PanDepth, an ultrafast and efficient genomic tool for coverage calculation.

Coverage quantification is required in many sequencing datasets within the field of genomics research. However, most existing tools fail to provide comprehensive statistical results and exhibit limited performance gains from multithreading. Here, we present PanDepth, an ultra-fast and efficient tool for calculating coverage and depth from sequencing alignments. PanDepth outperforms other tools in computation time and memory efficiency for both BAM and CRAM-format alignment files from sequencing data, regardless of read length. It employs chromosome parallel computation and optimized data structures, resulting in ultrafast computation speeds and memory efficiency. It accepts sorted or unsorted BAM and CRAM-format alignment files as well as GTF, GFF and BED-formatted interval files or a specific window size. When provided with a reference genome sequence and the option to enable GC content calculation, PanDepth includes GC content statistics, enhancing the accuracy and reliability of copy number variation analysis. Overall, PanDepth is a powerful tool that accelerates scientific discovery in genomics research.

Achieving Ultra-Broad Microwave Absorption Bandwidth Around Millimeter-Wave Atmospheric Window Through an Intentional Manipulation on Multi-Magnetic Resonance Behavior.

The utilization of electromagnetic waves is rapidly advancing into the millimeter-wave frequency range, posing increasingly severe challenges in terms of electromagnetic pollution prevention and radar stealth. However, existing millimeter-wave absorbers are still inadequate in addressing these issues due to their monotonous magnetic resonance pattern. In this work, rare-earth La3+ and non-magnetic Zr4+ ions are simultaneously incorporated into M-type barium ferrite (BaM) to intentionally manipulate the multi-magnetic resonance behavior. By leveraging the contrary impact of La3+ and Zr4+ ions on magnetocrystalline anisotropy field, the restrictive relationship between intensity and frequency of the multi-magnetic resonance is successfully eliminated. The magnetic resonance peak-differentiating and imitating results confirm that significant multi-magnetic resonance phenomenon emerges around 35 GHz due to the reinforced exchange coupling effect between Fe3+ and Fe2+ ions. Additionally, Mössbauer spectra analysis, first-principle calculations, and least square fitting collectively identify that additional La3+ doping leads to a profound rearrangement of Zr4+ occupation and thus makes the portion of polarization/conduction loss increase gradually. As a consequence, the La3+-Zr4+ co-doped BaM achieves an ultra-broad bandwidth of 12.5 + GHz covering from 27.5 to 40 + GHz, which holds remarkable potential for millimeter-wave absorbers around the atmospheric window of 35 GHz.

Mechanistic Insights into the Inhibition of a Common CTLA-4 Gene Mutation in the Cytoplasmic Domain.

Cytotoxic T-lymphocyte antigen 4 (CTLA-4) is a pivotal immune checkpoint receptor, playing a crucial role in modulating T-cell activation. In this study, we delved into the underlying mechanism by which a common mutation, G199R, in the cytoplasmic domain of CTLA-4 impacts its inhibitory function. Utilizing nuclear magnetic resonance (NMR) spectroscopy and biochemical techniques, we mapped the conformational changes induced by this mutation and investigated its role in CTLA-4 activity. Our findings reveal that this mutation leads to a distinct conformational alteration, enhancing protein-membrane interactions. Moreover, functional assays demonstrated an improved capacity of the G199R mutant to downregulate T-cell activation, underscoring its potential role in immune-related disorders. These results not only enhance our understanding of CTLA-4 regulatory mechanisms but also provide insights for targeted therapeutic strategies addressing immune dysregulation linked to CTLA-4 mutations.

Lipidomics analysis of rice bran during storage unveils mechanisms behind dynamic changes in functional lipid molecular species.

Rice bran, recognized for its rich lipids and health-beneficial bioactive compounds, holds considerable promise in applications such as rice bran oil production. However, its susceptibility to lipid hydrolysis and oxidation during storage presents a significant challenge. In response, we conducted an in-depth metabolic profiling of rice bran over a storage period of 14 days. We focused on the identification of bioactive compounds and functional lipid species (25 acylglycerols and 53 phospholipids), closely tracking their dynamic changes over time. Our findings revealed significant reductions in these lipid molecular species, highlighting the impact of rancidity processes. Furthermore, we identified 19 characteristic lipid markers and elucidated that phospholipid and glycerolipid metabolism were key metabolic pathways involved. By shedding light on the mechanisms driving lipid degradation in stored rice bran, our study significantly advanced the understanding of lipid stability. These information provided valuable insights for countering rancidity and optimizing rice bran preservation strategies.

