Daytime temperature is sensed by phytochrome B in Arabidopsis through a transcriptional activator HEMERA.

Ambient temperature sensing by phytochrome B (PHYB) in Arabidopsis is thought to operate mainly at night. Here we show that PHYB plays an equally critical role in temperature sensing during the daytime. In daytime thermosensing, PHYB signals primarily through the temperature-responsive transcriptional regulator PIF4, which requires the transcriptional activator HEMERA (HMR). HMR does not regulate PIF4 transcription, instead, it interacts directly with PIF4, to activate the thermoresponsive growth-relevant genes and promote warm-temperature-dependent PIF4 accumulation. A missense allele hmr-22, which carries a loss-of-function D516N mutation in HMR's transcriptional activation domain, fails to induce the thermoresponsive genes and PIF4 accumulation. Both defects of hmr-22 could be rescued by expressing a HMR22 mutant protein fused with the transcriptional activation domain of VP16, suggesting a causal relationship between HMR-mediated activation of PIF4 target-genes and PIF4 accumulation. Together, this study reveals a daytime PHYB-mediated thermosensing mechanism, in which HMR acts as a necessary activator for PIF4-dependent induction of temperature-responsive genes and PIF4 accumulation

CIA-Net: Robust Nuclei Instance Segmentation with Contour-aware Information Aggregation

Accurate segmenting nuclei instances is a crucial step in computer-aided image analysis to extract rich features for cellular estimation and following diagnosis as well as treatment. While it still remains challenging because the wide existence of nuclei clusters, along with the large morphological variances among different organs make nuclei instance segmentation susceptible to over-/under-segmentation. Additionally, the inevitably subjective annotating and mislabeling prevent the network learning from reliable samples and eventually reduce the generalization capability for robustly segmenting unseen organ nuclei. To address these issues, we propose a novel deep neural network, namely Contour-aware Informative Aggregation Network (CIA-Net) with multi-level information aggregation module between two task-specific decoders. Rather than independent decoders, it leverages the merit of spatial and texture dependencies between nuclei and contour by bi-directionally aggregating task-specific features. Furthermore, we proposed a novel smooth truncated loss that modulates losses to reduce the perturbation from outliers. Consequently, the network can focus on learning from reliable and informative samples, which inherently improves the generalization capability. Experiments on the 2018 MICCAI challenge of Multi-Organ-Nuclei-Segmentation validated the effectiveness of our proposed method, surpassing all the other 35 competitive teams by a significant margin.Comment: Accepted for the 26th Conference on Information Processing in Medical Imaging (IPMI 2019

Tissue-independent and tissue-specific patterns of DNA methylation alteration in cancer

BACKGROUND: There is growing evidence that DNA methylation alterations contribute to carcinogenesis. While cancer tissue exhibits widespread DNA methylation changes, the proportion of tissue-specific versus tissue-independent DNA methylation alterations in cancer is unclear. In addition, it is unknown which factors determine the patterns of aberrant DNA methylation in cancer. RESULTS: Using HumanMethylation450 BeadChips (450k), we here analyze genome-wide DNA methylation patterns of ten types of fetal tissue, in addition to matched normal-cancer data for corresponding tissue types, encompassing over 3000 samples. We demonstrate that the level of aberrant cancer DNA methylation in gene promoters and gene bodies is highly correlated between cancer types. We estimate that up to 60 % of the DNA methylation variation in a cancer genome of a given tissue type is explained by the corresponding variation in a cancer genome of another type, implying that much of the cancer DNA methylation landscape is tissue independent. We further show that histone marks in normal cells are better predictors of aberrant cancer DNA methylation than the corresponding signals in human embryonic stem cells. We build predictors of cancer DNA methylation patterns and show that although inclusion of three histone marks (H3K4me3, H3K27me3 and H3K36me3) improves model accuracy, the bivalent marks are the most predictive. Finally, we show that chromatin accessibility of gene promoters in normal tissue dictates the promoter's propensity to acquire aberrant DNA methylation in cancer in so far as it determines its level of DNA methylation in normal tissue. CONCLUSIONS: Our data show that a considerable fraction of the aberrant cancer DNA methylation landscape results from a mechanism that is largely tissue specific. Histone marks as specified in the normal cell of origin provide highly predictive models of aberrant cancer DNA methylation and outperform those derived from the same marks in hESCs

