Single-Cell RNA Sequencing of hESC-Derived 3D Retinal Organoids Reveals Novel Genes Regulating RPC Commitment in Early Human Retinogenesis.

The development of the mammalian retina is a complicated process involving the generation of distinct types of neurons from retinal progenitor cells (RPCs) in a spatiotemporal-specific manner. The progression of RPCs during retinogenesis includes RPC proliferation, cell-fate commitment, and specific neuronal differentiation. In this study, by performing single-cell RNA sequencing of cells isolated from human embryonic stem cell (hESC)-derived 3D retinal organoids, we successfully deconstructed the temporal progression of RPCs during early human retinogenesis. We identified two distinctive subtypes of RPCs with unique molecular profiles, namely multipotent RPCs and neurogenic RPCs. We found that genes related to the Notch and Wnt signaling pathways, as well as chromatin remodeling, were dynamically regulated during RPC commitment. Interestingly, our analysis identified that CCND1, a G1-phase cell-cycle regulator, was coexpressed with ASCL1 in a cell-cycle-independent manner. Temporally controlled overexpression of CCND1 in retinal organoids demonstrated a role for CCND1 in promoting early retinal neurogenesis. Together, our results revealed critical pathways and novel genes in early retinogenesis of humans

Viruses mobilize plant immunity to deter nonvector insect herbivores.

A parasite-infected host may promote performance of associated insect vectors; but possible parasite effects on nonvector insects have been largely unexplored. Here, we show that Begomovirus, the largest genus of plant viruses and transmitted exclusively by whitefly, reprogram plant immunity to promote the fitness of the vector and suppress performance of nonvector insects (i.e., cotton bollworm and aphid). Infected plants accumulated begomoviral βC1 proteins in the phloem where they were bound to the plant transcription factor WRKY20. This viral hijacking of WRKY20 spatiotemporally redeployed plant chemical immunity within the leaf and had the asymmetrical benefiting effects on the begomoviruses and its whitefly vectors while negatively affecting two nonvector competitors. This type of interaction between a parasite and two types of herbivores, i.e., vectors and nonvectors, occurs widely in various natural and agricultural ecosystems; thus, our results have broad implications for the ecological significance of parasite-vector-host tripartite interactions

Survival outcomes of autologous breast reconstruction after mastectomy: A matched case-control study

BackgroundDue to the lack of strong evidence-based medical evidence, the relationship between autologous breast reconstruction (ABR) after mastectomy and long-term prognosis is unclear. This study aims to explore if ABR after mastectomy is associated with the prognosis of breast cancer (BC) patients based on the data from the Surveillance, Epidemiology, and End Results (SEER) database.MethodsWe collected data for all cases diagnosed with BC who underwent or did not undergo ABR after mastectomy from 2010-2015 in the SEER database. The primary outcome of our study was overall survival (OS) and cancer specific survival (CSS). The Propensity Score-Matched (PSM) analysis was used to eliminate the effects of non-random statistics, setting the caliper as 0.0001 to balance the baseline variables within the groups. Chi-square test, Kaplan-Meier method, univariate and multivariate cox regression analysis were used to analyze the data and subgroup analysis was performed to find the subgroups of people who might benefit from ABR.ResultOf 27893 eligible patients, 11038 patients were matched. The cohort consisted of 5519 (50%) ABR patients and 5519 (50%) non-ABR patients after PSM. After PSM, on multivariate cox regression analysis, ABR still exerted a significant influence on the OS (hazard ratio (HR), 0.83, P< 0.05). However, no statistical difference was shown on CSS (HR, 0.93, P = 0.31). Kaplan-Meier survival analysis showed ABR group had better OS (P = 0.001), but similar CSS (P = 0.174) between ARB and mastectomy groups. Subgroup analysis showed that after matching, those with 50-59 years old, earlier stages of disease, without a marital partner and living in urban areas had better OS after ABR.ConclusionsABR after mastectomy was associated with better OS, but not affect CSS

Proteomics Analysis of the Spinal Dorsal Horn in Diabetic Painful Neuropathy Rats With Electroacupuncture Treatment

BackgroundClinical evidence demonstrates that electro-acupuncture (EA) of the Zu sanli (ST36) and Shen shu (BL23) acupoints is effective in relieving diabetic painful neuropathy (DPN); however, the underlying molecular mechanism requires further investigation, including the protein molecules associated with EA’s effects on DPN.MethodsSprague-Dawley adult male rats (n =36) were randomly assigned into control, DPN, and EA groups (n=12 each). After four weeks of EA treatment, response to mechanical pain and fasting blood glucose were analyzed. A tandem mass tag (TMT) labeling approach coupled with liquid chromatography with tandem mass spectrometry was used to identify potential biomarkers in the spinal dorsal horn. Further, proteomics analysis was used to quantify differentially expressed proteins (DEPs), and gene ontology, KEGG pathways, cluster, and string protein network interaction analyses conducted to explore the main protein targets of EA.ResultsCompared with the DPN model group, the mechanical pain threshold was significantly increased, while the fasting blood glucose levels were clearly decreased in EA group rats. Proteomics analysis was used to quantify 5393 proteins, and DEPs were chosen for further analyses, based on a threshold of 1.2-fold difference in expression level (P < 0.05) compared with control groups. Relative to the control group, 169 down-regulated and 474 up-regulated proteins were identified in the DPN group, while 107 and 328 proteins were up- and down-regulated in the EA treatment group compared with the DPN group. Bioinformatics analysis suggested that levels of proteins involved in oxidative stress injury regulation were dramatically altered during the EA effects on DPN.ConclusionsOur results provide the valuable protein biomarkers, which facilitates unique mechanistic insights into the DPN pathogenesis and EA analgesic, antioxidant stress and hypoglycemic effect

