Sportify: Question Answering with Embedded Visualizations and Personified Narratives for Sports Video.

As basketball's popularity surges, fans often find themselves confused and overwhelmed by the rapid game pace and complexity. Basketball tactics, involving a complex series of actions, require substantial knowledge to be fully understood. This complexity leads to a need for additional information and explanation, which can distract fans from the game. To tackle these challenges, we present Sportify, a Visual Question Answering system that integrates narratives and embedded visualization for demystifying basketball tactical questions, aiding fans in understanding various game aspects. We propose three novel action visualizations (i.e., Pass, Cut, and Screen) to demonstrate critical action sequences. To explain the reasoning and logic behind players' actions, we leverage a large-language model (LLM) to generate narratives. We adopt a storytelling approach for complex scenarios from both first and third-person perspectives, integrating action visualizations. We evaluated Sportify with basketball fans to investigate its impact on understanding of tactics, and how different personal perspectives of narratives impact the understanding of complex tactic with action visualizations. Our evaluation with basketball fans demonstrates Sportify's capability to deepen tactical insights and amplify the viewing experience. Furthermore, third-person narration assists people in getting in-depth game explanations while first-person narration enhances fans' game engagement.

Progress of researches on the mechanism of acupuncture treatment for Alzheimer's disease by modulating synaptic plasticity. / é’ˆåˆºè°ƒèŠ‚çªè§¦å¯å¡‘æ€§æ²»ç–—é˜¿å°”èŒ¨æµ·é»˜ç— æœºåˆ¶çš„ç ”ç©¶è¿›å±•.

Alzheimer's disease (AD) is a neurodegenerative disease with high incidence in the elderly population, and the synaptic changes in central neurons are the key pathological feature. The clinical effect of acupuncture and moxibustion in the treatment of AD is positive, and the research on the mechanism of acupuncture intervention of AD from the perspective of central synaptic plasticity regulation has been conducted uninterruptedly. In the present paper, we made a summation about the relevant experimental studies in recent years, and analyzed its mechanisms underlying improvement of AD by regulating synaptic plasticity from 1) repairing synaptic structure (synaptic contact area ï¼»total number of synapses, synaptic surface density, synaptic number densityï¼½, postsynaptic dense zone thickness, synaptic gap width, and interface curvature), 2) improving synaptic transmission efficiency (regulating long-term potentiation and long-term depression), 3) promoting the expression of synapse related proteins (synaptophysin, postsynaptic density protein 95, growth associated protein 43), 4) regulating the expression of neurotransmitters (acetylcholine, monoamines, amino acids, etc.) and receptors (α7 nicotinic acetylcholine receptor, glutaminergic receptor, etc.), and 5) improving the level of neurotrophic factors (brain derived neurotrophic factor, BDNF) and BDNF/SYN/microtubule-associated protein 2 signaling, etc., hoping to provide a reference for future studies.

Study on the Effects of Acupuncture with the "Yizhi Tiaoshen" Acupoint Formula on Blood Oxygen Metabolism and Neural Function in Key Brain Regions of AD Rats.

Purpose: Exploring the effects of acupuncture at the "Yizhi Tiaoshen" acupoint on blood oxygen metabolism and neurological function changes in the brain regions of AD model rats. Methods: The AD model was replicated by intraperitoneal injection of D-galactose combined with bilateral hippocampal CA1 injection of Okadaic acid (OA). Thirty rats with successfully replicated model were selected through Morris water maze experiment and randomly divided into model group, donepezil hydrochloride group, and acupuncture group, with 10 rats in each group. After treatment, fNIRs were used to detect changes in Oxy Hb, Deoxy Hb, and Total Hb in the cerebral cortex of rats in each group, in order to evaluate the neurological function changes in key brain areas. Results: The escape latency of the donepezil hydrochloride group and the acupuncture group was shortened, the number of crossings through the original platform increased, and the duration of stay in the quadrant where the original platform was located was prolonged. Based on fNIRs detection, the main differential channels of blood oxygen metabolism in AD rats were identified as 2-2 and 8-7, corresponding to the prefrontal and parietal lobes, respectively. The concentrations of Oxy Hb and Total Hb were significantly increased in both treatment groups, while the concentration of Deoxy Hb was significantly decreased. Conclusion: Acupuncture with the "Yizhi Tiaoshen" acupoint formula and donepezil hydrochloride can improve the learning and memory function of AD rats, and its mechanism may be related to improving blood oxygen metabolism in the prefrontal and parietal regions and protecting neuronal function.

