bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydrogen diffusion in NaH as derived from isotope exchange experiments
Authors: Borgschulte A. , Pendolino F. , Gremaud R. , Züttel A.
Published: March 2009

We report on hydrogen-deuterium-exchange experiments on NaH probed by thermogravimetry. From the measurements a diffusion parameter of deuterium in NaH of D=1.1×10−17 m2/s at 523 K is derived. The activation energy of tracer diffusion of D in NaH is found to be 1.0 eV. The results are hints for a diffusion process mediated by neutral hydrogen vacancies.
Maximization of granular outflow by oblique exits and by obstacles
Authors: Zelinski Björn , Goles Eric , Markus Mario
Published: March 2009

We investigate experimentally the intermittent discharge of a granular medium out of an exit at the bottom of a vertically shaken box. Changing the orientation of the bottom shows that there exists an angle (around 20°–25° with respect to the horizontal) at which the mean discharge rate increases up to a factor 1.9, as compared to the rate with horizontal bottom. Furthermore, adjusting the diameter and the distance of a cylindrical obstacle above the exit on the (horizontal) bottom, allows to optimize the mean rate of discharge up to 3.5 times the rate without obstacle.
Multilayered optical bit memory with a high signal-to-noise ratio in fluorescent polymethylmethacrylate
Authors: Nie Zhaogang , Lee Heungyeol , Yoo Hyeonggeun , Lee Youlee , Kim Younshil , Lim Ki-Soo , Lee Myeongkyu
Published: March 2009

We report on the three-dimensional optical memory utilizing a photoluminescence (PL) change in polymethylmethacrylate. Irradiation with a femtosecond pulsed laser (800 nm, 1 kHz, 100 fs) induced a strong PL spectrum in the visible range, which may result from the photogeneration of emissive radicals. Multilayered patterns were recorded inside the bulk sample by tightly focusing a pulsed laser beam. The pattern images were read out by a reflection-type fluorescent confocal microscope which detected the blue-green emission at 410–510 nm. The stored bits were retrieved with a high signal-to-noise ratio in the absence of any cross-talk.
Control performance of a single-chip white light emitting diode by adjusting strain in InGaN underlying layer
Authors: Wang X. H. , Guo L. W. , Jia H. Q. , Xing Z. G. , Wang Y. , Pei X. J. , Zhou J. M. , Chen H.
Published: March 2009

Light emission from green to white in a single-chip light emitting diode is modulated by adjusting the strain in InGaN underlying layer (UL) embedded below an active layer of InGaN/GaN multiple quantum wells. Transmission electron microscopy combined with x-ray reciprocal space mapping reveals that indium phase separation in InGaN quantum well active layer is enhanced by using a partly relaxed InGaN UL and In-rich quantum dots with different size and indium composition are formed. They emit multicolor lights whose mixing produces white light. Quality of the white light could be controlled by modulation on relaxation degree of the InGaN UL.
N-Glycoside Complexes of Nickel(II); Probing Carbohydrate - Transition Metal Interactions
Authors: Jones Dale , van Holst Marcelis , Yano Shigenobu , Tanase Tomoaki , Aldrich-Wright Janice
Published: March 2009

Nickel(ii) complexes prepared from d- and l-arabinose (d-ara and l-ara) and 1,2-diaminoethane (en), [Ni(en-d-ara)2](ClO4)2·2H2O 1 and [Ni(en-l-ara)2](ClO4)2·2H2O 2 (where en-d-ara is 1-((2-aminoethyl)amino)-1-deoxy-d-arabinose) were synthesized and characterized by absorption spectroscopy, circular dichroism (CD), and X-ray crystallography. The CD spectra of 1 and 2 in the d–d transition region indicate a C2 chiral configuration around the metal centre. X-ray crystallography of 1 revealed that two 1-((2-aminoethyl)amino)-1-deoxy-d-arabinose ligands coordinate to the nickel atom in nearly C2 symmetry, through the C(2) hydroxy group of the arabinose moiety and two nitrogen atoms of the diamine in a meridional mode. This results in a Λ-C2-helical configuration around the metal centre. The arabinose ring adopts the rare α-1C4 chair conformation and the carbohydrate–chelate ring conformation is δ.
Can Molecular Sieves be Used as Water Scavengers in Microwave Chemistry?
Authors: Baghbanzadeh Mostafa , Kappe C. Oliver
Published: March 2009

The use of sealed-vessel microwave-assisted organic synthesis in combination with 4 Å molecular sieves as water scavengers is investigated. Two classical model transformations, namely acetal formation and imine formation, are evaluated under both conventional heating and microwave dielectric heating. The results obtained in these studies indicate that molecular sieves cannot be used effectively as water scavengers in microwave-assisted transformations owing to the fact that these zeolites are generally most effective in adsorbing water at room temperature. For both acetal and imine formation, performing these reversible reactions at a higher temperature in the presence of molecular sieves leads to significantly reduced conversions compared with experiments at room temperature.
Microwave-Assisted Tandem Processes for the Synthesis of N-Heterocycles
Authors: Abid Mohammed , Török Béla , Huang Xudong
Published: March 2009

