bluuebunny/crossref_metadata_2025 huggingface dataset:
Economic and energy analysis of domestic ground source heat pump systems in four Canadian cities
Authors: Le Dû M. , Dutil Y. , Rousse D. R. , Paradis P. L. , Groulx D.
Published: October 2015

This study provides an economic and energy analysis of the implementation of geothermal systems to meet the needs of a typical 130 m2 dwelling of a Canadian individual. The objective is to determine the monetary balance after 22 years, the net present value, the internal return rate, and annual savings for the same system operating under different climatic conditions and in different provinces (legislations, costs of fuel) to determine whether or not an individual should implement such a system in 2014. The geothermal system is used for both space heating and cooling, and to provide for 25% of the total amount of domestic hot water. The simulations are performed with RETScreen® for four Canadian cities: Halifax, Montreal, Toronto, and Vancouver. For the investigated configurations, it appeared that the cost of energy and its sources, which varied greatly according to the location, are the factors that most strongly influenced the economic viability of the proposed geothermal system, while climate was only a secondary impact. The impact of carbon taxes and equivalent monetary subsidies does not significantly modify the economic outcomes for Halifax and Montreal. However, for Toronto and Vancouver, these would need to reach between 280 and 300 Can$/tCO2eq to attain economic balance.
Symmetry reductions, exact solutions, and conservation laws of the generalized Zakharov equations
Authors: Buhe Eerdun , Bluman George W.
Published: October 2015

In this paper, the generalized Zakharov equations, which describe interactions between high- and low-frequency waves in plasma physics are studied from the perspective of Lie symmetry analysis and conservation laws. Based on some subalgebras of symmetries, several reductions and numerous new exact solutions are obtained. All of these solutions represent modified traveling waves. The obtained solutions include expressions involving Airy functions, Bessel functions, Whittaker functions, and generalized hypergeometric functions. Previously unknown conservation laws are constructed for the generalized Zakharov equations using the direct method. Profiles are presented for some of these new solutions.
Simultaneous dynamic electrical and structural measurements of functional materials
Authors: Vecchini C. , Thompson P. , Stewart M. , Muñiz-Piniella A. , McMitchell S. R. C. , Wooldridge J. , Lepadatu S. , Bouchenoire L. , Brown S. , Wermeille D. , Bikondoa O. , Lucas C. A. , Hase T. P. A. , Lesourd M. , Dontsov D. , Cain M. G.
Published: October 2015

A new materials characterization system developed at the XMaS beamline, located at the European Synchrotron Radiation Facility in France, is presented. We show that this new capability allows to measure the atomic structural evolution (crystallography) of piezoelectric materials whilst simultaneously measuring the overall strain characteristics and electrical response to dynamically (ac) applied external stimuli.
Exciton hopping probed by picosecond time-resolved cathodoluminescence
Authors: Shahmohammadi Mehran , Jacopin Gwénolé , Fu Xuewen , Ganière Jean-Daniel , Yu Dapeng , Deveaud Benoît
Published: October 2015

The exciton transport is studied in high quality ZnO microwires using time resolved cathodoluminescence. Owing to the available picosecond temporal and nanometer spatial resolution, a direct estimation of the exciton average speed has been measured. When raising the temperature, a strong decrease of the effective exciton mobility (hopping speed of donor-bound excitons) has been observed in the absence of any remarkable change in the effective lifetime of excitons. Additionally, the exciton hopping speed was observed to be independent of the strain gradient value, revealing the hopping nature of exciton movement. These experimental results are in good agreement with the behavior predicted for impurity-bound excitons in our previously published theoretical model based on Monte-Carlo simulations, suggesting the hopping process as the main transport mechanism of impurity-bound excitons at low temperatures.
An edge-magnetoplasmon Mach-Zehnder interferometer
Authors: Hiyama N. , Hashisaka M. , Fujisawa T.
Published: October 2015

We report an edge-magnetoplasmon (EMP) Mach-Zehnder (MZ) interferometer in a quantum Hall system. The MZ interferometer, which is based on the interference of two EMP beams traveling in chiral one-dimensional edge channels, is constructed by tailoring edge channels with functional devices such as splitters and delay lines. We measured 1 GHz EMP beams transmitted through the interferometer while tuning the phase evolution along two interference paths using tunable delay lines. Clear interference patterns as a function of the phase difference ensure the MZ interference. Moreover, the MZ interferometry is applied to evaluate the EMP transport through an attenuator interposed in one of the paths. This technique will be useful for investigating the functionalities of devices in plasmonics.
A new solid state extractor pulser for the FNAL magnetron ion source
Authors: Bollinger D. S. , Lackey J. , Larson J. , Triplett K.
Published: October 2015

A new solid state extractor pulser has been installed on the Fermi National Accelerator Laboratory (FNAL) magnetron ion source, replacing a vacuum tube style pulser that was used for over 40 years. The required ion source extraction voltage is 35 kV for injection into the radio frequency quadrupole. At this voltage, the old pulser had a rise time of over 150 μs due to the current limit of the vacuum tube. The new solid state pulsers are capable of 50 kV, 100 A peak current pulses and have a rise time of 9 μs when installed in the operational system. This paper will discuss the pulser design and operational experience to date.
Enhancement of Rashba interaction in GaAs/AlGaAs quantum wells due to the incorporation of bismuth
Authors: Simmons R. A. , Jin S. R. , Sweeney S. J. , Clowes S. K.
Published: October 2015

