bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamics of glass-forming liquids. XIII. Microwave heating in slow motion
Authors: Huang Wei , Richert Ranko
Published: May 2009

Using time-resolved nonlinear dielectric relaxation measurements at fields as high as 450 kV/cm, the nonthermal effects of energy absorption are studied for simple and associating polar liquids in their supercooled state. The experiment is a low frequency analog of microwave heating and facilitates tracking the flow of energy in time, as it accumulates in slow degrees of freedom and transfers eventually to the vibrational heat bath of the liquid. Most findings agree with a phenomenological model of heterogeneous relaxation regarding structure and configurational temperature. The relevant thermal behavior of monohydroxy alcohols differs considerably from the cases of simple nonassociating liquids due to their distinct origins of the prominent dielectric absorption mode for the two classes of liquids. Nonthermal effects are observed as dynamics that are accelerated without increasing sample temperature, but for the present low frequencies the changes remain too small to explain the high efficiencies reported for microwave chemistry. Limitations as to how rapidly the faster relaxation time constants are able to adjust to temperature separate the modes of the dispersive α-relaxation into a “relaxation” and an “aging” regime, thereby explaining the incompatibility of heterogeneous dynamics with common physical aging observations.
Absolute x-ray yields from laser-irradiated germanium-doped low-density aerogels
Authors: Fournier K. B. , Satcher J. H. , May M. J. , Poco J. F. , Sorce C. M. , Colvin J. D. , Hansen S. B. , MacLaren S. A. , Moon S. J. , Davis J. F. , Girard F. , Villette B. , Primout M. , Babonneau D. , Coverdale C. A. , Beutler D. E.
Published: May 2009

The x-ray yields from laser-irradiated germanium-doped ultra-low-density aerogel plasmas have been measured in the energy range from sub-keV to ≈15 keV at the OMEGA laser facility at the Laboratory for Laser Energetics, University of Rochester. The targets’ x-ray yields have been studied for variation in target size, aerogel density, laser pulse length, and laser intensity. For targets that result in plasmas with electron densities in the range of ≈10% of the critical density for 3ω light, one can expect 10–11 J/sr of x rays with energies above 9 keV, and 600–800 J/sr for energies below 3.5 keV. In addition to the x-ray spectral yields, the x-ray temporal waveforms have been measured and it is observed that the emitted x rays generally follow the delivered laser power, with late-time enhancements of emitted x-ray power correlated with hydrodynamic compression of the hot plasma. Further, the laser energy reflected from the target by plasma instabilities is found to be 2%–7% of the incident energy for individual beam intensities ≈1014–1015 W/cm2. The propagation of the laser heating in the target volume has been characterized with two-dimensional imaging. Source-region heating is seen to be correlated with the temporal profile of the emitted x-ray power.
A central role for venom in predation by
Varanus komodoensis
(Komodo Dragon) and the extinct giant
Varanus
(
Megalania
)
priscus
Authors: Fry Bryan G. , Wroe Stephen , Teeuwisse Wouter , van Osch Matthias J. P. , Moreno Karen , Ingle Janette , McHenry Colin , Ferrara Toni , Clausen Phillip , Scheib Holger , Winter Kelly L. , Greisman Laura , Roelants Kim , van der Weerd Louise , Clemente Christofer J. , Giannakis Eleni , Hodgson Wayne C. , Luz Sonja , Martelli Paolo , Krishnasamy Karthiyani , Kochva Elazar , Kwok Hang Fai , Scanlon Denis , Karas John , Citron Diane M. , Goldstein Ellie J. C. , Mcnaughtan Judith E. , Norman Janette A.
Published: May 2009

The predatory ecology of
Varanus komodoensis
(Komodo Dragon) has been a subject of long-standing interest and considerable conjecture. Here, we investigate the roles and potential interplay between cranial mechanics, toxic bacteria, and venom. Our analyses point to the presence of a sophisticated combined-arsenal killing apparatus. We find that the lightweight skull is relatively poorly adapted to generate high bite forces but better adapted to resist high pulling loads. We reject the popular notion regarding toxic bacteria utilization. Instead, we demonstrate that the effects of deep wounds inflicted are potentiated through venom with toxic activities including anticoagulation and shock induction. Anatomical comparisons of
V. komodoensis
with
V.
(
Megalania
)
priscus
fossils suggest that the closely related extinct giant was the largest venomous animal to have ever lived.
Elucidating geological and biological processes underlying the diversification of Sulawesi tarsiers
Authors: Merker Stefan , Driller Christine , Perwitasari-Farajallah Dyah , Pamungkas Joko , Zischler Hans
Published: May 2009

