bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of polarization force and fast electrons on DA shock waves in a strongly coupled dusty plasma
Authors: PERVIN S. , DUHA S. S. , ASADUZZAMAN M. , MAMUN A. A.
Published: August 2012

A strongly coupled dusty plasma system consisting of non-thermal electrons, Maxwellian ions, and negatively charged dust in presence of polarization force has been considered. The nonlinear propagation of dust-acoustic shock waves in such a dusty plasma system has been theoretically investigated by employing the reductive perturbation method. The effects of the polarization force and non-thermal electrons, on the properties of these dust-acoustic shock waves are briefly discussed. It is shown that the strong correlation among the charged dust grains is a source of dissipation, and is responsible for the formation of the dust-acoustic shock waves. It has been found that the effects of polarization force and non-thermal electrons significantly modify the basic features of such shock waves. It has been proposed to design a new laboratory experiment, which will be able to identify the basic features of the dust-acoustic shock waves predicted in this present investigation.
Risk factors associated with surgical site infections following vascular surgery at a German university hospital
Authors: OTT E. , BANGE F.-Ch. , SOHR D. , TEEBKEN O. , MATTNER F.
Published: August 2012

Surgical site infection (SSI) after vascular surgery is a serious complication increasing morbidity, mortality, and costs for healthcare systems. A 4-year retrospective cohort study was performed in a university hospital with patients who had undergone arterial vascular surgery below the aortic arch. Investigated variables included demographics and clinical data. Forty-four of 756 patients experienced SSI, 29 of which were superficial, five were deep, and 10 had organ/space infections. Coagulase-negative staphylococci (22%), enterococci (20%), and Staphylococcus aureus (18%) were the most common pathogens. Independent risk factors for SSIs were femoral grafting [odds ratio (OR) 6·7], peripheral atherosclerotic disease, Fontaine stages III–IV (OR 4·1), postoperative drainage >5 days (OR 3·6), immunosuppression (OR 2·8), duration of operation >214 min (OR 2·8), and body mass index >29 (OR 2·6). The application of perioperative antibiotic prophylaxis was an independent protective factor (OR 0·2). Patients with certain risk factors for SSIs warrant special attention for infection prevention.
Measurement and Inference in Wine Tasting
Authors: Quandt Richard E.
Published: August 2012

The paper has three basic objectives: (1) to discuss and analyze the subtleties of ranking wines in blind tastings, (2) to analyze the degree of agreement or disagreement among the tasters (judges) and (3) to shed some light on the problem of identifying the wines and to determine when the identifications of the judges might be called statistically significant. The first issue utilizes the rank sums or the related measure, “votes against,” and discusses the appropriateness of a statistical test introduced by Kramer. The second introduces Kendall's W coefficient of concordance and discusses some other, related measures. The third derives the finite sample distribution of the number of correct identifications under the null hypothesis of random identifications, from which critical values can be obtained, both for the case in which each wine has to be identified exactly and the case in which there is a small number of different types of wine that have to be identified. (JEL Classification numbers: C12, C15, C49, C59)
Merkmale von Alkoholklienten der ambulanten Suchthilfe in Selbsthilfegruppen
Authors: Fuchs Walter , Kuhn Silke , Martens Marcus-Sebastian , Verthein Uwe
Published: August 2012

Fragestellung: Die Arbeit untersucht, ob sich alkoholabhängige Klienten, die zusätzlich zur ambulanten Betreuung in der professionellen Suchthilfe Selbsthilfegruppen aufsuchen, von solchen Klienten unterscheiden, die das nicht tun. Methodik: Es wurde ein Datensatz der Hamburger Basisdatendokumentation der ambulanten Suchthilfe (BADO) – die eine zeitliche Verlaufsbetrachtung ermöglicht – analysiert. Ergebnisse: Klienten, die neben der ambulanten Suchthilfe an Selbsthilfegruppen teilnehmen, sind sowohl zu Beginn als auch zu Ende der Betreuungsepisode häufiger abstinent. Obwohl sie über günstigere psychosoziale Ressourcen als solche Klienten verfügen, die das nicht tun, berichten sie häufiger über traumatische sexuelle Gewalterfahrungen. An Selbsthilfegruppen teilnehmende Klienten leiden seltener unter Schlafstörungen. Alkoholabhängige in der ambulanten Suchthilfe, die über einen längeren Zeitraum hinweg Selbsthilfegruppen aufgesucht haben, leiden schließlich seltener unter Leberschäden. Schlussfolgerung: Alkoholklienten, die neben ihrer ambulanten Betreuung Selbsthilfegruppen aufsuchen, weisen mehr Ressourcen und einen besseren Verlauf auf. Dies mag auf Wirkungen der Selbsthilfegruppe als ergänzende Hilfe oder auf Selektionseffekte zurückgehen.
Evolution of the global wind wave climate in CMIP5 experiments
Authors: Dobrynin M. , Murawsky J. , Yang S.
Published: August 2012

