bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation of tunneling field-effect transistors with extended source structures
Authors: Yang Yue , Guo Pengfei , Han Genquan , Lu Low Kain , Zhan Chunlei , Yeo Yee-Chia
Published: June 2012

In this paper, we perform a study of novel source structures in double-gate (DG) Tunneling Field-Effect Transistors (TFETs) by two-dimensional numerical simulation of source structures in double gate tunneling field effect. Extended source structures are employed in both pure Ge TFETs and Ge-source Si-body TFETs, and on-state current enhancement is observed in simulation results. Compared with conventional p+-p−-n+ TFETs, the p+ region in extended source TFETs extends underneath the gates. When large gate bias is applied, high electric field ξ, which distributes along p+-p− junction edge extends into the middle of the channel. More tunneling paths with short lengths are available in the on-state, effectively boosting the drive current of TFET. In addition, the extent of performance enhancement depends on the geometry of the extended source. By incorporating heterojunction, TFET drive current can be increased further, which is up to 0.8 mA/μm at VGS = VDS = 0.7 V.
On-line thermal dependence study of the main solar cell electrical photoconversion parameters using low thermal emission lamps
Authors: Gallardo J. J. , Navas J. , Alcántara R. , Fernández-Lorenzo C. , Aguilar T. , Martín-Calleja J.
Published: June 2012

This paper presents a non-conventional methodology and an instrumental system to measure the effect of temperature on the photovoltaic properties of solar cells. The system enables the direct measurement of the evolution of open-circuit voltage and short-circuit current intensity in relation to a continuously decreasing temperature. The system uses a high-intensity white light-emitting diode light source with low emissions of radiation in the infrared region of the electromagnetic spectrum, resulting in a reduced heating of the photovoltaic devices by the irradiation source itself. To check the goodness of the system and the methodology designed, several measurements were performed with monocrystalline silicon solar cells, dye-sensitized solar cells, and thin-film amorphous silicon solar cells, showing similar tendencies to those reported in the literature.
Chaotification of complex networks with impulsive control
Authors: Guan Zhi-Hong , Liu Feng , Li Juan , Wang Yan-Wu
Published: June 2012

This paper investigates the chaotification problem of complex dynamical networks (CDN) with impulsive control. Both the discrete and continuous cases are studied. The method is presented to drive all states of every node in CDN to chaos. The proposed impulsive control strategy is effective for both the originally stable and unstable CDN. The upper bound of the impulse intervals for originally stable networks is derived. Finally, the effectiveness of the theoretical results is verified by numerical examples.
Magnetization dynamics and reversal mechanism of Fe filled Ni80Fe20 antidot nanostructures
Authors: Liu X. M. , Ding J. , Adeyeye A. O.
Published: June 2012

We investigate the magnetization dynamics and reversal mechanism of Fe filled Ni80Fe20 antidot nanostructures. The mutual magnetostatic coupling between the two ferromagnetic nanostructures leads to a significant modification to the magnetization reversal mechanism and ferromagnetic resonance mode profiles when compared with reference Fe dots and Ni80Fe20 antidot array. Our experimental results are in qualitative agreement with both the static and dynamic micromagnetic simulations.
Revised mechanism of complement lectin-pathway activation revealing the role of serine protease MASP-1 as the exclusive activator of MASP-2
Authors: Héja Dávid , Kocsis Andrea , Dobó József , Szilágyi Katalin , Szász Róbert , Závodszky Péter , Pál Gábor , Gál Péter
Published: June 2012

The lectin pathway of complement activation is an important component of the innate immune defense. The initiation complexes of the lectin pathway consist of a recognition molecule and associated serine proteases. Until now the autoactivating mannose-binding lectin-associated serine protease (MASP)-2 has been considered the autonomous initiator of the proteolytic cascade. The role of the much more abundant MASP-1 protease was controversial. Using unique, monospecific inhibitors against MASP-1 and MASP-2, we corrected the mechanism of lectin-pathway activation. In normal human serum, MASP-2 activation strictly depends on MASP-1. MASP-1 activates MASP-2 and, moreover, inhibition of MASP-1 prevents autoactivation of MASP-2. Furthermore we demonstrated that MASP-1 produces 60% of C2a responsible for C3 convertase formation.
Acetylation modulates cellular distribution and DNA sensing ability of interferon-inducible protein IFI16
Authors: Li Tuo , Diner Benjamin A. , Chen Jin , Cristea Ileana M.
Published: June 2012

