bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting risk for oral and written language learning difficulties in students educated in a second language
Authors: ERDOS CAROLINE , GENESEE FRED , SAVAGE ROBERT , HAIGH CORINNE
Published: January 2013

The extent to which risk for French as a second language (L2) reading and language learning impairment are distinct and can be predicted using first language (L1) predictors was examined in English-speaking students in total French immersion programs. A total of 86 children were tested in fall of kindergarten, spring kindergarten, and spring Grade 1 using an extensive battery of L1 predictor tests (in kindergarten) and L2 outcome tests (in Grade 1). Analyses of the kindergarten predictor scores revealed distinct underlying components, one related to reading and one to oral language. Further analyses revealed that phonological awareness, phonological access, and letter-sound knowledge in L1 were significant predictors of risk for reading difficulties in L2 while performance on L1 sentence repetition, phonological awareness, and tense marking tests in kindergarten were the best predictors of risk for L1 and L2 oral language difficulties. Both fall- and spring-kindergarten predictors predicted Grade 1 outcomes to a significant extent, with the spring-kindergarten predictors being more accurate. These results provide support for distinctive risk profiles for L2 oral language and reading difficulty and, furthermore, argue that assessment of L1 abilities can be used to make reasonably accurate predictions of later reading and/or oral language learning difficulties in L2 students.
A method to reduce ambiguities of qualitative reasoning for conceptual design applications
Authors: D'Amelio Valentina , Chmarra Magdalena K. , Tomiyama Tetsuo
Published: January 2013

Qualitative reasoning can generate ambiguous behaviors due to the lack of quantitative information. Despite many different research results focusing on ambiguities reduction, fundamentally it is impossible to totally remove ambiguities with only qualitative methods and to guarantee the consistency of results. This prevents the wide use of qualitative reasoning techniques in practical situations, particularly in conceptual design, where qualitative reasoning is considered intrinsically useful. To improve this situation, this paper initially investigates the origin of ambiguities in qualitative reasoning. Then it proposes a method based on intelligent interventions of the user who is able to detect ambiguities, to prioritize interventions on these ambiguities, and to reduce ambiguities based on the least commitment strategy. This interaction method breaks through the limit of qualitative reasoning in practical applications to conceptual design. The method was implemented as a new feature in a software tool called the Knowledge Intensive Engineering Framework in order to be tested and used for a printer design.
Five Supernova Survey Galaxies in the Southern Hemisphere: Supernova Ia Rates
Authors: Hakobyan A. A. , Petrosian A. R. , Mamon G. A. , McLean B. , Kunth D. , Turatto M. , Cappellaro E. , Mannucci F. , Allen R. J. , Panagia N. , Valle M. Della , Petrosyan G. V.
Published: January 2013

Based on the database of 56 supernovae (SNe) events discovered in 3838 galaxies of the southern hemisphere, we compute the rate of SNe of different types along the Hubble sequence normalized to the optical and near-infrared (NIR) luminosities as well as to the stellar mass of the galaxies. We find that the rates of Type Ia SNe show a dependence on both morphology and colors of the galaxies, and therefore, on the star-formation activity. The rate of SNe Ia can be explained by assuming that at least 15% of Ia events in spiral galaxies originate in relatively young stellar populations. We also find that the rates show no modulation with nuclear activity or environment.
The Appearance of Type Ia Supernova Progenitors: If Not SSSs, then What Do They Look Like?
Authors: Di Stefano Rosanne
Published: January 2013

“What do the progenitors of Type Ia supernovae (SNe Ia) look like? How can we hope to find them?” We focus on the epoch during which mass is incident on a white dwarf (WD) at high rates (> 10−7M⊙ yr−1). Such epochs are expected in single-degenerate (SD) progenitors, double-degenerate (DD) progenitors, and in a wide range of binaries with WDs that will not achieve the Chandrasekhar mass, MCh. High-rate accretion onto a WD produces high luminosities through accretion alone; in addition, most calculations show that quasisteady or episodic nuclear burning can occur, increasing the luminosity by more than an order of magnitude. If the photosphere is not much larger than the WD, the emission will have values of kT in the range of tens of eV, and the source will appear as a luminous supersoft x-ray source (SSS). Studies of local SSSs that are good candidates for nuclear-burning WDs (NBWDs) suggest that many have low duty cycles of SSS activity. This is consistent with the fact that binary WD models predict about 100 times as many SSSs in external galaxies of all types as are actually detected. Interstellar absorption does not appear to be the problem. Instead, it is likely that the ~1037−1038 erg s−1 emitted by NBWDs emerges in other wavebands. The challenge we face is to search for highly luminous systems within the Milky Way and nearby galaxies that have unusual properties consistent with NBWDs, and inconsistent with other physical models. Model tests can then be conducted for individual candidates, allowing us to identify large numbers of progenitors years before explosion.
Single Degenerate Progenitors of Type Ia Supernovae
Authors: Bours Madelon , Toonen Silvia , Nelemans Gijs
Published: January 2013

There is a general agreement that Type Ia supernovae correspond to the thermonuclear runaway of a white dwarf (WD) in a compact binary. The details of these progenitor systems are still unclear. Using the population synthesis code SeBa and several assumption for the WD retention efficiency, we estimate the delay times and supernova rates for the single degenerate scenario.
Constraining the Properties of SNe Ia Progenitors from Light Curves
Authors: Sadler B. , Hoeflich Peter , Baron E. , Krisciunas K. , Folatelli G. , Hamuy M. , Khokhlov M. , Phillips M. , Suntzeff N. , Wang L.
Published: January 2013

