bluuebunny/crossref_metadata_2025 huggingface dataset:
Salt intake and insulin sensitivity in healthy human volunteers
Authors: Townsend Raymond R. , Kapoor Shiv , McFadden Christopher B.
Published: July 2007

The literature on salt intake and insulin sensitivity presents a mixed picture, as some studies have shown an increase, whereas others have shown a decrease, in insulin action as sodium intake is enhanced. In some cases, this may relate to the study of salt intake in patients with co-morbidities such as hypertension or diabetes. In the present study, we selected healthy normotensive lean volunteers who underwent a euglycaemic clamp following 6 days of a low-salt diet (20 mmol sodium daily) and, subsequently, 6 days of a high-salt diet (200 mmol sodium daily). Our results show an increase in insulin-mediated glucose disposal during euglycaemic clamp conditions that was significantly higher following the high-salt diet compared with the low-salt diet (7.41±0.41 compared with 6.11±0.40 mg·kg−1 of body weight·min−1 respectively; P=0.03). We measured calf blood flow before and during insulin infusion (no significant change after the two dietary salt interventions was detected) and plasma non-esterified fatty acids (also no significant differences were detected). We observed the expected increases in renin concentration and aldosterone activity in subjects on the low-salt diet, and also observed a significantly less increase in plasma noradrenaline concentration during euglycaemic insulin infusion following the high-salt compared with the low-salt diet. We propose that the 4–5-fold increase in serum aldosterone and the greater increase in plasma noradrenaline concentration following the low-salt intervention compared with the high-salt period may have contributed to the differences in insulin sensitivity following the adjustment in dietary sodium intake.
A Comparison of Two Techniques for Wood Fibre Isolation ‐ Evaluation by Tensile Tests on Single Fibres with Different Microfibril Angle
Authors: Burgert I. , Keckes J. , Frühmann K. , Fratzl P. , Tschegg S. E.
Published: July 2007

Abstract: Fibres (tracheids) of spruce (Picea abies [L.] Karst.) were isolated by means of two isolation techniques. On the one hand, a soft chemical treatment with Jeffrey solution was used. The isolation was carried out with a reduced time of treatment (2 h), just to achieve the state where the fibres could be separated easily with tweezers. On the other hand, fibres were directly peeled out with tweezers, taking advantage of the low shear strength between them. Following this approach, a chemical treatment could be avoided completely. In order to compare the isolation techniques, single tracheids from tissue types with different microfibril angle (earlywood, latewood, juvenile wood, opposite wood, compression wood) were tested in the dry state. The microfibril angles were determined by X‐ray diffraction. Single tracheids handled with both isolation techniques were strained in microtensile tests and load‐strain diagrams were obtained. The chemically treated fibres were found to have much lower strength and stiffness compared to the mechanically isolated fibres, even though the influence of microfibril angle was still obvious for both kinds of treatment. The results clearly show the importance of single fibre extraction to preserve as much as possible the original properties.
The Role of Druse and Raphide Calcium Oxalate Crystals in Tissue Calcium Regulation in Pistia stratiotes Leaves
Authors: Volk G. M. , Lynch‐Holm V. J. , Kostman T. A. , Goss L. J. , Franceschi V. R.
Published: July 2007

Abstract: Ca oxalate crystal formation was examined in Pistia stratiotes L. leaves during excess Ca and Ca‐deficient conditions. Pistia produces druse crystal idioblasts in the adaxial mesophyll and raphide idioblasts in the abaxial aerenchyma. Raphide crystals were previously found to grow bidirectionally, and here we show that Ca is incorporated along the entire surfaces of developing druse crystals, which are coated with membrane‐bound microprojections. Leaves formed on plants grown on 0 Ca medium have fewer and smaller druse crystals than leaves formed under 5 mM Ca (“control”) conditions, while raphide crystal formation is completely inhibited. When plants were moved from 0 to 15 mM (“high”) Ca, the size and number of crystals in new leaves returned to (druse) or exceeded (raphide) control levels. High Ca also induced formation of druse, but not raphide, crystals in differentiating chlorenchyma cells. When plants were transferred from 15 mM Ca to 0 Ca, young druse crystals were preferentially partially dissolved. Oxalate oxidase, an enzyme that degrades oxalate, increased during Ca deficiency and was localized to the crystal surfaces. The more dynamic nature of druse crystals is not due to hydration form as both crystal types are shown to be monohydrate. Part of the difference may be because raphide idioblasts have developmental constraints that interfere with a more flexible response to changing Ca. These studies demonstrate that excess Ca can be stored as Ca oxalate, the Ca can be remobilized under certain conditions, and different forms of Ca oxalate have different roles in bulk Ca regulation.
Simplifying additivity problems using direct sum constructions
Authors: Fukuda Motohisa , Wolf Michael M.
Published: July 2007

We study the additivity problems for the classical capacity of quantum channels, the minimal output entropy, and its convex closure. We show for each of them that additivity for arbitrary pairs of channels holds if and only if it holds for arbitrary equal pairs, which in turn can be taken to be unital. In a similar sense, weak additivity is shown to imply strong additivity for any convex entanglement monotone. The implications are obtained by considering direct sums of channels (or states) for which we show how to obtain several information theoretic quantities from their values on the summands. This provides a simple and general tool for lifting additivity results.
Effect of different metal deposition methods on the growth behaviors of carbon nanotubes
Authors: Sohn Jung Inn , Ok Young-Woo , Seong Tae-Yeon , Lee Seonghoon
Published: July 2007

