Single-cell bisulfite-free 5mC and 5hmC sequencing with high sensitivity and scalability.

Existing single-cell bisulfite-based DNA methylation analysis is limited by low DNA recovery, and the measurement of 5hmC at single-base resolution remains challenging. Here, we present a bisulfite-free single-cell whole-genome 5mC and 5hmC profiling technique, named Cabernet, which can characterize 5mC and 5hmC at single-base resolution with high genomic coverage. Cabernet utilizes Tn5 transposome for DNA fragmentation, which enables the discrimination between different alleles for measuring hemi-methylation status. Using Cabernet, we revealed the 5mC, hemi-5mC and 5hmC dynamics during early mouse embryo development, uncovering genomic regions exclusively governed by active or passive demethylation. We show that hemi-methylation status can be used to distinguish between pre- and post-replication cells, enabling more efficient cell grouping when integrated with 5mC profiles. The property of Tn5 naturally enables Cabernet to achieve high-throughput single-cell methylome profiling, where we probed mouse cortical neurons and embryonic day 7.5 (E7.5) embryos, and constructed the library for thousands of single cells at high efficiency, demonstrating its potential for analyzing complex tissues at substantially low cost. Together, we present a way of high-throughput methylome and hydroxymethylome detection at single-cell resolution, enabling efficient analysis of the epigenetic status of biological systems with complicated nature such as neurons and cancer cells.

Heterovalent Metal Pair Sites on Metal-Organic Framework Ordered Macropores for Multimolecular Co-Activation.

The precise design of catalytic metal centers with multiple chemical states to facilitate sophisticated reactions involving multimolecular activation is highly desirable but challenging. Herein, we report an ordered macroporous catalyst with heterovalent metal pair (HMP) sites comprising CuII-CuI on the basis of a microporous metal-organic framework (MOF) system. This macroporous HMP catalyst with proximity heterovalent dual copper sites, whose distance is controlled to ∼2.6 Å, on macropore surface exhibits a co-activation behavior of ethanol at CuII and alkyne at CuI, and avoids microporous restriction, thereby promoting additive-free alkyne hydroboration reaction. The desired yield enhances dramatically compared with the pristine MOF and ordered macroporous MOF both with solely isovalent CuII-CuII sites. Density functional theory calculations reveal that the Cu-HMP sites can stabilize the Bpin-CuII-CuI-alkyne intermediate and facilitate C-B bond formation, resulting in a smooth alkyne hydroboration process. This work provides new perspectives to design multimolecular activation catalysts for sophisticated matter transformations.

Manipulating the Host-Guest Chemistry of Cucurbituril to Propel Highly Reversible Zinc Metal Anodes.

Rechargeable aqueous zinc-ion batteries are practically plagued by the short lifespan and low Coulombic efficiency (CE) of Zn anodes resulting from random dendrite deposition and parasitic reactions. Herein, the host-guest chemistry of cucurbituril additive with Zn2+ to achieve longstanding Zn anodes is manipulated. The macrocyclic molecule of cucurbit[5]uril (CB[5]) is delicately designed to reconstruct both the CB[5]-adsorbed electric-double layer (EDL) structure at the Zn interface and the hydrated sheath of Zn2+ ions. Especially benefiting from the desirable carbonyl rims and suitable hydrophobic cavities, the CB[5] has a strong host-guest interaction with Zn2+ ions, which exclusively permits rapid Zn2+ flux across the EDL interface but retards the H2O radicals and SO4 2-. Accordingly, such a unique particle redistributor warrants long-lasting dendrite-free deposition by homogenizing Zn nucleation/growth and significantly improved CE by inhibiting side reactions. The Zn anode can deliver superior reversibility in CB[5]-containing electrolyte with a ninefold increase of cycle lifetime and an elevated CE of 99.7% under harsh test conditions (10 mA cm-2/10 mA h cm-2). The work opens a new avenue from the perspective of host-guest chemistry to propel the development of rechargeable Zn metal batteries and beyond.