Because of their exceptionally long independent evolution, a range diminution of their Eocene relatives, and a remarkable subsequent diversification in Southeast Asia, tarsiers are of particular importance to evolutionary primatologists. Little is known, however, on the processes shaping the radiation of these small enigmatic primates—especially on the Indonesian island of Sulawesi, their center of endemism. Geological reconstructions and progress in applying DNA sequence information to divergence dating now provide us with the tools and background to comprehend tarsier dispersal. Here, we describe effects of plate-tectonic movements, Pleistocene sea level changes, and hybridization on the divergence of central Sulawesi tarsiers. We analyzed 12 microsatellites, the cytochrome
b
gene, the hypervariable region I of the mitochondrial control region, and the sex-determining region on the Y-chromosome from 144 specimens captured along a transect crossing a species boundary and a contact zone between 2 microplates. Based on these differentially inherited genetic markers, geographic information, and recordings of vocalizations, we demonstrate that the species boundary coincides with a tectonic suture. We estimate the most recent common ancestor of the 2 taxa to have lived 1.4 Mya, we describe asymmetrical introgressive hybridization, and we give evidence of unbiased dispersal in one species and male-biased dispersal in another species. This study exemplifies that the distribution of tarsier acoustic forms on Sulawesi is consistent with the allocation of genetic variability and that plate-tectonic and glacial events have left traceable marks in the biogeography of this island's unique fauna.
Over three millennia of mercury pollution in the Peruvian Andes
Authors: Cooke Colin A. , Balcom Prentiss H. , Biester Harald , Wolfe Alexander P.
Published: May 2009

We present unambiguous records of preindustrial atmospheric mercury (Hg) pollution, derived from lake-sediment cores collected near Huancavelica, Peru, the largest Hg deposit in the New World. Intensive Hg mining first began
ca.
1400 BC, predating the emergence of complex Andean societies, and signifying that the region served as a locus for early Hg extraction. The earliest mining targeted cinnabar (HgS) for the production of vermillion. Pre-Colonial Hg burdens peak
ca.
500 BC and
ca.
1450 AD, corresponding to the heights of the Chavín and Inca states, respectively. During the Inca, Colonial, and industrial intervals, Hg pollution became regional, as evidenced by a third lake record ≈225 km distant from Huancavelica. Measurements of sediment-Hg speciation reveal that cinnabar dust was initially the dominant Hg species deposited, and significant increases in deposition were limited to the local environment. After conquest by the Inca (
ca.
1450 AD), smelting was adopted at the mine and Hg pollution became more widely circulated, with the deposition of matrix-bound phases of Hg predominating over cinnabar dust. Our results demonstrate the existence of a major Hg mining industry at Huancavelica spanning the past 3,500 years, and place recent Hg enrichment in the Andes in a broader historical context.
Impaired interferon signaling is a common immune defect in human cancer
Authors: Critchley-Thorne Rebecca J. , Simons Diana L. , Yan Ning , Miyahira Andrea K. , Dirbas Frederick M. , Johnson Denise L. , Swetter Susan M. , Carlson Robert W. , Fisher George A. , Koong Albert , Holmes Susan , Lee Peter P.
Published: May 2009

Immune dysfunction develops in patients with many cancer types and may contribute to tumor progression and failure of immunotherapy. Mechanisms underlying cancer-associated immune dysfunction are not fully understood. Efficient IFN signaling is critical to lymphocyte function; animals rendered deficient in IFN signaling develop cancer at higher rates. We hypothesized that altered IFN signaling may be a key mechanism of immune dysfunction common to cancer. To address this, we assessed the functional responses to IFN in peripheral blood lymphocytes from patients with 3 major cancers: breast cancer, melanoma, and gastrointestinal cancer. Type-I IFN (IFN-α)-induced signaling was reduced in T cells and B cells from all 3 cancer-patient groups compared to healthy controls. Type-II IFN (IFN-γ)-induced signaling was reduced in B cells from all 3 cancer patient groups, but not in T cells or natural killer cells. Impaired-IFN signaling was equally evident in stage II, III, and IV breast cancer patients, and downstream functional defects in T cell activation were identified. Taken together, these findings indicate that defects in lymphocyte IFN signaling arise in patients with breast cancer, melanoma, and gastrointestinal cancer, and these defects may represent a common cancer-associated mechanism of immune dysfunction.
Competitive facilitation of drug-resistant
Plasmodium falciparum
malaria parasites in pregnant women who receive preventive treatment
Authors: Harrington W. E. , Mutabingwa T. K. , Muehlenbachs A. , Sorensen B. , Bolla M. C. , Fried M. , Duffy P. E.
Published: May 2009

Intermittent preventive treatment in pregnancy (IPTp) is used to prevent
Plasmodium falciparum
malaria. However, parasites resistant to the IPTp drug sulfadoxine-pyrimethamine (SP) have emerged worldwide, and infections with mixed resistant and susceptible parasites are exacerbated by pyrimethamine in mice. In a prospective delivery cohort in Muheza, Tanzania, we examined the effects of SP IPTp on parasite resistance alleles, parasite diversity, level of parasitemia, and inflammation in the placenta. IPTp use was associated with an increased fraction of parasites carrying the resistance allele at DHPS codon 581, an increase in the level of parasitemia, and more intense placental inflammation. The lowest mean level of parasite diversity and highest mean level of parasitemia occurred in women after recent IPTp use. These findings support a model of parasite release and facilitation, whereby the most highly resistant parasites out-compete less fit parasite populations and overgrow under drug pressure. Use of partially effective anti-malarial agents for IPTp may exacerbate malaria infections in the setting of widespread drug resistance.
Distinct subsets of unmyelinated primary sensory fibers mediate behavioral responses to noxious thermal and mechanical stimuli
Authors: Cavanaugh Daniel J. , Lee Hyosang , Lo Liching , Shields Shannon D. , Zylka Mark J. , Basbaum Allan I. , Anderson David J.
Published: May 2009