Ocean wind waves follow shifts in atmospheric circulation and wind regimes caused by climate change and variability. We use a wave model (WAM) forced by winds from an Earth system model (EC‐Earth) to study the evolution of global wave climate in terms of trends in wind speed and wave height, their rates and anomalies over the 250 years. Historical period and future scenarios (RCP8.5 and RCP4.5) are calculated within the fifth phase of the Coupled Model Intercomparison Project. Both scenarios indicate a future increase of wind speed and wave height in the Arctic and Southern Ocean and a decrease in the Pacific Ocean. Some regions, e.g., the North Atlantic show a change of sign from currently positive to negative trends in this century. Swell dominated regions, connected to the Southern Ocean show opposite trends for winds and waves. Calculated trends are evaluated taking into account natural variability estimated from a simulation with pre–industrial climate. We conclude that projected wave heights are still within natural variability, whereas wind speed exceeds it in the Arctic and Southern Ocean. Probability estimates show that extreme winds and waves become more dominant in the Southern Hemisphere, Arctic and Indian Ocean. Low and medium winds and waves are highly probable in the North and Equatorial Atlantic and Pacific.
Turbulence and high‐frequency variability in a deep gravity current outflow
Authors: Nash Jonathan D. , Peters Hartmut , Kelly Samuel M. , Pelegrí Josep L. , Emelianov Mikhail , Gasser Marc
Published: August 2012

Intensive sampling of the deep Mediterranean outflow 70 km W of the Strait of Gibraltar reveals a strong, tidally modulated gravity current embedded with large‐amplitude oscillations and energetic turbulence. The flow appears to be hydraulically controlled at a small topographic constriction, with turbulence and internal waves varying together and increasing dramatically downstream of the choke point. These data suggest that a significant fraction of energy dissipation, mixing, and entrainment stress in gravity currents may occur in localized regions controlled by time‐varying flow interactions with fine‐scale topography. These findings highlight the important role of processes that are not resolved by global climate models (GCMs), which do not contain tides or mixing due to fine‐scale topographic interactions.
Fast and slow responses of the South Asian monsoon system to anthropogenic aerosols
Authors: Ganguly Dilip , Rasch Philip J. , Wang Hailong , Yoon Jin‐ho
Published: August 2012

Using a global climate model with fully predictive aerosol life cycle, we investigate the fast and slow responses of the South Asian monsoon system to anthropogenic aerosol forcing. Our results show that the feedbacks associated with sea surface temperature (SST) change caused by aerosols play a more important role than the aerosol's direct impact on radiation, clouds and land surface (rapid adjustments) in shaping the total equilibrium climate response of the monsoon system to aerosol forcing. Inhomogeneous SST cooling caused by anthropogenic aerosols eventually reduces the meridional tropospheric temperature gradient and the easterly shear of zonal winds over the region, slowing down the local Hadley cell circulation, decreasing the northward moisture transport, and causing a reduction in precipitation over South Asia. Although total responses in precipitation are closer to the slow responses in general, the fast component dominates over land areas north of 25°N. Our results also show an east‐west asymmetry in the fast responses to anthropogenic aerosols causing increases in precipitation west of 80°E but decreases east of it.
Measurements of 18O18O and 17O18O in the atmosphere and the role of isotope‐exchange reactions
Authors: Yeung Laurence Y. , Young Edward D. , Schauble Edwin A.
Published: August 2012

Of the six stable isotopic variants of O2, only three are measured routinely. Observations of natural variations in 16O18O/16O16O and 16O17O/16O16O ratios have led to insights in atmospheric, oceanographic, and paleoclimate research. Complementary measurements of the exceedingly rare 18O18O and 17O18O isotopic variants might therefore broaden our understanding of oxygen cycling. Here we describe a method to measure natural variations in these multiply substituted isotopologues of O2. Its accuracy is demonstrated by measuring isotopic effects for Knudsen diffusion and O2 electrolysis in the laboratory that are consistent with theoretical predictions. We then report the first measurements of 18O18O and 17O18O proportions relative to the stochastic distribution of isotopes (i.e., Δ36 and Δ35 values, respectively) in tropospheric air. Measured enrichments in 18O18O and 17O18O yield Δ36 = 2.05 ± 0.24‰ and Δ35 = 1.4 ± 0.5‰ (2σ). Based on the results of our electrolysis experiment, we suggest that autocatalytic O(3P) + O2 isotope exchange reactions play an important role in regulating the distribution of 18O18O and 17O18O in air. We constructed a box model of the atmosphere and biosphere that includes the effects of these isotope exchange reactions, and we find that the biosphere exerts only a minor influence on atmospheric Δ36 and Δ35 values. O(3P) + O2 isotope exchange in the stratosphere and troposphere is therefore expected to govern atmospheric Δ36 and Δ35 values on decadal timescales. These results suggest that the ‘clumped’ isotopic composition of atmospheric O2in ice core records is sensitive to past variations in atmospheric dynamics and free‐radical chemistry.
Vitamin A and Carotenoids
Authors: Greaves Ronda , Petkovich M , Miyazawa T , Albertini Beatrice , Baskaran V , Bohn T , Jia L , Czeczuga-Semeniuk Ewa , Tode C , Kim M K , Tajmir-Riahi H A , Gentili Alessandra. , Khillan J. S , Patel N A , Woollard Gerald , Lin J , Oberholster Anita , De Lera Angel R , Chauveau-Duriot B , Granado-Lorencio F. , Antonacci D , Zeb Alam , Napoli J L , Barber Teresa , Stephensen Charles B , Biesalski H K , Wieringa Frank , Mello C V
Published: August 2012