Multi-omics reveal toxicity mechanisms underpinning nanoplastic in redclaw crayfish (Cherax quadricarinatus).

We investigated the effects of different nanoplastic (NP, size = 100 nm) concentrations on red crayfish (Cherax quadricarinatus) and examined toxicity mechanisms. We established four concentration groups (control (CK): 0 µg/L; Low: 100 µg/L; Medium: 500 µg/L; and High: 1000 µg/L) and analyzed toxicity effects in C. quadricarinatus hepatopancreas using histopathological, transcriptomic, metabolomic, and fluorescence methods. NP exposure caused histological lesions and oxidative stress in hepatopancreas, and also significantly decreased glutathione (GSH) (P < 0.05) but significantly increased malondialdehyde content (MDA) (P < 0.05) in NP-treated groups. By analyzing different metabolic indicators, total cholesterol (T-CHO) content significantly increased (P < 0.05) and triglyceride (TG) content significantly decreased in Medium and High (P < 0.05). Transcriptomic analyses revealed that NPs influenced apoptosis, drug metabolism-cytochrome P450, and P53 signaling pathways. Metabolomic analyses indicated some metabolic processes were affected by NPs, including bile secretion, primary bile acid biosynthesis, and cholesterol metabolism. Caspase 3, 8, and 9 distribution levels in hepatopancreatic tissues were also determined by immunofluorescence; positive caspase staining increased with increased NP concentrations. Additionally, by examining relative Bcl-2, Bax, Apaf-1, and p53 mRNA expression levels, Bcl-2 expression was significantly decreased with increasing NP concentrations; and the expression of Bcl-2 was increasing significantly with the NPs concentration increasing. Bax expression in Low, Medium, and High groups was also significantly higher when compared with the CK group (P < 0.05); with High group levels significantly higher than in Low and Medium groups (P < 0.05). P53 expression was significantly increased in Low, Medium, and High groups (P < 0.05). Thus, NPs induced apoptosis in C. quadricarinatus hepatopancreatic cells, concomitant with increasing NP concentrations. Therefore, we identified mechanisms underpinning NP toxicity in C. quadricarinatus and provide a theoretical basis for exploring NP toxicity in aquatic organisms.

Evaluating the efficiency of online course resource allocation in universities of China.

Curriculum is the core element of talent cultivation in universities, and its quality directly determines that of the talent cultivation. However, the efficiency of online course resource allocation in universities of China is unacceptable, and the corresponding driving mechanisms are unclear. Based on the data of iCourses platform for a top university (H University) of China, this paper develops the DEA-Malmquist index and Tobit regression model to evaluate the efficiency of university online course resource allocation and explore its main influencing factors. The empirical results indicate that, first of all, humanities and social sciences outperform natural sciences in the resource allocation efficiency of online courses. Compared with non-national premium online courses, the resource investment redundancy of national premium online courses appears relatively lower. Secondly, from the perspective of temporal changes, the total factor productivity of online course resource allocation generally has a downward trend. The innovation effect of technological progress is more significant, while the catch-up effect of technical efficiency is clearly insufficient. Scale efficiency is the main factor hindering its improvement. Finally, in terms of the factors affecting the efficiency of online course resource allocation, teachers' research guidance capability, teaching research skills, and the number of courses offered have significantly positive impact.

SARC-F, SARC-CalF, and SARC-F+EBM as practical predictive tools for the risk of pneumonia in patients with stable schizophrenia-a prospective study.

