bluuebunny/crossref_metadata_2025 huggingface dataset:
A simple method to selectively scale down the self-interaction correction
Authors: Vydrov Oleg A. , Scuseria Gustavo E.
Published: May 2006

The method of Perdew and Zunger is commonly used to correct the self-interaction error of approximate density functionals. However, it has been shown that this orbital-based self-interaction correction (SIC) tends to overcorrect and often impairs molecular properties. We have recently proposed a method to improve the performance of the SIC by scaling it down in many-electron regions. In this communication, we present a simplification of this scheme. For every occupied orbital, we introduce a scaling factor determined by the ratio of the orbital density to the total spin-density. Thus, the magnitude of the correction is adjusted depending on how much orbital densities overlap with one another. Such a modification of the Perdew-Zunger SIC does not add any appreciable time to the computation, but significantly improves the accuracy for a number of benchmark properties.
Three-dimensional simulation of super-radiant Smith-Purcell radiation
Authors: Li D. , Imasaki K. , Yang Z. , Park Gun-Sik
Published: May 2006

A simulation of coherent and super-radiant Smith-Purcell radiation is performed in the gigahertz regime using a three-dimensional particle-in-cell code. The simulation model supposes a rectangular grating to be driven by a single electron bunch and a train of periodic bunches, respectively. The true Smith-Purcell radiation is distinguished from the evanescent wave, which has an angle independent frequency lower than the minimum allowed Smith-Purcell frequency. We also find that the super-radiant radiations excited by periodic bunches are emitted at higher harmonics of the bunching frequency and at the corresponding Smith-Purcell angles.
Comparing responses to phosphorus of field pea (Pisum sativum), canola (rape, Brassica napus) and spring wheat (Triticum aestivum)
Authors: Bolland M. D. A. , Brennan R. F. , White P. F
Published: May 2006

The phosphorus (P) requirements of spring wheat (Triticum aestivum L.) are well known for all soils in south-western Australia; but the P requirements of field pea (Pisum sativum L.) and canola (Brassica napus L.), which are grown in rotation with wheat on marginally acidic to alkaline soils in the region, are not known. In a glasshouse study, the P requirements of field pea and wheat were compared for 16 soils collected throughout the agricultural region. Ten of the 16 soils were also used to compare the P requirements of canola and wheat. The P was applied as powdered single superphosphate, and yield of dried shoots of 42-day-old plants was measured. The amount of P required to produce 90% of the maximum yield of dried shoots (PR90 values) was used to compare the P requirements of the species. To produce 90% of the maximum yield, field pea required less P than wheat in 5 soils, similar P in 2 soils, and more P in 9 soils. Canola required less P than wheat in all 10 soils. We conclude the P requirements of field pea or canola relative to wheat depend on a complex interaction between plant and soil, particularly for field pea relative to wheat. Per unit of applied P, the P concentration in dried shoots decreased in the order canola > wheat > field pea, indicating the order in which plant roots of the 3 species were able to access P from soil.
Occurrence and severity of the weeds Anthriscus caucalis and Torilis nodosa in pyrethrum
Authors: Rawnsley R. P. , Lane P. A. , Brown P. H. , Groom T.
Published: May 2006

Pyrethrum [Tanacetum cinerariifolium (Trevis.) Sch.Bip.] is a short-lived, perennial horticultural crop grown for the production of pyrethrins. Weed management in pyrethrum is heavily reliant on chemical use and has unintentionally selected for a range of species. One of the major concerns to the pyrethrum industry is the presence of Apiaceae species, Anthriscus caucalis M. Bieb and Torilis nodosa (L.) Gaertn. Increased occurrence and severity of infestation of these species in pyrethrum is a threat to the industry through reduced crop yields and increased costs for their control. To determine the severity of this threat, pyrethrum crops were surveyed for the presence and level of infestation of A. caucalis and T. nodosa over 2 years. More than 30% of all pyrethrum crops had either 1 or both species present, with A. caucalis the more prevalent of the 2 species. Although the level of infestation was generally low, 23 pyrethrum crops had a severe or very severe infestation of the species in 2001. The severity of infestation was generally low, although older crops were found to have a higher level of infestation than newly established crops. All pyrethrum crops, which had undergone 4 annual harvests, were found to have Apiaceae weeds present. This work has documented the severity of occurrence of these species and highlighted the need to develop strategic control procedures to reduce their immediate impact and potential threat.
Constructing Race and Civility in Urban America
Authors: Lee Jennifer
Published: May 2006

Images of violence and conflict often go hand-in-hand with life in Black, urban communities, an association buttressed by the sensational media accounts that highlight crime, firebombings and riots. Past scholarly research also depicts interethnic relations in Black neighbourhoods as conflict-ridden, with immigrant merchants pitted against Black customers. However, this paper argues that previous research has been biased toward conflict and controversy and does not reflect the full range of commercial life in Black communities. Based on in-depth interviews and ethnographic research, it investigates both interethnic conflict and co-operation between African American, Jewish and Korean merchants on the one hand and their Black customers on the other, in five predominantly Black neighbourhoods in New York City and Philadelphia. The paper dispels the myth of the ubiquity of urban conflict and argues that civility, routine and 'business as usual' are the norm.
Respectable or Respectful? (In)civility and the City
Authors: Bannister Jon , Fyfe Nick , Kearns Ade
Published: May 2006

