Single-cell RNA sequencing (scRNA-seq) has enabled researchers to study gene expression at a cellular resolution. However, noise due to amplification and dropout may obstruct analyses, so scalable ...denoising methods for increasingly large but sparse scRNA-seq data are needed. We propose a deep count autoencoder network (DCA) to denoise scRNA-seq datasets. DCA takes the count distribution, overdispersion and sparsity of the data into account using a negative binomial noise model with or without zero-inflation, and nonlinear gene-gene dependencies are captured. Our method scales linearly with the number of cells and can, therefore, be applied to datasets of millions of cells. We demonstrate that DCA denoising improves a diverse set of typical scRNA-seq data analyses using simulated and real datasets. DCA outperforms existing methods for data imputation in quality and speed, enhancing biological discovery.
CRISPR-guided DNA cytosine and adenine base editors are widely used for many applications
but primarily create DNA base transitions (that is, pyrimidine-to-pyrimidine or purine-to-purine). Here we ...describe the engineering of two base editor architectures that can efficiently induce targeted C-to-G base transversions, with reduced levels of unwanted C-to-W (W = A or T) and indel mutations. One of these C-to-G base editors (CGBE1), consists of an RNA-guided Cas9 nickase, an Escherichia coli-derived uracil DNA N-glycosylase (eUNG) and a rat APOBEC1 cytidine deaminase variant (R33A) previously shown to have reduced off-target RNA and DNA editing activities
. We show that CGBE1 can efficiently induce C-to-G edits, particularly in AT-rich sequence contexts in human cells. We also removed the eUNG domain to yield miniCGBE1, which reduced indel frequencies but only modestly decreased editing efficiency. CGBE1 and miniCGBE1 enable C-to-G edits and will serve as a basis for optimizing C-to-G base editors for research and therapeutic applications.
Immune-checkpoint blockade has revolutionized cancer therapy. In particular, inhibition of programmed cell death protein 1 (PD-1) has been found to be effective for the treatment of metastatic ...melanoma and other cancers. Despite a dramatic increase in progression-free survival, a large proportion of patients do not show durable responses. Therefore, predictive biomarkers of a clinical response are urgently needed. Here we used high-dimensional single-cell mass cytometry and a bioinformatics pipeline for the in-depth characterization of the immune cell subsets in the peripheral blood of patients with stage IV melanoma before and after 12 weeks of anti-PD-1 immunotherapy. During therapy, we observed a clear response to immunotherapy in the T cell compartment. However, before commencing therapy, a strong predictor of progression-free and overall survival in response to anti-PD-1 immunotherapy was the frequency of CD14
CD16
HLA-DR
monocytes. We confirmed this by conventional flow cytometry in an independent, blinded validation cohort, and we propose that the frequency of monocytes in PBMCs may serve in clinical decision support.
The circadian clock is an important timing system that controls physiological responses to abiotic stresses in plants. However, there is little information on the effects of the clock on stress ...adaptation in important crops, like barley. In addition, we do not know how osmotic stress perceived at the roots affect the shoot circadian clock. Barley genotypes, carrying natural variation at the photoperiod response and clock genes Ppd‐H1 and HvELF3, were grown under control and osmotic stress conditions to record changes in the diurnal expression of clock and stress‐response genes and in physiological traits. Variation at HvELF3 affected the expression phase and shape of clock and stress‐response genes, while variation at Ppd‐H1 only affected the expression levels of stress genes. Osmotic stress up‐regulated expression of clock and stress‐response genes and advanced their expression peaks. Clock genes controlled the expression of stress‐response genes, but had minor effects on gas exchange and leaf transpiration. This study demonstrated that osmotic stress at the barley root altered clock gene expression in the shoot and acted as a spatial input signal into the clock. Unlike in Arabidopsis, barley primary assimilation was less controlled by the clock and more responsive to environmental perturbations, such as osmotic stress.
The cytokines interleukin (IL)-4 and IL-13, signaling via the IL-4 receptor (IL-4R), orchestrate type 2 immunity to helminth infections and toxins. Activation of epithelial and myeloid cells, and a ...transient neutrophils influx initiates type 2 immune responses, which are dominated by basophils, eosinophils, mast cells, B cell immunoglobulin E production, and type 2 T helper and T follicular helper cells. Interestingly, IL-4 and IL-13 can curtail chemotaxis and several effector functions of neutrophils in mice and humans. This inhibitory role of IL-4 and IL-13 probably developed to limit tissue damage by neutrophils during type 2 immunity where a "weep and sweep" response aims at expulsion and decreased fecundity, instead of killing, of macroparasites. Here, we review when IL-4R signaling cytokines appeared during evolution relative to neutrophils and adaptive immunity. Neutrophil-like granular phagocytes were present in invertebrates throughout the bilaterian clade, but we were unable to find data on IL-4, IL-13, or their receptors in invertebrates. Conversely, vertebrates had both adaptive immunity and IL-4, IL-13, and IL-4Rs, suggesting that type 2 cytokines evolved together with adaptive immunity. Further studies are necessary to determine whether IL-4R signaling in neutrophils was established simultaneously with the appearance of adaptive immunity or later.
