Cell transcriptomic atlas of the non-human primate Macaca fascicularis.

Studying tissue composition and function in non-human primates (NHPs) is crucial to understand the nature of our own species. Here we present a large-scale cell transcriptomic atlas that encompasses over 1 million cells from 45 tissues of the adult NHP Macaca fascicularis. This dataset provides a vast annotated resource to study a species phylogenetically close to humans. To demonstrate the utility of the atlas, we have reconstructed the cell-cell interaction networks that drive Wnt signalling across the body, mapped the distribution of receptors and co-receptors for viruses causing human infectious diseases, and intersected our data with human genetic disease orthologues to establish potential clinical associations. Our M. fascicularis cell atlas constitutes an essential reference for future studies in humans and NHPs.

Single-cell profiling identifies LIN28A mRNA targets in the mouse pluripotent-to-2C-like transition and somatic cell reprogramming.

RNA-binding proteins (RBPs) regulate totipotency, pluripotency maintenance, and induction. The intricacies of how they modulate these processes through their interaction with RNAs remain to be elucidated. Here we employed Targets of RBPs Identified By Editing (TRIBE) with single-cell resolution (scTRIBE) to profile the mRNA targets of the key pluripotency regulator LIN28A in mouse embryonic stem cells (ESCs), 2-cell embryo-like cells (2CLCs) and somatic cell reprogramming. LIN28A is known to act by controlling the maturation of the let-7 microRNA but, in addition, it binds to multiple mRNAs and influences their stability and translation efficiency. However, the mRNA targets of LIN28A in 2CLCs and reprogramming are unclear. Through quantitative single-cell analysis of the scTRIBE dataset, we observed a marked increase in the binding of LIN28A to mRNAs of ribosome biogenesis factors and a selected group of totipotency factors in 2CLCs within ESC cultures. Our results suggest that LIN28A extends the half-life of at least some of these mRNAs, providing new insights into its role in the totipotent state. We also uncovered the distinct trajectory-specific LIN28A-mRNA networks in reprogramming, helping explain how LIN28A facilitates the mesenchymal-to-epithelial transition and pluripotency acquisition. Our study not only clarifies the multifunctional role of LIN28A in these processes but also highlights the importance of decoding RNA-protein interactions at the single-cell level.

Role and mechanism of histone demethylase PHF8 in weightlessness osteoporosis.

Weightlessness osteoporosis, which progresses continuously and has limited protective effects, has become one of the major problems that need to be solved in manned spaceflight. Our study aims to investigate the regulatory role of PHF8 in disuse osteoporosis by observing the expression of PHF8 in bone marrow mesenchymal stem cells (BMSCs) under simulated weightlessness conditions. Therefore, we used the model of ground-based microgravity simulated by disuse osteoporosis patients and tail suspension in mice to simulate microgravity in vivo, and measured the expression of PHF8 in bone tissue. Subsequently, we used the 2D gyroscope to simulate the weightless effect on bone marrow mesenchymal stem cells. In the weightless condition, we detected the proliferation, apoptosis, osteogenesis, and osteogenic differentiation functions of BMSCs. We also detected the expression of osteogenic-related transcription factors after knocking down and overexpressing PHF8. Our results show that the weightless effect can inhibit the proliferation, osteogenesis, and osteogenic differentiation functions of BMSCs, while enhancing their apoptosis; and overexpression of PHF8 can partially alleviate the osteoporosis caused by simulated weightlessness, providing new ideas and clues for potential drug targets to prevent weightlessness and disuse osteoporosis.

An Unexpected Decrease in Vibrational Entropy of Multicomponent Rutile Oxides.

