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1.
Chem Commun (Camb) ; 2024 Jun 03.
Article in English | MEDLINE | ID: mdl-38828544

ABSTRACT

We synthesized a low metal-to-sulfur atomic ratio (0.5) FeCoS4, exhibiting high reversible specific capacity. Reduced graphene oxide was covered on the surface to improve the cycling stability and rate performance further. Density functional theory calculations show that composite materials can effectively increase the adsorption energy and enhance the diffusion kinetics.

2.
Nanomicro Lett ; 16(1): 189, 2024 May 02.
Article in English | MEDLINE | ID: mdl-38698120

ABSTRACT

Monolithic textured perovskite/silicon tandem solar cells (TSCs) are expected to achieve maximum light capture at the lowest cost, potentially exhibiting the best power conversion efficiency. However, it is challenging to fabricate high-quality perovskite films and preferred crystal orientation on commercially textured silicon substrates with micrometer-size pyramids. Here, we introduced a bulky organic molecule (4-fluorobenzylamine hydroiodide (F-PMAI)) as a perovskite additive. It is found that F-PMAI can retard the crystallization process of perovskite film through hydrogen bond interaction between F- and FA+ and reduce (111) facet surface energy due to enhanced adsorption energy of F-PMAI on the (111) facet. Besides, the bulky molecular is extruded to the bottom and top of perovskite film after crystal growth, which can passivate interface defects through strong interaction between F-PMA+ and undercoordinated Pb2+/I-. As a result, the additive facilitates the formation of large perovskite grains and (111) preferred orientation with a reduced trap-state density, thereby promoting charge carrier transportation, and enhancing device performance and stability. The perovskite/silicon TSCs achieved a champion efficiency of 30.05% based on a silicon thin film tunneling junction. In addition, the devices exhibit excellent long-term thermal and light stability without encapsulation. This work provides an effective strategy for achieving efficient and stable TSCs.

3.
Sci Rep ; 14(1): 10175, 2024 05 03.
Article in English | MEDLINE | ID: mdl-38702356

ABSTRACT

Acute myocardial infarction (AMI) commonly precedes ventricular remodeling, heart failure. Few dynamic molecular signatures have gained widespread acceptance in mainstream clinical testing despite the discovery of many potential candidates. These unmet needs with respect to biomarker and drug discovery of AMI necessitate a prioritization. We enrolled patients with AMI aged between 30 and 70. RNA-seq analysis was performed on the peripheral blood mononuclear cells collected from the patients at three time points: 1 day, 7 days, and 3 months after AMI. PLC/LC-MS analysis was conducted on the peripheral blood plasma collected from these patients at the same three time points. Differential genes and metabolites between groups were screened by bio-informatics methods to understand the dynamic changes of AMI in different periods. We obtained 15 transcriptional and 95 metabolite expression profiles at three time points after AMI through high-throughput sequencing. AMI-1d: enrichment analysis revealed the biological features of 1 day after AMI primarily included acute inflammatory response, elevated glycerophospholipid metabolism, and decreased protein synthesis capacity. Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) might stand promising biomarkers to differentiate post-AMI stage. Anti-inflammatory therapy during the acute phase is an important direction for preventing related pathology. AMI-7d: the biological features of this stage primarily involved the initiation of cardiac fibrosis response and activation of platelet adhesion pathways. Accompanied by upregulated TGF-beta signaling pathway and ECM receptor interaction, GP5 help assess platelet activation, a potential therapeutic target to improve haemostasis. AMI-3m: the biological features of 3 months after AMI primarily showed a vascular regeneration response with VEGF signaling pathway, NOS3 and SHC2 widely activated, which holds promise for providing new therapeutic approaches for AMI. Our analysis highlights transcriptional and metabolomics signatures at different time points after MI, which deepens our understanding of the dynamic biological responses and associated molecular mechanisms that occur during cardiac repair.


