A Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing.

Chimera artifacts in nanopore direct RNA sequencing (dRNA-seq) can significantly distort transcriptome analyses, yet their detection and removal remain challenging due to limitations in existing basecalling models. We present DeepChopper, a genomic language model that precisely identifies and removes adapter sequences from base-called dRNA-seq long reads at single-base resolution, operating independently of raw signal or alignment information to effectively eliminate chimeric read artifacts. By removing these artifacts, DeepChopper substantially improves the accuracy of critical downstream analyses, such as transcript annotation and gene fusion detection, thereby enhancing the reliability and utility of nanopore dRNA-seq for transcriptomics research.

Structure Distortion Endows Copper Nanoclusters with Surface-Active Uncoordinated Sites for Boosting Catalysis.

The utilization of structure distortion to modulate the electronic structure and alter catalytic properties of metallic nanomaterials is a well-established practice, but accurately identifying and comprehensively understanding these distortions present significant challenges. Ligand-stabilized metal nanoclusters with well-defined structures serve as exemplary model systems to illustrate the structure chemistry of nanomaterials, among which few studies have investigated nanocluster models that incorporate structural distortions. In this work, a novel copper hydride nanocluster, Cu(PPh)(RS)(CFCOO)(CHO)H (Cu; PPh is triphenylphosphine and RSH is 2,4-dichlorophenylthiol), with a highly twisted structure has been synthesized in a simple way.

Development and validation of prognostic nomograms for adult with papillary renal cell carcinoma: A retrospective study.

Objective: The aim of the study was to create two consensus nomograms for predicting Overall Survival (OS) and Cancer-Specific Survival (CSS) in adults with papillary Renal Cell Carcinoma (pRCC).

Methods: Using the Surveillance, Epidemiology, and End Results databases, a retrospective analysis of 1,074 adults with pRCC from 2004 to 2015 was performed. These patients were then randomly divided into two independent cohorts with a ratio of 7:3 (training cohort: 752; validation cohort: 322).

Supramolecular nanodrug targeting CDK4/6 overcomes BAG1 mediated cisplatin resistance in oral squamous cell carcinoma.

Chemoresistance to cisplatin remains a significant challenge affecting the prognosis of advanced oral squamous cell carcinoma (OSCC). However, the specific biomarkers and underlying mechanisms responsible for cisplatin resistance remain elusive. Through comprehensive bioinformatic analyses, we identified a potential biomarker, BCL2 associated athanogene-1 (BAG1), showing elevated expression in head and neck squamous cell carcinoma (HNSCC).

Eight-Electron Copper Nanoclusters for Photothermal Conversion.

Owing to distinct physicochemical properties in comparison to gold and silver counterparts, atomically precise copper nanoclusters are attracting embryonic interest in material science. The introduction of copper cluster nanomaterials in more interesting fields is currently urgent and desired. Reported in this work are novel copper nanoclusters of [XCuCl(BuS)(NO)] (X=S or none, BuSH=2-methyl-2-propanethiol), which exhibit high performance in photothermal conversion.

Peptide KN-17-Loaded Supramolecular Hydrogel Induces the Regeneration of the Pulp-Dentin Complex.

Regenerating the pulp-dentin complex remains a decisive factor during apexification for immature permanent teeth. Peptide KN-17, which was modified based on the structure of cecropin B, could effectively interfere with bacterial growth and induce the migration of human bone marrow stromal cells (hBMSCs). This study aimed to investigate the effect of KN-17 on the tissue regeneration.

ScanNeo2: a comprehensive workflow for neoantigen detection and immunogenicity prediction from diverse genomic and transcriptomic alterations.

Motivation: Neoantigens, tumor-specific protein fragments, are invaluable in cancer immunotherapy due to their ability to serve as targets for the immune system. Computational prediction of these neoantigens from sequencing data often requires multiple algorithms and sophisticated workflows, which are currently restricted to specific types of variants, such as single-nucleotide variants or insertions/deletions. Nevertheless, other sources of neoantigens are often overlooked.

Tuning Lignite Structure via Hydromodification To Promote the Formation of Coal-Based CNTs: Exploration for the Carbon Source of CNTs.

Although the preparation of coal-based carbon nanotubes (CNTs) has been realized in many studies, the relationship between carbon source structure of coal and CNT growth has not been studied in depth. In this study, we used lignite and KOH as raw material and catalyst and tuned lignite structure via hydrothermal modification to promote the formation of CNTs during catalytic pyrolysis. The main carbon source of CNTs was explored from the change of coal structure and pyrolysis characteristics.