It is generally known that the catalyst particles promote tip or base growth of carbon nanotubes depending on the contact force between the catalyst particles and the substrate. We have investigated the correlation between the growth modes of vertically aligned carbon nanotubes (CNTs) and the adhesion of Ni catalyst particles to the Si substrates. It is shown that Ni films (10 nm thick) deposited by pulsed laser deposition (PLD) and electron beam evaporation are broken up into nanoparticles and/or islands when pretreated in NH3 gas ambient at 850 °C for 20 min. It is found that CNT growth on the PLD substrate proceeds by base growth mode, whereas CNT growth on the electron-beam evaporated substrate is operated by tip growth mode. The different CNT growth behaviors are explained in terms of the difference of the adhesion between the Ni catalyst particles and the substrate due to the different kinetic energy of depositing Ni particles.
Effect of ablated particle flux on MgO nanowire growth by pulsed laser deposition
Authors: Marcu Aurelian , Yanagida Takeshi , Nagashima Kazuki , Tanaka Hidekazu , Kawai Tomoji
Published: July 2007

Oxide nanowire growth using a pulsed laser deposition (PLD) is a promising process since this essentially allows incorporating a rich functionality of various transition metal oxides into nanowires via the heterostructures. Here we investigate the effect of ablated particle flux on magnesium oxide nanowire growth by PLD. When varying the distance between the ablated material and the substrate, the small variation in ablated particle flux generated by a different plume expansion time influences mainly the growth rate while keeping the growth regime. However, varying the laser energy changes not only the growth rate but also the growth regime. Below a critical value of the laser energy the surface morphology tends to show an island growth rather than a nanowire growth. We attribute the existence of such a threshold to the desorption process from the catalyst droplet.
Nonlinear effects in collision cascades and high energy shock waves during ta-C:H growth
Authors: Piazza F. , Resto O. , Morell G.
Published: July 2007

The surface topography of hydrogenated tetrahedral amorphous carbon (ta-C:H) is critical for various applications such as microelectromechanical devices, magnetic and optical storage devices, and medical implants. The surface topography of ta-C:H films deposited by distributed electron cyclotron resonance plasma from C2H2 gas precursor was investigated. The effects of pressure, together with ion flux and energy, are studied by atomic force microscopy in relation to the structural evolution of the films. The results are compared with the predictions of the Edward-Wilkinson model [Proc. R. Soc. London, Ser. A 44, 1039 (1966)] recently proposed to account for ta-C:H growth and with previous interpretations based on hypersonic shock waves. The random hillocks observed on the smooth surfaces of ta-C:H films deposited at high pressure are thought to result from the interference of high energy shock waves triggered by C4Hx+ ions that produce overlapping collision cascades and induce nonlinear effects.
Composites with tuned effective magnetic permeability
Authors: Amirkhizi Alireza V. , Nemat-Nasser Sia
Published: July 2007

Pendry et al. [J. B. Pendry, A. J. Holden, D. J. Robbins, and W. J. Stewart, IEEE Trans. Microwave Theory Tech. 47, 2075 (1999)] and Smith et al. [D. R. Smith, W. J. Padilla, D. C. Vier, S. C. Nemat-Nasser, and S. Schultz, Phys. Rev. Lett. 84, 4184 (2000)] have shown that the effective magnetic permeability, μ, of free space can be rendered negative over a certain frequency range by a periodic arrangement of very thin conductors with suitable magnetic resonance properties, the so-called split-ring resonators. Because of its rather bulky architecture, this structure does not lend itself to a proper integration into a reasonably thin real composite structural panel. To remedy this fundamental barrier, we invented a new magnetic resonator consisting of very thin folded plates that are suitably nested within one another to form folded-doubled resonators (FDRs) that can be integrated into an actual composite panel. Measurements, using a focused beam electromagnetic characterization system combined with time-domain numerical simulations of the reflection and transmission coefficients of such a composite slab have revealed that indeed the composite has a negative μ over a frequency range of about 9.1–9.35 GHz [S. Nemat-Nasser, S. C. Nemat-Nasser, T. A. Plaisted, A. Starr, and A. Vakil Amirkhizi, in Biomimetics: Biologically Inspired Technologies, edited by Y. Bar Cohen (CRC Press, Boca Raton, FL, 2006)]. Thus, it has become possible to construct a structural composite panel with negative index of refraction by simultaneously creating negative effective ε and μ [V. G. Veselago, Sov. Phys. Usp. 10, 509 (1968); R. A. Shelby, D. R. Smith, and S. Schultz, Science 292, 77 (2001); A. F. Starr, P. M. Rye, D. R. Smith, and S. Nemat-Nasser, Phys. Rev. B 70, 113102 (2004)].
Construction of a versatile ultralow temperature scanning tunneling microscope
Authors: Kambara H. , Matsui T. , Niimi Y. , Fukuyama Hiroshi
Published: July 2007