Subject(s)
Metabolomics , Myocardial Infarction , Humans , Myocardial Infarction/metabolism , Myocardial Infarction/genetics , Myocardial Infarction/blood , Middle Aged , Male , Female , Metabolomics/methods , Aged , Adult , Transcriptome , Biomarkers/metabolism , Biomarkers/blood , Leukocytes, Mononuclear/metabolism , Gene Expression Profiling
4.
Adv Mater ; : e2405165, 2024 May 17.
Article in English | MEDLINE | ID: mdl-38758975

ABSTRACT

Solid nanoparticle-mediated drug delivery systems are usually confined to nanoscale due to the enhanced permeability and retention (EPR) effect. However, they remain a great challenge for malignant glioma chemotherapy because of poor drug delivery efficiency and insufficient tumor penetration resulting from the blood-brain barrier/blood-brain tumor barrier (BBB/BBTB). Inspired by biological microparticles (e.g., cells) with excellent adaptive deformation, we demonstrate that the adaptive microdrugs (even up to 3.0 µm in size) are more efficient than their nanodrugs (less than 200 nm in size) to cross BBB/BBTB and penetrate into tumor tissues, achieving highly efficient chemotherapy of malignant glioma. The distinct delivery of the adaptive microdrugs is mainly attributed to the enhanced interfacial binding and endocytosis via adaptive deformation. As expected, the obtained adaptive microdrugs exhibited enhanced accumulation, deep penetration, and cellular internalization into tumor tissues in comparison with nanodrugs, significantly improving the survival rate of glioblastoma mice. We believe that the bioinspired adaptive microdrugs enable them to efficiently cross physiological barriers and deeply penetrate tumor tissues for drug delivery, providing an avenue for the treatment of solid tumors. This article is protected by copyright. All rights reserved.

5.
Molecules ; 29(10)2024 May 08.
Article in English | MEDLINE | ID: mdl-38792055

ABSTRACT

The present study aimed to develop low-sodium curing agents for dry-cured meat products. Four low-sodium formulations (SPMA, SPM, SP, and SM) were used for dry-curing meat. The physicochemical properties and flavor of the dry-cured meat were investigated. The presence of Mg2+ ions hindered the penetration of Na+ into the meat. The weight loss, moisture content, and pH of all low-sodium salt groups were lower than those of S. Mg2+ addition increased the water activity (Aw) of SPMA, SPM, and SM. Dry-curing meat with low-sodium salts promoted the production of volatile flavor compounds, with Mg2+ playing a more prominent role. Furthermore, low-sodium salts also promoted protein degradation and increased the content of free amino acids in dry-cured meat, especially in SM. Principal component analysis (PCA) showed that the low-sodium salts containing Mg2+ were conducive to improving the quality of dry-cured meat products. Therefore, low-sodium salts enriched with Mg2+ become a desirable low-sodium curing agent for achieving salt reduction in dry-cured meat products.


Subject(s)
Magnesium , Meat Products , Meat Products/analysis , Magnesium/analysis , Magnesium/chemistry , Animals , Sodium/analysis , Sodium/chemistry , Salts/chemistry , Taste , Flavoring Agents/analysis , Flavoring Agents/chemistry , Hydrogen-Ion Concentration , Amino Acids/analysis , Amino Acids/chemistry , Food Handling/methods
6.
CNS Neurosci Ther ; 30(5): e14739, 2024 05.
Article in English | MEDLINE | ID: mdl-38702935

ABSTRACT

AIMS: The hippocampus has been reported to be morphologically and neurochemically altered in schizophrenia (SZ). Hyperlocomotion is a characteristic SZ-associated behavioral phenotype, which is associated with dysregulated dopamine system function induced by hippocampal hyperactivity. However, the neural mechanism of hippocampus underlying hyperlocomotion remains largely unclear. METHODS: Mouse pups were injected with N-methyl-D-aspartate receptor antagonist (MK-801) or vehicle twice daily on postnatal days (PND) 7-11. In the adulthood phase, one cohort of mice underwent electrode implantation in field CA1 of the hippocampus for the recording local field potentials and spike activity. A separate cohort of mice underwent surgery to allow for calcium imaging of the hippocampus while monitoring the locomotion. Lastly, the effects of atypical antipsychotic (aripiprazole, ARI) were evaluated on hippocampal neural activity. RESULTS: We found that the hippocampal theta oscillations were enhanced in MK-801-treated mice, but the correlation coefficient between the hippocampal spiking activity and theta oscillation was reduced. Consistently, although the rate and amplitude of calcium transients of hippocampal neurons were increased, their synchrony and correlation to locomotion speed were disrupted. ARI ameliorated perturbations produced by the postnatal MK-801 treatment. CONCLUSIONS: These results suggest that the disruption of neural coordination may underly the neuropathological mechanism for hyperlocomotion of SZ.