This paper reports on the predicted increase in the Rashba interaction due to the incorporation of Bi in GaAs/AlGaAs heterostructures. Band structure parameters obtained from the band anti-crossing theory have been used in combination with self-consistent Schrödinger-Poisson calculations and k.p models to determine the electron spin-splitting caused by structural inversion asymmetry and increased spin-orbit interaction. A near linear seven fold increase in the strength of the Rashba interaction is predicted for a 10% concentration of Bi in a GaAsBi/AlGaAs quantum well heterostructure.
Thermal diffusivity and heat capacity of SiGe/Si superlattice from 374 K to 674 K
Authors: Davidson Anthony L. , Twigg Mark , Thompson Phillip E. , Worchesky Terrance , Aifer Edward
Published: October 2015

In this work, we examine the thermal diffusivity of Si/SiGe thin-film superlattice (SL) structures and use these results with pervious thermal conductivity results to calculate the heat capacity from 374 K to 674 K. The thermal properties of semiconductor layered structures can be altered through the use of SL structures. This alteration occurs through two possible mechanisms: increased phonon scattering due to rough interfaces and phonon zone folding due to boundary conditions of the propagating waves. Examining the heat capacity allows for the observation of phonon zone folding effects while limiting effects due to scattering. Structures studied here consist of SiGe SLs grown at different temperatures and with varying SL spacing allowing the examination of period and crystallinity effects on thermal properties. Previously reported results show that for SL structures both crystalline and polycrystalline have a thermal conductivity of approximately 1 W/mK measured over temperatures ranging from 374 K to 674 K. In this work, thermal diffusivity was measured through laser flash analysis, with crystalline SL structures showing values <1 mm2/s, while the thermal diffusivity of the polycrystalline structure was found to be twice that of the crystalline structure over the temperature range. In all instances, the heat capacities for the SL structures are found to be lower than that for a uniform thin film alloy, indicating a significant contribution of phonon dispersion modification to the heat capacity.
Ferroelectric domain engineering by focused infrared femtosecond pulses
Authors: Chen Xin , Karpinski Pawel , Shvedov Vladlen , Koynov Kaloian , Wang Bingxia , Trull Jose , Cojocaru Crina , Krolikowski Wieslaw , Sheng Yan
Published: October 2015

We demonstrate infrared femtosecond laser-induced inversion of ferroelectric domains. This process can be realised solely by using tightly focused laser pulses without application of any electric field prior to, in conjunction with, or subsequent to the laser irradiation. As most ferroelectric crystals like LiNbO3, LiTaO3, and KTiOPO4 are transparent in the infrared, this optical poling method allows one to form ferroelectric domain patterns much deeper inside a ferroelectric crystal than by using ultraviolet light and hence can be used to fabricate practical devices. We also propose in situ diagnostics of the ferroelectric domain inversion process by monitoring the Čerenkov second harmonic signal, which is sensitive to the appearance of ferroelectric domain walls.
High-field electrical transport in amorphous phase-change materials
Authors: Kaes Matthias , Le Gallo Manuel , Sebastian Abu , Salinga Martin , Krebs Daniel
Published: October 2015

Electrical transport in chalcogenide-based phase change materials is an active area of research owing to the prominent role played by these materials in the field of information technology. Here, we present transport measurements (IV curves) obtained on line-cells of as-deposited amorphous phase change materials (Ge2Sb2Te5, GeTe, Ag4In3Sb66Te27) over a wide voltage and temperature range (300 K to 160 K). The well defined geometry of our devices enables a description of the transport behavior in terms of conductivity vs. electric field. At higher temperatures (300 K ≥ T ≥ 220 K) and low to intermediate fields (F < 20 V/μm), the data can be described within the framework of a previously developed model, which is based on multiple trapping transport together with 3D Poole-Frenkel emission from a two-center Coulomb potential. Based on this model, we observe a temperature dependence of the inter-trap distance, which we can relate to a temperature dependence in the occupation of the defect creating the Coulomb potential governing Poole-Frenkel emission. At higher fields and lower temperatures, the dependency of the IV curve on the electric field can be described by ln(I/I0) = (F/Fc)2. By combining this contribution with that of the Poole-Frenkel emission, we can show that the slope at high fields, Fc, is independent of temperature. We argue that models based on direct tunneling or thermally assisted tunneling from a single defect into the valence band cannot explain the observed behavior quantitatively.
Carbon as a source for yellow luminescence in GaN: Isolated CN defect or its complexes
Authors: Christenson Sayre G. , Xie Weiyu , Sun Y. Y. , Zhang S. B.
Published: October 2015

We study three carbon defects in GaN, isolated CN and its two complexes with donors CN–ON, and CN–SiGa, as a cause of the yellow luminescence using accurate hybrid density functional calculation, which includes the semi-core Ga 3d electrons as valence electrons and uses a larger 300-atom supercell. We show that the isolated CN defect yields good agreement with experiment on the photoluminescence (PL) peak position, zero-phonon line, and thermodynamic defect transition level. We find that the defect state of the complexes that is involved in the PL process is the same as that of the CN defect. The role of the positively charged donors (ON or SiGa) next to CN is to blue-shift the PL peak. Therefore, the complexes cannot be responsible for the same PL peak as isolated CN. Our detailed balance analysis further suggests that under thermal equilibrium at typical growth temperature, the concentration of isolated CN defect is orders of magnitude higher than the defect complexes, which is a result of the small binding energy in these complexes.
High performance, room temperature, broadband II-VI quantum cascade detector
Authors: Ravikumar Arvind P. , De Jesus Joel , Tamargo Maria C. , Gmachl Claire F.
Published: October 2015

