Functional Differences Research Articles

Identification of prognostic biomarkers in neuroblastoma using WGCNA and multi-omics analysis

BackgroundNeuroblastoma (NB) is one of the most frequent parenchymal tumors among children, with a high degree of heterogeneity and wide variation in clinical presentation. Despite significant therapeutic advances in recent years, long-term survival in high-risk patients remains low, emphasizing the urgent need to find new biomarkers and construct reliable prognostic models.MethodsIn this study, data from neuroblastoma samples in the ArrayExpress database were utilized to identify key gene modules and pivotal genes associated with NB prognosis by weighted gene co-expression network analysis (WGCNA). The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis was performed using the DAVID database. Based on these hub genes, survival prognosis models were constructed and validated on an independent validation set in the Gene Expression Omnibus (GEO) database. Differences in biological functions and immune microenvironments and the sensitivity to pharmacological and immunotherapeutic treatments of patients in the high- and low-risk groups were examined by gene set enrichment analysis (GSEA) and immune infiltration analysis.ResultsWGCNA identified 14 gene modules and screened the module with the highest relevance to the International Neuroblastoma Staging System (INSS), containing 60 pivotal genes. GO and KEGG analyses demonstrated that these pivotal genes were mainly implicated in biological processes and signaling pathways including DNA replication, cell division, mitotic cell cycle, and cell cycle. Based on Lasso regression and COX regression analysis, a prognostic model containing DHFR, GMPS and E2F3 was constructed, and the RiskScore was significantly correlated with the 1-, 3- and 5-year survival of the patients. GSEA and immune infiltration analyses revealed significant differences in the levels of cell cycle-related pathways and immune cell infiltration between the high and low RiskScore groups. In particular, patients in the high-risk group are less likely to benefit from immunotherapy and may be better suited for treatment with drugs such as Oxaliplatin and Alpelisib.ConclusionThis research systematically identified biomarkers related to NB prognosis and developed a reliable prognostic model applying WGCNA and multiple bioinformatics methods. The model has important application value in predicting patients’ prognosis, evaluating drug sensitivity and immunotherapy effect, and provides new ideas and directions for precise treatment of neuroblastoma.

Transcriptomic correlates of state modulation in GABAergic interneurons: A cross-species analysis

GABAergic inhibitory interneurons comprise many subtypes that differ in their molecular, anatomical and functional properties. In mouse visual cortex, they also differ in their modulation with an animal’s behavioural state, and this state modulation can be predicted from the first principal component (PC) of the gene expression matrix. Here, we ask whether this link between transcriptome and state-dependent processing generalises across species. To this end, we analysed seven single-cell and single-nucleus RNA sequencing datasets from mouse, human, songbird, and turtle forebrains. Despite homology at the level of cell types, we found clear differences between transcriptomic PCs, with greater dissimilarities between evolutionarily distant species. These dissim­ilarities arise from two factors: divergence in gene expression within homologous cell types and divergence in cell type abundance. We also compare the expression of cholinergic receptors, which are thought to causally link transcriptome and state modulation. Several cholinergic receptors predictive of state modulation in mouse interneurons are differentially expressed between species. Circuit modelling and mathematical analyses suggest conditions under which these expression differences could translate into functional differences.Significance StatementThe brain is a complex network of many different cell types. A particularly diverse group of cells is that of inhibitory interneurons, named for their suppressive effect. These interneurons change their activity depending on an animal’s behavioural state—at least in mice. Here, we investigate if this finding generalises to other species by comparing gene expression patterns of human, turtle, and zebra finch interneurons. Despite sharing an evolutionary past, we find that only human and mouse interneurons have similar gene expression patterns associated with state modulation. A mathematical model suggests which expression differences in individual cells translate into functional differences at the network level.

Evaluation of Early Accommodation Outcomes Following Femtosecond Laser-Assisted in situ Keratomileusis and Small Incision Lenticule Extraction

