Deep learning combining mammography and ultrasound images to predict the malignancy of BI-RADS US 4A lesions in women with dense breasts: a diagnostic study

OBJECTIVES

The authors aimed to assess the performance of a deep learning (DL) model, based on a combination of ultrasound (US) and mammography (MG) images, for predicting malignancy in breast lesions categorized as Breast Imaging Reporting and Data System (BI-RADS) US 4A in diagnostic patients with dense breasts.

METHODS

A total of 992 patients were randomly allocated into the training cohort and the test cohort at a proportion of 4:1. Another, 218 patients were enrolled to form a prospective validation cohort. The DL model was developed by incorporating both US and MG images. The predictive performance of the combined DL model for malignancy was evaluated by sensitivity, specificity, and area under the receiver operating characteristic curve (AUC). The combined DL model was then compared to a clinical nomogram model and to the DL model trained using US image only and to that trained MG image only.

RESULTS

The combined DL model showed satisfactory diagnostic performance for predicting malignancy in breast lesions, with an AUC of 0.940 (95% CI: 0.874-1.000) in the test cohort, and an AUC of 0.906 (95% CI: 0.817-0.995) in the validation cohort, which was significantly higher than the clinical nomogram model, and the DL model for US or MG alone ( P <0.05).

CONCLUSIONS

The study developed an objective DL model combining both US and MG imaging features, which was proven to be more accurate for predicting malignancy in the BI-RADS US 4A breast lesions of patients with dense breasts. This model may then be used to more accurately guide clinicians' choices about whether performing biopsies in breast cancer diagnosis.

Insights on the NF-κB system in polycystic ovary syndrome, attractive therapeutic targets

The nuclear factor κappa B (NF-κB) signaling plays a well-known function in inflammation and regulates a wide variety of biological processes. Low-grade chronic inflammation is gradually considered to be closely related to the pathogenesis of Polycystic ovary syndrome (PCOS). In this review, we provide an overview on the involvement of NF-κB in the progression of PCOS particularly, such as hyperandrogenemia, insulin resistance, cardiovascular diseases, and endometrial dysfunction. From a clinical perspective, progressive recognition of NF-κB pathway provides opportunities for therapeutic interventions aimed at inhibiting pathway-specific mechanisms. With the accumulation of basic experimental and clinical data, NF-κB signaling pathway was recognized as a therapeutic target. Although there have been no specific small molecule NF-κB inhibitors in PCOS, a plethora of natural and synthetic compound have emerged for the pharmacologic intervention of the pathway. The traditional herbs developed for NF-κB pathway have become increasingly popular in recent years. Abundant evidence elucidated that NF-κB inhibitors can significantly improve the symptoms of PCOS. Herein, we summarized evidence relating to how NF-κB pathway is involved in the development and progression of PCOS. Furthermore, we present an in-depth overview of NF-κB inhibitors for therapy interventions of PCOS. Taken together, the NF-κB signaling may be a futuristic treatment strategy for PCOS.

[Incidence of hypogammaglobulinaemia in children with steroid-dependent/frequently relapsing nephrotic syndrome treated with rituximab and its association with severe infections]

Objective: To investigate the incidence and influencing factors of hypogammaglobulinemia (HGG) in children with steroid-dependent/frequently relapsing nephrotic syndrome (SDNS/FRNS) treated with rituximab (RTX), and its relationship with the risk of severe infections. Methods: The clinical data of children with SDNS/FRNS treated with RTX at the Department of Pediatrics of the First Affiliated Hospital of Zhengzhou University from December 2020 to January 2023 were retrospectively analyzed. RTX treatment was performed using a B-cell-guided regimen (a single dose of 375 mg/m2, a maximum of 500 mg/dose, and an additional one dose when reassessment of peripheral blood CD19+B cells≥1%). Patients were divided into HGG and non-HGG groups according to the presence or absence of HGG during the follow-up period. A multivariate logistic regression model was used to analyze the influencing factors of HGG, and the predictive value of each influencing factor on HGG was assessed by plotting the receiver operating characteristic (ROC) curve. Results: A total of 59 SDNS/FRNS children (48 males and 11 females) were included, and aged [M (Q1, Q3)] 9.4 (6.5, 12.2) years at the time of the first RTX treatment, with a median application of 3 (2, 4) doses of RTX. During the follow-up period of 15.5 (9.9, 22.8) months, the HGG was present in 16 (27.1%) children, of which seven persisted for more than 1 year. Compared with non-HGG group, HGG group had a shorter duration of the disease [3.3 (2.1, 3.6) vs 4.6 (2.4, 8.0) years, P=0.030], younger age at the time of the first RTX treatment [6.2 (5.6, 7.4) vs 11.3 (8.8, 13.3) years, P<0.001], and lower serum IgG levels [5.9 (4.9, 6.4) vs 7.5 (6.1, 8.2) g/L, P<0.001]. Multivariate logistic regression analysis showed that young age at the time of the first RTX treatment (OR=0.52, 95%CI: 0.35-0.78, P=0.002) was an influencing factor of HGG. The area under the curve (AUC) for age at first RTX treatment to predict HGG was 0.887 (95%CI: 0.778-0.955, P<0.001), with an optimal cut-off value of 8.3 years. During the follow-up period, six children (10.2%) developed severe infectious, and there was no statistically significant difference in the incidence of serious infections between the HGG and non-HGG groups [12.5% (2/16) vs 9.3% (4/43), P=1.000]. Conclusions: HGG is frequent in children with SDNS/FRNS treated with RTX, and nearly half of HGG persists for more than 1 year. The possibility of HGG is greater in those≤8.3 years at the first RTX treatment, but HGG does not increase the risk of severe infections in children.

Differential diagnosis of breast mucinous carcinoma with an oval shape from fibroadenoma based on ultrasonographic features

BACKGROUND

Approximately 50% of breast mucinous carcinomas (MCs) are oval and have the possibility of being misdiagnosed as fibroadenomas (FAs). We aimed to identify the key features that can help differentiate breast MC with an oval shape from FA on ultrasonography (US).

METHODS

Seventy-six MCs from 71 consecutive patients and 50 FAs with an oval shape from 50 consecutive patients were included in our study. All lesions pathologically diagnosed. According to the Breast Imaging Reporting and Data System (BI-RADS), first, the ultrasonographic features of the MCs and FAs were recorded and a final category was assessed. Then, the differences in ultrasonographic characteristics between category 4 A (low-risk group) and category 4B-5 (medium-high- risk group) MCs were identified. Finally, other ultrasonographic features of MC and FA both with an oval shape were compared to determine the key factors for differential diagnosis. The Mann-Whitney test, χ2 test or Fisher's exact test was used to compare data between groups.

RESULTS

MCs with an oval shape (81.2%) and a circumscribed margin (25%) on US were more commonly assessed in the low-risk group (BI-RADS 4 A) than in the medium-high-risk group (BI-RADS 4B-5) (20%, p < 0.001 and 0%, p = 0.001, respectively). Compared with those with FA, patients with MC were older, and tended to have masses with non-hypoechoic patterns, not circumscribed margins, and a posterior echo enhancement on US (p < 0.001, p < 0.001, and p = 0.003, respectively).

CONCLUSION

The oval shape was the main reason for the underestimation of MCs. On US, an oval mass found in the breast of women of older age with non-hypoechoic patterns, not circumscribed margins, and a posterior echo enhancement was associated with an increased risk of being an MC, and should be subjected to active biopsy.

Diagnostic Efficacy of High-frequency Ultrasound (HFU) in Early Diagnosis of Congenital Hip Dysplasia

BACKGROUND

Hip dysplasia is one of the most prevalent disorders in children and one of the three primary congenital orthopedic deformities. Although there are numerous existing methods (e.g., CT, MRI and arthrography) for early identification of hip dysplasia, their diagnostic criteria differ widely. It is critical to establish a safe, accurate, and reliable way for early diagnosis and treatment of hip dysplasia.

OBJECTIVE

This study aimed to analyze the diagnostic efficacy of high-frequency ultrasound (HFU) for congenital developmental hip dysplasia and hip dislocation and to provide a reference for the early diagnosis of congenital hip dysplasia in the future.

METHODS

A total of 104 infants and children suspected of having congenital hip dislocation or developmental hip dysplasia admitted to our hospital from April 2019 to August 2022 were enrolled as study subjects. All the infants and children were subjected to HFU and X-ray examination in our hospital. The diagnostic efficacy of HFU for congenital hip dysplasia was observed using X-ray as the gold standard.

RESULTS

HFU confirmed 79 cases of congenital hip dysplasia, while X-ray confirmed 71 cases. The sensitivity and specificity of HFU were 77.42% and 83.33%, respectively, in the diagnosis of congenital developmental hip dysplasia, 76.47% and 96.55% in the diagnosis of congenital hip dislocation, and 77.22% and 60% in the diagnosis of congenital hip abnormality, which is very close to the gold standard. According to statistics on infants and children, the majority of patients were girls, and the left joint was more likely to be affected.

