BGF-YOLO: Enhanced YOLOv8 with Multiscale Attentional Feature Fusion for Brain Tumor Detection

You Only Look Once (YOLO)-based object detectors have shown remarkable accuracy for automated brain tumor detection. In this paper, we develop a novel BGF-YOLO architecture by incorporating Bi-level Routing Attention (BRA), Generalized feature pyramid networks (GFPN), and Fourth detecting head into YOLOv8. BGF-YOLO contains an attention mechanism to focus more on important features, and feature pyramid networks to enrich feature representation by merging high-level semantic features with spatial details. Furthermore, we investigate the effect of different attention mechanisms and feature fusions, detection head architectures on brain tumor detection accuracy. Experimental results show that BGF-YOLO gives a 4.7% absolute increase of mAP$_{50}$ compared to YOLOv8x, and achieves state-of-the-art on the brain tumor detection dataset Br35H. The code is available at https://github.com/mkang315/BGF-YOLO

Effects of mowing utilization on forage yield and quality in five oat varieties in alpine area of the eastern Qinghai-Tibetan Plateau

Oat (Avena sativa) is grown to provide feed in winter for livestock production in the alpine area of Qinghai-Tibetan Plateau. The effect of early cutting (T1), late cutting (T2) as well as once cutting andtwice cutting (T3) on forage yields and qualities were investigated for five oat varieties (YTA, CNC, B3, Q473 and Q444). The cutting frequency and time significantly affected forage yield and quality of five varieties with the effects being different among the five varieties. T3 increased hay yield and crude protein yield than T2. The dry hay yield and crude protein yield of T2 were all significantly lower when compared to T1. YTA presented the maximum fresh grass yields, total hay yields and total crude proteinyields under all cutting treatments among five varieties. T3 also improved feed quality on S/L ratio, F/D ratio, CP, CF and CA compared to T2 treatment. The results showed that utilization of two cuttings ofoat artificial grasslands can be used to supply forage for livestock in alpine area. YTA is a good oat introduced variety which has higher hay yield and feeding quality even with two cuttings in alpine area

Graph-Regularized Manifold-Aware Conditional Wasserstein GAN for Brain Functional Connectivity Generation

Common measures of brain functional connectivity (FC) including covariance and correlation matrices are semi-positive definite (SPD) matrices residing on a cone-shape Riemannian manifold. Despite its remarkable success for Euclidean-valued data generation, use of standard generative adversarial networks (GANs) to generate manifold-valued FC data neglects its inherent SPD structure and hence the inter-relatedness of edges in real FC. We propose a novel graph-regularized manifold-aware conditional Wasserstein GAN (GR-SPD-GAN) for FC data generation on the SPD manifold that can preserve the global FC structure. Specifically, we optimize a generalized Wasserstein distance between the real and generated SPD data under an adversarial training, conditioned on the class labels. The resulting generator can synthesize new SPD-valued FC matrices associated with different classes of brain networks, e.g., brain disorder or healthy control. Furthermore, we introduce additional population graph-based regularization terms on both the SPD manifold and its tangent space to encourage the generator to respect the inter-subject similarity of FC patterns in the real data. This also helps in avoiding mode collapse and produces more stable GAN training. Evaluated on resting-state functional magnetic resonance imaging (fMRI) data of major depressive disorder (MDD), qualitative and quantitative results show that the proposed GR-SPD-GAN clearly outperforms several state-of-the-art GANs in generating more realistic fMRI-based FC samples. When applied to FC data augmentation for MDD identification, classification models trained on augmented data generated by our approach achieved the largest margin of improvement in classification accuracy among the competing GANs over baselines without data augmentation.Comment: 10 pages, 4 figure

Adrenal computed tomography and NP-59 usefulness for diagnosing aldosterone-producing adenomas and idiopathic hyperaldosteronism in primary hyperaldosteronism

AbstractObjectivesTwo major causes of primary aldosteronism are aldosterone-producing adenomas (APA) and idiopathic hyperaldosteronism (IHA). In this study, we attempted to determine the role of NP-59 in identifying APA prior to adrenalectomy, especially when diagnostic computer tomography (CT) is equivocal.MethodsWe performed a retrospective analysis in patients with a clinical diagnosis of primary aldosteronism. The medical records of 36 patients were reviewed, which included 25 patients who had received adrenalectomy. All patients underwent adrenal CT alone or a combination of adrenal CT and NP-59 prior to surgery for the subtyping of primary aldosteronism, based on the protocols established in our institution. The accuracy of the adrenal CT and NP-59 findings was determined by a comparison with the pathologic findings and postoperative outcomes.ResultsTwenty-three patients received unilateral adrenalectomy under the diagnosis of APA. The diagnoses were based on CT findings in 11 patients and on CT and NP-59 findings in 12 patients. The results of pathology were adrenal cortical adenoma in these 23 patients and the positive predictive value was 100%. Blood pressure and potassium levels significantly improved after surgery in these patients (p < 0.01). Serum biochemistry and adrenal size of the limbs and bodies of patients with IHA were not significantly different from those of patients with APA.ConclusionFor the subtyping of primary aldosteronism, the imaging modality of adrenal CT alone or the combination of adrenal CT and NP-59 adrenal scan has a high positive predictive value for APAs. We suggest that all patients undergo an adrenal CT as their initial study, after confirming the diagnosis of primary aldosteronism, and to use NP-59 when adrenal CT findings are atypical or inconclusive. Lateralization by this modality prior to adrenalectomy can reduce unnecessarily invasive examinations such as adrenal venous sampling and also provide excellent treatment outcomes

