bluuebunny/crossref_metadata_2025 huggingface dataset:
Ionic liquid gating reveals trap-filled limit mobility in low temperature amorphous zinc oxide
Authors: Bubel S. , Meyer S. , Kunze F. , Chabinyc M. L.
Published: October 2013

In low-temperature solution processed amorphous zinc oxide (a-ZnO) thin films, we show the thin film transistor (TFT) characteristics for the trap-filled limit (TFL), when the quasi Fermi energy exceeds the conduction band edge and all tail-states are filled. In order to apply gate fields that are high enough to reach the TFL, we use an ionic liquid tape gate. Performing capacitance voltage measurements to determine the accumulated charge during TFT operation, we find the TFL at biases higher than predicted by the electronic structure of crystalline ZnO. We conclude that the density of states in the conduction band of a-ZnO is higher than in its crystalline state. Furthermore, we find no indication of percolative transport in the conduction band but trap assisted transport in the tail-states of the band.
Monte Carlo methods for estimating depletion potentials in highly size-asymmetrical hard sphere mixtures
Authors: Ashton D. J. , Sánchez-Gil V. , Wilding N. B.
Published: October 2013

We investigate Monte Carlo simulation strategies for determining the effective (“depletion”) potential between a pair of hard spheres immersed in a dense sea of much smaller hard spheres. Two routes to the depletion potential are considered. The first is based on estimates of the insertion probability of one big sphere in the presence of the other; we describe and compare three such methods. The second route exploits collective (cluster) updating to sample the depletion potential as a function of the separation of the big particles; we describe two such methods. For both routes, we find that the sampling efficiency at high densities of small particles can be enhanced considerably by exploiting “geometrical shortcuts” that focus the computational effort on a subset of small particles. All the methods we describe are readily extendable to particles interacting via arbitrary potentials.
Acridine orange as a biosensitive photovoltaic material
Authors: Sharifi Faranak , Bauld Reg , Fanchini Giovanni
Published: October 2013

Acridine orange (AO), a biosensitive molecule that is customarily used for labeling nucleic acids including DNA and RNA, is here investigated as a cost effective, water soluble, and photoactive material for the fabrication of potentially biosensitive organic photovoltaics. The electronic energy levels of AO are determined using Kelvin Probe Force Microscopy (KPFM) and UV-Visible spectroscopy. The effect of anticrystallization agents, as well as low-temperature annealing, on the work function of AO is investigated: amorphous AO films are shown to possess a significantly higher work function than microcrystalline AO films and the work function also increases by annealing. Photo-induced processes in AO films are investigated by considering the changes of the KPFM signal under illumination. We demonstrate that acridine orange is able to photogenerate electron-hole pairs at rates comparable to the most commonly used solar-grade photovoltaic materials, including polythiophenes. In addition, the effect of the morphology of different types of AO thin films spun from different solvents is studied in bilayer photovoltaic devices fabricated from stacks of AO and phenyl-C61-butyric acid methyl ester thin films.
An in-depth simulation study of thermal reset transitions in resistive switching memories
Authors: Villena M. A. , Jiménez-Molinos F. , Roldán J. B. , Suñé J. , Long S. , Lian X. , Gámiz F. , Liu M.
Published: October 2013

An in-depth characterization of the thermal reset transition in RRAM has been performed based on coupling self-consistent simulations to experimental results. A complete self-consistent simulator accounting for the electrical and thermal descriptions of the conductive filaments (CFs) has been developed for the numerical study of the temporal evolution of the reset transition in RRAM. The CFs series resistance, including the contributions of the setup and Maxwell components, has been included in the calculations. Using this simulation tool, we have been able to reproduce many experimental details of the experimental reset data obtained in Cu/HfO2/Pt devices. In doing so, we explained the current steps observed in some reset cycles by considering CFs with several coupled branches that break down at different times. The reset voltage dependence on the initial resistance of the CF has been analyzed and the relevant role played by the CF shape has also been demonstrated. In this respect, devices with a same initial resistance but different CF shape can switch at different voltages. A simulation study of the reset voltage distribution obtained for these devices has also been performed in order to explain the variability of the experimental samples.
Thermally assisted spatially directed pore formation in poly-dimethylsiloxane (PDMS)
Authors: Banait A. , Vishwakarma V. , Choobineh L. , Jain A.
Published: October 2013

This paper reports a method for spatially directed, self-assembled pore formation in poly-dimethylsiloxane (PDMS) that results in through-membrane pores only at desired locations. This method is based on bubble generation in uncured PDMS and subsequent bubble motion towards a hot region in a microfabricated chip containing a heater device due to thermocapillary effect. Pore formation in straight-line and semi-circular shapes is demonstrated. Coupled physics behind the pore formation and alignment process is described. Results show that the mechanism of pore formation can be controlled by changing the microheater temperature.
Dielectric probe for scattering-type terahertz scanning near-field optical microscopy
Authors: Kurihara T. , Yamaguchi K. , Watanabe H. , Nakajima M. , Suemoto T.
Published: October 2013

