Machine learning and deep learning enabled age estimation on medial clavicle CT images.

The medial clavicle epiphysis is a crucial indicator for bone age estimation (BAE) after hand maturation. This study aimed to develop machine learning (ML) and deep learning (DL) models for BAE based on medial clavicle CT images and evaluate the performance on normal and variant clavicles. This study retrospectively collected 1049 patients (mean± SD: 22.50±4.34 years) and split them into normal training and test sets, and variant training and test sets. An additional 53 variant clavicles were incorporated into the variant test set. The development stages of normal MCE were used to build a linear model and support vector machine (SVM) for BAE. The CT slices of MCE were automatically segmented and used to train DL models for automated BAE. Comparisons were performed by linear versus ML versus DL, and normal versus variant clavicles. Mean absolute error (MAE) and classification accuracy was the primary parameter of comparison. For BAE, the SVM had the best MAE of 1.73 years, followed by the commonly-used CNNs (1.77-1.93 years), the linear model (1.94 years), and the hybrid neural network CoAt Net (2.01 years). In DL models, SE Net 18 was the best-performing DL model with similar results to SVM in the normal test set and achieved an MAE of 2.08 years in the external variant test. For age classification, all the models exhibit superior performance in the classification of 18-, 20-, 21-, and 22-year thresholds with limited value in the 16-year threshold. Both ML and DL models produce desirable performance in BAE based on medial clavicle CT.

Automated bone age assessment from knee joint by integrating deep learning and MRI-based radiomics.

Bone age assessment (BAA) is a crucial task in clinical, forensic, and athletic fields. Since traditional age estimation methods are suffered from potential radiation damage, this study aimed to develop and evaluate a deep learning radiomics method based on multiparametric knee MRI for noninvasive and automatic BAA. This retrospective study enrolled 598 patients (age range,10.00-29.99 years) who underwent MR examinations of the knee joint (T1/T2*/PD-weighted imaging). Three-dimensional convolutional neural networks (3D CNNs) were trained to extract and fuse multimodal and multiscale MRI radiomic features for age estimation and compared to traditional machine learning models based on hand-crafted features. The age estimation error was greater in individuals aged 25-30 years; thus, this method may not be suitable for individuals over 25 years old. In the test set aged 10-25 years (n = 95), the 3D CNN (a fusion of T1WI, T2*WI, and PDWI) demonstrated the lowest mean absolute error of 1.32 ± 1.01 years, which is higher than that of other MRI modalities and the hand-crafted models. In the classification for 12-, 14-, 16-, and 18- year thresholds, accuracies and the areas under the ROC curves were all over 0.91 and 0.96, which is similar to the manual methods. Visualization of important features showed that 3D CNN estimated age by focusing on the epiphyseal plates. The deep learning radiomics method enables non-invasive and automated BAA from multimodal knee MR images. The use of 3D CNN and MRI-based radiomics has the potential to assist radiologists or medicolegists in age estimation.

Ocular biomarkers of cognitive decline based on deep-learning retinal vessel segmentation.

BACKGROUND: The current literature shows a strong relationship between retinal neuronal and vascular alterations in dementia. The purpose of the study was to use NFN+ deep learning models to analyze retinal vessel characteristics for cognitive impairment (CI) recognition. METHODS: We included 908 participants from a community-based cohort followed for over 15 years (the prospective KaiLuan Study) who underwent brain magnetic resonance imaging (MRI) and fundus photography between 2021 and 2022. The cohort consisted of both cognitively healthy individuals (N = 417) and those with cognitive impairment (N = 491). We employed the NFN+ deep learning framework for retinal vessel segmentation and measurement. Associations between Retinal microvascular parameters (RMPs: central retinal arteriolar / venular equivalents, arteriole to venular ratio, fractal dimension) and CI were assessed by Pearson correlation. P < 0.05 was considered statistically significant. The correlation between the CI and RMPs were explored, then the correlation coefficients between CI and RMPs were analyzed. Random Forest nonlinear classification model was used to predict whether one having cognitive decline or not. The assessment criterion was the AUC value derived from the working characteristic curve. RESULTS: The fractal dimension (FD) and global vein width were significantly correlated with the CI (P < 0.05). Age (0.193), BMI (0.154), global vein width (0.106), retinal vessel FD (0.099), and CRAE (0.098) were the variables in this model that were ranked in order of feature importance. The AUC values of the model were 0.799. CONCLUSIONS: Establishment of a predictive model based on the extraction of vascular features from fundus images has a high recognizability and predictive power for cognitive function and can be used as a screening method for CI.

