bluuebunny/crossref_metadata_2025 huggingface dataset:
Globalization of twisted partial actions
Authors: Dokuchaev M. , Exel R. , Simón J.
Published: April 2010

Let

A

\mathcal {A}

be a unital ring which is a product of possibly infinitely many indecomposable rings. We establish a criteria for the existence of a globalization for a given twisted partial action of a group on

A

.

\mathcal {A}.

If the globalization exists, it is unique up to a certain equivalence relation and, moreover, the crossed product corresponding to the twisted partial action is Morita equivalent to that corresponding to its globalization. For arbitrary unital rings the globalization problem is reduced to an extendibility property of the multipliers involved in the twisted partial action.
Representation and index theory for Toeplitz operators
Authors: Murphy G.
Published: April 2010

We study Toeplitz operators on the Hardy spaces of connected compact abelian groups and of tube-type bounded symmetric domains. A representation theorem for these operators and for classes of abstract Toeplitz elements in C*-algebras is proved. This is used to give a unified treatment to index theory in this setting, and a variety of new index theorems are proved that generalize the Gohberg–Krein theorem for Toeplitz operators on the Hardy space of the unit circle in the plane.
A signal–noise model for significance analysis of ChIP-seq with negative control
Authors: Xu Han , Handoko Lusy , Wei Xueliang , Ye Chaopeng , Sheng Jianpeng , Wei Chia-Lin , Lin Feng , Sung Wing-Kin
Published: April 2010

Motivation:ChIP-seq is becoming the main approach to the genome-wide study of protein–DNA interactions and histone modifications. Existing informatics tools perform well to extract strong ChIP-enriched sites. However, two questions remain to be answered: (i) to which extent is a ChIP-seq experiment able to reveal the weak ChIP-enriched sites? (ii) are the weak sites biologically meaningful? To answer these questions, it is necessary to identify the weak ChIP signals from background noise.

Results: We propose a linear signal–noise model, in which a noise rate was introduced to represent the fraction of noise in a ChIP library. We developed an iterative algorithm to estimate the noise rate using a control library, and derived a library-swapping strategy for the false discovery rate estimation. These approaches were integrated in a general-purpose framework, named CCAT (Control-based ChIP-seq Analysis Tool), for the significance analysis of ChIP-seq. Applications to H3K4me3 and H3K36me3 datasets showed that CCAT predicted significantly more ChIP-enriched sites that the previous methods did. With the high sensitivity of CCAT prediction, we revealed distinct chromatin features associated to the strong and weak H3K4me3 sites.

Availability:  http://cmb.gis.a-star.edu.sg/ChIPSeq/tools.htm

Contact:  sungk@gis.a-star.edu.sg; asflin@ntu.edu.sg

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Modular analysis of gene expression data with R
Authors: Csárdi Gábor , Kutalik Zoltán , Bergmann Sven
Published: April 2010

Summary: Large sets of data, such as expression profiles from many samples, require analytic tools to reduce their complexity. The Iterative Signature Algorithm (ISA) is a biclustering algorithm. It was designed to decompose a large set of data into so-called ‘modules’. In the context of gene expression data, these modules consist of subsets of genes that exhibit a coherent expression profile only over a subset of microarray experiments. Genes and arrays may be attributed to multiple modules and the level of required coherence can be varied resulting in different ‘resolutions’ of the modular mapping. In this short note, we introduce two BioConductor software packages written in GNU R: The isa2 package includes an optimized implementation of the ISA and the eisa package provides a convenient interface to run the ISA, visualize its output and put the biclusters into biological context. Potential users of these packages are all R and BioConductor users dealing with tabular (e.g. gene expression) data.

Availability:  http://www.unil.ch/cbg/ISA

Contact:  sven.bergmann@unil.ch
Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures
Authors: Wirawan Adrianto , Kwoh Chee Keong , Schmidt Bertil
Published: March 2010

Summary: Multiple sequence alignment is an important tool in bioinformatics. Although efficient heuristic algorithms exist for this problem, the exponential growth of biological data demands an even higher throughput. The recent emergence of multi-core technologies has made it possible to achieve a highly improved execution time for many bioinformatics applications. In this article, we introduce an implementation that accelerates the distance matrix computation on x86 and Cell Broadband Engine, a homogeneous and heterogeneous multi-core system, respectively. By taking advantage of multiple processors as well as Single Instruction Multiple Data vectorization, we were able to achieve speed-ups of two orders of magnitude compared to the publicly available implementation utilized in ClustalW.

Availability and Implementation: Source codes in C are publicly available at https://sourceforge.net/projects/distmatcomp/

Contact:  adri0004@ntu.edu.sg
The Role of Callose Deposition Along Plasmodesmata in Nematode Feeding Sites
Authors: Hofmann Julia , Youssef-Banora Mohamed , de Almeida-Engler Janice , Grundler Florian M. W.
Published: April 2010

