bluuebunny/crossref_metadata_2025 huggingface dataset:
Limnological characteristics of Canada's poorly known large lakes
Authors: Minns C. K.
Published: June 2010

Canada holds several of the world's large lakes (⩾100 km2). Many of these lakes, apart from the largest like the Great Lakes, are almost unknown beyond their location and area. This study documents a recent compilation and analyses of some key limnological features of these lakes: drainage area, lake area, maximum and mean depth, pH, Secchi depth, and total dissolved solids. The analyses showed the relationships among these features and with their primary watershed and ecozone assignments. Lake area and maximum depth were good predictors of some of the other lake variables. Ecozone was generally a better predictor than primary watershed of regional variation in lake variables with lake area or maximum depth as a covariate scaling for lake size. To enable regional impact assessments of cumulative environmental pressures of Canada's large lakes, these predictive regression models provide a stop-gap means for estimating key lake characteristics when data are missing. However, as cumulative pressures increase, Canada needs to increase efforts to undertake limnological inventories and learn more first hand about these poorly known lakes.
Use of aquatic protected areas in the management of large lakes
Authors: Hedges Kevin J. , Koops Marten A. , Mandrak Nicholas E. , Johannsson Ora E.
Published: June 2010

There is considerable variation in the strategies used to manage large lakes. Management targets and resources for monitoring, assessment, planning and enforcement (e.g. personnel, equipment, policy, legislation) can differ considerably among countries and lakes. With a growing interest and body of research regarding Marine Protected Areas, assessments of similar freshwater areas are timely, especially considering current concerns over the global loss of biodiversity and increased interest in ecosystem-based management and the Precautionary Principle. This paper examines the use of various types of Aquatic Protected Areas in the management of large lakes (e.g. Marine Protected Area equivalents, fish sanctuaries, parks). Potential and actual benefits and drawbacks, relative uses in current management strategies, purposes for which different types of areas have been created, and related trends are discussed. Very few true equivalents of Marine Protected Areas, that permanently protect both species and their habitats from exploitation and development, have been created in freshwater systems. Most protected areas within lakes exist as fish sanctuaries, which limit or prevent harvest of one or more species, and aquatic or terrestrial (shoreline) parks, which protect aquatic and riparian habitats by preventing development or resource extraction (e.g. logging or mining). Because many Aquatic Protected Areas are established in legislation the retirement of established areas is relatively difficult and the number of Aquatic Protected Areas is increasing. Although Aquatic Protected Areas have considerable potential for improving large lake management, it is essential that management goals are compatible with the function of Aquatic Protected Areas and that factors affecting their success are determined to facilitate efficient use of resources and political will.
Contemporary trends of temperature, nutrient loading, and water quality in large Lakes Peipsi and Võrtsjärv, Estonia
Authors: Nõges Tiina , Tuvikene Lea , Nõges Peeter
Published: June 2010

From 1961–2004, surface water temperature in large and shallow Lakes Peipsi and Võrtsjärv in Estonia increased significantly in April and August; respectively 0.37–0.75 and 0.32–0.42 degrees per decade reflecting the changes in air temperature. The average annual amount of precipitation in the catchment increased significantly. Reflecting practices in agriculture and wastewater treatment, nutrient loadings to the lakes increased rapidly in the 1980s and decreased again in the early 1990s. As total nitrogen (TN) loading decreased faster than total phosphorus (TP) loading, the TN/TP ratio in the loadings decreased. Both the increased temperature and low TN/TP ratio favoured the development of cyanobacteria blooms in Lake Peipsi. In Võrtsjärv, where the TN/TP mass ratio is about two times higher than in Peipsi, blooms did not occur. Recently, the TN/TP ratio has shown a tendency of increase in both lakes suggesting a certain reduction of blooms to be expected also in Lake Peipsi. Nutrient dynamics in the lakes followed the changes in loadings, showing the ability of shallow lake ecosystems to react sensitively to changes in catchment management as well as in climate.
Use of satellite remote sensing tools for the Great Lakes
Authors: Watkins Jim
Published: June 2010

Satellite-based sensors provide synoptic measurements of surface parameters useful in detecting physical and biological conditions of the Great Lakes. Satellite surface temperature measurements using infrared spectra are compatible with buoy measurements and the time series now covers more than two decades in length. This time-series tracks seasonal warming patterns and localized upwelling events. The use of visible spectra for remote sensing of water clarity and particle composition is improving with new algorithms to separate chlorophyll-a, inorganic particles, and dissolved organic matter. The use of satellites to measure these variables holds promise for future quantification of phytoplankton production, calcite precipitation (whiting), and suspended sediment from rivers and resuspension events. Satellite imagery has also been useful for interpreting ship-collected data such as those associated with the bi-national Lake Ontario Lower Foodweb Assessment (LOLA) in 2003.
Changes in abundance of Nile shrimp,Caridina nilotica(Roux) following the decline of Nile perch and recovery of native haplochromine fishes, Lake Victoria, Tanzanian waters
Authors: Ngupula G. W. , Mlaponi E.
Published: June 2010