Dielectric material was used as the probe material for a scattering-type terahertz scanning near-field optical microscope (THz S-SNOM). It was found that the dielectric probe exhibits a strong near-field scattering signal with an amplitude comparable to that of the metallic probe. The behavior of the electric near-field around the tip was calculated using the finite-difference time-domain method, showing the field enhancement comparable to that of the metallic probe. The dielectric probe also exhibited a faster temporal response compared to the response of the metallic probe. Introduction of a non-metallic probe would enlarge the application field of the THz S-SNOM technique.
Electric-field-assisted magnetization switching in FePd/Pb(Mg1/3Nb2/3)O3-PbTiO3 heterostructure at room temperature
Authors: Yang Y. T. , Wang D. H. , Song Y. Q. , Gao J. L. , Lv L. Y. , Cao Q. Q. , Du Y. W.
Published: October 2013

We demonstrate an electric-field-assisted magnetization switching in FePd/PMN-PT heterostructure at room temperature. Not only the remanent magnetization but also the coercivity exhibits an obvious response with the electric field. Without the aid of magnetic bias field, the remanent magnetization of the FePd film shows an analogous on-off behavior with the electric field switching on and off alternatively. The magnetization switching can be electrically controlled in this heterostructure due to the variation of coercivity caused by electric field.
High-contrast, all-silicon waveguiding platform for ultra-broadband mid-infrared photonics
Authors: Chiles Jeff , Khan Saeed , Ma Jichi , Fathpour Sasan
Published: October 2013

Suspended silicon-membrane ridge waveguides are fabricated and characterized on a single-material photonic device platform. By using direct bonding, a thin layer of silicon is fused to a bulk silicon substrate, which is patterned with narrow trenches. Waveguides are etched on the resulting suspended membranes and are characterized at mid- and near-infrared wavelengths. Transverse magnetic-mode propagation losses of 2.8 ± 0.5 and 5.6 ± 0.3 dB/cm at 3.39 and 1.53 μm wavelengths are measured, respectively. This all-silicon optical platform is capable of continuous low-loss waveguiding from wavelengths of 1.2–8.5 μm, enabling numerous applications in frequency conversion and spectral analysis.
Holocene dynamics of the Florida Everglades with respect to climate, dustfall, and tropical storms
Authors: Glaser Paul H. , Hansen Barbara C. S. , Donovan Joe J. , Givnish Thomas J. , Stricker Craig A. , Volin John C.
Published: October 2013

Significance

Wind-blown dust is seldom considered an important source for nutrients in large peatlands, such as the Everglades. However, a sedimentary record suggests that high loadings of dust-borne nutrients once prevailed in the central Everglades during a period of moister climate with intense tropical storms that ended 2,800 y ago. Afterwards, a drier climatic regime with a steep decline in dustfall may have been the impetus for the striking surface patterning of the Everglades. This study provides additional support for the importance of aeolian dust in ecosystem development.
Cancer cell exosomes depend on cell-surface heparan sulfate proteoglycans for their internalization and functional activity
Authors: Christianson Helena C. , Svensson Katrin J. , van Kuppevelt Toin H. , Li Jin-Ping , Belting Mattias
Published: October 2013

Significance

Exosome-mediated intercellular transfer of proteins and nucleic acids has attracted considerable attention as exosomes may promote the development of cancer and other pathological conditions; however, the mechanism of exosome uptake by target cells and how this may be inhibited remain as important questions. We provide evidence that heparan sulfate proteoglycans (HSPGs) function as receptors of cancer cell-derived exosomes. Importantly, our data indicate that the HSPG-dependent uptake route is highly relevant for the biological activity of exosomes, and thus a potential target for inhibition of exosome-mediated tumor development. Given that several viruses have previously been shown to enter cells through HSPGs, our data implicate HSPG as a convergence point during cellular uptake of endogenous vesicles and virus particles.
Molecular understanding of atmospheric particle formation from sulfuric acid and large oxidized organic molecules
Authors: Schobesberger Siegfried , Junninen Heikki , Bianchi Federico , Lönn Gustaf , Ehn Mikael , Lehtipalo Katrianne , Dommen Josef , Ehrhart Sebastian , Ortega Ismael K. , Franchin Alessandro , Nieminen Tuomo , Riccobono Francesco , Hutterli Manuel , Duplissy Jonathan , Almeida João , Amorim Antonio , Breitenlechner Martin , Downard Andrew J. , Dunne Eimear M. , Flagan Richard C. , Kajos Maija , Keskinen Helmi , Kirkby Jasper , Kupc Agnieszka , Kürten Andreas , Kurtén Theo , Laaksonen Ari , Mathot Serge , Onnela Antti , Praplan Arnaud P. , Rondo Linda , Santos Filipe D. , Schallhart Simon , Schnitzhofer Ralf , Sipilä Mikko , Tomé António , Tsagkogeorgas Georgios , Vehkamäki Hanna , Wimmer Daniela , Baltensperger Urs , Carslaw Kenneth S. , Curtius Joachim , Hansel Armin , Petäjä Tuukka , Kulmala Markku , Donahue Neil M. , Worsnop Douglas R.
Published: October 2013

Significance

The formation of nanoparticles by condensable vapors in the atmosphere influences radiative forcing and therefore climate. We explored the detailed mechanism of particle formation, in particular the role of oxidized organic molecules that arise from the oxidation of monoterpenes, a class of volatile organic compounds emitted from plants. We mimicked atmospheric conditions in a well-controlled laboratory setup and found that these oxidized organics form initial clusters directly with single sulfuric acid molecules. The clusters then grow by the further addition of both sulfuric acid and organic molecules. Some of the organics are remarkably highly oxidized, a critical feature that enables them to participate in forming initial stable molecular clusters and to facilitate the first steps of atmospheric nanoparticle formation.
Identification and grafting of a unique peptide-binding site in the Fab framework of monoclonal antibodies
Authors: Donaldson Joshua M. , Zer Cindy , Avery Kendra N. , Bzymek Krzysztof P. , Horne David A. , Williams John C.
Published: October 2013

