Mechanisms and clinical landscape of N6-methyladenosine (m6A) RNA modification in gastrointestinal tract cancers.

Epigenetics encompasses reversible and heritable chemical modifications of non-nuclear DNA sequences, including DNA and RNA methylation, histone modifications, non-coding RNA modifications, and chromatin rearrangements. In addition to well-studied DNA and histone methylation, RNA methylation has emerged as a hot topic in biological sciences over the past decade. N6-methyladenosine (m6A) is the most common and abundant modification in eukaryotic mRNA, affecting all RNA stages, including transcription, translation, and degradation. Advances in high-throughput sequencing technologies made it feasible to identify the chemical basis and biological functions of m6A RNA. Dysregulation of m6A levels and associated modifying proteins can both inhibit and promote cancer, highlighting the importance of the tumor microenvironment in diverse biological processes. Gastrointestinal tract cancers, including gastric, colorectal, and pancreatic cancers, are among the most common and deadly malignancies in humans. Growing evidence suggests a close association between m6A levels and the progression of gastrointestinal tumors. Global m6A modification levels are substantially modified in gastrointestinal tumor tissues and cell lines compared to healthy tissues and cells, possibly influencing various biological behaviors such as tumor cell proliferation, invasion, metastasis, and drug resistance. Exploring the diagnostic and therapeutic potential of m6A-related proteins is critical from a clinical standpoint. Developing more specific and effective m6A modulators offers new options for treating these tumors and deeper insights into gastrointestinal tract cancers.

Negative expression of CD117 predicted inferior OS and PFS in acute promyelocytic leukemia.

INTRODUCTION: In recent years, the correlation between CD117 antigen and the prognosis of hematological malignancies has been demonstrated. However, there is limited literature on the clinical significance of CD117 antigen in acute promyelocytic leukemia (APL). The aim of this study was to retrospectively analyze the clinical features and prognostic significance of CD117 in APL. METHODS: In this study, we retrospectively investigated the clinicopathological characteristics, outcome, and prognostic impact of negative CD117 expression (CD117-) in 169 APL patients treated with all-trans retinoic acid (ATRA) and arsenic trioxide (ATO) containing regimen. RESULTS: The median follow-up period was 63.0 months. CD117- was detected in 13 APL patients (7.7%). No significant differences were found in baseline characteristics between CD117+ and CD117- subgroups. However, compared to CD117+ APL, the incidence of early death (ED) was significantly higher in CD117- APL (p = 0.023). By multivariate analysis, CD117- was an independent adverse prognostic factor for overall survival (OS) and progression-free survival (PFS) (p = 0.022 and p = 0.014, respectively). CONCLUSIONS: To sum up, CD117- is associated with greater risk of ED and has the statistical power to predict inferior OS and PFS, this marker may be considered to build prognostic scores for risk-adapted therapeutic strategies in APL management.

Acetylcytidine modification of Amotl1 by N-acetyltransferase 10 contributes to cardiac fibrotic expansion in mice after myocardial infarction.

Cardiac fibrosis is a pathological scarring process that impairs cardiac function. N-acetyltransferase 10 (Nat10) is recently identified as the key enzyme for the N4-acetylcytidine (ac4C) modification of mRNAs. In this study, we investigated the role of Nat10 in cardiac fibrosis following myocardial infarction (MI) and the related mechanisms. MI was induced in mice by ligation of the left anterior descending coronary artery; cardiac function was assessed with echocardiography. We showed that both the mRNA and protein expression levels of Nat10 were significantly increased in the infarct zone and border zone 4 weeks post-MI, and the expression of Nat10 in cardiac fibroblasts was significantly higher compared with that in cardiomyocytes after MI. Fibroblast-specific overexpression of Nat10 promoted collagen deposition and induced cardiac systolic dysfunction post-MI in mice. Conversely, fibroblast-specific knockout of Nat10 markedly relieved cardiac function impairment and extracellular matrix remodeling following MI. We then conducted ac4C-RNA binding protein immunoprecipitation-sequencing (RIP-seq) in cardiac fibroblasts transfected with Nat10 siRNA, and revealed that angiomotin-like 1 (Amotl1), an upstream regulator of the Hippo signaling pathway, was the target gene of Nat10. We demonstrated that Nat10-mediated ac4C modification of Amotl1 increased its mRNA stability and translation in neonatal cardiac fibroblasts, thereby increasing the interaction of Amotl1 with yes-associated protein 1 (Yap) and facilitating Yap translocation into the nucleus. Intriguingly, silencing of Amotl1 or Yap, as well as treatment with verteporfin, a selective and potent Yap inhibitor, attenuated the Nat10 overexpression-induced proliferation of cardiac fibroblasts and prevented their differentiation into myofibroblasts in vitro. In conclusion, this study highlights Nat10 as a crucial regulator of myocardial fibrosis following MI injury through ac4C modification of upstream activators within the Hippo/Yap signaling pathway.