The abundance of Nile shrimp, Caridina nilotica (Roux) in Lake Victoria has fluctuated significantly over time, from the periods of 1900–1950s, 1980s–1990s and from 2000s to present day. To elucidate its current abundance, its contribution to the Rastrineobola argentea fishery catches, and its importance to the composition of the diet of Nile perch (Lates niloticus L.), and to the bottom trawl catches, were investigated. From August 2006 to January 2007, the mean C. nilotica CPUE was 1.68 ± 1.20 kg boat−1 day−1 at Kijiweni and Igombe, and its 0.37% contribution to the R. argentea total catches was insignificant. Of the 230 Nile perch stomachs containing prey items, C. nilotica comprised 54% by volume of the diet of fish <50 cm TL; while haplochromines contributed 41% to the diet of fish >50 cm TL. Mean catch rates of C. nilotica in bottom trawls in 8 months between 2005 and 2008 ranged between 0 and 2.45 ± 2.50 kg hr−1. Low catches of the C. nilotica in the R. argentea fishery, and the dietary shift of Nile perch of >50 cm TL to once again include haplochromines, may indicate a decrease in C. nilotica's abundance in the lake, and vice versa. Overfishing and the selectivity of the fishery to take only large Nile perch for fish filleting factories, have resulted in reduced stocks and dominance of juveniles in the perch's populations. The highly reduced Nile perch stocks are currently leading to an apparent reversal of the 1980s regime with a shift to a new cichlid-dominated and C. nilotica low abundance state. Increase in predation on juvenile C. nilotica by the recovering haplochromines, and juvenile perches, as well as environmental degradation, especially eutrophication and pollution, along with the effects of global warming impacts, account for the observed decline in C. nilotica.
Development of aerobic fitness of individuals with substance abuse/dependence following long‐term individual physical activity
Authors: Mamen Asgeir , Martinsen Egil W.
Published: June 2010

Thirty‐three individuals with substance abuse who completed a training programme 7.5 months (s=4.1) in duration were evaluated on development of aerobic power and performance on a lactate profile test using directly measured VO2max and measurement of blood lactate concentration. The group improved moderately on aerobic power (4%, s x =2, P=0.020) and on performance at the lactate threshold (running: 7%, s x =3, P=0.03; cycling: 13%, s x =5, P=0.03). The low improvement rate compared with other studies may be attributed to the use of directly measured VO2max, as indirect tests used in previous studies are prone to exaggerate the improvement. Those individuals whose aerobic fitness improved performed more of the training above threshold heart rate than those who did not improve (P=0.006), although the amount of training during the programme (315 h, s x =97 vs. 279 h, s x =89; P=0.30) did not differ significantly. The programme is the first to show that direct testing of fitness using maximal tests is feasible for this patient group. The programme is also pioneering in the use of training partners to help patients with substance abuse and dependence conduct large amounts of training.
The influence of stretcher height on posture in ergometer rowing
Authors: Caplan Nicholas , Gardner Trevor
Published: June 2010

The aim of this investigation was to determine the effect on rower posture of raising the stretchers. Nine male university rowers completed a single 30‐s trial at each of three stretcher heights on an ergometer, at 30 strokes min−1. The first ten strokes with complete data were averaged and data for four time points during the stroke extracted: catch, mid‐drive, finish, and mid‐recovery. Ankle angle was shown to increase significantly at all points during the stroke (P<0.01) as the stretchers were raised. Knee angle was only significantly increased into a more extended posture at mid‐drive (P<0.05) and mid‐recovery (P<0.01) for the higher stretcher positions, hip angle was significantly reduced into a more flexed posture at the catch (P<0.05) and at mid‐recovery (P<0.05), and the trunk was significantly extended at the catch (P<0.01), finish (P<0.01), and mid‐recovery (P<0.05) as the stretchers were raised. Our results show that the increase in stretcher height caused the rower's body to rotate posteriorly in the sagittal plane. This we suggest reduced the vertical component of stretcher force, thus achieving a more mechanically effective position, which could have led to the slower rate of fatigue reported previously for the two raised stretcher positions (Caplan & Gardner, 2005). The increased flexion of the hip should not be ignored, however, as this may lead to overstretching of the hip extensors if the stretchers are raised too high. Further research is required to determine the extent to which the stretchers can be raised in on‐water rowing.
Measuring the effectiveness of offensive match‐play in professional soccer
Authors: Tenga Albin , Ronglan Lars T. , Bahr Roald
Published: June 2010

The broader measures of offensive effectiveness, such as scoring opportunities and shots at goal, are commonly used as an alternative to goals scored due to the naturally low probability of scoring (about 1%) in soccer match‐play. These measures may enable soccer practitioners to objectively see behind single match results, which are often influenced by chance. The purpose of this study was to examine the relationship between broader measures (scoring opportunities and score box possessions) and the ultimate measure (goals scored) of offensive effectiveness. We analysed data from videotapes of 163 of 182 (90%) matches played in the Norwegian men's professional league during the 2004 season. Multiple logistic regression analyses showed very similar results when comparing the effectiveness of different offensive tactics, regardless of which outcome was used. For example, counterattacks were more effective than elaborate attacks in producing goals (odds ratio OR=2.07, 95% confidence interval: 1.40 to 3.05), scoring opportunities (OR=2.30, 95% confidence interval: 1.28 to 4.15), and score box possessions (OR=2.12, 95% confidence interval: 1.39 to 3.25). The receiver‐operating characteristic function statistical procedure was used to examine the association between each of the three measures of offensive effectiveness: scoring opportunities, score box possessions, and goals scored. No significant difference was observed between the area under the curve (AUC) for the broader measures (scoring opportunities and score box possessions) and the ultimate measure (goals scored) of offensive effectiveness. The 95% confidence interval of the AUC for both scoring opportunities (0.74–0.84) and score box possessions (0.68–0.76) includes the AUC for goals scored (0.74). Thus, the results are very similar regardless of which outcome measure for offensive effectiveness is used. This indicates that scoring opportunities and score box possessions (shooting opportunities) can be used as a proxy for goals scored when comparing the effectiveness of different playing tactics in soccer. Compared with goals scored, using scoring opportunities or score box possessions requires smaller match samples for meaningful analyses, and may therefore be more feasible alternatives.
Effective attacking strategies in rugby union
Authors: Wheeler Keane W. , Askew Christopher D. , Sayers Mark G.
Published: June 2010

