bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of optimised conditions for inductively coupled plasma‐reactive ion etching of quartz substrates and its optical applications
Authors: Tang Yu‐Hsiang , Lin Yu‐Hsin , Chen Po‐Li , Shiao Ming‐Hua , Hsiao Chien‐Nan
Published: June 2014

A C4F8/He inductively coupled plasma‐reactive ion etching (ICP‐RIE) was studied to improve the etching conditions of quartz glass. The influences of C4F8 flow rate, He flow rate, chamber pressure, inductively coupled plasma (ICP) power, bias power and cooling temperature were investigated. A report is presented on an optimum etching condition for fabricating quartz‐based optical components considering their application in diffractive optical element (DOE) devices. As per these etching results, the etched microstructure exhibited a depth of 44.2 μm and a vertical sidewall angle of 89° resulting from an ICP power of 3000 W, a bias power of 200 W, a chamber pressure of 2.5 mTorr and an etching time of 120 min in a mixture of C4F8 and He gases with 30 and 100 sccm flow rates, respectively. The successful fabrication of the DOE component by ICP‐RIE is reported. This can be used to provide the uniform light intensity distribution for a DOE device.
Preparation of Ag2SO3 sub‐microparticles with high visible‐light photocatalytic activity
Authors: Dong Chao , Wu Kong‐Lin , Wei Xian‐Wen , Wang Jing , Liu Li , Hu Yu , Xia Shan‐Hui
Published: June 2014

A visible‐light sensitive Ag2SO3 semiconductor photocatalyst with size of ca. 500 nm was prepared by a simple precipitation method. This photocatalyst exhibits high‐efficiency degradation ability for typical three dyes, which can be ascribed to the efficient photosensitised electron injection and slow electron recombination. The photocatalytic reaction follows a pseudo‐first‐order reaction and the rate constant of Ag2SO3 for the degradation of rhodamine B is estimated to be 1.7 times that of commercial TiO2. The stability of unstable Ag2SO3 was remarkably enhanced by the addition of Na2SO3. The h+ and •O2− played relatively major roles during the photocatalytic reaction.
Identifiability analysis of rotational diffusion tensor and electronic transition moments measured in time-resolved fluorescence depolarization experiment
Authors: Szubiakowski Jacek P.
Published: June 2014

The subject of this paper is studies of the deterministic identifiability of molecular parameters, such as rotational diffusion tensor components and orientation of electronic transition moments, resulting from the time-resolved fluorescence anisotropy experiment. In the most general case considered, a pair of perpendicularly polarized emissions enables the unique determination of all the rotational diffusion tensor's principal components. The influence of the tensor's symmetry and the associated degeneration of its eigenvalues on the identifiability of the electronic transitions moments is systematically investigated. The analysis reveals that independently of the rotational diffusion tensor's symmetry, the transition moments involved in photoselection and emission processes cannot be uniquely identified without a priori information about their mutual orientation or their orientation with respect to the principal axes of the tensor. Moreover, it is shown that increasing the symmetry of the rotational diffusion tensor deteriorates the degree of the transition moments identifiability. To obtain these results analytically, a novel approach to solve bilinear system of equations for Markov parameters is applied. The effect of the additional information, obtained from fluorescence measurements for different molecular mobilities, to improve the identifiability at various levels of analysis is shown. The effectiveness and reliability of the target analysis method for experimental determination of the molecular parameters is also discussed.
Rashba-Zeeman-effect-induced spin filtering energy windows in a quantum wire
Authors: Xiao Xianbo , Chen Zhaoxia , Nie Wenjie , Zhou Guanghui , Li Fei
Published: June 2014

We perform a numerical study on the spin-resolved transport in a quantum wire (QW) under the modulation of both Rashba spin-orbit coupling (SOC) and a perpendicular magnetic field by using the developed Usuki transfer-matrix method in combination with the Landauer-Büttiker formalism. Wide spin filtering energy windows can be achieved in this system for unpolarized spin injection. In addition, both the width of energy window and the magnitude of spin conductance within these energy windows can be tuned by varying Rashba SOC strength, which can be apprehended by analyzing the energy dispersions and spin-polarized density distributions inside the QW, respectively. Further study also demonstrates that these Rashba-SOC-controlled spin filtering energy windows show a strong robustness against disorders. These findings may not only benefit to further understand the spin-dependent transport properties of a QW in the presence of external fields but also provide a theoretical instruction to design a spin filter device.
Two chaotic global models for cereal crops cycles observed from satellite in northern Morocco
Authors: Mangiarotti Sylvain , Drapeau Laurent , Letellier Christophe
Published: June 2014