CONCLUSION

HFU has excellent diagnostic efficiency for congenital developmental hip dysplasia and hip dislocation, which can be considered an early assessment method for congenital hip dysplasia in the future.

One-Shot Weakly-Supervised Segmentation in 3D Medical Images

Deep neural networks typically require accurate and a large number of annotations to achieve outstanding performance in medical image segmentation. One-shot and weakly-supervised learning are promising research directions that reduce labeling effort by learning a new class from only one annotated image and using coarse labels instead, respectively. In this work, we present an innovative framework for 3D medical image segmentation with one-shot and weakly-supervised settings. Firstly a propagation-reconstruction network is proposed to propagate scribbles from one annotated volume to unlabeled 3D images based on the assumption that anatomical patterns in different human bodies are similar. Then a multi-level similarity denoising module is designed to refine the scribbles based on embeddings from anatomical- to pixel-level. After expanding the scribbles to pseudo masks, we observe the miss-classified voxels mainly occur at the border region and propose to extract self-support prototypes for the specific refinement. Based on these weakly-supervised segmentation results, we further train a segmentation model for the new class with the noisy label training strategy. Experiments on three CT and one MRI datasets show the proposed method obtains significant improvement over the state-of-the-art methods and performs robustly even under severe class imbalance and low contrast. Code is publicly available at https://github.com/LWHYC/OneShot_WeaklySeg.

BMP4 participates in the pathogenesis of PCOS by regulating glucose metabolism and autophagy in granulosa cells under hyperandrogenic environment

Polycystic ovary syndrome (PCOS) is a complex reproductive endocrine disease characterized by ovulation dysfunction with multiple etiologies and manifestations, and it is widely believed that the disorders of hyper-androgen and glucose metabolism play a key role in its progression. There has been evidence that bone morphogenetic protein 4 (BMP4) is essential for the regulation of granulosa cells, but whether it regulates metabolism level of granulosa cells under hyperandrogenic environment remains unclear. In this study, Gene Expression Omnibus, clinical data and serum of PCOS patient were collected to detect androgen and BMP4 levels. KGN cells exposed to androgens as a model for simulating PCOS granulosa cells. Lactate/pyruvate kits, and Extracellular Acidification Rate and Oxygen Consumption Rate assay were performed to detect glycolysis and autophagy levels of granulosa cells. Lentivirus infection was used to investigate the effects of BMP4 on granulosa cells. RNA-seq were performed to explore the special mechanism. We found that BMP4 was increased in PCOS patients with hyper-androgen and granulosa cells with dihydrotestosterone treatment. Mechanically, on the one hand, hyperandrogenemia can up-regulate BMP4 secretion and induce glycolysis and autophagy levels. On the other hand, we found that hyperandrogenic-induced YAP1 upregulation may mediate BMP4 to increase glycolysis level and decrease autophagy, which plays a protective role in granulosa cells to ensure subsequent energy utilization and mitochondrial function. Overall, we innovated on the protective effect of BMP4 on glycolysis and autophagy disorders induced by excessive androgen in granulosa cells. Our study will provide guidance for future understanding of PCOS from a metabolic perspective and for exploring treatment options.

UPL-SFDA: Uncertainty-Aware Pseudo Label Guided Source-Free Domain Adaptation for Medical Image Segmentation

Domain Adaptation (DA) is important for deep learning-based medical image segmentation models to deal with testing images from a new target domain. As the source-domain data are usually unavailable when a trained model is deployed at a new center, Source-Free Domain Adaptation (SFDA) is appealing for data and annotation-efficient adaptation to the target domain. However, existing SFDA methods have a limited performance due to lack of sufficient supervision with source-domain images unavailable and target-domain images unlabeled. We propose a novel Uncertainty-aware Pseudo Label guided (UPL) SFDA method for medical image segmentation. Specifically, we propose Target Domain Growing (TDG) to enhance the diversity of predictions in the target domain by duplicating the pre-trained model's prediction head multiple times with perturbations. The different predictions in these duplicated heads are used to obtain pseudo labels for unlabeled target-domain images and their uncertainty to identify reliable pseudo labels. We also propose a Twice Forward pass Supervision (TFS) strategy that uses reliable pseudo labels obtained in one forward pass to supervise predictions in the next forward pass. The adaptation is further regularized by a mean prediction-based entropy minimization term that encourages confident and consistent results in different prediction heads. UPL-SFDA was validated with a multi-site heart MRI segmentation dataset, a cross-modality fetal brain segmentation dataset, and a 3D fetal tissue segmentation dataset. It improved the average Dice by 5.54, 5.01 and 6.89 percentage points for the three tasks compared with the baseline, respectively, and outperformed several state-of-the-art SFDA methods.

Prognostic prediction of left ventricular myocardial noncompaction using machine learning and cardiac magnetic resonance radiomics

Background

Although there are many studies on the prognostic factors of left ventricular myocardial noncompaction (LVNC), the determinants are varied and not entirely consistent. This study aimed to build predictive models using radiomics features and machine learning to predict major adverse cardiovascular events (MACEs) in patients with LVNC.

Methods

In total, 96 patients with LVNC were included and randomly divided into training and test cohorts. A total of 105 cine cardiac magnetic resonance (CMR)-derived radiomics features and 35 clinical characteristics were extracted. Five different oversampling algorithms were compared for selection of the optimal imbalanced processing. Feature importance was assessed with extreme gradient boosting (XGBoost). We compared the performance of 5 machine learning classification methods with different sample:feature ratios to determine the optimal hybrid classification strategy. Subsequently, radiomics, clinical, and combined radiomics-clinical models were developed and compared.

Results

The machine learning pipeline included an adaptive synthetic (ADASYN) algorithm for imbalanced processing, XGBoost feature selection with a sample:feature ratio of 10, and support vector machine (SVM) modeling. The areas under the receiver operating characteristic curves (AUCs) of the radiomics model, clinical model, and combined model in the validation cohort were 0.87 (sensitivity 83.33%, specificity 64.29%), 0.65 (sensitivity 16.67%, specificity 78.57%), and 0.92 (specificity 33.33%, sensitivity 100.00%), respectively. The radiomics model performed similarly to the clinical and combined models (P=0.124 and P=0.621, respectively). The performance of the combined model was significantly better than that of the clinical model (P=0.003).

Conclusions

The machine learning-based cine CMR radiomics model performed well at predicting MACEs in patients with LVNC. Adding radiomics features offered incremental prognostic value over clinical factors alone.

CDDSA: Contrastive domain disentanglement and style augmentation for generalizable medical image segmentation

Generalization to previously unseen images with potential domain shifts is essential for clinically applicable medical image segmentation. Disentangling domain-specific and domain-invariant features is key for Domain Generalization (DG). However, existing DG methods struggle to achieve effective disentanglement. To address this problem, we propose an efficient framework called Contrastive Domain Disentanglement and Style Augmentation (CDDSA) for generalizable medical image segmentation. First, a disentangle network decomposes the image into domain-invariant anatomical representation and domain-specific style code, where the former is sent for further segmentation that is not affected by domain shift, and the disentanglement is regularized by a decoder that combines the anatomical representation and style code to reconstruct the original image. Second, to achieve better disentanglement, a contrastive loss is proposed to encourage the style codes from the same domain and different domains to be compact and divergent, respectively. Finally, to further improve generalizability, we propose a style augmentation strategy to synthesize images with various unseen styles in real time while maintaining anatomical information. Comprehensive experiments on a public multi-site fundus image dataset and an in-house multi-site Nasopharyngeal Carcinoma Magnetic Resonance Image (NPC-MRI) dataset show that the proposed CDDSA achieved remarkable generalizability across different domains, and it outperformed several state-of-the-art methods in generalizable segmentation. Code is available at https://github.com/HiLab-git/DAG4MIA.

TP53RK Drives the Progression of Chronic Kidney Disease by Phosphorylating Birc5

Renal fibrosis is a common characteristic of various chronic kidney diseases (CKDs) driving the loss of renal function. During this pathological process, persistent injury to renal tubular epithelial cells and activation of fibroblasts chiefly determine the extent of renal fibrosis. In this study, the role of tumor protein 53 regulating kinase (TP53RK) in the pathogenesis of renal fibrosis and its underlying mechanisms is investigated. TP53RK is upregulated in fibrotic human and animal kidneys with a positive correlation to kidney dysfunction and fibrotic markers. Interestingly, specific deletion of TP53RK either in renal tubule or in fibroblasts in mice can mitigate renal fibrosis in CKD models. Mechanistic investigations reveal that TP53RK phosphorylates baculoviral IAP repeat containing 5 (Birc5) and facilitates its nuclear translocation; enhanced Birc5 displays a profibrotic effect possibly via activating PI3K/Akt and MAPK pathways. Moreover, pharmacologically inhibiting TP53RK and Birc5 using fusidic acid (an FDA-approved antibiotic) and YM-155(currently in clinical phase 2 trials) respectively both ameliorate kidney fibrosis. These findings demonstrate that activated TP53RK/Birc5 signaling in renal tubular cells and fibroblasts alters cellular phenotypes and drives CKD progression. A genetic or pharmacological blockade of this axis serves as a potential strategy for treating CKDs.

