A road surface reconstruction dataset for autonomous driving.

Recent developments in intelligent robot systems, especially autonomous vehicles, put forward higher requirements for safety and comfort. Road conditions are crucial factors affecting the comprehensive performance of ground vehicles. Nonetheless, existing environment perception datasets for autonomous driving lack attention to road surface areas. In this paper, we introduce the road surface reconstruction dataset, providing multi-modal, high-resolution, and high-precision data collected by real-vehicle platform in diverse driving conditions. It covers common road types containing approximately 16,000 pairs of stereo images, point clouds, and ground-truth depth/disparity maps, with accurate data processing pipelines to ensure its quality. Preliminary evaluations reveal the effectiveness of our dataset and the challenge of the task, underscoring substantial opportunities of it as a valuable resource for advancing computer vision techniques. The reconstructed road structure and texture contribute to the analysis and prediction of vehicle responses for motion planning and control systems.

Characterization of the Fatty Acyl-CoA Reductase (FAR) Gene Family and Its Response to Abiotic Stress in Rice (Oryza sativa L.).

Fatty acyl-CoA reductase (FAR) is an important NADPH-dependent enzyme that can produce primary alcohol from fatty acyl-CoA or fatty acyl-carrier proteins as substrates. It plays a pivotal role in plant growth, development, and stress resistance. Herein, we performed genome-wide identification and expression analysis of FAR members in rice using bioinformatics methods. A total of eight OsFAR genes were identified, and the OsFARs were comprehensively analyzed in terms of phylogenetic relationships, duplication events, protein motifs, etc. The cis-elements of the OsFARs were predicted to respond to growth and development, light, hormones, and abiotic stresses. Gene ontology annotation analysis revealed that OsFAR proteins participate in biological processes as fatty acyl-CoA reductase during lipid metabolism. Numerous microRNA target sites were present in OsFARs mRNAs. The expression analysis showed that OsFARs were expressed at different levels during different developmental periods and in various tissues. Furthermore, the expression levels of OsFARs were altered under abiotic stresses, suggesting that FARs may be involved in abiotic stress tolerance in rice. The findings presented here serve as a solid basis for further exploring the functions of OsFARs.

Regulation of TRI5 expression and deoxynivalenol biosynthesis by a long non-coding RNA in Fusarium graminearum.

Deoxynivalenol (DON) is the most frequently detected mycotoxin in cereal grains and processed food or feed. Two transcription factors, Tri6 and Tri10, are essential for DON biosynthesis in Fusarium graminearum. In this study we conduct stranded RNA-seq analysis with tri6 and tri10 mutants and show that Tri10 acts as a master regulator controlling the expression of sense and antisense transcripts of TRI6 and over 450 genes with diverse functions. TRI6 is more specific for regulating TRI genes although it negatively regulates TRI10. Two other TRI genes, including TRI5 that encodes a key enzyme for DON biosynthesis, also have antisense transcripts. Both Tri6 and Tri10 are essential for TRI5 expression and for suppression of antisense-TRI5. Furthermore, we identify a long non-coding RNA (named RNA5P) that is transcribed from the TRI5 promoter region and is also regulated by Tri6 and Tri10. Deletion of RNA5P by replacing the promoter region of TRI5 with that of TRI12 increases TRI5 expression and DON biosynthesis, indicating that RNA5P suppresses TRI5 expression. However, ectopic constitutive overexpression of RNA5P has no effect on DON biosynthesis and TRI5 expression. Nevertheless, elevated expression of RNA5P in situ reduces TRI5 expression and DON production. Our results indicate that TRI10 and TRI6 regulate each other's expression, and both are important for suppressing the expression of RNA5P, a long non-coding RNA with cis-acting inhibitory effects on TRI5 expression and DON biosynthesis in F. graminearum.

A non-pheromone GPCR is essential for meiosis and ascosporogenesis in the wheat scab fungus.