Infective second-stage juveniles of the obligate plant-parasitic root-knot and cyst nematodes invade plant roots to induce specialized feeding structures. Here, we present data on the distribution of plasmodesmata in cell walls of syncytia and giant cells induced by cyst and root-knot nematodes. An Arabidopsis and a tobacco line were used, containing viral movement proteins fused to green fluorescent protein as a localization marker for plasmodesmata. Plasmodesmata were detected in walls between giant cells but also in walls toward neighboring cells. In syncytia, plasmodesmata were mainly detected at later stages. In young syncytia, few plasmodesmata were observed and a specific temporal callose deposition along plasmodesmata indicated impaired symplasmic exchange. In order to study the relevance of callose deposition for successful cyst nematode development in Arabidopsis, two mutant lines inhibited in callose synthesis and degradation, respectively, were used in nematode infection assays. Histological analyses showed that syncytia were smaller when callose degradation was reduced, indicating a significant importance of this process to cyst nematode development.
dl-β-Aminobutyric Acid–Induced Resistance of Potato Against Phytophthora infestans Requires Salicylic Acid but Not Oxylipins
Authors: Eschen-Lippold Lennart , Altmann Simone , Rosahl Sabine
Published: April 2010

Inducing systemic resistance responses in crop plants is a promising alternative way of disease management. To understand the underlying signaling events leading to induced resistance, functional analyses of plants defective in defined signaling pathway steps are required. We used potato, one of the economically most-important crop plants worldwide, to examine systemic resistance against the devastating late blight pathogen Phytophthora infestans, induced by treatment with dl-β-aminobutyric acid (BABA). Transgenic plants impaired in either the 9-lipoxygenase pathway, which produces defense-related compounds, or the 13-lipoxygenase pathway, which generates jasmonic acid–derived signals, expressed wild-type levels of BABA-induced resistance. Plants incapable of accumulating salicylic acid (SA), on the other hand, failed to mount this type of induced resistance. Consistently, treatment of these plants with the SA analog 2,6-dichloroisonicotinic acid restored BABA-induced resistance. Together, these results demonstrate the indispensability of a functional SA pathway for systemic resistance in potato induced by BABA.
Interaction ofRhizoctonia solaniandRhizopus stoloniferCausing Root Rot of Sugar Beet
Authors: Hanson L. E.
Published: April 2010

In recent years, growers in Michigan and other sugar beet (Beta vulgaris) production areas of the United States have reported increasing incidence of root rot with little or no crown or foliar symptoms in sugar beet with Rhizoctonia crown and root rot. In addition, Rhizoctonia-resistant beets have been reported with higher levels of disease than expected. In examining beets with Rhizoctonia root rot in Michigan, over 50% of sampled roots had a second potential root rot pathogen, Rhizopus stolonifer. Growing conditions generally were not conducive to disease production by this pathogen alone, so we investigated the potential for interaction between these two pathogens. In greenhouse tests, four of five sugar beet varieties had more severe root rot symptoms when inoculated with both pathogens than when inoculated with either pathogen alone. This synergism occurred under conditions that were not conducive to disease production by R. stolonifer. Host resistance to Rhizoctonia crown and root rot reduced diseases severity, but was insufficient to control the disease when both pathogens were present. This raises concerns about correct disease diagnosis and management practices and indicates that a root rot complex may be important on sugar beet in Michigan.
Bemisia afersensu lato, a Vector ofSweet potato chlorotic stunt virus
Authors: Gamarra Heidy A. , Fuentes Segundo , Morales Francisco J. , Glover Rachel , Malumphy Chris , Barker Ian
Published: April 2010

Bemisia tabaci biotype B is considered to be the primary vector of Sweet potato chlorotic stunt virus (SPCSV, Crinivirus). However, Trialeurodes abutiloneus also has been shown to transmit SPCSV in a semipersistent manner. Mixed infection of SPCSV with the aphid-transmitted Sweet potato feathery mottle virus (SPFMV, Potyvirus) causes sweetpotato (Ipomoea batatas) virus disease (SPVD), the major virus disease affecting this crop. High populations of B. afer sensu lato are seasonally associated with sweetpotato in Peru during times of low B. tabaci incidence. The transmission of SPCSV (in single and double infection with SPFMV) by laboratory-reared B. afer sensu lato and B. tabaci biotype B was investigated. For SPCSV transmission efficiency, individual adult insects were allowed 48 h for acquisition and inoculation access periods at both 20 and 25°C. SPCSV was transmitted by both whiteflies, with similar transmission efficiency when the virus was acquired from plants singly infected by SPCSV or doubly infected with SPCSV and SPFMV, at 20 and 25°C. We conclude that B. afer sensu lato is a newly identified vector of SPCSV. This finding may have important epidemiological significance for the spread of SPCSV and SPVD.
Molecular Genetic Characterization of Olpidium virulentus Isolates Associated with Big-Vein Diseased Lettuce Plants
Authors: Maccarone L. D. , Barbetti M. J. , Sivasithamparam K. , Jones R. A. C.
Published: April 2010