S3R: Shape and Semantics-Based Selective Regularization for Explainable Continual Segmentation Across Multiple Sites

In clinical practice, it is desirable for medical image segmentation models to be able to continually learn on a sequential data stream from multiple sites, rather than a consolidated dataset, due to storage cost and privacy restrictions. However, when learning on a new site, existing methods struggle with a weak memorizability for previous sites with complex shape and semantic information, and a poor explainability for the memory consolidation process. In this work, we propose a novel Shape and Semantics-based Selective Regularization ( [Formula: see text]) method for explainable cross-site continual segmentation to maintain both shape and semantic knowledge of previously learned sites. Specifically, [Formula: see text] method adopts a selective regularization scheme to penalize changes of parameters with high Joint Shape and Semantics-based Importance (JSSI) weights, which are estimated based on the parameter sensitivity to shape properties and reliable semantics of the segmentation object. This helps to prevent the related shape and semantic knowledge from being forgotten. Moreover, we propose an Importance Activation Mapping (IAM) method for memory interpretation, which indicates the spatial support for important parameters to visualize the memorized content. We have extensively evaluated our method on prostate segmentation and optic cup and disc segmentation tasks. Our method outperforms other comparison methods in reducing model forgetting and increasing explainability. Our code is available at https://github.com/jingyzhang/S3R.

Interleukin-23 Regulates Inflammatory Osteoclastogenesis via Activation of CLEC5A(+) Osteoclast Precursors

OBJECTIVE

To investigate the role of interleukin-23 (IL-23) in pathologic bone remodeling in inflammatory arthritis.

METHODS

In this study we investigated the role of IL-23 in osteoclast differentiation and activation using in vivo gene transfer techniques in wild-type and myeloid DNAX-activation protein 12-associating lectin-1 (MDL-1)-deficient mice, and by performing in vitro and in vivo osteoclastogenesis assays using spectral flow cytometry, micro-computed tomography analysis, Western blotting, and immunoprecipitation.

RESULTS

Herein, we show that IL-23 induces the expansion of a myeloid osteoclast precursor population and supports osteoclastogenesis and bone resorption in inflammatory arthritis. Genetic ablation of C-type lectin domain family member 5A, also known as MDL-1, prevents the induction of osteoclast precursors by IL-23 that is associated with bone destruction, as commonly observed in inflammatory arthritis. Moreover, osteoclasts derived from the bone marrow of MDL-1-deficient mice showed impaired osteoclastogenesis, and MDL-1-/- mice had increased bone mineral density.

CONCLUSION

Our data show that IL-23 signaling regulates the availability of osteoclast precursors in inflammatory arthritis that could be effectively targeted for the treatment of inflammatory bone loss in inflammatory arthritis.

Effects of stay-at-home orders on skill requirements in vacancy postings

The COVID-19 pandemic and containment policies have had profound economic impacts on the labor market. Stay-at-home orders (SAHOs) implemented across most of the United States changed the way of people worked. In this paper, we quantify the effect of SAHO durations on skill demands to study how firms adjust labor demand within occupation. We use skill requirement information from the 2018 to 2021 online job vacancy posting data from Burning Glass Technologies, exploit the spatial variations in the SAHO duration, and use instrumental variables to correct for the endogeneity in the policy duration related to local social and economic factors. We find that policy durations have persistent impacts on the labor demand after restrictions are lifted. Longer SAHOs motivate management style transformation from people-oriented to operation-oriented by requiring more of operational and administrative skills and less of personality and people management skills to carry out standard workflows. SAHOs also change the focus of interpersonal skill demands from specific customer services to general communication such as social and writing skills. SAHOs more thoroughly affect occupations with partial work-from-home capacity. The evidence suggests SAHOs change management structure and communication in firms.

IL-27 attenuates IL-23 mediated inflammatory arthritis

Interleukin 27 has both pro-inflammatory and anti-inflammatory properties in autoimmunity. The anti-inflammatory effects of IL-27 are linked with inhibition of Th17 differentiation but the IL-27 effect on myeloid cells is less studied. Herein we demonstrate that IL-27 inhibits IL-23-induced inflammation associated not only with Th17 cells but also with myeloid cell infiltration in the joints and splenic myeloid populations of CD11b⁺ GR1⁺ and CD3^-CD11b⁺CD11c^-GR1^- cells. The IL-27 anti-inflammatory response was associated with reduced levels of myeloid cells in the spleen and bone marrow. Overall, our data demonstrate that IL-27 has an immunosuppressive role that affects IL-23-dependent myelopoiesis in the bone marrow and its progression to inflammatory arthritis and plays a crucial role in controlling IL-23 driven joint inflammation by negatively regulating the expansion of myeloid cell subsets.

PyMIC: A deep learning toolkit for annotation-efficient medical image segmentation

BACKGROUND AND OBJECTIVE

Open-source deep learning toolkits are one of the driving forces for developing medical image segmentation models that are essential for computer-assisted diagnosis and treatment procedures. Existing toolkits mainly focus on fully supervised segmentation that assumes full and accurate pixel-level annotations are available. Such annotations are time-consuming and difficult to acquire for segmentation tasks, which makes learning from imperfect labels highly desired for reducing the annotation cost. We aim to develop a new deep learning toolkit to support annotation-efficient learning for medical image segmentation, which can accelerate and simplify the development of deep learning models with limited annotation budget, e.g., learning from partial, sparse or noisy annotations.

METHODS

Our proposed toolkit named PyMIC is a modular deep learning library for medical image segmentation tasks. In addition to basic components that support development of high-performance models for fully supervised segmentation, it contains several advanced components that are tailored for learning from imperfect annotations, such as loading annotated and unannounced images, loss functions for unannotated, partially or inaccurately annotated images, and training procedures for co-learning between multiple networks, etc. PyMIC is built on the PyTorch framework and supports development of semi-supervised, weakly supervised and noise-robust learning methods for medical image segmentation.

RESULTS

We present several illustrative medical image segmentation tasks based on PyMIC: (1) Achieving competitive performance on fully supervised learning; (2) Semi-supervised cardiac structure segmentation with only 10% training images annotated; (3) Weakly supervised segmentation using scribble annotations; and (4) Learning from noisy labels for chest radiograph segmentation.

CONCLUSIONS

The PyMIC toolkit is easy to use and facilitates efficient development of medical image segmentation models with imperfect annotations. It is modular and flexible, which enables researchers to develop high-performance models with low annotation cost. The source code is available at:https://github.com/HiLab-git/PyMIC.

First Report of radish tubers rot caused by Enterobacter asburiae in China

Radish (Raphanus sativus L.) is a widely consumed vegetable in China. However, radish is susceptible to diseases, which limits its yield and development in Harbin, China. In September 2021, rotten white radish tubers were observed in the field. The incidence of this disease reached 70% in October 2021, which led to huge economic losses (i.e., 30%-40%). Water-soaked lesions appeared on the radish tubers and appeared brown-yellow, which looked similar to ginger tuber rot caused by Enterobacter asburiae (Zhang et al. 2020). The interior was rotten with no considerable smell. Over time, the lesions gradually spread into all tubers of radish. Small square pieces of radish (0.5 cm × 0.5 cm) were excised from the junction of diseased and healthy tuber, disinfected with 75% alcohol, and washed three times with distilled water then ground to prepare tissue suspensions for plating. Under 28 ℃ for 16h, single colonies were isolated from the beef extract culture medium. Single colonies appeared oval, white, and smooth, with bright and slightly raised surfaces, and with moist neat edges. Gram-negative bacterial strain CCGL 988 was obtained, with an average size of 1-2 µm × 0.5-1 µm, and 3-4 flagella. Physiological and biological test results showed that strain CCGL 988 produced acid utilizing sucrose, glucose, maltobiose, D-Sorbitol, and mannitol; negative for Voges-Proskauer, methyl red, malanate, ornithine decarboxylase, arginine decarboxylase, and lysine decarboxylase. According to the results, strain CCGL 988 was identified as Enterobacter asburiae (Hoffmann et al. 2005). The 16S rDNA region of the strain was amplified using PCR with 27F/1492R primers (López et al. 2019), and partial gyrB, atpD, rpoB genes were amplified according to Zhang et al. (2020), infB gene was amplified with primers (F:TCAATGCGTGCTCGTGGTGCTC; R: TCGATACAGTGCCACTTCACG). The 16S rDNA, gyrB, atpD, rpoB and infB sequences were deposited in GenBank under accession numbers: ON999069, OP006448, OP006449, OP006450, and OP542231, respectively. These five sequences shared 99.80%, 100%, 100%, 100% and 100% of identity with E. asburiae (GenBank Accession: NO. CP011863). Maximum-likelihood phylogenetic tree clustered CCGL 988 with E. asburiae (MEGA7, bootstrap n = 1,000). Strain CCGL 988 was able to produce pectate lyases, polygalacturonases, cellulases, proteases, and extracellular polysaccharide using the methods described by Hugouviex-Cotte-Pattat et al. (2014), and Condemine et al. (1999). Koch's postulates were conducted by inoculating 20 µl of the bacterial suspension (108 CFU/ml) on the needle wound on the surface of six healthy radish tubers; six radish tubers incubated with sterile water were negative controls. Radish tubers were incubated at 28 ℃ with 80% humidity. The inoculated radish was slightly rotten after 7 days. Water-soaked lesions with light yellow were initially observed; after 12 days, the lesions expanded gradually and appeared deep yellow. No symptoms were found in the control radish. This experiment was carried out three times, each time with three replications. The bacterium was reisolated from infected radish tuber and was confirmed to be E. asburiae by the same molecular and morphological characterization as described above. This study is the first report of E. asburiae causing radish tuber rot in China. It serves as a basis for future studies to develop management strategies for the disease to prevent radish yield loss.