High-entropy oxides (HEOs), featuring infinite chemical composition and exceptional physicochemical properties, are attracting much attention. The configurational entropy caused by a component disorder of HEOs is popularly believed to be the main driving force for thermal stability, while the role of vibrational entropy in the thermodynamic landscape has been neglected. In this study, we systematically investigated the vibrational entropy of multicomponent rutile oxides (including Fe0.5Ta0.5O2, Fe0.333Ti0.333Ta0.333O2, Fe0.25Ti0.25Ta0.25Sn0.25O2, and Fe0.21Ti0.21Ta0.21Sn0.21Ge0.16O2) by precise heat capacity measurements. It is found that vibrational entropy gradually decreases with increasing component disorder, beyond what one could expect from an equilibrium thermodynamics perspective. Moreover, all multicomponent rutile oxides exhibit a positive excess vibrational entropy at 298.15 K. Upon examinations of configuration disorder, size mismatch, phase transition, and polyhedral distortions, we demonstrate that the excess vibrational entropy plays a pivotal role in lowering the crystallization temperature of multicomponent rutile oxides. These findings represent the first experimental confirmation of the role of lattice vibrations in the thermodynamic landscape of rutile HEOs. In particular, vibrational entropy could serve as a novel descriptor to guide the predictive design of multicomponent oxide materials.

Graph-Based Method for Calibration of High-Resolution Mass Spectra of Natural Organic Matter.

Inaccuracies in ion detection and signal processing can undermine confidence in the molecular formula assignment of high-resolution mass spectrometry, which relies on precise matching of the mass-to-charge ratio (m/z). This study proposes a novel graph-based spectra calibration method, MSCMcalib, which implements coordinate transformation and pattern detection. MSCMcalib maps uncalibrated m/z data onto a modified 2D mass defect plot, facilitating the automatic calibration of detected lines, i.e., the calibration of uncalibrated peaks aligned with these lines. The "propagation" method is subsequently employed to accurately and automatically calibrate 605 m/z values across multiple lines, encompassing 98% of the m/z range. The calibrated m/z values divide the m/z range of the spectrum into multiple subintervals, with each subinterval undergoing a process of "scaling" calibration. The utilization of narrower partitions effectively mitigates divergence issues at both ends that arise from the polynomial fitting of errors against m/z. The effectiveness of MSCMcalib is validated through the calibration of SRFA data with m/z error ranges spanning from -10 to -6 ppm, resulting in an additional assignment of 11%-30% more molecular formulas compared to the quadratic fitting calibration.

Vapor-Solid Interface Synthesis of Highly Crystalline Covalent Triazine Frameworks for Use as Efficient Photocatalysts.

Harsh synthetic conditions for crystalline covalent triazine frameworks (CTFs) and associated limitations on structural diversities impede not only further development of functional CTFs, but also practical large-scale synthesis. Herein, a mild and universal vapor-solid interface synthesis strategy is developed for highly crystalline CTFs employing trifluoromethanesulfonic acid vapor as catalysts. A series of highly ordered simple and functional CTFs (CTF-TJUs) can be facilely produced. In particular, the porphyrin-involved functional CTF (CTF-TJU-Por1) with high crystallinity is synthesized for the first time via this universal approach. The mechanism of vapor-catalyzed trimerization of nitrile monomers is thoroughly investigated through semi in situ characterizations. As a proof of concept, the photocatalytic performance of synthesized CTFs for water splitting is evaluated. CTF-TJU-133 exhibits significantly greater photocatalytic rates for hydrogen (4.35 µmol h-1) and oxygen (2.18 µmol h-1) evolutions during overall water splitting under visible light irradiations compared to other CTF-TJUs, representing one of the highest values among reported CTF photocatalysts. Further studies reveal that enhanced photocatalytic performance of CTF-TJU-133 results from optimized band structure, extended visible-light absorption, and high carrier separation efficiency. This study provides a promising strategy to synthesize various simple and functional CTFs, which significantly enriched diversities of CTF family for different application purposes.

Barbier Polymerization-Induced Emission towards Fully Substituted Polyethylene Analogues with Non-Traditional Intrinsic Luminescence.

The properties of polyethylene are highly dependent on the variety and quantity of substitutions. Generally, polyethylene can only be fully substituted with fluorine atoms, mainly e. g., polytetrafluoroethylene and nafion, because atomic radius of fluorine atom is small enough. The preparation of fully substituted polyethylene analogues (FSPEA) and their non-traditional intrinsic luminescence (NTIL) are attractive, especially for substitutions with relatively larger atomic radii than a fluorine atom. Here, Barbier polymerization-induced emission (PIE) is demonstrated as a universal method for the molecular design of NTIL type FSPEAs with intriguing aggregation-induced emission (AIE) behaviors. Through Barbier polymerization of diphenyldichloromethane and different peroxyesters in the presence of Mg in one pot, a series of FSPEAs, including polytriphenylethanol (PTPE), polydiphenylfurylethanol (PDPFE), polydiphenylthiophenylethanol (PDPTE) and polydiphenylnaphthylethanol (PDPNE) have been successfully prepared. Further potential applications for explosive detection, artificial light-harvesting system and white phosphor-converted light-emitting diode are investigated. Therefore, this work opens up a new approach for the molecular design of FSPEA with non-conjugated luminescence, which may cause inspirations to different research fields like polyolefin and luminescent materials.

