IAnimal: a cross-species omics knowledgebase for animals.

With the exponential growth of multi-omics data, its integration and utilization have brought unprecedented opportunities for the interpretation of gene regulation mechanisms and the comprehensive analyses of biological systems. IAnimal (https://ianimal.pro/), a cross-species, multi-omics knowledgebase, was developed to improve the utilization of massive public data and simplify the integration of multi-omics information to mine the genetic mechanisms of objective traits. Currently, IAnimal provides 61 191 individual omics data of genome (WGS), transcriptome (RNA-Seq), epigenome (ChIP-Seq, ATAC-Seq) and genome annotation information for 21 species, such as mice, pigs, cattle, chickens, and macaques. The scale of its total clean data has reached 846.46 TB. To better understand the biological significance of omics information, a deep learning model for IAnimal was built based on BioBERT and AutoNER to mine 'gene' and 'trait' entities from 2 794 237 abstracts, which has practical significance for comprehending how each omics layer regulates genes to affect traits. By means of user-friendly web interfaces, flexible data application programming interfaces, and abundant functional modules, IAnimal enables users to easily query, mine, and visualize characteristics in various omics, and to infer how genes play biological roles under the influence of various omics layers.

CompleteInst: An Efficient Instance Segmentation Network for Missed Detection Scene of Autonomous Driving.

As a fundamental computer vision task, instance segmentation is widely used in the field of autonomous driving because it can perform both instance-level distinction and pixel-level segmentation. We propose CompleteInst based on QueryInst as a solution to the problems of missed detection with a network structure designed from the feature level and the instance level. At the feature level, we propose Global Pyramid Networks (GPN) to collect global information of missed instances. Then, we introduce the semantic branch to complete the semantic features of the missed instances. At the instance level, we implement the query-based optimal transport assignment (OTA-Query) sample allocation strategy which enhances the quality of positive samples of missed instances. Both the semantic branch and OTA-Query are parallel, meaning that there is no interference between stages, and they are compatible with the parallel supervision mechanism of QueryInst. We also compare their performance to that of non-parallel structures, highlighting the superiority of the proposed parallel structure. Experiments were conducted on the Cityscapes and COCO dataset, and the recall of CompleteInst reached 56.7% and 54.2%, a 3.5% and 3.2% improvement over the baseline, outperforming other methods.

Allosteric modulation of SHP2: Quest from known to unknown.

Src homology-2 domain-containing protein tyrosine phosphatase-2 (SHP2) is a key regulatory factor in the cell cycle and its activating mutations play an important role in the development of various cancers, making it an important target for antitumor drugs. Due to the highly conserved amino acid sequence and positively charged nature of the active site of SHP2, it is difficult to discover inhibitors with high affinity for the catalytic site of SHP2 and sufficient cell permeability, making it considered an "undruggable" target. However, the discovery of allosteric regulation mechanisms provides new opportunities for transforming undruggable targets into druggable ones. Given the limitations of orthosteric inhibitors, SHP2 allosteric inhibitors have become a more selective and safer research direction. In this review, we elucidate the oncogenic mechanism of SHP2 and summarize the discovery methods of SHP2 allosteric inhibitors, providing new strategies for the design and improvement of SHP2 allosteric inhibitors.

An updated review of the new hadron states.

The past decades witnessed the golden era of hadron physics. Many excited open heavy flavor mesons and baryons have been observed since 2017. We shall provide an updated review of the recent experimental and theoretical progresses in this active field. Besides the conventional heavy hadrons, we shall also review the recently observed open heavy flavor tetraquark statesX(2900) andTcc+(3875)as well as the hidden heavy flavor multiquark statesX(6900),Pcs(4459)0,Zcs(3985)-,Zcs(4000)+, andZcs(4220)+. We will also cover the recent progresses on the glueballs and light hybrid mesons, which are the direct manifestations of the non-AbelianSU(3) gauge interaction of the Quantum Chromodynamics in the low-energy region.

Novel Coupled Channel Framework Connecting the Quark Model and Lattice QCD for the Near-threshold D_{s} States.

A novel framework is proposed to extract near-threshold resonant states from finite-volume energy levels of lattice QCD and is applied to elucidate structures of the positive parity D_{s}. The quark model, the quark-pair-creation mechanism and D^{(*)}K interaction are incorporated into the Hamiltonian effective field theory. The bare 1^{+} cs[over ¯] states are almost purely given by the states with heavy-quark spin bases. The physical D_{s0}^{*}(2317) and D_{s1}^{*}(2460) are the mixtures of bare cs[over ¯] core and D^{(*)}K component, while the D_{s1}^{*}(2536) and D_{s2}^{*}(2573) are almost dominated by bare cs[over ¯]. Furthermore, our model reproduces the clear level crossing of the D_{s1}^{*}(2536) with the scattering state at a finite volume.

