bluuebunny/crossref_metadata_2025 huggingface dataset:
Global distribution of convection penetrating the tropical tropopause
Authors: Liu Chuntao , Zipser Edward J.
Published: December 2005

Tropical deep convection with overshooting tops is identified by defining five different reference heights using a 5‐year TRMM database. The common properties of these extreme convective systems are examined from a global perspective. It is found that 1.3% of tropical convection systems reach 14 km and 0.1% of them may even penetrate the 380 K potential temperature level. Overshooting convection is more frequent over land than over water, especially over central Africa, Indonesia and South America. The seasonal, diurnal and geodistribution patterns of overshooting deep convection show very little sensitivity to the definition of the reference level. The global distribution of overshooting area, volume and precipitating ice mass shows that central Africa makes a disproportionately large contribution to overshooting convection. A semiannual cycle of total overshooting area, volume and precipitating ice mass is found.
Inferring carbon monoxide pollution changes from space‐based observations
Authors: Shindell Drew T. , Faluvegi Greg , Emmons Louisa K.
Published: December 2005

We compare space‐based measurements of carbon monoxide (CO) during April 1994 and October 1984 and 1994 from the early MAPS instrument with those during 2000–2004 from the MOPITT instrument. We show that a three‐dimensional global composition model can be used to account for differences in retrieval sensitivity between the two instruments and between the different years of MOPITT data. This allows direct comparison of CO amounts over most of the globe at different times. These types of changes in short‐lived constituents cannot be assessed with local measurements. Though the existing space‐based data are too sparse both temporally and geographically to allow trend estimates, we find substantial variations in midtropospheric CO between the different years in many continental‐scale regions. During April, average CO is ∼12–18 ppbv (∼10–20%) greater during 2000–2004 than during 1994 over North America, southeast Asia and North Africa though the global mean value is nearly the same. During October 1994, observations show CO enhancements of 15–20 ppbv relative to 1984 or 2000–2004 over South America and a similar, though slightly smaller (9–19 ppbv), enhancement globally. Southeast Asia, Europe and North America all show similar October CO levels in 1994 and 2000–2004, with both times showing substantially more pollution (13–29 ppbv) than 1984. Variations over Europe and Africa are consistent in both seasons, while changes elsewhere are not. Changes over southeast Asia and North Africa are substantially in excess of interannual variability, while those over North and South America and southern Africa are only marginally so. Model sensitivity studies examining the response to changes in emissions indicate probable causes of the CO changes over different regions. Over southeast Asia and North America, CO is most sensitive to industrial and biomass burning emissions, implying that changes in these sources likely account for the 13–29 ppbv increases seen there between 2000–2004 and earlier years. Over North Africa, CO is strongly influenced by numerous sources as well as meteorology, precluding attribution of increases to particular factors. Over South America and southern Africa, variations in both biomass burning and isoprene emissions likely contributed to the ∼10–20 ppbv changes.
A study of the NOAA 16 AMSU‐A brightness temperatures observed over Amazon rain forest
Authors: Mo Tsan
Published: December 2005

Angular distributions of brightness temperatures over the Amazon rain forest observed by the NOAA 16 Advanced Microwave Sounding Unit‐A (AMSU‐A) window channels are studied and simulated with a radiative transfer model. The model is based on a combination of the atmospheric radiative transfer model and a vegetation canopy model which treats the rain forest as a uniform layer with an effective canopy temperature. Since emission from the ground surface is heavily attenuated by the rain forest canopy, only radiations from the rain forest canopy and the atmospheric medium contribute to the measurements. The measured angular distributions of brightness temperatures at the four window channels 1–3 and 15 (with frequencies centered at 23.8, 31.4, 50.3, and 89 GHz, respectively), have relatively small angular dependence that is attributed to the atmospheric path length since the canopy radiation is angular‐independent. Data used in this study are collected from April 2001 to October 2002 for 1 month in each season. Angular distributions of the data from each month show remarkably stable patterns which can be well simulated by the model developed in this study. For the four window channels, ascending (day time 2 PM in the Sun) and descending (nighttime 2 AM in dark) measurements differ by 3–8 K, depending on channels. The root‐mean‐square (RMS) differences between 2 years' angular distributions for all four channels and the three overlapping months (April, July, and October) are 0.82 K for the ascending passes, and 0.47 K for the descending passes, respectively. The stable pattern and small variation of angular distributions can be potentially useful for postlaunch calibration of future microwave instruments.
Strain at radially fractured centers on Venus
Authors: Grindrod Peter M. , Nimmo Francis , Stofan Ellen R. , Guest John E.
Published: December 2005

Radially fractured centers (RFCs) on Venus are distinctive, ∼100 km long radiating systems of graben, fissures, and fractures arranged around a central topographic high. We use cycle 1 and cycle 3 Magellan images to determine the depths and wall dip angles of several large radial graben, using two different methods, at four RFCs: Becuma Mons, Didilia Corona, H'uraru Corona, and Pavlova Corona. We record graben depths of 0.3–0.9 km and mean wall dip angles of about 36°, which we interpret as a primary talus slope rather than a fault plane. Using the calculated depths and a more realistic fault dip of 60°, we find extension of between 0.5 and 1 km on graben between about 5 and 10 km wide. We use this extension to estimate the hoop strain at each RFC. Maximum measured strains on the flanks are typically between ∼1 and 4% and may be up to 7% toward the center. We conclude that this strain is too large to be explained by current plume‐related uplift models and also by magma chamber inflation. We conclude that dikes are probably responsible for the majority of the strain at the large radial graben.
Morphology of drainage basins as an indicator of climate on early Mars
Authors: Stepinski T. F. , Stepinski A. P.
Published: December 2005