CD276 enhances sunitinib resistance in clear cell renal cell carcinoma by promoting DNA damage repair and activation of FAK-MAPK signaling pathway.

OBJECTIVE: This study aimed to explore the effect of CD276 expression on the sunitinib sensitivity of clear cell renal cell carcinoma (ccRCC) cell and animal models and the potential mechanisms involved. METHODS: CD276 expression levels of ccRCC and normal samples were analyzed via online databases and real-time quantitative PCR (RT-qPCR). CD276 was knocked down in ccRCC cell models (sunitinib-resistant 786-O/R cells and sunitinib-sensitive 786-O cells) using shRNA transfection, and the cells were exposed to a sunitinib (2 µM) environment. Cells proliferation was then analyzed using MTT assay and colony formation experiment. Alkaline comet assay, immunofluorescent staining, and western blot experiments were conducted to assess the DNA damage repair ability of the cells. Western blot was also used to observe the activation of FAK-MAPK pathway within the cells. Finally, a nude mouse xenograft model was established and the nude mice were orally administered sunitinib (40 mg/kg/d) to evaluate the in vivo effects of CD276 knockdown on the therapeutic efficacy of sunitinib against ccRCC. RESULTS: CD276 was significantly upregulated in both ccRCC clinical tissue samples and cell models. In vitro experiments showed that knocking down CD276 reduced the survival rate, IC50 value, and colony-forming ability of ccRCC cells. Knocking down CD276 increased the comet tail moment (TM) values and γH2AX foci number, and reduced BRCA1 and RAD51 protein levels. Knocking down CD276 also decreased the levels of p-FAK, p-MEK, and p-ERK proteins. CONCLUSION: Knocking down CD276 effectively improved the sensitivity of ccRCC cell and animal models to sunitinib treatment.

KMTLabeler: An Interactive Knowledge-Assisted Labeling Tool for Medical Text Classification.

The process of labeling medical text plays a crucial role in medical research. Nonetheless, creating accurately labeled medical texts of high quality is often a time-consuming task that requires specialized domain knowledge. Traditional methods for generating labeled data typically rely on rigid rule-based approaches, which may not adapt well to new tasks. While recent machine learning (ML) methodologies have mitigated the manual labeling efforts, configuring models to align with specific research requirements can be challenging for labelers without technical expertise. Moreover, automated labeling techniques, such as transfer learning, face difficulties in in directly incorporating expert input, whereas semi-automated methods, like data programming, allow knowledge integration through rules or knowledge bases but may lack continuous result refinement throughout the entire labeling process. In this study, we present a collaborative human-ML teaming workflow that seamlessly integrates visual cluster analysis and active learning to assist domain experts in labeling medical text with high efficiency. Additionally, we introduce an innovative neural network model called the embedding network, which incorporates expert insights to generate task-specific embeddings for medical texts. We integrate the workflow and embedding network into a visual analytics tool named KMTLabeler, equipped with coordinated multi-level views and interactions. Two illustrative case studies, along with a controlled user study, provide substantial evidence of the effectiveness of KMTLabeler in creating an efficient labeling environment for medical text classification.

Single-structure 3-axis Lorentz force magnetometer based on an AlN-on-Si MEMS resonator.