Behavioral responses to painful stimuli require peripheral sensory neurons called nociceptors. Electrophysiological studies show that most C-fiber nociceptors are polymodal (i.e., respond to multiple noxious stimulus modalities, such as mechanical and thermal); nevertheless, these stimuli are perceived as distinct. Therefore, it is believed that discrimination among these modalities only occurs at spinal or supraspinal levels of processing. Here, we provide evidence to the contrary. Genetic ablation in adulthood of unmyelinated sensory neurons expressing the G protein-coupled receptor Mrgprd reduces behavioral sensitivity to noxious mechanical stimuli but not to heat or cold stimuli. Conversely, pharmacological ablation of the central branches of TRPV1+nociceptors, which constitute a nonoverlapping population, selectively abolishes noxious heat pain sensitivity. Combined elimination of both populations yielded an additive phenotype with no additional behavioral deficits, ruling out a redundant contribution of these populations to heat and mechanical pain sensitivity. This double-dissociation suggests that the brain can distinguish different noxious stimulus modalities from the earliest stages of sensory processing.
Crystal structure of the EutL shell protein of the ethanolamine ammonia lyase microcompartment
Authors: Sagermann Martin , Ohtaki Akashi , Nikolakakis Kiel
Published: May 2009

Bacterial microcompartments (BMCs) are specialized organelles that use proteinaceous membranes to confine chemical reaction spaces. The ethanolamine ammonialyase microcompartment of
Escherichia coli
represents such a class of cytosolic organelles that enables bacteria to survive on small organic molecules such as ethanolamine as the sole source for carbon and nitrogen. We present here the crystal structure of the shell protein EutL at 2.2-Å resolution. With 219 residues, it is the largest representative of this BMC's shell proteins. In the crystal, EutL forms a trimer that exhibits a hexagonally shaped tile structure. The tiles arrange into a tightly packed 2D array that is likely to resemble the proteinaceous membrane of the intact BMC. In contrast to other BMC shell proteins, which have only 1 pore per tile, EutL exhibits 3 pores per tile, thereby significantly increasing the overall porosity of this protein membrane. Each of the individual pores is lined with negatively charged residues and aromatic residues that are proposed to facilitate passive transport of specific solutes. The characteristic shape of the hexagonal tile, which is also found in the microcompartments of carbon-fixating bacteria, may present an inherent and fundamental building unit that may provide a general explanation for the formation of differently sized microcompartments.
The influence of BMI, smoking, and age on vaginal erosions after synthetic mesh repair of pelvic organ prolapses. A multicenter study
Authors: ARACO FRANCESCO , GRAVANTE GIANPIERO , SORGE ROBERTO , OVERTON JOHN , DE VITA DAVIDE , PRIMICERIO MARIO , DATI STEFANO , ARACO PLACIDO , PICCIONE EMILIO
Published: May 2009

Objective. To study the influence of body mass index (BMI), smoking, and age on the risk of vaginal erosions after mesh repair of pelvic prolapses. Design. Retrospective study. Setting. Three university and community hospitals. Population and sample. Patients that underwent mesh correction of prolapses between 2002 and 2007. Excluded were those with stress urinary incontinence, ongoing clinical infections, with a complete antibiotic course in the last six months and with systemic diseases affecting tissue oxygenation. Methods. Revision of medical notes. Main outcome measures. Risk contributions for age, smoking, and BMI on the occurrence of vaginal erosions. Results. Data were collected from 460 patients. Postoperative erosions were present in 7%. BMI greater than 30 conferred a 10.1‐fold increase in the risk of developing erosions, smoking a 3.7‐fold increase, and age greater than 60 years a 2.2‐fold increase. A cut‐off value of seven pack years was determined for smoking where the risk associated with light smokers was similar to that of non‐smokers. Conclusions. BMI, smoking, and age are important risk factors for pelvic organ prolapse surgery. Our data could be used to stratify patients according to their risk so that preventative measures can be taken in high‐risk patients.
Computed tomography appearance of ovarian fibrothecomas with and without torsion
Authors: Mak Chee-Wai , Tzeng Wen-Sheng , Chen Chin-Yu
Published: May 2009

Background: Fibrothecomas are the most common solid ovarian tumors and may undergo torsion. Early diagnosis of these tumors is important in order to allow prompt surgical treatment.

Purpose: To describe the features of ovarian fibrothecoma on computed tomography (CT) and to determine the possibility of detecting tumor torsion in this kind of tumor.

Material and Methods: The CT images of 11 patients with ovarian fibrothecomas in the past 8 years at our hospital were retrospectively reviewed. The CT attenuation values of each tumor were measured in both non-enhanced and enhanced scans. The size and degree of enhancement were evaluated and correlated with tumor torsion. All cases were pathologically proven.

Results: Three kinds of tumor pattern were found: 1) homogeneous tumor with significant enhancement containing scattered, low-attenuated regions after contrast injection; 2) heterogeneous tumor with mild enhancement after contrast injection; and 3) low-attenuated soft-tissue mass with no obvious enhancement after contrast injection.