The dynamics underlying cereal crops in the northern region of Morocco is investigated using a global modelling technique applied to a vegetation index time series derived from satellite measurements, namely, the normalized difference vegetation index from 1982 to 2008. Two three-dimensional chaotic global models of reduced size (14-term and 15-term models) are obtained. The model validation is performed by comparing their horizons of predictability with those provided in previous studies. The attractors produced by the two global models have a complex foliated structure—evidenced in a Poincaré section—rending a topological characterization difficult to perform. Thus, the Kaplan-Yorke dimension is estimated from the synthetic data produced by our global models. Our results suggest that cereal crops in the northern Morocco are governed by a weakly dissipative three-dimensional chaotic dynamics.
High performance TiN gate contact on AlGaN/GaN transistor using a mechanically strain induced P-doping
Authors: Soltani A. , Rousseau M. , Gerbedoen J.-C. , Mattalah M. , Bonanno P. L. , Telia A. , Bourzgui N. , Patriarche G. , Ougazzaden A. , BenMoussa A.
Published: June 2014

High performance titanium nitride sub-100 nm rectifying contact, deposited by sputtering on AlGaN/GaN high electron mobility transistors, shows a reverse leakage current as low as 38 pA/mm at VGS = −40 V and a Schottky barrier height of 0.95 eV. Based on structural characterization and 3D simulations, it is found that the polarization gradient induced by the gate metallization forms a P-type pseudo-doping region under the gate between the tensile surface and the compressively strained bulk AlGaN barrier layer. The strain induced by the gate metallization can compensate for the piezoelectric component. As a result, the gate contact can operate at temperatures as high as 700 °C and can withstand a large reverse bias of up to −100 V, which is interesting for high-performance transistors dedicated to power applications.
Intermittent bursts induced by double tearing mode reconnection
Authors: Wei Lai , Wang Zheng-Xiong
Published: June 2014

Reversed magnetic shear (RMS) configuration is assumed to be the steady-state operation scenario for the future advanced tokamaks like International Thermonuclear Experimental Reactor. In this work, we numerically discover a phenomenon of violent intermittent bursts induced by self-organized double tearing mode (DTM) reconnection in the RMS configuration during the very long evolution, which may continuously lead to annular sawtooth crashes and thus badly impact the desired steady-state operation of the future advanced RMS tokamaks. The key process of the intermittent bursts in the off-axis region is similar to that of the typical sawtooth relaxation oscillation in the positive magnetic shear configuration. It is interestingly found that in the decay phase of the DTM reconnection, the zonal field significantly counteracts equilibrium field to make the magnetic shear between the two rational surfaces so weak that the residual self-generated vortices of the previous DTM burst are able to trigger a reverse DTM reconnection by curling the field lines.
Effects of Ti-doping on evolution of coexisting magnetic phases in BaFeO3–δ thin films at room temperature
Authors: Aziz Fozia , Chandra Mahesh , Khare Amit , Pandey Parul , Mavani K. R.
Published: June 2014

BaFeO3–δ (BFO) thin films are deposited on different MgO single-crystal substrates with (001), (110), and (111) structural orientations and investigated for the structural and magnetic properties. These films show weak ferromagnetism and magnetocrystalline anisotropy, where (111) axis is found to be hard-axis of magnetization. As Ti-doping should reduce oxygen deficiencies, we have studied the effects of Ti-doping on BFO/MgO (001) system. This doping of nonmagnetic Ti4+ ions (with 3d0 orbital) at Fe-site in BaFeO3−δ largely enhances the magnetization at room temperature. After oxygen annealing of the undoped and doped films deposited on MgO (001), the films show further alteration of magnetization and structure depending on Ti-doping. These films either show a pinched magnetic hysteresis at zero field or a larger coercivity, which was otherwise absent in the untreated thin films. Our results reveal that such changes in magnetic hystereses take place due to the magnetocrystalline anisotropy and/or coexisted soft and hard (or less soft) magnetic phases in annealed films. The annealing-induced hard magnetic phase gets completely suppressed by Ti-doping in BFO film.
Study of the relation between oxygen vacancies and ferromagnetism in Fe-doped TiO2 nano-powders
Authors: Mudarra Navarro Azucena M. , Rodríguez Torres Claudia E. , Bilovol Vitaliy , Fabiana Cabrera A. , Errico L. A. , Weissmann M.
Published: June 2014

In this work, we present an experimental and theoretical study of structural and magnetic properties of Fe doped rutile TiO2 nanopowders. We show that Fe-doping induces the formation of oxygen vacancies in the first-sphere coordination of iron ions, which are in +2 and +3 oxidation states. We found that Fe ions form dimers that share one oxygen vacancy in the case of Fe3+ and two oxygen vacancies in the case of Fe2+. The saturation magnetization is almost independent of iron concentration and slightly increases with the relative fraction of Fe2+. Ab initio calculations show that two Fe ions sharing an oxygen vacancy are coupled ferromagnetically, forming a bound magnetic polaron (BMP), but two neighbor BMPs are aligned antiparallel to each other. Extra electron doping plays a fundamental role mediating the magnetic coupling between the ferromagnetic entities: carriers, possibly concentrated at grain boundaries, mediate between the BMP to produce ferromagnetic alignment.
Asymmetric “melting” and “freezing” kinetics of the magnetostructural phase transition in B2-ordered FeRh epilayers
Authors: de Vries M. A. , Loving M. , McLaren M. , Brydson R. M. D. , Liu X. , Langridge S. , Lewis L. H. , Marrows C. H.
Published: June 2014

