bluuebunny/crossref_metadata_2025 huggingface dataset:
Bushes protect tortoises from lethal overheating in arid areas of Morocco
Authors: LAGARDE F. , LOUZIZI T. , SLIMANI T. , EL MOUDEN H. , BEN KADDOUR K. , MOULHERAT S. , BONNET X.
Published: January 2012

Arid Mediterranean regions that shelter unique biodiversity are threatened by increasing anthropogenic pressures, such as urbanization, overgrazing and climate change. In Morocco, one of the main bush species in arid areas, the jujube (Ziziphus lotus), suffers from officially promoted programmes of removal. The Moorish tortoise (Testudo graeca soussensis) is threatened by such habitat loss. Like most animals, the Moorish tortoise must navigate between microhabitats to find essential feeding resources and thermal refuges. This study combined radio-tracking of free-ranging individuals, microhabitat temperature monitoring and transects in a range of habitats. Tortoises were found to depend on the occurrence of large and relatively abundant bushes to escape lethal overheating. Thus, (1) current official encouragements for the destruction of the jujube bushes should be reappraised; (2) habitat restoration relying on replanting jujube bush should be encouraged; and (3) large-scale monitoring of critical bush densities should be used to better organize conservation plans (protection and/or restoration of areas) for the Moorish tortoise.
Mostly-unsupervised statistical segmentation of Japanese kanji sequences
Authors: ANDO RIE KUBOTA , LEE LILLIAN
Published: January 2012

Given the lack of word delimiters in written Japanese, word segmentation is generally
considered a crucial first step in processing Japanese texts. Typical Japanese segmentation
algorithms rely either on a lexicon and syntactic analysis or on pre-segmented data; but these
are labor-intensive, and the lexico-syntactic techniques are vulnerable to the unknown word
problem. In contrast, we introduce a novel, more robust statistical method utilizing unsegmented
training data. Despite its simplicity, the algorithm yields performance on long kanji sequences
comparable to and sometimes surpassing that of state-of-the-art morphological analyzers
over a variety of error metrics. The algorithm also outperforms another mostly-unsupervised
statistical algorithm previously proposed for Chinese. Additionally, we present a two-level
annotation scheme for Japanese to incorporate multiple segmentation granularities, and
introduce two novel evaluation metrics, both based on the notion of a compatible bracket,
that can account for multiple granularities simultaneously.
Effekte von früher Zweisprachigkeit auf das deduktive Schließen im Grundschulalter
Authors: Kempert Sebastian , Hardy Ilonca
Published: January 2012

Zusammenfassung. Im vorliegenden Beitrag werden mehrsprachigkeitsbedingte Vorteile in den exekutiven Funktionen anhand von Konditionalaussagen der Form „Wenn P, dann Q” untersucht. Dabei interessieren v.a. Aufgaben mit kontraintuitiven und abstrakten Inhalten, da diese Arten von Syllogismen besondere Anforderungen an die Aufmerksamkeitskontrolle und Inhibitionsfähigkeit stellen. In einer Studie mit N = 54 monolingual deutschen und bilingual deutsch-englischen Schülerinnen und Schülern der dritten Klasse konnten die angenommenen Vorteile für Zweisprachige belegt werden. Zudem konnten in Abgrenzung dazu keine Unterschiede in den Lösungsraten bei Syllogismen mit konkreten Inhalten sowie mit erleichternden oder erschwerenden Zusatzinformationen beobachtet werden. Die Ergebnisse werden hinsichtlich der Entwicklung des deduktiven Schließens sowie der Relevanz für schulisches Lernen diskutiert.
Dielectric map of the Martian northern hemisphere and the nature of plain filling materials
Authors: Mouginot Jérémie , Pommerol Antoine , Beck Pierre , Kofman Wlodek , Clifford Stephen M.
Published: January 2012

A number of observations suggest that an extended ocean once covered a significant part of the Martian northern hemisphere. By probing the physical properties of the subsurface to unprecedented depth, the MARSIS/Mars Express provides new geophysical evidences for the former existence of a Late Hesperian ocean. The Vastitas Borealis formation, located inside a putative shoreline of the ancient ocean, has a low dielectric constant compared with that of typical volcanic materials. We show that the measured value is only consistent with low‐density sedimentary deposits, massive deposits of ground‐ice, or a combination of the two. In contrast, radar observations indicate a distribution of shallow ground ice in equilibrium with the atmosphere in the south polar region. We conclude that the northern plains are filled with remnants of a late Hesperian ocean, fed by water and sediments from the outflow channels about 3 Gy ago.
Inverted fluvial features in the Aeolis‐Zephyria Plana, western Medusae Fossae Formation, Mars: Evidence for post‐formation modification
Authors: Lefort Alexandra , Burr Devon M. , Beyer Ross A. , Howard Alan D.
Published: January 2012

