119 in their promoter regions. CUL4B mutations result in upregulated PP2A activity, which causes inhibition of AKT and ERK, leading to premature cell cycle exit. Activation of AKT and ERK or inhibition of PP2A activity in CUL4B mutant organoids rescues the neurogenesis defect. Our work unveils an essential role of CUL4B in human cortical development.

Approaching expert-level accuracy for differentiating ACL tear types on MRI with deep learning.

Treatment for anterior cruciate ligament (ACL) tears depends on the condition of the ligament. We aimed to identify different tear statuses from preoperative MRI using deep learning-based radiomics with sex and age. We reviewed 862 patients with preoperative MRI scans reflecting ACL status from Hunan Provincial People's Hospital. Based on sagittal proton density-weighted images, a fully automated approach was developed that consisted of a deep learning model for segmenting ACL tissue (ACL-DNet) and a deep learning-based recognizer for ligament status classification (ACL-SNet). The efficacy of the proposed approach was evaluated by using the sensitivity, specificity and area under the receiver operating characteristic curve (AUC) and compared with that of a group of three orthopedists in the holdout test set. The ACL-DNet model yielded a Dice coefficient of 98% ± 6% on the MRI datasets. Our proposed classification model yielded a sensitivity of 97% and a specificity of 97%. In comparison, the sensitivity of alternative models ranged from 84 to 90%, while the specificity was between 86 and 92%. The AUC of the ACL-SNet model was 99%, demonstrating high overall diagnostic accuracy. The diagnostic performance of the clinical experts as reflected in the AUC was 96%, 92% and 88%, respectively. The fully automated model shows potential as a highly reliable and reproducible tool that allows orthopedists to noninvasively identify the ACL status and may aid in optimizing different techniques, such as ACL remnant preservation, for ACL reconstruction.

Microplastics as potential barriers to ultraviolet light emitting diode inactivation of MS2 bacteriophage: Influence of water-quality parameters.

Microplastics have emerged as a concerning contaminant in drinking water sources, potentially interacting with pathogenic microorganisms and affecting the disinfection processes. In this study, MS2 was selected as an alternative for the human enteric virus. The influence of microplastics polyvinylchloride (MPs-PVC) on ultraviolet light emitting diode (UV-LED) inactivation of MS2 was investigated under various water chemistry conditions, such as MPs-PVC concentration, pH, salinity, and humic acid concentration. The results revealed that higher concentrations of MPs-PVC led to the reduced inactivation of MS2 by decreased UV transmittance, hindering the disinfection process. Additionally, the inactivation efficiency of MS2 in the presence of MPs-PVC was influenced by pH, and acidic solution (pH at 4, 5, and 6) exhibited higher efficiency compared to alkaline solution (pH at 8 and 9) and neutral solution (pH at 7). The low Na+ concentrations (0-50 mM) had a noticeable effect on MS2 inaction efficiency in the presence of MPs-PVC, while the addition of Ca2+ posed an insignificant effect due to the preferential interaction with MPs-PVC. Furthermore, the inactivation rate of MS2 initially increased and then decreased with increasing the concentration of humic acid, which was significantly different without MPs-PVC. These findings shed light on the complex interactions between MPs-PVC and MS2 in the UV-LED disinfection process under various water-quality parameters, contributing to drinking water safety and treatment.