Over the years, microwave-assisted organic synthesis (MAOS) became a commonly applied mainstream tool for the synthesis of heterocyclic compounds. The broad range of emerging applications in this field is mainly due to the significant contribution of MAOS to the development of ecofriendly processes. Various transformations have been developed for the synthesis of N-heterocycles under microwave conditions, including fast and selective processes. Tandem reactions involving greener reaction media, solvent-free conditions, and solid-phase synthesis are of exceptional interest in this area. In most transformations, microwave conditions dramatically enhanced reaction rates, as well as provided improved yields. This account highlights the most recent advancements in MAOS-based tandem processes for the synthesis of N-heterocycles.
Microwave-Assisted Synthesis of a New Hydantoin Monomer for Antibacterial Polymeric Materials
Authors: Iannelli Mauro , Bergamelli Fabio , Galli Giancarlo
Published: March 2009

11-(4,4-Dimethyl-2,5-dioxoimidazolidin-1-yl)undecyl acrylate was synthesized in a two-step procedure using microwave irradiation. Poly(acrylates) containing fluorinated and hydantoin (5,5-dimethylimidazolidine-2,4-dione) moieties were prepared by free radical polymerization of 2-(perfluorooctyl)ethyl acrylate and the synthesized monomer with the aim of obtaining low surface energy polymeric materials with properties of contact-active biocides. Polymeric films were treated with a bleaching solution in order to convert the hydantoin units to N-halamines, well-known contact-active biocides. The reversibility of the chlorination reaction, necessary to impart a renewable biocide effect, was investigated by Fourier Transform-Attenuated Total Reflection. Preliminary biological tests conducted against Bacillus megaterium demonstrated the effective biocide properties of the prepared materials.
Solubilization and Functionalization of Cellulose Assisted by Microwave Irradiation
Authors: Semsarilar Mona , Perrier Sébastien
Published: March 2009

The dissolution and functionalization of cellulose in the DMAc/LiCl system assisted by microwave irradiation is investigated. Cellulose solutions were prepared using mono- and multimodal microwave radiation, as well as using a conventional heating method. The effect of microwave irradiation on the dissolution of cellulose was evaluated by comparison of physical properties such as the viscosity of the resulting solution and the size distribution of the cellulosic chains in solution. We demonstrate that monomodal microwave irradiation allows for a faster and easier dissolution of cellulose, when compared with the use of multimodal microwave irradiation, or conventional heating. Furthermore, we show that monomodal microwave irradiation can be used for a one-pot modification of cellulose undertaken in two steps, first dissolution of the cellulose followed by reaction of the functional groups. The concept is illustrated by the modification of cellulose with lauroyl chloride.
High Temperature Initiator-Free RAFT Polymerization of Methyl Methacrylate in a Microwave Reactor
Authors: Paulus Renzo M. , Becer C. Remzi , Hoogenboom Richard , Schubert Ulrich S.
Published: March 2009

The reversible addition–fragmentation chain transfer (RAFT) polymerization of methyl methacrylate (MMA) was investigated under microwave irradiation. At first, a comparison was made between microwave and thermal heating for the RAFT polymerization of MMA with azobis(isobutyronitrile) (AIBN) as initiator and 2-cyano-2-butyldithiobenzoate (CBDB) as RAFT agent, revealing comparable polymerization kinetics indicating the absence of non-thermal microwave effects. Second, the CBDB-mediated RAFT polymerization of MMA was investigated at high temperatures (120°C, 150°C, and 180°C, respectively) in the absence of a radical initiator, showing a linear increase of the molar masses with conversion. The polydispersity indices remained below 1.5 up to 25% MMA conversion at 120°C and 150°C, indicating a controlled polymerization. This control over the polymerization was confirmed by the ability to control the molar masses by the concentration of RAFT agent.
Simultaneous Bayesian gene tree reconstruction and reconciliation analysis
Authors: Åkerborg Örjan , Sennblad Bengt , Arvestad Lars , Lagergren Jens
Published: March 2009

We present GSR, a probabilistic model integrating gene duplication, sequence evolution, and a relaxed molecular clock for substitution rates, that enables genomewide analysis of gene families. The gene duplication and loss process is a major cause for incongruence between gene and species tree, and deterministic methods have been developed to explain such differences through tree reconciliations. Although probabilistic methods for phylogenetic inference have been around for decades, probabilistic reconciliation methods are far less established. Based on our model, we have implemented a Bayesian analysis tool, PrIME-GSR, for gene tree inference that takes a known species tree into account. Our implementation is sound and we demonstrate its utility for genomewide gene-family analysis by applying it to recently presented yeast data. We validate PrIME-GSR by comparing with previous analyses of these data that take advantage of gene order information. In a case study we apply our method to the ADH gene family and are able to draw biologically relevant conclusions concerning gene duplications creating key yeast phenotypes. On a higher level this shows the biological relevance of our method. The obtained results demonstrate the value of a relaxed molecular clock. Our good performance will extend to species where gene order conservation is insufficient.
Extremely low-frequency electromagnetic fields disrupt magnetic alignment of ruminants
Authors: Burda Hynek , Begall Sabine , Červený Jaroslav , Neef Julia , Němec Pavel
Published: March 2009

Resting and grazing cattle and deer tend to align their body axes in the geomagnetic North-South direction. The mechanism(s) that underlie this behavior remain unknown. Here, we show that extremely low-frequency magnetic fields (ELFMFs) generated by high-voltage power lines disrupt alignment of the bodies of these animals with the geomagnetic field. Body orientation of cattle and roe deer was random on pastures under or near power lines. Moreover, cattle exposed to various magnetic fields directly beneath or in the vicinity of power lines trending in various magnetic directions exhibited distinct patterns of alignment. The disturbing effect of the ELFMFs on body alignment diminished with the distance from conductors. These findings constitute evidence for magnetic sensation in large mammals as well as evidence of an overt behavioral reaction to weak ELFMFs in vertebrates. The demonstrated reaction to weak ELFMFs implies effects at the cellular and molecular levels.
Structure of granzyme C reveals an unusual mechanism of protease autoinhibition
Authors: Kaiserman Dion , Buckle Ashley M. , Van Damme Petra , Irving James A. , Law Ruby H. P. , Matthews Antony Y. , Bashtannyk-Puhalovich Tanya , Langendorf Chris , Thompson Philip , Vandekerckhove Joël , Gevaert Kris , Whisstock James C. , Bird Phillip I.
Published: March 2009

