bluuebunny/crossref_metadata_2025_split huggingface dataset:
The wide skirt of the bashful ballerina: Hemispheric asymmetry of the heliospheric magnetic field in the inner and outer heliosphere
Authors: Mursula K. , Virtanen I. I. 
Published: July 2012

We reanalyze the observations of the heliospheric magnetic field (HMF) made by the Pioneer 10 and 11 and Voyager 1 and 2 heliospheric probes since 1972, and calculate the HMF sector occurrence ratios and tangential component strengths in the different regions of the heliosphere. Observations at the distant probes and at 1 AU show a very consistent picture of the HMF sector structure in the entire heliosphere, and even beyond the termination shock. HMF observations by the probes also support the southward shift of the heliospheric current sheet (the bashful ballerina phenomenon), which is observed earlier at 1–2 AU by the Ulysses probe and Earth‐orbiting satellites, and verify the HCS shift over a wide range of radial distances until the distant heliosphere. Pioneer 11 and Voyager 1 show that the development of northern polar coronal holes was very systematic and active during all the four solar minima since mid‐1970s, while Voyager 2 observations show a less systematic and delayed development of southern coronal holes in 1980s, 1990s and 2000s. This delay in the evolution of southern coronal holes with respect to the rapid and systematic evolution of northern coronal holes leads to a larger extent of northern coronal holes and the southward shift of the HCS for a few years in the late declining phase of each solar cycle. Although evidence for the connection between the different evolution of polar coronal holes and the bashful ballerina phenomenon is obtained here only for three solar cycles, this may be a common pattern for solar coronal hole evolution since the southward shift of the HCS has occurred at least since solar cycle 16.
Comparison of penetration electric fields created by the solar wind with Jicamarca data using SWAGE
Authors: Rothwell P. L. , Jasperse J. R. , Grossbard N. J. 
Published: July 2012

SWAGE (Solar Wind Acting on the Geophysical Environment) calculates the global ionospheric electric field generated by high‐latitude electrodynamics drivers determined from the time‐shifted solar wind data measured at L1 by joining the Hill‐Siscoe polar cap potential model with the N‐C ionospheric potential solver. Of particular interest are the conditions under which the eastward equatorial penetration electric field near twilight contributes to the pre‐reversal enhancement (PRE). In the present model, it is found that a steeper terminator conductance gradient leads to a more pronounced PRE. The model is statistically consistent with the Jicamarca vertical drift data at twilight during quiet times for eighty‐two days in the years 1998–2005. The model is also consistent with the Jicamarca vertical drift data during the November 2004 magnetic superstorms (Dst < −250 nT) and highlights the importance of including the LT dependence of the ionospheric response. In this comparison, disturbance dynamo (DD) effects are also included. Comparison is much better using the conductance model with a shallower terminator gradient and indicates that the conductance LT profile was relatively unchanged throughout the storms.
A comparison of the effects of CIR‐ and CME‐induced geomagnetic activity on thermospheric densities and spacecraft orbits: Case studies
Authors: Chen Guang‐ming , Xu Jiyao , Wang Wenbin , Lei Jiuhou , Burns Alan G. 
Published: July 2012

So far studies of the effect of geomagnetic storms on thermospheric density and satellite orbits have been mainly focused on severe storm events caused by Coronal Mass Ejections (CMEs). The effect of long‐duration, less intensive geomagnetic activity that is related to Corotating Interaction Regions (CIRs) has not been fully explored. In this paper, thermospheric densities observed by the CHAMP satellite and its orbit parameters are used to compare the responses of satellite orbital altitudes to geomagnetic activity caused by CMEs and CIRs. Three cases are investigated in this paper. Each case had one or two CME storm(s) and one CIR storm that occurred successively. In these cases three out of four CME‐storms were stronger than their corresponding CIR‐storms, but the durations of these CME‐storms were much shorter. Thus, the satellite orbit decay rates during CME‐storms are usually larger than those during CIR‐storms. However, CIR‐storms often had long durations that perturbed satellite orbits for longer periods of time. As a result, the total thermospheric density changes and satellite orbit decays for the entire periods of CIR‐storms were much greater than those for the CME‐storms since these parameters were related to the total energy deposited into the thermosphere/ionosphere, which depended on both the strengths and the durations of the storms. This study indicates that more attention should be paid to CIR storms during the declining phase and during solar minimum, when they occur frequently and periodically. Whereas fewer CME storms occurring under these conditions. We also found that changes in thermospheric densities and CHAMP orbit decay rates correlated well with variations of auroral hemispheric power, but lagging by about 3–6 h.
Identification of a haem domain in human soluble adenylate cyclase
Authors: Middelhaufe Sabine , Leipelt Martina , Levin Lonny R. , Buck Jochen , Steegborn Clemens 
Published: July 2012