Lettuce plants showing symptoms of lettuce big-vein disease were collected from fields in the Perth Metropolitan region of southwest Australia. When root extracts from each plant were tested by polymerase chain reaction (PCR) using primers specific to the rDNA internal transcribed spacer (ITS) region of Olpidium brassicae and O. virulentus, only O. virulentus was detected in each of them. The nucleotide sequences of the complete rDNA ITS regions of isolates from five of the root samples and 10 isolates of O. virulentus from Europe and Japan showed 97.9 to 100% identities. However, with the six O. brassicae isolates, their identities were only 76.9 to 79.4%. On phylogenetic analysis of the complete rDNA-ITS region sequences of the five Australian isolates and 10 others, the Australian isolates fitted within two clades of O. virulentus (I and II), and within clade I into two of its four subclades (Ia and Id). Japanese isolates had greatest sequence diversity fitting into both clades and into all of clade I subclades except Ib, while European isolates were restricted to subclades Ib and Id. When the partial rDNA-ITS region sequences of two additional southwest Australian isolates, four from Europe, and four from the Americas were included in the analyses, the Australian isolates were within O. virulentus subclades Ia and Id, the European isolates within subclade Ic, and the American isolates within subclades Ia and Ib. These findings suggest that there may have been at least three separate introductions of O. virulentus into the isolated Australian continent since plant cultivation was introduced following its colonization by Europeans. They also have implications regarding numbers of different introductions to other isolated regions. Lettuce big-vein associated virus and Mirafiori lettuce big-vein virus were both detected when symptomatic lettuce leaf tissue samples corresponding to the root samples from southwest Australia were tested using virus-specific primers in reverse transcription–PCR, so presence of both viruses was associated with O. virulentus occurrence.
Development of Anthracnose on Grain Sorghum Hybrids Inoculated with Recently Described Pathotypes of Colletotrichum sublineolum Found in Arkansas
Authors: Moore J. W. , Ditmore M. , TeBeest D. O.
Published: April 2010

Sorghum anthracnose, caused by Colletotrichum sublineolum, is found in most grain-sorghum-producing areas, including Arkansas. Yield losses can be severe in susceptible sorghum hybrids, suggesting that host resistance will continue to be critical for maintaining high yields. However, genetic control is often unsuccessful because of haplotype and pathotype variability within the C. sublineolum population. The objective of this research was to assess the levels of resistance of selected grain sorghum hybrids to isolates of the recently described pathotypes of C. sublineolum found in Arkansas. Field experiments were conducted in 2005 and 2006 to evaluate the reaction of 10 sorghum hybrids to eight C. sublineolum pathotypes by collecting anthracnose severity ratings at 7, 14, 21, and 28 days after inoculation. Based on these disease severity ratings, the area under the disease progress curve was calculated for each pathotype by hybrid interaction. These data showed that different levels of resistance are available in the current grain sorghum hybrids to different pathotypes. Cargill 888Y was resistant to all pathotypes in both years. However, Asgrow A571, DEKALB DKS53-11, FFR 318, and Pioneer 84G62 were moderately susceptible to susceptible to all pathotypes tested in both years. Pathotype 9 caused the most disease on 7 of the 10 hybrids evaluated in 2005 but, in 2006, pathotypes 12 and 13 surpassed pathotype 9 for disease severity on 9 of the 10 hybrids. More work is needed to assess host resistance and the effect of sorghum anthracnose on yield parameters of grain sorghum hybrids planted in Arkansas.
Simulated Rainfall and Mowing Impact Fungicide Performance When Targeting Dollar Spot in Creeping Bentgrass
Authors: Pigati R. L. , Dernoeden P. H. , Grybauskas A. P. , Momen B.
Published: April 2010

In this 2-year field study, four chemically diverse fungicides (i.e., chlorothalonil, boscalid, iprodione, and propiconazole) were evaluated for their ability to control dollar spot (Sclerotinia homoeocarpa) in creeping bentgrass (Agrostis stolonifera) as affected by simulated rain and mowing timing. Simulated rain (25 to 32 mm) was imposed about 30 min after fungicide application and was compared to rain-free plots. One set of plots was mowed in the morning when the canopy was wet with dew and compared to plots that were mowed when the canopy was dry in the afternoon. The percent reduction in dollar spot control associated with simulated-rain versus rain-free treatments in 2007 and 2008, respectively, was as follows: chlorothalonil 67 and 83%; propiconazole 42 and 79%; boscalid 48 and 70%; and iprodione 33 and 66%. When disease pressure was low, all fungicides subjected to simulated rain provided effective dollar spot control for 7 or more days following the initial application in each year. Across all fungicide-treated plots over 2 years, the average percent reduction in dollar spot associated with morning mowing ranged from 54 to 65%. The reduction in dollar spot severity in morning-mowed plots improved the performance of all fungicides.
Effects of Chemical Control, Cultivar Resistance, and Structure of Cultivar Root System on Black Shank Incidence of Tobacco
Authors: Antonopoulos Dimitrios F. , Melton Thomas , Mila Asimina L.
Published: April 2010

Black shank, caused by the hemibiotrophic oomycete Phytophthora parasitica var. nicotianae, is a major disease of tobacco (Nicotiana tabacum). The rise of race 1 in the late 1990s, after extensive cropping of cultivars possessing the Php gene, confirming immunity to race 0 of P. parasitica var. nicotianae, imposed new challenges to black shank management. The effects of tobacco cultivars and chemical controls with mefenoxam (Ridomil Gold) on black shank incidence were investigated in naturally infested fields. Twenty-five cultivars were tested and the highest resistance for races 0 and 1 of P. parasitica var. nicotianae was provided by RJR 75 and SP 227 based on field and laboratory studies. When race 1 was prevalent, mefenoxam was effective to control black shank. An initial application at an early stage of tobacco growth, such as a few days before or after transplant, was essential to successfully control the disease. In greenhouse experiments, cultivars carrying the Php gene produced fewer and shorter adventitious roots than cultivars possessing only partial resistance to all races of P. parasitica var. nicotianae. Strategies such as use of mefenoxam, especially at an early stage, when adventitious roots are emerging, and planting a cultivar with high partial resistance or possessing the Ph gene when race 1 or race 0, respectively, predominates are critical factors in reducing loss due to P. parasitica var. nicotianae.
Infection and Colonization of Turf-Type Bermudagrass by Ophiosphaerella herpotricha Expressing Green or Red Fluorescent Proteins
Authors: Caasi Oliver C. , Walker Nathan R. , Marek Stephen M. , Enis James N. , Mitchell Thomas K.
Published: April 2010