Evasive change‐of‐direction manoeuvres (agility skills) are a fundamental ability in rugby union. In this study, we explored the attributes of agility skill execution as they relate to effective attacking strategies in rugby union. Seven Super 14 games were coded using variables that assessed team patterns and individual movement characteristics during attacking ball carries. The results indicated that tackle‐breaks are a key determinant of try‐scoring ability and team success in rugby union. The ability of the attacking ball carrier to receive the ball at high speed with at least two body lengths from the defence line against an isolated defender promoted tackle‐breaks. Furthermore, the execution of a side‐step evasive manoeuvre at a change of direction angle of 20–60° and a distance of one to two body lengths from the defence, and then straightening the running line following the initial direction change at an angle of 20–60°, was associated with tackle‐breaks. This study provides critical insight regarding the attributes of agility skill execution that are associated with effective ball carries in rugby union.
Evaluative Conditioning and Conscious Knowledge of Contingencies: A Correlational Investigation with Large Samples
Authors: Bar-Anan Yoav , De Houwer Jan , Nosek Brian A.
Published: June 2010

Evaluative conditioning (EC) is a change in the valence of a stimulus that results from pairing the stimulus with an affective stimulus. Two high-powered studies (total N = 1,161) investigated the nature of the relationship between EC and contingency awareness measured as contingency memory. Stronger EC occurred among people with more accurate and more confident memory of the pairings. Awareness was a necessary condition for EC, but EC was not necessary for awareness. Supporting a propositional account of EC, we found evidence for intentional reliance on the contingency for the evaluation of stimuli. We also found evidence that contingency memory was based both on the actual contingency and on preexisting attitudes.
Disruption of short-term memory by distractor speech: Does content matter?
Authors: Bell Raoul , Mund Iris , Buchner Axel
Published: June 2010

Four experiments replicate the finding that auditory distractors that are lexically identical to the visual target items dramatically increase the irrelevant-speech effect on serial recall. This effect was previously attributed to interference of incompatible order cues. The present results suggest that a different interpretation of this effect is required. Experiment 2 replicates the order congruence effect observed by Hughes and Jones (2005), but shows that this effect is most likely due to an attenuation of interference that is caused by strategic attention shifts to the nominally irrelevant material. Experiments 3 and 4 show that the between-stream similarity effect generalizes to a condition in which the distractor items were drawn from the same category as the targets, but were not identical to them. By showing that nonacoustic distractor features can increase interference in serial recall of lists of supposedly “meaningless” items such as digits or consonants, the results are most consistent with models that postulate an integration of short-term and long-term memory such as the embedded-processes model and the feature model and are inconsistent with classical structural accounts of memory.
Si nanocone array optimization on crystalline Si thin films for solar energy harvesting
Authors: Li Junshuai , Yu HongYu , Wong She Mein , Zhang Gang , Lo Guo-Qiang , Kwong Dim-Lee
Published: June 2010

In this paper, the effects of structural parameters on the optical characteristics of crystalline Si thin films with the surface decorated by Si nanocone (SiNC) arrays are investigated by simulation. It is found that the SiNC base diameter should be equal to the array periodicity for efficient solar energy harvesting, and the optimized light absorption could already be realized when the SiNC height reaches ∼400 nm. An ultimate efficiency of ∼31.5% can be achieved when the periodicity is ∼600 nm for an 800 nm thick Si film with a 400 nm high nanocone array although the total thickness is only 1200 nm. And the ultimate efficiency could be further increased to some extent due to the enhanced light absorption in the low energy region by appropriately increasing the Si film thickness. The underlying physics is also discussed in this work.
A comparative study of the surface recombination of nitrogen atoms on various materials at atmospheric pressure
Authors: Oinuma Gaku , Inanaga Yasutaka , Tanimura Yasuhiro , Kuzumoto Masaki , Tabata Yoichiro , Watanabe Kensuke
Published: June 2010

The surface recombination of nitrogen atoms on various materials was investigated at atmospheric pressure. The afterglows of pure nitrogen discharge are injected into a surface loss test unit, whose path wall is composed of the materials to be examined. Measurement of the nitrogen atom densities at several points in the flowing afterglows reveals the temporal decay characteristics. The results are compared with two-dimensional numerical simulations to obtain the surface loss probability γ. Among the seven materials we studied (stainless steel, aluminium, titanium, alumina, Pyrex glass, aluminium nitride and boron nitride), stainless steel was found to have the highest γ value: 1.8 × 10−3; the lowest was for boron nitride: 4.8 × 10−5. The dependence of γ on surface roughness and temperature was also examined.
An investigation on two-phase mixture discharges: the effects of macroparticle sizes
Authors: Deng Heming , He Zhenghao , Xu Yuhang , Ma Jun , Liu Junxiang , Guo Runkai
Published: June 2010