We present an analysis of high precision V light curves (LC) for 18 local Type Ia supernovae (SNe Ia) as obtained with the same telescope and setup at the Las Campanas Observatory (LCO). This homogeneity provides an intrinsic accuracy of a few hundredths of a magnitude with respect to individual LCs and between different objects. Based on the single degenerate (SD) scenario, we identify patterns which have been predicted by model calculations as signatures of the progenitor and accretion rate which change the explosion energy and the amount of electron capture, respectively. Using these templates as principle components and the overdetermined system of SNe pairs, we reconstruct the properties of progenitors and progenitor systems. All LCO SNe Ia follow the brightness decline relation except 2001ay. After subtraction of the two components, the remaining scatter is reduced to ≈0.01m−0.03m. SNe Ia seem to originate from progenitors with main-sequence masses MMS > 3 M⊙ with the exception of two subluminous SNe Ia with MMS < 2 M⊙. The component analysis indicates a wide range of accretion rates in the progenitor systems closing the gap to accretion induced collapses (AIC). SN1991t-like objects show differences in decline rate (dm15) but no tracers of our secondary parameters. This may point to a different origin such as the double degenerate or pulsating delayed detonation scenarios. SN2001ay does not follow the decline relation. It can be understood in the framework of C-rich white dwarfs (WDs), and this group may produce an anti-Phillips relation. We suggest that this may be a result of a common envelope phase and mixing during central He burning as in SN1987A.
The role of van der Waals forces in water adsorption on metals
Authors: Carrasco Javier , Klimeš Jiří , Michaelides Angelos
Published: January 2013

The interaction of water molecules with metal surfaces is typically weak and as a result van der Waals (vdW) forces can be expected to be of importance. Here we account for the systematic poor treatment of vdW forces in most popular density functional theory exchange-correlation functionals by applying accurate non-local vdW density functionals. We have computed the adsorption of a variety of exemplar systems including water monomer adsorption on Al(111), Cu(111), Cu(110), Ru(0001), Rh(111), Pd(111), Ag(111), Pt(111), and unreconstructed Au(111), and small clusters (up to 6 waters) on Cu(110). We show that non-local correlations contribute substantially to the water-metal bond in all systems, whilst water-water bonding is much less affected by non-local correlations. Interestingly non-local correlations contribute more to the adsorption of water on the reactive transition metal substrates than they do on the noble metals. The relative stability, adsorption sites, and adsorption geometries of competing water adstructures rarely differ when comparing results obtained with semi-local functionals and the non-local vdW density functionals, which explains the previous success of semi-local functionals in characterizing adsorbed water structures on a number of metal surfaces.
Experimental demonstration of simplified quantum process tomography
Authors: Wu Z. , Li S. , Zheng W. , Peng X. , Feng M.
Published: January 2013

The essential tool to characterize dynamics of an open quantum system is quantum process tomography (QPT). Although standard QPT methods are hard to be scalable, simplified QPT approach is available if we have the prior knowledge that the system Hamiltonian commutes with the system-environment interaction Hamiltonian. Using a nuclear magnetic resonance (NMR) quantum simulator, we experimentally simulate dephasing channels to demonstrate the simplified QPT as well as the standard QPT method as a comparison. The experimental results agree well with our predictions which confirm the validity and better efficiency of the simplified QPT.
Influence of organic layer thickness on structure, magnetic, and transport properties of Langmuir-Blodgett ttb-CuPc/CoFe
Authors: Yu T. , Zhang Q. T. , Liu D. P. , Han X. F.
Published: January 2013

In this letter, the ill-defined layer in organic/metal vertical structure was examined using ttb-CuPc/CoFe films. The ill-defined layer thickness was estimated. Beside the usually observed damages to organic underlayer, it is found that ill-defined layer may also influence film properties by modulating the growth of top metal layer. In our case, granular rather than continuous CoFe film was found as increasing ttb-CuPc underlayer thickness with a corresponding change in film's magnetic and transport properties.
Effect of magnetic order on nucleation in undercooled Co80Pd20 melts
Authors: Zhou Shengyin , Hu Rui , Li Jinshan , Chang Hui , Kou Hongchao , Zhou Lian
Published: January 2013

Co80Pd20 melts have been undercooled below Curie temperature of the liquids (TCL) by employing the method of molten glass denucleation combined with cyclic superheating. The largest undercooling achieved is 465 K, which indicates that the nucleation temperature is below TCL more than 100 K and then the ferromagnetic liquid is obtained. The nucleation behavior is analyzed using the classical nucleation theory extended by magnetic contributions to the Gibbs free energy. The results reveal that the onset of magnetic order facilitates rather than stimulates nucleation. Consequently, Co80Pd20 melts can be undercooled below TCL.
12% magnetic field-induced strain in Ni-Mn-Ga-based non-modulated martensite
Authors: Sozinov A. , Lanska N. , Soroka A. , Zou W.
Published: January 2013