Do we stand before a rising tide of incivility, of disrespect? Or, is this the latest moral panic? Examining (the UK) New Labour's approach to incivility in the city, as manifest in the respect and urban renaissance agendas, this paper argues that the current zero-tolerance approach to incivility is based upon a confused understanding of anti-social behaviour and contradictory evidence of its occurrence and impact. Ultimately, it is proposed that a version of urbanity that endeavours to enforce respect and create the respectable city will prove counter-productive. Rather, respect and the respectful city require tolerance of, and engagement with, incivility.
Governing Neighbours: Anti-social Behaviour Orders and New Forms of Regulating Conduct in the UK
Authors: Flint John , Nixon Judy
Published: May 2006

Discourses on anti-social behaviour in the UK are embedded within a wider politics of conduct based around concepts of citizenship, self-regulation, welfare conditionality, obligations to communities and rights and responsibilities. This paper explores how the regulation of behaviour is framed within ideas of community and contractual governance and identifies the central role for housing within strategies aimed at tackling anti-social behaviour and promoting civility. It discusses the use of Anti-social Behaviour Orders in governing conduct within a wider package of regulatory mechanisms including Acceptable Behaviour Contracts and tenancy agreements. An increasing focus on governing the interactions between neighbours is identified along with techniques to achieve this, including the growing use of conditionality in welfare entitlement. The paper argues that the regulation of conduct is symbolic of significant realignments of the roles of various actors in policing residential areas and raises fundamental questions about the link between conduct, citizenship rights and the scope and ambition of governance interventions aimed at reducing anti-social behaviour at individual and community levels.
Ectopic Uterine Ovarian Tissue in Cynomolgus Monkeys
Authors: Kuwamura Yuki , Kakehi Kimiyo , Hirakawa Kimiaki , Miyajima Hiroaki
Published: May 2006

Spontaneous ectopic uterine ovarian tissue was found in 9 of 118 cynomolgus monkeys (Macaca fascicularis), an incidence of 7.6%. These ectopic tissues were minute and were incidentally observed in the parametrium by microscopic examination. They were composed of primordial or primary follicles and ovarian stroma. Ectopic ovarian tissue may result from disturbed migration of the ovarian primordium during embryogenesis.
Nasal Dosimetry of Inhaled Gases and Particles: Where Do Inhaled Agents Go in the Nose?
Authors: Kimbell J. S.
Published: May 2006

The anatomical structure of the nasal passages differs significantly among species, affecting airflow and the transport of inhaled gases and particles throughout the respiratory tract. Since direct measurement of local nasal dose is often difficult, 3-dimensional, anatomically accurate, computational models of the rat, monkey, and human nasal passages were developed to estimate regional transport and dosimetry of inhaled material. The computational models predicted that during resting breathing, a larger portion of inspired air passed through olfactory-lined regions in the rat than in the monkey or human. The models also predicted that maximum wall mass flux (mass per surface area per time) of inhaled formaldehyde in the nonsquamous epithelium was highest in monkeys (anterior middle turbinate) and similar in rats and humans (dorsal medial meatus in the rat and mid-septum in the human, near the squamous/nonsquamous epithelial boundary in both species). For particles that are 5 μm in aerodynamic diameter, preliminary simulations at minute volume flow rates predicted nasal deposition efficiencies of 92%, 11% and 25% in the rat, monkey, and human, respectively, with more vestibular deposition in the rat than in the monkey or human. Estimates such as these can be used to test hypotheses about mechanisms of toxicity and supply species-specific information for risk assessment, thus reducing uncertainty in extrapolating animal data to humans.
Nitrous oxide analgesia for intubating preterm neonates: A pilot study
Authors: Milesi Christophe , Pidoux Odile , Sabatier Elisabeth , Badr Malia , Cambonie Gilles , Picaud Jean Charles
Published: May 2006

Aim: To evaluate the administration of an equimolar mixture of N2O and O2 for intratracheal intubation in preterm neonates with respiratory distress syndrome (RDS). Design: Prospective evaluation of N2O/O2 in premature neonates with RDS. Setting: Tertiary neonatal unit from March to August 2003. Patients: Twenty‐six of 79 neonates admitted for RDS within 48 h of birth. Intervention: N2O/O2 was administered until muscle tone was suppressed. Surfactant was given intratracheally. Patients were extubated as soon as possible. Main outcome measures: The time needed for N2O/O2 to suppress muscle tone, an evaluation of sedation/analgesia through movements of the limbs, and indicators of stress‐related haemodynamic change, all recorded by an independent observer. Results: In the 26 patients, gestational age was 30.5 (25th, 75th percentile: 30, 32) wk and median body weight was 1540 (1220, 1900) g. Postnatal age at intubation was 2 (2, 3) h. N2O/O2 administration time was 8 (6, 10) min (range 4–15 min). Sedation/analgesia was complete in 77% of patients. No significant differences between pre‐procedure and post‐procedure values were found for heart rate (p=0.29) or mean arterial blood pressure (p=0.13) (paired Wilcoxon test). Time needed for intubation was 30 (20, 37) s (range 10–60 s). Side effects included transient agitation (3/26) and retching (2/26). Extubation occurred 5 (5, 10) min (range 2–15 min) after surfactant instillation. Apnoeas occurred in 3/26 patients within 2 h after extubation. Two patients required reintubation to repeat surfactant administration within 24 h after extubation.

