bluuebunny/crossref_metadata_2025 huggingface dataset:
Linear colour correction for multiple illumination changes and non‐overlapping cameras
Authors: Torres Juan , Schutte Klamer , Bouma Henri , Menéndez Jose‐Manuel
Published: October 2014

Many image processing methods, such as techniques for people re‐identification, assume photometric constancy between different images. This study addresses the correction of photometric variations based upon changes in background areas to correct foreground areas. The authors assume a multiple light source model where all light sources can have different colours and will change over time. In training mode, the authors learn per‐location relations between foreground and background colour intensities. In correction mode, the authors apply a double linear correction model based on learned relations. This double linear correction includes a dynamic local illumination correction mapping as well as an inter‐camera mapping. The authors evaluate their illumination correction by computing the similarity between two images based on the earth mover's distance. The authors compare the results to a representative auto‐exposure algorithm found in the recent literature plus a colour correction one based on the inverse‐intensity chromaticity. Especially in complex scenarios the authors’ method outperforms these state‐of‐the‐art algorithms.
Output pulse width of mode‐locked ring laser based on Er3+ ‐doped fibre amplifier and semiconductor optical amplifier
Authors: Zhang Liping , Wang Xiaofei , Li Xinzhong , Liu Huihui
Published: October 2014

The time width and the spectral width of the output pulse of ring laser based on Er3+ ‐doped fibre amplifier and semiconductor optical amplifier have been investigated theoretically. Influences of Er3+ ‐doped concentration, active region width, input current, the length of the cavity imposed on the spectral bandwidth of the output pulse have been analysed and discussed. By using the analyses and conclusions in this study, the authors can control the pulse width by adjusting the related parameters and optimise the structure of the mode‐locked laser system.
Modelling and analysis of turbulent datasets using Auto Regressive Moving Average processes
Authors: Faranda Davide , Pons Flavio Maria Emanuele , Dubrulle Bérengère , Daviaud François , Saint-Michel Brice , Herbert Éric , Cortet Pierre-Philippe
Published: October 2014

We introduce a novel way to extract information from turbulent datasets by applying an Auto Regressive Moving Average (ARMA) statistical analysis. Such analysis goes well beyond the analysis of the mean flow and of the fluctuations and links the behavior of the recorded time series to a discrete version of a stochastic differential equation which is able to describe the correlation structure in the dataset. We introduce a new index Υ that measures the difference between the resulting analysis and the Obukhov model of turbulence, the simplest stochastic model reproducing both Richardson law and the Kolmogorov spectrum. We test the method on datasets measured in a von Kármán swirling flow experiment. We found that the ARMA analysis is well correlated with spatial structures of the flow, and can discriminate between two different flows with comparable mean velocities, obtained by changing the forcing. Moreover, we show that the Υ is highest in regions where shear layer vortices are present, thereby establishing a link between deviations from the Kolmogorov model and coherent structures. These deviations are consistent with the ones observed by computing the Hurst exponents for the same time series. We show that some salient features of the analysis are preserved when considering global instead of local observables. Finally, we analyze flow configurations with multistability features where the ARMA technique is efficient in discriminating different stability branches of the system.
Fabrication and characterization of large arrays of mesoscopic gold rings on large-aspect-ratio cantilevers
Authors: Ngo D. Q. , Petković I. , Lollo A. , Castellanos-Beltran M. A. , Harris J. G. E.
Published: October 2014

We have fabricated large arrays of mesoscopic metal rings on ultrasensitive cantilevers. The arrays are defined by electron beam lithography and contain up to 105 rings. The rings have a circumference of 1 μm, and are made of ultrapure (6N) Au that is deposited onto a silicon-on-insulator wafer without an adhesion layer. Subsequent processing of the SOI wafer results in each array being supported at the end of a free-standing cantilever. To accommodate the large arrays while maintaining a low spring constant, the cantilevers are nearly 1 mm in both lateral dimensions and 100 nm thick. The extreme aspect ratio of the cantilevers, the large array size, and the absence of a sticking layer are intended to enable measurements of the rings' average persistent current ⟨I⟩ in the presence of relatively small magnetic fields. We describe the motivation for these measurements, the fabrication of the devices, and the characterization of the cantilevers' mechanical properties. We also discuss the devices' expected performance in measurements of ⟨I⟩.
Chirality of weakly bound complexes: The potential energy surfaces for the hydrogen-peroxide−noble-gas interactions
Authors: Roncaratti L. F. , Leal L. A. , Pirani F. , Aquilanti V. , e Silva G. M. , Gargano R.
Published: October 2014

We consider the analytical representation of the potential energy surfaces of relevance for the intermolecular dynamics of weakly bound complexes of chiral molecules. In this paper we study the H2O2−Ng (Ng=He, Ne, Ar, Kr, and Xe) systems providing the radial and the angular dependence of the potential energy surface on the relative position of the Ng atom. We accomplish this by introducing an analytical representation which is able to fit the ab initio energies of these complexes in a wide range of geometries. Our analysis sheds light on the role that the enantiomeric forms and the symmetry of the H2O2 molecule play on the resulting barriers and equilibrium geometries. The proposed theoretical framework is useful to study the dynamics of the H2O2 molecule, or other systems involving O–O and S–S bonds, interacting by non-covalent forces with atoms or molecules and to understand how the relative orientation of the O–H bonds changes along collisional events that may lead to a hydrogen bond formation or even to selectivity in chemical reactions.
An ultra-low temperature scanning Hall probe microscope for magnetic imaging below 40 mK
Authors: Karcı Özgür , Piatek Julian O. , Jorba Pau , Dede Münir , Rønnow Henrik M. , Oral Ahmet
Published: October 2014

