bluuebunny/crossref_metadata_2025 huggingface dataset:
Sea surface temperature cooling mode in the Pacific cold tongue
Authors: Zhang Wenjun , Li Jianping , Zhao Xia
Published: December 2010

Long‐term variability in sea surface temperature (SST) in the equatorial Pacific and its relationship with global warming were investigated using three SST data sets (Hadley Center Global Sea Ice and Sea Surface Temperature, extended reconstruction sea surface temperature, and Kaplan), atmospheric fields from National Centers for Environmental Prediction/National Center for Atmospheric Research reanalysis, and subsurface sea temperature from the Simple Ocean Data Assimilation data set. A cooling mode in the equatorial Pacific cold tongue is evident in all three SST data sets for two periods: 1870–2007 and 1948–2007. This cooling, which is indicated by the second empirical orthogonal function mode, is characterized by cooling in the Pacific cold tongue and warming elsewhere in the tropical Pacific. Its principal component time series is highly correlated with global mean surface temperature combining air temperature and SST. In association with the SST cooling mode, atmospheric fields and subsurface sea temperature are coupled in the tropical Pacific during recent decades. Moreover, for the coupled models in the 20th century run (20C3M), obtained from the Intergovernmental Panel on Climate Change Fourth Assessment Report database, those with realistic features of El Niño‐Southern Oscillation (ENSO) events can well show the cooling mode. However, the cooling mode is not shown in these coupled models in a preindustrial scenario with no forcing attributed to global warming. Results from observations and models suggest that the cooling mode is very likely caused by global warming. This conclusion is supported by a hypothesis that considers dynamic effects in the equatorial Pacific Ocean in response to global warming.
Comparison of rain fractions over tropical and sub‐tropical ocean obtained from precipitation retrieval algorithms for microwave sounders
Authors: Kida Satoshi , Shige Shoichi , Manabe Takeshi
Published: December 2010

We compare the fractional occurrence of precipitation (rain fraction) over ocean derived using the Global Satellite Mapping of Precipitation algorithm for the Advanced Microwave Sounding Unit (GSMaP_AMSU) and the Microwave Surface and Precipitation Products System Day 2 rainfall algorithm (NOAA_AMSU) for the Kwajalein radar site and over tropical and subtropical ocean. The rain fractions of GSMaP_AMSU and NOAA_AMSU are lower than that of Kwajalein radar estimates because of failure to detect areas of light rain. Over tropical and subtropical ocean, the rain fraction of GSMaP_AMSU is closer to that obtained using a microwave imager (MWI) and little different from that of Tropical Rainfall Measuring Mission Precipitation Radar (PR) data, whilethe rain fraction of NOAA_AMSU is much smaller than that obtained using MWI or PR data. In the case of the edge of the South Pacific Convergence Zone where the PR observes scattered shallow rain, while NOAA_AMSU fails to detect the scattered rain, GSMaP_AMSU detects the scattered rain through consideration of the scattering index, which is the difference in brightness temperature (Tb) between 89 and 150 GHz. Although the scattering index is designed on the basis that Tb decreases in response to scattering by precipitation at these frequencies and increases rapidly with frequency, there are emission and scattering regimes. Furthermore, the scattering index also responds to emission in light rain with a low concentration of cloud liquid water. As a result, the light rain pixel can be detected using the scattering index to take advantage of the emission signature from raindrops.
Precipitation and cloud statistics in the deep tropical convective regime
Authors: Shen Xinyong , Wang Yi , Zhang Nan , Li Xiaofan
Published: December 2010

Precipitation and cloud statistics in the deep tropical convective regime is investigated through the analysis of grid‐scale data from a two‐dimensional, cloud‐resolving model simulation. The model is forced by large‐scale vertical velocity, zonal wind, horizontal advection, and sea surface temperature observed and derived from the Tropical Ocean Global Atmosphere Coupled Ocean Atmosphere Response Experiment. The analysis is conducted by categorizing the grid‐scale data into eight rainfall types based on precipitation processes: Water vapor convergence, local vapor change, and hydrometeor change/convergence. Among the eight rainfall types, the rainfall with local atmospheric drying, water vapor divergence, and hydrometeor loss/convergence has the largest contribution (30.8%) to the total rainfall because of large rainfall coverage (35.3%). The hydrometeor loss is mainly caused by water clouds through precipitation and the evaporation of rain. For the three other rainfall types with water vapor divergence, each rainfall type contributes to the total rainfall by less than 5%. Of the total rainfall, 61% is attributed to the four rainfall types with water vapor convergence. Although the rainfall with local atmospheric drying, water vapor convergence, and hydrometeor loss/convergence shows the largest surface rain rate (27.8 mm h−1), it only accounts for a small part (10%) of the total rainfall due to its small rainfall coverage (1.2%). For the three other rainfall types with water vapor convergence, each rainfall type contributes to the total rainfall by 14–19%. The grid‐scale precipitation statistics are significantly different from the model domain mean precipitation statistics found by Shen et al. (2010), suggesting a spatial‐scale dependence of precipitation statistics.
Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics
Authors: Weber Marc , Teeling Hanno , Huang Sixing , Waldmann Jost , Kassabgy Mariette , Fuchs Bernhard M , Klindworth Anna , Klockow Christine , Wichels Antje , Gerdts Gunnar , Amann Rudolf , Glöckner Frank Oliver
Published: December 2010

