Associations of ambient air pollution exposure and lifestyle factors with incident dementia in the elderly: A prospective study in the UK Biobank.

OBJECTIVE: Dementia is an important disease burden among the elderly, and its occurrence may be profoundly affected by environmental factors. Evidence of the relationship between air pollution and dementia is emerging, but the extent to which this can be offset by lifestyle factors remains ambiguous. METHODS: This study comprised 155,828 elder adults aged 60 years and above in the UK Biobank who were dementia-free at baseline. Cox proportional hazard models were conducted to examine the associations of annual average levels of air pollutants in 2010, including nitrogen dioxide (NO2), nitrogen oxides (NOX), particulate matter (PM2.5, PM10, and PMcoarse) and lifestyle factors recorded at baseline [physical activity (PA), sleep patterns, or smoking status] with incident risk of dementia, and their interactions on both multiplicative and additive scales. RESULTS: During a 12-year period of follow-up, 4,389 incidents of all-cause dementia were identified. For each standarddeviationincrease in ambient NO2, NOX or PM2.5, all-cause dementia risk increases by 1.07-fold [hazard ratio (HR) and 95 % confidence interval (CI) = 1.07 (1.04, 1.10)], 1.05-fold (95 % CI: 1.02, 1.08) and 1.07-fold (95 % CI: 1.04, 1.10), whereas low levels of PA, poor sleep patterns, and smoking are associated with an elevated risk of dementia [HR (95 % CI) = 1.17 (1.09, 1.26), 1.13 (1.00, 1.27), and 1.14 (1.07, 1.21), respectively]. Furthermore, these air pollutants show joint effects with low PA, poor sleep patterns, and smoking on the onset of dementia. The moderate to high levels of PA could significantly or marginally significantly modify the associations between NO2, NOX or PM2.5 (P-int = 0.067, 0.036, and 0.067, respectively) and Alzheimer's disease (AD), but no significant modification effects are found for sleep patterns or smoking status. CONCLUSION: The increased exposures of NO2, NOX, or PM2.5 are associated with elevated risk of dementia among elderly UK Biobank population. These air pollutants take joint effects with low PA, poor sleep patterns, and smoking on the development of dementia. In addition, moderate to high levels of PA could attenuate the incident risk of AD caused by air pollution. Further prospective researches among other cohort populations are warranted to validate these findings.

Solvent-Free Enzymatic Synthesis of Ethyl 3-Oxobutyrate Derivative: Characterization and Optimization of Reaction Condition.

It was first found that porcine pancreatic lipase (PPL) could catalyze the Knoevenagel condensation of aromatic aldehydes and ethyl acetoacetate under solvent-free conditions in this paper. Under solvent-free conditions, the highest yield of PPL catalytic reaction was 99.38%, and the Z/E selectivity of the product was 3.93. In addition, the reaction conditions were optimized, and the factors affecting the product structure were studied.

Altered landscape of total RNA, tRNA and sncRNA modifications in the liver and spleen of mice infected by Toxoplasma gondii.

BACKGROUND: Pathogens can impact host RNA modification machinery to establish a favorable cellular environment for their replication. In the present study, we investigated the effect of Toxoplasma gondii infection on host RNA modification profiles and explored how these modifications may influence the host-parasite interaction. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed the modification levels of ∼ 80 nt tRNA and 17-50 nt sncRNAs in mouse liver, spleen, and serum using liquid chromatography and tandem mass spectrometry analysis. The results revealed alterations in RNA modification profiles, particularly during acute infection. The liver exhibited more differentially abundant RNA modifications than the spleen. RNA modification levels in serum were mostly downregulated during acute infection compared to control mice. Correlations were detected between different RNA modifications in the liver and spleen during infection and between several RNA modifications and many cytokines. Alterations in RNA modifications affected tRNA stability and protein translation. CONCLUSIONS/SIGNIFICANCE: These findings provide new insight into the role of RNA modifications in mediating the murine host response to T. gondii infection.

Development of apple pectin/soy protein isolate-based edible films containing punicalagin for strawberry preservation.