Vitamin A has an important role to play in vision, bone growth, reproduction, cell division, and cell differentiation. With the focus on Vitamin A and Carotenoids, this book includes the latest research in these areas and starts with an overview putting the compounds in context with other vitamins, supplementation and discussing the importance of beta-carotene. Details of the chemistry, structure and biochemistry of the compounds begins with nomenclature followed by information on encapsulation, thermal degradation and occurrence. Developments in analytical and bioanalytical techniques concerning these compounds in plant, milk and human tissue systems are covered in detail. Finally, the book covers the extensive functions and effects of Vitamin A on eg developmental growth, immune function, cancer risk, the brain and lungs as well as vision. Delivering high quality information, this book will be of benefit to anyone researching this area of health and nutritional science. It will bridge scientific disciplines so that the information is more meaningful and applicable to health in general. Part of a series of books, it is specifically designed for chemists, analytical scientists, forensic scientists, food scientists, dieticians and health care workers, nutritionists, toxicologists and research academics. Due to its interdisciplinary nature it could also be suitable for lecturers and teachers in food and nutritional sciences and as a college or university library reference guide.
Structural and functional characterization of Rpn12 identifies residues required for Rpn10 proteasome incorporation
Authors: Boehringer Jonas , Riedinger Christiane , Paraskevopoulos Konstantinos , Johnson Eachan O. D. , Lowe Edward D. , Khoudian Christina , Smith Dominique , Noble Martin E. M. , Gordon Colin , Endicott Jane A.
Published: August 2012

The ubiquitin–proteasome system targets selected proteins for degradation by the 26S proteasome. Rpn12 is an essential component of the 19S regulatory particle and plays a role in recruiting the extrinsic ubiquitin receptor Rpn10. In the present paper we report the crystal structure of Rpn12, a proteasomal PCI-domain-containing protein. The structure helps to define a core structural motif for the PCI domain and identifies potential sites through which Rpn12 might form protein–protein interactions. We demonstrate that mutating residues at one of these sites impairs Rpn12 binding to Rpn10 in vitro and reduces Rpn10 incorporation into proteasomes in vivo.
A new family of covalent inhibitors block nucleotide binding to the active site of pyruvate kinase
Authors: Morgan Hugh P. , Walsh Martin J. , Blackburn Elizabeth A. , Wear Martin A. , Boxer Matthew B. , Shen Min , Veith Henrike , McNae Iain W. , Nowicki Matthew W. , Michels Paul A. M. , Auld Douglas S. , Fothergill-Gilmore Linda A. , Walkinshaw Malcolm D.
Published: August 2012

PYK (pyruvate kinase) plays a central role in the metabolism of many organisms and cell types, but the elucidation of the details of its function in a systems biology context has been hampered by the lack of specific high-affinity small-molecule inhibitors. High-throughput screening has been used to identify a family of saccharin derivatives which inhibit LmPYK (Leishmania mexicana PYK) activity in a time- (and dose-) dependent manner, a characteristic of irreversible inhibition. The crystal structure of DBS {4-[(1,1-dioxo-1,2-benzothiazol-3-yl)sulfanyl]benzoic acid} complexed with LmPYK shows that the saccharin moiety reacts with an active-site lysine residue (Lys335), forming a covalent bond and sterically hindering the binding of ADP/ATP. Mutation of the lysine residue to an arginine residue eliminated the effect of the inhibitor molecule, providing confirmation of the proposed inhibitor mechanism. This lysine residue is conserved in the active sites of the four human PYK isoenzymes, which were also found to be irreversibly inhibited by DBS. X-ray structures of PYK isoforms show structural differences at the DBS-binding pocket, and this covalent inhibitor of PYK provides a chemical scaffold for the design of new families of potentially isoform-specific irreversible inhibitors.
Adsorption of ions on surfaces modified with brushes of polyampholytes
Authors: Borówko M. , Sokołowski S. , Staszewski T. , Sokołowska Z. , Ilnytskyi J. M.
Published: August 2012

We apply density functional theory to study adsorption of ions, treated in the framework of the restricted primitive model (RPM), on surfaces modified by tethered polyampholytes. The residual electrostatic contribution to the free energy functional is approximated by using the approach proposed by Wang et al. [J. Phys.: Condens. Matter 23, 175002 (2011)]10.1088/0953-8984/23/17/175002 for simple nonuniform RPMs systems. Our research concentrates on the problems how the distribution of the charges within chains of polyampholytes changes the selectivity of adsorption of ions species, the structure of the surface layer, and its electric properties.
Photoelectrochemical properties of CdS sensitized ZnO nanorod arrays: Effect of nanorod length
Authors: Vanalakar S. A. , Mali S. S. , Pawar R. C. , Tarwal N. L. , Moholkar A. V. , Kim J. H. , Patil P. S.
Published: August 2012

