LLM4THP: a computing tool to identify tumor homing peptides by molecular and sequence representation of large language model based on two-layer ensemble model strategy.

Tumor homing peptides (THPs) have a distinctive capacity to specifically attach to tumor cells, providing a promising approach for targeted cancer treatment and detection. Although THPs have the potential for significant impact, their detection by conventional methods is both time-consuming and expensive. To tackle this issue, we provide LLM4THP, an innovative computational approach that utilizes large language models (LLMs) to quickly and effectively detect THPs. LLM4THP utilizes two protein LLMs, ESM2 and Prot_T5_XL_UniRef50, to encode peptide sequences. This allows for the capture of complex patterns and relationships within the peptide data. In addition, we utilize inherent sequence characteristics such as Amino Acid Composition (AAC), Pseudo Amino Acid Composition (PAAC), Amphiphilic Pseudo Amino Acid Composition (APAAC), and Composition, Transition, and Distribution (CTD) to improve the representation of peptides. The RDKitDescriptors feature representation approach transforms peptide sequences into molecular objects and computes chemical characteristics, resulting in enhanced THP identification. The LLM4THP ensemble strategy incorporates various features into a two-layer learning architecture. The first layer consists of LightGBM, XGBoost, Random Forest, and Extremely Randomized Trees, which generate a set of meta results. The second layer utilizes Logistic Regression to further refine the identification of sequences as either THP or non-THP. LLM4THP exhibits exceptional performance compared to the most advanced methods, showcasing enhancements in accuracy, Matthew's correlation coefficient, F1 score, area under the curve, and average precision. The source code and dataset can be accessed at the following URL: https://github.com/abcair/LLM4THP.

UV wavelength-dependent photoionization quantum yields for the dark 1nπ* state of aqueous thymidine.

Despite the important role of the dark 1nπ* state in the photostability of thymidine in aqueous solution, no detailed ultraviolet (UV) wavelength-dependent investigation of the 1nπ* quantum yield (QY) in aqueous thymidine has been experimentally performed. Here, we investigate the wavelength-dependent photoemission spectra of aqueous thymidine from 266.7 to 240 nm using liquid-microjet photoelectron spectroscopy. Two observed ionization channels are assigned to resonant ionizations from 1ππ* to the cationic ground state D0 (π-1) and 1nπ* to the cationic excited state D1 (n-1). The weak 1nπ* → D1 ionization channel appears due to ultrafast 1ππ* → 1nπ* internal conversion within the pulse duration of ∼180 fs. The obtained 1nπ* quantum yields exhibit a strong wavelength dependence, ranging from 0 to 0.27 ± 0.01, suggesting a hitherto uncharacterized 1nπ* feature. The corresponding vertical ionization energies (VIEs) of D0 and D1 of aqueous thymidine are experimentally determined to be 8.47 ± 0.12 eV and 9.22 ± 0.29 eV, respectively. Our UV wavelength-dependent QYs might indicate that different structural critical points to connect the multidimensional 1ππ*/1nπ* conical intersection seam onto the multidimensional potential energy surface of the 1ππ* state might exist and determine the relaxation processes of aqueous thymidine upon UV excitation.

Oxygen Doping Cooperated with Co-N-Fe Dual-Catalytic Sites: Synergistic Mechanism for Catalytic Water Purification within Nanoconfined Membrane.

Atom-site catalysts, especially for graphitic carbon nitride-based catalysts, represents one of the most promising candidates in catalysis membrane for water decontamination. However, unravelling the intricate relationships between synthesis-structure-properties remains a great challenge. This study addresses the impacts of coordination environment and structure units of metal central sites based on Mantel test, correlation analysis, and evolution of metal central sites. An optimized unconventional oxygen doping cooperated with Co-N-Fe dual-sites (OCN Co/Fe) exhibits synergistic mechanism for efficient peroxymonosulfate activation, which benefits from a significant increase in charge density at the active sites and the regulation in the natural population of orbitals, leading to selective generation of SO4 •-. Building upon these findings, the OCN-Co/Fe/PVDF composite membrane demonstrates a 33 min-1 ciprofloxacin (CIP) rejection efficiency and maintains over 96% CIP removal efficiency (over 24 h) with an average permeance of 130.95 L m-2 h-1. This work offers a fundamental guide for elucidating the definitive origin of catalytic performance in advance oxidation process to facilitate the rational design of separation catalysis membrane with improved performance and enhanced stability.

