bluuebunny/crossref_metadata_2025 huggingface dataset:
Powder diffraction analysis of cerium dioxide at high pressure
Authors: Gerward L. , Olsen J. Staun
Published: January 2013

CeO2 transforms to an orthorhombic PbCl2-type structure at a pressure of about 31 GPa. The phase transition is accompanied by a 9.8% volume contraction. The bulk modulus of the low-pressure fluorite-type structure is 236(4) GPa. Comparisons are made with the high-pressure behaviour of UO2 and ThO2.
Powder Data for Ba3Ca2Ti2O9
Authors: Meden A. , Ceh M.
Published: January 2013

Powder data for the title compound have been published by Kwestroo and Paping (1959) (PDF 13-325) but neither unit cell nor indices were given. A diffractogram of this compound has been successfully indexed by the program TREOR (Eriksson and Westdahl, 1985) and the unit cell subsequently refined by a least squares procedure (Table 1).
X-ray powder diffraction pattern for lactitol and lactitol monohydrate
Authors: Valkonen J. , Perkkalainen P. , Pitkänen I. , Rautiainen H.
Published: January 2013

Diffraction patterns were recorded, and unit cell dimensions refined by the least-squares method, for lactitol and lactitol monohydrate. Refined unit cell parameters for lactitol are: a =7.622(1) Å, b = 10.764(2) Å, c = 9.375(1) Å, β= 108.25(1)° in space group P21, and those for lactitol monohydrate a =7.844(1) Å, b = 12.673(2) Å, c = 15.942(2) Å in space group P212121.
The lattice distortion and possible causes of the lazurite incommensurate and commensurate modulation structure
Authors: Sapozhnikov A. N. , Vasil'ev E. K.
Published: January 2013

By methods of X-ray structure analysis commensurate (one dimensional) and incommensurate (three-dimensional) modulations of the lazurite structure from Baikal deposits are considered. The analysis of the X-ray diffraction powder and single crystal data showed that the one-dimensional (anisotropic) modulation deforms the lazurite cubic structure and is manifested in a broadening and splitting of sublattice lines on the powder diffraction pattern of the mineral. At a three-dimensional modulation, the cubic structure is maintained. It is concluded that a density modulation is a cause of the incommensurate modulation of the lazurite structure. Due to this arrangement, a crystallographic equivalency of subcells is maintained. The cause of the commensurate modulation is an ordered distribution of intraframework units and the displacement modulation where all atoms of the mineral structure participate.
An environmental chamber for powder diffractometers and for temperatures up to 1200 °C under various atmospheres and vacuum
Authors: Anselmi-Tamburini Umberto , Campari Gualtiero , Ghigna Paolo , Spinolo Giorgio
Published: January 2013

An attachment for commercial X-ray powder diffractometers is described. The device is made of four different parts that are largely independent of each other, and can be freely interchanged or replaced, and aligned independently. It can be home-built, or modified, with high flexibility according to user requirements, and has been tested on different problems concerning high-temperature phase transitions and solid-state reactions up to 1200 °C under vacuum, under inert gas or under various oxygen partial pressures. Examples are given of possible designs of the various parts.
Incorporation of microabsorption corrections into Rietveid analysis
Authors: Pitschke W. , Mattern N. , Hermann H.
Published: January 2013

Surface roughness of planar samples causes an additional attenuation of X-ray diffraction intensity measured in Bragg–Brentano geometry. The decrease of intensity becomes stronger with decreasing scattering angle. This is part of the microabsorption effect. Two quantitative expressions describing the microabsorption effect are incorporated into the DBWS 9006-PC Rietveid program [D. B. Wiles and R. A. Young, J. Appl. Crystallogr. 15, 149–151 (1981)]. The procedure is applied to scattering data obtained from YBa2Cu3O7-powder samples with different degree of surface roughness but approximately identical bulk structure. The procedure is proved to work well. However, the values obtained for the parameters of the temperature factors and the microabsorption effect are correlated, and careful discussion is necessary to interpret the results.
JCPDS—International Centre for Diffraction Data statistical process control method development
Authors: Blanton T. N. , Schreiner W. N. , Dann J. N. , Hamill G. P. , Hamilton R. F.
Published: January 2013

A task group of the JCPDS—International Centre for Diffraction Data (ICDD) was established for the purpose of investigating a methodology which would be applicable for statistical process control monitoring of X-ray powder diffractometers. A procedure for collecting X-ray diffraction data for statistical process control purposes and the incorporation of these data into control charts are presented. The results of this task group show that, through the use of statistical process control methods, noncontrol situations for diffractometers were detected, the causes of these problems were identified, and these problems were corrected and noted on control charts.
The City, Still the Hope of Democracy? From Jane Addams and Mary Parker Follett to the Arab Spring
Authors: Flanagan Maureen A.
Published: January 2013

This essay, an expanded version of the presidential address presented to SHGAPE in April 2012, poses the essential question of whether the City can ever be a true site of democracy if women do not possess free, equal, and safe access to a city's public spaces. The essay compares the writings, proposals, and actions of men and women in the Anglo-Atlantic world early in the twentieth century to reveal the distinct gendered ideas behind various reform movements directed at improving the urban built environment. It uses theoretical frameworks provided by feminist historians and social scientists to demonstrate that from the Progressive Era to events of the contemporary Arab Spring, the city has not been a place of democratic equality for women. Fear of women's public presence, of the disorder of women, has motivated men to construct cities to reinforce their desires to embound women in the private domestic space and to punish women for transgressing the boundary between the public and the private.
Short- and full-season soybean in stale seedbeds versus rolled-crimped winter rye mulch
Authors: Forcella Frank
Published: January 2013