Synchrotron X-ray diffraction was used to study the phase transformation processes during the magnetostructural transition in a B2-ordered FeRh (001)-oriented epilayer grown on MgO by sputtering. Out-of-plane lattice constant measurements within the hysteretic regime of the transition reveal a microstructure consistent with the coexistence of lattice-expanded and contracted phases in spatially distinct regions. It was found that the phase separation is more pronounced during cooling than heating. Furthermore, whilst lattice-expanded domains that span the height of the film can be undercooled by several kelvins, there is no equivalent superheating. This asymmetry between the cooling and heating processes in FeRh is consistent with the difference in the kinetics of generic freezing and melting transitions.
Effects of sub-bandgap illumination on electrical properties and detector performances of CdZnTe:In
Authors: Xu Lingyan , Jie Wanqi , Zha Gangqiang , Feng Tao , Wang Ning , Xi Shouzhi , Fu Xu , Zhang Wenlong , Xu Yadong , Wang Tao
Published: June 2014

The effects of sub-bandgap illumination on electrical properties of CdZnTe:In crystals and spectroscopic performances of the fabricated detectors were discussed. The excitation process of charge carriers through thermal and optical transitions at the deep trap could be described by the modified Shockley-Read-Hall model. The ionization probability of the deep donor shows an increase under illumination, which should be responsible for the variation of electrical properties within CdZnTe bulk materials with infrared (IR) irradiation. By applying Ohm's law, diffusion model and interfacial layer-thermionic-diffusion theory, we obtain the decrease of bulk resistivity and the increase of space charge density in the illuminated crystals. Moreover, the illumination induced ionization will further contribute to improving carrier transport property and charge collection efficiency. Consequently, the application of IR irradiation in the standard working environment is of great significance to improve the spectroscopic characteristics of CdZnTe radiation detectors.
Co-fired magnetoelectric transformer
Authors: Zhou Yuan , Yan Yongke , Priya Shashank
Published: June 2014

In this study, we demonstrate a co-fired magnetoelectric (ME) laminate consisting of piezoelectric/magnetostrictive/piezoelectric layers with unipoled piezoelectric transformer structure. The ME transformer was characterized by quantifying the voltage gain variation and resonance frequency shift as a function of applied DC magnetic field. We delineate the magnetic tunability feature by considering the magnetoelectric coupling and delta-E effect, where E represents the modulus of magnetic material. The ME response of the composite structure was found to be 473 mV/cm.Oe exhibiting DC field sensitivity of 100 nT under AC field of 1 Oe at 1 kHz. At a magnetic bias of 60 Oe, the transformer exhibited large frequency tunability of the order of 1.4 Hz/Oe. These results present significant advancement towards developing on-chip magnetic-field-tunable devices.
Influence of Chemically Inert Cations on the Hydrogen-bond Network in the Bray-Liebhafsky Oscillatory Reaction
Authors: Stanisavljev Dragomir R. , Ljubić Ivana Ž. , Milenković Maja C.
Published: June 2014

The influence of the chemically inert alkali metal cations on the Bray-Liebhafsky oscillatory reaction dynamics was investigated by the addition of the same amount of various sulfates to the reaction mixture. Beside the expected changes related to the altered acidity of the sulfuric acid solution, subtle changes dependent on cation dimensions were noticed. Larger cations have more impact on the Bray-Liebhafsky reaction dynamics. Analysing the mean ionic activity of salts, it is suggested that the effects may be related to the altered extent of water hydrogen bonding and specific role of bulk water in the reaction mechanism.
Yield response in chickpea cultivars and wheat following crop rotations affecting population densities of Pratylenchus thornei and arbuscular mycorrhizal fungi
Authors: Reen R. A. , Thompson J. P. , Clewett T. G. , Sheedy J. G. , Bell K. L.
Published: June 2014

In Australia, root-lesion nematode (RLN; Pratylenchus thornei) significantly reduces chickpea and wheat yields. Yield losses from RLN have been determined through use of nematicide; however, nematicide does not control nematodes in Vertosol subsoils in Australia’s northern grains region. The alternative strategy of assessing yield response, by using crop rotation with resistant and susceptible crops to manipulate nematode populations, is poorly documented for chickpea. Our research tested the effectiveness of crop rotation and nematicide against P. thornei populations for assessing yield loss in chickpea. First-year field plots included canola, linseed, canaryseed, wheat and a fallow treatment, all with and without the nematicide aldicarb. The following year, aldicarb was reapplied and plots were re-cropped with four chickpea cultivars and one intolerant wheat cultivar. Highest P. thornei populations were after wheat, at 0.45–0.6 m soil depth. Aldicarb was effective to just 0.3 m for wheat and 0.45 m for other crops, and increased subsequent crop grain yield by only 6%. Canola, linseed and fallow treatments reduced P. thornei populations, but low mycorrhizal spore levels in the soil after canola and fallow treatments were associated with low chickpea yield. Canaryseed kept P. thornei populations low throughout the soil profile and maintained mycorrhizal spore densities, resulting in grain yield increases of up to 25% for chickpea cultivars and 55% for wheat when pre-cropped with canaryseed compared with wheat. Tolerance indices for chickpeas based on yield differences after paired wheat and canaryseed plots ranged from 80% for cv. Tyson to 95% for cv. Lasseter and this strategy is recommended for future use in assessing tolerance.
In vitro fermentation, digestibility and methane production of tropical perennial grass species
Authors: Gemeda Belete Shenkute , Hassen Abubeker
Published: June 2014

