On nonhydrostatic coastal model simulations of shear instabilities in a stratified shear flow at high Reynolds number

Author Posting. © American Geophysical Union, 2017. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 122 (2017): 3081–3105, doi:10.1002/2016JC012334.The nonhydrostatic surface and terrain-following coastal model NHWAVE is utilized to simulate a continually forced stratified shear flow in a straight channel, which is a generic problem to test the existing nonhydrostatic coastal models' capability in resolving shear instabilities in the field scale. The resolved shear instabilities in the shear layer has a Reynolds number of about 1.4 × 106, which is comparable to field observed value. Using the standard Smagorinsky closure with a grid size close to the Ozmidov length scale, simulation results show that the resolved energy cascade exceeds 1 order of magnitude and the evolution and turbulent mixing characteristics are predicted well. Two different approaches are used to estimate the turbulent dissipation rate, namely using the resolved turbulent energy spectrum and the parameterized subgrid turbulent dissipation rate, and the predicted results provide the upper and lower bounds that encompass the measured values. Model results show significantly higher turbulence in braids of shear instabilities, which is similar to field observations while both the subgrid turbulent dissipation rate and resolved vorticity field can be used as surrogates for measured high acoustic backscatter signals. Simulation results also reveal that the surface velocity divergence/convergence is an effective identifier for the front of the density current and the shear instabilities. To guide future numerical studies in more realistic domains, an evaluation on the effects of different grid resolutions and subgrid viscosity on the resolved flow field and subgrid dissipation rate are discussed.Office of Naval Research Grant Numbers: N00014-15-1-2612 , N00014-16-1-2948; National Science Foundation Grant Numbers: OCE-1334325 , OCE-1232928; Extreme Science and Engineering Discovery Environment (XSEDE) SuperMIC Grant Number: TG-OCE1000152017-10-1

Detection of Novel Variations Related to Litter Size in BMP15 Gene of Luzhong Mutton Sheep ( Ovis aries )

SIMPLE SUMMARY: BMP15 is a critical gene in sheep reproduction. Most of its variations have been reported in European sheep. In this study, the entire open reading frame (ORF) region of BMP15 was sequenced in 154 Luzhong mutton sheep. Among 13 identified variations, six were novel. Four SNPs (ENSOART00000010201.1:c.352+342C>A, c.352+1232T>C, c.352+1165A>G and c.353-2036T>A) were significantly associated with litter size, and could be used as candidate genetic markers for improving litter size. The results also suggested possible interaction between BMP15 and FecB/GDF9. ABSTRACT: Litter size is an important economic trait in the mutton sheep industry. BMP15 is one of the key candidate genes for litter size in sheep. In this study, the entire ORF region of BMP15 was sequenced in 154 Luzhong mutton ewes, and the novel variations were determined. The association between polymorphism in BMP15 and litter size was analyzed using a general linear model. Six out of a total of thirteen variations were identified to be novel. Association analysis indicated that four (SNPs ENSOART00000010201.1:c.352+342C>A, c.352+1232T>C, c.352+1165A>G and c.353-2036T>A) were significantly associated with litter size. The joint analysis among three major genes (BMP15, BMPR1B and GDF9) exhibited significant interaction effects in three combinations (FecB and c.352+1232T>C of BMP15; FecB and c.352+1165A>G of BMP15; c.352+342C>A of BMP15 and ENSOART00000014382.1:c.994G>A of GDF9). For the SNPs c.352+1232T>C and c.352+342C>A, the global distribution of allele frequencies showed that the highest variation frequency occurs in Western Europe. In conclusion, the results demonstrated that BMP15 is a major gene for litter size in Luzhong mutton sheep and candidate SNPs associated with litter size were identified

Cumulative Evidence for Relationships Between 8q24 Variants and Prostate Cancer

Multiple independent cancer susceptibility loci at chromosome 8q24 have been identified by GWAS (Genome-wide association studies). Forty six articles including 60,293 cases and 62,971 controls were collected to conduct a meta-analysis to evaluate the associations between 21 variants in 8q24 and prostate cancer risk. Of the 21 variants located in 8q2\5 were significantly associated with the risk of prostate cancer. In particular, both homozygous AA and heterozygous CA genotypes of rs16901979, as well as the AA and CA genotypes of rs1447295, were associated with the risk of prostate cancer. Our study showed that variants in the 8q24 region are associated with prostate cancer risk in this large-scale research synopsis and meta-analysis. Further studies are needed to explore the role of the 8q24 variants involved in the etiology of prostate cancer