Stale seedbeds are used by organic growers to reduce weed populations prior to crop planting. Rye mulches, derived from mechanically killed (rolled and crimped) winter rye cover crops, can serve the same purpose for spring-planted organic crops. Both methods can also be employed by conventional growers who face looming problems with herbicide resistant weeds. The objective of this research was to compare these methods over 2 years in central Minnesota in terms of weed seedling emergence, populations, biomass and manual-weeding times, as well as stands and yields of short-season and full-season soybean varieties planted late, in mid June. Rye mulch greatly lowered both pre- and post-planting weed populations of common annual weeds, which substantially affected necessity for augmented weed control. For instance, the need for within-crop manual-weeding was low for soybean planted into rye mulch (0–6 h ha−1), but ranged from 15 to 66 h ha−1of labor for soybean planted in stale seedbeds and augmented by inter-row cultivation. However, rye mulch lowered soybean yield potential by 800–1000 kg ha−1compared with stale seedbeds in 1 of 2 years. With organic feed-grade soybean seed valued at $1 kg−1, conventional soybean seed at $0.5 kg−1, and labor for manual-weeding at $10 h−1, the use of rye mulch compared with stale seedbeds augmented by manual-weeding are equally rational choices for organic growers in central Minnesota (assuming labor is available for hand-weeding), but rye mulches probably would be a wise financial option for conventional growers compared with hand-weeding. Lastly, full-season soybean had higher yields than short-season soybean and probably represents a prudent selection in central Minnesota, regardless of the late planting date requirements for both the rye mulch and stale seedbed systems.
Controlled variations in stimulus similarity during learning determine visual discrimination capacity in freely moving mice
Authors: Treviño Mario , Oviedo Tatiana , Jendritza Patrick , Li Shi-Bin , Köhr Georg , De Marco Rodrigo J.
Published: January 2013

The mouse is receiving growing interest as a model organism for studying visual perception. However, little is known about how discrimination and learning interact to produce visual conditioned responses. Here, we adapted a two-alternative forced-choice visual discrimination task for mice and examined how training with equiprobable stimuli of varying similarity influenced conditioned response and discrimination performance as a function of learning. Our results indicate that the slope of the gradients in similarity during training determined the learning rate, the maximum performance and the threshold for successful discrimination. Moreover, the learning process obeyed an inverse relationship between discrimination performance and discriminative resolution, implying that sensitivity within a similarity range cannot be improved without sacrificing performance in another. Our study demonstrates how the interplay between discrimination and learning controls visual discrimination capacity and introduces a new training protocol with quantitative measures to study perceptual learning and visually-guided behavior in freely moving mice.
Predictors of Hearing Aid Use Time in Children With Mild-to-Severe Hearing Loss
Authors: Walker Elizabeth A. , Spratford Meredith , Moeller Mary Pat , Oleson Jacob , Ou Hua , Roush Patricia , Jacobs Shana
Published: January 2013

Purpose

This study investigated predictors of hearing aid (HA) use time for children with mild-to-severe hearing loss (HL). Barriers to consistent HA use and reliability of parent report measures were also examined.

Method

Participants included parents of 272 children with HL. Parents estimated the amount of time the child used HAs daily. Regression analysis examined the relationships among independent variables and HA use time. To determine parental accuracy of HA use time, datalogging from the HAs was compared to the parents' estimates.

Results

Longer HA use related to older age, poorer hearing, and higher maternal education. Parental consistency ratings revealed similar findings—younger children and children with milder HL wore HAs less consistently than older children and children with more severe HL. Parents' estimates and datalogging were significantly correlated; however, results suggested that parents overestimate the amount of time their children wear their HAs.

Conclusion

Certain variables were significantly related to the amount of time children wore their HAs. Consistency rating scales provided insight into circumstances that were challenging for families. Use of both parent reports and datalogging may allow clinicians and researchers to obtain a general estimate of HA use time.
Carrier heating and electron-phonon energy exchange effects on nonlinear transport phenomena in semiconductor films
Authors: Gonzalez de la Cruz G. , Gurevich Yu. G.
Published: January 2013

Theory of nonlinear size effects is developed in semiconductor films in the presence of an external dc electric field. The electron and phonon temperatures are calculated self-consistently with the electron-phonon energy interaction taken into account and its influence on the electron current density is considered. The temperature distributions are calculated using appropriate boundary conditions at the surfaces of the semiconductor film. It is shown that the electron and phonon temperatures depend on the electron-phonon coupling factor and the film thickness. Because the electrical conductivity is a function of the electron and phonon temperature distributions, the electron current density in the semiconductor film becomes nonlinear as a function of the heating electric field. We discuss the nonlinear effects for different special cases.
Giant negative uniaxial magnetocrystalline anisotropy of Co80Ir20 sputtered films with perfect hexagonal-close-packed and composition-modulated atomic layer stacking
Authors: Nozawa Naoki , Saito Shin , Kimura Takuya , Shibuya Kazunari , Hoshino Kazuya , Hinata Shintaro , Takahashi Migaku
Published: January 2013