This work presents a single-structure 3-axis Lorentz force magnetometer (LFM) based on an AlN-on-Si MEMS resonator. The operation of the proposed LFM relies on the flexible manipulation of applied excitation currents in different directions and frequencies, enabling the effective actuation of two mechanical vibration modes in a single device for magnetic field measurements in three axes. Specifically, the excited out-of-plane drum-like mode at 277 kHz is used for measuring the x- and y-axis magnetic fields, while the in-plane square-extensional mode at 5.4 MHz is used for measuring the z-axis magnetic field. The different configurations of applied excitation currents ensure good cross-interference immunity among the three axes. Compared to conventional capacitive LFMs, the proposed piezoelectric LFM utilizes strong electromechanical coupling from the AlN layer, which allows it to operate at ambient pressure with a high sensitivity. To understand and analyze the measured results, a novel equivalent circuit model for the proposed LFM is also reported in this work, which serves to separate the effect of Lorentz force from the unwanted capacitive feedthrough. The demonstrated 3-axis LFM exhibits measured magnetic responsivities of 1.74 ppm/mT, 1.83 ppm/mT and 6.75 ppm/mT in the x-, y- and z-axes, respectively, which are comparable to their capacitive counterparts.

Pro-cancer role of CD276 as a novel biomarker for clear cell renal cell carcinoma.

OBJECTIVE: Renal cell carcinoma (RCC) is a common malignant tumor with a high incidence in males and the elderly, and clear cell RCC (ccRCC) is the most common RCC subtype. ccRCC is highly metastatic with a poor prognosis. Therefore, it is crucial to obtain a detailed understanding of the molecular mechanism of ccRCC and to identify suitable biomarkers to realize early diagnosis and improve prognosis. METHODS: We analyzed data from the Cancer Genome Atlas, investigated the overall differential expression of CD276 in ccRCC, and evaluated the influence of CD276 on patient survival and prognosis. We also performed gene set enrichment analysis (GSEA) and pathway enrichment analysis and investigated cell infiltration and drug responsiveness to further assess the regulatory effect of CD276 on ccRCC. Furthermore, we verified CD276 expression in RCC cell lines and control cell lines. RESULTS: The CD276 expression level in ccRCC samples was higher than that in corresponding samples adjacent to the tumors. Moreover, high CD276 expression levels were positively correlated with poor prognosis in patients with RCC. GSEA revealed that CD276 was significantly involved in immune-related pathways, and the level of CD276 expression was confirmed as associated with immune cell infiltration to some extent. Notably, some drugs were predicted to act on CD276, and this was confirmed by molecular docking. Furthermore, high levels of CD276 expression in RCC cell lines were verified. CONCLUSION: CD276 expression was significantly increased in ccRCC tissues and cells and positively correlated with patient prognosis. CD276 is a potential prognostic biomarker of ccRCC. Overall, this study provides a potential therapeutic strategy for ccRCC.

Use of Dixon in magnetic resonance breast contrast-enhanced T1 weighted high-resolution imaging for mastectomy patients at 3T: A prospective study in single center.

BACKGROUND: For patients with complete breast resection, conventional contrast-enhanced T1-weighted imaging (CE-T1WI) with frequency-selective spectral attenuated inversion recovery (SPAIR) provides limited fat suppression on the postoperative side due to the uneven skin surface, inhomogeneous tissue environment, and frequency-selective feature of the SPAIR scheme, leading to difficulties in precise diagnosis. This study aimed to investigate the image quality and performance of the Dixon method compared with SPAIR in breast high-resolution CE-T1WI for mastectomy patients. MATERIALS AND METHODS: Sixty female patients who had not performed any breast surgeries were randomly selected retrospectively as the control group. Postmastectomy female patients were enrolled to undergone high-resolution CE-T1WI with SPAIR and Dixon breast scans. Subjective scores were rated using a 5-point scale. Objective parameters, including contrast-to-noise ratio (CNR), edge sharpness, and signal uniformity were measured and calculated. The Wilcoxon rank-sum test and Kappa statistic were used. RESULTS: A total of 114 consecutive postmastectomy patients were included. Subjective scores of T1WI-SPAIR in the control group were all significantly better than those with SPAIR on the postoperative side of mastectomy patients (P < 0.01). Dixon outperformed SPAIR with significantly better subjective scores in regards to uniformity and degree of fat-suppression, anatomical structures depiction, lesion conspicuity, and axillary visibility (p < 0.05) in both post- and non-operative sides and bilateral axillary areas through the paired comparison. The objective parameters of Dixon were significantly better than those of SPAIR. CONCLUSION: The Dixon method provided better image uniformity and higher fat suppression efficiency, and showed significant advantages in delineating the anatomical structures, with better axillary and lesion visibilities, especially on the completely removed breast side.