We describe the design of a low temperature scanning Hall probe microscope (SHPM) for a dilution refrigerator system. A detachable SHPM head with 25.4 mm OD and 200 mm length is integrated at the end of the mixing chamber base plate of the dilution refrigerator insert (Oxford Instruments, Kelvinox MX−400) by means of a dedicated docking station. It is also possible to use this detachable SHPM head with a variable temperature insert (VTI) for 2 K–300 K operations. A microfabricated 1μm size Hall sensor (GaAs/AlGaAs) with integrated scanning tunneling microscopy tip was used for magnetic imaging. The field sensitivity of the Hall sensor was better than 1 mG/√Hz at 1 kHz bandwidth at 4 K. Both the domain structure and topography of LiHoF4, which is a transverse-field Ising model ferromagnet which orders below TC = 1.53 K, were imaged simultaneously below 40 mK.
Global solution of the electromagnetic field-particle system of equations
Authors: Falconi Marco
Published: October 2014

In this paper we discuss global existence of the solution of the Maxwell and Newton system of equations, describing the interaction of a rigid charge distribution with the electromagnetic field it generates. A unique solution is proved to exist (for regular charge distributions) on suitable homogeneous and non-homogeneous Sobolev spaces, for the electromagnetic field, and on coordinate and velocity space for the charge; provided initial data belong to the subspace that satisfies the divergence part of Maxwell's equations.
The influence of surface functionalisation on the electrical properties and thermal stability of nanodiamonds
Authors: Welch Joseph O , Li Pei , Chaudhary Aysha , Edgington Robert , Jackman Richard B.
Published: October 2014

Detonation nanodiamond (ND) has recently emerged as a useful new class of diamond material. However, to date there has been little investigation of the electrical properties of this material. Due to the nanoscale dimensions, the surface functionalisation of the individual ND is of particular importance to the characteristics of ND films. Here, hydrogen and oxygen termination of ND, verified using Fourier transform infrared spectroscopy, are shown to strongly influence the electronic properties of NDs. Hydrogen terminated ND exhibiting a far greater resilience to thermal decomposition when compared to the oxygen terminated NDs. Moreover, H-NDs also displayed so-called “surface conductivity,” a property displayed by hydrogen-terminated bulk diamond films, whilst O-NDs display properties high resistivity. These results indicate that under the correct conditions ND layers can display similar electrical properties to “bulk” diamond thin films.
Indium phosphide-based monolithically integrated PIN waveguide photodiode readout for resonant cantilever sensors
Authors: Siwak N. P. , Fan X. Z. , Kanakaraju S. , Richardson C. J. K. , Ghodssi R.
Published: October 2014

An integrated photodiode displacement readout scheme for a microelectromechanical cantilever waveguide resonator sensing platform is presented. III-V semiconductors are used to enable the monolithic integration of passive waveguides with active optical components. This work builds upon previously demonstrated results by measuring the displacement of cantilever waveguide resonators with on-chip waveguide PIN photodiodes. The on-chip integration of the readout provides an additional 70% improvement in mass sensitivity compared to off-chip photodetector designs due to measurement stability and minimized coupling loss. In addition to increased measurement stability, reduced packaging complexity is achieved due to the simplicity of the readout design. We have fabricated cantilever waveguides with integrated photodetectors and experimentally characterized these cantilever sensors with monolithically integrated PIN photodiodes.
Controlling the sharpness of metal-insulator transition in epitaxial (La1−xPrx)0.67Ca0.33MnO3 (0 ≤ x ≤ 0.35) films
Authors: Chen Pingfan , Huang Zhen , Tan Xuelian , Chen Binbin , Zhi Bowen , Gao Guanyin , Chen Feng , Wu Wenbin
Published: October 2014

We report that epitaxial strain and chemical doping can be used cooperatively to tune the sharpness of metal-insulator transition (MIT) in epitaxial (La1−xPrx)0.67Ca0.33MnO3 (LPCMO) films. Compared to multiple MITs in anisotropically strained LPCMO/(LaAlO3)0.3(SrAl0.5Ta0.5O3)0.7(001)C (LSAT) films with a phase-separated ground state, the lattice-matched LPCMO/NdGaO3(110)Or (NGO) films show a sharp MIT near the Curie temperature (TC), with a ferromagnetic-metallic ground state. The sharpness of MIT, as evaluated by the temperature coefficient of resistance (TCR), can be two times larger in LPCMO/NGO films than in LPCMO/LSAT films. Moreover, for LPCMO/NGO films, TCR greatly relies on the Pr doping level x, where a maximum TCR value of 88.17% K−1 can be obtained at x = 0.25, but shows less dependence on the film thicknesses. These results suggest that the combination of epitaxial strain and chemical doping could be employed to control not only the ground state of the manganite films, but the sharpness of MIT at various TC, providing the feasibility to design manganite-based infrared devices in a broad temperature range.
First principles assessment of helium trapping in Y2TiO5 in nano-featured ferritic alloys
Authors: Jin Yanan , Jiang Yong , Yang Litong , Lan Guoqiang , Robert Odette G. , Yamamoto Takuya , Shang Jiacheng , Dang Ying
Published: October 2014

