MMGan: a multimodal MR brain tumor image segmentation method.

Computer-aided diagnosis has emerged as a rapidly evolving field, garnering increased attention in recent years. At the forefront of this field is the segmentation of lesions in medical images, which is a critical preliminary stage in subsequent treatment procedures. Among the most challenging tasks in medical image analysis is the accurate and automated segmentation of brain tumors in various modalities of brain tumor MRI. In this article, we present a novel end-to-end network architecture called MMGan, which combines the advantages of residual learning and generative adversarial neural networks inspired by classical generative adversarial networks. The segmenter in the MMGan network, which has a U-Net architecture, is constructed using a deep residual network instead of the conventional convolutional neural network. The dataset used for this study is the BRATS dataset from the Brain Tumor Segmentation Challenge at the Medical Image Computing and Computer Assisted Intervention Society. Our proposed method has been extensively tested, and the results indicate that this MMGan framework is more efficient and stable for segmentation tasks. On BRATS 2019, the segmentation algorithm improved accuracy and sensitivity in whole tumor, tumor core, and enhanced tumor segmentation. Particularly noteworthy is the higher dice score of 0.86 achieved by our proposed method in tumor core segmentation, surpassing those of stateof-the-art models. This study improves the accuracy and sensitivity of the tumor segmentation task, which we believe is significant for medical image analysis. And it should be further improved by replacing different loss functions such as cross-entropy loss function and other methods.

Effect of metronidazole on the growth of vaginal lactobacilli in female athletes

Lactobacillus strains isolated from female athletes were tested. MRS broth was supplemented with a range of Metronidazole concentrations from 128 to 2000 μg/ml. The growth of these strains was monitored by measuring optical density at 3-hour intervals over 24 hours. Results: It was observed that at Metronidazole concentrations up to 128 μg/ml, there was no significant impact on the growth of the Lactobacillus strains. However, at concentrations above 512 μg/ml, Metronidazole significantly inhibited their growth. The response to Metronidazole varied among different Lactobacillus strains. For instance, at a concentration of 256 μg/ml, Lactobacillus delbrueckii, Lactobacillus jensenii, and Lactobacillus vaginalis showed notable inhibition, whereas Lactobacillus crispatus, Lactobacillus gasseri, and Lactobacillus fermentum were not significantly affected. Discussion: High concentrations of Metronidazole were found to inhibit the growth of the six Lactobacillus strains isolated from female athletes. Lower concentrations had negligible effects. The differential response of Lactobacillus strains to varying concentrations of Metronidazole (between 128 μg/ml and 512 μg/ml) highlights the need for careful consideration of Metronidazole use in managing vaginal microbiota health in female athletes (AU)

Proteomics analyses of acute kidney injury biomarkers in a rat exertional heat stroke model.

The frequency of exertional heat stroke (EHS) increases with the gradual elevation of global temperatures during summer. Acute kidney injury (AKI) is a common complication of EHS, and its occurrence often indicates the worsening of a patient's condition or a poor prognosis. In this study, a rat model of AKI caused by EHS was established, and the reliability of the model was evaluated by HE staining and biochemical assays. The expression of kidney tissue proteins in the EHS rats was analyzed using label-free liquid chromatography-tandem mass spectrometry. A total of 3,129 differentially expressed proteins (DEPs) were obtained, and 10 key proteins were finally identified, which included three upregulated proteins (Ahsg, Bpgm, and Litaf) and seven downregulated proteins (medium-chain acyl-CoA synthetase 2 (Acsm2), Hadha, Keg1, Sh3glb1, Eif3d, Ambp, and Ddah2). The qPCR technique was used to validate these 10 potential biomarkers in rat kidney and urine. In addition, Acsm2 and Ahsg were double-validated by Western blotting. Overall, this study identified 10 reliable biomarkers that may provide potential targets for the treatment of AKI caused by EHS.

Construction of Imatinib Controlled Release Film-Forming System Based on Drug Ion-Pair and Oligomeric Ionic Liquids for the Long Local Therapy of Cutaneous Melanoma.

