Mixing of moiré-surface and bulk states in graphite.

Van der Waals assembly enables the design of electronic states in two-dimensional (2D) materials, often by superimposing a long-wavelength periodic potential on a crystal lattice using moiré superlattices1-9. This twistronics approach has resulted in numerous previously undescribed physics, including strong correlations and superconductivity in twisted bilayer graphene10-12, resonant excitons, charge ordering and Wigner crystallization in transition-metal chalcogenide moiré structures13-18 and Hofstadter's butterfly spectra and Brown-Zak quantum oscillations in graphene superlattices19-22. Moreover, twistronics has been used to modify near-surface states at the interface between van der Waals crystals23,24. Here we show that electronic states in three-dimensional (3D) crystals such as graphite can be tuned by a superlattice potential occurring at the interface with another crystal-namely, crystallographically aligned hexagonal boron nitride. This alignment results in several Lifshitz transitions and Brown-Zak oscillations arising from near-surface states, whereas, in high magnetic fields, fractal states of Hofstadter's butterfly draw deep into the bulk of graphite. Our work shows a way in which 3D spectra can be controlled using the approach of 2D twistronics.

Structural basis for self-cleavage prevention by tag:anti-tag pairing complementarity in type VI Cas13 CRISPR systems.

Bacteria and archaea apply CRISPR-Cas surveillance complexes to defend against foreign invaders. These invading genetic elements are captured and integrated into the CRISPR array as spacer elements, guiding sequence-specific DNA/RNA targeting and cleavage. Recently, in vivo studies have shown that target RNAs with extended complementarity with repeat sequences flanking the target element (tag:anti-tag pairing) can dramatically reduce RNA cleavage by the type VI-A Cas13a system. Here, we report the cryo-EM structure of Leptotrichia shahii LshCas13acrRNA in complex with target RNA harboring tag:anti-tag pairing complementarity, with the observed conformational changes providing a molecular explanation for inactivation of the composite HEPN domain cleavage activity. These structural insights, together with in vitro biochemical and in vivo cell-based assays on key mutants, define the molecular principles underlying Cas13a's capacity to target and discriminate between self and non-self RNA targets. Our studies illuminate approaches to regulate Cas13a's cleavage activity, thereby influencing Cas13a-mediated biotechnological applications.

The evolution of lineage-specific regulatory activities in the human embryonic limb.

The evolution of human anatomical features likely involved changes in gene regulation during development. However, the nature and extent of human-specific developmental regulatory functions remain unknown. We obtained a genome-wide view of cis-regulatory evolution in human embryonic tissues by comparing the histone modification H3K27ac, which provides a quantitative readout of promoter and enhancer activity, during human, rhesus, and mouse limb development. Based on increased H3K27ac, we find that 13% of promoters and 11% of enhancers have gained activity on the human lineage since the human-rhesus divergence. These gains largely arose by modification of ancestral regulatory activities in the limb or potential co-option from other tissues and are likely to have heterogeneous genetic causes. Most enhancers that exhibit gain of activity in humans originated in mammals. Gains at promoters and enhancers in the human limb are associated with increased gene expression, suggesting they include molecular drivers of human morphological evolution.

Electronic phase separation in multilayer rhombohedral graphite.

Of the two stable forms of graphite, hexagonal and rhombohedral, the former is more common and has been studied extensively. The latter is less stable, which has so far precluded its detailed investigation, despite many theoretical predictions about the abundance of exotic interaction-induced physics1-6. Advances in van der Waals heterostructure technology7 have now allowed us to make high-quality rhombohedral graphite films up to 50 graphene layers thick and study their transport properties. Here we show that the bulk electronic states in such rhombohedral graphite are gapped8 and, at low temperatures, electron transport is dominated by surface states. Because of their proposed topological nature, the surface states are of sufficiently high quality to observe the quantum Hall effect, whereby rhombohedral graphite exhibits phase transitions between a gapless semimetallic phase and a gapped quantum spin Hall phase with giant Berry curvature. We find that an energy gap can also be opened in the surface states by breaking their inversion symmetry by applying a perpendicular electric field. Moreover, in rhombohedral graphite thinner than four nanometres, a gap is present even without an external electric field. This spontaneous gap opening shows pronounced hysteresis and other signatures characteristic of electronic phase separation, which we attribute to emergence of strongly correlated electronic surface states.

