bluuebunny/crossref_metadata_2025 huggingface dataset:
Can RNAi‐mediated hsp90α knockdown in combination with 17‐AAG be a therapy for glioma?
Authors: Mehta Adi , Shervington Amal , Howl John , Jones Sarah , Shervington Leroy
Published: June 2013

Heat shock protein 90 promotes tumor progression and survival and has emerged as a vital therapeutic target. Previously we reported that the combinatorial treatment of 17AAG/sihsp90α significantly downregulated Hsp90α mRNA and protein levels in Glioblastoma Multiforme (GBM). Here we investigated the ability of cell penetrating peptide (Tat48–60 CPP)‐mediated siRNA‐induced hsp90α knockdown as a single agent and in combination with 17‐allylamino‐17‐demethoxygeldanamycin (17‐AAG) to induce tumor growth inhibition in GBM and whether it possessed therapeutic implications. GBM and non‐tumorigenic cells exposed to siRNA and/or 17‐AAG were subsequently assessed by qRT‐PCR, immunofluorescence, FACS analysis, quantitative Akt, LDH leakage and cell viability assays. PAGE was performed for serum stability assessment. A combination of siRNA/17‐AAG treatment significantly induced Hsp90α gene and protein knockdown by 95% and 98%, respectively, concomitant to 84% Akt kinase activity attenuation, induced cell cycle arrest and tumor‐specific cytotoxicity by 88%. Efficient complex formation between CPP and siRNA exhibited improved serum stability of the siRNA with minimal intrinsic toxicity in vitro. The preliminary in vivo results showed that combination therapy induced hsp90α knockdown and attenuated Akt kinase activity in intracranial glioblastoma mouse models. The results imply that RNAi‐mediated hsp90α knockdown increases 17‐AAG treatment efficacy in GBM. In addition, the cytotoxic response observed was the consequence of downregulation of hsp90α gene expression, reduced Akt kinase activity and S‐G2/M cell cycle arrest. These results are novel and highlight the ability of Tat to efficiently deliver siRNA in GBM and suggest that the dual inhibition of Hsp90 has therapeutic potentials.
Linear and nonlinear obliquely propagating ion-acoustic waves in magnetized negative ion plasma with non-thermal electrons
Authors: MISHRA M. K. , JAIN S. K.
Published: June 2013

Ion-acoustic solitons in magnetized low-β plasma consisting of warm adiabatic positive and negative ions and non-thermal electrons have been studied. The reductive perturbation method is used to derive the Korteweg–de Vries (KdV) equation for the system, which admits an obliquely propagating soliton solution. It is found that due to the presence of finite ion temperature there exist two modes of propagation, namely fast and slow ion-acoustic modes. In the case of slow-mode if the ratio of temperature to mass of positive ion species is lower (higher) than the negative ion species, then there exist compressive (rarefactive) ion-acoustic solitons. It is also found that in the case of slow mode, on increasing the non-thermal parameter (γ) the amplitude of the compressive (rarefactive) soliton decreases (increases). In fast ion-acoustic mode the nature and characteristics of solitons depend on negative ion concentration. Numerical investigation in case of fast mode reveals that on increasing γ, the amplitude of compressive (rarefactive) soliton increases (decreases). The width of solitons increases with an increase in non-thermal parameters in both the modes for compressive as well as rarefactive solitons. There exists a value of critical negative ion concentration (αc), at which both compressive and rarefactive ion-acoustic solitons appear as described by modified KdV soliton. The value of αc decreases with increase in γ.
TRANSACTION COSTS, NONFUNDAMENTAL UNCERTAINTY, AND THE EXCHANGE RATE DISCONNECT
Authors: Li Nan
Published: June 2013

Exchange rates display excessive volatility and are disconnected from macroeconomic fundamentals. This paper presents a two-country general equilibrium model in which nonfundamental uncertainty (“sunspots”) in part drives stochastic fluctuations in the exchange rate in a class of rational expectation equilibria. In the model, a combination of financial frictions—incomplete asset markets and a proportional transaction cost associated with trading foreign-currency-denominated bonds—breaks the tight link between exchange rates and fundamentals. Moreover, the model generates a negative Backus–Smith correlation between relative consumption and the real exchange rate, because relative prices, acting as a source of shocks as opposed to shock absorbers, directly affect relative output and generate a large wealth effect on relative consumption. Using a random walk as an example of sunspot shocks, the volatility of exchange rates relative to that of output and consumption is found to be large in the presence of nontradable goods and distribution services.
Relative validity and reproducibility of a quantitative FFQ for assessing nutrient intakes of vegetarians in Taiwan
Authors: Chiu Tina HT , Huang Hui-Ya , Chen Kuan-Ju , Wu Yu-Ru , Chiu Jason PC , Li Yi-Hwei , Chiu Brian C-H , Lin Chin-Lon , Lin Ming-Nan
Published: June 2013

Objective

To assess the relative validity and reproducibility of the quantitative FFQ used in the Tzu Chi Health Study (TCHS).

