Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression.

Alternative polyadenylation (APA) is a major mechanism of post-transcriptional regulation in various cellular processes including cell proliferation and differentiation, but the APA heterogeneity among single cells remains largely unknown. Single-cell RNA sequencing (scRNA-seq) has been extensively used to define cell subpopulations at the transcription level. Yet, most scRNA-seq data have not been analyzed in an "APA-aware" manner. Here, we introduce dynamic analysis of APA from single-cell RNA-seq (scDaPars), a bioinformatics algorithm to accurately quantify APA events at both single-cell and single-gene resolution using either 3'-end (10x Chromium) or full-length (Smart-seq2) scRNA-seq data. Validations in both real and simulated data indicate that scDaPars can robustly recover missing APA events caused by the low amounts of mRNA sequenced in single cells. When applied to cancer and human endoderm differentiation data, scDaPars not only revealed cell-type-specific APA regulation but also identified cell subpopulations that are otherwise invisible to conventional gene expression analysis. Thus, scDaPars will enable us to understand cellular heterogeneity at the post-transcriptional APA level.

Subclinical cardiac impairments in fetuses conceived through assisted reproductive technology by speckle tracking echocardiography.

OBJECTIVES: To evaluate the changes of cardiac morphology and function in fetuses conceived through assisted reproductive technologies (ART) by speckle tracking echocardiography. METHODS: A retrospective study was conducted in 101 spontaneously conceived (SC) fetuses and 99 ART-conceived ones. Fetal echocardiography was performed, fetal cardiac morphology and function were analyzed using two-dimensional speckle tracking software, including global sphericity index (GSI), global longitudinal strain (GLS), fractional area change (FAC) of the left and right ventricles, as well as segmental sphericity index (SI), end-diastolic diameter (ED), and fractional shortening (FS) in 24 segments. RESULTS: Compared to the SC fetuses, the ART-conceived fetuses exhibited decreased GSI (median [interquartile range], 1.22 [1.16-1.27] vs. 1.18 [1.11-1.24], p=0.007), decreased right ventricular GLS (24.9 [21.5-27.6] vs. 23.2 [20.4-26.8], p=0.026), and decreased right ventricular FAC (mean ± standard deviation, 39.7 ± 6.4 vs. 37.2 ± 7.1, p=0.003). Analysis of the 24 segments showed that ART-conceived fetuses had reduced SI in the apical segments of right ventricle and increased ED in several segments of the right ventricle. CONCLUSIONS: Fetuses conceived through ART had a more spherical shape of the global heart and predominantly right-sided cardiac remodeling and systolic function impairment.

Ultrasound evaluation of the cardiovascular system in offspring conceived through assisted reproductive technology.

With the widespread application of assisted reproductive technology, the health issues of offspring conceived through assisted reproductive technology have also received increasing attention. Animal experiments and clinical studies have found subclinical adverse changes in the cardiovascular system of assisted reproductive offspring. Assisted reproductive technology itself may be just one of the many factors contributing to this phenomenon, with epigenetics playing an important role. Ultrasound technology can be used to assess the morphological structure and function of the cardiovascular system in assisted reproductive offspring from the fetal stage, providing the possibility to study the potential cardiovascular damage in this large population. This review aims to explore the effects and mechanisms of assisted reproductive technology on the cardiovascular system of offspring and provide a review of the research progress in ultrasound technology in this area.

NUDT21 alters glioma migration through differential alternative polyadenylation of LAMC1.