Nano-scale Y2Ti2O7 and Y2TiO5 oxides are the major features that provide high strength and irradiation tolerance in nano-structured ferritic alloys. Here, we employ density functional theory to study helium trapping in Y2TiO5. The results suggest that helium is more deeply trapped in Y2TiO5 compared to Y2Ti2O7. Helium occupies open channels in Y2TiO5, where it weakly chemically interacts with neighboring oxygen anions, and results in less volume expansion compared to Y2Ti2O7, reducing strains in the iron matrix. The corresponding helium mobility in these channels is very high. While its ultimate fate is to form oxide/matrix interface bubbles, transient deep trapping of helium in oxides plays a major role in the ability of NFA to manage helium distribution.
Spatial modulation of in-plane magnetic anisotropy in epitaxial Co(111) films grown on macrostep-bunched Si(111)
Authors: Davydenko A. V. , Kozlov A. G. , Chebotkevich L. A.
Published: October 2014

We compared magnetic properties of epitaxial Co(111) films grown on microstep- and macrostep-bunched vicinal Si(111) substrates. A surface of the microstep-bunched Si(111) substrate represents regular array of step-bunches with height of 1.7 nm divided from each other by flat microterraces with a width of 34 nm. A surface of the macrostep-bunched Si(111) substrate is constituted by macrostep bunches with a height of 75–85 nm divided by atomically flat macroterraces. The average sum width of a macrostep bunch and a macroterrace is 2.3 μm. While in-plane magnetic anisotropy was spatially uniform in Co(111) films grown on the microstep-bunched Si(111), periodic macromodulation of the topography of the Si(111) substrate induced spatial modulation of in-plane magnetic anisotropy in Co(111) film grown on the macrostep-bunched Si(111) surface. The energy of uniaxial magnetic anisotropy in the areas of the Co(111) film deposited on the Si(111) macrosteps was higher more than by the order of magnitude than the energy of the magnetic anisotropy in the areas grown on macroterraces. Magnetization reversal in the areas with different energy of the magnetic anisotropy occurred in different magnetic fields. We showed the possibility of obtaining high density of domain walls in Co(111) film grown on the macrostep-bunched Si(111) by tuning the spatial step density of the Si(111) substrate.
Increased piezoelectric energy harvesting from human footstep motion by using an amplification mechanism
Authors: Xie Longhan , Cai Mingjing
Published: October 2014

In this paper, we propose a piezoelectric energy harvester to scavenge the impact energy from human footsteps at low input frequencies. The device consists of an amplification mechanism and piezoelectric bimorphs. When a human foot strikes the proposed harvester, the amplification mechanism deforms the piezoelectric bimorphs in the 31-mode to produce a large mechanical strain, meaning that the output power can be generated with high efficiency. A maximum output power of 27.5 mW was generated by the proposed harvester at an input frequency of 1.5 Hz (representing fast walking), while 18.6 mW was generated at 1.0 Hz (representing slow walking). Comparison experiments also showed that the proposed harvester can produce much a higher output power than that the same harvester operating in the 33-mode under the same working conditions.
Electrically pumped single-photon emission at room temperature from a single InGaN/GaN quantum dot
Authors: Deshpande Saniya , Frost Thomas , Hazari Arnab , Bhattacharya Pallab
Published: October 2014

We demonstrate a semiconductor quantum dot based electrically pumped single-photon source operating at room temperature. Single photons emitted in the red spectral range from single In0.4Ga0.6N/GaN quantum dots exhibit a second-order correlation value g(2)(0) of 0.29, and fast recombination lifetime ∼1.3 ±0.3 ns at room temperature. The single-photon source can be driven at an excitation repetition rate of 200 MHz.
Reversible elastic deformation of functionalized sp2 carbon at pressures of up to 33 GPa
Authors: Soignard Emmanuel , Hochheimer Hans D. , Yarger Jeff , Raj Rishi
Published: October 2014

We show that sp2 carbon bonded to silicon and oxygen can withstand reversible elastic deformation at pressures of up to 33 GPa. These experiments were carried out in a diamond anvil cell. In-situ Raman spectroscopy was employed to record the reversibility of elastic deformation by measuring the movement in the D and G peaks of carbon. Above 33 GPa the material, a silicon oxycarbide, transforms into an unidentified state which is retained upon unloading down to ambient pressure. Thermodynamical analysis suggests that the material could have transformed into a crystalline state at these ultrahigh pressures, driven by mechanical work.
Opportunities for plant improvement to increase the value of forage shrubs on low-rainfall mixed farms
Authors: Monjardino M. , Bathgate A. , Llewellyn R.
Published: October 2014

