Proceedings of RIKEN BNL Research Center Workshop: Brookhaven Summer Program on Quarkonium Production in Elementary and Heavy Ion Collisions

Understanding the structure of the hadron is of fundamental importance in subatomic physics. Production of heavy quarkonia is arguably one of the most fascinating subjects in strong interaction physics. It offers unique perspectives into the formation of QCD bound states. Heavy quarkonia are among the most studied particles both theoretically and experimentally. They have been, and continue to be, the focus of measurements in all high energy colliders around the world. Because of their distinct multiple mass scales, heavy quarkonia were suggested as a probe of the hot quark-gluon matter produced in heavy-ion collisions; and their production has been one of the main subjects of the experimental heavy-ion programs at the SPS and RHIC. However, since the discovery of J/psi at Brookhaven National Laboratory and SLAC National Accelerator Laboratory over 36 years ago, theorists still have not been able to fully understand the production mechanism of heavy quarkonia, although major progresses have been made in recent years. With this in mind, a two-week program on quarkonium production was organized at BNL on June 6-17, 2011. Many new experimental data from LHC and from RHIC were presented during the program, including results from the LHC heavy ion run. To analyze and correctly interpret these measurements, and in order to quantify properties of the hot matter produced in heavy-ion collisions, it is necessary to improve our theoretical understanding of quarkonium production. Therefore, a wide range of theoretical aspects on the production mechanism in the vacuum as well as in cold nuclear and hot quark-gluon medium were discussed during the program from the controlled calculations in QCD and its effective theories such as NRQCD to various models, and to the first principle lattice calculation. The scientific program was divided into three major scientific parts: basic production mechanism for heavy quarkonium in vacuum or in high energy elementary collisions; the formation of quarkonium in nuclear medium as well as the strong interacting quark-gluon matter produced in heavy ion collisions; and heavy quarkonium properties from the first principle lattice calculations. The heavy quarkonium production at a future Electron-Ion Collider (EIC) was also discussed at the meeting. The highlight of the meeting was the apparent success of the NRQCD approach at next-to-leading order in the description of the quarkonium production in proton-proton, electron-proton and electron positron collisions. Still many questions remain open in lattice calculations of in-medium quarkonium properties and in the area of cold nuclear matter effects

An evolutionary dynamic multi-objective optimization algorithm based on center-point prediction and sub-population autonomous guidance

Dynamic multi-objective optimization problems (DMOPs) provide a challenge in that objectives conflict each other and change over time. In this paper, a hybrid approach based on prediction and autonomous guidance is proposed, which responds the environmental changes by generating a new population. According to the position of historical population, a part of the population is generated by predicting roughly and quickly. In addition, another part of the population is generated by autonomous guidance. A sub-population from current population evolves several generations independently, which guides the current population into the promising area. Compared with other three algorithms on a series of benchmark problems, the proposed algorithm is competitive in convergence and diversity. Empirical results indicate its superiority in dealing with dynamic environments

Differential Protein Expression in Sugarcane during Sugarcane-Sporisorium scitamineum Interaction Revealed by 2-DE and MALDI-TOF-TOF/MS

To understand the molecular basis of a specific plant-pathogen interaction, it is important to identify plant proteins that respond to the pathogen attack. Two sugarcane varieties, NCo376 and Ya71-374, were used in this study. By applying 2-dimensional electrophoresis (2-DE), the protein expression profile of sugarcane after inoculating with Sporisorium scitamineum was analyzed. In total, 23 differentially expressed proteins were identified by MALDI-TOF-TOF/MS. Bioinformatics analysis revealed that the functions of these 20 differential proteins were associated with such functions as photosynthesis, signal transduction, and disease resistance, while the function of the remaining three proteins was not determined. From above, we can assume that the protein regulatory network during the interaction between sugarcane and S. scitamineum is complicated. This represents the first proteomic investigation focused on highlighting the alterations of the protein expression profile in sugarcane exposed to S. scitamineum, and it provides reference information on sugarcane response to S. scitamineum stress at the protein level