Energy and Environmental Efficiency Evaluation of Transportation Systems in China’s 255 Cities

China’s transportation sector suffers from excessive energy consumption and serious pollutant emissions. There is increasing pressure to improve energy and environmental efficiency (EEE). This paper researches the EEE of transportation systems in 255 Chinese cities from 2015 to 2019 with the assistance of the super-efficiency SBM model. Research results show that the five-year average EEE of the Chinese transportation system is 0.4420, indicating an overall low performance, with most regions still needing improvement. There are significant differences in the transportation system EEE between cities, with Guangzhou, Maoming, and Zhoushan ranking in the top three, and Heihe, Xining, and Taiyuan in the bottom. Cities with a better economic base, developed water systems and more relevant policy documents do better in energy use and environmental protection compared to other cities. Moreover, the development of the transportation systems is uneven, with noticeable regional differences. The general trend is that cities located in the eastern have better transportation systems EEE than cities in other economic zones. The findings should have a far-reaching impact on the sustainable development of cities. It also provides an essential reference for the research on EEE efficiency of transportation systems in China and other countries

The global state of research in stem cells therapy for spinal cord injury (2003–2022): a visualized analysis

ObjectiveOur study aimed to visualize the global status and frontiers in stem cell therapy for spinal cord injury by using bibliometric methodology.MethodsPublication citation information related to stem cell therapy for spinal cord injury (SCI) studies between 2003 and 2022 was retrieved from the Web of Science Core Collection database. For the visualized study, VOS viewer software and Graph Pad Prism 9.5 were used to perform bibliometric analysis of included data and publication number statistics in stem cell therapy for the SCI domain.ResultsA total of 6,686 publications were retrieved. The USA and China made the highest contributions to global research with the highest number of citations and link strength. The journal Experimental Neurology ranks as the top journal, combining the publication amount and bibliometrics results. The University of Toronto, based in Canada, was the first-ranking institution. The directions of the current study could be divided into five clusters. The research of Transplantation and Regenerative Medicine and Neurosciences Mechanism Research may be the emerging frontiers in this domain.ConclusionIn summary, stem cell therapy for spinal cord injuries is poised for more valuable advances

Identification of Genome-Wide Variations among Three Elite Restorer Lines for Hybrid-Rice

Rice restorer lines play an important role in three-line hybrid rice production. Previous research based on molecular tagging has suggested that the restorer lines used widely today have narrow genetic backgrounds. However, patterns of genetic variation at a genome-wide scale in these restorer lines remain largely unknown. The present study performed re-sequencing and genome-wide variation analysis of three important representative restorer lines, namely, IR24, MH63, and SH527, using the Solexa sequencing technology. With the genomic sequence of the Indica cultivar 9311 as the reference, the following genetic features were identified: 267,383 single-nucleotide polymorphisms (SNPs), 52,847 insertion/deletion polymorphisms (InDels), and 3,286 structural variations (SVs) in the genome of IR24; 288,764 SNPs, 59,658 InDels, and 3,226 SVs in MH63; and 259,862 SNPs, 55,500 InDels, and 3,127 SVs in SH527. Variations between samples were also determined by comparative analysis of authentic collections of SNPs, InDels, and SVs, and were functionally annotated. Furthermore, variations in several important genes were also surveyed by alignment analysis in these lines. Our results suggest that genetic variations among these lines, although far lower than those reported in the landrace population, are greater than expected, indicating a complicated genetic basis for the phenotypic diversity of the restorer lines. Identification of genome-wide variation and pattern analysis among the restorer lines will facilitate future genetic studies and the molecular improvement of hybrid rice

High Diversity of the Fungal Community Structure in Naturally-Occurring Ophiocordyceps sinensis