We show that drainage basin morphology correlates with climate. Computational analysis of the 46 basins extracted from the western slopes of the Andes reveals the existence of four different basin morphologic classes. This purely geomorphic partition correlates with division of the same basins on the grounds of climate types. Basins are compared using circularity functions as their formal representations. Self‐organizing maps and dendrograms are employed to provide basin classification. One class of basin morphologies corresponds to sites in the arid Atacama Desert, and the other class corresponds to sites in the Atacama exhibiting groundwater sapping landforms. Using the same technique, we study a larger sample of 94 basins that, in addition to the Andean basins, includes other terrestrial basins and 26 basins from Martian sites that show prominent valley networks. The classification of this larger set shows that morphologies of Martian and terrestrial basins bifurcate at the root of the dendrogram, forming two separate domains of basin morphologies. The similarity map reveals that, of all the terrestrial basins, the Atacama Desert basins are morphologically closest to the Martian basins. Extrapolating the terrestrial morphology‐climate linkage to Mars points to formation of valley networks in a hyperarid climatic environment. We submit that the Atacama Desert provides the best possible terrestrial morphologic analog to valley network sites on Mars. We discuss climatic and hydrologic particularities of the Atacama Desert and hypothesize that a similar environment existed on early Mars.
Laboratory‐simulated acid‐sulfate weathering of basaltic materials: Implications for formation of sulfates at Meridiani Planum and Gusev crater, Mars
Authors: Golden D. C. , Ming Douglas W. , Morris Richard V. , Mertzman Stanley A.
Published: December 2005

Acid‐sulfate weathering of basaltic materials is a candidate formation process for the sulfate‐rich outcrops and rocks at the MER rover Opportunity and Spirit landing sites. To determine the style of acid‐sulfate weathering on Mars, we weathered basaltic materials (olivine‐rich glassy basaltic sand and plagioclase feldspar‐rich basaltic tephra) in the laboratory under different oxidative, acid‐sulfate conditions and characterized the alteration products. We investigated alteration by (1) sulfuric‐acid vapor (acid fog), (2) three‐step hydrothermal leaching treatment approximating an “open system,” and (3) single‐step hydrothermal batch treatment approximating a “closed system.” In acid fog experiments, Al‐, Fe‐, and Ca‐sulfates and amorphous silica formed from plagioclase‐rich tephra, and Mg‐ and Ca‐sulfates and amorphous silica formed from the olivine‐rich sands. In three‐step leaching experiments, only amorphous Si formed from the plagioclase‐rich basaltic tephra, and jarosite, Mg‐, and Ca‐sulfates and amorphous silica formed from olivine‐rich basaltic sand. Amorphous silica formed under single‐step experiments for both starting materials. On the basis of our experiments, jarosite formation in Meridiani outcrop is potential evidence for an open system acid‐sulfate weathering regime. Waters rich in sulfuric acid percolated through basaltic sediment, dissolving basaltic phases (e.g., olivine) and forming jarosite, other sulfates, and iron oxides. Aqueous alteration of outcrops and rocks on the West Spur of the Columbia Hills may have occurred when vapors rich in SO2 from volcanic sources reacted with basaltic materials. Soluble ions from the host rock (e.g., olivine) reacted with S to form Ca‐, Mg‐, and other sulfates along with iron oxides and oxyhydroxides.
An intense terminal epoch of widespread fluvial activity on early Mars: 2. Increased runoff and paleolake development
Authors: Irwin Rossman P. , Howard Alan D. , Craddock Robert A. , Moore Jeffrey M.
Published: December 2005

To explain the much higher denudation rates and valley network development on early Mars (>∼3.6 Gyr ago), most investigators have invoked either steady state warm/wet (Earthlike) or cold/dry (modern Mars) end‐member paleoclimates. Here we discuss evidence that highland gradation was prolonged, but generally slow and possibly ephemeral during the Noachian Period, and that the immature valley networks entrenched during a brief terminal epoch of more erosive fluvial activity in the late Noachian to early Hesperian. Observational support for this interpretation includes (1) late‐stage breaching of some enclosed basins that had previously been extensively modified, but only by internal erosion and deposition; (2) deposition of pristine deltas and fans during a late stage of contributing valley entrenchment; (3) a brief, erosive response to base level decline (which was imparted as fretted terrain developed by a suite of processes unrelated to surface runoff) in fluvial valleys that crosscut the highland‐lowland boundary scarp; and (4) width/contributing area relationships of interior channels within valley networks, which record significant late‐stage runoff production with no evidence of recovery to lower‐flow conditions. This erosion appears to have ended abruptly, as depositional landforms generally were not entrenched with declining base level in crater lakes. A possible planetwide synchronicity and common cause to the late‐stage fluvial activity are possible but remain uncertain. This increased activity of valley networks is offered as a possible explanation for diverse features of highland drainage basins, which were previously cited to support competing warm, wet and cold, dry paleoclimate scenarios.
A method for filling in the cohesive ends of double‐stranded DNA using Pfu DNA polymerase
Authors: Yang Shaohui , Li Xin , Ding Dongfeng , Hou Jianhua , Jin Zhaoxia , Yu Xinchun , Bo Tao , Li Weidong , Li Minggang
Published: December 2005