Magnetic field-induced strain (MFIS) of 12% is reported in ferromagnetic Ni46Mn24Ga22Co4Cu4 martensite exhibiting non-modulated (NM) tetragonal crystal structure with lattice parameter ratio c/a>1. The strain was measured at ambient temperature in a magnetic field of the order of 1 T. The twinning stress σTW and the magnetic stress σMAG were also measured and the condition for a giant MFIS observation σTW<σMAG was confirmed. The MFIS was achieved in NM Ni46Mn24Ga22Co4Cu4 martensite by considerable lowering of the σTW value as compared to the values for NM martensites in ternary Ni-Mn-Ga system.
Asymmetrical stripline based method for retrieving the electromagnetic properties of metamaterials
Authors: Gómez S. , Quéffélec P. , Chevalier A. , Tarot A. C. , Sharaiha A.
Published: January 2013

An experimental characterization technique for determining the electromagnetic properties of metamaterials in the microwave frequency band is presented. The method consists in measuring the S-parameters of an asymmetrical stripline partially filled with the sample to be characterized. For retrieving the characteristic parameters, two different approaches based on quasi-static approximations are compared. This measurement cell allows an “in situ” characterization because it reproduces the electromagnetic environment frequently found in planar technologies for microwave applications of metamaterials. The whole sample is uniformly excited in magnitude and direction by the interacting electromagnetic field which guarantees representativeness of extracted permittivity and permeability and avoids possible inconsistencies due to anisotropy and heterogeneity of metamaterials.
Band gap engineering of graphene/h-BN hybrid superlattices nanoribbons
Authors: Li Shilong , Ren Zhaoyu , Zheng Jiming , Zhou Yixuan , Wan Yun , Hao Ling
Published: January 2013

The electronic properties of one-dimensional superlattices which are alternately composed of graphene nanoribbon (GNR) and boron nitride nanoribbon (BNNR) with different unit ratio (GNR:BNNR) have been investigated by applying first-principles methods. The results show that the band gap of the superlattices is regulated in a wide range for both zigzag and armchair edges with increasing the BN proportion. With the increase of the BN proportion, the band gap increases either for zigzag edges superlattices or armchair edges superlattices. From analyzing the band structures, the local density of states, and the charge densities, the engineering mechanism is explored. Furthermore, the present results are coincidence with the conclusion of Kronig-Penney model.
Polarization-dependent optical absorption of graphene under total internal reflection
Authors: Ye Qing , Wang Jin , Liu Zhibo , Deng Zhi-Chao , Kong Xian-Tian , Xing Fei , Chen Xu-Dong , Zhou Wen-Yuan , Zhang Chun-Ping , Tian Jian-Guo
Published: January 2013

It is shown that graphene exhibits strong polarization-dependent optical absorption under total internal reflection. Compared with universal absorbance of 2.3%, larger absorption was observed in monolayer, bilayer, and few-layer graphenes for transverse electric (TE) wave under total internal reflection. Our result indicates that reflectance ratio of transverse magnetic wave to TE waves can easily provide the information of number of graphene layers. Furthermore, the enhanced light-graphene coupling in a wide spectral range will be great potential in many applications such as photodetector, photovoltaics, and optical sensor.
Magnetic properties and magnetocaloric effects in Er3−xGdxCo intermetallic compounds
Authors: Mo Zhao-Jun , Shen Jun , Yan Li-Qin , Wu Jian-Feng , Tang Cheng-Chun , Shen Bao-Gen
Published: January 2013

A series of intermetallic Er3−xGdxCo (x = 0.5–3) compounds were synthesized and their magnetic properties and magnetocaloric effects were investigated. The Neél temperature (TN) could be tuned from 28 to 129 K by partially replacement of Gd with Er. For a field change of 5 T, the Er1.5Gd1.5Co exhibited a minimum −ΔSM of 9.8 J/kg K and maximum refrigerant capacity power (RCP) value of 629 J/kg which originated from an enlarged temperature span of magnetic entropy change in the compound. Results demonstrate that it is a feasible way to search for a large RCP material from the compounds with two magnetic transitions and controlled temperature region.
The effects of sodium gluconate and microbial phytase on performance and mineral utilisation in broiler chicks
Authors: Günal M.
Published: January 2013

An experiment was conducted to investigate the effects of sodium gluconate and microbial phytase (MP) (Natuphos 1000G) supplementation of diets on performance, mineral retention and bone mineralisation in male broiler chicks from a day old to 21 days of age. The experiment was carried out using a completely randomised design with a 3 by 2 factorial arrangement (0, 2 and 4% sodium gluconate and 0 and 750 U MP/kg diet). Diets were formulated with deficient contents of available phosphorus (aP) (2.4 g/kg). Ten replicate cages of four chicks per replicate cage were fed experimental diets. MP supplementation of diets with deficient contents of aP significantly improved weight gain (P < 0.05) and feed efficiency (P < 0.01). The performance results were similar in birds fed the diets without sodium gluconate and the diets with 2% sodium gluconate. However, the dietary inclusion of sodium gluconate at 4% depressed (P < 0.05) the growth of broiler chickens compared with the diet without sodium gluconate. Compared with the diets supplemented with 2% sodium gluconate, the diets supplemented with 4% sodium gluconate decreased (P < 0.05) weight gain and increased (P < 0.05) feed efficiency. MP supplementation increased (P < 0.01) Ca, P, Mg, Zn retention, and tibia ash, Ca and P contents in tibia ash. Diets with sodium gluconate increased (P < 0.05) P and Zn retention. Diets containing sodium gluconate without phytase increased (P < 0.05) Mg retention and P content in tibia ash. The diet with 2% sodium gluconate without phytase also increased (P < 0.05) Ca retention. The dietary inclusion of sodium gluconate at 2% improved (P < 0.05) tibia ash and Ca content in tibia ash. Sodium gluconate and MP had significant interactions in Ca and Mg retention (P < 0.01), and P content (P < 0.05) in tibia ash. In conclusion, the results indicated that phytase and sodium gluconate supplementation of corn–soybean meal low AP diets increased Ca, P, Mg and Zn mineral retention and bone mineralisation in chicks. The addition of MP improved the performance. However, the supplementation of diets with 4% sodium gluconate depressed the performance.
Liveweight prediction from hip height, condition score, fetal age and breed in tropical female cattle
Authors: Fordyce Geoffry , Anderson Angela , McCosker Kieren , Williams Paul J. , Holroyd Richard G. , Corbet Nick J. , Sullivan Michael S.
Published: January 2013