Lithography-Free Nanofabrication on Various Semiconductors by the Codeposition Etching Technique.

Nano-/microstructures can be formed with the aid of small amounts of impurities during deposition with noble gas plasma irradiation, which is referred to as codeposition etching. This can be a new method for lithography-free semiconductor nanofabrication. Here, the codeposition etching method was employed with argon plasma and molybdenum (Mo) impurities on various semiconductors. Structures can be formed only on substrates that have a lower sputtering yield than the seed impurity. The density, area, and height of structures are related to both the impurity deposition rate and the substrate material. Moreover, two mechanisms of impurity nucleation are proposed according to time dependence results for the formation of the structures.

Online LC-Orbitrap MS method for the rapid molecular characterization of dissolved organic matter.

RATIONALE: High-resolution mass spectrometry (HRMS) combined with electrospray ionization (ESI) has been the most useful technique for molecular characterization of dissolved organic matter (DOM) derived from diverse sources. However, the comprehensive detection of DOM composition was hindered by ionization suppression observed in ESI sources. HRMS coupled with liquid chromatography (LC) is a potential tool for comprehensive molecular characterization of DOM. METHODS: The Suwannee River fulvic acids (SRFAs) and two DOM samples from seawater and refinery wastewater extracted by solid phase extraction (SPE) were analyzed by LC-Orbitrap MS coupled with ESI. The mobile phases, solvent composition, and gradient in the LC-Orbitrap MS analysis were optimized. RESULTS: The number of detected molecular formulae of SRFAs by online LC-Orbitrap MS was significantly increased by approximately 40% compared to direct injection. These additional detected compounds are mainly protein and lignin-like compounds, with a low O/C ratio and high H/C ratio. For the SRFAs, the relative standard deviations (%) of reproducibility are 5.51, 2.33, 7.97, and 1.80 for average O/C, H/C, double bond equivalent, and modified aromaticity index, respectively. CONCLUSIONS: This study proposed a simple and rapid method based on LC-Orbitrap MS for an in-depth analysis of the molecular composition of DOM, achieving a remarkable analysis time of only 5 min per sample. The rapid method provides a dependable and efficient approach for the molecular characterization of DOM, thereby advancing our comprehension and investigation of DOM across diverse ecosystems.

Temporal Variations in Fire Impacts on Characteristics and Composition of Soil-Derived Dissolved Organic Matter at Qipan Mountain, China.

Dissolved organic matter (DOM), the most reactive fraction of forest soil organic matter, is increasingly impacted by wildfires worldwide. However, few studies have quantified the temporal changes in soil DOM quantity and quality after fire. Here, soil samples were collected after the Qipan Mountain Fire (3-36 months) from pairs of burned and unburned sites. DOM contents and characteristics were analyzed using carbon quantification and various spectroscopic and spectrometric techniques. Compared with the unburned sites, burned sites showed higher contents of bulk DOM and most DOM components 3 months after the fire but lower contents of them 6-36 months after the fire. During the sharp drop of DOM from 3 to 6 months after the fire, carboxyl-rich alicyclic molecule-like and highly unsaturated compounds had greater losses than condensed aromatics. Notably, the burned sites had consistently higher abundances of oxygen-poor dissolved black nitrogen and fluorescent DOM 3-36 months after the fire, particularly the abundance of pyrogenic C2 (excitation/emission maxima of <250/∼400 nm) that increased by 150% before gradually declining. This study advances the understanding of temporal variations in the effects of fire on different soil DOM components, which is crucial for future postfire environmental management.

Revealing the backbone structures of land-based fulvic acids derived from river and soil through n-butylsilane reduction.