Comparison of Changes in Retinal Vascular Parameters and Density in Patients with Moyamoya Disease: A Retrospective Study.

INTRODUCTION: This study aimed to compare retinal vascular parameters and density in patients with moyamoya disease using the optical coherence tomography angiography. METHODS: This clinical trial totally enrolls 78 eyes from 39 participants, and all these patients with moyamoya disease (N = 13) are set as experimental group and participants with health who matched with age and gender are considered as the control group (N = 26). Then all these participants receive optical coherence tomography angiography detection. Participants' general data are collected and analyzed. Skeleton density (SD) value, vessel density (VD) value, fractal dimension (FD) value, vessel diameter index (VDI) value, foveal avascular zone (FAZ) value are analyzed. RESULTS: A total of 39 participants are included in this study. The SD value in the experimental group was significantly lower than that in control group (0.175 [0.166, 0.181] vs. 0.184 [0.175, 0.188], p = 0.017). Similarly, the VD value in the experimental group was significantly lower than that in the control group (0.333 [0.320, 0.350] vs. 0.354 [0.337, 0.364], p = 0.024). Additionally, the FD value in the experimental group was significantly lower than that in the control group (2.088 [2.083, 2.094] vs. 2.096 [2.090, 2.101], p = 0.022). As for the VDI and FAZ, VDI and FAZ values in the experimental group were lower than those in the control group, there was no significant difference in VDI and FAZ values between the two groups. CONCLUSIONS: Our study, using non-invasive and rapid OCTA imaging, confirmed decreased retinal vascular parameters and density in patients with moyamoya disease.

The novel amylase function of the carboxyl terminal domain of Amy63.

α-amylase plays a crucial role in regulating metabolism and health by hydrolyzing of starch and glycogen. Despite comprehensive studies of this classic enzyme spanning over a century, the function of its carboxyl terminal domain (CTD) with a conserved eight ß-strands is still not fully understood. Amy63, identified from a marine bacterium, was reported as a novel multifunctional enzyme with amylase, agarase and carrageenase activities. In this study, the crystal structure of Amy63 was determined at 1.8 Å resolution, revealing high conservation with some other amylases. Interestingly, the independent amylase activity of the carboxyl terminal domain of Amy63 (Amy63_CTD) was newly discovered by the plate-based assay and mass spectrometry. To date, the Amy63_CTD alone could be regarded as the smallest amylase subunit. Moreover, the significant amylase activity of Amy63_CTD was measured over a wide range of temperature and pH, with optimal activity at 60 °C and pH 7.5. The Small-angle X-ray scattering (SAXS) data showed that the high-order oligomeric assembly gradually formed with increasing concentration of Amy63_CTD, implying the novel catalytic mechanism as revealed by the assembly structure. Therefore, the discovery of the novel independent amylase activity of Amy63_CTD suggests a possible missing step or a new perspective in the complex catalytic process of Amy63 and other related α-amylases. This work may shed light on the design of nanozymes to process marine polysaccharides efficiently.

Small-Angle X-ray Scattering for PEGylated Liposomal Doxorubicin Drugs: An Analytical Model Comparison Study.

