Deep learning-based bronchial tree-guided semi-automatic segmentation of pulmonary segments in computed tomography images.

Background: Pulmonary segments are valuable because they can provide more precise localization and intricate details of lung cancer than lung lobes. With advances in precision therapy, there is an increasing demand for the identification and visualization of pulmonary segments in computed tomography (CT) images to aid in the precise treatment of lung cancer. This study aimed to integrate multiple deep-learning models to accurately segment pulmonary segments in CT images using a bronchial tree (BT)-based approach. Methods: The proposed segmentation method for pulmonary segments using the BT-based approach comprised the following five essential steps: (I) segmentation of the lung using a U-Net (R231) (public access) model; (II) segmentation of the lobes using a V-Net (self-developed) model; (III) segmentation of the airway using a combination of a differential geometric approach method and a BronchiNet (public access) model; (IV) labeling of the BT branches based on anatomical position; and (V) segmentation of the pulmonary segments based on the distance of each voxel to the labeled BT branches. This five-step process was applied to 14 high-resolution breath-hold CT images and compared against manual segmentations for evaluation. Results: For the lung segmentation, the lung mask had a mean dice similarity coefficient (DSC) of 0.98±0.03. For the lobe segmentation, the V-Net model had a mean DSC of 0.94±0.06. For the airway segmentation, the average total length of the segmented airway trees per image scan was 1,902.8±502.1 mm, and the average number of the maximum airway tree generations was 8.5±1.3. For the segmentation of the pulmonary segments, the proposed method had a DSC of 0.73±0.11 and a mean surface distance of 6.1±2.9 mm. Conclusions: This study demonstrated the feasibility of combining multiple deep-learning models for the auxiliary segmentation of pulmonary segments on CT images using a BT-based approach. The results highlighted the potential of the BT-based method for the semi-automatic segmentation of the pulmonary segment.

The correlation between medial pattern of intracranial arterial calcification and white matter hyperintensities.

BACKGROUND AND AIMS: Despite reported correlations between intracranial arterial calcification (IAC) and white matter hyperintensities (WMH), little is known about the relationship between IAC pattern and WMH. By differentiating intimal and medial IAC, we aimed to investigate the relationship between IAC pattern and WMH. METHODS: Consecutive acute stroke patients were included. IAC pattern was categorized as intimal or medial on plain brain CT. The number of cerebral arteries involved by IAC for each patient was recorded. IAC severity was defined as focal or diffuse. On brain MRI, the burden of WMH was visually graded and classified as absent mild, moderate and severe. Multiple logistic regression was performed to examine the relationship between IAC and WMH. RESULTS: Among 265 patients, intimal IAC was detected in 54.7% patients and medial IAC in 48.5% patients. Diffuse IAC was present in 27.9% patients, all of which were medial. WMH was found in 75.5% patients, including 39.6% patients with mild WMH, 26.0% with moderate WMH, and 9.8% with severe WMH. The severity of medial IAC was correlated with WMH occurrence (p < 0.001). Chi-square linear trend suggested the number of arteries involved by medial IAC (p < 0.001) and the severity of medial IAC (p < 0.001) were correlated with WMH burden. Multiple ordinal logistic regression demonstrated a positive correlation of WMH burden with the number of arteries involved by medial IAC (p < 0.001) and the severity of medial IAC (p < 0.001). CONCLUSIONS: Medial IAC was correlated with WMH. The dose-effect relationship between medial IAC and WMH suggests underlying shared mechanisms of intracranial large artery disease and small vessel disease.

Chloroplast Genome Structure and Phylogenetic Analysis of 13 Lamiaceae Plants in Tibet.

BACKGROUND: The chloroplast (cp) genome has unique and highly conserved characteristics and is therefore widely used in species identification and classification, as well as to improve the in-depth understanding of plant evolution. METHODS: In this study, the cp genomes of 13 Lamiaceae plants in the Tibet Autonomous Region of China were sequenced, assembled and annotated using bioinformatics methods. Phylogenetic trees were constructed to reveal the phylogenetic relationship of related species in the Lamiaceae. RESULTS: The results showed that all 13 cp genomes had a typical four-segment structure, including one large single-copy (LSC) region, one pair of inverted repeat (IR) regions and one small single-copy (SSC) region. The sequence lengths of the 13 cp genomes were between 149,081 bp and 152,312 bp, and the average GC content was 37.6%. These genomes contained 131-133 annotated genes, including 86-88 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. A total of 542 SSR loci were detected using MISA software. The repeat types were mostly single-nucleotide repeats, accounting for 61% of simple repeats. A total of 26,328-26,887 codons were detected in 13 cp genomes. According to the RSCU value analysis, the codons mostly ended with A/T. Analysis of IR boundaries showed that the other species were relatively conserved, except for Nepeta laevigata (D. Don) Hand.-Mazz., which differed in gene type and location on both sides of the boundary. By analysing nucleotide diversity, two highly mutated regions located in the LSC and SSC regions were identified in the 13 cp genomes. CONCLUSIONS: Using the cp genome of Lycium ruthenicum Murray as the outgroup, 97 cp genomes of the Lamiaceae were used to construct an Maximum Likehood (ML) phylogenetic tree, in which these species were divided into eight major clades, corresponding to eight subfamilies based on morphological classification. The phylogenetic results based on monophyletic relationships were consistent with the morphological classification status at the tribe level.

