bluuebunny/crossref_metadata_2025 huggingface dataset:
Application of Trichoderma harzianum SQR‐T037 bio‐organic fertiliser significantly controls Fusarium wilt and affects the microbial communities of continuously cropped soil of cucumber
Authors: Chen Li‐Hua , Huang Xin‐Qi , Zhang Feng‐Ge , Zhao Di‐Kun , Yang Xing‐Ming , Shen Qi‐Rong
Published: April 2012

BACKGROUND: The reduction in diversity of the soil microbial community causes the disorder of continuous cropping. The aim of this study was to determine the effects of applying Trichoderma harzianum SQR‐T037 bio‐organic fertiliser (BIO) on the microbial community in continuously cropped cucumber soil. Four treatments were set: (1) control, where neither seedling nursery soil (N) nor transplanted soil (T) was amended with BIO; (2) N treatment, where nursery soil was amended with BIO (1% w/w) but transplanted soil was not; (3) N + T treatment, where BIO was added to both nursery soil (1% w/w) and transplanted soil (0.5% w/w); (4) uncropped soil, where soil was left uncropped consistently.

RESULTS: A disease index of 72.2% was found for the control treatment, while the N and N + T treatments had disease indices of only 25 and 15% respectively. Analysis of the denaturing gradient gel electrophoresis (DGGE) profiles showed that the bacterial communities of the N and N + T treatments were similar to those of the uncropped soil but distinct from those of the control soil. The fungal communities of the N and N + T treatments differed from those of both the uncropped soil and the control.

CONCLUSION: Addition of BIO to both the nursery soil and the transplanted soil can diversify the microbial community in continuously cropped cucumber soil and thus effectively control Fusarium wilt of cucumber plants. Copyright © 2012 Society of Chemical Industry
Phenylboronic‐Acid‐Modified Amphiphilic Polyether as a Neutral Gene Vector
Authors: Chen Fujie , Zhang Zhenguo , Cai Mengmeng , Zhang Xiaojin , Zhong Zhenlin , Zhuo Renxi
Published: April 2012

A phenylboronic‐acid‐modified amphiphilic block polyether is prepared via reaction of polyglycidol‐block‐poly(ethylene oxide)‐block‐poly(propylene oxide)‐block‐poly(ethylene oxide)‐block‐polyglycidol (Pluronic‐PG) with 2‐(N,N‐dimethylaminomethyl)‐5‐aminomethyl phenylboronic acid using phosgene as a coupling reagent. The boronic‐acid‐modified non‐cationic polymer binds plasmid pGL3 effectively, forms sub‐µm polymer/DNA complex particles, and greatly facilitates the cell uptake of the plasmid. The efficiency of the polymer as a gene vector is evaluated in vitro by transfection of pGL3 to HeLa, COS‐7 and HepG2 cells. Pluronic‐PG‐BA enhances the transfection efficiency by 100 to 1000 times compared with Pluronic‐PG. The presence of serum does not significantly affect the transfection efficiency.

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Bladder inhibition by intermittent pudendal nerve stimulation in cat using transdermal amplitude‐modulated signal (TAMS)
Authors: Tai Changfeng , Shen Bing , Wang Jicheng , Subbaroyan Jeyakumar , Roppolo James R. , de Groat William C.
Published: April 2012

Aims

To determine if intermittent stimulation of the pudendal nerve using a transcutaneous stimulation method can inhibit reflex bladder activity. Intermittent stimulation consumes less electrical power than continuous stimulation, requiring a smaller battery and reducing the size of the stimulator for neuromodulation therapy.

Methods

A non‐invasive stimulation method employing a transdermal amplitude‐modulated signal (TAMS) was used in 18 α‐chloralose anesthetized cats to stimulate the pudendal nerve via electrodes attached to the skin surface. Intermittent stimulation of different duty cycles was applied during repeated cystometrograms (CMGs) to inhibit reflex bladder activity. The bladder capacity measured during each CMG was used to indicate the inhibitory effect induced by the stimulation.

Results

Continuous stimulation maximally increased bladder capacity to 172.6 ± 15% of the control capacity, while intermittent stimulation at the duty cycles of 30/30, 5/5, and 1/1 (“on/off” in seconds) significantly (P < 0.05) increased bladder capacity to 132 ± 7.5%, 154.2 ± 20%, and 165.5 ± 28%, respectively. The inhibitory effect was gradually reduced as the “on/off” ratio was decreased.

Conclusions

This pre‐clinical study indicated that intermittent stimulation of the pudendal nerve could be as effective as continuous stimulation to inhibit reflex bladder activity. These results are useful for the design and development of new stimulator technology to treat overactive bladder, and are also important for understanding pudendal neuromodulation therapy. Neurourol. Urodynam. 31:1181–1184, 2012. © 2012 Wiley Periodicals, Inc.
Fetal varicella – diagnosis, management, and outcome
Authors: Mandelbrot Laurent
Published: April 2012