Proteases act in important homeostatic pathways and are tightly regulated. Here, we report an unusual structural mechanism of regulation observed by the 2.5-Å X-ray crystal structure of the serine protease, granzyme C. Although the active-site triad residues adopt canonical conformations, the oxyanion hole is improperly formed, and access to the primary specificity (S1) pocket is blocked through a reversible rearrangement involving Phe-191. Specifically, a register shift in the 190-strand preceding the active-site serine leads to Phe-191 filling the S1 pocket. Mutation of a unique Glu–Glu motif at positions 192–193 unlocks the enzyme, which displays chymase activity, and proteomic analysis confirms that activity of the wild-type protease can be released through interactions with an appropriate substrate. The 2.5-Å structure of the unlocked enzyme reveals unprecedented flexibility in the 190-strand preceding the active-site serine that results in Phe-191 vacating the S1 pocket. Overall, these observations describe a broadly applicable mechanism of protease regulation that cannot be predicted by template-based modeling or bioinformatic approaches alone.
The cost of gene expression underlies a fitness trade-off in yeast
Authors: Lang Gregory I. , Murray Andrew W. , Botstein David
Published: March 2009

Natural selection optimizes an organism's genotype within the context of its environment. Adaptations to one environment can decrease fitness in another, revealing evolutionary trade-offs. Here, we show that the cost of gene expression underlies a trade-off between growth rate and mating efficiency in the yeast
Saccharomyces cerevisiae
. During asexual growth, mutations that eliminate the ability to mate provide an ≈2% per-generation growth-rate advantage. Some strains, including most laboratory strains, carry an allele of
GPA1
(an upstream component of the mating pathway) that increases mating efficiency by ≈30% per round of mating at the cost of an ≈1% per-generation growth-rate disadvantage. In addition to demonstrating a trade-off between growth rate and mating efficiency, our results illustrate differences in the selective pressures defining fitness in the laboratory versus the natural environment and show that selection, acting on the cost of gene expression, can optimize expression levels and promote gene loss.
Cooperative learning that features a culturally appropriate pedagogy
Authors: Phuong‐Mai Nguyen , Terlouw Cees , Pilot Albert , Elliott Julian
Published: March 2009

Many recent intercultural studies have shown that people cooperate with each other differently across cultures. We argue that cooperative learning (CL), an educational method originating in the USA and with fundamental psychological assumptions based on Western values, should be adjusted to be culturally appropriate for any non‐Western cultures in which it is applied. In the light of this assertion, this paper reports a series of experiments conducted in Vietnamese upper‐secondary schools. One group was provided with a series of lessons designed according to mainstream CL practice. Another group was provided with similar lessons but these were modified so as to be more culturally appropriate in terms of leadership, reward allocation and group composition. Findings show that (1) the role and the type of leadership, although not a key element of mainstream CL theories and practice, proved to be influential; (2) groupings based upon existing friendships, rather than upon cognitive ability, appeared to be important. A key finding was that the group receiving a culturally modified programme appeared to work harder during, and gain more satisfaction from, collaborative learning activities.
EPS Prize Lecture: Decision by sampling: The role of the decision environment in risky choice
Authors: Stewart Neil
Published: March 2009

Decision by sampling (DbS) is a theory about how our environment shapes the decisions that we make. Here, I review the application of DbS to risky decision making. According to classical theories of risky decision making, people make stable transformations between outcomes and probabilities and their subjective counterparts using fixed psychoeconomic functions. DbS offers a quite different account. In DbS, the subjective value of an outcome or probability is derived from a series of binary, ordinal comparisons with a sample of other outcomes or probabilities from the decision environment. In this way, the distribution of attribute values in the environment determines the subjective valuations of outcomes and probabilities. I show how DbS interacts with the real-world distributions of gains, losses, and probabilities to produce the classical psychoeconomic functions. I extend DbS to account for preferences in benchmark data sets. Finally, in a challenge to the classical notion of stable subjective valuations, I review evidence that manipulating the distribution of attribute values in the environment changes our subjective valuations just as DbS predicts.
Accounting for Incomplete Postdischarge Follow-Up During Surveillance of Surgical Site Infection by Use of the National Nosocomial Infections Surveillance System's Risk Index
Authors: Biscione Fernando Martín , Couto Renato Camargos , Pedrosa Tânia M. G.
Published: March 2009

Objective.

We examined the usefulness of a simple method to account for incomplete postdischarge follow-up during surveillance of surgical site infection (SSI) by use of the National Nosocomial Infections Surveillance (NNIS) system's risk index.

Design.

Retrospective cohort study that used data prospectively collected from 1993 through 2006.

Setting.

Five private, nonuniversity healthcare facilities in Belo Horizonte, Brazil.

Patients.

Consecutive patients undergoing the following NNIS operative procedures: 20,981 operations on the genitourinary system, 11,930 abdominal hysterectomies, 7,696 herniorraphies, 6,002 cholecystectomies, and 6,892 laparotomies.

Methods.