Multimodal Data Integration to Predict Severe Acute Oral Mucositis of Nasopharyngeal Carcinoma Patients Following Radiation Therapy.

(1) Background: Acute oral mucositis is the most common side effect for nasopharyngeal carcinoma patients receiving radiotherapy. Improper or delayed intervention to severe AOM could degrade the quality of life or survival for NPC patients. An effective prediction method for severe AOM is needed for the individualized management of NPC patients in the era of personalized medicine. (2) Methods: A total of 242 biopsy-proven NPC patients were retrospectively recruited in this study. Radiomics features were extracted from contrast-enhanced CT (CECT), contrast-enhanced T1-weighted (cT1WI), and T2-weighted (T2WI) images in the primary tumor and tumor-related area. Dosiomics features were extracted from 2D or 3D dose-volume histograms (DVH). Multiple models were established with single and integrated data. The dataset was randomized into training and test sets at a ratio of 7:3 with 10-fold cross-validation. (3) Results: The best-performing model using Gaussian Naive Bayes (GNB) (mean validation AUC = 0.81 ± 0.10) was established with integrated radiomics and dosiomics data. The GNB radiomics and dosiomics models yielded mean validation AUC of 0.6 ± 0.20 and 0.69 ± 0.14, respectively. (4) Conclusions: Integrating radiomics and dosiomics data from the primary tumor area could generate the best-performing model for severe AOM prediction.

Integrated transcriptomic and metabolomic analyses revealed the molecular mechanism of terpenoid formation for salicylic acid resistance in Pulsatilla chinensis callus.

As a kind of traditional Chinese medicine, Pulsatilla chinensis (Bunge) Regel is well known for its anti-inflammation and anti-cancer activities, which are attributed to its active components including total saponins and monomers. To clarify the synthesis and metabolism mechanisms of class components in callus terpenes of P. chinensis, a certain concentration of salicylic acid (SA) hormone elicitor was added to the callus before being analysed by transcriptomic and metabolomic techniques. Results showed that the content of Pulsatilla saponin B4 in the callus suspension culture was significantly increased up to 1.99% with the addition of SA. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the differentially expressed genes were mainly enriched in 122 metabolic pathways, such as terpenoid metabolism-related pathways: terpenoid skeleton synthesis pathway, monoterpenoid biosynthesis pathways, diterpenoid biosynthesis pathways, and ubiquinone and other terpenoid-quinone biosynthesis pathways. A total of 31 differentially accumulated metabolites were obtained from four differential groups. Amongst 21 kinds of known chemical components in P. chinensis, deoxyloganic acid was the only monoterpenoid; the others are triterpenoids. In summary, this study found that SA elicitors can affect the metabolic changes of terpenoids in P. chinensis callus, which provided a basis for analysing the genetic regulation of terpenoid components of leucons.

Validation of the Meta-Analysis Global Group in Chronic Heart Failure risk score for the prediction of 1-year mortality in a Chinese cohort.