Co80Ir20 films with negative uniaxial magnetocrystalline anisotropy (Ku) are investigated with respect to the regularity of the stacking sequence and atomic site arrangement. Substrate heating at 600 °C enhances the negative Ku of Co80Ir20 to −9.6 × 106 erg/cm3. X-ray diffraction analysis and scanning transmission electron microscopy of the Co80Ir20 film fabricated at 600 °C indicate (1) a near perfect hexagonal-close-packed (hcp) stacking structure and (2) an atomic layered structure that consists of randomly sequenced Ir-rich and Ir-poor layers. These hcp and composition-modulated atomic layer stacking structures are considered to be the reason for the enhancement of the negative Ku.
Characterization of Hall effect thruster propellant distributors with flame visualization
Authors: Langendorf S. , Walker M. L. R.
Published: January 2013

A novel method for the characterization and qualification of Hall effect thruster propellant distributors is presented. A quantitative measurement of the azimuthal number density uniformity, a metric which impacts propellant utilization, is obtained from photographs of a premixed flame anchored on the exit plane of the propellant distributor. The technique is demonstrated for three propellant distributors using a propane-air mixture at reservoir pressure of 40 psi (gauge) (377 kPa) exhausting to atmosphere, with volumetric flow rates ranging from 15-145 cfh (7.2–68 l/min) with equivalence ratios from 1.2 to 2.1. The visualization is compared with in-vacuum pressure measurements 1 mm downstream of the distributor exit plane (chamber pressure held below 2.7 × 10−5 Torr-Xe at all flow rates). Both methods indicate a non-uniformity in line with the propellant inlet, supporting the validity of the technique of flow visualization with flame luminosity for propellant distributor characterization. The technique is applied to a propellant distributor with a manufacturing defect in a known location and is able to identify the defect and characterize its impact. The technique is also applied to a distributor with numerous small orifices at the exit plane and is able to resolve the resulting non-uniformity. Luminosity data are collected with a spatial resolution of 48.2–76.1 μm (pixel width). The azimuthal uniformity is characterized in the form of standard deviation of azimuthal luminosities, normalized by the mean azimuthal luminosity. The distributors investigated achieve standard deviations of 0.346 ± 0.0212, 0.108 ± 0.0178, and 0.708 ± 0.0230 mean-normalized luminosity units respectively, where a value of 0 corresponds to perfect uniformity and a value of 1 represents a standard deviation equivalent to the mean.
Anomalous phonon behavior of carbon nanotubes: First-order influence of external load
Authors: Aghaei Amin , Dayal Kaushik , Elliott Ryan S.
Published: January 2013

External loads typically have an indirect influence on phonon curves, i.e., they influence the phonon curves by changing the state about which linearization is performed. In this paper, we show that in nanotubes, the axial load has a direct first-order influence on the long-wavelength behavior of the transverse acoustic (TA) mode. In particular, when the tube is force-free, the TA mode frequencies vary quadratically with wave number and have curvature (second derivative) proportional to the square-root of the nanotube's bending stiffness. When the tube has non-zero external force, the TA mode frequencies vary linearly with wave number and have slope proportional to the square-root of the axial force. Therefore, the TA phonon curves—and associated transport properties—are not material properties but rather can be directly tuned by external loads. In addition, we show that the out-of-plane shear deformation does not contribute to this mode and the unusual properties of the TA mode are exclusively due to bending. Our calculations consist of 3 parts: First, we use a linear chain of atoms as an illustrative example that can be solved in close-form; second, we use our recently developed symmetry-adapted phonon analysis method to present direct numerical evidence; and finally, we present a simple mechanical model that captures the essential physics of the geometric nonlinearity in slender nanotubes that couples the axial load directly to the phonon curves. We also compute the density of states and show the significant effect of the external load.
Ultrasonic estimate of the modulus of rupture and quantification of the frequency dependent dynamic modulus in Norway Spruce
Authors: Salmi Ari , Karppinen Timo , Montonen Risto , Saranpää Pekka , Hæggström Edward
Published: January 2013

Ultrasonic measurements allow non-destructive evaluation of mechanical properties of wood. However, it is unclear how these ultrasonically determined properties relate to comparable values obtained by traditional mechanical experiments, e.g., three point bending performed at different probing frequencies. In addition, although a link between the modulus of rupture (MOR) and the modulus of elasticity (MOE) obtained with static methods is established, little research exists on the correlation between the ultrasonically determined dynamic elastic modulus and MOR. Therefore, we set out to link the modulus values obtained by three-point bending to those obtained by ultrasonic measurements at different frequencies. We compared the modalities using a fractional derivative model that theoretically predicts a frequency dependency of the dynamic elastic modulus. We determined MOE and MOR in 102 Norway Spruce samples (340 to 510 kg/m3 density) by three-point bending followed by ultrasonic through-transmission measurements that quantified the dynamic modulus at 500 kHz, 4 MHz, and 8 MHz. This is the first report on such a frequency series for Norway Spruce. Our results provide a conversion factor that permits comparing ultrasonically and statically measured MOE values. Depending on the ultrasonic frequency, correlations ranging from 0.3 to 0.53 between the ultrasonic dynamic modulus and MOR were found.
Resistive switching of oxygen enhanced TiO2 thin-film devices
Authors: Salaoru Iulia , Prodromakis Themistoklis , Khiat Ali , Toumazou Christofer
Published: January 2013