For each operative procedure category, 2 SSI risk models were specified. First, a model based on the NNIS system's risk index variables was specified (hereafter referred to as the NNIS-based model). Second, a modified model (hereafter referred to as the modified NNIS-based model), which was also based on the NNIS system's risk index, was specified with a postdischarge surveillance indicator, which was assigned the value of 1 if the patient could be reached during follow-up and a value of 0 if the patient could not be reached. A formal comparison of the capabilities of the 2 models to assess the risk of SSI was conducted using measures of calibration (by use of the Pearson goodness-of-fit test) and discrimination (by use of receiver operating characteristic curves). Goodman-Kruskal correlations (G) were also calculated.

Results.

The rate of incomplete postdischarge follow-up varied between 29.8% for abdominal hysterectomies and 50.5% for cholecystectomies. The modified NNIS-based model for laparotomy did not show any significant benefit over the NNIS-based model in any measure. For all other operative procedures, the modified NNIS-based model showed a significantly improved discriminatory ability and higher G statistics, compared with the NNIS-based model, with no significant impairment in calibration, except if used to assess the risk of SSI after operations on the genitourinary system or after a cholecystectomy.

Conclusions.

Compared with the NNIS-based model, the modified NNIS-based model added potentially useful clinical information regarding most of the operative procedures. Further work is warranted to evaluate this method for accounting for incomplete postdischarge follow-up during surveillance of SSI.
Vancomycin Use During Left Ventricular Assist Device Support
Authors: Eyler Rachel F. , Butler Simona O. , Walker Paul C. , DePestel Daryl D. , Spoor Martinus T. , Pagani Francis D. , Malani Preeti N.
Published: March 2009

We reviewed the frequency and duration of vancomycin use during 93 left ventricular assist device placements. Vancomycin prophylaxis was administered for a mean duration (± standard deviation) of 10.5 ± 11 days. Empirical vancomycin use was frequent, with a mean duration (± standard deviation) of therapy of 9.8 ± 9 days (median, 8 days) given during 81 (87%) of the implantations. The most common indications for empirical vancomycin treatment were isolated leukocytosis or driveline drainage. Strategies to improve vancomycin use during left ventricular assist device support should be considered.
First Report of Powdery Mildew of Poison-Hemlock Caused by Erysiphe heraclei in North America
Authors: Koike Steven T. , Glawe Dean A.
Published: March 2009

Poison-hemlock is a widely distributed biennial especially known for its toxic piperidine alkaloids that can poison livestock that eat this plant. In 2008, a powdery mildew was observed on poison-hemlock growing in coastal California. The causal agent was determined to be Erysiphe heraclei DC., previously unreported on this host in North America.

Accepted for publication 18 December 2008. Published 12 March 2009.
Cotton Cultivars Evaluated for Tolerance to Reniform Nematode
Authors: Stetina Salliana R. , Sciumbato Gabriel L. , Young Lawrence D. , Blessitt Julie A.
Published: March 2009

Thirty-nine commercial cotton (Gossypium hirsutum) cultivars were evaluated to identify those with tolerance to reniform nematode (Rotylenchulus reniformis). Trials were conducted for three years at two west-central Mississippi field locations naturally infested with reniform nematode. Main plots were cultivars and subplots were either not treated or treated with nematicide. Reniform nematode soil population densities were assessed throughout the growing season. At harvest, seed cotton yields were determined, and fiber quality was evaluated for select samples. Data were pooled from all years and locations, and t-tests were used to identify tolerant cultivars. Cultivars were judged tolerant if nematicide did not improve yield, although the nematode population was reduced at a midseason sampling interval. Only Deltapine 449 BR, Paymaster 1218 BR, and Suregrow 215 BR met these criteria. Additionally, tolerance indices were calculated for nine cultivars showing suppressed nematode populations in nematicide-treated plots at any point during the growing season. The three tolerant cultivars identified based on the t-tests ranked first (Suregrow 215 BR), second (Paymaster 1218 BR), and fifth (Deltapine 449 BR) with respect to tolerance index. Because they do not appear to suffer significant yield loss due to reniform nematode, these three cultivars may benefit growers.

Accepted for publication 12 January 2009. Published 12 March 2009.
Report of a Watermelon mosaic potyvirus Strain in Kentucky Undetected by ELISA
Authors: Vincelli Paul , Seebold Kenneth
Published: March 2009

These results indicate that a strain of WMV is present in Kentucky which does not react to a widely used assay for detection of this economically important virus. Prior to this report, it has been unknown whether the recent, widespread occurrence of PVG-positive/CVS-negative cucurbit samples was due to a new variant of a previously recognized potyvirus or a new potyvirus. This report identifies the causal agent for at least some of these anomalous cases.

Accepted for publication 2 January 2009. Published 13 March 2009.
Iris recognition in the presence of ocular disease
Authors: Aslam Tariq Mehmood , Tan Shi Zhuan , Dhillon Baljean
Published: March 2009

