Comparative analysis of the image quality and diagnostic performance of the zooming technique with diffusion-weighted imaging using different b-values for thyroid papillary carcinomas and benign nodules.

Objective: To compare image quality and diagnostic performance using different b-values for the zooming technique with diffusion-weighted imaging (ZOOMit-DWI) in thyroid nodules. Materials and methods: A total of 51 benign thyroid nodules and 50 thyroid papillary carcinomas were included. ZOOMit-DWI was performed with b-values of 0, 500, 1000, 1500 and 2000 s/mm2. The sharpness was evaluated as subjective index. The signal intensity ratio (SIR), signal-to-noise ratio (SNR) and apparent diffusion coefficient (ADC) were measured as objective indices. Pairwise comparisons were performed among the different b-value groups using the Friedman test. A receiver operating characteristic curve of the ADC value was used to evaluate diagnostic performance. The DeLong test was used to compare diagnostic effectiveness among the different b-value groups. Results: In both the papillary carcinoma group (P = 0.670) and the benign nodule group (P = 0.185), the sharpness of nodules was similar between b-values of 1000 s/mm2and 1500 s/mm2. In the papillary carcinoma group, the SIRnodule was statistically higher in DWI images with a b-value of 1500 s/mm2than in DWI images with b-values of 500 s/mm2(P = 0.004), 1000 s/mm2(P = 0.002), and 2000 s/mm2(P = 0.003). When the b-values were 1500 s/mm2(P = 0.008) and 2000 s/mm2(P = 0.009), the SIRnodule significantly differed between the papillary carcinoma group and the benign nodule group. When b = 500 s/mm2, the ADC had an AUC of 0.888. When b = 1000 s/mm2, the ADC had an AUC of 0.881. When b = 1500 s/mm2, the ADC had an AUC of 0.896. When b = 2000 s/mm2, the ADC had an AUC of 0.871. The DeLong test showed comparable diagnostic effectiveness among the different b-value groups except for between b-values of 2000 s/mm2and 1500 s/mm2, with a b-value of 2000 s/mm2showing lower effectiveness. Conclusion: This study suggests that 1500 s/mm2may be a suitable b-value to differentiate benign and malignant thyroid nodules in ZOOMit-DWI images, which yielded better image quality.

N-acetyltransferase NAT10 controls cell fates via connecting mRNA cytidine acetylation to chromatin signaling.

Cell fate transition involves dynamic changes of gene regulatory network and chromatin landscape, requiring multiple levels of regulation, yet the cross-talk between epitranscriptomic modification and chromatin signaling remains largely unknown. Here, we uncover that suppression of N-acetyltransferase 10 (NAT10), the writer for mRNA N4-acetylcytidine (ac4C) modification, can notably affect human embryonic stem cell (hESC) lineage differentiation and pluripotent reprogramming. With integrative analysis, we identify that NAT10-mediated ac4C modification regulates the protein levels of a subset of its targets, which are strongly enriched for fate-instructive chromatin regulators, and among them, histone chaperone ANP32B is experimentally verified and functionally relevant. Furthermore, NAT10-ac4C-ANP32B axis can modulate the chromatin landscape of their downstream genes (e.g., key regulators of Wnt and TGFß pathways). Collectively, we show that NAT10 is an essential regulator of cellular plasticity, and its catalyzed mRNA cytidine acetylation represents a critical layer of epitranscriptomic modulation and uncover a previously unrecognized, direct cross-talk between epitranscriptomic modification and chromatin signaling during cell fate transitions.

First report of Fusarium ussurianum causing leaf spot on Hemerocallis citrina in Sichuan Basin of China.