Meiosis is essential for generating genetic diversity and sexual spores, but the regulation of meiosis and ascosporogenesis is not clear in filamentous fungi, in which dikaryotic and diploid cells formed inside fruiting bodies are not free living and independent of pheromones or pheromone receptors. In this study, Gia1, a non-pheromone GPCR (G protein-coupled receptor) with sexual-specific expression in Fusarium graminearum, is found to be essential for ascosporogenesis. The gia1 mutant was normal in perithecium development, crozier formation, and karyogamy but failed to undergo meiosis, which could be partially rescued by a dominant active mutation in GPA1 and activation of the Gpmk1 pathway. GIA1 orthologs have conserved functions in regulating meiosis and ascosporogenesis in Sordariomycetes. GIA1 has a paralog, GIP1, in F. graminearum and other Hypocreales species which is essential for perithecium formation. GIP1 differed from GIA1 in expression profiles and downstream signaling during sexual reproduction. Whereas the C-terminal tail and IR3 were important for intracellular signaling, the N-terminal region and EL3 of Gia1 were responsible for recognizing its ligand, which is likely a protein enriched in developing perithecia, particularly in the gia1 mutant. Taken together, these results showed that GIA1 encodes a non-pheromone GPCR that regulates the entry into meiosis and ascosporogenesis via the downstream Gpmk1 MAP kinase pathway in F. graminearum and other filamentous ascomycetes.

The synthesis and functionalization of metal organic frameworks and their applications for the selective separation of proteins/peptides.

Recently, proteins separation has drawn great interest for the full investigation of a proteome because the proteins separation is the precondition when conducting clinical research or proteomics research. Metal organic frameworks (MOFs) are fabricated via covalent connection between organic ligands and metal ions/clusters units. MOFs have attracted much attention due to the ultra-high specific surface area, tunable structure, more metal site or unsaturated site, and chemical stability. Over the past decade, different functionalization types of MOFs have been reported in combination with amino acids, nucleic acids, proteins, polymers, and nanoparticles for various applications. In this review, the synthesis and functionalization of MOFs have been thoroughly discussed, and we introduced the existing problems and development trends in these fields. Furthermore, MOFs as advanced adsorbents for selective separation of proteins/peptides are summarized. Additionally, we present a comprehensive prospects and challenges in the preparation of robust functional MOFs-based adsorbents and make a final outlook on their future development prospects in selective separation of proteins/peptides.

Single Nanovesicles Tracking Reveals Their Heterogeneous Extracellular Adsorptions.

The vigorous nanomedicine offers significant possibilities for effective therapeutics of various diseases, and nanovesicles (NVs) represented by artificial liposomes and natural exosomes and cytomembranes especially show great potential. However, their complex interactions with cells, particularly the heterogeneous extracellular adsorptions, are difficult to analyze spatiotemporally due to the transient dynamics. In this study, by single NVs tracking, the extracellular NVs adsorptions are directly observed and their heterogeneous characteristics are revealed. Briefly, plenty of NVs adsorbed on HCT116 cells are tracked and classified, and it is discovered that they exhibit various diffusion properties from different extracellular regions: stable adsorptions on the rear surface and restricted adsorptions on the front protrusion. After the hydrolysis of hyaluronic acid in the extracellular matrix by hyaluronidase, the restricted adsorptions are further weakened and manifested as dissociative adsorptions, which demonstrated reduced total NVs adsorptions from a single-cell and single-particle perspective. Compared with traditional static analysis, the spatiotemporal tracking and heterogeneous results not only reveal the extracellular NVs-cell interactions but also inspire a wide variety of nanomedicine and their nano-investigations.

Bioactive Constituents of Verbena officinalis Alleviate Inflammation and Enhance Killing Efficiency of Natural Killer Cells.

Natural killer (NK) cells play key roles in eliminating pathogen-infected cells. Verbena officinalis (V. officinalis) has been used as a medical plant in traditional and modern medicine for its anti-tumor and anti-inflammatory activities, but its effects on immune responses remain largely elusive. This study aimed to investigate the potential of V. officinalis extract (VO extract) to regulate inflammation and NK cell functions. We examined the effects of VO extract on lung injury in a mouse model of influenza virus infection. We also investigated the impact of five bioactive components of VO extract on NK killing functions using primary human NK cells. Our results showed that oral administration of VO extract reduced lung injury, promoted the maturation and activation of NK cells in the lung, and decreased the levels of inflammatory cytokines (IL-6, TNF-α and IL-1ß) in the serum. Among five bioactive components of VO extract, Verbenalin significantly enhanced NK killing efficiency in vitro, as determined by real-time killing assays based on plate-reader or high-content live-cell imaging in 3D using primary human NK cells. Further investigation showed that treatment of Verbenalin accelerated the killing process by reducing the contact time of NK cells with their target cells without affecting NK cell proliferation, expression of cytotoxic proteins, or lytic granule degranulation. Together, our findings suggest that VO extract has a satisfactory anti-inflammatory effect against viral infection in vivo, and regulates the activation, maturation, and killing functions of NK cells. Verbenalin from V. officinalis enhances NK killing efficiency, suggesting its potential as a promising therapeutic to fight viral infection.

