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Integrated gene network analysis and experimental validation identify key hub genes in potato response to Potato Virus Y infection
Potato (Solanum tuberosum) is a staple food crop that supports global food security, ranking as the world’s third most important food crop after rice and wheat in terms of human consumption, and it is threatened by Potato virus Y (PVY), which causes severe yield losses. This study integrates bioinformatics analysis and experimental approaches to elucidate molecular defense mechanisms against PVY infection. Using transcriptomic data from PVY-infected potato plants, we constructed protein-protein interaction (PPI) networks and identified hub genes central to defense responses. The qPCR validation showed that three hub genes (NAD1, NAD2, NAD3) were upregulated in resistant Sante plants but downregulated in susceptible Agria. Among these, NAD2 showed a striking 5.58-fold increase in Sante, highlighting its critical role in stress signaling and antiviral defense. Network analysis revealed interactions with microRNAs (miRNAs), including stu-miR8015-5p and stu-miR396-5p, suggesting complex regulatory networks. Codon usage bias analysis highlighted adaptive codon preferences optimized for translational efficiency, supporting potential strategies like codon deoptimization to impair viral fitness. Promoter motif analysis identified stress-responsive cis-regulatory elements linked to abscisic acid signaling, critical for antiviral responses. This comprehensive study establishes a framework for targeting hub genes and miRNAs to engineer PVY-resistant cultivars, thereby offering a sustainable solution.
Timescales for stochastic barrier crossing: Inferring the potential from nonequilibrium data
Kramers’s rate theory forms a cornerstone for thermally activated barrier crossing. However, its reliance on equilibrium quantities excludes the analysis of nonequilibrium dynamics at early times. Most studies have thus focused on obtaining rates and transition time and path distributions in equilibrium. Instead, here we consider early-time nonequilibrium dynamics in a model system of a particle with overdamped dynamics hopping over the barrier in a double-well potential, using the Smoluchowski equation (SE) and stochastic path integral (SPI) mapping of the Langevin equation. We identify several key timescales relevant to nonequilibrium dynamics and quantify them using the SE and SPI approaches. The shortest timescale corresponds to equilibration in a well at time t ≪ τB, where τB is the Brownian diffusion time. The second important timescale is when an inflexion point appears in the effective potential constructed from the density at t ⪅ τB. Shortly after, the existence of a second potential well can be inferred from sufficient sampling of the dynamics. Interestingly, this timescale decreases with increasing barrier height. We find significant deviations from the equilibrium limit unless t ≫ τB. We further calculate the current at the barrier for bistable and asymmetric potentials and find that it crosses over to that from equilibrium rate theory at a time that does not appear to depend on the barrier height. Our results have important implications for controlling activated processes at finite times and demonstrate the importance of reaching long enough times to faithfully construct potential landscapes from experimental or simulation data.
Nonlinear relationship between digital and intelligent transformation and energy conservation and emission reduction in China
Shredder species identity over diversity: Insights into litter decomposition in ponds
Many freshwater ecosystems rely on the decomposition of organic matter as a key process for nutrient cycling and energy flow. Small lentic freshwater ecosystems, such as ponds, often derive a large amount of energy from allochthonous detritus due to their close connection with the terrestrial environment. However, the process of leaf litter decomposition in ponds remains poorly understood. We conducted a microcosm experiment in a pond environment to investigate intra- and inter-specific variation in organic matter processing by three shredders (Tipula sp., Sericostoma sp. and Gammarus fossarum) and to assess the effects of shredder community characteristics on the mass loss of black alder (Alnus glutinosa) leaf litter. We developed a novel approach to quantify functional traits directly related to litter processing. Detailed gut content analysis revealed significant inter- and intra-specific variation in the organic matter particles ingested by individual shredder taxa. Our results showed that neither taxonomic nor functional diversity reliably predicts leaf litter decomposition rates in ponds. Instead, the keystone shredder Sericostoma showed a pronounced effect on decomposition rates driven by their unique feeding behaviour and density-dependent shifts in particle size preferences. These findings highlight the importance of a detailed understanding of species-specific functional traits and behaviour in shaping ecosystem processes, as the role of keystone species can outweigh the contributions of overall diversity measures in driving ecosystem processes.