A review of the open charm and open bottom systems.

Since the discovery of the first charmed meson in 1976, many open-charm and open-bottom hadrons were observed. In 2003 two narrow charm-strange states [Formula: see text] and D s1(2460) were discovered by the BaBar and CLEO Collaborations, respectively. After that, more excited heavy hadrons were reported. In this work, we review the experimental and theoretical progress in this field.

The genome of the pear (Pyrus bretschneideri Rehd.).

The draft genome of the pear (Pyrus bretschneideri) using a combination of BAC-by-BAC and next-generation sequencing is reported. A 512.0-Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 194× coverage. High-density genetic maps comprising 2005 SNP markers anchored 75.5% of the sequence to all 17 chromosomes. The pear genome encodes 42,812 protein-coding genes, and of these, ~28.5% encode multiple isoforms. Repetitive sequences of 271.9 Mb in length, accounting for 53.1% of the pear genome, are identified. Simulation of eudicots to the ancestor of Rosaceae has reconstructed nine ancestral chromosomes. Pear and apple diverged from each other ~5.4-21.5 million years ago, and a recent whole-genome duplication (WGD) event must have occurred 30-45 MYA prior to their divergence, but following divergence from strawberry. When compared with the apple genome sequence, size differences between the apple and pear genomes are confirmed mainly due to the presence of repetitive sequences predominantly contributed by transposable elements (TEs), while genic regions are similar in both species. Genes critical for self-incompatibility, lignified stone cells (a unique feature of pear fruit), sorbitol metabolism, and volatile compounds of fruit have also been identified. Multiple candidate SFB genes appear as tandem repeats in the S-locus region of pear; while lignin synthesis-related gene family expansion and highly expressed gene families of HCT, C3'H, and CCOMT contribute to high accumulation of both G-lignin and S-lignin. Moreover, alpha-linolenic acid metabolism is a key pathway for aroma in pear fruit.

Decoding the X(5568) as a Fully Open-Flavor sub[over ¯]d[over ¯] Tetraquark State.

We investigate the recent evidence for a charged X(5568) meson as an exotic open-flavor tetraquark state sub[over ¯]d[over ¯] with J^{P}=0^{+}/1^{+} in the framework of QCD sum rules. We use the color antisymmetric [3[over ¯]_{c}]_{su}⊗[3_{c}]_{b[over ¯]d[over ¯]} tetraquark currents in both scalar and axial-vector channels to perform evaluations and numerical analyses. Our results imply that the X(5568) can be interpreted as both the scalar sub[over ¯]d[over ¯] tetraquark state and the axial-vector one, which are in good agreement with the experimental measurement. We also discuss the possible decay patterns of the X(5568) and suggest to search for its neutral partner in the radiative decay into B_{s}^{0}γ and B_{s}^{*}γ, which can be used to determine its spin-parity quantum numbers. Moreover, we predict its charmed partner state around 2.55 GeV with the quark content suc[over ¯]d[over ¯] and J^{P}=0^{+}/1^{+}.

Identifying Exotic Hidden-Charm Pentaquarks.

The LHCb Collaboration at the Large Hadron Collider at CERN discovered two pentaquark states P_{c}(4380) and P_{c}(4450). These two hidden-charm states are interpreted as the loosely bound Σ_{c}(2455)D^{*} and Σ_{c}^{*}(2520)D^{*} molecular states in the boson exchange interaction model, which provides an explanation for why the experimental width of P_{c}(4450) is much narrower than that of P_{c}(4380). The discovery of the new resonances P_{c}(4380) and P_{c}(4450), indeed, opens a new page for hadron physics. The partners of P_{c}(4380) and P_{c}(4450) should be pursued in future experiments.

Towards Exotic Hidden-Charm Pentaquarks in QCD.

Inspired by P(c)(4380) and P(c)(4450) recently observed by LHCb, a QCD sum rule investigation is performed, by which they can be identified as exotic hidden-charm pentaquarks composed of an anticharmed meson and a charmed baryon. Our results suggest that P(c)(4380) and P(c)(4450) have quantum numbers J(P)=3/2(-) and 5/2(+), respectively. Furthermore, two extra hidden-charm pentaqurks with configurations D̅Σ(c)(*) and D̅(*)Σ(c)(*) are predicted, which have spin-parity quantum numbers J(P)=3/2(-) and J(P)=5/2(+), respectively. As an important extension, the mass predictions of hidden-bottom pentaquarks are also given. Searches for these partners of P(c)(4380) and P(c)(4450) are especially accessible at future experiments like LHCb and BelleII.

Corrigendum: Untreated depression and anxiety in patients with common skin diseases: a cross-sectional study in China.

[This corrects the article DOI: 10.3389/fpsyg.2023.1150998.].

