REBOUND is a new multi-purpose N-body code which is freely available under an open-source license. It was designed for collisional dynamics such as planetary rings but can also solve the classical ...N-body problem. It is highly modular and can be customized easily to work on a wide variety of different problems in astrophysics and beyond. REBOUND comes with three symplectic integrators: leap-frog, the symplectic epicycle integrator (SEI) and a Wisdom-Holman mapping (WH). It supports open, periodic and shearing-sheet boundary conditions. REBOUND can use a Barnes-Hut tree to calculate both self-gravity and collisions. These modules are fully parallelized with MPI as well as OpenMP. The former makes use of a static domain decomposition and a distributed essential tree. Two new collision detection modules based on a plane-sweep algorithm are also implemented. The performance of the plane-sweep algorithm is superior to a tree code for simulations in which one dimension is much longer than the other two and in simulations which are quasi-two dimensional with less than one million particles. In this work, we discuss the different algorithms implemented in REBOUND, the philosophy behind the code’s structure as well as implementation specific details of the different modules. We present results of accuracy and scaling tests which show that the code can run efficiently on both desktop machines and large computing clusters.
Metastasis is a major contributor to cancer-associated deaths. It is characterized by a multistep process that occurs through the acquisition of molecular and phenotypic changes enabling cancer cells ...from a primary tumour to disseminate and colonize at distant organ sites. Over the past decade, the discovery and characterization of long noncoding RNAs (lncRNAs) have revealed the diversity of their regulatory roles, including key contributions throughout the metastatic cascade. Here, we review how lncRNAs promote metastasis by functioning in discrete pro-metastatic steps including the epithelial-mesenchymal transition, invasion and migration and organotrophic colonization, and by influencing the metastatic tumour microenvironment, often by interacting within ribonucleoprotein complexes or directly with other nucleic acid entities. We discuss well-characterized lncRNAs with in vivo phenotypes and highlight mechanistic commonalities such as convergence with the TGFβ-ZEB1/ZEB2 axis or the nuclear factor-κB pathway, in addition to lncRNAs with controversial mechanisms and the influence of methodologies on mechanistic interpretation. Furthermore, some lncRNAs can help identify tumours with increased metastatic risk and spur novel therapeutic strategies, with several lncRNAs having shown potential as novel targets for antisense oligonucleotide therapy in animal models. In addition to well-characterized examples of lncRNAs functioning in metastasis, we discuss controversies and ongoing challenges in lncRNA biology. Finally, we present areas for future study for this rapidly evolving field.
Recent clinical successes of cancer immunotherapy necessitate the investigation of the interaction between malignant cells and the host immune system. However, elucidation of complex tumor-immune ...interactions presents major computational and experimental challenges. Here, we present Tumor Immune Estimation Resource (TIMER; cistrome.shinyapps.io/timer) to comprehensively investigate molecular characterization of tumor-immune interactions. Levels of six tumor-infiltrating immune subsets are precalculated for 10,897 tumors from 32 cancer types. TIMER provides 6 major analytic modules that allow users to interactively explore the associations between immune infiltrates and a wide spectrum of factors, including gene expression, clinical outcomes, somatic mutations, and somatic copy number alterations. TIMER provides a user-friendly web interface for dynamic analysis and visualization of these associations, which will be of broad utilities to cancer researchers.
.
Summary
Porcine reproductive and respiratory syndrome virus (PRRSV) is a major economically significant pathogen that has adversely affected China's swine industry. Currently, a novel type 2 PRRSV, ...called the NADC30‐like strain, is epidemic in numerous provinces of China, and commercial vaccines provide limited protection for infected animals. The extensive recombination phenomenon among NADC30‐like PRRSVs is identified as a unique molecular characteristic of the virus. However, our understanding of how recombination influences NADC30‐like PRRSVs is largely inadequate. In this study, we analysed the genetic characteristics of a recombinant NADC30‐like PRRSV (SC‐d) and examined its pathogenicity compared with a non‐recombinant NADC30‐like PRRSV (SD‐A19) and a highly pathogenic PRRSV (HuN4). SC‐d has three discontinuous deletions in nsp2, consistent with NADC30 isolated from the United States in 2008. Furthermore, we identified four recombination breakpoints in the SC‐d genome, which separated the SC‐d genome into four regions (regions A, B, C and D). Regions A and C are closely related to the JXA1‐like strain, one of the earliest Chinese HP‐PRRSV strains, and regions B and D are closely related to the NADC30 strain. Moreover, SC‐d inoculated piglets exhibited a persistent fever, moderate weight loss, mild thymus atrophy and obvious microscopic lung lesions. In summary, the recombinant NADC30‐like PRRSV SC‐d strain displayed a higher pathogenicity than the non‐recombinant NADC30‐like PRRSV SD‐A19 strain; however, the pathogenicity of the NADC30‐like PRRSV SC‐d was lower compared with the HP‐PRRSV HuN4 strain in piglets. Our findings demonstrate that recombination is responsible for the enormous genetic diversity and pathogenicity variance of the NADC30‐like PRRSV in China. This study provides a theoretical basis for developing a more reasonable PRRSV control and prevention strategy.
Abstract
Inspired by the relevance between the asymmetric coupling amplitude and the imaginary gauge field, we construct the counterpart of the non-Hermitian SSH model. The idea is the nonzero ...imaginary magnetic flux vanishing when the boundary condition changes from periodic to open. The zero imaginary magnetic flux of the counterpart leads to the eliminating of the non-Hermitian skin effect and the non-Hermitian Aharonov–Bohm effect which ensures the recovery of the conventional bulk-boundary correspondence from the non-Bloch bulk-boundary correspondence. We explain how some the non-Hermitian models can be transformed to the non-Hermitian SSH models and how the non-reciprocal hopping in the non-Hermitian SSH models can be transformed from one term to the other terms by the similarity transformations. We elaborate why the effective imaginary magnetic flux disappears due to the interplay of the non-reciprocal hoppings in the partner of the non-Hermitian SSH model. As the results, we obtain the topological invariants of the non-Hermitian SSH model in analytical form defined in conventional Brillouin zone. The non-Hermitian SSH model in domain configuration on a chain is discussed with this method. The technique gives an alternative way to study the topological properties of non-Hermitian systems.