Liposomal delivery systems are recognized as efficient and safe platforms for chemotherapeutic agents, with doxorubicin-loaded liposomes being the most representative nanopharmaceuticals. Characterizing the structure of liposomal nanomedicines in high spatial and temporal resolution is critical to analyze and evaluate their stability and efficacy. Small-angle X-ray scattering (SAXS) is a powerful tool increasingly used to investigate liposomal delivery systems. In this study, we chose a Doxil-like PEGylated liposomal doxorubicin (PLD) as an example and characterized the liposomal drug structure using synchrotron SAXS. Classical analytical models, including the spherical-shell or flat-slab geometries with Gaussian or uniform electron density profiles, were used to model the internal structure of the liposomal membrane. A cylinder model was applied to fit the scattering from the drug crystal loaded in the liposomes. The high-resolution structures of the original drug, Caelyx, and a similar research drug prepared in our laboratory were characterized using these analytical models. The structural parameters of PLDs, including the thickness of the liposomal membrane and morphology of the drug crystal, were further compared. The results demonstrated that both spherical-shell and flat-slab geometries with Gaussian electron density distribution were suitable to elucidate the structural features of the liposomal membrane under a certain range of scattering vectors, while models with uniform electron density distribution exhibited poor fitting performance. This study highlights the technical features of SAXS, which provides structural information at the nanoscale for liposomal drugs. The demonstrated methods are reliable and easy-to-use for the structural analysis of liposomal drugs, which are helpful for a broader application of SAXS in the production and regulation of nanopharmaceuticals.

Deep learning enables automatic adult age estimation based on CT reconstruction images of the costal cartilage.

OBJECTIVE: Adult age estimation (AAE) is a challenging task. Deep learning (DL) could be a supportive tool. This study aimed to develop DL models for AAE based on CT images and compare their performance to the manual visual scoring method. METHODS: Chest CT were reconstructed using volume rendering (VR) and maximum intensity projection (MIP) separately. Retrospective data of 2500 patients aged 20.00-69.99 years were obtained. The cohort was split into training (80%) and validation (20%) sets. Additional independent data from 200 patients were used as the test set and external validation set. Different modality DL models were developed accordingly. Comparisons were hierarchically performed by VR versus MIP, single-modality versus multi-modality, and DL versus manual method. Mean absolute error (MAE) was the primary parameter of comparison. RESULTS: A total of 2700 patients (mean age = 45.24 years ± 14.03 [SD]) were evaluated. Of single-modality models, MAEs yielded by VR were lower than MIP. Multi-modality models generally yielded lower MAEs than the optimal single-modality model. The best-performing multi-modality model obtained the lowest MAEs of 3.78 in males and 3.40 in females. On the test set, DL achieved MAEs of 3.78 in males and 3.92 in females, which were far better than the MAEs of 8.90 and 6.42 respectively, for the manual method. For the external validation, MAEs were 6.05 in males and 6.68 in females for DL, and 6.93 and 8.28 for the manual method. CONCLUSIONS: DL demonstrated better performance than the manual method in AAE based on CT reconstruction of the costal cartilage. CLINICAL RELEVANCE STATEMENT: Aging leads to diseases, functional performance deterioration, and both physical and physiological damage over time. Accurate AAE may aid in diagnosing the personalization of aging processes. KEY POINTS: • VR-based DL models outperformed MIP-based models with lower MAEs and higher R2 values. • All multi-modality DL models showed better performance than single-modality models in adult age estimation. • DL models achieved a better performance than expert assessments.

The tetrameric assembly of 2-aminomuconic 6-semialdehyde dehydrogenase is a functional requirement of cofactor NAD+ binding.

The bacterium Pseudomonas sp. AP-3 is able to use the environmental pollutant 2-aminophenol as its sole source of carbon, nitrogen, and energy. Eight genes (amnA, B, C, D, E, F, G, and H) encoding 2-aminophenol metabolizing enzymes are clustered into a single operon. 2-Aminomuconic 6-semialdehyde dehydrogenase (AmnC), a member of the aldehyde dehydrogenase (ALDH) superfamily, is responsible for oxidizing 2-aminomuconic 6-semialdehyde to 2-aminomuconate. In contrast to many other members of the ALDH superfamily, the structural basis of the catalytic activity of AmnC remains elusive. Here, we present the crystal structure of AmnC, which displays a homotetrameric quaternary assembly that is directly involved in its enzymatic activity. The tetrameric state of AmnC in solution was also presented using small-angle X-ray scattering. The tetramerization of AmnC is mediated by the assembly of a protruding hydrophobic beta-strand motif and residues V121 and S123 located in the NAD+ -binding domain of each subunit. Dimeric mutants of AmnC dramatically lose NAD+ binding affinity and failed to oxidize the substrate analogue 2-hydroxymuconate-6-semialdehyde to α-hydroxymuconic acid, indicating that tetrameric assembly of AmnC is functional requirement.