In this study, we developed punicalagin-loaded antimicrobial films based on soy protein isolate (SPI) and apple pectin (AP). The AP was derived from apple pomace waste while the punicalagin was obtained from pomegranate peel. Punicalagin was identified to exist in both α- and ß-isomers, with the ß-type being predominant. The composite films were characterized using scanning electron microscopy, Fourier transformed infrared spectroscopy, X-ray diffraction, and thermogravimetric analysis. Our results demonstrated that the incorporation of AP significantly enhanced the mechanical strength, heat resistance, and barrier properties of the films. Moreover, the composite films integrated with punicalagin exhibited excellent antimicrobial activities against Staphylococcus aureus (with a minimum bactericidal concentration value of 0.25 %), Escherichia coli (with a minimum bactericidal concentration value of 0.50 %), and Aspergillus niger. Finally, these antimicrobial film solutions were tested as coatings on strawberries and found to have significantly better effects on reducing weight loss, improving shelf-life, and maintaining the freshness of strawberries compared to coatings without punicalagin. The results indicate that antimicrobial coatings loaded with punicalagin hold great promise as multifunctional active packaging materials for fruit preservation.

Mitochondrial DNA copy number mediated the associations between perfluoroalkyl substances and breast cancer incidence: A prospective case-cohort study.

Epidemiologic studies have reported the relationships between perfluoroalkyl substances (PFASs) and breast cancer incidence, yet the underlying mechanisms are not well understood. This study aimed to elucidate the mediation role of mitochondrial DNA copy number (mtDNAcn) in the relationships between PFASs exposure and breast cancer risk. We conducted a case-cohort study within the Dongfeng-Tongji cohort, involving 226 incident breast cancer cases and a random sub-cohort (n = 990). Their plasma concentrations of six PFASs [including perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), perfluorodecanoic acid (PFDA), perfluoroheptanoic acid (PFHpA), perfluorooctane sulfonic acid (PFOS) and perfluorohexane sulfonic acid (PFHxS)], and peripheral blood levels of mtDNAcn, were detected at baseline by using ultraperformance liquid chromatography-tandem mass spectrometry and quantitative real-time PCR, respectively. Linear regression and Barlow-weighted Cox models were employed separately to assess the relationships of mtDNAcn with PFASs and breast cancer risk. Mediation analysis was further conducted to quantify the mediating effects of mtDNAcn on PFAS-breast cancer relationships. We observed increased blood mtDNAcn levels among participants with the highest PFNA and PFHpA exposure [Q4 vs. Q1, ß(95%CI) = 0.092(0.022, 0.162) and 0.091(0.022, 0.160), respectively], while no significant associations were observed of PFOA, PFDA, PFOS, or PFHxS with mtDNAcn. Compared to participants within the lowest quartile subgroup of mtDNAcn, those with the highest mtDNAcn levels exhibited a significantly increased risk of breast cancer and postmenopausal breast cancer [Q4 vs. Q1, HR(95%CI) = 3.34(1.80, 6.20) and 3.71(1.89, 7.31)]. Furthermore, mtDNAcn could mediate 14.6 % of the PFHpA-breast cancer relationship [Indirect effect, HR(95%CI) = 1.02(1.00, 1.05)]. Our study unveiled the relationships of PFNA and the short-chain PFHpA with mtDNAcn and the mediation role of mtDNAcn in the PFHpA-breast cancer association. These findings provided insights into the potential biological mechanisms linking PFASs to breast cancer risk.

Identification of nuclear membrane SUN proteins and components associated with wheat fungal stress responses.