Hip height, body condition, subcutaneous fat, eye muscle area, percentage Bos taurus, fetal age and diet digestibility data were collected at 17 372 assessments on 2181 Brahman and tropical composite (average 28% Brahman) female cattle aged between 0.5 and 7.5 years of age at five sites across Queensland. The study validated the subtraction of previously published estimates of gravid uterine weight to correct liveweight to the non-pregnant status. Hip height and liveweight were linearly related (Brahman: P < 0.001, R2 = 58%; tropical composite P < 0.001, R2 = 67%). Liveweight varied by 12–14% per body condition score (5-point scale) as cows differed from moderate condition (P < 0.01). Parallel effects were also found due to subcutaneous rump fat depth and eye muscle area, which were highly correlated with each other and body condition score (r = 0.7–0.8). Liveweight differed from average by 1.65–1.66% per mm of rump fat depth and 0.71–0.76% per cm2 of eye muscle area (P < 0.01). Estimated dry matter digestibility of pasture consumed had no consistent effect in predicting liveweight and was therefore excluded from final models. A method developed to estimate full liveweight of post-weaning age female beef cattle from the other measures taken predicted liveweight to within 10 and 23% of that recorded for 65 and 95% of cases, respectively. For a 95% chance of predicted group average liveweight (body condition score used) being within 5, 4, 3, 2 and 1% of actual group average liveweight required 23, 36, 62, 137 and 521 females, respectively, if precision and accuracy of measurements matches that used in the research. Non-pregnant Bos taurus female cattle were calculated to be 10–40% heavier than Brahmans at the same hip height and body condition, indicating a substantial conformational difference. The liveweight prediction method was applied to a validation population of 83 unrelated groups of cattle weighed in extensive commercial situations on 119 days over 18 months (20 917 assessments). Liveweight prediction in the validation population exceeded average recorded liveweight for weigh groups by an average of 19 kg (~6%) demonstrating the difficulty of achieving accurate and precise animal measurements under extensive commercial grazing conditions.
Synthetic Studies Concerning the Crinine Alkaloid Haemultine
Authors: Gao Nadia (Yuqian) , Ma Xinghua , Petit Laurent , Schwartz Brett D. , Banwell Martin G. , Willis Anthony C. , Cade Ian A. , Rae A. David
Published: January 2013

The racemic form, (±)-1, of the structure originally assigned to the crinine alkaloid haemultine has been prepared for the first time. A key step involved the conversion of compound (±)-4 into the isomeric cis-C3a-arylhexahydroindole (±)-3 using a Pd0-catalysed intramolecular Alder-ene reaction. The amino-alcohol (±)-2 derived from the latter compound reacted with paraformaldehyde in the presence of trifluoroacetic acid to give, via a Pictet–Spengler reaction, the target (±)-1. The diastereoisomeric Mosher esters 15 and 16 obtained by coupling the racemate (±)-1 with the R-form, 14, of the Mosher acid could be separated chromatographically and then reductively cleaved to give the enantiomerically pure compounds (+)-1 and (–)-1, respectively. The physical and spectroscopic data derived from the former enantiomer are consistent with the proposition that the title natural product is, in fact, a mixture of (+)-1 and its Δ2,3-double bond isomer.
Coordination Polymers of Silver(I) with the Flexible Tritopic Ligand 1,3,5-Tri(4-cyanophenoxy)benzene: Guest Inclusion and Luminescent Properties
Authors: Roy Sandipan , Biradha Kumar
Published: January 2013

A new flexible tritopic ligand, 1,3,5-tri(4-cyanophenoxy)benzene (1), was synthesised by the reaction of phloroglucinol and para-fluorobenzonitrile. Compound 1 crystallises in the non-centrosymmetric space group Pna21. The reaction of ligand 1 with AgBF4 in the presence of different aromatic guest molecules was found to result in coordination polymers, namely, {[Ag3(1)2(BF4)3(H2O)2]·2C7H8·2CH2Cl2}n (2), {[Ag3(1)2(BF4)3(H2O)2]·2C6H6·2CH2Cl2}n (3). The crystal structures of 2 and 3 reveal that ligand 1 is linked by AgI ions into three-dimensional networks containing channels that are occupied by dichloromethane and aromatic guest molecules. The luminescent properties of crystalline 1 and 3 differ significantly.
Soil water storage, drainage, and leaching in four irrigated cotton-based cropping systems sown in a Vertosol with subsoil sodicity
Authors: Hulugalle N. R. , Weaver T. B. , Finlay L. A.
Published: January 2013