Spring dead spot, caused by Ophiosphaerella herpotricha, is the most important disease of turf-type bermudagrass (Cynodon spp.) in the transition zone of the United States. Despite the importance of the disease, only limited information is available about the host–pathogen interaction at the cellular level. To evaluate the host plant interaction, an isolate of O. herpotricha expressing green fluorescent proteins (GFP) or red fluorescent proteins (tdTomato) was used to study the infection and colonization of roots and stolons of several bermudagrass cultivars. Roots of cultivars Tifway 419 and Midlawn were colonized similarly, resulting in extensive root necrosis, whereas an accession of Cynodon transvaalensis was less necrotic. The stele of C. transvaalensis roots was colonized but not those of Tifway 419 and Midlawn. For intact stolons, colonization was limited to the epidermis and defined macroscopic necrotic lesions were observed on Tifway 419 and Midlawn while C. transvaalensis stolon tissues remained mostly nonnecrotic. Internal colonization of stolons occurred when hyphae grew into wounds, resulting in necrosis in Tifway 419 and Midlawn, but not in C. transvaalensis. These studies suggest that the interaction of O. herpotricha with bermudagrass varies across host genotypes and the host tissues infected. The limited necrosis in C. transvaalensis tissues, though colonized, suggests an inherent tolerance to O. herpotricha.
Century-Old Mystery of Puccinia striiformis Life History Solved with the Identification of Berberis as an Alternate Host
Authors: Jin Yue , Szabo Les J. , Carson Martin
Published: April 2010

The life history of Puccinia striiformis remains a mystery because the alternate host has never been identified. Inoculation of grasses using aeciospores from naturally infected Berberis chinensis and B. koreana resulted in infection on Poa pratensis, producing uredinia typical of stripe rust caused by P. striiformis. Analyses using real-time polymerase chain reaction and DNA sequence confirmed the rust fungus as P. striiformis. Pycnia and aecia were produced on B. chinensis, B. holstii, B. koreana, and B. vulgaris after inoculation using germinating telia of P. striiformis f. sp. tritici. Wheat inoculated with aeciospores from B. chinensis resulted in uredinia, which demonstrated that Berberis spp. also serve as alternate hosts for the wheat stripe rust pathogen. The elucidation of the complete life history for P. striiformis f. sp. tritici will provide a powerful tool to rapidly advance our knowledge of the genetics of this rust fungus, and will lead to the development of improved strategies for a better control of stripe rust.
Quantitative Trait Loci for Resistance to Pyrenophora tritici-repentis Race 1 in a Chinese Wheat
Authors: Sun Xiao-Chun , Bockus William , Bai Guihua
Published: April 2010

Tan spot, caused by Pyrenophora tritici-repentis, is an economically important foliar disease of wheat worldwide. Eight races of the pathogen have been characterized on the basis of their ability to cause necrosis or chlorosis in a set of differential wheat lines. Race 1 produces two host-selective toxins, Ptr ToxA and Ptr ToxC, that induce necrosis and chlorosis, respectively, on leaves of sensitive wheat genotypes. A population of recombinant inbred lines was developed from a cross between Chinese landrace Wangshuibai (resistant) and Chinese breeding line Ning7840 (highly susceptible) to identify chromosome regions harboring quantitative trait loci (QTL) or genes for tan spot resistance. Plants were inoculated at the four-leaf stage in a greenhouse and percent leaf area diseased was scored 7 days after inoculation. Two QTL for resistance to race 1 were mapped to the short arms of chromosomes 1A and 2B in the population. The QTL on 1AS, designated as QTs.ksu-1AS, showed a major effect and accounted for 39% of the phenotypic variation; the QTL on 2BS, designated as QTs.ksu-2BS, explained 4% of the phenotypic variation for resistance. A toxin infiltration experiment demonstrated that both parents were insensitive to Ptr ToxA, suggesting that the population was most likely segregating for reaction to chlorosis, not necrosis. The markers closely linked to the QTL should be useful for marker-assisted selection in wheat-breeding programs.
Genetic Diversity of the Mating Type and Toxin Production Genes in Pyrenophora tritici-repentis
Authors: Lepoint P. , Renard M.-E. , Legrève A. , Duveiller E. , Maraite H.
Published: April 2010