In this work, we investigate the effect of oxygen-enhanced TiO2 thin films on the switching dynamics of Pt/TiO2/Pt memristive nanodevices. We demonstrate that such devices can be used as resistive random access memory (RRAM) cells without required electroforming. We experimentally demonstrate that devices based on TiO2 films fabricated via sputtering with partial pressures of Ar/O2 6/6 sccm and 2/10 sccm show OFF/ON ratios of six and two orders of magnitude, respectively. Additionally, it was found that a lower O2 flow during sputtering of TiO2 allows for lower energy requirements for switching the devices from a high to low resistive state.
Dihydride structures of deuterium on germanium (001) surfaces
Authors: Sarhan Abdulla , Yi Ching Ong , Nakanishi Hiroshi , Fukutani Katsuyuki , Kasai Hideaki
Published: January 2013

Structures of deuterium (D) adsorbed on germanium (001) surface were studied by the density functional theory (DFT) calculations and by the scanning tunneling microscope (STM). Two structures of dihydride adsorption were identified on the Ge (001) surface by STM measurements and confirmed by DFT calculated topographies. Also, differences in structural stabilities were explained based on binding strength differences with Ge and on hybridization effect of the s-orbital of D with the Ge p states. The excitation mode of 0.18 eV observed in the STM dI/dV spectrum was found to correspond to the DFT calculated D-Ge stretching vibration mode of 0.17 eV.
Separation of tumor cells with dielectrophoresis-based microfluidic chip
Authors: Alshareef Mohammed , Metrakos Nicholas , Juarez Perez Eva , Azer Fadi , Yang Fang , Yang Xiaoming , Wang Guiren
Published: January 2013

The present work demonstrates the use of a dielectrophoretic lab-on-a-chip device in effectively separating different cancer cells of epithelial origin for application in circulating tumor cell (CTC) identification. This study uses dielectrophoresis (DEP) to distinguish and separate MCF-7 human breast cancer cells from HCT-116 colorectal cancer cells. The DEP responses for each cell type were measured against AC electrical frequency changes in solutions of varying conductivities. Increasing the conductivity of the suspension directly correlated with an increasing frequency value for the first cross-over (no DEP force) point in the DEP spectra. Differences in the cross-over frequency for each cell type were leveraged to determine a frequency at which the two types of cell could be separated through DEP forces. Under a particular medium conductivity, different types of cells could have different DEP behaviors in a very narrow AC frequency band, demonstrating a high specificity of DEP. Using a microfluidic DEP sorter with optically transparent electrodes, MCF-7 and HCT-116 cells were successfully separated from each other under a 3.2 MHz frequency in a 0.1X PBS solution. Further experiments were conducted to characterize the separation efficiency (enrichment factor) by changing experimental parameters (AC frequency, voltage, and flow rate). This work has shown the high specificity of the described DEP cell sorter for distinguishing cells with similar characteristics for potential diagnostic applications through CTC enrichment.
Ultrahigh-frequency surface acoustic wave generation for acoustic charge transport in silicon
Authors: Büyükköse S. , Vratzov B. , van der Veen J. , Santos P. V. , van der Wiel W. G.
Published: January 2013

We demonstrate piezo-electrical generation of ultrahigh-frequency surface acoustic waves on silicon substrates, using high-resolution UV-based nanoimprint lithography, hydrogen silsequioxane planarization, and metal lift-off. Interdigital transducers were fabricated on a ZnO layer sandwiched between two SiO2 layers on top of a Si substrate. Excited modes up to 23.5 GHz were observed. Depth profile calculations of the piezoelectric field show this multilayer structure to be suitable for acoustic charge transport in silicon at extremely high frequencies with moderate carrier mobility requirements.
Electrically driven quantum dot single-photon source at 2 GHz excitation repetition rate with ultra-low emission time jitter
Authors: Hargart F. , Kessler C. A. , Schwarzbäck T. , Koroknay E. , Weidenfeld S. , Jetter M. , Michler P.
Published: January 2013

The influence of the bias voltage on emission properties of a red emitting InP/GaInP quantum dot based single-photon source was investigated. Under pulsed electrical excitation, we can influence the band bending of the p-i-n diode with the applied bias voltage and thus the charge carrier escape by quantum tunneling. This leads to control over the non-radiative decay channel and allows carrier escape times as low as 40 ps, effectively reducing the time jitter of the photon emission. We realized high excitation repetition rates of up to 2 GHz while autocorrelation measurements with g(2)(0)-values of 0.27 attest dominant single-photon emission.
A Novel Organic Electron Donor Derived from N-Methylisatin
Authors: Sword Ryan , O'Sullivan Steven , Murphy John A.
Published: January 2013

We report the reactivity of an electron donor derived from N-methylisatin on reduction by sodium amalgam. Transfer of a clear supernatant solution to iodoarenes affords the products of two-electron reduction. Reductions of sulfones, activated arenesulfonamides, and Weinreb amides are also reported.
The anatomical basis of the link between density and mechanical strength in mangrove branches
Authors: Santini Nadia S. , Schmitz Nele , Bennion Vicki , Lovelock Catherine E.
Published: January 2013