Prediction of the shear wave speed of seafloor sediments in the northern South China Sea based on an XGBoost algorithm

Based on data on the shear wave speed and physical properties of the shallow sediment samples collected in the northwest South China Sea, the hyperparameter selection and contribution of the characteristic factors of the machine learning model for predicting the shear wave speed of seafloor sediments were studied using the eXtreme Gradient Boosting (XGBoost) algorithm. An XGBoost model for predicting the shear wave speed of seafloor sediments was established based on four physical parameters of the sediments: porosity (n), water content (w), density (ρ), and average grain size (MZ). The result reveals that: (1) The shear wave speed has a good correlation with n, w, ρ, and MZ, and their Pearson correlation coefficients are all above 0.75, indicating that they can be used as the suitable characteristic parameters for predicting the shear wave speed based on the XGBoost model; (2) When the number of weak learners (n_estimators) is 115 and the maximum depth of the tree (max_depth) is 6, the XGBoost model has a very high goodness of fit (R2) of the validation data of 0.914, the very low mean absolute error (MAE) and mean absolute percentage error (MAPE) of the predicted shear wave speed are 3.366 m/s and 9.90%, respectively; (3) Compared with grain-shearing (GS) model and single- and dual-parameter regression equation prediction models, the XGBoost model for the shear wave speed of seafloor sediments has higher fitting goodness and lower prediction error

Gene knockout of glutathione reductase results in increased sensitivity to heavy metals in Acidithiobacillus caldus

Acidithiobacillus caldus plays an important role in bioleaching of low-grade metal ore. It can promote the release of heavy metals in mining-associated habitats and survive in high concentrations of heavy metals. Functions of glutathione reductase (GR) in cell defense against reactive oxygen species caused by heavy metals have been elucidated in some eukaryotic cells and bacteria; however, no information is available in A. caldus. In this research, the methods of bioinformatics, gene expression, GR activity assays were used to detect and characterize the glutathione reductase gene from the A. caldus MTH-04 strain. Then, A. caldus gr knockout mutant and gr overexpression strain were constructed, and the heavy metal tolerant properties and transcriptional levels of ROS related genes of them were compared to study the function of GR. The results showed that, a putative gr gene F0726_RS04210 was detected in the genome of A. caldus MTH-04. The purified recombinant protein of F0726_RS04210 showed remarkable GR activity at optimal pH 7.0 and 30°C using in vitro assay. The evolutionary relationship of GR from A. caldus MTH-04 was close to that from Escherichia coli K12. Gene knockout or overexpression of gr in A. caldus did not affect the growth rate on S0 medium, suggesting that GR did not play a key role in the activation of sulfur. Deletion of gr resulted in increased sensitivity to heavy metals (Cu2+ and Zn2+) in A. caldus, and the gr overexpression strain showed enhanced tolerance to heavy metals. Furthermore, transcription analysis also revealed strong correlations between GR and the antioxidant pathway. The above results suggest that GR can play an important role in heavy metal tolerance in A. caldus

Trans-lymphatic Contrast-Enhanced Ultrasound in Combination with Blue Dye Injection is Feasible for Detection and Biopsy of Sentinel Lymph Nodes in Breast Cancer

Objective: The best method for sentinel lymph node biopsy (SLNB) in early-staged breast cancer (EBC) remains controversial. This study aimed to evaluate a novel method by combining trans-lymphatic contrast-enhanced ultrasound (TLCEUS) with blue dye injection as a guidance of SLNB. Methods: TLCEUS was performed in 88 patients with newly diagnosed EBC. Methylene blue dye was percutaneously injected into enhanced sentinel lymph nodes (SLNs) under ultrasound guidance, followed by standard SLNB and axillary lymph node dissection. Enhancement patterns and the arriving time (AT) of contrast agent within SLNs were evaluated. Histopathological examination of dissected nodes was performed to confirm metastasis. Results: A total of 95 enhanced SLNs were identified and biopsied in 86 of 88 patients with identification rate of 97.7%. The specificity was 75.0%, sensitivity was 83.3%, and false-negative rate was 16.7%. Contrast-enhanced SLNs with type I, type II, and type III patterns had a metastatic positive rate of 11.4% (5/44), 57.1% (12/21) and 80.0% (24/30), respectively. Metastatic positive SLNs showed a mean AT of 61.6 ± 58.7 s while metastatic negative SLNs showed a mean AT of 41.3 ± 19.9 s, which was statistically significantly different. Conclusion: The TLCEUS/blue dye method can be used as an alternative to the radioisotope/blue dye method for its feasibility and accuracy