Conclusion: Fibrothecomas usually appear as a homogeneous solid tumor with varying degrees of enhancement. Calcification may be present and, as these tumors enlarge, myxoid or cystic degeneration may occur, resulting in a heterogeneous pattern. The larger the tumor, the greater is the chance of torsion. Lack of tumor enhancement is the most reliable sign for detection of ovarian torsion and should facilitate prompt surgical intervention to remove damaged tissue.
The protective role of telmisartan against nephrotoxicity induced by X-ray contrast media in rat model
Authors: Duan Shao Bin , Wang Yu Hui , Liu Fu You , Xu Xiang Qing , Wang Pian , Zou Qin , Peng You Ming
Published: May 2009

Background: Contrast-induced nephropathy is a serious complication of diagnostic and interventional procedures.

Purpose: To evaluate the nephrotoxicity of high- and low-osmolar contrast media (HOCM, LOCM) on kidneys in Sprague-Dawley rats. Telmisartan was administered to confirm its protective role against nephrotoxicity induced by contrast media.

Material and Methods: Sixty male rats were randomly divided into six groups ( n=10/group). Glycerin was given to all rats except controls to induce renal injury. HOCM (diatrizoate) or LOCM (iohexol) (10 ml/kg b.w., 300 mg I/ml) was given through a caudal vein. Serum creatinine level was measured by an automatical biochemical analyzer. Caspase-3 activity and Angiotensin II (Ang II) level of renal tissue were detected by fluorometric method and radioimmunoassay, respectively. The renal injury was also assessed by hematoxylin and eosin and TdT-mediated deoxyuridine nick end-labeling staining.

Results: In diatrizoate-injected rats, serum creatinine level was increased ( P<0.001). There was no significant difference between iohexol animals and glycerol controls in the level of serum creatinine. The renal caspase-3 activity and Ang II levels in HOCM and LOCM groups were higher than those in glycerol control group ( P<0.001). The percentage of apoptotic tubular cells and pathological scores were lower in the iohexol animals than that in the diatrizoate animals ( P<0.001). In the groups pretreated with telmisartan, no increase in the levels of serum creatinine, renal Ang II, and caspase-3 activity was observed ( P>0.05). The renal injuries induced by contrast media were alleviated.

Conclusion: Both HOCM (diatrizoate) and LOCM (iohexol) could cause renal tubular cell apoptosis in the kidneys damaged by glycerin. LOCM was less toxic to rat kidneys than HOCM. Caspase-3 and Ang II might play a role in renal tubular cell apoptosis induced by contrast media. Telmisartan protected the renal tissue from nephrotoxicity induced by contrast media.
An over‐represented minority! Non‐mainland French athletes in L’Équipe (1946–1968)
Authors: Bretin‐Maffiuletti Karen , Erard Carine
Published: May 2009

After the Second World War, the French athletics team included many sportsmen from outside mainland France, mainly from Maghreb (Morocco, Algeria, and Tunisia), Black Africa, and Overseas, who distinguished themselves by their performances at the highest national and indeed international levels. How did the French sports press, in particular the mainland press, report these performances, which overturned colonial hierarchies and challenged “white superiority”?

This article will describe the coverage, from a quantitative perspective, of these non‐mainland athletes in the columns of L’Équipe, France's main multi‐sports daily newspaper (after first determining the origin of the members of the French athletics team and pinpointing the arrival and gradual integration of athletes born outside mainland France). [Observations are limited here to male athletes. Women born outside mainland France joined the French athletic elite later than men, making it difficult to include both male and female athletes in the context of a single study. After 1945, the first French woman born outside mainland France to join the athletic elite was Martinique's Emma Sulter in 1970. In the United States, no African‐born American woman picked up a gold medal until the 1948 Olympic Games.] Our objective is to test the hypothesis that these coloured athletes from the French colonies were discriminated against in the media. Indeed, American studies with comparable subject matter have shown different media coverage for “white” and “black” sportsmen.

Our results show that the French athletic elite opened its doors to the colonies during the second half of the twentieth century, as the first wave of non‐mainland athletes was integrated into the French team between 1946 and 1968. In fact, athletes from Maghreb were present in relatively high numbers; those from Overseas were starting to be integrated, and the numbers of people coming from Black Africa were reaching their highest levels. During this period, L’Équipe gave non‐mainland athletes proportionately higher coverage than was warranted by their presence in the elite. This over‐representation was even more marked in the case of athletes from Overseas and Black Africa (while it seems that North Africans had slightly less coverage compared with their presence in the French team). It would appear, therefore, that in terms of quantity France's main sports daily did not discriminate against athletes who were not born on the mainland, but quite the reverse, with the relative exception of athletes from Maghreb. Several interpretations of this over‐representation will be considered, including: a disparity in terms of practice level between the groups of athletes; the particular features of French colonial history with regard to racial stereotypes; and the effect of mental categorization.
Influence of resistance exercise volume on recovery energy expenditure in women
Authors: Benton Melissa J. , Swan Pamela D.
Published: May 2009