The Aeolis and Zephyria Plana contain the western‐most portion of the Medusae Fossae Formation (MFF), an enigmatic and extensive light‐toned deposit located in the Martian equatorial region and dated from the Hesperian to Amazonian epochs. This area hosts a large population of sinuous ridges (SRs), interpreted as inverted fluvial features, formed by precipitation, indurated by chemical cementation, buried by subsequent deposition, and finally exhumed. This interpretation of SRs as uniformly fluvial represents a modification to an earlier hypothesis for one particular SR of possible glaciofluvial (i.e. esker) formation. These SRs provide a tool to investigate the degree and character of post‐fluvial modification processes in this region. We combined digital terrain models made from Context Camera (CTX) and High Resolution Imaging Science Experiment (HiRISE) stereo image pairs with individual data points from the Mars Orbiter Laser Altimeter (MOLA) to estimate relief, cross‐sectional profiles, longitudinal profiles and slope directions of selected SRs. Longitudinal profiles of several SRs display undulations with amplitudes of up to order 100 m. While some of the lower amplitude undulations may be due to differential erosion, undulations having amplitudes in excess of SR relief require alternative explanations. Our combined morphologic and topographic analysis suggests that multiple post‐flow processes, including compaction of the deposits and tectonic displacements, have modified the original SR profiles. Specification of the type(s) and magnitudes of these modification processes will contribute to understanding both the potential of post‐flow modification of fluvial profiles elsewhere on Mars as well as the nature and properties of the MFF.
Pore‐scale simulation of mixing‐induced calcium carbonate precipitation and dissolution in a microfluidic pore network
Authors: Yoon Hongkyu , Valocchi Albert J. , Werth Charles J. , Dewers Thomas
Published: January 2012

We develop a 2‐D pore scale model of coupled fluid flow, reactive transport, and calcium carbonate (CaCO3) precipitation and dissolution. The model is used to simulate transient experimental results of CaCO3 precipitation and dissolution under supersaturated conditions in a microfluidic pore network (i.e., micromodel) in order to improve understanding of coupled reactive transport systems perturbed by geological CO2 injection. In the micromodel, precipitation is induced by transverse mixing along the centerline in pore bodies. The reactive transport model includes the impact of pH upon carbonate speciation and a CaCO3 reaction rate constant, the effect of changing reactive surface area upon the reaction, and the impact of pore blockage from CaCO3 precipitation on diffusion and flow. Overall, the pore scale model qualitatively captured the precipitate morphology, precipitation rate, and maximum precipitation area using parameter values from the literature. In particular, we found that proper estimation of the effective diffusion coefficient (Deff) and the reactive surface area is necessary to adequately simulate precipitation and dissolution rates. In order to match the initial phase of fast precipitation, it was necessary to consider the top and bottom of the micromodel as additional reactive surfaces. In order to match a later phase when dissolution occurred, it was necessary to increase the dissolution rate compared to the precipitation rate, but the simulated precipitate area was still higher than the experimental results after ∼30 min, highlighting the need for future study. The model presented here allows us to simulate and mechanistically evaluate precipitation and dissolution of CaCO3 observed in a micromodel pore network. This study leads to improved understanding of the fundamental physicochemical processes of CaCO3precipitation and dissolution under far‐from‐equilibrium conditions.
Juan de Fuca subduction zone from a mixture of tomography and waveform modeling
Authors: Chu Risheng , Schmandt Brandon , Helmberger Don V.
Published: January 2012

Seismic tomography images of the upper mantle structures beneath the Pacific Northwestern United States display a maze of high‐velocity anomalies, many of which produce distorted waveforms evident in the USArray observations indicative of the Juan de Fuca (JdF) slab. The inferred location of the slab agrees quite well with existing contour lines defining the slab's upper interface. Synthetic waveforms generated from a recent tomography image fit teleseismic travel times quite well and also some of the waveform distortions. Regional earthquake data, however, require substantial changes to the tomographic velocities. By modeling regional waveforms of the 2008 Nevada earthquake, we find that the uppermost mantle of the 1D reference model AK135, the reference velocity model used for most tomographic studies, is too fast for the western United States. Here, we replace AK135 with mT7, a modification of an older Basin‐and‐Range model T7. We present two hybrid velocity structures satisfying the waveform data based on modified tomographic images and conventional slab wisdom. We derive P and SH velocity structures down to 660 km along two cross sections through the JdF slab. Our results indicate that the JdF slab is subducted to a depth of 250 km beneath the Seattle region, and terminates at a shallower depth beneath Portland region of Oregon to the south. The slab is about 60 km thick and has a P velocity increase of 5% with respect to mT7. In order to fit waveform complexities of teleseismic Gulf of Mexico and South American events, a slab‐like high‐velocity anomaly with velocity increases of 3% for P and 7% for SH is inferred just above the 660 discontinuity beneath Nevada.
Effects of Energy Content and Energy Density of Pre‐Portioned Entrées on Energy Intake
Authors: Blatt Alexandria D. , Williams Rachel A. , Roe Liane S. , Rolls Barbara J.
Published: January 2012