Hemerocallis citrina is a popular vegetable crop in China, due to abundant nutrients in its edible flower buds. In March 2021, serious symptoms of leaf spot were observed on nearly 90% cultivated H. citrina seedlings in the fields of Dazhou city (31°17'56″ N, 107°31'59″ E), Sichuan, China. Symptomatic leaves were collected from 15 seedlings in five different sampling sites (3 seedlings per site). Small pieces (5 × 3 mm) of lesion margin were excised, surface disinfected in 70% ethanol for 20 s and 1% sodium hypochlorite (NaClO) for 40 s, washed, dried, placed on potato dextrose agar (PDA) amended with streptomycin sulfate (50 mg/L) and incubated in dark at 25 ℃ for two days. Finally, eight purified isolates, HHC-FL22, HHC-FL23, HHC-FL25, HHC-FL26, HHC-FL27, HHC-FL28, HHC-FL29 and HHC-FL30, showing similar morphology were obtained through transferring hyphal tips to fresh PDA plates. On PDA plates, mycelia were initially white but gradually became light yellow, and scarlet diffusible pigments were also produced with time. On carnation leaf agar, our isolates produced slightly curved macroconidia with 4 to 8 septa that measured 3.1 to 5.7 × 36.8 to 69.3 µm (n = 30). Microconidia and chlamydospores were not observed. Our isolates were initially identified as Fusarium species based on morphological features (Leslie and Summerell 2006). To further confirm accurate identity, primers EF1/EF2 (O'Donnell et al. 2010), TRI1015B/TRI1013E (Hao et al. 2017), RPB1-F5/RPB1-G2R (O'Donnell et al. 2010), and fRPB2-5F/fRPB2-11aR and RPB2-5f2/RPB2-7cr (O'Donnell et al. 2012) were used to amplify gene sequences of translation elongation factor-1 alpha (TEF1), 3-O-acetyltransferase (Tri101), and DNA-directed RNA polymerase II largest (RPB1) and second largest subunit (RPB2), respectively. Our sequences were deposited in GenBank under accession numbers OQ860946 to OQ860953 (TEF1), OR393245 to OR393252 (Tri101), OP131893 to OP131900 (RPB1), and OQ860954 to OQ860961 and OP131885 to OP131892 (RPB2), respectively. BLASTN searches of our sequences showed 99 ~ 100% identity with TEF1 (FJ240301.1), Tri101 (FJ240345.1), RPB1 (MW233297.1) and RPB2 (KM361666.1) of F. ussurianum NRRL 45681, and 99.05 ~ 100% identity with TEF1 (FJ240305.1) and Tri101 (FJ240349.1) of F. ussurianum NRRL 45833, respectively. Two independent maximum-likelihood phylogenetic trees based on different combined datasets of TEF1, Tri101, RPB1 and RPB2 of Fusarium species confirmed that our isolates were F. ussurianum. To test pathogenicity, conidial suspension from HHC-FL23 (106 conidia / mL) were sprayed to seedlings of cultivar "chuanhuanghua No.1" (n = 3) and incubated in a greenhouse (25°C under 90% relative humidity, 16/8 h light/dark cycle). Controls were treated with ddH2O. Ten days post-inoculation, natural symptoms appeared on leaves inoculated with HHC-FL23, but control group seedlings remained disease-free. This experiment was repeated three times. All re-isolated pathogens from diseased leaves were molecularly and morphologically identified using methods described above. Consequently, the re-isolated fungi were identical to these inoculated. The leaf spot disease could cause foliar damage and even drastic yield loss of flower buds under severe conditions. To our knowledge, this is the first report of F. ussurianum causing leaf spot in H. citrina worldwide. Our study will assist in monitoring causal agent diversity of leaf spot and breeding new resistant varieties in H. citrina.

Targeting proteasomal deubiquitinases USP14 and UCHL5 with b-AP15 reduces 5-fluorouracil resistance in colorectal cancer cells.