Objectives: Individuals diagnosed with schizophrenia have a high incidence and fatality rates due to pneumonia. Sarcopenia is a contributing factor to the development of pneumonia in patients with schizophrenia. In this study, we examine the effectiveness of three simple screening questionnaires, namely SARC-F, SARC-CalF, and SARC-F + EBM, in predicting the occurrence of pneumonia in stable patients with schizophrenia who are experiencing sarcopenia. Design: A prospective study. Setting: Patients with stable schizophrenia patients aged ≥50 years in two psychiatric hospitals in western China. Methods: Medical data from patients were collected from September 1 to September 30, 2020. Data specifically from patients diagnosed with pneumonia were collected for a period of one year, from October 2020 to October 2021. Three hundred thirty-five stable schizophrenia patients, among whom 229 were males (68.36 %.), were enrolled in the prospective study. The risk of sarcopenia was evaluated using the SARC-F, SARC-CalF, and SARC-F + EBM scores, with values of ≥4, 11, and 12 indicating an elevated risk of sarcopenia. The collected data were analyzed using logistic regression analysis to establish the association between the scores of these screening tools and the risk of pneumonia in individuals with stable schizophrenia. Results: The rate of pneumonia in stable schizophrenia individuals was 24.48 %. Among the included stable schizophrenia patients, the incidence of pneumonia in individuals with SARC-CalF scores ≥11 was higher than in those with SARC-CalF scores less than 11 (29.91 % vs 14.88 %, P = 0.002). In individuals with SARC-F + EBM scores ≥12, the pneumonia occurrence was higher than that in those with SARC-F + EBM scores less than 12 (37.33 % vs 20.77 %, P = 0.003). However, this pattern was not found in patients with stable schizophrenia who had SARC-F scores of 4 or above and less than 4. Following the implementation of logistic regression data analysis, it has been discovered that persons with SARC-CalF scores greater than or equal to 11 were at a significantly increased risk of having pneumonia compared to patients with SARC-CalF scores less than 11 (OR = 2.441, 95 % CI: 1.367-4.36). After adjusting the possible confounders, patients with SARC-CalF scores ≥11 had a greater danger of pneumonia (OR = 2.518, 95%CI: 1.36-4.665). As a result, it was found that individuals with SACR-F+EBM scores ≥12 were more likely to acquire pneumonia (OR = 2.273, 95%CI: 1.304-3.961) when compared to those with scores <12 (OR = 2.273, 95%CI: 1.304-3.961). The results of this study, which controlled for potential confounders, indicated that patients with SARC-F + EBM scores ≥12 were more inclined to acquire pneumonia (OR = 2.181, 95%CI: 1.182-4.026). However, in stable schizophrenia patients with SARC-F scores ≥4 and < 4, this study has not yet observed a similar pattern for pneumonia risk. Conclusions and implications: These results demonstrate, in stable adults with schizophrenia, a relationship between pneumonia risk and SARC-F + EBM and SARC-CalF scores. It is, therefore, advised to use these scores to determine whether these patients have pneumonia, especially in hospitals that cannot diagnose sarcopenia.

Review of laser and energy-based devices to treat rosacea in skin of color.

The prevalence of rosacea in skin of color (SOC) populations is estimated to be as high as 10% in some countries. Traditionally, intense pulsed light (IPL) and pulsed dye laser (PDL) have been the laser and energy-based devices (EBDs) used to treat rosacea. However, not all laser and EBDs are safe for SOC (Fitzpatrick skin types IV-VI) due to increased absorption of energy in pigmented skin and increased risk of post-inflammatory hyperpigmentation and scarring. This review summarizes the use of the top seven laser and EBDs for treating rosacea in SOC.

GTAM: a molecular pretraining model with geometric triangle awareness.

MOTIVATION: Molecular representation learning is pivotal for advancing deep learning applications in quantum chemistry and drug discovery. Existing methods for molecular representation learning often fall short of fully capturing the intricate interactions within chemical bonds of 2D topological graphs and the multifaceted effects of 3D geometric conformations. RESULTS: To overcome these challenges, we present a novel contrastive learning strategy for molecular representation learning, named Geometric Triangle Awareness Model (GTAM). This method integrates innovative molecular encoders for both 2D graphs and 3D conformations, enabling the accurate capture of geometric dependencies among edges in graph-based molecular structures. Furthermore, GTAM is bolstered by the development of two contrastive training objectives designed to facilitate the direct transfer of edge information between 2D topological graphs and 3D geometric conformations, enhancing the functionality of the molecular encoders. Through extensive evaluations on a range of 2D and 3D downstream tasks, our model has demonstrated superior performance over existing approaches. AVAILABILITY AND IMPLEMENTATION: The test code and data of GTAM are available online at https://github.com/StellaHxy/GTAM.

Mass spectrometry-based proteomic landscape of rice reveals a post-transcriptional regulatory role of N6-methyladenosine.

Rice is one of the most important staple food and model species in plant biology, yet its quantitative proteomes are largely uncharacterized. Here we quantify the relative protein levels of over 15,000 genes across major rice tissues using a tandem mass tag strategy followed by intensive fractionation and mass spectrometry. We identify tissue-specific and tissue-enriched proteins that are linked to the functional specificity of individual tissues. Proteogenomic comparison of rice and Arabidopsis reveals conserved proteome expression, which differs from mammals in that there is a strong separation of species rather than tissues. Notably, profiling of N6-methyladenosine (m6A) across the rice major tissues shows that m6A at untranslated regions is negatively correlated with protein abundance and contributes to the discordance between RNA and protein levels. We also demonstrate that our data are valuable for identifying novel genes required for regulating m6A methylation. Taken together, this study provides a paradigm for further research into rice proteogenome.