A fast two-stage algorithm for non-negative matrix factorization in smoothly varying data

This article reports the study of algorithms for non-negative matrix factorization (NMF) in various applications involving smoothly varying data such as time or temperature series diffraction data on a dense grid of points. Utilizing the continual nature of the data, a fast two-stage algorithm is developed for highly efficient and accurate NMF. In the first stage, an alternating non-negative least-squares framework is used in combination with the active set method with a warm-start strategy for the solution of subproblems. In the second stage, an interior point method is adopted to accelerate the local convergence. The convergence of the proposed algorithm is proved. The new algorithm is compared with some existing algorithms in benchmark tests using both real-world data and synthetic data. The results demonstrate the advantage of the algorithm in finding high-precision solutions.

[Study on long-term morphological stability of three-dimensional-printed photosensitive resin dental models]

Objective: To study the long-term morphological stability of three-dimensional (3D) printed photosensitive resin dental models under natural light and dark conditions. Methods: Eighty sets of resin dental models were made by the desktop 3D printer from one digital standard model set, and randomly divided into two groups, namely natural light group (40 sets) and dark group (40 sets). All resin models were stored in sealed bags, with 4 model sets from each group randomly collected after 1, 3, 5, 7, 14, 21, 28, 40, 60, or 90 days of storage and 3D scanned using an optical model scanner. The root-mean-square error (RMSE) was calculated to represent the mean deviation of the difference between the digital standard model and the scanned resin model. Meanwhile, three linear indexes (the width between the canines, the width between the first molars, and the arch length) of the resin dental model were measured and compared with the corresponding values of the standard model. RMSE and the linear measurements between the digital standard model and the scanned resin models were compared between the natural light group and the dark group and among models from different time points. Results: Compared with the digital standard model, the RMSE values of 96.9% (155/160) resin dental models were less than 0.1 mm within 90-day storage. Also, at the same time point, there was no significant difference in the RMSE between the natural light group and the dark group (P>0.05). 75.0% (360/480) of the absolute values of the linear differences (differences in inter-canine width, intra-molar width, and arch length between the digital standard model and the scanned resin model) were within 0.2 mm, and about 0.1% (3/480) of the linear differences were greater than 0.5 mm, and all of the linear differences were within 0.6 mm. Conclusions: 3D-printed resin dental models can be stored stably under natural light and dark conditions for a long time.

BraVRG, a novel protein of Brassica rapa, is induced by vernalization and promotes flowering in Arabidopsis thaliana

Plant flowering is an important economical characteristic for the transformation from vegetative growth to reproductive growth, especially for biennial crops. Additionally, bolting or flowering time is more important for vegetable plants due to their different harvest organs, such as flower for cauliflower and broccoli and leafy heads for cabbage and Chinese cabbage. The flowering time of Arabidopsis thaliana has six classical regulated pathways, and some key regulated genes are identified in Brassicaceae crops. However, the regulatory mechanism needs further exploration. Here, we reported an novel protein BraVRG (Vernalization Related Gene) of Chinese cabbage induced by vernalization. The expression of BraVRG increased rapidly at 14 day of vernalization in the semi-winter type of Brassica rapa and 21 days for the winter types. Meanwhile the modifications of H3K4me3 deposited on BraVRG increased but H3K27me3 decreased. Moreover, BraVRG promoted flowering in transgenic A. thaliana compared with the wild types accompanied the downregulated expression of FLC caused by the decrease of H3K4me3 enrichment and the increase of H3K27me3 on FLC with or without vernalization conditions.

Contrastive Semi-Supervised Learning for Domain Adaptive Segmentation Across Similar Anatomical Structures

Convolutional Neural Networks (CNNs) have achieved state-of-the-art performance for medical image segmentation, yet need plenty of manual annotations for training. Semi-Supervised Learning (SSL) methods are promising to reduce the requirement of annotations, but their performance is still limited when the dataset size and the number of annotated images are small. Leveraging existing annotated datasets with similar anatomical structures to assist training has a potential for improving the model's performance. However, it is further challenged by the cross-anatomy domain shift due to the image modalities and even different organs in the target domain. To solve this problem, we propose Contrastive Semi-supervised learning for Cross Anatomy Domain Adaptation (CS-CADA) that adapts a model to segment similar structures in a target domain, which requires only limited annotations in the target domain by leveraging a set of existing annotated images of similar structures in a source domain. We use Domain-Specific Batch Normalization (DSBN) to individually normalize feature maps for the two anatomical domains, and propose a cross-domain contrastive learning strategy to encourage extracting domain invariant features. They are integrated into a Self-Ensembling Mean-Teacher (SE-MT) framework to exploit unlabeled target domain images with a prediction consistency constraint. Extensive experiments show that our CS-CADA is able to solve the challenging cross-anatomy domain shift problem, achieving accurate segmentation of coronary arteries in X-ray images with the help of retinal vessel images and cardiac MR images with the help of fundus images, respectively, given only a small number of annotations in the target domain. Our code is available at https://github.com/HiLab-git/DAG4MIA.

Comprehensive Analysis of Transcriptomics and Genetic Alterations Identifies Potential Mechanisms Underlying Anthracycline Therapy Resistance in Breast Cancer

Anthracycline is a mainstay of treatment for breast cancer patients because of its antitumor activity. However, anthracycline resistance is a critical barrier in treating breast cancer. Thus, it is of great importance to uncover the molecular mechanisms underlying anthracycline resistance in breast cancer. Herein, we integrated transcriptome data, genetic alterations data, and clinical data of The Cancer Genome Atlas (TCGA) to identify the molecular mechanisms involved in anthracycline resistance in breast cancer. Two hundred and four upregulated genes and 1376 downregulated genes were characterized between the anthracycline-sensitive and anthracycline-resistant groups. It was found that drug resistance-associated genes such as ABCB5, CYP1A1, and CYP4Z1 were significantly upregulated in the anthracycline-resistant group. The gene set enrichment analysis (GSEA) suggested that the P53 signaling pathway, DNA replication, cysteine, and methionine metabolism pathways were associated with anthracycline sensitivity. Somatic TP53 mutation was a common genetic abnormality observed in the anthracycline-sensitive group, while CDH1 mutation was presented in the anthracycline-resistant group. Immune infiltration patterns were extremely different between the anthracycline-sensitive and anthracycline-resistant groups. Immune-associated chemokines and cytokines, immune regulators, and human leukocyte antigen genes were significantly upregulated in the anthracycline-sensitive group. These results reveal potential molecular mechanisms associated with anthracycline resistance.

MiR-93-5p promotes granulosa cell apoptosis and ferroptosis by the NF-kB signaling pathway in polycystic ovary syndrome

Polycystic ovary syndrome (PCOS) is one of the most common endocrine disorders in women of reproductive age. miR-93-5p has been reported to be elevated in granulosa cells of PCOS patients. However, the mechanism by which miR-93-5p drives granulosa cell (GC) progression remains unclear. Thus, this study focuses on the roles and mechanisms of miR-93-5p in the GCs of PCOS.

METHODS

KGN cells have similar ovarian physiological characteristics and are used to study the function and regulatory mechanism of GCs. In this study, KGN cells were transfected with si-NC, si-miR93-5p, oe-NC and oe-miR93-5p. A cell counting kit-8 assay, flow cytometry and western blotting were performed to observe the proliferation and apoptosis of KGN in different groups. Subsequently, the levels of reactive oxygen species, malondialdehyde, GPX4, SLC7A11 and Nrf2, which are indicators of ferroptosis, were measured by a dihydroethidium fluorescent dye probe, biochemical kit, western blotting and reverse transcription quantitative polymerase chain reaction. Ultimately, bioinformatic analysis and experimental methods were used to examine the interaction between miR-93-5p and the NF-κB signaling pathway.

