SproutAngio: an open-source bioimage informatics tool for quantitative analysis of sprouting angiogenesis and lumen space

Three-dimensional image analyses are required to improve the understanding of the regulation of blood vessel formation and heterogeneity. Currently, quantitation of 3D endothelial structures or vessel branches is often based on 2D projections of the images losing their volumetric information. Here, we developed SproutAngio, a Python-based open-source tool, for fully automated 3D segmentation and analysis of endothelial lumen space and sprout morphology. To test the SproutAngio, we produced a publicly available in vitro fibrin bead assay dataset with a gradually increasing VEGF-A concentration ( https://doi.org/10.5281/zenodo.7240927 ). We demonstrate that our automated segmentation and sprout morphology analysis, including sprout number, length, and nuclei number, outperform the widely used ImageJ plugin. We also show that SproutAngio allows a more detailed and automated analysis of the mouse retinal vasculature in comparison to the commonly used radial expansion measurement. In addition, we provide two novel methods for automated analysis of endothelial lumen space: (1) width measurement from tip, stalk and root segments of the sprouts and (2) paired nuclei distance analysis. We show that these automated methods provided important additional information on the endothelial cell organization in the sprouts. The pipelines and source code of SproutAngio are publicly available ( https://doi.org/10.5281/zenodo.7381732 ).

Study on the influence of shot peening strengthening before shot peen forming on 2024-T351 aluminum alloy fatigue crack growth rate

It is sparse and inconclusive that research on the subject whether the fatigue life of the structure will be reduced by shot peening strengthening before shot peen forming (S + F), and this study investigates accordingly. First, the crack growth rate test of the machine-processing plate and shot peening strengthening before shot peen forming plate demonstrate that both plates' final crack growth rate and length are similar. However, the test shows the "fluctuation phenomenon" of crack growth rate and the "intersection phenomenon" in the Paris curve. This study is based on a self-developed simulation plugin for crack growth paths. The results verify that "fluctuation" causes the differential distribution of the overall stress intensity factor in the strengthened (4.5% increase compared to machine-processing) and formed (9.8% decrease compared to machine-processing) crater areas of the shot peening strengthening before shot peen forming plate. Comparing to the full coverage strengthening area, the forming area (only 30% coverage) in the early stage of growth as well as the gain amplitude of the residual stress in the late stage of growth gradually decrease and tend to be the same as that of the machine-processing, as validated by the "intersection phenomenon".

Measurement of Sequential ϒ Suppression in Au+Au Collisions at sqrt[s_{NN}]=200 GeV with the STAR Experiment

We report on measurements of sequential ϒ suppression in Au+Au collisions at sqrt[s_{NN}]=200  GeV with the STAR detector at the Relativistic Heavy Ion Collider (RHIC) through both the dielectron and dimuon decay channels. In the 0%-60% centrality class, the nuclear modification factors (R_{AA}), which quantify the level of yield suppression in heavy-ion collisions compared to p+p collisions, for ϒ(1S) and ϒ(2S) are 0.40±0.03(stat)±0.03(sys)±0.09(norm) and 0.26±0.08(stat)±0.02(sys)±0.06(norm), respectively, while the upper limit of the ϒ(3S) R_{AA} is 0.17 at a 95% confidence level. This provides experimental evidence that the ϒ(3S) is significantly more suppressed than the ϒ(1S) at RHIC. The level of suppression for ϒ(1S) is comparable to that observed at the much higher collision energy at the Large Hadron Collider. These results point to the creation of a medium at RHIC whose temperature is sufficiently high to strongly suppress excited ϒ states.