Tree branches are important as they support the canopy, which controls photosynthetic carbon gain and determines ecological interactions such as competition with neighbours. Mangrove trees are subject to high wind speeds, strong tidal flows and waves that can damage their branches. The survival and establishment of mangroves partly depend on the structural and mechanical characteristics of their branches. In addition, mangroves are exposed to soils that vary in salinity. Highly saline conditions can increase the tension in the water column, imposing mechanical stresses on the xylem vessels. Here, we investigated how mechanical strength, assessed as the modulus of elasticity (MOE) and the modulus of rupture (MOR), and density relate to the anatomical characteristics of intact mangrove branches from southeast Queensland and whether the mechanical strength of branches varies among mangrove species. Mechanical strength was positively correlated with density of mangrove intact branches. Mechanical strength (MOE) varied among species, with Avicennia marina (Forssk.) Vierh. branches having the highest mechanical strength (2079 ± 176 MPa), and Rhizophora stylosa Griff. and Bruguiera gymnorrhiza (L.) Savigny ex Lam. and Poiret having the lowest mechanical strength (536.8 ± 39.2 MPa in R. stylosa and 554 ± 58.2 MPa in B. gymnorrhiza). High levels of mechanical strength were associated with reductions in xylem vessel lumen area, pith content and bark content, and positively associated with increases in fibre wall thickness. The associations between mechanical strength and anatomical characteristics in mangrove branches suggest trade-offs between mechanical strength and water supply, which are linked to tree growth and survival.
Mating system and local dispersal patterns of an endangered potoroid, the northern bettong (Bettongia tropica)
Authors: Pope L. C. , Vernes K. , Goldizen A. W. , Johnson C. N.
Published: January 2013

The northern bettong (Bettongia tropica) (Potoroidae), is an endangered macropod with a restricted distribution. We combined radio-tracking and trapping data with microsatellite genotypes to infer the mating system and local dispersal patterns of this species, and discuss their relevance to translocations. We defined the mating system as ‘overlap promiscuity’ (sensu Wittenberger 1979), though we cannot rule out serial monogamy. We found significant effects of proximity (average distance between parents = 190 m) and male weight, but not size, on the likelihood of paternity, suggesting that closer, heavier males have greater mating success. The average distance between putative pairs of relatives suggested that most dispersal occurred over short distances, with the distance between ‘related’ females significantly lower than that between related males (0.9 km versus 1.3 km). A spatial autocorrelation analysis showed high female relatedness across distances of up to 435 m, equivalent to half an average home range width. Conversely, male pairs had low relatedness across 0 to 870 m. These results suggested that female young often settle next to their mother, while males avoid nesting within their father’s home range. Both limited natal and ‘mating’ dispersal may have contributed to the strong genetic structure previously reported for this species.
H1 linker histone promotes epigenetic silencing by regulating both DNA methylation and histone H3 methylation
Authors: Yang Seung-Min , Kim Byung Ju , Norwood Toro Laura , Skoultchi Arthur I.
Published: January 2013

Epigenetic silencing in mammals involves DNA methylation and posttranslational modifications of core histones. Here we show that the H1 linker histone plays a key role in regulating both DNA methylation and histone H3 methylation at the
H19
and
Gtl2
loci in mouse ES cells. Some, but not all, murine H1 subtypes interact with DNA methyltransferases DNMT1 and DNMT3B. The interactions are direct and require a portion of the H1 C-terminal domain. Expression of an H1 subtype that interacts with DNMT1 and DNMT3B in ES cells leads to their recruitment and DNA methylation of the
H19
and
Gtl2
imprinting control regions. H1 also interferes with binding of the SET7/9 histone methyltransferase to the imprinting control regions, inhibiting production of an activating methylation mark on histone H3 lysine 4. H1-dependent recruitment of DNMT1 and DNMT3B and interference with the binding of SET7/9 also were observed with chromatin reconstituted in vitro. The data support a model in which H1 plays an active role in helping direct two processes that lead to the formation of epigenetic silencing marks. The data also provide evidence for functional differences among the H1 subtypes expressed in somatic mammalian cells.
Virulence and stress-related periplasmic protein (VisP) in bacterial/host associations
Authors: Moreira Cristiano G. , Herrera Carmen M. , Needham Brittany D. , Parker Christopher T. , Libby Stephen J. , Fang Ferric C. , Trent M. Stephen , Sperandio Vanessa
Published: January 2013