Detection of pathogenic nucleic acids is essential for mammalian innate immunity. IFN-inducible protein IFI16 has emerged as a critical sensor for detecting pathogenic DNA, stimulating both type I IFN and proinflammatory responses. Despite being predominantly nuclear, IFI16 can unexpectedly sense pathogenic DNA in both the cytoplasm and the nucleus. However, the mechanisms regulating its localization and sensing ability remain uncharacterized. Here, we propose a two-signal model for IFI16 sensing. We first identify an evolutionarily conserved multipartite nuclear localization signal (NLS). Next, using FISH and immunopurification, we demonstrate that IFI16 detects HSV-1 DNA primarily in the nucleus, requiring a functional NLS. Furthermore, we establish a localization-dependent IFN-β induction mediated by IFI16 in response to HSV-1 infection or viral DNA transfection. To identify mechanisms regulating the secondary cytoplasmic localization, we explored IFI16 posttranslation modifications. Combinatorial MS analyses identified numerous acetylations and phosphorylations on endogenous IFI16 in lymphocytes, in which we demonstrate an IFI16-mediated IFN-β response. Importantly, the IFI16 NLS was acetylated in lymphocytes, as well as in macrophages. Mutagenesis and nuclear import assays showed that NLS acetylations promote cytoplasmic localization by inhibiting nuclear import. Additionally, broad-spectrum deacetylase inhibition triggered accumulation of cytoplasmic IFI16, and we identify the acetyltransferase p300 as a regulator of IFI16 localization. Collectively, these studies establish acetylation as a molecular toggle of IFI16 distribution, providing a simple and elegant mechanism by which this versatile sensor detects pathogenic DNA in a localization-dependent manner.
New meta-analysis tools reveal common transcriptional regulatory basis for multiple determinants of behavior
Authors: Ament Seth A. , Blatti Charles A. , Alaux Cedric , Wheeler Marsha M. , Toth Amy L. , Le Conte Yves , Hunt Greg J. , Guzmán-Novoa Ernesto , DeGrandi-Hoffman Gloria , Uribe-Rubio Jose Luis , Amdam Gro V. , Page Robert E. , Rodriguez-Zas Sandra L. , Robinson Gene E. , Sinha Saurabh
Published: June 2012

A fundamental problem in meta-analysis is how to systematically combine information from multiple statistical tests to rigorously evaluate a single overarching hypothesis. This problem occurs in systems biology when attempting to map genomic attributes to complex phenotypes such as behavior. Behavior and other complex phenotypes are influenced by intrinsic and environmental determinants that act on the transcriptome, but little is known about how these determinants interact at the molecular level. We developed an informatic technique that identifies statistically significant meta-associations between gene expression patterns and transcription factor combinations. Deploying this technique for brain transcriptome profiles fromca.400 individual bees, we show that diverse determinants of behavior rely on shared combinations of transcription factors. These relationships were revealed only when we considered complex and variable regulatory rules, suggesting that these shared transcription factors are used in distinct ways by different determinants. This regulatory code would have been missed by traditional gene coexpression orcis-regulatory analytic methods. We expect that our meta-analysis tools will be useful for a broad array of problems in systems biology and other fields.
Translating eyewitness accounts
Authors: Harding Sue-Ann Jane
Published: June 2012

This paper uses concepts from socio-narrative theory, particularly the notions of ‘narrator’ and ‘temporary narrator’, and a revised typology of narrative to examine how eyewitness accounts of the Beslan hostage-taking were incorporated into some of the news narratives constructed in response to the event. Using online articles published in both Russian and English by three different websites, the study considers the few eyewitnesses who are selected to narrate, and ways in which each website controls the sometimes contradictory, multivalent narratives of its eyewitnesses so that they reinforce, rather than challenge or undermine, its overall narrative position. It also considers the impact of translation on these processes and concludes that in translation, the contribution of these eyewitness accounts is further diminished and even removed altogether.
Uncovering ideology in translation
Authors: Ayyad Ahmad Y.
Published: June 2012

This paper examines aspects of political ideology as realised through translation in the context of a case study, the translations of the Roadmap Plan. The Roadmap is one of several peace plans or initiatives that have been launched in the last decades to resolve the Palestinian-Israeli conflict. Originally drafted in English in 2003 by the Quartet, the plan was subsequently translated into Arabic and Hebrew by different institutions and news media. This paper begins by examining the textual profiles of the different Arabic and Hebrew versions, focusing on their functions and principles of audience design. This study then moves on to establish how ideological factors inform translational choices as well as the interpretation of translated texts by readers. The main body of the analysis, informed by concepts and methods of descriptive translation studies and critical discourse analysis, focuses on the translator’s mediation of proper names (including protagonists of the conflict and toponyms); instances of deliberately ambiguous or vague drafting; and politically sensitive terms (e.g. ‘normalisation’ or ‘curfew’). The concluding section accounts for the findings of the analysis in terms of the social, political, and ideological constraints shaping the different language versions of the document under scrutiny.
Translation, self-translation andapartheid-imposed conflict
Authors: Kruger Alet
Published: June 2012

Translation has played a major role alongside original literature in each of the South African languages in aiding the construction of their cultural and literary identities. Because ofapartheid(literally, ‘apartness’), Afrikaans carried a political burden and literary authors in this language were considered the protectors of Afrikaner cultural and national identity. After outlining the historical origins and the consolidation of apartheid, this paper charts the emergence of aversetliteratuur(‘protest literature’) movement among disillusioned Afrikaans authors during the apartheid era. Growing censorship and the first banning of an Afrikaans novel under the 1974 Publications and Entertainment Act led to translation and self-translation (into English) being used as a tool of resistance by Afrikaans writers against the ideology of apartheid. The paper moves on to explore the effects of apartheid-imposed conflict on other authors such as South African authors writing in English. It then focuses on the ideological agenda informing the language policy-makers’ and Africanists’ selection of books to be translated into African languages, as part of the government’s attempts to promote mother tongue education in African schools and thus perpetuate the segregation of black South Africans. The concluding section discusses how changes in political life since 1990 have influenced the use of translation in South African literature.
Winter Feeding as an Overwintering Survival Strategy in Young‐of‐the‐Year Winter Flounder
Authors: Bell Richard J.
Published: June 2012