Next-generation sequencing (NGS) technologies have enabled the application of broad-scale sequencing in microbial biodiversity and metagenome studies. Biodiversity is usually targeted by classifying 16S ribosomal RNA genes, while metagenomic approaches target metabolic genes. However, both approaches remain isolated, as long as the taxonomic and functional information cannot be interrelated. Techniques like self-organizing maps (SOMs) have been applied to cluster metagenomes into taxon-specific bins in order to link biodiversity with functions, but have not been applied to broad-scale NGS-based metagenomics yet. Here, we provide a novel implementation, demonstrate its potential and practicability, and provide a web-based service for public usage. Evaluation with published data sets mimicking varyingly complex habitats resulted into classification specificities and sensitivities of close to 100% to above 90% from phylum to genus level for assemblies exceeding 8 kb for low and medium complexity data. When applied to five real-world metagenomes of medium complexity from direct pyrosequencing of marine subsurface waters, classifications of assemblies above 2.5 kb were in good agreement with fluorescence in situ hybridizations, indicating that biodiversity was mostly retained within the metagenomes, and confirming high classification specificities. This was validated by two protein-based classifications (PBCs) methods. SOMs were able to retrieve the relevant taxa down to the genus level, while surpassing PBCs in resolution. In order to make the approach accessible to a broad audience, we implemented a feature-rich web-based SOM application named TaxSOM, which is freely available at http://www.megx.net/toolbox/taxsom. TaxSOM can classify reads or assemblies exceeding 2.5 kb with high accuracy and thus assists in linking biodiversity and functions in metagenome studies, which is a precondition to study microbial ecology in a holistic fashion.
Ontology-Based Queries over Cancer Data
Authors: Gonzalez-Beltran Alejandra
Published: December 2010

The ever-increasing amount of data in biomedical research, and in cancer research in particular, needs to be managed to support efficient data access, exchange and integration. Existing software infrastructures, such as caGrid, support access to distributed information annotated with a domain ontology. However, caGrid's current querying functionality depends on the structure of individual data resources without exploiting the semantic annotations. In this paper, we present the design and development of an ontology-based querying functionality that consists of: the generation of OWL2 ontologies from the underlying data resources’ metadata and a query rewriting and translation process based on reasoning, which converts a query at the domain ontology level into queries at the software infrastructure level. We present a detailed analysis of our approach as well as an extensive performance evaluation. While the implementation and evaluation was performed for the caGrid infrastructure, the approach could be applicable to other model and metadata-driven environments for data sharing.
Dietary Adherence During Weight Loss Predicts Weight Regain
Authors: Del Corral Pedro , Bryan David R. , Garvey W. Timothy , Gower Barbara A. , Hunter Gary R.
Published: December 2010

This study examined the relationship between previous dietary adherence during a low‐calorie diet weight loss intervention and subsequent weight change during a 2‐year follow‐up for weight maintenance. One hundred and sixteen healthy, recently weight reduced (lost ∼12 kg, BMI 22–25 kg/m2) premenopausal women were studied. Dietary adherence was assessed by doubly labeled water (DLW) and body composition change. Comparisons were made between the upper and lower tertiles for previous dietary adherence and subsequent weight change at 1‐ and 2‐year follow‐up. Percent weight regained was significantly lower (30.9 ± 6.7% vs. 66.7 ± 9.4%; P < 0.05) in the upper compared to the lower adherence tertile for previous weight loss dietary adherence (49.9 ± 8.8% vs. 96.8 ± 12.8% P < 0.05) at 1‐ and 2‐year follow‐up, respectively. This difference was partly explained by increases in daily activity‐related energy expenditure (AEE) (+95 ± 45 kcal/day vs. −44 ± 42 kcal/day, P < 0.05) and lower daily energy intake (2,066 ± 71 kcal/day vs. 2,289 ± 62 kcal/day, P < 0.05) in the higher tertile for previous dietary adherence, compared to the lower. These findings suggest that higher adherence (i.e., higher tertile) to the previous low‐calorie diet predicts lower weight regain over 2‐year follow‐up for weight maintenance, which is explained by lower energy intake and higher physical activity. Finally, how well an individual adheres to a low‐calorie diet intervention during weight loss may be a useful tool for identifying individuals who are particularly vulnerable to subsequent weight regain.
Retinol‐Binding Protein 4 in Young Men With Low Versus Normal Birth Weight: Physiological Response to Short‐Term Overfeeding
Authors: Ribel‐Madsen Rasmus , Brøns Charlotte , Friedrichsen Martin , Poulsen Pernille , Vaag Allan
Published: December 2010