We constructed a dilution-refrigerator (DR)-based ultralow temperature scanning tunneling microscope (ULT-STM) which works at temperatures down to 30mK, in magnetic fields up to 6T and in ultrahigh vacuum (UHV). Besides these extreme operation conditions, this STM has several unique features not available in other DR-based ULT-STMs. One can load STM tips as well as samples with clean surfaces prepared in an UHV environment to a STM head keeping low temperature and UHV conditions. After then, the system can be cooled back to near the base temperature within 3h. Due to these capabilities, it has a variety of applications not only for cleavable materials but also for almost all conducting materials. The present ULT-STM has also an exceptionally high stability in the presence of magnetic field and even during field sweep. We describe details of its design, performance, and applications for low temperature physics.
Development and performance characterization of a new standard mercury manometer
Authors: Akram H. M. , Maqsood M. , Rashid Haris
Published: July 2007

A new standard mercury manometer has been developed to calibrate low vacuum gauges in the range from atmospheric pressure to 1mbar. It consists of a cistern that is a small stainless steel container used as mercury reservoir and also as the first Hg column connected to a long glass tube used as the second Hg column. Manometer scale covers the difference in Hg heights in two columns up to the length equivalent to 1000mbars. This is a novel low cost manometer with simple design, compact fabrication, better accuracy, easy operation, low vibration, and thermal stability. In order to evaluate the performance of the equipment, its generated pressures are compared with those of secondary standard, i.e., calibrated capacitance diaphragm gauge, giving the average correction factor 0.998. Different uncertainties of the generated pressures are discussed in detail along with the evaluation of correction factors. The relative uncertainty in the higher pressure side is found to be in the range of 10−4 which is within the limit (≈10−4).
Resistance to time-dependent deformation of nanoparticle/polymer composites
Authors: Yang Jinglei , Zhang Zhong , Friedrich Klaus , Schlarb Alois K.
Published: July 2007

Dimensional stability and structural reliability are major concerns for thermoplastics due to their nature of high mobility of polymer chains. Here the authors report the creep experiments on polypropylene filled with 1vol% TiO2 nanoparticles with diameter of 21 or 300nm at different load levels and temperatures, which show that the dimensional stability of the nanocomposites is significantly improved, especially by loading small sized nanoparticles. The creep strain and creep rate of nanoparticle-filled polypropylene are reduced by 46% and 80%, respectively, compared to those of the neat matrix. Additionally, creep lifetime is extended by 330% due to the addition of small nanoparticles.
Amplification of optical pulse sequences at a high repetition rate in a polymer slab waveguide
Authors: Amarasinghe D. , Ruseckas A. , Vasdekis A. E. , Turnbull G. A. , Samuel I. D. W.
Published: July 2007

Amplification of three short light pulses in a 140ps time window at 5kHz repetition rate has been demonstrated using a compact amplifier based on the conjugated polymer poly(9,9′-dioctylfluorene-co-benzothiadiazole). The amplifier was optically pumped and gratings were used to couple the signal into and out of the film. A gain of 22dB was observed for a signal pulse temporally aligned with the pump pulse in a 1mm waveguide. For a signal pulse delayed by 140ps, the maximum gain achieved was 14dB. The results are a step towards the use of polymer amplifiers in data communications.
Enhanced grain surface effect on magnetic properties of La0.5Gd0.2Sr0.3MnO3 nanoparticles: A comparison with bulk counterpart
Authors: Dey P. , Nath T. K. , Banerjee A.
Published: July 2007

Magnetization studies on La0.5Gd0.2Sr0.3MnO3 (LGSMO) nanoparticles (∼20nm) reveal superparamagnetic phase associated with this system and thereby contrasting from cluster glass (CG) phase of its bulk counterpart. Doping of Gd on La sites and its antiferromagnetic coupling with Mn lattices are expected to induce random magnetic disorder in the magnetic lattice of LGSMO system. Study reveals that random magnetic disorder, which results in CG phase in an otherwise long range ordered ferromagnetic host matrix of bulk, does not have similar significant effect when the uniformity of the host matrix reduces to nanosize. On the contrary, analysis brings out that magnetic properties of LGSMO nanoparticles are primarily decided by its nanodimension having physical size of ∼20nm, which yield single domain magnetic entities of dimension of ∼12nm surrounded by a magnetic dead layer of ∼4nm.
Amorphous ZnO transparent thin-film transistors fabricated by fully lithographic and etching processes
Authors: Hsieh Hsing-Hung , Wu Chung-Chih
Published: July 2007

Oxide-semiconductor-based thin-film transistors (TFTs), particularly the amorphous ones, are becoming an important emerging technology. Since oxide semiconductors easily form polycrystalline phases, usually more complicated oxide mixtures are needed for growing amorphous phases. In this letter, we report that by simply reducing the thickness, ZnO can be intentionally grown into the amorphous phase. Furthermore, both top-gate and bottom-gate amorphous ZnO TFTs of micrometer scales were effectively implemented using fully lithographic and etching processes. Rather high field-effect mobilities of 25 and 4cm2∕Vs and on∕off current ratios of >107 and >106 were achieved for top-gate and bottom-gate configurations, respectively.
Silicon-based light emitters fabricated by embedding Ge self-assembled quantum dots in microdisks
Authors: Xia J. S. , Nemoto K. , Ikegami Y. , Shiraki Y. , Usami N.
Published: July 2007

Silicon-based light emitters have been fabricated on silicon-on-insulator substrates by embedding Ge self-assembled quantum dots in microdisk resonators. Strong room-temperature resonant luminescence is observed from the microdisks under optical pumping. Photoluminescence from Ge quantum dots is significantly enhanced by the microdisk resonators. Different kinds of cavity modes, whispering-gallery modes, and Fabry-Pérot modes are observed in the wavelength range from 1.2to1.6μm for microdisks with different diameters.
Broadband efficient second harmonic generation in media with a short-range order
Authors: Sheng Yan , Dou Junhong , Ma Boqin , Cheng Bingying , Zhang Daozhong
Published: July 2007