Subject(s)
Antipsychotic Agents , Aripiprazole , Disease Models, Animal , Dizocilpine Maleate , Hippocampus , Hyperkinesis , Schizophrenia , Animals , Aripiprazole/pharmacology , Aripiprazole/therapeutic use , Schizophrenia/drug therapy , Hippocampus/drug effects , Antipsychotic Agents/pharmacology , Antipsychotic Agents/therapeutic use , Dizocilpine Maleate/pharmacology , Mice , Hyperkinesis/drug therapy , Male , Locomotion/drug effects , Locomotion/physiology , Excitatory Amino Acid Antagonists/pharmacology , Mice, Inbred C57BL , Animals, Newborn , Neurons/drug effects , Theta Rhythm/drug effects , Theta Rhythm/physiology
7.
ACS Nano ; 18(20): 12970-12980, 2024 May 21.
Article in English | MEDLINE | ID: mdl-38725336

ABSTRACT

Ionogels have grabbed significant interest in various applications, from sensors and actuators to wearable electronics and energy storage devices. However, current ionogels suffer from low strength and poor ionic conductivity, limiting their performance in practical applications. Here, inspired by the mechanical reinforcement of natural biomacromolecules through noncovalent aggregates, a strategy is proposed to construct nanofibril-based ionogels through complex coacervation-induced assembly. Cellulose nanofibrils (CNFs) can bundle together with poly(ionic liquid) (PIL) to form a superstrong nanofibrous network, in which the ionic liquid (IL) can be retained to form ionogels with high liquid inclusion and ionic conductivity. The strength of the CNF-PIL-IL ionogels can be tuned by the IL content over a wide range of up to 78 MPa. The optical transparency, high strength, and hygroscopicity enabled them to be promising candidates in moist-electricity generation and applications such as energy harvesting windows and wearable power generators. In addition, the ionogels are degradable and the ionogel-based generators can be recycled through dehydration. Our strategy suggests perspectives for the fabrication of high-strength and multifunctional ionogels for sustainable applications.

8.
Article in English | MEDLINE | ID: mdl-38739505

ABSTRACT

This study aims to tackle the intricate challenge of predicting RNA-small molecule binding sites to explore the potential value in the field of RNA drug targets. To address this challenge, we propose the MultiModRLBP method, which integrates multi-modal features using deep learning algorithms. These features include 3D structural properties at the nucleotide base level of the RNA molecule, relational graphs based on overall RNA structure, and rich RNA semantic information. In our investigation, we gathered 851 interactions between RNA and small molecule ligand from the RNAglib dataset and RLBind training set. Unlike conventional training sets, this collection broadened its scope by including RNA complexes that have the same RNA sequence but change their respective binding sites due to structural differences or the presence of different ligands. This enhancement enables the MultiModRLBP model to more accurately capture subtle changes at the structural level, ultimately improving its ability to discern nuances among similar RNA conformations. Furthermore, we evaluated MultiModRLBP on two classic test sets, Test18 and Test3, highlighting its performance disparities on small molecules based on metal and non-metal ions. Additionally, we conducted a structural sensitivity analysis on specific complex categories, considering RNA instances with varying degrees of structural changes and whether they share the same ligands. The research results indicate that MultiModRLBP outperforms the current state-of-the-art methods on multiple classic test sets, particularly excelling in predicting binding sites for non-metal ions and instances where the binding sites are widely distributed along the sequence. MultiModRLBP also can be used as a potential tool when the RNA structure is perturbed or the RNA experimental tertiary structure is not available. Most importantly, MultiModRLBP exhibits the capability to distinguish binding characteristics of RNA that are structurally diverse yet exhibit sequence similarity. These advancements hold promise in reducing the costs associated with the development of RNA-targeted drugs.