Retinol‐binding protein 4 (RBP4) is a plasma protein which is elevated in obesity and type 2 diabetes. We aimed to investigate whether RBP4 represents a mechanism underlying the associations between low birth weight (LBW), high‐fat diet, and insulin resistance. Forty‐six young, lean men with low (n = 20) or normal (n = 26) birth weight underwent a 5‐day high‐fat high‐calorie (HFHC) dietary intervention. In vivo glucose metabolism was assessed by euglycemic‐hyperinsulinemic clamp, glucose tracer and intravenous glucose tolerance test techniques. Body composition was measured by a dual‐energy x‐ray absorptiometry scan, and plasma RBP4 by an enzyme‐linked immunosorbent assay. RBP4 was not associated with birth weight, but with BMI (β = 0.9 µg/ml (0.08;1.8) (95% confidence interval), P = 0.03) and plasma levels of low‐density lipoprotein cholesterol (β = 5.3 µg/ml (1.9;8.7), P = 0.03) and triglycerides (β = 15.4 µg/ml (9.5;21.3), P < 0.001). Under baseline diet conditions, RBP4 was associated with decreased disposition index (Di) (β = −2.4% (−4.5%;−0.2%), P = 0.04) and increased basal hepatic glucose production rate (HGP) (β = 0.02 mg kg−1 min−1 (0.002;0.04), P = 0.03), but not associated with peripheral glucose disposal rate or hepatic insulin resistance index. RBP4 levels were not influenced by overfeeding or related to peripheral and hepatic insulin resistance provoked by the dietary intervention. In conclusion, plasma RBP4 in young men associates with components of the metabolic syndrome, but is not determined by birth weight and seems not to be involved in short‐term high‐fat diet‐induced insulin resistance.
Rescuing neurons in prion disease
Authors: Verity Nicholas C. , Mallucci Giovanna R.
Published: December 2010

One of the major current challenges to both medicine and neuroscience is the treatment of neurodegenerative diseases, which pose an ever-increasing medical, social and economic burden in the developed world. These disorders, which include Alzheimer's, Huntington's and Parkinson's diseases, and the rarer prion diseases, are separate entities clinically but have common features, including aggregates of misfolded proteins and varying patterns of neurodegeneration. A key barrier to effective treatment is that patients present clinically with advanced, irreversible, neuronal loss. Critically, mechanisms of neurotoxicity are poorly understood. Prevention of neuronal loss, ideally by targeting underlying pathogenic mechanisms, must be the aim of therapy. The present review describes the rationale and experimental approaches that have allowed such prevention, rescuing neurons in mice with prion disease. This rescue cured animals of a rapidly fatal neurodegenerative condition, resulting in symptom-free survival for their natural lifespan. Early pathological changes were reversed; behavioural, cognitive and neurophysiological deficits were recovered; and there was no neuronal loss. This was achieved by targeting the central pathogenic process in prion disease rather than the presumed toxic species, first by proof-of-principle experiments in transgenic mice and then by treatment using RNA interference for gene knockdown. The results have been a new therapeutic target for prion disease, further insight into mechanisms of prion neurotoxicity and the discovery of a window of reversibility in neuronal damage. Furthermore, the work gives rise to new concepts for treatment strategies for other neurodegenerative disorders, and highlights the need for clinical detection of early neuronal dysfunction, so that similar early rescue can also be achieved for these disorders.
Building water bridges in air: Electrohydrodynamics of the floating water bridge
Authors: Marín Álvaro G. , Lohse Detlef
Published: December 2010

The interaction of electrical fields and liquids can lead to a phenomenon that defies intuition. Some famous examples can be found in electrohydrodynamics as Taylor cones, whipping jets, or noncoalescing drops. A less famous example is the floating water bridge: a slender thread of water held between two glass beakers in which a high voltage difference is applied. Surprisingly, the water bridge defies gravity even when the beakers are separated at distances up to 2 cm. In this paper, experimental measurements and simple models are proposed and discussed for the stability of the bridge and the source of the flow, revealing an important role of polarization forces on the stability of the water bridge. On the other hand, the observed flow can only be explained due to the non-negligible free charge present in the surface. In this sense, the floating water bridge can be considered as an extreme case of a leaky dielectric liquid [J. R. Melcher and G. I. Taylor, Annu. Rev. Fluid Mech. 1, 111 (1969)].
Model of electron pressure anisotropy in the electron diffusion region of collisionless magnetic reconnection
Authors: Divin A. , Markidis S. , Lapenta G. , Semenov V. S. , Erkaev N. V. , Biernat H. K.
Published: December 2010

A new model of the electron pressure anisotropy in the electron diffusion region in collisionless magnetic reconnection is presented for the case of antiparallel configuration of magnetic fields. The plasma anisotropy is investigated as source of collisionless dissipation. By separating electrons in the vicinity of the neutral line into two broad classes of inflowing and accelerating populations, it is possible to derive a simple closure for the off-diagonal electron pressure component. The appearance of these two electron populations near the neutral line is responsible for the anisotropy and collisionless dissipation in the magnetic reconnection. Particle-in-cell simulations verify the proposed model, confirming first the presence of two particle populations and second the analytical results for the off-diagonal electron pressure component. Furthermore, test-particle calculations are performed to compare our approach with the model of electron pressure anisotropy in the inner electron diffusion region by Fujimoto and Sydora [Phys. Plasmas 16, 112309 (2009)].
Pseudomorphic strain induced strong anisotropic magnetoresistance over a wide temperature range in epitaxial La0.67Ca0.33MnO3/NdGaO3(001) films
Authors: Wang L. F. , Huang Z. , Tan X. L. , Chen P. F. , Zhi B. W. , Li G. M. , Wu W. B.
Published: December 2010

