Monitoring Local Changes in Granite Rock Under Biaxial Test: A Spatiotemporal Imaging Application With Diffuse Waves

International audienceDiffuse acoustic or seismic waves are highly sensitive to detect changes of mechanical properties in heterogeneous geological materials. In particular, thanks to acousto-elasticity, we can quantify stress changes by tracking acoustic or seismic relative velocity changes in the material at test.In this paper, we report on a small-scale laboratory application of an innovative time-lapse tomography technique named Locadiff to image spatio-temporal mechanical changes on a granite sample under biaxial loading, using diffuse waves at ultrasonic frequencies ( 300 kHz to 900 kHz). We demonstrate the ability of the method to image reversible stress evolution and deformation process, together with the development of reversible and irreversible localized micro-damage in the specimen at an early stage. Using full-field infrared thermography, we visualize stress induced temperature changes and validate stress images obtained from diffuse ultrasound. We demonstrate that the inversion with a good resolution can be achieved with only a limited number of receivers distributed around a single source, all located at the free surface of the specimen. This small-scale experiment is a proof of concept for frictional earthquake-like failure (e.g. stick slip) research at laboratory scale as well as large scale seismic applications, potentially including active fault monitoring

p97/VCP is highly expressed in the stem-like cells of breast cancer and controls cancer stemness partly through the unfolded protein response

p97/VCP, an evolutionarily concerned ATPase, partakes in multiple cellular proteostatic processes, including the endoplasmic reticulum (ER)-associated protein degradation (ERAD). Elevated expression of p97 is common in many cancers and is often associated with poor survival. Here we report that the levels of p97 positively correlated with the histological grade, tumor size, and lymph node metastasis in breast cancers. We further examined p97 expression in the stem-like cancer cells or cancer stem cells (CSCs), a cell population that purportedly underscores cancer initiation, therapeutic resistance, and recurrence. We found that p97 was consistently at a higher level in the CD4

Metabolic Disturbance and Th17/Treg Imbalance Are Associated With Progression of Gingivitis

ObjectiveThis study sought to explore the role of metabolic disturbance in immunoregulation of gingivitis targeting T helper 17 cells (Th17)/regulatory T cell (Treg).Materials and MethodsA total of 20 gingivitis patients and 19 healthy volunteers were recruited. Quantitative real time polymerase chain reaction (qRT-PCR) was used to evaluate expression patterns of Forkhead box protein P3 (Foxp3), transforming growth factor-β (TGF-β), retinoid-related orphan receptor-gammat (RORγt) and interleukin 17A (IL-17A) in the peripheral blood lymphocytes of subjects across the two groups. Moreover, the enzyme-linked immunosorbent assay (ELISA) technique was used to detect levels of TGF-β, IL-4, IL-6,TL-10 and L-17A secreted in the plasma as well as the SIgA secreted in saliva. Flow cytometry was used to detect the percentage of CD4+CD25+ Foxp3+Treg cells and the percentage of CD4+IL-17A+ Th17 cells in whole blood of subjects in both groups. Gas chromatography-mass spectrometry (GC-MS) was employed to analyze the plasma metabolites in the gingivitis patient group. Statistical analysis was applied to determine whether the plasma metabolites and related metabolic pathways significantly differed between gingivitis patients and healthy controls. Ingenuity pathway analysis (IPA) was employed to identify the potential relation between the metabolites and the Th17 and Treg related pathway.ResultsThe percentages of CD4+IL17A+Th17 cells and IL-17 significantly increased in the peripheral blood in the gingivitis group. Moreover, the upregulation of IL-17A mRNA and RORγt mRNA were also found in the gingivitis group. However, the percentage of CD4+CD25+ Foxp3+Treg cells and Foxp3 mRNA in the whole blood did not significantly change. However, TGF-β mRNA as well as TGF-β, IL-4, IL-6, IL-10 in the periperial blood and SIgA in the saliva were higher in the gingivitis group. Notably, that the ratio of Th17/Treg cells was significantly increased during peripheral circulation. Furthermore, we identified 18 different metabolites which were differentially expressed in plasma between the gingivitis and healthy control groups. Notably, the levels of cholesterol, glycerol 1-octadecanoate, d-glucose, uric acid, cyclohexaneacetic acid, 3-pyridine, tryptophan, and undecane 2,4-dimethyl were significantly up-regulated. whereas the levels of lactic acid, glycine, linoleic acid, monopalmitic acid, glycerol, palmitic acid, pyruvate, 1-(3-methylbutyl)-2,3,4,6-tetramethylbenzene, 1 5-anhydro d-altrol, and boric acid were down-regulated in the gingivitis group, relative to healthy controls. IPA showed that these metabolites are connected to IL17 signaling, TGF-B signaling, and IL10 signaling, which are related closely to Th17 and Treg pathway.ConclusionOverall, these results showed that disturbance to glycolysis as well as amino and fatty acid metabolism are associated with Th17/Treg balance in gingivitis. Impaired immunometabolism may influence some periodontally involved systemic diseases, hence it is a promising strategy in targeted development of treatment therapies