Computational spatiotemporal analysis identifies WAVE2 and cofilin as joint regulators of costimulation-mediated T cell actin dynamics

Fluorescence microscopy is one of the most important tools in cell biology research and it provides spatial and temporal information to investigate regulatory systems inside cells. This technique can generate data in the form of signal intensities at thousands of positions resolved inside individual live cells; however, given extensive cell-to-cell variation, methods do not currently exist to assemble these data into three- or four-dimensional maps of protein concentration that can be compared across different cells and conditions. Here, we have developed one such method and applied it to investigate actin dynamics in T cell activation. Antigen recognition in T cells by the T cell receptor (TCR) is amplified by engagement of the costimulatory receptor CD28 and we have determined how CD28 modulates actin dynamics. We imaged actin and eight core actin regulators under conditions where CD28 in the context of a strong TCR signal was engaged or blocked to yield over a thousand movies. Our computational analysis identified diminished recruitment of the activator of actin nucleation WAVE2 and the actin severing protein cofilin to F-actin as the dominant difference upon costimulation blockade. Reconstitution of WAVE2 and cofilin activity restored the defect in actin signaling dynamics upon costimulation blockade. Thus we have developed and validated an approach to quantify protein distributions in time and space for analysis of complex regulatory systems

An animal model of SARS produced by infection of Macaca mulatta with SARS coronavirus.

A new SARS animal model was established by inoculating SARS coronavirus (SARS-CoV) into rhesus macaques (Macaca mulatta) through the nasal cavity. Pathological pulmonary changes were successively detected on days 5-60 after virus inoculation. All eight animals showed a transient fever 2-3 days after inoculation. Immunological, molecular biological, and pathological studies support the establishment of this SARS animal model. Firstly, SARS-CoV-specific IgGs were detected in the sera of macaques from 11 to 60 days after inoculation. Secondly, SARS-CoV RNA could be detected in pharyngeal swab samples using nested RT-PCR in all infected animals from 5 days after virus inoculation. Finally, histopathological changes of interstitial pneumonia were found in the lungs during the 60 days after viral inoculation: these changes were less marked at later time points, indicating that an active healing process together with resolution of an acute inflammatory response was taking place in these animals. This animal model should provide insight into the mechanisms of SARS-CoV-related pulmonary disease and greatly facilitate the development of vaccines and therapeutics against SARS