Gram-negative bacteria have an outer membrane containing LPS. LPS is constituted of an oligosaccharide portion and a lipid-A moiety that embeds this molecule within the outer membrane. LPS is a pathogen-associated molecular pattern, and several pathogens modify their lipid-A as a stealth strategy to avoid recognition by the innate immune system and gain resistance to host factors that disrupt the bacterial cell envelope. An essential feature of
Salmonella enterica
Typhimurium pathogenesis is its ability to replicate within vacuoles in professional macrophages.
S
. Typhimurium modifies its lipid-A by hydroxylation by the Fe2+/α-ketoglutarate-dependent dioxygenase enzyme (LpxO). Here, we show that a periplasmic protein of the bacterial oligonucleotide/oligosaccharide-binding fold family, herein named virulence and stress-related periplasmic protein (VisP), on binding to the sugar moiety of peptidoglycan interacts with LpxO. This interaction inhibits LpxO function, leading to decreased LpxO-dependent lipid-A modifications and increasing resistance to stressors within the vacuole environment during intramacrophage replication promoting systemic disease. Consequently, Δ
visP
is avirulent in systemic murine infections, where VisP acts through LpxO. Several Gram-negative pathogens harbor both VisP and LpxO, suggesting that this VisP-LpxO mechanism of lipid-A modifications has broader implications in bacterial pathogenesis. Bacterial species devoid of LpxO (e.g.,
Escherichia coli
) have no lipid-A phenotypes associated with the lack of VisP; however, VisP also controls LpxO-independent phenotypes. VisP and LpxO act independently in the
S
. Typhimurium murine colitis model, with both mutants being attenuated for diverging reasons; Δ
visP
is less resistant to cationic antimicrobial peptides, whereas Δ
lpxO
is deficient for epithelial cell invasion. VisP converges bacterial cell wall homeostasis, stress responses, and pathogenicity.
Coffee Shops and Cigarettes: On the ‘Return’ to Tehran of Young Diasporic Iranians
Authors: Sreberny-Mohammadi Leili
Published: January 2013

This essay explores the experiences of a young community of diasporic Iranians living and working in Tehran during the years 2007–2009 when the author lived there. Through analysis of the lived experiences of this group, the article highlights a unique experience that is often absent from current discussions of “diaspora.” In the preliminary research, a redeployment of often taken-for-granted concepts such as “home” and “abroad” are proposed and a conceptualization of migration and diaspora that problematizes stasis and movement is reconsidered.
Saudi Arabia: local and regional challenges
Authors: Al-Rasheed Madawi
Published: January 2013

The Arab uprisings posed serious challenges to Saudi Arabia at the level of society and leadership. Activists engaged in intense debates, and both real and virtual protest, to which the leadership responded by fighting for security and survival. The uprisings added to the regime’s internal succession burdens as Islamists in other Arab countries won seats in elected parliaments. The regime responded by deploying tight security measures at home and adopting three strategies to contain the outcome of the Arab uprisings: containment, counter-revolution and revolution. This article examines the intersections between the local and regional challenges facing Saudi Arabia at a critical historical moment. It demonstrates that Arab revolutions and the empowerment of Islamists in neighbouring Arab countries contribute to Saudi Arabia’s losing its unique Islamic credentials. The regime is eager to contain the uprisings in such a way as to remain the sole Islamic model in the region.
Short‐ and Long‐Run Determinants of Commodity Price Volatility
Authors: Karali Berna , Power Gabriel J.
Published: January 2013

To explain price volatility in the U.S. agricultural, energy, and metal futures markets, we estimate a model of common and commodity‐specific, high‐ and low‐frequency factors by building on the spline‐GARCH model of Engle and Rangel (2008). A better model fit results from allowing the unconditional variance to slowly change over time. Moreover, the persistence of volatility shocks is shown to be much weaker than what standard GARCH models imply. Combining the volatility results with monthly macroeconomic indicator data, we find that decomposing realized volatility into high‐ and low‐frequency components better reveals the impact of slowly‐evolving aggregate variables on price volatility. Moreover, over the period 1990–2005, most of the macroeconomic variables had similar effects within the same commodity category (e.g. grain), but their effects differed across commodity groups (e.g. grain versus livestock). Over the period 2006–2009, however, commodity‐specific factors dominated common factors.
The Firm's Management in Production: Management, Firm, and Time Effects in an Indian Ocean Tuna Fishery
Authors: Wolff François-Charles , Squires Dale , Guillotreau Patrice
Published: January 2013

Exploiting variability in the managerial dimension, this paper presents firm management through firm and time effects in a production function that uses a three‐way fixed effect model and a unique panel dataset that tracks multiple managers for each firm from 1980–2007. We allow for time‐varying firm management through learning. The model is applied to the French purse‐seine fleet harvesting tuna in the Indian Ocean. We find that skippers' learning‐by‐doing as measured by experience and job tenure plays no significant role, meaning that managerial ability is time‐invariant.
SIBER: systematic identification of bimodally expressed genes using RNAseq data
Authors: Tong Pan , Chen Yong , Su Xiao , Coombes Kevin R.
Published: January 2013

Motivation: Identification of bimodally expressed genes is an important task, as genes with bimodal expression play important roles in cell differentiation, signalling and disease progression. Several useful algorithms have been developed to identify bimodal genes from microarray data. Currently, no method can deal with data from next-generation sequencing, which is emerging as a replacement technology for microarrays.

Results: We present SIBER (systematic identification of bimodally expressed genes using RNAseq data) for effectively identifying bimodally expressed genes from next-generation RNAseq data. We evaluate several candidate methods for modelling RNAseq count data and compare their performance in identifying bimodal genes through both simulation and real data analysis. We show that the lognormal mixture model performs best in terms of power and robustness under various scenarios. We also compare our method with alternative approaches, including profile analysis using clustering and kurtosis (PACK) and cancer outlier profile analysis (COPA). Our method is robust, powerful, invariant to shifting and scaling, has no blind spots and has a sample-size-free interpretation.

Availability: The R package SIBER is available at the website http://bioinformatics.mdanderson.org/main/OOMPA:Overview.

