CLEAPA: a framework for exploring the conformational landscape of cryo-EM using energy-aware pathfinding algorithm.

MOTIVATION: Cryo-electron microscopy (cryo-EM) is a powerful technique for studying macromolecules and holds the potential for identifying kinetically preferred transition sequences between conformational states. Typically, these sequences are explored within two-dimensional energy landscapes. However, due to the complexity of biomolecules, representing conformational changes in two dimensions can be challenging. Recent advancements in reconstruction models have successfully extracted structural heterogeneity from cryo-EM images using higher-dimension latent space. Nonetheless, creating high-dimensional conformational landscapes in the latent space and then searching for preferred paths continues to be a formidable task. RESULTS: This study introduces an innovative framework for identifying preferred trajectories within high-dimensional conformational landscapes. Our method encompasses the search for the minimum energy path in the graph, where edge weights are determined based on the energy estimation at each node using local density. The effectiveness of this approach is demonstrated by identifying accurate transition states in both synthetic and real-world datasets featuring continuous conformational changes. AVAILABILITY AND IMPLEMENTATION: The CLEAPA package is available at https://github.com/tengyulin/energy_aware_pathfinding/.

Phosphorylation of sugar transporter TST2 by protein kinase CPK27 enhances drought tolerance in tomato.

Drought is a major environmental stress threatening plant growth and productivity. Calcium-dependent protein kinases (CPKs) are plant-specific Ca2+ sensors with multifaceted roles in signaling drought responses. Nonetheless, the mechanisms underpinning how CPKs transmit downstream drought signaling remain unresolved. Through genetic investigations, our study unveiled that knocking out CPK27 reduced drought tolerance in tomato (Solanum lycopersicum) plants and impaired abscisic acid (ABA)-orchestrated plant response to drought stress. Proteomics and phosphoproteomics revealed that CPK27-dependent drought-induced proteins were highly associated with the sugar metabolism pathway, which was further verified by reduced soluble sugar content in the cpk27 mutant under drought conditions. Using protein-protein interaction assays and phosphorylation assessments, we demonstrated that CPK27 directly interacted with and phosphorylated tonoplast sugar transporter 2 (TST2), promoting intercellular soluble sugar accumulation during drought stress. Furthermore, Ca2+ and ABA enhanced CPK27-mediated interaction and phosphorylation of TST2, thus revealing a role of TST2 in tomato plant drought tolerance. These findings extend the toolbox of potential interventions for enhancing plant drought stress tolerance and provide a target to improve drought tolerance by manipulating CPK27-mediated soluble sugar accumulation for rendering drought tolerance in a changing climate.

Nesprin proteins: bridging nuclear envelope dynamics to muscular dysfunction.

This review presents a comprehensive exploration of the pivotal role played by the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex, with a particular focus on Nesprin proteins, in cellular mechanics and the pathogenesis of muscular diseases. Distinguishing itself from prior works, the analysis delves deeply into the intricate interplay of the LINC complex, emphasizing its indispensable contribution to maintaining cellular structural integrity, especially in mechanically sensitive tissues such as cardiac and striated muscles. Additionally, the significant association between mutations in Nesprin proteins and the onset of Dilated Cardiomyopathy (DCM) and Emery-Dreifuss Muscular Dystrophy (EDMD) is highlighted, underscoring their pivotal role in disease pathogenesis. Through a comprehensive examination of DCM and EDMD cases, the review elucidates the disruptions in the LINC complex, nuclear morphology alterations, and muscular developmental disorders, thus emphasizing the essential function of an intact LINC complex in preserving muscle physiological functions. Moreover, the review provides novel insights into the implications of Nesprin mutations for cellular dynamics in the pathogenesis of muscular diseases, particularly in maintaining cardiac structural and functional integrity. Furthermore, advanced therapeutic strategies, including rectifying Nesprin gene mutations, controlling Nesprin protein expression, enhancing LINC complex functionality, and augmenting cardiac muscle cell function are proposed. By shedding light on the intricate molecular mechanisms underlying nuclear-cytoskeletal interactions, the review lays the groundwork for future research and therapeutic interventions aimed at addressing genetic muscle disorders.

Reduced atopic march risk in pediatric atopic dermatitis patients prescribed dupilumab versus conventional immunomodulatory therapy: A population-based cohort study.