Fetal varicella syndrome (FVS) is due to transplacental infection by the Varicella zoster virus following maternal infection. The risks for the fetus and neonate depend on the timing. When varicella occurs around delivery, it often leads to disseminated neonatal varicella. When varicella occurs during pregnancy, transmission can occur, but is usually asymptomatic; some infants develop zoster postnatally and a few have FVS. Before 20 weeks' gestation, FVS can occur, with an incidence of about 1%. The lesions can affect the skin, limbs, central and autonomous nervous systems, eyes, cause calcifications, and growth retardation; mortality is high. Lesions typically follow one or several nerve territories, suggesting that damage results from in utero zoster following primary fetal infection. There has been little study of prenatal diagnosis of FVS. Serial ultrasound examination can detect various anomalies, magnetic resonance imaging can be of use to investigate for microphthamia and cerebral lesions, and amniocentesis can diagnose viral transmission. Prevention strategies include vaccination and post‐exposure prophylaxis with immune globulin and/or antivirals. Perspectives for treating infected fetuses in utero require further research. © 2012 John Wiley & Sons, Ltd.
Lightning occurrence characteristics in Japan for 17 years: observation results with lightning location systems of electric power utilities from 1992 to 2008
Authors: Shindo Takatoshi , Motoyama Hideki , Sakai Akira , Honma Noriyasu , Takami Jun , Shimizu Masahito , Tamura Kiyoshi , Shinjo Kazuo , Ishikawa Fumio , Ueno Yoshiyuki , Ikuta Masateru , Takahashi Daisuke
Published: April 2012

We summarize the lightning data for 17 years from 1992 to 2008 obtained with lightning location systems of nine electric power utilities in Japan and analyze them. The observed annual number of lightning flashes of which the current is more than 10 kA is 400 000–800 000 and the 50% value of the cumulative distribution of lightning peak currents is about 23 kA in recent times. The variation of lightning occurrence characteristics by areas, seasons, and so on, is clarified. Comparison of the obtained data with those obtained by another lightning location system is also made. The relationship between lightning occurrence and climate is discussed. © 2012 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Advanced error concealment for 1Seg video communication considering error propagation inside a frame
Authors: Wang Jun , Goto Satoshi
Published: April 2012

Transmission of compressed video over error‐prone channels may result in packet losses or errors, which can significantly degrade the image quality. Such degradation becomes even worse in 1Seg video broadcasting, which is widely used in Japan and Brazil for mobile phone TV services recently, where errors are drastically increased and the lost areas are contiguous. Therefore, the errors in the earlier concealed MBs (macro blocks) may propagate to the MBs later to be concealed inside the same frame (spatial domain). The error concealment (EC) is used to recover the lost data by the redundancy in videos. Aiming at spatial error propagation (SEP) reduction, this paper proposes an SEP‐reduction‐based EC (SEPEC). In SEPEC, besides the mismatch distortion in the current MB, the potential propagated mismatch distortion in the following to be concealed MBs is also minimized. Also, two extensions of SEPEC, i.e. SEPEC with refined search and SEPEC with multiple layer match, are discussed. Compared with previous work, the experiments show SEPEC achieves much better performance of video recovery and excellent trade‐off between quality and computation in 1Seg broadcasting. © 2012 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
A learning Fuzzy Petri net model
Authors: Feng Liangbing , Obayashi Masanao , Kuremoto Takashi , Kobayashi Kunikazu
Published: April 2012

Fuzzy Petri net (FPN) is a powerful modeling tool for the construction of knowledge systems. In this paper, we propose a new learning model tool—learning fuzzy Petri net (LFPN). In contrast with the existing FPN, there are three extensions in the new model: (i) the place can possess different tokens which represent different propositions; (ii) these propositions have different degrees of truth toward different transitions; and (iii) the truth degree of the proposition can be learned by adjusting the arc's weight function. The LFPN model obtains the capability of learning fuzzy production rules through truth degree updating. The LFPN learning algorithm which introduces network learning method into Petri net update is proposed and the convergence of algorithm is analyzed. Finally, for the purpose of certification of the effectiveness of the proposed model, LFPN is used to model the Web service discovery. The result of the simulation shows that the proposed LFPN is useful and effective. © 2012 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
A constant DC voltage control‐based strategy for an active power quality compensator in electrified railways with improved response
Authors: Ishikura Norio , Ishibashi Keisuke , Hiraki Eiji , Tanaka Toshihiko
Published: April 2012

This paper proposes a constant DC voltage control‐based strategy for an active power quality compensator (APQC) used in electrified railways. The proposed strategy consists of only an I‐PD‐based constant DC capacitor voltage control with an added moving‐average type low‐pass filter (LPF). The added LPF improves the response of the constant DC capacitor voltage control for the APQC. Thus we offer the simplest control method for the APQC used in electrified railways with improved response. The basic principle of the proposed control strategy is discussed in detail, and then confirmed by digital computer simulation using the PSIM software. A prototype experimental model is constructed and tested. Experimental results demonstrate that balanced source currents with unity power factor are obtained on the primary side of the Scott transformer in the traction substation systems, improving the response by one‐fourth as compared to that of the previously proposed control method. © 2012 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Transformation of China's sovereign wealth fund since the 2008‐2009 global crisis
Authors: Wu Friedrich , Goh Christine , Hajela Ruchi
Published: April 2012