MicroRNA-27a Promotes Proliferation, Migration and Invasion by Targeting MAP2K4

Background: Osteosarcoma is a high-grade malignant bone neoplasm. Although the introduction of chemotherapy has reduced its mortality, more than 50% of patients develop chemoresistance and have an extremely poor prognosis due to pulmonary metastasis. Several molecular pathways contributing to osteosarcoma development and progression have recently been discovered. Various studies have addressed the genes involved in the metastasis of osteosarcoma. However, the highly complex molecular mechanisms of metastasis are still poorly understood. Recently, the decisive role of microRNAs in the regulation of molecular pathways has been uncovered. miRNAs may function as either oncogenes or tumor suppressors, depending on their target genes. miR-27a, a member of an evolutionarily conserved miRNA family, is abnormally increased in several types of cancers. It has been shown to be upregulated in osteosarcoma and plays a pro-metastatic role in osteosarcoma cell lines. However, the effects of miR-27a on osteosarcoma have not been clearly elucidated. The present study thus addressed the miR-27a sensitive mechanisms in osteosarcoma. Methods: In this study, three biological programs were used to predict whether MAP2K4 was a target of miR-27a. A specific miR-27a inhibitor was used to inhibit the endogenous activity of miR-27a in the human osteosarcoma cell line MG63. Cell proliferation, colony formation, migration and invasion assays were performed to assess the effects of miR-27a on the proliferation, metastasis and invasion of MG63 cells. The expression levels of several proteins evolved in the JNK/p38 signaling pathway were detected using western blot analysis. Results: The luciferase activity of the wild-type pGL3-MAP2K4 3'UTR vector was significantly inhibited after the miR-27a precursor or the control precursor was transfected into the MG63 cells. However, the luciferase activity was not inhibited after transfection of the mutant pGL3-MAP2K4 3'UTR vector. The inhibition of miR-27a increased the luciferase activity of the wild-type pGL3-MAP2K4 3'UTR vector after MG63 cells were transfected with the miR-27a inhibitor or the control inhibitor. Thus, MAP2K4 is a potential target of miR-27a and can be directly regulated by miR-27a. Inhibition of miR-27a significantly suppressed cell proliferation after 72 hours compared to the negative control group. Inhibition of miR-27a significantly suppressed colony formation of the MG63 cells by 39 6%. Transwell migration and invasion assays demonstrated that the number of migratory and invasive cells transfected with the miR-27a inhibitor was reduced by 63.5% and 69.1%, respectively. After transfection of the miR-27a inhibitor into the MG63 cells, the level of phospho-JNK1 and phospho-p38 increased by 25% and 29%, respectively, along with the up-regulation of MAP2K4 protein. Conclusion: This is the first study showing that miR-27a can function as an oncogene by targeting MAP2K4 in the osteosarcoma MG63 cell line. Inhibition of miR-27a increases MAP2K4 expression, which in turn inhibits cell proliferation and migration through the JNK/p38 signaling pathway in MG63 cells. These findings may help us understand the molecular mechanism of miR-27a in the tumorigenesis of osteosarcoma and may provide new diagnostic and therapeutic options for the treatment of this neoplasia

The Caenorhabditis elegans CUB-like-domain containing protein RBT-1 functions as a receptor for Bacillus thuringiensis Cry6Aa toxin.

Plant-parasitic nematodes cause huge agricultural economic losses. Two major families of Bacillus thuringiensis crystal proteins, Cry5 and Cry6, show nematicidal activity. Previous work showed that binding to midgut receptors is a limiting step in Cry toxin mode of action. In the case of Cry5Ba, certain Caenorhabditis elegans glycolipids were identified as receptors of this toxin. However, the receptors for Cry6 toxin remain unknown. In this study, the C. elegans CUB-like-domain containing protein RBT-1, released by phosphatidylinositol-specific phospholipase C (PI-PLC), was identified as a Cry6Aa binding protein by affinity chromatography. RBT-1 contained a predicted glycosylphosphatidylinositol (GPI) anchor site and was shown to locate in lipid rafts in the surface of the midgut cells. Western ligand blot assays and ELISA binding analysis confirmed the binding interaction between Cry6Aa and RBT-1 showing high affinity and specificity. In addition, the mutation of rbt-1 gene decreased the susceptibility of C. elegans to Cry6Aa but not that of Cry5Ba. Furthermore, RBT-1 mediated the uptake of Cry6Aa into C. elegans gut cells, and was shown to be involved in triggering pore-formation activity, indicating that RBT-1 is required for the interaction of Cry6Aa with the nematode midgut cells. These results support that RBT-1 is a functional receptor for Cry6Aa

Multi-stage state of health estimation of lithium-ion battery with high tolerance to heavily-partial charging

State of health (SOH) is critical to the management of lithium-ion battery (LIB) due to its deep insight into the health diagnostic and protection. However, the absence of complete charging data, which is common in practice, risks impairing the charging-based SOH estimators. This paper proposes a multi-stage SOH estimation method with a broad scope of applications, including the unfavorable but practical scenarios of heavily-partial charging. In particular, different sets of health indicators (HIs), covering both the morphological IC features and the voltage entropy information, are extracted from the partial CC charging data with different initial charging voltage to characterize the aging status. Following this endeavor, artificial neural network (ANN)-based HI fusion is proposed to estimate the SOH of LIB precisely in real time. The proposed method is evaluated with long-term aging experiments performed on different types of LIBs. Results validate several superior merits of the proposed method, including high estimation accuracy, high tolerance to partial charging, strong robustness to cell inconsistency, and wide generality to different battery types