Identification of Myxobolus distalisensis n. sp. (Cnidaria: Myxozoa) infecting yellow catfish Tachysurus fulvidraco (Richardson), with a supplement description of M. voremkhai (Akhmerov, 1960) Landsberg and Lom, 1991.

With growing scale of intensive fish cultivation, the risk of parasite infection in commercial fish is increased. Precisely identifying and characterizing the parasites that infect the farmed fish is critical to understanding the dynamics of their communities. Here, two species of Myxobolus were identified in farmed yellow catfish Tachysurus fulvidraco (Richardson) in China.

Decorating an Anticuboctahedral Copper Kernel with Labile Surface Coatings for Controlling Optical and Catalytic Properties.

Manipulating the interfacial/surface structure of ligand-stabilized atomically precise metal nanoclusters (NCs) is one of the central tasks in nanoscience because surface motifs are directly related to key properties of nanomaterials. Although great progress has been made in engineering the surface of gold and silver nanoclusters, parallel studies on lighter copper analogues hitherto remain unexplored. In this work, we report the design, synthesis, and structure of a new class of copper nanoclusters featuring virtually identical kernels but different surface motifs.

PRMT2 promotes RCC tumorigenesis and metastasis via enhancing WNT5A transcriptional expression.

Protein arginine methyltransferase 2 (PRMT2) is involved in several biological processes via histone methylation and transcriptional regulation. Although PRMT2 has been reported to affect breast cancer and glioblastoma progression, its role in renal cell cancer (RCC) remains unclear. Here, we found that PRMT2 was upregulated in primary RCC and RCC cell lines.

How to Perform Intravesical Chemotherapy after Second TURBT for Non-Muscle-Invasive Bladder Cancer: A Single-Center Experience.

Purpose: The objective of this study aimed to explore whether the original IVC regimen should be continued after the second TURBT or whether the IVC induction phase should be restarted from the beginning.

Methods: A retrospective analysis was performed on 137 patients who underwent a second TURBT at the Affiliated Hospital of Xuzhou Medical University between April 2014 and June 2022. Based on the pathological findings, patients were divided into two groups: group A patients, who did not have a residual tumor on pathological examination after the second TURBT; and group B patients, who had residual tumor.

The methodology for preparing domperidone: strategies, routes and reaction processes.

Domperidone is a powerful peripheral dopamine receptor antagonist; however, a systematic review of the synthetic methods and processes of this drug has not been reported so far. This review summarizes the synthetic strategies, synthetic routes and reaction processes of domperidone in detail. Domperidone can be synthesized from the coupling reaction of two benzimidazolone derivatives (intermediates 1 and 2).

Transcriptomic Insights into the Diversity and Evolution of Myxozoa (Cnidaria, Endocnidozoa) Toxin-like Proteins.

Myxozoa is a speciose group of endoparasitic cnidarians that can cause severe ecological and economic effects. Their cnidarian affinity is affirmed by genetic relatedness and the presence of nematocysts, historically called "polar capsules". Previous studies have revealed the presence of toxin-like proteins in myxozoans; however, the diversity and evolution of venom in Myxozoa are not fully understood.

A clinical and biomechanical comparison of INFIX plus single versus double sacroiliac screw fixation for unstable pelvic ring injury.

Background: The aim of this study is to compare the clinical and biomechanical outcome of INFIX plus single with two sacroiliac screw fixation for unstable pelvic fractures of Type C.

Methods: Sixteen cadavers were randomly subjected to INFIX plus single or double sacroiliac screw fixations and then mounted onto the ElectroForce loading machine under different vertical loads. To investigate the clinical outcomes of the two techniques, nineteen patients were retrospectively analyzed.

A myxozoan genome reveals mosaic evolution in a parasitic cnidarian.

Background: Parasite evolution has been conceptualized as a process of genetic loss and simplification. Contrary to this model, there is evidence of expansion and conservation of gene families related to essential functions of parasitism in some parasite genomes, reminiscent of widespread mosaic evolution-where subregions of a genome have different rates of evolutionary change. We found evidence of mosaic genome evolution in the cnidarian Myxobolus honghuensis, a myxozoan parasite of fish, with extremely simple morphology.

Mitochondrion-targeted supramolecular "nano-boat" simultaneously inhibiting dual energy metabolism for tumor selective and synergistic chemo-radiotherapy.