RESULTS

miR-93-5p was upregulated in the GCs of PCOS patients. Overexpression of miR-93-5p promoted apoptosis and ferroptosis in KGN cells, while knockdown of miR-93-5p showed the reverse effect. Biological analysis and subsequent experiments demonstrated that miR-93-5p negatively regulates the NF- κB signaling pathway.

CONCLUSION

miR-93-5p promotes the apoptosis and ferroptosis in GC by regulating the NF-κB signaling pathway. Silencing of miR-93-5p protects against GC dysfunction. Our study identified miR-93-5p as a new molecular target for improving the function of GCs in PCOS patients.

Predicting the risk of axillary lymph node metastasis in early breast cancer patients based on ultrasonographic-clinicopathologic features and the use of nomograms: a prospective single-center observational study

OBJECTIVES

The purpose of this study was to establish two preoperative nomograms to evaluate the risk for axillary lymph node (ALN) metastasis in early breast cancer patients based on ultrasonographic-clinicopathologic features.

METHODS

We prospectively evaluated 593 consecutive female participants who were diagnosed with cT_1-3N_0-1M₀ breast cancer between March 2018 and May 2019 at Sun Yat-Sen Memorial Hospital. The participants were randomly classified into training and validation sets in a 4:1 ratio for the development and validation of the nomograms, respectively. Multivariate logistic regression analysis was performed to identify independent predictors of ALN status. We developed Nomogram A and Nomogram B to predict ALN metastasis (presence vs. absence) and the number of metastatic ALNs (≤ 2 vs. > 2), respectively.

RESULTS

A total of 528 participants were evaluated in the final analyses. Multivariable analysis revealed that the number of suspicious lymph nodes, long axis, short-to-long axis ratio, cortical thickness, tumor location, and histological grade were independent predictors of ALN status. The AUCs of nomogram A in the training and validation groups were 0.83 and 0.78, respectively. The AUCs of nomogram B in the training and validation groups were 0.87 and 0.87, respectively. Both nomograms were well-calibrated.

CONCLUSION

We developed two preoperative nomograms that can be used to predict ALN metastasis (presence vs. absence) and the number of metastatic ALNs (≤ 2 vs. > 2) in early breast cancer patients. Both nomograms are useful tools that will help clinicians predict the risk of ALN metastasis and facilitate therapy decision-making about axillary surgery.

KEY POINTS

• We developed two preoperative nomograms to predict axillary lymph node status based on ultrasonographic-clinicopathologic features. • Nomogram A was used to predict axillary lymph node metastasis (presence vs. absence). The AUCs in the training and validation groups were 0.83 and 0.78, respectively. Nomogram B was used to estimate the number of metastatic lymph nodes ( ≤ 2 vs. > 2). The AUCs in the training and validation group were 0.87 and 0.87, respectively. • Our nomograms may help clinicians weigh the risks and benefits of axillary surgery more appropriately.

The role of Sirtuin 1 in the pathophysiology of polycystic ovary syndrome

Polycystic ovarian syndrome (PCOS) is the most common multifactor heterogeneous endocrine and metabolic disease in women of childbearing age. PCOS is a group of clinical syndromes characterized by reproductive disorders, metabolic disorders, and mental health problems that seriously impact the physical and mental health of patients. At present, new studies suggest that human evolution leads to the body changes and the surrounding environment mismatch adaptation, but the understanding of the disease is still insufficient, the pathogenesis is still unclear. Sirtuin 1 (SIRT1), a member of the Sirtuin family, is expressed in various cells and plays a crucial role in cell energy conversion and physiological metabolism. Pathophysiological processes such as cell proliferation and apoptosis, autophagy, metabolism, inflammation, antioxidant stress and insulin resistance play a crucial role. Moreover, SIRT1 participates in the pathophysiological processes of oxidative stress, autophagy, ovulation disturbance and insulin resistance, which may be a vital link in the occurrence of PCOS. Hence, the study of the role of SIRT1 in the pathogenesis of PCOS and related complications will contribute to a more thorough understanding of the pathogenesis of PCOS and supply a basis for the treatment of patients.

Single-cell transcriptomic signatures and gene regulatory networks modulated by Wls in mammalian midline facial formation and clefts

Formation of highly unique and complex facial structures is controlled by genetic programs that are responsible for the precise coordination of three-dimensional tissue morphogenesis. However, the underlying mechanisms governing these processes remain poorly understood. We combined mouse genetic and genomic approaches to define the mechanisms underlying normal and defective midfacial morphogenesis. Conditional inactivation of the Wnt secretion protein Wls in Pax3-expressing lineage cells disrupted frontonasal primordial patterning, cell survival and directional outgrowth, resulting in altered facial structures, including midfacial hypoplasia and midline facial clefts. Single-cell RNA sequencing revealed unique transcriptomic atlases of mesenchymal subpopulations in the midfacial primordia, which are disrupted in the conditional Wls mutants. Differentially expressed genes and cis-regulatory sequence analyses uncovered that Wls modulates and integrates a core gene regulatory network, consisting of key midfacial regulatory transcription factors (including Msx1, Pax3 and Pax7) and their downstream targets (including Wnt, Shh, Tgfβ and retinoic acid signaling components), in a mesenchymal subpopulation of the medial nasal prominences that is responsible for midline facial formation and fusion. These results reveal fundamental mechanisms underlying mammalian midfacial morphogenesis and related defects at single-cell resolution.

First Report of Flower Stalk Wilting Caused by Rhizopus oryzae on Chinese cabbage in China

Chinese cabbage (Brassica rapa L. ssp. pekinensis) is one of the main biennial vegetables in China and its flowers can be produced in the second year. In May 2021, approximately 50% of the flower stalks of Chinese cabbage wilted in a field in Laizhou, China. Water-soaked lesions were first observed on the lateral shoots of flower stalks, leading to wilting at a later stage. Small diseased tissues were excised from the margin of lesions, surface disinfected in 75% alcohol, rinsed in distilled water twice, and transferred onto potato dextrose agar (PDA) medium for incubation at 28 ℃. Five fungal isolates were obtained using single spore isolation method. The fungal colonies were initially white and became gray or black within 5 days. The columella was globose to subglobose and 82.86±5.25 μm (n=5) in diameter; sporangiophores were smooth-walled, simple or branched; the globose sporangia were 86.06±15.37 μm (n=5) in diameter and black; the sporangiospores were subglobose and abundant and 5.23±0.98 μm (n=5) in diameter; and the rhizoids were dark brown and 5.69±1.82 μm (n=5) wide. A cetyl tri-methyl ammonium bromide method was used to extract DNA from 3-day-old hyphae (Ausubel et al. 1987). PCR was performed for ITS (White et al. 1990), the RNA polymerase II large subunit (RPB1) gene (Voigt et al. 2000) and the actin (ACT) gene (Stiller et al. 1997). The DNA sequences of the five isolates were identical, therefore, the sequence of Isolate RO21 was submitted to GenBank. According to BLAST search, the ITS (MZ452687), RPB1 (OK431470), and ACT (OK431471) sequences showed 99.66% similarity to Rhizopus oryzae Strain CBS 112.07 (NR103595), 100% to Strain CBS 127.08 (KJ566325) and 100% to Strain CBS 102660 (KJ551423), respectively. A neighbor-joining phylogenetic tree was reconstructed based on the ITS of Isolate RO21 and 14 other Rhizopus species sequences obtained from GenBank. Isolate RO21 was found to be most closely related to R. oryzae and far from other species. Based on morphological and phylogenetic characteristics, Isolate RO21 was identified as R. oryzae (Dolatabadi et al. 2014, Kwon et al. 2015, Palemón-Alberto et al. 2020). Sporangiospores were harvested from 5-day-old PDA cultures, suspended in sterilized distilled water, adjusted to 106 spores/ml and amended with 0.1% Tween-80. Chinese cabbage inbred line "A54-1" was inoculated near the middle of the flower stalk by applying 20 μl of spore suspension (106 spores/ml) to each of three sites wounded using a sterilized knife or to the unwounded site. Sterilized distilled water was used as the control. Forty flower stalks (20 for the inoculation treatment and the rest for the control) selected from ten plants were used for pathogenicity test. All plants were incubated in a growth chamber at 28/22 °C (day/night), with 80 to 90% of relative humidity. Wilting symptoms similar to those in the field were observed in the wounded flower stalks after 5 days and in the non-wounded flower stalks after 15 days. All control flower stalks remained asymptomatic. The fungus was re-isolated from the artificially infected flower stalks and identified as R. oryzae by morphological characteristics and sequencing to fulfill the Koch's postulates. To our knowledge, this is the first report that R. oryzae causes flower stalk wilting on Chinese cabbage in China. The results can provide the basis for future studies on the occurrence, prevention and management of this disease.