A two-phase mixture (TPM) is a mixture of gas and macroparticles of high concentration, and there has been significant interest in many technical applications and natural phenomena concerning two-phase mixture discharges (TPMDs), but until now there has been no widely accepted analysis for the propagation of discharges in TPMs. In this paper, 21 kinds of different dielectric materials are used to investigate the effects on TPMD. The diameters of macroparticles in 21 kinds of TPMs are measured by microscope, laser particle size analyzer, etc, and the volume fractions are measured by a video camera and particle image velocimetry system. Based on a direct comparison of the breakdown voltages and the percentages of the discharge path in TPMs with those in air, this work reveals that whether TPMs promote the discharge development or not depends mainly on the macroparticle sizes. These macroparticles in TPMs distort the electric field, interact with ions, electrons or photons, and produce corresponding enhancements or decreases in ionization and excitation as the streamer front encounters them, but the details of alterations on the discharge development are highly correlated with the macroparticle sizes.
Electronic and optical properties of Al2O3/SiO2 thin films grown on Si substrate
Authors: Tahir Dahlang , Kwon Hyuk Lan , Shin Hye Chung , Oh Suhk Kun , Kang Hee Jae , Heo Sung , Chung Jae Gwan , Lee Jae Cheol , Tougaard Sven
Published: June 2010

The electronic and optical properties of Al2O3/SiO2 dielectric thin films grown on Si(1 0 0) by the atomic layer deposition method were studied by means of x-ray photoelectron spectroscopy and reflection electron energy loss spectroscopy (REELS). The band gaps of the Al2O3/SiO2 thin films before annealing and after annealing were 6.5 eV and 7.5 eV, respectively, and those of the γ-Al2O3 and α-Al2O3 phases were 7.1 eV and 8.4 eV, respectively. All of these were estimated from the onset values of the REELS spectra. The dielectric functions were determined by comparing the effective cross-section determined from experimental REELS with a rigorous model calculation based on dielectric response theory, using available software packages. The determined energy loss function obtained from the Al2O3/SiO2 thin films before annealing showed a broad peak at 22.7 eV, which moved to the γ-Al2O3 position at 24.3 eV after annealing. The optical properties were determined from the dielectric function. The optical properties of the Al2O3/SiO2 thin films after annealing were in good agreement with those of γ-Al2O3. The changes in band gap, electronic and optical properties of the Al2O3/SiO2 thin films after annealing indicated a phase transition from an amorphous phase to the γ-Al2O3 phase after annealing.
LOX: inferring Level Of eXpression from diverse methods of census sequencing
Authors: Zhang Zhang , López-Giráldez Francesc , Townsend Jeffrey P.
Published: June 2010

Summary: We present LOX (Level Of eXpression) that estimates the Level Of gene eXpression from high-throughput-expressed sequence datasets with multiple treatments or samples. Unlike most analyses, LOX incorporates a gene bias model that facilitates integration of diverse transcriptomic sequencing data that arises when transcriptomic data have been produced using diverse experimental methodologies. LOX integrates overall sequence count tallies normalized by total expressed sequence count to provide expression levels for each gene relative to all treatments as well as Bayesian credible intervals.

Availability:  http://www.yale.edu/townsend/software.html

Contact:  jeffrey.townsend@yale.edu
A highly accurate statistical approach for the prediction of transmembrane β-barrels
Authors: Freeman Thomas C. , Wimley William C.
Published: June 2010

Motivation: Transmembrane β-barrels (TMBBs) belong to a special structural class of proteins predominately found in the outer membranes of Gram-negative bacteria, mitochondria and chloroplasts. TMBBs are surface-exposed proteins that perform a variety of functions ranging from nutrient acquisition to osmotic regulation. These properties suggest that TMBBs have great potential for use in vaccine or drug therapy development. However, membrane proteins, such as TMBBs, are notoriously difficult to identify and characterize using traditional experimental approaches and current prediction methods are still unreliable.

Results: A prediction method based on the physicochemical properties of experimentally characterized TMBB structures was developed to predict TMBB-encoding genes from genomic databases. The Freeman–Wimley prediction algorithm developed in this study has an accuracy of 99% and MCC of 0.748 when using the most efficient prediction criteria, which is better than any previously published algorithm.

Availability: The MS Windows-compatible application is available for download at http://www.tulane.edu/∼biochem/WW/apps.html

Contact:  wwimley@tulane.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Rationale and design of the ‘aldosterone receptor blockade in diastolic heart failure’ trial: a double‐blind, randomized, placebo‐controlled, parallel group study to determine the effects of spironolactone on exercise capacity and diastolic function in patients with symptomatic diastolic heart failure (Aldo‐DHF)
Authors: Edelmann Frank , Schmidt Albrecht G. , Gelbrich Götz , Binder Lutz , Herrmann‐Lingen Christoph , Halle Martin , Hasenfuss Gerd , Wachter Rolf , Pieske Burkert
Published: June 2010

Aims

Increasing evidence suggests that enhanced aldosterone signalling plays a key role in the onset and progression of diastolic heart failure (DHF). Aldo‐DHF will test the hypothesis that aldosterone receptor blockade by spironolactone will improve exercise capacity and diastolic function in patients with DHF.