Molecular Engineering to Regulate the Pseudo-Graphitic Structure of Hard Carbon for Superior Sodium Energy Storage.

Resin-derived hard carbons have shown great advantages in serving as promising anode materials for sodium-ion batteries due to their flexible microstructure tunability. However, it remains a daunting challenge to rationally regulate the pseudo-graphitic crystallite and defect of hard carbon toward advanced sodium storage performance. Herein, a molecular engineering strategy is demonstrated to modulate the cross-linking degree of phenolic resin and thus optimize the microstructure of hard carbon. Remarkably, the resorcinol endows resin with a moderate cross-linking degree, which can finely tune the pseudo-graphitic structure with enlarged interlayer spacing and restricted surface defects. As a consequence, the optimal hard carbon delivers a notable reversible capacity of 334.3 mAh g-1 at 0.02 A g-1, a high initial Coulombic efficiency of 82.1%, superior rate performance of 103.7 mAh g-1 at 2 A g-1, and excellent cycling durability over 5000 cycles. Furthermore, kinetic analysis and in situ Raman spectroscopy are performed to reveal the electrochemical advantage and sodium storage mechanism. This study fundamentally sheds light on the molecular design of resin-based hard carbons to advance sodium energy for scale-up applications.

Rheumatoid meningitis in the absence of rheumatoid arthritis: 2 cases.

Rheumatoid meningitis (RM) is a rare extra-articular manifestation of rheumatoid arthritis (RA) that has been increasingly recognized by neurologists. However, the diversity of its clinical manifestations makes its diagnosis difficult. RM does not have a unified diagnostic standard, and its link with RA needs to be studied further. Here we report two cases of RM without a history of RA. The first patient, an 80-year-old woman, presented with sudden unilateral limb weakness, with brain MR showing abnormal signals in the leptomeningeal of the right frontal parietal. Subarachnoid hemorrhage was excluded after imaging examination, and infectious meningitis was ruled out after cerebrospinal fluid (CSF) examination. The patient was diagnosed as having RM, she had increased levels of CCP and AKA, the markers of RA, but no history of the disease or other clinical manifestations of it. Another case, a 65-year-old man, was hospitalized with Bell's palsy. We found that he had intracranial imaging changes highly consistent with those characteristic of RM during his routine examination. Except for the left peripheral facial palsy, the patient had no other neurological signs or symptoms and no RA history. After a careful physical examination, we found no joint or other manifestations or serological abnormalities consistent with RA (RF, CCP, AKA, etc.). However, after excluding infection meningitis and considering the patient's unique imaging results, we diagnosed him as having RM. We report these two cases as references for clinical diagnosis and treatment of RM, providing a discussion of our rationale.

Association between famine exposure during infancy and childhood and the risk of chronic kidney disease in adulthood.

BACKGROUND: Famine exposure in childhood is proven to be associated with multiple chornic disease in adult but has not been studied with chronic kidney disease (CKD). AIMS: This study was conducted to identify the relationship between famine exposure during infancy and childhood - specifically, the Chinese famine of 1959-1961 - and the risk of adult-onset chronic kidney disease (CKD) among Chinese individuals. METHODS: This study included 2937 individuals from the Qingdao Diabetes Prevention Program. They were stratified by birth year into infancy-exposed (1956-1958), childhood-exposed (1950-1955) and unexposed (1963-1971) groups. The estimated glomerular filtration rate (eGFR) was calculated using the Chronic Kidney Disease Epidemiology Collaboration equation. CKD was defined as an eGFR of <90 mL/min/1.73 m2 . RESULTS: The mean eGFR values for the infancy-exposed and childhood-exposed groups were 107.23 ± 12.53 and 103.23 ± 12.44 mL/min/1.73 m2 , respectively, both of which were lower than that of the unexposed group (114.82 ± 13.39 mL/min/1.73 m2 ; P < 0.05). In the crude model, the odds ratio (OR) for CKD was 2.00 (95% confidence interval (CI): 1.39-2.88) in the infancy-exposed group and 2.92 (95% CI: 2.17-3.93) in the childhood-exposed group. Further adjustments for urban/rural residence, body mass index, age, current smoking, type 2 diabetes, systolic blood pressure, diastolic blood pressure and total cholesterol did not significantly alter the association between famine exposure and CKD. The corresponding ORs were 1.71 (95% CI: 1.17-2.50) and 2.48 (95% CI: 1.81-3.40) for the infancy-exposed and childhood-exposed groups respectively. CONCLUSIONS: Famine exposure during infancy and childhood is associated with a long-term decline in eGFR and an increased adult-onset CKD risk. Early intervention for high-risk individuals may mitigate the risk of adult-onset CKD.