Deciphering Cholesterol's Role in PD-L2 Stability: A Distinct Regulatory Mechanism From PD-L1.

Programmed cell death 1 ligand 2 (PD-L2), a member of the B7 immune checkpoint protein family, emerges as a crucial player in immune modulation. Despite its functional overlap with programmed cell death 1 ligand 1 (PD-L1) in binding to the programmed cell death protein 1 (PD-1) on T cells, PD-L2 exhibits a divergent expression pattern and a higher affinity for PD-1. However, the regulatory mechanisms of PD-L2 remain under-explored. Here, our investigations illustrate the pivotal role of cholesterol in modulating PD-L2 stability. Using advanced nuclear magnetic resonance (NMR) and biochemical analyses, we demonstrate a direct and specific binding between cholesterol and PD-L2, mediated by an F-xxx-V-xx-LR motif in its transmembrane domain, distinct from that in PD-L1. This interaction stabilizes PD-L2 and prevents its downstream degradation. Disruption of this binding motif compromises PD-L2's cellular stability, underscoring its potential significance in cancer biology. These findings not only deepen our understanding of PD-L2 regulation in the context of tumors, but also open avenues for potential therapeutic interventions.

Exploring Diacylglycerol Oil-Based Oleogels as Effective Stabilizers in Peanut Butter: Performance, Structural Insights, and Sensory Evaluation.

In the pursuit of reducing oil separation in peanut butter, oleogels synthesized from diacylglycerol (DAG)-rich peanut oils, using glycerol monostearate (GMS) as the gelator, were examined as alternative stabilizers. In comparison to triacylglycerol (TAG)-rich peanut oils, the DAG oil-based oleogels exhibited better oil-binding capacities across increasing GMS concentrations. Intriguingly, thermal and rheological assessments pointed to a weaker network structure in DAG oil oleogels, as evidenced by their lower crystallization temperatures and reduced viscoelastic parameters (G' and G''). Insight from infrared spectroscopy revealed that this could stem from heightened intermolecular hydrogen bonding between the DAG oil and the gelator. When applied to peanut butter, DAG oil oleogels demonstrated efficacy in minimizing oil separation. Extended storage trials affirmed the long-term stability of peanut butter formulations incorporating these oleogels. Furthermore, sensory evaluations by panelists underscored favorable impressions, suggesting potential consumer acceptance. Overall, this study illuminates the promising role of DAG oleogels as effective, alternative stabilizers in peanut butter formulations.

Comparison of different corneal residual bed thickness after small incision lenticule extraction (SMILE).

PURPOSE: To evaluate the corneal biological parameters stability between the different corneal residual bed thickness (RBT) after Small Incision Lenticule Extraction (SMILE). METHODS: In this prospective clinical trial, 127 eyes of 64 patients underwent SMILE. According to the corneal RBT, the patients were divided into the 250-270 µm, 270-290 µm and 290-310 µm groups. Corvis ST (Oculus Optikgeräte GmbH, Wetzlar, Germany) and Scheimpflug camera (Pentacam; Oculus Optikgeräte GmbH, Wetzlar, Germany) measurements were performed preoperatively, 1 day, 1week, 1month and 3 months after surgery. RESULTS: The keratometer values among the three groups were no significant differences in postoperative periods (each P > 0.05), except the corneal thickness values (each P < 0.05). In the 250-270 µm and 270-290 µm groups, the keratometer and corneal thickness values were decreased at postoperative 1 week and increased at 1 and 3 months. The 290-310 µm group significantly higher posterior maximum elevation (PME) than the 250-270 µm group at 1 and 3 months (P = 0.022, 0.022, respectively), and higher preoperative thinnest point (PTE) at 1 week and 1 month (P = 0.013, 0.035, respectively). The PME of the 290-310 µm group was higher than the 270-290 µm group at 3 months (P = 0.045), and higher PTE at 1 week and 3 months (P = 0.022, 0.02, respectively). In all three groups, the maximal deformation amplitude (DA) was significantly higher at 1 and 3 months compared to postoperative 1 day and 1 week, and the IOP was decreased at 1 month then recovered at 3 months (each P < 0.05).The DA of the 250-270 µm group was significantly higher than the 290-310 µm group at postoperative 1 week, 1 and 3 months (P = 0.001, 0.01, 0.02, respectively). The change of the posterior corneal elevation and biomechanical parameters values were no significant differences among the three groups in postoperative periods (each P > 0.05). CONCLUSIONS: The range of 250-310 µm RBT was safe and stable at the early postoperative of SMILE. The RBT may be positively correlated with the posterior corneal elevation.