Performance of a deep learning-based lung nodule detection system as an alternative reader in a Chinese lung cancer screening program

Objective: To evaluate the performance of a deep learning-based computer-aided detection (DL-CAD) system in a Chinese low-dose CT (LDCT) lung cancer screening program. Materials and methods: One-hundred-and-eighty individuals with a lung nodule on their baseline LDCT lung cancer screening scan were randomly mixed with screenees without nodules in a 1:1 ratio (total: 360 individuals). All scans were assessed by double reading and subsequently processed by an academic DL-CAD system. The findings of double reading and the DL-CAD system were then evaluated by two senior radiologists to derive the reference standard. The detection performance was evaluated by the Free Response Operating Characteristic curve, sensitivity and false-positive (FP) rate. The senior radiologists categorized nodules according to nodule diameter, type (solid, part-solid, non-solid) and Lung-RADS. Results: The reference standard consisted of 262 nodules ≥ 4 mm in 196 individuals; 359 findings were considered false positives. The DL-CAD system achieved a sensitivity of 90.1% with 1.0 FP/scan for detection of lung nodules regardless of size or type, whereas double reading had a sensitivity of 76.0% with 0.04 FP/scan (P = 0.001). The sensitivity for detection of nodules ≥ 4 - ≤ 6 mm was significantly higher with DL-CAD than with double reading (86.3% vs. 58.9% respectively; P = 0.001). Sixty-three nodules were only identified by the DL-CAD system, and 27 nodules only found by double reading. The DL-CAD system reached similar performance compared to double reading in Lung-RADS 3 (94.3% vs. 90.0%, P = 0.549) and Lung-RADS 4 nodules (100.0% vs. 97.0%, P = 1.000), but showed a higher sensitivity in Lung-RADS 2 (86.2% vs. 65.4%, P < 0.001). Conclusions: The DL-CAD system can accurately detect pulmonary nodules on LDCT, with an acceptable false-positive rate of 1 nodule per scan and has higher detection performance than double reading. This DL-CAD system may assist radiologists in nodule detection in LDCT lung cancer screening

Crop Diversity for Yield Increase

Traditional farming practices suggest that cultivation of a mixture of crop species in the same field through temporal and spatial management may be advantageous in boosting yields and preventing disease, but evidence from large-scale field testing is limited. Increasing crop diversity through intercropping addresses the problem of increasing land utilization and crop productivity. In collaboration with farmers and extension personnel, we tested intercropping of tobacco, maize, sugarcane, potato, wheat and broad bean – either by relay cropping or by mixing crop species based on differences in their heights, and practiced these patterns on 15,302 hectares in ten counties in Yunnan Province, China. The results of observation plots within these areas showed that some combinations increased crop yields for the same season between 33.2 and 84.7% and reached a land equivalent ratio (LER) of between 1.31 and 1.84. This approach can be easily applied in developing countries, which is crucial in face of dwindling arable land and increasing food demand

Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus) : applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis

High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1-8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species.Peer reviewe

Analysis of synonymous codon usage in Hepatitis A virus

<p>Abstract</p> <p>Background</p> <p>Hepatitis A virus is the causative agent of type A viral hepatitis, which causes occasional acute hepatitis. Nevertheless, little information about synonymous codon usage pattern of HAV genome in the process of its evolution is available. In this study, the key genetic determinants of codon usage in HAV were examined.</p> <p>Results</p> <p>The overall extent of codon usage bias in HAV is high in <it>Picornaviridae</it>. And the patterns of synonymous codon usage are quite different in HAV genomes from different location. The base composition is closely correlated with codon usage bias. Furthermore, the most important determinant that results in such a high codon bias in HAV is mutation pressure rather than natural selection.</p> <p>Conclusions</p> <p>HAV presents a higher codon usage bias than other members of <it>Picornaviridae</it>. Compositional constraint is a significant element that influences the variation of synonymous codon usage in HAV genome. Besides, mutation pressure is supposed to be the major factor shaping the hyperendemic codon usage pattern of HAV.</p