Improved bacterial composition and co-occurrence patterns of rhizosphere increased nutrient uptake and grain yield through cultivars mixtures in maize.

Crop diversification contributes to agricultural productivity and resources efficient utilization. However, whether cultivar mixtures in maize affects soil bacterial community, nutrient uptake, plant growth and yield remains unknown. A two-year lysimetric experiment was conducted using two maize cultivars (LY16 and JS501) with different root system architectures planted in monoculture or in mixture under normal fertilization (NF), reduced fertilization (RF) or no addition of fertilizer (CK) and was assessed at the silking stages. Cultivar mixtures and monoculture of LY16 had higher shoot biomass, nutrient uptake and total root length at silking stage, and grain yield than monoculture of JS501 under NF and RF conditions. Under NF and RF conditions, cultivar mixtures and monoculture of LY16 led to an increase in bacterial diversity, significant changes in community structure, and a high abundance of Bacteroidia and biomarkers of Chitinophagaceae and Saprospiraceae (Bacteroidia). Cultivar mixtures showed specific responses from modules of the rhizosphere bacterial community co-occurrence network, and the relative abundance of keystone taxa of cultivar mixtures was higher than that of monoculture of JS501. The keystone taxa had a broad and significant positive correlation with plant nutrient accumulation and grain yield. Cultivar mixtures showed similar assembly processes of Bacteroidia with monoculture of LY16, and the increased abundance of Chitinophagaceae may lead to a healthy rhizosphere bacterial community. Overall, our findings indicate that cultivar mixtures significantly affects the assembly and composition of the rhizosphere bacterial community, and thus benefits plant nutrient acquisition and plant growth. These findings could deepen our understanding of the facilitating effect of rhizosphere functional microbial community (e.g. plant nutrition uptake or immunity)of cultivar mixtures.

Deep Learning-Based Universal Expert-Level Recognizing Pathological Images of Hepatocellular Carcinoma and Beyond.

Background and Aims: We aim to develop a diagnostic tool for pathological-image classification using transfer learning that can be applied to diverse tumor types. Methods: Microscopic images of liver tissue with and without hepatocellular carcinoma (HCC) were used to train and validate the classification framework based on a convolutional neural network. To evaluate the universal classification performance of the artificial intelligence (AI) framework, histological images from colorectal tissue and the breast were collected. Images for the training and validation sets were obtained from the Xiamen Hospital of Traditional Chinese Medicine, and those for the test set were collected from Zhongshan Hospital Xiamen University. The accuracy, sensitivity, and specificity values for the proposed framework were reported and compared with those of human image interpretation. Results: In the human-machine comparisons, the sensitivity, and specificity for the AI algorithm were 98.0, and 99.0%, whereas for the human experts, the sensitivity ranged between 86.0 and 97.0%, while the specificity ranged between 91.0 and 100%. Based on transfer learning, the accuracies of the AI framework in classifying colorectal carcinoma and breast invasive ductal carcinoma were 96.8 and 96.0%, respectively. Conclusion: The performance of the proposed AI framework in classifying histological images with HCC was comparable to the classification performance achieved by human experts, indicating that extending the proposed AI's application to diagnoses and treatment recommendations is a promising area for future investigation.

Beneficial Effects of Gracillin From Rhizoma Paridis Against Gastric Carcinoma via the Potential TIPE2-Mediated Induction of Endogenous Apoptosis and Inhibition of Migration in BGC823 Cells.