Pre‐portioned entrées are commonly consumed to help control portion size and limit energy intake. The influence of entrée characteristics on energy intake, however, has not been well studied. We determined how the effects of energy content and energy density (ED, kcal/g) of pre‐portioned entrées combine to influence daily energy intake. In a crossover design, 68 non‐dieting adults (28 men and 40 women) were provided with breakfast, lunch, and dinner on 1 day a week for 4 weeks. Each meal included a compulsory, manipulated pre‐portioned entrée followed by a variety of unmanipulated discretionary foods that were consumed ad libitum. Across conditions, the entrées were varied in both energy content and ED between a standard level (100%) and a reduced level (64%). Results showed that in men, decreases in the energy content and ED of pre‐portioned entrées acted independently and added together to reduce daily energy intake (both P < 0.01). Simultaneously decreasing the energy content and ED reduced total energy intake in men by 16% (445 ± 47 kcal/day; P < 0.0001). In women, the entrée factors also had independent effects on energy intake at breakfast and lunch, but at dinner and for the entire day the effects depended on the interaction of the two factors (P < 0.01). Simultaneously decreasing the energy content and ED reduced daily energy intake in women by 14% (289 ± 35 kcal/day; P < 0.0001). Both the energy content and ED of pre‐portioned entrées affect daily energy intake and could influence the effectiveness of such foods for weight management.
Visceral and Not Subcutaneous Abdominal Adiposity Reduction Drives the Benefits of a 1‐Year Lifestyle Modification Program
Authors: Borel Anne‐Laure , Nazare Julie‐Anne , Smith Jessica , Alméras Natalie , Tremblay Angelo , Bergeron Jean , Poirier Paul , Després Jean‐Pierre
Published: January 2012

Excess visceral adipose tissue (VAT) is associated with an increased cardiometabolic risk. The study examined whether changes in cardiometabolic risk markers after a 1‐year lifestyle intervention in viscerally obese men were associated with changes in VAT or with changes in subcutaneous abdominal adipose tissue (SAT). The relative contributions of changes in global adiposity vs. changes in cardiorespiratory fitness to changes in VAT were also quantified. One hundred and forty four men were selected on the basis of an increased waist circumference (≥90 cm) associated with dyslipidemia (triglycerides ≥1.69 and/or high‐density lipoprotein (HDL)‐cholesterol <1.03 mmol/l); 117 men completed the 1‐year intervention which consisted in a healthy eating, physical activity/exercise program. Body weight, body composition, and fat distribution were assessed by anthropometry and dual‐energy X‐ray absorptiometry (DEXA)/computed tomography. Cardiorespiratory fitness, plasma adipokine/inflammatory markers, fasting lipoprotein‐lipid profile, and oral glucose tolerance test (OGTT) were assessed. VAT volume decreased by 26%, cardiorespiratory fitness improved by 20% (P < 0.0001) after 1 year. Plasma adipokine/inflammatory markers, lipids/lipoproteins, and glucose homeostasis were improved. One‐year changes in triglyceride (r = 0.29), apolipoprotein B (r = 0.21), 120‐min OGTT‐glucose (r = 0.27), and fasting insulin (r = 0.27) levels correlated with changes in VAT (all P < 0.05) after adjustment for changes in SAT. Using a multilinear regression model, VAT reduction was independently associated with SAT reduction and with improvement in cardiorespiratory fitness (R2 = 0.58, P < 0.0001). Therefore, this healthy eating‐physical activity/exercise program improved the cardiometabolic risk profile of viscerally obese men in relation to the reduction of VAT. Furthermore, the reduction in VAT was independently related to the reduction in global adiposity and to the improvement in cardiorespiratory fitness.
Obesity and Pain Are Associated in the United States
Authors: Stone Arthur A. , Broderick Joan E.
Published: January 2012

Recent small‐scale studies have shown a positive association between central obesity and self‐reported pain levels. This study attempts to replicate the finding in a survey of over 1,000,000 individuals in the United States. The Gallup Organization conducted a proprietary survey between 2008 through 2010 where 1,062,271 randomly selected individuals in the United States participated in a telephone interview. Survey questions included height and weight, from which BMI was computed, questions about pain conditions in the past year, and a question about pain experience yesterday. Only 19.2% of the sample was classified as Low‐Normal BMI, 21.4 were classified as Overweight, and the remainder was in the three categories of Obese. BMI and pain yesterday were reliably associated when demographic variables were controlled: the overweight group reported 20% higher rates of pain than Low‐Normal group, 68% higher for Obese I group, 136% higher for Obese II group, and 254% higher for Obese III group. The association held for both men and women and it became stronger in older age groups. Controlling the associations for other pain‐related medical conditions substantially reduced the associations, but they remained substantial for the Obese groups. We conclude that BMI and daily pain are positively correlated in the United States: people who are obese are considerably more prone to having daily pain. The association is robust and holds after controlling for several pain conditions and across gender and age. The increasing BMI‐pain association with older ages suggests a developmental process that, along with metabolic hypotheses, calls out for investigation.
Histone H4 histidine phosphorylation: kinases, phosphatases, liver regeneration and cancer
Authors: Besant Paul G. , Attwood Paul V.
Published: January 2012

Phosphorylation of histone H4 on one or both of its two histidine residues has been known to occur in liver cells for nearly 40 years and has been associated with proliferation of hepatocytes during regeneration of the liver following mechanical damage. More recently, large increases in histone H4 histidine kinase activity have been found to occur associated with proliferation and differentiation of liver progenitor cells following chemical damage that prevents hepatocyte proliferation. In addition, it has been shown this histone H4 histidine kinase activity is elevated nearly 100-fold in human foetal liver and several hundredfold in hepatocellular carcinoma tissue compared with normal adult liver. In the present paper, we review what is currently known about histone H4 histidine phosphorylation, the kinase(s) responsible and the phosphatases capable of catalysing its dephosphorylation, and briefly summarize the techniques used to detect and measure the histidine phosphorylation of histone H4 and the corresponding kinase activity.
Negative co-operativity in the EGF receptor
Authors: Pike Linda J.
Published: January 2012

