DPHL v.2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins.

A comprehensive pan-human spectral library is critical for biomarker discovery using mass spectrometry (MS)-based proteomics. DPHL v.1, a previous pan-human library built from 1,096 data-dependent acquisition (DDA) MS data of 16 human tissue types, allows quantifying of 10,943 proteins. Here, we generated DPHL v.2 from 1,608 DDA-MS data. The data included 586 DDA-MS data acquired from 18 tissue types, while 1,022 files were derived from DPHL v.1. DPHL v.2 thus comprises data from 24 sample types, including several cancer types (lung, breast, kidney, and prostate cancer, among others). We generated four variants of DPHL v.2 to include semi-tryptic peptides and protein isoforms. DPHL v.2 was then applied to two colorectal cancer cohorts. The numbers of identified and significantly dysregulated proteins increased by at least 21.7% and 14.2%, respectively, compared with DPHL v.1. Our findings show that the increased human proteome coverage of DPHL v.2 provides larger pools of potential protein biomarkers.

Precisely Tuning the Pore-Wall Surface Composition of Bioceramic Scaffolds Facilitates Angiogenesis and Orbital Bone Defect Repair.

Orbital bone damage (OBD) may result in severe post-traumatic enophthalmos, craniomaxillofacial deformities, vision loss, and intracranial infections. However, it is still a challenge to fabricate advanced biomaterials that can match the individual anatomical structure and enhance OBD repair in situ. Herein, we aimed to develop a selective surface modification strategy on bioceramic scaffolds and evaluated the effects of inorganic or organic functional coating on angiogenesis and osteogenesis, ectopically and orthotopically in OBD models. It was shown that the low thermal bioactive glass (BG) modification or layer-by-layer assembly of a biomimetic hydrogel (Biogel) could readily integrate into the pore wall of the bioceramic scaffolds. The BG and Biogel modification showed appreciable enhancement in the initial compressive strength (∼30-75%) or structural stability in vivo, respectively. BG modification could enhance by nearly 2-fold the vessel ingrowth, and the osteogenic capacity was also accelerated, accompanied with a mild scaffold biodegradation after 3 months. Meanwhile, the Biogel-modified scaffolds showed enhanced osteogenic differentiation and mineralization through calcium and phosphorus retention. The potential mechanism of the enhanced bone repair was elucidated via vascular and osteogenic cell responses in vitro, and the cell tests indicated that the Biogel and BG functional layers were both beneficial for in vitro osteoblastic differentiation and mineralization on bioceramics. Totally, these findings demonstrated that the bioactive ions or biomolecules could significantly improve the angiogenic and osteogenic capabilities of conventional bioceramics, and the integration of inorganic or organic functional coating in the pore wall is a highly flexible material toolbox that can be tailored directly to improve orbital bone defect repair.

Next-generation finely controlled graded porous antibacterial bioceramics for high-efficiency vascularization in orbital reconstruction.

Eyeball loss due to severe ocular trauma, intraocular malignancy or infection often requires surgical treatment called orbital implant reconstruction to rehabilitate the orbital volume and restore the aesthetic appearance. However, it remains a challenge to minimize the postoperative exposure and infection complications due to the inert nature of conventional orbital implants. Herein, we developed a novel Ca-Zn-silicate bioceramic implant with multi-functions to achieve the expected outcomes. The porous hardystonite (Ca2ZnSi2O7) scaffolds with triply periodic minimal surfaces (TPMS)-based pore architecture and graded pore size distribution from center to periphery (from 500 to 800 µm or vice versa) were fabricated through the digital light processing (DLP) technique, and the scaffolds with homogeneous pores (500 or 800 µm) were fabricated as control. The graded porous scaffolds exhibited a controlled bio-dissolving behavior and intermediate mechanical strength in comparison with the homogeneous counterparts, although all of porous implants presented significant antibacterial potential against S. aureus and E. coli. Meanwhile, the pore size-increasing scaffolds indicated more substantial cell adhesion, cell viability and angiogenesis-related gene expression in vitro. Furthermore, the gradually increasing pore feature exhibited a stronger blood vessel infiltrating potential in the dorsal muscle embedding model, and the spherical implants with such pore structure could achieve complete vascularization within 4 weeks in the eyeball enucleation rabbit models. Overall, our results suggested that the novel antibacterial hardystonite bioceramic with graded pore design has excellent potential as a next-generation orbital implant, and the pore topological features offer an opportunity for the improvement of biological performances in orbital reconstruction.

Clinicopathological analysis of 5146 eyelid tumours and tumour-like lesions in an eye centre in South China, 2000-2018: a retrospective cohort study.