5-Fluorouracil (5-FU) is the first-line treatment for colorectal cancer (CRC) patients, but the development of acquired resistance to 5-FU remains a big challenge. Deubiquitinases play a key role in the protein degradation pathway, which is involved in cancer development and chemotherapy resistance. In this study, we investigated the effects of targeted inhibition of the proteasomal deubiquitinases USP14 and UCHL5 on the development of CRC and resistance to 5-FU. By analyzing GEO datasets, we found that the mRNA expression levels of USP14 and UCHL5 in CRC tissues were significantly increased, and negatively correlated with the survival of CRC patients. Knockdown of both USP14 and UCHL5 led to increased 5-FU sensitivity in 5-FU-resistant CRC cell lines (RKO-R and HCT-15R), whereas overexpression of USP14 and UCHL5 in 5-FU-sensitive CRC cells decreased 5-FU sensitivity. B-AP15, a specific inhibitor of USP14 and UCHL5, (1-5 µM) dose-dependently inhibited the viability of RKO, RKO-R, HCT-15, and HCT-15R cells. Furthermore, treatment with b-AP15 reduced the malignant phenotype of CRC cells including cell proliferation and migration, and induced cell death in both 5-FU-sensitive and 5-FU-resistant CRC cells by impairing proteasome function and increasing reactive oxygen species (ROS) production. In addition, b-AP15 inhibited the activation of NF-κB pathway, suppressing cell proliferation. In 5-FU-sensitive and 5-FU-resistant CRC xenografts nude mice, administration of b-AP15 (8 mg·kg-1·d-1, intraperitoneal injection) effectively suppressed the growth of both types of tumors. These results demonstrate that USP14 and UCHL5 play an important role in the development of CRC and resistance to 5-FU. Targeting USP14 and UCHL5 with b-AP15 may represent a promising therapeutic strategy for the treatment of CRC.

A fast chemical reprogramming system promotes cell identity transition through a diapause-like state.

Cellular reprogramming by only small molecules holds enormous potentials for regenerative medicine. However, chemical reprogramming remains a slow process and labour intensive, hindering its broad applications and the investigation of underlying molecular mechanisms. Here, through screening of over 21,000 conditions, we develop a fast chemical reprogramming (FCR) system, which significantly improves the kinetics of cell identity rewiring. We find that FCR rapidly goes through an interesting route for pluripotent reprogramming, uniquely transitioning through a developmentally diapause-like state. Furthermore, FCR critically enables comprehensive characterizations using multi-omics technologies, and has revealed unexpected important features including key regulatory factors and epigenetic dynamics. Particularly, activation of pluripotency-related endogenous retroviruses via inhibition of heterochromatin significantly enhances reprogramming. Our studies provide critical insights into how only environmental cues are sufficient to rapidly reinstate pluripotency in somatic cells, and make notable technical and conceptual advances for solving the puzzle of regeneration.

A lightweight CNN-based knowledge graph embedding model with channel attention for link prediction.

Knowledge graph (KG) embedding is to embed the entities and relations of a KG into a low-dimensional continuous vector space while preserving the intrinsic semantic associations between entities and relations. One of the most important applications of knowledge graph embedding (KGE) is link prediction (LP), which aims to predict the missing fact triples in the KG. A promising approach to improving the performance of KGE for the task of LP is to increase the feature interactions between entities and relations so as to express richer semantics between them. Convolutional neural networks (CNNs) have thus become one of the most popular KGE models due to their strong expression and generalization abilities. To further enhance favorable features from increased feature interactions, we propose a lightweight CNN-based KGE model called IntSE in this paper. Specifically, IntSE not only increases the feature interactions between the components of entity and relationship embeddings with more efficient CNN components but also incorporates the channel attention mechanism that can adaptively recalibrate channel-wise feature responses by modeling the interdependencies between channels to enhance the useful features while suppressing the useless ones for improving its performance for LP. The experimental results on public datasets confirm that IntSE is superior to state-of-the-art CNN-based KGE models for link prediction in KGs.

Harnessing endogenous transcription factors directly by small molecules for chemically induced pluripotency inception.