The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads.

Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50) =694 kb, including contigs with N(50)=20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.

Polycation-Intercalated MXene Membrane with Enhanced Permselective and Anti-Microbial Properties.

Two-dimensional (2D) nanomaterial-based membranes feature attractive properties for molecular separation and transport, which exhibit huge potential in various chemical processes. However, the low permeability and bio-fouling of the MXene membrane in water treatment become huge obstacles to its practical application. Herein, a highly permselective and anti-bacterial 2D nanofiltration membrane is fabricated by intercalating a polycation of polydiallyldimethylammonium chloride (PDDA) into the Ti3C2Tx MXene laminar architecture through a facile and patternable electrostatic assembly strategy. As a result, the as-fabricated Ti3C2Tx/PDDA composite membrane exhibits higher water permeance up to 73.4 L m-2 h-1 with a rejection above 94.6% for MgCl2. The resultant membrane simultaneously possesses good resistance to swelling and long-term stability in water environments, even after 8 h. Additionally, the Ti3C2Tx/PDDA membrane also demonstrates a high flux recovery ratio of nearly 96.1% to bovine serum albumin proteins after being cleaned. More importantly, the current membrane shows excellent anti-adhesive and anti-microbial activity against Gram-negative Escherichia coli (E. coli) and Gram-positive Staphylococcus aureus (S. aureus), with inhibition rates of 90% and 95% against E. coli and S. aureus, respectively. This holds great potential for the application of the polyelectrolyte-intercalated MXene membrane in serving as a promising platform to separate molecules and/or ions in an aquatic environment.

Computational methods for in situ structural studies with cryogenic electron tomography.

Cryo-electron tomography (cryo-ET) plays a critical role in imaging microorganisms in situ in terms of further analyzing the working mechanisms of viruses and drug exploitation, among others. A data processing workflow for cryo-ET has been developed to reconstruct three-dimensional density maps and further build atomic models from a tilt series of two-dimensional projections. Low signal-to-noise ratio (SNR) and missing wedge are two major factors that make the reconstruction procedure challenging. Because only few near-atomic resolution structures have been reconstructed in cryo-ET, there is still much room to design new approaches to improve universal reconstruction resolutions. This review summarizes classical mathematical models and deep learning methods among general reconstruction steps. Moreover, we also discuss current limitations and prospects. This review can provide software and methods for each step of the entire procedure from tilt series by cryo-ET to 3D atomic structures. In addition, it can also help more experts in various fields comprehend a recent research trend in cryo-ET. Furthermore, we hope that more researchers can collaborate in developing computational methods and mathematical models for high-resolution three-dimensional structures from cryo-ET datasets.

Untreated depression and anxiety in patients with common skin diseases: a cross-sectional study in China.

Objective: The study aimed to analyze the current status and reasons for the neglect of the psychological need of patients with common skin diseases. Methods: This cross-sectional study was conducted in China using an online self-assessment questionnaire distributed via social media. Demographic, clinical and psychological data were collected, and the main outcomes, i.e., depression (evaluated using the 9-item Patient Health Questionnaire, PHQ-9) and anxiety (evaluated using Generalized Anxiety Disorder-7, GAD-7). Multivariate regression analysis was used for the prediction of variates of mental health service seeking behaviors. Results: A total of 1,010 patients participated in the survey, and 273 (27.0%) patients met the "with need" criteria, i.e., having the need for mental health intervention but not being treated. In the multivariate regression model, income (OR = 0.80, 95%CI: 0.65-0.99), duration of disease (OR = 0.68, 95%CI: 0.49-0.95) and suicide ideation (OR = 2.10, 95%CI: 1.14-3.87) were significant factors. For patients who did not receive mental health care, the lack of knowledge about the availability of mental health services, lack of knowledge of where to seek help, concerns about the side effects of treatment, failure to seek treatment for severe skin diseases, and absence of current psychological distress were associated with their need for psychological intervention. Conclusion: This study examined the current status of the need for psychological intervention and the reasons why the need was unmet in patients with skin diseases. Due to the confusion and a lack of knowledge about their mental health issues, mental health services are often underutilized.

Corrigendum: Untreated depression and anxiety in patients with common skin diseases: a cross-sectional study in China.

[This corrects the article DOI: 10.3389/fpsyg.2023.1150998.].

Advancing Strategies of Biofouling Control in Water-Treated Polymeric Membranes.