We report on the experimental demonstration of a room temperature, II-VI, ZnCdSe/ZnCdMgSe, broadband Quantum Cascade detector. The detector consists of 30 periods of 2 interleaved active-absorption regions centered at wavelengths 4.8 μm and 5.8 μm, respectively. A broad and smooth photocurrent spectrum between 3.3 μm and 6 μm spanning a width of 1030 cm–1 measured at 10% above baseline was obtained up to 280 K, corresponding to a ΔE/E of 47%. Calibrated blackbody responsivity measurements show a measured peak responsivity of 40 mA/W at 80 K, corresponding to a detectivity of about 3.1×1010 cmHz/W. Bias dependent photocurrent measurements revealed no significant change in the spectral shape, suggesting an impedance matched structure between the different active regions.
Effect of dielectric stoichiometry and interface chemical state on band alignment between tantalum oxide and platinum
Authors: Lebedinskii Yu. Yu. , Chernikova A. G. , Markeev A. M. , Kuzmichev D. S.
Published: October 2015

The tantalum oxide–platinum interface electronic properties determined by X-ray photoelectron spectroscopy are found to depend on the dielectric stoichiometry and platinum chemical state. We demonstrate the slow charging of the tantalum oxide in cases of Ta2O5/Pt and Ta2O5−y/Pt interfaces under the X-ray irradiation. This behavior is proposed to be related to the charge accumulation at oxygen vacancies induced traps. Based on the proposed methodology, we define the intrinsic conductive band offset (CBO) ∼1.3 eV (both for Ta2O5/Pt and Ta2O5−y/Pt) and CBO after the full saturation of the traps charging ∼0.5 eV, while the last one defines the energy position of charged traps below the bottom of conduction band. We demonstrate also the pining at the both Ta2O5/Pt and Ta2O5−y/Pt interfaces even in the “intrinsic” state, apparently induced by the presence of additional interfacial states. No shifts of Ta4f line and band alignment in over stoichiometric Ta2O5+x/Pt structure during X-ray irradiation, as well as the absence of pinning, resulting in increase of CBO up to 2.3 eV are found. This behavior is related to the PtO2 interfacing layer formation at Ta2O5+x/Pt, blocking the charging of the surface states and associated dipole formation.
Multi-gate synergic modulation in laterally coupled synaptic transistors
Authors: Zhu Li Qiang , Xiao Hui , Liu Yang Hui , Wan Chang Jin , Shi Yi , Wan Qing
Published: October 2015

Laterally coupled oxide-based synaptic transistors with multiple gates are fabricated on phosphorosilicate glass electrolyte films. Electrical performance of the transistor can be evidently improved when the device is operated in a tri-gate synergic modulation mode. Excitatory post-synaptic current and paired pulse facilitation (PPF) behavior of biological synapses are mimicked, and PPF index can be effectively tuned by the voltage applied on the modulatory terminal. At last, superlinear to sublinear synaptic integration regulation is also mimicked by applying a modulatory pulse on the third modulatory terminal. The multi-gate oxide-based synaptic transistors may find potential applications in biochemical sensors and neuromorphic systems.
Tetra-methyl substituted copper (II) phthalocyanine as a hole injection enhancer in organic light-emitting diodes
Authors: Wang Yu-Long , Xu Jia-Ju , Lin Yi-Wei , Chen Qian , Shan Hai-Quan , Yan Yan , Roy V. A. L. , Xu Zong-Xiang
Published: October 2015

We have enhanced hole injection and lifetime in organic light-emitting diodes (OLEDs) by incorporating the isomeric metal phthalocyanine, CuMePc, as a hole injection enhancer. The OLED devices containing CuMePc as a hole injection layer (HIL) exhibited higher luminous efficiency and operational lifetime than those using a CuPc layer and without a HIL. The effect of CuMePc thickness on device performance was investigated. Atomic force microscope (AFM) studies revealed that the thin films were smooth and uniform because the mixture of CuMePc isomers depressed crystallization within the layer. This may have caused the observed enhanced hole injection, indicating that CuMePc is a promising HIL material for highly efficient OLEDs.
Assessing spatial variation of seagrass habitat structure in New Caledonia: an integrated approach
Authors: Irving Andrew D. , Jackson Emma L. , Hendry Rebecca A.
Published: October 2015

Natural habitats can be described using an array of variables, but metrics that distil these multiple parameters into a single readily comparable value (e.g. a score) can prove useful for spatio-temporal comparisons as well as decisions concerning environmental resource management. In the lagoon of south-western New Caledonia, multiple habitat variables sampled from seagrass meadows were integrated into a single score for comparison of habitat structure across two spatial scales. Collectively, seagrass meadows scored at 69/100, indicating a ‘fair-to-good’ habitat structure. Spatial variation was evident, however, being greatest at the scale of ‘site’ (0.5–5 km) relative to ‘location’ (tens of kilometres). Key metrics of seagrass area, percentage cover and species identity appeared to drive spatial patterns in habitat structure scores. Although the causes of observed site-scale variation in seagrass structure are untested, differences in wave exposure among sites appear a likely contributing factor. Overall, integrated sampling techniques such as that used herein can provide a convenient way to rapidly compare seagrass habitats, and could be useful as early warning indicators of habitat change in regions where anthropogenic impacts that cause seagrass decline (e.g. eutrophication, sediment released from mining) are of concern.
Australian general practitioner attitudes to clinical practice guidelines and some implications for translating osteoarthritis care into practice
Authors: Basedow Martin , Runciman William B. , Lipworth Wendy , Esterman Adrian
Published: October 2015