OBJECTIVES: To describe the clinicopathological characteristics of patients with eyelid tumours and tumour-like lesions in South China, investigate possible factors affecting tumour constitution. DESIGN: Retrospective cohort study. SETTING: All patients diagnosed with eyelid tumours were included from a high-volume tertiary eye care centre from South China which caring for over 2000 patients per day. All biopsied specimens were reviewed by two senior pathologists and were classified according to the fourth edition of the WHO Classification of Skin Tumours. PARTICIPANT: A total of 5146 cases of eyelid lesions were reviewed from 2000 to 2018, being classified by histogenesis and pathologic diagnosis, being compared with data from previous literature containing different races. MAIN OUTCOME MEASURES: Age-specific and gender-specific incidence constitutions, time trends, tumour location, distribution in different age groups and relationship with Sociodmographic Index (SDI) were calculated. RESULTS: Benign tumours accounted for 85.08% (4378) of all cases, among which, nevus was most common (33.07%). Eight of top 10 benign lesions had higher occurrence in upper eyelids. The R² value of linear regression in patient annual number of benign lesions were 0.946 (p<0.01) for male and 0.914 (p<0.01) for female. More than 33.60% (1471/4378) were made up by patients younger than 40 years. The number of patients undergoing removal of benign lesions decreased with age. Among the malignant lesions, basal cell carcinoma (BCC) was most prevalent (48.70%), followed by sebaceous gland carcinoma (34.24%) and majority (81.8%) occurred in patients above 60 years. CONCLUSIONS: Over the past 19 years, most eyelid tumours occurred at our centre were benign lesions. The number of patients presenting with benign lesions increased in both genders, especially among young females who were more likely to request surgeries. Among malignant lesions, BCC remains the most common type, appears a higher incidence in countries with higher SDI.

Clinicopathological analysis of 719 pediatric and adolescents' ocular tumors and tumor-like lesions: a retrospective study from 2000 to 2018 in China.

AIM: To describe the clinicopathologic features and classification of pediatric and adolescent ocular tumors and tumor-like lesions. METHODS: A total of 719 cases of pathologically confirmed ocular tumors and tumor-like lesions in a pediatric population from two academic institutions over an 18-year period were retrospectively analyzed. The main outcome measures were the clinical and pathological features of the cases. RESULTS: Benign tumors accounted for 92.1% of all cases while malignant tumors accounted for 7.9%. The most common ocular benign tumors were (epi-)dermoid cysts (19.8%), nevi (15.2%), corneal dermoid tumors (9.8%), and calcified epitheliomas (8.8%). The most common ocular malignant tumors were retinoblastoma (80.8%), and rhabdomyosarcoma (3.9%). Eyelid and ocular surface tumors comprised 73.3% of benign tumors while intraocular and orbital cavity comprised 94.2% of malignant tumors. For tumor site, the upper eyelid was up to 1.79 times more than lower eyelid (P<0.05). Age at surgery and sex also had an association with different lesions (P=0.006, P=0.035, respectively). CONCLUSION: Most ocular tumors and tumor-like lesions in children and adolescents are benign. Pediatric ocular tumors are distinct from those in adults in terms of histological origin. (Epi-)dermoid cysts are the most common benign tumors while retinoblastomas the most common malignant tumors.

The prognostic landscape of adaptive immune resistance signatures and infiltrating immune cells in the tumor microenvironment of uveal melanoma.

Uveal melanoma (UM) is the most common primary intraocular malignancy in adults and has a high mortality rate. Tumor microenvironment (TME) is crucial in controlling and influencing the behavior of malignant tumors. Thus, illustrating the prognostic values of adaptive immune resistance signatures and infiltrating immune cells in the TME of UM may provide scientific rationales for immunotherapy. In this study, the gene expression data of 80 primary UM and 103 primary skin cutaneous melanoma (SKCM) samples with relevant clinical information were obtained from The Cancer Genome Atlas (TCGA) database. The TME was analyzed by the xCell, EPIC, ESTIMATE and TIMER algorithms. The relationships and prognostic values of immune infiltrates and mutated genes were further investigated. We found that primary UM and primary SKCM exhibited distinct TMEs. Higher levels of infiltrating stromal and immune cells in UM were related to more aggressive biology and poor prognosis. Increased CD8+ T cell level, as well as several adaptive immune resistance markers, was a predictive factor of poor prognosis in UM. Furthermore, some common mutations of UM were associated with its TME. This study analyzed the immune landscape of adaptive immune resistance signatures and infiltrating immune cells in the TME of UM. Identification of these immune-related biomarkers may thus enable the prediction of prognosis and the selection of optimal immunotherapy strategies in UM.

Automated identification of malignancy in whole-slide pathological images: identification of eyelid malignant melanoma in gigapixel pathological slides using deep learning.