Strong anisotropic magnetoresistance (AMR) was observed in La0.67Ca0.33MnO3 films grown coherently on the orthorhombic NdGaO3(001) substrates. With an increased orthorhombic lattice distortion due to the pseudomorphic strain, the films show not only a ferromagnetic-metal (FM) transition at TC of ∼265 K, but also the phase coexistence of FM and antiferromagnetic-insulator below ∼250 K. The phase competitions are very sensitive to the magnetic field, and more strikingly, to its orientations with respect to the crystal axes resulting in a large AMR in a broad temperature range, in addition to the conventional one peaked near TC. The films also show uniaxial magnetic anisotropy with the easy axis along the elongated b axis, suggesting that it is the strain induced spin-orbit-lattice coupling and the resultant phase competitions that control the AMR in epitaxial manganite films.
End-group effects on negative differential resistance and rectifying performance of a polyyne-based molecular wire
Authors: Qiu M. , Zhang Z. H. , Deng X. Q. , Pan J. B.
Published: December 2010

Based on first-principles approach, the end-group effects on negative differential resistance (NDR) and rectifying performance of polyyne-based molecular wires are investigated. The NDR behaviors are observed when the polyyne is attached to asymmetric (–NO2 and –NH2) or symmetric (double –S) end groups, and rectifying performance emerges with the presence of asymmetric groups. The analysis on microscopic nature reveals the intrinsic origin of these phenomena. Our results show the possibility of a multifunctional molecular device design simultaneously with NDR and rectifying performances by using a technology of capping certain end groups to polyyne.
Track heating study for current-induced domain wall motion experiments
Authors: Curiale J. , Lemaître A. , Faini G. , Jeudy V.
Published: December 2010

We investigate the Joule heating produced by current pulses in (Ga,Mn)(As,P) ferromagnetic semiconducting nanotracks. The transient and the stationary heating regimes are determined experimentally. A good quantitative agreement is obtained with simulations and analytical calculations. The temperature of the tracks is shown to be essentially determined by the heat diffusion through the substrate. Implications for current-induced domain wall motion experiments are discussed.
Fano profiles in transmission spectra of terahertz radiation through one-dimensional periodic metallic structures
Authors: Pradarutti B. , Torosyan G. , Theuer M. , Beigang R.
Published: December 2010

The transmission properties of broadband terahertz radiation through one-dimensional periodic metallic structures are investigated experimentally, and the obtained results are explained theoretically. Characteristic minima known as Wood’s anomalies are observed in the transmission spectra. The measured line shapes, the so-called Fano profiles, are caused by the coupling between resonant surface plasmons excited on the metallic grating and nonresonant diffraction orders. Numerical simulations using classical electrodynamics are in good agreement with the experiments.
The trapping and detrapping of short internal waves by an inertia wave
Authors: Vanderhoff Julie C. , Rottman James W. , Broutman Dave
Published: December 2010

The refraction of a spectrum of short internal waves by a packet of inertia waves is considered. It is found that a short inertia-wave packet produces a larger net change in a spectrum of short waves than a long inertia-wave packet, provided the short waves are trapped at some time during the interaction. Specifically, an incident narrow-banded short-wave spectrum broadens more quickly and more fully when refracted by the short inertia-wave packet. The results are explained in terms of a frequency conservation law, which constrains short-wave change in the limit of a long inertia-wave packet.
Road mortality reduces survival and population growth rates of tammar wallabies on Garden Island, Western Australia
Authors: Chambers Brian , Bencini Roberta
Published: December 2010

Context Although road mortality has the potential to affect the fate of populations, it is often confounded with other forms of environmental change. Therefore determining its impact separately from other factors is difficult because it requires an understanding of how road mortalities affect age- and sex-specific survival rates. Aims We determined the impact of high numbers of road-kills and habitat modification on the growth and survival of the population of tammar wallabies (Macropus eugenii) on Garden Island, off the coast of Western Australia. The increased supply of food from large areas of fertilised and irrigated lawns on a naval base was expected to increase the population growth rate (λ) and the road-kills were expected to offset the population response. Methods We conducted a mark-and-recapture study over three years to estimate rates of survival, reproduction and population growth rates in areas of the island that were either heavily affected by the presence of a naval base that included a network of roads and buildings, close enough to the naval base that animals could be affected by the disturbance there, and completely unaffected and lacking major roads or buildings. All road-kills were collected to estimate the impact of road mortality on the survival and growth rates of the population. Key results The growth rate, λ, for the population on the naval base was 1.02 ± 0.083 (s.e.) per year, which was much higher than in an area of adjacent bushland at 0.92 ± 0.065 per year and in undisturbed bushland at 0.93 ± 0.100 per year. When the impact of road mortality was removed, λ increased to 1.15 ± 0.101 per year on the naval base and 0.96 ± 0.076 per year in the bushland adjacent to the naval base. On the naval base road mortality reduced survival rates of one-year-old and adult animals by 0.14 ± 0.087 and 0.12 ± 0.012 per year (mean ± s.e.). Conclusions Road mortality counteracted the increase in the size of the tammar population caused by the habitat modification on the naval base. The impact of road mortality on the adjacent bushland population may result in its long-term decline, as the population may not be able to recover from the reduction in survival rates. Implications Road mortality has the potential to threaten susceptible populations but its impact should be quantified so that mitigation measures can be implemented where they will achieve the greatest benefits.
Completely phased genome sequencing through chromosome sorting
Authors: Yang Hong , Chen Xi , Wong Wing Hung
Published: December 2010