Tumor necrosis factor-α inducible protein-8 (TIPE2), initially recognized as a negative immune regulator, exerts an important role in suppressing the progression of numerous cancers. In our previous investigation, we found that TIPE2 expression displayed a decrease or absence in gastric tumor tissue, and the overexpression of TIPE2 suppressed the growth of gastric cancer tumors and cells, demonstrating that TIPE2 could be a potential medicinal target for gastric cancer treatment. However, it's seldomly reported that several medicinal agents or candidates targeted TIPE2 for treating diseases, including gastric cancer. To identify the candidate targeting TIPE2 to fight against gastric cancer, several extractions from traditional natural medicinal plants with anti-tumor functions were employed to screen the active compounds according to bioassay-guided isolation. Interestingly, gracillin, a component from the ethyl acetate extraction of Rhizoma Paridis, was identified to induce the expression of TIPE2 and inhibit the cell proliferation in gastric cancer BGC-823 cells. Furthermore, the underlying mechanisms that restrain gastric cancer were evaluated by clone formation, EdU staining, flow cytometry, and other assays. Meanwhile, the role of TIPE2 in the anti-tumor effect of gracillin was elucidated via the use of siTIPE2 RNA. It was determined that gracillin could fight against gastric cancer cells by inhibiting the cell proliferation participated by the PI3K/AKT pathway and cell cycle arrest, suppressing the EMT pathway-regulating cell migration, and inducing bcl2-associated mitochondrial apoptosis. Additionally, TIPE2 maybe contribute to the benefits of gracillin. These results of the present study are an important step toward the medicinal development of gracillin, and are also of use in understanding the effect of TIPE2 as a potential tumor target.

Obliquely Deposited Titanium Nitride Nanorod Arrays as Surface-Enhanced Raman Scattering Substrates.

In this work, titanium nitride (TiN) nanorod arrays were prepared as surface-enhanced Raman scattering (SERS) substrates using glancing angle deposition (GLAD) in a magnetron sputtering system. The nitrogen flow rate was varied from RN2 = 1 to 3 sccm, yielding five TiN uniform thin films and five TiN nanorod arrays. The figure of merit (FOM) of each TiN uniform film was measured and compared with the SERS signal of each TiN nanorod array. Rhodamine 6G (R6G) was used as the analyte in SERS measurement. For an R6G concentration of 10-6 M, the analytical enhancement factor (AEF) of the TiN nanorod array that was prepared at RN2 = 1.5 sccm was 104. The time-durable SERS performance of TiN nanorod arrays was also investigated.

Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation.

BACKGROUND: The importance of transcription factors (TFs) and epigenetic modifications in the control of gene expression is widely accepted. However, causal relationships between changes in TF binding, histone modifications, and gene expression during the response to extracellular stimuli are not well understood. Here, we analyze the ordering of these events on a genome-wide scale in dendritic cells in response to lipopolysaccharide (LPS) stimulation. RESULTS: Using a ChIP-seq time series dataset, we find that the LPS-induced accumulation of different histone modifications follows clearly distinct patterns. Increases in H3K4me3 appear to coincide with transcriptional activation. In contrast, H3K9K14ac accumulates early after stimulation, and H3K36me3 at later time points. Integrative analysis with TF binding data reveals potential links between TF activation and dynamics in histone modifications. Especially, LPS-induced increases in H3K9K14ac and H3K4me3 are associated with binding by STAT1/2 and were severely impaired in Stat1-/- cells. CONCLUSIONS: While the timing of short-term changes of some histone modifications coincides with changes in transcriptional activity, this is not the case for others. In the latter case, dynamics in modifications more likely reflect strict regulation by stimulus-induced TFs and their interactions with chromatin modifiers.

Capping metallic nanohelixes with SiO2 nanohelixes to enhance broadband and wide-angle light extinction.

In this work, an SiO2 nanohelix array is obliquely deposited upon a metal nanohelix array as an index matching layer to enhance light extinction. Firstly, an SiO2-Ag nanohelix array is fabricated with stronger light extinction than the Ag nanohelix array over wavelengths from 300 nm to 1000 nm at normal incidence. Next, the SiO2-Al-Ag nanohelix array is fabricated; it exhibits broadband and wide-angle light extinction that is stronger that reported for the Al-Ag nanohelix array. The unpolarized extinctance exceeds 90% over wavelengths from 400 nm to 2000 nm and angles of incidence from 0° to 70°.

Overexpression of miR-19a inhibits colorectal cancer angiogenesis by suppressing KRAS expression.