The vertically aligned ZnO nanorod arrays were achieved from aqueous chemical route on soda lime and transparent conducting oxide coated glass substrates. The length of nanorods was varied from 1.6 μm to 4.5 μm by varying deposition time. The aspect ratio of ZnO nanorod was increased with increasing deposition time. Cadmium sulfide (CdS) nanoparticles have been subjected to self-assemble onto ZnO nanorods (ZNRs) using chemical bath deposition method. The synthesized CdS/ZnO nanorod arrays were characterized for their optical, structural, and morphological properties with UV-visible absorption spectroscopy (UV-Vis), x-ray diffraction, energy-dispersive x-ray analysis, x-ray photoelectron spectroscopy, contact angle measurement, and scanning electron microscopy. The cross-section images of the samples clearly depict different lengths of ZnO nanorods. UV-vis absorption spectrum shows the significant red shifting after covering of the CdS nanoparticles over the ZnO nanorods. The lengths of ZnO nanorod arrays are an effective parameter to improve the photoelectrochemical performance of CdS nanoparticles sensitized ZnO solar cells. We obtain a highest total light-to-electricity power conversion efficiency of 1.2% for relatively larger area (1 cm2) solar cells.
Rapid topography mapping of scalar fields: Large molecular clusters
Authors: Yeole Sachin D. , López Rafael , Gadre Shridhar R.
Published: August 2012

An efficient and rapid algorithm for topography mapping of scalar fields, molecular electron density (MED) and molecular electrostatic potential (MESP) is presented. The highlight of the work is the use of fast function evaluation by Deformed-atoms-in-molecules (DAM) method. The DAM method provides very rapid as well as sufficiently accurate function and gradient evaluation. For mapping the topography of large systems, the molecular tailoring approach (MTA) is invoked. This new code is tested out for mapping the MED and MESP critical points (CP’s) of small systems. It is further applied to large molecular clusters viz. (H2O)25, (C6H6)8 and also to a unit cell of valine crystal at MP2/6-31+G(d) level of theory. The completeness of the topography is checked by extensive search as well as applying the Poincaré-Hopf relation. The results obtained show that the DAM method in combination with MTA provides a rapid and efficient route for mapping the topography of large molecular systems.
Fully integrated InGaAs/InP single-photon detector module with gigahertz sine wave gating
Authors: Liang Xiao-Lei , Liu Jian-Hong , Wang Quan , Du De-Bing , Ma Jian , Jin Ge , Chen Zeng-Bing , Zhang Jun , Pan Jian-Wei
Published: August 2012

InGaAs/InP single-photon avalanche diodes (SPADs) working in the regime of GHz clock rates are crucial components for the high-speed quantum key distribution (QKD). We have developed for the first time a compact, stable, and user-friendly tabletop InGaAs/InP single-photon detector system operating at a 1.25 GHz gate rate that fully integrates functions for controlling and optimizing SPAD performance. We characterize the key parameters of the detector system and test the long-term stability of the system for continuous operation of 75 h. The detector system can substantially enhance QKD performance and our present work paves the way for practical high-speed QKD applications.
Safe and consistent method of spot-welding platinum thermocouple wires and foils for high temperature measurements
Authors: Orr G. , Roth M.
Published: August 2012

A low-voltage (mV) electronically triggered spot welding system for fabricating fine thermocouples and thin sheets used in high-temperature characterization of materials’ properties is suggested. The system is based on the capacitance discharge method with a timed trigger for obtaining reliable and consistent welds. In contrast to existing techniques based on employing high voltage DC supplies for charging the capacitor or supplies with positive and negative rails, this method uses a simple, standard dual power supply available at most of the physical laboratories or can be acquired at a low cost. In addition, an efficient and simple method of fabricating non-sticking electrodes that do not contaminate the weld area is suggested and implemented.
Electronic structure and magnetism in M(=IA, IIA)C compounds with the rocksalt structure
Authors: Zhang Wenxu , Song Zhida , Peng Bin , Zhang Wanli
Published: August 2012

Electronic structures of MC, where M is the alkali and alkaline earth metals with the rocksalt structure, are calculated by full potential density functional codes. We find that the spin magnetic moment in the compounds is mainly contributed by the spin polarized p-orbitals of carbon. The large distance between the carbon makes the p-orbitals localized, which induces magnetic instability according to the Stoner criterion. The electronic structure can be mapped to the rigid band model. SrC, BaC, and RaC are half-metals, while KC, RbC, and CsC are magnetic semiconductors.
Long range temporal correlation in the chaotic oscillations of a dc glow discharge plasma
Authors: Lahiri S. , Roychowdhury D. , Sekar Iyengar A. N.
Published: August 2012

Long range temporal correlations in the fluctuations of the plasma floating potentials (measured using a Langmuir probe) are investigated in a dc glow discharge plasma. Keeping the neutral pressure constant, the discharge voltage was varied and at the formation of the plasma, quasi periodic oscillations were excited and on further increase of the discharge voltage they became chaotic (irregular) beyond a threshold voltage. We compared the Lyapunov exponent with the Hurst exponent obtained from R/S statistics which showed an opposite behaviour at the transition point. These results are perhaps new since we have not come across such comparative analysis for chaotic oscillations in a glow discharge plasma before.
Autonomous phagosomal degradation and antigen presentation in dendritic cells
Authors: Hoffmann Eik , Kotsias Fiorella , Visentin Géraldine , Bruhns Pierre , Savina Ariel , Amigorena Sebastian
Published: August 2012