HemoDL: Hemolytic peptides prediction by double ensemble engines from Rich sequence-derived and transformer-enhanced information.

Hemolytic peptides can trigger hemolysis by rupturing red blood cells' membranes and triggering cell disruption. Due to the labor-intensive and time-consuming in-lab identification process, accurate, high-throughput hemolytic peptide prediction is crucial for the growth of peptide sequence data in proteomics and peptidomics. In this study, we offer the HemoDL ensemble learning model, which learns the distinct distribution of sequence characteristics for predicting the hemolytic activity of peptides using a double LightGBM framework. To determine the most informative encoding features, we compare 17 widely used features across four benchmark datasets. Our investigation reveals that CTD, BPF, Charge, AAC, GDPC, ATC, QSO, and transformer-based features exhibit more positive contributions to detecting the hemolytic activity of peptides. Comparison with eight state-of-the-art methods demonstrates that HemoDL outperforms other models, attaining higher Matthews Correlation Coefficient values on four test datasets, ranging from 6.30% to 16.04%, 6.63%-11.26%, 4.76%-9.92%, and 7.41%-15.03%, respectively. Additionally, we provide the HemoDL with a user-friendly graphical interface available at https://github.com/abcair/HemoDL. In summary, the HemoDL model, leveraging CTD, BPF, Charge, AAC, GDPC, ATC, QSO and transformer-based encoding features within a double LightGBM learning framework, achieves high accuracy in predicting the hemolytic activity of peptides.

Tunable schiff-based networks with different bonding sites for enhanced photocatalytic activity under visible-light irradiation: The effects of steric hindrance.

Organic polymers hold great potential in photocatalysis considering their low cost, structural tailorability, and well-controlled degree of conjugation for efficient electron transfer. Among the polymers, Schiff base networks (SNWs) with high nitrogen content have been noticed. Herein, a series of SNWs is synthesized based on the melamine units and dialdehydes with different bonding sites. The chemical and structural variation caused by steric hindrance as well as the related photoelectric properties of the SNW samples are investigated, along with the application exploration on photocatalytic degradation and energy production. The results demonstrate that only SNW-o based on o-phthalaldehyde responds to visible light, which extends to over 550 nm. SNW-o shows the highest tetracycline degradation rate of 0.02516 min-1, under 60-min visible light irradiation. Moreover, the H2O2 production of SNW-o is 2.14 times higher than that of g-C3N4. The enhanced photocatalytic activity could be ascribed to the enlarged visible light adsorption and intramolecular electron transfer. This study indicates the possibility to regulate the optical and electrical properties of organic photocatalysts on a molecular level, providing an effective strategy for rational supramolecular engineering to the applications of organic materials in photocatalysis.

PPSNO: A Feature-Rich SNO Sites Predictor by Stacking Ensemble Strategy from Protein Sequence-Derived Information.

The protein S-nitrosylation (SNO) is a significant post-translational modification that affects the stability, activity, cellular localization, and function of proteins. Therefore, highly accurate prediction of SNO sites aids in grasping biological function mechanisms. In this document, we have constructed a predictor, named PPSNO, forecasting protein SNO sites using stacked integrated learning. PPSNO integrates multiple machine learning techniques into an ensemble model, enhancing its predictive accuracy. First, we established benchmark datasets by collecting SNO sites from various sources, including literature, databases, and other predictors. Second, various techniques for feature extraction are applied to derive characteristics from protein sequences, which are subsequently amalgamated into the PPSNO predictor for training. Five-fold cross-validation experiments show that PPSNO outperformed existing predictors, such as PSNO, PreSNO, pCysMod, DeepNitro, RecSNO, and Mul-SNO. The PPSNO predictor achieved an impressive accuracy of 92.8%, an area under the curve (AUC) of 96.1%, a Matthews correlation coefficient (MCC) of 81.3%, an F1-score of 85.6%, an SN of 79.3%, an SP of 97.7%, and an average precision (AP) of 92.2%. We also employed ROC curves, PR curves, and radar plots to show the superior performance of PPSNO. Our study shows that fused protein sequence features and two-layer stacked ensemble models can improve the accuracy of predicting SNO sites, which can aid in comprehending cellular processes and disease mechanisms. The codes and data are available at https://github.com/serendipity-wly/PPSNO .