Chemistry-alone approach has recently been applied for incepting pluripotency in somatic cells, representing a breakthrough in biology. However, chemical reprogramming is hampered by low efficiency, and the underlying molecular mechanisms remain unclear. Particularly, chemical compounds do not have specific DNA-recognition domains or transcription regulatory domains, and then how do small molecules work as a driving force for reinstating pluripotency in somatic cells? Furthermore, how to efficiently clear materials and structures of an old cell to prepare the rebuilding of a new one? Here, we show that small molecule CD3254 activates endogenous existing transcription factor RXRα to significantly promote mouse chemical reprogramming. Mechanistically, CD3254-RXRα axis can directly activate all the 11 RNA exosome component genes (Exosc1-10 and Dis3) at transcriptional level. Unexpectedly, rather than degrading mRNAs as its substrates, RNA exosome mainly modulates the degradation of transposable element (TE)-associated RNAs, particularly MMVL30, which is identified as a new barrier for cell-fate determination. In turn, MMVL30-mediated inflammation (IFN-γ and TNF-α pathways) is reduced, contributing to the promotion of successful reprogramming. Collectively, our study provides conceptual advances for translating environmental cues into pluripotency inception, particularly, identifies that CD3254-RXRα-RNA exosome axis can promote chemical reprogramming, and suggests modulation of TE-mediated inflammation via CD3254-inducible RNA exosome as important opportunities for controlling cell fates and regenerative medicine.

Production and characterization of cell-penetrating recombinant botulinum neurotoxin type A.

We recently reported that fusion of cell-penetrating peptides (CPPs) to botulinum neurotoxin type A (BoNTA) proteins could improve the efficiency of cellular uptake. Here, we describe steps to produce and evaluate CPP-BoNTA fusion proteins. We present procedures for the expression and purification of recombinant CPP-BoNTA using insect-cell-based baculovirus expression vector system and in vitro characterization of purified proteins. We also detail the analysis of cellular uptake in cell culture and examination of the in vivo performance in mice. For complete details on the use and execution of this protocol, please refer to Wei et al. (2022).1.

Piperlongumine overcomes imatinib resistance by inducing proteasome inhibition in chronic myelogenous leukemia cells.

ETHNOPHARMACOLOGICAL RELEVANCE: Piper longum L., an herbal medicine used in India and other Asian countries, is prescribed routinely for a range of diseases, including tumor. Piperlongumine, a natural product isolated from Piper longum L., has received widespread attention due to its various pharmacological activities, such as anti-inflammatory, antimicrobial, and antitumor effects. AIM OF THE STUDY: Chronic myelogenous leukemia (CML) is a hematopoietic disease caused by Bcr-Abl fusion gene, with an incidence of 15% in adult leukemias. Targeting Bcr-Abl by imatinib provides a successful treatment approach for CML. However, imatinib resistance is an inevitable issue for CML treatment. In particular, T315I mutant is the most stubborn of the Bcr-Abl point mutants associated with imatinib resistance. Therefore, it is urgent to find an alternative approach to conquer imatinib resistance. This study investigated the role of a natural product piperlongumine in overcoming imatinib resistance in CML. MATERIALS AND METHODS: Cell viability and apoptosis were evaluated by MTS assay and Annexin V/propidium iodide counterstaining assay, respectively. Levels of intracellular signaling proteins were assessed by Western blots. Mitochondrial membrane potential was reflected by the fluorescence intensity of rhodamine-123. The function of proteasome was detected using 20S proteasomal activity assay, proteasomal deubiquitinase activity assay, and deubiquitinase active-site-directed labeling. The antitumor effects of piperlongumine were assessed with mice xenografts. RESULTS: We demonstrate that (i) Piperlongumine inhibits proteasome function by targeting 20S proteasomal peptidases and 19S proteasomal deubiquitinases (USP14 and UCHL5) in Bcr-Abl-WT and Bcr-Abl-T315I CML cells; (ii) Piperlongumine inhibits the cell viability of CML cell lines and primary CML cells; (iii) Proteasome inhibition by piperlongumine leads to cell apoptosis and downregulation of Bcr-Abl; (iv) Piperlongumine suppresses the tumor growth of CML xenografts. CONCLUSIONS: These results support that blockade of proteasome activity by piperlongumine provides a new therapeutic strategy for treating imatinib-resistant CML.

Inhibition of proteasomal deubiquitinases USP14 and UCHL5 overcomes tyrosine kinase inhibitor resistance in chronic myeloid leukaemia.