BACKGROUND/AIMS: To develop a deep learning system (DLS) that can automatically detect malignant melanoma (MM) in the eyelid from histopathological sections with colossal information density. METHODS: Setting: Double institutional study. STUDY POPULATION: We retrospectively reviewed 225 230 pathological patches (small section cut from pathologist-labelled area from an H&E image), cut from 155 H&E-stained whole-slide images (WSI). OBSERVATION PROCEDURES: Labelled gigapixel pathological WSIs were used to train and test a model designed to assign patch-level classification. Using malignant probability from a convolutional neural network, the patches were embedded back into each WSI to generate a visualisation heatmap and leveraged a random forest model to establish a WSI-level diagnosis. MAIN OUTCOME MEASURE(S): For classification, the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity and specificity were used to evaluate the efficacy of the DLS in detecting MM. RESULTS: For patch diagnosis, the model achieved an AUC of 0.989 (95% CI 0.989 to 0.991), with an accuracy, sensitivity and specificity of 94.9%, 94.7% and 95.3%, respectively. We displayed the lesion area on the WSIs as graded by malignant potential. For WSI, the obtained sensitivity, specificity and accuracy were 100%, 96.5% and 98.2%, respectively, with an AUC of 0.998 (95% CI 0.994 to 1.000). CONCLUSION: Our DLS, which uses artificial intelligence, can automatically detect MM in histopathological slides and highlight the lesion area on WSIs using a probabilistic heatmap. In addition, our approach has the potential to be applied to the histopathological sections of other tumour types.

Simultaneous enhancement of vascularization and contact-active antibacterial activity in diopside-based ceramic orbital implants.

Rapid vascularization and long-term antibacterial property are desirable characteristics of the next-generation implants in orbital reconstruction. In this study, the new diopside-based orbital implants were developed by direct ink writing of diopside (CaMgSi2O6; DIO) and low-melt bioactive glass (BG)-assisted sintering approaches. The mechanical tests showed that the addition 5% or 10% BG could readily enhance the compressive strength of the DIO porous bioceramics after sintering at 1150 °C. The Tris buffer immersion test in vitro indicated that the porous bioceramics exhibited appreciable mechanical stability and very limited mass loss (<3.5%) after 8 weeks. The DIO/10BG porous bioceramic sintered at 1150 °C or 1250 °C could promote appreciable angiogenesis response at the early stage (2-6 weeks) of implantation in the rabbit panniculus carnosus muscle models in vivo. It is interesting that the steam autoclaved bioceramics exhibited outstanding contact-active inhibition against Staphylococcus aureus and Pseudomonas aeruginosa, but as-sintered bioceramics showed no antibacterial effect. It is reasonable to consider that our strategy paves the way toward a simple and effective approach to fabricate the multifunctional tailormade implants for orbital implantation, thus accelerating the clinical translation of biomaterials research.

Multifractal and lacunarity analyses of microvascular morphology in eyes with diabetic retinopathy: A projection artifact resolved optical coherence tomography angiography study.

OBJECTIVE: To evaluate the degree of microvascular impairment in DR using multifractal and lacunarity analyses and to compare the diagnostic ability between traditional Euclidean measures (fovea avascular zone area and vessel density) and fractal geometric features. METHODS: This retrospective cross-sectional study included a total of 143 eyes of 94 patients with different stages of DR. The retinal microvasculature was imaged by projection removed OCTA. We examined the degree of association between fractal metrics of the retinal microvasculature and DR severity. The area under the ROC curve was used to estimate the diagnostic performance. RESULTS: With increasing DR severity, the multifractal spectrum shifted toward the left bottom and exhibited less left skewness and asymmetry. The vessel density, multifractal features, and lacunarity measured from the DCP were strongly associated with DR severity. The multifractal feature D5 showed the highest diagnostic ability. The combination of multifractal features further improved the discriminating power. CONCLUSIONS: Multifractal and lacunarity analyses can be potentially valuable tools for assessment of microvascular impairments in DR. Multifractal geometric parameters exhibit a better discriminatory performance than Euclidean measures, particularly for detection of the early stages of DR.

Synergistic Effect of Copper-Containing Mesoporous Bioactive Glass Coating on Stimulating Vascularization of Porous Hydroxyapatite Orbital Implants in Rabbits.

Rapid and complete vascularization of the porous orbital implants after enucleation is vital for reducing postoperative complications, such as exposure and infection. In this study, the porous hydroxyapatite (pHA) scaffolds modified with the mesoporous bioactive glass with and without adding copper (MBG, Cu-MBG) were prepared by sol-gel technique and followed by evaporation induced self-assembly (EISA) process. The macro-/microstructure analysis of the modified scaffolds (i.e., MBG/pHA, Cu-MBG/pHA) showed highly interconnected macropores, and unique mesoporous structures in the pore wall with higher surface area. A primary angiogenic test in a panniculus carnosus muscle model in rabbit indicated that the Cu-MBG coating was significantly beneficial for the vascularization in the porous architecture of the scaffolds in the early stage. These results suggest that the Cu-MBG modification provides a simple and effective strategy to endow favorable biological performances with pHA implants and greater potential for future application in orbit reconstruction.