Significance

The identification and subsequent grafting of a unique peptide binding site within the Fab domain offers a unique means of adding functionality to monoclonal antibodies through a noncovalent interaction including improved pretargeted imaging, alternative payload delivery, and cross-linking of mAbs on cell surfaces to enhance their therapeutic potential.
TALEN-engineered AR gene rearrangements reveal endocrine uncoupling of androgen receptor in prostate cancer
Authors: Nyquist Michael D. , Li Yingming , Hwang Tae Hyun , Manlove Luke S. , Vessella Robert L. , Silverstein Kevin A. T. , Voytas Daniel F. , Dehm Scott M.
Published: October 2013

Significance

The androgen receptor (AR) is a master regulator in cells of prostatic origin, including prostate cancer. How AR activity can persist in tumors that are resistant to second-generation AR-targeted therapies remains unknown. This study describes the discovery of AR gene rearrangements in clinical prostate cancer tissues, and the use of genome engineering in prostate cancer cells with transcription activator-like effector nucleases to functionally classify these gene rearrangements as drivers of resistance. This knowledge is expected to lead to better patient management and enable the development of more effective therapies for advanced prostate cancer.
Arabidopsis
CRY2 and ZTL mediate blue-light regulation of the transcription factor CIB1 by distinct mechanisms
Authors: Liu Hongtao , Wang Qin , Liu Yawen , Zhao Xiaoying , Imaizumi Takato , Somers David E. , Tobin Elaine M. , Lin Chentao
Published: October 2013

Significance

Plants rely on many different types of photoreceptors to control light responses, but the molecular mechanisms underlying the coaction of different photoreceptors that regulate the same light response remains unclear. This study demonstrates a mechanism of the photoreceptor coaction. In
Arabidopsis
, the blue-light receptor cryptochrome 2 interacts with and activates the transcription factor CRYPTOCHROME-INTERACTING basic helix–loop–helix 1 (CIB1). It was found that CIB1 protein is degraded in the absence of blue light and that the light–oxygen–voltage-domain F-box blue-light receptor ZEITLUPE mediates blue-light suppression of CIB1 degradation.
Arginine oscillation explains Na
+
independence in the substrate/product antiporter CaiT
Authors: Kalayil Sissy , Schulze Sabrina , Kühlbrandt Werner
Published: October 2013

Significance

Many secondary-active transporters use a sodium gradient to translocate their substrate along with a sodium ion or ions across the membrane. In contrast to other, closely related transporters, the carnitine transporter CaiT does not depend on an ion gradient. We show here that the positively charged amino acid sidechain arginine 262 (R262) in CaiT replaces the sodium ion required by other transporters. Mutating R262 in CaiT makes substrate binding and transport sodium dependent. Modeling studies reveal that R262 adopts various orientations in different conformational states of the CaiT transport cycle. We propose that this oscillation of R262 mimics sodium binding and dissociation that is crucial for triggering conformational changes resulting in substrate translocation.
3D printing of microscopic bacterial communities
Authors: Connell Jodi L. , Ritschdorff Eric T. , Whiteley Marvin , Shear Jason B.
Published: October 2013

Significance

Bacteria within the human body commonly thrive within structured three-dimensional (3D) communities composed of multiple bacterial species. Organization of individuals and populations within bacterial aggregates is believed to play key roles in mediating community attributes, affecting, for example, the virulence of infections within the cystic fibrosis lung and oral cavity. To gain detailed insights into how geometry may influence pathogenicity, we describe a strategy for 3D printing bacterial communities in which physically distinct but chemically interactive populations of defined size, shape, and density can be organized into essentially any arrangement. Using this approach, we show that resistance of one pathogenic species to an antibiotic can enhance the resistance of a second species by virtue of their 3D relationship.
TERT
promoter mutations in bladder cancer affect patient survival and disease recurrence through modification by a common polymorphism
Authors: Rachakonda P. Sivaramakrishna , Hosen Ismail , de Verdier Petra J. , Fallah Mahdi , Heidenreich Barbara , Ryk Charlotta , Wiklund N. Peter , Steineck Gunnar , Schadendorf Dirk , Hemminki Kari , Kumar Rajiv
Published: October 2013

Significance

This study shows that the
telomerase reverse transcriptase
(
TERT
) promoter mutations, which create de novo E-twenty six/ternary complex factors (Ets/TCF) transcription binding sites, besides being the most common somatic genetic lesions, influence both survival and disease recurrence in bladder cancer patients. The effect of the
TERT
promoter mutations on both survival and recurrence is modified by a common polymorphism within the preexisting Ets binding site in the
TERT
promoter. The data were supported by the results from reporter assays carried out in two urothelial carcinoma cell lines. The findings of the study suggest that the
TERT
promoter mutations in conjunction with the common polymorphism have potential of being used as clinical biomarkers in bladder cancer.
Mitochondrial disulfide relay mediates translocation of p53 and partitions its subcellular activity
Authors: Zhuang Jie , Wang Ping-yuan , Huang Xinglu , Chen Xiaoyuan , Kang Ju-Gyeong , Hwang Paul M.
Published: October 2013