Plantings of forage shrubs such as saltbush (Atriplex spp.) in the drier part of the crop–livestock zone of southern Australia have the potential to help fill feed autumn gaps, provide valuable feed during drought periods, and provide year-round groundcover, shelter for livestock and options for management of saline soils. However, the proportion of farms with forage shrub plantings and the extent of those plantings remain relatively low, with the rate of new plantings slowing over the past decade. Development of new forage-shrub options has been occurring with the aim of improving the feed value and adoption of forage shrubs. Using a whole-farm bio-economic optimisation model for a crop–livestock farming system in the low-rainfall Mallee region of southern Australia (Mallee MIDAS—model of an integrated dryland agricultural system), we explored how key attributes of forage-shrub plantings and the associated pasture understorey, such as biomass growth, digestibility and ease of establishment, can make forage shrub plantings economically more attractive to farmers. We found that saltbush types and forage-shrub options with improved feed quality characteristics will offer the opportunity for improved economic returns and increased profitability from larger plantings compared with existing options. Improving feed quality was more important than increasing the growth rates of saltbush plants. Results still indicate only a niche role in farming systems, with profit typically being greatest when using relatively small areas (<10% of farm area) on the less productive soils of the farm. The results suggest that the profitability of forage shrubs will be greatest for those growers with larger areas of marginal cropping soils and greater reliance on livestock than cropping. Furthermore, the results demonstrate that, if cereal prices or yields fall significantly and/or lamb prices rise, the value of a forage shrub planting can increase substantially. The principles revealed have wide application beyond the region, although these need to be adapted on-farm and widely disseminated before potential contribution to Australian agriculture can be realised.
Shoot branching in response to nodal roots is mimicked by application of exogenous cytokinin in Trifolium repens
Authors: Thomas Roderick G. , Hay Michael J. M.
Published: October 2014

In nodally-rooting prostrate herbs the outgrowth of shoot axillary buds is highly influenced by the supply of a branch-promoting signal exported from nodal roots to the shoot. The aim of this study was to establish whether cytokinin could be a candidate for the positive component within this net root stimulus (NRS). The approach taken was based on the notion that should cytokinin be the activating signal, then the effects on bud outgrowth induced by exogenous supply of cytokinin (6-benzylaminopurine (BAP)) to plants should largely mimic the responses observed when experimental manipulations alter intra-plant supply of NRS. In Trifolium repens experimental results consistently indicated that supply of BAP into the stem vasculature induced responses mimicking those induced by manipulation of NRS supply: it induced the outgrowth of a similar number of distal axillary buds, activated buds to a similar extent, had similar properties of transport along stems, induced a similar dose dependent response in distal buds and also had the ability to induce bud outgrowth in P-deficient plants. These findings indicate a requirement for further detailed hormonal analytical work to confirm this result and identify the nature of the cytokinin(s) involved in the NRS signalling pathway.
Coarse woody debris reduces the rate of moisture loss from surface soils of cleared temperate Australian woodlands
Authors: Goldin Sarah R. , Hutchinson Michael F.
Published: October 2014

Reintroductions of coarse woody debris (CWD) to Australia’s temperate woodlands have been proposed to offset the impacts of long-term tree removal. However, the magnitude of the reduction in the rate of surface-soil moisture loss due to CWD is not known. Gravimetric soil moisture content was measured at different distances from CWD for 12 samples in a cleared temperate woodland. Sampling was conducted at regular intervals following a major rain event in late summer. Lower soil bulk densities near CWD indicated higher levels of soil carbon. A multivariate nonlinear statistical model was constructed to explain the observed soil moisture content as a function of time after rainfall, distance from CWD and CWD diameter. The model demonstrated that rates of soil moisture loss increased with increasing distance from CWD. Drying times near CWD were 40% longer than drying times at reference distances from CWD. The model also showed that CWD diameter influenced the rate of soil moisture loss, with larger diameters yielding reductions in soil moisture loss over greater distances from CWD. Locations of greater soil moisture availability associated with CWD may be particularly advantageous for organisms sensitive to low soil moisture levels and may increase productivity, particularly in water-limited ecosystems.
Following movement of domain IV of elongation factor G during ribosomal translocation
Authors: Salsi Enea , Farah Elie , Dann Jillian , Ermolenko Dmitri N.
Published: October 2014

Significance

The ribosome synthesizes proteins in all living organisms. During the process of protein synthesis, tRNAs and mRNA move through the ribosome, and this movement is catalyzed by the binding of a protein called elongation factor G (EF-G). The mechanism of EF-G–induced translocation of mRNA and tRNAs is not fully understood. In this work, we show that EF-G undergoes structural rearrangements and adopts at least two distinct conformations during translocation. Our work provides new insights into how EF-G promotes tRNA and mRNA translocation.
Gene coexpression measures in large heterogeneous samples using count statistics
Authors: Wang Y. X. Rachel , Waterman Michael S. , Huang Haiyan
Published: October 2014

Significance

Coexpression analysis is one of the earliest tools for inferring gene associations using expression data but faces new challenges in this “big data” era. In a large heterogeneous dataset, it is likely that gene relationships may change or only exist in a subset of the samples, and they can be nonlinear or nonfunctional. We propose two new robust count statistics to account for local patterns in gene expression profiles. The statistics are generalizable to detect statistical dependence in other application domains. The performance of the statistics is evaluated against a number of popular bivariate dependence measures, showing favorable results. The asymptotic studies of the statistics provide an interesting addition to the combinatorics literature.
Angler‐Caught Piscivore Diets Reflect Fish Community Changes in Lake Huron
Authors: Roseman Edward F. , Schaeffer Jeffrey S. , Bright Ethan , Fielder David G.
Published: October 2014

Examination of angler‐caught piscivore stomachs revealed that Lake Trout Salvelinus namaycush, Chinook Salmon Oncorhynchus tshawytscha, and Walleyes Sander vitreus altered their diets in response to unprecedented declines in Lake Huron's main‐basin prey fish community. Diets varied by predator species, season, and location but were nearly always dominated numerically by some combination of Alewife Alosa pseudoharengus, Rainbow Smelt Osmerus mordax, Emerald Shiner Notropis atherinoides, Round Goby Neogobius melanostomus, or terrestrial insects. Rainbow Trout Oncorhynchus mykiss (steelhead), Coho Salmon Oncorhynchus kisutch, and Atlantic Salmon Salmo salar had varied diets that reflected higher contributions of insects. Compared with an earlier (1983–1986) examination of angler‐caught predator fishes from Lake Huron, the contemporary results showed an increase in consumption of nontraditional prey (including conspecifics), use of smaller prey, and an increase in insects in the diet, suggesting that piscivores were faced with chronic prey limitation during this study. The management of all piscivores in Lake Huron will likely require consideration of the pervasive effects of changes in food webs, especially if prey fish remain at low levels.