Microscopic insights into the solvation of polyethylene glycol chains in water: A machine learning potential approach
Polyethylene glycol (PEG) is a structurally simple, nontoxic, and water-soluble polymer widely utilized in medical and pharmaceutical applications. Notably, when a PEG chain is immersed in water, the surrounding water molecules play a key role in driving conformational changes of this macromolecule. In this study, we explore the solvation behavior of PEG under mechanical strain using molecular dynamics simulations, with an interatomic potential obtained from machine learning. Our focus is on the transition from the favored coil-like conformation to an extended one under external force. Through analyses of radial distribution functions, hydrogen bonding, and solvation dynamics, we uncover how mechanical stretching influences the local hydration environment. Moreover, we disentangle the enthalpic and entropic contributions to the conformational stability of PEG in water. Surprisingly, our neural network potential model identifies dewetting of PEG C-atoms, and not water H-bonding with PEG O-atoms, as the main enthalpic driving force for the coiling of PEG in water.
Knowledge, attitude, and practice among non-breast cancer women towards breast cancer screening with a focus on economic factors
Risk stratification for the prediction of skeletal-related events in patients with castration-resistant prostate cancer with bone metastases
Skeletal-related events (SREs) are common in patients with bone metastases from castration-resistant prostate cancer (CRPC). Despite advances in prostate cancer treatment, clinically validated predictive models for SREs in CRPC patients with bone metastases remain elusive. This gap in prognostic tools hinders optimal patient management and treatment planning for this high-risk population. This study aimed to develop a prediction model for SRE by investigating potential risk factors and classifying them into different groups. This model can be used to identify patients at high risk of SREs who need close follow-up. Between 2004 and 2013, 68 male patients with bone metastases from CRPC who were treated at our institute were evaluated for survival without SREs and survival without SREs of the spinal cord. The study analyzed clinical data at enrollment to identify risk factors for initial and spinal SREs. Multivariate analysis revealed that a high count of metastatic vertebrae, along with visceral or lymph node metastases, were significant risk factors. Patients were categorized into four subgroups based on the number of vertebral metastases and presence of visceral or lymph node metastases: 1) extensive vertebral and both types of metastases, 2) extensive vertebral without additional metastases, 3) some vertebral with other metastases, 4) some vertebral without additional metastases. The first SRE and spinal SRE occurred significantly sooner in the first subgroup compared to others. Incidence rates at 12 months for the first SRE were 56%, 40%, 27%, and 5%, and for the first spinal SRE were 47%, 40%, 27%, and 0% respectively. Patients with extensive vertebral and additional metastases require vigilant monitoring to mitigate SREs.
Theoretical investigation of the photolysis mechanism of fluorinated Criegee intermediate HFCOO
Hydrofluoroolefins (HFOs) have emerged as promising alternatives for ozone-depleting chlorofluorocarbons (CFCs) and hydrochlorofluorocarbons (HCFCs) due to their drastically shorter atmospheric lifetimes (days to weeks vs years to decades for CFCs and HCFCs) and significantly lower global warming potential. While HFOs’ rapid degradation minimizes their direct environmental accumulation, the ecological risks posed by their reactive degradation intermediates—particularly hydrofluorocarbonyl oxide (HFCOO), a fluorinated Criegee intermediate generated via HFO-ozone reactions—require urgent mechanistic clarification. The atmospheric persistence and chemical reactivity of HFCOO are intrinsically governed by its excited-state dynamics, where competing photochemical pathways determine whether it undergoes ultrafast dissociation or survives to mediate secondary pollutant formation. In this paper, we examine the deactivation mechanism of HFCOO by employing high-level electronic structure calculations and on-the-fly surface hopping dynamic simulations. Our results reveal that the first excited singlet state (S1) of HFCOO is a dark state populated via nπ* transitions, while the second excited singlet state (S2), accessed through ππ* transitions, is crucial for O–O bond cleavage. We find that both syn- and anti-configurations of the S2 state exhibit rapid O–O bond dissociation, producing hydrofluorocarbonyl (HFCO) and excited oxygen atoms within 30 and 50 fs, respectively. Our study underscores the ultrafast photodissociation dynamics of HFCOO in the atmosphere, contributing valuable insights into the environmental safety assessment of HFOs and improving atmospheric models for predicting their ecological impacts.