This study characterised 16 tropical perennial grass species in terms of in vitro methane output and related their digestibility and rumen fermentation with methane output. The grass samples were collected, dried in a forced oven, and ground and analysed for nutrient composition. In vitro gas production and organic matter digestibility (IVOMD) were determined using rumen fluid collected, strained and anaerobically prepared. A semi-automated system was used to measure gas production through in vitro incubation at 39°C. Anthephora argentea and Stipagrostis ciliate produced the highest concentration of methane in terms of g kg–1 digestible dry matter (DDM) and g kg–1 digestible organic matter (IVOMD). Cenchrus ciliaris, Setaria verticillata and Panicum coloratum produced the lowest (P < 0.05) methane when expressed in terms of g kg–1 DDM and g kg–1 IVOMD. Ash, ether extract, non-fibrous carbohydrate, neutral and acid detergent insoluble nitrogen, and crude protein were negatively correlated with methane production. Methane production positively correlated with neutral and acid detergent fibre, cellulose and hemicellulose. It is important to focus on screening and selecting perennial grass with higher nitrogen content and low methane production to mitigate methane production under tropical conditions.
Amphidromy and marine larval phase of ancestral gobioids Rhyacichthys guilberti and Protogobius attiti (Teleostei: Rhyacichthyidae)
Authors: Tabouret H. , Tomadin M. , Taillebois L. , Iida M. , Lord C. , Pécheyran C. , Keith P.
Published: June 2014

Even if amphidromous fish species contribute most to the diversity of fish communities in the tropical insular rivers, their biological cycle remain poorly known. For the first time, the otolith elemental composition and microstructure of two ancestral gobioids, Rhyacichthys guilberti and Protogobius attiti, were investigated to describe their biological cycle and pelagic larval duration (PLD). The otolith analysis using a femtosecond laser ablation coupled to an inductively coupled plasma–mass spectrometer (fs-LA-ICP-MS) revealed an amphidromous life history for R. guilberti and it suggested a progressive habitat shift from a marine habitat to a freshwater environment for P. attiti. For the first time, an endemic species, P. attiti, showed longer and more variable PLD (55.2 ± 13.5 days) than did a widespread one (R. guilberti: ~30 days). These results need to be confirmed by analysing more samples but suggest that factors other than the PLD control endemism and dispersal processes. In association with this first description of the biological cycle for both species, such an approach is a prerequisite for the management and conservation of both patrimonial species.
Impact of sewage pollution on the structure and functioning of a rocky shore benthic community
Authors: Cabral-Oliveira J. , Dolbeth M. , Pardal M. A.
Published: June 2014

The secondary production of rocky shore macroinvertebrate assemblages impacted through sewage discharge was assessed, taking into account the trends of production among dominant species and feeding guilds. The present study was conducted on the Peniche peninsula (central-western Portuguese coast, temperate region), in three areas: one area near a sewage discharge and two undisturbed reference areas. Within each area, three intertidal zones were monitored ‐ littoral fringe, eulittoral and sublittoral fringe ‐ by taking seasonal samples during one year. The empirical model of Cusson and Bourget (2005) was used to evaluate secondary production. In the littoral fringe, no differences in the production values were found between impacted and reference areas. In the eulittoral, sewage discharge seemed to affect the natural competition between patellidae and barnacles by favouring suspension feeders (barnacles), presumably due to higher food resources near the sewage. In the sublittoral fringe, near the sewage discharge, an increase in the production values of tolerant species was observed to the detriment of the sensitive species, with higher production levels in the reference areas. Overall, secondary production was higher in the communities near the sewage affected areas, but this increase was mostly due to the production of tolerant species. The present study showed that the incorporation of secondary production in the biological assessment provided further insight into the health of the ecosystem, thus being an important tool for understanding differences in the functioning of the ecosystem.
Hyperbenthic and pelagic predators regulate alternate key planktonic copepods in shallow temperate estuaries
Authors: Wasserman R. J. , Vink T. J. F. , Kramer R. , Froneman P. W.
Published: June 2014

Although predation has been identified as an important community driver, the role of predator diversity in structuring estuarine zooplankton has not been assessed. As such, we investigated the effects of two different zooplanktivorous fish species on the estuarine zooplankton community during a 12-day mesocosm study. Three experimental treatments were established, whereby natural zooplankton communities were subject to either (1) no predatory pressure, (2) predation by a pelagic predator (Monodactylus falciformis) or (3) predation by a hyper-benthic predator (Glossogobius callidus). The pelagic feeding M. falciformis fed largely on the numerically dominant mid-water copepod species, Paracartia longipatella. In contrast, the hyper-benthic fish had a greater predatory impact on the less numerically dominant copepod, Pseudodiaptomus hessei, which demonstrates strong diel vertical migration. Variations in prey-population regulation are ascribed to the distinct behavioural differences of the predators, and mediated by the differences in behaviour of the copepod species.
Sexual system of the freshwater shrimps of the genus Potimirim Holthuis (Decapoda : Caridea : Atyidae): is there a pattern in this genus?
Authors: Grilli Natalia de Miranda , Terossi Mariana , Mantelatto Fernando L.
Published: June 2014