Clinical Implications of a New DDX58 Pathogenic Variant That Causes Lupus Nephritis due to RIG-I Hyperactivation.

BACKGROUND: Lupus nephritis (LN) is one of the most severe complications of systemic lupus erythematosus, with heterogeneous phenotypes and different responses to therapy. Identifying genetic causes of LN can facilitate more individual treatment strategies. METHODS: We performed whole-exome sequencing in a cohort of Chinese patients with LN and identified variants of a disease-causing gene. Extensive biochemical, immunologic, and functional analyses assessed the effect of the variant on type I IFN signaling. We further investigated the effectiveness of targeted therapy using single-cell RNA sequencing. RESULTS: We identified a novel DDX58 pathogenic variant, R109C, in five unrelated families with LN. The DDX58 R109C variant is a gain-of-function mutation, elevating type I IFN signaling due to reduced autoinhibition, which leads to RIG-I hyperactivation, increased RIG-I K63 ubiquitination, and MAVS aggregation. Transcriptome analysis revealed an increased IFN signature in patient monocytes. Initiation of JAK inhibitor therapy (baricitinib 2 mg/d) effectively suppressed the IFN signal in one patient. CONCLUSIONS: A novel DDX58 R109C variant that can cause LN connects IFNopathy and LN, suggesting targeted therapy on the basis of pathogenicity. PODCAST: This article contains a podcast at.

Quantification of dissipative effects in a complex Ginzburg-Landau equation governed laser system by tracing soliton dynamics.

The concept of dissipative solitons has provided new insight into the complex pulse dynamics in mode-locked lasers and stimulated novel laser cavity designs. However, most of these studies are restricted to qualitative regimes, because it is difficult to quantify dissipative effects in a mode-locked laser. Meanwhile, the quantification of dissipative effects is a general problem that can be also encountered in other dissipative systems. In this paper, we demonstrate a method for quantifying dissipative effects in a mode-locked laser based on analyzing the soliton dynamics traced by time-stretch dispersive Fourier transform. As a result, we are able to quantitatively reproduce the evolution of the pulse that seeds mode-locking through simulations and gain a deeper understanding of the whole process. The obtained physical picture of mode-locking allows us to propose a simple method to quantify the energy threshold for mode-locking buildup and the stability of mode-locked states. A parameter is introduced to evaluate mode-locking conditions, which can serve as a criterion for designing mode-locked lasers. This work opens up new possibilities in the diagnosis and improvement of mode-locked lasers and studies of soliton physics.

The identification of piecewise non-linear dynamical system without understanding the mechanism.

This paper designs an algorithm to distill the piecewise non-linear dynamical system from the data without prior knowledge. The system to be identified does not have to be written as a known model term or be thoroughly understood. We exploit the fact that an unknown piecewise non-linear system can be decomposed into the Fourier series as long as its equations of motion are Riemann integrable. Based on this property, we reduce the challenge of finding the correct model to discovering the Fourier series approximation. However, the Fourier series approximation of the piecewise function is inaccurate. The new method takes advantage of this weakness to determine whether the model has piecewise features and to find a way to discover the discontinuity set. Then, the dynamical system on each segment is identified as a pure Fourier series. Identification of intricate models can be achieved in simple steps. The results show that the method can accurately discover the equation of motion and precisely capture the non-smooth characteristic. Next, the prediction and further detailed analysis can be carried out.