For fish, the first winter of life can be a period of high mortality prior to recruitment. When resources are limiting or when fish are unable to feed due to low temperatures, starvation can often lead to size‐dependent overwintering mortality. Larger individuals are typically better able to survive starvation because they have a higher percentage of energy reserves and a lower metabolic rate per unit of body mass than small individuals. Alternatively, fish that can feed during the winter are able to maintain their lipid stores and reduce their chance of starvation. The aim of this study was to examine the overwintering mortality and physiology of young‐of‐the‐year (age‐0) winter flounderPseudopleuronectes americanusin relation to body size. Size‐dependent mortality was investigated with 17 years of length‐frequency data. In addition, I sampled the diet and whole‐body crude lipid content of 309 age‐0 winter flounder over the course of 1 year. Samples were taken in three estuaries in the northeastern USA during October–April. Whole‐body crude lipid content ranged from 4.7% to 12.4% of dry weight. Larger age‐0 winter flounder did not have higher lipid stores, and the age‐0 fish did not exhibit size‐dependent overwintering mortality. Age‐0 winter flounder fed on amphipods and polychaetes throughout the winter, and their whole‐body crude lipid content was maintained through the fall and winter. The physiology data lack temporal replication, but the spatial coherence in results (i.e., consistency among the three estuaries, representing two different stocks) suggests that the consumption and energy allocation patterns are real and that age‐0 winter flounder follow an alternative overwintering survival strategy.
Passage of Spawning Alabama Shad at Jim Woodruff Lock and Dam, Apalachicola River, Florida
Authors: Young Shawn P. , Ingram Travis R. , Tannehill Josh E. , Isely J. Jeffery
Published: June 2012

In 2005, a pilot study was initiated to evaluate the potential use of the navigation lock at Jim Woodruff Lock and Dam (JWLD), Florida, as a means for fish passage. The focal species was the Alabama shad Alosa alabamae. The Apalachicola River population is one of the last‐remaining, extant self‐sustaining populations, estimated adult spawning returns ranging from lows of 5,211 to 14,674 individuals in 2007 to highs of 51,417 to 127,251 individuals in 2010. We estimated the passage of migrating Alabama shad during spawning migrations during March–May 2005, 2007, 2010, and 2011. During 2005, 23 of 36 Alabama shad that were implanted with transmitters successfully passed from the lock into the reservoir 1–7 d after release, for a passage rate of 64% (95% CI = 48–80%). Advancing on the promising results from 2005, voluntary passage was evaluated during spring 2007, 2010, and 2011. During these years, 63–100% of implanted shad were relocated at the lock at least once, and voluntary passage ranged from 33% to 45%. Voluntary passage occurred 3–39 d postimplanting, most shad passing < 28 d after initial capture. Implanted Alabama shad were subsequently relocated upstream in both the Flint and Chattahoochee rivers. Based on these results, the navigation lock at JWLD was an effective means to pass migrating Alabama shad. Increased passage could be achieved by maximizing attraction flow near the lock entrance and increasing the time the upper gates are open during an afternoon locking cycle. By coupling passage and population estimates, the total number of shad that migrated through JWLD ranged from 2,137 in 2007 to 57,262 in 2010.
Emulating Riverine Landscape Controls of Beaver in Stream Restoration
Authors: DeVries Paul , Fetherston Kevin L , Vitale Angelo , Madsen Sue
Published: June 2012

Stream and floodplain restoration at the reach scale has ranged from expensive, heavy-handed modification of the channel and floodplain to simple, longer-term revegetation efforts. We have developed and implemented a simple approach that emulates the ecosystem engineering effects of beaver. This approach is less expensive and disruptive than typical large-scale engineering efforts and has the potential to restore both fish habitat and floodplain vegetation more rapidly than simply revegetating and waiting for the riparian zone to mature. The approach involves constructing log flow-choke structures that mimic the hydraulic function of a natural beaver dam during flooding. By placing these structures throughout a naturally entrenched stream reach at locations promoting increased frequency of flood connection with floodplain swales and relict channels, we set the stage to restore the riparian corridor and floodplain more quickly than could be achieved through revegetation alone. Monitoring shows that within just one to two years of implementation, beaver are building more persistent dams in close proximity to our structures, and we are seeing increased hydraulic connectivity with the floodplain. Our technique may therefore provide a cost-effective, natural process-based restoration tool with potential large-scale benefits.

RESUMEN

El gradiente de restauración ribereña y de planicies de inundación puede ir desde una importante modificación artificial de canales y llanuras inundables, hasta esfuerzos de reforestación a largo plazo. En este estudio se desarrolló e implementó un enfoque que emula los efectos a nivel de ecosistema que tienen las construcciones hechas por los castores. Este enfoque es menos costoso e invasivo que los típicos esfuerzos de ingeniería a gran escala, y tiene el potencial de poder restaurar tanto el hábitat de los peces como la vegetación de las planicies de inundación más rápidamente que la práctica de sólo reforestar y esperar a que el área ribereña madure por sí misma. Este enfoque consiste en la construcción de estructuras hechas a base de troncos que controlan el flujo de agua, emulando la función hidráulica de las presas construidas por los castores. La colocación de dichas estructuras en lugares donde el agua se confina de forma natural a lo largo de sitios que promueven la comunicación con canales tributarios y llanuras de inundación, representa la infraestructura que sirve para restaurar el corredor ribereño y las planicies de inundación más rápidamente que lo que pudiera lograrse sólo mediante la reforestación. Un seguimiento muestra que tras dos años de la implementación del enfoque, los castores están edificando presas más resistentes en sitios próximos a las estructuras, y se aprecia un incremento en la conectividad hidráulica con las llanuras de inundación. Esta técnica, por lo tanto, representa una herramienta de restauración de bajo costo y basada en un proceso natural con beneficios potenciales observables a gran escala.
Nutritional Composition and Use of Common Carp Muscle in Yellow Perch Diets
Authors: Schaeffer Travis W , Hennen Matthew J , Brown Michael L , Rosentrater Kurt A
Published: June 2012

