bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solar initiative at Oukaimeden Observatory
Authors: Benkaldoun Zouhair , Makela Jonathan J. , Meriwether John W. 
Published: July 2013

AbstractThe solar research program at Oukaimeden Observatory started in 1988 with the helioseimological IRIS network. The Moroccan researchers involved in this research have analyzed solar observations in order to detect and characterize the solar sphere modes of oscillations. In the coming year, the researchers at the Oukaimeden Observatory will add new research capabilities by joining the International Space Weather Initiative (ISWI), installing a suite of optical instruments, comprising a Remote Equatorial Nighttime Observatory of Ionospheric Regions (RENOIR). The scope and objectives to be achieved in this proposed project are to:
•deploy a Fabry-Perot interferometer and wide-angle imaging system to the Observatoire Astronomique Universitaire de LOukaimeden;•train students and researchers from Cadi Ayyad University on the operation of the equipment and related analysis techniques;•collect and analyze data from the equipment to study properties of upper-atmospheric winds and temperatures and how they relate to the occurrence of space weather; and•develop an international collaboration network with other researchers using similar instrumentation in Brazil and Peru. We will present here the plan we intend to develop for the Moroccan solar program in connection with ISWI.
Observations of interplanetary scintillation in China
Authors: Liu Li-Jia , Peng Bo 
Published: July 2013

AbstractThe Sun affects the Earth in multiple ways. In particular, the material in interplanetary space comes from coronal expansion in the form of solar wind, which is the primary source of the interplanetary medium. Ground-based Interplanetary Scintillation (IPS) observations are an important and effective method for measuring solar wind speed and the structures of small diameter radio sources. In this paper we will discuss the IPS observations in China.
An intelligent method for solar flare observation
Authors: Lin Jia Ben , Guo Juan , Deng Yuan Yong 
Published: July 2013

AbstractTo capture the fine structure of the flare kernel during it's explosive phase, we design a real time flare onset detecting algorithm named Near Saturation Area Threshold(NSAT), And an automatic CCD parameters control algorithm for the observing software. All the data from CCD, 48f/s, could be saved to the hard disk, and the GPS time of the flare onset also be saved in the log. These methods could avoid the data overflow and grab the fine structure data of the flare kernel. The simulation experiment works well and the software will be put into use in Huairou Solar Observatory soon.
Space environment during Solar Minimum of SC-23
Authors: Hady Ahmed A. 
Published: July 2013

AbstractGeomagnetic and solar storms and their occurrence rate with respect to the solar activity cycle is an important topic of space environment research. The minimum of solar activity during the solar cycle number 23 (SC-23) have detectable effects on the space environments, where the monthly mean of sunspot number and solar proton events effecting the space environment and produced many of Geophysical effects. A detailed study of the centers of activity produced the proton events are carried out. The electromagnetic emissions at the different bands during the impulsive phase of the flare are tabulated and discussed. The different Geophysical effects due to the events are studied. Conclusions about the proton solar events at minimum activity are presented.
The helicity, induced electric field and Poynting flux of AR 11158
and their relationship with the X-class flare
Authors: Liu Jihong , Su Jiangtao , Zhang Hongqi 
Published: July 2013

AbstractWith the photospheric vector magnetic fields provided by SDO/HMI team, the helicity accumulation, induced electric field and Poynting flux is calculated for AR 11158 by using the local correlation tracking technique (LCT). It is found that the helicity accumulation reaches 6000×1040Mx2, the average densities of the induced electric field about 0.15-0.35 V cm−1, and that of the Poynting flux about 50-240 W m−2, within 50 hours. One main flare of X2.2 occurs in the increasing phase of the helicity accumulation, which also corresponds to the decreasing phase of the induced electric field and the gradual change phase of the Poynting flux. Before the flare, all these quantities increase rapidly for about 20 hours firstly, then increase gradually or even decrease for 8-9 hours.
Probing the solar origin of energy build-up and release in solar energetic particles
Authors: Awasthi Arun Kumar , Jain Rajmal , Bhatt Nipa J. 
Published: July 2013