Significance

p53 is one of the most highly studied proteins in biomedical research because of its importance in preventing cancer and its direct or indirect role in many biological processes. It is best known as a nuclear protein that is critical for maintaining genomic integrity and regulating gene expression. We have uncovered a molecular mechanism by which p53 translocates into the mitochondria, depending on respiration, and facilitates the repair of oxidative damage to mitochondrial DNA. The dynamic partitioning of p53 between the nuclear and mitochondrial compartments has important implications for cancer and the many other essential functions of p53 in normal physiology.
Neofunctionalization of young duplicate genes in
Drosophila
Authors: Assis Raquel , Bachtrog Doris
Published: October 2013

Significance

Gene duplication is thought to play an important role in the evolution of complex phenotypes. Although studies have revealed that duplicate genes are abundant, there is considerable controversy about how they are maintained throughout evolution. In this study, we develop an approach for comparing genome-wide expression profiles of closely related species to disentangle the evolutionary forces operating on duplicate genes. Application of our approach to pairs of young duplicate genes in
Drosophila
reveals that nearly all duplicates are retained by the evolution of a novel function in one copy. Further analysis reveals that, although young genes are primarily expressed in testes, their expression broadens as they age, illustrating how new genes become integrated into diverse functional networks over time.
Unique caudal plumage of
Jeholornis
and complex tail evolution in early birds
Authors: O’Connor Jingmai , Wang Xiaoli , Sullivan Corwin , Zheng Xiaoting , Tubaro Pablo , Zhang Xiaomei , Zhou Zhonghe
Published: October 2013

Significance

We describe the presence of essentially two functional tails in the Early Cretaceous
Jeholornis
(the second most primitive bird)—one like that of some modern birds with a fan-shaped tract of feathers over the proximal tail vertebrae and another distal frond like that of feathered dinosaurs such as
Caudipteryx
and
Microraptor
. We suggest that the unique “two-tail” plumage in
Jeholornis
probably evolved as the result of complex interactions between natural and sexual selective pressures and served both aerodynamic (flight and balance, etc.) and ornamental functions (communication/display, etc.). Our aerodynamic analysis also provides a plausible functional explanation for the elongation of the boney tail in
Jeholornis
relative to
Archaeopteryx
.
Network model of top-down influences on local gain and contextual interactions in visual cortex
Authors: Piëch Valentin , Li Wu , Reeke George N. , Gilbert Charles D.
Published: October 2013

Significance

Perceptual grouping links line segments that define object contours and distinguishes them from background contours. This process is reflected in the responses to contours of neurons in primary visual cortex (V1), and depends on long-range horizontal cortical connections. We present a network model, based on an interaction between recurrent inputs to V1 and intrinsic connections within V1, which accounts for task-dependent changes in the properties of V1 neurons. The model simulates top-down modulation of effective connectivity of intrinsic cortical connections among biophysically realistic neurons. It quantitatively reproduces the magnitude and time course of the facilitation of V1 neuronal responses to contours.
Dialogue interpreting as intercultural mediation
Authors: Davitti Elena
Published: October 2013

Research on dialogue interpreting shows that interpreters do not simply convey speech content, but also perform crucial coordinating and mediating functions. This descriptive study, which is based on PhD research conducted at the University of Manchester, explores the activity of qualified dialogue interpreters in three video-recorded parent-teacher meetings involving immigrant mothers. English and Italian are the languages used, the meetings having taken place in the UK (one case) and Italy (two cases). The study focuses on interpreters’ handling of evaluative assessment, in many cases introduced by them in the target speech as an “upgrading rendition”. Transcribed extracts are examined in a micro-analytical perspective, the dynamics of each actor’s (dis)engagement towards interlocutors being studied in relation to gaze patterns annotated by dedicated software. Results show that the interpreter actively promotes alignment between the parties; however, s/he often does so by emphasising positive considerations to the mother. The outcome of this approach is that the mother accepts, but is not encouraged to co-construct a negotiated solution: she is assimilated, not empowered.
Serving two masters
Authors: De Smet Hendrik , Van de Velde Freek
Published: October 2013

This paper examines two cases of so-called syntactic amalgams. In syntactic amalgams a particular string that is shared by two constructions is exploited to combine them, in such a way that one of the constructions functions as a modifier of the other. Typical examples are after God knows how many years (< after many years + God knows how many years) and a big enough house (< a big house + big enough). In formal theories, these kinds of constructions have been insightfully described as ‘grafts’. However, the exact process through which these amalgams arise remains unexplored. When studied closely, these processes reveal form–function friction not fully accounted for by the graft metaphor.

Syntactic amalgams typically serve a subjective function and have been recruited for this purpose. However, because they consist of a syntagm that is still internally parsable, they tend to resist full reanalysis. More precisely, their original syntax continues to constrain their use. As such, amalgams get caught between their original syntax, which remains transparent, and their new function, which suggests a new syntactic status.

This appears clearly from contrastive studies of amalgams in Dutch and English that are functionally similar but whose use is constrained in different ways due to structural differences between the two languages. Our first case study deals with the Dutch and English amalgam wie weet / who knows. A contrastive analysis of the development of the respective items shows both the conservative effect of the origin of change and the attraction exerted by the target of change. The second case we discuss in detail involves so-called transparent free relatives. A contrastive analysis shows the role of the overall grammar of a language in licensing change, in this case with Dutch word order posing more difficulties to the new focusing function of transparent free relatives.