Methods

Aldo‐DHF is a randomized, placebo‐controlled, double‐blinded, two‐armed, multicentre, parallel group study. Four hundred and twenty patients with DHF will be randomly assigned to receive spironolactone 25 mg per day or placebo. The main inclusion criteria are: age ≥ 50 years, New York Heart Association II/III, preserved left ventricular ejection fraction (≥50%), and echocardiographic evidence of diastolic dysfunction. The two primary endpoints are changes in exercise capacity (peak VO2, spiroergometry) and in diastolic function (E/é, echocardiography) after 12 months. Secondary endpoints include effects of spironolactone on additional parameters of exercise performance and diastolic as well as systolic function, neurohumoral activation, and quality of life. Morbidity and mortality as well as safety aspects will also be assessed.

Conclusion

Aldo‐DHF is the first large‐scale clinical trial to evaluate the effects of aldosterone receptor blockade on exercise capacity and diastolic function in patients with DHF. Aldo‐DHF will provide important information about the clinical course of this condition and may have significant impact on treatment strategies and future trials in these patients.
Empirical Implications of Signaling Models: Estimation of Belief Updating in International Crisis Bargaining
Authors: Whang Taehee
Published: June 2010

Signaling models are ubiquitous in political science. An essential characteristic of these models is that actors can update their beliefs about their opponents. An actor observes the behavior of his opponent, and this behavior functions as a signal that allows the actor to learn more about his opponent's true “type.” As a result, the actor is able to adapt his own behavior. Current statistical models of strategic choice based on perfect Bayesian equilibrium, however, allow for very little, if any, belief updating. I explain why current models allow for little updating and offer in their stead a new, fully strategic choice estimator that calculates the correct amount of belief updating.
The degradation properties of co-continuous calcium phosphate polyester composites: insights with synchrotron micro-computer tomography
Authors: Ehrenfried Lisa M. , Farrar David , Cameron Ruth E.
Published: June 2010

This study investigates the
in vitro
degradation properties of composites consisting of a porous tricalcium phosphate (TCP) foam filled with degradable poly(
dl
-lactic acid) (PDLLA) via either
in situ
polymerization or infiltration. The motivation was to develop a material for bone repair that would be initially mechanically strong and would develop porosity during degradation of one of the components. A thorough analysis of the physical
in vitro
degradation properties has been conducted and reported by the same authors elsewhere. Synchrotron micro-computer tomography analysis (conducted at ID19, ESRF, Grenoble, France) allowed detailed insights to be gained into the process of the composites' degradation, which was discovered to be strongly influenced by the manufacturing method. The polymer phase of
in situ
-polymerized TCP–PDLLA degraded as a bulk sample, with faster degradation in the centre of the sample as a whole. In contrast, the polymer phase of infiltrated TCP–PDLLA degraded as individual polymer spheres with faster degradation in the centre of each sphere.
Watching sexy displays improves hatching success and offspring growth through maternal allocation
Authors: Loyau Adeline , Lacroix Frédéric
Published: June 2010

Male attractiveness can have tremendous effects on the fitness of his offspring via good genes, but also via enhanced maternal allocation of resources. Yet the proximate mechanisms influencing differential maternal allocation in relation to male sexiness are poorly known. Here, we studied the importance of visual stimulation for maternal allocation in the Houbara bustard, a vulnerable bird species bred in captivity to support wild populations. Artificial insemination allowed controlling for potential confounding factors, such as a male's territory quality, social interactions or sperm quality/quantity, probably linked to mate attractiveness. We show that artificially inseminated females stimulated by highly displaying males increased their hatching success, owing to increased fertilization success. The females also increased the allocation of maternal androgens in their eggs, leading to an increase of circulating testosterone and growth rate in chicks. Hence, visual stimulation of the females can promote differential maternal allocation and favour offspring fitness. Our results further suggest that using artificial insemination for species conservation without appropriate stimulation of the breeding females probably has negative impacts on their breeding performance and therefore on population viability.
An experimental study of the population and evolutionary dynamics ofVibrio choleraeO1 and the bacteriophage JSF4
Authors: Wei Yan , Ocampo Paolo , Levin Bruce R.
Published: June 2010

Studies ofVibrio choleraein the environment and infected patients suggest that the waning of cholera outbreaks is associated with rise in the density of lytic bacteriophage. In accordance with mathematical models, there are seemingly realistic conditions where phage predation could be responsible for declines in the incidence of cholera. Here, we present the results of experiments with the El Tor strain ofV. cholerae(N16961) and a naturally occurring lytic phage (JSF4), exploring the validity of the main premise of this model: that phage predation limits the density ofV. choleraepopulations. At one level, the results of our experiments are inconsistent with this hypothesis. JSF4-resistantV. choleraeevolve within a short time following their confrontation with these viruses and their populations become limited by resources rather than phage predation. At a larger scale, however, the results of our experiments are not inconsistent with the hypothesis that bacteriophage modulate outbreaks of cholera. We postulate that the resistant bacteria that evolved play an insignificant role in the ecology or pathogenicity ofV. cholerae. Relative to the phage-sensitive cells from whence they are derived, the evolved JSF4-resistantV. choleraehave fitness costs and other characters that are likely to impair their ability to compete with the sensitive cells in their natural habitat and may be avirulent in human hosts. The results of thisin vitrostudy make predictions that can be tested in natural populations ofV. choleraeand cholera-infected patients.
Growth-induced mass flows in fungal networks
Authors: Heaton Luke L. M. , López Eduardo , Maini Philip K. , Fricker Mark D. , Jones Nick S.
Published: June 2010

