Correction: High-resolution magic-angle spinning NMR metabolic profiling with spatially localized spectroscopy under slow sample spinning.

Correction for 'High-resolution magic-angle spinning NMR metabolic profiling with spatially localized spectroscopy under slow sample spinning' by Alan Wong, Anal. Methods, 2023, 15, 6302-6308, https://doi.org/10.1039/D3AY01812A.

Cardiovascular manifestations of Erdheim-Chester disease: A narrative review with two cases.

Erdheim-Chester disease (ECD) is a rare 'L' (Langerhans) group histiocytic neoplasm that affects a multitude of organ systems, causing osteosclerotic bone lesions, periaortic encasement ('coated' aorta), retroperitoneal fibrosis involving kidneys and ureters ('hairy kidney'), and infiltration of the central nervous system. Cardiovascular involvement can occur in up to 70% of patients and is usually found during computed tomography/magnetic resonance imaging evaluation. When present, cardiovascular symptoms can have wide variability in presentation from asymptomatic to pericarditis, fatal cardiac tamponade, myocardial infarction, conduction abnormalities, heart failure, renal artery stenosis, and claudication. Cardiac involvement found on imaging includes right atrial pseudotumor, right atrioventricular groove infiltration, and pericardial effusions. ECD can involve the large- and medium-sized arteries, often seen as periarterial thickening (commonly coating the aorta) with stenosis/occlusion. Although more cardiovascular ECD cases have begun to be published in the literature, more data are needed on the outcomes of these patients, as well as how cardiovascular manifestations respond to treatment of ECD.

Accurate top protein variant discovery via low-N pick-and-validate machine learning.

A strategy to obtain the greatest number of best-performing variants with least amount of experimental effort over the vast combinatorial mutational landscape would have enormous utility in boosting resource producibility for protein engineering. Toward this goal, we present a simple and effective machine learning-based strategy that outperforms other state-of-the-art methods. Our strategy integrates zero-shot prediction and multi-round sampling to direct active learning via experimenting with only a few predicted top variants. We find that four rounds of low-N pick-and-validate sampling of 12 variants for machine learning yielded the best accuracy of up to 92.6% in selecting the true top 1% variants in combinatorial mutant libraries, whereas two rounds of 24 variants can also be used. We demonstrate our strategy in successfully discovering high-performance protein variants from diverse families including the CRISPR-based genome editors, supporting its generalizable application for solving protein engineering tasks. A record of this paper's transparent peer review process is included in the supplemental information.

Folate depletion induces erythroid differentiation through perturbation of de novo purine synthesis.

Folate, an essential vitamin, is a one-carbon acceptor and donor in key metabolic reactions. Erythroid cells harbor a unique sensitivity to folate deprivation, as revealed by the primary pathological manifestation of nutritional folate deprivation: megaloblastic anemia. To study this metabolic sensitivity, we applied mild folate depletion to human and mouse erythroid cell lines and primary murine erythroid progenitors. We show that folate depletion induces early blockade of purine synthesis and accumulation of the purine synthesis intermediate and signaling molecule, 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR), followed by enhanced heme metabolism, hemoglobin synthesis, and erythroid differentiation. This is phenocopied by inhibition of folate metabolism using the inhibitor SHIN1, and by AICAR supplementation. Mechanistically, the metabolically driven differentiation is independent of mechanistic target of rapamycin complex 1 (mTORC1) and adenosine 5'-monophosphate-activated protein kinase (AMPK) and is instead mediated by protein kinase C. Our findings suggest that folate deprivation-induced premature differentiation of erythroid progenitor cells is a molecular etiology to folate deficiency-induced anemia.

Regulation of mast cells by overlapping but distinct protein interactions of Siglec-6 and Siglec-8.