Clinical Potential of Hypoxia Inducible Factors Prolyl Hydroxylase Inhibitors in Treating Nonanemic Diseases

Hypoxia inducible factors (HIFs) and their regulatory hydroxylases the prolyl hydroxylase domain enzymes (PHDs) are the key mediators of the cellular response to hypoxia. HIFs are normally hydroxylated by PHDs and degraded, while under hypoxia, PHDs are suppressed, allowing HIF-α to accumulate and transactivate multiple target genes, including erythropoiesis, and genes participate in angiogenesis, iron metabolism, glycolysis, glucose transport, cell proliferation, survival, and so on. Aiming at stimulating HIFs, a group of small molecules antagonizing HIF-PHDs have been developed. Of these HIF-PHDs inhibitors (HIF-PHIs), roxadustat (FG-4592), daprodustat (GSK-1278863), vadadustat (AKB-6548), molidustat (BAY 85-3934) and enarodustat (JTZ-951) are approved for clinical usage or have progressed into clinical trials for chronic kidney disease (CKD) anemia treatment, based on their activation effect on erythropoiesis and iron metabolism. Since HIFs are involved in many physiological and pathological conditions, efforts have been made to extend the potential usage of HIF-PHIs beyond anemia. This paper reviewed the progress of preclinical and clinical research on clinically available HIF-PHIs in pathological conditions other than CKD anemia.

Fired bullet signature correlation using the finite ridgelet transform (FRIT) and the gray level co-occurrence matrix (GLCM) methods

When a bullet is fired from a barrel, micro striation marks caused by the sliding motion of the bullet through the rifled barrel are one of the foremost factors in automated ballistic identification. This paper focuses on 3D topography images of land engraved areas (LEA) and proposes a bullet identification method incorporating the finite ridgelet transform (FRIT) and gray level co-occurrence matrix (GLCM) algorithms. The FRIT extracts the striation marks from the 3D micro image and the GLCM generates a linearly weighted weight corresponding to the texture features for 2D average profile calculation. The entire striation marks image is divided into several cells and a cell with valid correlation areas is assigned a large weight, but the one with invalid correlation areas is assigned a small weight along the vertical direction. The visible results show that the valid correlation areas are effectively identified and the negative effects of invalid correlation areas are suppressed. Tests were performed on a control set and an unknown set, giving a total of 35 bullet samples fired from pistols with 10 consecutively manufactured slides. The results included no false identifications or false exclusions and a clear separation between the matching index of the matching and non-matching LEA profiles, demonstrating excellent performance in striation mark capture and valid correlation areas extraction of FRIT and GLCM algorithms. The proposed method is capable of correctly matching toolmarked surfaces to the barrel used.

Advances in Research on the Mechanism of Heterosis in Plants

Heterosis is a common biological phenomenon in nature. It substantially contributes to the biomass yield and grain yield of plants. Moreover, this phenomenon results in high economic returns in agricultural production. However, the utilization of heterosis far exceeds the level of theoretical research on this phenomenon. In this review, the recent progress in research on heterosis in plants was reviewed from the aspects of classical genetics, parental genetic distance, quantitative trait loci, transcriptomes, proteomes, epigenetics (DNA methylation, histone modification, and small RNA), and hormone regulation. A regulatory network of various heterosis-related genes under the action of different regulatory factors was summarized. This review lays a foundation for the in-depth study of the molecular and physiological aspects of this phenomenon to promote its effects on increasing the yield of agricultural production.

A new nomogram for predicting the malignant diagnosis of Breast Imaging Reporting and Data System (BI-RADS) ultrasonography category 4A lesions in women with dense breast tissue in the diagnostic setting

Background

Biopsy has been recommended for Breast Imaging Reporting and Data System (BI-RADS) category 4 lesions. However, the malignancy rate of category 4A lesions is very low (2-10%). Therefore, most biopsies of category 4A lesions are benign, and the results will generally cause additional health care costs and patient anxiety.

Methods

A prediction model was developed based on an analysis of 418 BI-RADS ultrasonography (US) category 4A patients at Sun Yat-sen Memorial Hospital. Univariate and multivariate logistic regression analyses were applied to identify significant variables for inclusion in the final nomogram. The predictive accuracy and discriminative ability were evaluated using the concordance index (C-index) and calibration curves. An independent cohort of 97 patients from the Second Affiliated Hospital of Guangzhou Medical University was used for external validation.

Results

The independent risk factors from the multivariate analysis for the training cohort were family history of breast cancer (OR =4.588, P=0.004), US features [margin (OR =2.916, P=0.019), shape (irregular vs. oval, OR =2.474, P=0.044; round vs. oval, OR =1.935, P=0.276), parallel orientation vs. not parallel (OR =2.204, P=0.040)], low suspicious lymph nodes (OR =7.664, P=0.019), and suspicious calcifications on mammography (MG) (OR =6.736, P=0.001). The C-index was good in the training [0.813, 95% confidence interval (95% CI), 0.733 to 0.893] and validation cohorts (0.765, 95% CI, 0.584 to 0.946). The calibration curves showed optimal agreement between the nomogram prediction and actual observations for the probability of malignancy. Also, the cutoff score was set to 100 for discriminating high and low risk. The model performed well in discerning different risk groups.

Conclusions

We developed a well-discriminated and calibrated nomogram to predict the malignancy of BI-RADS US category 4A lesions in dense breast tissue, which may help clinicians identify patients at lower or higher risk.

Immunological Identification and Characterization of the Capsid Scaffold Protein Encoded by UL26.5 of Herpes Simplex Virus Type 2

Herpes simplex virus type 2 (HSV2), a pathogen that causes genital herpes lesions, interferes with the host immune system via various known and unknown mechanisms. This virus has been used to study viral antigenic composition. Convalescent serum from HSV2-infected patients was used to identify viral antigens via 2-D protein electrophoresis and immunoblotting. The serum predominantly recognized several capsid scaffold proteins encoded by gene UL26.5, mainly ICP35. This protein has been primarily reported to function temporarily in viral assembly but is not expressed in mature virus particles. Further immunological studies suggested that this protein elicits specific antibody and cytotoxic T lymphocyte (CTL) responses in mice, but these responses do not result in a clinical protective effect in response to HSV2 challenge. The data suggested that immunodominance of ICP35 might be used to design an integrated antigen with other viral glycoproteins.

Specimen number based diagnostic yields of suspicious axillary lymph nodes in core biopsy in breast cancer: clinical implications from a prospective exploratory study

Background

Ultrasound (US)-guided core needle biopsy (CNB) is widely applied in the pathological diagnosis of suspicious axillary lymph nodes (ALNs) in breast cancer. However, the number of specimens removed during biopsy is currently based on the preference of the individual radiologist. This study aims to analyze the specimen number based diagnostic yields of US guided CNB of suspicious ALNs in breast cancer.

Methods

Core biopsy specimens of suspicious lymph nodes were prospectively obtained from breast cancer patients treated at our hospital between November, 2018, and July, 2019. Four specimens were obtained from each patient and labeled 1-4 in the order they were removed. Each specimen underwent pathological evaluation to determine whether metastasis had occurred. The diagnostic yields of the specimens were calculated and differences in diagnostic accuracy according to the number of specimens were evaluated by McNemar's test.

Results

A total of 167 patients were enrolled, and 139 (83.2%) cases were identified as metastasis by CNB. The diagnostic yields were: 74.2% (specimen 1), 87.8% (specimens 1-2), 91.2% (specimens 1-3), and 94.6% (specimens 1-4). The increases in diagnostic yield from specimen 1 to 1-2 and from specimens 1-2 to 1-4 were significant; however, no significant differences were detected between specimens 1-3 and the first two, or between specimens 1-4 and the first three in this sample size. The lower diagnostic abilities for the first two specimens were associated with shorter long- and short-axis lengths of lymph nodes on US.

Conclusions

Although the second specimen contributed significant diagnostic yield of suspicious axillary lymph nodes in core biopsy in breast cancer, a minimum number cannot be determined by this study. Additional specimens may improve diagnostic yield particularly in patients with small nodes.

LncRNA RPPH1 attenuates Aβ25-35-induced endoplasmic reticulum stress and apoptosis in SH-SY5Y cells via miR-326/PKM2

BACKGROUND

The durative endoplasmic reticulum stress (ERS) and subsequent apoptosis contributes to the development and progression of Alzheimer's disease (AD). MiR-326 can reduce pyruvate kinase M2 (PKM2) expression, leading to ERS. Whereas, lncRNA RPPH1 is able to increase dendritic spine density and protect hippocampal pyramidal neurons through targeting miR-326. Our study aims to investigate the regulation of lncRNA RPPH1 and miR-326/PKM2 on ERS and related apoptosis in AD.

METHODS

SH-SY5Y cells treated with Aβ25-35 were selected as an in vitro AD model. RPPH1 and miR-326 overexpression and silencing cells were established by transforming vectors. The expression of RPPH1 and miR-326 were detected by qRT-PCR. MTT, flow cytometric, intracellular calcium assay and Western blot were used to test the functions of RPPH1 and miR-326 in SH-SY5Y cell proliferation, apoptosis and ERS. Dual-luciferase assay was used to detect the interaction among RPPH1, miR-326 and PKM2.