Cord-forming fungi form extensive networks that continuously adapt to maintain an efficient transport system. As osmotically driven water uptake is often distal from the tips, and aqueous fluids are incompressible, we propose that growth induces mass flows across the mycelium, whether or not there are intrahyphal concentration gradients. We imaged the temporal evolution of networks formed byPhanerochaete velutina, and at each stage calculated the unique set of currents that account for the observed changes in cord volume, while minimizing the work required to overcome viscous drag. Predicted speeds were in reasonable agreement with experimental data, and the pressure gradients needed to produce these flows are small. Furthermore, cords that were predicted to carry fast-moving or large currents were significantly more likely to increase in size than cords with slow-moving or small currents. The incompressibility of the fluids within fungi means there is a rapid global response to local fluid movements. Hence velocity of fluid flow is a local signal that conveys quasi-global information about the role of a cord within the mycelium. We suggest that fluid incompressibility and the coupling of growth and mass flow are critical physical features that enable the development of efficient, adaptive biological transport networks.
Deletion of the Correia element in the mtr gene complex of Neisseria meningitidis
Authors: Enríquez Rocío , Abad Raquel , Chanto Grettel , Corso Alejandra , Cruces Raquel , Gabastou Jean Marc , Gorla María Cecilia , Maldonado Aurora , Moreno Jaime , Muros-Le Rouzic Erwan , Sorhouet Cecilia , Vázquez Julio A.
Published: June 2010

The mtr gene complex in Neisseria meningitidis encodes an efflux pump that is responsible for export of antibacterial hydrophobic agents. The promoter region of the mtrCDE operon harbours an insertion sequence known as a Correia element, and a binding site for the integration host factor (IHF) is present at the centre of the Correia element. It has been suggested that the expression of the mtrCDE operon in meningococci is subject to transcriptional regulation by the IHF and post-transcriptional regulation by cleavage in the inverted repeat of the Correia element. The promoter region of the mtrCDE operon as well as the association of changes at that point with decreased susceptibility to antimicrobial drugs in 606 Neisseria meningitidis strains were analysed in this study. Two different deletions were present in the analysed region. The first one, found in seven strains, corresponded to absence of the Correia element. The second one, affecting the −10 region and first 100 bp of the mtrR gene and present in 57 isolates, was only found in ST-1624 isolates. None of the deletions were associated with decreased susceptibility to antimicrobial drugs. Although most of the meningococcal strains carry the Correia element at that position, its deletion is not an exception.
The human immunodeficiency virus type 1 Rev protein: ménage à trois during the early phase of the lentiviral replication cycle
Authors: Grewe Bastian , Überla Klaus
Published: June 2010

The Rev protein of human immunodeficiency viruses (HIV) has long been recognized to be essential for the late phase of the virus replication cycle, due to its strong enhancement of expression of viral structural proteins. Surprisingly, a number of recent papers have demonstrated that Rev can also interfere with integration of the reverse-transcribed cDNA into the host-cell genome. This seems to be due to Rev's binding to integrase and LEDGF/p75, an important cellular cofactor of HIV-1 integration. As Rev is presumably expressed at sufficiently high levels only after the encoding genome has already integrated, the main function of Rev during the early phase might be to reduce genotoxicity due to excessive integration events after superinfection of the same cell by subsequent viruses. Other potential consequences for HIV-1 replication and evolution after co-infection of the same cell with two viruses are discussed.
Predicting genetic modifier loci using functional gene networks
Authors: Lee Insuk , Lehner Ben , Vavouri Tanya , Shin Junha , Fraser Andrew G. , Marcotte Edward M.
Published: June 2010

Most phenotypes are genetically complex, with contributions from mutations in many different genes. Mutations in more than one gene can combine synergistically to cause phenotypic change, and systematic studies in model organisms show that these genetic interactions are pervasive. However, in human association studies such nonadditive genetic interactions are very difficult to identify because of a lack of statistical power—simply put, the number of potential interactions is too vast. One approach to resolve this is to predict candidate modifier interactions between loci, and then to specifically test these for associations with the phenotype. Here, we describe a general method for predicting genetic interactions based on the use of integrated functional gene networks. We show that in both Saccharomyces cerevisiae and Caenorhabditis elegans a single high-coverage, high-quality functional network can successfully predict genetic modifiers for the majority of genes. For C. elegans we also describe the construction of a new, improved, and expanded functional network, WormNet 2. Using this network we demonstrate how it is possible to rapidly expand the number of modifier loci known for a gene, predicting and validating new genetic interactions for each of three signal transduction genes. We propose that this approach, termed network-guided modifier screening, provides a general strategy for predicting genetic interactions. This work thus suggests that a high-quality integrated human gene network will provide a powerful resource for modifier locus discovery in many different diseases.
Development of a Novel Aluminum Tolerance Phenotyping Platform Used for Comparisons of Cereal Aluminum Tolerance and Investigations into Rice Aluminum Tolerance Mechanisms
Authors: Famoso Adam N. , Clark Randy T. , Shaff Jon E. , Craft Eric , McCouch Susan R. , Kochian Leon V.
Published: June 2010