An imatinib controlled release film-forming system (FFS) was developed based on the drug ion-pair and newly designed oligomeric ionic liquids (OILs) for the topical therapy of cutaneous melanoma, which avoided the systemic side-effect of oral administration and maintained a long local therapy effect. The OILs significantly improved the drug release capacity about 1.5-fold, and the formability and stability of FFSs (verified by AFM/PLM). The in vivo anti-tumor efficacy studies in melanoma tumor bearing mice showed that compared with the oral capsules, the topical application of the optimized imatinib FFS significantly (p < 0.01) increased tumor inhibition rate (67.54 ± 2.72%) and the amount of apoptotic cells. As confirmed by FT-IR and NMR, the partial protonation of OILs were demonstrated to have high hydrogen bond forming capacity, thus showing low polarity and good biocompatibility. More importantly, based on 13C-NMR study, OILs demonstrated higher hydrogen bond forming capacity, and formed bridge between drug ion-pair (O-H of counter-ion) and PVA (O-H), increased the molecular mobility of PVA, thus maintaining a long drug release capacity. Therefore, an imatinib FFS was developed with good therapeutic effect and the effect of drug ion-pair and OILs on increasing the drug skin retention and controlled release of imatinib FFS for topical therapy was clarified at the molecular level, which provided a safe and effective way for the treatment of cutaneous melanoma.

Expression of EMT-related genes in lymph node metastasis in endometrial cancer: a TCGA-based study.

BACKGROUND: Endometrial cancer (EC) with metastasis in pelvic/para-aortic lymph nodes suggests an unsatisfactory prognosis. Nevertheless, there is still rare literature focusing on the role of epithelial-mesenchymal transition (EMT) in lymph node metastasis (LNM) in EC. METHODS: Transcriptional data were derived from the TCGA database. Patients with stage IA-IIIC2 EC were included, constituting the LN-positive and LN-negative groups. To evaluate the extent of EMT, an EMT signature composed of 315 genes was adopted. The EMT-related genes (ERGs) were obtained from the dbEMT2 database, and the differentially expressed ERGs (DEERGs) between these two groups were screened. On the basis of DEERGs, pathway analysis was carried out. We eventually adopted the logistic regression model to build an ERG-based gene signature with predictive value for LNM in EC. RESULTS: A total of 498 patients were included, with 75 in the LN-positive group. Median EMT score of tumor tissues from LN-negative group was - 0.369, while that from the LN-positive group was - 0.296 (P < 0.001), which clearly exhibited a more mesenchymal phenotype for LNM cases on the EMT continuum. By comparing expression profiles, 266 genes were identified as DEERGs, in which 184 were upregulated and 82 were downregulated. In pathway analysis, various EMT-related pathways were enriched. DEERGs shared between molecular subtypes were comparatively few. The ROC curve and logistic regression analysis screened 7 genes with the best performance to distinguish between the LN-positive and LN-negative group, i.e., CIRBP, DDR1, F2RL2, HOXA10, PPARGC1A, SEMA3E, and TGFB1. A logistic regression model including the 7-gene-based risk score, age, grade, myometrial invasion, and histological subtype was built, with an AUC of 0.850 and a favorite calibration (P = 0.074). In the validation dataset composed of 83 EC patients, the model exhibited a satisfactory predictive value and was well-calibrated (P = 0.42). CONCLUSION: The EMT status and expression of ERGs varied in LNM and non-LNM EC tissues, involving multiple EMT-related signaling pathways. Aside from that, the distribution of DEERGs differed among molecular subtypes. An ERG-based gene signature including 7 DEERGs exhibited a desirable predictive value for LNM in EC, which required further validation based upon clinical specimens in the future.

Does Omega-3 Fatty Acid Supplementation Have Favorable Effects on the Lipid Profile in Postmenopausal Women? A Systematic Review and Dose-response Meta-analysis of Randomized Controlled Trials.