Clinical practice guidelines (CPGs) have been shown to improve processes of care and health outcomes, but there is often a discrepancy between recommendations for care and clinical practice. This study sought to explore general practitioner (GP) attitudes towards CPGs, in general and specifically for osteoarthritis (OA), with the implications for translating OA care into practice. A self-administered questionnaire was conducted in January 2013 with a sample of 228 GPs in New South Wales and South Australia. Seventy-nine GPs returned questionnaires (response rate 35%). Nearly all GPs considered that CPGs support decision-making in practice (94%) and medical education (92%). Very few respondents regarded CPGs as a threat to clinical autonomy, and most recognised that individual patient circumstances must be taken into account. Shorter CPG formats were preferred over longer and more comprehensive formats, with preferences being evenly divided among respondents for short, 2–3-page summaries, flowcharts or algorithms and single page checklists. GPs considered accessibility to CPGs to be important, and electronic formats were popular. Familiarity and use of The Royal Australian College of General Practitioners OA Guideline was poor, with most respondents either not aware of it (30%; 95% confidence interval (CI) 27 – 41%), had never used it (19%; 95% CI 12 – 29%) or rarely used it (34%; 95% CI 25–45%). If CPGs are to assist with the translation of evidence into practice, they must be easily accessible and in a format that encourages use.
The complex Lorentzian Leech lattice and the bimonster (II)
Authors: Basak Tathagata
Published: October 2015

LetDDbe the incidence graph of the projective plane overF3\mathbb {F}_3. The Artin group of the graphDDmaps onto the bimonster and a complex hyperbolic reflection groupΓ\Gammaacting on1313dimensional complex hyperbolic spaceYY. The generators of the Artin group are mapped to elements of order22(resp.33) in the bimonster (resp.Γ\Gamma). LetY∘⊆YY^{\circ } \subseteq Ybe the complement of the union of the mirrors ofΓ\Gamma. Daniel Allcock has conjectured that the orbifold fundamental group ofY∘/ΓY^{\circ }/\Gammasurjects onto the bimonster.

In this article we study the reflection groupΓ\Gamma. Our main result shows that there is homomorphism from the Artin group ofDDto the orbifold fundamental group ofY∘/ΓY^{\circ }/\Gamma, obtained by sending the Artin generators to the generators of monodromy around the mirrors of the generating reflections inΓ\Gamma. This answers a question in Allcock’s article “A monstrous proposal” and takes a step towards the proof of Allcock’s conjecture. The finite groupPGL⁡(3,F3)⊆Aut(D)\operatorname {PGL}(3, \mathbb {F}_3) \subseteq \mathrm {Aut}(D)acts onYYand fixes a complex hyperbolic line pointwise. We show that the restriction ofΓ\Gamma-invariant meromorphic automorphic forms onYYto the complex hyperbolic line fixed byPGL⁡(3,F3)\operatorname {PGL}(3, \mathbb {F}_3)gives meromorphic modular forms of level1313.
Dynamics of Farmland Ownership and Leasing: Implications for Young and Beginning Farmers
Authors: Katchova Ani L. , Ahearn Mary Clare
Published: October 2015

This study considers the transition into farming and growth of new farmers in U.S. agriculture by examining land ownership and leasing trends. Our approach is to characterize the entire distribution by farmer age and farmer experience rather than using young versus old and beginning versus established farmer categories. We also use a linked‐farms longitudinal approach to show trends over time in farmland expansion and contraction. We find that farms operated by older beginning farmers tend to be smaller and do not tend to grow over time. Our results show that it is mostly young farmers as opposed to all beginning farmers who rapidly expand their farm operations after entering agriculture. Our findings inform policy makers about the strategies that young and beginning farmers use to start their businesses and expand over time, and suggest more effective approaches for targeting loan programs to both young and beginning farmers.
Untangling cortico-striatal connectivity and cross-frequency coupling in L-DOPA-induced dyskinesia
Authors: Belić Jovana J. , Halje Pär , Richter Ulrike , Petersson Per , Hellgren Kotaleski Jeanette
Published: October 2015

We simultaneously recorded local field potentials in the primary motor cortex and sensorimotor striatum in awake, freely behaving, 6-OHDA lesioned hemi-parkinsonian rats in order to study the features directly related to pathological states such as parkinsonian state and levodopa-induced dyskinesia. We analysed the spectral characteristics of the obtained signals and observed that during dyskinesia the most prominent feature was a relative power increase in the high gamma frequency range at around 80 Hz, while for the parkinsonian state it was in the beta frequency range. Here we show that during both pathological states effective connectivity in terms of Granger causality is bidirectional with an accent on the striatal influence on the cortex. In the case of dyskinesia, we also found a high increase in effective connectivity at 80 Hz. In order to further understand the 80- Hz phenomenon, we performed cross-frequency analysis and observed characteristic patterns in the case of dyskinesia but not in the case of the parkinsonian state or the control state. We noted a large decrease in the modulation of the amplitude at 80 Hz by the phase of low frequency oscillations (up to ~10 Hz) across both structures in the case of dyskinesia. This may suggest a lack of coupling between the low frequency activity of the recorded network and the group of neurons active at ~80 Hz.
Local and population-level responses of Greater sage-grouse to oil and gas development and climatic variation in Wyoming
Authors: Ramey Rob R. , Thorley Joseph L. , Ivey Alexander S.
Published: October 2015

Background

Spatial scale is important when studying ecological processes. The Greater sage-grouse (Centrocercus urophasianus) is a large sexually dimorphic tetraonid that is endemic to the sagebrush biome of western North America. The impacts of oil and gas development at individual leks has been well-documented. However, no previous studies have quantified the population-level response.