China Investment Corporation (CIC) transformed its initial investment strategy of focusing mainly on the US financial sector during 2007‐2008 into a new strategy of diversified investments across geography and sectors since 2009. Massive financial losses and domestic political backlash during the global financial crisis of 2008 gave impetus to CIC's rethinking of strategy. In the midst of the crisis, CIC engineered a capacity‐building and reorganization exercise to reposition itself for a new strategy that has since allowed for more diversification of investments. A more receptive global investment climate for sovereign wealth funds has also aided CIC's efforts to present itself as a responsible global investor and facilitated its investments. Postcrisis, CIC's new strategy of diversification is characterized by continued investments in the financial sector, but with new investments increasingly directed to real sectors of energy, natural resources, and real estate in both developed and emerging economies. Notwithstanding a global recovery that is fraught with uncertainties, CIC's judicious timing in making diversified investments, and its attention to reducing risks and enhancing returns, have been rewarded by an impressive turnaround in performance since 2009. Going forward, the success and sustainability of the new strategy will be contingent on how well CIC can navigate domestic bureaucratic rivalry and the shifting climate of the international investment environment in the medium to long term. Ultimately, CIC's shareholder, the government of the People's Republic of China (PRC), holds the key to its future direction and goals. © 2012 Wiley Periodicals, Inc.
Esophagogastric Trauma in Scotland
Authors: Skipworth Richard J. E. , McBride Olivia M. B. , Kerssens Jan J. , Paterson‐Brown Simon
Published: April 2012

Background

This study was designed to investigate the incidence of esophageal (ET) and gastric trauma (GT) in Scotland and to identify factors associated with adverse outcome.

Methods

Population‐based study of a prospective multicenter database of 52,887 trauma patients, admitted to 25 hospitals from 1992 to 2002.

Results

Thirty patients [0.06 %; median age, 32 year (range, 15–79); 86.7 % male] sustained ET [17 (56.7 %) blunt vs. 13 (43.3 %) penetrating]. The most common causes of injury were road traffic accidents (RTAs; n = 11; 36.7 %) and assaults (n = 10; 33.3 %). Most patients (n = 25; 83.3 %) had injury severity scores (ISS) >15, consistent with severe trauma. Fifteen patients (50 %) underwent surgery, of whom 8 (53.3 %) died. Another 13 patients died, yielding an overall mortality rate of 70 %. In contrast, 149 patients [0.29 %; median age, 28 year (range, 13–74); 90.6 % male] sustained GT [124 (83.2 %) penetrating vs. 25 (16.8 %) blunt]. The predominant cause was assault (n = 119; 79.9 %). Most patients (n = 134; 89.9 %) underwent surgery, of which 23 (17.2 %) died. Another 12 patients died, yielding an overall mortality rate of 23.5 %. Factors associated independently with GT mortality included higher ISS, lower Glasgow coma scale (GCS), and hemodynamic compromise.

Conclusions

Esophagogastric trauma occurs predominantly in young males. The incidence of GT, although low, is five times that of ET. Predominant mechanisms of GT are penetrating compared with blunt for ET. Both ET and GT are commonly found in the presence of other multiple injuries, and are associated with high mortality. Operative management of GT is associated with reduced mortality, but outcome is worse for patients with hemodynamic compromise, low GCS, and high ISS.
Genetic Implications of Rare Uraninite and Pyrite in Quartz-Pebble Conglomerates from Sundargarh District of Orissa, Eastern India
Authors: Kumar Ajay , S.Venkatesh A. , Babu P. V. Ramesh , Nayak S.
Published: April 2012

Petrographic and EPMA studies reveal the presence of discrete grains of uraninite and pyrite are being reported for the first time in quartz-pebble conglomerates from western margin of Bonai granite pluton, Sundargarh district, Orissa. Uraninite grains (2-3 μ in size) are subrounded to muffin shaped which show variation in UO2 (63.86 to 71.73 wt %), ThO2 (5.48 to 6.42 wt %) and RE2O3 (1.57 to 2.23 wt %). Pegmatitic source of uraninite is revealed by comparing UO2, ThO2, PbO, CaO content and ratios of UO2/ThO2 and CaO/ThO2 in uraninites from pegmatite and other environments and areas. Subrounded to muffin shape of uraninite, their association with subrounded pyrite and heavies like zircon, tourmaline, chromite, monazite, magnetite and their comparable chemistry with well established quartz-pebble conglomerates of India and world are indicative of their detrital origin. Pyrite, minor chalcopyrite and rare galena are observed as sulphide phases in conglomerate. Variable shapes of pyrite, their low Co (up to 0.16 wt %) and Ni contents (up to 0.09 wt %) and Co/Ni ratio less than 1.0 (mean= 0.63) favours sedimentary/diagenetic origin.
Recommendations on follow-up strategies for idiopathic vocal fold paralysis: evidence-based review
Authors: Tsikoudas A , Paleri V , El-Badawey M Reda , Zammit-Maempel I
Published: April 2012

Introduction:

Vocal fold paralysis can be an early warning sign of serious extra-laryngeal pathology. Even if imaging investigations show no pathology, there is always concern about the emergence of new pathology in the future. There is currently no consensus on the best follow-up protocol for vocal fold paralysis patients with no abnormalities on investigation.

Methods:

Systematic review, using an Ovid and Medline database search of papers written in the English language and published in the last 20 years.

Results:

Eight relevant studies were identified. Not all of them were directly comparable. A narrative review of the studies is presented and conclusions are drawn.