In eukaryotes, the nuclear membrane that encapsulates genomic DNA is composed of an inner nuclear membrane (INM), an outer nuclear membrane (ONM), and a perinuclear space. SUN proteins located in the INM and KASH proteins in the ONM form the SUN-KASH NM-bridge, which functions as the junction of the nucleocytoplasmic complex junction. Proteins containing the SUN domain showed the highest correlation with differentially accumulated proteins (DAPs) in the wheat response to fungal stress. To understand the characteristics of SUN and its associated proteins in wheat responding to pathogen stress, here we investigated and comprehensive analyzed SUN- and KASH-related proteins among the DAPs under fungi infection based on their conserved motifs. In total, four SUN proteins, one WPP domain-interacting protein (WIP), four WPP domain-interacting tail-anchored proteins (WIT), two WPP proteins and one Ran GTPase activating protein (RanGAP) were identified. Following transient expression of Nicotiana benthamiana, TaSUN2, TaRanGAP2, TaWIT1 and TaWIP1 were identified as nuclear membrane proteins, while TaWPP1 and TaWPP2 were expressed in both the nucleus and cell membrane. RT-qPCR analysis demonstrated that the transcription of TaSUN2, TaRanGAP2 and TaWPP1 were strongly upregulated in response to fungal infection. Furthermore, using the bimolecular fluorescence complementation, the luciferase complementation and a nuclear and split-ubiquitin-based membrane yeast two-hybrid systems, we substantiated the interaction between TaSUN2 and TaWIP1, as well as TaWIP1/WIT1 and TaWPP1/WPP2. Silencing of TaSUN2, TaRanGAP2 and TaWPP1 in wheat leaves promoted powdery mildew infection and hyphal growth, and reduced the expression of TaBRI1, TaBAK1 and Ta14-3-3, indicating that these NM proteins play a positive role in resistance to fungal stress. Our study reveals the characteristics of NM proteins and propose the preliminary construction of SUN-WIP-WPP-RanGAP complex in wheat, which represents a foundation for detail elucidating their functions in wheat in future.

Identification of biomarkers and potential therapeutic targets for pancreatic cancer by proteomic analysis in two prospective cohorts.

Pancreatic cancer (PC) is the deadliest malignancy due to late diagnosis. Aberrant alterations in the blood proteome might serve as biomarkers to facilitate early detection of PC. We designed a nested case-control study of incident PC based on a prospective cohort of 38,295 elderly Chinese participants with ∼5.7 years' follow-up. Forty matched case-control pairs passed the quality controls for the proximity extension assay of 1,463 serum proteins. With a lenient threshold of p < 0.005, we discovered regenerating family member 1A (REG1A), REG1B, tumor necrosis factor (TNF), and phospholipase A2 group IB (PLA2G1B) in association with incident PC, among which the two REG1 proteins were replicated using the UK Biobank Pharma Proteomics Project, with effect sizes increasing steadily as diagnosis time approaches the baseline. Mendelian randomization analysis further supported the potential causal effects of REG1 proteins on PC. Taken together, circulating REG1A and REG1B are promising biomarkers and potential therapeutic targets for the early detection and prevention of PC.

Structural and functional characteristics of pectins from three cultivars of apple (Malus pumila Mill.) pomaces.

This study aimed to investigate the chemical composition, structural properties, and biological properties of pectin polysaccharides (AP-FS, AP-QG, and AP-HG) isolated from different varieties of apple pomace. Based on the methylation and nuclear magnetic resonance analyses, the structure of AP-FS was determined to be composed of an α-1,4-linked homogalacturonan backbone that exhibited high levels of O-6 methylation. All pectins exhibit potent inhibitory activity against human colon cancer and human liver cancer cells, along with immunostimulatory effects. Among them, AP-FS exhibited the highest activity level. Finally, we further investigated the underlying mechanism behind the effect of AP-FS on RAW 264.7 cells using proteomics analysis. Our findings revealed that AP-FS triggers RAW 264.7 macrophage activation via NOD-like receptor (NLR), NF-κB, and mitogen-activated protein kinase (MAPK) signaling pathways. Therefore, our research contributes to a better understanding of the structure-function relationship among apple pectins, and AP-FS has the potential to be applied to dietary supplements targeting immunomodulation.

Theabrownin as a Potential Prebiotic Compound Regulates Lipid Metabolism via the Gut Microbiota, Microbiota-Derived Metabolites, and Hepatic FoxO/PPAR Signaling Pathways.