Scatchard analyses of the binding of EGF (epidermal growth factor) to its receptor (EGFR) yield concave up Scatchard plots, indicative of some type of heterogenity in ligand-binding affinity. This was typically interpreted as being due to the presence of two independent binding sites: one of high affinity representing ≤10% of the receptor population, and one of low affinity making up the bulk of the receptors. However, the concept of two independent binding sites is difficult to reconcile with the X-ray structures of the dimerized EGFR that show symmetrical binding of the two ligands. A new approach to the analysis of 125I-EGF-binding data combined with the structure of the singly-occupied Drosophila EGFR have now shown that this heterogeneity is due to the presence of negative co-operativity in the EGFR. Concerns that negative co-operativity precludes ligand-induced dimerization of the EGFR confuse the concepts of linkage and co-operativity. Linkage refers to the effect of ligand on the assembly of dimers, whereas co-operativity refers to the effect of ligand binding to one subunit on ligand binding to the other subunit within a preassembled dimer. Binding of EGF to its receptor is positively linked with dimer assembly, but shows negative co-operativity within the dimer.
Organization of cAMP signalling microdomains for optimal regulation by Ca2+ entry
Authors: Willoughby Debbie
Published: January 2012

Cross-talk between cAMP and Ca2+ signalling pathways plays a critical role in cellular homoeostasis. Several AC (adenylate cyclase) isoforms, catalysing the production of cAMP from ATP, display sensitivity to submicromolar changes in intracellular Ca2+ and, as a consequence, are key sites for Ca2+ and cAMP interplay. Interestingly, these Ca2+-regulated ACs are not equally responsive to equivalent Ca2+ rises within the cell, but display a remarkable selectivity for regulation by SOCE (store-operated Ca2+ entry). Over the years, considerable efforts at investigating this phenomenon have provided indirect evidence of an intimate association between Ca2+-sensitive AC isoforms and sites of SOCE. Now, recent identification of the molecular components of SOCE [namely STIM1 (stromal interaction molecule 1) and Orai1], coupled with significant advances in the generation of high-resolution targeted biosensors for Ca2+ and cAMP, have provided the first detailed insight into the organization of the cellular microdomains associated with Ca2+-regulated ACs. In the present review, I summarize the findings that have helped to provide our most definitive understanding of the selective regulation of cAMP signalling by SOCE.
Morphological and functional aspects of STIM1-dependent assembly and disassembly of store-operated calcium entry complexes
Authors: Shen Wei-Wei , Demaurex Nicolas
Published: January 2012

The SOCE (store-operated Ca2+ entry) pathway is a central component of cell signalling that links the Ca2+-filling state of the ER (endoplasmic reticulum) to the activation of Ca2+-permeable channels at the PM (plasma membrane). SOCE channels maintain a high free Ca2+ concentration within the ER lumen required for the proper processing and folding of proteins, and fuel the long-term cellular Ca2+ signals that drive gene expression in immune cells. SOCE is initiated by the oligomerization on the membrane of the ER of STIMs (stromal interaction molecules) whose luminal EF-hand domain switches from globular to an extended conformation as soon as the free Ca2+ concentration within the ER lumen ([Ca2+]ER) decreases below basal levels of ~500 μM. The conformational changes induced by the unbinding of Ca2+ from the STIM1 luminal domain promote the formation of higher-order STIM1 oligomers that move towards the PM and exposes activating domains in STIM1 cytosolic tail that bind to Ca2+ channels of the Orai family at the PM and induce their activation. Both SOCE and STIM1 oligomerization are reversible events, but whether restoring normal [Ca2+]ER levels is sufficient to initiate the deoligomerization of STIM1 and to control the termination of SOCE is not known. The translocation of STIM1 towards the PM involves the formation of specialized compartments derived from the ER that we have characterized at the ultrastructural level and termed the pre-cortical ER, the cortical ER and the thin cortical ER. Pre-cortical ER structures are thin ER tubules enriched in STIM1 extending along microtubules and located deep inside cells. The cortical ER is located in the cell periphery in very close proximity (8–11 nm) to the plasma membrane. The thin cortical ER consists of thinner sections of the cortical ER enriched in STIM1 and devoid of chaperones that appear to be specialized ER compartments dedicated to Ca2+ signalling.
Regulation of MEK/ERK pathway output by subcellular localization of B-Raf
Authors: Andreadi Catherine , Noble Catherine , Patel Bipin , Jin Hong , Aguilar Hernandez Maria M. , Balmanno Kathryn , Cook Simon J. , Pritchard Catrin
Published: January 2012

The strength and duration of intracellular signalling pathway activation is a key determinant of the biological outcome of cells in response to extracellular cues. This has been particularly elucidated for the Ras/Raf/MEK [mitogen-activated growth factor/ERK (extracellular-signal-regulated kinase) kinase]/ERK signalling pathway with a number of studies in fibroblasts showing that sustained ERK signalling is a requirement for S-phase entry, whereas transient ERK signalling does not have this capability. A major unanswered question, however, is how a cell can sustain ERK activation, particularly when ERK-specific phosphatases are transcriptionally up-regulated by the pathway itself. A major point of ERK regulation is at the level of Raf, and, to sustain ERK activation in the presence of ERK phosphatases, sustained Raf activation is a requirement. Three Raf proteins exist in mammals, and the activity of all three is induced following growth factor stimulation of cells, but only B-Raf activity is maintained at later time points. This observation points to B-Raf as a regulator of sustained ERK activation. In the present review, we consider evidence for a link between B-Raf and sustained ERK activation, focusing on a potential role for the subcellular localization of B-Raf in this key physiological event.
Investigating extracellular in situ EGFR structure and conformational changes using FRET microscopy
Authors: Roberts Selene K. , Tynan Christopher J. , Winn Martyn , Martin-Fernandez Marisa L.
Published: January 2012