BACKGROUND: Chronic myeloid leukaemia (CML) is a haematological cancer featured by the presence of BCR-ABL fusion protein with abnormal tyrosine kinase activation. Classical tyrosine kinase inhibitor (TKI)-based therapies are available to patients with CML. However, acquired resistance to TKI has been a challenging obstacle, especially stubborn T315I mutation is the most common cause. Therefore, it is especially urgent to find more effective targets to overcome TKI resistance induced by BCR-ABLT315I . Proteasomal deubiquitinases (USP14 and UCHL5) have fundamental roles in the ubiquitin-proteasome system and possess multiple functions during cancer progression. METHODS: The human peripheral blood mononuclear cells were collected to measure the mRNA expression of USP14 and UCHL5, as well as to detect the toxicity effect of b-AP15. We explored the effect of b-AP15 on the activity of proteasomal deubiquitinases. We detected the effects of b-AP15 on BCR-ABLWT and BCR-ABLT315I CML cells in vitro and in the subcutaneous tumour model. We knocked down USP14 and/or UCHL5 by shRNA to explore whether these proteasomal deubiquitinases are required for cell proliferation of CML. RESULTS: In this study, we found that increased expression of the proteasomal deubiquitinase USP14 and UCHL5 in primary cancer cells from CML patients compared to healthy donors. b-AP15, an inhibitor of USP14 and UCHL5, exhibited potent tumour-killing activity in BCR-ABLWT and BCR-ABLT315I CML cell lines, as well as in CML xenografts and primary CML cells. Mechanically, pharmacological or genetic inhibition of USP14 and UCHL5 induced cell apoptosis and decreased the protein level of BCR-ABL in CML cells expressing BCR-ABLWT and BCR-ABLT315I . Moreover, b-AP15 synergistically enhanced the cytotoxic effect caused by TKI imatinib in BCR-ABLWT and BCR-ABLT315I CML cells. CONCLUSION: Collectively, our results demonstrate targeting USP14 and UCHL5 as a potential strategy for combating TKI resistance in CML.

Comparison of the Differential Diagnostic Performance of Intravoxel Incoherent Motion Imaging and Diffusion Kurtosis Imaging in Malignant and Benign Thyroid Nodules.

Objective: This study aimed to compare the diagnostic capacity between IVIM and DKI in differentiating malignant from benign thyroid nodules. Material and Methods: This study is based on magnetic resonance imaging data of the thyroid with histopathology as the reference standard. Spearman analysis was used to assess the relationship of IVIM-derived parameters D, f, D* and the DKI-derived parameters Dapp and Kapp. The parameters of IVIM and DKI were compared between the malignant and benign groups. Binary logistic regression analysis was performed to establish the diagnostic model, and receiver operating characteristic (ROC) curve analysis was subsequently performed. The DeLong test was used to compare the diagnostic effectiveness of different prediction models. Spearman analysis was used to assess the relationship of Ki-67 expression and parameters of IVIM and DKI. Results: Among the 93 nodules, 46 nodules were malignant, and 47 nodules were benign. The Dapp of DKI-derived parameter was related to the D (P < 0.001, r = 0.863) of IVIM-derived parameter. The Kapp of DKI-derived parameter was related to the D (P < 0.001, r = -0.831) of IVIM-derived parameters. The malignant group had a significantly lower D value (P < 0.001) and f value (P = 0.013) than the benign group. The malignant group had significantly higher Kapp and lower Dapp values (all P < 0.001). The D+f had an area under the curve (AUC) of 0.951. The Dapp+Kapp had an AUC of 0.943. The D+f+Dapp+Kapp had an AUC of 0.954. The DeLong test showed no statistical significance among there prediction models. The D (P = 0.007) of IVIM-derived parameters and Dapp (P = 0.045) of DKI-derived parameter were correlated to the Ki-67 expression. Conclusions: IVIM and DKI were alternative for each other in in differentiating malignant from benign thyroid nodules.

rFOV-DWI and SMS-RESLOVE-DWI in patients with thyroid nodules: Comparison of image quality and apparent diffusion coefficient measurements.