While ultra-high-resolution mass spectrometry has enabled the identification of the molecular composition of dissolved organic matter (DOM), elucidating its molecular structure remains a challenging endeavor. Here, two fulvic acids (FAs), one from river and the other from forest soil, were subjected to reduction using an optimized n-butylsilane (n-BS) reduction method. The reduction products were purified through a combination of liquid-liquid extraction and silica gel column chromatography, resulting in the separation into saturates, aromatics, and polar products. The polar products were analyzed by high-resolution mass spectrometry (HRMS), and the saturates and aromatics were analyzed using gas chromatography-mass spectrometry (GC-MS). HRMS results showed that the number of oxygen atoms and double-bond equivalent (DBE) values of FA decreased after reduction. GC-MS results revealed that a total of 270 hydrocarbon monomers were identified from the reduction products of a single sample, with the highest carbon number of cycloalkanes reaching C33. For the first time, steranes and hopanes were detected in the reduction products, potentially serving as evidence for the existence of carboxyl-rich alicyclic molecule (CRAM) precursors. Additionally, a significant number of polycyclic aromatic hydrocarbons were identified, and the potential sources of various compounds were preliminarily inferred based on their isomers. This study extends the knowledge of the possible backbone structure of the DOM and provides a new potential tool for investigating the origin and transformation mechanisms of DOM.

Fecal calprotectin: A novel predictor of ulcerated esophageal injury after atrial fibrillation catheter ablation.

BACKGROUND: Atrial esophageal fistula (AEF) is a lethal complication that can occur post atrial fibrillation (AF) ablation. Esophageal injury (EI) is likely to be the initial lesion leading to AEF. Endoscopic examination is the gold standard for a diagnosis of EI but extensive endoscopic screening is invasive and costly. This study was conducted to determine whether fecal calprotectin (Fcal), a marker of inflammation throughout the intestinal tract, may be associated with the existence of esophageal injury. METHODS: This diagnostic study was conducted in a cohort of 166 patients with symptomatic AF undergoing radiofrequency catheter ablation from May 2020 to June 2021. Fcal tests were performed 1-7 days after ablation. All patients underwent endoscopic ultrasonography 1 or 2 days after ablation. RESULTS: The levels of Fcal were significantly different between the EI and non-EI groups (404.9 µg/g (IQR 129.6-723.6) vs. 40.4 µg/g (IQR 15.0-246.2), p < .001). Analysis of ROC curves revealed that a Fcal level of 125 µg/g might be the optimal cut-off value for a diagnosis of EI, giving a 78.8% sensitivity and a 65.4% specificity. The negative predictive value of Fcal was 100% for ulcerated EI. CONCLUSIONS: The level of Fcal is associated with EI post AF catheter ablation. 125 µg/g might be the optimal cut-off value for a diagnosis of EI. Negative Fcal could predict the absence of ulcerated EI, which could be considered a precursor to AEF.

Deciphering dissolved organic matter characteristics and its fate in a glacier-fed desert river-the Tarim river, China.

The bioavailable diverse dissolved organic matter (DOM) present in glacial meltwater significantly contributes to downstream carbon cycling in mountainous regions. However, the comprehension of molecular-level characteristics of riverine DOM, from tributary to downstream and their fate in glacier-fed desert rivers remains limited. Herein, we employed spectroscopic and high-resolution mass spectrometry techniques to study both optical and molecular-level characteristics of DOM in the Tarim River catchment, northwest China. The results revealed that the DOC values in the downstream were higher than those in the tributaries, yet they remained comparable to those found in other glacier-fed streams worldwide. Five distinct components were identified using EEM-PARAFAC analysis in both tributary and downstream samples. The dominance of three protein-like components in tributary samples, contrasting with a higher presence of humic-like components in downstream samples, which implied that the dilution and alterations of the glacier DOM signature and overprinting with terrestrial-derived DOM. Molecular composition revealed that thousands of compounds with higher molecular weight and increased aromaticity were transformed, generated and introduced from terrestrial inputs during downstream transportation. The twofold rise in polycyclic aromatic and polyphenolic compounds observed downstream compared to tributaries indicated a greater influx of terrestrial organic matter introduced into the downstream during water transportation. The study suggests that the glacier-sourced DOM experienced minimal photodegradations, with limited influence from human activities, while also being shaped by terrestrial inputs during its transit in the alpine-arid region. This unique scenario offers valuable insights into comprehending the fate of DOM originating from glacial meltwater in arid mountainous regions.

