bluuebunny/crossref_metadata_2025 huggingface dataset:
Observation of momentum space semi-localization in Si-doped β-Ga2O3
Authors: Richard P. , Sato T. , Souma S. , Nakayama K. , Liu H. W. , Iwaya K. , Hitosugi T. , Aida H. , Ding H. , Takahashi T.
Published: December 2012

We performed an angle-resolved photoemission spectroscopy study of Si-doped β-Ga2O3. We observed very small photoemission intensity near the Fermi level corresponding to non-dispersive states assigned to Si impurities. We show evidence for a quantization of these states that is accompanied by a confinement in the momentum space consistent with a real-space finite confinement observed in a previous scanning tunneling microscopy study. Our results suggest that this semi-localization in the conjugate spaces plays a crucial role in the electronic conduction of this material.
Existence domains of arbitrary amplitude nonlinear structures in two-electron temperature space plasmas. II. High-frequency electron-acoustic solitons
Authors: Maharaj S. K. , Bharuthram R. , Singh S. V. , Lakhina G. S.
Published: December 2012

A three-component plasma model composed of ions, cool electrons, and hot electrons is adopted to investigate the existence of large amplitude electron-acoustic solitons not only for the model for which inertia and pressure are retained for all plasma species which are assumed to be adiabatic but also neglecting inertial effects of the hot electrons. Using the Sagdeev potential formalism, the Mach number ranges supporting the existence of large amplitude electron-acoustic solitons are presented. The limitations on the attainable amplitudes of electron-acoustic solitons having negative potentials are attributed to a number of different physical reasons, such as the number density of either the cool electrons or hot electrons ceases to be real valued beyond the upper Mach number limit, or, alternatively, a negative potential double layer occurs. Electron-acoustic solitons having positive potentials are found to be supported only if inertial effects of the hot electrons are retained and these are found to be limited only by positive potential double layers.
Thin-film encapsulation of inverted indium-tin-oxide-free polymer solar cells by atomic layer deposition with improvement on stability and efficiency
Authors: Li Kan , Fan Huanhuan , Huang Chaofan , Hong Xia , Fang Xu , Li Haifeng , Liu Xu , Li Chengshuai , Huang Zhuoyin , Zhen Hongyu
Published: December 2012

Atomic layer deposition (ALD) technology is employed to encapsulate inverted indium-tin-oxide-free polymer solar cells (IFSCs) with a structure of Al/TiOx/P3HT:PC61BM/PEDOT:PSS. The encapsulation layer, Al2O3, is deposited by ALD on the light incident surface. The thickness of the Al2O3 layer can thus be optimized through optical simulation to minimize light loss of IFSCs. Based on optical calculation, we encapsulated the device (85 nm thick active layer) with a 30 nm thick Al2O3 layer. The resulting ALD encapsulated IFSCs show much better device performance and higher stability than the glass-encapsulated ones.
An accurate determination of the surface energy of solid selenium
Authors: Guisbiers G. , Arscott S. , Snyders R.
Published: December 2012

Selenium is currently a key element for developing nano and micro-technologies. Nevertheless, the surface energy of solid selenium (γSe) reported in the literature is still questionable. In this work, we have measured γSe = 0.291 ± 0.025 J/m2 at 293 K using the sessile drop technique with different probe liquids, namely ethylene glycol, de-ionized water, mercury, and gallium. This value is in excellent agreement with theoretical predictions.
Correlation between interface energetics and open circuit voltage in organic photovoltaic cells
Authors: Wilke A. , Endres J. , Hörmann U. , Niederhausen J. , Schlesinger R. , Frisch J. , Amsalem P. , Wagner J. , Gruber M. , Opitz A. , Vollmer A. , Brütting W. , Kahn A. , Koch N.
Published: December 2012

We have used ultraviolet and inverse photoemission spectroscopy to determine the transport gaps (Et) of C60 and diindenoperylene (DIP), and the photovoltaic gap (EPVG) of five prototypical donor/acceptor interfaces used in organic photovoltaic cells (OPVCs). The transport gap of C60 (2.5 ± 0.1) eV and DIP (2.55 ± 0.1) eV at the interface is the same as in pristine films. We find nearly the same energy loss of ca 0.5 eV for all material pairs when comparing the open circuit voltage measured for corresponding OPVCs and EPVG.
Global gyrokinetic particle-in-cell simulations of internal kink instabilities
Authors: Mishchenko Alexey , Zocco Alessandro
Published: December 2012

Internal kink instabilities have been studied in straight tokamak geometry employing an electromagnetic gyrokinetic particle-in-cell (PIC) code. The ideal-MHD internal kink mode and the collisionless m=1 tearing mode have been successfully simulated with the PIC code. Diamagnetic effects on the internal kink modes have also been investigated.
Moving Away, Moving Onward: Displacement Pressures and Divergent Neighborhood Politics in Buenos Aires
Authors: Centner Ryan
Published: December 2012

This paper focuses on two Buenos Aires neighborhoods that face displacement pressures. Building on research about urban mobilization in a range of cities, this paper highlights how collaboration can vary in its configuration and orientation at the neighborhood level, despite similar circumstances. Data include ethnographic excerpts from the experiences of residents who fight to remain in their homes but ultimately leave, which trace out distinct neighborhood trajectories—moving onward and moving away. These accounts indicate divergence in how residents respond to displacement threats due to the differently situated, networked nature of the two sites as political spaces. Moreover, distinct logics of collaboration inflect ongoing displacement politics in the threatened neighborhoods as well as in the destinations of displaced residents.
God, Globalization, and Geopolitics: On West Jerusalem's Gated Communities
Authors: Yacobi Haim
Published: December 2012