Characterize direct protein interactions with enrichable, cleavable and latent bioreactive unnatural amino acids.

Latent bioreactive unnatural amino acids (Uaas) have been widely used in the development of covalent drugs and identification of protein interactors, such as proteins, DNA, RNA and carbohydrates. However, it is challenging to perform high-throughput identification of Uaa cross-linking products due to the complexities of protein samples and the data analysis processes. Enrichable Uaas can effectively reduce the complexities of protein samples and simplify data analysis, but few cross-linked peptides were identified from mammalian cell samples with these Uaas. Here we develop an enrichable and multiple amino acids reactive Uaa, eFSY, and demonstrate that eFSY is MS cleavable when eFSY-Lys and eFSY-His are the cross-linking products. An identification software, AixUaa is developed to decipher eFSY mass cleavable data. We systematically identify direct interactomes of Thioredoxin 1 (Trx1) and Selenoprotein M (SELM) with eFSY and AixUaa.

Micro/nano-plastics impacts in cardiovascular systems across species.

The widespread presence of microplastics and nanoplastics (MPs/NPs) in the environment has become a critical public health issue due to their potential to infiltrate and affect various biological systems. Our review is crucial as it consolidates current data and provides a comprehensive analysis of the cardiovascular impacts of MPs/NPs across species, highlighting significant implications for human health. By synthesizing findings from studies on aquatic and terrestrial organisms, including humans, this review offers insights into the ubiquity of MPs/NPs and their pathophysiological roles in cardiovascular systems. We demonstrated that exposure to MPs/NPs is linked to various cardiovascular ailments such as thrombogenesis, vascular damage, and cardiac impairments in model organisms, which likely extrapolate to humans. Our review critically evaluated methods for detecting MPs/NPs in biological tissues, assessing their toxicity, and understanding their behaviour within the vasculature. These findings emphasise the urgent need for targeted public health strategies and enhanced regulatory measures to mitigate the impacts of MP/NP pollution. Furthermore, the review underlined the necessity of advancing research methodologies to explore long-term effects and potential intergenerational consequences of MP/NP exposure. By mapping out the intricate links between environmental exposure and cardiovascular risks, our work served as a pivotal reference for future research and policymaking aimed at curbing the burgeoning threat of plastic pollution.

Multi-omics reveals the particle size effect of nanoplastics on the hepatopancreas and intestinal toxicity of crustacean model Neospoda palmata.

Nano-plastics (NPs) have emerged as prevalent contaminants in aquatic ecosystems, gaining significant research interest. Nonetheless, limited research has addressed the toxicity mechanisms associated with PS-NPs (polystyrene nanoplastics) of varying particle sizes. In this investigation, genotoxicity, growth patterns, hepatopancreatic damage, and intestinal flora alterations in freshwater shrimp Neocaridina palmata (Shen 1948), subjected to 35 days PS-NPs exposure (two size PS-NPs: 75 nm and 200 nm were used for this experiment, and five concentrations were set: 0 mg/L, 0.5 mg/L, 2.5 mg/L, 5 mg/L, and 10 mg/L concentrations PS-NP concentrations were examined using RNA sequencing, histopathological analyses, enzyme activity assessments, and 16S rRNA sequencing. Noteworthy variations in differentially expressed genes (DEGs) were identified across groups exposed to different PS-NPs sizes. We observed that PS-NPs predominantly instigated cellular component-related processes and induced apoptosis and oxidative stress across tissues via the mitochondrial pathway. Although the 200 nm-PS-NPs are stronger than the 75 nm-PS-NPs in terms of fluorescence intensity, 75 nm-PS-NPs are more likely to promote apoptosis than 200 nm-PS-NPs. PS-NPs impeded standard energy provision in N. palmata, potentially contributing to decreased body length and weight. Moreover, PS-NPs inflicted damage on intestinal epithelial and hepatopancreatic tissues and significantly modified intestinal microbial community structures. Specifically, PS-NPs-induced intestinal damage was marked by a decline in some probiotics (notably Lactobacilli) and a surge in pathogenic bacteria. Moreover, supplementing N. palmata with Lactobacilli appeared ameliorate oxidative stress and strengthen energy metabolism. Our findings provided valuable insights into crustacean toxicity mechanisms when subjected to PS-NPs and the potential risks that different PS-NPs sizes posed to terrestrial ecosystems.