Design

The reproducibility was evaluated by comparing the baseline FFQ with the 2-year follow-up FFQ. The validity was evaluated by comparing the baseline FFQ with 3 d dietary records and biomarkers (serum folate and vitamin B12). Median comparison, cross-classification and Spearman correlation with and without energy adjustment and deattenuation for day-to-day variation were assessed.

Setting

TCHS is a prospective cohort containing a high proportion of true vegetarians and part-time vegetarians (regularly consuming a vegetarian diet without completely avoiding meat).

Subject

Subsets of 103, seventy-eight and 1528 TCHS participants were included in the reproducibility, dietary record-validity and biomarker-validity studies, respectively.

Results

Correlations assessing the reproducibility for repeat administrations of the FFQ were in the range of 0·46–0·65 for macronutrients and 0·35–0·67 for micronutrients; the average same quartile agreement was 40%. The correlation between FFQ and biomarkers was 0·41 for both vitamin B12 and folate. Moderate to good correlations between the baseline FFQ and dietary records were found for energy, protein, carbohydrate, saturated and monounsaturated fat, fibre, vitamin C, vitamin A, K, Ca, Mg, P, Fe and Zn (average crude correlation: 0·47 (range: 0·37–0·66); average energy-adjusted correlation: 0·43 (range: 0·38–0·55); average energy-adjusted deattenuated correlation: 0·50 (range: 0·44–0·66)) with same quartile agreement rate of 39% (range: 35–45%), while misclassification to the extreme quartile was rare (average: 4% (range: 0–6%)).

Conclusions

The FFQ is a reliable and valid tool to rank relative intake of major nutrients for TCHS participants.
Philosophical issues in the search for extraterrestrial life and intelligence
Authors: Schneider Jean
Published: June 2013

In the search for extraterrestrial life and intelligence, it is essential to clarify what is to be meant by ‘life’ and ‘intelligence’. I first analyse what it means to ‘define’ these words. I will show that some philosophical prejudice is unavoidable. As a working hypothesis, I consider two types of philosophy: ‘natural philosophy’, seeking for some essence of things, and ‘critical (or analytical) philosophy’, devoted to the analysis of the procedures by which we claim to construct a reality. An extension of critical philosophy, epistemo-analysis (i.e. the psycho-analysis of concepts) is presented and applied to the definition of exolife and to extraterrestrial ‘intelligence’. Some pragmatic conclusions are finally drawn for future search strategies.
Perceived Competition Explains Regional Differences in the Stereotype Content of Immigrant Groups
Authors: Binggeli Steve , Krings Franciska , Sczesny Sabine
Published: June 2013

This research investigates differences in the stereotype content of immigrant groups between linguistic regions. We expected that immigrant groups who speak the local language of a specific linguistic region would be perceived as more competitive within this region than in another linguistic region. Further, we expected these differences would underlie regional differences in stereotype content, albeit only for the warmth dimension. Predictions were tested in the two largest linguistic regions of Switzerland. As expected, in the German-speaking region, locals perceived German immigrants as more competitive and thus as less warm, whereas in the French-speaking region, locals perceived French immigrants as more competitive and, consequently, as less warm. So, paradoxically, immigrants with strong integration potential are particularly disliked because they are regarded as direct competitors.
Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus
Authors: Rineau F , Shah F , Smits M M , Persson P , Johansson T , Carleer R , Troein C , Tunlid A
Published: June 2013

The majority of nitrogen in forest soils is found in organic matter–protein complexes. Ectomycorrhizal fungi (EMF) are thought to have a key role in decomposing and mobilizing nitrogen from such complexes. However, little is known about the mechanisms governing these processes, how they are regulated by the carbon in the host plant and the availability of more easily available forms of nitrogen sources. Here we used spectroscopic analyses and transcriptome profiling to examine how the presence or absence of glucose and/or ammonium regulates decomposition of litter material and nitrogen mobilization by the ectomycorrhizal fungus Paxillus involutus. We found that the assimilation of nitrogen and the decomposition of the litter material are triggered by the addition of glucose. Glucose addition also resulted in upregulation of the expression of genes encoding enzymes involved in oxidative degradation of polysaccharides and polyphenols, peptidases, nitrogen transporters and enzymes in pathways of the nitrogen and carbon metabolism. In contrast, the addition of ammonium to organic matter had relatively minor effects on the expression of transcripts and the decomposition of litter material, occurring only when glucose was present. On the basis of spectroscopic analyses, three major types of chemical modifications of the litter material were observed, each correlated with the expression of specific sets of genes encoding extracellular enzymes. Our data suggest that the expression of the decomposition and nitrogen assimilation processes of EMF can be tightly regulated by the host carbon supply and that the availability of inorganic nitrogen as such has limited effects on saprotrophic activities.
Visual Information Can Hinder Working Memory Processing of Speech
Authors: Mishra Sushmit , Lunner Thomas , Stenfelt Stefan , Rönnberg Jerker , Rudner Mary
Published: June 2013

Purpose

The purpose of the present study was to evaluate the new Cognitive Spare Capacity Test (CSCT), which measures aspects of working memory capacity for heard speech in the audiovisual and auditory-only modalities of presentation.