High market demand for marine fish meals coupled with increasing costs and questionable sustainability of wild stocks have led researchers to investigate a variety of alternative plant and animal protein sources for aquaculture feeds. Our objective was to evaluate the use of common carp Cyprinus carpio, a locally abundant, nonnative fish species, to offset the cost of marine fish meal in fish feed. We completed analyses of common carp whole muscle, formulated diets containing combinations of carp and Gulf menhaden Brevoortia patronus fish meal, and then evaluated test diets in a feeding trial with yellow perch Perca flavescens. Composition (dry matter basis [dmb]) of common carp flesh (crude protein [CP] = 73.4%, crude lipid [CL] = 25.7%) slightly differed from menhaden fish meal (MFM; CP = 71.0%, CL = 11.7%, dmb). Three experimental diets were formulated to include percentage ratios of 50:0, 25:25, or 0:50 of common carp muscle meal (CCMM) to MFM to obtain similar crude protein (29.7 ± 0.9% [mean ± SD]), crude lipid (15.0 ± 3.7%), and digestible energy (14.2 ± 0.3 kJ/g) levels. Juvenile yellow perch (initial weight = 18.1 ± 3.3 g) were randomly stocked (n = 7) in twelve 37-L tanks resulting in four replicate tanks per treatment. Fish fed 25% CCMM : 25% MFM had significantly higher weight gain, while fish fed 50% CCMM : 0% MFM had significantly higher food conversion ratios and lower visceral somatic indices. No statistically significant differences were observed for protein efficiency ratios, Fulton condition factors, hepatosomatic indices, or feed intake of fish fed the different diets. These results indicate that CCMM can be used to partially offset the use of MFM in yellow perch diets.
The Effect of Calcium Hardness on Hatching Success of Channel Catfish × Blue Catfish Hybrid Catfish Eggs
Authors: Chatakondi Nagaraj G , Torrans Eugene L
Published: June 2012

The present study was designed to determine the optimal level of calcium hardness in hatching waters to incubate channel catfish Ictalurus punctatus × blue catfish I. furcatus hybrid catfish eggs. Hatching success of hybrid catfish eggs was higher (P < 0.05) at a calcium hardness (CaCO3) of 75 mg/L in hatching waters than at a calcium hardness of 25 or 50 mg/L; however, further increases in calcium concentration did not improve hatching success. A minimum water hardness of CaCO3 at 75 mg/L is recommended for incubating hybrid catfish eggs.
Baffled and Standard Raceways: A Comparison of Juvenile Spring Chinook Salmon Performance and Smolt-to-Adult Survival
Authors: Brignon William R , Olson Douglas E , Peters Mary H , Gutenberger Susan K
Published: June 2012

We compared on-station mortality, growth (mm), feed conversion, health parameters, and smolt-to-adult survival rate of spring Chinook salmon Oncorhynchus tshawytscha reared in baffled and standard (unbaffled) raceways. Fish reared in baffled raceways survived from release to adulthood at a rate 0.85 times that of fish reared in unbaffled raceways. There was no difference in percent on-station mortality (range, 0.00–0.001), health, or average length gained (1–12 mm) between fish reared in baffled and unbaffled raceways. Average feed conversion was constant (1.20–2.25) throughout the period of juvenile rearing and was similar between fish reared in baffled and unbaffled raceways, a finding supported by adiposomatic and hepatosomatic indices. Overall, we found similar on-station performance between fish reared in baffled and unbaffled raceways. The difference between SARs of fish reared in baffled versus unbaffled raceways was not statistically significant (P = 0.08). However, it is suggestive of a biological difference between the two treatments. The self-cleaning characteristics of baffled raceways free up a substantial amount of hatchery personnel time to attend to other duties, which ultimately reduces the annual operation budget for any facility. In the end, the self-cleaning feature of baffled raceways needs to be weighed against any advantage in adult survival of fish reared in unbaffled raceways.
“By Instruments her Powers Appeare”: Music and Authority in the Reign of Queen Elizabeth I
Authors: Butler Katherine
Published: June 2012

Queen Elizabeth I’s musical talents and the elaborate music of her courtly entertainments are widely acknowledged. However, while the effect of Elizabeth’s gender on her authority as a ruler has been the subject of much historical research, the impact of this musical activity on the creation and representation of her authority has not been recognized. Gender stereotypes were both exploited and subverted as music became a symbol and tool of Elizabeth’s queenship. Poets and courtiers drew inspiration from Elizabeth’s music-making, combining traditional notions of the erotic power of female music with the idea of a musical harmony that governed the heavens, the political world, and the human soul to legitimize female power. By blending the talents of Elizabeth’s natural body with those of her political body, and by merging practical musicianship with speculative harmony, Elizabeth and her courtiers used music as a source of political authority.
Nuclear factor of activated T-cell c3 inhibition of mammalian target of rapamycin signaling through induction of regulated in development and DNA damage response 1 in human intestinal cells
Authors: Zhou Yuning , Wang Qingding , Guo Zheng , Weiss Heidi L. , Evers B. Mark
Published: June 2012