Among the genus Potimirim, the sexual system has been studied only in Potimirim mexicana, which was suggested as being a sequential protandric shrimp. The genus Potimirim comprises five described species that occur in drainages along the western Atlantic coast. We tested the hypothesis that there is a common shared sexual system pattern for the genus Potimirim, and that both species reported for Brazil (P. brasiliana and P. potimirim) are sequentially protandric. The animals were analysed with respect to sex, external morphology and nature of the gonads. We found similar results for both species: females were significantly larger than males; the appendix masculina increased significantly as the carapace enlarged; all adult males had cincinnuli and only well-developed testes; all females lacked cincinnuli and had only well-developed ovaries; and all males and females had a non-prehensile third pereopod. The absence of any characteristic that could be interpreted as evidence of sex change indicates that these species are gonochoric species. Therefore we concluded that there is no sexual system shared by all members of this genus. Additionally, we compared our results with a molecular phylogeny previously proposed for the genus Potimirim, as the baseline to discuss the sexual system in this genus.
Do recolonisation processes in intermittent streams have sustained effects on benthic algal density and assemblage composition?
Authors: Chester E. T. , Robson B. J.
Published: June 2014

When intermittent streams flow, benthic algae develop from both colonising propagules and regrowing dried biofilm. We aimed to determine whether colonisation processes influence algal densities and taxonomic composition beyond the period immediately following commencement of winter flows, and whether regulation modifies those processes, in the Victoria Range, Australia. Stones were placed in two unregulated streams, and upstream and downstream of weirs in three regulated streams, after dry biofilm was removed. Epilithic algae on treatment and control stones were collected after winter flows (12 weeks). Treatment effects were still apparent in one (unregulated) stream, but not in the other streams. Algal assemblages and densities upstream and downstream of weirs differed, but there was no systematic pattern among streams. In intermittent headwater streams, recolonisation processes may influence algal assemblages until spring; but in most streams, the duration of influence will be shorter, depending on the assemblage composition in regrowth and refuges, which is also shaped by conditions during the previous flow season. If the effects of regulation depend on how idiosyncratic flow regimes and assemblage compositions influence recolonisation, they may be difficult to predict. Similarly, recovery trajectories for stream communities after drought will differ among streams, depending on whether biofilm can develop during potentially short seasonal flows.
Transgenerational inheritance of ovarian development deficiency induced by maternal diethylhexyl phthalate exposure
Authors: Zhang Xi-Feng , Zhang Teng , Han Zhe , Liu Jing-Cai , Liu Yu-Ping , Ma Jun-Yu , Li Lan , Shen Wei
Published: June 2014

Diethylhexyl phthalate (DEHP) is a widely used industrial additive for increasing plastic flexibility. It disrupts the physiological functions of endogenous hormones and induces abnormal development of mammals. The objectives of the present study were to evaluate the effects of DEHP exposure on ovarian development of pregnant mice and whether the effects are inheritable. We found that the synthesis of oestradiol in pregnant mice after DEHP exposure was significantly decreased, and that the first meiotic progression of female fetal germ cells was delayed. Furthermore, the DNA methylation level of Stra8 was increased and the expression levels of Stra8 were significantly decreased. An accelerated rate of follicle recruitment in F1 mice was responsible for the depletion of the primordial-follicle pool. Maternal DEHP exposure also significantly accelerated the recruitment of primordial follicles in F2 mice. In conclusion, our results indicated that maternal DEHP exposure induced ovarian development deficiency, which was transgenerational in mice.
Women with disabilities: from discrimination and violence towards an ethics of reciprocity
Authors: Barbuto Rita , Napolitano Emilia
Published: June 2014

Since 2001 DPI Italia, the Italian section of Disabled People's International, has played an important role in a series of research projects in the European Commission's Daphne Programme on violence against women with disabilities. Several different types of violence have been identified, from sexual abuse to removal of women's control over their environment to invasion of their privacy in healthcare contexts to control of their reproductive capacity, particularly of women with intellectual disabilities. In the light of these projects, and of the CRPD's recognition of the multiple discriminations experienced by many women with disabilities, the article argues for a shift away from an ethics of care and dependency towards one of equal reciprocal relations between disabled women and others and to a bioethics grounded not in exceptional need but in everyday life. Peer counselling among disabled women is particularly important in effecting this shift.
Associations of people with disabilities in Italy: a short history
Authors: Schianchi Matteo
Published: June 2014