Drug-drug interaction prediction: databases, web servers and computational models.

In clinical treatment, two or more drugs (i.e. drug combination) are simultaneously or successively used for therapy with the purpose of primarily enhancing the therapeutic efficacy or reducing drug side effects. However, inappropriate drug combination may not only fail to improve efficacy, but even lead to adverse reactions. Therefore, according to the basic principle of improving the efficacy and/or reducing adverse reactions, we should study drug-drug interactions (DDIs) comprehensively and thoroughly so as to reasonably use drug combination. In this review, we first introduced the basic conception and classification of DDIs. Further, some important publicly available databases and web servers about experimentally verified or predicted DDIs were briefly described. As an effective auxiliary tool, computational models for predicting DDIs can not only save the cost of biological experiments, but also provide relevant guidance for combination therapy to some extent. Therefore, we summarized three types of prediction models (including traditional machine learning-based models, deep learning-based models and score function-based models) proposed during recent years and discussed the advantages as well as limitations of them. Besides, we pointed out the problems that need to be solved in the future research of DDIs prediction and provided corresponding suggestions.

Utility of methylated DNA markers for the diagnosis of malignant biliary strictures.

BACKGROUND AND AIMS: Early identification of malignant biliary strictures (MBS) is challenging, with up to 20% classified as indeterminants after preliminary testing and tissue sampling with endoscopic retrograde cholangiopancreatography (ERCP). We aimed to evaluate the use of methylated DNA markers (MDM) from biliary brushings to enhance MBS detection in a prospective cohort. METHODS: Candidate MDMs were evaluated for their utility in MBS diagnosis through a series of discovery and validation phases. DNA was extracted from biliary brushing samples, quantified, bisulfite-converted, and then subjected to methylation-specific Droplet Digital Polymerase Chain Reaction (ddPCR).  Patients were considered to have no malignancy if the sampling was negative and there was no evidence of malignancy after 1 year or definitive negative surgical histopathology. RESULTS: Fourteen candidate MDMs were evaluated in the discovery phase, with top-performing and new markers evaluated in the technical validation phase. The top four MDMs were TWIST1, HOXA1, VSTM2B, and CLEC11A, which individually achieved AUC values of 0.82, 0.81, 0.83, and 0.78, respectively, with sensitivities of 59.4%, 53.1%, 62.5%, and 50.0%, respectively, at high specificities for malignancy of 95.2-95.3% for the final biologic validation phase. When combined as a panel, the AUC was 0.86, achieving 73.4% sensitivity and 92.9% specificity, which outperformed cytology and fluorescent in situ hybridization (FISH). CONCLUSIONS: The selected methylated DNA markers demonstrated improved performance characteristics for the detection of MBS compared to cytology and FISH. ​ Therefore, MDMs should be considered viable candidates for inclusion in diagnostic testing algorithms.​.

Transcriptome-wide subtyping of pediatric and adult T cell acute lymphoblastic leukemia in an international study of 707 cases.

T cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy of T cell progenitors, known to be a heterogeneous disease in pediatric and adult patients. Here we attempted to better understand the disease at the molecular level based on the transcriptomic landscape of 707 T-ALL patients (510 pediatric, 190 adult patients, and 7 with unknown age; 599 from published cohorts and 108 newly investigated). Leveraging the information of gene expression enabled us to identify 10 subtypes (G1­G10), including the previously undescribed one characterized by GATA3 mutations, with GATA3R276Q capable of affecting lymphocyte development in zebrafish. Through associating with T cell differentiation stages, we found that high expression of LYL1/LMO2/SPI1/HOXA (G1­G6) might represent the early T cell progenitor, pro/precortical/cortical stage with a relatively high age of disease onset, and lymphoblasts with TLX3/TLX1 high expression (G7­G8) could be blocked at the cortical/postcortical stage, while those with high expression of NKX2-1/TAL1/LMO1 (G9­G10) might correspond to cortical/postcortical/mature stages of T cell development. Notably, adult patients harbored more cooperative mutations among epigenetic regulators, and genes involved in JAK-STAT and RAS signaling pathways, with 44% of patients aged 40 y or above in G1 bearing DNMT3A/IDH2 mutations usually seen in acute myeloid leukemia, suggesting the nature of mixed phenotype acute leukemia.