9.
J Mol Histol ; 2024 May 17.
Article in English | MEDLINE | ID: mdl-38758519

ABSTRACT

Cadmium is a toxic heavy metal, which is both an environmental pollutant, and a threat to human health. A fluorescent probe was developed to detect Cd2+ selectively, sensitively, and quickly. This study reports the successful development of a polypeptide fluorescent probe TPE-HC (TPE-His-Pro-Gly-Cys) which selectively detects Cd2+ by Aggregation-Induced Emission effect. After fluorescence excitation, Cd2+ can be effectively detected based on the change of fluorescence intensity. The detection limit of Cd2+ in buffer solution was determined to be 151 nM (R2 = 0.9933). This probe exhibits high sensitivity, high cell permeabilit y, and low biological toxicity, and can perform live cell imaging under biological conditions. This study indicates that TPE-HC can detect Cd2+ in biological environments.

10.
Materials (Basel) ; 17(9)2024 Apr 25.
Article in English | MEDLINE | ID: mdl-38730813

ABSTRACT

We present a surface modification technique that turns CuNi foam films with a high contact angle and non-sticking property into a sticky surface. By decorating with mesh-like biaxially oriented polypropylene (BOPP) and adjusting the surface parameters, the surface exhibits water-retaining capability even when being held upside down. The wetting transition process of droplets falling on its surface were systematically studied using the finite element simulation method. It is found that the liquid filled the surface microstructure and curvy three-phase contact line. Moreover, we experimentally demonstrated that this surface can be further applied to capture underwater air bubbles.

11.
Entropy (Basel) ; 26(4)2024 Apr 17.
Article in English | MEDLINE | ID: mdl-38667894

ABSTRACT

In order to find more excellent structural materials resistant to radiation damage, high-entropy alloys (HEAs) have been developed due to their characteristics of limited point defect diffusion such as lattice distortion and slow diffusion. Specially, refractory high-entropy alloys (RHEAs) that can adapt to a high-temperature environment are badly needed. In this study, TiZrHfNbMo0.1 RHEAs are selected for irradiation and nanoindentation experiments. We combined the mechanistic model for the depth-dependent hardness of ion-irradiated metals and the introduction of the scale factor f to modify the irradiation-hardening model in order to better describe the nanoindentation indentation process in the irradiated layer. Finally, it can be found that, with the increase in irradiation dose, a more serious lattice distortion caused by a higher defect density limits the expansion of the plastic zone.

12.
Medicine (Baltimore) ; 103(13): e37542, 2024 Mar 29.
Article in English | MEDLINE | ID: mdl-38552082

ABSTRACT

In this retrospective study conducted at Sichuan Jinxin Xinan Women and Children's Hospital spanning January 2015 to December 2021, our objective was to investigate the impact of embryo cryopreservation duration on outcomes in frozen embryo transfer. Participants, totaling 47,006 cycles, were classified into 3 groups based on cryopreservation duration: ≤1 year (Group 1), 1 to 6 years (Group 2), and ≥6 years (Group 3). Employing various statistical analyses, including 1-way ANOVA, Kruskal-Wallis test, chi-square test, and a generalized estimating equation model, we rigorously adjusted for confounding factors. Primary outcomes encompassed clinical pregnancy rate and Live Birth Rate (LBR), while secondary outcomes included biochemical pregnancy rate, multiple pregnancy rate, ectopic pregnancy rate, early and late miscarriage rates, preterm birth rate, neonatal birth weight, weeks at birth, and newborn sex. Patient distribution across cryopreservation duration groups was as follows: Group 1 (40,461 cycles), Group 2 (6337 cycles), and Group 3 (208 cycles). Postcontrolling for confounding factors, Group 1 exhibited a decreased likelihood of achieving biochemical pregnancy rate, clinical pregnancy rate, and LBR (OR < 1, aOR < 1, P < .05). Furthermore, an elevated incidence of ectopic pregnancy was observed (OR > 1, aOR > 1), notably significant after 6 years of freezing time [aOR = 4.141, 95% confidence intervals (1.013-16.921), P = .05]. Cryopreservation exceeding 1 year was associated with an increased risk of early miscarriage and preterm birth (OR > 1, aOR > 1). No statistically significant differences were observed in birth weight or sex between groups. However, male infant birth rates were consistently higher than those of female infants across all groups. In conclusion, favorable pregnancy outcomes align with embryo cryopreservation durations within 1 year, while freezing for more than 1 year may diminish clinical pregnancy and LBRs, concurrently elevating the risk of ectopic pregnancy and preterm birth.