Conclusion:

Current diagnostic modalities are sufficiently reliable and sensitive to diagnose any significant existing extra-laryngeal pathology. Thus, once initial investigation (including computed tomography) has concluded, no further follow up is necessary.
NEW LIGHT ON THE LABYRINTH FRESCO FROM THE PALACE AT KNOSSOS
Authors: Shaw M.C.
Published: April 2012

Considered here is the ‘Labyrinth Fresco’ (or ‘Maze Fresco’), fragments of which were found by Sir Arthur Evans in the Minoan palace at Knossos. Interestingly, the pattern was rendered through engraving, with the exclusively red colour used applied within the grooves. Oddly, this design is very similar to one shown as a patterned floor in a recently excavated wall painting discovered by the Austrian excavator Manfred Bietak, at Tell el Dab'a, in the Nile Delta area of Egypt, where it depicts an arena used for bull leaping. The present article therefore raises the question of whether the ‘Labyrinth Fresco’ from Knossos was actually decoration on a patterned plaster floor rather than a wall, and could have acted as the model for the one depicted in the Tell el Dab'a painting. One possible explanation for this phenomenon is that the Tell el Dab'a painters were Greek expatriate artists – a matter that prompts questions about actual international contacts between the Aegean and Egypt in the mid-second millenniumbcThe paintings in Egypt clearly imply travelling Aegean artists, though further and more formal contacts probably also existed between the two countries.
The heterogeneous multiscale method
Authors: Abdulle Assyr , Weinan E , Engquist Björn , Vanden-Eijnden Eric
Published: April 2012

The heterogeneous multiscale method (HMM), a general framework for designing multiscale algorithms, is reviewed. Emphasis is given to the error analysis that comes naturally with the framework. Examples of finite element and finite difference HMM are presented. Applications to dynamical systems and stochastic simulation algorithms with multiple time scales, spall fracture and heat conduction in microprocessors are discussed.
Mathematical cancer therapy planning in deep regional hyperthermia
Authors: Deuflhard Peter , Schiela Anton , Weiser Martin
Published: April 2012

This paper surveys the mathematics required for a typically challenging problem from computational medicine: cancer therapy planning in deep regional hyperthermia. In the course of many years of close cooperation with clinics, the medical problem has given rise to many subtle mathematical problems, some of which were unsolved when the project started. Efficiency of numerical algorithms, i.e., computational speed and monitored reliability, plays a decisive role in the medical treatment. Off-the-shelf software had turned out to be insufficient to meet the requirements of medicine. Instead, new mathematical theory as well as new numerical algorithms had to be developed. In order to make our algorithms useful in the clinical environment, new visualization software, i.e., a ‘virtual lab’, including three-dimensional geometry processing of individual virtual patients, had to be designed and implemented. Moreover, before the problems could be attacked by numerical algorithms, careful mathematical modelling had to be done. Finally, parameter identification and constrained optimization for the PDEs had to be newly analysed and realized over the individual patient's geometry. Our new techniques had an impact on the specificity of the treatment of individual patients and on the construction of an improved hyperthermia applicator.
Evaluation of snowmelt simulation in the Weather Research and Forecasting model
Authors: Jin Jiming , Wen Lijuan
Published: April 2012

The objective of this study is to better understand and improve snowmelt simulations in the advanced Weather Research and Forecasting (WRF) model by coupling it with the Community Land Model (CLM) Version 3.5. Both WRF and CLM are developed by the National Center for Atmospheric Research. The automated Snow Telemetry (SNOTEL) station data over the Columbia River Basin in the northwestern United States are used to evaluate snowmelt simulations generated with the coupled WRF‐CLM model. These SNOTEL data include snow water equivalent (SWE), precipitation, and temperature. The simulations cover the period of March through June 2002 and focus mostly on the snowmelt season. Initial results show that when compared to observations, WRF‐CLM significantly improves the simulations of SWE, which is underestimated when the release version of WRF is coupled with the Noah and Rapid Update Cycle (RUC) land surface schemes, in which snow physics is oversimplified. Further analysis shows that more realistic snow surface energy allocation in CLM is an important process that results in improved snowmelt simulations when compared to that in Noah and RUC. Additional simulations with WRF‐CLM at different horizontal spatial resolutions indicate that accurate description of topography is also vital to SWE simulations. WRF‐CLM at 10 km resolution produces the most realistic SWE simulations when compared to those produced with coarser spatial resolutions in which SWE is remarkably underestimated. The coupled WRF‐CLM provides an important tool for research and forecasts in weather, climate, and water resources at regional scales.
The role of the extracellular loops of the CGRP receptor, a family B GPCR
Authors: Barwell James , Woolley Michael J. , Wheatley Mark , Conner Alex C. , Poyner David R.
Published: April 2012

The CGRP (calcitonin gene-related peptide) receptor is a family B GPCR (G-protein-coupled receptor). It consists of a GPCR, CLR (calcitonin receptor-like receptor) and an accessory protein, RAMP1 (receptor activity-modifying protein 1). RAMP1 is needed for CGRP binding and also cell-surface expression of CLR. There have been few systematic studies of the ECLs (extracellular loops) of family B GPCRs. However, they are likely to be especially important for the interaction of the N-termini of the peptide agonists that are the natural agonists for these receptors. We have carried out alanine scans on all three ECLs of CLR, as well as their associated juxtamembrane regions. Residues within all three loops influence CGRP binding and receptor activation. Mutation of Ala203 and Ala206 on ECL1 to leucine increased the affinity of CGRP. Residues at the top of TM (transmembrane) helices 2 and 3 influenced CGRP binding and receptor activation. L351A and E357A in TM6/ECL3 reduced receptor expression and may be needed for CLR association with RAMP1. ECL2 seems especially important for CLR function; of the 16 residues so far examined in this loop, eight residues reduce the potency of CGRP at stimulating cAMP production when mutated to alanine.
Histone transfer among chaperones
Authors: Liu Wallace H. , Churchill Mair E.A.
Published: April 2012