ABSTRACT Purpose The aim of this study is to assess the changes and differences in early postoperative binocular accommodative function following femtosecond laser-assisted in situ keratomileusis (FS-LASIK) and small incision lenticule extraction (SMILE). Methods In this retrospective study, 120 patients (240 eyes) diagnosed with low-to-moderate and high myopia, who underwent either FS-LASIK or SMILE procedures were included. The assessment encompassed measurements of accommodative facility, accommodation time, relaxation time, and accommodation-to-relaxation ratio using a smart flipper. Measurements were taken preoperatively, as well as at 1 day, 1 week, and 1 month postoperatively. Additionally, the visual fatigue scale score was assessed and compared at the 1 month mark post-surgery. Changes in parameters were quantified by calculating the difference between preoperative values and those recorded at each postoperative time point. Results At 1 month post-surgery, both FS-LASIK and SMILE procedures demonstrated potential for recovery or even improvement in accommodative facility, accommodation time, relaxation time, and accommodation-to-relaxation ratio compared to preoperative levels. The FS-LASIK group exhibited a greater magnitude of change in accommodative facility postoperatively compared to the SMILE group. In the low-to-moderate myopia subgroup, the FS-LASIK group exhibited lower changes in accommodation time and visual fatigue scale score at 1 month post-surgery compared to the SMILE group, with all associated p-values <0.05. Conclusions Early postoperative recovery of accommodation function was slower following SMILE compared to FS-LASIK. Additionally, the severity of visual fatigue at 1 month post-surgery was greater in the SMILE group than in the FS-LASIK group. This difference in visual fatigue levels may be attributed to the delayed recovery observed in postoperative SMILE procedures.

Low Magnetic Field Exposure Alters Prostate Cancer Cell Properties

Prostate cancer is the second most common neoplasia and fifth-leading cause of cancer death in men worldwide. Electromagnetic and magnetic fields have been classified as possible human carcinogens, but current understanding of molecular and cellular pathways involved is very limited. Effects due to extremely low magnetic/hypomagnetic fields (LMF) are furthermore poorly understood. Extracellular vesicles (EVs) are crucial mediators of cellular communication with multifaceted roles in cancer progression, including via transport and uptake of various protein and microRNA (miRNA) EV-cargoes. miRNAs regulate gene expression and are implicated in cancer-related processes such as proliferation, metastasis, and chemoresistance. This study investigated the effects of LMF exposure (20 nT) by magnetic shielding on the prostate cancer cell line PC3 compared to the prostate epithelial cell line PNT2 under short-term (4 h) conditions. We examined EV profiles following a 4 h LMF exposure alongside associated functional enrichment KEGG and GO pathways for the EV proteomes. The 4 h LMF exposure significantly reduced cellular EV release and modified PC3 EV cargoes to a more inflammatory and metastatic profile, with 16 Disease Pathways and 95 Human Phenotypes associated specifically with the LMF-treated PC3 EV proteomes. These included cancerous, metabolic, blood, skin, cardiac and skeletal Disease Pathways, as well as pain and developmental disorders. In the normal PNT2 cells, less EV protein cargo was observed following LMF exposure compared with cells not exposed to LMF, and fewer associated functional enrichment pathways were identified. This pointed to some differences in various cellular functions, ageing, defence responses, oxidative stress, and disease phenotypes, including respiratory, digestive, immune, and developmental pathways. Furthermore, we analysed alterations in matrix metalloproteinases (MMPs) and miRNAs linked to metastasis, as this is crucial in cancer aggressiveness. The 4 h LMF exposure caused a significant increase in MMP2 and MMP9, as well as in onco-miRs miR-155, miR-210, miR-21, but a significant reduction in tumour-suppressor miRs (miR-200c and miR-126) in the metastatic PC3 cells, compared with normal PNT2 cells. In addition, 4 h LMF exposure significantly induced cellular invasion of PC3 cells. Overall, our findings suggest that changes in magnetic field exposures modulate EV-mediated and miR-regulatory processes in PCa metastasis, providing a basis for exploring novel therapeutic strategies.

The moderating function of sexual sanctification on the relation between sexual and relationship satisfaction: A registered report

Past research on sanctification has focused on the direct association between domain sanctification and domain satisfaction. This registered-report study focused on the predicted moderating function of sexual sanctification on the association between sexual and relationship satisfaction. An Internet panel sample of 740 women and 872 men, all married Jewish individuals residing in Israel, assessed the levels of their sexual and marital satisfaction, sexual sanctification, religiousness, and social desirability via an anonymous online questionnaire. As expected, sexual and marital satisfaction were highly correlated. As predicted, sexual sanctification was found to moderate the association between sexual and marital satisfaction for women even after controlling for age, religiousness, and social desirability. However, although the positive association between sexual and relationship satisfaction was predicted to be larger at higher levels of sanctification than at lower levels, the moderation analysis revealed a reverse pattern. In addition, the moderation effect was significant for men only after controlling for religiousness. Post hoc analyses for moderated moderation confirmed significant gender differences in the moderation function of sexual sanctification. The importance of examining gender differences in future sanctification studies and the theoretical implications for the independence of sanctification from religiousness is discussed.