Transcription factor SlWRKY50 enhances cold tolerance in tomato by activating the jasmonic acid signaling.

Tomato (Solanum lycopersicum) is a cold-sensitive crop but frequently experiences low-temperature stimuli. However, tomato responses to cold stress are still poorly understood. Our previous studies have shown that using wild tomato (Solanum habrochaites) as rootstock can significantly enhance the cold resistance of grafted seedlings, in which a high concentration of jasmonic acids (JAs) in scions exerts an important role, but the mechanism of JA accumulation remains unclear. Herein, we discovered that tomato SlWRKY50, a Group II WRKY transcription factor that is cold inducible, responds to cold stimuli and plays a key role in JA biosynthesis. SlWRKY50 directly bound to the promoter of tomato allene oxide synthase gene (SlAOS), and overexpressing SlWRKY50 improved tomato chilling resistance, which led to higher levels of Fv/Fm, antioxidative enzymes, SlAOS expression, and JA accumulation. SlWRKY50-silenced plants, however, exhibited an opposite trend. Moreover, diethyldithiocarbamate acid (a JA biosynthesis inhibitor) foliar treatment drastically reduced the cold tolerance of SlWRKY50-overexpression plants to wild-type levels. Importantly, SlMYC2, the key regulator of the JA signaling pathway, can control SlWRKY50 expression. Overall, our research indicates that SlWRKY50 promotes cold tolerance by controlling JA biosynthesis and that JA signaling mediates SlWRKY50 expression via transcriptional activation by SlMYC2. Thus, this contributes to the genetic knowledge necessary for developing cold-resistant tomato varieties.

Ultrathin Rh Nanosheets with Rich Grain Boundaries for Efficient Hydrogen Oxidation Electrocatalysis.

Two-dimensional (2D) Pt-group ultrathin nanosheets (NSs) are promising advanced electrocatalysts for energy-related catalytic reactions. However, improving the electrocatalytic activity of 2D Pt-group NSs through the addition of abundant grain boundaries (GBs) and understanding the underlying formation mechanism remain significant challenges. Herein, we report the controllable synthesis of a series of Rh-based nanocrystals (e.g., Rh nanoparticles, Rh NSs, and Rh NSs with GBs) through a CO-mediated kinetic control synthesis route. In light of the 2D NSs' structural advantages and GB modification, the Rh NSs with rich GBs exhibit an enhanced electrocatalytic activity compared to pure Rh NSs and commercial Pt/C toward the hydrogen oxidation reaction (HOR) in alkaline media. Both experimental results and theoretical computations corroborate that the GBs in the Rh NSs have the capacity to ameliorate the adsorption free energy of reaction intermediates during the HOR, thus resulting in outstanding HOR catalytic performance. Our work offers novel perspectives in the realm of developing sophisticated 2D Pt-group metal electrocatalysts with rich GBs for the energy conversion field.

Enhanced electrocatalytic hydrogen evolution from nitrogen plasma-tailored MoS2 nanostructures.

Two-dimensional (2D) layered transition metal dichalcogenides such as MoS2 have been viewed as the most favorable candidates for replacing noble metals in catalyzing the hydrogen evolution reaction in water splitting owing to their earth abundance, superb chemical stability, and appropriate Gibbs free energy. However, due to its low number of catalytic sites and basal catalytic inertia, the pristine MoS2 displayed intrinsically unsatisfactory HER catalytic activity. Here, the hydrogen evolution catalytic activities of nanostructured MoS2 powder before and after plasma modification with nitrogen doping were experimentally compared, and the influence of treatment parameters on the hydrogen evolution catalytic performance of MoS2 has been studied. The feasibility of regulating hydrogen evolution catalytic activity by nitrogen doping of MoS2 was verified based on density functional theory calculations. Our work demonstrates a more convenient and faster way to develop cheap and efficient MoS2-based catalysts for electrochemical hydrogen evolution reactions. Additionally, theoretical studies reveal that N-doped MoS2 exhibits strong hybridization between Mo-d and N-p states, causing magnetism to evolve, as confirmed by experiments.