Genome-Wide Identification and Expression Analysis of Dendrocalamus farinosus CCoAOMT Gene Family and the Role of DfCCoAOMT14 Involved in Lignin Synthesis.

As the main component of plant cell walls, lignin can not only provide mechanical strength and physical defense for plants, but can also be an important indicator affecting the properties and quality of wood and bamboo. Dendrocalamus farinosus is an important economic bamboo species for both shoots and timber in southwest China, with the advantages of fast growth, high yield and slender fiber. Caffeoyl-coenzyme A-O-methyltransferase (CCoAOMT) is a key rate-limiting enzyme in the lignin biosynthesis pathway, but little is known about it in D. farinosus. Here, a total of 17 DfCCoAOMT genes were identified based on the D. farinosus whole genome. DfCCoAOMT1/14/15/16 were homologs of AtCCoAOMT1. DfCCoAOMT6/9/14/15/16 were highly expressed in stems of D. farinosus; this is consistent with the trend of lignin accumulation during bamboo shoot elongation, especially DfCCoAOMT14. The analysis of promoter cis-acting elements suggested that DfCCoAOMTs might be important for photosynthesis, ABA/MeJA responses, drought stress and lignin synthesis. We then confirmed that the expression levels of DfCCoAOMT2/5/6/8/9/14/15 were regulated by ABA/MeJA signaling. In addition, overexpression of DfCCoAOMT14 in transgenic plants significantly increased the lignin content, xylem thickness and drought resistance of plants. Our findings revealed that DfCCoAOMT14 can be a candidate gene that is involved in the drought response and lignin synthesis pathway in plants, which could contribute to the genetic improvement of many important traits in D. farinosus and other species.

Recent Advances and Future Prospects of Mycosporine-like Amino Acids.

Mycosporine-like amino acids (MAAs) are a class of water-soluble active substances produced by various aquatic organisms. However, due to the limitations of low accumulation of MAAs in organisms, the cumbersome extraction process, difficult identification, and high cost, MAAs have not yet been widely used in human life. Recently, there has been an emergence of heterologous synthesis for MAAs, making increasing yield the key to the quantification and application of MAAs. This review summarizes the latest research progress of MAAs, including: (1) introducing the biodistribution of MAAs and the content differences among different species to provide a reference for the selection of research subjects; (2) elaborating the species and molecular information of MAAs; (3) dissecting the synthesis mechanism and sorting out the synthesis pathways of various MAAs; (4) summarizing the methods of extraction and identification, summarizing the advantages and disadvantages, and providing a reference for the optimization of extraction protocols; (5) examining the heterologous synthesis method; and (6) summarizing the physiological functions of MAAs. This paper comprehensively updates the latest research status of MAAs and the various problems that need to be addressed, especially emphasizing the potential advantages of heterologous synthesis in the future production of MAAs.

Study on the polarization dependence of nonlinear absorption of ultrafast laser pulses in bulk fused silica.

By studying the nonlinear absorption of ultrafast laser pulses in fused silica, we examine, both with experiments and numerical simulations, the different polarization dependence of multiphoton ionization and avalanche ionization. Results show multiphoton ionization and avalanche ionization play different roles in femtosecond and picosecond laser micromachining, and the contribution via avalanche ionization increases with pulse duration. Meanwhile, the spatial distribution of the free carriers generated by circularly polarized pulses is more concentrated than those generated by linear polarization for picosecond laser pulses. These properties make the circular polarized ultrafast laser a possible way to improve the ultrafast laser micromachining efficiency and spatial quality, and can help to reduce some problematic nonlinear effects in ultrafast laser micromachining of low energy band materials.

Energy deposition and incubation effects of nonlinear absorption of ultrashort laser pulses in dielectrics.