BACKGROUND: Ophiocordyceps sinensis (syn. Cordyceps sinensis), which is a parasite of caterpillars and is endemic to alpine regions on the Tibetan Plateau, is one of the most valuable medicinal fungi in the world. "Natural O. sinensis specimens" harbor various other fungi. Several of these other fungi that have been isolated from natural O. sinensis specimens have similar chemical components and/or pharmaceutical effects as O. sinensis. Nevertheless, the mycobiota of natural O. sinensis specimens has not been investigated in detail. METHODOLOGY/PRINCIPAL FINDINGS: Based on the technique of PCR-single-strand conformation polymorphism (PCR-SSCP), the mycobiota of three different sections (stromata, sclerotia, and mycelial cortices) from natural O. sinensis specimens were investigated using both culture-dependent and -independent methods. For the culture-dependent method, 572 fungal strains were isolated, and 92 putative operational taxonomic units (OTUs) were identified from 226 sequenced strains with the threshold of 97%. For the culture-independent method, 490 fungal clones were identified from about 3000 clones of ITS fragments from the whole-community DNA; based on PCR-SSCP analyses, 266 of these clones were selected to be sequenced, and 118 putative OTUs were detected. The overwhelming majority of isolates/clones and OTUs were detected from mycelial cortices; only a few were detected from stromata and sclerotia. The most common OTUs detected with both methods belonged to Ascomycota; however, only 13 OTUs were detected simultaneously by both methods. Potential novel lineages were detected by each of the two methods. CONCLUSIONS/SIGNIFICANCE: A great number of fungal species present in the mycobiota of naturally-occurring O. sinensis specimens were detected, and many of them may represent undescribed lineages. That only a few of the same OTUs were detected by both methods indicated that different methods should be used. This study increased our understanding about the fungal community structure of this valuable medicinal herb

miR-200 Enhances Mouse Breast Cancer Cell Colonization to Form Distant Metastases

BACKGROUND: The development of metastases involves the dissociation of cells from the primary tumor to penetrate the basement membrane, invade and then exit the vasculature to seed, and colonize distant tissues. The last step, establishment of macroscopic tumors at distant sites, is the least well understood. Four isogenic mouse breast cancer cell lines (67NR, 168FARN, 4TO7, and 4T1) that differ in their ability to metastasize when implanted into the mammary fat pad are used to model the steps of metastasis. Only 4T1 forms macroscopic lung and liver metastases. Because some miRNAs are dysregulated in cancer and affect cellular transformation, tumor formation, and metastasis, we examined whether changes in miRNA expression might explain the differences in metastasis of these cells. METHODOLOGY/PRINCIPAL FINDINGS: miRNA expression was analyzed by miRNA microarray and quantitative RT-PCR in isogenic mouse breast cancer cells with distinct metastatic capabilities. 4T1 cells that form macroscopic metastases had elevated expression of miR-200 family miRNAs compared to related cells that invade distant tissues, but are unable to colonize. Moreover, over-expressing miR-200 in 4TO7 cells enabled them to metastasize to lung and liver. These findings are surprising since the miR-200 family was previously shown to promote epithelial characteristics by inhibiting the transcriptional repressor Zeb2 and thereby enhancing E-cadherin expression. We confirmed these findings in these cells. The most metastatic 4T1 cells acquired epithelial properties (high expression of E-cadherin and cytokeratin-18) compared to the less metastatic cells. CONCLUSIONS/SIGNIFICANCE: Expression of miR-200, which promotes a mesenchymal to epithelial cell transition (MET) by inhibiting Zeb2 expression, unexpectedly enhances macroscopic metastases in mouse breast cancer cell lines. These results suggest that for some tumors, tumor colonization at metastatic sites might be enhanced by MET. Therefore the epithelial nature of a tumor does not predict metastatic outcome

Research on Construction and Practice of Precision Teaching Classroom for University Programming Courses

Facing the challenges of programming courses teaching in university, this study constructs a precision teaching classroom for programming courses that integrates precision teaching theory. Firstly, this paper analyzes the realization conditions for precision teaching in programming courses, then designs the implementation process of precision teaching including three teaching phases and five teaching links, and finally carried out teaching practice in C Language Programming course. The practice results showed that in the precision programming teaching classroom, teacher-student interactions were more frequent and students had higher programming learning efficiency than in ordinary programming teaching classroom. Compared with the control class, students in the experimental class were more capable of grasping programming knowledge and had better programming problem-solving abilities, and most of them were highly satisfied with teaching design of precision teaching classroom for C Language Programming. Precision programming teaching classroom constructed by this research provides a more optimized and effective teaching method for university programming teaching. On the other hand, this study provides a practical case for the integration and application of precision teaching theory and university curriculum teaching