Over the last two decades West Jerusalem's city centre has undergone wide-scale privatization of space which is expressed, for instance, in the extensive construction of gated-community housing compounds. This is a global process which can be seen in many cities where neoliberal policies are implemented, resulting in the expansion of the elite's private capital on the one hand and the weakening of the welfare state as part of globalization processes on the other. However, this explanation is not sufficient when analyzing the privatization of space in West Jerusalem's city centre, which is spatially and politically part of the ongoing Israeli—Arab conflict. In other words, my argument is that the case of West Jerusalem illustrates a combination both of local ethnosecurity discourses and of global neoliberal urban policies which do not contradict each other, but rather are complementary.
‘Stars’ and the Connectivity of Cultural Industry World Cities: An Empirical Social Network Analysis of Human Capital Mobility and its Implications for Economic Development
Authors: Currid-Halkett Elizabeth , Ravid Gilad
Published: December 2012

Many scholars have studied the role of human capital and its social networks in order to understand uneven economic development. The cultural industries have become a focal point in this line of inquiry. In this paper we study the linkages across cultural industry hubs, with particular focus on the role of ‘star’ human capital networks in the establishment of connectivity and dominance by a few particular cities. To date, no one has used a technique that directly connects individuals across space and empirically follows the social networks of human capital across major economic hubs. We use a unique dataset, Getty Images photographs, and undertake social network analysis to study the social networks and human capital movement within the cultural industries. We collected caption information on over 600 000 photographs, 6754 individuals, 12 777 industry social events, and 187 locations. We analyzed these photographic data to determine whether empirical social connections could tell us something meaningful about cultural industry human capital mobility and its impact on the places in which it locates. Our results empirically reaffirm preexisting knowledge of cultural hubs, but we go farther by articulating the connectivity between these places and identifying the social relations and human capital that appear to correlate with their competitive advantage.
Who Sprawls Most? Exploring the Patterns of Urban Growth across 26 European Countries
Authors: Siedentop Stefan , Fina Stefan
Published: December 2012

In recent years considerable progress has been made in the understanding of urban land-use change and its dynamic interrelationships with economic, social, and environmental systems. From a quantitative perspective, advancements in GIS technologies, the increased availability of high-resolution remote sensing data, and new GIS-based spatial metrics of urban form and urban growth have helped to establish methods for comparative spatial analysis. However, due to the lack of homogeneous data, very few empirical studies have systematically addressed urbanisation and urban growth at a cross-national level. With this background, this paper presents a comparative assessment of urban land-use change across twenty-six European countries. On two scales of analysis, country and 20 km cells, we found a surprising variability in terms of urban growth and its territorial shape. We argue that these differences cannot be explained by varying demographic or economic growth pressures alone. Indicators on the composition, pattern, and density of urban growth illustrate that country-specific drivers of urban land-use change play an important role for the shaping of Europe's settlement structure.
Network Governance Theory: A Gramscian Critique
Authors: Davies Jonathan S
Published: December 2012

Influential governance theories argue that we live increasingly in a world of networks either relegating hierarchy to the shadows or dismissing it altogether. This paper develops a Gramscian critique of these currents, advancing two key arguments. First, drawing on Gramsci's concepts of hegemony and passive revolution, it reinterprets the cultivation of networks as a prominent element in the hegemonic strategies of Western neoliberalism, exemplified by UK public policy. Second, however, governing networks struggle to cultivate trust, relying instead on hierarchy and closure. It is argued that network governance can therefore be understood as a form of Gramsci's integral state, a concept which highlights both the continuing centrality of coercion in the governance system and the limits of the networks project. It is concluded that conceiving of urban governing networks as micro configurations of the integral state offers a distinctive way of overcoming the ‘government to governance’ dualism.
Shape Detection of Gaborized Outline Versions of Everyday Objects
Authors: Sassi Michaël , Machilsen Bart , Wagemans Johan
Published: December 2012

We previously tested the identifiability of six versions of Gaborized outlines of everyday objects, differing in the orientations assigned to elements inside and outside the outline. We found significant differences in identifiability between the versions, and related a number of stimulus metrics to identifiability [Sassi, M., Vancleef, K., Machilsen, B., Panis, S., & Wagemans, J. (2010). Identification of everyday objects on the basis of Gaborized outline versions. i-Perception, 1(3), 121–142]. In this study, after retesting the identifiability of new variants of three of the stimulus versions, we tested their robustness to local orientation jitter in a detection experiment. In general, our results replicated the key findings from the previous study, and allowed us to substantiate our earlier interpretations of the effects of our stimulus metrics and of the performance differences between the different stimulus versions. The results of the detection task revealed a different ranking order of stimulus versions than the identification task. By examining the parallels and differences between the effects of our stimulus metrics in the two tasks, we found evidence for a trade-off between shape detectability and identifiability. The generally simple and smooth shapes that yield the strongest contour integration and most robust detectability tend to lack the distinguishing features necessary for clear-cut identification. Conversely, contours that do contain such identifying features tend to be inherently more complex and, therefore, yield weaker integration and less robust detectability.
Directionless Vection: A New Illusory Self-Motion Perception
Authors: Seno Takeharu , Yamada Yuki , Palmisano Stephen
Published: December 2012