Polymeric membranes, such as polyamide thin film composite membranes, have gained increasing popularity in wastewater treatment, seawater desalination, as well as the purification and concentration of chemicals for their high salt-rejection and water flux properties. Membrane biofouling originates from the attachment or deposition of organic macromolecules/microorganisms and leads to an increased operating pressure and shortened service life and has greatly limited the application of polymeric membranes. Over the past few years, numerous strategies and materials were developed with the aim to control membrane biofouling. In this review, the formation process, influence factors, and consequences of membrane biofouling are systematically summarized. Additionally, the specific strategies for mitigating membrane biofouling including anchoring of hydrophilic monomers, the incorporation of inorganic antimicrobial nanoparticles, coating/grafting of cationic bactericidal polymers, and the design of multifunctional material integrated multiple anti-biofouling mechanisms, are highlighted. Finally, perspectives on the challenges and opportunities in anti-biofouling polymeric membranes are shared, shedding light on the development of even better anti-biofouling materials in near future.

Carbon Nanotubes as Carriers in Drug Delivery for Non-Small Cell Lung Cancer, Mechanistic Analysis of Their Carcinogenic Potential, Safety Profiling and Identification of Biomarkers.

Non-small cell lung cancer (NSCLC) is a global burden leading to millions of deaths worldwide every year. Nanomedicine refers to the use of materials at the nanoscale for drug delivery and subsequent therapeutic approaches in cancer. Carbon nanotubes (CNTs) are widely used as nanocarriers for therapeutic molecules such as plasmids, siRNAs, antisense agents, aptamers and molecules related to the immunotherapy for several cancers. They are usually functionalized and loaded with standard drug molecules to improve their therapeutic efficiency. Functionalization and drug loading possibly decrease the genotoxic and carcinogenic potential of CNTs. In addition, the targeted cytotoxic properties of the drug improve and undesired toxicity decreases after drug loading and/or conjugation with proteins, including antibodies. For intended drug delivery, a lysosomal pH of 5.5 is more suitable and effective for the slow and extended release of cytotoxic drugs than a physiological of pH 7.4. Remarkably, CNTs possess intrinsic antitumor properties and are usually internalized by endocytosis. After being internalized, several mechanisms are involved in the therapeutic and carcinogenic effects of CNTs. They are generally safe for therapy, and their toxicity profile remains dependent on their physicochemical properties. Moreover, the dose, route, duration of exposure, surface properties and degradative potential determine the toxicity outcomes of CNTs locally or systemically. In summary, the use of CNTs in drug delivery and NSCLC therapy, as well as their genotoxic and carcinogenic potential and the possible mechanisms, has been discussed in this review. The therapeutic index is generally high for NSCLC cells treated with drug-loaded CNTs; therefore, they are effective carriers in implementing targeted therapy for NSCLC.

Universal detection of curved rice panicles in complex environments using aerial images and improved YOLOv4 model.

Accurate and rapid identification of the effective number of panicles per unit area is crucial for the assessment of rice yield. As part of agricultural development, manual observation of effective panicles in the paddy field is being replaced by unmanned aerial vehicle (UAV) imaging combined with target detection modeling. However, UAV images of panicles of curved hybrid Indica rice in complex field environments are characterized by overlapping, blocking, and dense distribution, imposing challenges on rice panicle detection models. This paper proposes a universal curved panicle detection method by combining UAV images of different types of hybrid Indica rice panicles (leaf-above-spike, spike-above-leaf, and middle type) from four ecological sites using an improved You Only Look Once version 4 (YOLOv4) model. MobileNetv2 is used as the backbone feature extraction network based on a lightweight model in addition to a focal loss and convolutional block attention module for improved detection of curved rice panicles of different varieties. Moreover, soft non-maximum suppression is used to address rice panicle occlusion in the dataset. This model yields a single image detection rate of 44.46 FPS, and mean average precision, recall, and F1 values of 90.32%, 82.36%, and 0.89%, respectively. This represents an increase of 6.2%, 0.12%, and 16.24% from those of the original YOLOv4 model, respectively. The model exhibits superior performance in identifying different strain types in mixed and independent datasets, indicating its feasibility as a general model for detection of different types of rice panicles in the heading stage.

Predicting the D‾s(*)Ds(*) bound states as the partners of X(3872).

In this work, we investigate the SU(3) flavor symmetry, heavy quark spin symmetry and their breaking effects in the di-meson systems. We prove the existence of the [Formula: see text] , [Formula: see text] , and [Formula: see text] bound states as the consequence of two prerequisites in the SU(3) flavor symmetry and heavy quark spin symmetry. The first prerequisite, the X(3872) as the weakly D‾∗D/D‾D∗ bound state is supported by its mass and decay branching ratios. The second prerequisite, the existence of the [Formula: see text] bound state is supported by the lattice QCD calculation and the observation of χc0(3930) by the LHCb Collaboration. We hope the future experimental analyses can search for these bound states in the B→D(s)(*)D‾(s)(*)h processes (h denotes the light hadrons). The [Formula: see text] bound state is also expected to be reconstructed in the J/ψϕ final state in the B→J/ψϕK decay.