Iris recognition systems are among the most accurate of all biometric technologies with immense potential for use in worldwide security applications. This study examined the effect of eye pathology on iris recognition and in particular whether eye disease could cause iris recognition systems to fail. The experiment involved a prospective cohort of 54 patients with anterior segment eye disease who were seen at the acute referral unit of the Princess Alexandra Eye Pavilion in Edinburgh. Iris camera images were obtained from patients before treatment was commenced and again at follow-up appointments after treatment had been given. The principal outcome measure was that of mathematical difference in the iris recognition templates obtained from patients' eyes before and after treatment of the eye disease. Results showed that the performance of iris recognition was remarkably resilient to most ophthalmic disease states, including corneal oedema, iridotomies (laser puncture of iris) and conjunctivitis. Problems were, however, encountered in some patients with acute inflammation of the iris (iritis/anterior uveitis). The effects of a subject developing anterior uveitis may cause current recognition systems to fail. Those developing and deploying iris recognition should be aware of the potential problems that this could cause to this key biometric technology.
Crosstalk between PTEN/Akt2 and TGFβ signaling involving EGF receptor down‐regulation during the tumor promotion process from the early stage in a rat two‐stage hepatocarcinogenesis model
Authors: Taniai Eriko , Kawai Masaomi , Dewa Yasuaki , Nishimura Jihei , Harada Tomoaki , Saegusa Yukie , Matsumoto Sayaka , Takahashi Miwa , Mitsumori Kunitoshi , Shibutani Makoto
Published: March 2009

The present study investigated the involvement of signaling of phosphatase and tensin homolog deleted on chromosome 10 (PTEN)/protein kinase B (Akt) and transforming growth factor‐β (TGFβ) as well as receptor tyrosine kinases in the tumor promotion processes in a two‐stage hepatocarcinogenesis model using male F344 rats. The cellular localization of related molecules was examined in liver cell foci expressing glutathione S‐transferase placental form (GST‐P) at the early stage of tumor promotion by fenbendazole (FB), piperonyl butoxide, or thioacetamide. Distribution in the liver cell foci and neoplastic lesions positive for GST‐P was also examined at the later stage of FB promotion. In contrast to the initiation‐alone cases, subpopulations of GST‐P‐positive foci induced by promotion for 6 weeks, regardless of the promoting chemicals used, enhanced down‐regulation of PTEN and up‐regulation of phosphorylated (active) Akt2 and phosphorylated substrate(s) of Akt‐kinase activity. Also, up‐regulation of TGFβ receptor I and down‐regulation of epidermal growth factor receptor (EGFR) were enhanced in the subpopulation of GST‐P‐positive foci in all promoted cases. A similar pattern of cellular distribution of these molecules was also observed in the neoplastic lesions at the late stage. These results suggest a crosstalk between Akt2 and TGFβ signaling that involves a mechanism requiring EGFR down‐regulation during the entire tumor promotion process starting from the early stage. In particular, a shift in subcellular localization of phosphorylated substrate(s) of Akt from the cell membrane in liver cell foci to the cytoplasm in carcinomas was observed, suggesting an alteration of the function or activity of the corresponding molecule(s). (Cancer Sci 2009; 100: 813–820)
A severe symptom phenotype in tomato in Mali is caused by a reassortant between a novel recombinant begomovirus (Tomato yellow leaf curl Mali virus) and a betasatellite
Authors: CHEN LI‐FANG , ROJAS MARIA , KON TATSUYA , GAMBY KADIATOU , XOCONOSTLE‐CAZARES BEATRIZ , GILBERTSON ROBERT L.
Published: March 2009

Tomato production in West Africa has been severely affected by begomovirus diseases, including yellow leaf curl and a severe symptom phenotype, characterized by extremely stunted and distorted growth and small deformed leaves. Here, a novel recombinant begomovirus from Mali, Tomato yellow leaf curl Mali virus (TYLCMLV), is described that, alone, causes tomato yellow leaf curl disease or, in combination with a betasatellite, causes the severe symptom phenotype. TYLCMLV is an Old World monopartite begomovirus with a hybrid genome composed of sequences from Tomato yellow leaf curl virus‐Mild (TYLCV‐Mld) and Hollyhock leaf crumple virus (HoLCrV). A TYLCMLV infectious clone induced leaf curl and yellowing in tomato, leaf curl, crumpling and yellowing in Nicotiana benthamiana and common bean, mild symptoms in N. glutinosa, and a symptomless infection in Datura stramonium. In a field‐collected sample from a tomato plant showing the severe symptom phenotype in Mali, TYLCMLV was detected together with a betasatellite, identified as Cotton leaf curl Gezira betasatellite (CLCuGB). Tomato plants co‐agroinoculated with TYLCMLV and CLCuGB developed severely stunted and distorted growth and small crumpled leaves. These symptoms were more severe than those induced by TYLCMLV alone, and were similar to the severe symptom phenotype observed in the field in Mali and in other West African countries. TYLCMLV and CLCuGB also induced more severe symptoms than TYLCMLV in the other solanaceous hosts, but not in common bean. The increased symptom severity was associated with hyperplasia of phloem‐associated cells, but relatively little increase in TYLCMLV DNA levels. In surveys of tomato virus diseases in West Africa, TYLCMLV was commonly detected in plants with leaf curl and yellow leaf curl symptoms, whereas CLCuGB was infrequently detected and always in association with the severe symptom phenotype. Together, these results indicate that TYLCMLV causes tomato yellow leaf curl disease throughout West Africa, whereas TYLCMLV and CLCuGB represent a reassortant that causes the severe symptom phenotype in tomato.
Maintenance of genetic variation in plants and pathogens involves complex networks of gene‐for‐gene interactions
Authors: HALL SHARON A. , ALLEN REBECCA L. , BAUMBER RACHEL E. , BAXTER LAURA A. , FISHER KATE , BITTNER‐EDDY PETER D. , ROSE LAURA E. , HOLUB ERIC B. , BEYNON JIM L.
Published: March 2009