The dysregulation of lipid metabolism poses a significant health threat, necessitating immediate dietary intervention. Our previous research unveiled the prebiotic-like properties of theabrownin. This study aimed to further investigate the theabrownin-gut microbiota interactions and their downstream effects on lipid metabolism using integrated physiological, genomic, metabolomic, and transcriptomic approaches. The results demonstrated that theabrownin significantly ameliorated dyslipidemia, hepatic steatosis, and systemic inflammation induced by a high-fat/high-cholesterol diet (HFD). Moreover, theabrownin significantly improved HFD-induced gut microbiota dysbiosis and induced significant alterations in microbiota-derived metabolites. Additionally, the detailed interplay between theabrownin and gut microbiota was revealed. Analysis of hepatic transcriptome indicated that FoxO and PPAR signaling pathways played pivotal roles in response to theabrownin-gut microbiota interactions, primarily through upregulating hepatic Foxo1, Prkaa1, Pck1, Cdkn1a, Bcl6, Klf2, Ppara, and Pparg, while downregulating Ccnb1, Ccnb2, Fabp3, and Plin1. These findings underscored the critical role of gut-liver axis in theabrownin-mediated improvements in lipid metabolism disorders and supported the potential of theabrownin as an effective prebiotic compound for targeted regulation of metabolic diseases.

Particulate matter pollution, polygenic risk score and mosaic loss of chromosome Y in middle-aged and older men from the Dongfeng-Tongji cohort study.

Mosaic loss of chromosome Y (mLOY) is the most common somatic alteration as men aging and may reflect genome instability. PM exposure is a major health concern worldwide, but its effects with genetic factors on mLOY has never been investigated. Here we explored the associations of PM2.5 and PM10 exposure with mLOY of 10,158 males measured via signal intensity of 2186 probes in male-specific chromosome-Y region from Illumina array data. The interactive and joint effects of PM2.5 and PM10 with genetic factors and smoking on mLOY were further evaluated. Compared with the lowest tertiles of PM2.5 levels in each exposure window, the highest tertiles in the same day, 7-, 14-, 21-, and 28-day showed a 0.005, 0.006, 0.007, 0.007, and 0.006 decrease in mLRR-Y, respectively (all P < 0.05), with adjustment for age, BMI, smoking pack-years, alcohol drinking status, physical activity, education levels, season of blood draw, and experimental batch. Such adverse effects were also observed in PM10-mLOY associations. Moreover, the unweighted and weighted PRS presented significant negative associations with mLRR-Y (both P < 0.001). Participants with high PRS and high PM2.5 or PM10 exposure in the 28-day separately showed a 0.018 or 0.019 lower mLRR-Y level [ß (95 %CI) = -0.018 (-0.023, -0.012) and - 0.019 (-0.025, -0.014), respectively, both P < 0.001], when compared to those with low PRS and low PM2.5 or PM10 exposure. We also observed joint effects of PM with smoking on exacerbated mLOY. This large study is the first to elucidate the impacts of PM2.5 exposure on mLOY, and provides key evidence regarding the interactive and joint effects of PM with genetic factors on mLOY, which may promote understanding of mLOY development, further modifying and increasing healthy aging in males.

Treatment of abdominal pain due to deficiency syndrome of the spleen and stomach with Bian stone plus TCM iontophoresis: A case report.

RATIONALE: Bian stone ironing and rubbing traditional Chinese medicine penetration method is based on the theory of regulating the middle and restoring balance. By using Bian stone to heat, ironing, and rubbing, pushing and rubbing in the epigastric area can regulate the spleen and stomach, restore the normal function of the middle jiao qi movement and the functions of the five organs. Bian stone hot ironing can harmonize stomach qi, nourish qi and assist yang, clear the internal organs and clear turbidity, regulate intestinal qi circulation, and promote qi stagnation. PATIENT CONCERNS: The VAS score for stomach pain is 6 points, and the SAS score is moderate anxiety, which seriously affects sleep and daily life. DIAGNOSES: epigastric pain, spleen, and stomach deficiency cold syndrome. INTERVENTIONS: Easy to digest diet, Western medicine provides famotidine acid inhibiting and protecting gastric mucosa, and mosapride promoting gastrointestinal peristalsis medication treatment; Traditional Chinese Medicine provides oral administration of Huangqi Jianzhong Tang and traditional Chinese medicine techniques such as Bianchi Ironing and Moxibustion for treatment. OUTCOMES: The patient's symptoms of stomach pain have significantly improved, with a decrease in the epigastric pain score to 0, improved anxiety, reduced fatigue, improved sleep, improved epigastric fullness, unobstructed bowel movements, and improved quality of life. The patient is very satisfied. LESSONS: The method of using Bian stone ironing and rubbing traditional Chinese medicine to treat stomach pain caused by the spleen and stomach deficiency cold can alleviate the symptoms of stomach pain in patients, and the improvement of symptoms shows a gradual increase, with significant effects. At the same time, it significantly improves patient anxiety and fatigue symptoms and can increase the sample size in future work to further clarify its clinical effects.