AbstractWe study the temporal and spatial evolution of magnetic field parameters, and multi-wavelength observations of the AR 11226 and AR 11261, observed during 02-09 June 2011 and 31 July to 06 August 2011 respectively, to probe the origin of the associated solar energetic particles (SEPs). The magnetic-field toplogy of both ARs shows complex magnetic structure of β and βγ configuration. The X-ray observations by GOES and RHESSI reveal that the AR 11226 as well as AR 11261 has been most turbulent to produce flares accompanying CMEs and SEPs. We restrict our study of magnetic field evolution of ARs to helio-longitudes E20-W70. The AR 11226 produced 28 flares (⩾ GOES C-class) and 8 CMEs as well as 5 SEPs. On the other hand, the AR 11261 produced 29 flares (⩾ GOES C class), 8 CMEs as well as 5 SEPs. We study the temporal evolution of magnetic field parameters viz. gradient, shear, rotation to probe the origin of the energy release in the flare and associated CME and SEP. We do not find convincing relationship in view of predicting SEPs.
Coordinate flares observed by TRACE
Authors: Kong Defang , Yan Xiaoli , Xue Zhike 
Published: July 2013

AbstractTwo flares occurred simultaneously in active region NOAA 9433 on 2001 April 25. The GOES X-ray fluxes show only one peak during the two flares. The negative magnetic polarities in the two flaring regions exhibited a clockwise rotation motion around the positive polarities, which can be seen from the evolution of the SOHO/MDI magnetograms. Through analyzing the potential fields extrapolated from the MDI magnetogram, we find that there is a channel strode by a group of magnetic field lines connecting the two flaring regions.
Polar jet kinetics and energetics analysed from STEREO/COR data
Authors: Feng Li , Gan Weiqun 
Published: July 2013

AbstractWe analyze coronagraph observations of a polar jet eruption observed by SECCHI/STEREO. The brightness distribution of the jet in white-light coronagraph images is compared with a kinetic particle model. In this first application, we consider only gravity as the dominant force on the jet particles along the magnetic field. The kinetic model explains well the observed brightness evolution. The initial particle velocity distribution is fitted by Maxwellian distributions and we find deviations of the high energy tail from the Maxwellian distributions. The jets total mass is between 3.2×1014 and 1.8×1015 g. The total kinetic energy of all the particles in the jet source region amounts from 2.1×1028 to 2.4×1029 ergs.
Peculiar microwave quasi-periodic pulsations with zigzag pattern in a CME-related Flare on 2005-01-15
Authors: Tan Baolin 
Published: July 2013

AbstractA microwave quasi-periodic pulsation with zigzag pattern (Z-QPP) in a solar flare on 2005-01-15 is observed by the Chinese Solar Broadband Spectrometer in Huairou (SBRS/Huairou) at 1.10-1.34 GHz. The zigzag pulsation occurred just in the early rising phase of the flare with weakly right-handed circular polarization. Its period is only several decades millisecond. Particularly, before and after the pulsation, there are many spectral fine structures, such as zebra patterns, fibers, and millisecond spikes. The microwave Z-QPP can provide some kinematic information of the source region in the early rising phase of the flare, and the source width changes from ~1000 km to 3300 km, even if we have no imaging observations. The abundant spectral fine structures possibly reflect the dynamic features of non-thermal particles.
A statistical study on photospheric active-region magnetic nonpotentiality and associated flares during solar cycles 22 – 23
Authors: Yang Xiao , Zhang HongQi , Lin GangHua , Gao Yu , Guo Juan 
Published: July 2013

AbstractUsing photospheric data obtained by vector magnetograph in Huairou Solar Observing Station of China, we have statistically studied the strength evolution of several magnetic nonpotentiality measures, along with a quantified parameter characterizing the active-region magnetic complexity – effective distance, and their relationship with associated flares during the latest 22nd and 23rd solar cycles. And the flare-prediction performance of these magnetic nonpotentiality and complexity parameters is verified by a machine learning technique.
Relaxation of magnetic field relative to plasma density during solar flares
Authors: Yu Sijie , Yan Yihua , Tan Baolin 
Published: July 2013