Triplex DNA Helix Sensor Based on Reduced Graphene Oxide and Electrodeposited Gold Nanoparticles for Sensitive Lead(II) Detection.

A triplex DNA electrochemical sensor based on reduced graphene oxide (rGO) and electrodeposited gold nanoparticles (EAu) was simply fabricated for Pb2+ detection. The glass carbon electrode (GCE) sequentially electrodeposited with rGO and EAu was further modified with a triplex DNA helix that consisted of a guanine (G)-rich circle and a stem of triplex helix based on T-A•T base triplets. With the existence of Pb2+, the DNA configuration which was formed via the Watson-Crick and Hoogsteen base pairings was split and transformed into a G-quadruplex. An adequate electrochemical response signal was provided by the signal indicator methylene blue (MB). The proposed sensor demonstrated a linear relationship between the differential pulse voltammetry (DPV) peak currents and the logarithm of Pb2+ concentrations from 0.01 to 100.00 µM with a detection limit of 0.36 nM. The proposed sensor was also tested with tap water, river and medical wastewater samples with qualified recovery and accuracy and represented a promising method for Pb2+ detection.

Effect of the inoculation of Phanerochaete chrysosporium on nitrogen migration and organic matter conversion during electrolytic manganese residue composting.

Composting has made it practicable to dispose electrolytic manganese residues (EMR) in a less toxic way, nevertheless, the decomposition and the loss of nitrogen is a critical issue. This study aimed to investigate the role of Phanerochaete chrysosporium (PC) inoculation on nitrogen migration and promotion of decomposing organic matter (OM), as well as the effect on bacterial community structure during EMR composting. The results exhibited that nitrogen loss tallied with the first-order kinetic model. PC inoculation increased the relative microbial abundance of Firmicutes, which improved the efficiency of nitrogen nitrification and OM degradation, and increased the germination index and total nitrogen content by 13.8% and 2.95 g/kg, respectively. Moreover, aromatic benzenes replaced heteropolysaccharides, alcohols and ethers as the main components of OM in fertilizer, leading up to a more stable humus structure. This study provides a rationale and a novel perspective on the resource and nutrient conservation of EMR-contaminated soils.

A sensitive and economical method for simultaneous determination of D/L- amino acids profile in foods by HPLC-UV: Application in fermented and unfermented foods discrimination.

This work described a sensitive and economical HPLC-UV method with FDAA derivatization to simultaneously detect 36 D/l-amino acids, which provides higher sensitivity and lower cost than other HPLC-based methods. It was validated for linearity range (8-1000 µmol/L), limits of detection (2.68-62.44 pmol/L), limits of quantification (2.93 to 208.13 pmol/L), intraday precision (0.30 % - 5.31 %), interday precision (1.96 % - 8.04 %) and accuracy (86.53 % - 121.46 %). This method was then applied in the determination of D/L- amino acids abundance in fermented and unfermented food materials and showed the characteristics of each type of foods. The method also demonstrated good performance in another application case for the discrimination of different types of food materials based on D/L- amino acids profile. It emphasizes the ability of the method to study the characteristics, distribution and abundance of d-amino acids in foods and their potential application in food quality control.

Polydatin activates the Nrf2/HO-1 signaling pathway to protect cisplatin-induced hearing loss in guinea pigs.

Irreversible sensorineural hearing loss is one of the most common side effects after cisplatin treatment. Prevention and reversal of hearing loss caused by cisplatin are of great importance for cancer patients, especially children. Oxidative stress is an important cause of hearing loss resulted from cisplatin, unfortunately, there is no drug yet available that can completely prevent and reverse the ototoxicity from cisplatin. Polydatin (PD) possesses excellent antioxidant and anti-inflammatory effects, however, its role in the cisplatin-induced hearing loss has not been investigated. Herein, we have explored the preventive and therapeutic effects of PD on cisplatin-induced hearing loss and the possible underlying mechanisms. In the in vivo setting with guinea pigs, we have demonstrated that PD can reduce the threshold shift of auditory brainstem response (ABR) caused by cisplatin, promote the nuclear translocation of Nuclear factor erythroid-2 related factor 2 (Nrf2), increase the expression of Nrf2 and heme oxygenase-1 (HO-1), and thus reduce the loss of outer hair cells (OHCs). PD can ameliorate cisplatin-induced hearing loss through activating the Nrf2/HO-1 signaling pathway. This study provides a potential strategy for preventing and improving hearing loss resulted from cisplatin treatment in clinics.