Metabolism of alcohol ethoxylates (AEs) in rat, hamster, and human hepatocytes and liver S9: a pilot study for metabolic stability, metabolic pathway, and metabolites identification in vitro and in silico.

Alcohol ethoxylates (AEs) are a well-known class of non-ionic surfactants widely used by the personal care market. The aim of this study was to evaluate and characterize the in vitro metabolism of AEs and identify metabolites. Five selected individual homologue AEs (C8EO4, C10EO5, C12EO4, C16EO8, and C18EO3) were incubated using human, rat, and hamster liver S9 fraction and cryopreserved hepatocytes. LC-MS was used to identify metabolites following the incubation of AEs by liver S9 and hepatocytes of all three species. All AEs were metabolized in these systems with a half-life ranging from 2 to 139 min. In general, incubation of AE with human liver S9 showed a shorter half-life compared to rat liver S9. While rat hepatocytes metabolized AEs faster than human hepatocytes. Both hydrophobic alkyl chain and hydrophilic EO head group groups of AEs were found to be target sites of metabolism. Metabolites were identified that show primary hydroxylation and dehydrogenation, followed by O-dealkylation (shortening of EO head groups) and glucuronidation. Additionally, the detection of whole EO groups indicates the cleavage of the ether bond between the alkyl chain and the EO groups as a minor metabolic pathway in the current testing system. Furthermore, no difference in metabolic patterns of each individual homologue AE investigated was observed, regardless of alkyl chain length or the number of EO groups. Moreover, there is an excellent agreement between the in vitro experimental data and the metabolite profile simulations using in silico approaches (OECD QSAR Toolbox). Altogether, these data indicate fast metabolism of all AEs with a qualitatively similar metabolic pathway with some quantitative differences observed in the metabolite profiles. These metabolic studies using different species can provide important reference values for further safety evaluation.

Pedestrian Pose Recognition Based on Frequency-Modulated Continuous-Wave Radar with Meta-Learning.

With the continuous advancement of autonomous driving and monitoring technologies, there is increasing attention on non-intrusive target monitoring and recognition. This paper proposes an ArcFace SE-attention model-agnostic meta-learning approach (AS-MAML) by integrating attention mechanisms into residual networks for pedestrian gait recognition using frequency-modulated continuous-wave (FMCW) millimeter-wave radar through meta-learning. We enhance the feature extraction capability of the base network using channel attention mechanisms and integrate the additive angular margin loss function (ArcFace loss) into the inner loop of MAML to constrain inner loop optimization and improve radar discrimination. Then, this network is used to classify small-sample micro-Doppler images obtained from millimeter-wave radar as the data source for pose recognition. Experimental tests were conducted on pose estimation and image classification tasks. The results demonstrate significant detection and recognition performance, with an accuracy of 94.5%, accompanied by a 95% confidence interval. Additionally, on the open-source dataset DIAT-µRadHAR, which is specially processed to increase classification difficulty, the network achieves a classification accuracy of 85.9%.

A Joint State and Fault Estimation Scheme for State-Saturated System with Energy Harvesting Sensors.

In this article, the issue of joint state and fault estimation is ironed out for delayed state-saturated systems subject to energy harvesting sensors. Under the effect of energy harvesting, the sensors can harvest energy from the external environment and consume an amount of energy when transmitting measurements to the estimator. The occurrence probability of measurement loss is computed at each instant according to the probability distribution of the energy harvesting mechanism. The main objective of the addressed problem is to construct a joint state and fault estimator where the estimation error covariance is ensured in some certain sense and the estimator gain is determined to accommodate energy harvesting sensors, state saturation, as well as time delays. By virtue of a set of matrix difference equations, the derived upper bound is minimized by parameterizing the estimator gain. In addition, the performance evaluation of the designed joint estimator is conducted by analyzing the boundedness of the estimation error in the mean-squared sense. Finally, two experimental examples are employed to illustrate the feasibility of the proposed estimation scheme.