Comparative study of the growth, stress status and reproductive capabilities of four wild-type zebrafish (Danio rerio) lines

BackgroundZebrafish are widely used in various research fields and to fulfil the diverse research needs, numerous zebrafish lines are available, each with a unique domestication background, potentially resulting in intraspecies differences in specific biological functions. Few studies have compared multiple zebrafish lines under identical conditions to investigate both inter- and intra-line variability related to different functions. However, such variability could pose a challenge for the reproducibility of results in studies utilising zebrafish, particularly when the line used is not clearly specified. This study assessed growth, stress status (cortisol, serotonin) and reproductive capabilities (maturity, fecundity, fertilisation rate, sperm quality) of four commonly used wild-type zebrafish lines (AB, SJD, TU, WIK) using standardized protocols.ResultsThe stress markers levels were found to be similar across the lines, indicating that the endocrine stress status is robust to diverse domestication histories. Variations were observed in the growth and reproductive parameters. The lines exhibited differences in the timing of puberty (86 dpf for AB and SJD lines vs. 107 dpf for the WIK line) despite achieving similar sizes, suggesting that there are line-specific variations in the induction of maturation. Additionally, the AB line demonstrated higher sperm quality than did the other lines and higher fecundity and fertilization rates than did the SJD line. The AB line also exhibiting a smaller adult size but a heavier brain relative to its body weight.ConclusionThese findings emphasize the importance of line selection for zebrafish research, indicating that researchers should consider line-specific traits to ensure the biological relevance and reproducibility of the results.

Similar short-term outcomes for bone-level implants with or without intermediate abutments.

A single-center (university-setting), prospective, longitudinal, split-mouth, single-blind, randomized controlled clinical trial investigated peri-implant parameters of bone-level implants restored with either screw-retained prostheses connected directly to the implants or with intermediate abutments over a 3-year period. The study adhered to the ethical principles of the Helsinki Declaration and the CONSORT guidelines. Ethical approval was granted, and the trial was registered at Clinicaltrials.gov . Participants included were over 18 years of age, had a plaque index below 25%, and were missing at least two adjacent teeth, allowing for rehabilitation with screw-retained fixed partial prostheses over two implants and 2-4 prosthetic units. Exclusion criteria included long-term use of medications affecting bone metabolism, smoking more than 10 cigarettes per day, history of local radiotherapy, untreated periodontitis, and the need for rehabilitation in the anterior sextant of the maxilla. The primary clinical outcome was marginal bone loss (MBL), while secondary outcomes included probing pocket depth (PPD), plaque index (PI), bleeding on probing (BOP), and patient-reported outcomes (PROs). The study schedule included a screening (visit 1), implant surgery (visit 2), stage-two 8 weeks post-surgery (visit 3), impressions taken 4 weeks post stage-two (visit 4), baseline standardized radiograph (visit 5), followed by 6-month (visit 6), 12-month (visit 7), and 36-month (visit 8) follow-up visits. Descriptive statistics and quantitative measures included means, standard deviations (SDs), minimum and maximum values, and 95% confidence intervals (CIs). Clinical parameters (six sites per implant) measured were MBL, PPD, PI, and BOP. Paired t tests were utilized for intragroup comparisons across different time points and intergroup comparisons at each time point. PROs at 36 months were compared using Student's t test. The alpha significance level was set at 0.05. The study included 36 patients (72 implants), with two not completing the follow-up due to death and relocation. No implants showed signs of inflammation or mobility. Mean interproximal bone level (IBL) at baseline was 0.13 mm ± 0.15 mm for the control group and 0.10 ± 0.13 mm for the test group. At the 36-month follow-up, mean IBL was 0.13 ± 0.18 mm for the control group and 0.20 ± 0.24 mm for the test group, with no significant differences (F(1, 32) = 1.06; p > 0.05). Clinical parameters (PPD, BOP, PI) at 36 months showed no significant differences between groups. Minor complications occurred in 6.7% of the control group and 5.3% of the test group. PROs indicated no significant differences in general satisfaction, esthetics, comfort, phonetics, and masticatory function between the groups. After a 36-month follow-up, bone-level implants restored with CAD/CAM prostheses directly connected to the implants displayed similar clinical outcomes, PROs, and marginal bone level changes as those restored with intermediate standardized abutments.

Posterior Cruciate Ligament Preservation versus Posterior Cruciate Ligament Sacrifice: Comparing Patient Outcomes in Medial Congruent Total Knee Arthroplasty.