Comparative studies of drainage and leaching in irrigated cotton (Gossypium hirsutum L.) based cropping systems in Australian Vertosols are sparse. Our objective was to quantify soil water storage, drainage, and leaching in four cotton-based cropping systems sown on permanent beds in an irrigated Vertosol with subsoil sodicity. Drainage was inferred using the chloride mass-balance method, and soil water storage and leaching were measured with a neutron moisture meter and ceramic-cup water samplers, respectively, from September 2005 to May 2011 in an ongoing experiment. The experimental treatments were: CC, cotton monoculture, summer cotton with winter fallow; CV, cotton–vetch (Vicia benghalensis L.) rotation with vetch stubble retained as in-situ mulch; CW, cotton–wheat (Triticum aestivum L.), with wheat stubble incorporated and a summer–winter fallow; and CWV, cotton–wheat–vetch, with wheat and vetch stubbles retained as in-situ mulch and summer and spring fallows. Soil water storage was generally highest under CW and CWV and least under CV. An untilled short fallow (~3 months) when combined with retention of crop residues as surface mulch, as in CWV, was as effective in harvesting rainfall as a tilled long fallow (~11 months) with stubble incorporation, as in CW. Drainage under cotton was generally in the order CW ≥ CWV > CC = CV, all of which were considerably greater than drainage during fallows. Except for very wet and dry winters, drainage under wheat rotation crops was greater than that under vetch. During wet winters, saturated soil in the 0–0.6 m depth of treatments under fallow resulted in more drainage than in the drier, cropped plots. No definitive conclusions could be made with respect to the effects of cropping systems on salt and nutrient leaching. Leachate contained less nitrate-nitrogen, magnesium, and potassium, but leachate electrical conductivity was ~6 times higher than infiltrated water. The greater salinity of the leachate may pose a risk to groundwater resources.
Nature of the clay - cation bond affects soil structure as verified by X-ray computed tomography
Authors: Marchuk Alla , Rengasamy Pichu , McNeill Ann , Kumar Anupama
Published: January 2013

Non-destructive X-ray computed tomography (µCT) scanning was used to characterise changes in pore architecture as influenced by the proportion of cations (Na, K, Mg, or Ca) bonded to soil particles. These observed changes were correlated with measured saturated hydraulic conductivity, clay dispersion, and zeta potential, as well as cation ratio of structural stability (CROSS) and exchangeable cation ratio. Pore architectural parameters such as total porosity, closed porosity, and pore connectivity, as characterised from µCT scans, were influenced by the valence of the cation and the extent it dominated in the soil. Soils with a dominance of Ca or Mg exhibited a well-developed pore structure and pore interconnectedness, whereas in soil dominated by Na or K there were a large number of isolated pore clusters surrounded by solid matrix where the pores were filled with dispersed clay particles. Saturated hydraulic conductivities of cationic soils dominated by a single cation were dependent on the observed pore structural parameters, and were significantly correlated with active porosity (R2 = 0.76) and pore connectivity (R2 = 0.97). Hydraulic conductivity of cation-treated soils decreased in the order Ca > Mg > K > Na, while clay dispersion, as measured by turbidity and the negative charge of the dispersed clays from these soils, measured as zeta potential, decreased in the order Na > K > Mg > Ca.
The results of the study confirm that structural changes during soil–water interaction depend on the ionicity of clay–cation bonding. All of the structural parameters studied were highly correlated with the ionicity indices of dominant cations. The degree of ionicity of an individual cation also explains the different effects caused by cations within a monovalent or divalent category. While sodium adsorption ratio as a measure of soil structural stability is only applicable to sodium-dominant soils, CROSS derived from the ionicity of clay–cation bonds is better suited to soils containing multiple cations in various proportions.
Single-particle EM reveals extensive conformational variability of the Ltn1 E3 ligase
Authors: Lyumkis Dmitry , Doamekpor Selom K. , Bengtson Mario H. , Lee Joong-Won , Toro Tasha B. , Petroski Matthew D. , Lima Christopher D. , Potter Clinton S. , Carragher Bridget , Joazeiro Claudio A. P.
Published: January 2013

Ltn1 is a 180-kDa E3 ubiquitin ligase that associates with ribosomes and marks certain aberrant, translationally arrested nascent polypeptide chains for proteasomal degradation. In addition to its evolutionarily conserved large size, Ltn1 is characterized by the presence of a conserved N terminus, HEAT/ARM repeats predicted to comprise the majority of the protein, and a C-terminal catalytic RING domain, although the protein’s exact structure is unknown. We used numerous single-particle EM strategies to characterize Ltn1’s structure based on negative stain and vitreous ice data. Two-dimensional classifications and subsequent 3D reconstructions of electron density maps show that Ltn1 has an elongated form and presents a continuum of conformational states about two flexible hinge regions, whereas its overall architecture is reminiscent of multisubunit cullin–RING ubiquitin ligase complexes. We propose a model of Ltn1 function based on its conformational variability and flexibility that describes how these features may play a role in cotranslational protein quality control.
Synchronization in complex oscillator networks and smart grids
Authors: Dörfler Florian , Chertkov Michael , Bullo Francesco
Published: January 2013