We report a new visual illusion, “directionless vection.” When expanding and contracting optic flows are simultaneously presented in the same depth plane, observers can perceive illusory self-motion (vection) without direction.
“Exorcist Illusion”: Twisting Necks in the Hollow-Face and Hollow-Torso Illusions
Authors: Papathomas Thomas V. , De Heer Marcel , Zhuang Xiaohua , Grace Tom , Bunkin Robert
Published: December 2012

We combine a convex facial mask with a concave torso—or vice versa—thus creating a single rigid object with a transition area at the neck, where convexity changes to concavity. This combination creates stunning illusions when the rigid object is set to motion. The two simplest effects are (1) when the object is rotated about its axis, the head appears to twist with respect to the torso, as in “The Exorcist” film (2) when it is rotated around an axis parallel to the shoulders, the head appears to hinge around the torso. More complex illusory effects result from more complex motions. The involvement of higher-level perceptual processes may account for the illusory effects.
Why Do Most Faces Look Thinner Upside Down?
Authors: Thompson Peter , Wilson Jennie
Published: December 2012

Faces are found generally to be perceived as thinner when viewed upside down. When a face is viewed upright, the internal features are thought to influence the perception of face shape. However, when inverted, it has been proposed that disruption to holistic processing means that these factors can no longer be used to judge the shape of a face. We show that it is not the case that an inverted face reverts to some average shape whereby fat faces appear thinner upside down whereas thin faces appear fatter. The fact that the illusion appears to occur for most face shapes is discussed with regard to the horizontal–vertical illusion.
Population dynamics of the invasive, annual species, Carrichtera annua, in Australia
Authors: Cooke J. , Ash J. E. , Groves R. H.
Published: December 2012

Carrichtera annua (L.) DC. (Brassicaceae) is a widespread weed of the southern rangelands of Australia and there is currently no effective control strategy for this weed outside agricultural systems. Field and glasshouse experiments were used to target various stages of the life cycle of C. annua that, from initial field observations and a review of the literature, appeared to be important or were poorly understood in Australia. Seed production was found to be prodigious with up to 30 000 seed m–2 recorded in the field and extensive collection of dry-dispersed seed by ants was documented, similar to that in the native range of C. annua. Two seedbanks, an aerial pod seedbank and a soil seedbank, are key features contributing to the success of this invasive species as the seedbanks are subject to, and protected from, contrasting pressures. The aerial seedbank, usually the larger of the two, protects seed from collection by ants but is susceptible to vertebrate grazing and fire, while the soil seedbank is depleted by ants and seed decay although the adhesive nature of wetted seeds helps stabilise this seedbank. The population can be replenished by either seedbank in one generation, hence both seedbanks need to be targeted to allow successful control. Inhibition of germination by high temperatures in unfavourable conditions and the potential to reach maturation and fruit production very quickly also contribute to the high seed production of this species.
Microfluidic Western blotting
Authors: Hughes Alex J. , Herr Amy E.
Published: December 2012

Rapid, quantitative Western blotting is a long-sought bioanalytical goal in the life sciences. To this end, we describe a Western blotting assay conducted in a single glass microchannel under purely electronic control. The μWestern blot is comprised of multiple steps: sample enrichment, protein sizing, protein immobilization (blotting), and in situ antibody probing. To validate the microfluidic assay, we apply the μWestern blot to analyses of human sera (HIV immunoreactivity) and cell lysate (NFκB). Analytical performance advances are achieved, including: short durations of 10–60 min, multiplexed analyte detection, mass sensitivity at the femtogram level, high-sensitivity 50-pM detection limits, and quantitation capability over a 3.6-log dynamic range. Performance gains are attributed to favorable transport and reaction conditions on the microscale. The multistep assay design relies on a photopatternable (blue light) and photoreactive (UV light) polyacrylamide gel. This hydrophilic polymer constitutes both a separation matrix for protein sizing and, after brief UV exposure, a protein immobilization scaffold for subsequent antibody probing of immobilized protein bands. We observe protein capture efficiencies exceeding 75% under sizing conditions. This compact microfluidic design supports demonstration of a 48-plex μWestern blot in a standard microscope slide form factor. Taken together, the μWestern blot establishes a foundation for rapid, targeted proteomics by merging exceptional specificity with the throughput advantages of multiplexing, as is relevant to a broad range of biological inquiry.
CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice
Authors: Guo Ya , Monahan Kevin , Wu Haiyang , Gertz Jason , Varley Katherine E. , Li Wei , Myers Richard M. , Maniatis Tom , Wu Qiang
Published: December 2012

The closely linked human protocadherin (
Pcdh
) α, β, and γ gene clusters encode 53 distinct protein isoforms, which are expressed in a combinatorial manner to generate enormous diversity on the surface of individual neurons. This diversity is a consequence of stochastic promoter choice and alternative pre-mRNA processing. Here, we show that
Pcdhα
promoter choice is achieved by DNA looping between two downstream transcriptional enhancers and individual promoters driving the expression of alternate Pcdhα isoforms. In addition, we show that this DNA looping requires specific binding of the CTCF/cohesin complex to two symmetrically aligned binding sites in both the transcriptionally active promoters and in one of the enhancers. These findings have important implications regarding enhancer/promoter interactions in the generation of complex
Pcdh
cell surface codes for the establishment of neuronal identity and self-avoidance in individual neurons.
Non-local residue–residue contacts in proteins are more conserved than local ones
Authors: Noivirt-Brik Orly , Hazan Gershon , Unger Ron , Ofran Yanay
Published: December 2012