Pyrenophora tritici-repentis, the causal agent of tan spot on wheat, is a homothallic loculoascomycete with a complex race structure. The objectives of this study were to confirm the homothallic nature of the pathogen, characterize mating type diversity and toxin production genes in a global collection of strains, and analyze how these traits are associated between each other and with existing races. The pseudothecia production capacity, race identification, mating type locus (MAT), internal transcribed spacer, and glyceraldehyde-3-phosphate dehydrogenase regions were analyzed in a selection of 88 strains originating from Europe, North and South America, North Africa, and Central and South Asia. Some (60%) strains produced pseudothecia containing ascospores, independent of their origin. Race identification obtained using the multiplex polymerase chain reaction targeting host-selective toxin (HST) genes was consistent, overall, with the results based on the inoculation of a set of differential wheat cultivars and confirmed the predominance of race 1/2 strains (≈83%). However, discrepancies in race identification, differences from the reference tester strains, and atypical ToxA profiles suggest the presence of new races and HSTs. The MAT1-1 and MAT1-2 coding regions are consecutively arranged in a single individual, suggesting putative heterothallic origin of P. tritici-repentis. Upstream from the MAT is an open reading frame of unknown function (ORF1) containing a MAT-specific degenerate carboxy-terminus. The phylogenetic analysis of the MAT locus reveals two distinct groups, unlinked to geographical origin or ToxA profile. Group I, the best-represented group, is associated with typical tan spot lesions caused by races 1, 2, 3, and 5 on wheat. It is more homogenous than group II encompassing race 4 strains, as well as isolates associated primarily with small spot lesions on wheat leaves or other hosts. Group II could contain several distinct taxa.
Comparison of Surgical Stress Index-guided Analgesia with Standard Clinical Practice during Routine General Anesthesia
Authors: Chen Xinzhong , Thee Carsten , Gruenewald Matthias , Wnent Jan , Illies Christoph , Hoecker Jan , Hanss Robert , Steinfath Markus , Bein Berthold
Published: April 2010

Background

Surgical stress index (SSI), a novel multivariate index, has recently been proven to react well to surgical nociceptive stimuli and analgesic drug concentration changes during general anesthesia. We investigated the feasibility of application of SSI for guidance of remifentanil administration during propofol-remifentanil anesthesia.

Methods

Eighty patients scheduled for elective ear-nose-throat surgery were randomized into two groups, SSI-guided analgesia group (SSI group) and standard practice analgesia group (control group). In both groups, anesthesia was maintained with a propofol target-controlled infusion and adjusted stepwise by 0.5 microg/ml to keep bispectral index values between 40 and 60. In the SSI group, the predicted effect-site concentration of remifentanil was adjusted stepwise by 1 ng/ml to keep SSI values between 20 and 50, whereas in the control group, predicted effect-site concentration of remifentanil was adjusted according to traditional inadequate analgesia criteria. Anesthetics consumption, recovery times, and incidence of unwanted events were recorded.

Results

Remifentanil consumption (average normalized infusion rate) was lower in the SSI group than in the control group (mean +/- SD, 9.5 +/- 3.8 microg . kg(-1) . h(-1) vs. 12.3 +/- 5.2 microg . kg(-1) . h(-1); P < 0.05). The number of unwanted events was less in the SSI group (84) than in the control group (556; P < 0.01). Recovery times were comparable between groups. No patient reported intraoperative recall.

Conclusions

SSI-guided anesthesia resulted in lower remifentanil consumption, more stable hemodynamics, and a lower incidence of unwanted events.
A New Technique to Assist Epidural Needle Placement
Authors: Ting Chien-Kun , Tsou Mei-Yung , Chen Pin-Tarng , Chang Kuang-Yi , Mandell M. Susan , Chan Kwok-Hon , Chang Yin
Published: April 2010

Background

Up to 10% of epidurals fail due to incorrect catheter placement. We describe a novel optical method to assist epidural catheter insertion in a porcine model.

Methods

Optical emissions were tested on ex vivo tissues from porcine paravertebral tissues to identify optical reflective spectra. The wavelengths of 650 and 532 nm differentiated epidural space from the ligamentum flavum. We then used a hollow stylet that contained optical fibers to place epidural needles in anesthetized pigs. Real-time data were displayed on an oscilloscope and stored for analysis. A total of 50 punctures were done in four laboratory pigs. Data were expressed as mean +/- SD.

Results

Paired t test shows significant optical differences between the epidural space and the ligamentum flavum at both 650 nm (P < 0.001) and 532 nm (P = 0.014). Mean magnitudes for 650 nm, 532 nm, and their ratio were 3.565 +/- 0.194, 2.542 +/- 0.145, and 0.958 +/- 0.172 at epidural space and 3.842 +/- 0.191, 2.563 +/- 0.131, and 1.228 +/- 0.244 at ligamentum flavum, respectively. There were no differences in the optical characteristics of the ligamentum flavum and epidural space at different levels in the lumbar and thoracic region (two-way ANOVA P > 0.05).

Conclusions

This is the first study to introduce a new optical method to localize epidural space in a porcine model. Epidural space could be identified by the changes in the reflective pattern of light emitted at 650 nm, which were specific for the ligamentum flavum and dural tissue. Real-time optical information successfully guided a modified Tuohy needle into the epidural space.
Ketamine Activates Cell Cycle Signaling and Apoptosis in the Neonatal Rat Brain
Authors: Soriano Sulpicio G. , Liu Qian , Li Jing , Liu Jia-Ren , Han Xiao Hui , Kanter Jennifer L. , Bajic Dusica , Ibla Juan C.
Published: April 2010

Background

Prolonged exposure to ketamine results in accelerated neurodegeneration and neurocognitive deficits in the neonatal rats. Experimental models of neurodegeneration have implicated reentry of postmitotic neurons into the cell cycle, leading to cell death. The authors hypothesize that the ketamine-induced neuroapoptosis is partially due to aberrant cycle cell reentry. To explore this hypothesis, the authors characterized the effect of ketamine on the cell cycle signaling pathway in the developing rodent brain in vivo and in vitro.