The acute effects of resistance exercise on energy expenditure in the post‐exercise period have not been well studied in women, even though they are at high risk for weight gain and so would benefit greatly from exercise‐related increases in energy expenditure. The purpose of this study was to identify factors that influence recovery energy expenditure in women after an acute bout of resistance exercise. Seventeen healthy women aged 40–55 years completed an acute bout of resistance exercise followed by measurement of energy expenditure for 120 min of recovery. Body composition was measured via air displacement plethysmography. The resistance exercise bout consisted of three sets of 8–12 repetitions of eight exercises at 50% of one‐repetition maximum (1‐RM) for the first set and 80% 1‐RM for the second and third sets. Oxygen consumption (VO2) was measured before and for 120 min after resistance exercise. Post‐exercise energy expenditure data were analysed as 4‐min means at 0, 20, 40, 60, 90, and 120 min of recovery. Mean (± s x) training volume was 7604.1±450.64 kg and overall mean recovery energy expenditure was 133±6 kcal. Pearson's correlation analysis found no significant relationship between post‐exercise energy expenditure and age, body mass index, exercise time or delay between cessation of exercise and commencement of metabolic measurement. Absolute (kg) lean mass was also not significantly related to energy expenditure at any time post‐exercise, although relative (%) lean mass was during the late recovery period only (40 min of recovery: r = 0.49, P = 0.05; 60 min: r = 0.51, P = 0.04; 90 min: r = 0.63, P < 0.01). The factor most consistently related to post‐exercise energy expenditure was total exercise volume, which had a moderately strong relationship through 90 min of the recovery period (0 min of recovery: r=0.49. P = 0.05; 20 min: r = 0.52, P = 0.03; 40 min: r = 0.53, P = 0.03; 60 min: r = 0.50, P = 0.04; 90 min: r=0.48, P = 0.05). In the present sample of women, acute post‐exercise energy expenditure was influenced primarily by total training volume, although lean mass had a limited effect. Based on these findings, it is recommended that women be encouraged to lift at higher intensities (70–80% 1‐RM) to maximize post‐exercise energy expenditure and potentially promote fat loss.
A multi‐component assessment model for monitoring training distress among athletes
Authors: Main Luana , Grove J. Robert
Published: May 2009

We report the initial validation of a multi‐component assessment model for monitoring training distress among athletes. The model combines measures of mood disturbance with measures of perceived stress and symptom intensity. Altogether, 492 athletes completed the 10‐item Perceived Stress Scale (PSS‐10; Cohen et al., 1983), the 24‐item Brunel Mood Scale (BRUMS; Terry et al., 2003), and a checklist of 19 symptoms associated with acute overtraining (Fry et al., 1994). Six training distress factors were identified by an exploratory factor analysis: “depressed mood”, “perceived vigour”, “physical symptoms”, “sleep disturbance”, “perceived stress”, and “general fatigue”. Comparisons of group means of these factors with a previously validated inventory were consistent with theoretical predictions and provided evidence of construct validity. Internal consistency of the subscales was also confirmed, with Cronbach alphas ranging from 0.72 to 0.86. Together, these findings suggest that this multi‐component model provides a sound conceptual basis for the assessment of training distress among athletes.
Sport, women, and leadership: Results of a project on executives in German sports organizations
Authors: Pfister Gertrud , Radtke Sabine
Published: May 2009

Throughout the world, women are a small minority within the governing bodies of organized sport. This paper presents the results of three empirical studies that have been undertaken within a German research project. The representative survey of all male and female executives in German sports federations (N=697) included questions concerning their socio‐demography, their careers as executive members of sports organizations, as well as their careers in sport and their chosen occupation. The survey reveals significant gender differences in terms of, for example, age, family situation, responsibilities in the executive committees, duration of office, and career barriers. Furthermore, we conducted 23 in‐depth, semi‐structured interviews with women in leadership positions to explore the women's individual perspectives. The aim of a second interview study (“drop‐out” study) was to identify barriers in the voluntary careers of seven male and nine female leaders who left office prematurely (i.e. earlier than they had originally planned). These informants can be seen as experts who have an excellent insight into their organizations and who have also experienced barriers that caused them to “drop out”. The respondents’ statements showed similarities with regard to socio‐economic background but considerable differences in terms of gender‐specific experiences, attitudes, and evaluations. The demands placed on the sports leaders were much more in line with the biographies of the men interviewed than with the personal circumstances of the women.
Unc93B1 biases Toll-like receptor responses to nucleic acid in dendritic cells toward DNA- but against RNA-sensing
Authors: Fukui Ryutaro , Saitoh Shin-ichiroh , Matsumoto Fumi , Kozuka-Hata Hiroko , Oyama Masaaki , Tabeta Koichi , Beutler Bruce , Miyake Kensuke
Published: May 2009

Toll-like receptors (TLRs) 3, 7, and 9 recognize microbial nucleic acids in endolysosomes and initiate innate and adaptive immune responses. TLR7/9 in dendritic cells (DCs) also respond to self-derived RNA/DNA, respectively, and drive autoantibody production. Remarkably, TLR7 and 9 appear to have mutually opposing, pathogenic or protective, impacts on lupus nephritis in MRL/lpr mice. Little is known, however, about the contrasting relationship between TLR7 and 9. We show that TLR7 and 9 are inversely linked by Unc93B1, a multiple membrane-spanning endoplasmic reticulum (ER) protein. Complementation cloning with a TLR7-unresponsive but TLR9-responsive cell line revealed that amino acid D34 in Unc93B1 repressed TLR7-mediated responses. D34A mutation rendered Unc93B1-deficient DCs hyperresponsive to TLR7 ligand but hyporesponsive to TLR9 ligand, with TLR3 responses unaltered. Unc93B1 associates with and delivers TLR7/9 from the ER to endolysosomes for ligand recognition. The D34A mutation up-regulates Unc93B1 association with endogenous TLR7 in DCs, whereas Unc93B1 association with TLR9 was down-regulated by the D34A mutation. Consistently, the D34A mutation up-regulated ligand-induced trafficking of TLR7 but down-regulated that of TLR9. Collectively, TLR response to nucleic acids in DCs is biased toward DNA-sensing by Unc93B1.
Reconsidering Perceptual Content
Authors: Wojtach William T.
Published: May 2009