Non-covalent residue–residue contacts drive the folding of proteins and stabilize them. They may be local—i.e. involve residues that are close in sequence, or non-local. It has been suggested that, in most proteins, local contacts drive protein folding by providing crucial constraints of the conformational space, thus allowing proteins to fold. We compared residues that are involved in local contacts to residues that are involved in non-local contacts and found that, in most proteins, residues in non-local contacts are significantly more conserved evolutionarily than residues in local contacts. Moreover, non-local contacts are more structurally conserved: a contact between positions that are distant in sequence is more likely to exist in many structural homologues compared with a contact between positions that are close in sequence. These results provide new insights into the mechanisms of protein folding and may allow for better prediction of critical intra-chain contacts.

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  yanay@ofranlab.org
Nonomuraea solani sp. nov., an actinomycete isolated from eggplant root (Solanum melongena L.)
Authors: Wang Xiangjing , Zhao Junwei , Liu Chongxi , Wang Jidong , Shen Yue , Jia Feiyu , Wang Liang , Zhang Ji , Yu Chao , Xiang Wensheng
Published: December 2012

A novel actinomycete, designated strain NEAU-Z6T, was isolated from eggplant (Solanum melongena L.) root. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain NEAU-Z6T belonged to the genus

Nonomuraea

, with highest sequence similarity to

Nonomuraea monospora

PT 708T (98.83 %),

Nonomuraea rosea

GW 12687T (98.55 %) and

Nonomuraea rhizophila

YIM 67092T (98.02 %). Sequence similarities between strain NEAU-Z6T and other species of the genus

Nonomuraea

ranged from 97.94 % (

Nonomuraea candida

HMC10T) to 96.30 % (

Nonomuraea wenchangensis

210417T). Key morphological, physiological and chemotaxonomic characteristics of strain NEAU-Z6T were congruent with the description of the genus

Nonomuraea

. The G+C content of the genomic DNA was 64.51 mol%. DNA–DNA relatedness and comparative analysis of physiological, biochemical and chemotaxonomic data allowed genotypic and phenotypic differentiation of strain NEAU-Z6T from closely related species. Thus, strain NEAU-Z6T represents a novel species of the genus

Nonomuraea

, for which the name Nonomuraea solani sp. nov. is proposed. The type strain is NEAU-Z6T ( = CGMCC 4.7037T = DSM 45729T).
Naasia aerilata gen. nov., sp. nov., a member of the family

Microbacteriaceae

isolated from air
Authors: Weon Hang-Yeon , Kim Soo-Jin , Jang Yun-Hee , Hamada Moriyuki , Tamura Tomohiko , Ahn Jae-Hyung , Suzuki Ken-ichiro , Kwon Soon-Wo
Published: December 2012

A Gram-positive, aerobic, rod-shaped bacterial strain, 5116S-4T, was isolated from an air sample collected in Suwon city, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain was a new member of the family

Microbacteriaceae

. The sequence similarities of this strain to the members of the family

Microbacteriaceae

were less than 97 %, with the highest values observed with

Cryobacterium mesophilum

MSL-15T (96.3 %),

Cryobacterium roopkundense

RuGl7T (96.2 %),

Labedella gwakjiensis

KSW2-17T (96.2 %),

Cryobacterium luteum

Hh15T (96.2 %),

Cryobacterium psychrophilum

DSM 4854T (96.2 %),

Klugiella xanthotipulae

44C3T (96.0 %) and

Amnibacterium kyonggiense

KSL51201-037T (96.0 %). According to the phylogenetic tree, strain 5116S-4T formed a cluster with

A. kyonggiense

KSL51201-037T,

Labedella gwakjiensis

KSW2-17T and
Lysinimonas soli
SGM3-12T (95.3 % sequence similarity) on the support of high bootstrap values. Cells were motile with single polar flagellum and showed optimum growth at 30 °C and pH 7 without NaCl. Predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Polar lipids were diphosphatidylglycerol, dimannosyldiacylglycerol, phosphatidylglycerol, one unknown glycolipid, one unknown phospholipid and one unknown lipid. The acyl type of the cell-wall muramic acid was the acetyl type. Peptidoglycan was supposed to be the type B1 with 2,4-diaminobutyric acid on position 3. Strain 5116S-4T was clearly distinguishable from the phylogenetically related genera in the family

Microbacteriaceae

in terms of chemotaxonomic characteristics. On the basis of the chemotaxonomic and phylogenetic characteristics, a novel genus and species are proposed, Naasia aerilata gen. nov., sp. nov. The type strain of Naasia aerilata is 5116S-4T ( = KACC 15517T  = NBRC 108725T).
Microbacterium oryzae sp. nov., an actinobacterium isolated from rice field soil
Authors: Kumari Prabla , Bandyopadhyay Saumya , Das Subrata K.
Published: December 2012