Methods

Postnatal day 7 rat pups and primary neurons were used for the experiments. Each rat pup received five intraperitoneal doses of either saline or ketamine (5, 10, and 20 mg/kg/dose) at 90-min intervals over 6 h. Primary neurons were exposed to varying concentrations of ketamine to determine the dose and duration effects. The expression of cell cycle proteins (cyclin D1, cyclin-dependent kinase 4, and E2F1), Bcl2-interacting mediator of cell death (Bim), and activated caspase-3 was determined. The effect of cyclin D1 knockdown by small interfering RNA was also examined in primary neurons incubated in ketamine.

Results

Ketamine mediated a dose- and time-dependent increase in expression of cell cycle proteins and activated caspase-3. Cyclin D1, cyclin-dependent kinase 4, E2F1, Bim, and cleaved caspase-3 expression increased at 12 h and peaked at 24 h in vitro. Knockdown of cyclin D1 by small interfering RNA attenuated Bim and cleaved caspase-3 expression.

Conclusion

These findings support a model in which ketamine induces aberrant cell cycle reentry, leading to apoptotic cell death in the developing rat brain.
Association of Perioperative Risk Factors and Cumulative Duration of Low Bispectral Index with Intermediate-term Mortality after Cardiac Surgery in the B-Unaware Trial
Authors: Kertai Miklos D. , Pal Nirvik , Palanca Ben J. A. , Lin Nan , Searleman Sylvia A. , Zhang Lini , Burnside Beth A. , Finkel Kevin J. , Avidan Michael S.
Published: April 2010

Background

Current data suggest that mortality after noncardiac surgery may be associated with persistent hypotension and the cumulative duration of low processed electroencephalogram-based bispectral index (BIS). This study assessed the relationships among cumulative duration of low BIS (BIS < 45), intermediate-term mortality, and anesthetic dose after cardiac surgery.

Methods

The authors studied 460 patients (mean age, 63.0 +/- 13.1 yr; 287 men) who underwent cardiac surgery between September 2005 and October 2006 at Washington University Medical Center, St Louis, Missouri. By using multivariable Cox regression analysis, perioperative factors were evaluated for their potential association with intermediate-term all-cause mortality.

Results

A total of 82 patients (17.8%) died during a median follow-up of 3 yr (interquartile range, 2.7-3.3 yr). Comparing patients who died with those who survived, there was no statistically significant difference in the relationship between end-tidal anesthetic gas concentrations during the anesthetic maintenance phase and the BIS. Cumulative duration of low BIS was independently associated with intermediate-term mortality. The 1.29 adjusted hazard ratio (95% CI, 1.12-1.49) for intermediate-term mortality with cumulative duration of low BIS translated into a 29% increased risk of death for every cumulative hour spent with a BIS less than 45. The final multivariable Cox regression model showed a good discriminative ability (c-index of 0.78).

Conclusions

This study found an association between cumulative duration of low BIS and mortality in the setting of cardiac surgery. Notably, this association was independent of both volatile anesthetic concentration and duration of anesthesia, suggesting that intermediate-term mortality after cardiac surgery was not causally related to excessive anesthetic dose.
How to characterize the dynamics of cold atoms in non-dissipative optical lattices?
Authors: Hennequin D. , Verkerk Ph.
Published: April 2010

We examine here the classical dynamics of cold atoms in square optical lattices, i.e. lattices obtained with two orthogonal stationary plane waves. Contrary to many of the past studies in this domain, the potential here is time independent and non-dissipative. We show that, as a function of the experimental parameters, very different behaviours are obtained, both for the dynamics of atoms trapped inside individual sites and for atoms travelling between sites: inside the sites, chaos may be the main regime or, on the contrary, it may be negligible; outside the sites, chaos sometimes coexists with other regimes. We discuss the consequences of these differences on the macroscopic behaviour of the atoms in the lattice, and we propose experimental measurements able to characterize these dynamics and to distinguish between the different cases.
Mapping Plant Interactomes Using Literature Curated and Predicted Protein–Protein Interaction Data Sets
Authors: Lee KiYoung , Thorneycroft David , Achuthan Premanand , Hermjakob Henning , Ideker Trey
Published: April 2010

Most cellular processes are enabled by cohorts of interacting proteins that form dynamic networks within the plant proteome. The study of these networks can provide insight into protein function and provide new avenues for research. This article informs the plant science community of the currently available sources of protein interaction data and discusses how they can be useful to researchers. Using our recently curated IntAct Arabidopsis thaliana protein–protein interaction data set as an example, we discuss potentials and limitations of the plant interactomes generated to date. In addition, we present our efforts to add value to the interaction data by using them to seed a proteome-wide map of predicted protein subcellular locations.
Convergent Evolution of Syringyl Lignin Biosynthesis via Distinct Pathways in the Lycophyte Selaginella and Flowering Plants
Authors: Weng Jing-Ke , Akiyama Takuya , Bonawitz Nicholas D. , Li Xu , Ralph John , Chapple Clint
Published: April 2010