An important class of teleological theories cannot explain the representational content of visual states because they fail to address the relationship between the world, projected retinal stimuli, and perception. A different approach for achieving a naturalized theory of visual content is offered that rejects the traditional internalism/externalism debate in favor of what is termed “empirical externalism.” This position maintains that, while teleological considerations can underwrite a broad understanding of representation, the content of visual representation can only be determined empirically according to accumulated past experience. A corollary is that a longstanding problem concerning the indeterminacy of visual content is dissolved.
How to Confirm the Conjunction of Disconfirmed Hypotheses
Authors: Atkinson David , Peijnenburg Jeanne , Kuipers Theo
Published: May 2009

Could some evidence confirm a conjunction of two hypotheses more than it confirms either of the hypotheses separately? We show that it might, moreover under conditions that are the same for ten different measures of confirmation. Further, we demonstrate that it is even possible for the conjunction of two disconfirmed hypotheses to be confirmed by the same evidence.
Past Longevity as Evidence for the Future
Authors: Pisaturo Ronald
Published: May 2009

Gott (1993) has used the ‘Copernican principle’ to derive a probability distribution for the total longevity of any phenomenon, based solely on the phenomenon's past longevity. Leslie (1996) and others have used an apparently similar probabilistic argument, the ‘Doomsday Argument’, to claim that conventional predictions of longevity must be adjusted, based on Bayes's Theorem, in favor of shorter longevities. Here I show that Gott's arguments are flawed and contradictory, but that one of his conclusions is plausible and mathematically equivalent to Laplace's famous—and notorious—‘rule of succession’. On the other hand, the Doomsday Argument, though it appears consistent with some common-sense grains of truth, is fallacious; the argument's key error is to conflate future longevity and total longevity. Applying the work of Hill (1968) and Coolen (1998, 2006) in the field of nonparametric predictive inference, I propose an alternative argument for quantifying how past longevity of a phenomenon does provide evidence for future longevity. In so doing, I identify an objective standard by which to choose among counting time intervals, counting population, or counting any other measure of past longevity in predicting future longevity.
ISMB/ECCB 2009 Stockholm
Authors: Sagot Marie-France , McKay B.J. Morrison , Myers Gene
Published: May 2009

The International Society for Computational Biology (ISCB; http://www.iscb.org) presents the Seventeenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), organized jointly with the Eighth Annual European Conference on Computational Biology (ECCB; http://bioinf.mpi-inf.mpg.de/conferences/eccb/eccb.htm), in Stockholm, Sweden, 27 June to 2 July 2009. The organizers are putting the finishing touches on the year's premier computational biology conference, with an expected attendance of 1400 computer scientists, mathematicians, statisticians, biologists and scientists from other disciplines related to and reliant on this multi-disciplinary science. ISMB/ECCB 2009 (http://www.iscb.org/ismbeccb2009/) follows the framework introduced at the ISMB/ECCB 2007 (http://www.iscb.org/ismbeccb2007/) in Vienna, and further refined at the ISMB 2008 (http://www.iscb.org/ismb2008/) in Toronto; a framework developed to specifically encourage increased participation from often under-represented disciplines at conferences on computational biology. During the main ISMB conference dates of 29 June to 2 July, keynote talks from highly regarded scientists, including ISCB Award winners, are the featured presentations that bring all attendees together twice a day. The remainder of each day offers a carefully balanced selection of parallel sessions to choose from: proceedings papers, special sessions on emerging topics, highlights of the past year's published research, special interest group meetings, technology demonstrations, workshops and several unique sessions of value to the broad audience of students, faculty and industry researchers. Several hundred posters displayed for the duration of the conference has become a standard of the ISMB and ECCB conference series, and an extensive commercial exhibition showcases the latest bioinformatics publications, software, hardware and services available on the market today. The main conference is preceded by 2 days of Special Interest Group (SIG) and Satellite meetings running in parallel to the fifth Student Council Symposium on 27 June, and in parallel to Tutorials on 28 June. All scientific sessions take place at the Stockholmsmässan/Stockholm International Fairs conference and exposition facility.

Contact:  bj@iscb.org
Efficient computation of all perfect repeats in genomic sequences of up to half a gigabyte, with a case study on the human genome
Authors: Becher Verónica , Deymonnaz Alejandro , Heiber Pablo
Published: May 2009

Motivation: There is a significant ongoing research to identify the number and types of repetitive DNA sequences. As more genomes are sequenced, efficiency and scalability in computational tools become mandatory. Existing tools fail to find distant repeats because they cannot accommodate whole chromosomes, but segments. Also, a quantitative framework for repetitive elements inside a genome or across genomes is still missing.