Methods

Hierarchical models were used to estimate the effects of the areal disturbance due to well pads as well as climatic variation on individual lek counts and Greater sage-grouse populations (management units) over 32 years. The lek counts were analyzed using General Linear Mixed Models while the management units were analyzed using Gompertz Population Dynamic Models. The models were fitted using frequentist and Bayesian methods. An information-theoretic approach was used to identify the most important spatial scale and time lags. The relative importance of oil and gas and climate at the local and population-level scales was assessed using information-theoretic (Akaike’s weights) and estimation (effect size) statistics.

Results

At the local scale, oil and gas was an important negative predictor of the lek count. At the population scale, there was only weak support for oil and gas as a predictor of density changes but the estimated impacts on the long-term carrying capacity were consistent with summation of the local impacts. Regional climatic variation, as indexed by the Pacific Decadal Oscillation, was an important positive predictor of density changes at both the local and population-level (particularly in the most recent part of the time series).

Conclusions

Additional studies to reduce the uncertainty in the range of possible effects of oil and gas at the population scale are required. Wildlife agencies need to account for the effects of regional climatic variation when managing sage-grouse populations.
Fast and accurate long-range phasing in a UK Biobank cohort
Authors: Loh Po-Ru , Palamara Pier Francesco , Price Alkes L
Published: October 2015

Recent work has leveraged the extensive genotyping of the Icelandic population to perform long-range phasing (LRP), enabling accurate imputation and association analysis of rare variants in target samples typed on genotyping arrays. Here, we develop a fast and accurate LRP method, Eagle, that extends this paradigm to populations with much smaller proportions of genotyped samples by harnessing long (>4cM) identical-by-descent (IBD) tracts shared among distantly related individuals. We applied Eagle toN=150K samples (0.2% of the British population) from the UK Biobank, and we determined that it is 1–2 orders of magnitude faster than existing methods while achieving similar or better phasing accuracy (switch error rate ≈0.3%, corresponding to perfect phase in most 10Mb segments). We also observed that when used within an imputation pipeline, Eagle pre-phasing improved downstream imputation accuracy compared to pre-phasing in batches using existing methods (as necessary to achieve comparable computational cost).
A genome-wide resource for the analysis of protein localisation inDrosophila
Authors: Sarov Mihail , Barz Chritiane , Jambor Helena , Hein Marco Y. , Schmied Christopher , Suchold Dana , Stender Bettina , Janosch Stephan , Vikas Vinay K.J. , Krisnan R.T. , Aishwarya K. , Ferreira Irene R.S. , Ejsmont Radoslaw K. , Finkl Katja , Hasse Susanne , Kämpfer Philipp , Plewka Nicole , Vinis Elisabeth , Schloissnig Siegfried , Knust Elisabeth , Hartenstein Volker , Mann Matthias , Ramaswami Mani , VijayRaghavan K. , Tomancak Pavel , Schnorrer Frank
Published: October 2015

TheDrosophilagenome contains >13,000 protein coding genes, the majority of which remain poorly investigated. Important reasons include the lack of antibodies or reporter constructs to visualise these proteins. Here we present a genome-wide fosmid library of ≈10,000 GFP-tagged clones, comprising tagged genes and most of their regulatory information. For 880 tagged proteins we have created transgenic lines and for a total of 207 lines we have assessed protein expression and localisation in ovaries, embryos, pupae or adults by stainings and live imaging approaches. Importantly, we can visualise many proteins at endogenous expression levels and find a large fraction of them localising to subcellular compartments. Using complementation tests we demonstrate that two-thirds of the tagged proteins are fully functional. Moreover, our clones also enable interaction proteomics from developing pupae and adult flies. Taken together, this resource will enable systematic analysis of protein expression and localisation in various cellular and developmental contexts.
Mitochondrial introgression suggests extensive ancestral hybridization events amongSaccharomycesspecies
Authors: Peris David , Arias Armando , Orlić Sandi , Belloch Carmela , Pérez-Través Laura , Querol Amparo , Barrio Eladio
Published: October 2015

1.