The second messengers cAMP and cGMP mediate a multitude of physiological processes. In mammals, these cyclic nucleotides are formed by related Class III nucleotidyl cyclases, and both ACs (adenylate cyclases) and GCs (guanylate cyclases) comprise transmembrane receptors as well as soluble isoforms. Whereas sGC (soluble GC) has a well-characterized regulatory HD (haem domain) that acts as a receptor for the activator NO (nitric oxide), very little is known about the regulatory domains of the ubiquitous signalling enzyme sAC (soluble AC). In the present study, we identify a unique type of HD as a regulatory domain in sAC. The sAC-HD (sAC haem domain) forms a larger oligomer and binds, non-covalently, one haem cofactor per monomer. Spectral analyses and mutagenesis reveal a 6-fold co-ordinated haem iron atom, probably with non-typical axial ligands, which can bind both NO and CO (carbon monoxide). Splice variants of sAC comprising this domain are expressed in testis and skeletal muscle, and the HD displays an activating effect on the sAC catalytic core. Our results reveal a novel mechanism for regulation of cAMP signalling and suggest a need for reanalysis of previous studies on mechanisms of haem ligand effects on cyclic nucleotide signalling, particularly in testis and skeletal muscle.
Geochemical evidence for possible natural migration of Marcellus Formation brine to shallow aquifers in Pennsylvania
Authors: Warner Nathaniel R. , Jackson Robert B. , Darrah Thomas H. , Osborn Stephen G. , Down Adrian , Zhao Kaiguang , White Alissa , Vengosh Avner 
Published: July 2012

The debate surrounding the safety of shale gas development in the Appalachian Basin has generated increased awareness of drinking water quality in rural communities. Concerns include the potential for migration of stray gas, metal-rich formation brines, and hydraulic fracturing and/or flowback fluids to drinking water aquifers. A critical question common to these environmental risks is the hydraulic connectivity between the shale gas formations and the overlying shallow drinking water aquifers. We present geochemical evidence from northeastern Pennsylvania showing that pathways, unrelated to recent drilling activities, exist in some locations between deep underlying formations and shallow drinking water aquifers. Integration of chemical data (Br, Cl, Na, Ba, Sr, and Li) and isotopic ratios (
87
Sr/
86
Sr,
2
H/H,
18
O/
16
O, and
228
Ra/
226
Ra) from this and previous studies in 426 shallow groundwater samples and 83 northern Appalachian brine samples suggest that mixing relationships between shallow ground water and a deep formation brine causes groundwater salinization in some locations. The strong geochemical fingerprint in the salinized (Cl > 20 mg/L) groundwater sampled from the Alluvium, Catskill, and Lock Haven aquifers suggests possible migration of Marcellus brine through naturally occurring pathways. The occurrences of saline water do not correlate with the location of shale-gas wells and are consistent with reported data before rapid shale-gas development in the region; however, the presence of these fluids suggests conductive pathways and specific geostructural and/or hydrodynamic regimes in northeastern Pennsylvania that are at increased risk for contamination of shallow drinking water resources, particularly by fugitive gases, because of natural hydraulic connections to deeper formations.
Magnetic characterization of isolated candidate vertebrate magnetoreceptor cells
Authors: Eder Stephan H.K. , Cadiou Hervé , Muhamad Airina , McNaughton Peter A. , Kirschvink Joseph L. , Winklhofer Michael 
Published: July 2012