The microRNA miR-19a is closely related to tumor formation and development and is a key oncogene. Previous studies have demonstrated that miR-19a is upregulated in multiple cancer types, including colorectal cancer (CRC). However, most of these experiments were performed in vitro, and consequently, the mechanisms underlying the effects of miR-19a on CRC are still unclear. Therefore, in the present study, we investigated the role of miR-19a in the development of solid CRC tumors. We generated KRAS 3'UTR-Mut by deleting the predicted binding site for miR-19a in KRAS, and observed that the expression of a reporter gene containing the KRAS 3'UTR in HCT116 cells was suppressed by miR-19a, while that of a reporter gene with mutant KRAS 3'UTR was unaffected by miR-19a. We observed that high miR-19a levels reduced KRAS expression. In the tube formation assay, overexpression of miR-19a exhibited anti-angiogenesis effects, which were rescued by KRAS expression. We established a nude mouse xenograft model to investigate the specific role of miR-19a in solid tumors. The results revealed that the sizes of xenograft tumors and density of blood vessels developed from HCT116 cells expressing miR-19a were smaller/lower compared with those of the control. KRAS and VEGFA levels were also reduced. In conclusion, our results revealed that miR-19a overexpression supressed KRAS expression and angiogenesis in CRC, indicating possibilities of using miR-19a in future therapeutic applications.

Liver cirrhosis caused by chronic Budd-Chiari syndrome.

Chronic Budd-Chiari syndrome (BCS) is a rare cause of liver cirrhosis (LC) and tends to be misdiagnosed in clinical practice. In order to characterize LC caused by chronic BCS, we conducted this retrospective observational study. Medical records of all patients who were initially diagnosed as chronic BCS with LC when discharged from our department from January, 2011 to October, 2016 were reviewed. Cirrhotic patients with known causes and cases lacked key data were excluded. Data of remaining patients was collected and analyzed. A total of 15 cases were included in this study. Patients with LC caused by chronic BCS were characterized by preserved liver function and prominent portal hypertension (PH). Abdominal distention and edema of lower extremities were most common initial manifestations. Intra- or extrahepatic collaterals on imaging studies were of great importance for differential diagnosis. Most of these patients received interventional angioplasty followed by anticoagulation with warfarin and survived without obvious complications of PH. Chronic BCS was a rare but important cause of LC and should always be considered in patients with chronic liver disease and so-called cryptogenic LC. Early diagnosis and timely treatment may improve outcome. Correct interpretation of imaging examinations was fundamental to avoiding misdiagnosis.

aCGH Analysis to Estimate Genetic Variations among Domesticated Chickens.

Chickens have been familiar to humans since ancient times and have been used not only for culinary purposes but also for cultural purposes including ritual ceremonies and traditional entertainment. The various chicken breeds developed for these purposes often display distinct morphological and/or behavioural traits. For example, the Japanese Shamo is larger and more aggressive than other domesticated chickens, reflecting its role as a fighting cock breed, whereas Japanese Naganakidori breeds, which have long-crowing behaviour, were bred instead for their entertaining and aesthetic qualities. However, the genetic backgrounds of these distinct morphological and behavioural traits remain unclear. Therefore, the question arises as to which genomic regions in these chickens were acted upon by selective pressures through breeding. We compared the entire genomes of six chicken breeds domesticated for various cultural purposes by utilizing array comparative genomic hybridization. From these analyses, we identified 782 regions that underwent insertions, deletions, or mutations, representing man-made selection pressure in these chickens. Furthermore, we found that a number of genes diversified in domesticated chickens bred for cultural or entertainment purposes were different from those diversified in chickens bred for food, such as broilers and layers.

An interference coating of metamaterial as an ultrathin light absorber in the violet-to-infrared regime.