Phagocytosis plays a critical role in both innate and adaptive immunity. Phagosomal fusion with late endosomes and lysosomes enhances proteolysis, causing degradation of the phagocytic content. Increased degradation participates in both innate protection against pathogens and the production of antigenic peptides for presentation to T lymphocytes during adaptive immune responses. Specific ligands present in the phagosomal cargo influence the rate of phagosome fusion with lysosomes, thereby modulating both antigen degradation and presentation. Using a combination of cell sorting techniques and single phagosome flow cytometry-based analysis, we found that opsonization with IgG accelerates antigen degradation within individual IgG-containing phagosomes, but not in other phagosomes present in the same cell and devoid of IgG. Likewise, IgG opsonization enhances antigen presentation to CD4+T lymphocytes only when antigen and IgG are present within the same phagosome, whereas cells containing phagosomes with either antigen or IgG alone failed to present antigen efficiently. Therefore, individual phagosomes behave autonomously, in terms of both cargo degradation and antigen presentation to CD4+T cells. Phagosomal autonomy could serve as a basis for the intracellular discrimination between self and nonself antigens, resulting in the preferential presentation of peptides derived from opsonized, nonself antigens.
Soybean susceptibility to manufactured nanomaterials with evidence for food quality and soil fertility interruption
Authors: Priester John H. , Ge Yuan , Mielke Randall E. , Horst Allison M. , Moritz Shelly Cole , Espinosa Katherine , Gelb Jeff , Walker Sharon L. , Nisbet Roger M. , An Youn-Joo , Schimel Joshua P. , Palmer Reid G. , Hernandez-Viezcas Jose A. , Zhao Lijuan , Gardea-Torresdey Jorge L. , Holden Patricia A.
Published: August 2012

Based on previously published hydroponic plant, planktonic bacterial, and soil microbial community research, manufactured nanomaterial (MNM) environmental buildup could profoundly alter soil-based food crop quality and yield. However, thus far, no single study has at once examined the full implications, as no studies have involved growing plants to full maturity in MNM-contaminated field soil. We have done so for soybean, a major global commodity crop, using farm soil amended with two high-production metal oxide MNMs (nano-CeO
2
and -ZnO). The results provide a clear, but unfortunate, view of what could arise over the long term: (
i
) for nano-ZnO, component metal was taken up and distributed throughout edible plant tissues; (
ii
) for nano-CeO
2
, plant growth and yield diminished, but also (
iii
) nitrogen fixation—a major ecosystem service of leguminous crops—was shut down at high nano-CeO
2
concentration. Juxtaposed against widespread land application of wastewater treatment biosolids to food crops, these findings forewarn of agriculturally associated human and environmental risks from the accelerating use of MNMs.
Structural insights into
Helicobacter pylori
oncoprotein CagA interaction with β1 integrin
Authors: Kaplan-Türköz Burcu , Jiménez-Soto Luisa F. , Dian Cyril , Ertl Claudia , Remaut Han , Louche Arthur , Tosi Tommaso , Haas Rainer , Terradot Laurent
Published: August 2012

Infection with the gastric pathogen
Helicobacter pylori
is a risk factor for the development of gastric cancer. Pathogenic strains of
H. pylori
carry a type IV secretion system (T4SS) responsible for the injection of the oncoprotein CagA into host cells.
H. pylori
and its
cag
-T4SS exploit α5β1 integrin as a receptor for CagA translocation. Injected CagA localizes to the inner leaflet of the host cell membrane, where it hijacks host cell signaling and induces cytoskeleton reorganization. Here we describe the crystal structure of the N-terminal ∼100-kDa subdomain of CagA at 3.6 Å that unveils a unique combination of folds. The core domain of the protein consists of an extended single-layer β-sheet stabilized by two independent helical subdomains. The core is followed by a long helix that forms a four-helix helical bundle with the C-terminal domain. Mapping of conserved regions in a set of CagA sequences identified four conserved surface-exposed patches (CSP1–4), which represent putative hot-spots for protein–protein interactions. The proximal part of the single-layer β-sheet, covering CSP4, is involved in specific binding of CagA to the β1 integrin, as determined by yeast two-hybrid and in vivo competition assays in
H. pylori
cell-culture infection studies. These data provide a structural basis for the first step of CagA internalization into host cells and suggest that CagA uses a previously undescribed mechanism to bind β1 integrin to mediate its own translocation.
Conditional control of gene function by an invertible gene trap in zebrafish
Authors: Ni Terri T. , Lu Jianjun , Zhu Meiying , Maddison Lisette A. , Boyd Kelli L. , Huskey Lindsey , Ju Bensheng , Hesselson Daniel , Zhong Tao P. , Page-McCaw Patrick S. , Stainier Didier Y. , Chen Wenbiao
Published: August 2012

Conditional mutations are essential for determining the stage- and tissue-specific functions of genes. Here we achieve conditional mutagenesis in zebrafish using FT1, a gene-trap cassette that can be stably inverted by both Cre and Flp recombinases. We demonstrate that intronic insertions in the gene-trapping orientation severely disrupt the expression of the host gene, whereas intronic insertions in the neutral orientation do not significantly affect host gene expression. Cre- and Flp-mediated recombination switches the orientation of the gene-trap cassette, permitting conditional rescue in one orientation and conditional knockout in the other. To illustrate the utility of this system we analyzed the functional consequence of intronic FT1 insertion in
supv3l1
, a gene encoding a mitochondrial RNA helicase. Global
supv311
mutants have impaired mitochondrial function, embryonic lethality, and agenesis of the liver. Conditional rescue of
supv311
expression in hepatocytes specifically corrected the liver defects. To test whether the liver function of
supv311
is required for viability we used Flp-mediated recombination in the germline to generate a neutral allele at the locus. Subsequently, tissue-specific expression of Cre conditionally inactivated the targeted locus. Hepatocyte-specific inactivation of
supv311
caused liver degeneration, growth retardation, and juvenile lethality, a phenotype that was less severe than the global disruption of
supv311
. Thus,
supv311
is required in multiple tissues for organismal viability. Our mutagenesis approach is very efficient and could be used to generate conditional alleles throughout the zebrafish genome. Furthermore, because FT1 is based on the promiscuous Tol2 transposon, it should be applicable to many organisms.
Third target of rapamycin complex negatively regulates development of quiescence in
Trypanosoma brucei
Authors: Barquilla Antonio , Saldivia Manuel , Diaz Rosario , Bart Jean-Mathieu , Vidal Isabel , Calvo Enrique , Hall Michael N. , Navarro Miguel
Published: August 2012