Method

In Experiment 1, 20 young adults with normal hearing performed the CSCT and an independent battery of cognitive tests. In the CSCT, they listened to and recalled 2-digit numbers according to instructions inducing executive processing at 2 different memory loads. In Experiment 2, 10 participants performed a less executively demanding free recall task using the same stimuli.

Results

CSCT performance demonstrated an effect of memory load and was associated with independent measures of executive function and inference making but not with general working memory capacity. Audiovisual presentation was associated with lower CSCT scores but higher free recall performance scores.

Conclusions

CSCT is an executively challenging test of the ability to process heard speech. It captures cognitive aspects of listening related to sentence comprehension that are quantitatively and qualitatively different from working memory capacity. Visual information provided in the audiovisual modality of presentation can hinder executive processing in working memory of nondegraded speech material.
Who's Who? Memory Updating and Character Reference in Children's Narratives
Authors: Whitely Cristy , Colozzo Paola
Published: June 2013

Purpose

The capacity to update and monitor the contents of working memory is an executive function presumed to play a critical role in language processing. The current study used an individual differences approach to consider the relationship between memory updating and accurate reference to story characters in the narratives of typically developing children.

Method

English-speaking children from kindergarten to grade 2 (N= 63;Mage= 7.0 years) completed updating tasks, short-term memory tasks, and narrative productions. The authors used multiple regression to test whether updating accounted for independent variability in referential adequacy.

Results

The capacity to update working memory was related to adequate character reference beyond the effects of age and of short-term memory capacity, with the strongest relationship emerging for maintaining reference over multiple utterances.

Conclusions

This individual differences study is the first to show a link between updating and performance in a discourse production task for young school-age children. The findings contribute to the growing body of research investigating the role of working memory in shaping language production. This study invites extension to children of different ages and language abilities as well as to other language production tasks.
AAC Assessment and Intervention in Pediatric ICU/Acute Care: From Referral Through Continuum of Care
Authors: Santiago Rachel , Costello John M.
Published: June 2013

AAC supports in the ICU/Acute Care vary by patient presentation. Our 20+ years of bedside service delivery reveals trends in patient needs for AAC across the continuum of care. We detail three phases of AAC assessment and intervention and the role of SLP in the assessment/feature matching process.
Meeting the Needs of Limited English Proficiency Patients
Authors: Hurtig Richard , Czerniejewski Emily , Bohnenkamp Laura , Na Jiyoung
Published: June 2013

The number of patients in U.S. hospitals with limited English proficiency (LEP) is growing. There is a body of evidence that suggests that inadequate patient-provider communication is responsible for a range of adverse events, including death. In recognition of this, the Joint Commission has set standards requiring hospitals to address the communication needs of the diverse hospitalized population. Although the optimal approach for LEP patients would involve having certified interpreters at the bedside around the clock, this is unfortunately not practically or economically feasible. Speech-generating devices (SGDs) can offer patients a means of communicating with their caregivers and an opportunity to participate more actively in their care. The University of Iowa Assistive Devices Lab has developed a series of bilingual communication templates suited for use in acute and critical care settings. They developed these templates for use by LEP patients who are speakers of diverse languages, as well as by Deaf patients who use a sign language as their primary means of communication.
Estimating communication costs for distributed XML query processing
Authors: Park Jong‐Hyun , Kang Ji‐Hoon
Published: June 2013

In distributed query processing, good estimation algorithms of communication costs are critical for query processing, including distributed XML queries. There are techniques that estimate a communication cost for distributed SQL query processing, and some of techniques are adopted in numerous distributed SQL processors. Therefore adopting the processing techniques for SQL queries for the communication cost‐based processing of the distributed XML queries seems natural. Unfortunately, however, the tree‐structured XML document is different from the table‐shaped relational data. These structural differences make adopting the techniques for SQL queries difficult. This study defines some of the considerations for estimating the communication cost of distributed XML queries, and proposes a method for communication cost‐based query processing. The experiments show that the proposed algorithm is reasonable for estimating the communication cost for distributed XML queries.
Capacity analysis of Rayleigh fading channels in low signal‐to‐noise ratio regime for maximal ratio combining diversity because of combining errors
Authors: Janarthanan Subhashini , Bhaskar Vidhyacharan
Published: June 2013

In this research work, the authors derive closed‐form expressions for capacity per unit bandwidth (spectrum efficiency) of correlated Rayleigh fading channels under maximal ratio combining diversity at low signal‐to‐noise ratios (SNRs). Spectrum efficiency expressions are derived for M diversity branches under adaptation policies, such as: (i) optimal power and rate adaptation (OPRA) policy, (ii) optimal rate adaptation (ORA) policy and (iii) truncated channel inversion with fixed rate (TIFR) policy. Even at low SNRs, if space diversity is exercised using a single‐input multiple‐output system, spectrum efficiency achieved is higher compared with that achieved when signals are uncorrelated and have no diversity. This forms the focal point of this study. Analytical results show accurately that OPRA policy provides highest capacity over other adaptation policies. The spectrum efficiency for the three policies and outage probability for the low SNR case are derived, plotted and analysed in detail in this work.
On an extension problem for density matrices
Authors: Carlen Eric A. , Lebowitz Joel L. , Lieb Elliott H.
Published: June 2013