Occluded Facial Pain Assessment in the ICU using Action Units Guided Network.

Untreated pain in critically ill patients can lead to immunosuppression and increased metabolic activity, with severe clinical consequences such as tachypnea and delirium. Continuous pain assessment is challenging due to nursing shortages and intensive care unit (ICU) workload. Mechanical ventilation equipment obscures the facial features of many patients in the ICU, making previous facial pain detection methods based on full-face images inapplicable. This paper proposes a facial Action Units (AUs) guided pain assessment network for faces under occlusion. The network consists of an AU-guided (AUG) module, a texture feature extraction (TFE) module, and a pain assessment (PA) module. The AUG module automatically detects AUs in the non-occluded areas of the face. In contrast, the TFE module detects the facial landmarks and crops prior knowledge patches, a random exploration patch, and a global feature patch. Then these patches are fed into two convolutional networks to extract texture features. Afterward, the designed AU guidances and texture features are fused in the PA module to assess the pain state. Extensive validation is conducted on a public dataset and two datasets created in this work. The proposed network architecture achieves superior performance in binary classification, four-class classification, and intensity regression tasks. In addition, we have successfully applied the network to actual data collected in the laboratory environment with excellent results.

Candidate regulators of drought stress in tomato revealed by comparative transcriptomic and proteomic analyses.

Drought is among the most common abiotic constraints of crop growth, development, and productivity. Integrating different omics approaches offers a possibility for deciphering the metabolic pathways and fundamental mechanisms involved in abiotic stress tolerance. Here, we explored the transcriptional and post-transcriptional changes in drought-stressed tomato plants using transcriptomic and proteomic profiles to determine the molecular dynamics of tomato drought stress responses. We identified 22467 genes and 5507 proteins, among which the expression of 3765 genes and 294 proteins was significantly changed under drought stress. Furthermore, the differentially expressed genes (DEGs) and differentially abundant proteins (DAPs) showed a good correlation (0.743). The results indicated that integrating different omics approaches is promising in exploring the multilayered regulatory mechanisms of plant drought resistance. Gene ontology (GO) and pathway analysis identified several GO terms and pathways related to stress resistance, including response to stress, abiotic stimulus, and oxidative stress. The plant hormone abscisic acid (ABA) plays pivotal roles in response to drought stress, ABA-response element binding factor (AREB) is a key positive regulator of ABA signaling. Moreover, our analysis indicated that drought stress increased the abscisic acid (ABA) content, which activated AREB1 expression to regulate the expression of TAS14, GSH-Px-1, and Hsp, ultimately improving tomato drought resistance. In addition, the yeast one-hybrid assay demonstrated that the AREB1 could bind the Hsp promoter to activate Hsp expression. Thus, this study involved a full-scale analysis of gene and protein expression in drought-stressed tomato, deepening the understanding of the regulatory mechanisms of the essential drought-tolerance genes in tomato.

Microtubule-associated protein SlMAP70 interacts with IQ67-domain protein SlIQD21a to regulate fruit shape in tomato.

Tomato (Solanum lycopersicum) fruit shape is related to microtubule organization and the activity of microtubule-associated proteins (MAPs). However, insights into the mechanism of fruit shape formation from a cell biology perspective remain limited. Analysis of the tissue expression profiles of different microtubule regulators revealed that functionally distinct classes of MAPs, including members of the plant-specific MICROTUBULE-ASSOCIATED PROTEIN 70 (MAP70) and IQ67 DOMAIN (IQD, also named SUN in tomato) families, are differentially expressed during fruit development. SlMAP70-1-3 and SlIQD21a are highly expressed during fruit initiation, which relates to the dramatic microtubule pattern rearrangements throughout this developmental stage of tomato fruits. Transgenic tomato lines overexpressing SlMAP70-1 or SlIQD21a produced elongated fruits with reduced cell circularity and microtubule anisotropy, while their loss-of-function mutants showed the opposite phenotype, harboring flatter fruits. Fruits were further elongated in plants coexpressing both SlMAP70-1 and SlIQD21a. We demonstrated that SlMAP70s and SlIQD21a physically interact and that the elongated fruit phenotype is likely due to microtubule stabilization induced by the SlMAP70-SlIQD21a interaction. Together, our results identify SlMAP70 proteins and SlIQD21a as important regulators of fruit elongation and demonstrate that manipulating microtubule function during early fruit development provides an effective approach to alter fruit shape.