Although ultrashort laser has been widely employed in micromachining thanks to its excellent processing precision, one of the main challenges it faces when applied to 3D modification inside dielectrics is its processing efficiency. Many applications require multiple pulses to achieve significant modification to create structure such as microlenses. We report incubation experiments on energy deposition and the control of material modification in fused silica. This allows us to develop a practical incubation model by taking account different ionization mechanisms, in which coefficients relating to multiphoton and avalanche ionization change with laser shots due to accumulating defects. We then extend our study to the scheme where a pre-pulse is used to limit the absorption volume through pre-seeding. Both experiments and simulations show that the efficiency of laser processing can be significantly improved without sacrificing the spatial resolution with this method, especially for longer pulses.

Simple and cost-effective broad bandwidth fiber chirped pulse amplification laser system seeded by a nonlinear amplifier.

In this paper, we demonstrate a simple and cost-effective fiber chirped pulse amplification (CPA) laser system, where a nonlinear amplifier is employed to generate broadband seeding pulses. The nonlinear amplifier can generate stable pulses with 50 nm spectral bandwidth and linear chirp. With such a seeding configuration being adapted into a fiber CPA laser system, the output bandwidth can be expanded from 7 nm to 20 nm, with only minor changes to a standard industrial fiber CPA system. The increased bandwidth allows for pulse durations of less than 100 fs, which is significantly shorter than the original configuration's 250 fs. When combined with a Fourier pulse shaper, such a fiber laser system is expected to produce pulses with energy exceeding 100 µJ and duration shorter than 100 fs.

Single-shot method to study high order solitons in all-polarization-maintaining soliton mode-locked fiber lasers.

A single-shot experimental method is proposed to study non-repetitive evolutions of high order solitons. In our experiments, high order solitons are prepared in the building up process of a soliton fiber laser, and the order of high order soliton is controlled via changing the parameters of the laser. The evolution of high order soliton is recorded by the single-shot spectral measurements-time stretch dispersive Fourier transform. A 4th order soliton evolution under perturbations of gain saturation and saturable loss is studied, showing how a leading pulse wins the competition against the tailing one. Our work provides a controllable technique to study the high order solitons evolutions, which can be applied in the research of ultrafast laser amplifications and supercontinuum generations.

Optimal conditions for self-starting of soliton mode-locked fiber lasers with a saturable absorber.

With the recently developed single-shot time-stretch dispersive Fourier transform technique, we investigate the buildup process of an all-polarization-maintaining soliton mode-locked fiber laser. Considering the multi-pulse competitions and the evolution of the survived pulse, we find an optimal range of intra-cavity energy for self-starting related to the saturation energy of the employed saturable absorber. Under the conditions, one dominant pulse can build up quickly against the others, and it finally drives to single-pulse operation. The conclusions drawn here hold for other soliton mode-locked lasers.

The stochastic bifurcation of the vibro-impact system on the impact surface via a new path integration method.

In this paper, a new path integration algorithm is proposed for the non-autonomous vibro-impact system. It can be used to obtain the stochastic response of the system at the impact instant. The innovation of this algorithm is that the fixed excitation phase at the impact instant is introduced. The fixed excitation phase and the impact surface are combined as the special impact surface, and the algorithm sets up the different evolution methods of the probability density function and the impact completion condition. It can directly capture the stochastic response of the system at the impact instant without any non-smooth approximations. The non-smooth characteristics of the impact can be well preserved. This new path integration algorithm has good applicability. It has no limitation on the restitution coefficient. The design idea of this algorithm may provide a framework for the non-smooth system subject to the periodic excitation. In the end, a linear vibro-impact system and a nonlinear vibro-impact system excited by the external periodic force are used as examples to show how our method could be implemented. The stochastic P-bifurcation phenomena induced by parameters also are considered. The Monte Carlo simulations verify the effectiveness and accuracy of the proposed path integration algorithm.

Breakfast replacement with a liquid formula improves glycaemic variability in patients with type 2 diabetes: a randomised clinical trial.