This study aimed to compare outcomes and complication rates between posterior cruciate ligament (PCL) retention and excision utilizing a medial congruent (MC) polyethylene insert in total knee arthroplasty (TKA) in a specialized ambulatory surgery center (ASC) dedicated to hip and knee arthroplasty. A retrospective review was performed between May 2023 and October 2023 analyzing 398 patients who underwent primary MC TKA by high-volume joint arthroplasty surgeons (n = 9) with either PCL preservation (n = 264) or sacrifice (n = 134) in a single free-standing ASC. Patients were matched chronologically on a 2:1 basis. Demographics, baseline function, 90-day complications, and patient-reported outcomes were recorded for each patient. There were no differences in preoperative baseline function or patient-reported outcome measures, Charlson Comorbidity Index, or American Society of Anesthesiologists class among patient groups. The PCL-preserve and PCL-sacrifice cohorts showed significant variation in 12-week postoperative Knee Injury and Osteoarthritis Outcome, Junior (KOOS, JR.) scores. Specifically, the number of patients who achieved the minimal clinically important difference (MCID) in KOOS, JR. scores was higher in the PCL-sacrifice group (p < 0.05). Yet, no complications within the 90-day period were associated with PCL status and other patient-reported outcomes. This study comparing outcomes between MC TKAs with PCL retention and sacrifice suggests that both techniques are viable options with similar functional outcomes, pain scores, and complication rates, which may have benefits in an ASC setting. The PCL-sacrifice group exhibited a statistically significant increase in patients who achieved the MCID in KOOS, JR. score compared with the PCL-preserving at early follow-up. Future research should employ prospective, randomized designs to further validate these findings and explore long-term implications.

Selectivity Modulation of Multistep Reduction Reactions by Gold Nanoclusters

The selective synthesis of valuable azo‐ and azoxyaromatic chemicals via transfer coupling of nitroaromatic compounds has been achieved by fine‐tuning the catalyst structure. Here, a direct method to modulate nitrobenzene reduction and selectively alter the product from azobenzene to azoxybenzene by employing the size effect of Au is reported. Au nanoclusters (NCs) with smaller sizes embedded in ZIF‐8 controllably converted nitrobenzene into azoxybenzene, while supported Au nanoparticles (NPs) catalyzed nitrobenzene reduction to azobenzene. X‐ray photoelectron spectroscopy (XPS) and Diffuse reflectance infrared Fourier transform spectroscopy on CO adsorption (CO‐DRIFTS) of Au NC/ZIF‐8 revealed a higher valence state and a lower electron density of Au than that of Au NP/ZIF‐8, combined with the desorption of azoxybenzene from the Au NC and Au NP surface, suggesting that the Au NCs with lower electron density exhibit stronger adsorption. Density functional theory (DFT) calculations and charge density difference maps indicated that azoxybenzene bonded to Au NC/ZIF‐8 with greater adsorption energy, resulting in more electron transfer between azoxybenzene and the generated Au sites, which inhibited further reduction of azoxybenzene and resulted in high azoxybenzene selectivity. The application of the size effect of Au particles to regulate nitrobenzene transfer coupling provided new insights into the structure‐selectivity relationships.

Host preference and physiological performance of the invasive hemiparasite of coastal communities &lt;i&gt;Cassytha filiformis&lt;/i&gt; L. (Lauraceae)

Background: Invasive parasitic species have barely been studied despite their impact on the communities they invade. Questions: What is the host range used by the invasive parasite Cassytha filiformis in the coastal scrubland of northern Yucatan? Does C. filiformis show host preference? Does the physiological performance of C. fliformis (water deficit and chlorophyll content) vary among hosts on which it establishes and reproduces? Study species: Cassytha filiformis, an invasive hemiparasitic vine of coastal communities. Study sites and dates: Telchac, Yucatán, México. The study lasted from October 2022 to June 2023. Methods: The incidence of C. filiformis parasitism was recorded. Histological analysis confirmed parasitism, and the water potential and chlorophyll concentration of C. filiformis in its main hosts were determined. Results: C. filiformis parasitized 10 species, showing a preference for shrubs. Its main hosts were Scaevola plumieri, Phitecellobium keyense and Croton punctatus. Differences between hosts were observed in water potential variation and total chlorophyll concentration. Differences between stem types (young and mature) in chlorophyll concentration were also observed. Conclusions: C. filiformis prefers shrub species to establish. The physiological performance of C. filiformis varied depending on host identity. Differences in chlorophyll concentration between stem types of C. filiformis suggest functional physiological differences between them.

Selectivity Modulation of Multistep Reduction Reactions by Gold Nanoclusters.