Gradient Nitrogen Doping in the Garnet Electrolyte for Highly Efficient Solid-State-Electrolyte/Li Interface by N2 Plasma.

Solid-state lithium batteries (SSBs) have been widely researched as next-generation energy storage technologies due to their high energy density and high safety. However, lithium dendrite growth through the solid electrolyte usually results from the catastrophic interface contact between the solid electrolyte and lithium metal. Herein, a gradient nitrogen-doping strategy by nitrogen plasma is introduced to modify the surface and subsurface of the garnet electrolyte, which not only etches the surface impurities (e.g., Li2CO3) but also generates an in situ formed Li3N-rich interphase between the solid electrolyte and lithium anode. As a result, the Li/LLZTON-3/Li cells show a low interfacial resistance (3.50 Ω cm2) with a critical current density of about 0.65 mA cm-2 at room temperature and 1.60 mA cm-2 at 60 °C, as well as a stable cycling life for over 1300 h at 0.4 mA cm-2 at room temperature. A hybrid solid-state full cell paired with a LiFePO4 cathode exhibits excellent cycling durability and rate performance at room temperature. These results demonstrate a rational strategy to enable lithium utilization in SSBs.

Three-Dimensional Collision Avoidance Method for Robot-Assisted Minimally Invasive Surgery.

In the robot-assisted minimally invasive surgery, if a collision occurs, the robot system program could be damaged, and normal tissues could be injured. To avoid collisions during surgery, a 3-dimensional collision avoidance method is proposed in this paper. The proposed method is predicated on the design of 3 strategic vectors: the collision-with-instrument-avoidance (CI) vector, the collision-with-tissues-avoidance (CT) vector, and the constrained-control (CC) vector. The CI vector demarcates 3 specific directions to forestall collision among the surgical instruments. The CT vector, on the other hand, comprises 2 components tailored to prevent inadvertent contact between the robot-controlled instrument and nontarget tissues. Meanwhile, the CC vector is introduced to guide the endpoint of the robot-controlled instrument toward the desired position, ensuring precision in its movements, in alignment with the surgical goals. Simulation results verify the proposed collision avoidance method for robot-assisted minimally invasive surgery. The code and data are available at https://github.com/cynerelee/collision-avoidance.

Unveiling the Structural Self-Reconstruction and Identifying the Reactive Center of a V, Fe Co-Doped Cobalt Precatalyst toward Enhanced Overall Water Splitting by Operando Raman Spectroscopy.

The development of efficient and stable bifunctional electrocatalysts based on non-noble metals for water electrolysis is both urgent and challenging. However, unresolved issues remain regarding the challenge of identifying the active phase and gaining a comprehensive understanding of its surface reconstruction and functionality throughout the reaction process. In this study, we have combined doping and heterostructure construction by a one-step electrodeposition and a subsequent activation treatment to synthesize Fe, V co-doped Co3O4/Co(OH)2 and Co/Co(OH)2 heterointerfaces (referred to as A-Co60Fe1.1V). These heterointerfaces, composed of Co/Co(OH)2 and Co3O4/Co(OH)2, are proposed to facilitate charge transfer process during catalysis. X-ray photoelectron spectroscopy (XPS) analysis demonstrates that the introduction of V and Fe dopants increases the valence state of Co centers in Co3O4 and Co(OH)2. Further operando Raman spectroscopy reveals that Co(OH)2 and Co3O4 with the high-valence Co centers remain stable during the hydrogen evolution reaction (HER) process. These high-valence Co centers are believed to promote the crucial water dissociation step and therefore enhance the overall HER catalysis. On the other hand, during the oxygen evolution reaction (OER), Fe, V co-doping leads to an earlier formation of the active CoOOH species, while Fe doping can further help stabilize the more reactive ß-CoOOH species instead of the less reactive γ-CoOOH. As a result, the A-Co60Fe1.1V catalyst exhibits significantly improved catalytic activity for both HER and OER that it requires low overpotentials of 51 and 250 mV, respectively, to attain a current density of 10 mA cm-2. Moreover, when utilized as both the cathode and anode in alkaline water electrolysis, the A-Co60Fe1.1V catalyst can operate at a mere 1.54 V voltage while maintaining 10 mA cm-2, surpassing the majority of non-noble metal catalysts. Remarkably, it also exhibits stability for at least 40 h at ∼100 mA cm-2.