The emergence of synchronization in a network of coupled oscillators is a fascinating topic in various scientific disciplines. A widely adopted model of a coupled oscillator network is characterized by a population of heterogeneous phase oscillators, a graph describing the interaction among them, and diffusive and sinusoidal coupling. It is known that a strongly coupled and sufficiently homogeneous network synchronizes, but the exact threshold from incoherence to synchrony is unknown. Here, we present a unique, concise, and closed-form condition for synchronization of the fully nonlinear, nonequilibrium, and dynamic network. Our synchronization condition can be stated elegantly in terms of the network topology and parameters or equivalently in terms of an intuitive, linear, and static auxiliary system. Our results significantly improve upon the existing conditions advocated thus far, they are provably exact for various interesting network topologies and parameters; they are statistically correct for almost all networks; and they can be applied equally to synchronization phenomena arising in physics and biology as well as in engineered oscillator networks, such as electrical power networks. We illustrate the validity, the accuracy, and the practical applicability of our results in complex network scenarios and in smart grid applications.
Monkeys are perceptually tuned to facial expressions that exhibit a theta-like speech rhythm
Authors: Ghazanfar Asif A. , Morrill Ryan J. , Kayser Christoph
Published: January 2013

Human speech universally exhibits a 3- to 8-Hz rhythm, corresponding to the rate of syllable production, which is reflected in both the sound envelope and the visual mouth movements. Artificial perturbation of the speech rhythm outside the natural range reduces speech intelligibility, demonstrating a perceptual tuning to this frequency band. One theory posits that the mouth movements at the core of this speech rhythm evolved through modification of ancestral primate facial expressions. Recent evidence shows that one such communicative gesture in macaque monkeys, lip-smacking, has motor parallels with speech in its rhythmicity, its developmental trajectory, and the coordination of vocal tract structures. Whether monkeys also exhibit a perceptual tuning to the natural rhythms of lip-smacking is unknown. To investigate this, we tested rhesus monkeys in a preferential-looking procedure, measuring the time spent looking at each of two side-by-side computer-generated monkey avatars lip-smacking at natural versus sped-up or slowed-down rhythms. Monkeys showed an overall preference for the natural rhythm compared with the perturbed rhythms. This lends behavioral support for the hypothesis that perceptual processes in monkeys are similarly tuned to the natural frequencies of communication signals as they are in humans. Our data provide perceptual evidence for the theory that speech may have evolved from ancestral primate rhythmic facial expressions.
Correlations between cannabis use and IQ change in the Dunedin cohort are consistent with confounding from socioeconomic status
Authors: Rogeberg Ole
Published: January 2013

Does cannabis use have substantial and permanent effects on neuropsychological functioning? Renewed and intense attention to the issue has followed recent research on the Dunedin cohort, which found a positive association between, on the one hand, adolescent-onset cannabis use and dependence and, on the other hand, a decline in IQ from childhood to adulthood [Meier et al. (2012)
Proc Natl Acad Sci USA
109(40):E2657–E2664]. The association is given a causal interpretation by the authors, but existing research suggests an alternative confounding model based on time-varying effects of socioeconomic status on IQ. A simulation of the confounding model reproduces the reported associations from the Dunedin cohort, suggesting that the causal effects estimated in Meier et al. are likely to be overestimates, and that the true effect could be zero. Further analyses of the Dunedin cohort are proposed to distinguish between the competing interpretations. Although it would be too strong to say that the results have been discredited, the methodology is flawed and the causal inference drawn from the results premature.
Ecological analysis of antigen-specific CTL repertoires defines the relationship between naïve and immune T-cell populations
Authors: Thomas Paul G. , Handel Andreas , Doherty Peter C. , La Gruta Nicole L.
Published: January 2013

Ecology is typically thought of as the study of interactions organisms have with each other and their environment and is focused on the distribution and abundance of organisms both within and between environments. On a molecular level, the capacity to probe analogous questions in the field of T-cell immunology is imperative as we acquire substantial datasets both on epitope-specific T-cell populations through high-resolution analyses of T-cell receptor (TCR) use and on global T-cell populations analyzed via high-throughput DNA sequencing. Here, we present the innovative application of existing statistical measures (used typically in the field of ecology), together with unique statistical analyses, to comprehensively assess how the naïve epitope-specific CD8
+
cytotoxic T lymphocyte (CTL) repertoire translates to that found following an influenza-virus–specific immune response. Such interrogation of our extensive, cumulated TCR CDR3β sequence datasets, derived from both naïve and immune CD8
+
T-cell populations specific for four different influenza-derived epitopes (D
b
NP
366
, influenza nucleoprotein amino acid residues 366–374; D
b
PA
224
, influenza acid polymerase amino acid residues 224–233; D
b
PB1-F2
62
, influenza polymerase B 1 reading frame 2 amino acid residues 62–70; K
b
NS2
114
, and influenza nonstructural protein 2 amino acid residues 114–121), demonstrates that epitope-specific TCR use in an antiviral immune response is the consequence of a complex interplay between the intrinsic characteristics of the naïve cytotoxic T lymphocyte precursor pool and extrinsic (likely antigen driven) influences, the contribution of which varies in an epitope-specific fashion.
Optimal and Preferred Eye Landing Positions in Objects and Scenes
Authors: Foulsham Tom , Kingstone Alan
Published: January 2013