Over the past 50 y, behavioral experiments have produced a large body of evidence for the existence of a magnetic sense in a wide range of animals. However, the underlying sensory physiology remains poorly understood due to the elusiveness of the magnetosensory structures. Here we present an effective method for isolating and characterizing potential magnetite-based magnetoreceptor cells. In essence, a rotating magnetic field is employed to visually identify, within a dissociated tissue preparation, cells that contain magnetic material by their rotational behavior. As a tissue of choice, we selected trout olfactory epithelium that has been previously suggested to host candidate magnetoreceptor cells. We were able to reproducibly detect magnetic cells and to determine their magnetic dipole moment. The obtained values (4 to 100 fAm
2
) greatly exceed previous estimates (0.5 fAm
2
). The magnetism of the cells is due to a μ
m
-sized intracellular structure of iron-rich crystals, most likely single-domain magnetite. In confocal reflectance imaging, these produce bright reflective spots close to the cell membrane. The magnetic inclusions are found to be firmly coupled to the cell membrane, enabling a direct transduction of mechanical stress produced by magnetic torque acting on the cellular dipole in situ. Our results show that the magnetically identified cells clearly meet the physical requirements for a magnetoreceptor capable of rapidly detecting small changes in the external magnetic field. This would also explain interference of ac powerline magnetic fields with magnetoreception, as reported in cattle.
RETRACTED: Stabilization of vaccines and antibiotics in silk and eliminating the cold chain
Authors: Zhang Jeney , Pritchard Eleanor , Hu Xiao , Valentin Thomas , Panilaitis Bruce , Omenetto Fiorenzo G. , Kaplan David L. 
Published: July 2012

Sensitive biological compounds, such as vaccines and antibiotics, traditionally require a time-dependent “cold chain” to maximize therapeutic activity. This flawed process results in billions of dollars worth of viable drug loss during shipping and storage, and severely limits distribution to developing nations with limited infrastructure. To address these major limitations, we demonstrate self-standing silk protein biomaterial matrices capable of stabilizing labile vaccines and antibiotics, even at temperatures up to 60 °C over more than 6 months. Initial insight into the mechanistic basis for these findings is provided. Importantly, these findings suggest a transformative approach to the cold chain to revolutionize the way many labile therapeutic drugs are stored and utilized throughout the world.
Transcriptome and methylome interactions in rice hybrids
Authors: Chodavarapu Ramakrishna K. , Feng Suhua , Ding Bo , Simon Stacey A. , Lopez David , Jia Yulin , Wang Guo-Liang , Meyers Blake C. , Jacobsen Steven E. , Pellegrini Matteo 
Published: July 2012

DNA methylation is a heritable epigenetic mark that controls gene expression, is responsive to environmental stresses, and, in plants, may also play a role in heterosis. To determine the degree to which DNA methylation is inherited in rice, and how it both influences and is affected by transcription, we performed genome-wide measurements of these patterns through an integrative analysis of bisulfite-sequencing, RNA-sequencing, and siRNA-sequencing data in two inbred parents of the Nipponbare (NPB) and
indica
(93–11) varieties of rice and their hybrid offspring. We show that SNPs occur at a rate of about 1/253 bp between the two parents and that these are faithfully transmitted into the hybrids. We use the presence of these SNPs to reconstruct the two chromosomes in the hybrids according to their parental origin. We found that, unlike genetic inheritance, epigenetic heritability is quite variable. Cytosines were found to be differentially methylated (epimutated) at a rate of 7.48% (1/15 cytosines) between the NPB and 93–11 parental strains. We also observed that 0.79% of cytosines were epimutated between the parent and corresponding hybrid chromosome. We found that these epimutations are often clustered on the chromosomes, with clusters representing 20% of all epimutations between parental ecotypes, and 2–5% in F1 plants. Epimutation clusters are also strongly associated with regions where the production of siRNA differs between parents. Finally, we identified genes with both allele-specific expression patterns that were strongly inherited as well as those differentially expressed between hybrids and the corresponding parental chromosome. We conclude that much of the misinheritance of expression levels is likely caused by epimutations and
trans
effects.
Fasting improves static apnea performance in elite divers without enhanced risk of syncope
Authors: Schagatay Erika , Lodin‐Sundström Angelica 
Published: July 2012