The selective synthesis of valuable azo- and azoxyaromatic chemicals via transfer coupling of nitroaromatic compounds has been achieved by fine-tuning the catalyst structure. Here, a direct method to modulate nitrobenzene reduction and selectively alter the product from azobenzene to azoxybenzene by employing the size effect of Au is reported. Au nanoclusters (NCs) with smaller sizes embedded in ZIF-8 controllably converted nitrobenzene into azoxybenzene, while supported Au nanoparticles (NPs)catalyzed nitrobenzene reduction to azobenzene. X-ray photoelectron spectroscopy (XPS) and Diffuse reflectance infrared Fourier transform spectroscopy on CO adsorption (CO-DRIFTS) of Au NC/ZIF-8 revealed a higher valence state and a lower electron density of Au than that of Au NP/ZIF-8, combined with the desorption of azoxybenzene from the Au NC and Au NP surface, suggesting that the Au NCs with lower electron density exhibit stronger adsorption. Density functional theory (DFT) calculations and charge density difference maps indicated that azoxybenzene bonded to Au NC/ZIF-8 with greater adsorption energy, resulting in more electron transfer between azoxybenzene and the generated Au sites, which inhibited further reduction of azoxybenzene and resulted in high azoxybenzene selectivity. The application of the size effect of Au particles to regulate nitrobenzene transfer coupling provided new insights into the structure-selectivity relationships.

Psychological and social difficulties in young non-help-seeking adolescents at risk for psychosis: insights from a large cohort study

BackgroundThis study used data from the Norwegian Mother, Father, and Child Cohort Study (MoBa), and explored the psychological and social challenges of 14-year-olds who report psychotic symptoms. Research on help-seeking youths indicates comorbid symptoms of depression, anxiety, and social deterioration, but less is known about non-help-seeking individuals who may not use healthcare services, possibly skewing comorbidity profiles. Also, findings suggest that adolescents manifesting psychotic symptoms refrain from pursuing help. This gap underscores the necessity of studying non-help-seeking adolescents to better understand their needs and the risks they face without intervention.MethodsWe analyzed responses from adolescents who completed the 14-year questionnaire in MoBa (N = 127), identifying those as at risk by their high scores on psychosis-risk items, within the top 0.4% (N = 58). Comparative analyses were conducted against matched controls to assess differences in psychological and social functioning (N = 69).ResultsResults indicated that the at-risk adolescents experience significantly more depression and anxiety and have lower self-esteem and poorer social functioning than controls. Social functioning parameters, including leisure activities, social competence, quality of parental relationship, and sense of school belonging, were significantly worse than those observed in controls. The results indicate a pronounced vulnerability among non-help-seeking adolescents at-risk, similar to issues seen in help-seeking youths.ConclusionThese findings highlight the importance of early identification and intervention strategies that reach beyond traditional clinical settings, suggesting the efficacy of population or community-based screenings to prevent long-term adverse outcomes. The study proposes a broader understanding of psychosis risk, stressing the importance of inclusive approaches to support at-risk adolescents effectively.

Nonlinear Seismic Response of Tunnel Structures under Traveling Wave Excitation

Tunnels traditionally regarded as resilient to seismic events have recently garnered significant attention from engineers owing to a rise in incidents of seismic damage. In this paper, the reflection characteristics of the elastic plane wave incident on the free surface are analyzed, and the matrix analysis method SWIM (Seismic Wave Input Method) for the calculation of equivalent nodal loads with artificial truncated boundary conditions for seismic wave oblique incidence is established by using coordinate transformation technology, according to the displacement velocity and stress characteristics of a plane wave. The results show that the oblique incidence method is more effective in reflecting the traveling wave effect, and the “rotational effect” induced by oblique incidence must be considered for P wave and SV wave incidence, including the associated stress and deformation. This effect exhibits markedly distinct rotational phenomenon. In particular, the P wave incidence should be focused on the vault and the inverted arch due to the expansion wave. With the increase of the oblique incidence angle, the structural stress and deformation are rotated to a certain extent, and the values are significantly increased. Simultaneously, the shear action of the SV wave may result in “ovaling” of the tunnel structure, thereby facilitating damage to the arch shoulder and the sidewall components. As the oblique incidence angle, the potentially damaging effects of the “rotational effect” to the vault and the inverted arch, but the numerical value does not change significantly. In addition, in comparison to a circular cross-section, the low-frequency amplification of seismic waves in the surrounding rock and the difference of frequency response function in different parts of the lining are more pronounced. In particular, the dominant frequency characteristics are significant at P wave incidence and the seismic wave signal attenuation tends to be obvious with increasing incidence angle. In contrast, SV waves exhibit more uniform characteristics.