The crystallographic structures of functional fragments of ErbBs have provided excellent insights into the geometry of growth factor binding and receptor dimerization. By placing together receptor fragments to build structural models of entire receptors, we expect to understand how these enzymes are allosterically regulated; however, several predictions from these models are inconsistent with experimental evidence from cells. The opening of this gap underlines the need to investigate intact ErbBs by combining cellular and structural studies into a full picture.
Multi-pathway network analysis of mammalian epithelial cell responses in inflammatory environments
Authors: Clarke David C. , Lauffenburger Douglas A.
Published: January 2012

Inflammation is a key physiological response to infection and injury and, although usually beneficial, it can also be damaging to the host. The liver is a prototypical example in this regard because inflammation helps to resolve liver injury, but it also underlies the aetiology of pathologies such as fibrosis and hepatocellular carcinoma. Liver cells sense their environment, including the inflammatory environment, through the activities of receptor-mediated signal transduction pathways. These pathways are organized in a complex interconnected network, and it is becoming increasingly recognized that cellular adaptations result from the quantitative integration of multi-pathway network activities, rather than isolated pathways causing particular phenotypes. Therefore comprehending liver cell signalling in inflammation requires a scientific approach that is appropriate for studying complex networks. In the present paper, we review our application of systems analyses of liver cell signalling in response to inflammatory environments. Our studies feature broad measurements of cell signalling and phenotypes in response to numerous experimental perturbations reflective of inflammatory environments, the data from which are analysed using Boolean and fuzzy logic models and regression-based methods in order to quantitatively relate the phenotypic responses to cell signalling network states. Our principal biological insight from these studies is that hepatocellular carcinoma cells feature uncoupled inflammatory and growth factor signalling, which may underlie their immune evasion and hyperproliferative properties.
Exploring the function of the JNK (c-Jun N-terminal kinase) signalling pathway in physiological and pathological processes to design novel therapeutic strategies
Authors: Davies Clare , Tournier Cathy
Published: January 2012

JNK (c-Jun N-terminal kinase) is a member of the MAPK (mitogen-activated protein kinase) family that regulates a range of biological processes implicated in tumorigenesis and neurodegenerative disorders. For example, genetic studies have demonstrated that the removal of specific Jnk genes can reduce neuronal death associated with cerebral ischaemia. As such, targeting JNK signalling constitutes an obvious opportunity for therapeutic intervention. However, MAPK inhibitors can display toxic effects. Consequently, dual-specificity MKKs (MAPK kinases) may represent more attractive targets. In particular, evidence that blocking JNK activation by removing MKK4 offers an effective therapy to treat pathological conditions has started to emerge. MKK4 was the first JNK activator identified. The remaining level of JNK activity in cells lacking MKK4 expression led to the discovery of a second activator of JNK, named MKK7. Distinct phenotypic abnormalities associated with the targeted deletion of Mkk4 and Mkk7 in mice have revealed that MKK4 and MKK7 have non-redundant function in vivo. Further insights into the specific functions of the JNK activators in cancer cells and in neurons will be of critical importance to validate MKK4 and MKK7 as promising drug targets.
The glycerophosphoinositols and their cellular functions
Authors: Corda Daniela , Zizza Pasquale , Varone Alessia , Bruzik Karol S. , Mariggiò Stefania
Published: January 2012

Interest in the glycerophosphoinositols has been increasing recently, on the basis of their biological activities. The cellular metabolism of these water-soluble bioactive phosphoinositide metabolites has been clarified, with the identification of the specific enzyme involved in their synthesis, PLA2IVα (phospholipase A2 IVα), and the definition of their phosphodiesterase-based catabolism, and thus inactivation. The functional roles and mechanisms of action of these compounds have been investigated in different cellular contexts. This has led to their definition in the control of various cell functions, such as cell proliferation in the thyroid and actin cytoskeleton organization in fibroblasts and lymphocytes. Roles for the glycerophosphoinositols in immune and inflammatory responses are also being defined. In addition to these physiological functions, the glycerophosphoinositols have potential anti-metastatic activities that should lead to their pharmacological exploitation.
How phosphoinositide 3-phosphate controls growth downstream of amino acids and autophagy downstream of amino acid withdrawal
Authors: Ktistakis Nicholas T. , Manifava Maria , Schoenfelder Priya , Rotondo Sergio
Published: January 2012