PURPOSE: Gliomas and their surrounding microenvironment constantly interact to promote tumorigenicity, yet the underlying posttranscriptional regulatory mechanisms that govern this interplay are poorly understood. METHODS: Utilizing our established PAC-seq approach and PolyAMiner bioinformatic analysis pipeline, we deciphered the NUDT21-mediated differential APA dynamics in glioma cells. RESULTS: We identified LAMC1 as a critical NUDT21 alternative polyadenylation (APA) target, common in several core glioma-driving signaling pathways. qRT-PCR analysis confirmed that NUDT21-knockdown in glioma cells results in the preferred usage of the proximal polyA signal (PAS) of LAMC1. Functional studies revealed that NUDT21-knockdown-induced 3'UTR shortening of LAMC1 is sufficient to cause translational gain, as LAMC1 protein is upregulated in these cells compared to their respective controls. We demonstrate that 3'UTR shortening of LAMC1 after NUDT21 knockdown removes binding sites for miR-124/506, thereby relieving potent miRNA-based repression of LAMC1 expression. Remarkably, we report that the knockdown of NUDT21 significantly promoted glioma cell migration and that co-depletion of LAMC1 with NUDT21 abolished this effect. Lastly, we observed that LAMC1 3'UTR shortening predicts poor prognosis of low-grade glioma patients from The Cancer Genome Atlas. CONCLUSION: This study identifies NUDT21 as a core alternative polyadenylation factor that regulates the tumor microenvironment through differential APA and loss of miR-124/506 inhibition of LAMC1. Knockdown of NUDT21 in GBM cells mediates 3'UTR shortening of LAMC1, contributing to an increase in LAMC1, increased glioma cell migration/invasion, and a poor prognosis.

Ab initio theory of noble gas atoms in bcc transition metals.

Systematic ab initio calculations based on density functional theory have been performed to gain fundamental understanding of the interactions between noble gas atoms (He, Ne, Ar and Kr) and bcc transition metals in groups 5B (V, Nb and Ta), 6B (Cr, Mo and W) and 8B (Fe). Our charge density analysis indicates that the strong polarization of nearest-neighbor metal atoms by noble gas interstitials is the electronic origin of their high formation energies. Such polarization becomes more significant with an increasing gas atom size and interstitial charge density in the host bcc metal, which explains the similar trend followed by the unrelaxed formation energies of noble gas interstitials. Upon allowing for local relaxation, nearby metal atoms move farther away from gas interstitials in order to decrease polarization, albeit at the expense of increasing the elastic strain energy. Such atomic relaxation is found to play an important role in governing both the energetics and site preference of noble gas atoms in bcc metals. Our most notable finding is that the fully relaxed formation energies of noble gas interstitials are strongly correlated with the elastic shear modulus of the bcc metal, and the physical origin of this unexpected correlation has been elucidated by our theoretical analysis based on the effective-medium theory. The kinetic behavior of noble gas atoms and their interaction with pre-existing vacancies in bcc transition metals have also been discussed in this work.

Monte Carlo simulation of magnetic domain structure and magnetic properties near the morphotropic phase boundary.

The morphotropic phase boundary (MPB), which is the boundary separating a tetragonal phase from a rhombohedral phase by varying the composition or mechanical pressure in ferroelectrics, has been studied extensively for decades because it can lead to strong enhancement of piezoelectricity. Recently, a parallel ferromagnetic MPB was experimentally reported in the TbCo2-DyCo2 ferromagnetic system and this discovery proposes a new way to develop potential materials with giant magnetostriction. However, the role of magnetic domain switching and spin reorientation near the MPB region is still unclear. For the first time, we combine micromagnetic theory with Monte Carlo simulation to investigate the evolution of magnetic domain structures and the corresponding magnetization properties near the MPB region. It is demonstrated that the magnetic domain structure and the corresponding magnetization properties are determined by the interplay among anisotropy energy, magnetostatic energy and exchange energy. If the anisotropy energy barrier is large compared with the magnetostatic energy barrier and the exchange energy barrier, the MPB region is a T and R mixed structure and magnetic domain switching is the dominant mechanism. If the anisotropy energy barrier is small, the MPB region will also contain M phases and spin reorientation is the dominant mechanism. Our work could provide a guide for the design of advanced ferromagnetic materials with enhanced magnetostriction.

Neck Computed Tomography Measurements Associated With Cardiovascular Risk Factors.