Progress in Antiviral Fullerene Research.

Unlike traditional small molecule drugs, fullerene is an all-carbon nanomolecule with a spherical cage structure. Fullerene exhibits high levels of antiviral activity, inhibiting virus replication in vitro and in vivo. In this review, we systematically summarize the latest research regarding the different types of fullerenes investigated in antiviral studies. We discuss the unique structural advantage of fullerenes, present diverse modification strategies based on the addition of various functional groups, assess the effect of structural differences on antiviral activity, and describe the possible antiviral mechanism. Finally, we discuss the prospective development of fullerenes as antiviral drugs.

Facile synthesis of cadmium-doped graphite carbon nitride for photocatalytic degradation of tetracycline under visible light irradiation.

In recent years, using semiconductor photocatalysts for antibiotic contaminant degradation under visible light has become a hot topic. Herein, a novel and ingenious cadmium-doped graphite phase carbon nitride (Cd-g-C3N4) photocatalyst was successfully constructed via the thermal polymerization method. Experimental and characterization results revealed that cadmium (Cd) was well doped at the g-C3N4 surface and exhibited high intercontact with g-C3N4. Additionally, the introduction of cadmium significantly improved the photocatalytic activity, and the optimum degradation efficiency of tetracycline (TC) reached 98.1%, which was exceeded 2.0 times that of g-C3N4 (43.9%). Meanwhile, the Cd-doped sample presented a higher efficiency of electrical conductivity, light absorption property, and photogenerated electron-hole pair migration compared with g-C3N4. Additionally, the quenching experiments and electron spin-resonance tests exhibited that holes (h+), hydroxyl radicals (•OH), superoxide radicals (•O2-) were the main active species involved in TC degradation. The effects of various conditions on photocatalytic degradation, such as pH, initial TC concentrations, and catalyst dosage, were also researched. Finally, the degradation mechanism was elaborated in detail. This work gives a reasonable point to synthesizing high-efficiency and economic metal-doped photocatalysts.

Cobalt Single Atoms Anchored on Oxygen-Doped Tubular Carbon Nitride for Efficient Peroxymonosulfate Activation: Simultaneous Coordination Structure and Morphology Modulation.

Simultaneous regulation of the coordination environment of single-atom catalysts (SACs) and engineering architectures with efficient exposed active sites are efficient strategies for boosting peroxymonosulfate (PMS) activation. We isolated cobalt atoms with dual nitrogen and oxygen coordination (Co-N3 O1 ) on oxygen-doped tubular carbon nitride (TCN) by pyrolyzing a hydrogen-bonded cyanuric acid melamine-cobalt acetate precursor. The theoretically constructed Co-N3 O1 moiety on TCN exhibited an impressive mass activity of 7.61×105  min-1 mol-1 with high 1 O2 selectivity. Theoretical calculations revealed that the cobalt single atoms occupied a dual nitrogen and oxygen coordination environment, and that PMS adsorption was promoted and energy barriers reduced for the key *O intermediate that produced 1 O2 . The catalysts were attached to a widely used poly(vinylidene fluoride) microfiltration membrane to deliver an antibiotic wastewater treatment system with 97.5 % ciprofloxacin rejection over 10 hours, thereby revealing the suitability of the membrane for industrial applications.

Effects of Ilisha elongata proteins on proliferation and adhesion of Lactobacillus plantarum.

The effects of aquatic proteins on the proliferation and adhesion of intestinal probiotic bacteria were investigated by in vitro fermentation and mouse in vitrointestinal tissue models. Compared with the control group, the Illisha elongata protein reduced the growth time of Lactobacillus plantarum (LP45) by 34.25% and increased the total number of colonies by 6.61%. The Ilisha elongata salt-solubale protein performed better than water-soluble protein in vitro proliferation of LP45. Ilisha elongata salt-soluble protein significantly increased the number of viable bacteria adhering to intestinal, and caused changes in the amount of polysaccharides, proteins and biofilms in the intestinal tissue model. These results indicate that the Ilisha elongata protein is beneficial to the proliferation and adhesion of probiotics in the intestinal, and can be used as an active protein beneficial to intestinal health.