Conclusion: N2O/O2 may be helpful for intubation in preterm neonates. Larger randomized, double‐blind studies are needed for a thorough evaluation of effectiveness and safety.
Synchronizing a multicellular system by external input: an artificial control strategy
Authors: Wang Ruiqi , Chen Luonan , Aihara Kazuyuki
Published: May 2006

Motivation: Although there are significant advances on elucidating the collective behaviors on biological organisms in recent years, the essential mechanisms by which the collective rhythms arise remain to be fully understood, and further how to synchronize multicellular networks by artificial control strategy has not yet been well explored.

Results: A control strategy is developed to synchronize gene regulatory networks in a multicellular system when spontaneous synchronization cannot be achieved. We first construct an impulsive control system to model the process of periodically injecting coupling substances with constant or random impulsive control amounts into the common extracellular medium, and further study its effects on the dynamics of individual cells. We derive the threshold of synchronization induced by the periodic substance input. Therefore, we can synchronize the multicellular network to a specific collective behavior by changing the frequency and amplitude of the periodic stimuli. Moreover, a two-stage scheme is proposed to facilitate the synchronization in this paper. We show that the presence of the external input may also initiate different dynamics. The multicellular network of coupled repressilators is used to show the effectiveness of the proposed method. The results not only provide a perspective to understand the interactions between external stimuli and intrinsic physiological rhythms, but also may lead to development of realistic artificial control strategy and medical therapy.

Availability:

Contact:  aihara@sat.t.u-tokyo.ac.jp
Anecdotes, data and regulatory modules
Authors: Balmer James E , Blomhoff Rune
Published: May 2006

Beginning in the late 1980s, Eric Davidson's group at Cal Tech developed a modularity hypothesis of developmental gene regulation, showing that in an expanding number of cases, particular aspects of development were governed by compact ‘modules’ of transcription factor binding sites (TFBSs), and that these modules were separable, complex and interconnected. Davidson made no attempt to further generalize the hypothesis, but others took up the idea, transported it out of development and extended it to a general rule of clustering. Despite such misbegotten origins, the ‘extended’ modularity hypothesis—that TFBSs in general tend to come in compact clusters—has been highly productive, yet it has never been challenged with a large, diverse and unbiased dataset to see how universal it actually is. The aim of the present paper is to do so. Applying human–mouse–rat phylogenetic footprinting to neighbourhoods of a diverse set of TFBSs, including both developmental and non-developmental signals, we find that the extended hypothesis holds in at least 93.5% of cases. Based on this particular sample, we found a mean module length of 609 nucleotides containing, on an average, 24.5 presumptive regulatory signals of length greater than 5 and averaging 8.5 nucleotides each.
Palaeoclimates: the first two billion years
Authors: Kasting James F , Ono Shuhei
Published: May 2006

Earth's climate during the Archaean remains highly uncertain, as the relevant geologic evidence is sparse and occasionally contradictory. Oxygen isotopes in cherts suggest that between 3.5 and 3.2 Gyr ago (Ga) the Archaean climate was hot (55–85 °C); however, the fact that these cherts have experienced only a modest amount of weathering suggests that the climate was temperate, as today. The presence of diamictites in the Pongola Supergroup and the Witwatersrand Basin of South Africa suggests that by 2.9 Ga the climate was glacial. The Late Archaean was relatively warm; then glaciation (possibly of global extent) reappeared in the Early Palaeoproterozoic, around 2.3–2.4 Ga.

Fitting these climatic constraints with a model requires high concentrations of atmospheric CO2or CH4, or both. Solar luminosity was 20–25% lower than today, so elevated greenhouse gas concentrations were needed just to keep the mean surface temperature above freezing. A rise in O2at approximately 2.4 Ga, and a concomitant decrease in CH4, provides a natural explanation for the Palaeoproterozoic glaciations. The Mid-Archaean glaciations may have been caused by a drawdown in H2and CH4caused by the origin of bacterial sulphate reduction. More work is needed to test this latter hypothesis.
The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation
Authors: Roger Andrew J , Hug Laura A
Published: May 2006

Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes.

Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods used and their assumptions. Accurate dating of divergence times among the major eukaryote lineages will require a robust tree of eukaryotes, a much richer Proterozoic fossil record of microbial eukaryotes assignable to extant groups for calibration, more sophisticated relaxed molecular clock methods and many more genes sampled from the full diversity of microbial eukaryotes.
Suppression of human immunodeficiency virus type 1 replication by arginine deiminase of Mycoplasma arginini
Authors: Kubo Makoto , Nishitsuji Hironori , Kurihara Kiyoshi , Hayashi Takaya , Masuda Takao , Kannagi Mari
Published: May 2006

It was found previously that human immunodeficiency virus type 1 (HIV-1)-irrelevant CD8+ cytotoxic T lymphocytes (CTLs) from uninfected donors suppressed HIV-1 replication in a cell-contact-dependent manner. However, one of these CTL lines (CTL-3) also significantly suppressed HIV-1 replication through its supernatant. Here, the suppressive fraction from CTL-3 supernatant was purified and analysed by mass spectrometry. A protein band specific for the suppressive fraction was identified as arginine deiminase from Mycoplasma arginini, which catalyses the hydrolysis of arginine to citrulline. Addition of l-arginine or the use of antibiotics against mycoplasma restored supernatant-mediated but not cell-contact-dependent suppression of HIV-1 replication by CTL-3, clearly indicating that arginine deiminase of M. arginini in the supernatants suppressed HIV-1 replication, which is independent of CD8+ T-cell-mediated HIV-1 suppression via cell contact. Arginine deiminase is known to be a chemotherapeutic agent against arginine-requiring tumours and these results suggest that it also has potential application in antiviral therapy.
Human immunodeficiency virus type 1 Tat increases cooperation between AP-1 and NFAT transcription factors in T cells
Authors: Hidalgo-Estévez Alicia M. , González Esther , Punzón Carmen , Fresno Manuel
Published: May 2006

Human immunodeficiency virus type 1 (HIV-1) Tat affects cellular gene expression through modulation of the activity of different transcription factors. Here, the role of Tat in the cooperation between nuclear factor of activated T cells (NFAT) and activator protein 1 (AP-1) transcription factors was investigated. Constitutive or transient Tat expression in Jurkat T cells enhanced cooperative NFAT/AP-1- but not AP-1-dependent transcription independent of its ability to transactivate the HIV-1 LTR. The enhancing effect of Tat took place after nuclear translocation of NFAT. Furthermore, transactivation of an NFAT/AP-1 reporter by transfection of NFAT and c-Jun was strongly enhanced by simultaneous Tat transfection. Moreover, intracellular Tat expression increased the binding of NFAT/AP-1 complexes to the interleukin 2 promoter without significantly altering NFAT- and AP-1-independent binding. HIV-1 Tat interacted with NFAT but not c-Jun. These results indicate that Tat interacts with NFAT, affecting its cooperation with AP-1, without altering independent binding of these transcription factors to DNA.
In vitro and in vivo mapping of the Prunus necrotic ringspot virus coat protein C-terminal dimerization domain by bimolecular fluorescence complementation
Authors: Aparicio Frederic , Sánchez-Navarro Jesús A. , Pallás Vicente
Published: May 2006

Interactions between viral proteins are critical for virus viability. Bimolecular fluorescent complementation (BiFC) technique determines protein interactions in real-time under almost normal physiological conditions. The coat protein (CP) of Prunus necrotic ringspot virus is required for multiple functions in its replication cycle. In this study, the region involved in CP dimerization has been mapped by BiFC in both bacteria and plant tissue. Full-length and C-terminal deleted forms of the CP gene were fused in-frame to the N- and C-terminal fragments of the yellow fluorescent protein. The BiFC analysis showed that a domain located between residues 9 and 27 from the C-end plays a critical role in dimerization. The importance of this C-terminal region in dimer formation and the applicability of the BiFC technique to analyse viral protein interactions are discussed.
Silencing T cells or T-cell silencing: concepts in virus-induced immunosuppression
Authors: Schneider-Schaulies Sibylle , Dittmer Ulf
Published: May 2006

The ability to evade or suppress the host's immune response is a property of many viruses, indicating that this provides an advantage for the pathogen to spread efficiently or even to establish a persistent infection. The type and complexity of its genome and cell tropism but also its preferred type of host interaction are important parameters which define the strategy of a given virus to modulate the immune system in an optimal manner. Because they take a central position in any antiviral defence, the activation and function of T cells are the predominant target of many viral immunosuppressive regimens. In this review, two different strategies whereby this could be achieved are summarized. Retroviruses can infect professional antigen-presenting cells and impair their maturation and functional properties. This coincides with differentiation and expansion of silencing T cells referred to as regulatory T cells with suppressive activity, mainly to CD8+effector T cells. The second concept, outlined for measles virus, is a direct, contact-mediated silencing of T cells which acquire a transient paralytic state.
Genotyping Hepatitis B virus from whole- and sub-genomic fragments using position-specific scoring matrices in hbv
star
Authors: Myers Richard , Clark Caroline , Khan Arshad , Kellam Paul , Tedder Richard
Published: May 2006