The authors demonstrate broadband efficient quasiphase matched second harmonic generation (SHG) in nonlinear LiNbO3 crystals. The distribution of ferroelectric domains in a short-range order provides the possibility for broadband second harmonic generation in the visible range. This process is similar to the broadband SHG in random media, but it results in much higher conversion efficiency. The unique distribution of reciprocal vectors provided by the structural short-range order plays an important role in the enhancement. The achieved broadband SHG with high conversion efficiency will aid in the development of optics integration and multiple-channel devices.
Terahertz wave emission and detection using photoconductive antennas made on low-temperature-grown InGaAs with 1.56μm pulse excitation
Authors: Takazato A. , Kamakura M. , Matsui T. , Kitagawa J. , Kadoya Y.
Published: July 2007

Photoconductive antennas made on low-temperature-grown Be doped InxGa1−xAs (0.45⩽x⩽0.53) have been investigated focusing on the terahertz emission properties. In the antenna of x=0.45, the resistance as high as 3MΩ enabled us to increase the bias field up to 60kV∕cm, and the terahertz waves emitted from the antenna were significantly enhanced. In addition, terahertz waves with the spectral range over 2.5THz and the peak to noise ratio of 45dB were generated and detected using only 1.56μm pulses.
Most luminous supernova ever seen may be manifesting a new eruption mechanism
Authors: Schwarzschild Bertram
Published: July 2007

A supernova is conventionally taken to be a star’s death knell. For the very brightest supernovae, that presumption may well be wrong.
Engineering the energy levels in quantum dots leads to optical gain
Authors: Wilson Mark
Published: July 2007

The achievement charts a straightforward path to the first colloidal quantum-dot lasers.
From the archives: SCIENCE and the War on...
Authors: Crewe Albert V.
Published: July 2007

Scientists can and must take the initiative in helping society solve such problems as air and water pollution and crime. We need new instruments to measure pollution and new ways to reduce it. Because the crime rate is rising so rapidly, we require new methods of detection and deterrence.
Cartographic Anxiety and the Search for Regionality
Authors: Painter Joe
Published: July 2007

Despite the rise of relational and antiessentialist approaches to regional theory, many accounts of regionality continue to work with territorial conceptions of regions as bounded wholes or totalities. The author suggests that this tendency can be explained in part by the continuing effect of cartographic anxiety and Eurocentrism on dominant understandings of regionality. The paper examines the relationships between regional theory, different forms of totality and the cartographic impulse, and discusses possible reasons for the Eurocentric cast of some regional research. It concludes with a consideration of how regional theory might respond to cartographic anxiety and Eurocentrism.
Fertility and Spatial Mobility in the Life Course: Evidence from Austria
Authors: Kulu Hill
Published: July 2007

There is a growing body of literature looking at the interplay between an individual's residential and other careers in the life course. Previous research has mostly studied the impact of partnership and employment changes on spatial mobility. The author focuses on the effect of child-bearing on migrations and residential moves. The study is based on retrospective event-history data from Austria, to which intensity (or hazard) regression is applied. The analysis suggests, first, that the birth of a child triggers housing-related and environment-related residential relocations. These are mostly moves within a labour-market area, but there are also migrations from cities to rural areas. Second, growing family size significantly reduces couples' wishes to and chances of moving over long distances for a job. The event of first conception also induces moves related to partnership formation.
Modeling Urban Growth in Data-Sparse Environments: A New Approach
Authors: Fragkias Michail , Seto Karen C
Published: July 2007

Although there exist numerous urban growth models, most have significant data input requirements, limiting their utility in a developing-world context. Yet, it is precisely in the developing world where there is an urgent need for urban growth models and scenarios since most expected urban growth in the next two decades will occur in such countries. This paper describes a physical urban growth model that requires few, but widely available, spatially explicit data. Utilizing binary urban/nonurban maps generated by satellite imaging, our model can inform urban planners and policy makers about the most probable locations and periods of future urban land-use change. Using a discrete choice framework, the model employs a spatially explicit logistic regression analysis to evaluate probabilities of urban growth for a baseline period. It calibrates parameters, validates results, predicts urban land-use change and examines future growth scenarios. Future growth scenarios can be generated through the inclusion of land prohibited from development, transportation routes, or new planned urban developments. A novel and important element of the model is the incorporation of an explicit policy-making framework that captures and reduces model uncertainty (theory and specification uncertainties), effectively addressing problems of predictive bias; this framework also allows the user or policy maker to associate predictions with a loss function. The model is applied to three cities in southern China that have experienced dramatic urban land growth in the last two decades. From 1988 to 1999, urban land in the region increased by 451.6% or at an annual rate of approximately 16.5%. Results show that the model achieves 73% – 77% accuracy for different cities at 30 m and 60 m resolutions. Aggregating the predictions to the county/administrative district shows that prediction through thresholding underperforms in comparison to the technique of sample enumeration.
Making Sense of Mankind's Scholarly Knowledge and Expertise: Collecting, Interlinking, and Organizing What We Know and Different Approaches to Mapping (Network) Science
Authors: Börner Katy
Published: July 2007