RESULTS

RPPH1 overexpression enhanced the viability of SH-SY5Y cells, and attenuated the apoptosis of of SH-SY5Y cells. Moreover, RPPH1 overexpression down-regulated ER stress related proteins such as GRP78, CHOP and cleaved caspase-12. Mechanistically, RPPH1 directly targeted miR-326, thereby counteracting its inhibitory effect on PKM2 expression, contributing to attenuation of apoptosis and ERS induced by Aβ25-35.

CONCLUSION

Aβ25-35-induced ERS and apoptosis in SH-SY5Y cells can be attenuated by lncRNA RPPH1 through regulating miR-326/PKM2 axis. This study provided therapeutic options for AD patients.

Validation of non-negative matrix factorization for rapid assessment of large sets of atomic pair distribution function data

The use of the non-negative matrix factorization (NMF) technique is validated for automatically extracting physically relevant components from atomic pair distribution function (PDF) data from time-series data such as in situ experiments. The use of two matrix-factorization techniques, principal component analysis and NMF, on PDF data is compared in the context of a chemical synthesis reaction taking place in a synchrotron beam, applying the approach to synthetic data where the correct composition is known and on measured PDFs from previously published experimental data. The NMF approach yields mathematical components that are very close to the PDFs of the chemical components of the system and a time evolution of the weights that closely follows the ground truth. Finally, it is discussed how this would appear in a streaming context if the analysis were being carried out at the beamline as the experiment progressed.

Genome-Wide Identification and Analysis of CC-NBS-LRR Family in Response to Downy Mildew and Black Rot in Chinese Cabbage

The nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family is the largest group of plant disease resistance (R) genes widespread in response to viruses, bacteria, and fungi usually involved in effector triggered immunity (ETI). Forty members of the Chinese cabbage CC type NBS-LRR family were investigated in this study. Gene and protein characteristics, such as distributed locations on chromosomes and gene structures, were explored through comprehensive analysis. CC-NBS-LRR proteins were classified according to their conserved domains, and the phylogenetic relationships of CC-NBS-LRR proteins in Brassica rapa, Arabidopsis thaliana, and Oryza sativa were compared. Moreover, the roles of BrCC-NBS-LRR genes involved in pathogenesis-related defense were studied and analyzed. First, the expression profiles of BrCC-NBS-LRR genes were detected by inoculating with downy mildew and black rot pathogens. Second, sensitive and resistant Chinese cabbage inbred lines were screened by downy mildew and black rot. Finally, the differential expression levels of BrCC-NBS-LRR genes were monitored at 0, 1, 3, 6, 12 and 24 h for short and 0, 3, 5, 7, 10 and 14 days for long inoculation time. Our study provides information on BrCC-NBS-LRR genes for the investigation of the functions and mechanisms of CC-NBS-LRR genes in Chinese cabbage.

Simple and rapid detection Aspergillus fumigatus by loop-mediated isothermal amplification coupled with lateral flow biosensor assay

AIMS

We have developed a new diagnostic technique, termed loop-mediated isothermal amplification coupled with lateral flow biosensor (LAMP-LFB), which has been successfully applied to the detection of Aspergillus fumigatus.

MATERIAL AND METHODS

A set of six LAMP primers was designed according to the A. fumigatus-specific anxC4 gene, which specifically recognized eight different regions of the target sequence. The LFB was employed for reporting the A. fumigatus-LAMP results, and the visual readouts were obtained within 2 min. The strains of A. fumigatus species and non-A. fumigatus species were used to test the assay's sensitivity and examine the analytical specificity of the target assay. Optimal LAMP conditions were 66°C for 50 min. The limit of detection is 100 fg. No cross-reactions were obtained, and the specificity of LAMP-LFB assay was 100%. The whole process of the assay, including 20 min of DNA preparation, 50 min of constant temperature amplification, and 2 min of detection by the sensor strip, took a total of 72 min (less than 75 min). Among 89 sputum specimens for clinical evaluation, 10 (11·23%) samples were A. fumigatus-positive by LAMP-LFB and traditional culture method, 9 (10·11%) samples were A. fumigatus-positive by PCR method. Compared with culture method, the diagnostic accuracy of LAMP-LFB method was 100%.

CONCLUSIONS

The novel LAMP-LFB detection technology established in the current research is a rapid and reliable detection tool for A. fumigatus.

SIGNIFICANCE AND IMPACT OF THE STUDY

This novel LAMP-LFB assay can quickly, specifically and sensitively detect A. fumigatus, thereby speeding up the detection process and increasing the detection rate. In addition, it can also be used as a new molecular method for detection of A. fumigatus in clinical and laboratory areas.

CA-Net: Comprehensive Attention Convolutional Neural Networks for Explainable Medical Image Segmentation

Accurate medical image segmentation is essential for diagnosis and treatment planning of diseases. Convolutional Neural Networks (CNNs) have achieved state-of-the-art performance for automatic medical image segmentation. However, they are still challenged by complicated conditions where the segmentation target has large variations of position, shape and scale, and existing CNNs have a poor explainability that limits their application to clinical decisions. In this work, we make extensive use of multiple attentions in a CNN architecture and propose a comprehensive attention-based CNN (CA-Net) for more accurate and explainable medical image segmentation that is aware of the most important spatial positions, channels and scales at the same time. In particular, we first propose a joint spatial attention module to make the network focus more on the foreground region. Then, a novel channel attention module is proposed to adaptively recalibrate channel-wise feature responses and highlight the most relevant feature channels. Also, we propose a scale attention module implicitly emphasizing the most salient feature maps among multiple scales so that the CNN is adaptive to the size of an object. Extensive experiments on skin lesion segmentation from ISIC 2018 and multi-class segmentation of fetal MRI found that our proposed CA-Net significantly improved the average segmentation Dice score from 87.77% to 92.08% for skin lesion, 84.79% to 87.08% for the placenta and 93.20% to 95.88% for the fetal brain respectively compared with U-Net. It reduced the model size to around 15 times smaller with close or even better accuracy compared with state-of-the-art DeepLabv3+. In addition, it has a much higher explainability than existing networks by visualizing the attention weight maps. Our code is available at https://github.com/HiLab-git/CA-Net.

Ultrasound-Guided Vacuum-assisted Biopsy Versus Surgical Resection in Patients With Breast Desmoid Tumor

BACKGROUND

Recent studies suggest that desmoid tumors can be managed more conservatively rather than undergoing wide surgical resection (SR). Ultrasound-guided vacuum-assisted biopsy (UGVAB) is a minimally invasive technique. This retrospective study aimed to compare the outcome in patients with breast desmoid tumor (BDT) who received UGVAB alone versus SR.

MATERIALS AND METHODS

The pathology database was searched for patients diagnosed with BDT ≤ 3 cm from 2007 to 2019. All patients underwent breast ultrasound examination and were then performed UGVAB alone or local SR. The Kaplan-Meier method with a log-rank test was used as a univariate analysis to compare the relapse-free survival (RFS) rates between UGVAB and SR groups. Cox regression analysis was used for multivariate analysis.

RESULTS

A total of 39 patients were included. The median follow-up was 41 mo (range, 5-110 mo). The incidence of tumor recurrence was 23.1% (9/39). The 3-y cumulative RFS was 83.1% and 95.8% in the UGVAB and SR group, respectively, which was not significantly different between the two groups (P = 0.131, log-rank test). Multivariate analysis also revealed that treatment strategy (UGVAB versus SR) was not associated with an increased risk of relapse events (P = 0.274).

CONCLUSIONS

Small desmoid tumors (≤3 cm) after UGVAB alone did not have a significantly compromised RFS compared with those who underwent SR. UGVAB may be an alternative and relatively conservative method for the diagnosis and local control of BDT with a smaller size. A prospective, randomized study with large sample size is needed to confirm this observation.

Roles of CsBRC1-like in leaf and lateral branch development in cucumber

TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) family genes, as plant-specific transcription factors, play vital roles in flower pattern, leaf development and plant architecture. Our recent study shows that the TCP gene BRANCHED1 (CsBRC1) specifically regulates shoot branching in cucumber. Here, we found CsBRC1 had a closely related paralogous gene CsBRC1-like. The synteny analysis revealed that these two genes originated from a segmental duplication. CsBRC1-like displayed different expression patterns in cucumber compared with CsBRC1, indicating that they may have functional differentiation. Ectopic expression of CsBRC1-like in Arabidopsis brc1-1 mutant resulted in reduced rosette branches and rosette leaves, whereas silencing CsBRC1-like in cucumber only led to a deformed true leaf of seedling rather than affecting the shoot branching. RNA-seq analysis of wild-type and CsBRC1-like-RNAi plants implicated that CsBRC1-like might regulate early leaf development through affecting the transcripts of auxin and cytokinin related genes in cucumber. Moreover, CsBRC1-like directly interacts with CsTCP10a and CsBRC1 in vivo. Our results demonstrated that CsBRC1-like has a specific role in regulating leaf development, and CsBRC1-like and CsBRC1 may have overlapping roles in shoot branching.