Dynamic genomic changes in methotrexate-resistant human cancer cell lines beyond DHFR amplification suggest potential new targets for preventing drug resistance.

BACKGROUND: Although DHFR gene amplification has long been known as a major mechanism for methotrexate (MTX) resistance in cancer, the early changes and detailed development of the resistance are not yet fully understood. METHODS: We performed genomic, transcriptional and proteomic analyses of human colon cancer cells with sequentially increasing levels of MTX-resistance. RESULTS: The genomic amplification evolved in three phases (pre-amplification, homogenously staining region (HSR) and extrachromosomal DNA (ecDNA)). We confirm that genomic amplification and increased expression of DHFR, with formation of HSRs and especially ecDNAs, is the major driver of resistance. However, DHFR did not play a detectable role in the early phase. In the late phase (ecDNA), increase in FAM151B protein level may also have an important role by decreasing sensitivity to MTX. In addition, although MSH3 and ZFYVE16 may be subject to different posttranscriptional regulations and therefore protein expressions are decreased in ecDNA stages compared to HSR stages, they still play important roles in MTX resistance. CONCLUSION: The study provides a detailed evolutionary trajectory of MTX-resistance and identifies new targets, especially ecDNAs, which could help to prevent drug resistance. It also presents a proof-of-principal approach which could be applied to other cancer drug resistance studies.

Derived energy storage systems from Brayton cycle.

Various energy storage systems (ESS) can be derived from the Brayton cycle, with the most representative being compressed air energy storage and pumped thermal electricity storage systems. Although some important studies on above ESS are reported, the topological structure behind those systems (i.e., derivations of the Brayton cycle) has not been studied, and the underlying thermodynamic ideas still need to be further explored. This paper first introduces the topological structure and the symmetry of ESS and their based Brayton cycles. The formation method of ESS based on paths and separation points is specified. It is found that round-trip path can form ESS directly. Then various ESS formed are compared. Finally, the synergistic effect and gain principle of thermal cycle and ESS are revealed. This work helps to reveal the intrinsic relationship between thermal cycles and ESS, understand the general laws behind ESS, and guide the combination of thermal cycles and ESS.

SeFilter-DIA: Squeeze-and-Excitation Network for Filtering High-Confidence Peptides of Data-Independent Acquisition Proteomics.

Mass spectrometry is crucial in proteomics analysis, particularly using Data Independent Acquisition (DIA) for reliable and reproducible mass spectrometry data acquisition, enabling broad mass-to-charge ratio coverage and high throughput. DIA-NN, a prominent deep learning software in DIA proteome analysis, generates peptide results but may include low-confidence peptides. Conventionally, biologists have to manually screen peptide fragment ion chromatogram peaks (XIC) for identifying high-confidence peptides, a time-consuming and subjective process prone to variability. In this study, we introduce SeFilter-DIA, a deep learning algorithm, aiming at automating the identification of high-confidence peptides. Leveraging compressed excitation neural network and residual network models, SeFilter-DIA extracts XIC features and effectively discerns between high and low-confidence peptides. Evaluation of the benchmark datasets demonstrates SeFilter-DIA achieving 99.6% AUC on the test set and 97% for other performance indicators. Furthermore, SeFilter-DIA is applicable for screening peptides with phosphorylation modifications. These results demonstrate the potential of SeFilter-DIA to replace manual screening, providing an efficient and objective approach for high-confidence peptide identification while mitigating associated limitations.

Distribution and Drug Resistance of Common Pathogens Causing Lower Respiratory Tract Infection in Xinjiang Region.