PURPOSE: Menopause is associated with disturbances in the metabolism of lipids. Moreover, during the postmenopausal period, female subjects are more prone to develop dyslipidemia. Omega-3 fatty acids, which exert cardioprotective, anti-inflammatory, and lipid-lowering actions, are commonly recommended in postmenopausal women. However, their effect on serum lipids in this population remains unclear. This systematic review and meta-analysis of randomized controlled trials (RCTs) was conducted to clarify this research question. METHODS: We systematically searched the Web of Science, Scopus, PubMed/MEDLINE, and EMBASE databases from their inception until January 3, 2022. The DerSimonian and Laird random-effects model was used to combine effect sizes. FINDINGS: Omega-3 fatty acid supplementation resulted in a decrease in triglyceride concentrations (weighted mean difference [WMD], -17.8 mg/dL; 95% CI, -26 to -9.6; P < 0.001), particularly in the RCTs that lasted ≤16 weeks (WMD, -18.6 mg/dL), when the baseline triglyceride concentrations were ≥150 mg/dL (WMD, -22.8 mg/dL), in individuals with a body mass index ≥30 kg/m2 (WMD, -19.3 mg/dL), and when the dose of omega-3 fatty acids was ≥1 g/d (WMD, -21.10 mg/dL). LDL-C (WMD, 4.1 mg/dL; 95% CI, 1.80 to 6.36; P < 0.001) and HDL-C (WMD, 2.1 mg/dL; 95% CI, 0.97 to 3.2; P < 0.001) values increased. Total cholesterol levels (WMD, -0.15 mg/dL; 95% CI, -4 to 3.74; P = 0.94) remained unchanged after administration of omega-3 fatty acids. IMPLICATIONS: In postmenopausal women, supplementation with omega-3 fatty acids resulted in a significant reduction in triglyceride concentrations and a modest elevation in HDL-C and LDL-C levels, whereas this intervention did not affect total cholesterol values.

Rapid and accurate determination of diesel multiple properties through NIR data analysis assisted by machine learning.

The rapid and accurate detection of diesel multiple properties is an important research topic in petrochemical industry that is conducive to diesel quality assessment and environmental pollution mitigation. To that end, this paper developed a new machine learning model for near infrared (NIR) spectroscopy capable of simultaneously determining diesel density, viscosity, freezing point, boiling point, cetane number and total aromatics. The model combined improved XY co-occurrence distance (ISPXY) and differential evolution-gray wolf optimization support vector machine (DEGWO-SVM) to attain the goal of rapidity and accuracy. Experimental results indicated that the average recovery, mean square error, mean absolute percentage error and determination coefficient of the presented method outperformed those of the existing machine learning methods. The proposed hybrid model provides superior solution to the problem of low efficiency and high cost of diesel quality detection, and has the potential to be utilized as a promising tool for diesel routine monitoring.

Complete genome sequence of a distinct rosadnavirus isolated from Viola plants in China.

In 2019, plants of the genus Viola showing yellow mottling symptoms were collected in Liaoning, China. RNA sequencing and PCR both confirmed the presence of a reverse-transcribing DNA virus. The novel virus was named "viola yellow mottle virus" (VYMV), and its 9,872-bp genome was found to contain eight open reading frames. The polymerase (RT + RNase H) gene shared the most similarity (31.6% nucleotide and 41.6% amino acid sequence identity) with that of rose yellow vein virus (RYVV, NC_020999), which is currently the only member of the genus Rosadnavirus. Phylogenetic analysis indicated a close relationship between these viruses, suggesting that VYMV should be considered a new member of the genus Rosadnavirus.

Complete genome sequence of a putative new and distinct caulimovirus from Metaplexis japonica (Thunb.) Makino in China.

In 2019, a new disease characterized by yellow mottling on leaves was observed on Metaplexis japonica (Thunb.) Makino plants in Liaoning, China. Using RNA sequencing and PCR with overlapping primers, the complete nucleotide sequence of the circular double-stranded DNA genome of a new virus similar to caulimoviruses in diseased samples was determined. The genome comprised 7733 base pairs and was predicted to encode six proteins. It had the closest relationship to a caulimovirus, strawberry vein banding virus, based on sequence comparisons and phylogenetic analysis. Species-level sequence divergences from caulimoviruses were also observed in the conserved genomic regions. A complete episomal viral genome sequence in symptomatic M. japonica plants was identified, and the name "metaplexis yellow mottle-associated virus" is proposed for this virus.

Highly sensitive nanoparticle sensing based on a hybrid cavity in a freely suspended microfiber.