Tumor energy metabolism has been a well-appreciated target of cancer therapy; however, the metabolism change of cancer cells between oxidative phosphorylation and glycolysis poses a challenge to the above. In this study, we constructed an innovative mitochondrion-targeted supramolecular "nano-boat" based on peptide self-assembly for tumor combined chemo-radiotherapy by simultaneously inhibiting the dual energy metabolism. A lipophilic self-assembled peptide and a positively charged cyclen were integrated to fabricate a brand new mitochondrion-targeted nano-platform for the first time.

Quantitative Insights into the Contribution of Nematocysts to the Adaptive Success of Cnidarians Based on Proteomic Analysis.

Nematocysts are secretory organelles in cnidarians that play important roles in predation, defense, locomotion, and host invasion. However, the extent to which nematocysts contribute to adaptation and the mechanisms underlying nematocyst evolution are unclear. Here, we investigated the role of the nematocyst in cnidarian evolution based on eight nematocyst proteomes and 110 cnidarian transcriptomes/genomes.

Structure of Self-assembled Peptide Determines the Activity of Aggregation-Induced Emission Luminogen-Peptide Conjugate for Detecting Alkaline Phosphatase.

The unique property of turning on their fluorescence after aggregation or assembly makes aggregation-induced emission luminogens (AIEgens) ideal luminescent molecules for the construction of self-assembled peptide-based nanoprobes. However, the characteristic highly twisted or propeller-shaped molecular conformation of AIEgens tends to prevent the assembly of AIEgen-peptides. Here, we show that (i) the distance between tetraphenylethene (TPE) and assembled peptides should not be too far (less than five glycines), otherwise the self-assembly of peptides cannot limit the intramolecular rotation of conjugated TPE and the luminous efficiency of TPE-peptide to alkaline phosphatase (ALP) will decrease; (ii) properly increasing the number of amino acids with self-assembly ability (three phenylalanines) can improve their ALP-responsive self-assembly and luminescence ability; (iii) the strategy of co-assembly with a non-AIEgen-capped self-assembled peptide is a simple and effective way to realize the efficient assembly and luminescence of AIEgen-peptides; and (iv) the hydrophilic and hydrophobic balance of the probe should always be considered in the construction of an efficient AIEgen-peptide probe.

Paclitaxel-based supramolecular hydrogel loaded with mifepristone for the inhibition of breast cancer metastasis.

Breast cancer is the leading cause of cancer death among women and almost all of the breast cancer-caused mortality is related to metastasis. It has been reported that glucocorticoid facilitates the metastasis of breast cancer in mice, and mifepristone can antagonize the effect of glucocorticoid. Paclitaxel is one of the important drugs in the treatment of breast cancer.

Role of FeS Catalyst in the Hydromodification of Lignite in a Subcritical Water-CO System.

The impacts of FeS catalysts on the hydromodification and structural evolution of lignite were investigated using Fourier transform infrared spectroscopy, nuclear magnetic resonance, and X-ray photoelectron spectroscopy. The results indicate that the caking property of lignite can be significantly improved in the presence of the FeS catalyst. When 6.

Fins infestation induced by Myxobolus xiantaoensis in yellow catfish Tachysurus fulvidraco Richardson, 1846: Some pathophysiological and molecular insights.

The myxozoan parasite Myxobolus xiantaoensis is a fin pathogen of commercially important yellow catfish Tachysurus fulvidraco Richardson, 1846, in the freshwater ponds of China. In the present work, four geographical isolates of M. xiantaoensis were sampled from the fins of yellow catfish.

Supramolecular nanofibers increase the efficacy of 10-hydroxycamptothecin by enhancing nuclear accumulation and depleting cellular ATP.

Poor nuclear delivery and accumulation are the main reasons for the reduced drug efficacy of many anticancer drugs that target DNA or enzymes in the nucleus, and it is a major obstacle to successful cancer therapy. To address this problem, developing practical drug delivery systems for nuclear delivery is urgently needed. Here we develop a supramolecular hydrogel by conjugating the anticancer agent 10-hydroxycamptothecine (HCPT) and macrocyclic polyamine cyclen to a self-assembling peptide.

A coassembled peptide hydrogel boosts the radiosensitization of cisplatin.

We constructed a novel supramolecular hydrogel by carrying out a coassembly of cisplatin and short naproxen-capped peptides. This procedure boosted the radiosensitization effect of cisplatin by increasing the number of Pt-DNA adducts, arresting the cell cycle, and inhibiting cyclooxygenase-2.