BACKGROUND: The Meta-Analysis Global Group in Chronic Heart Failure (MAGGIC) risk score was developed in 2013 to predict survival in heart failure (HF) patients. However, it has yet to be validated in a Chinese population. Our study aimed to investigate the ability of the score to predict 1-year mortality in a Chinese population. METHODS: Consecutive patients with HF were retrospectively selected from the inpatient electronic medical records of the cardiology department in a regional hospital in China. A total integer score was calculated for each enrolled patient based on the value of each risk factor in the MAGGIC scoring system. Each enrolled patient was followed for at least 1 year. The observational endpoint of this study was all-cause mortality. The predictive ability of the MAGGIC score was assessed by comparing observed and predicted mortality within 1 year. RESULTS: Between January 2018 and December 2020, a total of 635 patients were included in the study: 57 (9.0%) of whom died within 1 year after discharge. The average age of all patients was 74.6 ±â€Š11.2 years, 264 of them (41.6%) were male, and the average left ventricular ejection fraction was 50.7% ±â€Š13.2%. The area under the receiver operating characteristic curve was 0.840 (95% confidence interval: 0.779, 0.901), which indicated a fair discriminatory ability of the score. The Hosmer-Lemeshow test result ( χ2  = 12.902, degree of freedom = 8, P   =  0.115) indicated that the MAGGIC score had good calibration. The decision curve analysis showed that the MAGGIC score yielded a good clinical net benefit and net reduction in interventions. CONCLUSIONS: This validation of the MAGGIC score showed that it has a good ability to predict 1-year mortality in Chinese patients with HF after discharge. Due to regional and inter-hospital differences, external validation studies need to be further confirmed in other centers.

Role of skeletal macrophages in fracture repair: A systematic review.

In the field of bone research, the importance of the function of skeletal macrophages (sMΦ) and their crucial role in immune homeostasis and bone regeneration has been extensively studied. The aim of the present systematic review was to summarize the role of sMΦ in bone fracture healing and to evaluate their potential for immunoregulatory therapy in bone regeneration. A systematic literature search of PubMed and Embase® was performed to retrieve studies on the role of sMΦ in bone injury repair. The Systematic Review Centre for Laboratory animal Experimentation tool was used to assess the risk of bias of the studies included. A total of four articles were included in the present review. A relatively high risk of bias was identified in the included articles as none of the assessors in these studies were blinded. sMΦ were defined by the surface markers F4/80+, Mac-2- / low, TRAP-, CD169+, Ly6G- and CD115low. All of the studies provided support for the essential role of sMΦ in intramembranous ossification or endochondral ossification during fracture healing. F4/80+Mac-2-CD169+ sMΦ are a promising therapeutic target for immunoregulatory therapy of bone repair due to their essential role in bone formation and homeostasis. Future studies aimed at profiling and modulating sMΦ to promote bone regeneration are required.

Mitochondria-targeted aggregation-induced emission active near infrared fluorescent probe for real-time imaging.

Mitochondria are essential organelles in eukaryotic cells and act as the energy powerhouse and biosynthetic compartment. Fluorescent dyes are widely used powerful molecular tools for analytical sensing and optical imaging. Low photostability, short excitation and emission wavelengths, and aggregation-induced quenching effects restrict the application of traditional commercial mitochondrial fluorescent probes for bioimaging. In this study, using rhodamine as the acceptor and phenothiazine as the donor, we synthesized a novel mitochondrial-targeted near infrared (NIR) fluorescent probe, MIT-PZR. Due to low cytotoxicity, great photostability and high specificity for mitochondria targeting, MIT-PZR has enormous potential for cell imaging. Furthermore, with a sizeable Stokes shift (emission peak at 705 nm), MIT-PZR penetrated tissues providing stable red fluorescence for imaging in vivo. The histological assessment of various tissues after treatment with MIT-PZR indicated that it has good biocompatibility. Thus, MIT-PZR is a promising mitochondrial NIR fluorescent probe for future application in clinical diagnosis and modern biological research.

A Novel Kunitzin-Like Trypsin Inhibitor Isolated from Defensive Skin Secretion of Odorrana versabilis.

Protease inhibitors that were identified from amphibian skin secretions with low molecular weights and potent inhibitory activity were thought to be potential candidates for novel peptide drugs. Here, a novel peptide with trypsin inhibitory activity was found in the skin secretion of the Chinese bamboo leaf odorous frog, Odorrana versabilis. Based on the sequence alignments of sequencing results, the novel peptide (ALKYPFRCKAAFC) was named as Kunitzin-OV. The synthetic replicate of Kunitzin-OV was subjected to a series of functional assays, and it exhibited a trypsin inhibitory activity with a Ki value of 3.042 µM, whereas, when Lys-9 at P1 position was substituted by Phe, trypsin inhibitory activity was undetected and the chymotrypsin inhibitory activity was optimized with a Ki value of 2.874 µM. However, its protease-binding loop was catabolized by trypsin during the trypsin cleavage test. In conclusion, Kunizin-OV is a novel peptide with trypsin inhibitory activity as a member of kunitzins, which is a non-typical Kunitz-like trypsin inhibitor with a highly conserved reactive site (K-A) and quite a short sequence.