BACKGROUND: Sialic acid-binding immunoglobulin-like lectin (Siglec)-6 and Siglec-8 are closely related mast cell (MC) receptors with broad inhibitory activity, but whose functional differences are incompletely understood. METHODS: Proteomic profiling using quantitative mass spectrometry was performed on primary mouse MCs to identify proteins associated with Siglec-6 and Siglec-8. For functional characterization, each receptor was evaluated biochemically and in ex vivo and in vivo inhibition models of IgE and non-IgE-mediated MC activation in Siglec-6- or Siglec-8-expressing transgenic mice. RESULTS: Siglec-6 and Siglec-8 were found in MCs within large complexes, interacting with 66 and 86 proteins, respectively. Strikingly, Siglec-6 and Siglec-8 interacted with a large cluster of proteins involved in IgE and non-IgE-mediated MC activation, including the high affinity IgE receptor, stem cell factor (SCF) receptor KIT/CD117, IL-4 and IL-33 receptors, and intracellular kinases LYN and JAK1. Protein interaction networks revealed Siglec-6 and Siglec-8 had overlapping yet distinct MC functions, with a potentially broader regulatory role for Siglec-6. Indeed, Siglec-6 preferentially interacted with the mature form of KIT at the cell surface, and treatment with an anti-Siglec-6 antibody significantly inhibited SCF-mediated MC activation more in comparison to targeting Siglec-8. CONCLUSION: These data demonstrate a central role for Siglec-6 and Siglec-8 in controlling MC activation through interactions with multiple activating receptors and key signaling molecules. Our findings suggest that Siglec-6 has a role distinct from that of Siglec-8 in regulating MC function and represents a distinct potential therapeutic target in mast cell-driven diseases.

High-resolution magic-angle spinning NMR metabolic profiling with spatially localized spectroscopy under slow sample spinning.

Owing to its feasibility and versatility, High-Resolution Magic-Angle Spinning (HRMAS) NMR spectroscopy is considered an essential analytical technique in metabolomics for assessing the biochemical composition of tissue samples. Localized profiling with HRMAS has recently emerged and shown promise for spatial resolution of metabolic profiles within the sampling tissues. However, the requisite sample spinning in a few kHz can perturb the tissues spatially and morphologically. This study explored a simple approach to slow sample spinning experiments at 500 Hz without needing pulse-assist sideband suppression experiments to acquire localized spectral data. Slow-spinning localized one-and two-dimensional spectroscopy, including Total Correlation Spectroscopy (TOCSY), were explored on soft tissues for metabolic profiling. We also examined inhomogeneous radiofrequency B1 field distribution across the sampling volume, which can affect the quantification analysis.

High-throughput screening of genetic and cellular drivers of syncytium formation induced by the spike protein of SARS-CoV-2.

Mapping mutations and discovering cellular determinants that cause the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to induce infected cells to form syncytia would facilitate the development of strategies for blocking the formation of such cell-cell fusion. Here we describe high-throughput screening methods based on droplet microfluidics and the size-exclusion selection of syncytia, coupled with large-scale mutagenesis and genome-wide knockout screening via clustered regularly interspaced short palindromic repeats (CRISPR), for the large-scale identification of determinants of cell-cell fusion. We used the methods to perform deep mutational scans in spike-presenting cells to pinpoint mutable syncytium-enhancing substitutions in two regions of the spike protein (the fusion peptide proximal region and the furin-cleavage site). We also used a genome-wide CRISPR screen in cells expressing the receptor angiotensin-converting enzyme 2 to identify inhibitors of clathrin-mediated endocytosis that impede syncytium formation, which we validated in hamsters infected with SARS-CoV-2. Finding genetic and cellular determinants of the formation of syncytia may reveal insights into the physiological and pathological consequences of cell-cell fusion.

Discovery of regulatory motifs in 5' untranslated regions using interpretable multi-task learning models.