The RPP13 [recognition of Hyaloperonospora arabidopsidis (previously known as Peronospora parasitica)] resistance (R) gene in Arabidopsis thaliana exhibits the highest reported level of sequence diversity among known R genes. Consistent with a co‐evolutionary model, the matching effector protein ATR13 (A. thaliana‐recognized) from H. arabidopsidis reveals extreme levels of allelic diversity. We isolated 23 new RPP13 sequences from a UK metapopulation, giving a total of 47 when combined with previous studies. We used these in functional studies of the A. thaliana accessions for their resistance response to 16 isolates of H. arabidopsidis. We characterized the molecular basis of recognition by the expression of the corresponding ATR13 genes from these 16 isolates in these host accessions. This allowed the determination of which alleles of RPP13 were responsible for pathogen recognition and whether recognition was dependent on the RPP13/ATR13 combination. Linking our functional studies with phylogenetic analysis, we determined that: (i) the recognition of ATR13 is mediated by alleles in just a single RPP13 clade; (ii) RPP13 alleles in other clades have evolved the ability to detect other pathogen ATR protein(s); and (iii) at least one gene, unlinked to RPP13 in A. thaliana, detects a different subgroup of ATR13 alleles.
NSAID‐induced antral ulcers are associated with distinct changes in mucosal gene expression
Authors: DESAI J. C. , GOO T. , FUKATA M. , SANYAL S. , DIKMAN A. , MILLER K. , COHEN L. , BROOKS A. , WANG Q. , ABREU M. T. , AISENBERG J.
Published: March 2009

Background  The basis for individual variation in gastroduodenal vulnerability to NSAIDs is not well understood.

Aim  To assess whether a gene expression signature is associated with susceptibility to gastroduodenal ulcerations.

Methods  Twenty‐five Helicobacter pylori negative adults were treated for 7 days with naproxen 500 mg b.d. Subjects underwent baseline and post‐treatment endoscopy, during which biopsies were taken from antrum and duodenum. RNA extraction and cDNA synthesis were performed, followed by PCR of 23 genes relevant to mucosal injury and repair. Fold changes in gene expression were compared between subjects who developed ulcers and those who did not.

Results  Compared with subjects who did not develop ulcers (n = 18), subjects who developed antral ulcers (n = 7) had significantly greater mucosal up‐regulation of interleukin‐8 [Fold change = 33.5 (S.E.M. = 18.5) vs. −7.7 (3.2)] and of cyclo‐oxygenase‐2 [2.3 (1.7) vs. −10.8 (2.2)]. Conversely, non‐ulcer subjects had significantly greater up‐regulation of toll‐like receptor‐4, cyclo‐oxygenase‐1 and hepatocyte growth factor [14.0 (2.2) vs. −0.8 (1.0), 9.8 (2.4) vs. 0.0 (0.7) and 8.2 (2.6) vs. −2.2 (0.3) respectively].

Conclusions  NSAID‐induced antral ulcers are associated with a specific pattern of gastroduodenal mucosal gene expression. These patterns may provide an insight into the molecular basis of individual susceptibility to mucosal injury.
Suppressor of cytokine signalling 1 (SOCS1) is a physiological regulator of the asthma response
Authors: Lee C. , Kolesnik T. B. , Caminschi I. , Chakravorty A. , Carter W. , Alexander W. S. , Jones J. , Anderson G. P. , Nicholson S. E.
Published: March 2009

Background
The molecular determinants of the severity and persistence of allergic asthma remain poorly understood. Suppressor of cytokine signalling 1 (SOCS1) is a negative regulator of IL‐4‐dependent pathways in vitro and might therefore control T‐helper type 2 (Th2) immunity associated traits, such as IgE levels, mucin production, IL‐5 and IL‐13 induction, and eosinophilic mucosal inflammation, which are implicated in allergic asthma.

Objective
To investigate the role of SOCS1 in regulating Th2‐associated disease traits in a murine sub‐chronic aeroallergen‐driven asthma model.

Methods
Following sensitization and challenge with ovalbumin (OVA), bronchoalveolar lavage and serum were collected from mice lacking the Socs1 gene on an IFN‐γ null background (Socs1−/−Ifnγ−/−). The composition of infiltrating cells in the lung, serum IgE and IgG1 levels and cytokine levels were analysed.

Results
Serum IgE levels and infiltrating eosinophils were considerably increased in the lungs of OVA‐treated Socs1−/−Ifnγ−/− mice compared with Ifnγ−/− and C57BL/6 controls. Expression of the Th2 cytokines, IL‐4, IL‐5 and IL‐13 was increased in CD4+ cells and lung tissue from OVA‐treated Socs1−/−Ifnγ−/− mice. IgE, IL‐5 levels and infiltrating eosinophils were also elevated in saline‐treated Socs1−/−Ifnγ−/− mice, suggesting that in the absence of SOCS1, mice are already biased towards a Th2 response. It is at present unclear whether the elevated cytokine levels are sufficient to result in the exacerbated Th2 response to OVA challenge or whether enhanced intra‐cellular signalling also contributes. Surprisingly, of the various IL‐4/IL‐13 responsive genes tested, only Arginase I appeared to be modestly up‐regulated in the lungs of OVA‐treated Socs1−/−Ifnγ−/− mice, suggesting that regulation by SOCS1 occurs primarily in haematopoietic cells and not in the airway epithelium.

Conclusions
Together these results indicate that SOCS1 is an important regulator of the Th2 response.
Characterization of NVX‐207, a novel betulinic acid‐derived anti‐cancer compound
Authors: Willmann M. , Wacheck V. , Buckley J. , Nagy K. , Thalhammer J. , Paschke R. , Triche T. , Jansen B. , Selzer E.
Published: March 2009

Background Development of betulinic acid derivatives for clinical use has been hampered by adverse pharmacological and physico‐chemical characteristics of this class of compounds. We here present a novel semi‐synthetic betulinic acid‐derived drug candidate well suited for further clinical development.