AbstractIn competitive apnea divers, the nutritional demands may be essentially different from those of, for example, endurance athletes, where energy resources need to be maximised for successful performance. In competitive apnea, the goal is instead to limit metabolism, as the length of the sustainable apneic period will depend to a great extent on minimising oxygen consumption. Many but not all elite divers fast before performing static apnea in competition. This may increase oxygen consumption as mainly lipid stores are metabolised but could also have beneficial effects on apneic duration. Our aim was to determine the effect of over‐night fasting on apnea performance. Six female and seven male divers performed a series of three apneas after eating and fasting, respectively. The series consisted of two 2‐min apneas spaced by 3 min rest and, after 5 min rest, one maximal effort apnea. Apneas were performed at supine rest and preceded by normal respiration and maximal inspiration. Mean (±SD) time since eating was 13 h (±2 h 43 min) for the fasting and 1 h 34 min (±33 min) for the eating condition (P < 0.001). Mean blood glucose was 5.1 (±0.4) mmol/L after fasting and 5.9 (±0.7) mmol/L after eating (P<0.01). Lung volumes were similar in both conditions (NS). For the 2‐min apneas, nadir SaO2 during fasting was 95 (±1)% and 92 (±2)% (P < 0.001) on eating and ETCO2 was lower in the fasting condition (P < 0.01) while heart rate (HR) during apnea was 74 (±10) bpm for fasting and 80 (±10) bpm for eating conditions (P < 0.01). Maximal apnea durations were 4 min 41 s (±43 s) during fasting and 3 min 51 s (±37 s) after eating (P < 0.001), and time without respiratory contractions was 31 s (25%) longer after fasting (P < 0.01). At maximal apnea termination, SaO2 and ETCO2 were similar in both conditions (NS) and apneic HR was 63 (±9) bpm for fasting and 70 (±10) bpm for eating (P < 0.01). The 22% longer apnea duration after fasting with analogous end apnea SaO2 levels suggests that fasting is beneficial for static apnea performance in elite divers, likely via metabolism‐limiting mechanisms. The oxygen‐conserving effect of the more pronounced diving response and possibly other metabolism‐limiting mechanisms related to fasting apparently outweigh the enhanced oxygen consumption caused by lipid metabolism.
Separate control between geometrical and electrical asymmetry effects in capacitively coupled plasmas
Authors: Zhang Quan-Zhi , Zhao Shu-Xia , Jiang Wei , Wang You-Nian 
Published: July 2012

Abstract
Both geometrical and electrical asymmetry effects in capacitive argon discharges are investigated using a two-dimensional particle-in-cell coupled with Monte Carlo collision model. When changing the ratio of the top and bottom electrode surface areas and the phase shift between the two applied harmonics, the induced self-bias was found to develop separately. By adjusting the ratio between the high and low harmonic amplitudes, the electrical asymmetry effect at a fixed phase shift can be substantially optimized. However, the self-bias caused by the geometrical asymmetry hardly changed. Moreover, the separate control of these two asymmetry effects can also be demonstrated from their power absorption profiles. Both the axial and radial plasma density distributions can be modulated by the electrical asymmetry effect.
Effect of hyperbaric oxygen on Vibrio vulnificus and murine infection caused by it
Authors: Tamura Tetsuro , Iida Ken‐ichiro , Saito Mitsumasa , Shiota Susumu , Nakayama Hiroaki , Yoshida Shin‐ichi 
Published: July 2012

ABSTRACTVibrio vulnificus is a bacterium known to cause fatal necrotizing soft tissue infection in humans. Here, a remarkable therapeutic effect of hyperbaric oxygen (HBO) on V. vulnificus infection provoked by its injection into mouse footpads is described. HBO was shown to be bactericidal to this bacterium in vitro as well as in the infected tissue. The bactericidal activity of HBO was shown to be due to reactive oxygen species (ROS), the efficacy of HBO against V. vulnificus infection being accounted for by the high sensitivity of this bacterium to ROS. Besides being somewhat weak in ROS‐inactivating enzyme activities, this bacterium is also unusually sensitive to ultraviolet light and other DNA‐damaging agents. It seems likely that the sensitivity of V. vulnificus to HBO is mainly due to its poor ability to repair oxidative damage to DNA. These findings encourage clinical application of HBO against potentially fatal V. vulnificus infection in humans.
Phagocytosis of apoptotic cells by macrophages in anti-neutrophil cytoplasmic antibody-associated systemic vasculitis
Authors: Ohlsson S M , Pettersson Å , Ohlsson S , Selga D , Bengtsson A A , Segelmark M , Hellmark T 
Published: July 2012