High-Temperature Superlubricity in MoS2/Graphene van der Waals Heterostructures.

Achieving high-temperature superlubricity is essential for modern extreme tribosystems. Solid lubrication is the sole viable alternative due to the degradation of liquid ones but currently suffers from notable wear, instability, and high friction coefficient. Here, we report robust superlubricity in MoS2/graphene van der Waals heterostructures at high temperatures up to ∼850 K, achieved through localized heating to enable reliable friction testing. The ultralow friction of the MoS2/graphene heterostructure is found to be notably further reduced at elevated temperature and dominantly contributed by the MoS2 edge. The observation can be well described by a multi-contact model, wherein the thermally activated rupture of edge-contacts facilitates the sliding. Our results should be applicable to other van der Waals heterostructures and shed light on their applications for superlubricity at elevated temperature.

Redox-Sensitive NiOx Stabilizing Perovskite Films for High-Performance Photovoltaics.

Metal halide perovskite materials inherently possess imperfections, particularly under nonequilibrium conditions, such as exposure to light or heat. To tackle this challenge, we introduced stearate ligand-capped nickel oxide (NiOx), a redox-sensitive metal oxide with variable valence, into perovskite intermediate films. The integration of NiOx improved the efficiency and stability of perovskite solar cells (PSCs) by offering multifunctional roles: (1) chemical passivation for ongoing defect repair, (2) energetic passivation to bolster defect tolerance, and (3) field-effect passivation to mitigate charge accumulation. Employing a synergistic approach that tailored these three passivation mechanisms led to a substantial increase in the devices' efficiencies. The target cell (0.12 cm2) and module (18 cm2) exhibited efficiencies of 24.0 and 22.9%, respectively. Notably, the encapsulated modules maintained almost 100 and 87% of the initial efficiencies after operating for 1100 h at the maximum power point (60 °C, 50% RH) and 2000 h of damp-heat testing (85 °C, 85% RH), respectively. Outdoor real-time tests further validated the commercial viability of the NiOx-assisted PSMs. The proposed passivation strategy provides a practical and uncomplicated approach for fabricating high-efficiency and stable photovoltaics.

Atomic Design of Alkyne Semihydrogenation Catalysts via Active Learning.

Alkyne hydrogenation on palladium-based catalysts modified with silver is currently used in industry to eliminate trace amounts of alkynes in alkenes produced from steam cracking and alkane dehydrogenation processes. Intensive efforts have been devoted to designing an alternative catalyst for improvement, especially in terms of selectivity and catalyst cost, which is still far away from that as expected. Here, we describe an atomic design of a high-performance Ni-based intermetallic catalyst aided by active machine learning combined with density functional theory calculations. The engineered NiIn catalyst exhibits >97% selectivity to ethylene and propylene at the full conversion of acetylene and propyne at mild temperature, outperforming the reported Ni-based catalysts and even noble Pd-based ones. Detailed mechanistic studies using theoretical calculations and advanced characterizations elucidate that the atomic-level defined coordination environment of Ni sites and well-designed hybridization of Ni 3d with In 5p orbital determine the semihydrogenation pathway.

Disentangling Thermal from Electronic Contributions in the Spectral Response of Photoexcited Perovskite Materials.