Forensic age prediction and age classification for critical age thresholds via 3.0T magnetic resonance imaging of the knee in the Chinese Han population.

OBJECTIVES: To assess the performance of knee MRI for forensic age prediction and classification for 12-, 14-, 16-, and 18-year thresholds. METHODS: The ossification stages of distal femoral epiphyses and proximal tibial epiphyses were assessed using an integrated staging system by Schmeling et al. and Kellinghaus et al. for knee 3.0T MRI with T1-weighted turbo spin-echo (T1-TSE) in sagittal orientation among 852 Chinese Han individuals (483 males and 369 females) aged 7-30 years. Regression models for age prediction were constructed and their performances were evaluated based on mean absolute deviation (MAD) values. In addition, the performances of age classification were assessed using receiver operating characteristic (ROC) analyses. RESULTS: The intra- and inter-observer agreement levels were very good (κ > 0.80). The complete fusion of those two types of epiphyses took place before 18.0 years in our study participants. The minimum MAD values were 2.51 years (distal femur) and 2.69 years (proximal tibia) in males, and 2.75 years (distal femur) and 2.87 years (proximal tibia) in females. The specificity values of constructed prediction models were all above 90% for the 12-, 14-, and 16-year thresholds, compared to the 74.8-84.6% for the 18-year threshold. Better performances of age prediction and classification were observed in males by distal femoral epiphyses. CONCLUSIONS: Ossification stages via 3.0T MRI of the knee with T1-TSE sequence using an integrated staging system could be a reliable noninvasive method for age prediction or for age classification for 12-, 14-, and 16-year thresholds, especially in males by distal femoral epiphyses. However, assessments based on the full bony fusion of the distal femoral epiphysis and proximal tibial epiphysis seemed not reliable for age classification for the 18-year threshold in the Chinese Han population.

Clinicopathological study of the polypoidal lesions of polypoidal choroidal vasculopathy.

PURPOSE: To investigate the pathogenic features of the polypoidal lesions from the specimens of polypoidal choroidal vasculopathy extracted from human subjects. METHODS: Seven specimens of polypoidal lesions extracted from five eyes of six patients (mean age, 60.16 ± 10.41 years) of polypoidal choroidal vasculopathy were examined. The polypoidal lesions were obtained by surgical excision. Thereafter, a histopathological analysis of the specimens was performed. RESULTS: The polypoidal lesions were oval nodules located underneath the retinal pigment epithelium. A pathological study of the lesions revealed that Bruch's membrane schisis was observed in all specimens and they were all located in the Bruch's membrane. The Bruch's membrane schisis and serosanguineous materials constituted the main structure of the lesions in five of the seven specimens, with small vessels being observed in two specimens. One specimen was composed of two polypoidal lesions of different characteristics, and one specimen had a neovessel membrane complex with several polypoidal lesions. Inflammatory cells and blood vessels were observed in the polypoidal lesion of the specimen with neovessel membrane complex. CONCLUSION: Polypoidal lesions of polypoidal choroidal vasculopathy are abnormalities of the Bruch's membrane. The lesions are characterized by the Bruch's membrane schisis, which is filled with serosanguineous materials. The lesions are progressive and may contain inflammatory cells and blood vessels.

The Second Class of Tetrahydrofolate (THF-II) Riboswitches Recognizes the Tetrahydrofolic Acid Ligand via Local Conformation Changes.

Riboswitches are regulatory noncoding RNAs found in bacteria, fungi and plants, that modulate gene expressions through structural changes in response to ligand binding. Understanding how ligands interact with riboswitches in solution can shed light on the molecular mechanisms of this ancient regulators. Previous studies showed that riboswitches undergo global conformation changes in response to ligand binding to relay information. Here, we report conformation switching models of the recently discovered tetrahydrofolic acid-responsive second class of tetrahydrofolate (THF-II) riboswitches in response to ligand binding. Using a combination of selective 2'-hydroxyl acylation, analyzed by primer extension (SHAPE) assay, 3D modeling and small-angle X-ray scattering (SAXS), we found that the ligand specifically recognizes and reshapes the THF-II riboswitch loop regions, but does not affect the stability of the P3 helix. Our results show that the THF-II riboswitch undergoes only local conformation changes in response to ligand binding, rearranging the Loop1-P3-Loop2 region and rotating Loop1 from a ~120° angle to a ~75° angle. This distinct conformation changes suggest a unique regulatory mechanism of the THF-II riboswitch, previously unseen in other riboswitches. Our findings may contribute to the fields of RNA sensors and drug design.