Subject(s)
Abortion, Spontaneous , Pregnancy, Ectopic , Premature Birth , Child , Pregnancy , Female , Male , Infant, Newborn , Humans , Pregnancy Outcome/epidemiology , Retrospective Studies , Abortion, Spontaneous/epidemiology , Abortion, Spontaneous/etiology , Birth Weight , Premature Birth/epidemiology , Premature Birth/etiology , Live Birth , Embryo Transfer/adverse effects , Pregnancy Rate , Cryopreservation , Pregnancy, Ectopic/epidemiology , Pregnancy, Ectopic/etiology
13.
Foods ; 13(5)2024 Mar 01.
Article in English | MEDLINE | ID: mdl-38472889

ABSTRACT

To expound on the correlation between the microorganism communities and the formation of off-odour in Xuanwei ham, the microorganism communities and volatile compounds were investigated in the biceps femoris (BF) and semimembranosus (SM) of Xuanwei ham with different quality grades (normal ham and spoiled ham). The single molecule real-time sequencing showed that differential bacteria and fungi were more varied in normal hams than in spoiled hams. Headspace solid-phase microextraction-gas chromatography (HS-SPME-GC-MS) results indicated that aldehydes and alcohols were significantly higher in spoiled hams than those in normal hams (p < 0.05). The off-odour of spoiled hams was dominated by ichthyic, malodourous, sweaty, putrid, sour, and unpleasant odours produced by compounds such as trimethylamine (SM: 13.05 µg/kg), hexanal (BF: 206.46 µg/kg), octanal (BF: 59.52 µg/kg), methanethiol (SM: 12.85 µg/kg), and valeric acid (BF: 15.08 µg/kg), which are positively correlated with Bacillus cereus, Bacillus subtilis, Bacillus licheniformis, Pseudomonas sp., Aspergillus ruber, and Moraxella osloensis. Furthermore, the physicochemical property and quality characteristics results showed that high moisture (BF: 56.32 g/100 g), pH (BF: 6.63), thiobarbituric acid reactive substances (TBARS) (SM: 1.98 MDA/kg), and low NaCl content (SM: 6.31%) were also responsible for the spoilage of hams with off-odour. This study provided a deep insight into the off-odour of Xuanwei ham from the perspective of microorganism communities and a theoretical basis for improving the flavour and overall quality of Xuanwei hams.

14.
Lab Chip ; 24(6): 1782-1793, 2024 03 12.
Article in English | MEDLINE | ID: mdl-38358122

ABSTRACT

Non-invasive droplet manipulation with no physical damage to the sample is important for the practical value of manipulation tools in multidisciplinary applications from biochemical analysis and diagnostics to cell engineering. It is a challenge to achieve this for most existing photothermal, electric stimuli, and magnetic field-based technologies. Herein, we present a droplet handling toolbox, the ferrofluid transporter, for non-invasive droplet manipulation in an oil environment. It involves the transport of droplets with high robustness and efficiency owing to low interfacial friction. This capability caters to various scenarios including droplets with varying components and solid cargo. Moreover, we fabricated a droplet array by transporter positioning and achieved droplet gating and sorting for complex manipulation in the droplet array. Benefiting from the ease of scale-up and high biocompatibility, the transporter-based droplet array can serve as a digital microfluidic platform for on-chip droplet-based bioanalysis, cell spheroid culture, and downstream drug screening tests.


Subject(s)
Colloids , Microfluidics , Cell Engineering , Cell Culture Techniques
15.
Diabetes Metab Syndr Obes ; 17: 865-880, 2024.
Article in English | MEDLINE | ID: mdl-38406269