Introduction Neck adiposity has been related to cardiovascular risk in healthy and nonhealthy individuals. Our objective was to evaluate the utility of anatomic neck measurements extracted from computed tomography (CT) examinations as a predictor of cardiovascular disease and its risk factors. Methods We investigated patients who had a CT neck examination with intravenous contrast performed at two hospitals between 2013 and 2020. Patients with a neck malignancy, prior neck surgery, age <18 years, incomplete demographic information, and inadequate image quality were excluded. We performed 18 separate measurements of neck anatomy which were correlated with cardiovascular risk factors and disease, as well as relevant lab values and medications. All multivariable linear regressions were controlled for gender and BMI. Associations with p<0.05 were considered statistically significant. The measurements were then used to predict hypertension using random forest, a non-linear prediction algorithm. Results Approximately 20,000 neck CT examinations with contrast were performed between 2013-2020. After applying the inclusion criteria, 458 patients remained in the study population. Eight measurements (all of which include a component of neck adiposity) showed a statistically significant association between anatomic measurements and cardiovascular risk factors. The risk factor most often associated with increases in CT measurements was type 2 diabetes. Accordingly, patients on insulin treatment had a significantly higher average for all eight measurements. Significant measurement increases were also found in those previously diagnosed with hyperlipidemia and in those being treated with hypertension medications. The area under the receiver operating characteristic (AUROC) value of the random forest prediction algorithm was 0.68, meaning our measurements were a good predictor of hypertensive disease status. Conclusion Adipose tissue measurements extracted from CT examinations of the neck are associated with cardiovascular risk factors including hypertension, diabetes, and hyperlipidemia. Machine learning models of anatomic neck measurements can potentially identify patients at risk for cardiovascular disease.

Improvements of myocardial strain and work in diabetes patients with normal ejection fraction after empagliflozin treatment.

AIMS/INTRODUCTION: To assess the effect of empagliflozin treatment on left ventricular (LV), right ventricular (RV) and left atrial (LA) functions in diabetes patients with normal ejection fraction. MATERIALS AND METHODS: The study included a total of 128 diabetes patients with multiple cardiovascular risk factors who were subjected to a 6-month follow up from the initiation of empagliflozin treatment. Before and after treatment with empagliflozin, LV, RV and LA strain, and noninvasive myocardial work parameters were evaluated by speckle tracking echocardiography. RESULTS: In 128 diabetes patients (mean age 56 ± 8 years, 85 men) with multiple cardiovascular risk factors, myocardial strain and work parameters were impaired, despite the absence of significant clinical symptoms of heart failure. After 6-month treatment with empagliflozin, the absolute value of LV strain in all directions increased, represented by LV global longitudinal strain (-18.0 ± 1.7% to -19.2 ± 1.7% [mean ± SD]). The same trend in LV global work efficiency (93 [91-94] % to 94 [93-95] % [median (IQR)]), RV free-wall longitudinal strain (-24.0 ± 2.7% to -25.0 ± 2.8%), LA reservoir (31 ± 5% to 34 ± 5%) and conduit strain (-14 ± 4% to -16 ± 4%) was also observed. LV mass index (106.9 ± 16.8-103.6 ± 16.4 g/m2) and LV global wasted work (143 [111-185] mmHg% to 108 [88-141] mmHg%) decreased after treatment (P < 0.05 for all). LV volume and LA volume index remained unchanged after treatment. In the multivariable analysis, the change in LA reservoir strain (ß = 0.050, P = 0.035) and baseline global longitudinal strain (ß = -0.488, P < 0.001) were independent predictors of improvement in LV global longitudinal strain. CONCLUSIONS: This study suggests that 6-month treatment with empagliflozin improved LV, RV and LA functions in diabetes patients with normal ejection fraction.

Isthmin-1 Improves Aging-Related Cardiac Dysfunction in Mice through Enhancing Glycolysis and SIRT1 Deacetylase Activity.

Aging-related cardiac dysfunction poses a major risk factor of mortality for elderly populations, however, efficient treatment for aging-related cardiac dysfunction is far from being known. Isthmin-1 (ISM1) is a novel adipokine that promotes glucose uptake and acts indispensable roles in restraining inflammatory and fibrosis. The present study aims to investigate the potential role and molecular mechanism of ISM1 in aging-related cardiac dysfunction. Aged and matched young mice were overexpressed or silenced with ISM1 to investigate the role of ISM1 in aging-related cardiac dysfunction. Moreover, H9C2 cells were stimulated with D-galactose (D-gal) to examine the role of ISM1 in vitro. Herein, we found that cardiac-specific overexpression of ISM1 significantly mitigated insulin resistance by promoting glucose uptake in aging mice. ISM1 overexpression alleviated while ISM1 silencing deteriorated cellular senescence, cardiac inflammation, and dysfunction in natural and accelerated cardiac aging. Mechanistically, ISM1 promoted glycolysis and activated Sirtuin-1 (SIRT1) through increasing glucose uptake. ISM1 increased glucose uptake via translocating GLUT4 to the surface, thereby enhancing glycolytic flux and hexosamine biosynthetic pathway (HBP) flux, ultimately leading to increased SIRT1 activity through O-GlcNAc modification. ISM1 may serve as a novel potential therapeutic target for preventing aging-related cardiac disease in elderly populations. ISM1 prevents aging-related cardiac dysfunction by promoting glycolysis and enhancing SIRT1 deacetylase activity, making it a promising therapeutic target for aging-related cardiac disease.