African trypanosomes are protozoan parasites transmitted by a tsetse fly vector to a mammalian host. The life cycle includes highly proliferative forms and quiescent forms, the latter being adapted to host transmission. The signaling pathways controlling the developmental switch between the two forms remain unknown.
Trypanosoma brucei
contains two target of rapamycin (TOR) kinases, TbTOR1 and TbTOR2, and two TOR complexes, TbTORC1 and TbTORC2. Surprisingly, two additional TOR kinases are encoded in the
T. brucei
genome. We report that TbTOR4 associates with an Armadillo domain-containing protein (TbArmtor), a major vault protein, and LST8 to form a unique TOR complex, TbTORC4. Depletion of TbTOR4 caused irreversible differentiation of the parasite into the quiescent form. AMP and hydrolysable analogs of cAMP inhibited TbTOR4 expression and induced the stumpy quiescent form. Our results reveal unexpected complexity in TOR signaling and show that TbTORC4 negatively regulates differentiation of the proliferative form into the quiescent form.
Bayesian probabilistic population projections for all countries
Authors: Raftery Adrian E. , Li Nan , Ševčíková Hana , Gerland Patrick , Heilig Gerhard K.
Published: August 2012

Projections of countries’ future populations, broken down by age and sex, are widely used for planning and research. They are mostly done deterministically, but there is a widespread need for probabilistic projections. We propose a Bayesian method for probabilistic population projections for all countries. The total fertility rate and female and male life expectancies at birth are projected probabilistically using Bayesian hierarchical models estimated via Markov chain Monte Carlo using United Nations population data for all countries. These are then converted to age-specific rates and combined with a cohort component projection model. This yields probabilistic projections of any population quantity of interest. The method is illustrated for five countries of different demographic stages, continents and sizes. The method is validated by an out of sample experiment in which data from 1950–1990 are used for estimation, and applied to predict 1990–2010. The method appears reasonably accurate and well calibrated for this period. The results suggest that the current United Nations high and low variants greatly underestimate uncertainty about the number of oldest old from about 2050 and that they underestimate uncertainty for high fertility countries and overstate uncertainty for countries that have completed the demographic transition and whose fertility has started to recover towards replacement level, mostly in Europe. The results also indicate that the potential support ratio (persons aged 20–64 per person aged 65+) will almost certainly decline dramatically in most countries over the coming decades.
Muscle synergy patterns as physiological markers of motor cortical damage
Authors: Cheung Vincent C. K. , Turolla Andrea , Agostini Michela , Silvoni Stefano , Bennis Caoimhe , Kasi Patrick , Paganoni Sabrina , Bonato Paolo , Bizzi Emilio
Published: August 2012

The experimental findings herein reported are aimed at gaining a perspective on the complex neural events that follow lesions of the motor cortical areas. Cortical damage, whether by trauma or stroke, interferes with the flow of descending signals to the modular interneuronal structures of the spinal cord. These spinal modules subserve normal motor behaviors by activating groups of muscles as individual units (muscle synergies). Damage to the motor cortical areas disrupts the orchestration of the modules, resulting in abnormal movements. To gain insights into this complex process, we recorded myoelectric signals from multiple upper-limb muscles in subjects with cortical lesions. We used a factorization algorithm to identify the muscle synergies. Our factorization analysis revealed, in a quantitative way, three distinct patterns of muscle coordination—including preservation, merging, and fractionation of muscle synergies—that reflect the multiple neural responses that occur after cortical damage. These patterns varied as a function of both the severity of functional impairment and the temporal distance from stroke onset. We think these muscle-synergy patterns can be used as physiological markers of the status of any patient with stroke or trauma, thereby guiding the development of different rehabilitation approaches, as well as future physiological experiments for a further understanding of postinjury mechanisms of motor control and recovery.
Blocking antibody to the β-subunit of FSH prevents bone loss by inhibiting bone resorption and stimulating bone synthesis
Authors: Zhu Ling-Ling , Blair Harry , Cao Jay , Yuen Tony , Latif Rauf , Guo Lida , Tourkova Irina L. , Li Jianhua , Davies Terry F. , Sun Li , Bian Zhuan , Rosen Clifford , Zallone Alberta , New Maria I. , Zaidi Mone
Published: August 2012