In this paper I discuss and compare different approaches to collecting, interlinking, organizing, and making sense of scholarly knowledge and expertise in a comprehensive and timely fashion. ‘Comprehensive’ refers to the need for collecting and interlinking multilingual, multidisciplinary records from multiple sources such as publications, patents, grants, and others to truly capture all relevant knowledge. By ‘timely’ I want to emphasize that there has to be a way to integrate the most recent—that is, today's—publications with existing holdings of scholarly knowledge and expertise. I then discuss the advantages and limitations of using search engines to access, and text mining and data mining to help extract, meaning from mankind's wisdom. Next I suggest the usage of semantic association networks as a viable and complementary alternative for interlinking and making sense of scholarly knowledge and expertise. The second part of the paper exemplifies and contrasts three approaches that can be used to delineate and make sense of scholarly knowledge. The first approach uses questionnaire data, the second uses citation data from a major digital library, and the third uses personal bibliography files. These approaches are exemplified by mapping the emerging research area of network science. A particular focus is the identification of major experts, papers, and research areas and geospatial locations in which network science research is conducted. The paper concludes with a summary and outlook.
Revisiting the Hidden Transcript: Oral Tradition and Black Cultural Politics in the Colombian Pacific Coast Region
Authors: Oslender Ulrich
Published: July 2007

The role of oral traditions in the reconstruction and the politicisation of collective memory has widely been recognised in post-colonial theories. Yet, the concrete application of these oral traditions by subaltern groups in projects of cultural politics has often been an ambiguous and discontinuous process. Moreover, poststructural interventions on cultural politics in social movement research, while theorising culture as a collective and dynamic process that produces meaning and shapes social relations, only rarely look at specific cultural manifestations as a privileged site for examining the construction of a subaltern politics of resistance on the ground. In this paper, I argue for oral traditions to be considered as one such specific manifestation in a subaltern cultural politics. I will elaborate this argument drawing on James Scott's conceptual framework on the public and hidden transcripts of social interaction between dominant and subordinate social groups. Beyond the restricted meaning that Scott ascribes to the hidden transcript as dialectically related to contexts of domination, however, I will extend its meaning and significance by focusing on the processes of transition of certain offstage discourses and practices when they ‘storm the stage’ and become part of the public transcript. Empirically, I will show this to be the case of the changing dynamics of mobilising oral traditions among black communities in Colombia. Through a selection of poems, verse, and stories that I recorded among black populations in the Pacific coast region of this South American country, I will show how these poetic forms as offstage discourses (and hidden transcripts) challenge dominant representations of space and are increasingly mobilised as powerful political tools (and public transcripts) in the struggle for cultural and territorial rights. All quotes, interview transcripts, and poems from the original Spanish into English have been translated by myself.
Locally controlled inhibitory mechanisms are involved in eukaryotic GPCR-mediated chemosensing
Authors: Xu Xuehua , Meier-Schellersheim Martin , Yan Jianshe , Jin Tian
Published: July 2007

Gprotein–coupled receptor (GPCR) signaling mediates a balance of excitatory and inhibitory activities that regulate Dictyostelium chemosensing to cAMP. The molecular nature and kinetics of these inhibitors are unknown. We report that transient cAMP stimulations induce PIP3 responses without a refractory period, suggesting that GPCR-mediated inhibition accumulates and decays slowly. Moreover, exposure to cAMP gradients leads to asymmetric distribution of the inhibitory components. The gradients induce a stable accumulation of the PIP3 reporter PHCrac-GFP in the front of cells near the cAMP source. Rapid withdrawal of the gradient led to the reassociation of G protein subunits, and the return of the PIP3 phosphatase PTEN and PHCrac-GFP to their pre-stimulus distribution. Reapplication of cAMP stimulation produces a clear PHCrac-GFP translocation to the back but not to the front, indicating that a stronger inhibition is maintained in the front of a polarized cell. Our study demonstrates a novel spatiotemporal feature of currently unknown inhibitory mechanisms acting locally on the PI3K activation pathway.
Deficiency in glutamine but not glucose induces MYC-dependent apoptosis in human cells
Authors: Yuneva Mariia , Zamboni Nicola , Oefner Peter , Sachidanandam Ravi , Lazebnik Yuri
Published: July 2007

The idea that conversion of glucose to ATP is an attractive target for cancer therapy has been supported in part by the observation that glucose deprivation induces apoptosis in rodent cells transduced with the proto-oncogene MYC, but not in the parental line. Here, we found that depletion of glucose killed normal human cells irrespective of induced MYC activity and by a mechanism different from apoptosis. However, depletion of glutamine, another major nutrient consumed by cancer cells, induced apoptosis depending on MYC activity. This apoptosis was preceded by depletion of the Krebs cycle intermediates, was prevented by two Krebs cycle substrates, but was unrelated to ATP synthesis or several other reported consequences of glutamine starvation. Our results suggest that the fate of normal human cells should be considered in evaluating nutrient deprivation as a strategy for cancer therapy, and that understanding how glutamine metabolism is linked to cell viability might provide new approaches for treatment of cancer.
Molecular epidemiology identifies only a single rabies virus variant circulating in complex carnivore communities of the Serengeti
Authors: Lembo T , Haydon D.T , Velasco-Villa A , Rupprecht C.E , Packer C , Brandão P.E , Kuzmin I.V , Fooks A.R , Barrat J , Cleaveland S
Published: July 2007