Development of Rat Caries-Induced Pulpitis Model for Vital Pulp Therapy

Rodent animal models for vital pulp therapy are commonly used in dental research because their tooth anatomy and cellular processes are similar to the anatomy and processes in humans. However, most studies have been conducted using uninfected sound teeth, which makes it difficult to adequately assess the inflammatory shift after vital pulp therapy. In the present study, we aimed to establish a caries-induced pulpitis model based on the conventional rat caries model and then evaluate inflammatory changes during the wound-healing process after pulp capping in a model of reversible pulpitis induced by carious infection. To establish the caries-induced pulpitis model, the pulpal inflammatory status was investigated at different stages of caries progression by immunostaining targeted to specific inflammatory biomarkers. Immunohistochemical staining revealed that both Toll-like receptor 2 and proliferating cell nuclear antigen were expressed in moderate and severe caries-stimulated pulp, indicating that an immune reaction occurred at both stages of caries progression. M2 macrophages were predominant in moderate caries-stimulated pulp, whereas M1 macrophages were predominant in the severe caries-stimulated pulp. Pulp capping in teeth with moderate caries (i.e., teeth with reversible pulpitis) led to complete tertiary dentin formation within 28 d after treatment. Impaired wound healing was observed in teeth with severe caries (i.e., teeth with irreversible pulpitis). During the wound-healing process in reversible pulpitis after pulp capping, M2 macrophages were predominant at all time points; their proliferative capacity was upregulated in the early stage of wound healing compared with healthy pulp. In conclusion, we successfully established a caries-induced pulpitis model for studies of vital pulp therapy. M2 macrophages have an important role in the early stages of the wound-healing process in reversible pulpitis.

Novel Functional Peptide for Next-Generation Vital Pulp Therapy

Although vital pulp therapy should be performed by promoting the wound-healing capacity of dental pulp, existing pulp-capping materials were not developed with a focus on the pulpal repair process. In previous investigations of wound healing in dental pulp, we found that organic dentin matrix components (DMCs) were degraded by matrix metalloproteinase-20, and DMC degradation products containing protein S100A7 (S100A7) and protein S100A8 (S100A8) promoted the pulpal wound-healing process. However, the direct use of recombinant proteins as pulp-capping materials may cause clinical problems or lead to high medical costs. Thus, we hypothesized that functional peptides derived from recombinant proteins could solve the problems associated with direct use of such proteins. In this study, we identified functional peptides derived from the protein S100 family and investigated their effects on dental pulp tissue. We first performed amino acid sequence alignments of protein S100 family members from several mammalian sources, then identified candidate peptides. Next, we used a peptide array method that involved human dental pulp stem cells (hDPSCs) to evaluate the mineralization-inducing ability of each peptide. Our results supported the selection of 4 candidate functional peptides derived from proteins S100A8 and S100A9. Direct pulp-capping experiments in a rat model demonstrated that 1 S100A8-derived peptide induced greater tertiary dentin formation compared with the other peptides. To investigate the mechanism underlying this induction effect, we performed liquid chromatography-tandem mass spectrometry analysis using hDPSCs and the S100A8-derived peptide; the results suggested that this peptide promotes tertiary dentin formation by inhibiting inflammatory responses. In addition, this peptide was located in a hairpin region on the surface of S100A8 and could function by direct interaction with other molecules. In summary, this study demonstrated that a S100A8-derived functional peptide promoted wound healing in dental pulp; our findings provide insights for the development of next-generation biological vital pulp therapies.

Beam Energy Dependence of Fifth- and Sixth-Order Net-Proton Number Fluctuations in Au+Au Collisions at RHIC