OBJECTIVES: To compare reduced field of view technique diffusion-weighted imaging (rFOV-DWI) and simultaneous multislice readout segmentation of long variable echo-trains diffusion-weighted imaging (SMS-RESOLVE-DWI) in terms of image quality and diagnostic performance of the apparent diffusion coefficient (ADC) for thyroid nodules. MATERIALS AND METHODS: A total of 27 benign thyroid nodules and 26 malignant thyroid nodules were enrolled. rFOV-DWI and SMS-RESOLVE-DWI were performed at b values of 0 and 1000 s/mm2. Subjective image quality was evaluated in terms of sharpness, distortion and artifacts. Objective indices reflecting distortion, the contrast-to-noise ratio and the ADC were measured. Paired-samples t-tests or Wilcoxon U tests were applied to assess whether significant differences existed among different sequences. According to the pathological results, the nodules were divided into the benign and malignant groups. The receiver operating characteristic (ROC) curve of the ADC values was used to predict malignant nodules. The DeLong test was used to compare the diagnostic effectiveness between rFOV-DWI and SMS-RESOLVE-DWI. RESULTS: The rFOV-DWI images exhibited better sharpness (P < 0.001) and fewer artifacts (P = 0.003) for the thyroid than the SMS-RESOLVE-DWI images. The overall image quality of nodules (P < 0.001) was better in rFOV-DWI images than in SMS-RESOLVE-DWI images. The rFOV-DWI images also showed less deformation than the SMS-RESOLVE-DWI images (P = 0.002, 0.006). The ADC values of both rFOV-DWI and SMS-RESOLVE-DWI revealed equivalent excellent diagnostic performance. The DeLong test revealed no statistically significant differences between rFOV-DWI and SMS-RESOLVE-DWI. CONCLUSION: This study suggested that rFOV-DWI exhibited better image quality than SMS-RESOLVE-DWI and similar performance in differential diagnosis.

Cyclin-dependent kinase 7/9 inhibitor SNS-032 induces apoptosis in diffuse large B-cell lymphoma cells.

Approximately 40% of patients with diffuse large B-cell lymphoma (DLBCL) are refractory or relapse to standard chemotherapy, and most of them are activated B cell-like DLBCLs (ABC-DLBCL) and germinal center B cell-like DLBCLs (GCB-DLBCL). SNS-032, a novel and selective CDK7/9 inhibitor, that the first phase clinical trials approved by US FDA for cancer treatment have been completed. In this study, we investigated the anti-tumor effect of SNS-032 in ABC- and GCB-DLBCL subtypes. We report that SNS-032 induced growth inhibition and cell apoptosis in both DLBCL cells in vitro, and inhibited the growth of both DLBCL xenografts in nude mice. Mechanistically, SNS-032 inhibited RNA polymerase II, which led to transcriptional-dependent suppression of NF-κB signaling pathway and its downstream targets involved in cell survival; SNS-032 also downregulates BCL-2 and c-MYC in both mRNA and protein levels. Significantly, these findings provide pre-clinical evidence for application of targeting the CDK7/9 in DLBCL.

miR-125a attenuates the malignant biological behaviors of cervical squamous cell carcinoma cells through Rad51.

Cervical squamous cell carcinoma (CSCC), the most common cervical malignancy, is more likely to invade and metastasize than other cervical cancers. miR-125a, a tumor suppressor gene, has been confirmed to be associated with cancer metastasis. However, the role of miR-125a in CSCC and the underlying mechanism are unknown. miR-125a expression was confirmed by real-time quantitative PCR (RT-qPCR), and the Rad51 expression level was measured by western blotting analysis. CSCC cell proliferation, migration and invasion were assessed with functional assays, including CCK-8, colony formation, wound healing and Transwell assays. Our data confirmed that miR-125a is expressed at low levels in CSCC tissues and cells. Functionally, the overexpression of miR-125a greatly prevented the proliferation, migration and invasion of CSCC cells, and the inhibition of miR-125a expression strongly enhanced these behaviors in CSCC cells. Moreover, the expression of Rad51, a miR-125a target gene, greatly reversed the miR-125-mediated inhibition of CSCC cell proliferation, migration and invasion. In addition, we discovered that miR-125a downregulated the levels of phosphorylated PI3K, AKT and mTOR through Rad51 in CSCC cells. miR-125a, a tumor suppressor, can attenuate the malignant behaviors of CSCC cells by targeting Rad51. Therefore, the miR-125a/Rad51 axis might be a target for CSCC therapy.