Diverse behavior clustering of students on campus with macroscopic attention
Comparative proteomics of HepG2 cells reveals NGLY1 as an important regulator of ferroptosis resistance and iron uptake
NGLY1 deficiency is a rare genetic disorder caused by mutations in the NGLY1 gene. This disorder presents a wide range of clinical symptoms, and its severity varies among affected individuals. Previous studies have focused on understanding the influence of NGLY1 on energy metabolism, revealing dysregulation in lipid metabolism following NGLY1 deletion. In this study, we investigated the consequences of the loss of NGLY1 on ferroptosis and iron homeostasis using human hepatocellular carcinoma cells, HepG2. Comparative proteomics analysis revealed significant alterations in protein quantities in NGLY1 -deficient HepG2 cells, indicating that these cells are under “pro-ferroptotic” stress state. Moreover, dysregulated iron uptake and increased reactive oxygen species production were observed in the absence of NGLY1, indicating a novel perspective on the consequences of the loss of NGLY1 . These findings provide important insights into the molecular pathways affected by NGLY1 deletion and may contribute to the development of potential therapeutic strategies for individuals with NGLY1 deficiency.
Influence of NH⋯N and OH⋯N hydrogen bonds in the aggregation of flexible molecules: A combined experimental and computational study
Hydrogen bond formation is an important mechanism of molecular aggregation and, therefore, its understanding is crucial to modeling this fundamental process. While extensive literature exists regarding the OH⋯O interaction, NamineH⋯N interactions have been more occasionally studied in gas phase. Here, we study the formation of those two interactions in the context of dimerization of flexible molecules. Using supersonic expansions, we created the conditions to form 2-phenylethylamine homodimers and 2-phenylethylamine⋯2-phenylethanol heterodimers. Structural information was then extracted using mass-resolved excitation spectroscopy. The experimental data were interpreted on the light of computational predictions carried out at the B3LYP-D3(BJ)/def2-TZVP level. Both dimers present a collection of interactions, in addition to the formation of hydrogen bonds. Clearly, the OH⋯N interaction is stronger than the NH⋯N interaction due to the better donor character of the hydroxyl group. However, despite the difference in hydrogen bond strength, both dimers present similar behavior and structure. Comparison with other systems based on similar interactions helps in understanding these results.
Effect of ultrasound-microbubble exposure on acute myeloid leukemia cancer cell proteome
Visuospatial information transfer and task self-assessment within and between autistic and non-autistic adults
Previous research has demonstrated that autistic people transmit verbal information as effectively as non-autistic people; however, when autistic and non-autistic people interact less information is transmitted. We tested whether these findings generalised to a task requiring the transmission of primarily visual information and examined how accurately participants self-assessed their performance. 310 adults (154 autistic) were allocated to one of three, six-person diffusion chain conditions: (i) autistic, (ii) non-autistic, (iii) mixed autistic and non-autistic. Participant 1 in each chain watched a video of an experimenter creating a dog shape from a puzzle toy that could be manipulated. Participant 1 showed Participant 2 how to make a dog shape, Participant 2 showed Participant 3, and so on until the end of the chain. Objective Performance was scored as the number of puzzle pieces in the correct location; self-assessment was measured on a 100-point scale, and the similarity of this self-assessment was calculated by comparing it to Objective Performance. Analyses indicated no difference in the amount of information transmitted between autistic, non-autistic, or mixed chains, or in self-assessment ratings and the similarity of these. Both autistic and non-autistic participants shared information with others and evaluated their performance similarly, aligning with previous work on the transmission of verbal information. However, the predicted breakdown in information sharing in the mixed chains did not occur. It is possible that a mismatch in neurotype may not impact information transmission that is less-verbal and more visuospatial. The heterogeneity of the sample may also have overshadowed any effect of neurotype.