Intraoperative fat embolism syndrome associated with implantation of titanium sacroiliac joint fusion implants: a report of two cases.

Background: For patients undergoing long-construct fusion surgeries, simultaneous sacroiliac joint (SIJ) fusion is a growing trend in spine surgery. Some options for posterior SIJ fusion include 3D-printed triangular titanium implants or self-harvesting SIJ screws. Both implants require fixation within the sacrum and ileum. Fat embolism syndrome is a rare but known complication of lumbar pedicle instrumentation but has never been reported in association with SIJ fusion, regardless of implant type. We report the first two known cases of fat embolism associated with placement of SIJ fusion devices during long construct posterior spine fusion. Case Description: Case 1-a 50-year-old female with multiple previous spine surgeries complicated by osteomyelitis/diskitis that was successfully eradicated, underwent T10-pelvis posterior spinal fusion (PSF), L4 pedicle-subtracting-osteotomy, and bilateral SIJ fusion. During implantation of each SIJ fusion device, the patient's hemodynamic status deteriorated necessitating vasopressor support, intravenous fluid bolus, and hyperventilation, but quickly resolved. The case was completed without further issue, and she had an uneventful post-operative course. Case 2-a 71-year-old female with a past medical history of ankylosing spondylitis, previous L2-L5 PSF, rheumatoid arthritis on chronic steroids, underwent a T9-pelvis PSF, bilateral SIJ fusion, L4 pedicle subtraction osteotomy, T10-L1 Smith Peterson osteotomies. After implantation of the second SIJ fusion device, she became hypotensive and tachycardic, pulses were absent, and cardiopulmonary resuscitation was initiated. Pulses returned quickly, the index surgery was terminated, and she was transferred to the intensive care unit (ICU). In the ICU she was quickly weaned off the ventilator on post-operative day 1. On post-operative day 4, the patient returned to the operating room for completion of the surgery and had an extended, but uneventful, recovery afterwards. Conclusions: We report on the first two known cases of fat embolism syndrome occurring immediately after implantation of SIJ fusion devices. Spine surgeons should be aware of this rare, but potentially fatal, complication. Collaboration with the anesthesia team and optimization of the patient's hemodynamic status prior to implantation may help prevent catastrophic complications.

Genetic interactions reveal distinct biological and therapeutic implications in breast cancer.

Co-occurrence and mutual exclusivity of genomic alterations may reflect the existence of genetic interactions, potentially shaping distinct biological phenotypes and impacting therapeutic response in breast cancer. However, our understanding of them remains limited. Herein, we investigate a large-scale multi-omics cohort (n = 873) and a real-world clinical sequencing cohort (n = 4,405) including several clinical trials with detailed treatment outcomes and perform functional validation in patient-derived organoids, tumor fragments, and in vivo models. Through this comprehensive approach, we construct a network comprising co-alterations and mutually exclusive events and characterize their therapeutic potential and underlying biological basis. Notably, we identify associations between TP53mut-AURKAamp and endocrine therapy resistance, germline BRCA1mut-MYCamp and improved sensitivity to PARP inhibitors, and TP53mut-MYBamp and immunotherapy resistance. Furthermore, we reveal that precision treatment strategies informed by co-alterations hold promise to improve patient outcomes. Our study highlights the significance of genetic interactions in guiding genome-informed treatment decisions beyond single driver alterations.

Novel STAT3 oligonucleotide compounds suppress tumor growth and overcome the acquired resistance to sorafenib in hepatocellular carcinoma.