BACKGROUND: Dupilumab effectively treats atopic dermatitis (AD); however, its role in halting the atopic march remains uncertain. OBJECTIVE: To investigate dupilumab's effect on atopic march in pediatric AD patients versus conventional immunomodulators. METHODS: This retrospective cohort study utilized data from the TriNetX US Collaborative Network (2011-2024). Pediatric AD patients (≤18 years) were categorized into DUPI-cohort (newly prescribed dupilumab) or CONV-cohort (prescribed conventional immunomodulators without dupilumab). After 1:1 propensity-score matching, we analyzed atopic march progression, defined by the incident asthma or allergic rhinitis (AR). Cumulative incidence was plotted using Kaplan-Meier, with risk assessment via Cox regression. RESULTS: The study included 2192 patients in each cohort. The 3-year cumulative incidence of atopic march progression was lower in the DUPI-cohort than the CONV-cohort (20.09% vs 27.22%; P < .001). The DUPI-cohort demonstrated significant risk reduction in atopic march progression (hazard ratio [HR] 0.68, 95% CI 0.55-0.83), individual asthma (HR 0.60, 0.45-0.81), and individual AR (HR 0.69, 0.54-0.88). Younger patients on dupilumab exhibited a greater risk reduction for atopic march progression and individual asthma, contrasting with the opposite age-related pattern for individual AR. LIMITATIONS: Observational study. CONCLUSION: Among pediatric AD patients, dupilumab was associated with reduced risk of atopic march progression compared with conventional therapies.

The Tumor Necrosis Factor-α Level in Platelet-Rich Plasma Might Be Associated with Treatment Outcome in Patients with Interstitial Cystitis/Bladder Pain Syndrome or Recurrent Urinary Tract Infection.

Using platelet-rich plasma (PRP) injections to treat urological diseases has attracted great attention. This study investigated the impact of cytokine concentrations in PRP on the treatment outcome of patients with recurrent urinary tract infection (rUTI) and interstitial cystitis/bladder pain syndrome (IC/BPS). Forty patients with IC/BPS and twenty-one patients with rUTI were enrolled for four-monthly repeated PRP injections. PRP was collected at the first injection and analyzed with multiplex immunoassays for 12 target cytokines. In patients with IC/BPS, a Global Response Assessment (GRA) score ≥ 2 was defined as a successful outcome. In rUTI patients, ≤2 episodes of UTI recurrence during one year of follow-up was considered a successful outcome. Nineteen (47.5%) patients with IC/BPS and eleven (52.4%) patients with rUTI had successful outcomes. The IC/BPS patients with successful outcomes had significantly lower levels of tumor necrosis factor-α (TNF-α) in their PRP than those with unsuccessful outcomes (p = 0.041). The rUTI patients with successful outcomes also had a lower level of TNF-α (p = 0.025) and a higher level of epidermal growth factor (p = 0.035) and transforming growth factor-ß2 (p = 0.024) in PRP than those with unsuccessful outcomes. A lower level of TNF-α in PRP might be a potentially predictive factor of treatment outcome.

Identification of Skin Lesions by Snapshot Hyperspectral Imaging.

This study pioneers the application of artificial intelligence (AI) and hyperspectral imaging (HSI) in the diagnosis of skin cancer lesions, particularly focusing on Mycosis fungoides (MF) and its differentiation from psoriasis (PsO) and atopic dermatitis (AD). By utilizing a comprehensive dataset of 1659 skin images, including cases of MF, PsO, AD, and normal skin, a novel multi-frame AI algorithm was used for computer-aided diagnosis. The automatic segmentation and classification of skin lesions were further explored using advanced techniques, such as U-Net Attention models and XGBoost algorithms, transforming images from the color space to the spectral domain. The potential of AI and HSI in dermatological diagnostics was underscored, offering a noninvasive, efficient, and accurate alternative to traditional methods. The findings are particularly crucial for early-stage invasive lesion detection in MF, showcasing the model's robust performance in segmenting and classifying lesions and its superior predictive accuracy validated through k-fold cross-validation. The model attained its optimal performance with a k-fold cross-validation value of 7, achieving a sensitivity of 90.72%, a specificity of 96.76%, an F1-score of 90.08%, and an ROC-AUC of 0.9351. This study marks a substantial advancement in dermatological diagnostics, thereby contributing significantly to the early and precise identification of skin malignancies and inflammatory conditions.

Assessing the Efficacy of the Spectrum-Aided Vision Enhancer (SAVE) to Detect Acral Lentiginous Melanoma, Melanoma In Situ, Nodular Melanoma, and Superficial Spreading Melanoma.