The present paper reports a highly efficient method of making blunt ends from cohesive ends of double‐stranded DNA. Klenow fragment and Pfu DNA polymerases were used to fill in the cohesive ends. Since the transformation efficiency can directly reflect the filling‐in efficiency, similar ligation and transformation conditions were used, and the filling‐in efficiency was compared with the corresponding transformation efficiency. The results indicate that the filling‐in efficiency of Pfu DNA polymerase was 1.96 times that of Klenow fragment and its efficiency was markedly higher than that of Klenow fragment (P<0.01). The optimization experiments on reaction conditions indicate, when the pH is 8.5 and the temperature is 74 °C, that the filling‐in efficiency was highest upon using a buffer containing 3 mM MgSO4 and 300 μM dNTP.
Cystatins may confer viral resistance in plants by inhibition of a virus‐induced cell death phenomenon in which cysteine proteinases are active: cloning and molecular characterization of a cDNA encoding cysteine‐proteinase inhibitor (celostatin) from Celosia cristata (crested cock's comb)
Authors: Gholizadeh Ashraf , Santha Ittiaparambu Mana , Kohnehrouz Bahram Baghban , Lodha Madan Lal , Kapoor Harish Chander
Published: December 2005

Cystatins (cysteine proteinase inhibitors) have been recently used in plants as antiviral strategy against those viruses whose replication involves cysteine proteinase activity. We proposed an idea that cystatins may confer resistance by inhibition of a virus‐induced cell‐death phenomenon in which cysteine proteinases are active. To test this idea, a full‐length cDNA library was constructed from the preflowering stage of Celosia cristata (crested cock's comb) leaves, and a cDNA clone with cystatin domain was isolated using an oligonucleotide probe designed on the basis of the conserved peptide of plant cystatins. It was expressed in an Escherichia coli expression system as a fusion protein. The purified recombinant product, termed ‘celostatin’ (Celosia cystatin), inhibited the enzymatic activity of papain indicating its cystatin activity and prevented TMV (tobacco mosaic virus)‐induced hypersensitive‐response cell death in Nicotiana glutinosa (a wild species of tobacco) leaves by 65–70% at the concentration of approx. 50 ng/ml. It also offered resistance against TMV and caused normal growth of the test plant. Since the activity of cysteine proteinases is not involved in the TMV replication process, we speculated that inhibition of the hypersensitive response by celostatin may be due to the inactivation of proteolysis involved in the plant cell death programme, a phenomenon that has already been reported in animal systems.
A general one‐step method for the cloning of PCR products
Authors: Bolchi Angelo , Ottonello Simone , Petrucco Stefania
Published: December 2005

A very fast, highly efficient, versatile and low‐cost cloning of PCR products is described. PCR amplicons, obtained with any set of primers, is directly integrated into circular plasmid vectors by means of a one‐step restriction–ligation procedure. When using proof‐reading DNA polymerases, 100% cloning efficiency is easily achieved, implying that direct cloning into ‘final‐use’ vectors (i.e. avoiding any intermediate cloning step) is a feasible task. Albeit with a lower efficiency, the same procedure is also suitable for the cloning of PCR products generated by ‘non‐proof‐reading’ DNA polymerases. Furthermore, with a simple modification of the vector polylinker site, the present method can be easily adapted to the directional cloning of open‐reading‐frame‐encoding amplicons. This one‐step procedure thus couples high efficiency with high reliability and versatility, and lends itself as the method of choice for routine cloning of PCR products.
Purification of transferrin from Cohn supernatant I using ion‐exchange chromatography
Authors: McCann Karl B. , Hughes Ben , Wu John , Bertolini Joseph , Gomme Peter T.
Published: December 2005

The present paper describes an anion‐exchange chromatography method to separate iron‐free apo‐Tf (apo‐transferrin) from albumin and IgG in Cohn supernatant I. The method uses DEAE‐fast flow Sepharose chromatography along with optimized protein concentration (5%, w/v) and column operation conditions (40 g/l, conductivity <1.0 mS/cm) to resolve apo‐Tf from IgG and albumin. The single step purifies apo‐Tf to >90% and provides an efficient means to obtain commercial quantities of the protein.
Desferrioxamine release from gelatin‐based systems
Authors: Ulubayram Kezban , Kiziltay Aysel , Yilmaz Elvan , Hasirci Nesrin
Published: December 2005

The conventional treatment with regular red‐blood‐cell transfusions and simultaneous chelation of excess iron with DFO (desferrioxamine) improves quality of life of thalassaemic patients while increasing their rate of survival considerably. Although DFO is the main iron‐ chelating drug currently utilized, it has various drawbacks, including high cost, poor oral effectiveness, toxicity and short plasma half‐life. It has to be administered by slow, subcutaneous infusion during blood transfusion for 8–12 h at night, 5–7 nights a week, and this leads to a very poor patient compliance. In order to avoid frequent and uncomfortable infusions of DFO, application of controlled‐release systems might be alternative routes in the supportive treatment of thalassaemia. In the present study, GMs (gelatin microspheres) and GFs (gelatin films) were prepared by coacervation and casting methods respectively to develop controlled DFO‐release systems. Cross‐linking by glutaraldehyde and carbodi‐imide were performed to increase the stability of gelatin matrices. Microspheres and films prepared without the addition of cross‐linker degraded completely in 4 h. On the other hand, addition of cross‐linker extended this time from hours to weeks depending on the added amount. Therefore the amount of DFO released from microspheres in 7 days was found to be in the range 12–82%, whereas the amount permeated through the films in 5.0 h was found to be in the range 34–67%. GFs were elastic and demonstrated good mechanical properties. Films achieved 0.14–0.69 MPa tensile strength, with 0.12–1.29 MPa elastic modulus and 26.49–109.38% strain values at break point. These studies showed that gelatin‐based controlled‐release systems could be improved and could be good candidates for the production of long‐term DFO‐carrying systems.
Expression and characterization of human‐elastin‐repeat‐based temperature‐responsive protein polymers for biotechnological purposes
Authors: Bandiera Antonella , Taglienti Anna , Micali Fulvio , Pani Bianca , Tamaro Marisa , Crescenzi Vittorio , Manzini Giorgio
Published: December 2005