Contact: kcoombes@mdanderson.org

Supplementary information: Supplementary data are available at Bioinformatics online.
Elizabeth I’s Former Tutor Reports on the Parliament of 1559: Johannes Spithovius to the Chancellor of Denmark, 27 February 1559
Authors: Adams Simon , Gehring David Scott
Published: January 2013

The fragmentary nature of the evidence for the proceedings of the Parliament of 1559 is one of the more obvious reasons for the continuing debate over the Elizabethan religious settlement. Philip II’s representative, the count of Feria, whose reports have been in print for more than a century, has been the primary diplomatic source.1 As a consequence of the war with France, there was no French diplomatic representation at the English court. However, in February 1559 three further envoys arrived on relatively brief missions. George, count of Helfenstein, the Emperor Ferdinand I’s ambassador in Brussels, was commissioned to greet Elizabeth I on her accession, but also to assess her intentions over religion and marriage. He has left a reasonably well-known series of reports.2 The other two envoys are more or less unknown, but both were Lutherans. One was Ludovico Vergerio, nephew of Pier Paulo Vergerio, spiritual advisor to Christopher, duke of Württemberg.3 The last envoy was sent by Dorothea, the recently widowed queen of Denmark.4 His sole surviving report is the only known commentary on the situation in England in February 1559 by a foreign Protestant observer. But he was not a stranger; he had previously been one of Elizabeth’s tutors.
Baseline and serial measurements of galectin‐3 in patients with heart failure: relationship to prognosis and effect of treatment with valsartan in the Val‐HeFT
Authors: Anand Inder S. , Rector Thomas S. , Kuskowski Michael , Adourian Aram , Muntendam Pieter , Cohn Jay N.
Published: January 2013

Aims

This study was conducted to determine whether galectin‐3, a β‐galactoside‐binding lectin, plays a role in the pathogenesis of heart failure (HF).

Methods and results

Galectin‐3 was measured at baseline (n = 1650), after 4 months (n = 1346), and after 12 months (n = 1097) in the Valsartan Heart Failure Trial (Val‐HeFT). Galectin‐3 levels at baseline ranged from 4.8 to 53 ng/mL. Higher levels were associated with features of worse HF. In a fully adjusted Cox regression model comprising 23 other prognostic variables, baseline galectin‐3 was not associated with the risks of all‐cause mortality, the composite of the first morbid event, or hospitalization for HF. However, when changes in galectin‐3 over time were examined, the increases in galectin‐3 between baseline and 4 months were independently and significantly associated with the risks of subsequent all‐cause mortality, first morbid event, and hospitalizations for HF, even after adjusting for all baseline and concurrent changes in all variables including estimated glomerular filtration rate (eGFR) and NT‐proBNP. The strongest correlate of galectin‐3 levels was eGFR, which accounted for 20% of the variability in galectin‐3 levels at baseline. There was a significant interaction (P = 0.03) between baseline galectin‐3 and the effect of valsartan on hospitalizations for HF. Valsartan caused a significant 44% reduction in hospitalizations for HF in patients with galectin‐3 levels below the median level of 16.2 ng/mL, but not in patients with levels above the median.

Conclusions

Galectin‐3 levels are elevated in a substantial proportion of patients with HF, particularly those with more severe HF and renal dysfunction. Galectin‐3 increased over time in this cohort, and the increase was independently associated with worse outcomes. Valsartan use was associated with a reduction in hospitalizations for HF in patients with low galectin‐3, but not in those with higher levels of galectin‐3.
Double dose vs. standard dose influenza vaccination in patients with heart failure: a pilot study
Authors: Van Ermen Amy , Hermanson Matthew P. , Moran John M. , Sweitzer Nancy K. , Johnson Maryl R. , Vardeny Orly
Published: January 2013

Aims

Influenza infection leads to increased morbidity and mortality in those with heart failure, and individuals with heart failure exhibit reduced antibody responses to influenza vaccine. We hypothesized that patients with heart failure randomized to double dose (DD) influenza vaccine will mount more vigorous humoral immune responses compared with those given standard dose (SD) vaccine.

Methods and results

We randomized 28 heart failure patients to DD (30 μg/strain) or SD (15 μg/strain) influenza vaccine. We assessed antibody production by haemagglutination inhibition assay (reported as log haemagglutination units) prior to, at 2–4 weeks and at 4–6 months following vaccination. Baseline antibody titres between DD (n = 12, mean age 64 ± 10 years) and SD (n = 16, mean age 63 ± 9 years) did not differ significantly. At 2–4 weeks, DD haemagglutination unit changes were significantly higher than those of SD (3.3 vs. 1.6 for A/H3N2, P < 0.001; 1.9 and 1.1 for A/H1N1, P = 0.009; and 1.7 and 1 for B‐type, P = 0.02). At 4–6 weeks, there were no differences in titres in any of the virus types between treatment groups and, although titres decreased, levels remained above the seroprotective threshold.