The sequence in the 5' untranslated regions (UTRs) is known to affect mRNA translation rates. However, the underlying regulatory grammar remains elusive. Here, we propose MTtrans, a multi-task translation rate predictor capable of learning common sequence patterns from datasets across various experimental techniques. The core premise is that common motifs are more likely to be genuinely involved in translation control. MTtrans outperforms existing methods in both accuracy and the ability to capture transferable motifs across species, highlighting its strength in identifying evolutionarily conserved sequence motifs. Our independent fluorescence-activated cell sorting coupled with deep sequencing (FACS-seq) experiment validates the impact of most motifs identified by MTtrans. Additionally, we introduce "GRU-rewiring," a technique to interpret the hidden states of the recurrent units. Gated recurrent unit (GRU)-rewiring allows us to identify regulatory element-enriched positions and examine the local effects of 5' UTR mutations. MTtrans is a powerful tool for deciphering the translation regulatory motifs.

Guideline-based and restricted fluid resuscitation strategy in sepsis patients with heart failure: A systematic review and meta-analysis.

OBJECTIVES: To examine whether a fluid resuscitation strategy based on guidelines (at least 30 mL/kg IV crystalloids) vs. a restrictive approach with <30 mL/kg within three hours affects in-hospital mortality in patients with sepsis and a history of heart failure (HF). DATA SOURCES: On 03/07/2023, we searched Embase, PubMed, and Scopus for peer-reviewed papers and abstracts using the PRISMA guidelines. STUDY SELECTION: The language was limited to English. Studies published since 2016 included if they had sepsis patients with a history of HF, or a subgroup of patients with HF, and in-hospital mortality data on these patients that did or did not meet the 30 mL/kg by 3 h (30 × 3) goal. Duplicate studies, studies that focused on a broader period than 3 h from the diagnosis of sepsis or without mortality breakdown for HF patients or with unrelated title/abstract, or without an IRB approval were excluded. DATA EXTRACTION: In-hospital mortality data was taken from the final studies for HF patients with sepsis who did or did not meet the 30 × 3 goal. DATA SYNTHESIS: The meta-analysis was performed using the Review Manager 5.4 program with ORs as the effect measure. The ProMeta program version 3.0 was used to evaluate the publication bias. Egger's linear regression and Berg and Mazumdar's rank correlation was used to evaluate the publication bias. The result was visually represented by a funnel plot. To estimate the proportion of variance attributable to heterogeneity, the I2 statistic was calculated. RESULTS: The search yielded 26,069 records, which were narrowed down to 4 studies. Compared to those who met the 30 × 3 goal, the <30 × 3 group had a significantly higher risk of in-hospital mortality (OR = 1.81, 95% CI = 1.13-2.89, P = 0.01). CONCLUSIONS: Restrictive fluid resuscitation increased the risk of in-hospital mortality in HF patients with sepsis. More rigorous research is required to determine the optimal fluid resuscitation strategy for this population.

Predicting Degradation Mechanisms in Lithium Bistriflimide "Water-In-Salt" Electrolytes For Aqueous Batteries.

Aqueous solutions are crucial to most domains in biology and chemistry, including in energy fields such as catalysis and batteries. Water-in-salt electrolytes (WISEs), which extend the stability of aqueous electrolytes in rechargeable batteries, are one example. While the hype for WISEs is huge, commercial WISE-based rechargeable batteries are still far from reality, and there remain several fundamental knowledge gaps such as those related to their long-term reactivity and stability. Here, we propose a comprehensive approach to accelerating the study of WISE reactivity by using radiolysis to exacerbate the degradation mechanisms of concentrated LiTFSI-based aqueous solutions. We find that the nature of the degradation species depends strongly on the molality of the electrolye, with degradation routes driven by the water or the anion at low or high molalities, respectively. The main aging products are consistent with those observed by electrochemical cycling, yet radiolysis also reveals minor degradation species, providing a unique glimpse of the long-term (un)stability of these electrolytes.

Parallel engineering and activity profiling of a base editor system.