The nuclear factor of activated T-cell (NFAT) proteins are a family of transcription factors (NFATc1–c4) involved in the regulation of cell differentiation. We identified REDD1, a negative regulator of mammalian target of rapamycin (mTOR) through the tuberous sclerosis complex (TSC1/2 complex), as a new molecular target of NFATc3. We show that treatment with a combination of phorbol 12-myristate 13-acetate (PMA) plus ionophore A23187 (Io), which induces NFAT activation, increased REDD1 mRNA and protein expression and inhibited mTOR signaling; pretreatment with the calcineurin inhibitor cyclosporin A (CsA), an antagonist of NFAT signaling, decreased REDD1 induction and mTOR inhibition. Knockdown of NFATc3, not NFATc1, NFATc2, or NFATc4, attenuated PMA/Io-induced REDD1 expression. Treatment with PMA/Io increased REDD1 promoter activity and increased NFATc3 binding to the REDD1 promoter. Overexpression of NFATc3 increased REDD1 mRNA and protein expression and increased PMA/Io-mediated REDD1 promoter activity. Treatment with PMA/Io increased expression of the goblet cell differentiation marker MUC2; these changes were attenuated by pretreatment with CsA or knockdown of REDD1 or NFATc3. Overexpression of NFATc3 increased, while knockdown of TSC2 decreased, MUC2 expression. We provide evidence showing NFATc3 inhibits mTOR via induction of REDD1. Our results suggest a role for the NFATc3/REDD1/TSC2 axis in the regulation of intestinal cell differentiation.
SORTALLER: predicting allergens using substantially optimized algorithm on allergen family featured peptides
Authors: Zhang Lida , Huang Yuyi , Zou Zehong , He Ying , Chen Ximo , Tao Ailin
Published: June 2012

Summary: SORTALLER is an online allergen classifier based on allergen family featured peptide (AFFP) dataset and normalized BLAST E-values, which establish the featured vectors for support vector machine (SVM). AFFPs are allergen-specific peptides panned from irredundant allergens and harbor perfect information with noise fragments eliminated because of their similarity to non-allergens. SORTALLER performed significantly better than other existing software and reached a perfect balance with high specificity (98.4%) and sensitivity (98.6%) for discriminating allergenic proteins from several independent datasets of protein sequences of diverse sources, also highlighting with the Matthews correlation coefficient (MCC) as high as 0.970, fast running speed and rapidly predicting a batch of amino acid sequences with a single click.

Availability and implementation:  http://sortaller.gzhmc.edu.cn/.

Contact:  taoailin@gzhmc.edu.cn

Supplementary Information: Supplementary data are available at Bioinformatics online.
mcaGUI: microbial community analysis R-Graphical User Interface (GUI)
Authors: Copeland Wade K. , Krishnan Vandhana , Beck Daniel , Settles Matt , Foster James A. , Cho Kyu-Chul , Day Mitch , Hickey Roxana , Schütte Ursel M.E. , Zhou Xia , Williams Christopher J. , Forney Larry J. , Abdo Zaid
Published: June 2012

Summary: Microbial communities have an important role in natural ecosystems and have an impact on animal and human health. Intuitive graphic and analytical tools that can facilitate the study of these communities are in short supply. This article introduces Microbial Community Analysis GUI, a graphical user interface (GUI) for the R-programming language (R Development Core Team, 2010). With this application, researchers can input aligned and clustered sequence data to create custom abundance tables and perform analyses specific to their needs. This GUI provides a flexible modular platform, expandable to include other statistical tools for microbial community analysis in the future.

Availability: The mcaGUI package and source are freely available as part of Bionconductor at http://www.bioconductor.org/packages/release/bioc/html/mcaGUI.html

Contact:  wade@kingcopeland.com; zabdo@uidaho.edu

Supplementary Information:  Supplementary data and figures are available at Bioinformatics online.
Variation Among Phytophthora cinnamomi Isolates from Oak Forest Soils in the Eastern United States
Authors: Eggers J. E. , Balci Y. , MacDonald W. L.
Published: June 2012

Phytophthora cinnamomi isolates from geographically diverse oak forest soils in the Mid-Atlantic regions were studied to determine the extent of genotypic, phenotypic, and pathogenic variation. Four microsatellite loci were targeted for genetic analysis. Phenotypic characteristics measured included sexual and asexual spore dimensions and colony growth rate and morphology. Red oak (Quercus rubra) logs were inoculated with selected isolates to determine relative pathogenicity. Microsatellite analysis showed that the genetic variability of P. cinnamomi isolates was low, with two predominant microsatellite fingerprint groups (MFG). Isolates in MFG1 (48% of the total isolates examined) were characterized by DNA fragment lengths of 120 and 122 bp at locus d39, 169 and 170 bp at locus e16, and 254 and 255 bp at locus g13. MFG2 isolates were characterized by marker sizes of 122 and 124 bp at locus d39, 161 and 163 bp at locus e16, and 247 and 248 bp at locus g13. Asexual and sexual spore dimensions varied greatly among isolates but were similar to previously published descriptions. Phenotypic differences were most pronounced when data were grouped by MFG; the most significant were colony morphology and growth rate. Neither characteristic was a reliable predictor of isolate genotype. Differences in growth rates of MFGs were observed, with MFG1 being less tolerant at higher incubation temperatures. No variation in pathogenicity was observed on red oak logs. The low level of phenotypic and genotypic variation of P. cinnamomi suggest that other factors such as climate might play a more important role in its northern distribution and the diseases it causes.
Postoperative QT Interval Prolongation in Patients Undergoing Noncardiac Surgery under General Anesthesia
Authors: Nagele Peter , Pal Swatilika , Brown Frank , Blood Jane , Miller J. Philipp , Johnston Joshua
Published: June 2012