Horizontal Gene Transfer (HGT) in eukaryotic plastids and mitochondrial genomes is common, and plays an important role in organism evolution. In yeasts, recent mitochondrial HGT has been suggested betweenS. cerevisiaeandS. paradoxus. However, few strains have been explored due to the lack of accurate mitochondrial genome annotations. Mitochondrial genome sequences are important to understand how frequent these introgressions occur and their role in cytonuclear incompatibilities and fitness. In fact, most of the Bateson-Dobzhansky-Muller genetic incompatibilities described in yeasts are driven by cytonuclear incompatibilities. In this study, we have explored the mitochondrial inheritance of several worldwide distributedSaccharomycesspecies isolated from different sources and geographic origins. We demonstrated the existence of several recombination points in the mitochondrial regionCOX2-ORF1, likely mediated by the transfer of two different types ofORF1(F-SceIII), encoding a freestanding homing endonuclease, or mostly facilitated by A+T tandem repeats and regions of integration of GC clusters. These introgressions were shown to occur at intra- as well as at interspecific levels. This suggest a complex model ofSaccharomycesevolution which involve several ancestral hybridization events in wild environments.
Evolving synergetic interactions
Authors: Wu Bin , Arranz Jordi , Du Jinming , Zhou Da , Traulsen Arne
Published: October 2015

The outcome of a major evolutionary transition is the aggregation of independent entities into a new synergetic level of organisation. Classical models involve either pairwise interactions between individuals or a linear superposition of these interactions. However, major evolutionary transitions display synergetic effects: their outcome is not just the sum of its parts. Multiplayer games can display such synergies, as their payoff can be different from the sum of any collection of two-player interactions. Assuming that all interactions start from pairs, how can synergetic multiplayer games emerge from simpler pairwise interaction? Here, we present a mathematical model that captures the transition from pairwise interactions to synergetic multiplayer ones. We assume that different social groups have different breaking rates. We show that non-uniform breaking rates do foster the emergence of synergy, even though individuals always interact in pairs. Our work sheds new light on the mechanisms underlying a major evolutionary transition.
Exome sequencing results in successful riboflavin treatment of a rapidly progressive neurological condition
Authors: Petrovski Slavé , Shashi Vandana , Petrou Steven , Schoch Kelly , McSweeney Keisha Melodi , Dhindsa Ryan S. , Krueger Brian , Crimian Rebecca , Case Laura E. , Khalid Roha , El-Dairi Maysantoine A. , Jiang Yong-Hui , Mikati Mohamad A. , Goldstein David B.
Published: October 2015

Genetically targeted therapies for rare Mendelian conditions are improving patient outcomes. Here, we present the case of a 20-mo-old female suffering from a rapidly progressing neurological disorder. Although diagnosed initially with a possible autoimmune condition, analysis of the child's exome resulted in a diagnosis of Brown–Vialetto–Van Laere syndrome 2 (BVVLS2). This new diagnosis led to a change in the therapy plan from steroids and precautionary chemotherapy to high-dose riboflavin. Improvements were reported quickly, including in motor strength after 1 mo. In this case, the correct diagnosis and appropriate treatment would have been unlikely in the absence of exome sequencing and careful interpretation. This experience adds to a growing list of examples that emphasize the importance of early genome-wide diagnostics.
Sustained therapeutic response to riboflavin in a child with a progressive neurological condition, diagnosed by whole-exome sequencing
Authors: Shashi Vandana , Petrovski Slavé , Schoch Kelly , Crimian Rebecca , Case Laura E. , Khalid Roha , El-Dairi Maysantoine A. , Jiang Yong-Hui , Mikati Mohamad A. , Goldstein David B.
Published: October 2015

One of the most promising outcomes of whole-exome sequencing (WES) is the alteration of medical management following an accurate diagnosis in patients with previously unresolved disorders. Although case reports of targeted therapies resulting from WES have been published, there are few reports with long-term follow-up that confirm a sustained therapeutic response. Following a diagnosis by WES of Brown–Vialetto–Van Laere Syndrome 2 (BVVLS2), high-dose riboflavin therapy was instituted in a 20-mo-old child. An immediate clinical response with stabilization of signs and symptoms was noted over the first 2–4 wk. Subsequent clinical follow-up over the following 8 mo demonstrates not just stabilization, but continuing and sustained improvements in all manifestations of this usually fatal condition, which generally includes worsening motor weakness, sensory ataxia, hearing, and vision impairments. This case emphasizes that early application of WES can transform patient care, enabling therapy that in addition to being lifesaving can sometimes reverse the disabling disease processes in a progressive condition.
A case of me: clinical cancer sequencing and the future of precision medicine
Authors: Wartman Lukas D.
Published: October 2015

In this invited Perspective, I detail how my own experience as a patient with acute lymphoblastic leukemia (ALL) exemplifies several key concepts central to the implementation of cancer sequencing and precision medicine into clinical practice.
De novo POGZ mutations are associated with neurodevelopmental disorders and microcephaly
Authors: Ye Yizhou , Cho Megan T. , Retterer Kyle , Alexander Nora , Ben-Omran Tawfeg , Al-Mureikhi Mariam , Cristian Ingrid , Wheeler Patricia G. , Crain Carrie , Zand Dina , Weinstein Veronique , Vernon Hilary J. , McClellan Rebecca , Krishnamurthy Vidya , Vitazka Patrik , Millan Francisca , Chung Wendy K.
Published: October 2015

Seven patients with similar phenotypes of developmental delay and microcephaly were found by whole-exome sequencing to have de novo loss-of-function mutations in POGZ. POGZ is a pogo transposable element-derived protein with a zinc finger cluster. The protein is involved in normal kinetochore assembly and mitotic sister chromatid cohesion and mitotic chromosome segregation. POGZ deficiency may affect mitosis, disrupting brain development and function.
Complete hematologic response of early T-cell progenitor acute lymphoblastic leukemia to the γ-secretase inhibitor BMS-906024: genetic and epigenetic findings in an outlier case
Authors: Knoechel Birgit , Bhatt Ami , Pan Li , Pedamallu Chandra S. , Severson Eric , Gutierrez Alejandro , Dorfman David M. , Kuo Frank C. , Kluk Michael , Kung Andrew L. , Zweidler-McKay Patrick , Meyerson Matthew , Blacklow Stephen C. , DeAngelo Daniel J. , Aster Jon C.
Published: October 2015