Received December 19, 2013; accepted June 30, 2014
Spatial and Temporal Variation of the Gill Rakers of Gizzard Shad and Silver Carp in Three Midwestern Rivers
Authors: Walleser Liza R. , Sandheinrich Mark B. , Howard David R. , Gaikowski Mark P. , Amberg Jon J.
Published: October 2014

Improved management of invasive Silver Carp Hypophthalmichthys molitrix in the upper Mississippi River basin may be possible by better understanding the feeding abilities of this population. Food collection for filter-feeding fishes, such as Silver Carp, is influenced by the species-specific structure of their gill rakers. To investigate structural variation in gill rakers of Silver Carp, the morphology of gill rakers was quantified and compared with that of a native filter-feeding fish species which may compete with Silver Carp for food resources, Gizzard Shad Dorosoma cepedianum. Intra- and interspecies variation of gill rakers was examined in both species collected from three locations among four months. Interspecies analysis indicated the size of pores in gill rakers of Silver Carp were much larger than the interraker spacings of Gizzard Shad (95% CI ranged from 80.69 to 185.75 μm versus 16.72 to 47.36 μm, respectively). Intraspecies variation of gill rakers from Silver Carp was related to the overall size of fish and occurred only among sites where dissimilar sizes of fish were collected. This suggested the size of particles filtered by Silver Carp may be dependent upon ontogenic development rather than phenotypic plasticity in response to spatial or temporal factors. Intraspecies variation of gill rakers from Gizzard Shad occurred among site and monthly sampling data; however, variation was only attributable to overall size of fish for monthly sampling data. This suggested ontogeny may influence the filter-feeding ability of this species within a habitat. However, variation noted among sites, which was not attributable to size of fish, may indicate gill rakers are phenotypically plastic among Gizzard Shad populations of various river systems of the upper Mississippi River basin.

Received January 16, 2014; accepted April 13, 2014
Effects of Fish Length and Anatomical Placement on Retention of Visible Implant Alpha Tags in Hatchery-Reared Rainbow Trout
Authors: Davis Jacob L. , Barnes Michael E. , Kientz Jeremy L. , Galinat Austin G.
Published: October 2014

We examined the effects of anatomical placement and fish TL on 8-month retention of standard-sized (1.2 × 2.7 mm) visible implant alpha (VIA) tags in 255 Rainbow Trout Oncorhynchus mykiss (128–368 mm TL) at 14-d intervals in a hatchery setting. Anatomical placement was strongly associated with tag retention at each sampling period following day 154, culminating with significantly fewer (P < 0.05) VIA tags retained in anal fin tissue (25%) than in postorbital adipose tissue (55%) on day 224. Logistic regression models suggested that TL was more strongly associated with retention when VIA tags were placed in postorbital adipose tissue than in anal fins. Visible implant alpha tag retention was significantly associated with TL for placement in the postorbital adipose tissue at each 14-d interval. Tag retention in anal fin tissue was associated with TL during the first 6-month period of the study and became less significant after day 182. Overall tag retention rates were lowest for fish < 200 mm TL at 15% and 25% for anal fin and postorbital adipose placement, respectively, but rose to 28% and 63% for fish 200–300 mm TL and 30% and 75% for fish >300 mm TL. Due to the effects of fish size and tagging location on tag retention in Rainbow Trout, we recommend VIA tag use only in fish > 200 mm, with placement in postorbital tissue. Estimates of VIA tag retention should also be considered before or during marking studies involving Rainbow Trout.

Received January 8, 2014; accepted June 4, 2014
Annual Variation of Spawning Cutthroat Trout in a Small Western USA Stream: A Case Study with Implications for the Conservation of Potamodromous Trout Life History Diversity
Authors: Bennett Stephen , Al-Chokhachy Robert , Roper Brett B. , Budy Phaedra
Published: October 2014