A novel aerobic soil actinobacterium (strain MB10T) belonging to the genus

Microbacterium

was isolated from rice field soil samples collected from Jagatpur, Orissa, India. Cells were Gram-stain positive, short rod-shaped and motile. The strain was oxidase-negative and catalase-positive. Heterotrophic growth was observed at pH 5.0–11.0 and at 16–37 °C; optimum growth was observed at 28 °C and pH 7.0–9.0. The DNA G+C content was 71.6 mol%. Predominant cellular fatty acids of strain MB10T were iso-C14 : 0, anteiso-C15 : 0, C16 : 0, iso-C16 : 0 and anteiso-C17 : 0. Cell wall sugars were galactose, glucose and rhamnose. The major isoprenoid quinones were MK-9 (10 %), MK-10 (43 %) and MK-11 (36 %). The peptidoglycan represents the peptidoglycan type B2β. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid and unknown glycolipids. 16S rRNA gene sequence identity revealed the strain MB10T clustered within the radiation of the genus

Microbacterium

and showed 99.2 % similarity with

Microbacterium barkeri

DSM 20145T. However, DNA–DNA similarity study was 37.0 % with

Microbacterium barkeri

DSM 20145T, the nearest phylogenetic relative. On the basis of phenotypic and chemotaxonomic properties, 16S rRNA gene sequence analysis and DNA–DNA reassociation studies, it is proposed that strain MB10T represents a novel species of the genus

Microbacterium

, for which the name Microbacterium oryzae sp. nov. is proposed; the type strain is MB10T ( = JCM 16837T = DSM 23396
T
).
Leptospira

idonii sp. nov., isolated from environmental water
Authors: Saito Mitsumasa , Villanueva Sharon Y. A. M. , Kawamura Yoshiaki , Iida Ken-ichiro , Tomida Junko , Kanemaru Takaaki , Kohno Eri , Miyahara Satoshi , Umeda Akiko , Amako Kazunobu , Gloriani Nina G. , Yoshida Shin-ichi
Published: December 2012

Strain Eri-1T was isolated from a water sample on the campus of Kyushu University, Fukuoka, Japan. The motility and morphology of the isolate were similar to those of members of the genus

Leptospira

, but the spiral structure of the isolate was sharper under dark-field microscopy. Cells were 10.6±1.3 µm long and 0.2 µm in diameter, with a wavelength of 0.9 µm and an amplitude of 0.4 µm. Strain Eri-1T grew in Korthof’s medium at both 13 and 30 °C, and also in the presence of 8-azaguanine. 16S rRNA gene-based phylogenetic analysis placed strain Eri-1T within the radiation of the genus

Leptospira

where it formed a unique lineage within the clade of the known saprophytic species of the genus

Leptospira

. The strain was not pathogenic to hamsters. Strain Eri-1T exhibited low levels (11.2–12.6 %) of similarity by DNA–DNA hybridization to the three most closely related species of the genus

Leptospira

. The DNA G+C content of the genome of strain Eri-1T was 42.5±0.1 mol%. These results suggest that strain Eri-1T represents a novel species of the genus

Leptospira

, for which the name

Leptospira

idonii sp. nov. is proposed. The type strain is Eri-1T ( = DSM 26084T = JCM 18486T).
Aureimonas ferruginea sp. nov. and Aureimonas rubiginis sp. nov., two siderophore-producing bacteria isolated from rusty iron plates
Authors: Lin Shih-Yao , Hameed Asif , Liu You-Cheng , Hsu Yi-Han , Lai Wei-An , Shen Fo-Ting , Young Li-Sen , Tsai Chia-Fang , Young Chiu-Chung
Published: December 2012

Two novel siderophore-producing strains designated CC-CFT023T and CC-CFT034T, isolated from a rusty iron plate, are characterized in this study. Cells of both strains were catalase- and oxidase-positive. Strain CC-CFT023T showed a high pairwise 16S rRNA gene sequence similarity to

Aureimonas altamirensis

LMG 23375T (96.0 %), whereas, strain CC-CFT034T shared a maximum similarity to

Aureimonas ureilytica

DSM 18598T (95.8 %). The predominant quinone system was ubiquinone (Q-10) and the DNA G+C contents of CC-CFT023T and CC-CFT034T were 69.5 mol% and 67.7 mol%, respectively. The major fatty acids of these strains were C16 : 0, C18 : 0, C19 : 0 cyclo ω8c, C18 : 1 2-OH and summed features 3 and 8, consisting of C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c, respectively. Polar lipid profiles of both of these isolates include diphosphatidylglycerol (DPG), phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and most importantly sulfoquinovosyldiacylglycerol (SQDG), which is one of the typical molecular features reported to delineate the members of the genus

Aureimonas

from their closest relatives, species of the genus

Aurantimonas

. Based on the phylogenetic, phenotypic and chemotaxonomic features, strains CC-CFT023T and CC-CFT034T represent two novel species within the genus

Aureimonas

, for which the names Aureimonas ferruginea sp. nov. (type strain CC-CFT023T = BCRC 80439T = JCM 18444T) and Aureimonas rubiginis sp. nov. (type strain CC-CFT034T = BCRC 80440T = JCM 18445T) are proposed.
Wickerhamiella dulcicola sp. nov. and Wickerhamiella cachassae sp. nov., yeasts isolated from cachaça fermentation in Brazil
Authors: Badotti Fernanda , Silva Pollyana A. B. , Mendonça Michelle C. , Gomes Fatima C. O. , Morais Paula B. , Lachance Marc-André , Rosa Carlos A.
Published: December 2012