Background

Abnormal cardiac repolarization, indicated by a prolongation of the QT interval, increases the risk for torsades de pointes, a potentially life-threatening arrhythmia. Many perioperatively administered drugs and conditions prolong the QT interval. Despite several reports of perioperative torsades de pointes, systematic evidence regarding perioperative QT interval prolongation is limited.

Methods

Serial postoperative 12-lead electrocardiograms were obtained from 469 adult patients undergoing major noncardiac surgery under general anesthesia. Heart rate corrected QT-interval duration (Fridericia formula) was the primary outcome. All perioperatively administered drugs were recorded. Emphasis was placed on absolute QTc prolongation greater than 500 ms and relative increases of 30 and 60 ms.

Results

At the end of surgery, 80% of the patients (345 of 429) experienced a significant QTc interval prolongation (ΔQTc 23 ± 26 ms (mean and SD), 95% CI 20-25 ms, P less than 0.001). Approximately 51% (219 of 429) had a QTc greater than 440 ms, and 4% (16 of 429) a QTc greater than 500 ms. In 39% (166 of 429), the ΔQTc was greater than 30 ms, in 8% (34 of 429) >60 ms, and in greater than 0.5% (2 of 429) >100 ms. No changes in ΔQTc occurred at subsequent time points. One patient developed torsades de pointes with a ΔQTc: 29 ms (0.4% incidence rate). Several drugs had a large effect on ΔQTc: isoflurane, methadone, ketorolac, cefoxitin, zosyn, unasyn, epinephrine, ephedrine, and calcium. Postoperative body temperature had a weak negative correlation with ΔQTc (r = -0.15, P = 0.02); serum magnesium, potassium, and calcium concentrations were not correlated.

Conclusion

Postoperative QT-interval prolongation is common. Several perioperatively administered drugs are associated with a substantial QT-interval prolongation. The exact cause and its clinical relevance are, however, unclear. Nevertheless, an association between postoperative QT prolongation and risk for torsades de pointes is likely.
Infants prefer the faces of strangers or mothers to morphed faces: an uncanny valley between social novelty and familiarity
Authors: Matsuda Yoshi-Taka , Okamoto Yoko , Ida Misako , Okanoya Kazuo , Myowa-Yamakoshi Masako
Published: June 2012

The ‘uncanny valley’ response is a phenomenon involving the elicitation of a negative feeling and subsequent avoidant behaviour in human adults and infants as a result of viewing very realistic human-like robots or computer avatars. It is hypothesized that this uncanny feeling occurs because the realistic synthetic characters elicit the concept of ‘human’ but fail to satisfy it. Such violations of our normal expectations regarding social signals generate a feeling of unease. This conflict-induced uncanny valley between mutually exclusive categories (human and synthetic agent) raises a new question: could an uncanny feeling be elicited by other mutually exclusive categories, such as familiarity and novelty? Given that infants prefer both familiarity and novelty in social objects, we address this question as well as the associated developmental profile. Using the morphing technique and a preferential-looking paradigm, we demonstrated uncanny valley responses of infants to faces of mothers (i.e. familiarity) and strangers (i.e. novelty). Furthermore, this effect strengthened with the infant's age. We excluded the possibility that infants detect and avoid traces of morphing. This conclusion follows from our finding that the infants equally preferred strangers’ faces and the morphed faces of two strangers. These results indicate that an uncanny valley between familiarity and novelty may accentuate the categorical perception of familiar and novel objects.
Dynamic self-cleaning in gecko setae via digital hyperextension
Authors: Hu Shihao , Lopez Stephanie , Niewiarowski Peter H. , Xia Zhenhai
Published: June 2012

Gecko toe pads show strong adhesion on various surfaces yet remain remarkably clean around everyday contaminants. An understanding of how geckos clean their toe pads while being in motion is essential for the elucidation of animal behaviours as well as the design of biomimetic devices with optimal performance. Here, we test the self-cleaning of geckos during locomotion. We provide, to our knowledge, the first evidence that geckos clean their feet through a unique dynamic self-cleaning mechanism via digital hyperextension. When walking naturally with hyperextension, geckos shed dirt from their toes twice as fast as they would if walking without hyperextension, returning their feet to nearly 80 per cent of their original stickiness in only four steps. Our dynamic model predicts that when setae suddenly release from the attached substrate, they generate enough inertial force to dislodge dirt particles from the attached spatulae. The predicted cleaning force on dirt particles significantly increases when the dynamic effect is included. The extraordinary design of gecko toe pads perfectly combines dynamic self-cleaning with repeated attachment/detachment, making gecko feet sticky yet clean. This work thus provides a new mechanism to be considered for biomimetic design of highly reuseable and reliable dry adhesives and devices.
Towards excimer-laser-based stereolithography: a rapid process to fabricate rigid biodegradable photopolymer scaffolds
Authors: Beke S. , Anjum F. , Tsushima H. , Ceseracciu L. , Chieregatti E. , Diaspro A. , Athanassiou A. , Brandi F.
Published: June 2012