The eukaryotic processes of nucleosome assembly and disassembly govern chromatin dynamics, in which histones exchange in a highly regulated manner to promote genome accessibility for all DNA-dependent processes. This regulation is partly carried out by histone chaperones, which serve multifaceted roles in co-ordinating the interactions of histone proteins with modification enzymes, nucleosome remodellers, other histone chaperones and nucleosomal DNA. The molecular details of the processes by which histone chaperones promote delivery of histones among their many functional partners are still largely undefined, but promise to offer insights into epigenome maintenance. In the present paper, we review recent findings on the histone chaperone interactions that guide the assembly of histones H3 and H4 into chromatin. This evidence supports the concepts of histone post-translational modifications and specific histone chaperone interactions as guiding principles for histone H3/H4 transactions during chromatin assembly.
The mechanical properties of kinesin-1: a holistic approach
Authors: Jeppesen George M. , Hoerber J.K. Heinrich
Published: April 2012

During the last 25 years, a vast amount of research has gone into understanding the mechanochemical cycle of kinesin-1 and similar processive motor proteins. An experimental method that has been widely used to this effect is the in vitro study of kinesin-1 molecules moving along microtubules while pulling a bead, the position of which is monitored optically while trapped in a laser focus. Analysing results from such experiments, in which thermally excited water molecules are violently buffeting the system components, can be quite difficult. At low loads, the effect of the mechanical properties of the entire molecule must be taken into account, as stalk compliance means the bead position recorded is only weakly coupled to the movement of the motor domains, the sites of ATP hydrolysis and microtubule binding. In the present review, findings on the mechanical and functional properties of the various domains of full-length kinesin-1 molecules are summarized and a computer model is presented that uses this information to simulate the motion of a bead carried by a kinesin molecule along a microtubule, with and without a weak optical trap present. A video sequence made from individual steps of the simulation gives a three-dimensional visual insight into these types of experiment at the molecular level.
H1 and HMGB1: modulators of chromatin structure
Authors: Thomas Jean O. , Stott Katherine
Published: April 2012

Histone H1 and HMGB1 (high-mobility group protein B1) are the most abundant chromosomal proteins apart from the core histones (on average, one copy per nucleosome and per ten nucleosomes respectively). They are both highly mobile in the cell nucleus, with high on/off rates for binding. In vivo and in vitro evidence shows that both are able to organize chromatin structure, with H1 binding resulting in a more stable structure and HMGB1 binding in a less stable structure. The binding sites for H1 and HMGB1 in chromatin are partially overlapping, and replacement of H1 by HMGB1 through the highly dynamic nature of their binding, possibly facilitated by interaction between them, could result in switching of chromatin states. Binding of HMGB1 to DNA or chromatin is regulated by its long and highly acidic tail, which is also involved in H1 binding. The present article focuses mainly on HMGB1 and its interaction with chromatin and H1, as well as its chaperone role in the binding of certain transcription factors (e.g. p53) to their cognate DNA.
Automated gene-model curation using global discriminative learning
Authors: Bernal Axel , Crammer Koby , Pereira Fernando
Published: April 2012

Motivation: Gene-model curation creates consensus gene models by combining multiple sources of protein-coding evidence that may be incomplete or inconsistent. To date, manual curation still produces the highest quality models. However, manual curation is too slow and costly to be completed even for the most important organisms. In recent years, machine-learned ensemble gene predictors have become a viable alternative to manual curation. Current approaches make use of signal and genomic region consistency among sources and some voting scheme to resolve conflicts in the evidence. As a further step in that direction, we have developed eCRAIG (ensemble CRAIG), an automated curation tool that combines multiple sources of evidence using global discriminative training. This allows efficient integration of different types of genomic evidence with complex statistical dependencies to maximize directly annotation accuracy. Our method goes beyond previous work in integrating novel non-linear annotation agreement features, as well as combinations of intrinsic features of the target sequence and extrinsic annotation features.

Results: We achieved significant improvements over the best ensemble predictors available for Homo sapiens, Caenorhabditis elegans and Arabidopsis thaliana. In particular, eCRAIG achieved a relative mean improvement of 5.1% over Jigsaw, the best published ensemble predictor in all our experiments.