AbstractWe investigated the variations of 74 microwave ZP structures observed by Chinese Solar Broadband Radio Spectrometer at 2.6–3.8 GHz in 9 solar flares, found that the ratio between the plasma density scale height LN and the magnetic field scale height LB in emission source displays a tendency of decrease during the flaring process, indicates that LB increases faster than the LN during solar flares. The detailed analysis of the step-wise decrease of LN/LB in three typical X-class flares reveals the magnetic field relaxation relative to the plasma density.
Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight
Authors: Chow Cheryl-Emiliane T , Sachdeva Rohan , Cram Jacob A , Steele Joshua A , Needham David M , Patel Anand , Parada Alma E , Fuhrman Jed A 
Published: July 2013

Abstract
Time-series are critical to understanding long-term natural variability in the oceans. Bacterial communities in the euphotic zone were investigated for over a decade at the San Pedro Ocean Time-series station (SPOT) off southern California. Community composition was assessed by Automated Ribosomal Intergenic Spacer Analysis (ARISA) and coupled with measurements of oceanographic parameters for the surface ocean (0–5 m) and deep chlorophyll maximum (DCM, average depth ∼30 m). SAR11 and cyanobacterial ecotypes comprised typically more than one-third of the measured community; diversity within both was temporally variable, although a few operational taxonomic units (OTUs) were consistently more abundant. Persistent OTUs, mostly Alphaproteobacteria (SAR11 clade), Actinobacteria and Flavobacteria, tended to be abundant, in contrast to many rarer yet intermittent and ephemeral OTUs. Association networks revealed potential niches for key OTUs from SAR11, cyanobacteria, SAR86 and other common clades on the basis of robust correlations. Resilience was evident by the average communities drifting only slightly as years passed. Average Bray-Curtis similarity between any pair of dates was ∼40%, with a slight decrease over the decade and obvious near-surface seasonality; communities 8–10 years apart were slightly more different than those 1–4 years apart with the highest rate of change at 0–5 m between communities &lt;4 years apart. The surface exhibited more pronounced seasonality than the DCM. Inter-depth Bray-Curtis similarities repeatedly decreased as the water column stratified each summer. Environmental factors were better predictors of shifts in community composition than months or elapsed time alone; yet, the best predictor was community composition at the other depth (that is, 0–5 m versus DCM).
Histidine kinases from bacteria to humans
Authors: Attwood Paul V. 
Published: July 2013

It is more than 50 years since protein histidine phosphorylation was first discovered in 1962 by Boyer and co-workers; however, histidine kinases are still much less well recognized than the serine/threonine and tyrosine kinases. The best-known histidine kinases are the two-component signalling kinases that occur in bacteria, fungi and plants. The mechanisms and functions of these kinases, their cognate response regulators and associated phosphorelay proteins are becoming increasingly well understood. When genomes of higher eukaryotes began to be sequenced, it did not appear that they contained two-component histidine kinase system homologues, apart from a couple of related mitochondrial enzymes that were later shown not to function as histidine kinases. However, as a result of the burgeoning sequencing of genomes from a wide variety of eukaryotic organisms, it is clear that there are proteins that correspond to components of the two-component histidine kinase systems in higher eukaryotes and that operational two-component kinase systems are likely to occur in these organisms. There is unequivocal direct evidence that protein histidine phosphorylation does occur in mammals. So far, only nucleoside diphosphate kinases have been shown to be involved in protein histidine phosphorylation, but their mechanisms of action are not well understood. It is clear that other, yet to be identified, histidine kinases also exist in mammals and that protein histidine phosphorylation may play important roles in higher eukaryotes.
Intron excision from precursor tRNA molecules in mammalian cells requires ATP hydrolysis and phosphorylation of tRNA-splicing endonuclease components
Authors: Mair Barbara , Popow Johannes , Mechtler Karl , Weitzer Stefan , Martinez Javier 
Published: July 2013