Low estrogen levels undoubtedly underlie menopausal bone thinning. However, rapid and profuse bone loss begins 3 y before the last menstrual period, when serum estrogen is relatively normal. We have shown that the pituitary hormone FSH, the levels of which are high during late perimenopause, directly stimulates bone resorption by osteoclasts. Here, we generated and characterized a polyclonal antibody to a 13-amino-acid-long peptide sequence within the receptor-binding domain of the FSH β-subunit. We show that the FSH antibody binds FSH specifically and blocks its action on osteoclast formation in vitro. When injected into ovariectomized mice, the FSH antibody attenuates bone loss significantly not only by inhibiting bone resorption, but also by stimulating bone formation, a yet uncharacterized action of FSH that we report herein. Mesenchymal cells isolated from mice treated with the FSH antibody show greater osteoblast precursor colony counts, similarly to mesenchymal cells isolated from FSH receptor (
FSHR
)
−/−
mice. This suggests that FSH negatively regulates osteoblast number. We confirm that this action is mediated by signaling-efficient FSHRs present on mesenchymal stem cells. Overall, the data prompt the future development of an FSH-blocking agent as a means of uncoupling bone formation and bone resorption to a therapeutic advantage in humans.
Implementing the Opening Minds curriculum in a secondary school in England: an alternative to the one‐size‐fits‐all National Curriculum?
Authors: Stanley Grant , Jones Marion , Murphy Jan
Published: August 2012

The Importance of Teaching: The Schools White Paper 2010, which grants schools increased autonomy in curriculum development and implementation, heralded a new era of curriculum reform in England. This article critically examines how this process took place in a Catholic secondary school that decided to use the RSA Opening Minds (OM) curriculum with its Year 7 students. The discussion will be shaped by a range of perspectives, including the RSA point of view, literature on cross‐curricular learning and Catholic education, student responses to a post‐transition questionnaire, and the experiences and perceptions of the school's OM coordinator. From this, the following aspects have been identified as warranting critical consideration and further investigation: adequate staffing and resourcing; staff expertise to ensure teaching competence across a wide range of subject areas; achieving a balance between creative approaches to learning that promote engagement and a focus on in‐depth subject knowledge and academic achievement. Finally, we pose the question whether the implementation of the OM curriculum as practised in this particular school can assist students from disadvantaged backgrounds, who may have limited access to life‐transforming educational experiences outside of school, to acquire cultural capital and ‘high status knowledge’.
The 38th Sir Frederick Bartlett Lecture Why we need cognitive explanations of autism
Authors: Frith Uta
Published: August 2012

In the 70 years since autism was described and named there have been huge changes in the conceptualization of this enigmatic condition. This review takes a personal perspective on the history of autism research. The origins of the first cognitive theories of autism, theory of mind and weak central coherence, are discussed and updated to inform future developments. Selected experimental findings are interpreted in the historical context of changes that have been brought about by advances in methodology. A three-level framework graphically illustrates a causal chain between brain, mind, and behaviour to facilitate the identification of phenotypes in neurodevelopmental disorders. Cognition is placed at the centre of the diagram to reveal that it can link together brain and behaviour, when there are complex multiple mappings between the different levels.
Familiarity and face processing
Authors: Osborne Cara D. , Stevenage Sarah V.
Published: August 2012

The results of three experiments explore the role of familiarity in face processing. Using the complete-over-part advantage (Experiment 1) and the chimeric faces task (Experiment 2), the results revealed evidence for what may be termed “holistic processing” of unfamiliar, newly learned, and famous faces. Notably, the extent of holistic processing on both tasks was not moderated by the familiarity of the stimuli. Experiment 3 replicated this pattern using a simultaneous chimeric task to rule out a simple explanation through memory demands. Taken together, these three experiments provide robust and convergent evidence to suggest that all faces regardless of familiarity can be processed in a holistic fashion. On the basis of these results, discussion is presented regarding the value of considering different “types” of facial processing over and above a more simple consideration of task difficulty.
Tomography of fast-ion velocity-space distributions from synthetic CTS and FIDA measurements
Authors: Salewski M. , Geiger B. , Nielsen S.K. , Bindslev H. , García-Muñoz M. , Heidbrink W.W. , Korsholm S.B. , Leipold F. , Meo F. , Michelsen P.K. , Moseev D. , Stejner M. , Tardini G.
Published: August 2012

We compute tomographies of 2D fast-ion velocity distribution functions from synthetic collective Thomson scattering (CTS) and fast-ion D
α
(FIDA) 1D measurements using a new reconstruction prescription. Contradicting conventional wisdom we demonstrate that one single 1D CTS or FIDA view suffices to compute accurate tomographies of arbitrary 2D functions under idealized conditions. Under simulated experimental conditions, single-view tomographies do not resemble the original fast-ion velocity distribution functions but nevertheless show their coarsest features. For CTS or FIDA systems with many simultaneous views on the same measurement volume, the resemblance improves with the number of available views, even if the resolution in each view is varied inversely proportional to the number of views, so that the total number of measurements in all views is the same. With a realistic four-view system, tomographies of a beam ion velocity distribution function at ASDEX Upgrade reproduce the general shape of the function and the location of the maxima at full and half injection energy of the beam ions. By applying our method to real many-view CTS or FIDA measurements, one could determine tomographies of 2D fast-ion velocity distribution functions experimentally.
treePL: divergence time estimation using penalized likelihood for large phylogenies
Authors: Smith Stephen A. , O’Meara Brian C.
Published: August 2012

Summary: Ever larger phylogenies are being constructed due to the explosion of genetic data and development of high-performance phylogenetic reconstruction algorithms. However, most methods for calculating divergence times are limited to datasets that are orders of magnitude smaller than recently published large phylogenies. Here, we present an algorithm and implementation of a divergence time method using penalized likelihood that can handle datasets of thousands of taxa. We implement a method that combines the standard derivative-based optimization with a stochastic simulated annealing approach to overcome optimization challenges. We compare this approach with existing software including r8s, PATHd8 and BEAST.