Voluntary associations of persons with disabilities have played an important role in bringing issues related to disability onto the national agenda in Italy in the absence of effective provision by the state or representation by other bodies, such as the political parties and trades unions. At the same time, the nature of Italy's welfare state – weak, clientelistic, particularistic – and its way of conceiving disability as a set of bodily deficits has also shaped the character of disabled persons' organisations in Italy and the ways in which they have framed their demands and policies. These organisations have tended either to represent fragmented subsets of people with disabilities or, more recently, to form large federations that, while they reflect a more comprehensive understanding of disability, have left some categories of people with disabilities feeling excluded or under-represented
Aesthetic experience and analytic process
Authors: Winborn Mark Douglas
Published: June 2014

In this paper, it is proposed that all individuals have an innate (archetypal) aesthetic urge that is a central organizing influence for our actions, experiences, perceptions, self-perceptions, and relationships. The attitudes towards aesthetics held by Freud, Jung, and later theorists are reviewed. Drawing on ideas from aesthetic philosophy and neuroscience, it is suggested that many of the experiences associated with analytic process – such as the experience of depth, the emergence of meaning, transcendence, coherence, narrative flow, or moments of meeting – can be viewed through the lens of aesthetic experience. This aesthetic substratum is discussed in terms of analytic narrative and interpretation as well as exploring the impact that various artistic modalities, such as poetry and music, can have on analytic process.
Archetypal aesthetics: viewing art through states of consciousness
Authors: Potash Jordan S.
Published: June 2014

A Jungian and archetypal psychology approach to aesthetics includes noticing which archetypes are activated when viewing or engaging with art. Archetypes provide vitality to art and can be accessed by viewers through attention to bodily responses and emotional awareness enhanced by imagination. Connecting these personal experiences to the collective requires framing viewers' responses within comprehensible patterns. Joan Kellogg's theory ‘The Archetypal Stages of the Great Round of Mandala’ offers a system for identifying archetypes as states of consciousness and making them accessible to a wide audience in order to aid understanding of one's responses to art.
Cohomological support loci of varieties of Albanese fiber dimension one
Authors: Jiang Zhi , Sun Hao
Published: June 2014

Let

X
X

be a smooth projective variety of Albanese fiber dimension 1 and of general type. We prove that the translates through

0
0

of all components of

V
0

(

ω
X

)

V^0(\omega _X)

generate

Pic
0

⁡
(
X
)

\operatorname {Pic}^0(X)

. We then study the pluricanonical maps of

X
X

. We show that

|

4

K
X

|

|4K_X|

induces a birational map of

X
X

.
Cdk1 promotes cytokinesis in fission yeast through activation of the septation initiation network
Authors: Rachfall Nicole , Johnson Alyssa E. , Mehta Sapna , Chen Jun-Song , Gould Kathleen L.
Published: June 2014

In Schizosaccharomyces pombe, late mitotic events are coordinated with cytokinesis by the septation initiation network (SIN), an essential spindle pole body (SPB)–associated kinase cascade, which controls the formation, maintenance, and constriction of the cytokinetic ring. It is not fully understood how SIN initiation is temporally regulated, but it depends on the activation of the GTPase Spg1, which is inhibited during interphase by the essential bipartite GTPase-activating protein Byr4-Cdc16. Cells are particularly sensitive to the modulation of Byr4, which undergoes cell cycle–dependent phosphorylation presumed to regulate its function. Polo-like kinase, which promotes SIN activation, is partially responsible for Byr4 phosphorylation. Here we show that Byr4 is also controlled by cyclin-dependent kinase (Cdk1)–mediated phosphorylation. A Cdk1 nonphosphorylatable Byr4 phosphomutant displays severe cell division defects, including the formation of elongated, multinucleate cells, failure to maintain the cytokinetic ring, and compromised SPB association of the SIN kinase Cdc7. Our analyses show that Cdk1-mediated phosphoregulation of Byr4 facilitates complete removal of Byr4 from metaphase SPBs in concert with Plo1, revealing an unexpected role for Cdk1 in promoting cytokinesis through activation of the SIN pathway.
Spatial Approaches to American Religious Studies
Authors: Carroll Bret E.
Published: June 2014

Space is a basic yet complex dimension in American religion. Historically and historiographically, conceptually and in practice, it has been central to believers’ experiences of what they consider “sacred” and to the models that scholars have developed to understand religious practices in the United States. First assumed as an unexamined given by 19th-century scholars, it became recognized as an explanatory factor in its own right during the 20th century and was the focus of ongoing modern and postmodern attempts at conceptualization from the mid-20th century into the early 21st.

Until the late 20th century, work in American religious studies conceptualized space as an objectively existing container for human activity, and scholars considered a presumed abundance of it a defining determinant of American religious experience. Church historians prior to the mid-20th century typically argued that the vastness and relative isolation of American space, initially subsumed under the historiographic idea of an American “frontier,” allowed the development of uniquely American religious freedom and revivalism. Although the frontier thesis was challenged during the latter half of the 20th century, the concept of space persisted and proved useful as U.S. religious historians gave increasing attention to pluralism, urban experience, transnationalism, and everyday practice.