There is emerging evidence that glycaemic variability (GV) plays an important role in the development of diabetic complications. The current study aimed to compare the effects of lifestyle intervention (LI) with and without partial meal replacement (MR) on GV. A total of 123 patients with newly diagnosed and untreated type 2 diabetes (T2D) were randomised to receive either LI together with breakfast replacement with a liquid formula (LI+MR) (n 62) or LI alone (n 61) for 4 weeks and completed the study. Each participant was instructed to have three main meals per d and underwent 72-h continuous glucose monitoring (CGM) both before and after intervention. Measures of GV assessed by CGM included the incremental AUC of postprandial blood glucose (AUCpp), standard deviation of blood glucose (SDBG), glucose CV and mean amplitude of glycaemic excursions (MAGE). After a 4-week intervention, the improvements in systolic blood pressure (P=0·046) and time in range (P=0·033) were more pronounced in the LI+MR group than in the LI group. Furthermore, LI+MR caused significantly greater improvements in all GV metrics including SDBG (P=0·005), CV (P=0·002), MAGE (P=0·016) and AUCpp (P<0·001) than did LI. LI+MR (v. LI) was independently associated with improvements in GV after adjustment of covariates (all P<0·05). Our study showed that LI+MR led to significantly greater improvements in GV compared with LI, suggesting that LI+MR could be an effective treatment to alleviate glucose excursions.

Metabolic perturbations of post-load hyperglycemia vs. fasting hyperglycemia.

There is evidence that post-load/post-meal hyperglycemia is a stronger risk factor for cardiovascular disease than fasting hyperglycemia. The underlying mechanism remains to be elucidated. The current study aimed to compare the metabolic profiles of post-load hyperglycemia and fasting hyperglycemia. All subjects received an oral glucose tolerance test (OGTT) and were stratified into fasting hyperglycemia (FH) or post-load hyperglycemia (PH). Forty-six (FH, n = 23; PH, n = 23) and 40 patients (FH, n = 20; PH, n = 20) were recruited as the exploratory and the validation set, respectively, and underwent metabolic profiling. Eighty-seven subjects including normal controls (NC: n = 36; FH: n = 22; PH: n = 29) were additionally enrolled and assayed with enzyme-linked immunosorbent assay (ELISA). In the exploratory set, 10 metabolites were selected as differential metabolites of PH (vs. FH). Of them, mannose and 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) were confirmed in the validation set to be significantly higher in FH than in PH. In the 87 subjects measured with ELISA, FH had numerically higher mannose (466.0 ± 179.3 vs. 390.1 ± 140.2 pg/ml) and AICAR (523.5 ± 164.8 vs. 512.1 ± 186.0 pg/ml) than did PH. In the pooled dataset comprising 173 subjects, mannose was independently associated with FPG (ß = 0.151, P = 0.035) and HOMA-IR (ß = 0.160, P = 0.026), respectively. The associations of AICAR with biochemical parameters did not reach statistical significance. FH and PH exhibited distinct metabolic profiles. The perturbation of mannose may be involved in the pathophysiologic disturbances in diabetes.

Smart nanoparticles assembled by endogenous molecules for siRNA delivery and cancer therapy via CD44 and EGFR dual-targeting.

We developed an anticancer siRNA delivery system (named HLPR) through modular assembly of endogenous molecules. The structure of HLPR was a tightly condensed siRNA-peptide inner core in turn surrounded by the disordered lipid layer and thin HA coating from which the EGFR-targeted amino acid sequences of YHWYGYTPQNVI partially protrude outside of cell surfaces. Both HA and YHWYGYTPQNVI anchored on HLPR were responsible for targeting CD44 and EGFR overexpressed on the tumor cell surfaces, respectively. HLPR was relatively stable in the blood circulation and reached the tumor tissue in vivo through passive and active targeting. Then HLPR entered tumor cells mainly through EGFR-mediated pathway followed by the separation of HA from the remaining parts of nanocomplexes. The HA-uncoated complexes escaped the endosome through the membrane fusion function of DOPE and released cargoes (siRNA and peptide/siRNA) in the cytoplasm. HLPR significantly inhibited the growth of implanted subcutaneous liver tumors without toxicity.