Tailoring Functional Terminals on Solution-Processable Fullerene Electron Transporting Materials for High Performance Perovskite Solar Cells.

Widely known as an excellent electron transporting material (ETM), pristine fullerene C60 plays a critical role in improving the photovoltaic performance of inverted structure perovskite solar cells (PSCs). However, the imperfect perovskite/C60 interface significantly limits the promotion of device performance and stability due to the weak coordination interactions between bare carbon cages and perovskite. Here, we designed and synthesized three functionalized fulleropyrrolidine ETMs (abbreviated as CEP, CEPE, and CECB), each of which was modified with the same primary terminal (cyanoethyl) and various secondary terminals (phenyl, phenethyl, and chlorobutyl). The resulting CECB-based PSC has a power conversion efficiency (PCE) over 19% and exceptional photo-stability over 1800 h. This work provides significant insight into the targeted terminal design of novel fullerene ETMs for efficient and stable PSCs.

A Novel Zinc Exporter CtpG Enhances Resistance to Zinc Toxicity and Survival in Mycobacterium bovis.

Zinc is a microelement essential for the growth of almost all organisms, but it is toxic at high concentrations and represents an antimicrobial strategy for macrophages. Mycobacterium tuberculosis and Mycobacterium bovis are two well-known intracellular pathogens with strong environmental adaptability, including zinc toxicity. However, the signaling pathway and molecular mechanisms on sensing and resistance to zinc toxicity remains unclear in mycobacteria. Here, we first report that P1B-type ATPase CtpG acts as a zinc efflux transporter and characterize a novel CmtR-CtpG-Zn2+ regulatory pathway that enhances mycobacterial resistance to zinc toxicity. We found that zinc upregulates ctpG expression via transcription factor CmtR and stimulates the ATPase activity of CtpG. The APC residues in TM6 is essential for CtpG to export zinc and enhance M. bovis BCG resistance to zinc toxicity. During infection, CtpG inhibits zinc accumulation in the mycobacteria, and aids bacterial survival in THP-1 macrophage and mice with elevated inflammatory responses. Our findings revealed the existence of a novel regulatory pathway on mycobacteria responding to and adapting to host-mediated zinc toxicity. IMPORTANCE Tuberculosis is caused by the bacillus Mycobacterium tuberculosis and is one of the major sources of mortality. M. tuberculosis has developed unique mechanisms to adapt to host environments, including zinc deficiency and toxicity, during infection. However, the molecular mechanism by which mycobacteria promote detoxification of zinc, and the associated signaling pathways remains largely unclear. In this study, we first report that P1B-type ATPase CtpG acts as a zinc efflux transporter and characterize a novel CmtR-CtpG-Zn2+ regulatory pathway that enhances mycobacterial resistance to zinc toxicity in M. bovis. Our findings reveal the existence of a novel excess zinc-triggered signaling circuit, provide new insights into mycobacterial adaptation to the host environment during infection, and might be useful targets for the treatment of tuberculosis.

Metal-organic frameworks as a good platform for the fabrication of multi-metal nanomaterials: design strategies, electrocatalytic applications and prospective.

MOF-derived multi-metal nanomaterials are attracting numerous attentions in widespread applications such as catalysis, sensors, energy storage and conversion, and environmental remediation. Compared to the monometallic counterparts, the presence of foreign metal is expected to bring new physicochemical properties, thus exhibiting synergistic effect for enhanced performance. MOFs have been proved as a good platform for the fabrication of polymetallic nanomaterials with requisite features. Herein, various design strategies related to constructing multi-metallic nanomaterials from MOFs are summarized for the first time, involving metal nodal substitution, seed epitaxial growth, ion-exchange strategy, guest species encapsulation, solution impregnation and combination with extraneous substrate. Afterwards, the recent advances of multi-metallic nanomaterials for electrocatalytic applications, including oxygen reduction reaction (ORR), oxygen evolution reaction (OER) and hydrogen evolution reaction (HER), are systematically discussed. Finally, a personal outlook on the future trends and challenges are also presented with hope to enlighten deeper understanding and new thoughts for the development of multi-metal nanomaterials from MOFs.