We report a hybrid cavity structure based on a suspended microfiber with a diameter of 1.7 µm applied to nanoparticle sensing in water. The proposed hybrid cavity is composed of two symmetrical reflectors with a slotted Au layer in the middle. After being characterized by the finite-difference time-domain method, the obtained strong reflection and sufficiently wide band gap provide the potential to realize an ultrasmall mode volume, which can improve sensitivity and lower loss. In addition, an ultrahigh Q/V ratio of 8.2 × 106 (λ/n)-3 and high resonance transmittance of T = 0.53 can be obtained through optimization analysis. After analyzing the trapping force and resonance shift caused by the change in local electric field, it is proven that our proposed cavity exhibits a high sensitivity and offers a convenient and stable method for particle sensing in water.

Diversity, structure and function of the coiled-coil domains of plant NLR immune receptors.

Plant nucleotide-binding, leucine-rich repeat receptors (NLRs) perceive pathogen avirulence effectors and activate defense responses. Nucleotide-binding, leucine-rich repeat receptors are classified into coiled-coil (CC)-containing and Toll/interleukin-1 receptor (TIR)-containing NLRs. Recent advances suggest that NLR CC domains often function in signaling activation, especially for induction of cell death. In this review, we outline our current understanding of NLR CC domains, including their diversity/classification and structure, their roles in cell death induction, disease resistance, and interaction with other proteins. Furthermore, we provide possible directions for future work.

First report of tomato spotted wilt virus (TSWV) isolated from nasturtium (Tropaeolum majus L.) with a serious leaf mosaic disease in China.

Tomato spotted wilt virus (TSWV, Genus Orthotospovirus, Family Tospoviridae) is a thrips-transmitted negative-stranded RNA virus with a large host range. Major economic losses caused by TSWV have been recorded in various crops such as tomato, pepper and lettuce (Pappu et al., 2009; Adams et al., 2017). Nasturtium (Tropaeolum majus L.), a common flowering plant species native to Peru, is generally cultivated as a garden and greenhouse ornamental plant in China. It is also known for its medical, edible and cosmetic values (Jakubczyk et al., 2018). In June 2019, a serious leaf mosaic disease (Figure S1) was observed in ~77% of T. majus plants in Beiling Park in Shenyang City, Liaoning, China. To reveal the possible viral agent associated with the disease, leaf tissue was collected from 9 symptomatic and 2 asymptomatic plants, followed by total RNA extraction from each of the samples using RNASimple Total RNA Kit (Tiangen, Beijing, China). The RNA from one representative symptomatic sample (Figure S1, d) was used to construct an rRNA-depleted library using the Ribo-Zero™ rRNA Removal Kit (Plant Leaf) (Illumina, CA, USA). The library was subjected to RNA-Seq using a BGISEQ platform (Shenzhen Huada Gene Science and Technology Service Co., Ltd., Shenzhen, China). A total of 109,279,540 quality-filtered reads were obtained using the CLC Genomics Workbench 9.5 software (Qiagen, Valencia, CA, USA). Clean reads were assembled into 88,091 contigs ranging in length from 200 to 19,695 bp using Velvet (Zerbino and Birney 2008). Among the contigs, three sized at 8801, 4617 and 2909 bp were found to share a sequence identity of 98.74-99.35% with the RNA segments (L, M and S) of TSWV. No sequences of other viruses, viroids included, were detected. Ten primer pairs were designed based on the TSWV contigs to obtain the full genome sequence of the virus (Table S1). Five, three, and two amplicons were obtained for the TSWV RNA segments L, M and S, respectively, from the same RNA sample used in the RNA-Seq process. These amplicons were then cloned into the pMD18T vector (TaKaRa, Dalian, China) and Sanger sequenced. The resulting sequences were assembled and analyzed using the DNAMAN version 8.0 (LynnonBiosoft, Quebec, Canada) and DNAStar version 6.0 software (DNAStar Inc, Madison, WI, USA) (Table S1). The RNA segments were determined to be 8,914 nt (L, accession no. MT241883), 4,791 nt (M, MT241884) and 2,922 nt (S, MT241885) in length. They shared a sequence identity of >99% with the "LL-N.05" (segment L, KP008128) and "SPAIN-1" (segment S, AY744479) isolates from tomatoes in Spain and the "Beijing" isolate (segment M, MH717046) from chrysanthemum in China. These results, together with phylogenetic analysis, suggest that the isolate (designated as isolate LN-HJL) was likely resulted from genome reassortment between other isolates. No reliable recombination events were detected in the RNA segments of LN-HJL by the RDP4 program (Martin et al., 2015). RT-PCR assay with primer pair S-1F/1R on all samples led to positive detection of TSWV only in the symptomatic samples (Figure S1, g), indicating that the virus was likely responsible for the disease symptoms observed in T. majus. To the best of our knowledge, this is the first report of the TSWV infection in T. majus in China, and the second in the world since the first report in the USA (Ie, 1964). TSWV-infected T. majus plants not only lose their aesthetic and economic values (Figure S1, f), but also may act as reservoirs for the spread of TSWV to other important crops. T. majus should therefore be monitored regularly for the virus and managed accordingly in China.