Comparison of 20nm silver nanoparticles synthesized with and without a gold core: Structure, dissolution in cell culture media, and biological impact on macrophages

Widespread use of silver nanoparticles raises questions of environmental and biological impact. Many synthesis approaches are used to produce pure silver and silver-shell gold-core particles optimized for specific applications. Since both nanoparticles and silver dissolved from the particles may impact the biological response, it is important to understand the physicochemical characteristics along with the biological impact of nanoparticles produced by different processes. The authors have examined the structure, dissolution, and impact of particle exposure to macrophage cells of two 20 nm silver particles synthesized in different ways, which have different internal structures. The structures were examined by electron microscopy and dissolution measured in Rosewell Park Memorial Institute media with 10% fetal bovine serum. Cytotoxicity and oxidative stress were used to measure biological impact on RAW 264.7 macrophage cells. The particles were polycrystalline, but 20 nm particles grown on gold seed particles had smaller crystallite size with many high-energy grain boundaries and defects, and an apparent higher solubility than 20 nm pure silver particles. Greater oxidative stress and cytotoxicity were observed for 20 nm particles containing the Au core than for 20 nm pure silver particles. A simple dissolution model described the time variation of particle size and dissolved silver for particle loadings larger than 9 μg/ml for the 24-h period characteristic of many in-vitro studies

Memory-built-in quantum teleportation with photonic and atomic qubits

The combination of quantum teleportation and quantum memory of photonic qubits is essential for future implementations of large-scale quantum communication and measurement-based quantum computation. Both steps have been achieved separately in many proof-of-principle experiments, but the demonstration of memory-built-in teleportation of photonic qubits remains an experimental challenge. Here, we demonstrate teleportation between photonic (flying) and atomic (stationary) qubits. In our experiment, an unknown polarization state of a single photon is teleported over 7 m onto a remote atomic qubit that also serves as a quantum memory. The teleported state can be stored and successfully read out for up to 8 micro-second. Besides being of fundamental interest, teleportation between photonic and atomic qubits with the direct inclusion of a readable quantum memory represents a step towards an efficient and scalable quantum network.Comment: 19 pages 3 figures 1 tabl

Characterization and Comparison of 2 Distinct Epidemic Community-Associated Methicillin-Resistant Staphylococcus aureus Clones of ST59 Lineage.

Sequence type (ST) 59 is an epidemic lineage of community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) isolates. Taiwanese CA-MRSA isolates belong to ST59 and can be grouped into 2 distinct clones, a virulent Taiwan clone and a commensal Asian-Pacific clone. The Taiwan clone carries the Panton-Valentine leukocidin (PVL) genes and the staphylococcal chromosomal cassette mec (SCCmec) VT, and is frequently isolated from patients with severe disease. The Asian-Pacific clone is PVL-negative, carries SCCmec IV, and a frequent colonizer of healthy children. Isolates of both clones were characterized by their ability to adhere to respiratory A549 cells, cytotoxicity to human neutrophils, and nasal colonization of a murine and murine sepsis models. Genome variation was determined by polymerase chain reaction of selected virulence factors and by multi-strain whole genome microarray. Additionally, the expression of selected factors was compared between the 2 clones. The Taiwan clone showed a much higher cytotoxicity to the human neutrophils and caused more severe septic infections with a high mortality rate in the murine model. The clones were indistinguishable in their adhesion to A549 cells and persistence of murine nasal colonization. The microarray data revealed that the Taiwan clone had lost the ø3-prophage that integrates into the β-hemolysin gene and includes staphylokinase- and enterotoxin P-encoding genes, but had retained the genes for human immune evasion, scn and chps. Production of the virulence factors did not differ significantly in the 2 clonal groups, although more α-toxin was expressed in Taiwan clone isolates from pneumonia patients. In conclusion, the Taiwan CA-MRSA clone was distinguished by enhanced virulence in both humans and an animal infection model. The evolutionary acquisition of PVL, the higher expression of α-toxin, and possibly the loss of a large portion of the β-hemolysin-converting prophage likely contribute to its higher pathogenic potential than the Asian-Pacific clone