Selecting the most suitable existing base editors and engineering new variants for installing specific base conversions with maximal efficiency and minimal undesired edits are pivotal for precise genome editing applications. Here, we present a platform for creating and analyzing a library of engineered base editor variants to enable head-to-head evaluation of their editing performance at scale. Our comprehensive comparison provides quantitative measures on each variant's editing efficiency, purity, motif preference, and bias in generating single and multiple base conversions, while uncovering undesired higher indel generation rate and noncanonical base conversion for some of the existing base editors. In addition to engineering the base editor protein, we further applied this platform to investigate a hitherto underexplored engineering route and created guide RNA scaffold variants that augment the editor's base-editing activity. With the unknown performance and compatibility of the growing number of engineered parts including deaminase, CRISPR-Cas enzyme, and guide RNA scaffold variants for assembling the expanding collection of base editor systems, our platform addresses the unmet need for an unbiased, scalable method to benchmark their editing outcomes and accelerate the engineering of next-generation precise genome editors.

Selective processing in attention and memory in schizophrenia: A meta-analysis of the negative priming effect.

Individuals with schizophrenia show impairments in a variety of selective attention tasks. Research on the negative priming (NP) effect in schizophrenia has yielded mixed evidence. This meta-analysis aimed to examine the NP effect exhibited by patients with schizophrenia and the impact of study methodology on findings. The methods and reporting of this meta-analysis followed the PRISMA guideline. Eligible studies were identified through primary literature search in MEDLINE, PsycInfo, PsycArticles, and Embase and secondary search based on included studies and important reviews. Three-level random effects-models were used to summarize between-group differences in the raw NP score, as well as the NP ratio and baseline reaction time (RT) as secondary outcomes. We identified 1383 studies published between 1966 and 2022 and reviewed 27 studies that consist of 627 patients with schizophrenia and 653 controls in total. Compared to healthy controls, patients with schizophrenia showed a mildly reduced raw NP score with marginal significance, Hedges' g = -0.16, 95% confidence interval (CI) -0.35 to 0.02, p = 0.084. However, analysis of a subsample of studies indicated a significant, moderate reduction in the NP ratio among patients, g = -0.52, 95% CI -0.91 to -0.14; p = 0.014. Moderator analyses revealed a longer illness duration as predictive of a more reduced NP effect. This meta-analysis lends tentative evidence to impaired attention or memory process as measured by the NP task in schizophrenia. More research is needed to substantiate our results and clarify the impact of study design and patient characteristics on findings.

Cycloguanil and Analogues Potently Target DHFR in Cancer Cells to Elicit Anti-Cancer Activity.

Dihydrofolate reductase (DHFR) is an established anti-cancer drug target whose inhibition disrupts folate metabolism and STAT3-dependent gene expression. Cycloguanil was proposed as a DHFR inhibitor in the 1950s and is the active metabolite of clinically approved plasmodium DHFR inhibitor Proguanil. The Cycloguanil scaffold was explored to generate potential cancer therapies in the 1970s. Herein, current computational and chemical biology techniques were employed to re-investigate the anti-cancer activity of Cycloguanil and related compounds. In silico modeling was employed to identify promising Cycloguanil analogues from NCI databases, which were cross-referenced with NCI-60 Human Tumor Cell Line Screening data. Using target engagement assays, it was found that these compounds engage DHFR in cells at sub-nanomolar concentrations; however, growth impairments were not observed until higher concentrations. Folinic acid treatment rescues the viability impairments induced by some, but not all, Cycloguanil analogues, suggesting these compounds may have additional targets. Cycloguanil and its most promising analogue, NSC127159, induced similar metabolite profiles compared to established DHFR inhibitors Methotrexate and Pyrimethamine while also blocking downstream signaling, including STAT3 transcriptional activity. These data confirm that Cycloguanil and its analogues are potent inhibitors of human DHFR, and their anti-cancer activity may be worth further investigation.

An early perceptual locus of absolute pitch.