Rapid progress has been made in the design and synthesis of oligomers and polymers that emulate the properties of natural proteins. Molecular bioengineering offers the chance to design and produce artificial polymeric proteins with tailored polymeric properties. The elastin‐like polypeptides are a well‐defined family of polymers with noteworthy characteristic based on the VPGVG repeated motif of bovine elastin. In the human homologue, the most regular sequence is represented by the repetition of the VAPGVG hexapeptidic motif. On the basis of this sequence, a synthetic gene has been designed, cloned and expressed in Escherichia coli to obtain artificial protein polymers. The rapid one‐step in‐frame cloning of any biologically active sequence can be achieved directly in the expression vector, allowing further improvement of the potential of the resulting product.
Trafficking mechanism of water channel aquaporin‐2
Authors: Noda Yumi , Sasaki Sei
Published: December 2005

Targeted positioning of the water channel AQP2 (aquaporin‐2) strictly regulates body water homoeostasis. Trafficking of AQP2 to the apical membrane is critical for the reabsorption of water in renal collecting ducts. In addition to the cAMP‐mediated effect of vasopressin on AQP2 trafficking to the apical membrane, other signalling cascades can also induce this sorting. Recently, AQP2‐binding proteins which could regulate this trafficking have been discovered; SPA‐1 (signal‐induced proliferation‐associated gene‐1), a GAP (GTPase‐activating protein) for Rap1, and the cytoskeletal protein actin. This review summarizes recent advances related to the trafficking mechanisms of AQP2.
Once upon a time there was β‐catenin in cadherin‐mediated signalling
Authors: Gavard Julie , Mège René‐Marc
Published: December 2005

β‐Catenin was initially characterized as a protein interacting with the cadherin cytoplasmic tail and regulating cell—cell contacts and actin cytoskeleton interactions. Moreover, the gene coding for the Drosophila orthologue of β‐catenin, armadillo, was independently identified downstream of wingless in the segment‐polarity signalling pathway. In fact, β‐catenin/Armadillo turned out to be key mediators of the Wnt/Wingless pathways in vertebrates and invertebrates. β‐Catenin participates in both adhesion and signalling functions in a mutually exclusive manner; bound to cadherins at the plasma membrane or ‘unbound’ in cytosolic or nuclear complexes. This model had placed β‐catenin at the crossroads between cadherin and Wnt signalling, leading to the dogma of inhibition of β‐catenin signalling by cadherins.
Purkinje cell protein-2 (Pcp2) stimulates differentiation in PC12 cells by Gβγ-mediated activation of Ras and p38 MAPK
Authors: Guan Jiazhen , Luo Yuan , Denker Bradley M.
Published: December 2005

Purkinje cell protein-2 (Pcp2 or L7) is highly expressed in cerebellar Purkinje cells and retinal bipolar neurons and interacts with the Gαi/o family of G-proteins. Although the expression pattern of Pcp2 in the developing central nervous system suggests a role in differentiation, its function remains unknown. We established Tet-off inducible expression of Pcp2 in PC12 cells (rat pheochromocytoma cells) to determine whether Pcp2 regulates neuronal differentiation. Utilizing a polyclonal antibody, Pcp2 was localized in the cell body and throughout neurites of differentiated PC12 cells, similar to its localization in cerebellar Purkinje cells. Pcp2 expression in PC12 cells stimulated process formation (5-fold) and NGF (nerve growth factor)-stimulated neurite length (2-fold). Under basal conditions, Pcp2-PC12 cells demonstrated a 5-fold increase in Ras activation relative to non-induced PC12 cells and there was no change in extracellular-signal-regulated kinase 1/2 activity with Pcp2 expression. However, Pcp2 induction led to a >3-fold increase in basal p38 MAPK (mitogen-activated protein kinase) activity and the addition of NGF significantly stimulated both Ras and p38 MAPK in Pcp2-PC12 cells relative to the controls. Pretreatment of Pcp2-PC12 cells with the p38-specific inhibitor SB203580 blocked both the increased neurite formation and NGF-stimulated neurite growth. Pertussis toxin treatment had no effect on neurite growth in control cells, but completely blocked Pcp2-mediated increased neurite growth. Transient transfection of the β-adrenergic receptor kinase C-terminus to prevent signalling through Gβγ in Pcp2-PC12 cells also inhibited the Pcp2-induced phenotype and reduced the Pcp2-stimulated Ras activation. Taken together, these findings demonstrate that Pcp2 induces differentiation in PC12 cells, in part through Gβγ-mediated Ras and p38 MAPK activation and suggest the potential for similar signalling mechanisms in Purkinje cells.
Suppression of the pro-apoptotic function of cytochrome c by singlet oxygen via a haem redox state-independent mechanism
Authors: Suto Daisuke , Sato Kazuaki , Ohba Yoshihiro , Yoshimura Tetsuhiko , Fujii Junichi
Published: December 2005