Relative apical sparing obtained with speckle tracking echocardiography is not a sensitive parameter for diagnosing light-chain cardiac amyloidosis.

Background: Distinguishing light-chain cardiac amyloidosis (AL CA) from left ventricular wall thickening (LVWT) resulted from other etiologies has proven to be challenging. This study aimed to determine the sensitivity and specificity of relative apical sparing in diagnosing AL CA and investigate the differences in clinical and echocardiographic characteristics between AL CA patients with apical sparing and those with non-apical sparing. Methods: A total of 63 consecutive patients with AL CA, 102 consecutive patients with LVWT (including 51 hypertrophic cardiomyopathy (HCM) and 51 hypertension) and 33 healthy individuals were recruited retrospectively at Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology. Conventional and speckle tracking echocardiography were performed on all subjects. Results: Although wall thickening was observed in all patients, almost all functional parameters were worse in AL CA, except for relative apical longitudinal strain (LS) (P=0.906). Of 63 patients with AL CA, only 17.5% (n=11) showed an apical sparing pattern. Patients with apical sparing had poorer cardiac performance than those with non-apical sparing. Relative apical sparing showed the lowest diagnostic accuracy with an area under the curve (AUC) of 0.58 [95% confidence interval (CI): 0.49-0.67, sensitivity: 17.5%, specificity: 98.0%, P=0.095] to detect AL CA, but right ventricular strain (RVS) (AUC: 0.86, P<0.001) showed the highest among all echocardiographic parameters. When diagnosing AL CA patients with non-apical sparing, RVS continued to maintain excellent diagnostic accuracy (AUC: 0.84, P<0.001), followed by left atrial reservoir strain (LASr) (AUC: 0.77, P<0.001). Conclusions: The diagnostic value of relative apical sparing for AL CA was limited with low sensitivity. In clinical practice, the diagnosis of early AL CA patients should not solely rely on relative apical sparing.

Potential Utility of C-reactive Protein for Tuberculosis Risk Stratification Among Patients With Non-Meningitic Symptoms at HIV Diagnosis in Low- and Middle-income Countries.

Background: The World Health Organization recommends initiating same-day antiretroviral therapy (ART) while tuberculosis (TB) testing is under way for patients with non-meningitic symptoms at HIV diagnosis, though safety data are limited. C-reactive protein (CRP) testing may improve TB risk stratification in this population. Methods: In this baseline analysis of 498 adults (>18 years) with TB symptoms at HIV diagnosis who were enrolled in a trial of rapid ART initiation in Haiti, we describe test characteristics of varying CRP thresholds in the diagnosis of TB. We also assessed predictors of high CRP as a continuous variable using generalized linear models. Results: Eighty-seven (17.5%) participants were diagnosed with baseline TB. The median CRP was 33.0 mg/L (interquartile range: 5.1, 85.5) in those with TB, and 2.6 mg/L (interquartile range: 0.8, 11.7) in those without TB. As the CRP threshold increased from ≥1 mg/L to ≥10 mg/L, the positive predictive value for TB increased from 22.4% to 35.4% and negative predictive value decreased from 96.9% to 92.3%. With CRP thresholds varying from <1 to <10 mg/L, a range from 25.5% to 64.9% of the cohort would have been eligible for same-day ART and 0.8% to 5.0% would have untreated TB at ART initiation. Conclusions: CRP concentrations can be used to improve TB risk stratification, facilitating same-day decisions about ART initiation. Depending on the CRP threshold, one-quarter to two-thirds of patients could be eligible for same-day ART, with a reduction of 3- to 20-fold in the proportion with untreated TB, compared with a strategy of same-day ART while awaiting TB test results.