Skin cancer is the predominant form of cancer worldwide, including 75% of all cancer cases. This study aims to evaluate the effectiveness of the spectrum-aided visual enhancer (SAVE) in detecting skin cancer. This paper presents the development of a novel algorithm for snapshot hyperspectral conversion, capable of converting RGB images into hyperspectral images (HSI). The integration of band selection with HSI has facilitated the identification of a set of narrow band images (NBI) from the RGB images. This study utilizes various iterations of the You Only Look Once (YOLO) machine learning (ML) framework to assess the precision, recall, and mean average precision in the detection of skin cancer. YOLO is commonly preferred in medical diagnostics due to its real-time processing speed and accuracy, which are essential for delivering effective and efficient patient care. The precision, recall, and mean average precision (mAP) of the SAVE images show a notable enhancement in comparison to the RGB images. This work has the potential to greatly enhance the efficiency of skin cancer detection, as well as improve early detection rates and diagnostic accuracy. Consequently, it may lead to a reduction in both morbidity and mortality rates.

Life satisfaction components and all-cause and cause-specific mortality: A large prospective cohort study.

BACKGROUND: Which life satisfaction components could be a target of positive psychological interventions for longevity is largely unknown. We aimed to investigate association of the composite measure of life satisfaction and its individual components with mortality. METHODS: This cohort study included UK Biobank participants who responded to questions concerning five components of life satisfaction at baseline. We generated a composite score representing overall life satisfaction, ranging from 0 (lowest) to 5 (highest). The outcomes were all-cause and cause-specific mortality. We used multivariable Cox regression to estimate hazard ratios (HR) for the associations of interest. RESULTS: Among 165,842 eligible participants, 12,261 all-cause deaths were observed over a median of 12.9-year follow-up. Overall life satisfaction was inversely associated with all-cause mortality (adjusted HR 0.94 [95% CI: 0.93-0.95] per 1 score increment). Health satisfaction showed the strongest association with all-cause mortality, with a fully adjusted HR of 0.52 (95% CI: 0.49-0.55) for high/extreme satisfaction and 0.63 (95% CI: 0.59-0.66) for moderate satisfaction, compared with unsatisfaction (P-trend<0.001), independent of other satisfaction components, regardless of physical health and sociodemographics. The association for family, friendship, work and financial satisfaction was attenuated when adjusted for other life satisfaction components. Similar findings were observed for cause-specific mortality. LIMITATIONS: Observational study with single baseline measurement of life satisfaction precludes the ability to establish causal relationship. CONCLUSIONS: Higher overall life satisfaction was associated with lower mortality. As the major contributor to lower mortality regardless of physical health and sociodemographics, health satisfaction could be an important target of positive psychological interventions for longevity.

The Relationship between Muscle Ultrasound Parameters and Diabetic Peripheral Neuropathy among Patients with Type 2 Diabetes Mellitus: A Cross-Sectional Study.

Background: Muscle dysfunction is an early complication of diabetic peripheral neuropathy (DPN). As a convenient and low-cost tool, muscle ultrasound has been used to assess muscle quality and muscle mass. However, the relationship between different muscle ultrasound parameters and DPN is unclear. Objectives: This study was designed to investigate the relationship between ultrasound parameters of different muscles and DPN among patients with type 2 diabetes mellitus, including the rectus femoris (RF), tibialis anterior (TA), and medial head of gastrocnemius (MG). Materials and Methods: The research enrolled 90 patients with type 2 diabetes mellitus (T2DM). All images were attained from both sides. Muscle measurements contained muscle thickness (MT), cross-sectional area (CSA), echo intensity (EI), and corrected EI. The binary logistic regression and multiple linear regression were used to investigate the association between muscle ultrasound parameters and DPN or vibration perception threshold (VPT). Results: EI, corrected EI, MT of MG, and EI of TA were associated with DPN separately after adjusting other clinical variates. Among these muscle parameters, the EI of MG had a better predictive value (OR: 1.114, 95% CI: 1.039, 1.196) of DPN. Combined with CSA of RF, peripheral artery disease (PAD), and sex, the corrected EI of MG was associated with the vibration perception threshold (VPT) (standard ß = 0.242, p < 0.001), better than the EI of MG (standard ß = 0.215, p = 0.002). Conclusions: MG (MT, EI, and corrected EI) and TA (EI) were associated with DPN, respectively. CSA of RF and corrected EI or EI of MG combined with PAD and sex were associated with VPT significantly, which supported that muscle ultrasound might be a substantial quantitative tool for detecting the exercise benefits for DPN.