Stimuli for apoptotic signalling typically induce release of cyt c (cytochrome c) from mitochondria. Cyt c then initiates the formation of the apoptosome, comprising Apaf-1 (apoptotic protease-activating factor 1), caspase-9 and other cofactors. The issue of whether the redox state of the haem in cyt c affects the initiation of the apoptotic pathway is currently a subject of debate. In a cell-free reconstitution system, we found that only oxidized cyt c was capable of activating the caspase cascade. Oxidized cyt c was reduced by the physiological reductants cysteine and glutathione, after which it was unable to activate the caspase cascade. It is thus likely that cyt c with oxidized haem is in a conformation capable of interaction with Apaf-1 and forming apoptosomes. When either oxidized or reduced cyt c was treated with submillimolar concentrations of endoperoxide, which affected less than 3% of the redox state of haem, the ability of the oxidized cyt c to activate the caspase cascade was abolished. Higher amounts of singlet oxygen were required to affect the optical spectral change of haem, suggesting that the suppressed pro-apoptotic function of oxidized cyt c is a mechanism that is separate from the redox state of haem. Oxidative protein modification of cyt c by singlet oxygen was evident, on the basis of elevated contents of carbonyl compounds. Our data suggest that singlet oxygen eliminates the pro-apoptotic ability of oxidized cyt c not via the reduction of haem, but via the modification of amino acid residues that are required for apoptosome formation.
Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway
Authors: Orton Richard J. , Sturm Oliver E. , Vyshemirsky Vladislav , Calder Muffy , Gilbert David R. , Kolch Walter
Published: December 2005

The MAPK (mitogen-activated protein kinase) pathway is one of the most important and intensively studied signalling pathways. It is at the heart of a molecular-signalling network that governs the growth, proliferation, differentiation and survival of many, if not all, cell types. It is de-regulated in various diseases, ranging from cancer to immunological, inflammatory and degenerative syndromes, and thus represents an important drug target. Over recent years, the computational or mathematical modelling of biological systems has become increasingly valuable, and there is now a wide variety of mathematical models of the MAPK pathway which have led to some novel insights and predictions as to how this system functions. In the present review we give an overview of the processes involved in modelling a biological system using the popular approach of ordinary differential equations. Focusing on the MAPK pathway, we introduce the features and functions of the pathway itself before comparing the available models and describing what new biological insights they have led to.
Identification of glucoselysine-6-phosphate deglycase, an enzyme involved in the metabolism of the fructation product glucoselysine
Authors: Wiame Elsa , Lamosa Pedro , Santos Helena , Van Schaftingen Emile
Published: December 2005

The metabolism of the glycation product fructose-ϵ-lysine in Escherichia coli involves its ATP-dependent phosphorylation by a specific kinase (FrlD), followed by the conversion of fructoselysine 6-phosphate into glucose 6-phosphate and lysine by fructoselysine-6-phosphate deglycase (FrlB), which is distantly related to the isomerase domain of glucosamine-6-phosphate synthase. As shown in the present work, several bacterial operons comprise: (1) a homologue of fructoselysine-6-phosphate deglycase; (2) a second homologue of the isomerase domain of glucosamine-6-phosphate synthase, more closely related to it; and (3) components of a novel phosphotransferase system, but no FrlD homologue. The FrlB homologue (GfrF) and the closer glucosamine-6-phosphate synthase homologue (GfrE) encoded by an Enterococcus faecium operon were expressed in E. coli and purified. Similar to FrlB, GfrF catalysed the reversible conversion of fructoselysine 6-phosphate into glucose 6-phosphate and lysine. When incubated with fructose 6-phosphate and elevated concentrations of lysine, GfrE catalysed the formation of a compound identified as 2-ϵ-lysino-2-deoxy-6-phospho-glucose (glucoselysine 6-phosphate) by NMR. GfrE also catalysed the reciprocal conversion, i.e. the formation of fructose 6-phosphate (but not glucose 6-phosphate) from glucoselysine 6-phosphate. The equilibrium constant of this reaction (0.8 M) suggests that the enzyme serves to degrade glucoselysine 6-phosphate. In conclusion, GfrF and GfrE serve to metabolize glycation products formed from lysine and glucose (fructoselysine) or fructose (glucoselysine), via their 6-phospho derivatives. The latter are presumably formed by the putative phosphotransferase system encoded by gfrA–gfrD. The designation gfr (glycation and fructation product degradation) is proposed for this operon. This is the first description of an enzyme participating in the metabolism of fructation products.
A novel regulation of IRS1 (insulin receptor substrate-1) expression following short term insulin administration
Authors: Ruiz-Alcaraz Antonio J. , Liu Hui-Kang , Cuthbertson Daniel J. , Mcmanus Edward J. , Akhtar Simeen , Lipina Christopher , Morris Andrew D. , Petrie John R. , Hundal Hari S. , Sutherland Calum
Published: December 2005