Religion scholars and anthropologists, meanwhile, proposed from the early 20th century that religious practice involved fundamental spatial distinctions between sacred and profane, inside and outside, center and periphery, and up and down that provided believers with a sense of social, geographic, and cosmic orientation. By the 1970s and 1980s, cultural theorists began conceiving of space as a subjective experience, a situationally located social and cultural construction “produced” through active efforts at definition, appropriation, and control by human beings. According to this newer conceptualization, space comes into being as an inherently contested medium as believers make specific and concrete the meanings of their beliefs through rituals, relationships, and symbols and create distinct physical and geographically located manifestations of their belief systems.

This new approach sparked a “spatial turn” that extended across the humanities and social sciences and moved spatial analysis to a central position in American religious studies. Attention to the spatial dimensions of religious practice generated fruitful research on and new studies of churches and other built environments, American “civil religion,” domestic religious practice, urban religion, the dynamics of pluralism, immigrant communities, and global diasporas. The spatial turn has also generated new concepts of space as scholars attuned to postmodern and transnational experiences have rejected standard emphases on spatial separation and fragmentation in favor of an emphasis on continuity and interconnection.
Thought Experiments and Religion
Authors: Fehige Yiftach
Published: June 2014

Thought experiments are basically imagined scenarios with a significant experimental character. Some of them justify claims about the world outside of the imagination. Originally they were a topic of scholarly interest exclusively in philosophy of science. Indeed, a closer look at the history of science strongly suggests that sometimes thought experiments have more than merely entertainment, heuristic, or pedagogic value. But thought experiments matter not only in science. The scope of scholarly interest has widened over the years, and today we know that thought experiments play an important role in many areas other than science, such as philosophy, history, and mathematics. Thought experiments are also linked to religion in a number of ways. Highlighted in this article are those links that pertain to the core of religions (first link), the relationship between science and religion in historical and systematic respects (second link), the way theology is conducted (third link), and the relationship between literature and religion (fourth link).
Evaluating synteny for improved comparative studies
Authors: Ghiurcuta Cristina G. , Moret Bernard M. E.
Published: June 2014

Motivation: Comparative genomics aims to understand the structure and function of genomes by translating knowledge gained about some genomes to the object of study. Early approaches used pairwise comparisons, but today researchers are attempting to leverage the larger potential of multi-way comparisons. Comparative genomics relies on the structuring of genomes into syntenic blocks: blocks of sequence that exhibit conserved features across the genomes. Syntenic blocs are required for complex computations to scale to the billions of nucleotides present in many genomes; they enable comparisons across broad ranges of genomes because they filter out much of the individual variability; they highlight candidate regions for in-depth studies; and they facilitate whole-genome comparisons through visualization tools. However, the concept of syntenic block remains loosely defined. Tools for the identification of syntenic blocks yield quite different results, thereby preventing a systematic assessment of the next steps in an analysis. Current tools do not include measurable quality objectives and thus cannot be benchmarked against themselves. Comparisons among tools have also been neglected—what few results are given use superficial measures unrelated to quality or consistency.

Results: We present a theoretical model as well as an experimental basis for comparing syntenic blocks and thus also for improving or designing tools for the identification of syntenic blocks. We illustrate the application of the model and the measures by applying them to syntenic blocks produced by three different contemporary tools (DRIMM-Synteny, i-ADHoRe and Cyntenator) on a dataset of eight yeast genomes. Our findings highlight the need for a well founded, systematic approach to the decomposition of genomes into syntenic blocks. Our experiments demonstrate widely divergent results among these tools, throwing into question the robustness of the basic approach in comparative genomics. We have taken the first step towards a formal approach to the construction of syntenic blocks by developing a simple quality criterion based on sound evolutionary principles.

Contact:  cristinagabriela.ghiurcuta@epfl.ch
BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles
Authors: Videm Pavankumar , Rose Dominic , Costa Fabrizio , Backofen Rolf
Published: June 2014

Summary: Non-coding RNAs (ncRNAs) play a vital role in many cellular processes such as RNA splicing, translation, gene regulation. However the vast majority of ncRNAs still have no functional annotation. One prominent approach for putative function assignment is clustering of transcripts according to sequence and secondary structure. However sequence information is changed by post-transcriptional modifications, and secondary structure is only a proxy for the true 3D conformation of the RNA polymer. A different type of information that does not suffer from these issues and that can be used for the detection of RNA classes, is the pattern of processing and its traces in small RNA-seq reads data. Here we introduce BlockClust, an efficient approach to detect transcripts with similar processing patterns. We propose a novel way to encode expression profiles in compact discrete structures, which can then be processed using fast graph-kernel techniques. We perform both unsupervised clustering and develop family specific discriminative models; finally we show how the proposed approach is scalable, accurate and robust across different organisms, tissues and cell lines.

Availability: The whole BlockClust galaxy workflow including all tool dependencies is available at http://toolshed.g2.bx.psu.edu/view/rnateam/blockclust_workflow.

Contact:  backofen@informatik.uni-freiburg.de; costa@informatik.uni-freiburg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Detecting independent and recurrent copy number aberrations using interval graphs
Authors: Wu Hsin-Ta , Hajirasouliha Iman , Raphael Benjamin J.
Published: June 2014

Motivation: Somatic copy number aberrations (SCNAs) are frequent in cancer genomes, but many of these are random, passenger events. A common strategy to distinguish functional aberrations from passengers is to identify those aberrations that are recurrent across multiple samples. However, the extensive variability in the length and position of SCNAs makes the problem of identifying recurrent aberrations notoriously difficult.