We report the beam energy and collision centrality dependence of fifth and sixth order cumulants (C_{5}, C_{6}) and factorial cumulants (κ_{5}, κ_{6}) of net-proton and proton number distributions, from center-of-mass energy (sqrt[s_{NN}]) 3 GeV to 200 GeV Au+Au collisions at RHIC. Cumulant ratios of net-proton (taken as proxy for net-baryon) distributions generally follow the hierarchy expected from QCD thermodynamics, except for the case of collisions at 3 GeV. The measured values of C_{6}/C_{2} for 0%-40% centrality collisions show progressively negative trend with decreasing energy, while it is positive for the lowest energy studied. These observed negative signs are consistent with QCD calculations (for baryon chemical potential, μ_{B}≤110  MeV) which contains the crossover transition range. In addition, for energies above 7.7 GeV, the measured proton κ_{n}, within uncertainties, does not support the two-component (Poisson+binomial) shape of proton number distributions that would be expected from a first-order phase transition. Taken in combination, the hyperorder proton number fluctuations suggest that the structure of QCD matter at high baryon density, μ_{B}∼750  MeV at sqrt[s_{NN}]=3  GeV is starkly different from those at vanishing μ_{B}∼24  MeV at sqrt[s_{NN}]=200  GeV and higher collision energies.

Deformable Motion Compensation for Intraprocedural Vascular Cone-beam CT with Sequential Projection Domain Targeting and Vessel-Enhancing Autofocus

Purpose

Cone-beam CT (CBCT) is used in interventional radiology (IR) for identification of complex vascular anatomy, difficult to visualize in 2D fluoroscopy. However, long acquisition time makes CBCT susceptible to soft-tissue deformable motion that degrades visibility of fine vessels. We propose a targeted framework to compensate for deformable intra-scan motion via learned full-sequence models for identification of vascular anatomy coupled to an autofocus function specifically tailored to vascular imaging.

Methods

The vessel-targeted autofocus acts in two stages: (i) identification of vascular and catheter targets in the projection domain; and, (ii) autofocus optimization for a 4D vector field through an objective function that quantifies vascular visibility. Target identification is based on a deep learning model that operates on the complete sequence of projections, via a transformer encoder-decoder architecture that uses spatial-temporal self-attention modules to infer long-range feature correlations, enabling identification of vascular anatomy with highly variable conspicuity. The vascular autofocus function is derived through eigenvalues of the local image Hessian, which quantify the local image structure for identification of bright tubular structures. Motion compensation was achieved via spatial transformer operators that impart time dependent deformations to NPAR = 90 partial angle reconstructions, allowing for efficient minimization via gradient backpropagation. The framework was trained and evaluated in synthetic abdominal CBCTs obtained from liver MDCT volumes and including realistic models of contrast-enhanced vascularity with 15 to 30 end branches, 1 - 3.5 mm vessel diameter, and 1400 HU contrast.

Results

The targeted autofocus resulted in qualitative and quantitative improvement in vascular visibility in both simulated and clinical intra-procedural CBCT. The transformer-based target identification module resulted in superior detection of target vascularity and a lower number of false positives, compared to a baseline U-Net model acting on individual projection views, reflected as a 1.97x improvement in intersection-over-union values. Motion compensation in simulated data yielded improved conspicuity of vascular anatomy, and reduced streak artifacts and blurring around vessels, as well as recovery of shape distortion. These improvements amounted to an average 147% improvement in cross correlation computed against the motion-free ground truth, relative to the un-compensated reconstruction.

Conclusion

Targeted autofocus yielded improved visibility of vascular anatomy in abdominal CBCT, providing better potential for intra-procedural tracking of fine vascular anatomy in 3D images. The proposed method poses an efficient solution to motion compensation in task-specific imaging, with future application to a wider range of imaging scenarios.

Multi-Stage Adaptive Spline Autofocus (MASA) with a Learned Metric for Deformable Motion Compensation in Interventional Cone-Beam CT

Purpose

Cone-beam CT (CBCT) is widespread in abdominal interventional imaging, but its long acquisition time makes it susceptible to patient motion. Image-based autofocus has shown success in CBCT deformable motion compensation, via deep autofocus metrics and multi-region optimization, but it is challenged by the large parameter dimensionality required to capture intricate motion trajectories. This work leverages the differentiable nature of deep autofocus metrics to build a novel optimization strategy, Multi-Stage Adaptive Spine Autofocus (MASA), for compensation of complex deformable motion in abdominal CBCT.