Reduced insulin-mediated glucose transport in skeletal muscle is a hallmark of the pathophysiology of T2DM (Type II diabetes mellitus). Impaired intracellular insulin signalling is implicated as a key underlying mechanism. Attention has focused on early signalling events such as defective tyrosine phosphorylation of IRS1 (insulin receptor substrate-1), a major target for the insulin receptor tyrosine kinase. This is required for normal induction of signalling pathways key to many of the metabolic actions of insulin. Conversely, increased serine/threonine phosphorylation of IRS1 following prolonged insulin exposure (or in obesity) reduces signalling capacity, partly by stimulating IRS1 degradation. We now show that IRS1 levels in human muscle are actually increased 3-fold following 1 h of hyperinsulinaemic euglycaemia. Similarly, transient induction of IRS1 (3-fold) in the liver or muscle of rodents occurs following feeding or insulin injection respectively. The induction by insulin is also observed in cell culture systems, although to a lesser degree, and is not due to reduced proteasomal targeting, increased protein synthesis or gene transcription. Elucidation of the mechanism by which insulin promotes IRS1 stability will permit characterization of the importance of this novel signalling event in insulin regulation of liver and muscle function. Impairment of this process would reduce IRS1 signalling capacity, thereby contributing to the development of hyperinsulinaemia/insulin resistance prior to the appearance of T2DM.
Combining fixed- and moving-grid methods to study direct dissociation processes involving nonadiabatic transitions
Authors: Gindensperger Etienne , Meier Christoph , Beswick J. Alberto , Parlant Gérard
Published: December 2005

We present a novel quantum-dynamics approach suitable for computing direct dissociation processes, including electronic transitions. This approach combines quantum trajectories in the Lagrangian reference frame with standard fixed-grid wave packets in order to overcome the limitations and difficulties of both techniques. As a model application, we consider the ultrafast photodissociation of H2 excited by a femtosecond extreme UV laser pulse.
The dynamics of solvation of an electron in the image potential state by a layer of polar adsorbates
Authors: Sebastian K. L. , Chakraborty Aniruddha , Tachiya M.
Published: December 2005

Recently, ultrafast two-photon photoemission has been used to study electron solvation at a two-dimensional metal∕polar adsorbate interfaces [A. Miller et al., Science 297, 1163 (2002)]. The electron is bound to the surface by the image interaction. Earlier we have suggested a theoretical description of the states of the electron interacting with a two-dimensional layer of the polar adsorbate [K. L. Sebastian et al., J. Chem. Phys. 119, 10350 (2003)]. In this paper we have analyzed the dynamics of electron solvation, assuming a trial wave function for the electron and the solvent polarization and then using the Dirac-Frenkel variational method to determine it. The electron is initially photoexcited to a delocalized state, which has a finite but large size, and causes the polar molecules to reorient. This reorientation acts back on the electron and causes its wave function to shrink, which will cause further reorientation of the polar molecules, and the process continues until the electron gets self-trapped. For reasonable values for the parameters, we are able to obtain fair agreement with the experimental observations.
Density-functional theory for fluid mixtures of charged chain particles and spherical counterions in contact with charged hard wall: Adsorption, double layer capacitance, and the point of zero charge
Authors: Pizio O. , Bucior K. , Patrykiejew A. , Sokołowski S.
Published: December 2005

We consider a density-functional theory to describe nonuniform fluids composed of chain molecules, containing a charged segment each, and spherical counterions. The chain molecules are modeled as freely jointed chains of hard spheres, the counterions are oppositely charged spheres of the same diameter as all segments of chain molecules. The theory is applied to study the structure of adsorbed layers, the excess adsorption isotherms, the capacitance of the double layer, and the potential of the zero charge. We show that all electric properties are strongly dependent on the length of the chain molecules. Moreover, these properties are also dependent on the position of the charged segment in the chain.
Heat capacity of water in nanopores
Authors: Tombari E. , Salvetti G. , Ferrari C. , Johari G. P.
Published: December 2005

Heat capacity of controlled amounts of water in Vycor’s 2nm radius pores has been determined in real time during the course of water’s isothermal nanoconfinement from bulk state at 358K, by using temperature-modulated calorimetry. As water transfers from bulk to nanopores via the vapor phase, its heat capacity per molecule increases asymptotically toward a limiting value of 1.4 times the heat capacity of bulk water for 1.8wt% water in Vycor and 1.04 times for 10.0wt%. The observations indicate that vibrational and configurational contributions to the heat capacity are highest when the amount of water is insufficient to completely cover the pore wall, and they decrease as more water is present in the nanopores and water clusters form. The heat capacity of water in completely filled nanopores approaches the value for bulk water, thus indicating that the heat capacity varies with the water molecules’ position in the nanopores.
The structure of ultrathin Langmuir-Blodgett films of cadmium behenate
Authors: Peng J. B. , Foran G. J. , Barnes G. T. , Gentle I. R.
Published: December 2005

Grazing incidence x-ray-diffraction investigations of the structures of Langmuir-Blodgett films of cadmium behenate with 1, 2, 3, 5, and 21 monolayers are reported. The single monolayer film, deposited on a hydrophilic substrate, showed a hexagonal structure, whereas the bilayer film, deposited on a hydrophobic substrate, had a rectangular structure with herringbone orientation of the acyl chains. With multilayer films formed on a hydrophilic substrate, it was possible to detect that the hexagonal structure of the first layer was retained when additional layers were deposited and that the additional layers had the same rectangular structure as the bilayer.
Determination of in-depth probe response function using spectral perturbation methods
Authors: Wan Keshu , Zhu Wenliang , Pezzotti Giuseppe
Published: December 2005