Phenotypic convergence in unrelated lineages arises when different organisms adapt similarly under comparable selective pressures. In an apparent example of this process, syringyl lignin, a fundamental building block of plant cell walls, occurs in two major plant lineages, lycophytes and angiosperms, which diverged from one another more than 400 million years ago. Here, we show that this convergence resulted from independent recruitment of lignin biosynthetic cytochrome P450-dependent monooxygenases that route cell wall monomers through related but distinct pathways in the two lineages. In contrast with angiosperms, in which syringyl lignin biosynthesis requires two phenylpropanoid meta-hydroxylases C3′H and F5H, the lycophyte Selaginella employs one phenylpropanoid dual meta-hydroxylase to bypass several steps of the canonical lignin biosynthetic pathway. Transgenic expression of the Selaginella hydroxylase in Arabidopsis thaliana dramatically reroutes its endogenous lignin biosynthetic pathway, yielding a novel lignin composition not previously identified in nature. Our findings demonstrate a unique case of convergent evolution via distinct biochemical strategies and suggest a new way to genetically reconstruct lignin biosynthesis in higher plants.
Moderator effects of organizational tenure on the relationship between psychological climate and affective commitment
Authors: English Brian , Morrison David , Chalon Christopher
Published: April 2010

Purpose

Previous research is equivocal about: whether affective organizational commitment increases or decreases with increasing tenure; and which psychological climate variables correlated with affective commitment are important as tenure increases. The study's purpose is to examine whether the relationship between psychological climate and affective commitment is moderated by tenure.

Design/methodology/approach

The total workforce of a public sector agency in Western Australia (n=1,117) was surveyed with a response rate of 53 per cent. The moderating role of tenure was examined for employees with less than one year's tenure (n=87), one to nine years (n=232) and more than nine years (n=258).

Findings

Affective commitment was found to be stronger for employees with longer tenure; however, perceptions of psychological climate appear to be less positive for these employees. The finding of a moderation effect for tenure appeared to be attributable to the importance of supervisor involvement to affective commitment for employees with one to nine years' tenure.

Practical implications

Building affective commitment is an important issue for managers as it is strongly related to withdrawal cognitions and employee turnover. The findings of the study suggest that the criteria against which an organization is assessed by employees tends to shift with time and impacts on affective commitment.

Originality/value

The three‐way relationship between tenure, psychological climate and affective commitment has received little attention. The findings of the study suggest that the strength of affective commitment may depend on the extent to which the specific interests and capabilities of individual employees at different stages of tenure are met.
Performance measurement in the food supply chain: a balanced scorecard approach
Authors: Bigliardi Barbara , Bottani Eleonora
Published: April 2010

Purpose

The primary objective of this paper is to develop a balanced scorecard (BSC) model that is designed and delimited for performance measurement in the food supply chain.

Design/methodology/approach

The research methodology is a combination of literature analysis, Delphi technique and case study‐based research. Starting from the literature concerning performance measurement and metrics, the food industry and the BSC model, the relevant financial and non‐financial indicators, suitable to be used for companies belonging to the food industry, were first identified. Indicators were submitted to a panel of experts, which operated following the Delphi technique, to gather possible suggestions or amendments. In its final form, the resulting BSC model was tested on two companies operating in the food industry, for a final validation.

Findings

Results of the case studies show that the companies examined have a similar view for three of the four perspectives of the BSC, which can be thus considered as validated. Conversely, some diverging results were observed concerning the learning and growth perspective.

Research limitations/implications

By focusing on the specific context of the food supply chain, this study completes previous works, which proposed a generic BSC model for supply chain management. On the other hand, the fact that a specific industry field was examined could be seen as a limitation of the work as the results presented are not suitable to be generalized or extended to other contexts, although some extrapolations can be made.

Originality/value

The paper provides a structured performance measurement system tailored for the food supply chain. The BSC model developed could serve as a reference for the food industry, to establish applicable performance appraisal indicators, and it is believed that both researchers and practitioners would benefit from the tool developed.
Scaleprinting: individual identification based on scale patterns
Authors: Morgado‐Santos M. , Matos I. , Vicente L. , Collares‐Pereira M. J.
Published: April 2010

A non‐intrusive method for individual identification of Iberian cyprinid complex Squalius alburnoides is presented, with possible application to other fish complexes and species. The proposed methodology is based on scale patterns that vary greatly between individuals.
Enhanced tumorigenesis of forestomach tumors induced by N‐Methyl‐N′‐nitro‐N‐nitrosoguanidine in rats with hypoinsulinemic diabetes
Authors: Kodama Yasushi , Ozaki Kiyokazu , Sano Tomoya , Matsuura Tetsuro , Narama Isao
Published: April 2010