The simple phosphoinositide PtdIns3P has been shown to control cell growth downstream of amino acid signalling and autophagy downstream of amino acid withdrawal. These opposing effects depend in part on the existence of distinct complexes of Vps34 (vacuolar protein sorting 34), the kinase responsible for the majority of PtdIns3P synthesis in cells: one complex is activated after amino acid withdrawal to induce autophagy and another regulates mTORC1 (mammalian target of rapamycin complex 1) activation when amino acids are present. However, lipid-dependent signalling almost always exhibits a spatial dimension, related to the site of formation of the lipid signal. In the case of PtdIns3P-regulated autophagy induction, recent data suggest that PtdIns3P accumulates in a membrane compartment dynamically connected to the endoplasmic reticulum that constitutes a platform for the formation of some autophagosomes. For PtdIns3P-regulated mTORC1 activity, a spatial context is not yet known: several possibilities can be envisaged based on the known effects of PtdIns3P on the endocytic system and on recent data suggesting that activation of mTORC1 depends on its localization on lysosomes.
The essential role of cAMP/Ca2+ signalling in mammalian circadian timekeeping
Authors: O'Neill John S. , Reddy Akhilesh B.
Published: January 2012

Approximately daily, or circadian, rhythms are ubiquitous across eukaryotes. They are manifest in the temporal co-ordination of metabolism, physiology and behaviour, thereby allowing organisms to anticipate and synchronize with daily environmental cycles. Although cellular rhythms are self-sustained and cell-intrinsic, in mammals, the master regulator of timekeeping is localized within the hypothalamic SCN (suprachiasmatic nucleus). Molecular models for mammalian circadian rhythms have focused largely on transcriptional–translational feedback loops, but recent data have revealed essential contributions by intracellular signalling mechanisms. cAMP and Ca2+ signalling are not only regulated by the cellular clock, but also contribute directly to the timekeeping mechanism, in that appropriate manipulations determine the canonical pacemaker properties of amplitude, phase and period. It is proposed that daily auto-amplification of second messenger activity, through paracrine neuropeptidergic coupling, is necessary and sufficient to account for the increased amplitude, accuracy and robustness of SCN timekeeping.
Triggering of Ca2+ signals by NAADP-gated two-pore channels: a role for membrane contact sites?
Authors: Patel Sandip , Brailoiu Eugen
Published: January 2012

NAADP (nicotinic acid–adenine dinucleotide phosphate) is a potent Ca2+-mobilizing messenger implicated in many Ca2+-dependent cellular processes. It is highly unusual in that it appears to trigger Ca2+ release from acidic organelles such as lysosomes. These signals are often amplified by archetypal Ca2+ channels located in the endoplasmic reticulum. Recent studies have converged on the TPCs (two-pore channels) which localize to the endolysosomal system as the likely primary targets through which NAADP mediates its effects. ‘Chatter’ between TPCs and endoplasmic reticulum Ca2+ channels is disrupted when TPCs are directed away from the endolysosomal system. This suggests that intracellular Ca2+ release channels may be closely apposed, possibly at specific membrane contact sites between acidic organelles and the endoplasmic reticulum.
Large-amplitude dynamics in vinyl radical: The role of quantum tunneling as an isomerization mechanism
Authors: Sharma Amit R. , Bowman Joel M. , Nesbitt David J.
Published: January 2012

We report tunneling splittings associated with the large amplitude 1,2 H-atom migration to the global minima in the vinyl radical. These are obtained using a recent full-dimensional ab initio potential energy surface (PES) [A. R. Sharma, B. J. Braams, S. Carter, B. C. Shepler, and J. M. Bowman, J. Chem. Phys. 130(17), 174301 (2009)] and independently, directly calculated “reaction paths.” The PES is a multidimensional fit to coupled cluster single and double and perturbative treatment of triple excitations coupled-cluster single double triple (CCSD(T)) with the augmented correlation consistent triple zeta basis set (aug-cc-pVTZ). The reaction path potentials are obtained from a series of CCSD(T)/aug-cc-pVnTZ calculations extrapolated to the complete basis set limit. Approximate 1D calculations of the tunneling splitting for these 1,2-H atom migrations are obtained using each of these potentials as well as quite different 1D Hamiltonians. The splittings are calculated over a large energy ranges, with results from the two sets of calculations in excellent agreement. Though negligibly slow (>1 s) for the vibrational ground state, this work predicts tunneling-promoted 1,2 hydride shift dynamics in vinyl to exhibit exponential growth with internal vibrational excitation, specifically achieving rates on the sub-μs time scale at energies above E ≈ 7500 cm−1. Most importantly, these results begin to elucidate the possible role of quantum isomerization through barriers without dissociation, in competition with the more conventional picture of classical roaming permitted over a much narrower window of energies immediately below the bond dissociation limit. Furthermore, when integrated over a Boltzmann distribution of thermal energies, these microcanonical tunneling rates are consistent with sub-μs time scales for 1,2 hydride shift dynamics at T > 1400 K. These results have potential relevance for combustion modeling of low-pressure flames, as well as recent observations of nuclear spin statistical mixing from high-resolution IR/microwave spectroscopy on vinyl radical.
Understanding hydrogen sorption in a polar metal-organic framework with constricted channels
Authors: Stern Abraham C. , Belof Jonathan L. , Eddaoudi Mohamed , Space Brian
Published: January 2012