Availability: Source code, example files, binaries and documentation for treePL are available at https://github.com/blackrim/treePL.

Contact:  eebsmith@umich.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Systematic review: early infant feeding and the prevention of coeliac disease
Authors: Szajewska H. , Chmielewska A. , Pieścik‐Lech M. , Ivarsson A. , Kolacek S. , Koletzko S. , Mearin M. L. , Shamir R. , Auricchio R. , Troncone R. ,   PREVENTCD Study Group
Published: August 2012

Background

PREVENTCD, Prevent Coeliac Disease, is an international project investigating the hypothesis of possible induction of tolerance to gluten in genetically predisposed children through introducing small quantities of gluten during the period of breastfeeding.

Aim

To summarise current knowledge on the possible relationship between early feeding practices and the risk of coeliac disease (CD).

Methods

The Cochrane Library, MEDLINE, and EMBASE databases were searched in May 2011, and the search was updated in January 2012, and again in July 2012.

Results

Breastfeeding (BF) and CD: some studies show a protective effect of BF, while others show no effect. No studies have shown a long‐term preventive effect. BF at the time of gluten introduction and CD: Results from a meta‐analysis of five observational case‐control studies suggest that BF at gluten introduction is associated with a lower risk of CD compared with formula feeding. It is unclear whether BF provides a permanent protection or only delays the onset of CD. Timing of gluten introduction: The data suggest that both early (≤4 months) and late (≥7 months) introduction of gluten may increase the risk of CD. Amount of gluten at weaning (and later) and CD: One incident case‐referent study documented that the introduction of gluten in large amounts compared with small or medium amounts increased the risk of CD.

Conclusions

In the absence of clear evidence, in order to decrease the risk of later coeliac disease, it is reasonable to avoid both early (<4 months) and late (≥7 months) introduction of gluten, and to introduce gluten while the infant is still being breastfed. Future studies may clarify the remaining uncertainties.
The Function of Click Call Emission in Capybaras (Hydrochoerus hydrochaeris)
Authors: Nogueira Selene S. C. , Pedroza Janine P. , Nogueira‐Filho Sérgio L. G. , Tokumaru Rosana S.
Published: August 2012

Contact calls are used to promote cohesion among individuals that live in social groups. Capybaras are very gregarious and often vocalize. This species emits a vocalization known as a click, which has been observed during aggregating and foraging behaviors, suggesting contact or monitoring call function. We carried out a playback experiment to evaluate behavioral responses to the capybara's click call and to a bird call, used as control in ten capybaras. We compared animals' latency to respond to stimuli, the time spent in behavioral patterns, alertness, head orientation toward the sound source, and approach to the sound source. All capybaras responded to the emission of the click call playback. Most of them assumed an alert position, showed head orientation toward the sound source, and approached the sound source. They promptly reacted to the first click call emission, while few reacted to the first bird call emission, used as control. All subjects showed behavioral changes after the second emission of the click call, and some responded to the third emission. Just three individuals answered after the first control emission, while none of them responded to the second and third emission of the playback. Therefore, click call playback promotes prompt behavioral changes in capybaras, including approach to the sound source. These results indicate that this vocalization functions as a contact or monitoring call in the species.
Response of Captive Raptors to Avian Mobbing Calls: the Roles of Mobber Size and Raptor Experience
Authors: Consla Donald J. , Mumme Ronald L.
Published: August 2012

The ‘move on’ hypothesis for avian mobbing proposes that mobbing induces stress in potential predators, thereby provoking them into moving elsewhere. We tested whether mobbing is stress inducing by subjecting captive owls, hawks, and falcons to the mobbing calls of four species of co‐occurring passerine birds that vary considerably in body size. Test subjects comprised 15 individuals of seven species of birds of prey that were housed at a wildlife rehabilitation center in northwestern Pennsylvania, USA. Playback treatments included mobbing calls of the black‐capped chickadee (Poecile atricapillus), blue‐headed vireo (Vireo solitarius), blue jay (Cyanocitta cristata), and American crow (Corvus brachyrhynchos), which vary in size from 12 g (chickadee) to 500 g (crow). A non‐mobbing vocalization (song of the black‐capped chickadee) was included in the playback treatments as a control. Playback treatment produced pronounced effects on three behavioral indicators of probable stress: head orientation toward the playback speaker, raising of feathers or spreading of wings, and changing of perch positions. Test subjects responded more vigorously to mobbing calls of the large passerines (jays and crows) than to those of the smaller passerines (chickadees and vireos). In addition, raptors that had entered the rehabilitation facility as adults generally responded more vigorously to the mobbing calls of jays and crows than did naive individuals that had entered the facility as fledglings or young juveniles. Our results are therefore consistent with the ‘move on’ hypothesis and suggest (1) that the mobbing calls of large passerines are more effective in provoking stress and altering the behavior of potential predators than are the mobbing calls of small passerines and (2) that a raptor's previous experience with mobbing in the wild can exaggerate the strength of its response, particularly to the mobbing calls of large passerines.