Objective: This study aims to analyze the composition and distribution of pathogenic bacteria in lower respiratory tract infections (LRTI) and their antimicrobial resistance patterns in a hospital in Xinjiang, to guide more effective antibiotic selection and inform clinical management. Methods: We retrospectively analyzed 545 strains isolated from various clinical specimens like sputum and blood, collected between June 2020 and June 2023, using the LIST system. The strains were subjected to drug resistance testing, and statistical analyses included t tests and Chi-square tests. Results: Among gram-negative bacilli, Acinetobacter baumannii dominated, accounting for 32.11%, followed by Pseudomonas aeruginosa, accounting for 18.35%. Among gram-positive bacteria, thrombin-negative staphylococcus was at the top of the list, followed by Staphylococcus aureus. Among Acinetobacter baumannii (AB), carbapenem-resistant Acinetobacter baumannii plays a dominant role. The sensitivity rate of these strains to tigecycline and amikacin could reach more than 80%. The sensitivity of Pseudomonas aeruginosa (PA) to piperacillin, gentamicin, imipenem, meropenem, ciprofloxacin and levofloxacin ranged from 50% to 80%. It is worth mentioning that the sensitivity rate of PA to amikacin, cefoperazone, and tobramycin exceeded 80%. Amikacin was more than 60% sensitive to carbapenem, ß-lactam inhibitors, tigecycline, quinolones, and aminoglycosides of ESBL producing Klebsiella pneumoniae. Among gram-positive coccus, methicillin-resistant coagulase-negative staphylococcus was 100% sensitive to duration, e, tigecycline, and vancomycin. In addition, the susceptibility rate of these strains to rifampicin and linezolid was greater than 70%. Conclusions: In patients with lower respiratory tract infection (LRTI) in a hospital in Xinjiang, the most common pathogenic bacteria are gram-negative bacilli, mainly Acinetobacter baumannii and Pseudomonas aeruginosa. Both resistant and non-resistant strains showed sensitivity to amikacin and tigecycline. Additionally, staphylococcus accounted for half of the total number of gram-positive bacteria, among which methicillin-resistant strains were more sensitive to vancomycin and linezolid.

The interaction effects of zinc and polygenic risk score with benzo[a]pyrene exposure on lung cancer risk: A prospective case-cohort study among Chinese populations.

The relationship of exposure to benzo[a]pyrene (BaP) with lung cancer risk has been firmly established, but whether this association could be modified by other environmental or genetic factors remains to be explored. To investigate whether and how zinc (Zn) and genetic predisposition modify the association between BaP and lung cancer, we performed a case-cohort study with a 5.4-year median follow-up duration, comprising a representative subcohort of 1399 participants and 359 incident lung cancer cases. The baseline concentrations of benzo[a]pyrene diol epoxide-albumin adduct (BPDE-Alb) and Zn were quantified. We also genotyped the participants and computed the polygenic risk score (PRS) for lung cancer. Our findings indicated that elevated BPDE-Alb and PRS were linked to increased lung cancer risk, with the HR (95%CI) of 1.54 (1.36, 1.74) per SD increment in ln-transformed BPDE-Alb and 1.27 (1.14, 1.41) per SD increment in PRS, but high plasma Zn level was linked to a lower lung cancer risk [HR (95%CI)=0.77 (0.66, 0.91) per SD increment in ln-transformed Zn]. There was evidence of effect modification by Zn on BaP-lung cancer association (P for multiplicative interaction = 0.008). As Zn concentrations increased from the lowest to the highest tertile, the lung cancer risk per SD increment in ln-transformed BPDE-Alb decreased from 2.07 (1.48, 2.89) to 1.33 (0.90, 1.95). Additionally, we observed a significant synergistic interaction of BPDE-Alb and PRS [RERI (95%CI) = 0.85 (0.03, 1.67)], with 42% of the incident lung cancer cases among individuals with high BPDE-Alb and high PRS attributable to their additive effect [AP (95%CI) = 0.42 (0.14, 0.69)]. This study provided the first prospective epidemiological evidence that Zn has protective effect against BaP-induced lung tumorigenesis, whereas high genetic risk can enhance the harmful effect of BaP. These findings may provide novel insight into the environment-environment and environment-gene interaction underlying lung cancer development, which may help to develop prevention and intervention strategies to manage BaP-induced lung cancer.