ABSTRACT

Purpose: Polycystic ovary syndrome (PCOS) is a frequent cause of infertility in reproductive-age women. Our work aims to evaluate the effects of glucagon-like peptide-1 receptor agonists (GLP-1RAs) on gut microbiota, with metabolic parameters including body weight and the hormone profile in PCOS. Patients and Methods: Dehydroepiandrosterone (DHEA)-induced PCOS mice were established and then treated with two GLP-1RAs: liraglutide and novel form semaglutide for four weeks. Changes in body weight and metabolic parameters were measured. Fecal samples were collected and analyzed using metagenomic sequencing. Results: Liraglutide and semaglutide modulated both alpha and beta diversity of the gut microbiota in PCOS. Liraglutide increased the Bacillota-to-Bacteroidota ratio through up-regulating the abundance of butyrate-producing members of Bacillota like Lachnospiraceae. Moreover, liraglutide showed the ability to reverse the altered microbial composition and the disrupted microbiota functions caused by PCOS. Semaglutide increased the abundance of Helicobacter in PCOS mice (p < 0.01) which was the only bacteria found negatively correlated with body weight. Moreover, pathways involving porphyrin and flavonoids were increased after semaglutide intervention. Conclusion: Liraglutide and semaglutide improved reproductive and metabolic disorders by modulating the whole structure of gut microbiota in PCOS. The greater efficacy in weight loss compared with liraglutide observed after semaglutide intervention was positively related with Helicobacter. The study may provide new ideas in the treatment and the underlying mechanisms of GLP-1RAs to improve PCOS.

16.
Foods ; 13(4)2024 Feb 19.
Article in English | MEDLINE | ID: mdl-38397606

ABSTRACT

This study aimed to investigate the synergistic effects of high-intensity ultrasound (0, 5, 10, 15, and 20 min) in combination with L-lysine (15 mM) on improving the solubility and flavour adsorption capacity of myofibrillar proteins (MPs) in low-ion-strength media. The results revealed that the ultrasound treatment for 20 min or the addition of L-lysine (15 mM) significantly improved protein solubility (p < 0.05), with L-lysine (15 mM) showing a more pronounced effect (p < 0.05). The combination of ultrasound treatment and L-lysine further increased solubility, and the MPs treated with ultrasound at 20 min exhibited the best dispersion stability in water, which corresponded to the lowest turbidity, highest absolute zeta potential value, and thermal stability (p < 0.05). Based on the reactive and total sulfhydryl contents, Fourier transform infrared spectroscopy, and fluorescence spectroscopy analysis, the ultrasound treatment combined with L-lysine (15 mM) promoted the unfolding and depolymerization of MPs, resulting in a larger exposure of SH groups on the surface, aromatic amino acids in a polar environment, and a transition of protein conformation from α-helix to ß-turn. Moreover, the combined treatment also increased the hydrophobic bonding sites, hydrogen-bonding sites, and electrostatic effects, thereby enhancing the adsorption capacity of MPs to bind kenone compounds. The findings from this study provide a theoretical basis for the production and flavour improvement of low-salt MP beverages and the utilisation of meat protein.

17.
J Am Chem Soc ; 146(9): 6125-6133, 2024 Mar 06.
Article in English | MEDLINE | ID: mdl-38323980

ABSTRACT

Chemical analysis of ions and small organic molecules in liquid samples is crucial for applications in chemistry, biology, environmental sciences, and health monitoring. Mainstream electrochemical and chromatographic techniques often suffer from complex and lengthy sample preparation and testing procedures and require either bulky or expensive instrumentation. Here, we combine triboelectrification and charge transfer on the surface of electrical insulators to demonstrate the concept of triboelectric spectroscopy (TES) for chemical analysis. As a drop of the liquid sample slides along an insulating reclined plane, the local triboelectrification of the surface is recorded, and the charge pattern along the sample trajectory is used to build a fingerprinting of the charge transfer spectroscopy. Chemical information extracted from the charge transfer pattern enables a new nondestructive and ultrafast (<1 s) tool for chemical analysis. TES profiles are unique, and through an automated identification, it is possible to match against standard and hence detect over 30 types of common salts, acids, bases and organic molecules. The qualitative and quantitative accuracies of the TES methodology is close to 93%, and the detection limit is as low as ppb levels. Instruments for TES chemical analysis are portable and can be further miniaturized, opening a path to in situ and rapid chemical detection relying on inexpensive, portable low-tech instrumentation.