Development of new all-optical signal regeneration technique

All-optical signal regeneration have been the active research area since last decade due to evolution of nonlinear optical signal processing. Existing all-optical signal regeneration techniques are agitated in producing low Bit Error Rate (BER) of 10-10 at below than -10 dBm power received. In this paper, a new all-optical signal regeneration technique is developed by using phase sensitive amplification and designed optical phase locked signal mechanism. The developed all-optical signal regeneration technique is tested for different 10 Gb/s Differential Phase Shift Keying degraded signals. It is determined that the designed all-optical signal regeneration technique is able to provide signal regeneration with noise mitigation for degraded signals. It is analyzed that overall, for all degraded test signals, average BER of 10-13 is achieved at received power of -14 dBm. The designed technique will be helpful to enhance the performance of existing signal regeneration systems in the presence of severe noise by providing minimum BER at low received power

New and simple algorithms for stable flow problems

Stable flows generalize the well-known concept of stable matchings to markets in which transactions may involve several agents, forwarding flow from one to another. An instance of the problem consists of a capacitated directed network, in which vertices express their preferences over their incident edges. A network flow is stable if there is no group of vertices that all could benefit from rerouting the flow along a walk. Fleiner established that a stable flow always exists by reducing it to the stable allocation problem. We present an augmenting-path algorithm for computing a stable flow, the first algorithm that achieves polynomial running time for this problem without using stable allocation as a black-box subroutine. We further consider the problem of finding a stable flow such that the flow value on every edge is within a given interval. For this problem, we present an elegant graph transformation and based on this, we devise a simple and fast algorithm, which also can be used to find a solution to the stable marriage problem with forced and forbidden edges. Finally, we study the stable multicommodity flow model introduced by Kir\'{a}ly and Pap. The original model is highly involved and allows for commodity-dependent preference lists at the vertices and commodity-specific edge capacities. We present several graph-based reductions that show equivalence to a significantly simpler model. We further show that it is NP-complete to decide whether an integral solution exists

Fano resonances in plasmonic core-shell particles and the Purcell effect

Despite a long history, light scattering by particles with size comparable with the light wavelength still unveils surprising optical phenomena, and many of them are related to the Fano effect. Originally described in the context of atomic physics, the Fano resonance in light scattering arises from the interference between a narrow subradiant mode and a spectrally broad radiation line. Here, we present an overview of Fano resonances in coated spherical scatterers within the framework of the Lorenz-Mie theory. We briefly introduce the concept of conventional and unconventional Fano resonances in light scattering. These resonances are associated with the interference between electromagnetic modes excited in the particle with different or the same multipole moment, respectively. In addition, we investigate the modification of the spontaneous-emission rate of an optical emitter at the presence of a plasmonic nanoshell. This modification of decay rate due to electromagnetic environment is referred to as the Purcell effect. We analytically show that the Purcell factor related to a dipole emitter oriented orthogonal or tangential to the spherical surface can exhibit Fano or Lorentzian line shapes in the near field, respectively.Comment: 28 pages, 10 figures; invited book chapter to appear in "Fano Resonances in Optics and Microwaves: Physics and Application", Springer Series in Optical Sciences (2018), edited by E. O. Kamenetskii, A. Sadreev, and A. Miroshnichenk