Availability: The source code and datasets are both available at http://www.seas.upenn.edu/abernal/ecraig.tgz

Contact:  abernal@seas.upenn.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Voter Turnout and the National Election Studies
Authors: Burden Barry C.
Published: April 2012

Though the overreporting of voter turnout in the National Election Study (NES) is widely known, this article shows that the problem has become increasingly severe. The gap between NES and official estimates of presidential election turnout has more than doubled in a nearly linear fashion, from 11 points in 1952 to 24 points in 1996. This occurred because official voter turnout fell steadily from 1960 onward, while NES turnout did not. In contrast, the bias in House election turnout is always smaller and has increased only marginally. Using simple bivariate statistics, I find that worsening presidential turnout estimates are the result mostly of declining response rates rather than instrumentation, question wording changes, or other factors. As more peripheral voters have eluded interviewers in recent years, the sample became more saturated with self-reported voters, thus inflating reported turnout.
The Rising Hazards of Party Incumbency: A Discrete Renewal Analysis
Authors: Lin Tse-Min , Guillén Montserrat
Published: April 2012

Recent interest in voters' anti-incumbent sentiments focuses on generational change as well as public weariness with partisan control of a long duration. Theories on the electoral effects of such behaviors predict partisan cycles that suggest rising hazards of party incumbency. This article provides an analytical framework for examining changes and durations of party control in presidential elections as a discrete point process. We introduce the discrete Weibull distribution for testing contagion in the context of renewal theory and develop the notion of pseudo-periodicity for a binary process. Our findings based on this event history approach confirm the claim that party incumbency engenders rising hazards. The partisan cycles that we identified have a pseudo-period of approximately six to eight presidential terms.
Conceptions and Paradoxes of Sets
Authors: ANTONELLI G. ALDO
Published: April 2012

This paper is concerned with the way different axiom systems for set theory can be justified by appeal to such intuitions as limitation of size, predicativity, stratification, etc. While none of the different conceptions historically resulting from the impetus to provide a solution to the paradoxes turns out to rest on an intuition providing an unshakeable foundation,'each supplies a picture of the set-theoretic universe that is both useful and internally well motivated. The same is true of more recently proposed axiom systems for non-well-founded universes, and an attempt is made to motivate such axiom systems on the basis of an old and respected ‘algebraic’ intuition.
Finite Mathematics and the Justification of the Axiom of Choice
Authors: MIRAGLIA PIERLUIGI
Published: April 2012

I discuss a difficulty concerning the justification of the Axiom of Choice in terms of such informal notions such as that of iterative set. A recent attempt to solve the difficulty is by S. Lavine, who claims in his Understanding the Infinite that the axioms of set theory receive intuitive justification from their being self-evidently true in Fin(ZFC), a finite counterpart of set theory. I argue that Lavine's explanatory attempt fails when it comes to AC: in this respect Fin(ZFC) is no better off than the iterative notion.
mdv1-miR-M7-5p, located in the newly identified first intron of the latency-associated transcript of Marek’s disease virus, targets the immediate-early genes ICP4 and ICP27
Authors: Strassheim S. , Stik G. , Rasschaert D. , Laurent S.
Published: April 2012

Marek’s disease virus serotype 1 (MDV-1) is an oncogenic alphaherpesvirus causing fatal T-cell lymphoma in chickens. MDV latency is characterized by the production of latency-associated transcripts (LATs), a family of non-protein-coding spliced RNAs. A cluster of four microRNAs (cluster mdv1-miR-M8-M10) was identified, but not formally mapped, at the predicted LAT 5′ end. We established a LAT cDNA library from latently MDV-infected cell line MSB-1. We identified 22 highly variable LATs, which were due to the extensive alternative splicing of a total of 14 introns. RACE PCR confirmed the predicted 3′ end and allowed identification of the 5′ end, 400 nt upstream of the previously predicted LAT end. The LATs share their transcription start site with the microRNA-expressing transcript described previously, localizing the microRNAs to the first LAT intron and identifying the LATs as the primary transcripts of the microRNAs. We identified MDV immediate-early (IE) genesICP4andICP27as putative targets of mdv1-miR-M7-5p, the third microRNA of the cluster mdv1-miR-M8-M10. Endogenously expressed mdv1-miR-M7-5p in MSB-1 cells reduced luciferase activity significantly when microRNA-responsive elements fromICP4orICP27were cloned in the 3′ UTR of the firefly luciferase gene. ICP27 protein levels were decreased by 70 % when the mdv1-miR-M7-5p precursor was co-expressed with anICP27expression plasmid. Additionally, we showed a negative correlation between the decreased expression of mdv1-miR-M7-5p and an increase in ICP27 expression during virus reactivation. Our results suggest that, by targeting two IE genes, MDV microRNAs produced from LAT transcripts may contribute to establish and/or maintain latency.
Water HyacinthEichhornia crassipes(Mart.) Solms-Laubach Dynamics and Succession in the Nyanza Gulf of Lake Victoria (East Africa): Implications for Water Quality and Biodiversity Conservation
Authors: Gichuki John , Omondi Reuben , Boera Priscillar , Okorut Tom , Matano Ally Said , Jembe Tsuma , Ofulla Ayub
Published: April 2012

This study, conducted in Nyanza Gulf of Lake Victoria, assessed ecological succession and dynamic status of water hyacinth. Results show that water hyacinth is the genesis of macrophyte succession. On establishment, water hyacinth mats are first invaded by native emergent macrophytes,Ipomoea aquaticaForsk., andEnydra fluctuansLour., during early stages of succession. This is followed by hippo grassVossia cuspidata(Roxb.) Griff. in mid- and late stages whose population peaks during climax stages of succession with concomitant decrease in water hyacinth biomass. Hippo grass depends on water hyacinth for buoyancy, anchorage, and nutrients. The study concludes that macrophyte succession alters aquatic biodiversity and that, since water hyacinth infestation and attendant succession are a symptom of broader watershed management and pollution problems, aquatic macrophyte control should include reduction of nutrient loads and implementing multifaceted approach that incorporates biological agents, mechanical/manual control with utilization of harvested weed for cottage industry by local communities.
Lithium-Acetate-Mediated Biginelli One-Pot Multicomponent Synthesis under Solvent-Free Conditions and Cytotoxic Activity against the Human Lung Cancer Cell Line A549 and Breast Cancer Cell Line MCF7
Authors: Sachdeva Harshita , Dwivedi Diksha
Published: April 2012