AIMS: The influence of bacterial species/strains in agitated culture was investigated on the morphology and structure characteristics of bacterial cellulose. METHODS AND RESULTS: Komagataeibacter ...nataicola Y19 and Gluconacetobacter entanii ACCC10215 were inoculated in Hestrin–Schramm (HS) medium and subjected to agitated cultivation. Different kinds of BCs were obtained including flocky asterisk‐like BC by G. entanii ACCC10215 and solid sphere‐like BC by K. nataicola Y19. The SEM results showed that the asterisk‐like BC had larger pores than the solid sphere‐like BC. The FT‐IR and X‐ray diffraction results showed the asterisk‐like BC had lower crystallinity (81·43%), higher cellulose Iα mass fraction (79·74%) and smaller crystallite size. CONCLUSIONS: The different species/strains can influence the morphology and structure characteristics of BC in agitated culture. SIGNIFICANCE AND IMPACT OF THE STUDY: We examined the influence of different species/strains on the morphology, macro‐ and microstructure of BCs produced in agitated culture for the first time, which suggest that different BCs with potential applications could be obtained by choosing different species or strains and fermentation method.
Enhancing heat transfer surface are used in many engineering applications such as heat exchanger, air conditioning, chemical reactor and refrigeration systems, hence many techniques have been ...investigated on enhancement of heat transfer rate and decrease the size and cost of the involving equipment especially in heat exchangers. One of the most important techniques used are passive heat transfer technique. These techniques when adopted in Heat exchanger proved that the overall thermal performance improved significantly. This paper reviews experimental and numerical works taken by researchers on this technique since 2004 such as twisted tape, wire coil, swirl flow generator,… etc. to enhance the thermal efficiency in heat exchangers and useful to designers implementing passive augmentation techniques in heat exchange. The authors found that variously developed twisted tape inserts are popular researched and used to strengthen the heat transfer efficiency for heat exchangers. The other techniques used for specific work environments are studied in this paper. Twisted tape inserts perform better in laminar flow than turbulent flow. However, the other several passive techniques such as ribs, conical nozzle, and conical ring, etc. are generally more efficient in the turbulent flow than in the laminar flow.
To evaluate a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and compare it with RT-PCR.
...We designed primers specific to the orf1ab and S genes of SARS-CoV-2. Total viral RNA was extracted using the QIAamp Viral RNA Mini Kit. We optimized the RT-LAMP assay, and evaluated it for its sensitivity and specificity of detection using real-time turbidity monitoring and visual observation.
The primer sets orf1ab-4 and S-123 amplified the genes in the shortest times, the mean (±SD) times were 18 ± 1.32 min and 20 ± 1.80 min, respectively, and 63°C was the optimum reaction temperature. The sensitivities were 2 × 101 copies and 2 × 102 copies per reaction with primer sets orf1ab-4 and S-123, respectively. This assay showed no cross-reactivity with 60 other respiratory pathogens. To describe the availability of this method in clinical diagnosis, we collected 130 specimens from patients with clinically suspected SARS-CoV-2 infection. Among them, 58 were confirmed to be positive and 72 were negative by RT-LAMP. The sensitivity was 100% (95% CI 92.3%–100%), specificity 100% (95% CI 93.7%–100%). This assay detected SARS-CoV-2 in a mean (±SD) time of 26.28 ± 4.48 min and the results can be identified with visual observation.
These results demonstrate that we developed a rapid, simple, specific and sensitive RT-LAMP assay for SARS-CoV-2 detection among clinical samples. It will be a powerful tool for SARS-CoV-2 identification, and for monitoring suspected patients, close contacts and high-risk groups.
The prevalence of diabetes in China is among the highest in the world. For this reason, findings from the 2016 Global Burden of Disease (GBD) study were used to calculate the burden of hyperglycaemia ...and diabetes in China.
Following the general analytical strategy used in GBD 2016, diabetes prevalence and mortality were analyzed by age and gender. Trends in disability-adjusted life years (DALYs) due to diabetes were assessed in 33 province-level administrative units from 1990 to 2016, and similar data were provided for chronic kidney disease (CKD) related to diabetes and, as an overall summarizing measure, for hyperglycaemia expressed as high fasting plasma glucose (HFPG).
From 1990 to 2016, all-age prevalence of diabetes rose from 3.7% to 6.6%, and all-age diabetes and diabetes-related CKD mortality rates increased by 63.5% and 33.3%, respectively, with both rates increasing more rapidly in diabetes patients aged 15–49 years than in any other age groups. In 2016, HFPG became China's sixth leading cause of DALYs, and the attributable DALYs burden was 1802.3/100,000 population. Although the number of diabetes DALYs increased by 95% from 1990 to 2016, age-standardized diabetes DALYs rates increased by only 2.3%. Also, from 1990 to 2016, rates of age-standardized DALYs due to diabetes decreased in 14 provinces, but increased in 19 provinces. High BMI Scores and diets low in whole grains, nuts and seeds were the most important risk factors for diabetes in 2016.
Diabetes and hyperglycaemia constitute a huge health burden in China. The substantial increase in diabetes-related burden represents an ongoing challenge, given the rapidly ageing Chinese population. Thus, a targeted control and preventative strategy needs to be developed at risk factor level to reduce this burden.
PDF