Calix4pyrroles are readily synthesized in one step from pyrroles and ketones. For several decades, these macrocycles have been exploited as powerful anion receptors or ligands for transition and ...rare-earth metals. In contrast, calix4pyrrolates as ligands for p-block elements were established only in 2018. The present feature article reviews these developments, together with the recent progress on s-, d-, and f-block element complexes of the calix4pyrroles. Particular focus is given on the calix4pyrrolato aluminate and the corresponding silane, both featuring square planar-coordinated p-block elements in their highest oxidation states. These unique "anti-van't-Hoff-Le-Bel" structures introduce valuable characteristics into main-group element chemistry, such as agostic interactions or ligand-to-metal charge transfer absorptions. The most vital reactivities are highlighted, which rely on properties ranging from amphoterism, redox-activity, and a small HOMO-LUMO gap up to the ability to provide a platform for additional external stimuli. Overall, these developments underscore the beneficial impact of structural constraint of p-block elements and element-ligand cooperativity to enhance the functionality of the most abundant elements in their native oxidation states.
Calix4pyrroles are a highly versatile class of ligands. This feature article highlights recent developments, with focus on the p-block elements.
Background
Spontaneous breathing is desirable in most ventilated patients. We therefore studied the influence of isoflurane versus propofol sedation on early spontaneous breathing in ventilated ...surgical intensive care patients and evaluated potential mediation by opioids and arterial carbon dioxide during the first 20 h of study sedation.
Methods
We included a single‐center subgroup of 66 patients, who participated in a large multi‐center trial assessing efficacy and safety of isoflurane sedation, with 33 patients each randomized to isoflurane or propofol sedation. Both sedatives were titrated to a sedation depth of −4 to −1 on the Richmond Agitation Sedation Scale. The primary outcome was the fraction of time during which patients breathed spontaneously.
Results
Baseline characteristics of isoflurane and propofol‐sedated patients were well balanced. There were no substantive differences in management or treatment aside from sedation, and isoflurane and propofol provided nearly identical sedation depths. The mean fraction of time spent spontaneously breathing was 82% 95% CI: 69, 90 in patients sedated with isoflurane compared to 35% 95% CI: 22, 51 in those assigned to propofol: median difference: 61% 95% CI: 14, 89, p < .001. After adjustments for sufentanil dose and arterial carbon dioxide partial pressure, patients sedated with isoflurane were twice as likely to breathe spontaneously than those sedated with propofol: adjusted risk ratio: 2.2 95%CI: 1.4, 3.3, p < .001.
Conclusions
Isoflurane compared to propofol sedation promotes early spontaneous breathing in deeply sedated ventilated intensive care patients. The benefit appears to be a direct effect isoflurane rather than being mediated by opioids or arterial carbon dioxide.
Human lungs enable efficient gas exchange and form an interface with the environment, which depends on mucosal immunity for protection against infectious agents. Tightly controlled interactions ...between structural and immune cells are required to maintain lung homeostasis. Here, we use single-cell transcriptomics to chart the cellular landscape of upper and lower airways and lung parenchyma in healthy lungs, and lower airways in asthmatic lungs. We report location-dependent airway epithelial cell states and a novel subset of tissue-resident memory T cells. In the lower airways of patients with asthma, mucous cell hyperplasia is shown to stem from a novel mucous ciliated cell state, as well as goblet cell hyperplasia. We report the presence of pathogenic effector type 2 helper T cells (T
2) in asthmatic lungs and find evidence for type 2 cytokines in maintaining the altered epithelial cell states. Unbiased analysis of cell-cell interactions identifies a shift from airway structural cell communication in healthy lungs to a T
2-dominated interactome in asthmatic lungs.
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![Calix[4]pyrroles as ligands...](http://api.summon.serialssolutions.com/2.0.0/image/issn/XR4PS5YY4K/1359-7345/small "Calix[4]pyrroles as ligands: recent progress with a focus on the emerging p-block element chemistry")