Association of systemic inflammation index with psoriasis risk and psoriasis severity: A retrospective cohort study of NHANES 2009 to 2014.

To investigate the association of systemic inflammation index (SII) with psoriasis risk and psoriasis severity. This is a retrospective cohort study based on data from the National Health and Nutrition Examination Survey database from 2009 to 2014. The psoriasis information was obtained from the questionnaire data, and the SII was calculated as neutrophil × platelet/lymphocyte. We performed matching by controlling age and gender to reach a 1:2 ratio for better statistical power. Weighted logistic regression analysis, subgroup analysis, restricted cubic spline analysis, and threshold analysis were used to evaluate the association of SII with psoriasis risk. Besides, mediation analysis was conducted to assess the possible regulatory path. Finally, the receiver operating characteristic curve was plotted to analyze the predictive value of SII for psoriasis severity. The study involved 16,466 participants including 16,020 no-psoriasis participants and 446 psoriasis participants. After matching, psoriasis and non-psoriasis individuals were 446 and 892, respectively. SII was significantly higher in the psoriasis group than the non-psoriasis group (P < .05). Additionally, white blood cells and monocytes were significantly linked to psoriasis risk and SII scores (P < .05). Besides, SII elevation was an independent predictor for upregulated psoriasis risk (P < .05). There was a nonlinear relationship between SII and psoriasis risk (P nonlinear < .05), which was not mediated by white blood cells and monocytes. Unexpectedly, SII had no significance in predicting SII severity (P > .05). SII can independently predict psoriasis risk but has no impact on psoriasis severity. Further, SII serves as a potential and robust biomarker for identifying high-risk psoriasis individuals.

AttnPep: A Self-Attention-Based Deep Learning Method for Peptide Identification in Shotgun Proteomics.

In shotgun proteomics, the proteome search engine analyzes mass spectra obtained by experiments, and then a peptide-spectra match (PSM) is reported for each spectrum. However, most of the PSMs identified are incorrect, and therefore various postprocessing software have been developed for reranking the peptide identifications. Yet these methods suffer from issues such as dependency on distribution, reliance on shallow models, and limited effectiveness. In this work, we propose AttnPep, a deep learning model for rescoring PSM scores that utilizes the Self-Attention module. This module helps the neural network focus on features relevant to the classification of PSMs and ignore irrelevant features. This allows AttnPep to analyze the output of different search engines and improve PSM discrimination accuracy. We considered a PSM to be correct if it achieves a q-value <0.01 and compared AttnPep with existing mainstream software PeptideProphet, Percolator, and proteoTorch. The results indicated that AttnPep found an average increase in correct PSMs of 9.29% relative to the other methods. Additionally, AttnPep was able to better distinguish between correct and incorrect PSMs and found more synthetic peptides in the complex SWATH data set.

Macro CD5L+ deteriorates CD8+T cells exhaustion and impairs combination of Gemcitabine-Oxaliplatin-Lenvatinib-anti-PD1 therapy in intrahepatic cholangiocarcinoma.

Intratumoral immune status influences tumor therapeutic response, but it remains largely unclear how the status determines therapies for patients with intrahepatic cholangiocarcinoma. Here, we examine the single-cell transcriptional and TCR profiles of 18 tumor tissues pre- and post- therapy of gemcitabine plus oxaliplatin, in combination with lenvatinib and anti-PD1 antibody for intrahepatic cholangiocarcinoma. We find that high CD8 GZMB+ and CD8 proliferating proportions and a low Macro CD5L+ proportion predict good response to the therapy. In patients with a poor response, the CD8 GZMB+ and CD8 proliferating proportions are increased, but the CD8 GZMK+ proportion is decreased after the therapy. Transition of CD8 proliferating and CD8 GZMB+ to CD8 GZMK+ facilitates good response to the therapy, while Macro CD5L+-CD8 GZMB+ crosstalk impairs the response by increasing CTLA4 in CD8 GZMB+. Anti-CTLA4 antibody reverses resistance of the therapy in intrahepatic cholangiocarcinoma. Our data provide a resource for predicting response of the combination therapy and highlight the importance of CD8+T-cell status conversion and exhaustion induced by Macro CD5L+ in influencing the response, suggesting future avenues for cancer treatment optimization.