Signal transducer and activator of transcription 3 (STAT3) plays an important role in the occurrence and progression of tumors, leading to resistance and poor prognosis. Activation of STAT3 signaling is frequently detected in hepatocellular carcinoma (HCC), but potent and less toxic STAT3 inhibitors have not been discovered. Here, based on antisense technology, we designed a series of stabilized modified antisense oligonucleotides targeting STAT3 mRNA (STAT3 ASOs). Treatment with STAT3 ASOs decreased the STAT3 mRNA and protein levels in HCC cells. STAT3 ASOs significantly inhibited the proliferation, survival, migration, and invasion of cancer cells by specifically perturbing STAT3 signaling. Treatment with STAT3 ASOs decreased the tumor burden in an HCC xenograft model. Moreover, aberrant STAT3 signaling activation is one of multiple signaling pathways involved in sorafenib resistance in HCC. STAT3 ASOs effectively sensitized resistant HCC cell lines to sorafenib in vitro and improved the inhibitory potency of sorafenib in a resistant HCC xenograft model. The developed STAT3 ASOs enrich the tools capable of targeting STAT3 and modulating STAT3 activity, serve as a promising strategy for treating HCC and other STAT3-addicted tumors, and alleviate the acquired resistance to sorafenib in HCC patients. A series of novel STAT3 antisense oligonucleotide were designed and showed potent anti-cancer efficacy in hepatocellular carcinoma in vitro and in vivo by targeting STAT3 signaling. Moreover, the selected STAT3 ASOs enhance sorafenib sensitivity in resistant cell model and xenograft model.

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In the clinical diagnosis and treatment of children with short stature, mental health issues merit special attention. It is widely acknowledged that the psychological well-being of children with short stature is lower than that of their peers with normal height. Therefore, during the diagnosis, treatment, and care of short stature, it is crucial to actively monitor the mental health of these children, promptly identify potential psychological and behavioral issues, and intervene accordingly. Such measures play a positive role in enhancing the quality of life of these children and improving their physical and mental health. This article analyses and discusses the current state of psychological assessment and psycho-behavioral interventions for children with short stature, aiming to provide insights for improving their mental health.

The Epidemiology, Management and Therapeutic Outcomes of Subdural Empyema in Neonates with Acute Bacterial Meningitis.

Background: Subdural empyema is one of the more serious complications of bacterial meningitis and therapeutic challenges to clinicians. We aimed to evaluate the clinical characteristics, treatment, and outcome of subdural empyema in neonates with bacterial meningitis. Methods: A retrospective cohort study was conducted in two medical centers in Taiwan that enrolled all cases of neonates with subdural empyema after bacterial meningitis between 2003 and 2020. Results: Subdural empyema was diagnosed in 27 of 153 (17.6%) neonates with acute bacterial meningitis compared with cases of meningitis without subdural empyema. The demographics and pathogen distributions were comparable between the study group and the controls, but neonates with subdural empyema were significantly more likely to have clinical manifestations of fever (85.2%) and seizure (81.5%) (both p values < 0.05). The cerebrospinal fluid results of neonates with subdural empyema showed significantly higher white blood cell counts, lower glucose levels and higher protein levels (p = 0.011, 0.003 and 0.006, respectively). Neonates with subdural empyema had a significantly higher rate of neurological complications, especially subdural effusions and periventricular leukomalacia. Although the final mortality rate was not increased in neonates with subdural empyema when compared with the controls, they were often treated much longer and had a high rate of long-term neurological sequelae. Conclusions: Subdural empyema is not uncommon in neonates with acute bacterial meningitis and was associated with a high risk of neurological complications, although it does not significantly increase the final mortality rate. Close monitoring of the occurrence of subdural empyema is required, and appropriate long-term antibiotic treatment after surgical intervention may lead to optimized outcomes.

60Co-γ Irradiation-Induced Shift and Polarity Reversal in the Triboelectric Series of Poly(ether sulfone)s.