Hepatitis B virus (HBV) genomes have been classified into eight genotypes based on phylogenetic analysis of sequence variation. Identifying and tracking the movement of HBV genotypes is important in terms of both monitoring infection rates and predicting disease and treatment. An HBV genotyping tool has been developed that compares query sequences with position-specific scoring matrices representing the eight HBV genotypes. This tool (hbv
star) is rapid, robust and accurate and assigns genotype based on a statistically defined scoring model. hbv
star confidently assigned 90 % of 590 full-length HBV genomes to an HBV genotype (Z score >2.0). Thirty-two of the residual 48 sequences were identified as non-human primate viruses and 16 sequences were identified as recombinant or putative recombinants. Receiver-Operated Characteristic (ROC) analysis was used to compare the accuracy of genotype prediction using basal core promoter sequences and surface and core genes with the accuracy achieved by using full-length sequences. A web interface to hbv
star is available at http://www.vgb.ucl.ac.uk/starn.shtml.
Infectivity of nanovirus DNAs: induction of disease by cloned genome components of Faba bean necrotic yellows virus
Authors: Timchenko T. , Katul L. , Aronson M. , Vega-Arreguín J. C. , Ramirez B. C. , Vetten H. J. , Gronenborn B.
Published: May 2006

Circumstantial evidence suggests that the genome of Faba bean necrotic yellows virus (FBNYV), a nanovirus, consists of eight distinct, circular, single-stranded DNAs, each of about 1 kb and encoding only one protein. Here, the use of cloned full-length FBNYV DNAs for reproducing FBNYV-like symptoms in Vicia faba, the principal natural host of FBNYV, is reported. Characteristic symptoms of FBNYV infection were obtained in faba bean plants following biolistic DNA delivery or agroinoculation with all eight FBNYV DNAs. Although the eight different DNAs have been invariably detected in field samples infected with the various geographical FBNYV isolates, experimental infection with different combinations of fewer than eight DNAs also led to typical FBNYV symptoms. Even only five genome components, DNA-R, DNA-S, DNA-M, DNA-U1 and DNA-U2, were sufficient for inducing disease symptoms in V. faba upon agroinoculation. Symptomatic plants agroinoculated or bombarded with eight DNAs contained typical FBNYV virions; however, the virus was not transmitted by Aphis craccivora or Acyrthosiphon pisum, two efficient aphid vectors of FBNYV.
In vivo characterization of a group II nucleopolyhedrovirus isolated from Mamestra brassicae (Lepidoptera: Noctuidae) in Japan
Authors: Mukawa Shigeyuki , Goto Chie
Published: May 2006

A Japanese isolate ofMamestra brassicaenucleopolyhedrovirus (MabrNPV) was identified phylogenetically as a group II nucleopolyhedrovirus (NPV) that is related closely to other NPVs isolated fromMamestraspp. based on nucleotide sequence data of itspolh,egtandlef-3genes. The multiplication of MabrNPV inM. brassicaelarvae was characterized following inoculation at various doses and in combination with the fluorescent brightener Tinopal by measuring temporal changes in the concentrations of its viral DNA using real-time quantitative PCR. The growth curves of budded-virus replication were analysed by fitting the data of viral DNA concentration in the host haemolymph to a modified Gompertz model. When fifth-instar larvae were inoculated with an LD95equivalent dose of MabrNPV and Tinopal, the time lag between the onset of primary and secondary infection was estimated to be 25 h. Another 65 h was required to reach a plateau titre equivalent to a level of 109virions ml−1in the haemolymph. All larvae died during the sixth instar following this inoculation regime. In contrast, following inoculation with a 1000-fold higher dose of MabrNPV and Tinopal, the time lag between the onset of primary and secondary infection was only 20 h. Subsequently, the same plateau titre was reached after a further 20 h. Following this inoculation regime, most larvae died during the fifth instar. Quantification of viral DNA by real-time quantitative PCR and application of the Gompertz model are valuable for the characterization of baculovirus replicationin vivo.
Genome‐wide transcriptional profiling in human squamous cell carcinoma of the skin identifies unique tumor‐associated signatures
Authors: KATHPALIA Vinnie P. , MUSSAK Erich N. , CHOW Selwyn S. , LAM Phillip H. , SKELLEY Nathan , TIME Michael , MARKELEWICZ Robert J. , KANDUC Darja , LOMAS Lucy , XIANG Zhaoying , SINHA Animesh A.
Published: May 2006

The elucidation of specific genetic changes associated with human cancer pathogenesis has focused efforts to relate such changes to the neoplastic phenotype. To further our understanding of the genetic basis of human squamous cell carcinoma (SCC) of the skin, this study used a genome‐wide (12 627 sequences) approach to determine transcriptional signatures in lesional and nonlesional sites from five SCC patients. Several novel genes involving the p53 pathway, anti‐apoptotic pathways, signal transduction, structural loss and DNA replication, including BCL2A1, MUC4, PTPN11 (SHP2) and FGF9, are upregulated in SCC and could warrant further study regarding their role in disease pathogenesis. SCC pathology is likely combinatorial in nature involving the compounded changes from several cellular processes.
Successful treatment of diabetic gangrene with topical application of a mixture of peripheral blood mononuclear cells and basic fibroblast growth factor
Authors: ASAI Jun , TAKENAKA Hideya , ICHIHASHI Kaori , UEDA Eiichiro , KATOH Norito , KISHIMOTO Saburo
Published: May 2006

