Massively parallel characterization of CRISPR activator efficacy in human induced pluripotent stem cells and neurons.

CRISPR activation (CRISPRa) is an important tool to perturb transcription, but its effectiveness varies between target genes. We employ human pluripotent stem cells with thousands of randomly integrated barcoded reporters to assess epigenetic features that influence CRISPRa efficacy. Basal expression levels are influenced by genomic context and dramatically change during differentiation to neurons. Gene activation by dCas9-VPR is successful in most genomic contexts, including developmentally repressed regions, and activation level is anti-correlated with basal gene expression, whereas dCas9-p300 is ineffective in stem cells. Certain chromatin states, such as bivalent chromatin, are particularly sensitive to dCas9-VPR, whereas constitutive heterochromatin is less responsive. We validate these rules at endogenous genes and show that activation of certain genes elicits a change in the stem cell transcriptome, sometimes showing features of differentiated cells. Our data provide rules to predict CRISPRa outcome and highlight its utility to screen for factors driving stem cell differentiation.

Correction: Fan et al. Progress in the Preclinical and Clinical Study of Resveratrol for Vascular Metabolic Disease. Molecules 2022, 27, 7524.

Text Correction [...].

High-dimensional principal component analysis with heterogeneous missingness.

We study the problem of high-dimensional Principal Component Analysis (PCA) with missing observations. In a simple, homogeneous observation model, we show that an existing observed-proportion weighted (OPW) estimator of the leading principal components can (nearly) attain the minimax optimal rate of convergence, which exhibits an interesting phase transition. However, deeper investigation reveals that, particularly in more realistic settings where the observation probabilities are heterogeneous, the empirical performance of the OPW estimator can be unsatisfactory; moreover, in the noiseless case, it fails to provide exact recovery of the principal components. Our main contribution, then, is to introduce a new method, which we call primePCA, that is designed to cope with situations where observations may be missing in a heterogeneous manner. Starting from the OPW estimator, primePCA iteratively projects the observed entries of the data matrix onto the column space of our current estimate to impute the missing entries, and then updates our estimate by computing the leading right singular space of the imputed data matrix. We prove that the error of primePCA converges to zero at a geometric rate in the noiseless case, and when the signal strength is not too small. An important feature of our theoretical guarantees is that they depend on average, as opposed to worst-case, properties of the missingness mechanism. Our numerical studies on both simulated and real data reveal that primePCA exhibits very encouraging performance across a wide range of scenarios, including settings where the data are not Missing Completely At Random.

Progress in the Preclinical and Clinical Study of Resveratrol for Vascular Metabolic Disease.

Vascular metabolic dysfunction presents in various diseases, such as atherosclerosis, hypertension, and diabetes mellitus. Due to the high prevalence of these diseases, it is important to explore treatment strategies to protect vascular function. Resveratrol (RSV), a natural polyphenolic phytochemical, is regarded as an agent to regulate metabolic pathways. Many studies have proven that RSV has beneficial effects on improving metabolism in endothelial cells (ECs) and vascular smooth muscle cells (VSMCs), which provide new directions to treat vascular metabolic diseases. Herein, we overviewed that RSV could regulate cell metabolism activity by inhibiting glucose uptake, suppressing glycolysis, preventing cells from fatty acid-related damages, reducing lipogenesis, increasing fatty acid oxidation, enhancing lipolysis, elevating uptake and synthesis of glutamine, and increasing NO release. Furthermore, in clinical trials, although the results from different studies remain controversial, we proposed that RSV had better therapeutic effects at high concentrations and for patients with metabolic disorders.

Resveratrol Promotes Angiogenesis in a FoxO1-Dependent Manner in Hind Limb Ischemia in Mice.