The sensitivity of triboelectric nanogenerators (TENGs) to the surface charge density highlights the significance of triboelectric materials and their modifications. Efforts have been directed toward developing effective strategies for increasing the surface charge density, expanding the potential applications of TENGs. This study proposes the use of irradiation technology for grafting to modify the electron-donating capability of poly(ether sulfone) (PES), thereby affording a dual benefit of enhancing the surface charge density and inducing a shift in the position of PES from negative to positive within the triboelectric series. The TENG based on grafted PES has resulted in a significant 3-fold increase in surface charge density compared to that of pristine PES, reaching 263 µC m-2. The surface charge density can be further increased to 502 µC m-2 through charge pumping. Notably, irradiation technology presents advantages over chemical grafting methods, particularly in terms of sustainability and environmental friendliness. This innovative approach shows great potential in advancing the domain of TENGs.

A Novel Three-Point Localization Method for Bladder Volume Estimation.

The measurement of bladder volume is crucial for the diagnosis and treatment of urinary system diseases. Ultrasound imaging, with its non-invasive, radiation-free, and repeatable scanning capabilities, has become the preferred method for measuring residual urine volume. Nevertheless, it still faces some challenges, including complex imaging methods leading to longer measurement times and lower spatial resolution. Here, we propose a novel three-point localization method that does not require ultrasound imaging to calculate bladder volume. A corresponding triple-element ultrasound probe has been designed based on this method, enabling the ultrasound probe to transmit and receive ultrasound waves in three directions. Furthermore, we utilize the Hilbert Transform algorithm to extract the envelope of the ultrasound signal to enhance the efficiency of bladder volume measurements. The experiment indicates that bladder volume estimation can be completed within 5 s, with a relative error rate of less than 15%. These results demonstrate that this novel three-point localization method offers an effective approach for bladder volume measurement in patients with urological conditions.

Equivariant Line Graph Neural Network for Protein-Ligand Binding Affinity Prediction.

Binding affinity prediction of three-dimensional (3D) protein-ligand complexes is critical for drug repositioning and virtual drug screening. Existing approaches usually transform a 3D protein-ligand complex to a two-dimensional (2D) graph, and then use graph neural networks (GNNs) to predict its binding affinity. However, the node and edge features of the 2D graph are extracted based on invariant local coordinate systems of the 3D complex. As a result, these approaches can not fully learn the global information of the complex, such as the physical symmetry and the topological information of bonds. To address these issues, we propose a novel Equivariant Line Graph Network (ELGN) for binding affinity prediction of 3D protein-ligand complexes. The proposed ELGN firstly adds a super node to the 3D complex, and then builds a line graph based on the 3D complex. After that, ELGN uses a new E(3)-equivariant network layer to pass the messages between nodes and edges based on the global coordinate system of the 3D complex. Experimental results on two real datasets demonstrate the effectiveness of ELGN over several state-of-the-art baselines.

Clustering single-cell multi-omics data via graph regularized multi-view ensemble learning.

MOTIVATION: Single-cell clustering plays a crucial role in distinguishing between cell types, facilitating the analysis of cell heterogeneity mechanisms. While many existing clustering methods rely solely on gene expression data obtained from single-cell RNA sequencing techniques to identify cell clusters, the information contained in mono-omic data is often limited, leading to suboptimal clustering performance. The emergence of single-cell multi-omics sequencing technologies enables the integration of multiple omics data for identifying cell clusters, but how to integrate different omics data effectively remains challenging. In addition, designing a clustering method that performs well across various types of multi-omics data poses a persistent challenge due to the data's inherent characteristics. RESULTS: In this paper, we propose a graph-regularized multi-view ensemble clustering (GRMEC-SC) model for single-cell clustering. Our proposed approach can adaptively integrate multiple omics data and leverage insights from multiple base clustering results. We extensively evaluate our method on five multi-omics datasets through a series of rigorous experiments. The results of these experiments demonstrate that our GRMEC-SC model achieves competitive performance across diverse multi-omics datasets with varying characteristics. AVAILABILITY AND IMPLEMENTATION: Implementation of GRMEC-SC, along with examples, can be found on the GitHub repository: https://github.com/polarisChen/GRMEC-SC.

MARS: a motif-based autoregressive model for retrosynthesis prediction.