We investigate the problem of the existence of a density matrix ρ123 on a Hilbert space \documentclass[12pt]{minimal}\begin{document}${\mathcal {H} }_{1}\otimes {\mathcal {H} }_2\otimes {\mathcal {H} }_3$\end{document}H1⊗H2⊗H3 with given partial traces ρ12 = Tr3 ρ123 and ρ23 = Tr1 ρ123. While we do not solve this problem completely, we offer partial results in the form of some necessary and some sufficient conditions on ρ12 and ρ23. The quantum case differs markedly from the classical (commutative) case, where the obvious necessary compatibility condition suffices, namely, Tr1 ρ12 = Tr3ρ23.
Time-resolved measurement of the tunnel magneto-Seebeck effect in a single magnetic tunnel junction
Authors: Boehnke Alexander , Walter Marvin , Roschewsky Niklas , Eggebrecht Tim , Drewello Volker , Rott Karsten , Münzenberg Markus , Thomas Andy , Reiss Günter
Published: June 2013

Recently, several groups have reported spin-dependent thermoelectric effects in magnetic tunnel junctions. In this paper, we present a setup for time-resolved measurements of thermovoltages and thermocurrents of a single micro- to nanometer-scaled tunnel junction. An electrically modulated diode laser is used to create a temperature gradient across the tunnel junction layer stack. This laser modulation technique enables the recording of time-dependent thermovoltage signals with a temporal resolution only limited by the preamplifier for the thermovoltage. So far, time-dependent thermovoltage could not be interpreted. Now, with the setup presented in this paper, it is possible to distinguish different Seebeck voltage contributions to the overall measured voltage signal in the μs time regime. A model circuit is developed that explains those voltage contributions on different sample types. Further, it will be shown that a voltage signal arising from the magnetic tunnel junction can only be observed when the laser spot is directly centered on top of the magnetic tunnel junction, which allows a lateral separation of the effects.
Note: Synchronous energy extraction through four output ports of microwave compressor
Authors: Avgustinovich V. A. , Artemenko S. N. , Novikov S. A. , Yushkov Yu. G.
Published: June 2013

The energy stored in a resonant cavity was extracted through four output ports and added in phase in a common line. Operation of a single switch provided synchronism and the power portions transmitted through the ports were combined in a waveguide turnstile junction. Estimation shows that the compressor peak power can reach a value eight times as much as the switched wave power, provided the output pulsewidth is shortened by the same factor with reference to the cavity double transit time. The performance of the X-band compressor prototype was investigated. Signals radiated through each of four output ports had identical envelope shapes and equal peak power values. The reflected wave did not accompany the power combining. The pulses of 1.2 MW peak power and 1.6 ns pulse width were obtained when the compressor was driven by the 50 kW pulse power magnetron generator.
Electric charge and potential distribution in twisted multilayer graphene
Authors: Zimbovskaya Natalya A. , Mele Eugene
Published: June 2013

The specifics of charge screening and electrostatic potential spatial distribution in multilayered graphene films placed in between charged substrates is theoretically analyzed. It is shown that by varying the areal charge densities on the substrates and/or the thickness of the graphene stack one may tune the doped carriers distribution over the system. When the charge densities on the substrates are weak, the carriers distribution and electrostatic potential profile agree with semimetallic properties of graphene. However, when the amount of the donated charge is sufficiently large the transition to a metallic-like behavior of the graphene layers occurs. The possibilities for experimental observation of the predicted transition are discussed.
Tncs' Technology Linkages with Domestic Firms: An Investigation of the Ict Industry in Suzhou, China
Authors: Liao Felix Haifeng , Wei Yehua H Dennis
Published: June 2013

On the basis of a comprehensive survey in the information and communication technology industry in China's Suzhou municipality, we examine the determinants of the technology linkages that transnational corporations (TNCs) make with domestic firms. We found that TNCs' domestic supply and client linkages and their decentralization of decision making had a significant and positive effect on technological interactions between domestic firms and TNCs. However, such linkages were constrained by the technology gap between TNCs and domestic firms and they are focused on new product developments for the domestic Chinese market. The results highlight the challenges that domestic Chinese firms face in establishing ‘global pipelines’ of knowledge exchange. The implications of the findings on technology and foreign direct investment policies in China are also assessed, and we argue that China has potential to pave a new way of technology development by taking advantage of its indigenous capacity and sizable domestic market.
Europeanisation of Regional Policy Making: A Boolean Analysis of Norwegian Counties' Participation in the Eu's Interreg Programme
Authors: Fitjar Rune Dahl , Leknes Einar , Thygesen Janne
Published: June 2013

How does the EU affect policy making by regional governments in Norway, a unitary nonmember state? We address this question through examining the impact of participation in the Interreg programme on Norwegian county councils' regional development policies. We examine forty-four acts of participation by Norwegian counties in Interreg projects, tracking their effects on both incremental policy changes and radical changes of policy direction. We find that most of the projects have resulted in policy changes by the county council and sometimes by other actors, and almost a third have resulted in a completely or partly new policy direction. Examining which projects had the greatest impact, we find that the county council's ability to shape the project according to regional concerns, especially in newly formed networks, is an important mediating condition. This could indicate that regional governments are using Interreg as a channel for policy entrepreneurship, building activities in new policy areas.
Evidence, Policy, and the Politics of Regional Development: The Case of High-Speed Rail in the United Kingdom
Authors: Tomaney John , Marques Pedro
Published: June 2013