In general, both case studies show the formation of syntactic amalgams to be sensitive to system pressures both in the course of their development and in the eventual outcome of change.
Sluiceway Operations for Adult Steelhead Downstream Passage at The Dalles Dam, Columbia River, USA
Authors: Khan Fenton , Royer Ida M. , Johnson Gary E. , Tackley Sean C.
Published: October 2013

Sluiceways at hydroelectric dams are designed to enable floating ice and debris to pass through the dams and may be used as an effective, nonturbine, surface route for out-migrating fishes to pass through dams. Each year, the sluiceway at The Dalles Dam on the Columbia River, USA, is normally operated between 1 April and 30 November and the spillway between 10 April and 31 August to enable downstream-migrating juvenile Pacific salmonids to pass. The only route available for fishes to pass the dam between 1 December and 31 March is through the turbines. This study evaluated downstream passage of adult steelhead Oncorhynchus mykiss at The Dalles Dam during various periods between 1 November and 10 April for years 2008 through 2010. The purpose of the study was to determine the efficacy of operating the sluiceway between 1 December and 31 March to provide a relatively safe, nonturbine, surface outlet for downstream passage of adult steelhead that overwinter in the lower Columbia River (i.e., fallbacks) or for adult steelhead attempting to emigrate back to the marine environment after spawning (i.e., kelts). We applied a fixed-location hydroacoustic technique to estimate downstream passage rates at the sluiceway and turbines. The sluiceway was used by 91–99% of the adult steelhead during all sampling periods; the remaining 1–9% passed through the turbines. This implies that adult steelhead preferred the sluiceway for downstream passage at the dam. Our results indicate that keeping the sluiceway open between 1 December and 31 March may provide an optimal, nonturbine surface route for downstream passage of overwintering or postspawned adult steelhead at The Dalles Dam. Similar operations are relevant at hydroelectric dams with surface-flow outlets, such as sluiceways, for safe downstream passage of fish species of management concern.

Received July 19, 2012; accepted March 27, 2013
Impacts of Anchor Tag Loss on Walleye Management in the Winnebago System
Authors: Koenigs Ryan P. , Bruch Ronald M. , Kamke Kendall K.
Published: October 2013

Rates of tag loss should be estimated and accounted for when using mark–recapture surveys and angler tag returns to estimate fish population abundance and exploitation rates. Walleyes Sander vitreus sampled during April 2010 spawning assessments conducted in the Winnebago system, Wisconsin, were marked with anchor tags and upper caudal fin clips to estimate tag loss rates during three time intervals: 0–11 d posttagging, 0–90 d posttagging, and 1 year posttagging. Tag loss was negligible (<0.5%) within the first 11 d but increased to 4.7% within the first 90 d and to 21.9% after 1 year. After we corrected for the tag loss occurring within the first 90 d, estimates of population abundance decreased 4.3% for females and 4.4% for males, while estimates of exploitation increased 4.9% for both sexes. Accounting for 21.9% annual tag loss led to more severe decreases in the estimates of population abundance (20.0% for females and 21.2% for males) and increases in the estimates of exploitation (28.0% for both sexes) than not accounting for any tag loss. Higher exploitation rates resulted in higher estimates of fishing mortality and lower estimates of natural mortality. When used in yield-per-recruit models, the estimated natural mortality rates derived from exploitation rates that accounted for tag loss resulted in higher yields through the implementation of larger minimum length limits to maximize yield. We recommend that managers evaluate the effectiveness of their tagging operations by estimating tag loss and assessing the potential impacts of quantified loss on management metrics. We also caution against the application of population models without an accurate estimate of tag loss and the associated impacts on estimates of population abundance and exploitation and, in turn, fishing and natural mortality rates.

Received May 22, 2013; accepted June 11, 2013
Predicting Paddlefish Roe Yields Using an Extension of the Beverton–Holt Equilibrium Yield-per-Recruit Model
Authors: Colvin Michael E. , Bettoli Phillip W. , Scholten George D.
Published: October 2013

Equilibrium yield models predict the total biomass removed from an exploited stock; however, traditional yield models must be modified to simulate roe yields because a linear relationship between age (or length) and mature ovary weight does not typically exist. We extended the traditional Beverton–Holt equilibrium yield model to predict roe yields of Paddlefish Polyodon spathula in Kentucky Lake, Tennessee–Kentucky, as a function of varying conditional fishing mortality rates (10–70%), conditional natural mortality rates (cm; 9% and 18%), and four minimum size limits ranging from 864 to 1,016 mm eye-to-fork length. These results were then compared to a biomass-based yield assessment. Analysis of roe yields indicated the potential for growth overfishing at lower exploitation rates and smaller minimum length limits than were suggested by the biomass-based assessment. Patterns of biomass and roe yields in relation to exploitation rates were similar regardless of the simulated value of cm, thus indicating that the results were insensitive to changes in cm. Our results also suggested that higher minimum length limits would increase roe yield and reduce the potential for growth overfishing and recruitment overfishing at the simulated cm values. Biomass-based equilibrium yield assessments are commonly used to assess the effects of harvest on other caviar-based fisheries; however, our analysis demonstrates that such assessments likely underestimate the probability and severity of growth overfishing when roe is targeted. Therefore, equilibrium roe yield-per-recruit models should also be considered to guide the management process for caviar-producing fish species.