A high fidelity molecular model is developed for a metal-organic framework (MOF) with narrow (approximately 7.3 Å) nearly square channels. MOF potential models, both with and neglecting explicit polarization, are constructed. Atomic partial point charges for simulation are derived from both fragment-based and fully periodic electronic structure calculations. The molecular models are designed to accurately predict and retrodict material gas sorption properties while assessing the role of induction for molecular packing in highly restricted spaces. Thus, the MOF is assayed via grand canonical Monte Carlo (GCMC) for its potential in hydrogen storage. The confining channels are found to typically accommodate between two to three hydrogen molecules in close proximity to the MOF framework at or near saturation pressures. Further, the net attractive potential energy interactions are dominated by van der Waals interactions in the highly polar MOF – induction changes the structure of the sorbed hydrogen but not the MOF storage capacity. Thus, narrow channels, while providing reasonably promising isosteric heat values, are not the best choice of topology for gas sorption applications from both a molecular and gravimetric perspective.
Reduced density matrix hybrid approach: An efficient and accurate method for adiabatic and non-adiabatic quantum dynamics
Authors: Berkelbach Timothy C. , Reichman David R. , Markland Thomas E.
Published: January 2012

We present a new approach to calculate real-time quantum dynamics in complex systems. The formalism is based on the partitioning of a system's environment into “core” and “reservoir” modes with the former to be treated quantum mechanically and the latter classically. The presented method only requires the calculation of the system's reduced density matrix averaged over the quantum core degrees of freedom which is then coupled to a classically evolved reservoir to treat the remaining modes. We demonstrate our approach by applying it to the spin-boson problem using the noninteracting blip approximation to treat the system and core, and Ehrenfest dynamics to treat the reservoir. The resulting hybrid methodology is accurate for both fast and slow baths, since it naturally reduces to its composite methods in their respective regimes of validity. In addition, our combined method is shown to yield good results in intermediate regimes where neither approximation alone is accurate and to perform equally well for both strong and weak system-bath coupling. Our approach therefore provides an accurate and efficient methodology for calculating quantum dynamics in complex systems.
Carrier dynamics in bulk GaN
Authors: Šcˇajev Patrik , Jarašiūnas Kęstutis , Okur Serdal , Özgür Ümit , Morkoç Hadis
Published: January 2012

Carrier dynamics in hydride vapor phase epitaxy grown bulk GaN with very low density of dislocations, 5–8 × 105 cm−2, have been investigated by time-resolved photoluminescence (PL), free carrier absorption, and light-induced transient grating techniques in the carrier density range of 1015 to ∼1019 cm−3 under single and two photon excitation. For two-photon carrier injection to the bulk (527 nm excitation), diffusivity dependence on the excess carrier density revealed a transfer from minority to ambipolar carrier transport with the ambipolar diffusion coefficient Da saturating at 1.6 cm2/s at room temperature. An extremely long lifetime value of 40 ns, corresponding to an ambipolar diffusion length of 2.5 μm, was measured at 300 K. A nearly linear increase of carrier lifetime with temperature in the 80–800 K range and gradual decrease of D pointed out a prevailing mechanism of diffusion-governed nonradiative recombination due to carrier diffusive flow to plausibly the grain boundaries. Under single photon excitation (266 and 351 nm), subnanosecond transients of PL decay and their numerical modeling revealed fast processes of vertical carrier diffusion, surface recombination, and reabsorption of emission, which mask access to pure radiative decay.
Cavitation inception during the interaction of a pair of counter-rotating vortices
Authors: Chang Natasha A. , Choi Jaehyug , Yakushiji Ryo , Ceccio Steven L.
Published: January 2012

Pairs of unequal strength, counter-rotating vortices were produced to examine the inception and dynamics of vortex cavitation as the vortices undergo a long-wavelength instability. The instability causes the weaker, secondary vortex to be turned and stretched by the stronger primary vortex. Folding and stretching of the secondary vortices result in sharp reductions of the core pressure. Here, these sharp and transient reductions in the secondary vortex core pressure produced incipient cavitation at static pressures that were as much as 20 times higher than that required for inception in the core of the unstretched secondary vortex. In addition, the majority of nuclei measured was of the order of 1 μm in size, which requires tension on the order of 100 kPa for cavitation inception to occur. The flow parameters that lead to the instability and cavitation inception in the secondary vortex are examined, and the measured event rates are correlated to freestream nuclei populations and static pressure. These measurements, combined with observations of the elongated bubbles themselves, suggest that stretching produced large tensions in the core of the secondary vortex due to both a reduction in the secondary vortex core size and the creation of a jetting flow in the vortex core.
Thermoelectric properties of Cu doped ZnSb containing Zn3P2 particles
Authors: Valset K. , Böttger P. H. M. , Taftø J. , Finstad T. G.
Published: January 2012

We prepared ZnSb containing Zn3P2 particles of size ranging from a few tens to several hundred nanometers by melting powders of Zn, Sb, and P. Materials with Zn3P2 content up to 3.75% were made and subsequently ball-milled and hot pressed. A reduction in the thermal conductivity of 15% was achieved. By adding 0.2% Cu the carrier concentration increased an order of magnitude, to 2.0 × 1019 cm−3, while the mobility remained unaffected. The resulting increase in electrical conductivity together with the reduced thermal conductivity, led to a significant increase in the dimensionless figure of merit, in excess of 0.9 around 550 K.
Inelastic carrier lifetime in bilayer graphene
Authors: Park Cheol-Hwan , Giustino Feliciano , Spataru Catalin D. , Cohen Marvin L. , Louie Steven G.
Published: January 2012