Understanding the transmission dynamics of generalist pathogens that infect multiple host species is essential for their effective control. Only by identifying those host populations that are critical to the permanent maintenance of the pathogen, as opposed to populations in which outbreaks are the result of ‘spillover’ infections, can control measures be appropriately directed. Rabies virus is capable of infecting a wide range of host species, but in many ecosystems, particular variants circulate among only a limited range of potential host populations. The Serengeti ecosystem (in northwestern Tanzania) supports a complex community of wild carnivores that are threatened by generalist pathogens that also circulate in domestic dog populations surrounding the park boundaries. While the combined assemblage of host species appears capable of permanently maintaining rabies in the ecosystem, little is known about the patterns of circulation within and between these host populations. Here we use molecular phylogenetics to test whether distinct virus–host associations occur in this species-rich carnivore community. Our analysis identifies a single major variant belonging to the group of southern Africa canid-associated viruses (Africa 1b) to be circulating within this ecosystem, and no evidence for species-specific grouping. A statistical parsimony analysis of nucleoprotein and glycoprotein gene sequence data is consistent with both within- and between-species transmission events. While likely differential sampling effort between host species precludes a definitive inference, the results are most consistent with dogs comprising the reservoir of rabies and emphasize the importance of applying control efforts in dog populations.
Promoting transcriptome diversity
Authors: L. Strausberg Robert , Levy Samuel
Published: July 2007

Although the number of protein-encoding human genes is more limited than many had estimated, the human transcript repertoire is much more diverse than anticipated. In part, transcript diversity is generated through the use of alternative promoters and alternate splicing. In addition, based on discoveries using technologies such as full-length cDNA libraries and whole genome tiling microarrays, it is now likely that non-protein-encoding transcripts comprise a substantial fraction of the human RNA population. Much attention is currently focused on understanding the role of alternative promoters in generating transcript diversity, both for non-protein-encoding (ncRNAs) and protein-encoding RNAs.
Recommended Steps for a FASTA Search
Authors: Mount David W.
Published: July 2007

INTRODUCTION

The following strategy is recommended for searches with FASTA for finding the most homologous sequences in a database search while avoiding false-negative matches.
Steps Used by the BLAST Algorithm: Figure 2.
Authors: Mount David W.
Published: July 2007

INTRODUCTION

The BLAST algorithm performs DNA and protein sequence similarity searches by an algorithm that is faster than FASTA but considered to be equally as sensitive. BLAST is very popular due to availability of the program on the World Wide Web through a large server at the National Center for Biotechnology Information (NCBI) and at many other sites. The BLAST algorithm has evolved to provide a set of very powerful search tools for the molecular biologist that are freely available to run on many computer platforms. This article provides a list of steps that describe how the BLAST algorithm searches a sequence database.
Cre Recombinase Gene Transfer In Vitro and Detection of loxP-Dependent Recombination: Figure 1.
Authors: Ohtsubo Kazuaki , Marth Jamey D.
Published: July 2007

INTRODUCTION

Altering the genome of intact cells and organisms by site-specific DNA recombination has become an important gene-transfer methodology. The inclusion of exogenous recombinase target sequences within transferred DNA segments allows subsequent modifications to previously altered genomic structure that increase the utility of gene transfer and enhance experimental design. In this protocol, correctly targeted mouse embryonic stem (ES) cell clones bearing the F[tkneo] allele (containing several loxP sites) are subjected to in vitro Cre gene transfer to generate ES cell subclones bearing either Type 1 (Δ) or Type 2 (F) alleles. Type 2 ES cells are used to generate chimeric mice that are then crossed to germ-line Cre-expressing mice, such as ZP3-Cre transgenic mates. The additional time needed to breed the mice (~2-3 mo) is typically less troublesome than the cost and effort of maintaining multiple clone-derived lines of mice.
Imaging Retinotectal Synaptic Connectivity
Authors: Cohen-Cory Susana
Published: July 2007

INTRODUCTION

This protocol describes a method for imaging synaptic sites in individual axon or dendritic terminals in live, developing embryos. By selectively targeting expression of green fluorescent protein (GFP)-tagged pre- and post-synaptic proteins to developing neurons in vivo, it is possible to visualize synaptic sites and to correlate their distribution and dynamics with changes in the morphology of axon or dendritic arbors labeled with a red fluorescent molecule. The techniques described here may be applied to almost any neuronal circuit or neuron type, as long as the embryonic tissues are accessible for transfection and the neurons of interest are located at a depth that is within the working distance of the objective. These techniques have been optimized for Xenopus embryos, but they are applicable to other vertebrate systems such as zebrafish and chick embryos.
Maize Tissue Preparation and Extraction of RNA from Target Cells for Genotyping
Authors: Ohtsu Kazuhiro , Schnable Patrick S.
Published: July 2007

INTRODUCTION

The use of RNA for genotyping analysis can be advantageous because transcriptomes are significantly smaller than genomes and typically contain far fewer repetitive sequences. Laser capture microdissection (LCM) has been used successfully to isolate sequences (especially rare transcripts) that accumulate in specific tissues. Where the quantity of isolated material is limiting, amplification can be used to increase the amount of product. Upon conversion to cDNA, the product serves as template for 454 sequencing to produce expressed sequence tags for subsequent SNP analysis and detection.