The process of tRNA splicing entails removal of an intron by TSEN (tRNA–splicing endonuclease) and ligation of the resulting exon halves to generate functional tRNAs. In mammalian cells, the RNA kinase CLP1 (cleavage and polyadenylation factor I subunit) associates with TSEN and phosphorylates the 3′ exon at the 5′ end in vitro, suggesting a role for CLP1 in tRNA splicing. Interestingly, recent data suggest that the ATP-binding and/or hydrolysis capacity of CLP1 is required to enhance pre-tRNA cleavage. In vivo, the lack of CLP1 kinase activity leads to progressive motor neuron loss and accumulation of novel 5′ leader–5′ exon tRNA fragments. We have extended the investigation of the biochemical requirements in pre-tRNA splicing and found that β–γ-hydrolysable ATP is crucial for the productive generation of exon halves. In addition, we provide evidence that phosphorylation of the TSEN complex components supports efficient pre-tRNA cleavage. Taken together, our data improve the mechanistic understanding of mammalian pre-tRNA processing and its regulation.
The kinase triad, AMPK, mTORC1 and ULK1, maintains energy and nutrient homoeostasis
Authors: Dunlop Elaine A. , Tee Andrew R. 
Published: July 2013

In order for cells to divide in a proficient manner, they must first double their biomass, which is considered to be the main rate-limiting phase of cell proliferation. Cell growth requires an abundance of energy and biosynthetic precursors such as lipids and amino acids. Consequently, the energy and nutrient status of the cell is acutely monitored and carefully maintained. mTORC1 [mammalian (or mechanistic) target of rapamycin complex 1] is often considered to be the master regulator of cell growth that enhances cellular biomass through up-regulation of protein translation. In order for cells to control cellular homoeostasis during growth, there is close signalling interplay between mTORC1 and two other protein kinases, AMPK (AMP-activated protein kinase) and ULK1 (Unc-51-like kinase 1). This kinase triad collectively senses the energy and nutrient status of the cell and appropriately dictates whether the cell will actively favour energy- and amino-acid-consuming anabolic processes such as cellular growth, or energy- and amino-acid-generating catabolic processes such as autophagy. The present review discusses important feedback mechanisms between these three homoeostatic protein kinases that orchestrate cell growth and autophagy, with a particular focus on the mTORC1 component raptor (regulatory associated protein of mammalian target of rapamycin), as well as the autophagy-initiating kinase ULK1.
Role of PI3K, mTOR and Akt2 signalling in hepatic tumorigenesis via the control of PKM2 expression
Authors: Nemazanyy Ivan , Espeillac Catherine , Pende Mario , Panasyuk Ganna 
Published: July 2013

To sustain increased growth, rapidly proliferating cells, such as tumour cells, undergo metabolic adaptations. In recent years, the mechanisms of glycolysis activation as a key metabolic adaptation in proliferating cells became the topic of intense research. Although this phenomenon was described more than 50 years ago by Otto Warburg, the molecular mechanisms remained elusive. Only recently, it was demonstrated that the expression of specific glycolytic enzymes, namely PKM2 (pyruvate kinase M2) and HK2 (hexokinase 2), occurs simultaneously with the glycolytic addiction of cancer cells. The PI3K (phosphoinositide 3-kinase)/mTOR [mammalian (or mechanistic) target of rapamycin] signalling pathway is a central signalling hub co-ordinating the growth in response to growth factor signalling and nutrient availability. Not surprisingly, it is found to be activated in the majority of the tumour cells. In the present article, we discuss the requirement of different PI3K/mTOR downstream effectors for the metabolic adaptation in liver cancer cells driven by this signalling pathway. We provide evidence for a selective involvement of the mTOR target Akt2 in tumoral growth. In addition, PTEN (phosphatase and tensin homologue deleted on chromosome 10)-negative human hepatocellular carcinoma cell lines display an up-regulation of PKM2 expression in an Akt2-dependent manner, providing an advantage for cell proliferation and anchorage-independent growth. Our data have implications on the link between the metabolic action of insulin signal transduction and tumorigenesis, identifying Akt2 as a potential therapeutical target in liver malignancies depending on cancer genotype.
Nuclear receptor-binding protein 1: a novel tumour suppressor and pseudokinase
Authors: Kerr Jason S. , Wilson Catherine H. 
Published: July 2013