The two haploid genome sequences that a person inherits from the two parents represent the most fundamentally useful type of genetic information for the study of heritable diseases and the development of personalized medicine. Because of the difficulty in obtaining long-range phase information, current sequencing methods are unable to provide this information. Here, we introduce and show feasibility of a scalable approach capable of generating genomic sequences completely phased across the entire chromosome.
Categorical implicit learning in real-world scenes: Evidence from contextual cueing
Authors: Goujon Annabelle
Published: December 2010

The present study examined the extent to which learning mechanisms are deployed on semantic-categorical regularities during a visual searching within real-world scenes. The contextual cueing paradigm was used with photographs of indoor scenes in which the semantic category did or did not predict the target position on the screen. No evidence of a facilitation effect was observed in the predictive condition compared to the nonpredictive condition when participants were merely instructed to search for a target T or L (Experiment 1). However, a rapid contextual cueing effect occurred when each display containing the search target was preceded by a preview of the scene on which participants had to make a decision regarding the scene's category (Experiment 2). A follow-up explicit memory task indicated that this benefit resulted from implicit learning. Similar implicit contextual cueing effects were also obtained when the scene to categorize was different from the subsequent search scene (Experiment 3) and when a mere preview of the search scene preceded the visual searching (Experiment 4). These results suggested that if enhancing the processing of the scene was required with the present material, such implicit semantic learning can nevertheless take place when the category is task irrelevant.
Variable selection for discriminant analysis with Markov random field priors for the analysis of microarray data
Authors: Stingo Francesco C. , Vannucci Marina
Published: December 2010

Motivation: Discriminant analysis is an effective tool for the classification of experimental units into groups. Here, we consider the typical problem of classifying subjects according to phenotypes via gene expression data and propose a method that incorporates variable selection into the inferential procedure, for the identification of the important biomarkers. To achieve this goal, we build upon a conjugate normal discriminant model, both linear and quadratic, and include a stochastic search variable selection procedure via an MCMC algorithm. Furthermore, we incorporate into the model prior information on the relationships among the genes as described by a gene–gene network. We use a Markov random field (MRF) prior to map the network connections among genes. Our prior model assumes that neighboring genes in the network are more likely to have a joint effect on the relevant biological processes.

Results: We use simulated data to assess performances of our method. In particular, we compare the MRF prior to a situation where independent Bernoulli priors are chosen for the individual predictors. We also illustrate the method on benchmark datasets for gene expression. Our simulation studies show that employing the MRF prior improves on selection accuracy. In real data applications, in addition to identifying markers and improving prediction accuracy, we show how the integration of existing biological knowledge into the prior model results in an increased ability to identify genes with strong discriminatory power and also aids the interpretation of the results.

Contact:  marina@rice.edu
Colonic Diverticulosis, Diverticular Disease and Diverticulitis: A Clinical Review
Authors: Patel Meera , Takhar Arun , Stephenson James A. , Metcalfe Matthew , Dennison Ashley
Published: December 2010

By the age of 50 years, 50% of the population will have diverticula of the large bowel. Ten to 20% will experience a clinically significant complication, principally diverticulitis and haemorrhage. As the elderly population grows, a concomitant rise in these patients will occur. Early diagnosis including the recognition of complications is key in reducing morbidity and mortality.
Strong and weak divergence in finite time of Euler's method for stochastic differential equations with non-globally Lipschitz continuous coefficients
Authors: Hutzenthaler Martin , Jentzen Arnulf , Kloeden Peter E.
Published: December 2010

The stochastic Euler scheme is known to converge to the exact solution of a stochastic differential equation (SDE) with globally Lipschitz continuous drift and diffusion coefficients. Recent results extend this convergence to coefficients that grow, at most, linearly. For superlinearly growing coefficients, finite-time convergence in the strong mean-square sense remains. In this article, we answer this question to the negative and prove, for a large class of SDEs with non-globally Lipschitz continuous coefficients, that Euler’s approximation converges neither in the strong mean-square sense nor in the numerically weak sense to the exact solution at a finite time point. Even worse, the difference of the exact solution and of the numerical approximation at a finite time point diverges to infinity in the strong mean-square sense and in the numerically weak sense.
Feedback-induced instability in tapping mode atomic force microscopy: theory and experiment
Authors: Payton O. , Champneys A. R. , Homer M. E. , Picco L. , Miles M. J.
Published: December 2010