Diabetic gangrene is a non‐healing skin ulcer that is often resistant to most common treatments. It is caused by microvascular disorders and an immunocompromised state which are induced by diabetes mellitus. We report a 65‐year‐old man with an aggressive, refractory diabetic gangrene on his left foot. Treatment of his diabetic gangrene with topical application of a mixture of peripheral blood mononuclear cells (PBMC) and basic fibroblast growth factor (bFGF) resulted in a dramatic improvement in a short time. The ulcer was completely closed and, in the past 6 months, no new ulceration has been observed. The patient is able to stand and walk by himself. Topical application of a mixture of PBMC and bFGF appears to be a useful, non‐invasive and convenient method for the treatment of diabetic gangrene.
Public sector managed care: a comparative evaluation of substance abuse treatment in three counties
Authors: Beattie Martha , McDaniel Patricia , Bond Jason
Published: May 2006

Aims  A study of publicly funded substance abuse treatment systems compared MidState, a county that reorganized its treatment system using managed care principles, to two other California counties that took different approaches, NorthState and SouthState. It was hypothesized that MidState would have better outcomes due to its emphasis on quality of care.

Design  This natural experiment compared the ‘experimental’ county, MidState, to two ‘control’ counties, assessing client outcomes following treatment. Administrative and historical exigencies that may affect system differences were explored in interviews with treatment program managers and staff.

Settings  Comparison counties were selected using treatment system and county census data, maximizing similarities to enhance internal validity.

Participants  Adult clients (n = 681) were interviewed when beginning treatment and 12 months later (81% response rate). In addition, 50 treatment program managers and staff members across the three counties were interviewed during the year of client recruitment.

Measurements  Client interviews assessed functioning in the seven Addiction Severity Index domains—alcohol, drug, psychiatric, legal, employment, medical and family/social.

Findings  Outcomes (differences between baseline and 12 month composite scores) did not differ between counties in six of seven domains; in the seventh, psychiatric functioning, SouthState had better outcomes than MidState. Staff interviews indicated generally similar treatment strategies across counties, with MidState supplying greater oversight and performance standards.

Conclusions  Managed care in public sector treatment generally did not result in poorer outcomes. Future attention in MidState to the barriers to successful implementation of individualized treatment, and to dual diagnosis treatment, might bring more positive results.
Nicotine dependence is associated with compulsive alcohol craving
Authors: Hillemacher Thomas , Bayerlein Kristina , Wilhelm Julia , Frieling Helge , Thürauf Norbert , Ziegenbein Marc , Kornhuber Johannes , Bleich Stefan
Published: May 2006

Aims  To investigate a possible association of nicotine dependence and alcohol craving.

Design  A prospective cross‐sectional study on patients diagnosed with alcohol dependence.

Setting  Detoxification unit of a regional psychiatric hospital.

Participants  A total of 127 smoking male patients were included in the study at admission for detoxification from alcohol.

Measurements  The Fagerström Test for Nicotine Dependence (FTND) was used to assess the severity of nicotine dependence while the Obsessive Compulsive Craving Scale (OCDS) was used to measure alcohol craving. The OCDS was assessed at admission and after 7 days of withdrawal treatment, distinguishing the total score, the obsessive and the compulsive subscale.

Findings  Spearman’s correlation revealed a significant association between the extent of alcohol craving and the FTND score (day 0, n = 127: OCDS total score r = 0.238, P = 0.007; OCDS compulsive score r = 0.280, P = 0.001; day 7; n = 94: OCDS total score r = 0.212, P = 0.040; OCDS compulsive score r = 0.225, P = 0.029).

Conclusions  The severity of nicotine dependence is associated with higher craving in alcohol‐dependent patients. These results point towards shared pathophysiological mechanisms in alcohol craving and nicotine addiction.
Prevalence and sociodemographics of reflux symptoms in Germany – results from a national survey
Authors: NOCON M. , KEIL T. , WILLICH S. N.
Published: May 2006

Background

Although gastro‐oesophageal reflux disease is a common gastrointestinal disorder, the prevalence rates differ depending on the population studied.

Aim

To determine the prevalence of reflux symptoms in the German adult population and any associations with age, gender or socio‐economic status.

Methods

A total of 7124 subjects were interviewed as part of the German National Health Interview and Examination Survey, which is a representative sample of the general adult population. The prevalence of mild, moderate or severe heartburn or regurgitation was calculated. Logistic regression models were developed to determine the relationship between reflux symptoms and sociodemographic factors such as age, gender and socio‐economic status.

Results

The overall prevalence of moderate and severe reflux symptoms was 14% and 4%, respectively. The prevalence increased with age and was highest in the age group 60–69 years with 25% of these subjects reporting moderate or severe reflux symptoms. Being male, it increased the risk of mild, but not of moderate or severe symptoms. Lower socio‐economic status was associated with moderate or severe symptoms.