Viewing position effects are commonly observed in reading, but they have only rarely been investigated in object perception or in the realistic context of a natural scene. In two experiments, we explored where people fixate within photorealistic objects and the effects of this landing position on recognition and subsequent eye movements. The results demonstrate an optimal viewing position—objects are processed more quickly when fixation is in the centre of the object. Viewers also prefer to saccade to the centre of objects within a natural scene, even when making a large saccade. A central landing position is associated with an increased likelihood of making a refixation, a result that differs from previous reports and suggests that multiple fixations within objects, within scenes, occur for a range of reasons. These results suggest that eye movements within scenes are systematic and are made with reference to an early parsing of the scene into constituent objects.
Excitation-induced exchange of Na+, K+, and Cl− in rat EDL muscle in vitro and in vivo: Physiology and pathophysiology
Authors: Clausen Torben
Published: January 2013

In skeletal muscle, excitation leads to increased [Na+]i, loss of K+, increased [K+]o, depolarization, and Cl− influx. This study quantifies these changes in rat extensor digitorum longus (EDL) muscles in vitro and in vivo using flame photometric determination of Na+ and K+ and 36Cl as a tracer for Cl−. In vitro, 5-Hz stimulation for 300 s increased intracellular Na+ content by 4.6 ± 1.2 µmol/g wet wt (P < 0.002) and decreased intracellular K+ content by 5.5 ± 2.3 µmol/g wet wt (P < 0.03). This would increase [K+]o by 28 ± 12 mM, sufficient to cause severe loss of excitability as the result of inactivation of Na+ channels. In rat EDL, in vivo stimulation at 5 Hz for 300 s or 60 Hz for 60 s induced significant loss of K+ (P < 0.01), sufficient to increase [K+]o by 71 ± 22 mM and 73 ± 15 mM, respectively. In spite of this, excitability may be maintained by the rapid and marked stimulation of the electrogenic Na+,K+ pumps already documented. This may require full utilization of the transport capacity of Na+,K+ pumps, which then becomes a limiting factor for physical performance. In buffer containing 36Cl, depolarization induced by increasing [K+]o to 40–80 mM augmented intracellular 36Cl by 120–399% (P < 0.001). Stimulation for 120–300 s at 5–20 Hz increased intracellular 36Cl by 100–188% (P < 0.001). In rats, Cl− transport in vivo was examined by injecting 36Cl, where electrical stimulation at 5 Hz for 300 s or 60 Hz for 60 s increased 36Cl uptake by 81% (P < 0.001) and 84% (P < 0.001), respectively, indicating excitation-induced depolarization. Cl− influx favors repolarization, improving K+ clearance and maintenance of excitability. In conclusion, excitation-induced fluxes of Na+, K+, and Cl− can be quantified in vivo, providing new evidence that in working muscles, extracellular accumulation of K+ is considerably higher than previously observed and the resulting depression of membrane excitability may be a major cause of muscle fatigue.
Cubic surfaces with special periods
Authors: Carlson James , Toledo Domingo
Published: January 2013

We study special values of the point in the unit ball (period) associated to a cubic surface. We show that this point has coordinates in

Q

(

−
3

)

\mathbb {Q}(\sqrt {-3})

if and only if the abelian variety associated to the surface is isogenous to the product of five Fermat elliptic curves. The proof uses an explicit formula for the embedding of the ball in the Siegel upper half plane. We give explicit constructions of abelian varieties with complex multiplication by fields of the form

K
0

(

−
3

)

K_0(\sqrt {-3})

, where

K
0

K_0

is a totally real quintic field, which arise from smooth cubic surfaces. We include Sage code for finding such fields and conclude with a list of related problems.
cAMP-stimulated phosphorylation of diaphanous 1 regulates protein stability and interaction with binding partners in adrenocortical cells
Authors: Li Donghui , Dammer Eric B. , Lucki Natasha C. , Sewer Marion B.
Published: January 2013

Diaphanous homologue 1 (DIAPH1) is a Rho effector protein that coordinates cellular dynamics by regulating microfilament and microtubule function. We previously showed that DIAPH1 plays an integral role in regulating the production of cortisol by controlling the rate of mitochondrial movement, by which activation of the adrenocorticotropin (ACTH)/cAMP signaling pathway stimulates mitochondrial trafficking and promotes the interaction between RhoA and DIAPH1. In the present study we use mass spectrometry to identify DIAPH1 binding partners and find that DIAPH1 interacts with several proteins, including RhoA, dynamin-1, kinesin, β-tubulin, β-actin, oxysterol-binding protein (OSBP)–related protein 2 (ORP2), and ORP10. Moreover, DIAPH1 is phosphorylated in response to dibutyryl cAMP (Bt2cAMP) at Thr-759 via a pathway that requires extracellular signal-related kinase (ERK). Alanine substitution of Thr-759 renders DIAPH1 more stable and attenuates the interaction between DIAPH1 and kinesin, ORP2, and actin but has no effect on the ability of the protein to interact with RhoA or β-tubulin. Finally, overexpression of a DIAPH1 T759A mutant significantly decreases the rate of Bt2cAMP-stimulated mitochondrial movement. Taken together, our findings establish a key role for phosphorylation in regulating the stability and function of DIAPH1.
NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets
Authors: Breese Marcus R. , Liu Yunlong
Published: January 2013

Summary: NGSUtils is a suite of software tools for manipulating data common to next-generation sequencing experiments, such as FASTQ, BED and BAM format files. These tools provide a stable and modular platform for data management and analysis.