Little is known about the variability in the spatial and temporal distribution of spawning potamodromous trout despite decades of research directed at salmonid spawning ecology and the increased awareness that conserving life history diversity should be a focus of management. We monitored a population of fluvial–resident Bonneville Cutthroat Trout Oncorhynchus clarkii utah in a tributary to the Logan River, Utah, from 2006 to 2012 to gain insight into the distribution and timing of spawning and what factors may influence these spawning activities. We monitored Bonneville Cutthroat Trout using redd surveys with multiple observers and georeferenced redd locations. We documented an extended spawning period that lasted from late April to mid-July. The onset, median, and end of spawning was best predicted by the mean maximum water temperature during the first 13 weeks of the year (F = 130. 4, df = 5, R2 = 0.96, P < 0.0001) with spawning beginning and ending earlier in years that had warmer water temperatures prior to spawning. The distribution of redds was clumped each year and the relative density of redds was greater in a reach dominated by dams constructed by beavers Castor canadensis. Both dam failure and construction appeared to be responsible for creating new spawning habitat that was quickly occupied, demonstrating rapid temporal response to local habitat changes. Bonneville Cutthroat Trout appeared to establish and defend a redd for up to 2 d, and spawning most often occurred between similar-sized individuals. Spawning surveys for potamodromous trout are an underutilized tool that could be used to better understand the distribution and timing of spawning as well as determine the size and trends of the reproducing portion of populations of management concern. Without efforts to document the diversity of this important aspect of potamodromous trout life history, prioritization of conservation will be problematic.
A Morphometric Approach for Stocking Walleye Fingerlings in Lakes Invaded by Rainbow Smelt
Authors: Lawson Zach J. , Carpenter Stephen R.
Published: October 2014

Invasive Rainbow Smelt Osmerus mordax have been associated with reductions in Walleye Sander vitreus recruitment, and predation by adult smelt on age-0 Walleyes has been identified as one of the potential mechanisms contributing to recruitment failure. Predation effects could be mitigated by stocking Walleye fingerlings based on smelt and Walleye morphometric relationships. By combining 0.95 quantile regression of smelt gape size on TL and 0.05 quantile regression of Walleye body depth on TL, we constructed a stocking tool to determine the appropriate size to stock Walleye fingerlings in lakes invaded by smelt such that few Walleyes are vulnerable to predation by smelt. In lakes where the largest smelt TL is known, Walleye fingerlings can be stocked according to the model: TLWYE = 0.819(TLRWS) − 23.838. In cases where the smelt population size structure is unknown, Walleyes should be stocked at sizes larger than 142 mm, which would be a sufficient size for Walleye fingerlings to avoid predation by Rainbow Smelt in all lakes in this study.

Received January 16, 2014; accepted June 30, 2014
Laboratory Evaluation of a Bioacoustic Bubble Strobe Light Barrier for Reducing Walleye Escapement
Authors: Flammang Mark K. , Weber Michael J. , Thul Megan D.
Published: October 2014

Fish escapement is a largely overlooked challenge to managing reservoir fisheries. Physical barriers may help retain fish in reservoirs but are often not practical due to high reservoir debris loads and maintenance requirements of these structures. As an alternative, nonphysical barriers may also be successful at increasing fish retention in reservoirs through the use of negative stimuli that divert fish away from targeted locations. However, the effectiveness of nonphysical barriers can vary considerably among barrier stimuli and fish species because the barrier's success is dependent upon on a behavioral response from fish. We conducted a laboratory experiment to evaluate the effectiveness of a bioacoustic bubble–strobe light barrier at reducing Walleye Sander vitreus escapement rates. We hypothesized that increasing the number and frequency of barrier stimuli would result in Walleyes approaching the barrier less frequently, reduced escapement, and increased amount of time before escapement occurred. Walleyes approached the barrier and were successfully deterred most often when lights were off and sound was on. Walleye escapement rates declined from 89.3% with the barrier off to 44.1% with low and medium sound, whereas up to 100% of the fish escaped with the addition of light. Mean time before escapement and time to 50% escapement increased with the use of sound, whereas fish escaped in less time when light was used as a deterrent. Most Walleyes escaped around sunset indicating that fish were most active during the crepuscular period. Despite reductions in escapement associated with sound–bubble barriers, we recommend that alternative nonphysical barriers be evaluated for their potential to further increase retention of Walleyes before installation of sound barrier deterrent systems in reservoirs.

Received December 23, 2013; accepted June 27, 2014
The miR-155–PU.1 axis acts on Pax5 to enable efficient terminal B cell differentiation
Authors: Lu Dong , Nakagawa Rinako , Lazzaro Sandra , Staudacher Philipp , Abreu-Goodger Cei , Henley Tom , Boiani Sara , Leyland Rebecca , Galloway Alison , Andrews Simon , Butcher Geoffrey , Nutt Stephen L. , Turner Martin , Vigorito Elena
Published: October 2014

A single microRNA (miRNA) can regulate the expression of many genes, though the level of repression imparted on any given target is generally low. How then is the selective pressure for a single miRNA/target interaction maintained across long evolutionary distances? We addressed this problem by disrupting in vivo the interaction between miR-155 and PU.1 in mice. Remarkably, this interaction proved to be key to promoting optimal T cell–dependent B cell responses, a previously unrecognized role for PU.1. Mechanistically, miR-155 inhibits PU.1 expression, leading to Pax5 down-regulation and the initiation of the plasma cell differentiation pathway. Additional PU.1 targets include a network of genes whose products are involved in adhesion, with direct links to B–T cell interactions. We conclude that the evolutionary adaptive selection of the miR-155–PU.1 interaction is exercised through the effectiveness of terminal B cell differentiation.
Alternative splicing of humanNT5Ein cirrhosis and hepatocellular carcinoma produces a negative regulator of ecto-5′-nucleotidase (CD73)
Authors: Snider Natasha T. , Altshuler Peter J. , Wan Shanshan , Welling Theodore H. , Cavalcoli James , Omary M. Bishr
Published: October 2014