Six strains of two novel yeast species were isolated from sugar-cane juice and fermentation vats of cachaça production in Brazil. The sequences of the D1/D2 domains of the large-subunit rRNA gene showed that these species belong to the Wickerhamiella clade, and their closest described relative in terms of sequence similarity is Candida (iter. nom. Wickerhamiella) drosophilae. The type strain of Wickerhamiella cachassae sp. nov. is UFMG-D5L7T ( = CBS 12587T  = CBMAI 1469T) and the type strain of Wickerhamiella dulcicola sp. nov. is UFMG-TOL15T ( = CBS 12588T  = CBMAI 1468T).
Generation and characterization of a new panel of broadly reactive anti-NS1 mAbs for detection of influenza A virus
Authors: Rahim Md Niaz , Selman Mohammed , Sauder Patricia J. , Forbes Nicole E. , Stecho William , Xu Wanhong , Lebar Mark , Brown Earl G. , Coombs Kevin M.
Published: December 2012

Influenza A virus (IAV) non-structural protein 1 (NS1) has multiple functions, is essential for virus replication and may be a good target for IAV diagnosis. To generate broadly cross-reactive NS1-specific mAbs, mice were immunized with A/Hong Kong/1/1968 (H3N2) 6×His-tagged NS1 and hybridomas were screened with glutathione S-transferase-conjugated NS1 of A/Puerto Rico/8/1934 (H1N1). mAbs were isotyped and numerous IgG-type clones were characterized further. Most clones specifically recognized NS1 from various H1N1 and H3N2 IAV types by both immunoblot and immunofluorescence microscopy in mouse M1, canine Madin–Darby canine kidney and human A549 cells. mAb epitopes were mapped by overlapping peptides and selective reactivity to the newly described viral NS3 protein. These mAbs detected NS1 in both the cytoplasm and nucleus by immunostaining, and some detected NS1 as early as 5 h post-infection, suggesting their potential diagnostic use for tracking productive IAV replication and characterizing NS1 structure and function. It was also demonstrated that the newly identified NS3 protein is localized in the cytoplasm to high levels.
Human immunodeficiency virus-1 BF intersubtype recombinant viral protein U second alpha helix plays an important role in viral release and BST-2 degradation
Authors: De Candia Cristian , Espada Constanza , Duette Gabriel , Salomón Horacio , Carobene Mauricio
Published: December 2012

We previously reported a naturally occurring BF intersubtype recombinant viral protein U (Vpu) variant with an augmented capacity to enhance viral replication. Structural analysis of this variant revealed that its transmembrane domain and α-helix I in the cytoplasmic domain (CTD) corresponded to subtype B, whereas the α-helix II in the CTD corresponded to subtype F1. In this study, we aimed to evaluate the role of the Vpu cytoplasmic α-helix II domain in viral release enhancement and in the down-modulation of BST-2 and CD4 from the cell surface. In addition, as serine residues in Vpu amino acid positions 61 or 64 have been shown to regulate Vpu intracellular half-life, which in turn could influence the magnitude of viral release, we also studied the impact of these residues on the VpuBF functions, since S61 and S64 are infrequently found among BF recombinant Vpu variants. Our results showed that the exchange of Vpu α-helix II between subtypes (B→F) directly correlated with the enhancement of viral release and, to a lesser extent, with changes in the capacity of the resulting chimera to down-modulate BST-2 and CD4. No differences in viral release and BST-2 down-modulation were observed between VpuBF and VpuBF-E61S. On the other hand, VpuBF-A64S showed a slightly reduced capacity to enhance viral production, but was modestly more efficient than VpuBF in down-modulating BST-2. In summary, our observations clearly indicate that α-helix II is actively involved in Vpu viral-release-promoting activity and that intersubtype recombination between subtypes B and F1 created a protein variant with a higher potential to boost the spread of the recombinant strain that harbours it.
Identification and characterization of novel porcine astroviruses (PAstVs) with high prevalence and frequent co-infection of individual pigs with multiple PAstV types
Authors: Xiao Chao-Ting , Giménez-Lirola Luis G. , Gerber Priscilla F. , Jiang Yong-Hou , Halbur Patrick G. , Opriessnig Tanja
Published: December 2012

Many astrovirus (AstV) species are associated with enteric disease, although extraintestinal manifestations in mammalian and avian hosts have also been described. In this study, the prevalence rates of porcine AstV types 1–5 (PAstV1–PAstV5) were investigated using faecal samples from 509 pigs of which 488 (95.9 %) came from farms with a history of diarrhoea. All of the five known PAstV types were found to circulate in pigs in the USA, and co-infection of a single pig with two or more PAstV types was frequently observed. A high overall prevalence of 64.0 % (326/509) of PAstV RNA-positive samples was detected, with 97.2 % (317/326) of the PAstV RNA-positive pigs infected with PAstV4. Further genomic sequencing and characterization of the selected isolates revealed low sequence identities (49.2–89.0 %) with known PAstV strains, indicating novel types or genotypes of PAstV2, PAstV4 and PAstV5. Some new features of the genomes of the PAstVs were also discovered. The first complete genome of a PAstV3 isolate was obtained and showed identities of 50.5–55.3 % with mink AstV and the novel human AstVs compared with 38.4–42.7 % with other PAstV types. Phylogenetic analysis revealed that PAstV1, PAstV2 and PAstV3 were more closely related to AstVs from humans and other animals than to each other, indicating past cross-species transmission and the zoonotic potential of these PAstVs.
Greenhouse Gas Emission Accounting and Management of Low-Carbon Community
Authors: Song Dan , Su Meirong , Yang Jin , Chen Bin
Published: December 2012