We demonstrate high-resolution photocross-linking of biodegradable poly(propylene fumarate) (PPF) and diethyl fumarate (DEF) using UV excimer laser photocuring at 308 nm. The curing depth can be tuned in a micrometre range by adjusting the total energy dose (total fluence). Young's moduli of the scaffolds are found to be a few gigapascal, high enough to support bone formation. The results presented here demonstrate that the proposed technique is an excellent tool for the fabrication of stiff and biocompatible structures on a micrometre scale with defined patterns of high resolution in all three spatial dimensions. Using UV laser photocuring at 308 nm will significantly improve the speed of rapid prototyping of biocompatible and biodegradable polymer scaffolds and enables its production in a few seconds, providing high lateral and horizontal resolution. This short timescale is indeed a tremendous asset that will enable a more efficient translation of technology to clinical applications. Preliminary cell tests proved that PPF : DEF scaffolds produced by excimer laser photocuring are biocompatible and, therefore, are promising candidates to be applied in tissue engineering and regenerative medicine.
Rapid magnetic cell delivery for large tubular bioengineered constructs
Authors: Gonzalez-Molina J. , Riegler J. , Southern P. , Ortega D. , Frangos C. C. , Angelopoulos Y. , Husain S. , Lythgoe M. F. , Pankhurst Q. A. , Day R. M.
Published: June 2012

Delivery of cells into tubular tissue constructs with large diameters poses significant spatial and temporal challenges. This study describes preliminary findings for a novel process for rapid and uniform seeding of cells onto the luminal surface of large tubular constructs. Fibroblasts, tagged with superparamagnetic iron oxide nanoparticles (SPION), were directed onto the luminal surface of tubular constructs by a magnetic field generated by a k4-type Halbach cylinder device. The spatial distribution of attached cells, as measured by the mean number of cells, was compared with a conventional, dynamic, rotational cell-delivery technique. Cell loading onto the constructs was measured by microscopy and magnetic resonance imaging. The different seeding techniques employed had a significant effect on the spatial distribution of the cells (
p
< 0.0001). The number of attached cells at defined positions within the same construct was significantly different for the dynamic rotation technique (
p
< 0.05). In contrast, no significant differences in the number of cells attached to the luminal surface were found between the defined positions on the construct loaded with the Halbach cylinder. The technique described overcomes limitations associated with existing cell-delivery techniques and is amenable to a variety of tubular organs where rapid loading and uniform distribution of cells for therapeutic applications are required.
Within-host competition and diversification of macro-parasites
Authors: Guilhem Rascalou , Šimková Andrea , Morand Serge , Gourbière Sébastien
Published: June 2012

Although competitive speciation is more and more regarded as a plausible mechanism for sympatric speciation of non-parasite species, virtually no empirical or theoretical study has considered this evolutionary process to explain intra-host diversification of parasites. We expanded the theory of competitive speciation to parasite species looking at the effect of macro-parasite life history on the conditions for sympatric speciation under the so-called pleiotropic scenario. We included within-host competition in the classical Anderson and May framework assuming that individuals exploit within-host resources according to a quantitative trait. We derived the invasion fitness function of mutants considering different distributions of individuals among hosts. Although the mutant fitness depends on parameters describing the key features of macro-parasite life history, and on the relative distributions of mutant and residents in hosts, the conditions for competitive speciation of macro-parasites are exactly the same as those previously established for free-living species. As an interesting by-product, within-host competitive speciation is expected not to depend on the aggregation level of the parasites. This theoretical pattern is confirmed by comparing the speciation rate of weakly and strongly aggregated monogenean parasites.
Thermal fluctuations of haemoglobin from different species: adaptation to temperature via conformational dynamics
Authors: Stadler A. M. , Garvey C. J. , Bocahut A. , Sacquin-Mora S. , Digel I. , Schneider G. J. , Natali F. , Artmann G. M. , Zaccai G.
Published: June 2012

Thermodynamic stability, configurational motions and internal forces of haemoglobin (Hb) of three endotherms (platypus,
Ornithorhynchus anatinus
; domestic chicken,
Gallus gallus domesticus
and human,
Homo sapiens
) and an ectotherm (salt water crocodile,
Crocodylus porosus
) were investigated using circular dichroism, incoherent elastic neutron scattering and coarse-grained Brownian dynamics simulations. The experimental results from Hb solutions revealed a direct correlation between protein resilience, melting temperature and average body temperature of the different species on the 0.1 ns time scale. Molecular forces appeared to be adapted to permit conformational fluctuations with a root mean square displacement close to 1.2 Å at the corresponding average body temperature of the endotherms. Strong forces within crocodile Hb maintain the amplitudes of motion within a narrow limit over the entire temperature range in which the animal lives. In fully hydrated powder samples of human and chicken, Hb mean square displacements and effective force constants on the 1 ns time scale showed no differences over the whole temperature range from 10 to 300 K, in contrast to the solution case. A complementary result of the study, therefore, is that one hydration layer is not sufficient to activate all conformational fluctuations of Hb in the pico- to nanosecond time scale which might be relevant for biological function. Coarse-grained Brownian dynamics simulations permitted to explore residue-specific effects. They indicated that temperature sensing of human and chicken Hb occurs mainly at residues lining internal cavities in the β-subunits.
Helical buckling of Skyrme–Faddeev solitons
Authors: Foster David , Harland Derek
Published: June 2012