18.
Respir Res ; 25(1): 18, 2024 Jan 04.
Article in English | MEDLINE | ID: mdl-38178073

ABSTRACT

OBJECTIVE: We aim to molecularly stratify stage IA lung adenocarcinoma (LUAD) for precision medicine. METHODS: Twelve multi-institution datasets (837 cases of IA) were used to classify the high- and low-risk types (based on survival status within 5 years), and the biological differences were compared. Then, a gene-based classifying score (IA score) was trained, tested and validated by several machine learning methods. Furthermore, we estimated the significance of the IA score in the prognostic assessment, chemotherapy prediction and risk stratification of stage IA LUAD. We also developed an R package for the clinical application. The SEER database (15708 IA samples) and TCGA Pan-Cancer (1881 stage I samples) database were used to verify clinical significance. RESULTS: Compared with the low-risk group, the high-risk group of stage IA LUAD has obvious enrichment of the malignant pathway and more driver mutations and copy number variations. The effect of the IA score on the classification of high- and low-risk stage IA LUAD was much better than that of classical clinicopathological factors (training set: AUC = 0.9, validation set: AUC = 0.7). The IA score can significantly predict the prognosis of stage IA LUAD and has a prognostic effect for stage I pancancer. The IA score can effectively predict chemotherapy sensitivity and occult metastasis or invasion in stage IA LUAD. The R package IAExpSuv has a good risk probability prediction effect for both groups and single stages of IA LUAD. CONCLUSIONS: The IA score can effectively stratify the risk of stage IA LUAD, offering good assistance in precision medicine.


Subject(s)
Adenocarcinoma of Lung , Lung Neoplasms , Humans , DNA Copy Number Variations , Adenocarcinoma of Lung/diagnosis , Adenocarcinoma of Lung/genetics , Databases, Factual , Lung Neoplasms/diagnosis , Lung Neoplasms/genetics , Risk Assessment , Prognosis
19.
Bioinformatics ; 40(1)2024 01 02.
Article in English | MEDLINE | ID: mdl-38175759

ABSTRACT

MOTIVATION: Binding of peptides to major histocompatibility complex (MHC) molecules plays a crucial role in triggering T cell recognition mechanisms essential for immune response. Accurate prediction of MHC-peptide binding is vital for the development of cancer therapeutic vaccines. While recent deep learning-based methods have achieved significant performance in predicting MHC-peptide binding affinity, most of them separately encode MHC molecules and peptides as inputs, potentially overlooking critical interaction information between the two. RESULTS: In this work, we propose RPEMHC, a new deep learning approach based on residue-residue pair encoding to predict the binding affinity between peptides and MHC, which encode an MHC molecule and a peptide as a residue-residue pair map. We evaluate the performance of RPEMHC on various MHC-II-related datasets for MHC-peptide binding prediction, demonstrating that RPEMHC achieves better or comparable performance against other state-of-the-art baselines. Moreover, we further construct experiments on MHC-I-related datasets, and experimental results demonstrate that our method can work on both two MHC classes. These extensive validations have manifested that RPEMHC is an effective tool for studying MHC-peptide interactions and can potentially facilitate the vaccine development. AVAILABILITY: The source code of the method along with trained models is freely available at https://github.com/lennylv/RPEMHC.


Subject(s)
Deep Learning , Protein Binding , Peptides/chemistry , Major Histocompatibility Complex , Histocompatibility Antigens Class I/metabolism
20.
Molecules ; 29(2)2024 Jan 11.
Article in English | MEDLINE | ID: mdl-38257274

ABSTRACT

4-Nitrophenol (4-NP) is considered a priority organic pollutant with high toxicity. Many authors have been committed to developing efficient, green, and environmentally friendly technological processes to treat wastewater containing 4-NP. Here, we investigated how the addition of Ca2+ affects the catalytic degradation of 4-NP with AgInS2 when exposed to light. We synthesized AgInS2 (AIS) and Ca2+-doped AgInS2 (Ca-AIS) with varying amounts of Ca2+ using a low-temperature liquid phase method. The SEM, XRD, XPS, HRTEM, BET, PL, and UV-Vis DRS characteristics were employed to analyze the structure, morphology, and optical properties of the materials. The effects of different amounts of Ca2+ on the photocatalytic degradation of 4-NP were investigated. Under visible light illumination for a duration of 120 min, a degradation rate of 63.2% for 4-Nitrophenol (4-NP) was achieved. The results showed that doping with an appropriate amount of Ca2+ could improve the visible light catalytic activity of AIS. This work provides an idea for finding suitable cheap alkaline earth metal doping agents to replace precious metals for the improvement of photocatalytic activities.

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