Received December 13, 2012; accepted June 20, 2013
Evaluation of an Alternative Technique for Attaching External Transmitters to Blue Catfish
Authors: Bodine Kristopher A. , Fleming B. Paul
Published: October 2013

Attaching telemetry transmitters to catfishes (family Ictaluridae) has historically been problematic. Current attachment techniques produce low retention rates or high mortality, or cause altered physiological or behavioral effects. We investigated an alternative attachment technique during three experiments in which external transmitters were fastened to the supraoccipital bone of Blue Catfish Ictalurus furcatus. We hypothesized that attaching a transmitter to the skeletal structure would improve retention rates and minimize negative health effects. In a 2-month pilot study, retention was 100% (N = 20; TL range = 435–638 mm) and fish appeared to be in excellent condition. However, in a subsequent laboratory experiment, retention was poor (41.7% at 2 months and 0% at 6 months; N = 24, TL range = 600–995 mm), which may be attributed to excessive handling during the experiment. The attachment technique was also field tested as part of a larger telemetry study. Fifty Blue Catfish (TL range = 600–995 mm) were tagged and monitored for up to 17 months in Lake Buchanan, Texas. Retention in the field was 40% at 6 months and 19% at 12 months, which was comparable to current free-floating internal transmitter retention rates. Although our procedure produces lower retention than internal transmitters fastened to the pectoral girdle (60–93% annual retention), we believe this modified attachment procedure has future utility despite our mixed results. Our procedure avoids negative health effects (i.e., transmitters absorbed in the intestine or stomach or passed through the body wall) associated with internal tags fixed to the pectoral girdle and has retention rates similar to free-floating internal tags without the need for surgical implantation. Our work demonstrates an alternative transmitter attachment method and suggests future direction (i.e., attaching transmitters to the skeletal structure) in further improving attachment procedures for Blue Catfish.

Received March 12, 2013; accepted June 20, 2013
A Comparison of Different Age Estimation Methods for the Northern Snakehead
Authors: Gu Pang-hua , Xiang Jian-guo , Chen Yi-fang , Li Yan-liang , Tang Jun , Xie Song-guang , Chen Yushun
Published: October 2013

We used otoliths, scales, pectoral fins, dorsal fins, basioccipital bones, opercular bones, interopercular bones, vertebrae, teeth, and cleithra sampled from 221 known-age Northern Snakeheads Channa argus argus representing five age-groups to determine and compare age estimation methods for this species. Results showed that accuracy of age estimation methods varied among structures: 85.68% of otoliths, 68.91% of scales, 49.25% of pectoral fin rays, and 27.67% of opercular bones yielded age estimates that were consistent with the actual fish ages. Ages determined from other structures, such as interopercular bones, dorsal fins, basioccipital bones, and vertebrae, had lower rates of agreement (<20%) with actual ages. The current results suggest that age estimation with otoliths, especially sagittal otoliths, is the most accurate method for use with Northern Snakeheads. Furthermore, analysis of scales can be used as a supplementary approach, especially for younger (age < 3) Northern Snakeheads.

Received March 14, 2013; accepted June 27, 2013
Prescribed-Fire Effects on an Aquatic Community of a Southwest Montane Grassland System
Authors: Caldwell Colleen A. , Jacobi Gerald Z. , Anderson Michael C. , Parmenter Robert R. , McGann Jeanine , Gould William R. , DuBey Robert , Jacobi M. Donna
Published: October 2013

The use of prescription fire has long been recognized as a reliable management tool to suppress vegetative succession processes and to reduce fuel loading to prevent catastrophic wildfires, but very little attention has been paid to the effects on aquatic systems. A late-fall prescribed burn was implemented to characterize effects on an aquatic community within a montane grassland system in north-central New Mexico. The fire treatment was consistent with protocols of a managed burn except that the fire was allowed to burn through the riparian area to the treatment stream to replicate natural fire behavior. In addition to summer and fall preburn assessment of the treatment and reference stream, we characterized immediate postfire effects (within a week for macroinvertebrates and within 6 months for fish) and seasonal effects over a 2-year period. Responses within the treatment stream were compared with an unburned reference stream adjacent to the prescription burn. During the burn, the diel range in air temperature increased by 5°C while diel range in water temperature did not change. Carbon–nitrogen ratios did not differ between treatment and reference streams, indicating the contribution of ash from the surrounding grassland was negligible. Although total taxa and species richness of aquatic macroinvertebrates were not altered, qualitative indices revealed departure from preburn condition due to loss of sensitive taxa (mayflies [order Ephemeroptera] and stoneflies [order Plecoptera]) and an increase in tolerant taxa (midges [order Chironomidae]) following the burn. Within 1 year of the burn, these attributes returned to preburn conditions. The density and recruitment of adult Brown Trout Salmo trutta did not differ between pre- and postburn collections, nor did fish condition differ. Fire is rarely truly replicated within a given study. Although our study represents one replication, the results will inform managers about the importance in timing (seasonality) of prescription burn and anticipated effects on aquatic communities.