Solitons in the Skyrme–Faddeev model on

are shown to undergo buckling transitions as the circumference of the
S
1
is varied. These results support a recent conjecture that solitons in this field theory are well-described by a much simpler model of elastic rods.
Historical ecology with real numbers: past and present extent and biomass of an imperilled estuarine habitat
Authors: Zu Ermgassen Philine S. E. , Spalding Mark D. , Blake Brady , Coen Loren D. , Dumbauld Brett , Geiger Steve , Grabowski Jonathan H. , Grizzle Raymond , Luckenbach Mark , McGraw Kay , Rodney William , Ruesink Jennifer L. , Powers Sean P. , Brumbaugh Robert
Published: June 2012

Historic baselines are important in developing our understanding of ecosystems in the face of rapid global change. While a number of studies have sought to determine changes in extent of exploited habitats over historic timescales, few have quantified such changes prior to late twentieth century baselines. Here, we present, to our knowledge, the first ever large-scale quantitative assessment of the extent and biomass of marine habitat-forming species over a 100-year time frame. We examined records of wild native oyster abundance in the United States from a historic, yet already exploited, baseline between 1878 and 1935 (predominantly 1885–1915), and a current baseline between 1968 and 2010 (predominantly 2000–2010). We quantified the extent of oyster grounds in 39 estuaries historically and 51 estuaries from recent times. Data from 24 estuaries allowed comparison of historic to present extent and biomass. We found evidence for a 64 per cent decline in the spatial extent of oyster habitat and an 88 per cent decline in oyster biomass over time. The difference between these two numbers illustrates that current areal extent measures may be masking significant loss of habitat through degradation.
Immune activation decreases sperm viability in both sexes and influences female sperm storage
Authors: Radhakrishnan Preethi , Fedorka Kenneth M.
Published: June 2012

All animals are under the constant threat of pathogenic infection. However, little is known regarding the influence of acute infection on sperm viability, particularly in female insects. This information is crucial for our understanding of mating and immune system coevolution, considering that females store sperm and serve as the site of sperm competition. Using the fruitfly,
Drosophila melanogaster
, we examined the influence of infection on sperm viability and storage. Twenty-four hours after haemocoel inoculation with a pathogen mimic (peptidoglycan, PGN) both sexes exhibited reduced sperm viability, indicating that systemic immune activation played a significant role in gamete survival. Surprisingly, sperm death did not appear to result from a reproductive-immune system trade-off, considering that sperm survived 24 h
in vitro
once removed from their somatic resources. Instead, our results are most consistent with death owing to immune effector collateral damage. We also examined the potential for sexually transmitted pathogens to influence sperm storage. Females mated with ‘infected’ males (created by dipping genitalia into a PGN solution) exhibited a higher proportion of empty sperm stores 48 h after mating compared to their controls. Remarkably, these data indicate that females may increase their fitness by removing ‘infected’ ejaculates from storage over time.
Evolution of foraging behaviour in response to chronic malnutrition in
Drosophila melanogaster
Authors: Vijendravarma Roshan K. , Narasimha Sunitha , Kawecki Tadeusz J.
Published: June 2012

Chronic exposure to food of low quality may exert conflicting selection pressures on foraging behaviour. On the one hand, more active search behaviour may allow the animal to find patches with slightly better, or more, food; on the other hand, such active foraging is energetically costly, and thus may be opposed by selection for energetic efficiency. Here, we test these alternative hypotheses in
Drosophila
larvae. We show that populations which experimentally evolved improved tolerance to larval chronic malnutrition have shorter foraging path length than unselected control populations. A behavioural polymorphism in foraging path length (the rover–sitter polymorphism) exists in nature and is attributed to the
foraging
locus (
for
). We show that a sitter strain (
for
s2
) survives better on the poor food than the rover strain (
for
R
), confirming that the sitter foraging strategy is advantageous under malnutrition. Larvae of the selected and control populations did not differ in global
for
expression. However, a quantitative complementation test suggests that the
for
locus may have contributed to the adaptation to poor food in one of the selected populations, either through a change in
for
allele frequencies, or by interacting epistatically with alleles at other loci. Irrespective of its genetic basis, our results provide two independent lines of evidence that sitter-like foraging behaviour is favoured under chronic larval malnutrition.
Disaster‐Relief Logistics With Limited Fuel Supply
Authors: Suzuki Yoshinori
Published: June 2012

Disaster‐relief logistics consists of providing adequate emergency supplies rapidly to the affected people so as to minimize human suffering and death. This study empirically examines the impact that the shortage of fuel, a commonly encountered problem in many disaster situations, can have on the effectiveness of disaster‐relief logistics operations. We focus on investigating the following two issues: (1) whether the shortage of fuel is more damaging in attaining logistical goals than the equivalent‐sized shortage in emergency supplies themselves, and (2) what types of vehicles should be used when the fuel supply is limited. Results suggest that the shortage of fuel may be more damaging than the shortage of emergency supplies, and that smaller trucks may be preferred to larger trucks when the shortage of fuel becomes severe.