Impact of propofol versus desflurane anesthesia on postoperative hepatic and renal functions in infants with living-related liver transplantation: a randomized controlled trial

BackgroundThe effects of anesthetics on liver and kidney functions after infantile living-related liver transplantation (LRLT) are unclear. This study aimed to investigate the effects of propofol-based total intravenous anesthesia (TIVA) or desflurane-based inhalation anesthesia on postoperative liver and kidney functions in infant recipients after LRLT and to evaluate hepatic ischemia–reperfusion injury (HIRI).MethodsSeventy-six infants with congenital biliary atresia scheduled for LRLT were randomly divided into two anesthesia maintenance groups: group D with continuous inhalation of desflurane and group P with an infusion of propofol. The primary focus was to assess alterations of liver transaminase and serum creatinine (Scr) levels within the first 7 days after surgery. And the peak aminotransferase level within 72 h post-surgery was used as a surrogate marker for HIRI.ResultsThere were no differences in preoperative hepatic and renal functions between the two groups. Upon the intensive care unit (ICU) arrival, the levels of aspartate aminotransferase (AST, P = 0.001) and alanine aminotransferase (ALT, P = 0.005) in group P were significantly lower than those in group D. These changes persisted until the fourth and sixth days after surgery. The peak AST and ALT levels within 72 h after surgery were also lower in group P than in group D (856 (552, 1221) vs. 1468 (732, 1969) U/L, P = 0.001 (95% CI: 161–777) and 517 (428, 704) vs. 730 (541, 1100) U/L, P = 0.006, (95% CI: 58–366), respectively). Patients in group P had lower levels of Scr upon the ICU arrival and on the first day after surgery, compared to group D (17.8 (15.2, 22.0) vs. 23.0 (20.8, 30.8) μmol/L, P < 0.001 (95% CI: 3.0–8.7) and 17.1 (14.9, 21.0) vs. 20.5 (16.5, 25.3) μmol/L, P = 0.02 (95% CI: 0.0–5.0) respectively). Moreover, the incidence of severe acute kidney injury was significantly lower in group P compared to that in group D (15.8% vs. 39.5%, P = 0.038).ConclusionsPropofol-based TIVA might improve liver and kidney functions after LRLT in infants and reduce the incidence of serious complications, which may be related to the reduction of HIRI. However, further biomarkers will be necessary to prove these associations.

Developing a Novel Prognostic Model Based on Muscle-Invasive Bladder Cancer Types: A Multicenter RetrospectiveCohort Study of Patients Who Received Radical Cystectomy and Chemotherapy.

To develop a prognostic model to manage patients with muscle-invasive bladder cancer (MIBC) undergoing radical cystectomy (RC) and chemotherapy. Clinicopathologic characteristics and survival data were collated from a North American database to develop a model. Genomic and clinicopathologic data were also obtained from European and Asian databases to externally validate the model. Patients were classified as either "primary" or "progressive" MIBC according to non-muscle invasive stage history. Optimized cancer-specific survival (CSS) models, based on MIBC types, were constructed using Cox's proportional hazard regression. Differences of biological function and tumor immunity, between two risk-based groups stratified according to the prognostic model, were estimated. There were 2631 participants in the American cohort, 291 in the European cohort and 142 in the Asian cohort. Under Cox's regression analysis, tumor stage, lymph node stage, age, ethnicity, and MIBC types were independent CSS predictors (all p < 0.05). The constructed nomogram, whichintegratedthese variables, improved the predictivepower. This model had good discrimination and calibration. Patients were categorized into high- or low-risk groups according to the total points calculated. Kaplan-Meier curves revealed that patients in the high-risk group had poorer survival (p < 0.001). This was confirmed with two external validation cohorts (both with p < 0.001). Higher stromal scores and increased M0 and M2 macrophage numbers were observed in samples from the high-risk group, whereas regulatory T cells had lower infiltration in these populations (all with p < 0.05). This MIBC type-based nomogram provides accurate CSS predictions, which could help improve patient management and clinical decision-making.

Abstract B084: Comparative functional analysis of TP53 alleles in pancreatic ductal adenocarcinoma in vivo