Geographers have often reflected on the impact of their research on policy making. Contributions usually focus on the (ir)relevance of research topics or on the pressures to ‘publish or perish’ that discourage academics from engaging with applied work. In this paper we will focus instead on the difficulty in engaging with the political process, even when the evidence appears robust and if policy implications are relatively clear. We use the example of high-speed rail and its impacts on territorial inequalities to reflect on the decision-making process in the UK, where the government is currently considering building a new high-speed line. We argue that, despite fairly strong evidence suggesting that high-speed rail is likely to deepen inequalities between the regions in the UK, currently this project is still being hailed as a strategy to spread economic activity and ‘rebalance’ the British economy. We identify some of the reasons for this perverse outcome.
Changing Landscapes of Support in the Lives of Chinese Urban Elders: Voices from Wuhan Neighbourhoods
Authors: Gilroy Rose
Published: June 2013

The change from a Soviet-style planned economy to one influenced by the market has rippled through all areas of Chinese life. This paper explores how changes to state financial support together with changing family dynamics are impacting on urban Chinese elders. Drawing on exploratory fieldwork in Wuhan, the paper takes an everyday-life approach to reveal new inequalities for older people. Changes to health-care costs are causing anxiety among many elders and plunging others into poverty. However, it is the family that emerges as pivotal to older people's economic and social well-being. For those with decently employed children there are emerging opportunities for independence in later life; conversely, where children are low paid or out of work, it is parental income that is taking the strain. The paper concludes by setting these findings in a broader global context.
Mangroves as maternity roosts for a colony of the rare east-coast free-tailed bat (Mormopterus norfolkensis) in south-eastern Australia
Authors: McConville Anna , Law Bradley S. , Mahony Michael J.
Published: June 2013

Context
Maternity roosts of insectivorous bats (where females raise young) are critical to the conservation of threatened species as roost quality can influence reproductive success. Additionally, threatened species may have specialised requirements or unusual behaviour, which may be overlooked without targeted investigation.

Aims
To explore which factors influence the roost selection of Mormopterus norfolkensis, by comparing day roosts, identified via radio-tracking, with environmental variables collected at tree, patch and landscape scales.

Methods
We collected a range of variables describing maternity roosts and surrounding patches, including internal measurements of hollows and microclimate. Additionally, we derived landscape-scale variables using a geographic information system. We then explored which variables best explained roost occurrence using logistic regression.

Key results
Nineteen lactating females and two male M. norfolkensis were tracked to 40 roost trees, mostly grey mangrove, Avicennia marina subsp. australasica. Lactating females were found to be faithful to two patches of mangrove forest close to where they were captured, regularly switched roosts and roosted in hollows singularly or in small groups. The attributes of mangrove patches, especially a high proportion of hollows, better predicted roosting by lactating females than roost-tree or landscape characteristics. Additionally, although the microclimate of roost hollows was not significantly different from ambient mangrove conditions, the mangrove forest was slightly more stable and had higher humidity than did other nearby habitats.

Conclusions
Contrary to predictions, maternity roosting group sizes were relatively small, indicating that bats were not deriving thermoregulatory benefits from communal living. However, we suggest that lactating females may benefit from the operation of a fission–fusion society among the colony as a whole. Additionally, the mature mangrove forest could offer unique roosting opportunities for bats because they support high densities of hollow-bearing trees, a stable microclimate and potentially low abundances of predators and competitors.

Implications
This is one of few international bat–mangrove studies and it illustrates that threatened species can behave unexpectedly and may be overlooked in conservation strategies that are based largely on anecdotal observations. We encourage further research into the value of mangrove forests to terrestrial fauna globally.
Influence of Lineage, Broodstock Conditioning, and Hormone Injection on Gila Trout Reproductive Success and Egg Fatty Acid Composition
Authors: Hill Heidi , Twibell Ronald , Conway Jeff , Gannam Ann , Seals John
Published: June 2013

Successful reproduction of captive-reared fishes depends on hatchery practices and proper broodstock nutrition. Nutrient requirements and environmental conditions stimulating reproductive development are unknown for many threatened and endangered species and may differ between lineages within species. Accordingly, prior to spawning, Main Diamond Gila Trout Oncorhynchus gilae broodstock were exposed to different thermal cycles and hormonal injection to improve reproductive success. Additionally, egg fatty acid composition and hatching success of Main and South Diamond Gila Trout were evaluated to determine the extent of phenotypic differences between lineages. Thermal conditioning of broodstock accompanied with injections of exogenous luteinizing hormone releasing hormone analog (LHRHa) prior to spawning improved progeny survival over historic hatchery means as well as means for broodstock reared in raceways at constant temperatures without LHRHa. Egg n-6 fatty acid content appears to be associated with this improvement. Eggs from Main and South Diamond broodstock fed the same feeds had similar hatch rates but could be differentiated on the basis of fatty acid profile. Future trials should further evaluate the influence of dietary fatty acids on egg deposition and hatch rate, while acknowledging that changes in reproductive performance may differ across lineages. Broodstocks should continue to be conditioned with thermal cycling and use of LHRHa to induce ovulation, as these techniques resulted in significantly better hatch rates in the current study than use of only photoperiod manipulation to stimulate reproductive development.
Potential of Asian Carp from the Illinois River as a Source of Raw Materials for Fish Meal Production
Authors: Bowzer John , Trushenski Jesse , Glover David C.
Published: June 2013