Hyperinsulinemia and hyperglycemia in prediabetic and diabetic patients are thought to increase the risk of developing neoplasms because insulin is a growth factor with pre‐eminent metabolic but also mitogenic effects. To determine the effect of hypoinsulinemic diabetic conditions on carcinogenesis, we examined N‐Methyl‐N′‐nitro‐N‐nitrosoguanidine (MNNG)‐induced forestomach carcinogenesis in hypoinsulinemic diabetic WBN/Kob rats aged about 45 weeks (DM) compared with non‐diabetic younger WBN/Kob rats (C1), non‐diabetic Wistar rats age‐matched to DM (C2), and non‐diabetic Wistar rats age‐matched to C1 (C3). All rats were treated with MNNG by gavage and were killed at 40 weeks after dosing. Various‐sized tumors were disseminated throughout the forestomach of all rats, and the ratio of the area of tumors to the whole forestomach area was 23.3% in the DM group and was higher than in the C1–3 (4.2–14.3%) groups. The incidence of carcinoma was much higher in the DM group (36.8%) than in the C1–3 (7.1–16.7%) groups, and the incidence of papilloma was also significantly higher in the DM group (84.2%) than in the C1–3 (28.5–50.0%) groups. The average thickness of the squamous epithelium in the non‐neoplastic mucosa was significantly greater in the DM group (50.8 μm) than in the C1–3 (29.6–37.9 μm) groups. Immunohistochemically, the Ki‐67‐positive index in the non‐tumorous mucosa of the DM group (42.0%) was significantly higher than that of the C1–3 groups (18.8–33.3%). These results suggest that prolonged hyperglycemic conditions without hyperinsulinemia enhance tumorigenesis of MNNG‐induced tumors by enhanced proliferative activity of the squamous epithelium in the rat forestomach. (Cancer Sci 2010)
Haematological emergencies managing hypercalcaemia in adults and children with haematological disorders
Authors: Sargent Jeremy T. S. , Smith Owen P.
Published: April 2010

Hypercalcaemia is a common metabolic complication of malignant disease often requiring emergency intervention. Although it is more frequently associated with solid tumours, malignancy‐associated hypercalcaemia (MAH) is seen in a significant number of patients with blood diseases. Its association with myeloma and adult T‐cell leukaemia/lymphoma is well recognized but the incidence of hypercalcaemia in other haematological neoplasms, affecting adults and children, is less clearly defined. Haematologists need to be familiar with the clinical manifestations of, the differential diagnosis to be considered and the most effective management strategies that are currently available for MAH. The key components of management of MAH include aggressive rehydration, specific therapy to inhibit bone resorption and, crucially, treatment of the underlying malignancy. Bisphosphonates have revolutionized the management of MAH over the last 20 years, however the elucidation of molecular pathways implicated in MAH is facilitating the development of more targeted approaches to treatment.
Myogenic differentiation in atrium‐derived adult cardiac pluripotent cells and the transcriptional regulation of GATA4 and myogenin on ANP promoter
Authors: Kamrul Hasan Md , Komoike Yuta , Tsunesumi Shin‐ichiro , Nakao Ryota , Nagao Hiroaki , Matsuoka Rumiko , Kawaguchi Nanako
Published: April 2010

We established cardiac pluripotent stem‐like cells from the left atrium (LA‐PCs) of adult rat hearts. These cells could differentiate not only into beating myocytes but also into cells of other lineages, including adipocytes and endothelial cells in the methylcellulose‐based medium containing interleukin‐3 (IL‐3), interleukin‐6 (IL‐6), and stem cell factor (SCF). In particular, IL‐3 and SCF contributed to the differentiation into cardiac troponin I‐positive cells. Notably, small population of LA‐PCs coexpressed GATA4 and myogenin, which are markers specific to cardiomyocytes and skeletal myocytes, respectively, and could differentiate into both cardiac and skeletal myocytes. Therefore, we investigated the involvement of these two tissue‐specific transcription factors in the cardiac transcriptional activity. Coexpression of GATA4 and myogenin synergistically activated GATA4‐specific promoter of the atrial natriuretic peptide gene. This combinatorial function was shown to be dependant on the GATA site, but independent of the E‐box. The results of chromatin immunoprecipitation and electrophoretic mobility shift assays suggested that myogenin bound to GATA4 on the GATA elements and the C‐terminal Zn‐finger domain of GATA4 and the N‐terminal region of myogenin were required for this synergistic activation of transcription. Taken together, these two transcription factors could be involved in the myogenesis of LA‐PCs.
Simultaneous expression of different transgenes in neurons and glia by combining in utero electroporation with the Tol2 transposon‐mediated gene transfer system
Authors: Yoshida Ayako , Yamaguchi Yoshifumi , Nonomura Keiko , Kawakami Koichi , Takahashi Yoshiko , Miura Masayuki
Published: April 2010

In utero electroporation is widely used to study neuronal development and function by introducing plasmid DNA into neural progenitors during embryogenesis. This is an effective and convenient method of introducing plasmid DNA into neural precursors and is suitable for manipulating gene expression in cells of the CNS. However, the applicability of this technique is comparatively limited to neuronal research, as the plasmid DNA introduced into neural progenitors during embryogenesis is diluted by cell proliferation and is not stably maintained in glial cells generated around and after birth. To overcome this limitation, we applied the Tol2 transposon system, which integrates a transgene into the genome of the host cell, to in utero electroporation. With this system, we confirmed that the transgene was effectively maintained in the progeny of embryonic neural precursors, astrocytes and oligodendrocytes. Using the glial promoters GFAP and S100β, targeted and stable expressions of transgenes in glia were obtained, which enabled the expression of different transgenes simultaneously in neurons and glia. Glia‐targeted expression of the transgene that causes neuronal migration defect was achieved without the defect. Thus, use of the Tol2 transposon system in combination with in utero electroporation is a powerful method for studying glia‐neuron interactions in vivo.