Plant NLR immune receptor Tm-22 activation requires NB-ARC domain-mediated self-association of CC domain.

The nucleotide-binding, leucine-rich repeat-containing (NLR) class of immune receptors of plants and animals recognize pathogen-encoded proteins and trigger host defenses. Although animal NLRs form oligomers upon pathogen recognition to activate downstream signaling, the mechanisms of plant NLR activation remain largely elusive. Tm-22 is a plasma membrane (PM)-localized coiled coil (CC)-type NLR and confers resistance to Tobacco mosaic virus (TMV) by recognizing its viral movement protein (MP). In this study, we found that Tm-22 self-associates upon recognition of MP. The CC domain of Tm-22 is the signaling domain and its function requires PM localization and self-association. The nucleotide-binding (NB-ARC) domain is important for Tm-22 self-interaction and regulates activation of the CC domain through its nucleotide-binding and self-association. (d)ATP binding may alter the NB-ARC conformation to release its suppression of Tm-22 CC domain-mediated cell death. Our findings provide the first example of signaling domain for PM-localized NLR and insight into PM-localized NLR activation.

Missing data recovery combined with Parallel factor analysis model for eliminating Rayleigh scattering in the process of detecting pesticide mixture.

Excitation-Emission Matrix (EEM) fluorescence spectroscopy combined with Parallel factor analysis (PARAFAC) provides a widely used method to extract useful information containing unknown components. However, the inherent scattering especially Rayleigh scattering will influence the accuracy of PARAFAC so that appropriate procedure to the scattering becomes an essential problem when processing the EEM data. Many methods have been proposed to solve the problems about eliminating scattering. Missing data recovery combined with PARAFAC model has been discussed in this paper. For EEM data, this method extracted the signal values in the missing area which can effectively correct scattering region. It can eliminate Rayleigh scattering effectively by choosing Gaussian contour constraint. The results of the correlation coefficient (R), the root mean square error of prediction (RMSEP) and average recovery rate (AR) are better which can prove that the combined method is easier to implement and provide better concentration prediction results in detecting pesticide mixture.

A GA-BP method of detecting carbamate pesticide mixture based on three-dimensional fluorescence spectroscopy.

In this paper, we have proposed a method to detect a mixture of carbamate pesticides using a back propagation network (BP), which is optimized by genetic algorithm (GA) for quantitative analysis. This method aims to combine the advantages of BP and GA to remedy their drawbacks. The training samples were taken as input, some performance indexes such as the predicted values, iteration time, mean squared error, correlation coefficient and recovery rate were compared between BP neural network and the constructed GA-BP model to evaluate the performance of two neural networks. Results show that the optimized GA-BP model can effectively predict the concentrations, the mean squared error and recovery rate are better. In addition, the correlation coefficient has a significant improvement. This study can provide a new way for detection of the pesticides mixture and help to analysis in a reliable way.

Full genome sequence of a novel potexvirus from Euonymus bungeanus Maxim based on RNA-Seq analysis.