Notch pathway antagonists such as γ-secretase inhibitors (GSIs) are being tested in diverse cancers, but exceptional responses have yet to be reported. We describe the case of a patient with relapsed/refractory early T-cell progenitor acute lymphoblastic leukemia (ETP-ALL) who achieved a complete hematologic response following treatment with the GSI BMS-906024. Whole-exome sequencing of leukemic blasts revealed heterozygous gain-of-function driver mutations in NOTCH1, CSF3R, and PTPN11, and a homozygous/hemizygous loss-of-function mutation in DNMT3A. The three gain-of-function mutations were absent from remission marrow cells, but the DNMT3A mutation persisted in heterozygous form in remission marrow, consistent with an origin for the patient's ETP-ALL from clonal hematopoiesis. Ex vivo culture of ETP-ALL blasts confirmed high levels of activated NOTCH1 that were repressed by GSI treatment, and RNA-seq documented that GSIs downregulated multiple known Notch target genes. Surprisingly, one potential target gene that was unaffected by GSIs was MYC, a key Notch target in GSI-sensitive T-ALL of cortical T-cell type. H3K27ac super-enhancer landscapes near MYC showed a pattern previously reported in acute myeloid leukemia (AML) that is sensitive to BRD4 inhibitors, and in line with this ETP-ALL blasts downregulated MYC in response to the BRD4 inhibitor JQ1. To our knowledge, this is the first example of complete response of a Notch-mutated ETP-ALL to a Notch antagonist and is also the first description of chromatin landscapes associated with ETP-ALL. Our experience suggests that additional attempts to target Notch in Notch-mutated ETP-ALL are merited.
SalivaryFOXP2expression and oral feeding success in premature infants
Authors: Zimmerman Emily , Maki Monika , Maron Jill
Published: October 2015

The objective of the study is to determine whether salivaryFOXP2gene expression levels at the initiation of oral feeding attempts are predictive of oral feeding success in the premature newborn. In this prospective study, saliva samples from 21 premature infants (13 males; birth gestational age [GA]: 30–34 wk) were collected around the initiation of oral feeding trials. Total RNA was extracted and underwent reverse transcription-quantitative polymerase chain reaction amplification forFOXP2.Oral feeding success was denoted by the days required to attain full oral feeds. A linear regression model, controlling for sex, birth GA, and weight at salivary collection, revealed thatFOXP2expression was significantly associated with oral feeding success (P= 0.002). The higher the expression level ofFOXP2, the shorter the duration to feed. SalivaryFOXP2expression levels are significantly associated with oral feeding success in the preterm infant.FOXP2may serve as a novel and informative biomarker to noninvasively assess infant feeding skills to reduce morbidities and length of stay.
Symmetries and color symmetries of a family of tilings with a singular point
Authors: Evidente Imogene F. , Felix Rene P. , Loquias Manuel Joseph C.
Published: October 2015

Tilings with a singular point are obtained by applying conformal maps on regular tilings of the Euclidean plane and their symmetries are determined. The resulting tilings are then symmetrically colored by applying the same conformal maps on colorings of regular tilings arising from sublattice colorings of the centers of the tiles. In addition, conditions are determined in order that the coloring of a tiling with singularity that is obtained in this manner is perfect.
Urbanization as A Process of State Building: Local Governance Reforms in China
Authors: Wai Wong Siu
Published: October 2015

Existing scholarship suggests that local transformation in reform‐era China has been a process of decentralization of state power driving extractive local governments to pursue economic growth through rapacious land appropriation and producing many miserable landless villagers. This study puts forward an alternative perspective by arguing that local governance reforms in China to advance urban development should also be interpreted as a process of state building, whereby local government reshaped its governance strategy so as to mitigate potential social unrest and strengthen its political legitimacy in governing rapidly urbanizing areas. Based on intensive fieldwork in a periurban district in southern China, this research examines how the local state has heightened its control over urbanizing villages through its day‐to‐day governance practices and the pursuit of a complex policy agenda comprising social welfare provision, shareholding reforms and intervention in grassroots politics. The findings of this study shed new light on understanding local state transformation in periurban China and on explaining why the country still maintains tremendous urban growth despite incessant land disputes and numerous social tensions at different localities.
Ultimate concerns in late modernity: Archer, Bourdieu and reflexivity
Authors: Farrugia David , Woodman Dan
Published: October 2015