Critical limb ischemia (CLI) is a severe form of peripheral artery diseases (PAD) and seriously endangers the health of people. Therapeutic angiogenesis represents an important treatment strategy for CLI; various methods have been applied to enhance collateral circulation. However, the current development drug therapy to promote angiogenesis is limited. Resveratrol (RSV), a polyphenol compound extracted from plants, has various properties such as anti-oxidative, anti-inflammatory and anti-cancer effects. Whether RSV exerts protective effects on CLI remains elusive. In the current study, we demonstrated that oral intake of RSV significantly improved hind limb ischemia in mice, and increased the expression of phosphorylated Forkhead box class-O1 (FoxO1). RSV treatment in human umbilical vein endothelial cells (HUVECs) could increase the phosphorylation of FoxO1 and its cytoplasmic re-localization to promote angiogenesis. Then we manipulated FoxO1 in HUVECs to further verify that the effect of RSV on angiogenesis is in a FoxO1-dependent manner. Furthermore, we performed metabolomics to screen the metabolic pathways altered upon RSV intervention. We found that the pathways of pyrimidine metabolism, purine metabolism, as well as alanine, aspartate and glutamate metabolism, were highly correlated with the beneficial effects of RSV on the ischemic muscle. This study provides a novel direction for the medical therapy to CLI.

The impact of severe acute kidney injury requiring renal replacement therapy on survival and renal function of heart transplant recipients - a UK cohort study.

Severe acute kidney injury (AKI), defined as requiring renal replacement therapy (RRT), is associated with higher mortality postheart transplantation, but its long-term renal consequences are not known. Anonymized data of 3365 patients, who underwent heart transplantation between 1995 and 2017, were retrieved from the UK Transplant Registry. Multivariable binary logistic regression was performed to identify risk factors for severe AKI requiring RRT, Kaplan-Meier analysis to compare survival and renal function deterioration of the RRT and non-RRT groups, and multivariable Cox regression model to identify predicting factors of mortality and end-stage renal disease (ESRD). 26.0% of heart recipients received RRT post-transplant. The RRT group has lower survival rates at all time points, especially in the immediate post-transplant period. However, conditional on 3 months survival, older age, diabetes and coronary heart disease, but not post-transplant RRT, were the risk factors for long-term survival. The predicting factors for ESRD were insulin-dependent diabetes, renal function at transplantation, eGFR decline in the first 3 months post-transplant, post-transplant severe AKI and transplantation era. Severe AKI requiring RRT post-transplant is associated with worse short-term survival, but has no impact on long-term mortality. It also accelerates recipients' renal function deterioration in the long term.

Inference in High-Dimensional Online Changepoint Detection.

We introduce and study two new inferential challenges associated with the sequential detection of change in a high-dimensional mean vector. First, we seek a confidence interval for the changepoint, and second, we estimate the set of indices of coordinates in which the mean changes. We propose an online algorithm that produces an interval with guaranteed nominal coverage, and whose length is, with high probability, of the same order as the average detection delay, up to a logarithmic factor. The corresponding support estimate enjoys control of both false negatives and false positives. Simulations confirm the effectiveness of our methodology, and we also illustrate its applicability on the U.S. excess deaths data from 2017 to 2020. The supplementary material, which contains the proofs of our theoretical results, is available online.

Gut microbial co-metabolite 2-methylbutyrylcarnitine exacerbates thrombosis via binding to and activating integrin α2ß1.

Thrombosis represents the leading cause of death and disability upon major adverse cardiovascular events (MACEs). Numerous pathological conditions such as COVID-19 and metabolic disorders can lead to a heightened thrombotic risk; however, the underlying mechanisms remain poorly understood. Our study illustrates that 2-methylbutyrylcarnitine (2MBC), a branched-chain acylcarnitine, is accumulated in patients with COVID-19 and in patients with MACEs. 2MBC enhances platelet hyperreactivity and thrombus formation in mice. Mechanistically, 2MBC binds to integrin α2ß1 in platelets, potentiating cytosolic phospholipase A2 (cPLA2) activation and platelet hyperresponsiveness. Genetic depletion or pharmacological inhibition of integrin α2ß1 largely reverses the pro-thrombotic effects of 2MBC. Notably, 2MBC can be generated in a gut-microbiota-dependent manner, whereas the accumulation of plasma 2MBC and its thrombosis-aggravating effect are largely ameliorated following antibiotic-induced microbial depletion. Our study implicates 2MBC as a metabolite that links gut microbiota dysbiosis to elevated thrombotic risk, providing mechanistic insight and a potential therapeutic strategy for thrombosis.