Reoxygenation Mitigates Intermittent Hypoxia-Induced Systemic Inflammation and Gut Microbiota Dysbiosis in High-Fat Diet-Induced Obese Rats.

Background: Obstructive sleep apnea (OSA) is a prevalent sleep breathing disorder characterized by intermittent hypoxia (IH), with continuous positive airway pressure (CPAP) as its standard treatment. However, the effects of intermittent hypoxia/reoxygenation (IH/R) on weight regulation in obesity and its underlying mechanism remain unclear. Gut microbiota has gained attention for its strong association with various diseases. This study aims to explore the combined influence of IH and obesity on gut microbiota and to investigate the impact of reoxygenation on IH-induced alterations. Methods: Diet-induced obese (DIO) rats were created by 8-week high-fat diet (HFD) feeding and randomly assigned into three groups (n=15 per group): normoxia (NM), IH (6% O2, 30 cycles/h, 8 h/day, 4 weeks), or hypoxia/reoxygenation (HR, 2-week IH followed by 2-week reoxygenation) management. After modeling and exposure, body weight and biochemical indicators were measured, and fecal samples were collected for 16S rRNA sequencing. Results: DIO rats in the IH group showed increased weight gain (p=0.0016) and elevated systemic inflammation, including IL-6 (p=0.0070) and leptin (p=0.0004). Moreover, IH rats exhibited greater microbial diversity (p<0.0167), and significant alterations in the microbial structure (p=0.014), notably the order Clostridiales, accompanied by an upregulation of bile acid metabolism predicted pathway (p=0.0043). Reoxygenation not only improved IH-exacerbated obesity, systemic inflammation, leptin resistance, and sympathetic activation, but also showed the potential to restore IH-induced microbial alterations. Elevated leptin levels were associated with Ruminococcaceae (p=0.0008) and Clostridiales (p=0.0019), while body weight was linked to Blautia producta (p=0.0377). Additionally, the abundance of Lactobacillus was negatively correlated with leptin levels (p=0.0006) and weight (p=0.0339). Conclusion: IH leads to gut dysbiosis and metabolic disorders, while reoxygenation therapy demonstrates a potentially protective effect by restoring gut homeostasis and mitigating inflammation. It highlights the potential benefits of CPAP in reducing metabolic risk among obese patients with OSA.

Macrophages in CRSwNP: Do they deserve more attention?

Chronic rhinosinusitis (CRS) represents a heterogeneous disorder primarily characterized by the persistent inflammation of the nasal cavity and paranasal sinuses. The subtype known as chronic rhinosinusitis with nasal polyposis (CRSwNP) is distinguished by a significantly elevated recurrence rate and augmented challenges in the management of nasal polyps. The pathogenesis underlying this subtype remains incompletely understood. Macrophages play a crucial role in mediating the immune system's response to inflammatory stimuli. These cells exhibit remarkable plasticity and heterogeneity, differentiating into either the pro-inflammatory M1 phenotype or the anti-inflammatory and reparative M2 phenotype depending on the surrounding microenvironment. In CRSwNP, macrophages demonstrate reduced production of Interleukin 10 (IL-10), compromised phagocytic activity, and decreased autophagy. Dysregulation of pro-resolving mediators may occur during the inflammatory resolution process, which could potentially hinder the adequate functioning of anti-inflammatory macrophages in facilitating resolution. Collectively, these factors may contribute to the prolonged inflammation observed in CRSwNP. Additionally, macrophages may enhance fibrin cross-linking through the release of factor XIII-A (FAXIII), promoting fibrin deposition and plasma protein retention. Macrophages also modulate vascular permeability by releasing Vascular endothelial growth factor (VEGF). Moreover, they may disrupt the balance between Matrix Metalloproteinases (MMPs) and Tissue Inhibitors of Metalloproteinases (TIMPs), which favors extracellular matrix (ECM) degradation, edema formation, and pseudocyst development. Accumulating evidence suggests a close association between macrophage infiltration and CRSwNP; however, the precise mechanisms underlying this relationship warrant further investigation. In different subtypes of CRSwNP, different macrophage phenotypic aggregations trigger different types of inflammatory features. Increasing evidence suggests that macrophage infiltration is closely associated with CRSwNP, but the mechanism and the relationship between macrophage typing and CRSwNP endophenotyping remain to be further explored. This review discusses the role of different types of macrophages in the pathogenesis of different types of CRSwNP and their contribution to polyp formation, in the hope that a better understanding of the role of macrophages in specific CRSwNP will contribute to a precise and individualized understanding of the disease.