Incentivizing overfishing through the creation of high‐value markets for Silver Carp Hypophthalmichthys molitrix and Bighead Carp H. nobilis has been proposed as a management strategy for controlling Asian carp in the Illinois River. Asian carp may be rendered into a protein‐dense fish meal, and one of the most attractive, high‐value end uses for such a product is aquafeed manufacturing. However, the nutritional content and shelf stability of Asian carp as a raw material must be determined to assess its suitability for rendering and subsequent use as a protein source in aquafeeds, which was the focus of this study. To determine seasonal, geographical, and species variation in body composition, fatty acids, and oxidative stability, Asian carp were collected from five reaches of the Illinois River during the fall, spring, and summer (up to 12 individuals of each species per reach per season) and analyzed. Slight geographical, seasonal, and species variation exists in the body composition and fatty acid profiles of adult Asian carp from the Illinois River. There was an apparent trend of increasing lipid content from lower to upper reaches and from fall to summer. Bighead Carp tended to be leaner (higher protein, moisture, and ash content) than Silver Carp (higher lipid content). Although Asian carp generally appear to be a good source of long‐chain polyunsaturated fatty acids regardless of capture location or season, the concentration of these nutrients was highest in the fall. Oxidative stability analysis indicated Asian carp meal will need stabilizers to increase shelf life. Collectively, our results suggest Asian carp‐based fish meals would be nutritionally suitable for use in aquafeeds, if precautions are taken to stabilize the product during storage. Creating demand for carp meal in the aquafeed manufacturing sector may prove a valuable strategy for aiding in the control of Asian carp populations in the Illinois River.
Motion of variable-length MreB filaments at the bacterial cell membrane influences cell morphology
Authors: Reimold Christian , Defeu Soufo Herve Joel , Dempwolff Felix , Graumann Peter L.
Published: June 2013

The maintenance of rod-cell shape in many bacteria depends on actin-like MreB proteins and several membrane proteins that interact with MreB. Using superresolution microscopy, we show that at 50-nm resolution, Bacillus subtilis MreB forms filamentous structures of length up to 3.4 μm underneath the cell membrane, which run at angles diverging up to 40° relative to the cell circumference. MreB from Escherichia coli forms at least 1.4-μm-long filaments. MreB filaments move along various tracks with a maximal speed of 85 nm/s, and the loss of ATPase activity leads to the formation of extended and static filaments. Suboptimal growth conditions lead to formation of patch-like structures rather than extended filaments. Coexpression of wild-type MreB with MreB mutated in the subunit interface leads to formation of shorter MreB filaments and a strong effect on cell shape, revealing a link between filament length and cell morphology. Thus MreB has an extended-filament architecture with the potential to position membrane proteins over long distances, whose localization in turn may affect the shape of the cell wall.
Intranuclear DNA density affects chromosome condensation in metazoans
Authors: Hara Yuki , Iwabuchi Mari , Ohsumi Keita , Kimura Akatsuki
Published: June 2013

Chromosome condensation is critical for accurate inheritance of genetic information. The degree of condensation, which is reflected in the size of the condensed chromosomes during mitosis, is not constant. It is differentially regulated in embryonic and somatic cells. In addition to the developmentally programmed regulation of chromosome condensation, there may be adaptive regulation based on spatial parameters such as genomic length or cell size. We propose that chromosome condensation is affected by a spatial parameter called the chromosome amount per nuclear space, or “intranuclear DNA density.” Using Caenorhabditis elegans embryos, we show that condensed chromosome sizes vary during early embryogenesis. Of importance, changing DNA content to haploid or polyploid changes the condensed chromosome size, even at the same developmental stage. Condensed chromosome size correlates with interphase nuclear size. Finally, a reduction in nuclear size in a cell-free system from Xenopus laevis eggs resulted in reduced condensed chromosome sizes. These data support the hypothesis that intranuclear DNA density regulates chromosome condensation. This suggests an adaptive mode of chromosome condensation regulation in metazoans.
Exact algorithms for haplotype assembly from whole-genome sequence data
Authors: Chen Zhi-Zhong , Deng Fei , Wang Lusheng
Published: June 2013

Motivation: Haplotypes play a crucial role in genetic analysis and have many applications such as gene disease diagnoses, association studies, ancestry inference and so forth. The development of DNA sequencing technologies makes it possible to obtain haplotypes from a set of aligned reads originated from both copies of a chromosome of a single individual. This approach is often known as haplotype assembly. Exact algorithms that can give optimal solutions to the haplotype assembly problem are highly demanded. Unfortunately, previous algorithms for this problem either fail to output optimal solutions or take too long time even executed on a PC cluster.