Results: We introduce a combinatorial approach to the problem of identifying independent and recurrent SCNAs, focusing on the key challenging of separating the overlaps in aberrations across individuals into independent events. We derive independent and recurrent SCNAs as maximal cliques in an interval graph constructed from overlaps between aberrations. We efficiently enumerate all such cliques, and derive a dynamic programming algorithm to find an optimal selection of non-overlapping cliques, resulting in a very fast algorithm, which we call RAIG (Recurrent Aberrations from Interval Graphs). We show that RAIG outperforms other methods on simulated data and also performs well on data from three cancer types from The Cancer Genome Atlas (TCGA). In contrast to existing approaches that employ various heuristics to select independent aberrations, RAIG optimizes a well-defined objective function. We show that this allows RAIG to identify rare aberrations that are likely functional, but are obscured by overlaps with larger passenger aberrations.

Availability:  http://compbio.cs.brown.edu/software.

Contact:  braphael@brown.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data
Authors: Hajirasouliha Iman , Mahmoody Ahmad , Raphael Benjamin J.
Published: June 2014

Motivation: High-throughput sequencing of tumor samples has shown that most tumors exhibit extensive intra-tumor heterogeneity, with multiple subpopulations of tumor cells containing different somatic mutations. Recent studies have quantified this intra-tumor heterogeneity by clustering mutations into subpopulations according to the observed counts of DNA sequencing reads containing the variant allele. However, these clustering approaches do not consider that the population frequencies of different tumor subpopulations are correlated by their shared ancestry in the same population of cells.

Results: We introduce the binary tree partition (BTP), a novel combinatorial formulation of the problem of constructing the subpopulations of tumor cells from the variant allele frequencies of somatic mutations. We show that finding a BTP is an NP-complete problem; derive an approximation algorithm for an optimization version of the problem; and present a recursive algorithm to find a BTP with errors in the input. We show that the resulting algorithm outperforms existing clustering approaches on simulated and real sequencing data.

Availability and implementation: Python and MATLAB implementations of our method are available at http://compbio.cs.brown.edu/software/

Contact:  braphael@cs.brown.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Gene network inference by probabilistic scoring of relationships from a factorized model of interactions
Authors: Žitnik Marinka , Zupan Blaž
Published: June 2014

Motivation: Epistasis analysis is an essential tool of classical genetics for inferring the order of function of genes in a common pathway. Typically, it considers single and double mutant phenotypes and for a pair of genes observes whether a change in the first gene masks the effects of the mutation in the second gene. Despite the recent emergence of biotechnology techniques that can provide gene interaction data on a large, possibly genomic scale, few methods are available for quantitative epistasis analysis and epistasis-based network reconstruction.

Results: We here propose a conceptually new probabilistic approach to gene network inference from quantitative interaction data. The approach is founded on epistasis analysis. Its features are joint treatment of the mutant phenotype data with a factorized model and probabilistic scoring of pairwise gene relationships that are inferred from the latent gene representation. The resulting gene network is assembled from scored pairwise relationships. In an experimental study, we show that the proposed approach can accurately reconstruct several known pathways and that it surpasses the accuracy of current approaches.

Availability and implementation: Source code is available at http://github.com/biolab/red.

Contact:  blaz.zupan@fri.uni-lj.si

Supplementary information:  Supplementary data are available at Bioinformatics online.
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
Authors: Bao Ergude , Jiang Tao , Girke Thomas
Published: June 2014

Motivation:  De novo assemblies of genomes remain one of the most challenging applications in next-generation sequencing. Usually, their results are incomplete and fragmented into hundreds of contigs. Repeats in genomes and sequencing errors are the main reasons for these complications. With the rapidly growing number of sequenced genomes, it is now feasible to improve assemblies by guiding them with genomes from related species.

Results: Here we introduce AlignGraph, an algorithm for extending and joining de novo-assembled contigs or scaffolds guided by closely related reference genomes. It aligns paired-end (PE) reads and preassembled contigs or scaffolds to a close reference. From the obtained alignments, it builds a novel data structure, called the PE multipositional de Bruijn graph. The incorporated positional information from the alignments and PE reads allows us to extend the initial assemblies, while avoiding incorrect extensions and early terminations. In our performance tests, AlignGraph was able to substantially improve the contigs and scaffolds from several assemblers. For instance, 28.7–62.3% of the contigs of Arabidopsis thaliana and human could be extended, resulting in improvements of common assembly metrics, such as an increase of the N50 of the extendable contigs by 89.9–94.5% and 80.3–165.8%, respectively. In another test, AlignGraph was able to improve the assembly of a published genome (Arabidopsis strain Landsberg) by increasing the N50 of its extendable scaffolds by 86.6%. These results demonstrate AlignGraph’s efficiency in improving genome assemblies by taking advantage of closely related references.

Availability and implementation: The AlignGraph software can be downloaded for free from this site: https://github.com/baoe/AlignGraph.

Contact:  thomas.girke@ucr.edu