Pseudokinases are a class of kinases which are structurally designated as lacking kinase activity. Despite the lack of kinase domain sequence conservation, there is increasing evidence that a number of pseudokinases retain kinase activity and/or have critical cellular functions, casting aside previous notions that pseudokinases simply exist as redundant kinases. Moreover, a number of recent studies have implicated pseudokinases as critical components in cancer formation and progression. The present review discusses the interactions and potential functions that nuclear receptor-binding protein 1, a pseudokinase recently described to have a tumour-suppressive role in cancer, may play in cellular homoeostasis and protein regulation. The recent findings highlighted in the present review emphasize the requirement to fully determine the function of pseudokinases in vitro and in vivo, the understanding of which may ultimately uncover new directions for drug discovery.
Attempting to rewrite History: challenges with the analysis of histidine-phosphorylated peptides
Authors: Gonzalez-Sanchez Maria-Belen , Lanucara Francesco , Helm Matthew , Eyers Claire E. 
Published: July 2013

A significant number of proteins in both eukaryotes and prokaryotes are known to be post-translationally modified by the addition of phosphate, serving as a means of rapidly regulating protein function. Phosphorylation of the amino acids serine, threonine and tyrosine are the focus of the vast majority of studies aimed at elucidating the extent and roles of such modification, yet other amino acids, including histidine and aspartate, are also phosphorylated. Although histidine phosphorylation is known to play extensive roles in signalling in eukaryotes, plants and fungi, roles for phosphohistidine are poorly defined in higher eukaryotes. Characterization of histidine phosphorylation aimed at elucidating such information is problematic due to the acid-labile nature of the phosphoramidate bond, essential for many of its biological functions. Although MS-based strategies have proven extremely useful in the analysis of other types of phosphorylated peptides, the chromatographic procedures essential for such approaches promote rapid hydrolysis of phosphohistidine-containing peptides. Phosphate transfer to non-biologically relevant aspartate residues during MS analysis further complicates the scenario.
2×2 Dominant achievement goal profiles in high‐level swimmers
Authors: Fernandez‐Rio Javier , Cecchini Estrada Jose A. , Mendez‐Giménez Antonio , Fernández‐Garcia Benjamín , Saavedra Pablo 
Published: July 2013

AbstractThe goal of this study was to assess achievement goal dominance, self‐determined situational motivation and competence in high‐level swimmers before and after three training sessions set at different working intensities (medium, sub‐maximal and maximal). Nineteen athletes (males, n=9, 18.00±2.32 years; females, n=10, 16.30±2.01 years, range = 14–18) agreed to participate. They completed a questionnaire that included the Dominant Achievement Goal assessment instrument, the 2×2 Achievement Goals Questionnaire for Sport (AGQ‐S), The Situational Motivation Scale (SIMS) and the Competence subscale of the Basic Psychological Needs in Exercise questionnaire (BPNES). Results indicated that participants overwhelmingly showed mastery‐approach achievement goal dominance, and it remained stable at the conclusion of the different training sessions under all intensity levels. This profile was positively correlated to self‐determined situational motivation and competence. However, swimmers' feelings of competence increased only after the medium intensity level training session. After the completion of the maximal intensity training session, swimmers' self‐determined motivation was significantly lower compared to the other two training sessions, which could be caused by a temporary period of burnout. Results indicated that high‐level swimmers had a distinct mastery‐approach dominant achievement goal profile that was not affected by the workload of the different training sessions. They also showed high levels of self‐determined situational motivation and competence. However, heavy workloads should be controlled because they can cause transitory burnout.
deltaGseg: macrostate estimation via molecular dynamics simulations and multiscale time series analysis
Authors: Low Diana H. P. , Motakis Efthymios 
Published: July 2013

Abstract
Summary: Binding free energy calculations obtained through molecular dynamics simulations reflect intermolecular interaction states through a series of independent snapshots. Typically, the free energies of multiple simulated series (each with slightly different starting conditions) need to be estimated. Previous approaches carry out this task by moving averages at certain decorrelation times, assuming that the system comes from a single conformation description of binding events. Here, we discuss a more general approach that uses statistical modeling, wavelets denoising and hierarchical clustering to estimate the significance of multiple statistically distinct subpopulations, reflecting potential macrostates of the system. We present the deltaGseg R package that performs macrostate estimation from multiple replicated series and allows molecular biologists/chemists to gain physical insight into the molecular details that are not easily accessible by experimental techniques.
Availability: deltaGseg is a Bioconductor R package available at http://bioconductor.org/packages/release/bioc/html/deltaGseg.html.
Contact: emotakis@hotmail.com