Metabolomics and microbiome co-analysis reveals altered innate immune responses in Charybdis japonica following Aeromonas hydrophila infection.

A comprehensive bioinformatics analysis was conducted to elucidate the innate immune response of Charybdis japonica following exposure to Aeromonas hydrophila. This study integrated metabolomics, 16S rRNA sequencing, and enzymatic activity data to dissect the immune mechanisms activated in response to infection. Infection with A. hydrophila resulted in an increased abundance of beneficial intestinal genera such as Photobacterium spp., Rhodobacter spp., Polaribacter spp., Psychrilyobacter spp., and Mesoflavibacter spp. These probiotics appear to suppress A. hydrophila colonization by competitively dominating the intestinal microbiota. Key metabolic pathways affected included fatty acid biosynthesis, galactose metabolism, and nitrogen metabolism, highlighting their role in the crab's intestinal response. Enzymatic analysis revealed a decrease in activities of hexokinase, phosphofructokinase, and pyruvate kinase, which are essential for energy homeostasis and ATP production necessary for stress responses. Additionally, reductions were observed in the activities of acetyl-CoA carboxylase and fatty acid synthase. Gene expression analysis showed downregulation in Peroxiredoxin 1 (PRDX1), Peroxiredoxin 2 (PRDX2), glutathione-S-transferase (GST), catalase (CAT), and glutathione (GSH), with concurrent increases in malondialdehyde (MDA) levels, indicating severe oxidative stress. This study provides insights into the molecular strategies employed by marine crabs to counteract bacterial invasions in their natural habitat.

Pan-cancer analyses reveal genomics and clinical outcome association of the fatty acid oxidation regulators in cancer.

Background: Fatty acid oxidation (FAO) is considered to play a vital part in tumor metabolic reprogramming. But the comprehensive description of FAO dysregulation in tumors has not been unknown. Methods: We obtained FAO genes, RNA-seq data and clinical information from the Msigdb, TCGA and GTEx databases. We assessed their prognosis value using univariate cox analysis, survival analysis and Kaplan-Meier curve. We determined the function of FAO genes using gene set variation analysis. The correlation analysis was calculated by corrplot R package. Immunotherapy response was assessed through TIDE scores. The protein expression levels of FAO genes were validated using immunohistochemistry (IHC). Results: The FAO scores were highest in COAD but lowest in PCPG. FAO scores were significantly associated with the prognosis of some cancers in OS, DSS, DFI and PFI. Besides, gene set variation analysis identified that FAO scores were related to immune-related pathways, and immune infiltration analysis showed FAO scores were positively related to cancer-associated fibroblasts and various immune-related genes. TIDE scores were significantly decreased in ACC, CHOL, ESCA, GBM, LAML, SARC, SKCM and THCA compared with normal samples, while it was significantly increased in BLCA, LUAD, LUSC, PCPG, PRAD and STAD. Besides, most FAO genes were downregulated in pan-cancer compared with normal samples. Moreover, we found copy number variation (CNV) of FAO genes played a positive role in their mRNA expression, while methylation was negative. We determined FAO genes were closely related to some drugs in pan-cancer. Conclusions: FAO score is a novel and promising factor for predicting outcomes.

An effective strategy for assembling the sex-limited chromosome.

BACKGROUND: Most currently available reference genomes lack the sequence map of sex-limited (such as Y and W) chromosomes, which results in incomplete assemblies that hinder further research on sex chromosomes. Recent advancements in long-read sequencing and population sequencing have provided the opportunity to assemble sex-limited chromosomes without the traditional complicated experimental efforts. FINDINGS: We introduce the first computational method, Sorting long Reads of Y or other sex-limited chromosome (SRY), which achieves improved assembly results compared to flow sorting. Specifically, SRY outperforms in the heterochromatic region and demonstrates comparable performance in other regions. Furthermore, SRY enhances the capabilities of the hybrid assembly software, resulting in improved continuity and accuracy. CONCLUSIONS: Our method enables true complete genome assembly and facilitates downstream research of sex-limited chromosomes.