Two calibration methods, besides the conventional defocus method, have been presented to determine the in-depth probe response function (i.e., the function characterizing the spectral intensity distribution within the probe volume along the sample in-depth direction) in photostimulated spectroscopy. One method is based on “perturbing” the detected spectral probe of a selected band by varying the aperture of a confocal pinhole placed in the light path to the spectrometer; the other method is based on perturbing the spectral position of a selected band using an applied (equibiaxial) linear stress field, superimposed on the sample by means of a biaxial bending jig. Using the R1 band of a sapphire film, the validity of these two methods for determining the in-depth probe response function, and their reciprocal consistency are demonstrated. The calibration methods, which allow one to maintain unchanged the position of the focal plane within the sample, appear to work well for determining the in-depth probe response function of films, coatings, or highly transparent thin plates, where the laser probe size is close to the sample thickness, and thus, the defocus method is hardly applicable.
Properties of the plasma channel in liquid discharges inferred from cathode local temperature measurements
Authors: Revaz B. , Witz G. , Flükiger R.
Published: December 2005

The properties of the plasma channel at the cathode surface in a liquid discharge have been studied by means of temperature measurements and heat transfer numerical analysis. The studied discharge (current: 5 A; duration: 100μs; gap: 10μm) is typical of electrical discharge machining (EDM) in the semifinishing operation. The temperature information is obtained from two independent experiments: (1) microthermocouples patterned on the cathode, close to the discharge have been used to record the temperature variation caused by a single discharge with a high local resolution and large bandwidth; (2) the geometry of the resolidified layer, which gives the maximum extension of the melting point temperature isotherm, has been measured. These temperature data have then been compared to numerical simulation using inverse calculations allowing the experimental determination of two fundamental quantities of the discharge cathode interaction: (1) the power fraction transferred from the discharge to the sample, which was found to be close to 10% and (2) the exponent n of the power law expansion of the plasma channel rplasma∝tn, which is n=0.2. The validity of the present analysis relies on the fact that the experimental temperature information is obtained for different values of the parameter rplasma∕t02, where t02 is the characteristic time of the experiment.
Impact of grain sizes on phonon thermal conductivity of bulk thermoelectric materials
Authors: Zheng Xiao Jing , Zhu Linli , Zhou You-He , Zhang Qingjie
Published: December 2005

We report a phonon transport model for a bulk thermoelectric material to investigate the effect of the grain diameter and the grain-boundary thickness on its thermal conductivity. The analysis results display that the bulk thermal conductivity is significantly reduced by decreasing the grain sizes when the grain diameter is less than 500nm, which provides us one feasible way to enhance the figure of merit ZT of the material, and the thermal conductivity is mainly attributed to the contribution of grains, while the grain-boundary thermal conductivity has to be considered when the grain diameter is less than 100nm.
Light emission of metal halide lamps under micro- and hypergravity conditions
Authors: Stoffels W. W. , Kemps P. C. M. , Beckers J. , Kroesen G. M. W. , Haverlag M.
Published: December 2005

The wavelength-integrated light output from a metal halide discharge lamp is measured for gravity conditions varying from 0to1.8g during parabolic flights. The results show that the changing gravity affects the convection flow in the lamp, which in turn changes the total light output. For vertically burning lamps, the sign and magnitude of the effect can be predicted using the demixing parameter: the ratio of typical diffusion to convection times. In horizontally burning lamps at 0g, the absence of convective mixing results in a reduced light emission.
Coupling of PbS quantum dots to photonic crystal cavities at room temperature
Authors: Fushman Ilya , Englund Dirk , Vučković Jelena
Published: December 2005

We demonstrate the coupling of PbS quantum dot emission to photonic crystal cavities at room temperature. The cavities are defined in 33% Al, AlGaAs membranes on top of oxidized AlAs. Quantum dots were dissolved in poly(methylmethacrylate) and spun on top of the cavities. Quantum dot emission is shown to map out the structure resonances. This technique may prove to be viable sources for room temperature cavity coupled single photon generation for quantum information processing applications. Moreover, our results also indicate that such commercially available quantum dots can be used for passive structure characterization. The deposition technique is versatile and allows layers with different dot densities and emission wavelengths to be redeposited on the same chip.
Turbulent thermal convection at high Rayleigh numbers for a Boussinesq fluid of constant Prandtl number
Authors: Amati G. , Koal K. , Massaioli F. , Sreenivasan K. R. , Verzicco R.
Published: December 2005

The results from direct numerical simulations of turbulent Boussinesq convection are briefly presented. The flow is computed for a cylindrical cell of aspect ratio 1∕2 in order to compare with the results from recent experiments. The results span eight decades of Ra from 2×106 to 2×1014 and form the baseline data for a strictly Boussinesq fluid of constant Prandtl number (Pr=0.7). A conclusion is that the Nusselt number varies nearly as the 1∕3 power of Ra for about four decades towards the upper end of the Ra range covered.
High-reflectance III-nitride distributed Bragg reflectors grown on Si substrates
Authors: Mastro M. A. , Holm R. T. , Bassim N. D. , Eddy C. R. , Gaskill D. K. , Henry R. L. , Twigg M. E.
Published: December 2005