MOTIVATION: Retrosynthesis is a critical task in drug discovery, aimed at finding a viable pathway for synthesizing a given target molecule. Many existing approaches frame this task as a graph-generating problem. Specifically, these methods first identify the reaction center, and break a targeted molecule accordingly to generate the synthons. Reactants are generated by either adding atoms sequentially to synthon graphs or by directly adding appropriate leaving groups. However, both of these strategies have limitations. Adding atoms results in a long prediction sequence that increases the complexity of generation, while adding leaving groups only considers those in the training set, which leads to poor generalization. RESULTS: In this paper, we propose a novel end-to-end graph generation model for retrosynthesis prediction, which sequentially identifies the reaction center, generates the synthons, and adds motifs to the synthons to generate reactants. Given that chemically meaningful motifs fall between the size of atoms and leaving groups, our model achieves lower prediction complexity than adding atoms and demonstrates superior performance than adding leaving groups. We evaluate our proposed model on a benchmark dataset and show that it significantly outperforms previous state-of-the-art models. Furthermore, we conduct ablation studies to investigate the contribution of each component of our proposed model to the overall performance on benchmark datasets. Experiment results demonstrate the effectiveness of our model in predicting retrosynthesis pathways and suggest its potential as a valuable tool in drug discovery. AVAILABILITY AND IMPLEMENTATION: All code and data are available at https://github.com/szu-ljh2020/MARS.

Generation of a human induced pluripotent stem cell line NTUHi004-A from a patient with Leigh syndrome harboring a homozygous missense mutation c.836 T > G (p.Met279Arg) in NDUFAF5 gene.

Leigh syndrome is a rare autosomal recessive disorder showcasing a diverse range of neurological symptoms. Classical Leigh syndrome is associated with mitochondrial complex I deficiency, primarily resulting from biallelic mutations in the NDUFAF5 gene, encoding the NADH:ubiquinone oxidoreductase complex assembly factor 5. Using the Sendai virus delivery system, we generated an induced pluripotent stem cell line from peripheral blood mononuclear cells of a 47-years-old female patient who carried a homozygous NDUFAF5 c.836 T > G (p.Met279Arg) mutation. This cellular model serves as a tool for investigating the underlying pathogenic mechanisms and for the development of potential treatments for Leigh syndrome.

De Novo Genome Assembly of the Whitespot Parrotfish (Scarus forsteni): A Valuable Scaridae Genomic Resource.

Scarus forsteni, a whitespot parrotfish from the Scaridae family, is a herbivorous fish inhabiting coral reef ecosystems. The deterioration of coral reefs has highly affected the habitats of the parrotfish. The decline in genetic diversity of parrotfish emphasizes the critical importance of conserving their genetic variability to ensure the resilience and sustainability of marine ecosystems for future generations. In this study, a genome of S. forsteni was assembled de novo through using Illumina and Nanopore sequencing. The 1.71-Gb genome of S. forsteni, was assembled into 544 contigs (assembly level: contig). It exhibited an N50 length of 17.97 Mb and a GC content percentage of 39.32%. Our BUSCO analysis revealed that the complete protein of the S. forsteni genome had 98.10% integrity. Combined with structure annotation data, 34,140 (74.81%) genes were functionally annotated out of 45,638 predicted protein-coding genes. Upon comparing the genome size and TE content of teleost fishes, a roughly linear relationship was observed between these two parameters. However, TE content is not a decisive factor in determining the genome size of S. forsteni. Population history analysis results indicate that S. forsteni experienced two major population expansions, both of which occurred before the last interglacial period. In addition, through a comparative genomic analysis of the evolutionary relationship of other species, it was found that S. forsteni had the closest relationship with Cheilinus undulatus, another member of the Labridae family. Our expansion and contraction analysis of the gene family showed that the expansion genes were mainly associated with immune diseases, organismal systems, and cellular processes. At the same time, cell transcription and translation, sex hormone regulation, and other related pathways were also more prominent in the positive selection genes. The genomic sequence of S. forsteni offers valuable resources for future investigations on the conservation, evolution, and behavior of fish species.