Sporosarcina jiandibaonis sp. nov., isolated from saline soil.

A Gram-stain-positive, aerobic, motile, rod-shaped bacterium, designated strain LAM9210T, was isolated from a saline soil sample collected from Lingxian County, Shandong Province, PR China. Analysis of the 16S rRNA gene sequence of the isolate revealed highest sequence similarities to the type strain of Sporosarcina pasteurii NCIMB 8841T (97.6 % sequence similarity). The genomic G+C content was 40.4 mol%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain LAM9210T and the type strain of the most closely related species S. pasteurii NCIMB 8841T were 73.6 and 20.6 %, respectively. Strain LAM9210T was found to grow at 10-40 °C (optimum, 30 °C), at pH 6.0-10.0 (optimum, pH 9.0) and with 0-6 % (w/v) NaCl (optimum, 0.5 %), respectively. The major fatty acids were anteiso-C15 : 0 and iso-C14 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid. Menaquinone-7 was detected as the predorminant respiratory quinone. Strain LAM9210T contained glycine, lysine, alanine and glutamic acid as the diagnostic amino acids in the cell-wall peptidoglycan. On the basis of phenotypic, phylogenetic and genotypic data, strain LAM9210T is considered to represent a novel species of the genus Sporosarcina, for which the name Sporosarcina jiandibaonis sp. nov. is proposed. The type strain is LAM9210T (=CGMCC 1.18607T=GDMCC 1.2002T=JCM 32514T).

Gap junctions mediate glucose transfer to promote colon cancer growth in three-dimensional spheroid culture.

In vivo tumor growth is characterized by a necrotic core generated by oxygen and nutrients gradients, which is replicated by in vitro three-dimensional (3D) tumor spheroids but not traditional two-dimensional cell monolayers. Gap junctions provide direct communication between adjacent cells and play a critical role in cancer development, but their effects are still debatable. In this study, we found that connexin 43 (Cx43) reduced the area of necrotic core in colon cancer 3D spheroids, thus providing a growth advantage. This impact is dependent on gap junction channel functions, as the channel blocker carbenoxolone or connexin channel death mutant reverses this effect. Additionally, enhanced glucose uptake was detected in Cx43-overexpressing spheroids, along with upregulated mTOR, downregulated AMPK signaling, increased ATP content, and enhanced oxygen consumption rate. Furthermore, the xenograft mouse model confirmed the growth advantage of Cx43 in vivo. RNAseq data and clinical information from The Cancer Genome Atlas (TCGA) database indicated a more heterogeneous expression pattern of Cx43 in colon cancer compared to normal colon tissue, and higher Cx43 level is associated with worse clinical outcomes. Our data suggest a novel function of connexin in tumor growth, that gap junctions may provide nutrients transmitting routes in lieu of vasculature to meet the increasing metabolic requirement of solid tumors.

Self-assembly hybridization of COFs and g-C3N4: Decipher the charge transfer channel for enhanced photocatalytic activity.

Organic semiconductors have been recognized as a new generation of photocatalysts for pollutants degradation and energy production. Herein, organic heterojunction (TpMa/CN) consisting of carbon nitride and ß-ketoenamine-based covalent organic framework is fabricated via a controllable self-assembly approach. The as-prepared TpMa/CN heterojunctions show enlarged visible-light absorption. The optimum TpMa/CN-5 photocatalyst achieves the highest photocatalytic activity towards tetracycline degradation, and its photocatalytic degradation rate is improved by 2.3 and 4.3 times than TpMa and CN, respectively. As a multifunctional photocatalyst, TpMa/CN-5 sample also shows remarkable photocatalytic activity for hydrogen peroxide production (880.494 µM h-1), which is 49 times higher than that of CN. Experimental and theoretical investigations indicate that a built-in electric field is formed at the interface of composite, which enables an accelerated charge transfer and separation. This work develops an effective strategy to design difunctional photocatalyst and deciphers the electronic properties and mechanisms of g-C3N4-based organic photocatalysts, which spurs further interests for organic heterojunction photocatalysts in the future.