We investigate a mathematical model of tapping mode atomic force microscopy (AFM), which includes surface interaction via both van der Waals and meniscus forces. We also take particular care to include a realistic representation of the integral control inherent to the real microscope. Varying driving amplitude, amplitude setpoint and driving frequency independently shows that the model can capture the qualitative features observed in AFM experiments on a flat sample and a calibration grid. In particular, the model predicts the onset of an instability, even on a flat sample, in which a large-amplitude beating-type motion is observed. Experimental results confirm this onset and also confirm the qualitative features of the dynamics suggested by the simulations. The simulations also suggest the mechanism behind the beating effect; that the control loop over-compensates for sufficiently high gains. The mathematical model is also used to offer recommendations on the effective use of AFMs in order to avoid unwanted artefacts.
Male genotype influences female reproductive investment in
Drosophila melanogaster
Authors: Pischedda Alison , Stewart Andrew D. , Little Monica K. , Rice William R.
Published: December 2010

In many species, males can influence the amount of resources their mates invest in reproduction. Two favoured hypotheses for this observation are that females assess male quality during courtship or copulation and alter their investment in offspring accordingly, or that males manipulate females to invest heavily in offspring produced soon after mating. Here, we examined whether there is genetic variation for males to influence female short-term reproductive investment in
Drosophila melanogaster
, a species with strong sexual selection and substantial sexual conflict. We measured the fecundity and egg size of females mated to males from multiple isofemale lines collected from populations around the globe. Although these traits were not strongly influenced by the male's population of origin, we found that 22 per cent of the variation in female short-term reproductive investment was attributable to the genotype of her mate. This is the first direct evidence that male
D. melanogaster
vary genetically in their proximate influence on female fecundity, egg size and overall reproductive investment.
Towards a scientific concept of free will as a biological trait: spontaneous actions and decision-making in invertebrates
Authors: Brembs Björn
Published: December 2010

Until the advent of modern neuroscience, free will used to be a theological and a metaphysical concept, debated with little reference to brain function. Today, with ever increasing understanding of neurons, circuits and cognition, this concept has become outdated and any metaphysical account of free will is rightfully rejected. The consequence is not, however, that we become mindless automata responding predictably to external stimuli. On the contrary, accumulating evidence also from brains much smaller than ours points towards a general organization of brain function that incorporates flexible decision-making on the basis of complex computations negotiating internal and external processing. The adaptive value of such an organization consists of being unpredictable for competitors, prey or predators, as well as being able to explore the hidden resource deterministic automats would never find. At the same time, this organization allows all animals to respond efficiently with tried-and-tested behaviours to predictable and reliable stimuli. As has been the case so many times in the history of neuroscience, invertebrate model systems are spearheading these research efforts. This comparatively recent evidence indicates that one common ability of most if not all brains is to choose among different behavioural options even in the absence of differences in the environment and perform genuinely novel acts. Therefore, it seems a reasonable effort for any neurobiologist to join and support a rather illustrious list of scholars who are trying to wrestle the term ‘free will’ from its metaphysical ancestry. The goal is to arrive at a scientific concept of free will, starting from these recently discovered processes with a strong emphasis on the neurobiological mechanisms underlying them.
The Smoking Abstinence Questionnaire: measurement of smokers' abstinence‐related expectancies
Authors: Hendricks Peter S. , Wood Sabrina B. , Baker Majel R. , Delucchi Kevin L. , Hall Sharon M.
Published: December 2010

Aims  To develop and validate a measure of smokers' expectancies for the abstinence process upon quitting smoking: the Smoking Abstinence Questionnaire (SAQ).

Design  Principal component analysis and other psychometric analyses of self‐report data.

Setting  San Francisco, California.

Participants  A total of 507 adult smokers of at least 10 cigarettes per day diverse in gender, sexual orientation and ethnoracial status.

Measurements  The primary measure was a draft version of the SAQ. Additional measures assessed a variety of other smoking‐related constructs.

Findings  Analyses yielded 10 scales of the SAQ: Withdrawal, Social Improvement/Non‐smoker Identity, Adverse Outcomes, Treatment Effectiveness, Common Reasons, Barriers to Treatment, Social Support, Optimistic Outcomes, Coffee Use and Weight Gain. The SAQ scales demonstrated internal consistencies ranging from 0.62 to 0.85 and were associated with tobacco dependence, motivation to quit, abstinence self‐efficacy, withdrawal symptoms, dietary restraint, shape and weight concern and tobacco use expectancies. The SAQ predicted smoking‐related constructs above and beyond tobacco use expectancies, suggesting that abstinence‐related expectancies and tobacco use expectancies are distinct from one another.