Materials and methods In vitroactivity and mode of action of NVX‐207 were determined using normal as well as cancer cell lines. Gene expression profiling was performed with Affymetrix U133 microarrays. NVX‐207 binding partners were identified using a heterobifunctional chemical crosslinker system. Potential binding proteins were identified by matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) analysis. Clinical studies were conducted in canine cancer patients suffering from spontaneously arising pre‐treated tumours.

Results NVX‐207 showed anti‐tumour activity (mean IC50 = 3·5 μM) against various human and canine cell lines. NVX‐207‐induced apoptosis was associated with activation of the intrinsic apoptotic pathway via cleavage of caspases ‐9, ‐3, ‐7 and of poly (ADP‐ribose) polymerase (PARP). Global gene expression profiling demonstrated regulation of genes associated with lipid metabolism, most notably an upregulation of genes coding for insulin‐induced gene 1 (Insig‐1), low‐density lipoprotein receptor (LDL‐R) and of 3‐hydroxy‐3‐methylglutaryl coenzyme A (HMG‐CoA). NVX‐207 bound to apolipoprotein A‐I, a major regulator of lipid metabolism and cholesterol transport. A phase I/II study in dogs suffering from naturally occurring cancer receiving local treatment of NVX‐207 (10 mg mL−1) showed excellent clinical responses including a complete remission in so far 5/5 treated animals.

Conclusions NVX‐207 is well tolerated and has significant anti‐cancer activityin vitroandin vivoin dogs with treatment‐resistant malignancies.
Biodiversity indicators in European ground waters: towards a predictive model of stygobiotic species richness
Authors: STOCH FABIO , ARTHEAU MALVINA , BRANCELJ ANTON , GALASSI DIANA M. P. , MALARD FLORIAN
Published: March 2009

1. Estimates of species richness obtained from exhaustive field inventories over large spatial scales are expensive and time‐consuming. For this reason, efficiency demands the use of indicators as ‘surrogates’ of species richness. Biodiversity indicators are defined herein as a limited suite of taxonomic groups the species richness of which is correlated with the species richness of all other taxonomic groups present in the survey area.

2. Species richness in ground water was assessed at different spatial scales using data collected from six regions in Europe. In total, 375 stygobiotic species were recorded across 1157 sites and 96 aquifers. The taxonomic groups collected from more than one site and with more than two species (Oligochaeta, Gastropoda, Cyclopoida, Harpacticoida, Ostracoda, Isopoda, Amphipoda, Bathynellacea and Acari) were used to develop nonparametric models to predict stygobiotic biodiversity at the aquifer scale.

3. Pair‐wise correlations between taxonomic groups were low, i.e. variation in species richness of a single taxonomic group did not usually reflect variation of the other groups. In contrast, multiple regressions calculated between species richness of any combination of taxa and extra‐group species richness along the six regions resulted in a number of significant relationships.

4. These results suggest that some taxonomic groups (mainly Copepoda and Amphipoda and, to a lesser extent, Oligochaeta and Gastropoda) combined in different ways across the regions, were good biodiversity indicators in European groundwater ecosystems. However, the uneven distribution of taxonomic groups prevented selection of a common set of indicators for all six regions. Faunal differences among regions are presumably related to both historical and ecological factors, including palaeogeography, palaeoecology, geology, aquifer fragmentation and isolation, and, less clearly, anthropogenic disturbance.
Environmental flows and the European Water Framework Directive
Authors: ACREMAN M. C. , FERGUSON A. J. D.
Published: March 2009

1. Environmental flows is now a widely accepted term that covers the quantity, timing, duration, frequency and quality of water flows required to sustain freshwater, estuarine and near‐shore ecosystems and the human livelihoods and well‐being that depend on them.

2. The Water Framework Directive (WFD) of the European Union does not use the term environmental flows explicitly, but requires member states to achieve good ecological status (GES) in all waterbodies, which is assessed by reference to aquatic biology. Nevertheless, it is accepted that ecologically appropriate hydrological regimes are necessary to meet this status. Implementing environmental flows will be a key measure for restoring and managing river ecosystems.

3. The WFD explicitly requires stakeholder involvement, but this has been interpreted as largely a dissemination exercise by national government agencies. Stakeholders are no longer involved in negotiation over ecological objectives as these are pre‐set in the WFD. However, stakeholders may be more involved in reviewing standards and agreeing to measures to restore river ecosystems to the status required by the WFD.

4. The U.K. has undertaken two major projects to set environmental standards for water resources (i) to define water abstraction limits that maintain a healthy river ecosystem and (ii) to define ecologically appropriate flow releases from reservoirs.

5. Implementation of environmental flows remains a major issue, but new ideas such as time‐limited licences and licence trading are being tried.
Reserve selection for conserving groundwater biodiversity
Authors: MICHEL GEORGES , MALARD FLORIAN , DEHARVENG LOUIS , DI LORENZO TIZIANA , SKET BORIS , DE BROYER CLAUDE
Published: March 2009

1. A possible conservation strategy to minimise the risk of groundwater biodiversity loss due to human activities consists in designing a network of reserve areas at the continental scale that collectively include most groundwater species. To this end, we compared the efficiency of three area selection methods (species richness hotspots, endemism hotspots and complementarity) and examined the influence of spatial constraints (reduced extent and increased aggregation of reserve areas) on the representation of 1059 groundwater species in six European regions.