Conclusions

Higher influenza vaccine doses may elicit increased antibody‐mediated responses in patients with heart failure; further studies should assess whether clinical outcomes are improved with this strategy.
Phenotype and function of B cells and dendritic cells from interferon regulatory factor 5-deficient mice with and without a mutation in DOCK2
Authors: Yasuda Kei , Nündel Kerstin , Watkins Amanda A. , Dhawan Tania , Bonegio Ramon G. , Ubellacker Jessalyn M. , Marshak-Rothstein Ann , Rifkin Ian R.
Published: January 2013

Interferon regulatory factor 5-deficient (IRF5−/−) mice have been used for many studies of IRF5 biology. A recent report identifies a mutation in dedicator of cytokinesis 2 (DOCK2) as being responsible for the abnormal B-cell development phenotype observed in the IRF5−/− line. Both dedicator of cytokinesis 2 (DOCK2) and IRF5 play important roles in immune cell function, raising the issue of whether immune effects previously associated with IRF5 are due to IRF5 or DOCK2. Here, we defined the insertion end-point of the DOCK2 mutation and designed a novel PCR to detect the mutation in genomic DNA. We confirmed the association of the DOCK2 mutation and the abnormal B-cell phenotype in our IRF5−/− line and also established another IRF5−/− line without the DOCK2 mutation. These two lines were used to compare the role of IRF5 in dendritic cells (DCs) and B cells in the presence or absence of the DOCK2 mutation. IRF5 deficiency reduces IFN-α, IFN-β and IL-6 production by Toll-like receptor 9 (TLR9)- and TLR7-stimulated DCs and reduces TLR7- and TLR9-induced IL-6 production by B cells to a similar extent in the two lines. Importantly however, IRF5−/− mice with the DOCK2 mutation have higher serum levels of IgG1 and lower levels of IgG2b, IgG2a/c and IgG3 than IRF5−/− mice without the DOCK2 mutation, suggesting that the DOCK2 mutation confers additional Th2-type effects. Overall, these studies help clarify the function of IRF5 in B cells and DCs in the absence of the DOCK2 mutation. In addition, the PCR described will be useful for other investigators using the IRF5−/− mouse line.
Glycodendrimers prevent HIV transmission via DC-SIGN on dendritic cells
Authors: Garcia-Vallejo Juan J. , Koning Nathalie , Ambrosini Martino , Kalay Hakan , Vuist Ilona , Sarrami-Forooshani Ramin , Geijtenbeek Teunis B. H. , van Kooyk Yvette
Published: January 2013

Dendritic cells (DCs) are antigen-presenting cells efficient in capturing pathogens, and processing their antigenic determinants for presentation to antigen-specific T cells to induce robust immune responses. Their location at peripheral tissues and the expression of pattern-recognition receptors, among them DC-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN), facilitates the capture of pathogens before spreading. However, some pathogens have developed strategies to escape the immune system. One of the most successful is HIV-1, which targets DC-SIGN for transport to the lymph node where the virus infects CD4 + T cells. Contact of HIV-1 with DC-SIGN is thus the first event in the pathogenic cascade and, therefore, it is the primary target point for therapies aimed at HIV infection prevention. DC-SIGN recognizes specific glycans on HIV-1 and this interaction can be blocked by competitive inhibition through glycans. Although the affinity of glycans is relatively low, multivalency may increase avidity and the strength to compete with HIV-1 virions. We have designed multivalent dendrimeric compounds based on Lewis-type antigens that bind DC-SIGN with high selectivity and avidity and that effectively block gp120 binding to DC-SIGN and, consequently, HIV transmission to CD4 + T cells. Binding to DC-SIGN and gp120 inhibition was higher on glycodendrimers with larger molecular diameter, indicating that the geometry of the compounds is an important factor determining their functionality. Our compounds elicited DC-SIGN internalization, a property of the receptor upon triggering, but did not affect the maturation status of DCs. Thus, Le X glycodendrimers could be incorporated into topic prophylactic approaches for the prevention of HIV-1 transmission.
Oxidants, antioxidants and the current incurability of metastatic cancers
Authors: Watson Jim
Published: January 2013

The vast majority of all agents used to directly kill cancer cells (ionizing radiation, most chemotherapeutic agents and some targeted therapies) work through either directly or indirectly generating reactive oxygen species that block key steps in the cell cycle. As mesenchymal cancers evolve from their epithelial cell progenitors, they almost inevitably possess much-heightened amounts of antioxidants that effectively block otherwise highly effective oxidant therapies. Also key to better understanding is why and how the anti-diabetic drug metformin (the world's most prescribed pharmaceutical product) preferentially kills oxidant-deficient mesenchymal p53
− −
cells. A much faster timetable should be adopted towards developing more new drugs effective against p53
− −
cancers.
ATR-like kinase Mec1 facilitates both chromatin accessibility at DNA replication forks and replication fork progression during replication stress
Authors: Rodriguez Jairo , Tsukiyama Toshio
Published: January 2013

Faithful DNA replication is essential for normal cell division and differentiation. In eukaryotic cells, DNA replication takes place on chromatin. This poses the critical question as to how DNA replication can progress through chromatin, which is inhibitory to all DNA-dependent processes. Here, we developed a novel genome-wide method to measure chromatin accessibility to micrococcal nuclease (MNase) that is normalized for nucleosome density, the NCAM (normalized chromatin accessibility to MNase) assay. This method enabled us to discover that chromatin accessibility increases specifically at and ahead of DNA replication forks in normal S phase and during replication stress. We further found that Mec1, a key regulatory ATR-like kinase in the S-phase checkpoint, is required for both normal chromatin accessibility around replication forks and replication fork rate during replication stress, revealing novel functions for the kinase in replication stress response. These results suggest a possibility that Mec1 may facilitate DNA replication fork progression during replication stress by increasing chromatin accessibility around replication forks.