Potential Utility of C-reactive Protein for Tuberculosis Risk Stratification among Patients with Non-Meningitic Symptoms at HIV Diagnosis in Low- and Middle-Income Countries.

Article Summary: We assessed the association between C-reactive protein (CRP) and Mycobacterium tuberculosis (TB) diagnosis in symptomatic patients at HIV diagnosis. We found that CRP concentrations can improve tuberculosis risk stratification, facilitating decision making about whether (specific) tuberculosis testing is indicated before antiretroviral therapy initiation. Background: The World Health Organization recommends initiating same-day ART while tuberculosis testing is underway for patients with non-meningitic symptoms at HIV diagnosis, though safety data are limited. C-reactive protein (CRP) testing may improve tuberculosis risk stratification in this population. Methods: In this baseline analysis of 498 adults (>18 years) with tuberculosis symptoms at HIV diagnosis who were enrolled in a trial of rapid ART initiation in Haiti, we describe test characteristics of varying CRP thresholds in the diagnosis of TB. We also assessed predictors of high CRP (≥3 mg/dL) using generalized linear models. Results: Eighty-seven (17.5%) patients were diagnosed with baseline TB. The median CRP was 33.0 mg/L (IQR: 5.1, 85.5) in those with TB, and 2.6 mg/L (IQR: 0.8, 11.7) in those without TB. As the CRP threshold increased from ≥1 mg/L to ≥10 mg/L, the positive predictive value for TB increased from 22.4% to 35.4%, and negative predictive value decreased from 96.9% to 92.3%. With CRP thresholds varying from <1 to <10 mg/L, a range from 25.5% to 64.9% of the cohort would have been eligible for same-day ART, and 0.8% to 5.0% would have untreated TB at ART initiation. Conclusions: CRP concentrations can be used to improve TB risk stratification, facilitating same-day decisions about ART initiation. Depending on the CRP threshold, one-quarter to two-thirds of patients could be eligible for same-day ART, with a reduction of 3-fold to 20-fold in the proportion with untreated TB, compared with a strategy of same-day ART while awaiting TB test results.

Microstructure map for self-organized phase separation during film deposition.

Drastically different two-phase microstructures have been reported for alloy epitaxial films, including self-organized nanoscale concentration modulations of vertical and lateral stripes. To understand the disparity of these microstructures, we study their formation mechanisms via spinodal decomposition during film deposition with the aid of computer simulations. Based on the simulation results, a microstructure map is established that describes relationships among the morphology of self-organized two-phase microstructure, initial alloy composition, and deposition rate relative to the phase separation kinetics in the film. Depending on the deposition rate relative to the kinetics of spinodal decomposition in the film, both laterally and vertically modulated microstructures could be obtained.

Computational analysis of alternative polyadenylation from standard RNA-seq and single-cell RNA-seq data.

Alternative polyadenylation (APA) is a major mechanism of post-transcriptional regulation in various cellular processes including cell proliferation and differentiation. Since conventional APA profiling methods have not been widely adopted, global APA studies are very limited. In this chapter, we summarize current computational methods for analyzing APA in standard RNA-seq and scRNA-seq data and describe two state-of-the-art bioinformatic algorithms DaPars and scDaPars in detail. The bioinformatic pipelines for both DaPars and scDaPars are presented and the application of both algorithms are highlighted.

Good's syndrome with a relapsed bloodstream infection induced by Alcaligenes sp. after thymectomy: A case report.

Good's syndrome (GS) or thymoma-associated immunodeficiency is a rare clinical syndrome with poor prognosis. The varied and unspecified clinical manifestations of GS commonly lead to a missed or delayed diagnosis. Thus, misdiagnosis and missed diagnosis are common. The present case study reports on a patient who suffered from a relapsed bloodstream infection caused by Alcaligenes sp. 6 months after thymectomy. The patient was finally diagnosed with GS after analyzing the clinical features and detecting T-lymphocyte subsets in the peripheral blood and humoral immune function. The patient's condition improved after anti-infection treatment and supplementation with intravenous immunoglobulin. Furthermore, no infection was observed during the 1-year follow-up.

Dissociated prismatic loop punching by bubble growth in FCC metals.