Compositional Characterization of Syngas-Based Glycolide Using Gas Chromatogram-Mass Spectrometry and Electrospray Ionization High-Resolution Mass Spectrometry.

Polyglycolic acid (PGA) is a biologically friendly material with a wide range of applications. The production of dimethyl oxalate using coal-based syngas and the hydrogenation of dimethyl oxalate can produce the polymerization raw material of PGA, glycolide, which requires a methyl glycolate polymerization and depolymerization process. The intermediate products of the production process were analyzed using gas chromatogram-mass spectrometry (GC-MS) and Orbitrap mass spectrometry (Orbitrap MS), which revealed the presence of cyclic and linear PGAs with different capped ends. The impurities present in the oligomer were mostly methyl-capped PGA and were retained in the subsequent depolymerization process to glycolide, solvent washing can be used to remove this part of the impurity and ultimately obtain a refined glycolide product. Furthermore, it is proposed that the use of the specialized Kendrick Mass Defect (KMD) to plot and analyze PGA compounds obtained using mass spectrometry can enable the direct classification of PGAs without the need for exact molecular formula assignment.

Spatiotemporal Utilization of Latent Heat in Erythritol-based Phase Change Materials as Solar Thermal Fuels.

Solar thermal fuels (STFs) have been particularly concerned as sustainable future energy due to their impressive ability to store solar energy in chemical bonds and controllably release thermal energy. However, currently studied STFs mainly focus on molecule-based materials with high photochemical activity, toxicity, and compromised features, which greatly restricts their applications in practical scenarios of solar energy utilization. Herein, we present a novel erythritol-based composite phase change material (PCM) as a new type of STFs with an outstanding capability to store solar energy as latent heat in its stable supercooling state and release thermal energy as needed. This composite PCM with stored thermal energy can be maintained stably at room temperature and subsequently release latent heat as high as 224.9 J/g during the crystallization process triggered by thermal stimuli. Remarkably, solar energy can be converted into latent heat stored in the composite PCM over months. Through mechanical stimulations, the released latent heat can increase the temperature of the composite up to 91 °C. This work presents a new concept of using spatiotemporal storage and release of latent heat in PCMs for solar energy utilization, making it a potential candidate as STFs for developing future clean energy techniques.

Intrinsically Flexible Phase Change Fibers for Intelligent Thermal Regulation.

Owing to the significant latent heat generated at constant temperatures, phase change fibers (PCFs) have recently received much attention in the field of wearable thermal management. However, the phase change materials involved in the existing PCFs still experience a solid-liquid transition process, severely restricting their practicality as wearable thermal management materials. Herein, we, for the first time, developed intrinsically flexible PCFs (polyethylene glycol/4,4'-methylenebis(cyclohexyl isocyanate) fibers, PMFs) through polycondensation and wet-spinning process, exhibiting an inherent solid-solid phase transition property, adjustable phase transition behaviors, and outstanding knittability. The PMFs also present superior mechanical strength (28 MPa), washability (>100 cycles), thermal cycling stability (>2000 cycles), facile dyeability, and heat-induced recoverability, all of which are highly significant for practical wearable applications. Additionally, the PMFs can be easily recycled by directly dissolving them in solvents for reprocessing, revealing promising applications as sustainable materials for thermal management. Most importantly, the applicability of the PMFs was demonstrated by knitting them into permeable fabrics, which exhibit considerably improved thermal management performance compared with the cotton fabric. The PMFs offer great potential for intelligent thermal regulation in smart textiles and wearable electronics.

The FASTQ+ format and PISA.

SUMMARY: The FASTQ+ format is designed for single-cell experiments. It extends various optional tags, including cell barcodes and unique molecular identifiers, to the sequence identifier and is fully compatible with the FASTQ format. In addition, PISA implements various utilities for processing sequences in the FASTQ format and alignments in the SAM/BAM/CRAM format from single-cell experiments, such as converting FASTQ format to FASTQ+, annotating alignments, PCR deduplication, feature counting and barcodes correction. The software is open-source and written in C language. AVAILABILITY AND IMPLEMENTATION: https://doi.org/10.5281/zenodo.7007056 or https://github.com/shiquan/PISA. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.