Conclusions

Because of their high prevalence, reflux symptoms are of major public health importance.
Inhalation induction using sevoflurane in children: the single‐breath vital capacity technique compared to the tidal volume technique*
Authors: Lejus C. , Bazin V. , Fernandez M. , Nguyen J. M. , Radosevic A. , Quere M. F. , Le Roux C. , Le Corre A. , Pinaud M.
Published: May 2006

The single‐breath vital capacity technique is suitable for inhalation induction of anaesthesia, using sevoflurane in children aged > 5 years. The purpose of this randomised trial was to compare the single breath vital capacity technique with the conventional tidal volume technique. Seventy‐ three ASA 1 or 2 children were instructed during the pre‐operative visit in the vital capacity technique. The main criterion measured was time to loss of the eyelash reflex. Induction was performed using a circle‐absorber breathing circuit primed with sevoflurane 7% in 50% nitrous oxide/oxygen with 6 l.min−1 fresh gas flow. Time required for induction, haemodynamic changes, airway tolerance and side‐effects were recorded. The children's opinion on the technique used was scored using a visual analogue scale (0–100) and a Smiley scale (0–10). The time to loss of the eyelash reflex was found to be reduced in the vital capacity group compared to the tidal volume group. The time to central myosis, to achieve bispectral index values 60 and 40, haemodynamic changes, respiratory events and side‐effect incidences were similar in both groups. However, we found that the vital capacity technique was preferred by the children to the tidal volume technique.
AluyMICB dimorphism within the class I region of the major histocompatibility complex is associated with asthma and airflow obstruction in the Busselton population
Authors: Hui J. , Palmer L. J. , James A. L. , Musk A. W. , Beilby J. P.
Published: May 2006

Aim
To examine the association between the Alu dimorphism within the first intron of the MICB gene and asthma and airflow obstruction.

Background
The highly polymorphic non‐classical MHC class I polypeptide‐related (MIC) genes, MICA and MICB, encode stress inducible glycoproteins, which are expressed on a variety of epithelial cells, including those of the lungs.

Methods
AluyMICB genotyping was performed on 1109 subjects from the Busselton Health Study. From a standard questionnaire, 359 individuals indicated that they had been diagnosed by a doctor with asthma. Lung function was assessed by the forced expired volume in 1 second (FEV1) and expressed as a percent of the predicted value. Airflow obstruction was defined as FEV1<80% predicted.

Results
In men, a dominant relationship was found between the AluyMICB DD genotype and asthma (P=0.006; χ22=7.65). Furthermore, multivariate analysis adjusted for age, height, weight and body mass index (BMI) showed a relationship between DD genotype and asthma in men in a dominant model (odds ratio (OR)=1.97; 95% confidence interval (CI)=1.11–3.51; P=0.021). In women, an association was found between the AluyMICB II genotype and FEV1 percent predicted as a continuous variable (P=0.001). When adjusted for age and BMI, it showed a significant relationship between AluyMICB and airflow obstruction in a dominant model (OR=14.11%, 95% CI 3.29–60.57, P<0.001). However, no association was found between the AluyMICB II genotypes and airflow obstruction in men.

Conclusion
These findings suggest the possible involvement of a MHC class I gene in abnormal airway structure in women and airway function in men.
Chemokine receptor expression and modulation by Mycobacterium tuberculosis antigens on mononuclear cells from human lymphoid tissues
Authors: Arias Mauricio A. , Pantoja Adelis E. , Jaramillo Gabriela , Paris Sara C. , Shattock Robin J. , García Luis F. , Griffin George E.
Published: May 2006

Chemokine receptor switching on lymphoid cells is an important factor regulating migration and homing, but little is known about the expression of such molecules during Mycobacterium tuberculosis infection in humans. We describe CCR2, CCR5 and CCR7 expression on human cells from blood, spleen and pulmonary hilar lymph nodes (PHLN) stimulated by M. tuberculosis antigens. CCR2 was not expressed by CD3+ cells regardless of the presence of antigen, but was highly expressed on CD14+ CD63+ monocytes/macrophages. CCR2 decreased on splenic monocytes/macrophages by nearly 50% in culture, independent of antigen, but remained high in blood and PHLN. CCR5 was low in CD3+ cells and was down‐regulated by M. tuberculosis antigens on blood and splenic cells but not in PHLN. CCR5 was highly expressed on monocytes/macrophages and was down‐regulated by M. tuberculosis antigens at 48 hr only in blood. Less than 15% of CD3+ cells from spleen and PHLN were CCR7+, whereas nearly 40% from blood expressed this receptor on primary isolation. However, CCR7 in PHLN increased in culture, independent of antigen. Monocytes/macrophages did not express CCR7. Thus, we characterize, for the first time, chemokine receptor expression and differential modulation by M. tuberculosis antigens on human mononuclear cells from spleen, blood and PHLN. Knowledge of chemokine receptor switching in human lymphoid tissue provides novel insight into mechanisms of the immune response to M. tuberculosis with potential effects on directing cell trafficking.
On plotting species abundance distributions
Authors: GRAY JOHN S. , BJØRGESÆTER ANDERS , UGLAND KARL. I.
Published: May 2006

There has been a revival of interest in species abundance distribution (SAD) models, stimulated by the claim that the log‐normal distribution gave an underestimate of the observed numbers of rare species in species‐rich assemblages. This led to the development of the neutral Zero Sum Multinomial distribution (ZSM) to better fit the observed data.