Counter-regulatory renin-angiotensin system in hypertension: Review and update in the era of COVID-19 pandemic.

Cardiovascular disease is the major cause of mortality and disability, with hypertension being the most prevalent risk factor. Excessive activation of the renin-angiotensin system (RAS) under pathological conditions, leading to vascular remodeling and inflammation, is closely related to cardiovascular dysfunction. The counter-regulatory axis of the RAS consists of angiotensin-converting enzyme 2 (ACE2), angiotensin (1-7), angiotensin (1-9), alamandine, proto-oncogene Mas receptor, angiotensin II type-2 receptor and Mas-related G protein-coupled receptor member D. Each of these components has been shown to counteract the effects of the overactivated RAS. In this review, we summarize the latest insights into the complexity and interplay of the counter-regulatory RAS axis in hypertension, highlight the pathophysiological functions of ACE2, a multifunctional molecule linking hypertension and COVID-19, and discuss the function and therapeutic potential of targeting this counter-regulatory RAS axis to prevent and treat hypertension in the context of the current COVID-19 pandemic.

Machine-Learning Approach for Predicting the Discharging Capacities of Doped Lithium Nickel-Cobalt-Manganese Cathode Materials in Li-Ion Batteries.

Understanding the governing dopant feature for cyclic discharge capacity is vital for the design and discovery of new doped lithium nickel-cobalt-manganese (NCM) oxide cathodes for lithium-ion battery applications. We herein apply six machine-learning regression algorithms to study the correlations of the structural, elemental features of 168 distinct doped NCM systems with their respective initial discharge capacity (IC) and 50th cycle discharge capacity (EC). First, a Pearson correlation coefficient study suggests that the lithium content ratio is highly correlated to both discharge capacity variables. Among all six regression algorithms, gradient boosting models have demonstrated the best prediction power for both IC and EC, with the root-mean-square errors calculated to be 16.66 mAhg-1 and 18.59 mAhg-1, respectively, against a hold-out test set. Furthermore, a game-theory-based variable-importance analysis reveals that doped NCM materials with higher lithium content, smaller dopant content, and lower-electronegativity atoms as the dopant are more likely to possess higher IC and EC. This study has demonstrated the exciting potentials of applying cutting-edge machine-learning techniques to accurately capture the complex structure-property relationship of doped NCM systems, and the models can be used as fast screening tools for new doped NCM structures with more superior electrochemical discharging properties.

INSIGHT: A population-scale COVID-19 testing strategy combining point-of-care diagnosis with centralized high-throughput sequencing.

We present INSIGHT [isothermal NASBA (nucleic acid sequence-based amplification) sequencing-based high-throughput test], a two-stage coronavirus disease 2019 testing strategy, using a barcoded isothermal NASBA reaction. It combines point-of-care diagnosis with next-generation sequencing, aiming to achieve population-scale testing. Stage 1 allows a quick decentralized readout for early isolation of presymptomatic or asymptomatic patients. It gives results within 1 to 2 hours, using either fluorescence detection or a lateral flow readout, while simultaneously incorporating sample-specific barcodes. The same reaction products from potentially hundreds of thousands of samples can then be pooled and used in a highly multiplexed sequencing-based assay in stage 2. This second stage confirms the near-patient testing results and facilitates centralized data collection. The 95% limit of detection is <50 copies of viral RNA per reaction. INSIGHT is suitable for further development into a rapid home-based, point-of-care assay and is potentially scalable to the population level.

Bi2MoO6 Quantum Dots In Situ Grown on Reduced Graphene Oxide Layers: A Novel Electron-Rich Interface for Efficient CO2 Reduction.