Various Biginelli compounds (dihydropyrimidinones) have been synthesized efficiently and in high yields under mild, solvent-free, and eco-friendly conditions in a one-pot reaction of 1,3-dicarbonyl compounds, aldehydes, and urea/thiourea/acetyl thiourea using lithium-acetate as a novel catalyst without the addition of any proton source. Comparative catalytic efficiency of lithium-acetate and polyphosphoric acid to catalyze Biginelli condensation is also studied under neat conditions. The reaction is carried out in the absence of any solvent and represents an improvement of the classical Biginelli protocol and an advantage in comparison with FeCl3·6H2O, NiCl2·6H2O and CoCl2·6H2O that were used with HCl as a cocatalyst. Compared to classical Biginelli reaction conditions, the present method has advantages of good yields, short reaction times, and experimental simplicity. The obtained products have been identified by spectral (1H NMR and IR) data and their melting points. The prepared compounds are evaluated for anticancer activity against two human cancer cell lines (lung cancer cell line A549 and breast cancer cell line MCF7).
Optimization of Ozonation Process for the Reduction of Excess Sludge Production from Activated Sludge Process of Sago Industry Wastewater Using Central Composite Design
Authors: Subha B. , Muthukumar M.
Published: April 2012

Sago industries effluent containing large amounts of organic content produced excess sludge which is a serious problem in wastewater treatment. In this study ozonation has been employed for the reduction of excess sludge production in activated sludge process. Central composite design is used to study the effect of ozone treatment for the reduction of excess sludge production in sago effluent and to optimise the variables such as pH, ozonation time, and retention time. ANOVA showed that the coefficient determination value (R2) of VSS and COD reduction were 0.9689 and 0.8838, respectively. VSS reduction (81%) was achieved at acidic pH 6.9, 12 minutes ozonation, and retention time of 10 days. COD reduction (87%) was achieved at acidic pH 6.7, 8 minutes of ozonation time, and retention time of 6 days. Low ozonation time and high retention time influence maximum sludge reduction, whereas low ozonation time with low retention time was effective for COD reduction.
Imaging Review of Skeletal Tumors of the Pelvis Malignant Tumors and Tumor Mimics
Authors: Girish Gandikota , Finlay Karen , Fessell David , Pai Deepa , Dong Qian , Jamadar David
Published: April 2012

Malignant lesions of the pelvis are not uncommon and need to be differentiated from benign lesions and tumor mimics. Appearances are sometimes nonspecific leading to consideration of a broad differential diagnosis. Clinical history, anatomic location, and imaging characterization can help narrow the differential diagnosis. The focus of this paper is to demonstrate the imaging features and the role of plain films, computed tomography, and magnetic resonance imaging for detecting and characterizing malignant osseous pelvic lesions and their common mimics.
Modeling Focused Ultrasound Exposure for the Optimal Control of Thermal Dose Distribution
Authors: Sassaroli E. , Li K. C. P. , O'Neill B. E.
Published: April 2012

Preclinical studies indicate that focused ultrasound at exposure conditions close to the threshold for thermal damage can increase drug delivery at the focal region. Although these results are promising, the optimal control of temperature still remains a challenge. To address this issue, computer-simulated ultrasound treatments have been performed. When the treatments are delivered without taking into account the cooling effect exerted by the blood flow, the resulting thermal dose is highly variable with regions of thermal damage, regions of underdosage close to the vessels, and areas in between these two extremes. When the power deposition is adjusted so that the peak thermal dose remains close to the threshold for thermal damage, the thermal dose is more uniformly distributed but under-dosage is still visible around the thermally significant vessels. The results of these simulations suggest that, for focused ultrasound, as for other delivery methods, the only way to control temperature is to adjust the average energy deposition to compensate for the presence of thermally significant vessels in the target area. By doing this, we have shown that it is possible to reduce the temperature heterogeneity observed in focused ultrasound thermal treatments.
Flavonoid-Deficient Mutants in Grass Pea (Lathyrus sativusL.): Genetic Control, Linkage Relationships, and Mapping with Aconitase and S-Nitrosoglutathione Reductase Isozyme Loci
Authors: Talukdar Dibyendu
Published: April 2012

Two flavonoid-deficient mutants, designated asfldL-1andfldL-2, were isolated in EMS-mutagenized (0.15%, 10 h) M2progeny of grass pea (Lathyrus sativusL.). Both the mutants contained total leaf flavonoid content only 20% of their mother varieties. Genetic analysis revealed monogenic recessive inheritance of the trait, controlled by two different nonallelic loci. The two mutants differed significantly in banding patterns of leaf aconitase (ACO) and S-nitrosoglutathione reductase (GSNOR) isozymes, possessing unique bands inAco 1, Aco 2,andGsnor 2loci. Isozyme loci inherited monogenically showing codominant expression in F2(1 : 2 : 1) and backcross (1 : 1) segregations. Linkage studies and primary trisomic analysis mappedAco 1andfld 1loci on extra chromosome of trisomic-I andAco 2,fld 2,andGsnor 2on extra chromosome of trisomic-IV in linked associations.
Efficacy of Some Botanical Extracts againstTrogoderma granariumin Wheat Grains with Toxicity Evaluation
Authors: Derbalah Aly S.
Published: April 2012