Received January 9, 2013; accepted June 27, 2013
IL-4 directly signals tissue-resident macrophages to proliferate beyond homeostatic levels controlled by CSF-1
Authors: Jenkins Stephen J. , Ruckerl Dominik , Thomas Graham D. , Hewitson James P. , Duncan Sheelagh , Brombacher Frank , Maizels Rick M. , Hume David A. , Allen Judith E.
Published: October 2013

Macrophages (MΦs) colonize tissues during inflammation in two distinct ways: recruitment of monocyte precursors and proliferation of resident cells. We recently revealed a major role for IL-4 in the proliferative expansion of resident MΦs during a Th2-biased tissue nematode infection. We now show that proliferation of MΦs during intestinal as well as tissue nematode infection is restricted to sites of IL-4 production and requires MΦ-intrinsic IL-4R signaling. However, both IL-4Rα–dependent and –independent mechanisms contributed to MΦ proliferation during nematode infections. IL-4R–independent proliferation was controlled by a rise in local CSF-1 levels, but IL-4Rα expression conferred a competitive advantage with higher and more sustained proliferation and increased accumulation of IL-4Rα+ compared with IL-4Rα− cells. Mechanistically, this occurred by conversion of IL-4Rα+ MΦs from a CSF-1–dependent to –independent program of proliferation. Thus, IL-4 increases the relative density of tissue MΦs by overcoming the constraints mediated by the availability of CSF-1. Finally, although both elevated CSF1R and IL-4Rα signaling triggered proliferation above homeostatic levels, only CSF-1 led to the recruitment of monocytes and neutrophils. Thus, the IL-4 pathway of proliferation may have developed as an alternative to CSF-1 to increase resident MΦ numbers without coincident monocyte recruitment.
Regulated vesicle fusion generates signaling nanoterritories that control T cell activation at the immunological synapse
Authors: Soares Helena , Henriques Ricardo , Sachse Martin , Ventimiglia Leandro , Alonso Miguel A. , Zimmer Christophe , Thoulouze Maria-Isabel , Alcover Andrés
Published: October 2013

How the vesicular traffic of signaling molecules contributes to T cell receptor (TCR) signal transduction at the immunological synapse remains poorly understood. In this study, we show that the protein tyrosine kinase Lck, the TCRζ subunit, and the adapter LAT traffic through distinct exocytic compartments, which are released at the immunological synapse in a differentially regulated manner. Lck vesicular release depends on MAL protein. Synaptic Lck, in turn, conditions the calcium- and synaptotagmin-7–dependent fusion of LAT and TCRζ containing vesicles. Fusion of vesicles containing TCRζ and LAT at the synaptic membrane determines not only the nanoscale organization of phosphorylated TCRζ, ZAP70, LAT, and SLP76 clusters but also the presence of phosphorylated LAT and SLP76 in interacting signaling nanoterritories. This mechanism is required for priming IL-2 and IFN-γ production and may contribute to fine-tuning T cell activation breadth in response to different stimulatory conditions.
Cross talk between Wnt/β-catenin and Irf8 in leukemia progression and drug resistance
Authors: Scheller Marina , Schönheit Jörg , Zimmermann Karin , Leser Ulf , Rosenbauer Frank , Leutz Achim
Published: October 2013

Progression and disease relapse of chronic myeloid leukemia (CML) depends on leukemia-initiating cells (LIC) that resist treatment. Using mouse genetics and a BCR-ABL model of CML, we observed cross talk between Wnt/β-catenin signaling and the interferon-regulatory factor 8 (Irf8). In normal hematopoiesis, activation of β-catenin results in up-regulation of Irf8, which in turn limits oncogenic β-catenin functions. Self-renewal and myeloproliferation become dependent on β-catenin in Irf8-deficient animals that develop a CML-like disease. Combined Irf8 deletion and constitutive β-catenin activation result in progression of CML into fatal blast crisis, elevated leukemic potential of BCR-ABL–induced LICs, and Imatinib resistance. Interestingly, activated β-catenin enhances a preexisting Irf8-deficient gene signature, identifying β-catenin as an amplifier of progression-specific gene regulation in the shift of CML to blast crisis. Collectively, our data uncover Irf8 as a roadblock for β-catenin–driven leukemia and imply both factors as targets in combinatorial therapy.
Antigen-loaded MR1 tetramers define T cell receptor heterogeneity in mucosal-associated invariant T cells
Authors: Reantragoon Rangsima , Corbett Alexandra J. , Sakala Isaac G. , Gherardin Nicholas A. , Furness John B. , Chen Zhenjun , Eckle Sidonia B.G. , Uldrich Adam P. , Birkinshaw Richard W. , Patel Onisha , Kostenko Lyudmila , Meehan Bronwyn , Kedzierska Katherine , Liu Ligong , Fairlie David P. , Hansen Ted H. , Godfrey Dale I. , Rossjohn Jamie , McCluskey James , Kjer-Nielsen Lars
Published: October 2013