Conclusions  A newly developed questionnaire, the Smoking Abstinence Questionnaire, appears to capture reliably smokers' expectancies for abstinence (Withdrawal, Social Improvement/Non‐smoker Identity, Adverse Outcomes, Common Reasons, Optimistic Outcomes, Coffee Use, and Weight Gain) and expectancies related to the success of a quit attempt (Treatment Effectiveness, Barriers to Treatment and Social Support). It remains to be seen how far any of these expectancies predict attempts to quit, withdrawal, treatment utilization and response and quitting success above and beyond existing measures.
Towards a national model for managing impaired driving offenders
Authors: Voas Robert B. , DuPont Robert L. , Talpins Stephen K. , Shea Corinne L.
Published: December 2010

Aims  To describe a proposed national model for controlling the risk presented by offenders convicted of driving while impaired (DWI) and promoting behavioral change to reduce future recidivism.

Setting  Traditional methods of controlling the risk they present to the driving public are not adequate, as indicated by the fact that approximately 1000 people are killed each year‐in alcohol‐related crashes involving drivers convicted of DWI in the previous three years. However, stimulated by the success of special drug courts for substance abusers and new technological methods for monitoring drug and alcohol use, new criminal justice programs for managing impaired driving offenders are emerging.

Intervention  A national model for a comprehensive system applicable to both drug and alcohol impaired drivers is proposed. The program focuses on monitoring offender drinking or the offender driving employing vehicle interlocks with swift, sure but moderate penalties for non‐compliance in which the ultimate sanction is based on offender performance in meeting monitoring requirements.

Findings  Several new court programs, such as the 24/7 Sobriety Project in South Dakota and North Dakota and the Hawaii's Opportunity Probation with Enforcement (HOPE) Project, which feature alcohol/drug consumption monitoring, have produced evidence that indicates even dependent drinkers can conform to abstinence monitoring requirements and avoid the short‐term jail consequence for failure.

Conclusions  Based on the apparent success of emerging court monitoring systems, it appears that the cost of incarcerating driving‐while‐impaired offenders can be minimized by employing low‐cost community correction programs paid for by the offender.
The ecology and emergence of diseases in fresh waters
Authors: JOHNSON PIETER T. J. , PAULL SARA H.
Published: December 2010

1. Freshwater ecosystems, including ponds, lakes, streams and rivers, represent an interaction nexus between environmental change and a wide variety of infectious diseases, including human malaria, salmonid whirling disease, amphibian chytridiomycosis, crayfish plague and many others. However, few studies have explicitly examined patterns of disease in fresh waters and how they are changing over time.

2. Freshwater environments can function as transmission foci for pathogens because of (i) the importance of fresh water for organism survival, (ii) the aquatic life histories of many vectors and intermediate hosts, (iii) the concentrated aggregations of species – both freshwater and terrestrial – in and around freshwater habitats and (iv) the highly altered condition of freshwater ecosystems, which can affect species interactions and disease pathology.

3. To determine whether water‐related diseases in wildlife are increasing, we used generalised additive models to quantitatively assess trends in the scientific literature (1970–2009) for major freshwater groups, including amphibians, molluscs, crayfishes, fishes, mammals, reptiles and birds. We further examined what types of pathogens were primarily responsible for observed patterns and whether recurrent groups or transmission modes could be identified.

4. After correcting for research effort and temporal autocorrelation, we find that reports of disease varied over time and across freshwater taxa, with significant increases in amphibians, fishes and crayfishes, a significant decrease in molluscs, and no significant change in freshwater reptiles, birds or mammals. The types and diversity of pathogens varied considerably among groups. Reports of infection in amphibians were dominated by helminths and a chytridiomycete, in crayfishes by viruses and fungi, in molluscs by digenetic trematodes, in birds, fishes and mammals by viruses, protists and helminths and in reptiles by helminths and bacteria.

5. These results provide some of the first quantitative evidence indicative of a long‐term increase in disease‐related research for freshwater taxa. Managing freshwater ecosystems to reduce or minimise human and wildlife disease risk – arguably one of the most significant ecosystem services – will require enhanced incorporation of ecological approaches alongside medical and veterinary tools.
Falls in older hospital inpatients and the effect of cognitive impairment: a secondary analysis of prevalence studies
Authors: Härlein Jürgen , Halfens Ruud JG , Dassen Theo , Lahmann Nils A
Published: December 2010

Aims and objectives.  The objective of this study was to compare fall rates in older hospital inpatients with and without cognitive impairment. Relationships between age, gender, mobility, cognitive impairment, care dependency, urinary incontinence and medical disciplines were investigated.

Background.  Falls are common in older people with cognitive impairment, but studies in the hospital setting are rare.

Design.  A secondary analysis of three nationwide prevalence studies in German hospitals from the years 2005, 2006 and 2007 was conducted.

Method.  Trained staff nurses used a standardised instrument to collect data about accidental falls within the last two weeks in their institutions and about other patient characteristics. Data from 9246 patients aged 65 years or older from 37 hospitals were analysed.