Bi2MoO6 quantum dots (BM QDs, 5 nm in diameter) are evenly in situ grown on reduced graphene oxide (rGO) layers, sensitizing the graphene with high visible light response and activity for efficient solar light-driven CO2 reduction. Under irradiation, small-sized BM QDs generate active electrons and donate them to the rGO layers. Since the formation of BM QDs and the reduction of GO are undergone simultaneously, a close connection between BM QDs and rGO enables the electron injection from excited Bi2MoO6 QDs to graphene scaffolds, and abundant electrons accommodated by the rGO layers offer an electron-rich interface for CO2 reduction. With the benefit of the improved electron extraction and transport over the BM QDs/rGO interface, 84.8 µmol g-1 of methanol and 57.5 µmol g-1 of ethanol are achieved on BM QDs/rGO in 4 h with optimal composition. The total output of alcohols over BM/rGO (142.3 µmol g-1) is 2.2 and 4.4 times that achieved on unmodified Bi2MoO6 QDs (64.0 µmol g-1) and flower-like Bi2MoO6 (32.2 µmol g-1), respectively.

Multicentre study of physical abuse and limb fractures in young children in the East Anglia Region, UK.

OBJECTIVE: To determine if the detection of physical abuse in young children with fractures is of uniform high standard in the East Anglia Region of the UK, and whether we can identify areas for improvement in our detection of high-risk groups. DESIGN: Multicentre retrospective 4-year study. SETTING: 7 hospitals across the East Anglia Region of Britain (East Anglia Paediatric Physical Abuse and Fractures study). PARTICIPANTS: Age groups and fractures indicated as being at higher risk for physical abuse (all children under 12 months of age, and fractures of humerus and femur in children under 36 months of age). OUTCOME MEASURES: Our criterion for physical abuse was the decision of a multiagency child protection case conference (CPCC). RESULTS: Probability of CPCC decision of physical abuse was highest in infants, ranging from 50% of fractures sustained in the first month of life (excluding obstetric injuries) to 10% at 12 months of age. Only 46%-86% of infants (under 12 months) with a fracture were assessed by a paediatrician for physical abuse after their fracture. Significant variation in the use of skeletal surveys and in CPCC decision of physical abuse was noted in children attending different hospitals. CONCLUSIONS: It is a concern that significant variation between hospitals was found in the investigation and detection of physical abuse as confirmed by CPCC decisions. To minimise failure to detect true cases of physical abuse, we recommend that all high-risk children should be assessed by a paediatrician prior to discharge from the emergency department. Our proposed criteria for assessment (where we found probability of CPCC decision of physical abuse was at least 10%) are any child under the age of 12 months with any fracture, under 18 months of age with femur fracture and under 24 months with humeral shaft fracture (not supracondylar).

Development of a Prognostic Model That Predicts Survival After Pancreaticoduodenectomy for Ampullary Cancer.

OBJECTIVES: The aims of this study were to (i) identify independent predictors of survival after pancreaticoduodenectomy for ampullary cancer and (ii) develop a prognostic model of survival. METHODS: Data were analyzed retrospectively on 110 consecutive patients who underwent pancreaticoduodenectomy between 2002 and 2013. Subjects were categorized into 3 nodal subgroups as per the recently proposed nodal subclassification: N0 (node negative), N1 (1-2 metastatic nodes), or N2 (≥3 metastatic nodes). Clinicopathological features and overall survival were compared by Kaplan-Meier and Cox regression analyses. RESULTS: The overall 1-, 3-, and 5-year survival rates were 79.8%, 42.2%, and 34.9%, respectively. The overall 1-, 3-, and 5-year survival rates for the N0 group were 85.2%, 71.9%, and 67.4%, respectively. The 1-, 3-, 5-year survival rates for the N1 and N2 subgroups were 81.5%, 49.4%, and 49.4% and 75%, 19.2%, and 6.4%, respectively (log rank, P < 0.0001). After performing a multivariate Cox regression analysis, vascular invasion and lymph node ratio were the only independent predictors of survival. Hence, a prediction model of survival was constructed based on those 2 variables. CONCLUSIONS: Using data from a carefully selected cohort of patients, we created a pilot prognostic model of postresectional survival. The proposed model may help clinicians to guide treatments in the adjuvant setting.