2. Presence data from a data base elaborated as part of a European initiative on groundwater biodiversity, the PASCALIS project, were referenced onto 4675 grid cells (0.2 by 0.2°). Complementary performed much better than traditional selection methods for maximising species representation in a reserve network arbitrarily limited to 10% of all the cells containing groundwater fauna. It captured 155 more species than areas selected on richness and 77 more species than areas selected on endemism hotspots.

3. Representing species in a specified proportion of their area of occupancy (i.e. 100%, 50% and 10% of the area of occupancy of species occurring in 1, ≤10, and >10 cells, respectively) required inclusion of 46% of the cells containing groundwater fauna. The reserve network needed to achieve this level of coverage may be too large and fragmented to be implemented and managed in practice.

4. Reduction of the reserve areas to 10% of the landscape containing groundwater fauna and their aggregation into a smaller number of cell clusters resulted in a more realistic reserve network that represented 73.8% (782 species) and 59.1% (274 endemics) of the total number of species and endemics, respectively.

5. We propose several research priorities to improve the design of effective groundwater reserve networks in Europe: (i) devising sampling strategies that reduce uncertainties in the placement of reserves and increase the number of alternative reserve networks and (ii) shifting from a grid‐cell selection approach to an aquifer‐selection approach that incorporates species representation targets, minimum space requirement and also socio‐economic costs related to the vulnerability of aquifers and degree of human activity in the catchment.
Influence of geographical extent on typology‐ and model‐based assessments of taxonomic completeness of river macroinvertebrates
Authors: AROVIITA JUKKA , MYKRÄ HEIKKI , MUOTKA TIMO , HÄMÄLÄINEN HEIKKI
Published: March 2009

1. River InVertebrate Prediction and Classification System (RIVPACS)‐type predictive models are increasingly used to assess the biological condition of freshwaters, but management schemes may also be based on a priori groupings of similar water bodies (typologies) to control for natural variation in biota. The two approaches may lead to disagreements of the biological status of a site, depending on, for example, the spatial scale at which assessments are conducted.

2. We used data from 96 reference and 134 potentially impacted sites from Western and Central Finland to compare RIVPACS‐type models and a simple size‐based typology of rivers for the assessment of taxonomic completeness (the quotient of the Observed‐to‐Expected number of predicted taxa, O / E) of riffle macroinvertebrates. We specifically examined how geographical extent influences bioassessment performance (accuracy, precision and sensitivity to detect impact) of the two approaches. To fully examine the behaviour of the O / E‐index with the two approaches at differing spatial scales, we performed all assessments with a full range of thresholds for predicted taxa occurrence probabilities (pt from 0+ to 0.9).

3. Both approaches performed consistently better than the corresponding null models. At the larger extent (i.e. assessment encompassing the whole study area), the RIVPACS‐approach performed in all aspects better than the typology‐approach. However, at the smaller extent (i.e. regional assessments) the RIVPACS‐type models and the typologies showed similar accuracy to predict the actual fauna (mean E), similar precision (SD) of cross‐validated O / E and similar sensitivity to detect sites with human impairment.

4. SD(O / E) decreased (i.e. precision increased) consistently with increasing pt. However, both approaches were most sensitive at intermediate pt:s (c. 0.2–0.6) when taxa with low predicted occurrence probabilities were excluded.

5. Our results show that RIVPACS‐type predictive models are less susceptible to variations in spatial scale, whereas the performance of a priori typologies increases with decreasing spatial extent. Thus, RIVPACS‐type models are more efficient for large‐scale bioassessments, but at restricted spatial scales, or with an otherwise biologically meaningful stratification, simple a priori classifications can be equally useful for the assessment of taxonomic completeness of river macroinvertebrates.
Overexpression of chromatin assembly factor‐1 (CAF‐1) p60 is predictive of adverse behaviour of prostatic cancer
Authors: Staibano Stefania , Mascolo Massimo , Mancini Francesco Paolo , Kisslinger Annamaria , Salvatore Gaetano , Di Benedetto Maria , Chieffi Paolo , Altieri Vincenzo , Prezioso Domenico , Ilardi Gennaro , De Rosa Gaetano , Tramontano Donatella
Published: March 2009

Aims:  Prostatic cancer may remain organ‐confined indefinitely; in a number of patients, however it gives rise to clinical symptoms and death. The biological behaviour of this tumour mostly remains difficult to predict. A promising tool for diagnosis and prognosis of some human tumours is the chromatin assembly factor‐1 (CAF‐1), involved in the control of higher order chromatin organization. The aim was to explore the role of CAF‐1/p60 protein as a new prognostic marker for prostatic cancer.

Methods and results:  The expression of CAF‐1/p60 was evaluated by immunohistochemistry and Western blotting in a selected series of prostatic cancers and in prostatic cancer cell lines. Results were compared with clinicopathological data and outcome of patients. CAF‐1/p60 was expressed in all cases, with a linear increase from low‐grade tumours (Gleason score <7) to high‐grade prostatic cancers (Gleason score >7). By comparing results with follow‐up data, a significant association between overexpression of CAF‐1/p60 and unfavourable behaviour of prostatic cancer emerged, and its predictive value was independent of classical prognostic factors.

Conclusions:  In our series of cases, overexpression of CAF‐1/p60 characterized prostatic cancers with a worse prognosis. CAF‐1/p60 has a potential role as a new reliable prognostic biomarker for prostatic cancer.