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, GEM and GPU-based aligners including BarraCUDA and CUSHAW, SOAP3-dp is two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60 percent. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1 percent FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides a scoring scheme same as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.Comment: 21 pages, 6 figures, submitted to PLoS ONE, additional files available at "https://www.dropbox.com/sh/bhclhxpoiubh371/O5CO_CkXQE". Comments most welcom

Coordinated regulation of core and accessory genes in the multipartite genome of Sinorhizobium fredii

Prokaryotes benefit from having accessory genes, but it is unclear how accessory genes can be linked with the core regulatory network when developing adaptations to new niches. Here we determined hierarchical core/accessory subsets in the multipartite pangenome (composed of genes from the chromosome, chromid and plasmids) of the soybean microsymbiont Sinorhizobium fredii by comparing twelve Sinorhizobium genomes. Transcriptomes of two S. fredii strains at mid-log and stationary growth phases and in symbiotic conditions were obtained. The average level of gene expression, variation of expression between different conditions, and gene connectivity within the co-expression network were positively correlated with the gene conservation level from strain-specific accessory genes to genus core. Condition-dependent transcriptomes exhibited adaptive transcriptional changes in pangenome subsets shared by the two strains, while strain-dependent transcriptomes were enriched with accessory genes on the chromid. Proportionally more chromid genes than plasmid genes were co-expressed with chromosomal genes, while plasmid genes had a higher within-replicon connectivity in expression than chromid ones. However, key nitrogen fixation genes on the symbiosis plasmid were characterized by high connectivity in both within- and between-replicon analyses. Among those genes with host-specific upregulation patterns, chromosomal znu and mdt operons, encoding a conserved high-affinity zinc transporter and an accessory multi-drug efflux system, respectively, were experimentally demonstrated to be involved in host-specific symbiotic adaptation. These findings highlight the importance of integrative regulation of hierarchical core/accessory components in the multipartite genome of bacteria during niche adaptation and in shaping the prokaryotic pangenome in the long run

Kondo spin liquid and magnetically long-range ordered states in the Kondo necklace model

A simplified version of the symmetric Kondo lattice model, the Kondo necklace model, is studied by using a representation of impurity and conduction electron spins in terms of local Kondo singlet and triplet operators. Within a mean field theory, a spin gap always appears in the spin triplet excitation spectrum in 1D, leading to a Kondo spin liquid state for any finite values of coupling strength $t/J$ (with $t$ as hopping and $J$ as exchange); in 2D and 3D cubic lattices the spin gaps are found to vanish continuously around $(t/J)_c\approx 0.70$ and $(t/J)_c\approx 0.38$, respectively, where quantum phase transitions occur and the Kondo spin liquid state changes into an antiferromagnetically long-range ordered state. These results are in agreement with variational Monte Carlo, higher-order series expansion, and recent quantum Monte Carlo calculations for the symmetric Kondo lattice modelComment: Revtex, four pages, three figures; to be published in Physical Review B1, 1 July (2000

SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60%. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1% FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A

A novel Hsp90 inhibitor AT13387 induces senescence in EBV-positive nasopharyngeal carcinoma cells and suppresses tumor formation

Background: Nasopharyngeal carcinoma (NPC) is an epithelial malignancy strongly associated with Epstein-Barr virus (EBV). AT13387 is a novel heat shock protein 90 (Hsp90) inhibitor, which inhibits the chaperone function of Hsp90 and reduces expression of Hsp90-dependent client oncoproteins. This study aimed to evaluate both the in vitro and in vivo antitumor effects of AT13387 in the EBV-positive NPC cell line C666-1.Results: Our results showed that AT13387 inhibited C666-1 cell growth and induced cellular senescence with the downregulation of multiple Hsp90 client oncoproteins EGFR, AKT, CDK4, and restored the protein expression of negative cell cycle regulator p27. We also studied the ability of AT13387 to restore p27 expression by downregulation of AKT and the p27 ubiquitin mediator, Skp2, using AKT inhibitor and Skp2 siRNA. In the functional study, AT13387 inhibited cell migration with downregulation of a cell migration regulator, HDAC6, and increased the acetylation and stabilization of α-tubulin. We also examined the effect of AT13387 on putative cancer stem cells (CSC) by 3-D tumor sphere formation assay. AT13387 effectively reduced both the number and size of C666-1 tumor spheres with decreased expression of NPC CSC-like markers CD44 and SOX2. In the in vivo study, AT13387 significantly suppressed tumor formation in C666-1 NPC xenografts.Conclusion: AT13387 suppressed cell growth, cell migration, tumor sphere formation and induced cellular senescence on EBV-positive NPC cell line C666-1. Also, the antitumor effect of AT13387 was demonstrated in an in vivo model. This study provided experimental evidence for the preclinical value of using AT13387 as an effective antitumor agent in treatment of NPC. © 2013 Chan et al.; licensee BioMed Central Ltd.published_or_final_versio