Availability and implementation: NGSUtils is available under a BSD license and works on Mac OS X and Linux systems. Python 2.6+ and virtualenv are required. More information and source code may be obtained from the website: http://ngsutils.org.

Contact:  yunliu@iupui.edu

Supplemental information:  Supplementary data are available at Bioinformatics online.
Fast alignment and comparison of RNA structures
Authors: Wiegels Tim , Bienert Stefan , Torda Andrew E.
Published: January 2013

Motivation: To recognize remote relationships between RNA molecules, one must be able to align structures without regard to sequence similarity. We have implemented a method, which is swift [O(n2)], sensitive and tolerant of large gaps and insertions. Molecules are broken into overlapping fragments, which are characterized by their memberships in a probabilistic classification based on local geometry and H-bonding descriptors. This leads to a probabilistic similarity measure that is used in a conventional dynamic programming method.

Results: Examples are given of database searching, the detection of structural similarities, which would not be found using sequence based methods, and comparisons with a previously published approach.

Availability and implementation: Source code (C and perl) and binaries for linux are freely available at www.zbh.uni-hamburg.de/fries.

Contact:  tim.wiegels@gmail.com
Reconciling differential gene expression data with molecular interaction networks
Authors: Poirel Christopher L. , Rahman Ahsanur , Rodrigues Richard R. , Krishnan Arjun , Addesa Jacqueline R. , Murali T. M.
Published: January 2013

Motivation: Many techniques have been developed to compute the response network of a cell. A recent trend in this area is to compute response networks of small size, with the rationale that only part of a pathway is often changed by disease and that interpreting small subnetworks is easier than interpreting larger ones. However, these methods may not uncover the spectrum of pathways perturbed in a particular experiment or disease.

Results: To avoid these difficulties, we propose to use algorithms that reconcile case-control DNA microarray data with a molecular interaction network by modifying per-gene differential expression P-values such that two genes connected by an interaction show similar changes in their gene expression values. We provide a novel evaluation of four methods from this class of algorithms. We enumerate three desirable properties that this class of algorithms should address. These properties seek to maintain that the returned gene rankings are specific to the condition being studied. Moreover, to ease interpretation, highly ranked genes should participate in coherent network structures and should be functionally enriched with relevant biological pathways. We comprehensively evaluate the extent to which each algorithm addresses these properties on a compendium of gene expression data for 54 diverse human diseases. We show that the reconciled gene rankings can identify novel disease-related functions that are missed by analyzing expression data alone.

Availability: C++ software implementing our algorithms is available in the NetworkReconciliation package as part of the Biorithm software suite under the GNU General Public License: http://bioinformatics.cs.vt.edu/∼murali/software/biorithm-docs.

Contact: murali@cs.vt.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
gKaKs: the pipeline for genome-level Ka/Ks calculation
Authors: Zhang Chengjun , Wang Jun , Long Manyuan , Fan Chuanzhu
Published: January 2013

Summary: gKaKs is a codon-based genome-level Ka/Ks computation pipeline developed and based on programs from four widely used packages: BLAT, BLASTALL (including bl2seq, formatdb and fastacmd), PAML (including codeml and yn00) and KaKs_Calculator (including 10 substitution rate estimation methods). gKaKs can automatically detect and eliminate frameshift mutations and premature stop codons to compute the substitution rates (Ka, Ks and Ka/Ks) between a well-annotated genome and a non-annotated genome or even a poorly assembled scaffold dataset. It is especially useful for newly sequenced genomes that have not been well annotated. We applied gKaKs to estimate the genome-wide substitution rates in five pairs of closely related species. The average Ka and Ks computed by gKaKs were consistent with previous studies. We also compared the Ka, Ks and Ka/Ks of mouse and rat orthologous protein-coding genes estimated by gKaKs and based on the alignments generated by PAL2NAL. Results from two methods are compatible.

Availability and implementation: gKaKs is implemented in Perl and is freely available on http://longlab.uchicago.edu/?q=gKaKs. The detailed user manual is available on the website.

Contact:  cfan@wayne.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution
Authors: Li Jing-Woei , Wan Raymond , Yu Chi-Shing , Co Ngai Na , Wong Nathalie , Chan Ting-Fung
Published: January 2013

Summary: Insertional mutagenesis from virus infection is an important pathogenic risk for the development of cancer. Despite the advent of high-throughput sequencing, discovery of viral integration sites and expressed viral fusion events are still limited. Here, we present ViralFusionSeq (VFS), which combines soft-clipping information, read-pair analysis and targeted de novo assembly to discover and annotate viral–human fusions. VFS was used in an RNA-Seq experiment, simulated DNA-Seq experiment and re-analysis of published DNA-Seq datasets. Our experiments demonstrated that VFS is both sensitive and highly accurate.

Availability: VFS is distributed under GPL version 3 at http://hkbic.cuhk.edu.hk/software/viralfusionseq

Contact: tf.chan@cuhk.edu.hk

Supplementary information: Supplementary data are available at Bioinformatics Online