Through a critique of Margaret Archer's theory of reflexivity, this paper explores the theoretical contribution of a Bourdieusian sociology of the subject for understanding social change. Archer's theory of reflexivity holds that conscious ‘internal conversations’ are the motor of society, central both to human subjectivity and to the ‘reflexive imperative’ of late modernity. This is established through critiques of Bourdieu, who is held to erase creativity and meaningful personal investments from subjectivity, and late modernity is depicted as a time when a ‘situational logic of opportunity’ renders embodied dispositions and the reproduction of symbolic advantages obsolete. Maintaining Archer's focus on ‘ultimate concerns’ in a context of social change, this paper argues that her theory of reflexivity is established through a narrow misreading and rejection of Bourdieu's work, which ultimately creates problems for her own approach. Archer's rejection of any pre‐reflexive dimensions to subjectivity and social action leaves her unable to sociologically explain the genesis of ‘ultimate concerns’, and creates an empirically dubious narrative of the consequences of social change. Through a focus on Archer's concept of ‘fractured reflexivity’, the paper explores the theoretical necessity of habitus and illusio for understanding the social changes that Archer is grappling with. In late modernity, reflexivity is valorized just as the conditions for its successful operation are increasingly foreclosed, creating ‘fractured reflexivity’ emblematic of the complex contemporary interaction between habitus, illusio, and accelerating social change.
Delivery mode and pelvic organ prolapse: a retrospective observational study
Authors: Trutnovsky G , Kamisan Atan I , Martin A , Dietz HP
Published: October 2015

Objective

To analyse the associations between delivery mode and symptoms and signs of pelvic organ prolapse (POP) in a cohort of symptomatic women.

Design

Retrospective observational study.

Population

A total of 1258 consecutive women attending a tertiary urogynaecological unit for the investigation of lower urinary tract or pelvic floor disorders between January 2012 and December 2014.

Methods

Obstetric history and clinical examination data were obtained from the unit database. Prolapse quantification on imaging was performed using stored four‐dimensional translabial ultrasound volume data sets. Women were grouped into four groups according to the most traumatic delivery reported. The presence of symptoms and signs of POP were compared between delivery groups while controlling for potential confounders.

Main outcome measures

Prolapse symptoms, visual analogue score for prolapse bother, International Continence Society Prolapse Quantification System findings and ultrasound findings of anterior, central and posterior compartment descent.

Results

Nulliparae showed the lowest prevalence of most measures of POP, followed by women exclusively delivered by caesarean section. Highest prevalences were consistently found in women delivered at least once by forceps, although the differences between this group and women delivered by normal vaginal delivery and/or vacuum extraction were significant in three out of eight measures only. Compared with women in the caesarean section group, the adjusted odds ratios for reporting symptoms of prolapse were 2.4 (95% CI 1.30–4.59) and 3.2 (95% CI 1.65–6.12) in the normal vaginal delivery/vacuum extraction group and forceps group, respectively.

Conclusions

There is a clear link between vaginal delivery and symptoms and signs of pelvic organ prolapse in urogynaecological patients.

Tweetable abstract

Compared with caesarean section a history of vaginal delivery more than doubles the risk for POP.
Endometriosis diagnosis and staging by operating surgeon and expert review using multiple diagnostic tools: an inter‐rater agreement study
Authors: Schliep KC , Chen Z , Stanford JB , Xie Y , Mumford SL , Hammoud AO , Boiman Johnstone E , Dorais JK , Varner MW , Buck Louis GM , Peterson CM
Published: October 2015

Objective

To determine agreement on endometriosis diagnosis between real‐time laparoscopy and subsequent expert review of digital images, operative reports, magnetic resonance imaging (MRI), and histopathology, viewed sequentially.

Design

Inter‐rater agreement study.

Setting

Five urban surgical centres.

Population

Women, aged 18–44 years, who underwent a laparoscopy regardless of clinical indication. A random sample of 105 women with and 43 women without a postoperative endometriosis diagnosis was obtained from the ENDO study.

Methods

Laparoscopies were diagnosed, digitally recorded, and reassessed.

Main outcome measures

Inter‐observer agreement of endometriosis diagnosis and staging according to the revised American Society for Reproductive Medicine criteria. Prevalence and bias‐adjusted kappa values (κ) were calculated for diagnosis, and weighted κ values were calculated for staging.

Results

Surgeons and expert reviewers had substantial agreement on diagnosis and staging after viewing digital images (n = 148; mean κ = 0.67, range 0.61–0.69; mean κ = 0.64, range 0.53–0.78, respectively) and after additionally viewing operative reports (n = 148; mean κ = 0.88, range 0.85–0.89; mean κ = 0.85, range 0.84–0.86, respectively). Although additionally viewing MRI findings (n = 36) did not greatly impact agreement, agreement substantially decreased after viewing histological findings (n = 67), with expert reviewers changing their assessment from a positive to a negative diagnosis in up to 20% of cases.

Conclusion

Although these findings suggest that misclassification bias in the diagnosis or staging of endometriosis via visualised disease is minimal, they should alert gynaecologists who review operative images in order to make decisions on endometriosis treatment that operative reports/drawings and histopathology, but not necessarily MRI, will improve their ability to make sound judgments.

Tweetable abstract

Endometriosis diagnosis and staging agreement between expert reviewers and operating surgeons was substantial.
Biology, Complexion, and Socioeconomic Status: Accounting for Nineteenth Century Body Mass Index by Race
Authors: Carson Scott Alan
Published: October 2015

Nineteenth‐centuryUSwhites were taller than their mulatto and darker complexionedAfrican‐American counterparts, a pattern known as the ‘MulattoAdvantage’. If this pattern was due to social preferences, fairer complexioned whites would have had greater body mass index (BMIs) values. This study shows that late nineteenth‐ and early twentieth‐centuryUS BMIsdiffered by race, and darker complexions were associated with greaterBMIvalues. Mulattos had greaterBMIreturns associated with socioeconomic characteristics, indicating that while blacks had greaterBMIsthan fairer complexioned whites and mulattos, part of the difference was offset by socioeconomic characteristics that favoured fairer complexions.