Dual-Functional Capping Agent-Mediated Transformation of Silver Nanotriangles to Silver Nanoclusters for Dual-Mode Biosensing.

The localized surface plasmon resonance (LSPR) property, depending on the structure (morphology and assembly) of nanoparticles, is very sensitive to the environmental fluctuation. Retaining the colorimetric effect derived from the LSPR property while introducing new optical properties (such as fluorescence) that provide supplementary information is an effective means to improve the controllability in structures and reproducibility in optical properties. DNA as a green and low-cost etching agent has been demonstrated to effectively control the morphology and optical properties (the blue shift of the LSPR peak) of the plasmonic nanoparticles. Herein, taking silver nanotriangles (AgNTs) as a proof of concept, we report a novel strategy to induce precisely tunable LSPR and fluorescence-composited dual-mode signals by using mono-DNA first as an etching agent for etching the morphology of AgNTs and later as a template for synthesizing fluorescent silver nanoclusters (AgNCs). In addition, common templates for synthesizing AgNCs, such as l-glutathione and bovine serum albumin, were demonstrated to have the capability to serve as etching agents. More importantly, these biomolecules as dual-functional capping agents (etching agents and templates) follow the size-dependent rule: as the size of the thiolated biomolecule increases, the blue shift of the LSPR peak increases; at the same time, the fluorescence intensity increases. The enzyme that can change the molecular weight (size) of the biomolecular substrates (DNA, peptides, and proteins) through an enzymatic cleavage reaction was explored to regulate the LSPR and fluorescent properties of the resulting nanoparticles (by etching of AgNTs and synthesis of AgNCs), achieving excellent performance in detection of cancer-related proteases. This study can be expanded to other biopolymers to impact both fundamental nanoscience and applications and provide powerful new tools for bioanalytical biosensors and nanomedicine.

Recent Advances of Seed-Mediated Growth of Metal Nanoparticles: from Growth to Applications.

Unprecedented advances in metal nanoparticle synthesis have paved the way for broad applications in sensing, imaging, catalysis, diagnosis, and therapy by tuning the optical properties, enhancing catalytic performance, and improving chemical and biological properties of metal nanoparticles. The central guiding concept for regulating the size and morphology of metal nanoparticles is identified as the precise manipulation of nucleation and subsequent growth, often known as seed-mediated growth methods. However, since the growth process is sensitive not only to the metal seeds but also to capping agents, metal precursors, growth solution, growth/incubation time, reductants, and other influencing factors, the precise control of metal nanoparticle morphology is multifactorial. Further, multiple reaction parameters are entangled with each other, so it is necessary to clarify the mechanism by which each factor precisely regulates the morphology of metal nanoparticles. In this review, to exploit the generality and extendibility of metal nanoparticle synthesis, the mechanisms of growth influencing factors in seed-mediated growth methods are systematically summarized. Second, a variety of critical properties and applications enabled by grown metal nanoparticles are focused upon. Finally, the current progress and offer insights on the challenges, opportunities, and future directions for the growth and applications of grown metal nanoparticles are reviewed.

An NIR fluorescent/photoacoustic dual-mode probe of NADPH for tumor imaging.

A novel probe was synthesized with a turn-on NIR fluorescent (NIRF)/photoacoustic (PA) response to NADPH, which was successfully applied in both monitoring intracellular NADPH and dual-modal imaging of tumor-bearing mice. It exhibits good potential in studying and understanding the tumor energy metabolism and treatment process related to NADPH.

Recent advances in development of functional magnetic adsorbents for selective separation of proteins/peptides.