Genome-wide analysis of CsWOX transcription factor gene family in cucumber (Cucumis sativus L.)

WUSCHEL-related homeobox (WOX) transcription factors are plant-specific members that characterized by the presence of a homeodomain. It has been shown that WOX members regulate several aspects of plant development, but the biological functions of this CsWOX gene family remain largely unknown in cucumber (Cucumis sativus L.). In this study, we identified and characterized 11 putative CsWOX genes in cucumber, which are also divided into three major clades (e.g., the Ancient clade, the Intermediate clade and the WUS clade). Expression pattern analysis revealed tissue-specific expression patterns of CsWOX genes, including that CsWOX9 is mainly expressed in developing fruit and also has lower expression in tip and axillary bud, which was further confirmed by in situ hybridization assay. Moreover, overexpression of CsWOX9 in Arabidopsis led to increased branches and rosette leaves, and shorter siliques. Together, these results indicated that CsWOX members may regulate cucumber growth and development.

Gene regulatory network controlling carpel number variation in cucumber

The WUSCHEL-CLAVATA3 pathway genes play an essential role in shoot apical meristem maintenance and floral organ development, and under intense selection during crop domestication. The carpel number is an important fruit trait that affects fruit shape, size and internal quality in cucumber, but the molecular mechanism remains elusive. Here, we found that CsCLV3 expression was negatively correlated with carpel number in cucumber cultivars. CsCLV3-RNAi led to increased number of petals and carpels, whereas overexpression of CsWUS resulted in more sepals, petals and carpels, suggesting that CsCLV3 and CsWUS function as a negative and a positive regulator for carpel number variation, respectively. Biochemical analyses indicated that CsWUS directly bound to the promoter of CsCLV3 and activated its expression. Overexpression of CsFUL1^A , a FRUITFULL-like MADS-box gene, resulted in more petals and carpels. CsFUL1^A can directly bind to the CsWUS promoter to stimulate its expression. Furthermore, we found that auxin participated in carpel number variation in cucumber through interaction of CsARF14 with CsWUS. Therefore, we have identified a gene regulatory pathway involving CsCLV3, CsWUS, CsFUL1^A and CsARF14 in determining carpel number variation in an important vegetable crop - cucumber.

The MADS-Box Gene CsSHP Participates in Fruit Maturation and Floral Organ Development in Cucumber

Cucumber is an important vegetable crop bearing fleshy pepo fruit harvested immature. Fruits left unpicked in time during summer production, as well as unfavorable environmental conditions during post-harvest shelf, will cause cucumber fruits to turn yellow and ripen, and thus impair the market value. Identification of maturity-related genes is of great agricultural and economic importance for cucumber production. Here, we isolated and characterized a MADS-box gene, Cucumis sativus SHATTERPROOF (CsSHP) in cucumber. Expression analysis indicated that CsSHP was specifically enriched in reproductive organs including stamens and carpels. Ectopic expression of CsSHP was unable to rescue the indehiscence silique phenotype of shp1 shp2 mutant plant in Arabidopsis. Instead, overexpression of CsSHP resulted in early flowering, precocious phenotypes, and capelloid organs in wild-type Arabidopsis. Biochemical analysis indicated that CsSHP directly interacted with cucumber SEPALLATA (SEP) proteins. CsSHP expression increased significantly during the yellowing stage of cucumber ripening, and was induced by exogenous application of abscisic acid (ABA). Therefore, CsSHP may participate in fruit maturation through the ABA pathway and floral organ specification via interaction with CsSEPs to form protein complex in cucumber.

Up-regulation of microRNA-375 ameliorates the damage of dopaminergic neurons, reduces oxidative stress and inflammation in Parkinson's disease by inhibiting SP1

Background: This study is conducted to investigate the protective role of elevated microRNA-375 (miR-375) in dopaminergic neurons in Parkinson’s disease through down-regulating transcription factor specificity protein 1 (SP1).

Results: The successfully modeled rats with Parkinson’s disease showed aggregated neurobehavioral change, increased neuroinflammatory response and oxidative stress, and lowered dopamine content. Parkinson’s disease rats treated with overexpressed miR-375 displayed improved neurobehavioral change, ameliorated neuroinflammatory response and oxidative stress, heightened dopamine content and abated neuronal apoptosis by down-regulating SP1. Up-regulation of SP1 reversed the protective effect of upregulated miR-375 on Parkinson’s disease.

Conclusion: Up-regulation of miR-375 ameliorated the damage of dopaminergic neurons, reduced oxidative stress and inflammation in Parkinson’s disease by inhibiting SP1.

Methods: Parkinson’s disease rat model was established by targeted injection of 6-hydroxydopamine to damage the substantia nigra striatum. The successfully modeled Parkinson’s disease rats were intracerebroventricularly injected with miR-375 mimics or pcDNA3.1-SP1. The functions of miR-375 and SP1 in neurobehavioral change, neuroinflammatory response, oxidative stress, dopamine content and expression of apoptosis-related proteins in the substantia nigra of Parkinson’s disease rats were evaluated. The target relation of miR-375 and SP1 was confirmed by bioinformatics analysis and dual luciferase reporter gene assay.

LncRNA Rpph1 protects amyloid-β induced neuronal injury in SK-N-SH cells via miR-122/Wnt1 axis

Objective: To investigate the role of lncRNA Rpph1 on amyloid-β induced neuronal injury in SK-N-SH cells and underlying mechanism.Methods: In vitro Alzheimer's disease (AD) model was established using the SK-N-SH cells treated with Aβ_25-35 peptide. APPswe/PS1ΔE9 double transgenic mice were used as AD animal model. Rpph1 was over-expressed and miR-122 was inhibited or overexpressed in SK-N-SH cells via transfection with pcDNA3.1-oe Rpph1 vector, miR-122 inhibitor or miR-122 mimic, respectively. Cell viabilities and apoptosis were evaluated using MTT or flow cytometry assay, respectively. Quantitative real-time PCR (RT-qPCR) was used to determine expression of Rpph1 and miR-122. Western blotting was used to determine the expression of apoptosis related proteins as well as Wnt/β-catenin signaling related proteins. Dual luciferase reporter assay was conducted to confirm the binding of miR-122 with predictive binding site in 3' UTR of Rpph1 and Wnt1.Results: Both lncRNA Rpph1 and miR-122 were up-regulated in AD mouse. Either over-expression of Rpph1 or inhibition of miR-122 restored the cell viability or decreased cell apoptosis rate in Aβ induced SK-N-SH cells. Overexpression of miR-122 inhibited the cell viability while did not influence the Aβ level in SK-N-SH cells. Furthermore, over-expression of Rpph1, as well as inhibition of miR-122, elevated Bcl-2, c-myc, Survivin and decreased Bax expression via activating Wnt/β-catenin signaling. Dual luciferase reporter assay showed that miR-122 could directly target to 3'UTR of Rpph1 and Wnt1.Conclusion: Both lncRNA Rpph1 and miR-122 were up-regulated in AD mouse and Rpph1 activated Wnt/β-catenin signaling to ameliorate amyloid-β induced neuronal apoptosis in SK-N-SH cells via direct targeting miR-122.

Olig2 regulates terminal differentiation and maturation of peripheral olfactory sensory neurons

The bHLH transcription factor Olig2 is required for sequential cell fate determination of both motor neurons and oligodendrocytes and for progenitor proliferation in the central nervous system. However, the role of Olig2 in peripheral sensory neurogenesis remains unknown. We report that Olig2 is transiently expressed in the newly differentiated olfactory sensory neurons (OSNs) and is down-regulated in the mature OSNs in mice from early gestation to adulthood. Genetic fate mapping demonstrates that Olig2-expressing cells solely give rise to OSNs in the peripheral olfactory system. Olig2 depletion does not affect the proliferation of peripheral olfactory progenitors and the fate determination of OSNs, sustentacular cells, and the olfactory ensheathing cells. However, the terminal differentiation and maturation of OSNs are compromised in either Olig2 single or Olig1/Olig2 double knockout mice, associated with significantly diminished expression of multiple OSN maturation and odorant signaling genes, including Omp, Gnal, Adcy3, and Olfr15. We further demonstrate that Olig2 binds to the E-box in the Omp promoter region to regulate its expression. Taken together, our results reveal a distinctly novel function of Olig2 in the periphery nervous system to regulate the terminal differentiation and maturation of olfactory sensory neurons.

Algorithm for distance list extraction from pair distribution functions

An algorithm is presented to extract the distance list from atomic pair distribution functions in a highly automated way. The algorithm is constructed via curve fitting based on a Debye scattering equation model. Because of the non-convex nature of the resulting optimization problem, a number of techniques are developed to overcome various computational difficulties. A key ingredient is a new approach to obtain a reasonable initial guess based on the theoretical properties of the mathematical model. Tests on various nanostructured samples show the effectiveness of the initial guess and the accuracy and overall good performance of the extraction algorithm. This approach could be extended to any spectrum that is approximated as a sum of Gaussian functions.