Bright and Efficient Sensitized Near-Infrared Photoluminescence from an Organic Neodymium-Containing Composite Material System.

Intense organic neodymium (Nd3+) emission is obtained with near-infrared (NIR) emission equivalent in intensity to that of an organic semiconductor emitting material. The advantage of Nd3+ emission is its narrow line width and NIR emission, which is enhanced by ∼3000 times at low excitation power through an efficient sensitization effect from a composite organic sensitizer. This performance is optimized at high concentrations of Nd3+ ions, and the organic perfluorinated system provides the ion excitations with a quantum efficiency of ∼40%. The material system is applicable to thin films that are compatible with integrated optics applications.

ATP/ADP modulates gp16-pRNA conformational change in the Phi29 DNA packaging motor.

Packaging of phage phi29 genome requires the ATPase gp16 and prohead RNA (pRNA). The highly conserved pRNA forms the interface between the connector complex and gp16. Understanding how pRNA interacts with gp16 under packaging conditions can shed light on the molecular mechanism of the packaging motor. Here, we present 3D models of the pRNA-gp16 complex and its conformation change in response to ATP or ADP binding. Using a combination of crystallography, small angle X-ray scattering and chemical probing, we find that the pRNA and gp16 forms a 'Z'-shaped complex, with gp16 specifically binds to pRNA domain II. The whole complex closes in the presence of ATP, and pRNA domain II rotates open as ATP hydrolyzes, before resetting after ADP is released. Our results suggest that pRNA domain II actively participates in the packaging process.

Biochemical characterization of SARS-CoV-2 nucleocapsid protein.

The nucleocapsid (N) protein is an important antigen for coronavirus, which participate in RNA package and virus particle release. In this study, we expressed the N protein of SARS-CoV-2 and characterized its biochemical properties. Static light scattering, size exclusive chromatography, and small-angle X-ray scattering (SAXS) showed that the purified N protein is largely a dimer in solution. CD spectra showed that it has a high percentage of disordered region at room temperature while it was best structured at 55 °C, suggesting its structural dynamics. Fluorescence polarization assay showed it has non-specific nucleic acid binding capability, which raised a concern in using it as a diagnostic marker. Immunoblot assays confirmed the presence of IgA, IgM and IgG antibodies against N antigen in COVID-19 infection patients' sera, proving the importance of this antigen in host immunity and diagnostics.

Association between Prediabetes and Renal Dysfunction from a Community-based Prospective Study.

Objective: Our study aimed to evaluate the association between prediabetes and renal dysfunction, and further assess which of glycemic indices of fasting plasma glucose (FPG), postprandial plasma glucose (PPG) and hemoglobin A1c (HbA1c) has a higher risk of renal dysfunction. Methods: This was a community-based prospective cohort study, which included 7015 participants from Beijing and Taian between May and October in 2015. The outcome was the renal dysfunction defined as estimated glomerular filtration rate (eGFR)<60 mL/min/1.73 m2. Univariate and multivariate logistic regression model was performed, and calculated the odds ratio (OR) and 95% confidence interval (95%CI) of renal dysfunction. Receiver operating curve (ROC) analysis was used to predict renal dysfunction for glycemic indices. Results: 121 renal dysfunction cases were identified. We found that the adjusted ORs (95%CI) of renal dysfunction were 1.72 (1.11-2.38), 1.48 (1.09-1.93), 1.97 (1.27-2.89) and 1.35 (1.07-2.13), respectively, for those with prediabetes, impaired fasting glucose (IFG), impaired glucose tolerance (IGT) and elevated HbA1c, compared with individuals with normal glucose tolerance. And IGT presented a higher risk of renal dysfunction than other glycemic indices. The similar results were obtained by performing the subgroup analysis. ROC analysis revealed the PPG had a higher predictive value for renal dysfunction. Conclusion: We found prediabetes was positively associated with the risk of renal dysfunction and PPG had a higher risk and predictive value of renal dysfunction than other glycemic indices of FPG and HbA1c.