Nowadays, proteins separation has attracted great attention in proteomics research. Because the proteins separation is helpful for making an early diagnosis of many diseases. Magnetic nanoparticles are an interesting and useful functional material, and have attracted extensive research interest during the past decades. Because of the excellent properties such as easy surface functionalization, tunable biocompatibility, high saturation magnetization etc, magnetic microspheres have been widely used in isolation of proteins/peptides. Notably, with the rapid development of surface decoration strategies, more and more functional magnetic adsorbents have been designed and fabricated to meet the growing demands of biological separation. In this review, we have collected recent information about magnetic adsorbents applications in selective separation of proteins/peptides. Furthermore, we present a comprehensive prospects and challenges in the field of protein separation relying on magnetic nanoparticles.

Genome-Wide Identification and Expression Analysis of the Stearoyl-Acyl Carrier Protein Δ9 Desaturase Gene Family under Abiotic Stress in Barley.

Stearoyl-acyl carrier protein (ACP) Δ9 desaturase (SAD) is a critical fatty acid dehydrogenase in plants, playing a prominent role in regulating the synthesis of unsaturated fatty acids (UFAs) and having a significant impact on plant growth and development. In this study, we conducted a comprehensive genomic analysis of the SAD family in barley (Hordeum vulgare L.), identifying 14 HvSADs with the FA_desaturase_2 domain, which were divided into four subgroups based on sequence composition and phylogenetic analysis, with members of the same subgroup possessing similar genes and motif structures. Gene replication analysis suggested that tandem and segmental duplication may be the major reasons for the expansion of the SAD family in barley. The promoters of HvSADs contained various cis-regulatory elements (CREs) related to light, abscisic acid (ABA), and methyl jasmonate (MeJA). In addition, expression analysis indicated that HvSADs exhibit multiple tissue expression patterns in barley as well as different response characteristics under three abiotic stresses: salt, drought, and cold. Briefly, this evolutionary and expression analysis of HvSADs provides insight into the biological functions of barley, supporting a comprehensive analysis of the regulatory mechanisms of oil biosynthesis and metabolism in plants under abiotic stress.

Mussel Inspired Trigger-Detachable Adhesive Hydrogel.

Adhesion to many kinds of surfaces, including biological tissues, is important in many fields but has been proved to be extremely challenging. Furthermore, peeling from strong adhesion is needed in many conditions, but is sometimes painful. Herein, a mussel inspired hydrogel is developed to achieve both strong adhesion and trigger-detachment. The former is actualized by electrostatic interactions, covalent bonds, and physical interpenetration, while the latter is triggered, on-demand, through combining a thixotropic supramolecular network and polymer double network. The results of the experiments show that the hydrogel can adhere to various material surfaces and tissues. Moreover, triggered by shear force, non-covalent interactions of the supramolecular network are destroyed. This adhesion can be peeled easily. The possible mechanism involved is discussed and proved. This work will bring new insight into electronic engineering and tissue repair like skin care for premature infants and burn victims.

Hexagonal WO3/3D Porous Graphene as a Novel Zinc Intercalation Anode for Aqueous Zinc-Ion Batteries.

Aqueous Zn-ion batteries (ZIBs) have acquired great attention because of their high safety and environmentally friendly properties. However, the uncontrollable Zn dendrites and the irreversibility of electrodes seriously affect their practical application. Herein, hexagonal WO3/three-dimensional porous graphene (h-WO3/3DG) is investigated as an intercalation anode for ZIBs. As a result, the h-WO3/3DG//Zn half-battery shows excellent electrochemical performance with a high capacity of 115.6 mAh g-1 at 0.1 A g-1 and 89% capacity retention at 2.0 A g-1 after 10 000 cycles. The reason could be that the crystalline structure of WO3, which has hexagonal channels, with a diameter of 5.36 Å, much higher than the diameter of Zn2+ (0.73 Å), accelerating the insertion/extraction of Zn ions. A zinc metal-free full battery using h-WO3/3DG as the anode and ZnMn2O4/carbon black (ZnMn2O4/CB) as the cathode is constructed, exhibiting an initial capacity of 66.8 mAh g-1 at 0.1 A g-1 corresponding to an energy density of 73.5 W h kg-1 (based on the total mass of anode and cathode-active materials) and a capacity retention of 76.6% after 1000 cycles at 0.5 A g-1. This work demonstrates the high potential of hexagonal WO3 as an advanced intercalation anode material for Zn metal-free batteries and may inspire new ideas for the development of other intercalation anode hosts for ZIBs.