Ecto-5′-nucleotidase (CD73), encoded by NT5E, is the major enzymatic source of extracellular adenosine. CD73 controls numerous pathophysiological responses and is a potential disease target, but its regulation is poorly understood. We examined NT5E regulation by alternative splicing. Genomic database analysis of human transcripts led us to identify NT5E-2, a novel splice variant that was expressed at low abundance in normal human tissues but was significantly up-regulated in cirrhosis and hepatocellular carcinoma (HCC). NT5E-2 encodes a shorter CD73 isoform we named CD73S. The presence of CD73S protein, which lacks 50 amino acids, was detected in HCC using an isoform-specific antibody. A noncanonical mouse mRNA, similar to human CD73S, was observed, but the corresponding protein was undetectable. The two human isoforms exhibited functional differences, such that ectopic expression of canonical CD73 (CD73L) in human HepG2 cells was associated with decreased expression of the proliferation marker Ki67, whereas CD73S expression did not have an effect on Ki67 expression. CD73S was glycosylated, catalytically inactive, unable to dimerize, and complexed intracellularly with the endoplasmic reticulum chaperone calnexin. Furthermore, CD73S complexed with CD73L and promoted proteasome-dependent CD73L degradation. The findings reveal species-specific CD73 regulation, with potential significance to cancer, fibrosis, and other diseases characterized by changes in CD73 expression and function.
Executive Summary: Clinical Practice Guideline for the Management of Chronic Kidney Disease in Patients Infected With HIV: 2014 Update by the HIV Medicine Association of the Infectious Diseases Society of America
Authors: Lucas Gregory M. , Ross Michael J. , Stock Peter G. , Shlipak Michael G. , Wyatt Christina M. , Gupta Samir K. , Atta Mohamed G. , Wools-Kaloustian Kara K. , Pham Paul A. , Bruggeman Leslie A. , Lennox Jeffrey L. , Ray Patricio E. , Kalayjian Robert C.
Published: October 2014

It is important to realize that guidelines cannot always account for individual variation among patients. They are not intended to supplant physician judgment with respect to particular patients or special clinical situations. IDSA considers adherence to these guidelines to be voluntary, with the ultimate determination regarding their application to be made by the physician in the light of each patient's individual circumstances.
From Bad to Worse: Anemia on Admission and Hospital-Acquired Anemia
Authors: Koch Colleen G. , Li Liang , Sun Zhiyuan , Hixson Eric D. , Tang Anne S. , Phillips Shannon C. , Blackstone Eugene H. , Henderson J. Michael
Published: October 2014

Background

Anemia at hospitalization is often treated as an accompaniment to an underlying illness, without active investigation, despite its association with morbidity. Development of hospital-acquired anemia (HAA) has also been associated with increased risk for poor outcomes. Together, they may further heighten morbidity risk from bad to worse.

Objectives

The aims of this study were to (1) examine mortality, length of stay, and total charges in patients with present-on-admission (POA) anemia and (2) determine whether these are exacerbated by development of HAA.

Design/Setting/Patients

In this cohort investigation, from January 1, 2009, to August 31, 2011, a total of 44,483 patients with POA anemia were admitted to a single health system compared with a reference group of 48,640 without POA anemia or HAA.

Measurements

Data sources included the University HealthSystem Consortium database and electronic medical records. Risk-adjustment methods included logistic and linear regression models for mortality, length of stay, and total charges. Present-on-admission anemia was defined by administrative coding. Hospital-acquired anemia was determined by changes in hemoglobin values from the electronic medical record.

Results

Approximately one-half of the patients experienced worsening of anemia with development of HAA. Risk for death and resource use increased with increasing severity of HAA. Those who developed severe HAA had 2-fold greater odds for death; that is, mild POA anemia with development of severe HAA resulted in greater mortality (odds ratio, 2.57; 95% confidence interval, 2.08–3.18; P < 0.001), increased length of stay (2.23; 2.16–2.31; P < 0.001), and higher charges (2.09; 2.03–2.15; P < 0.001).

Conclusions

Present-on-admission anemia is associated with increased mortality and resource use. This risk is further increased from bad to worse when patients develop HAA. Efforts to address POA anemia and HAA deserve attention.
Competition and cooperation in a synchronous bushcricket chorus
Authors: Hartbauer M. , Haitzinger L. , Kainz M. , Römer H.
Published: October 2014

Synchronous signalling within choruses of the same species either emerges from cooperation or competition. In our study on the katydidMecopoda elongata, we aim to identify mechanisms driving evolution towards synchrony. The increase of signal amplitude owing to synchronous signalling and the preservation of a conspecific signal period may represent cooperative mechanisms, whereas chorus synchrony may also result from the preference of females for leading signals and the resulting competition for the leader role. We recorded the timing of signals and the resulting communal signal amplitudes in small choruses and performed female choice experiments to identify such mechanisms. Males frequently timed their signals either as leader or follower with an average time lag of about 70 ms. Females selected males in such choruses on the basis of signal order and signal duration. Two-choice experiments revealed a time lag of only 70 ms to bias mate choice in favour of the leader. Furthermore, a song model with a conspecific signal period of 2 s was more attractive than a song model with an irregular or longer and shorter than average signal period. Owing to a high degree of overlap and plasticity of signals produced in ‘four male choruses’, peak and root mean square amplitudes increased by about 7 dB relative to lone singers. Modelling active space of synchronous males and solo singing males revealed a strongly increased broadcast area of synchronous signallers, but a slightly reducedper capitamating possibility compared with lone singers. These results suggest a strong leader preference of females as the ultimate causation of inter-male competition for timing signals as leader. The emerging synchrony increases the amplitude of signals produced in a chorus and has the potential to compensate a reduction of mating advantage in a chorus. We discuss a possible fitness benefit of males gained through a beacon effect and the possibility that signalling as follower is stabilized via natural selection.
A non-local free boundary problem arising in a theory of financial bubbles
Authors: Berestycki Henri , Monneau Regis , Scheinkman José A.
Published: October 2014