A metamaterial with brief and ultrathin structure performs high efficiency in light absorption. An upright aluminum nanorod array (Al NRA) is obliquely deposited, measured, and analyzed its optical property. The Al NRA performs high efficiency of light absorption and low reflectance simultaneously. Based on the measured refractive index and impedances, the wave propagation through the Al NRA is traced to demonstrate the destructive interference that leads to antireflection. According to the analysis of wave tracing, an Al semicontinuous film with thickness of 15nm is introduced under an Al NRA with thickness of only 245nm as a brief and thin two-layered structure. The broadband and polarization-independent light absorption is measured over the violet-to-infrared regime.

Metal/dielectric/metal sandwich film for broadband reflection reduction.

A film comprising randomly distributed metal/dielectric/metal sandwich nanopillars with a distribution of cross-sectional diameters, displayed extremely low reflectance over the blue-to-red regime, when coated on glass and illuminated normally. When it is illuminated by normally incident light, this sandwich film (SWF) has a low extinction coefficient, its phase thickness is close to a negative wavelength in the blue-to-red spectral regime, and it provides weakly dispersive forward and backward impedances, so that reflected waves from the two faces of the SWF interfere destructively. Broadband reflection-reduction, over a wide range of incidence angles and regardless of the polarization state of the incident light, was observed when the SWF was deposited on polished silicon.

Extended broadband achromatic reflective-type waveplate.

This work demonstrates the feasibility of applying a symmetrical film stack on a silver mirror, resulting in broadband phase retardation. While functioning as a reflective-type achromatic waveplate, the symmetrical film stack comprises at least one anisotropic thin film. Additionally, selecting the birefringence and thickness of the thin film allows for the design of uniform phase retardation in both the passband and stopband. A symmetrical film stack that is composed of an anisotropic Ta(2)O(5) thin film and isotropic Ta(2)O(5) thin film is investigated for its achromatic performance in phase retardation.

Biologically inspired achromatic waveplates for visible light.

Waveplates are planar devices used in optics and optoelectronics to change the polarization state of light. Made of anisotropic dielectric materials such as crystals and thin films, waveplates are not known to exhibit achromatic performance over the visible regime. Inspired by the microvillar structure of R8 cells functioning as polarization converters in the eyes of stomatopod crustaceans, we conceived, designed, fabricated and tested periodically multilayered structures comprising two different types of arrays of nanorods. Morphologically analogous to the ocular cells, here we show that the periodically multilayered structures can function as achromatic waveplates over the visible regime.

Effective gene collection from the metatranscriptome of marine microorganisms.

BACKGROUND: Metagenomic studies, accelerated by the evolution of sequencing technologies and the rapid development of genomic analysis methods, can reveal genetic diversity and biodiversity in various samples including those of uncultured or unknown species. This approach, however, cannot be used to identify active functional genes under actual environmental conditions. Metatranscriptomics, which is similar in approach to metagenomics except that it utilizes RNA samples, is a powerful tool for the transcriptomic study of environmental samples. Unlike metagenomic studies, metatranscriptomic studies have not been popular to date due to problems with reliability, repeatability, redundancy and cost performance. Here, we propose a normalized metatranscriptomic method that is suitable for the collection of genes from samples as a platform for comparative transcriptomics. RESULTS: We constructed two libraries, one non-normalized and the other normalized library, from samples of marine microorganisms taken during daylight hours from Hiroshima bay in Japan. We sequenced 0.6M reads for each sample on a Roche GS FLX, and obtained 0.2M genes after quality control and assembly. A comparison of the two libraries showed that the number of unique genes was larger in the normalized library than in the non-normalized library. Functional analysis of genes revealed that a small number of gene groups, ribosomal RNA genes and chloroplast genes, were dominant in both libraries. Taxonomic distribution analysis of the libraries suggests that Stramenopiles form a major taxon that includes diatoms. The normalization technique thus increases unique genes, functional categories of genes, and taxonomic richness. CONCLUSIONS: Normalization of the marine metatranscriptome could be useful in increasing the number of genes collected, and in reducing redundancies among highly expressed genes. Gene collection through the normalization method was effective in providing a foundation for comparative transcriptomic analysis.