PolarMask++: Enhanced Polar Representation for Single-Shot Instance Segmentation and Beyond.

Reducing complexity of the pipeline of instance segmentation is crucial for real-world applications. This work addresses this problem by introducing an anchor-box free and single-shot instance segmentation framework, termed PolarMask++, which reformulates the instance segmentation problem as predicting the contours of objects in the polar coordinate, leading to several appealing benefits. (1) The polar representation unifies instance segmentation (masks) and object detection (bounding boxes) into a single framework, reducing the design and computational complexity. (2) We carefully design two modules (soft polar centerness and polar IoU loss) to sample high-quality center examples and optimize polar contour regression, making the performance of PolarMask++ does not depend on the bounding box prediction and thus more efficient in training. (3) PolarMask++ is fully convolutional and can be easily embedded into most off-the-shelf detectors. To further improve the accuracy of the framework, a Refined Feature Pyramid is introduced to improve the feature representation at different scales. Extensive experiments demonstrate the effectiveness of PolarMask++, which achieves competitive results on COCO dataset, and new state-of-the-art results on text detection and cell segmentation datasets. We hope polar representation can provide a new perspective for designing algorithms to solve single-shot instance segmentation. Code is released at: github.com/xieenze/PolarMask.

Affimer-Based Europium Chelates Allow Sensitive Optical Biosensing in a Range of Human Disease Biomarkers.

The protein biomarker measurement has been well-established using ELISA (enzyme-linked immunosorbent assay), which offers good sensitivity and specificity, but remains slow and expensive. Certain clinical conditions, where rapid measurement or immediate confirmation of a biomarker is paramount for treatment, necessitate more rapid analysis. Biosensors offer the prospect of reagent-less, processing-free measurements at the patient's bedside. Here, we report a platform for biosensing based on chelated Eu3+ against a range of proteins including biomarkers of cardiac injury (human myoglobin), stroke (glial fibrillary acidic protein (GFAP)), inflammation (C-reactive protein (CRP)) and colorectal cancer (carcinoembryonic antigen (CEA)). The Eu3+ ions are chelated by modified synthetic binding proteins (Affimers), which offer an alternative targeting strategy to existing antibodies. The fluorescence characteristics of the Eu3+ complex with modified Affimers against human myoglobin, GFAP, CRP and CEA were measured in human serum using λex = 395 nm, λem = 590 and 615 nm. The Eu3+-Affimer based complex allowed sensitive detection of human myoglobin, GFAP, CRP and CEA proteins as low as 100 fM in (100-fold) diluted human serum samples. The unique dependence on Eu3+ fluorescence in the visible region (590 and 615 nm) was exploited in this study to allow rapid measurement of the analyte concentration, with measurements in 2 to 3 min. These data demonstrate that the Affimer based Eu3+ complexes can function as nanobiosensors with potential analytical and diagnostic applications.

Composable microfluidic spinning platforms for facile production of biomimetic perfusable hydrogel microtubes.

Microtissues with specific structures and integrated vessels play a key role in maintaining organ functions. To recapitulate the in vivo environment for tissue engineering and organ-on-a-chip purposes, it is essential to develop perfusable biomimetic microscaffolds. We developed facile all-aqueous microfluidic approaches for producing perfusable hydrogel microtubes with diverse biomimetic sizes and shapes. Here, we provide a detailed protocol describing the construction of the microtube spinning platforms, the assembly of microfluidic devices, and the fabrication and characterization of various perfusable hydrogel microtubes. The hydrogel microtubes can be continuously generated from microfluidic devices due to the crosslinking of alginate by calcium in the coaxial flows and collecting bath. Owing to the mild all-aqueous spinning process, cells can be loaded into the alginate prepolymer for microtube spinning, which enables the direct production of cell-laden hydrogel microtubes. By manipulating the fluid dynamics at the microscale, the composable microfluidic devices and platforms can be used for the facile generation of six types of biomimetic perfusable microtubes. The microfluidic platforms and devices can be set up within 3 h from commonly available and inexpensive materials. After 10-20 min required to adjust the platform and fluids, perfusable hydrogel microtubes can be generated continuously. We describe how to characterize the microtubes using scanning electron or confocal microscopy. As an example application, we describe how the microtubes can be used for the preparation of a vascular lumen and how to perform barrier permeability tests of the vascular lumen.