In an attempt to find alternative control methods for stored products insects, extracts of seven plant species (Cassia senna, Caesalpinia gilliesii, Thespesia populnea var. acutiloba, Chrysanthemum frutescens, Euonymus japonicus, Bauhinia purpurea, andCassia fistula) were evaluated under laboratory conditions for their ability to protect wheat (Triticumspp.) grains againstTrogoderma granariuminsect. Moreover, gas chromatography-mass spectrometry (GC-MS) analysis was carried to identify the chemical components of the most effective plant extract againstT. granarium. Furthermore, the safety of the most effective plant extract was evaluated with respect to biochemical and histological changes in treated rats relative to control. The results revealed that, the tested botanical extracts showed high efficiency againstT. granariumwith respect to mortality and progeny of the adults.C. sennawas the most effective botanical extract againstT. granarium. The GC-MS analysis of the most effective plant extract showed the presence of different bioactive compounds that is known by its insecticidal activity. The most effective plant extract showed no toxicity on treated rats relative to control with respect to biochemical and histological changes. The results suggest the ability of using these plant extracts for wheat grains protection as a safe alternative to insecticides.
Trace Metal Content of Sediments Close to Mine Sites in the Andean Region
Authors: Yacoub Cristina , Pérez-Foguet Agustí , Miralles Nuria
Published: April 2012

This study is a preliminary examination of heavy metal pollution in sediments close to two mine sites in the upper part of the Jequetepeque River Basin, Peru. Sediment concentrations of Al, As, Cd, Cu, Cr, Fe, Hg, Ni, Pb, Sb, Sn, and Zn were analyzed. A comparative study of the trace metal content of sediments shows that the highest concentrations are found at the closest points to the mine sites in both cases. The sediment quality analysis was performed using the threshold effect level of the Canadian guidelines (TEL). The sediment samples analyzed show that potential ecological risk is caused frequently at both sites by As, Cd, Cu, Hg, Pb, and Zn. The long-term influence of sediment metals in the environment is also assessed by sequential extraction scheme analysis (SES). The availability of metals in sediments is assessed, and it is considered a significant threat to the environment for As, Cd, and Sb close to one mine site and Cr and Hg close to the other mine site. Statistical analysis of sediment samples provides a characterization of both subbasins, showing low concentrations of a specific set of metals and identifies the main characteristics of the different pollution sources. A tentative relationship between pollution sources and possible ecological risk is established.
A decision‐support scheme that generates contingency plans and prioritizes action during pest outbreaks*
Authors: Sunley R. , Cannon R. , Eyre D. , Baker R. H. A. , Battisti A. , Giltrap N. , Griessinger D.
Published: April 2012

The decision‐support scheme (DSS) for action at outbreaks developed under PRATIQUE (Enhancements of Pest Risk Analysis Techniques) brings together a set of guidance and tools, using the CAPRA application. The DSS is initiated by the collation of key information on the current outbreak situation, and then compares candidate measures in order to derive a strategy for action and/or contingency. It is hoped that this deliverable will assist national plant protection organizations (NPPOs) to address and justify eradication campaigns effectively. The rationale behind the DSS and its key features are presented and discussed.
Analysis of exotic fruit fly trapping networks*
Authors: Quilici S. , Donner P.
Published: April 2012

This paper reviews the main networks of fruit fly trapping worldwide. The general result highlights the global effectiveness of large and structured fruit fly surveillance networks established according to current international standards. However, there is a considerable contrast among national approaches, depending mainly on the frequency of fruit fly detections. The cost of surveillance networks is high and frequently constitutes a limiting factor for their correct implementation according to the recommended standards. This highlights the importance of research to improve the effectiveness of trapping systems (which refers to the combination of an attractant, a dispenser and a type of trap). A cost‐benefit analysis to compare the actual cost of surveillance with a no‐surveillance strategy and the cost of expected damage would be a promising tool. Ideally, such analysis should take into account the complex of tephritid species already present in a given country and the estimated cost of increased damage on fruit production or increased control costs.
Modelling and mapping spread in pest risk analysis: a generic approach*
Authors: Kehlenbeck H. , Robinet C. , van der Werf W. , Kriticos D. , Reynaud P. , Baker R.
Published: April 2012

Assessing the likelihood and magnitude of spread is one of the cornerstones of pest risk analysis (PRA), and is usually based on qualitative expert judgment. This paper proposes a suite of simple ecological models to support risk assessors who also wish to estimate the rate and extent of spread, e.g. when modelling the dynamics of invasion and the economic impacts that may result. Models are based on simple ecological principles, such as logistic growth, radial range expansion and population growth in combination with dispersal. Different models capture different perspectives of the spread process, being based on pest density or simply presence/absence, and they compare spatially explicit and spatially implicit approaches. A case study on Diabrotica virgifera virgifera is provided for illustration. The suite of models requires further development and testing with the risk assessment community building familiarity before their more general application in PRA.