Distributed Bragg reflectors (DBRs) composed of an AlN∕AlGaN superlattice were grown of Si (111) substrates. The first high-reflectance III-nitride DBR on Si was achieved by growing the DBR directly on the Si substrate to enhance the overall reflectance due to the high index of refraction contrast at the Si∕AlN interface. For a 9× DBR, the measured peak reflectance of 96.8% actually exceeded the theoretical value of 96.1%. The AlN∕AlGaN superlattice served the added purpose of compensating for the large tensile strain developed during the growth of a crack-free 500nm GaN∕7× DBR/Si structure. This achievement opens the possibility to manufacture high-quality III-nitride optoelectronic devices without optical absorption in the opaque Si substrate.
Room-temperature operation of 3.26μm GaSb-based type-I lasers with quinternary AlGaInAsSb barriers
Authors: Grau M. , Lin C. , Dier O. , Lauer C. , Amann M.-C.
Published: December 2005

Quinternary AlGaInAsSb is introduced as a new barrier material for GaSb-based type-I laser diodes. For wavelengths beyond 3μm, this material improves the valence-band offset between GaInAsSb quantum wells and barriers as compared to standard GaInAsSb∕AlGaAsSb structures. The laser structures, which comprise three compressively strained GaInAsSb quantum wells and AlGaInAsSb barriers and waveguides, show good structural and optical quality. 3.26μm emission has been achieved with ridge waveguide lasers working in pulsed operation up to 50°C. With this emission wavelength, a strong absorption line of CH4 is accessible for gas absorption measurements.
Change in photovoltage due to an external magnetic field in a manganite-based heterojunction
Authors: Sheng Z. G. , Zhao B. C. , Song W. H. , Sun Y. P. , Sun J. R. , Shen B. G.
Published: December 2005

The effect of magnetic field on the photovoltaic effect (PVE) has been investigated for a manganite-based heterojunction composed of a La0.7Ce0.3MnO3 film and a 0.5 wt % Nb-doped SrTiO3 substrate. A linear decrease in the photovoltage (Voc) with magnetic fields is observed and the relative variation of Voc [defined as 1−Voc(H)∕Voc(0)] is larger than 10% under a field of 0.5 T at a temperature T=16.5K. There is a proportional relation between ΔVoc and the magnetoresistance of the heterojunction. We attribute the modulation of PVE to variation of magnetization and resistance of depletion layer by external magnetic fields.
High emission current density microwave-plasma-grown carbon nanotube arrays by postdepositional radio-frequency oxygen plasma treatment
Authors: Chen Z. , den Engelsen D. , Bachmann P. K. , van Elsbergen V. , Koehler I. , Merikhi J. , Wiechert D. U.
Published: December 2005

Highly stable field emission current densities of more than 6A∕cm2 along with scalable total field emission currents of ∼300μA per 70μm diameter carbon nanotube (CNT)-covered electron emitter dot are reported. Microwave-plasma chemical vapor deposition, along with a novel catalyst sandwich structure and postdepositional radio-frequency (rf) oxygen plasma treatment lead to well-structured vertically aligned CNTs with excellent and scalable emission properties. Scanning electron and transmission electron microscope investigations reveal that postdepositional treatment reduces not only the number but modifies the structure of the CNTs. Well-structured microwave-plasma-grown nanotubes become amorphous during rf oxygen plasma treatment and the measured work functions of CNTs change from 4.6eVto4.0eV before and after treatment, respectively. Our experiments outline a novel fabrication route for structured CNT arrays with improved and scalable field emission characteristics.
GaN blue photonic crystal membrane nanocavities
Authors: Choi Y.-S. , Hennessy K. , Sharma R. , Haberer E. , Gao Y. , DenBaars S. P. , Nakamura S. , Hu E. L. , Meier C.
Published: December 2005

GaN-based photonic-crystal membrane nanocavities with Q factors up to 800 have been realized at the wavelength of ∼480nm. The tuning behavior agrees well with numerical calculations using the finite-difference time-domain method. Theoretically, the lowest energy mode of a cavity that consists of seven missing holes in the Γ-K direction promises a Q factor as high as 4×104 with a mode volume of about 1.3×(λ∕n)3.
Observation and manipulation of subsurface hydride in Pd{111} and its effect on surface chemical, physical, and electronic properties
Authors: Sykes E. Charles H. , Fernández-Torres Luis C. , Nanayakkara Sanjini U. , Mantooth Brent A. , Nevin Ryan M. , Weiss Paul S.
Published: December 2005

We report the observation and manipulation of hydrogen atoms beneath the surface of a Pd{111} crystal by using low-temperature scanning tunneling microscopy. These subsurface hydride sites have been postulated to have critical roles in hydrogen storage, metal embrittlement, fuel cells, and catalytic reactions, but they have been neither observed directly nor selectively populated previously. We demonstrate that the subsurface region of Pd can be populated with hydrogen atoms from the bulk by applying voltage pulses from a scanning tunneling microscope tip. This phenomenon is explained with an inelastic excitation mechanism, whereby hydrogen atoms in the bulk are excited by tunneling electrons and are promoted to more stable sites in the subsurface region. We show that this selectively placed subsurface hydride affects the electronic, geometric, and chemical properties of the surface. Specifically, we observed the effects of hydride formation on surface deformation and charge and on adsorbed hydrogen on the surface. Hydrogen segregation and overlayer vacancy ordering on the Pd{111} have been characterized and explained in terms of the surface changes attributable to selective hydrogen occupation of subsurface hydride sites in Pd{111}.