Disentangling electronic and thermal effects in photoexcited perovskite materials is crucial for photovoltaic and optoelectronic applications but remains a challenge due to their intertwined nature in both the time and energy domains. In this study, we employed temperature-dependent variable-angle spectroscopic ellipsometry, density functional theory calculations, and broadband transient absorption spectroscopy spanning the visible to mid-to-deep-ultraviolet (UV) ranges on MAPbBr3 thin films. The use of deep-UV detection opens a new spectral window that enables the exploration of high-energy excitations at various symmetry points within the Brillouin zone, facilitating an understanding of the ultrafast responses of the UV bands and the underlying mechanisms governing them. Our investigation reveals that the photoinduced spectral features remarkably resemble those generated by pure lattice heating, and we disentangle the relative thermal and electronic contributions and their evolutions at different delay times using combinations of decay-associated spectra and temperature-induced differential absorption. The results demonstrate that the photoinduced transients possess a significant thermal origin and cannot be attributed solely to electronic effects. Following photoexcitation, as carriers (electrons and holes) transfer their energy to the lattice, the thermal contribution increases from ∼15% at 1 ps to ∼55% at 500 ps and subsequently decreases to ∼35-50% at 1 ns. These findings elucidate the intricate energy exchange between charge carriers and the lattice in photoexcited perovskite materials and provide insights into the limited utilization efficiency of photogenerated charge carriers.

Solvent-Templated Methylammonium-Based Ruddlesden-Popper Perovskites with Short Interlayer Distances.

Two-dimensional (2D) halide perovskites are exquisite semiconductors with great structural tunability. They can incorporate a rich variety of organic species that not only template their layered structures but also add new functionalities to their optoelectronic characteristics. Here, we present a series of new methylammonium (CH3NH3+ or MA)-based 2D Ruddlesden-Popper perovskites templated by dimethyl carbonate (CH3OCOOCH3 or DMC) solvent molecules. We report the synthesis, detailed structural analysis, and characterization of four new compounds: MA2(DMC)PbI4 (n = 1), MA3(DMC)Pb2I7 (n = 2), MA4(DMC)Pb3I10 (n = 3), and MA3(DMC)Pb2Br7 (n = 2). Notably, these compounds represent unique structures with MA as the sole organic cation both within and between the perovskite sheets, while DMC molecules occupy a tight space between the MA cations in the interlayer. They form hydrogen-bonded [MA···DMC···MA]2+ complexes that act as spacers, preventing the perovskite sheets from condensing into each other. We report one of the shortest interlayer distances (∼5.7-5.9 Å) in solvent-incorporated 2D halide perovskites. Furthermore, the synthesized crystals exhibit similar optical characteristics to other 2D perovskite systems, including narrow photoluminescence (PL) signals. The density functional theory (DFT) calculations confirm their direct-band-gap nature. Meanwhile, the phase stability of these systems was found to correlate with the H-bond distances and their strengths, decreasing in the order MA3(DMC)Pb2I7 > MA4(DMC)Pb3I10 > MA2(DMC)PbI4 ∼ MA3(DMC)Pb2Br7. The relatively loosely bound nature of DMC molecules enables us to design a thermochromic cell that can withstand 25 cycles of switching between two colored states. This work exemplifies the unconventional role of the noncharged solvent molecule in templating the 2D perovskite structure.

Planar Core and Macrocyclic Shell Stabilized Atomically Precise Copper Nanocluster Catalyst for Efficient Hydroboration of C-C Multiple Bond.

Atomically precise metal nanoclusters (NCs) have become an important class of catalysts due to their catalytic activity, high surface area, and tailored active sites. However, the design and development of bond-forming reaction catalysts based on copper NCs are still in their early stages. Herein, we report the synthesis of an atomically precise copper nanocluster with a planar core and unique shell, [Cu45(TBBT)29(TPP)4(C4H11N)2H14]2+ (Cu45) (TBBT: 4-tert-butylbenzenethiol; TPP: triphenylphosphine), in high yield via a one-pot reduction method. The resulting structurally well-defined Cu45 is a highly efficient catalyst for the hydroboration reaction of alkynes and alkenes. Mechanistic studies show that a single-electron oxidation of the in situ-formed ate complex enables the hydroboration via the formation of boryl-centered radicals under mild conditions. This work demonstrates the promise of tailored copper nanoclusters as catalysts for C-B heteroatom bond-forming reactions. The catalysts are compatible with a wide range of alkynes and alkenes and functional groups for producing hydroborated products.