Results: We present a new efficient algorithm and its implementation as a software tool to compute all perfect repeats in inputs of up to 500 million nucleotide bases, possibly containing many genomes. Our algorithm is based on a suffix array construction and a novel procedure to extract all perfect repeats in the entire input, that can be arbitrarily distant, and with no bound on the repeat length. We tested the software on the Homo sapiens DNA genome NCBI 36.49. We computed all perfect repeats of at least 40 bases occurring in any two chromosomes with exact matching. We found that each H.sapiens chromosome shares ∼10% of its full sequence with every other human chromosome, distributed more or less evenly among the chromosome surfaces. We give statistics including a quantification of repeats by diversity, length and number of occurrences. We compared the computed repeats against all biological repeats currently obtainable from Ensembl enlarged with the output of the dust program and all elements identified by TRF and RepeatMasker (ftp://ftp.ebi.ac.uk/pub/databases/ensembl/jherrero/.repeats/all_repeats.txt.bz2). We report novel repeats as well as new occurrences of repeats matching with known biological elements.

Availability: The source code, results and visualization of some statistics are accessible from http://kapow.dc.uba.ar/patterns/

Contact:  vbecher@dc.uba.ar
Genetic Diversity ofArmillariaspp. Infecting Highbush Blueberry in Northern Italy (Trentino Region)
Authors: Prodorutti D. , Vanblaere T. , Gobbin D. , Pellegrini A. , Gessler C. , Pertot I.
Published: May 2009

Armillaria spp. are the causal agents of root rots of several woody plants, including highbush blueberry. Since 2003, highbush blueberry plants infected by Armillaria spp. have been found in Valsugana Valley, Trentino region, northern Italy. Our aim was to identify the Armillaria spp. involved in these infections, as well as possible sources of inoculum in blueberry fields. Samples of Armillaria spp. were collected from diseased blueberry plants in 13 infected blueberry fields, from bark spread along the blueberry rows, from infected trees in the vicinity of the fields, and from four forest locations. The identification of Armillaria spp. was accomplished using a species-specific multiplex polymerase chain reaction method and by sequencing the rDNA at a specific locus. The differentiation between genotypes was performed by using simple-sequence repeat analysis. Armillaria mellea and A. gallica were the most frequently observed species infecting blueberry in the Valsugana Valley. Three to eight Armillaria genotypes were identified in each blueberry field. No individual genotypes were found in more than one blueberry field. Two-thirds of the genotypes found colonizing trees in the immediate vicinity of infected fields and two-thirds of the genotypes found colonizing the bark spread in blueberry rows were also isolated from blueberry plants in the field, indicating that bark used as mulch and infected trees surrounding the fields may be important sources of inoculum.
Simultaneous Detection of Acidovorax avenae subsp. citrulli and Didymella bryoniae in Cucurbit Seedlots Using Magnetic Capture Hybridization and Real-Time Polymerase Chain Reaction
Authors: Ha Y. , Fessehaie A. , Ling K. S. , Wechter W. P. , Keinath A. P. , Walcott R. R.
Published: May 2009

To improve the simultaneous detection of two pathogens in cucurbit seed, a combination of magnetic capture hybridization (MCH) and multiplex real-time polymerase chain reaction (PCR) was developed. Single-stranded DNA hybridization capture probes targeting DNA of Acidovorax avenae subsp. citrulli, causal agent of bacterial fruit blotch, and Didymella bryoniae, causal agent of gummy stem blight, were covalently attached to magnetic particles and used to selectively concentrate template DNA from cucurbit seed samples. Sequestered template DNAs were subsequently amplified by multiplex real-time PCR using pathogen-specific TaqMan PCR assays. The MCH multiplex real-time PCR assay displayed a detection threshold of A. avenae subsp. citrulli at 10 CFU/ml and D. bryoniae at 105 conidia/ml in mixtures of pure cultures of the two pathogens, which was 10-fold more sensitive than the direct real-time PCR assays for the two pathogens separately. Although the direct real-time PCR assay displayed a detection threshold for A. avenae subsp. citrulli DNA of 100 fg/μl in 25% (1/4 samples) of the samples assayed, MCH real-time PCR demonstrated 100% detection frequency (4/4 samples) at the same DNA concentration. MCH did not improve detection sensitivity for D. bryoniae relative to direct real-time PCR using conidial suspensions or seed washes from D. bryoniae-infested cucurbit seed. However, MCH real-time PCR facilitated detection of both target pathogens in watermelon and melon seed samples (n = 5,000 seeds/sample) in which 0.02% of the seed were infested with A. avenae subsp. citrulli and 0.02% were infested with D. bryoniae.
Stress Tolerance and Environmental Fitness of Pseudomonas fluorescens A506, Which Has a Mutation in rpoS
Authors: Hagen Mary J. , Stockwell Virginia O. , Whistler Cheryl A. , Johnson Kenneth B. , Loper Joyce E.
Published: May 2009