Methods

MASA poses the autofocus problem as a multi-stage adaptive sampling strategy of the motion trajectory, sampled with Hermite spline basis with variable amplitude and knot temporal positioning. The adaptive method permits simultaneous optimization of the sampling phase, local temporal sampling density, and time-dependent amplitude of the motion trajectory. The optimization is performed in a multi-stage schedule with increasing number of knots that progressively accommodates complex trajectories in late stages, preconditioned by coarser components from early stages, and with minimal increase in dimensionality. MASA was evaluated in controlled simulation experiments with two types of motion trajectories: i) combinations of slow drifts with sudden jerk (sigmoid) motion; and ii) combinations of periodic motion sources of varying frequency into multi-frequency trajectories. Further validation was obtained in clinical data from liver CBCT featuring motion of contrast-enhanced vessels, and soft-tissue structures.

Results

The adaptive sampling strategy provided successful motion compensation in sigmoid trajectories, compared to fixed sampling strategies (mean SSIM increase of 0.026 compared to 0.011). Inspection of the estimated motion showed the capability of MASA to automatically allocate larger sampling density to parts of the scan timeline featuring sudden motion, effectively accommodating complex motion without increasing the problem dimension. Experiments on multi-frequency trajectories with 3-stage MASA (5, 10, and 15 knots) yielded a twofold SSIM increase compared to single-stage autofocus with 15 knots (0.076 vs 0.040, respectively). Application of MASA to clinical datasets resulted in simultaneous improvement on the delineation of both contrast-enhanced vessels and soft-tissue structures in the liver.

Conclusion

A new autofocus framework, MASA, was developed including a novel multi-stage technique for adaptive temporal sampling of the motion trajectory in combination with fully differentiable deep autofocus metrics. This novel adaptive sampling approach is a crucial step for application of deformable motion compensation to complex temporal motion trajectories.

[Exploration of esophagojejunostomy after totally laparoscopic total gastrectomy]

The advantages of lymph node dissection through total laparoscopic total gastrectomy (TLTG) seem to be more and more accepted by the academic community. However, reconstruction of digestive tract is challenging and remains a focus of debate and research. Which way is better for esophagojejunostomy, circular stapler or linear stapler,remains to be answered. The authors believe that, under the conditions of existing anastomosis instruments, using of linear stapler for esophagojejunal side-to-side anastomosis may be the most common choice, but it must be used with strict indications, because there are still many problems to be solved. It is believed that with the breakthrough in the development of the circular stapler suitable for esophagojejunostomy in TLTG, the application of circular stapler for digestive tract reconstruction will become the mainstream again in future. Thus, the current routine clinical practice of TLTG should be cautious and the surgical indications should be strictly evaluated.

Prognostic Value of Four Preimplantation Malnutrition Estimation Tools in Predicting Heart Failure Hospitalization of the Older Diabetic Patients with Right Ventricular Pacing

OBJECTIVES

The prognostic value of preimplantation nutritional status is not yet known for older diabetic patients that received right ventricular pacing (RVP). The study aimed to investigate the clinical value of the four malnutrition screening tools for the prediction of heart failure hospitalization (HFH) in older diabetic patients that received RVP.

DESIGN

Retrospective observational cohort study.

SETTING AND PARTICIPANTS

This study was conducted between January 2017 and January 2018 at the Fuwai Hospital, Beijing, China, and included older (age ≥ 65 years) diabetic patients that received RVP for the first time Measurements: The Prognostic Nutritional Index (PNI), Geriatric Nutritional Risk Index (GNRI), Naples Prognostic Score (NPS), and the Controlling Nutritional Status (CONUT) score were used to estimate the preimplantation nutritional status of the patients. Univariate and multivariate Cox proportional hazard regression analyses were performed to investigate the association between preimplantation malnutrition and HFH.