Abstract TP53 is the second most mutated gene in pancreatic ductal adenocarcinoma (PDAC), bearing both truncal loss-of-function and missense point mutations. TP53 encodes a stress-induced transcription factor (p53) capable of activating tumor suppressive pathways mediating cell cycle arrest, apoptosis, senescence, and metabolic reprogramming. Despite high mutational frequency, how TP53 mutants function to suppress pancreatic tumorigenesis in vivo remains unclear. Previous studies indicate that the most frequent point mutations observed in human PDAC (TP53 R175H and R273H; mouse homologues Trp53 R172H and R270H) exhibit both dominant-negative (e.g., response to radiation in leukemia cells) and gain-of-function (e.g., increased liver metastasis in advanced PDAC models) roles compared to p53 null cells in various contexts. To rigorously explore the differential functions of p53 point and deletion mutants in PDAC progression, we performed an isogenic comparative analysis of Trp53 alleles in vivo using Mosaic Analysis with Double Markers (MADM) in mice. MADM uses stochastic mitotic recombination to induce two genotypically distinct daughter cells – created at 1-to-1 ratios – expressing different Trp53 variants dependent on the genotype of the mouse (+/+ vs. -/-, R172H/R172H vs. +/+, R172H/R172H vs. -/-, R270H/R270H vs. +/+, R270H/R270H vs. -/-) and simultaneously label them with unique genetically encoded fluorescent markers (TdTomato vs. GFP). We integrated MADM into a faithful Kras-driven model of pancreatic tumorigenesis (KC: Kras LSL-G12D/+ ; Pdx1-Cre) and used fluorescence microscopy to trace subclonal populations with various Trp53 alleles within the same mouse. By analyzing the ratio of TdTomato+ to GFP+ cells, we studied the functional differences between alleles in driving tumor initiation and expansion at various stages of progression. Strikingly, we found that Trp53 -/- cells exhibited greater expansion in preinvasive pancreatic intraepithelial neoplasias (PanINs) compared to not only Trp53 +/+ cells but also cells harboring either point mutation (Trp53 R172H/R172H or Trp53 R270H/R270H ). While Trp53 R270H/R270H cells predominated over Trp53 +/+ in PanINs, Trp53 R172H/R172H cells were surprisingly indistinguishable from Trp53 +/+ cells, suggesting that p53R172H retains tumor suppressive properties in early PDAC progression. Conversely, both Trp53 R172H/R172H and Trp53 R270H/R270H cells progressed to advanced PDAC with comparable PDAC incidence and survival as Trp53 -/- , arguing that Trp53 R172H is a separation-of-function mutant concordant with a distinct transcriptional profile relative to Trp53 -/- tumor cells. Together, these studies offer the strongest evidence to date for stage-specific functional differences between TP53 mutant variants in cancer progression in vivo and provide a faithful MADM-based PDAC model to define molecular mechanisms (through ongoing transcriptomic, epigenomic, and metabolomic studies) that govern functional differences amongst these diverse alleles. Citation Format: Sherry S. Agabiti, Andy Tang, Timothy Nottoli, Mandar D. Muzumdar. Comparative functional analysis of TP53 alleles in pancreatic ductal adenocarcinoma in vivo [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr B084.

Composting of Cow-Dung-Amended Soil by the Dung Beetle Catharsius molossus L. Improves Bacterial Ecological Functions Related to Nitrogen Mineralization and Human and Plant Pathogenesis

The Asian dung beetle (Catharsius molossus L.; Coleoptera: Scarabeidae) has been shown to positively affect soil bacterial diversity and the agronomic features of crop plants. In this study, we used bioinformatic tools to investigate the differences in bacterial functional phenotypes and ecological functions between control soil, cow dung-amended soil (CD), and cow dung-amended soil composted by dung beetles (DB). The soil bacterial metagenomes were sequenced and analyzed with the bioinformatic packages BugBase, PICRUSt2, Tax4Fun, and FAPROTAX to evaluate the effects of dung beetle-mediated composting on bacterial functions such as human and plant pathogenicity, trophic strategies, and soil nutrient transformation. BugBase proved useful for the determination of differences in major functional phenotypes, whereas FAPROTAX was effective at identifying differences in bacterial ecological functions between the treatments. Both tools suggested a relative decrease in human pathogens in the DB soil. This was corroborated by the pairwise comparison of abundances in bacterial species, which showed a significant reduction in the abundance of the broad-host-range pathogen Pseudomonas aeruginosa in the DB soil. In addition, FAPROTAX suggested a decrease in plant pathogens and an increase in chitinolytic bacteria, meaning that the DB treatment might be beneficial to the plant-growth-promoting bacteria involved in biological control. Finally, FAPROTAX revealed an array of ecological functions related to trophic strategies and macro- and micronutrient metabolism. According to these results, the activity of C. molossus beetles enhanced methanotrophy, ammonification, nitrification, sulfate reduction, and manganese oxidation, whereas iron respiration was decreased in the DB-treated soil. Our results represent a collection of general insights into the effects of C. molossus beetles on soil bacterial functions, which also reflect on the nutrient composition of dung beetle-composted soil.