As the major source of greenhouse gas (GHG) emission, cities have been under tremendous pressure of energy conservation and emission reduction for decades. Community is the main unit of urban housing, public facilities, transportation, and other properties of city's land use. The construction of low-carbon community is an important pathway to realize carbon emission mitigation in the context of rapid urbanization. Therefore, an efficient carbon accounting framework should be proposed for CO2emissions mitigation at a subcity level. Based on life-cycle analysis (LCA), a three-tier accounting framework for the carbon emissions of the community is put forward, including emissions from direct fossil fuel combustion, purchased energy (electricity, heat, and water), and supply chain emissions embodied in the consumption of goods. By compiling a detailed CO2emission inventory, the magnitude of carbon emissions and the mitigation potential in a typical high-quality community in Beijing are quantified within the accounting framework proposed. Results show that emissions from supply chain emissions embodied in the consumption of goods cannot be ignored. Specific suggestions are also provided for the urban decision makers to achieve the optimal resource allocation and further promotion of low-carbon communities.
The Effects of Piroxicam and Deracoxib on Canine Mammary Tumour Cell Line
Authors: Üstün Alkan Fulya , Üstüner Oya , Bakırel Tülay , Çınar Suzan , Erten Gaye , Deniz Günnur
Published: December 2012

Cyclooxygenase (COX) inhibitors, already widely used for the treatment of pain and inflammation, are considered as promising compounds for the prevention and treatment of neoplasia. The aim of our study was to determine the direct antiproliferative effects of nonsteroidal anti-inflammatory drugs (NSAIDs), piroxicam and deracoxib, at a variety of concentrations as both single and combined treatments on canine mammary carcinoma cell line CMT-U27 and to understand the mechanisms of cell death. MTT assay was performed to determine cell viability, and flow cytometric analyses were performed to evaluate apoptosis and cell cycle alterations. Significant decrease in cell viability was observed at high concentrations of piroxicam and deracoxib in both single and combined treatments after 72 h incubation. Combined treatment produced a significantly greater inhibition than that caused by either agent alone. Also apoptotic cell number was increased by both drugs at the cytotoxic concentrations. However, concomitant treatment of cells with piroxicam and deracoxib resulted in significant induction of apoptosis at lower concentrations and accumulation of cells in the G0/G1phase. Significant cytotoxic effects exhibited by the combination of piroxicam and deracoxib against canine mammary carcinoma cellsin vitrosuggest an attractive approach for the treatment of canine mammary carcinoma.
Tissue-Specific Silencing of ArabidopsisSU(VAR)3-9 HOMOLOG8by miR171a
Authors: Manavella Pablo A. , Koenig Daniel , Rubio-Somoza Ignacio , Burbano Hernán A. , Becker Claude , Weigel Detlef
Published: December 2012

MicroRNAs (miRNAs) are produced from double-stranded precursors, from which a short duplex is excised. The strand of the duplex that remains more abundant is usually the active form, the miRNA, while steady-state levels of the other strand, the miRNA*, are generally lower. The executive engines of miRNA-directed gene silencing are RNA-induced silencing complexes (RISCs). During RISC maturation, the miRNA/miRNA* duplex associates with the catalytic subunit, an ARGONAUTE (AGO) protein. Subsequently, the guide strand, which directs gene silencing, is retained, while the passenger strand is degraded. Under certain circumstances, the miRNA*s can be retained as guide strands. miR170 and miR171 are prototypical miRNAs in Arabidopsis (Arabidopsis thaliana) with well-defined targets. We found that the corresponding star molecules, the sequence-identical miR170* and miR171a*, have several features of active miRNAs, such as sequence conservation and AGO1 association. We confirmed that active AGO1-miR171a* complexes are common in Arabidopsis and that they trigger silencing of SU(VAR)3-9 HOMOLOG8, a new miR171a* target that was acquired very recently in the Arabidopsis lineage. Our study demonstrates that each miR171a strand can be loaded onto RISC with separate regulatory outcomes.
Marine cyanophages exhibit local and regional biogeography
Authors: Marston Marcia F. , Taylor Samantha , Sme Noel , Parsons Rachel J. , Noyes Timothy J. E. , Martiny Jennifer B. H.
Published: December 2012

Biogeographic patterns have been demonstrated for a wide range of microorganisms. Nevertheless, the biogeography of marine viruses has been slower to emerge. Here we investigate biogeographic patterns of marine cyanophages that infect Synechococcus sp. WH7803 across multiple spatial and temporal scales. We compared cyanophage myoviral communities from nine coastal sites in Southern New England (SNE), USA, one site in Long Island NY, and four sites from Bermuda's inshore waters by assaying cyanophage isolates using the myoviral g43 DNA polymerase gene. Cyanophage community composition varied temporally at each of the sites. Further, 6 years of sampling at one Narragansett Bay site revealed annual seasonal variations in community composition, driven by the seasonal reoccurrence of specific viral taxa. Although the four Bermuda communities were similar to one another, they were significantly different than the North American coastal communities, with almost no overlap of taxa between the two regions. Among the SNE sites, cyanophage community composition also varied significantly and was correlated with the body of water sampled (e.g. Narragansett Bay, Cape Cod Bay, Vineyard Sound), although here, the same viral taxa were found at multiple sites. This study demonstrates that marine cyanophages display striking seasonal and spatial biogeographic patterns.
Case for mandatory reporting of ‘body packers’
Authors: Mitra Biswadev , Smit De Villiers , O'Shea William P
Published: December 2012