Results: We develop an approach to finding optimal solutions for the haplotype assembly problem under the minimum-error-correction (MEC) model. Most of the previous approaches assume that the columns in the input matrix correspond to (putative) heterozygous sites. This all-heterozygous assumption is correct for most columns, but it may be incorrect for a small number of columns. In this article, we consider the MEC model with or without the all-heterozygous assumption. In our approach, we first use new methods to decompose the input read matrix into small independent blocks and then model the problem for each block as an integer linear programming problem, which is then solved by an integer linear programming solver. We have tested our program on a single PC [a Linux (x64) desktop PC with i7-3960X CPU], using the filtered HuRef and the NA 12878 datasets (after applying some variant calling methods). With the all-heterozygous assumption, our approach can optimally solve the whole HuRef data set within a total time of 31 h (26 h for the most difficult block of the 15th chromosome and only 5 h for the other blocks). To our knowledge, this is the first time that MEC optimal solutions are completely obtained for the filtered HuRef dataset. Moreover, in the general case (without the all-heterozygous assumption), for the HuRef dataset our approach can optimally solve all the chromosomes except the most difficult block in chromosome 15 within a total time of 12 days. For both of the HuRef and NA12878 datasets, the optimal costs in the general case are sometimes much smaller than those in the all-heterozygous case. This implies that some columns in the input matrix (after applying certain variant calling methods) still correspond to false-heterozygous sites.

Availability: Our program, the optimal solutions found for the HuRef dataset available at http://rnc.r.dendai.ac.jp/hapAssembly.html.

Contact:  zzchen@mail.dendai.ac.jp or cswangl@cityu.edu.hk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Biotic and abiotic factors influencing forage fish and pelagic nekton community in the Columbia River plume (USA) throughout the upwelling season 1999–2009
Authors: Litz Marisa N. C. , Emmett Robert L. , Bentley Paul J. , Claiborne Andrew M. , Barceló Caren
Published: June 2013

Litz, M. N. C., Emmett, R. L., Bentley, P. J., Claiborne, A. M., and Barceló, C. Biotic and abiotic factors influencing forage fish and pelagic nekton community in the Columbia River plume (USA) throughout the upwelling season 1999–2009. – ICES Journal of Marine Science, 71: . Large river plumes modify coastal environments and can impact production across multiple trophic levels. From 1999 to 2009, the assemblages of forage fish, predator fish, and other pelagic nekton were monitored in coastal waters associated with the Columbia River plume. Surveys were conducted at night to target vertically migrating species, and community structure evaluated to better understand ecological interactions. Distinct inshore and offshore communities were identified during spring and summer that were correlated with ocean temperature, salinity, plume volume, and upwelling intensity. Resident euryhaline forage fish species, such as smelts, anchovy, herring, market squid, juvenile salmon, and spiny dogfish, showed a high affinity for inshore habitat and the lower salinity plume during spring. Highly migratory species, such as sardine, piscivorous hake, sharks, and mackerels, were associated with warmer, saltier waters offshore, during strong upwelling periods in summer. Overall, our study of pelagic nekton revealed that temporal dynamics in abundance and community composition were associated with seasonal abiotic phenomenon, but not interannual, large-scale oceanographic processes. Forage fish assemblages differed seasonally and spatially from the assemblages of major piscivorous predators. This finding suggests a potential role of the plume as refuge for forage fish from predation by piscivorous fish in the northern California Current.
Identification of Two Tobacco rattle virus Sequence Variants Associated with Virus-like Mottle Symptom on Hosta in Ohio
Authors: Fisher John R.
Published: June 2013

Two Hosta sp. ‘So Sweet’ plants and one Hosta sieboldii (labeled as ‘Albo-marginata’) plant showing a suspected virus-like leaf mottle symptom tested negative for the Potyvirus group, Hosta virus X, Alfalfa mosaic virus, Arabis mosaic virus, Cucumber mosaic virus, Impatiens necrotic spot virus, Tobacco mosaic virus, Tobacco ringspot virus, Tomato ringspot virus, and Tomato spotted wilt virus by ELISA. DsRNA analysis produced a banding profile suggestive of a viral infection, and dsRNA was used as template to synthesize cDNAs for use with tobravirus group and Tobacco rattle virus (TRV) specific PCR primers. Amplicons were cloned and sequenced, and results showed two distinct populations of sequences: the two So Sweet isolates were ∼99% identical to each other but only ∼92% identical to the Albo-marginata isolate. These results represent the first confirmed report of TRV in Hosta in Ohio, and further demonstrate that there are at least two nucleotide sequence variants of the virus infecting Ohio Hosta.

Accepted for publication 21 December 2012. Published 30 March 2013.
A Quick and Simple Method to Evaluate Anisogramma anomala Ascospore Viability
Authors: Heckert Stephanie , Pscheidt Jay W. , Stone Jeff K.
Published: June 2013

Viability of ascospores of Anisogramma anomala, cause of eastern filbert blight on European hazelnut, was assessed using the vital stain trypan blue (working solution of 0.05% in lactoglycerol). Viable ascospores only had faint blue staining around their cell walls while non-viable ascospores absorbed the stain and turned dark blue. The number of viable (non-stained) ascospores as determined by trypan blue was similar to the proportion of ascospores germinating on culture media. Viability of field collected ascospores from rainwater spore traps ranged from 41 to 68%. Disease incidence of hazelnut seedlings was more closely related to differences in ascospore abundance than to differences in ascospore viability.