Dual-source dual-energy computed tomography-derived quantitative parameters combined with machine learning for the differential diagnosis of benign and malignant thyroid nodules.

BACKGROUND: This study aimed to investigate the ability of quantitative parameter-derived dual-source dual-energy computed tomography (DS-DECT) combined with machine learning to distinguish between benign and malignant thyroid nodules. METHODS: Patients with thyroid nodules and pathological surgical results who underwent preoperative DS-DECT were selected. Quantitative parameter-derived DS-DECT was applied to classify benign and malignant nodules. Then, machine learning and binary logistic regression analysis models were constructed using the DS-DECT quantitative parameters to distinguish between benign and malignant nodules. The receiver operating characteristic curve was used to assess the diagnostic performance. The DeLong test was used to compare the diagnostic efficacy. RESULTS: One hundred and thirty patients with 139 confirmed thyroid nodules were involved in the study. The malignant group had a significantly higher iodine concentrationnodule (arterial phase) (P=0.001), normalized iodine concentration (arterial phase) (P=0.002), iodine concentration difference (P<0.001), spectral curve slope (nonenhancement) (P=0.007), spectral curve slope (arterial phase) (P=0.001), effective atomic number (nonenhancement) (P<0.001), and effective atomic number (arterial phase) (P=0.039) than the benign group. The binary logistic regression analysis model had an AUC (area under the curve) of 0.76, a sensitivity of 0.821, and a specificity of 0.667. The machine learning model had an AUC of 0.86, a sensitivity of 0.822, specificity of 0.791 in the training cohort, an AUC of 0.84, a sensitivity of 0.727, and specificity of 0.750 in the testing cohort. CONCLUSIONS: Multiple quantitative parameters of DS-DECT combined with machine learning could differentiate between benign and malignant thyroid nodules.

The chloroplast genome of Elytrigia repens (L.) Nevski (Poaceae: Triticeae), a widespread perennial grass from Qinghai-Tibetan Plateau, China.

Elytrigia repens (L.) Nevski, belonging to Triticeae of Poaceae, is a wild-growing perennial grass, widely distributed in Qinghai-Tibetan Plateau of China. In this study, the complete chloroplast genome of E. repens was sequenced and analyzed. The complete chloroplast genome size is 134,749 bp with 38.3% GC content. It includes 136 genes, including 89 protein-coding genes, 39 tRNAs genes, and 8 rRNAs genes. Based on chloroplast genome sequences, further phylogenetic analyses between E. repens and other Triticeae species revealed that E. repens, Connorochloa tenuis and three Elymus species formed a distinct clade, showing closer relationships.

Identification and functional deciphering suggested the regulatory roles of long intergenic ncRNAs (lincRNAs) in increasing grafting pepper resistance to Phytophthora capsici.