RESULTS

Overall, 231 older diabetic patients receiving RVP were included. The median follow-up period after RVP was 53 months. HFH was reported for 19.9% of the included patients. Our results showed preimplantation malnutrition for 18.2%, 15.2%, 86.6% and 66.2% of the included patients based on the PNI, GNRI, NPS, and CONUT score, respectively. The cumulative rate of HFH during follow-up period was significantly higher for patients in the preimplantation malnutrition group based on the PNI (log-rank = 13.0, P = 0.001), GNRI (log-rank = 8.5, P = 0.01), and NPS (log-rank = 15.7, P < 0.001) compared to the normal nutrition group, but was not statistically significant for those in the preimplantation malnutrition group based on the CONUT score (log-rank = 2.7, P = 0.3). As continuous variables, all the nutritional indices showed significant correlation with HFH (all P < 0.05). However, multivariate analysis showed that only GNRI was independently associated with HFH (HR = 0.97, 95% CI: 0.937-0.997, P = 0.032). As categorical variables, PNI, GNRI, and NPS showed significant correlation with HFH. After adjustment of confounding factors, moderate-to-severe degree of malnutrition was an independent predictor of HFH based on the PNI (HR = 4.66, 95% CI: 1.03-21.00, P = 0.045) and GNRI (HR = 3.02, 95% CI: 1.02-9.00, P = 0.047).

CONCLUSION

Preimplantation malnutrition was highly prevalent in older diabetic patients that received RVP. The malnutrition prediction tools, PNI and GNRI, showed significant prognostic value in accurately predicting HFH in older diabetic patients with RVP.

Collision-System and Beam-Energy Dependence of Anisotropic Flow Fluctuations

Elliptic flow measurements from two-, four-, and six-particle correlations are used to investigate flow fluctuations in collisions of U+U at sqrt[s_{NN}]=193  GeV, Cu+Au at sqrt[s_{NN}]=200  GeV and Au+Au spanning the range sqrt[s_{NN}]=11.5-200  GeV. The measurements show a strong dependence of the flow fluctuations on collision centrality, a modest dependence on system size, and very little if any, dependence on particle species and beam energy. The results, when compared to similar LHC measurements, viscous hydrodynamic calculations, and trento model eccentricities, indicate that initial-state-driven fluctuations predominate the flow fluctuations generated in the collisions studied.

[Retrospective analysis and a cross-sectional questionnaire survey of lung cancer concomitant with interstitial lung disease]

Objective: To describe the clinical characteristics and prognosis of lung cancer concomitant with interstitial lung disease (LC-ILD), and to understand the current status of knowledge of LC-ILD by physicians in the departments related to the treatment of the disease. Methods: We conducted a retrospective analysis of in-hospitalized pathology identified lung cancer (LC) patients who were admitted to our hospital between January 2014 and December 2018. After reviewing their chest CT imagings and pathological reports, 70 patients who were concomitant with interstitial lung disease (ILD) were enrolled in our study. On the other hand, a cross-sectional survey using an online questionnaire was conducted in LC-ILD management doctors who came from 29 provincial hospitals. The perceptions of demographic features, LC characteristics and management, ILD characteristics and management, and the prognosis of LC-ILD were investigated. Results: Among the 70 enrolled LC-ILD cases, there were 52 males, and the mean age was (64.3±7.63) years (ranged from 49 years to 84 years). There were 51 patients who were older than 59 years. The most common pathological pattern of LC was adenocarcinoma. Most of them were diagnosed with LC and ILD simultaneously, and they were usually treated with chemotherapy while unresectable. There were 11 patients (15.7%) with positive EGFR or ALK mutation. Forty-five patients (64.3%) died during the follow-up, and 33 were died from LC progression. There were no significant differences between the surgical group and non-surgical group on age, pathological patterns, EGFR or ALK mutation. However, LC-ILD patients in the surgical group were diagnosed with earlier TNM classification and with better prognosis. A total of 1 014 doctors answered the questionnaire completely. In the feedback, patients aged 60 years and older (785 doctors/77.4%), and male patients (720 doctors/71%) were the predominant LC-ILD patients. Adenocarcinoma (390 doctors/38.5%), adenocarcinoma or squamous-cell cancer (SCC) (182 doctors/17.9%), and SCC (151 doctors/14.9%) were considered as the common pathological patterns of LC-ILD patients. In most doctors' feedback, the EGFR or ALK mutation was not common for LC-ILD: low (646 doctors/63.7%) or hardly (306 doctors/30.5%) positive mutation. The diagnosis of ILD was earlier than LC (506 doctors/49.9%) or there was no identified precedence of LC and ILD diagnosis (208 doctors/20.5%). Most of the doctors (693 doctors/68.3%) agreed that the vital factor for surgery or not was the severity of ILD for LC-ILD patients. There were great divergences on the treatment protocol both for the advanced LC and ILD. The patients with LC-ILD were died mostly from LC progression and ILD exacerbation (542 doctors/53.5%), followed by ILD exacerbation (237 doctors/23.4%) or LC progression (226 doctors/22.3%). Conclusions: The elderly male patients were predisposed to LC-ILD, and adenocarcinoma was the common pathological pattern. The LC-ILD patients with non-advanced LC who were performed with surgery had better prognosis. However, it is recommended to consider whether to perform surgery in combination with the severity of the ILD.