Exploring lithium-ion diffusion and electronic properties in defective graphite via molecular dynamics and density functional theory
The thermodynamic, kinetic, and mechanical properties of graphite anodes significantly influence the performance of lithium-ion batteries. Molecular dynamics simulations and density functional theory calculations were employed to examine the effects of defects in graphite on these properties. In particular, the influence of three types of defects—Stone–Wales (SW), single vacancy (SV), and double vacancy (DV)—at defect densities below 0.4% was analyzed, including their impact on graphite density, charge transfer, voltage, lithium-ion diffusion, and mechanical stability. The results show that defects in graphite form bridge, ylide, and spiro configurations, with structural stability decreasing in the order of SV > SW > DV. As defect density increases, the lithium-ion diffusion coefficient decreases significantly from 4.71 × 10−8 to 3.75 × 10−11 Å2/ps as lithium concentration increases from Li0.02C6 to LiC6. In contrast, for Li0.02C6, the diffusion coefficient rises with increasing defect density, from 2.94 × 10−9 to 1.29 × 10−9 Å2/ps. Mechanical analysis reveals that increasing defect density reduces Young’s modulus from 936.49 to 743.54 GPa and ultimate tensile strength from 94.59 to 58.50 GPa, highlighting the detrimental effect of defects on graphite's mechanical stability. Defects introduce localized electronic states within the bandgap, promoting lithium-ion diffusion at higher concentrations and disrupting the graphite structure to create new diffusion paths. These findings underscore the critical role of defect engineering in optimizing graphite anode performance and provide insights for the design of high-performance anode materials.
PTPRC is an immunotherapeutic predictor and serum biomarker in lung adenocarcinoma correlated with immune cell infiltration
Factors associated with stroke recurrence and mortality in ischemic and haemorrhagic stroke: Protocol for a systematic review and meta-analysis
Background and objectives Stroke is one of the leading causes of death and disability worldwide. People with stroke face a significant risk of recurrence, however, there is a lack of consensus on the risk factors for stroke recurrence. Previous systematic reviews in this area are either outdated, focus exclusively on clinical risk factors, or are limited by geographical region, stroke subtype or age group. This review aims to systematically identify clinical and lifestyle risk factors associated with stroke recurrence and mortality in people with stroke. Methods A systematic search will be conducted in four electronic databases (PubMed, EMBASE, CINAHL and PsycINFO) and grey literature sources. Only prospective cohort studies that estimate the association between risk factors and stroke recurrence and/or mortality in adults with ischemic and haemorrhagic stroke will be included. The exposures of interest are clinical and lifestyle risk factors, including vascular and cardiac factors such as hypertension or atrial fibrillation, and behavioural factors such as physical activity, nutrition, or smoking. Two independent reviewers will conduct screening, data extraction, and risk of bias assessment using the ROBINS-E tool, while the GRADE approach will be used to evaluate the certainty of evidence. A meta-analysis using a random-effects model will be used to determine the overall effect for each exposure on stroke recurrence and/or mortality. However, if a meta-analysis is not justified, a narrative synthesis will instead be conducted. Discussion Recurrent strokes are associated with greater mortality and poorer functional prognosis than first-time events, imposing greater economic burden on healthcare services. This review will identify factors that increase one’s risk for recurrence, thereby informing the development and refinement of clinical guidance for secondary stroke prevention; a key priority for both those living with stroke and the wider health service.