We present a first-principles calculation of the inelastic carrier lifetimes in pristine and doped bilayer graphene. The scattering rate arising from electron-electron interactions is smaller than that in graphene by 20–40% on average, and is highly anisotropic. On the other hand, the scattering rate arising from electron-phonon interactions is similar in magnitude to that in graphene and is isotropic.
Design and performance of the collective Thomson scattering receiver at ASDEX Upgrade
Authors: Furtula V. , Salewski M. , Leipold F. , Michelsen P. K. , Korsholm S. B. , Meo F. , Moseev D. , Nielsen S. K. , Stejner M. , Johansen T.
Published: January 2012

Here we present the design of the fast-ion collective Thomson scattering receiver for millimeter wave radiation installed at ASDEX Upgrade, a tokamak for fusion plasma experiments. The receiver can detect spectral power densities of a few eV against the electron cyclotron emission background on the order of 100 eV under presence of gyrotron stray radiation that is several orders of magnitude stronger than the signal to be detected. The receiver down converts the frequencies of scattered radiation (100–110 GHz) to intermediate frequencies (IF) (4.5–14.5 GHz) by heterodyning. The IF signal is divided into 50 IF channels tightly spaced in frequency space. The channels are terminated by square-law detector diodes that convert the signal power into DC voltages. We present measurements of the transmission characteristics and performance of the main receiver components operating at mm-wave frequencies (notch, bandpass, and lowpass filters, a voltage-controlled variable attenuator, and an isolator), the down-converter unit, and the IF components (amplifiers, bandpass filters, and detector diodes). Furthermore, we determine the performance of the receiver as a unit through spectral response measurements and find reasonable agreement with the expectation based on the individual component measurements
A dual-channel, focusing x-ray spectrograph with uniform dispersion for Z pinch plasmas measurement
Authors: Yang Qingguo , Li Zeren , Chen Guanhua , Ye Yan , Huang Xianbin , Cai Hongchun , Li Jing , Xiao Shali
Published: January 2012

A dual-channel, focusing x-ray spectrograph with uniform dispersion (i.e., the linear dispersion of this spectrograph is a constant) is described for measuring the x-ray spectra emission from the hot, dense Al Z pinch plasmas. The spectrograph uses double uniform-dispersed crystals (e.g., a Quartz 1010 crystal and a Mica 002 crystal) as dispersion elements and a double-film box as detector to achieve the simultaneous recording of the time integrated spectrum covering a wide spectral range of ∼5–9 Å. Since this spectrograph disperse the x-rays on the detector plane with uniform spacing for every wavelength, it needs not the calibration of the wavelength with spatial coordinate, thereby own the advantages of easiness and veracity for spectra identification. The design of this spectrograph and the example of experiment on the “Yang” accelerator are presented.
Acoustic metamaterial exhibiting four different sign combinations of density and modulus
Authors: Seo Yong Mun , Park Jong Jin , Lee Seung Hwan , Park Choon Mahn , Kim Chul Koo , Lee Sam Hyeon
Published: January 2012

We fabricated a double negative acoustic metamaterial which consisted of Helmholtz resonators and membranes. Experimental data on the transmission and dispersion relation are presented. The system exhibited three frequencies where the acoustic state makes sharp transitions from density negative (ρ-NG) to double negative (DNG), modulus negative (B-NG), and double positive (DPS) in sequence with the frequency. We observed a wide range of negative refractive indexes from −0.06 to −3.7 relative to air, which will allow for new acoustic transformation techniques.
New symbolic tools for differential geometry, gravitation, and field theory
Authors: Anderson I. M. , Torre C. G.
Published: January 2012

DifferentialGeometry is a Maple software package which symbolically performs fundamental operations of calculus on manifolds, differential geometry, tensor calculus, spinor calculus, Lie algebras, Lie groups, transformation groups, jet spaces, and the variational calculus. These capabilities, combined with dramatic recent improvements in symbolic approaches to solving algebraic and differential equations, have allowed for development of powerful new tools for solving research problems in gravitation and field theory. The purpose of this paper is to describe some of these new tools and present some advanced applications involving: Killing vector fields and isometry groups, Killing tensors, algebraic classification of solutions of the Einstein equations, and symmetry reduction of field equations.
A contactless methodology of picking up micro-particles from rigid surfaces by acoustic radiation force
Authors: Jia Kun , Yang Keji , Fan Zongwei , Ju Bing-Feng
Published: January 2012

Controlled movement and pick up of small object from a rigid surface is a primary challenge in many applications. In this paper, a contactless methodology of picking up micro-particles within deionized water from rigid surfaces by acoustic radiation force is presented. In order to achieve this, an acoustic radiation force was generated by 1.75 MHz transducers. A custom built setup facilitates the optimization of the sound field by varying the parameters such as sound source size and source position. The three-dimensional pressure distributions are measured and its relative sound field is also characterized accordingly. The standing wave field has been formed and it is mainly composed of two obliquely incident plane waves and their reflectors. We demonstrated the gripping and positioning of silica beads, SiO2, and aluminum micro-particles of 100 μm to 500 μm in size with this method using acoustic radiation force. The acoustic radiation force generated is well controlled, contactless, and in the tens of nano-Newton range which allowed us to manipulate relative big micro objects such as MEMS components as well as moving objects such as living cells. The proposed method provided an alternative form of contactless operating environment with scalable dimensions suitable for the manipulating of small objects. This permits high-throughput processing and reduction in time required for MEMS assembling, cell biomechanics, and biotechnology applications.