SummaryAnti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is a group of autoimmune diseases, including granulomatosis with polyangiitis (GPA) and microscopic polyangiitis (MPA). It is not known why ANCA develop, but it has been shown that they participate in pathogenesis by activating polymorphonuclear neutrophils (PMNs). In this study we hypothesize that dysregulation of phagocytosis in AAV leads to the accumulation of apoptotic neutrophils seen in association with blood vessels in AAV. These cells progress into secondary necrosis, contributing to tissue damage and autoantibody formation. Peripheral blood cells were counted, and phagocytosis was investigated using monocyte-derived macrophages (MØ) and PMNs from healthy blood donors (HBD), AAV patients and systemic lupus erythematosus (SLE) patients. Furthermore, the effect of serum was assessed. Phagocytosis was measured using flow cytometry. The results showed no deviation in monocyte subpopulations for AAV patients compared to HBDs, although there was a decrease in lymphocyte and pDC (plasmacytoid dendritic cell) populations (4·2 × 106 cells/l versus 10·4 × 106 cells/l, P &lt; 0·001). The number of neutrophils was increased (6·0 × 109 cells/l versus 3·8 × 109 cells/l, P &lt; 0·001). There were no differences found in the ability of MØs to engulf apoptotic cells, nor when comparing apoptotic PMNs to become engulfed. However, serum from AAV donors tended to decrease the phagocytosis ability of MØs (36%) compared to serum from HBDs (43%). In conclusion, there is no intrinsic dysfunction in the MØs or in the PMNs that have an effect on phagocytic activity, but ANCA may play a role by decreasing phagocytic ability.
The role of stromal cells in the persistence of chronic inflammation
Authors: Naylor A J , Filer A , Buckley C D 
Published: July 2012

SummaryInflammation is an unstable state; it either resolves or persists. Inflammatory reactions often have a propensity for specific anatomical sites. Why inflammation persists with specific tissue tropism remains obscure. Increasing evidence suggests that stromal cells which define tissue architecture are the key cells involved, and therefore make attractive therapeutic targets. Research on stromal cells in general and fibroblasts in particular has so far been hampered by a lack of fibroblast-specific cell markers. This review highlights our increasing understanding of the role of fibroblasts in inflammation, and suggests that these cells provide the cellular basis for site specific chronic inflammation.
CD8 T cell autoreactivity to preproinsulin epitopes with very low human leucocyte antigen class I binding affinity
Authors: Abreu J R F , Martina S , Verrijn Stuart A A , Fillié Y E , Franken K L M C , Drijfhout J W , Roep B O 
Published: July 2012

SummaryBeta cells presenting islet epitopes are recognized and destroyed by autoreactive CD8 T cells in type 1 diabetes. These islet-specific T cells are believed to react with epitopes binding with high affinity to human leucocyte antigen (HLA) expressed on beta cells. However, this assumption might be flawed in case of islet autoimmunity. We evaluated T cell recognition of the complete array of preproinsulin (PPI) peptides with regard to HLA binding affinity and T cell recognition. In a comprehensive approach, 203 overlapping 9–10mer PPI peptides were tested for HLA-A2 binding and subjected to binding algorithms. Subsequently, a high-throughput assay was employed to detect PPI-specific T cells in patient blood, in which conditional HLA ligands were destabilized by ultraviolet irradiation and HLA molecules refolded with arrays of PPI peptides, followed by quantum-dot labelling and T cell staining. Analysis of patient blood revealed high frequencies of CD8 T cells recognizing very low HLA binding peptides. Of 28 peptides binding to HLA-A2, a majority was predicted not to bind. Unpredicted peptides bound mainly with low affinities. HLA binding affinity and immunogenicity may not correlate in autoimmunity. Algorithms used to predict high-affinity HLA peptide binders discount the majority of low-affinity HLA binding epitopes. Appreciation that peptides binding HLA with very low affinity can act as targets of autoreactive T cells may help to understand loss of tolerance and disease pathogenesis and possibly point to tissue-specific immune intervention targets.