This protocol describes the preparation of acetone-fixed and paraffin-embedded maize seedling tissue sections. Once the sections are prepared, the PALM MicroBeam System, with its Laser Microdissection and Pressure Catapulting (LMPC) technology, is used to cut out cells of interest and “catapult” isolated tissues into collection caps. This tissue can then be used for RNA extraction.
SNP Mining from Maize 454 EST Sequences
Authors: Barbazuk W. Brad , Emrich Scott , Schnable Patrick S.
Published: July 2007

INTRODUCTION

In this protocol, 454 expressed sequence tags (ESTs) are generated by sequencing shoot apical meristem (SAM) cDNA from maize inbred lines on the 454 Life Sciences GS-20 sequencing system. The computational tool PolyBayes (Marth et al. 1999) is then used to identify single-nucleotide polymorphisms (SNPs). PolyBayes has been used successfully to identify SNPs in many different systems, including maize, and is particularly recommended for identifying SNPs in 454 sequences.
Single-Neuron Labeling Using the Genetic MARCM Method
Authors: Luo Liqun
Published: July 2007

INTRODUCTION

Our brain is composed of hundreds of billions of neurons, each of which has an elaborate shape and a complex pattern of connections. To untangle this complexity, it is often useful to visualize one neuron at a time. This protocol describes single-neuron labeling using the MARCM system (Mosaic Analysis with a Repressible Cell Marker). The system was developed in Drosophila, but could, in principle, also work in other genetic model organisms such as Caenorhabditis elegans, zebrafish, or mice.
Construction of a Heated Incubation Chamber around a Microscope Stage for Time-Lapse Imaging: Figure 1.
Authors: Kulesa Paul M. , Kasemeier-Kulesa Jennifer C.
Published: July 2007

INTRODUCTION

Intravital imaging of embryogenesis has the potential to provide valuable information on cell proliferation, cell shape changes, and cell migratory behaviors. However, most embryo model systems require a temperature-controlled environment. Several expensive commercially available temperature control devices have emerged, including microscope stages surrounded by custom-fit Plexiglas boxes, heated plates for culture dishes, and objective warmers for water-immersion lenses, that strictly control temperature and, in some cases, help control local gas mixtures. This protocol describes an easy-to-assemble, cost-effective, custom-made cardboard box and incubator, adaptable to each user’s specifications and microscope set-up. The cardboard box fits around the microscope, primarily the stage area, to assist in maintaining a prescribed temperature near the microscope stage. Warmed air, blown into the box enclosure from an incubator, circulates around the stage. The heated incubation box maintains a set temperature with minimal fluctuations and has been tested and utilized for studies of chick, mouse, and zebrafish embryogenesis.
Strategies for Sequence Similarity Database Searches
Authors: Mount David W.
Published: July 2007

INTRODUCTION

Database similarity search programs tend to produce large volumes of output. It can become difficult to screen this volume of material and to assess whether the more remotely related sequences are really related to the query sequence. Thus, it is important to limit the sequence output; there are some relatively simple procedures that may be followed for each program, as described in this article. For searches of protein databases, avoid repetitive alignments with the same sequence by limiting searches to the protein sequence databases that are well curated, such as SwissProt and PIR, or to a specific genome, as opposed to the entire set of translated GenBank sequences (the GenPept database).
Using the Basic Local Alignment Search Tool (BLAST)
Authors: Mount David W.
Published: July 2007

INTRODUCTION

The BLAST algorithm was developed as a way to perform DNA and protein sequence similarity searches by an algorithm that is faster than FASTA but considered to be equally as sensitive. Both of these methods follow a heuristic (tried-and-true) method that almost always works to find related sequences in a database search, but does not have the underlying guarantee of an optimal solution like the dynamic programming algorithm. FASTA finds short common patterns in query and database sequences and joins these into an alignment. BLAST is similar to FASTA, but gains a further increase in speed by searching only for rarer, more significant patterns in nucleic acid and protein sequences. BLAST is very popular due to its availability on the World Wide Web through a large server at the National Center for Biotechnology Information (NCBI) and at many other sites. The BLAST algorithm has evolved to provide molecular biologists with a set of very powerful search tools that are freely available to run on many computer platforms. This article is intended to be a “user’s guide” to the principles underlying BLAST.
Ethics Education
Authors: Lipman Hannah I.
Published: July 2007

Dr Lipman invites your submissions of case reports for analysis and discussion in future columns and/or your submission of papers detailing ethics educational initiatives; submissions may be made at www.lejacq.com/submit—Nanette Wenger, MD, Editor in Chief.
Heart Failure in the “Oldest Old”: Clinical and Echocardiographic Insights
Authors: Bouchard Joseph L. , Aurigemma Gerard P. , Goldberg Robert J. , Fournier John B. , Vinch Craig S. , Hill Jeffrey C. , Ennis Cynthia A. , Tighe Dennis A. , Meyer Theo E.
Published: July 2007