The genetic and physiological mechanisms of aluminum (Al) tolerance have been well studied in certain cereal crops, and Al tolerance genes have been identified in sorghum (Sorghum bicolor) and wheat (Triticum aestivum). Rice (Oryza sativa) has been reported to be highly Al tolerant; however, a direct comparison of rice and other cereals has not been reported, and the mechanisms of rice Al tolerance are poorly understood. To facilitate Al tolerance phenotyping in rice, a high-throughput imaging system and root quantification computer program was developed, permitting quantification of the entire root system, rather than just the longest root. Additionally, a novel hydroponic solution was developed and optimized for Al tolerance screening in rice and compared with the Yoshida's rice solution commonly used for rice Al tolerance studies. To gain a better understanding of Al tolerance in cereals, comparisons of Al tolerance across cereal species were conducted at four Al concentrations using seven to nine genetically diverse genotypes of wheat, maize (Zea mays), sorghum, and rice. Rice was significantly more tolerant than maize, wheat, and sorghum at all Al concentrations, with the mean Al tolerance level for rice found to be 2- to 6-fold greater than that in maize, wheat, and sorghum. Physiological experiments were conducted on a genetically diverse panel of more than 20 rice genotypes spanning the range of rice Al tolerance and compared with two maize genotypes to determine if rice utilizes the well-described Al tolerance mechanism of root tip Al exclusion mediated by organic acid exudation. These results clearly demonstrate that the extremely high levels of rice Al tolerance are mediated by a novel mechanism, which is independent of root tip Al exclusion.
Involvement of Auxin and Brassinosteroid in the Regulation of Petiole Elongation under the Shade
Authors: Kozuka Toshiaki , Kobayashi Junko , Horiguchi Gorou , Demura Taku , Sakakibara Hitoshi , Tsukaya Hirokazu , Nagatani Akira
Published: June 2010

Plants grown under a canopy recognize changes in light quality and modify their growth patterns; this modification is known as shade avoidance syndrome. In leaves, leaf blade expansion is suppressed, whereas petiole elongation is promoted under the shade. However, the mechanisms that control these responses are largely unclear. Here, we demonstrate that both auxin and brassinosteroid (BR) are required for the normal leaf responses to shade in Arabidopsis (Arabidopsis thaliana). The microarray analysis of leaf blades and petioles treated with end-of-day far-red light (EODFR) revealed that almost half of the genes induced by the treatment in both parts were previously identified as auxin-responsive genes. Likewise, BR-responsive genes were overrepresented in the EODFR-induced genes. Hence, the auxin and BR responses were elevated by EODFR treatment in both leaf blades and petioles, although opposing growth responses were observed in these two parts. The analysis of the auxin-deficient doc1/big mutant and the BR-deficient rot3/cyp90c1 mutant further indicates that auxin and BR were equally required for the normal petiole elongation response to the shade stimulus. In addition, the spotlight irradiation experiment revealed that phytochrome in leaf blades but not that in petioles regulated petiole elongation, which was probably mediated through regulation of the auxin/BR responses in petioles. On the basis of these findings, we conclude that auxin and BR cooperatively promote petiole elongation in response to the shade stimulus under the control of phytochrome in the leaf blade.
Enhanced antitumor efficacy of folate‐linked liposomal doxorubicin with TGF‐β type I receptor inhibitor
Authors: Taniguchi Yukimi , Kawano Kumi , Minowa Takuya , Sugino Takashi , Shimojo Yuki , Maitani Yoshie
Published: June 2010

Tumor cell targeting of drug carriers is a promising strategy and uses the attachment of various ligands to enhance the therapeutic potential of chemotherapy agents. Folic acid is a high‐affinity ligand for folate receptor, which is a functional tumor‐specific receptor. The transforming growth factor (TGF)‐β type I receptor (TβR‐I) inhibitor A‐83‐01 was expected to enhance the accumulation of nanocarriers in tumors by changing the microvascular environment. To enhance the therapeutic effect of folate‐linked liposomal doxorubicin (F‐SL), we co‐administrated F‐SL with A‐83‐01. Intraperitoneally injected A‐83‐01‐induced alterations in the cancer‐associated neovasculature were examined by magnetic resonance imaging (MRI) and histological analysis. The targeting efficacy of single intravenous injections of F‐SL combined with A‐83‐01 was evaluated by measurement of the biodistribution and the antitumor effect in mice bearing murine lung carcinoma M109. A‐83‐01 temporarily changed the tumor vasculature around 3 h post injection. A‐83‐01 induced 1.7‐fold higher drug accumulation of F‐SL in the tumor than liposome alone at 24 h post injection. Moreover F‐SL co‐administrated with A‐83‐01 showed significantly greater antitumor activity than F‐SL alone. This study shows that co‐administration of TβR‐I inhibitor will open a new strategy for the use of FR‐targeting nanocarriers for cancer treatment. (Cancer Sci 2010); 00: 000–000
The role of micronucleus scoring in fine needle aspirates of ductal carcinoma of the breast
Authors: Samanta S. , Dey P. , Nijhawan R.
Published: June 2010

S. Samanta, P. Dey and R. Nijhawan

The role of micronucleus scoring in fine needle aspirates of ductal carcinoma of the breast

Aims and objectives: Micronucleus (MN) scoring was carried out in benign (fibroadenoma) and malignant (infiltrating ductal carcinoma) breast lesions to evaluate the role of MN as a biomarker in breast carcinomas. We also compared MN scores among different cytological grades of breast carcinoma.