Establishment of suppressive populations of bacterial biological control agents on aerial plant surfaces is a critical phase in biologically based management of floral diseases. Periodically, biocontrol agents encounter inhospitable conditions for growth on plants; consequently, tolerance of environmental stresses may contribute to their fitness. In many gram-negative bacteria, including strains of Pseudomonas spp., the capacity to survive environmental stresses is influenced by the stationary phase sigma factor RpoS. This study focused on the role of RpoS in stress response and epiphytic fitness of Pseudomonas fluorescens A506, a well-studied bacterial biological control agent. We detected a frameshift mutation in the rpoS of A506 and demonstrated that the mutation resulted in a truncated, nonfunctional RpoS. Using site-directed mutagenesis, we deleted a nucleotide from rpoS, which then encoded a full-length, functional RpoS. We compared the stress response and epiphytic fitness of A506 with derivative strains having the functional full-length RpoS or a disrupted, nonfunctional RpoS. RpoS had little effect on stress response of A506 and no consistent influence on epiphytic population size of A506 on pear or apple leaves or flowers. Although the capacity of strain A506 to withstand exposure to environmental stresses was similar to that of other fluorescent pseudomonads, this capacity was largely independent of rpoS.
Field Assessment of a Model for Fungicide Effects on Intraplant Spread of Stem Rust in Perennial Ryegrass Seed Crops
Authors: Pfender W. F. , Eynard J.
Published: May 2009

Intraplant spread of stem rust (Puccinia graminis subsp. graminicola) in perennial ryegrass during tiller extension is a major determinant of epidemic severity and is dominated by stem extension dynamics. Simple equations for extension of inflorescence and internodes are presented and parameterized. These equations are combined with previously published equations for pathogen latent period and for postinfection efficacy of fungicides to produce a model for effects of fungicide type and timing on intraplant spread. The model is driven by thermal units, calculated from air temperature measurements. Three field experiments, conducted independently from the field experiments that provided data for plant growth model parameterization, were conducted to assess performance of the disease spread model. Either propiconazole or azoxystrobin, the two most commonly used fungicides for stem rust control, was applied to tillers that had stem rust pustules on the flag sheath and in which the inflorescence was partially extended. Intraplant spread of disease to the extending inflorescence (stem and flowerhead) was observed at several dates following treatment and compared with modeled severities. The model estimated accurately the severities of inflorescence infection for most treatments and observation times, with a correlation coefficient of 0.93 for modeled versus observed disease severities across the three experiments. The model correctly estimated the rank order of final severities among the treatments (fungicide type and timing). The model can be extended to intraplant spread of stem rust at all internodes and incorporated into decision support tools for fungicide type and timing in management of this disease.
Characterization of Bois Noir Isolates by Restriction Fragment Length Polymorphism of a Stolbur-Specific Putative Membrane Protein Gene
Authors: Pacifico D. , Alma A. , Bagnoli B. , Foissac X. , Pasquini G. , Tessitori M. , Marzachì C.
Published: May 2009

Bois noir phytoplasma (BNp), widespread in wine-producing areas of Europe and endemic in France and Italy, is classified in the 16SrXII-A subgroup, whose members are referred to as Stolbur phytoplasmas. The 16S rDNA gene of Stolbur phytoplasma shows low variability, and few non-ribosomal genes are available as markers to assess variation among isolates. We used the Stolbur-specific stol-1H10 gene, encoding a putative membrane-exposed protein, to investigate genetic diversity of French and Italian BNp isolates from plants and insects. Amplification of stol-1H10 from infected grapevines, weeds, and Hyalesthes obsoletus produced fragments of three sizes, and restriction fragment length polymorphism analysis divided these amplicons further into 12 profiles (V1 to V12). French BNp isolates were more variable than Italian ones, and different profiles were present in infected grapevines from France and Italy. Isolate V3, most abundant among Italian affected grapes but present among French ones, was found in one Urtica dioica sample and in all H. obsoletus collected on this species. Four Italian-specific profiles were represented among infected Convolvulus arvensis, the most frequent of which (V12) was also detected in H. obsoletus collected on this species. Most of the variability in the stol-1H10 sequence was associated with type II on the tuf gene.
Trans-Replication of, and Competition Between, DNA β Satellites in Plants Inoculated with Tomato yellow leaf curl China virus and Tobacco curly shoot virus
Authors: Qing Ling , Zhou Xueping
Published: May 2009

Tomato yellow leaf curl China virus (TYLCCNV) Y10 isolate (Y10) and Tobacco curly shoot virus (TbCSV) Y35 isolate (Y35), both obtained from Yunnan Province, were each found to be associated with a distinct species of satellite DNA (DNA β). Here, we demonstrate that both Y10 DNA β (Y10β) and Y35 DNA β (Y35β) were stably trans-replicated by the noncognate Begomovirus, although the noncognate DNA β accumulated in plants at a lower level than did the cognate DNA β. In Nicotiana benthamiana and N. glutinosa plants agroinoculated with Y10+Y10β+Y35β or with Y35+Y35β+Y10β, all components accumulated in the early stages of infection but, at later stages, the noncognate DNA β decreased in relative concentration and was undetectable at 80 to 120 days after inoculation. The helper viruses and cognate DNA β species persisted at higher levels throughout the experiments. When the initiation codon of the βC1 gene of the cognate DNA β was mutated, the dominance of the cognate over the noncognate DNA β in mixed infections was unimpaired. These results imply that the cognate DNA β competes with the noncognate DNA β and that the ability for selective maintenance of DNA β is not controlled by the βC1 protein.