Unveiling the impact of cell death-related genes and immune dynamics on drug resistance in lung adenocarcinoma: a risk score model and functional insights

Lung adenocarcinoma (LUAD), characterized by its heterogeneity and complex pathogenesis, is the focus of this study which investigates the association between cell death-related genes and LUAD. Through machine learning, a risk score model was developed using the Coxboost rsf algorithm, demonstrating strong prognostic accuracy in both validation (GSE30219, GSE31210, GSE72094) and training (TCGA-LUAD) datasets with C-indices of 0.93, 0.67, 0.68, and 0.64, respectively. The study reveals that the expression of Keratin 18 (KRT18), a key cytoskeletal protein, varies across LUAD cell lines (DV-90, PC-9, A549) compared to normal bronchial epithelial cells (BEAS-2B), suggesting its potential role in LUAD's pathogenesis. Kaplan–Meier survival curves further validate the model, indicating longer survival in the low-risk group. A comprehensive analysis of gene expression, functional differences, immune infiltration, and mutations underscores significant variations between risk groups, highlighting the high-risk group's immunological dysfunction. This points to a more intricate tumor immune environment and the possibility of alternative therapeutic strategies. The study also delves into drug sensitivity, showing distinct responses between risk groups, underscoring the importance of risk stratification in treatment decisions for LUAD patients. Additionally, it explores KRT18's epigenetic regulation and its correlation with immune cell infiltration and immune regulatory molecules, suggesting KRT18's significant role in the tumor immune landscape. This research not only offers a valuable prognostic tool for LUAD but also illuminates the complex interplay between cell death-related genes, drug sensitivity, and immune infiltration, positioning KRT18 as a potential therapeutic or prognostic target to improve patient outcomes by personalizing LUAD treatment strategies.

187 Exploring deep shotgun sequencing to understand the rumen microbial function in Angus bulls with divergent RFI EPD

Abstract We investigated the rumen microbiome of Angus bulls selected for Residual Feed Intake-Expected Progeny Difference (RFI-EPD) utilizing deep shotgun metagenomic sequencing. Negative RFI-EPD bulls (NegRFI: n = 10; RFI-EPD = -0.3883 kg/d) and Positive RFI-EPD bulls (PosRFI: n = 10; RFI-EPD = 0.2935 kg/d) were selected from a group of 59 Angus bulls [average body weight (BW) = 427.81 ± 18.77 kg] fed a high-forage total mixed ration after a 59-d testing period. At the end of the 59-d period, rumen fluid samples were collected for bacterial DNA extraction and subsequent shotgun metagenomic sequencing. Results of the metagenome analysis revealed greater gene richness in NegRFI bulls compared with PosRFI. Analysis of similarity revealed a significant difference (P = 0.05) in the rumen microbial community between the NegRFI and PosRFI. Linear Discriminant Analysis effect size (Lefse) was used to identify the differentially abundant taxa. The Lefse results showed that class Fibrobacteria (LDA = 5.1) and genus Fibrobacter (LDA = 4.8) were the most differentially enriched markers in NegRFI bulls, compared with PosRFI bulls. Relative abundance of the carbohydrate-active enzymes was also compared using lefse analysis. The results showed greater relative abundance of glycoside hydrolases and carbohydrate-binding modules such as GH5, CBM86, CBM35, GH43, and CBM6 (LDA &amp;gt; 3.0) in NegRFI bulls whereas GH13 and GT2 were greater in PosRFI. The distinct metabolic and microbial profiles observed in NegRFI, compared with PosRFI bulls, characterized by greater gene richness and specific taxa such as Fibrobacter, and variations in carbohydrate-active enzymes, underscore the potential genetic and functional differences in their rumen microbiome. These findings contribute to a deeper understanding of the interplay between host genetics, microbiota, and feed efficiency in Angus bulls, opening avenues for targeted interventions and advancements in livestock management practices.

Pinning Down Small Populations of Photoinduced Intermediates Using Transient Absorption Spectroscopy and Time-Dependent Density Functional Theory Difference Spectra to Provide Mechanistic Insight into Controlling Pyridine Azo Dynamics with Protons.

In this work, the impact of protonation on the photoisomerization (trans → cis) and reversion (cis → trans) of three pyridine-based azo dyes (PyrN) is investigated by using a combination of transient absorption spectroscopy and time-dependent density functional theory computed difference spectra. The photophysical behaviors of the PyrN dyes are altered by the addition of one or two protons. Protonation of basic pyridine nitrogens results in an ultrafast accelerated reversion mechanism after photoisomerization, while protonation of azo bond nitrogens restricts cis isomer formation entirely. Computed difference spectra provide spectral signatures that are critical for the assignment of low-population long-lived states, providing direct evidence of the accelerated reversion mechanism. Thus, the addition of organic acids can selectively control the photophysics of azo dyes for a wide range of applications, including materials design and pharmaceuticals.