High-Efficiency Circularly Polarized Light-Emitting Diodes Based on Chiral Metal Nanoclusters.

Circularly polarized light-emitting diodes (CP-LEDs) are critical for next-generation optical technologies, ranging from holography to quantum information processing. Currently deployed chiral luminescent materials, with their intricate synthesis and processing and limited efficiency, are the main bottleneck for CP-LEDs. Chiral metal nanoclusters (MNCs) are potential CP-LED materials, given their ease of synthesis and processability as well as diverse structures and excited states. However, their films are usually plagued by inferior electronic quality and aggregation-caused photoluminescence quenching, necessitating their incorporation into host materials; without such a scheme, MNC-based LEDs exhibit external quantum efficiencies (EQEs) < 10%. Herein, we achieve an efficiency leap for both CP-LEDs and cluster-based LEDs by using novel chiral MNCs with aggregation-induced emission enhancement. CP-LEDs using enantiopure MNC films attain EQEs of up to 23.5%. Furthermore, by incorporating host materials, the devices yield record EQEs of up to 36.5% for both CP-LEDs and cluster-based LEDs, along with electroluminescence dissymmetry factors (|gEL|) of around 1.0 × 10-3. These findings open a new avenue for advancing chiral light sources for next-generation optoelectronics.

Enhanced forward scattering of a cell in line optical tweezers with an astigmatic beam.

The line optical tweezers (LOT) has been proven to be an alternative technique to manipulating the biological cells because of the bigger potential compared with traditional optical tweezers with a highly focused spot. We deduce the 4 × 4 optical matrix of the astigmatic LOT to investigate the optical characteristics related to the systematic parameters. The comparison of the initial and scattered electric fields by the cell under the astigmatic and stigmatic LOT is implemented to illustrate that the forward scattered light from the astigmatic LOT is much stronger than that from the stigmatic LOT, so as to the cell deformations. It is demonstrated that the astigmatic LOT could provide a more efficient way to deform the cell not only in the focal plane, but also along the optical axis to screen large biomaterials in biomechanics.

Phase 1 trial of navitoclax and sorafenib in patients with relapsed or refractory solid tumors with hepatocellular carcinoma expansion cohort.

Navitoclax (ABT-263) is an oral BCL2 homology-3 mimetic that binds with high affinity to pro-survival BCL2 proteins, resulting in apoptosis. Sorafenib, an oral multi kinase inhibitor also promotes apoptosis and inhibits tumor angiogenesis. The efficacy of either agent alone is limited; however, preclinical studies demonstrate synergy with the combination of navitoclax and sorafenib. In this phase 1 study, we evaluated the combination of navitoclax and sorafenib in a dose escalation cohort of patients with refractory solid tumors, with an expansion cohort in hepatocellular carcinoma (HCC). Maximum tolerated dose (MTD) was determined using the continual reassessment method. Navitoclax and sorafenib were administered continuously on days 1 through 21 of 21-day cycles. Ten patients were enrolled in the dose escalation cohort and 15 HCC patients were enrolled in the expansion cohort. Two dose levels were tested, and the MTD was navitoclax 150 mg daily plus sorafenib 400 mg twice daily. Among all patients, the most common grade 3 toxicity was thrombocytopenia (5 patients, 20%): there were no grade 4 or 5 toxicities. Patients received a median of 2 cycles (range 1-36 cycles) and all patients were off study treatment at data cut off. Six patients in the expansion cohort had stable disease, and there were no partial or complete responses. Drug-drug interaction between navitoclax and sorafenib was not observed. The combination of navitoclax and sorafenib did not increase induction of apoptosis compared with navitoclax alone. Navitoclax plus sorafenib is tolerable but showed limited efficacy in the HCC expansion cohort. These findings do not support further development of this combination for the treatment of advanced HCC. This phase I trial was conducted under ClinicalTrials.gov registry number NCT01364051.

Natural variation in plant telomere length is associated with flowering time.