Nitrite-Responsive Hydrogel: Smart Drug Release Depending on the Severity of the Nitric Oxide-Related Disease.

Nitric oxide (NO) is known as one of the most important biomarkers of many diseases. However, the development of NO-triggered drug releasing platforms is challenging due to the low concentration and short lifetime of NO in vivo. In this work, a novel nitrite (NO2-)-responsive hydrogel (DHPL-GEL), which can be used for smart drug release depending on the severity of the NO-related disease, is demonstrated. A dihydropyridine cross-linking agent is designed to construct DHPL-GEL to enable the responsive degradation of the hydrogel triggered by NO2-. On-demand release of the drug loaded in DHPL-GEL was observed under the stimulation of various concentrations of NO2- at the physiological level both in vitro and in vivo. In the inflammatory arthritis rat model, the DHPL-GEL drug delivery system showed a better therapeutic effect and less side effects than the traditional therapy and nonresponsive hydrogel drug delivery system, demonstrating the promising application of the NO2--responsive hydrogel for the treatment of NO-related diseases.

Designed Fabrication of Polymer-Mediated MOF-Derived Magnetic Hollow Carbon Nanocages for Specific Isolation of Bovine Hemoglobin.

It is highly required to develop well-designed separation materials for the specific isolation of certain proteins in proteomic research. Herein, the new type of metal-organic framework (MOF)-derived polymer-mediated magnetic hollow nanocages was fabricated via stress-induced orientation contraction, which was further applied for specific enrichment of proteins. The core-shell nanocomposites comprised of polymer-mediated ZIF-67 cores and polydopamine (PDA) shells, after annealing, generated magnetic hollow carbon nanocages with hierarchical pores and structures. Particularly, the magnetic carbonized PDA@F127/ZIF-67 hollow nanocages exhibited a remarkable adsorption capacity toward bovine hemoglobin (BHB) up to 834.3 mg g-1, which was significantly greater than that of the directed carbonized ZIF-67 nanoparticles. The results also exhibited the notable specificity of the obtained nanocages on complex biosamples, including intact mixed proteins and fetal calf serum. The hierarchically hollow porous structure greatly improves the specific surface area and reduces the mass transfer resistance, leading to enhanced high adsorption for target protein BHB. This novel method will be promising for the applications in purification and enrichment of biomacromolecules for complex biosamples, which successfully solve the problem of low adsorption efficiency and tedious separating process of the previous MOF-derived materials.

Selective separation of bovine hemoglobin using magnetic mesoporous rare-earth silicate microspheres.

Selective separation of heme proteins and peptides from complicated biological samples before comprehensive identification and characterization of intact biomolecules which are low stoichiometry is indispensable for ongoing proteomics. Here, three magnetic mesoporous rare-earth silicate (rare-earth = Er, Tm, Yb) microspheres prepared by facile solvothermal method were used as novel adsorbents for the selective isolation of bovine hemoglobin (BHb), and magnetic mesoporous ytterbium silicate showed apparent adsorption efficiency in isolating BHb with a adsorption capacity of 304.4 mg/g after the comparison. The retained BHb could be eluted by using Na2CO3 as stripping reagent. Meanwhile, Circular dichroism spectra illustrated that the microspheres posed no effect on the secondary structure of BHb. The resultant magnetic particles were characterized by transmission electron microscope, scanning electron microscope, x-ray powder diffraction, vibrating sample magnetometer, Fourier transform infrared spectroscopy, N2 adsorption-desorption isotherm and zeta potential. The as-prepared magnetic microspheres showed high specificity for the separation of BHb from bovine plasma as corroborated by SDS-PAGE and MALDI-TOF MS analysis, which would be expected to possess potential application in isolation of other heme proteins in complex biological samples.