Absolute pitch (AP) refers to the naming of musical tone without external reference. The influential two-component model states that AP is limited by the late-emerging pitch labeling process only and not the earlier perceptual and memory processes. Over the years, however, support for this model at the neural level has been mixed with various methodological limitations. Here, the electroencephalography responses of 27 AP possessors and 27 non-AP possessors were recorded. During both name verification and passive listening, event-related potential analyses showed a difference between AP and non-AP possessors at about 200 ms in their response toward tones compared with noise stimuli. Multivariate pattern analyses suggested that pitch naming was subserved by a series of transient processes for the first 250 ms, followed by a stage-like process for both AP and non-AP possessors with no group differences between them. These findings are inconsistent with the predictions of the two-component model, and instead suggest the existence of an early perceptual locus of AP.

Are there associations between daily multitasking experience and multitasking performance?

Research showed mixed findings regarding the relationships between daily multitasking experience and laboratory multitasking performance. One measurement issue was the low reliability and validity of using a single measurement for daily multitasking experience. Another measurement issue was the popular use of simple laboratory paradigms that may or may not capture well cognitive processes underlying real-life multitasking. The current study revisited the relationship between daily multitasking experience and multitasking performance with a better design. Multiple measurements were used to ensure good reliability and validity. This included a mobile phone task switching measurement-an arguably better proxy for daily multitasking experience and three realistic multitasking paradigms that mimic real life multitasking situations. The results showed that (1) phone switching was not significantly associated with the media multitasking index, suggesting that they were measuring different aspects of multitasking experience; (2) indicators of the multitasking performance were moderately correlated among themselves, suggesting that different realistic multitasking paradigms were measuring overlapping multitasking abilities; and, intriguingly, (3) no significant association between multitasking experience and performance indicators was found. One possibility is that people can only benefit from daily multitasking practice when they engaged in daily multitasking activities with an intention to improve the performance. Other possibilities and implications were also discussed.

A roadmap to high-resolution standard microcoil MAS NMR spectroscopy for metabolomics.

Current microcoil probe technology has emerged as a significant advancement in NMR applications to biofluids research. It has continued to excel as a hyphenated tool with other prominent microdevices, opening many new possibilities in multiple omics fields. However, this does not hold for biological samples such as intact tissue or organisms, due to the considerable challenges of incorporating the microcoil in a magic-angle spinning (MAS) probe without relinquishing the high-resolution spectral data. Not until 2012 did a microcoil MAS probe show promise in profiling the metabolome in a submilligram tissue biopsy with spectral resolution on par with conventional high-resolution MAS (HR-MAS) NMR. This result subsequently triggered a great interest in the possibility of NMR analysis with microgram tissues and striving toward the probe development of "high-resolution" capable microcoil MAS NMR spectroscopy. This review gives an overview of the issues and challenges in the probe development and summarizes the advancements toward metabolomics.

Discovery of an agonistic Siglec-6 antibody that inhibits and reduces human mast cells.

Mast cells (MC) are key drivers of allergic and inflammatory diseases. Sialic acid-binding immunoglobulin-like lectin (Siglec)-6 is an immunoregulatory receptor found on MCs. While it is recognized that engaging Siglecs with antibodies mediates inhibition across immune cells, the mechanisms that govern this agonism are not understood. Here we generated Siglec-6 mAb clones (AK01 to AK18) to better understand Siglec-6-mediated agonism. Siglec-6 mAbs displayed epitope-dependent receptor internalization and inhibitory activity. We identified a Siglec-6 mAb (AK04) that required Fc-mediated interaction for receptor internalization and induced inhibition and antibody-dependent cellular phagocytosis against MCs. AK04-mediated MC inhibition required Siglec-6 immunoreceptor tyrosine-based inhibitory motif (ITIM) and ITIM-like domains and was associated with receptor cluster formation containing inhibitory phosphatases. Treatment of humanized mice with AK04 inhibited systemic anaphylaxis with a single dose and reduced MCs with chronic dosing. Our findings suggest Siglec-6 activity is epitope dependent and highlight an agonistic Siglec-6 mAb as a potential therapeutic approach in allergic disease.