Safety of HIF prolyl hydroxylase inhibitors for anemia in dialysis patients: a systematic review and network meta-analysis

Aim: We performed a systematic review and network meta-analysis evaluating the safety and efficacy of hypoxia-inducible factor prolyl hydroxylase inhibitors (HIF-PHIs) among dialysis chronic kidney disease patients.Methods: Safety was evaluated with any adverse events (AEs), serious adverse events (SAEs), and 12 common events. Efficacy was mainly analyzed with hemoglobin response. All reported results were summarized using mean difference and risk ratio (RR) with 95% confidence interval (CI). Publication bias was assessed through funnel plots.Results: Twenty trials (19 studies) with 14,947 participants were included, comparing six HIF-PHIs with erythropoiesis-stimulating agents (ESAs). No significant differences were indicated in overall AEs and SAEs between each HIF-PHI and ESA. The occurrence of gastrointestinal disorder was higher in enarodustat and roxadustat than in ESAs (RR: 6.92, 95% CI: 1.52–31.40, p = 0.01; RR: 1.30, 95% CI: 1.04–1.61, p = 0.02). The occurrence of hypertension was lower in vadadustat than in ESAs (RR: 0.81, 95% CI: 0.69–0.96, p = 0.01). The occurrence of vascular-access complications was higher in roxadustat (RR: 1.15, 95% CI: 1.04–1.27, p<0.01) and lower in daprodustat (RR: 0.78, 95% CI: 0.66–0.92, p<0.01) than in ESAs. In the risk of the other nine events, including cardiovascular events, no significant differences were observed between HIF-PHIs and ESAs. For hemoglobin response, network meta-analysis showed that compared with ESAs, significant increases were shown in roxadustat (RR: 1.04, 95% CI: 1.01–1.07, p<0.01) and desidustat (RR: 1.22, 95% CI: 1.01–1.48, p = 0.04), whereas noticeable reductions were indicated in vadadustat (RR: 0.88, 95% CI: 0.82–0.94, p<0.01) and molidustat (RR: 0.83, 95% CI: 0.70–0.98, p = 0.02). There was no significant difference between daprodustat and ESAs (RR: 0.97, 95% CI: 0.89–1.06, p = 0.47).Conclusion: Although HIF-PHIs did not show significant differences from ESAs in terms of overall AEs and SAEs, statistical differences in gastrointestinal disorder, hypertension, and vascular-access complications were observed between HIF-PHIs, which deserved to be noted in clinical decision making.Systematic review registration: This study is registered with PROSPERO (registration number CRD42022312252

Stability of important antibodies for kidney disease: pre-analytic methodological considerations

Background The importance of circulating antibodies as biomarkers of kidney disease has recently been recognized. However, no study has systematically described the methodology of sample preparation and storage regarding antibodies as biomarkers of kidney disease. It remains unknown whether repetitive freeze-thaw cycles, physical disturbances, storage at different temperatures or for different periods of time, or haemolytic or turbid serum samples affect antibody measurements. The aim of this study was to investigate the stabilities of antibodies associated with kidney disease in serum samples under various relevant clinical and research conditions. Methods We stored serum samples in the following different conditions: repetitive freeze-thaw cycles (1, 6 or 12 times), long-term storage (7 or 12 months at −80 °C), physical disturbance (1 or 8 h), and storage at 4 °C (1, 3 or 6 weeks) and room temperature (1 or 7 days). The stabilities of the anti-phospholipase A2 receptor (anti-PLA2R), anti-glomerular basement membrane, anti-myeloperoxidase and anti-proteinase 3 antibodies were evaluated with enzyme-linked immunosorbent assays (ELISA). Results We found that repetitive freeze-thaw cycles did not have a significant effect on the stabilities of the abovementioned antibodies in clear serum samples. The ELISA readings of haemolytic and turbid serum samples tended to increase and decrease, respectively. Neither long-term storage at −80 °C nor physical disturbance had a significant effect on anti-PLA2R antibody stability in sealed serum samples. The concentrations of most of these antibodies increased in unsealed serum samples that were stored at 4 °C for more than 6 weeks or at room temperature for more than 7 days. Discussion Our findings revealed that the abovementioned circulating antibodies that are used as biomarkers for kidney disease had stable physicochemical properties, structures and immunoreactivities such that they were not influenced by repetitive freeze-thaw cycles, physical disturbances or long-term storage at −80 °C. However, the ELISA readings tended to change for haemolytic, turbid and unsealed serum samples