Materials and methods: A total of 31 archival cases of fibroadenoma (FA) and 40 cases of infiltrating ductal carcinoma (IDC) were selected. The best May‐Grünwald–Giemsa (MGG) stained fine needle aspiration cytology (FNAC) smear of each case was selected. The MN scoring was carried out independently by two observers on 1000 epithelial cells in oil immersion magnification (100× objective). The MN scores in FA and IDC were compared. The IDC cases were graded and the MN scores in different cytological grades of IDC were compared.

Results: The mean MN scores (± standard deviation) in FA and IDC were 0.6 (± 1.1) and 13.6 (± 12.8), respectively, which were significantly different (P < 0.0001). There were seven grade 1, 13 grade 2, and 20 grade 3 IDCs. The mean MN scores (± standard deviation) of grade 1, 2 and 3 IDC were 4.3 (± 2.3), 11.95 (± 9.2) and 21.1 (± 16.7), respectively. An analysis of variance (anova) test showed a significant difference in MN score between all the grades of IDC (P < 0.05). However, there was no significant difference between fibroadenoma and grade 1 IDC. The Pearson’s correlation coefficient showed positive correlations between MN scoring in the different grades of IDC.

Conclusions: MN scoring on routinely stained smears of IDCs was significantly higher than in fibroadenoma and was relatively easy, reliable and reproducible. As MN scoring of grade 1 IDC was similar to fibroadenoma, a larger study should be conducted to compare grade 1 IDC with other benign breast lesions.
Grass snakes exploit anthropogenic heat sources to overcome distributional limits imposed by oviparity
Authors: Löwenborg Kristin , Shine Richard , Kärvemo Simon , Hagman Mattias
Published: June 2010

1. A lack of warm nest‐sites prevents oviparous reptile species from reproducing in cool climates; such areas are dominated by viviparous species because sun‐seeking pregnant females can maintain high temperatures for their developing offspring.

2. Our field and laboratory studies show that one oviparous species (the grass snake, Natrix natrix) escapes this cold‐climate constraint (and hence, extends much further north in Europe than do other oviparous taxa) by ovipositing in a thermally distinctive man‐made microhabitat (manure heaps on farms).

3. In the field, temperatures inside manure heaps averaged 30·7 °C, much higher than compost heaps (20·6 °C) or potential natural nest‐sites under logs and rocks (15·5 °C).

4. In the laboratory, higher incubation temperatures not only hastened hatching, but also increased hatching success and modified the body sizes, colours, and locomotor abilities of hatchlings. Incubation temperatures typical of manure heaps (rather than alternative nest‐sites) resulted in larger, faster offspring that hatched earlier in the season.

5. Thus, anthropogenic activities have generated potential nest‐sites offering thermal regimes not naturally available in the region; and grass snakes have exploited that opportunity to escape the thermal limits that restrict geographic distributions of other oviparous reptile taxa.
AATYK1A phosphorylation by Cdk5 regulates the recycling endosome pathway
Authors: Takano Tetsuya , Tsutsumi Koji , Saito Taro , Asada Akiko , Tomomura Mineko , Fukuda Mitsunori , Hisanaga Shin‐ichi
Published: June 2010

Trafficking of recycling endosomes (REs) is regulated by the small GTPase, Rab11A; however, the regulatory mechanism remains elusive. Apoptosis‐associated tyrosine kinase 1A (AATYK1A) is a Ser/Thr kinase expressed highly in brain. We have recently shown that AATYK1A localizes to Rab11A‐positive RE and is phosphorylated at Ser34 by cyclin‐dependent kinase 5 (Cdk5). Here, we have investigated a role of AATYK1A and its phosphorylation in recycling endosomal trafficking using Chinese hamster ovary‐K1 (CHO‐K1) cells. AATYK1A localizes predominantly to Rab11A‐positive pericentrosomal endocytic recycling compartment (ERC). Phosphorylation at Ser34 of AATYK1A disrupts its accumulation in the pericentrosomal ERC. Consistently, phosphorylation‐mimic mutant (AATYK1A‐S34D) did not accumulate in the ERC and additionally attenuated ERC formation. ERC formation suppression can be reversed by constitutively active Rab11A‐Q70L, suggesting a functional link between AATYK1A phosphorylation and Rab11A activity. Although no direct interaction between AATYK1A and Rab11A could be detected, the exchange of guanine nucleotides bound to Rab11A was significantly reduced in the presence of the phosphorylation‐mimic AATYK1A‐S34D. Together, our results reveal a regulatory role for AATYK1A in the formation of pericentrosomal ERC. They furthermore indicate that Cdk5 can disrupt ERC formation via Ser34 phosphorylation of AATYK1A. Finally, our data suggest a mechanism by which AATYK1A signaling couples Cdk5 to Rab11A activity.