While the incidence and prevalence of heart failure (HF) increase markedly with age, few studies have included data on a large series of patients aged 85 years and older. Clinical and echocardiographic data from 533 patients admitted to a tertiary care hospital for acute HF were obtained. Data from the oldest old (≥85 years; n=252; mean age, 91.9±3.6 years) were compared with data from those aged 65 to 74 years (n=123; mean age, 70.1±2.8 years) and 75 to 84 years (n=158; mean age, 79.4±2.9 years). Echocardiographic data were consistent with hypertensive remodeling. The proportion of patients with HF and a preserved left ventricular ejection fraction was greatest in the oldest patients (61%) in comparison to patients aged 65 to 74 years (48%) and 75 to 84 years (48%). Approximately three‐fourths of the oldest patients were women, and two‐thirds of women had a left ventricular ejection fraction ≥50%.
Safety and Efficacy of Extended‐Release Ranolazine in Patients Aged 70 Years or Older With Chronic Stable Angina Pectoris
Authors: Rich Michael W. , Crager Michael , McKay Charles R.
Published: July 2007

This analysis examined the safety and efficacy of extended‐release ranolazine among patients aged 70 years or older (n=363) compared with patients younger than 70 years (n=1024) enrolled in 2 large multinational prospective clinical trials. The primary end points were exercise capacity and number of weekly angina episodes. Beneficial effects of ranolazine, relative to placebo, were generally similar for each of these outcomes among older and younger participants. For example, at a ranolazine dose of 1000 mg bid, mean exercise duration increased by 19.8±13.1 seconds (mean ± SE) relative to placebo in patients younger than 70 years and by 32.4±19.7 seconds relative to placebo in patients 70 years or older. Adverse effects were more common in older than in younger patients, but the incidence of serious adverse effects attributable to ranolazine did not differ significantly between age groups. Outcomes were also similar at dosages of either 750 mg or 1000 mg bid. In conclusion, pooled data from 2 large randomized trials indicate that the efficacy of ranolazine is similar in older and younger patients but that adverse effects are more common in the elderly.
Changes of endocrine function of adipose tissue in anorexia nervosa: comparison of circulating levels versus subcutaneous mRNA expression
Authors: Dolezalova Radka , Lacinova Zdena , Dolinkova Marketa , Kleiblova Petra , Haluzikova Denisa , Housa Daniel , Papezova Hana , Haluzik Martin
Published: July 2007

Objective  To study the influence of chronic malnutrition in patients with anorexia nervosa on endocrine function of adipose tissue on both circulating and subcutaneous fat mRNA expression level.

Patients and design  A total of 12 patients with anorexia nervosa and 18 normal weight age‐matched women underwent anthropometric examination, single blood drawing and subcutaneous adipose tissue biopsy.

Measurements  Serum concentrations of high‐sensitive CRP (hsCRP), leptin, soluble leptin receptor, adiponectin, resistin, interleukin‐6 and insulin were measured by Luminex, enzyme‐linked immunosorbent assay (ELISA) and radioimmunoassay (RIA) kits. Subcutaneous adipose tissue mRNA expression of the same adipokines, adiponectin receptors 1 and 2 and immunocompetent cells marker CD68 was measured by real‐time polymerase chain reaction (PCR).

Results  Decreased body fat content of patients with anorexia nervosa was accompanied by reduced hsCRP, leptin and increased adiponectin and soluble leptin receptor. Resistin, interleukin‐6 and insulin levels did not differ from those of the control group. Fat mRNA adiponectin, leptin, interleukin‐6 and CD68 expression was reduced, resistin mRNA expression was increased and adiponectin receptor 1 and 2 expression were unchanged as compared to the control group.

Conclusions  Local perturbations in resistin, adiponectin and interleukin‐6 mRNA expression in subcutaneous adipose tissue are not reflected by its circulating levels. These changes could be involved in some local metabolic disturbances in subcutaneous adipose tissue of anorexia nervosa patients.
CXCR6 is expressed on T cells in both T helper type 1 (Th1) inflammation and allergen‐induced Th2 lung inflammation but is only a weak mediator of chemotaxis
Authors: Latta Markus , Mohan Karkada , Issekutz Thomas B.
Published: July 2007

Summary Numerous chemokine receptors are increased in number on T cells in inflamed tissues. Our objective was to examine CXCR6 expression on lymphocytes during immune and inflammatory reactions and its potential for mediating T‐cell recruitment. The cDNA for rat CXCR6 was cloned and monoclonal antibodies (mAbs) to CXCR6 were developed. CXCR6 was present on 4–6% of CD4 and CD8 T cells in blood, normal lymph nodes (LNs) and the spleen, primarily on memory T cells. In vitro antigen re‐stimulation of LN T cells from animals with autoimmune arthritis and experimental autoimmune encephalomyelitis (EAE) increased the proportion of CXCR6+ T cells to 35–50% and anti‐T‐cell receptor (TCR) activation to 60–80%. In vivo, after antigen challenge of LNs there was only a small increase in CXCR6+ T cells on the lymphoblasts in the LNs, and a much higher percentage of T cells were CXCR6+ in virus‐induced peritoneal exudates (∼47%) and in allergen‐induced lung inflammation (33%). Chemotaxis of CXCR6‐expressing inflammatory T cells to CXCL16 was poor, but that to CXCL10 was robust. We conclude that few T cells in normal and antigen‐challenged LNs are CXCR6+, whereas a high proportion of in vitro activated T cells and T cells from inflammatory sites are CXCR6+, but these cells migrate poorly to CXCL16. This suggests that CXCR6 may contribute to T‐cell positioning and activation, rather than recruitment. CXCR6 is also expressed on T cells not only in T helper type 1 (Th1) inflammation (arthritis and EAE) but also, as shown here, in Th2 inflammation, where it is increased after allergen challenge.