BACKGROUND: As a popular and valuable technique, grafting is widely used to protect against soil-borne diseases and nematodes in vegetable production. Growing evidences have revealed that long intergenic ncRNAs (lincRNAs) are strictly regulated and play essential roles in plants development and stress responses. Nevertheless, genome-wide identification and function deciphering of pepper lincRNAs, especially for their roles in improving grafting pepper resistance to Phytophthora capsici is largely unknown. RESULTS: In this study, RNA-seq data of grafting and control pepper plants with or without P. capsici inoculation were used to identify lincRNAs. In total, 2,388 reliable lincRNAs were identified. They were relatively longer and contained few exons than protein-coding genes. Similar to coding genes, lincRNAs had higher densities in euchromatin regions; and longer chromosome transcribed more lincRNAs. Expression pattern profiling suggested that lincRNAs commonly had lower expression than mRNAs. Totally, 607 differentially expressed lincRNAs (DE-lincRANs) were identified, of which 172 were found between P. capsici resistance grafting pepper sample GR and susceptible sample LDS. The neighboring genes of DE-lincRNAs and miRNAs competitively sponged by DE-lincRNAs were identified. Subsequently, the expression level of DE-lincRNAs was further confirmed by qRT-PCR and regulation patterns between DE-lincRNAs and neighboring mRNAs were also validated. Function annotation revealed that DE-lincRNAs increased the resistance of grafting prepper to P. capsici by modulating the expression of disease-defense related genes through cis-regulating and/or lincRNA-miRNA-mRNA interaction networks. CONCLUSIONS: This study identified pepper lincRNAs and suggested their potential roles in increasing the resistance level of grafting pepper to P. capsici.

Cullin 2-RBX1 E3 ligase and USP2 regulate antithrombin ubiquitination and stability.

Hemophilia A and B are congenital bleeding disorders caused by a deficiency in pro-coagulant factor VIII or IX that is treated by downregulation of antithrombin. However, the molecular mechanisms that regulate antithrombin expression remain poorly understood. Here, we identified Cullin 2 and USP2 (ubiquitin-specific peptidase-2) as novel regulators of antithrombin expression that act by modulating antithrombin ubiquitination. Inhibition of the proteasome caused accumulation of antithrombin and its ubiquitinated forms in HepG2 and SMMC7721 cells. Notably, inhibition of neddylation with MLN4924 suppressed both ubiquitination and degradation of antithrombin, which is recapitulated by silencing of the neddylation enzymes, NAE1, UBA3, and UBE2M, with small interfering RNA (siRNA). We identified Cullin 2 as the interaction partner of antithrombin, and siRNA-mediated Cullin 2 knockdown reduced antithrombin ubiquitination and increased antithrombin protein. We further found that USP2 interacted with antithrombin and regulated antithrombin expression, showing that overexpression of USP2 inhibits the ubiquitination and proteasomal clearance of antithrombin, whereas pharmacological inhibition or siRNA-mediated knockdown of USP2 downregulates antithrombin. Collectively, these results suggest that Cullin 2 E3 ubiquitin ligase and USP2 coordinately regulate antithrombin ubiquitination and degradation. Thus, targeting Cullin 2 and USP2 could be a potential strategy for treatment of hemophilia.

Association of Gyrification Pattern, White Matter Changes, and Phenotypic Profile in Patients With Parkinson Disease.

OBJECTIVE: To investigate the cortical gyrification changes as well as their relationships with white matter (WM) microstructural abnormalities in the akinetic-rigid (AR) and tremor-dominant (TD) subtypes of Parkinson disease (PD). METHODS: Sixty-four patients with the AR subtype, 26 patients with the TD subtype, and 56 healthy controls (HCs) were included in this study. High-resolution T1-weighted and diffusion-weighted images were acquired for each participant. We computed local gyrification index (LGI) and fractional anisotropy (FA) to identify the cortical gyrification and WM microstructural changes in the AR and TD subtypes. RESULTS: Compared with HCs, patients with the AR subtype showed decreased LGI in the precentral, postcentral, inferior and superior parietal, middle and superior frontal/temporal, anterior and posterior cingulate, orbitofrontal, supramarginal, precuneus, and some visual cortices, and decreased FA in the corticospinal tract, inferior and superior longitudinal fasciculus, inferior fronto-occipital fasciculus, forceps minor/major, and anterior thalamic radiation. Decreases in LGI and FA of the AR subtype were found to be tightly coupled. LGIs of the left inferior and middle frontal gyrus correlated with Mini-Mental State Examination and Hoehn & Yahr scores of patients with the AR subtype. Patients with the TD subtype showed no significant change in the LGI and FA compared with patients with the AR subtype and HCs. CONCLUSIONS: Our results suggest that cortical gyrification changes in PD are motor phenotype-specific and are possibly mediated by the microstructural abnormalities of the underlying WM tracts.