Stern–Gerlach deflection of cryogenically cold polyatomic molecules in superfluid nanodroplets
Beam deflection is capable of providing valuable information about the magnetic moments of molecules and clusters and about the relaxation dynamics of their spins. However, observations have been hampered by magnetic couplings to excited vibrational and rotational states of polyatomic systems, which are challenging to control, characterize, and systematize. In this work, we carried out deflection measurements on superfluid helium nanodroplets doped with high-spin FeCl2 and CoCl2 molecules and their complexes. This enabled quantitative determination of the magnetic moments of molecules and clusters at extremely low, and fully defined, temperature of all of their degrees of freedom. The spin magnetic moments become thermalized and oriented along the applied field. Dimers and trimers are found to be antiferromagnetically ordered. The issue of rates and mechanisms of molecular spin relaxation within the cryogenic helium matrix is highlighted.
Quasiparticle interaction originating from Bogoliubov Fermi surfaces under pressure in 18%-S substituted FeSe studied via NMR
Abstract S-substituted FeSe superconductors in the tetragonal phase display several unique features among iron-based superconductors, particularly the presence of zero-energy excitations in the superconducting (SC) state. The recent concept of Bogoliubov Fermi surfaces (BFSs)—a theoretical model describing ultranodal states—has attracted considerable interest. Nuclear magnetic resonance (NMR) studies on FeSe1 − x S x (x = 0.18) have revealed an anomalous low-energy spin fluctuations deep in the SC state. The low-energy spin fluctuations are enhanced with decreasing temperature, supporting strong Bogoliubov quasiparticle interactions associated with BFSs. Here, we further investigate these correlation effects through 77Se-NMR measurements of FeSe1 − x S x (x = 0.18) under pressures up to 2.0 GPa and temperatures down to ~ 100 mK. The results demonstrate that the anomalous enhancement is suppressed but persists under pressure, implying that quasiparticle interactions become weak by applying pressure. Furthermore, spin fluctuations in the normal state exhibit different temperature dependence from those deep in the SC state, suggesting that the nesting properties of normal electrons differ from those of Bogoliubov quasiparticles. These findings are consistent with the theoretical model of BFSs with C 2 symmetry and strengthen evidence for Bogoliubov quasiparticle interactions, providing insights into the unconventional pairing state of this system.
Association between Endothelial Activation and Stress Index and mortality in diabetic nephropathy ICU patients: A retrospective cohort study
Background Diabetic nephropathy (DN) is a serious complication of diabetes mellitus, often leading to poor outcomes in critically ill patients. Endothelial Activation and Stress Index (EASIX), a marker of endothelial dysfunction and systemic stress, has been associated with adverse outcomes in various diseases, but its role in predicting mortality in DN patients remains unclear. Methods A retrospective cohort study was conducted using the MIMIC-IV database. A total of 1,260 critically ill DN patients were included and stratified into tertiles based on their EASIX scores. Kaplan-Meier survival analysis, Cox proportional hazard models, and restricted cubic spline regression were applied to evaluate the association between EASIX and 30- and 60-day all-cause mortality. Subgroup analyses were also performed to assess interactions with key patient characteristics. Results Patients with higher EASIX scores had significantly increased ICU and in-hospital mortality rates. Cox regression analyses revealed that EASIX was an independent predictor of mortality after adjusting for age, sex, and comorbidities (HR: 1.14; 95% CI: 1.03–1.26; p = 0.01). Kaplan-Meier analysis showed significantly worse survival rates in the highest EASIX tertile. Subgroup analysis showed that higher EASIX scores were still associated with short-term survival in patients with DN in the presence of older age, male gender, and severe complications. Conclusion Higher EASIX scores are associated with increased short-term mortality in critically ill DN patients, highlighting its value as a prognostic biomarker for risk stratification and personalized management. Further studies are needed to validate these findings and explore therapeutic interventions targeting endothelial dysfunction.