Materials performance can be significantly degraded due to bubble generation. In this work, the bubble growth process is elaborated in Cu by atomistic modeling to bridge the gap of experimental observations. Upon continuous He implantation, bubble growth is accommodated first by nucleation of dislocation network from bubble surface, then formation of dissociated prismatic dislocation loop (DPDL), and final DPDL emission in [Formula: see text] directions. As the DPDL is found capable of collecting He atoms, this process is likely to assist the formation of self-organized bubble superlattice, which has been reported from experiments. Moreover, the pressurized bubble in solid state manifests the shape of an imperfect octahedron, built by Cu [Formula: see text] surfaces, consistent with experiments. These atomistic details integrating experimental work fill the gap of mechanistic understanding of athermal bubble growth in Cu. Importantly, by associating with nanoindentation testings, DPDL punching by bubble growth arguably applies to various FCC (face-centered cubic) metals such as Au, Ag, Ni, and Al.

An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability.

Genome-wide association studies have identified thousands of noncoding variants associated with human traits and diseases. However, the functional interpretation of these variants is a major challenge. Here, we constructed a multi-tissue atlas of human 3'UTR alternative polyadenylation (APA) quantitative trait loci (3'aQTLs), containing approximately 0.4 million common genetic variants associated with the APA of target genes, identified in 46 tissues isolated from 467 individuals (Genotype-Tissue Expression Project). Mechanistically, 3'aQTLs can alter poly(A) motifs, RNA secondary structure and RNA-binding protein-binding sites, leading to thousands of APA changes. Our CRISPR-based experiments indicate that such 3'aQTLs can alter APA regulation. Furthermore, we demonstrate that mapping 3'aQTLs can identify APA regulators, such as La-related protein 4. Finally, 3'aQTLs are colocalized with approximately 16.1% of trait-associated variants and are largely distinct from other QTLs, such as expression QTLs. Together, our findings show that 3'aQTLs contribute substantially to the molecular mechanisms underlying human complex traits and diseases.

Deformation pathway and defect generation in crystals: a combined group theory and graph theory description.

The generation and motion of crystalline defects during plastic deformation are critical processes that determine the mechanical properties of a crystal. The types of defect generated are not only related to the symmetry of a crystal but also associated with the symmetry-breaking process during deformation. Proposed here is a new mathematical framework to capture the intrinsic coupling between crystal symmetry and deformation-induced symmetry breaking. Using a combination of group theory and graph theory, a general approach is demonstrated for the systematic determination of the types of crystalline defect induced by plastic deformation, through the construction of a crystal deformation group and a deformation pathway graph. The types of defect generated in the deformation of a face-centered cubic crystal are analyzed through the deformation pathway graph and compared with experimental observations.

Bifurcation and Pattern Symmetry Selection in Reaction-Diffusion Systems with Kinetic Anisotropy.

Ordering and self-organization are critical in determining the dynamics of reaction-diffusion systems. Here we show a unique pattern formation mechanism, dictated by the coupling of thermodynamic instability and kinetic anisotropy. Intrinsically different from the physical origin of Turing instability and patterning, the ordered patterns we obtained are caused by the interplay of the instability from uphill diffusion, the symmetry breaking from anisotropic diffusion, and the reactions. To understand the formation of the void/gas bubble superlattices in crystals under irradiation, we establish a general theoretical framework to predict the symmetry selection of superlattice structures associated with anisotropic diffusion. Through analytical study and phase field simulations, we found that the symmetry of a superlattice is determined by the coupling of diffusion anisotropy and the reaction rate, which indicates a new type of bifurcation phenomenon. Our discovery suggests a means for designing target experiments to tailor different microstructural patterns.

Grand-potential-based phase-field model for multiple phases, grains, and chemical components.

Grand-potential-based phase-field model for multiple phases, grains, and chemical components is derived from a grand-potential functional. Due to the grand-potential formulation, the chemical energy does not contribute to the interfacial energy between phases, simplifying parametrization and decoupling interface thickness from interfacial energy, which can potentially allow increased interface thicknesses and therefore improved computational efficiency. Two-phase interfaces are stable with respect to the formation of additional phases, simplifying implementation and allowing the variational form of the evolution equations to be used. Additionally, we show that grand-potential-based phase-field models are capable of simulating phase separation, and we derive conditions under which this is possible.