Tailoring the Microstructure of Porous Carbon Spheres as High Rate Performance Anodes for Lithium-Ion Batteries.

Benefiting from their high surface areas, excellent conductivity, and environmental-friendliness, porous carbon nanospheres (PCSs) are of particular attraction for the anodes of lithium-ion batteries (LIBs). However, the regulation of carbon nanospheres with controlled pore distribution and graphitization for delivering high Li+ storage behavior is still under investigation. Here, we provide a facile approach to obtain PCSs with different microstructures via modulating the carbonization temperatures. With the processing temperature of 850 °C, the optimized PCSs exhibit an increased surface area, electrical conductivity, and enhanced specific capacity (202 mA h g-1 at 2 A g-1) compared to the PCSs carbonized at lower temperatures. Additionally, PCSs 850 provide excellent cyclability with a capacity retention of 83% for 500 cycles. Such work can pave a new pathway to achieve carbon nanospheres with excellent performances in LIBs.

Plant lysin motif extracellular proteins are required for arbuscular mycorrhizal symbiosis.

Arbuscular mycorrhizal fungi (AMF) can form a mutually beneficial symbiotic relationship with most land plants. They are known to secrete lysin motif (LysM) effectors into host root cells for successful colonization. Intriguingly, plants secrete similar types of LysM proteins; however, their role in plant-microbe interactions is unknown. Here, we show that Medicago truncatula deploys LysM extracellular (LysMe) proteins to facilitate symbiosis with AMF. Promoter analyses demonstrated that three M. truncatula LysMe genes MtLysMe1/2/3, are expressed in arbuscule-containing cells and those adjacent to intercellular hyphae. Localization studies showed that these proteins are targeted to the periarbuscular space between the periarbuscular membrane and the fungal cell wall of the branched arbuscule. M. truncatula mutants in which MtLysMe2 was knocked out via CRISPR/Cas9-targeted mutagenesis exhibited a significant reduction in AMF colonization and arbuscule formation, whereas genetically complemented transgenic plants restored wild-type level AMF colonization. In addition, knocking out the ortholog of MtLysMe2 in tomato resulted in a similar defect in AMF colonization. In vitro binding affinity precipitation assays suggested binding of MtLysMe1/2/3 with chitin and chitosan, while microscale thermophoresis (MST) assays revealed weak binding of these proteins with chitooligosaccharides. Moreover, application of purified MtLysMe proteins to root segments could suppress chitooctaose (CO8)-induced reactive oxygen species production and expression of reporter genes of the immune response without impairing chitotetraose (CO4)-triggered symbiotic responses. Taken together, our results reveal that plants, like their fungal partners, also secrete LysM proteins to facilitate symbiosis establishment.

SlZF3 regulates tomato plant height by directly repressing SlGA20ox4 in the gibberellic acid biosynthesis pathway.

Plant height is an important target trait for crop genetic improvement. Our previous work has identified a salt-tolerant C2H2 zinc finger, SlZF3, and its overexpression lines also showed a semi-dwarf phenotype, but the molecular mechanism remains to be elucidated. Here, we characterized the dwarf phenotype in detail. The dwarfism is caused by a decrease in stem internode cell elongation and deficiency of bioactive gibberellic acids (GAs), and can be rescued by exogenous GA3 treatment. Gene expression assays detected reduced expression of genes in the GA biosynthesis pathway of the overexpression lines, including SlGA20ox4. Several protein-DNA interaction methods confirmed that SlZF3 can directly bind to the SlGA20ox4 promoter and inhibit its expression, and the interaction can also occur for SlKS and SlKO. Overexpression of SlGA20ox4 in the SlZF3-overexpressing line can recover the dwarf phenotype. Therefore, SlZF3 regulates plant height by directly repressing genes in the tomato GA biosynthesis pathway.