In July 2018, a yellow mottle leaf disease was observed on the leaves of Euonymus bungeanus Maxim plants in Liaoning Province of China. Typical flexuous filaments (diameter, 13 nm; length, ca. 500 nm) were observed in extracts on the symptomatic leaves. Transcriptome sequencing indicated the presence of a potexvirus in the infected samples. The complete viral genome, determined to be 6,784 nucleotides in length, excluding the poly(A) tail, contains five open reading frames and is most closely related to that of euonymus yellow vein associated virus (EuYVAV, MF078061) (41.0%). Based on the coat protein gene, this virus shares the highest sequence similarity with cymbidium mosaic virus (CyMV, EF125179), with 43.9% nucleotide and 38.8% amino acid sequence identity, respectively. Phylogenetic analysis indicated that the virus clustered with potexviruses and is most closely related to EuYVaV. This virus is a distinct member of the genus Potexvirus, for which the name "euonymus yellow mottle associated virus" (EuYMaV) is proposed.

The complete nucleotide sequence and genome organization of a novel virus of the order Tymovirales isolated from Prunus davidiana (Carr.) Franch. in Liaoning, China.

In September 2017, a yellow spot leaf disease was noted on the leaves of Prunus davidiana (Carr.) Franch. plants in Liaoning, China, and spherical virions (approx. 30 nm in diameter) were later observed in preparations of symptomatic leaves. Subsequent deep sequencing of small RNA revealed the presence of a virus in these symptomatic leaves The complete genome of this viral isolate consists of 6,072 nucleotides, excluding the poly(A) tail. The virus showed the closest genetic relationship to grapevine-associated tymo-like virus, reported in Colmar, France (GaTLV, MH383239), which is the sole member of the newly proposed genus "Gratylivirus" within the order Tymovirales, which is currently unassigned to a particular family. The virus clustered closely with GaTLV in a phylogenetic tree constructed based on complete genomic sequences. On the basis of the nucleotide and amino acid sequences of the replicase and coat protein genes, this virus shares the highest (although still relatively low) sequence similarity with those of GaTLV (41.6%-60.8% identity), indicating that the virus is a distinct member of the order Tymovirales, for which the name "prunus yellow spot-associated virus" (PYSaV) is proposed. To our knowledge, this is the first report of a virus naturally infecting P. davidiana.

ARGONAUTE10 Inhibits In Vitro Shoot Regeneration Via Repression of miR165/166 in Arabidopsis thaliana.

Many plant cells retain their totipotency when cultured in vitro. The regulation of shoot regeneration from in vitro culture involves a number of gene products, but the nature of the associated post-transcriptional events remains largely unknown. Here, the post-transcriptional regulator ARGONAUTE10 (AGO10), a protein which is specifically expressed in the explant during the period when pro-shoot apical meristems (SAMs) are forming, has been known to inhibit shoot regeneration. In in vitro cultured explants of the loss-of-function mutant ago10, a much larger than normal number of SAMs was formed and, in these, the stem cell marker genes WUSCHEL, CLAVATA3 and SHOOT MERISTEMLESS were all strongly expressed. AGO10 repressed the accumulation of the microRNAs miR165/166, thereby up-regulating a suite of HD-ZIP III genes. The overproduction of miR166 was shown to promote shoot regeneration, while the absence of miR165/166 message resulted in a blockage to shoot regeneration and only a partial rescue of the phenotype of the ago10 mutant. The major conclusion was that the shoot regeneration inhibition determined by AGO10 functions via the repression of miR165/166.

Antiviral Resistance Protein Tm-22 Functions on the Plasma Membrane.

The tomato Tobacco mosaic virus resistance-22 (Tm-22 ) gene encodes a coiled-coil-nucleotide binding site-Leu-rich repeat protein lacking a conventional plasma membrane (PM) localization motif. Tm-22 confers plant extreme resistance against tobamoviruses including Tobacco mosaic virus (TMV) by recognizing the avirulence (Avr) viral movement protein (MP). However, the subcellular compartment where Tm-22 functions is unclear. Here, we demonstrate that Tm-22 interacts with TMV MP to form a protein complex at the PM We show that both inactive and active Tm-22 proteins are localized to the PM When restricted to PM by fusing Tm-22 to the S-acylated PM association motif, the Tm-22 fusion protein can still induce a hypersensitive response cell death, consistent with its activation at the PM Through analyses of viral MP mutants, we find that the plasmodesmata (PD) localization of the Avr protein MP is not required for Tm-22 function. These results suggest that Tm-22-mediated resistance takes place on PM without requirement of its Avr protein to be located to PD.