Accepted for publication 3 January 2013. Published 9 May 2013.
Climatic and Environmental Trends Observed During Epidemic and Non-epidemic Years of Soybean Sudden Death Syndrome in Iowa
Authors: Leandro Leonor F. S. , Robertson Alison E. , Mueller Daren S. , Yang Xiao-Bing
Published: June 2013

Soybean yield losses due to sudden death syndrome (SDS) have varied from year to year in Iowa since the disease was first reported in 1993. An SDS epidemic in 2010 resulted in significant yield losses and raised numerous concerns by farmers and agronomists regarding the potential for future outbreaks. Since infection and SDS development is highly dependent on temperature and soil moisture, our hypothesis was that SDS epidemics occur in years with above-average rainfall and below-average temperatures. To test this hypothesis, environmental conditions in southeast and central Iowa were compared among epidemic and non-epidemic years. Mean total precipitation and number of days with precipitation during each month of the growing season (April through August) tended to be greater in epidemic years (10.4 to 26.3 inches, 10 to 15 days) than non-epidemic years (8.9 to 15.4 inches, 9 to 12 days). Soil temperatures in April through July averaged less in epidemic years (9.0 to 24.7°C) than non-epidemic years (10.4 to 26.6°C). The widespread 2010 SDS epidemic in Iowa likely resulted from the concurrence of several weather conditions that were particularly favorable for disease. To reduce risk of yield losses in future years, soybean farmers should use an integrated disease management for SDS, focusing on using resistant varieties, avoiding soil compaction, and avoiding planting in cool wet soils.

Accepted for publication 31 January 2013. Published 29 May 2013.
Molecular phylogeography of tick-borne encephalitis virus in central Europe
Authors: Weidmann Manfred , Frey Stefan , Freire Caio C. M. , Essbauer Sandra , Růžek Daniel , Klempa Boris , Zubrikova Dana , Vögerl Maria , Pfeffer Martin , Hufert Frank T. , Zanotto Paolo M. , Dobler Gerhard
Published: June 2013

In order to obtain a better understanding of tick-borne encephalitis virus (TBEV) strain movements in central Europe the E gene sequences of 102 TBEV strains collected from 1953 to 2011 at 38 sites in the Czech Republic, Slovakia, Austria and Germany were determined. Bayesian analysis suggests a 350-year history of evolution and spread in central Europe of two main lineages, A and B. In contrast to the east to west spread at the Eurasian continent level, local central European spreading patterns suggest historic west to east spread followed by more recent east to west spread. The phylogenetic and network analyses indicate TBEV ingressions from the Czech Republic and Slovakia into Germany via landscape features (Danube river system), biogenic factors (birds, red deer) and anthropogenic factors. The identification of endemic foci showing local genetic diversity is of paramount importance to the field as these will be a prerequisite for in-depth analysis of focal TBEV maintenance and long-distance TBEV spread.
A genetic and developmental pathway from STAT3 to the OCT4–NANOG circuit is essential for maintenance of ICM lineages in vivo
Authors: Do Dang Vinh , Ueda Jun , Messerschmidt Daniel M. , Lorthongpanich Chanchao , Zhou Yi , Feng Bo , Guo Guoji , Lin Peiyu J. , Hossain Md Zakir , Zhang Wenjun , Moh Akira , Wu Qiang , Robson Paul , Ng Huck Hui , Poellinger Lorenz , Knowles Barbara B. , Solter Davor , Fu Xin-Yuan
Published: June 2013

Although it is known that OCT4–NANOG are required for maintenance of pluripotent cells in vitro, the upstream signals that regulate this circuit during early development in vivo have not been identified. Here we demonstrate, for the first time, signal transducers and activators of transcription 3 (STAT3)-dependent regulation of the OCT4–NANOG circuitry necessary to maintain the pluripotent inner cell mass (ICM), the source of in vitro-derived embryonic stem cells (ESCs). We show that STAT3 is highly expressed in mouse oocytes and becomes phosphorylated and translocates to the nucleus in the four-cell and later stage embryos. Using leukemia inhibitory factor (Lif)-null embryos, we found that STAT3 phosphorylation is dependent on LIF in four-cell stage embryos. In blastocysts, interleukin 6 (IL-6) acts in an autocrine fashion to ensure STAT3 phosphorylation, mediated by janus kinase 1 (JAK1), a LIF- and IL-6-dependent kinase. Using genetically engineered mouse strains to eliminate Stat3 in oocytes and embryos, we firmly establish that STAT3 is essential for maintenance of ICM lineages but not for ICM and trophectoderm formation. Indeed, STAT3 directly binds to the Oct4 and Nanog distal enhancers, modulating their expression to maintain pluripotency of mouse embryonic and induced pluripotent stem cells. These results provide a novel genetic model of cell fate determination operating through STAT3 in the preimplantation embryo and pluripotent stem cells in vivo.