Telomeres are highly repetitive DNA sequences found at the ends of chromosomes that protect the chromosomes from deterioration duringcell division. Here, using whole-genome re-sequencing and terminal restriction fragment assays, we found substantial natural intraspecific variation in telomere length in Arabidopsis thaliana, rice (Oryza sativa), and maize (Zea mays). Genome-wide association study (GWAS) mapping in A. thaliana identified 13 regions with GWAS-significant associations underlying telomere length variation, including a region that harbors the telomerase reverse transcriptase (TERT) gene. Population genomic analysis provided evidence for a selective sweep at the TERT region associated with longer telomeres. We found that telomere length is negatively correlated with flowering time variation not only in A. thaliana, but also in maize and rice, indicating a link between life-history traits and chromosome integrity. Our results point to several possible reasons for this correlation, including the possibility that longer telomeres may be more adaptive in plants that have faster developmental rates (and therefore flower earlier). Our work suggests that chromosomal structure itself might be an adaptive trait associated with plant life-history strategies.

Light sheet fluorescence microscopy with active optical manipulation.

We present a light sheet fluorescence microscopy (LSFM) with active optical manipulation by using linear optical tweezers (LOTs). In this method, two coaxially transmitting laser beams of different wavelengths are shaped using cylindrical lenses to form a linear optical trapping perpendicular to the optical axis and an excitation light sheet (LS) parallel to the optical axis, respectively. Multiple large-sized polystyrene fluorescent microspheres are stably captured by LOTs, and their rotation angles around specific rotation axes are precisely controlled. During a sample rotation, the stationary excitation LS scans the sample to obtain fluorescence sectioning images of the sample at different angles.

Ultrafast Axial Freezing in a Liquid-Filled Capillary Tube.

Liquid-filled capillary tubes are a kind of standard component in life science (e.g., blood vessels, interstitial pores, and plant vessels) and engineering (e.g., MEMS microchannel resonators, heat pipe wicks, and water-saturated soils). Under sufficiently low temperatures, the liquid in a capillary tube undergoes phase transition, forming an ice nucleus randomly on its inner wall. However, how an ice layer forms from the nucleus and then expands, either axially or radially to the tube inner wall, remains obscure. We demonstrated, both experimentally and theoretically, that axial freezing along the inner wall of a water-filled capillary tube occurs way ahead of radial freezing, at a nearly constant velocity 3 orders in magnitude faster than the latter. Rapid release of latent heat during axial freezing was identified as the determining factor for the short duration of recalescence, resulting in an exponential rise of the supercooling temperature from ice nucleation via axial freezing to radial freezing. The profile of the ice-water interface is strongly dependent upon the length-to-radius ratio of the capillary tube and the supercooling degree at ice nucleation. The results obtained in this study bridge the knowledge gap between the classical nucleation theory and the Stefan solution of phase transition.

Crosstalk in extrahepatic and hepatic system in NAFLD/NASH.

Non-alcoholic fatty liver disease (NAFLD) has emerged as the most prevalent chronic liver disease globally. Non-alcoholic steatohepatitis (NASH) represents an extremely progressive form of NAFLD, which, without timely intervention, may progress to cirrhosis or hepatocellular carcinoma. Presently, a definitive comprehension of the pathogenesis of NAFLD/NASH eludes us, and pharmacological interventions targeting NASH specifically remain constrained. The aetiology of NAFLD encompasses a myriad of external factors including environmental influences, dietary habits and gender disparities. More significantly, inter-organ and cellular interactions within the human body play a role in the development or regression of the disease. In this review, we categorize the influences affecting NAFLD both intra- and extrahepatically, elaborating meticulously on the mechanisms governing the onset and progression of NAFLD/NASH. This exploration delves into progress in aetiology and promising therapeutic targets. As a metabolic disorder, the development of NAFLD involves complexities related to nutrient metabolism, liver-gut axis interactions and insulin resistance, among other regulatory functions of extraneous organs. It further encompasses intra-hepatic interactions among hepatic cells, Kupffer cells (KCs) and hepatic stellate cells (HSCs). A comprehensive understanding of the pathogenesis of NAFLD/NASH from a macroscopic standpoint is instrumental in the formulation of future therapies for NASH.