A Scalp Metastatic Follicular Thyroid Carcinoma with a Silent Thyroid History and Normal Thyroid Uptake by PET-CT

Introduction/Objective

Follicular thyroid carcinoma (FTC) accounts for 10%-15% of all primary thyroid cancers. Follicular thyroid cancer is known to metastasize hematogenously, with distant metastasis occurring in 6-20% of cases. Scalp metastasis with an underlying thyroid carcinoma is an exceedingly rare clinical entity; there are less than 15 case reports in the literature. 1-2. Here, we present a case of widely invasive FTC with skull metastases located on the parietal calvarium. The scalp mass was confirmed as follicular thyroid carcinoma via microscopic morphology and positive immunoreactivity for Vimentin, TTF1, thyroglobulin, and PAX8. We present this case not only because of the diagnostic challenge and rare scalp metastasis, but also because of the patient’s unusual “silent” thyroid medical history and no abnormal thyroid uptake by PET-CT.

Methods/Case Report

81-year-old female presenting 2-year history of right parietal scalp mass, which was previously suspected for lipoma with attempted resection in Mexico but interrupted due to severe hemorrhage. No palpable thyroid nodule was noted. PET-CT showed avid lesions of the right breast with nipple retraction, as well as avid suspicious lesions of bilateral lungs, calvarium, xiphoid process, right acetabulum, T spine most c/f widely metastatic cancer, most likely a breast primary; evaluation of the neck demonstrates physiologic FDG-activity in the thyroid. Thyroid studies showed hyperthyroidism: TSH (L) &lt;0.010 uIU/mL; Free T3 (H) 4.7 pg/mL and Free T4 1.00 ng/d. The patient was performed Ultrasound-guided FNA and core biopsy of the large parietal scalp lesion, however, FNA of the cystic component was nondiagnostic (no malignant cells seen).

Results (if a Case Study enter NA)

NA.

Conclusion

Core biopsy of the large parietal mass the tumor cells tend to form follicular or microfollicular architecture with colloid present, but no papillary nuclear features. Rare mitotic figures are seen. IHC stain of tumor cells are positive for AE1/AE3, Cam5.2, CK7, TTF1, thyroglobulin, PAX8, and Vimentin, which show strong evidence for metastatic follicular thyroid carcinoma (FTC) origin. Tumor cells are negative for Napsin-A, P63, Synaptophysin, Ck5/6, Ck20, EMA, WT1, CDX2, GATA3, Mammaglobin, ER, PR, and BRST2, which helps rule out the primary malignancy from lung, breast, neuroendocrine or other adenocarcinomas.