We consider an evolution non-local free boundary problem that arises in the modelling of speculative bubbles. The solution of the model is the speculative component in the price of an asset. In the framework of viscosity solutions, we show the existence and uniqueness of the solution. We also show that the solution is convex in space, and establish several monotonicity properties of the solution and of the free boundary with respect to parameters of the problem. To study the free boundary, we use, in particular, the fact that the odd part of the solution solves a more standard obstacle problem. We show that the free boundary is

and describe the asymptotics of the free boundary as
c
, the cost of transacting the asset, goes to zero.
Serological characterization of surface-exposed proteins of Coxiella burnetii
Authors: Jiao Jun , Xiong Xiaolu , Qi Yong , Gong Wenping , Duan Changsong , Yang Xiaomei , Wen Bohai
Published: October 2014

The obligate intracellular Gram-negative bacterium Coxiella burnetii causes Q fever, a worldwide zoonosis. Here we labelled Cox
. burnetii with biotin and used biotin-streptavidin affinity chromatography to isolate surface-exposed proteins (SEPs). Using two-dimensional electrophoresis combined with mass spectrometry, we identified 37 proteins through bioinformatics analysis. Thirty SEPs expressed in Escherichia coli (recombinant SEPs, rSEPs) were used to generate microarrays, which were probed with sera from mice experimentally infected with Cox. burnetii or sera from Q fever patients. Thirteen rSEPs were recognized as seroreactive, and the majority reacted with at least 50 % of the sera from mice infected with Cox. burnetii but not with sera from mice infected with Rickettsia rickettsii, R. heilongjiangensis, or R. typhi. Further, 13 proteins that reacted with sera from patients with Q fever did not react with sera from patients with brucellosis or mycoplasma pneumonia. Our results suggest that these seroreactive SEPs have potential as serodiagnostic antigens or as subunit vaccine antigens against Q fever.
Skip and bin: pervasive alternative splicing triggers degradation by nuclear RNA surveillance in fission yeast
Authors: Bitton Danny A. , Atkinson Sophie R. , Rallis Charalampos , Smith Graeme C. , Ellis David A. , Jeffares Daniel C. , Chen Yuan Y.C. , Malecki Michal , Codlin Sandra , Lubas Michal , Lemay Jean-François , Bachand François , Cotobal Cristina , Marguerat Samuel , Mata Juan , Heick Jensen Torben , Bähler Jürg
Published: October 2014

Exon-skipping is considered a principal mechanism by which eukaryotic cells expand their transcriptome and proteome repertoires, creating different slice varaiants with distinct cellular functions. Here we analyze RNA-seq data from 116 transcriptomes in fission yeast (Schizosaccharomyces pombe), covering multiple physiological conditions as well as transcriptional and RNA processing mutants. We applied brute-force algorithms to detect all possible exon-skipping events, which were ubiquitous but rare compared to canonical splicing events. Exon-skipping events increased in cells deficient for the nuclear exosome or the 5’-3’ exonuclease Dhp1, and also at late stages of meiotic differentiation when nuclear-exosome transcripts were down-regulated. The pervasive exon-skipping transcripts were stochastic, did not increase in specific physiological conditions, and were mostly present at below 1 copy per cell, even in the absence of nuclear RNA surveillance and late during meiosis. These exon-skipping transcripts are therefore unlikely to be functional and may reflect splicing errors that are actively removed by nuclear RNA surveillance. The average splicing error-rate was ∼0.24% in wild-type and ∼1.75% in nuclear exonuclease mutants. Using an exhaustive search algorithm, we also uncovered thousands of previously unknown splice sites, indicating pervasive splicing, yet most of these novel splicing events were rare and targeted for nuclear degradation. Analysis of human transcriptomes revealed similar, albeit much weaker trends for pervasive exon-skipping transcripts, some of which being degraded by the nuclear exosome. This study highlights widespread, but low frequency alternative splicing which is targeted by nuclear RNA surveillance.
Epithelial flow into the optic cup facilitated by suppression of BMP drives eye morphogenesis
Authors: Heermann Stephan , Schütz Lucas , Lemke Steffen , Krieglstein Kerstin , Wittbrodt Joachim
Published: October 2014

The transformation of the oval optic vesicle to a hemispheric bi-layered optic cup involves major morphological changes during early vertebrate eye development. According to the classical view, the lens-averted epithelium differentiates into the retinal pigmented epithelium (RPE), while the lens-facing epithelium forms the neuroretina. We find a 4.7 fold increase of the entire basal surface of the optic cup.

Although the area an individual RPC demands at its basal surface declines during optic cup formation, we find a 4.7 fold increase of the entire basal surface of the optic cup. We demonstrate that the lens-averted epithelium functions as reservoir and contributes to the growing neuroretina by epithelial flow around the distal rims of the optic cup. This flow is negatively modulated by BMP, which arrests epithelial flow. This inhibition results in persisting neuroretina in the RPE domain and ultimately in coloboma.