Yet plots of SADs, purportedly of the same data, showed differences in frequencies of species and of statistical fits to the ZSM and log‐normal models due to the use of different binning methods.

We plot six different binning methods for the Barro Colorado Island (BCI) tropical tree data. The appearances of the curves are very different for the different binning methods. Consequently, the fits to different models may vary depending on the binning system used.

There is no agreed binning method for SAD plots. Our analysis suggests that a simple doubling of the number of individuals per species in each bin is perhaps the most practical one for illustrative purposes. Alternatively rank‐abundance plots should be used.

For fitting and testing models exact methods have been developed and application of these does not require binning of data. Errors are introduced unnecessarily if data are binned before testing goodness‐of‐fit to models.
Modelling the impacts of two exotic invasive species on a native butterfly: top‐down vs. bottom‐up effects
Authors: KEELER MARGARET S. , CHEW FRANCES S. , GOODALE BRITTON C. , REED J. MICHAEL
Published: May 2006

Exotic invasive species can influence population dynamics of native species through top‐down or bottom‐up forces. The present study examined separate and interactive effects of multiple exotic species invasions on the native mustard white butterfly, Pieris napi oleracea Harris (Lepidoptera: Pieridae), using a stochastic simulation model.

P. n. oleracea populations in North America have decreased regionally since the 1860s. Competition with an exotic congener (P. rapae L.), loss of native host plants and parasitism by the introduced broconid wasp (Cotesia glomerata L.), have been suggested to be independently responsible for its decline. The present study examined these hypotheses, as well as an alternative, invasion by an exotic crucifer, garlic mustard (Alliaria petiolata[Bieb.] Cavara & Grande).

A stochastic simulation model of P. n. oleracea population dynamics revealed that decreasing the number of host plants available for oviposition and larval development (i.e. habitat loss), sharply reduced the probability of populations persistence and decreased population size for those that persisted.

Simulated invasion by garlic mustard also substantially decreased both probability of persistence (= 0 at approximately 50% cover) and mean population size. Persistence probability never reached zero under any C. glomerata scenarios, even when larval mortality in the second generation due to parasitism was 100%. The impact of garlic mustard was intensified by the addition of C. glomerata parasitism.

Results suggest that bottom‐up forces, loss of host plants through forest understorey loss and/or garlic mustard invasion are the most important forces driving P. n. oleracea population decline. Parasitism by C. glomerata may interact to reduce P. n. oleracea populations more rapidly, but appears insufficient alone to cause local extinction.
Impact of transgenic potatoes expressing anti‐bacterial agents on bacterial endophytes is comparable with the effects of plant genotype, soil type and pathogen infection
Authors: RASCHE FRANK , VELVIS HENK , ZACHOW CHRISTIN , BERG GABRIELE , VAN ELSAS JAN D. , SESSITSCH ANGELA
Published: May 2006

Blackleg and soft rot disease of potatoes Solanum tuberosum L., mainly caused by the bacterial pathogen Erwinia carotovora ssp. atrospetica (Eca), lead to enormous yield losses world‐wide. Genetically modified (GM) potatoes producing anti‐bacterial agents, such as cecropin/attacin and T4 lysozyme, may offer effective future pathogen control strategies. Because of concerns about undesirable ecological side‐effects of GM crops, it is important to analyse the potential environmental impact of GM crops carefully. The objective of this study was to investigate the effect of GM potatoes with anti‐bacterial activity on the diversity and functional abilities of bacteria colonizing the intercellular spaces and vascular tissues (endosphere) of potato plants.

A greenhouse experiment was performed to analyse the effect of GM potatoes expressing either attacin/cecropin or T4 lysozyme on endophytic bacterial communities. Endophytic bacteria colonizing the GM potato lines as well as their nearly isogenic wild types were analysed at two vegetation stages. In order to compare GM‐related variations with impacts caused by changing environmental conditions, potatoes were cultivated in two different soil types, and challenged with the pathogen Eca. Endophytic diversity was assessed by 16S rRNA‐based terminal‐restriction fragment length polymorphism (T‐RFLP) analysis. Cultivated community members were identified by 16S rRNA gene analysis and screened for a range of plant growth‐promoting and plant pathogen‐antagonistic abilities.

Both genetic transformation events induced a differentiation in the community structures of associated bacterial populations and in the related functional abilities of cultivated bacterial endophytes. In comparison with the other factors analysed, the impact of both genetic modification types was minor or comparable with the variations caused by plant genotype, vegetation stage, pathogen exposure and soil type.

Synthesis and applications. This study has shown that the expression of anti‐bacterial proteins may affect bacterial endophytes; however, the impacts were no greater than those of other factors analysed. Future risk assessment studies of GM crops should consider different environmental factors. This study contributes to the ongoing risk assessment of GM crops and provides valuable baseline information for prospective GM crop assays.