Mucosal-associated invariant T cells (MAIT cells) express a semi-invariant T cell receptor (TCR) α-chain, TRAV1-2–TRAJ33, and are activated by vitamin B metabolites bound by the major histocompatibility complex (MHC)–related class I–like molecule, MR1. Understanding MAIT cell biology has been restrained by the lack of reagents to specifically identify and characterize these cells. Furthermore, the use of surrogate markers may misrepresent the MAIT cell population. We show that modified human MR1 tetramers loaded with the potent MAIT cell ligand, reduced 6-hydroxymethyl-8-d-ribityllumazine (rRL-6-CH2OH), specifically detect all human MAIT cells. Tetramer+ MAIT subsets were predominantly CD8+ or CD4−CD8−, although a small subset of CD4+ MAIT cells was also detected. Notably, most human CD8+ MAIT cells were CD8α+CD8β−/lo, implying predominant expression of CD8αα homodimers. Tetramer-sorted MAIT cells displayed a TH1 cytokine phenotype upon antigen-specific activation. Similarly, mouse MR1–rRL-6-CH2OH tetramers detected CD4+, CD4−CD8− and CD8+ MAIT cells in Vα19 transgenic mice. Both human and mouse MAIT cells expressed a broad TCR-β repertoire, and although the majority of human MAIT cells expressed TRAV1-2–TRAJ33, some expressed TRAJ12 or TRAJ20 genes in conjunction with TRAV1-2. Accordingly, MR1 tetramers allow precise phenotypic characterization of human and mouse MAIT cells and revealed unanticipated TCR heterogeneity in this population.
A Pseudomonas syringae Diversity Survey Reveals a Differentiated Phylotype of the Pathovar syringae Associated with the Mango Host and Mangotoxin Production
Authors: Gutiérrez-Barranquero José A. , Carrión Víctor J. , Murillo Jesús , Arrebola Eva , Arnold Dawn L. , Cazorla Francisco M. , de Vicente Antonio
Published: October 2013

Pseudomonas syringae pv. syringae, the causal agent of bacterial apical necrosis (BAN) in mango crops, has been isolated in different mango-producing areas worldwide. An extensive collection of 87 P. syringae pv. syringae strains isolated from mango trees affected by BAN from different countries, but mainly from Southern Spain, were initially examined by repetitive sequence-based polymerase chain reaction (rep-PCR) to analyze the genetic diversity with an epidemiological aim. rep-PCR was powerful in assessing intrapathovar distribution and also allowing clustering of the P. syringae pv. syringae strains isolated from mango, depending on the isolation area. A clear pattern of clustering was observed for all the P. syringae pv. syringae strains isolated from mango distinct from strains from other hosts, including strains for the same geographical regions as the mango isolates. For this reason, a representative group of 51 P. syringae pv. syringae strains isolated from mango and other hosts, as well as some P. syringae strains from other pathovars, were further characterized to determine their possible genetic, phenotypic, and phylogenetic relationships. Similar to the rep-PCR results, the randomly amplified polymorphic DNA PCR (RAPD-PCR) and catabolic diversity analysis using the Biolog GN2 profile grouped 90% of the mango isolates together in a unique cluster. Interestingly, the majority of P. syringae pv. syringae strains isolated from mango produced mangotoxin. The analysis of the phylogenetic distribution using the multilocus sequence typing analysis strongly supports the existence of a differentiated phylotype of the pathovar syringae mainly associated with the mango host and characterized by the mangotoxin production.
The fourth dimension of tool use: temporally enduring artefacts aid primates learning to use tools
Authors: Fragaszy D. M. , Biro D. , Eshchar Y. , Humle T. , Izar P. , Resende B. , Visalberghi E.
Published: October 2013

All investigated cases of habitual tool use in wild chimpanzees and capuchin monkeys include youngsters encountering durable artefacts, most often in a supportive social context. We propose that enduring artefacts associated with tool use, such as previously used tools, partly processed food items and residual material from previous activity, aid non-human primates to learn to use tools, and to develop expertise in their use, thus contributing to traditional technologies in non-humans. Therefore, social contributions to tool use can be considered as situated in the three dimensions of Euclidean space, and in the fourth dimension of time. This notion expands the contribution of social context to learning a skill beyond the immediate presence of a model nearby. We provide examples supporting this hypothesis from wild bearded capuchin monkeys and chimpanzees, and suggest avenues for future research.
Elongation as a factor in artefacts of humans and other animals: an Acheulean example in comparative context
Authors: Gowlett J. A. J.
Published: October 2013

Elongation is a commonly found feature in artefacts made and used by humans and other animals and can be analysed in comparative study. Whether made for use in hand or beak, the artefacts have some common properties of length, breadth, thickness and balance point, and elongation can be studied as a factor relating to construction or use of a long axis. In human artefacts, elongation can be traced through the archaeological record, for example in stone blades of the Upper Palaeolithic (traditionally regarded as more sophisticated than earlier artefacts), and in earlier blades of the Middle Palaeolithic. It is now recognized that elongation extends to earlier Palaeolithic artefacts, being found in the repertoire of both Neanderthals and more archaic humans. Artefacts used by non-human animals, including chimpanzees, capuchin monkeys and New Caledonian crows show selection for diameter and length, and consistent interventions of modification. Both chimpanzees and capuchins trim side branches from stems, and appropriate lengths of stave are selected or cut. In human artefacts, occasional organic finds show elongation back to about 0.5 million years. A record of elongation achieved in stone tools survives to at least 1.75 Ma (million years ago) in the Acheulean tradition. Throughout this tradition, some Acheulean handaxes are highly elongated, usually found with others that are less elongated. Finds from the million-year-old site of Kilombe and Kenya are given as an example. These findings argue that the elongation need not be integral to a design, but that artefacts may be the outcome of adjustments to individual variables. Such individual adjustments are seen in animal artefacts. In the case of a handaxe, the maker must balance the adjustments to achieve a satisfactory outcome in the artefact as a whole. It is argued that the need to make decisions about individual variables within multivariate objects provides an essential continuity across artefacts made by different species.