Structure-function analyses reveal the molecular architecture and neutralization mechanism of a bacterial HEPN-MNT toxin-antitoxin system.

Toxin-antitoxin (TA) loci in bacteria are small genetic modules that regulate various cellular activities, including cell growth and death. The two-gene module encoding a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain and a cognate MNT (minimal nucleotidyltransferase) domain have been predicted to represent a novel type II TA system prevalent in archaea and bacteria. However, the neutralization mechanism and cellular targets of the TA family remain unclear. The toxin SO_3166 having a HEPN domain and its cognate antitoxin SO_3165 with an MNT domain constitute a typical type II TA system that regulates cell motility and confers plasmid stability in the bacterium Shewanella oneidensis Here, we report the crystal structure and solution conformation of the SO_3166-SO_3165 pair, representing the first complex structures in this TA family. The structures revealed that SO_3165 and SO_3166 form a tight heterooctamer (at a 2:6 ratio), an organization that is very rare in other TA systems. We also observed that SO_3166 dimerization enables the formation of a deep cleft at the HEPN-domain interface harboring a composite RX4-6H active site that functions as an RNA-cleaving RNase. SO_3165 bound SO_3166 mainly through its two α-helices (α2 and α4), functioning as molecular recognition elements. Moreover, their insertion into the SO_3166 cleft sterically blocked the RX4-6H site or narrowed the cleft to inhibit RNA substrate binding. Structure-based mutagenesis confirmed the important roles of these α-helices in SO_3166 binding and inhibition. Our structure-function analysis provides first insights into the neutralization mechanism of the HEPN-MNT TA family.

Molecular-Barrier-Enhanced Aromatic Fluorophores in Cocrystals with Unity Quantum Efficiency.

Singlet-triplet conversion in organic light-emitting materials introduces non-emissive (dark) and long-lived triplet states, which represents a significant challenge in constraining the optical properties. There have been considerable attempts at separating singlets and triplets in long-chain polymers, scavenging triplets, and quenching triplets with heavy metals; nonetheless, such triplet-induced loss cannot be fully eliminated. Herein, a new strategy of crafting a periodic molecular barrier into the π-conjugated matrices of organic aromatic fluorophores is reported. The molecular barriers effectively block the singlet-to-triplet pathway, resulting in near-unity photoluminescence quantum efficiency (PLQE) of the organic fluorophores. The transient optical spectroscopy measurements confirm the absence of the triplet absorption. These studies provide a general approach to preventing the formation of dark triplet states in organic semiconductors and bring new opportunities for the development of advanced organic optics and photonics.

Surfactant 1-Hexadecyl-3-methylimidazolium Chloride Can Convert One-Dimensional Viologen Bromoplumbate into Zero-Dimensional.

A zero-dimensional N,N'-dibutyl-4,4'-dipyridinium bromoplumbate, [BV]6[Pb9Br30], with unusual discrete [Pb9Br30]12- anionic clusters was prepared via a facile surfactant-mediated solvothermal process. This bromoplumbate exhibits a narrower optical band gap relative to the congeneric one-dimensional viologen bromoplumbates.

Self-Healing Behavior in a Thermo-Mechanically Responsive Cocrystal during a Reversible Phase Transition.

The molecular-level motions of a coronene-based supramolecular rotator are amplified into macroscopic changes of crystals by co-assembly of coronene and TCNB (1,2,4,5-tetracyanobenzene) into a charge-transfer complex. The as-prepared cocrystals show remarkable self-healing behavior and thermo-mechanical responses during thermally-induced reversible single-crystal-to-single-crystal (SCSC) phase transitions. Comprehensive analysis of the microscopic observations as well as differential scanning calorimetry (DSC) measurements and crystal habits reveal that a thermally-reduced-rate-dependent dynamic character exists in the phase transition. The crystallographic studies show that the global similarity of the packing patterns of both phases with local differences, such as molecular stacking sequence and orientations, should be the origin of the self-healing behavior of these crystals.