Results.  The fall rate for cognitively impaired patients was 12·9%, while only 4·2% of older persons without cognitive impairment experienced a fall. Comparison between medical disciplines showed great differences concerning fall risk for confused and non‐confused inpatients. In multivariate logistic regression analysis, the odds‐ratio association of cognitive impairment and falls was 2·1 (CI 1·7–2·7). Higher age (OR 1·5, CI 1·2–1·9), greater care dependency (OR 1·6, CI 1·1–2·1), reduced mobility (OR 2·6, CI 1·9–3·7) and being a patient on a geriatric ward (OR 1·8, CI 1·1–2·9) were also statistically significant predictors in this model.

Conclusions.  Cognitively impaired older people constitute a high‐risk group for accidental falls in hospitals.

Relevance to clinical practice.  Fall prevention strategies in the hospital setting should address cognitively impaired inpatients as an important high‐risk group.
Nurses’ clinical assessments of older clients who are suspected victims of abuse: an exploratory study in community care in Norway
Authors: Sandmoe Astrid , Kirkevold Marit
Published: December 2010

Aim and objectives.  The aim of this study was to explore how nurses in community care experienced clinical assessment of suspected abuse cases and factors impacting on the assessment process.

Background.  Elder abuse is a serious problem affecting an older person’s health and well‐being. A considerable number of older victims of abuse receive health care services. Health professionals, such as nurses in community care, will very likely meet clients suffering from abuse. In Scandinavia, research about older abuse is quite limited. This also applies to research into nurses’ clinical assessments of older, abused clients under community care services.

Design.  Qualitative, hermeneutic approach.

Method.  Ten nurses were recruited by purposeful sampling and interviewed in‐depth. The analysis process was guided by Gadamer’s recommendations on understanding and interpreting oral and written text.

Results.  Three important phases in the clinical assessment were revealed, including the recognition of a possible abuse situation, an information gathering phase and, finally, judgement and conclusion. Two critical factors impacting on the process included the nurse’s ability to get into position to perform the necessary observations in the home and the quality of the information gathered about the client’s situation. In addition, factors related to the client and the community care organisation influenced the nurses’ work and thereby promoted, delayed or interrupted the clinical assessment.

Conclusions.  Nurses’ opportunities to identify older, abused clients might fail unless certain conditions are present that facilitate the clinical assessment. In particular, the involvement of the manager is important, in addition to the presence of alliances in the assessment process.

Relevance to clinical practice.  The findings indicate the need for a framework that may facilitate the systematic clinical assessment of suspected older, abused clients in community care. Such a framework might ensure the quality of the service provided to victims of abuse.
Conserved flanking microsatellite sequences (ReFS) differentiate between Lepidoptera species, and provide insight into microsatellite evolution
Authors: MOLODSTOVA DARIA , CROWE EMILY , OLSON AMBER , YEE JANET , FREELAND JOANNA R.
Published: December 2010

High rates of mutation and homoplasy mean that microsatellites generally are not considered to be useful molecular markers for inferring systematic relationships between species. However, an earlier pilot study suggested that conserved flanking microsatellite sequences, also known as repetitive flanking sequences (ReFS), may form a basis for a dominant marker that can differentiate between species of Lepidoptera. We present data that demonstrate that ReFS are quick and easy to use, and generate highly repeatable banding patterns from a range of Lepidoptera species. Sequence data from a subset of ReFS‐amplified bands revealed microsatellite families with flanking sequences that are more conserved within than among species: this is probably attributable to recombination‐mediated events, transposition of mobile elements or a combination of the two. Our data support the use of ReFS as dominant interspecific molecular markers, and add to the growing literature on the evolution of microsatellites in Lepidoptera.
An alternative strategy for perinatal verbal autopsy coding: single versus multiple coders
Authors: Engmann C. , Jehan I. , Ditekemena J. , Garces A. , Phiri M. , Mazariegos M. , Chomba E. , Pasha O. , Tshefu A. , McClure E. M. , Thorsten V. , Chakraborty H. , Goldenberg R. L. , Bose C. , Carlo W. A. , Wright L. L.
Published: December 2010

Objective  To determine the comparability between cause of death (COD) by a single physician coder and a two‐physician panel, using verbal autopsy.

Methods  The study was conducted between May 2007 and June 2008. Within a week of a perinatal death in 38 rural remote communities in Guatemala, the Democratic Republic of Congo, Zambia and Pakistan, VA questionnaires were completed. Two independent physicians, unaware of the others decisions, assigned an underlying COD, in accordance with the causes listed in the chapter headings of the International classification diseases and related health problems, 10th revision (ICD‐10). Cohen’s kappa statistic was used to assess level of agreement between physician coders.

Results  There were 9461 births during the study period; 252 deaths met study enrolment criteria and underwent verbal autopsy. Physicians assigned the same COD for 75% of stillbirths (SB) (K = 0.69; 95% confidence interval: 0.61–0.78) and 82% early neonatal deaths (END) (K = 0.75; 95% confidence interval: 0.65–0.84). The patterns and proportion of SBs and ENDs determined by the physician coders were very similar compared to causes individually assigned by each physician. Similarly, rank order of the top five causes of SB and END was identical for each physician.

Conclusion  This study raises important questions about the utility of a system of multiple coders that is currently widely accepted and speculates that a single physician coder may be an effective and economical alternative to VA programmes that use traditional two‐physician panels to assign COD.