Body packing is the term used to describe the ingestion of illicit substances for transport across control lines. Where the diagnosis of body packing is made independently in the ED, the issue of reporting the case to law enforcement officials poses a difficult scenario given the legal obligations of patient confidentiality. We describe a case of a body packer brought into the ED and subsequently reported to the police. The conflicts between patient confidentiality versus statutory exceptions to confidentiality along with case law regarding this scenario are discussed.
Cutoff Values for Alcoholic Liver Fibrosis Using Magnetic Resonance Elastography Technique
Authors: Bensamoun Sabine F. , Leclerc Gwladys E. , Debernard Laëtitia , Cheng Xiaobin , Robert Ludovic , Charleux Fabrice , Rhein Colette , Latrive Jean‐Paul
Published: December 2012

Background

Due to the lack of cutoff values validated for specific liver diseases, the purpose of this study was to set up specific magnetic resonance elastography (MRE) cutoff values for asymptomatic liver fibrosis in alcoholic patients.

Methods

Ninety patients underwent 3 clinical exams. The liver stiffness was measured locally with the Fibroscan, and globally through cartographies of shear modulus generated with MRE. The Fibroscan method was chosen as the gold standard to classify the fibrosis. The liver score was also obtained with the Fibrometer A, and the diagnostic performance of the methods was analyzed with receiver‐operating characteristic (ROC) curves and cutoff values were calculated.

Results

Spearman correlation and area under the ROC curve revealed that MRE is a better diagnostic method than the Fibrometer A, to identify various levels of fibrosis. The results showed that the Fibrometer A was adapted for severe fibrosis. The MRE cutoff values are F1:2.20 kPa, F2:2.57 kPa, F3:3.31 kPa, and F4:4 kPa and were not influenced by the glutamic oxaloacetic transaminase level. By using the ultrasound cutoff values attributed for alcoholism, 66% of patients had a similar liver fibrosis diagnosis as the MRE cutoffs. However, both imaging techniques did not provide the same distribution for minor fibrosis.

Conclusions

None of the imaging techniques (Fibroscan, MRE) could replace the gold standard of the biopsy. However, due to the risk and the unnecessary procedure for the present recruited alcoholic patients, the Fibroscan method was chosen as the reference. Since MRE is currently being used as a clinical exam, the present MRE cutoffs could aid clinicians with their diagnosis of liver fibrosis for alcoholism disease.
Mapping Tropical Forest Trees Using High‐Resolution Aerial Digital Photographs
Authors: Garzon‐Lopez Carol X. , Bohlman Stephanie A. , Olff Han , Jansen Patrick A.
Published: December 2012

The spatial arrangement of tree species is a key aspect of community ecology. Because tree species in tropical forests occur at low densities, it is logistically challenging to measure distributions across large areas. In this study, we evaluated the potential use of canopy tree crown maps, derived from high‐resolution aerial digital photographs, as a relatively simple method for measuring large‐scale tree distributions. At Barro Colorado Island, Panama, we used high‐resolution aerial digital photographs (~0.129 m/pixel) to identify tree species and map crown distributions of four target tree species. We determined crown mapping accuracy by comparing aerial and ground‐mapped distributions and tested whether the spatial characteristics of the crown maps reflect those of the ground‐mapped trees. Nearly a quarter (22%) of the common canopy species had sufficiently distinctive crowns to be good candidates for reliable mapping. The errors of commission (crowns misidentified as a target species) were relatively low, but the errors of omission (missed canopy trees of the target species) were high. Only 40 percent of canopy individuals were mapped on the air photographs. Despite failing to accurately predict exact abundances of canopy trees, crown distributions accurately reproduced the clumping patterns and spatial autocorrelation features of three of four tree species and predicted areas of high and low abundance. We discuss a range of ecological and forest management applications for which this method can be useful.
Effects of immunosuppressive agents on Th17 cells involved in transplantation
Authors: Wang Xiao‐Fei , van Velkinburgh Jennifer C. , Zhang Yi , Ni Bing , Yang Zhan‐Yu
Published: December 2012

The lymphocyte‐derived helper T (Th) cells are critical regulators of the adaptive immune response and are associated with inflammatory disease. The most recently recognized Th‐cell lineage, Th17, plays an important role in host defense against extracellular pathogens by secreting the proinflammatory cytokine, interleukin 17, and recruiting reactive oxygen species (ROS)‐producing monocytes to the site of infection. However, accumulating evidence has implicated Th17‐cell dysregulation as an underlying cause for some immune‐related pathogenic conditions, including allograft rejection. Recent studies of human transplant patients have indicated that Th17 cells exhibit resistance to current immunosuppressive therapies that would otherwise prevent allograft rejection. In this review, we will discuss the most current research findings related to Th17‐cell function in various kinds of allografts.