bluuebunny/crossref_metadata_2025 huggingface dataset:
Mode-specific tunneling using the Qim path: Theory and an application to full-dimensional malonaldehyde
Authors: Wang Yimin , Bowman Joel M.
Published: October 2013

We present a theory of mode-specific tunneling that makes use of the general tunneling path along the imaginary-frequency normal mode of the saddle point, Qim, and the associated relaxed potential, V(Qim) [Y. Wang and J. M. Bowman, J. Chem. Phys. 129, 121103 (2008)]. The novel aspect of the theory is the projection of the normal modes of a minimum onto the Qim path and the determination of turning points on V(Qim). From that projection, the change in tunneling upon mode excitation can be calculated. If the projection is zero, no enhancement of tunneling is predicted. In that case vibrationally adiabatic (VA) theory could apply. However, if the projection is large then VA theory is not applicable. The approach is applied to mode-specific tunneling in full-dimensional malonaldehyde, using an accurate full-dimensional potential energy surface. Results are in semi-quantitative agreement with experiment for modes that show large enhancement of the tunneling, relative to the ground state tunneling splitting. For the six out-of-plane modes, which have zero projection on the planar Qim path, VA theory does apply, and results from that theory agree qualitatively and even semi-quantitatively with experiment. We also verify the failure of simple VA theory for modes that show large enhancement of tunneling.
Exchange bias and its propagation in ferromagnetic/antiferromagnetic/ferromagnetic trilayers
Authors: Hu Yong , Shi Feng , Jia Ning , Liu Yan , Wu Haina , Du An
Published: October 2013

We establish a simple ferromagnetic/antiferromagnetic/ferromagnetic trilayer model, where the lower-interface coupling is varied and study its combined effect with cooling field or temperature on the upper-interface exchange bias effect. Exchange bias field is almost independent of cooling field, if the lower-interface coupling is ferromagnetic and large. Otherwise, its value becomes sensitive to cooling field, and the evolution trend of exchange bias with increasing cooling field depends on the sign and strength of lower-interface coupling. On the other hand, the blocking temperature, below which exchange bias emerges, is reduced (or elevated) in the trilayers with a large ferromagnetic (or antiferromagnetic) lower-interface coupling. The numerical results obtained are interpreted well in terms of the magnetization behaviors in the respective layers. A cooling field creates a low-temperature frozen configuration in the antiferromagnetic layer after cooling to generate exchange bias, while such a configuration related to exchange bias and blocking temperature may be rearranged due to existence of the second ferromagnetic layer on the backside of the antiferromagnetic layer. This work provides an insight into the exchange bias effect and its propagation in such a trilayer stack employing a rather thin antiferromagnetic layer.
Impact of interface properties on spin accumulation in dual-injection lateral spin valves
Authors: Idzuchi H. , Karube S. , Fukuma Y. , Aoki T. , Otani Y.
Published: October 2013

We study spin accumulation in dual-injection lateral spin valves (DLSVs) with Ni80Fe20(/MgO)/Ag or Co50Fe50/MgO/Ag junctions. In Ohmic NiFe/Ag junctions, there is negligible enhancement in the spin accumulation for the dual scheme compared with the conventional single scheme. In contrast, large spin valve signals of 233 and 480 m Ω are observed for DLSVs with NiFe/MgO/Ag and CoFe/MgO/Ag junctions, respectively. The experimental results are analyzed with a one-dimensional spin diffusion model, taking into account the junctions and their structures. The efficient generation of a pure spin current IS/IC up to 0.55 is realized.
A bulge-induced dehydration failure mode of nanocomposite hydrogel
Authors: Tang Jingda , Yu Zejun , Sun Youyi , Pei Yongmao , Fang Daining
Published: October 2013

Since hydrogels are very soft and usually weak in swollen state, they pose unique challenges to traditional mechanical experiments. The mechanical property of nanocomposite poly(N-isopropylacrylamide) hydrogel was characterized by the bulge test in this investigation. A dehydration failure phenomenon of the hydrogel was found and the failure mechanism was presented. A criterion is proposed that when strain reaches the threshold, water molecules migrate out of the polymer networks and the dehydration failure occurs. The critical strain keeps constant for orifices with different diameters. This failure mode can be applied in the controllable release of drugs.
Analysis of slope-intercept plots for arrays of electron field emitters
Authors: Persaud Arun
Published: October 2013

In electron field emission experiments, a linear relationship in plots of slope vs. intercept obtained from Fowler-Nordheim analysis is commonly observed for single tips or tip arrays. By simulating samples with many tips, it is shown here that the observed linear relationship results from the distribution of input parameters, assuming a log-normal distribution for the radius of each tip. Typically, a shift from the lower-left to the upper-right of a slope-intercept plot has been correlated with a shift in work function. However, as shown in this paper, the same effect can result from a variation in the number of emitters.
The relationship between depth-resolved composition and strain relaxation in InAlN and InGaN films grown by molecular beam epitaxy
Authors: Jiao Wenyuan , Kong Wei , Li Jincheng , Collar Kristen , Kim Tong-Ho , Brown April S.
Published: October 2013

A study of the relationship between strain and the incorporation of group III elements in ternary InGaN and InAlN grown by molecular beam epitaxy is reported. Using X-ray Photoelectron Spectroscopy compositional depth profiles with x-ray diffraction, we are able to find a clear relationship between strain and In incorporation including tensile-strained InAlN which has, to date, not been studied. The results show that fully strained films contain homogeneous indium composition while partially relaxed films have a non-homogeneous indium composition with depth. These results can be interpreted by considering the impurity formation energies of indium in host lattices.
Optimizing the spin-pumping induced inverse spin Hall voltage by crystal growth in Fe/Pt bilayers
Authors: Papaioannou Evangelos Th. , Fuhrmann Philipp , Jungfleisch Matthias B. , Brächer Thomas , Pirro Philipp , Lauer Viktor , Lösch Jörg , Hillebrands Burkard
Published: October 2013

We examine the influence of crystal growth on the spin-pumping induced inverse spin Hall effect in Fe/Pt bilayers. The morphology of the Fe/Pt interface influences the effective spin mixing conductance. The increase of growth temperature leads to smoother and larger grains at the interface that enhance the effective spin mixing conductance. The spin current injection efficiency into Pt, measured by the inverse spin Hall effect, is maximized by optimizing the epitaxy of Pt on Fe. In magnetic field dependent measurements, the presence of a strong magnetic anisotropy gives rise to two distinct inverse spin Hall effect voltage peaks.
Evaluating Collaborative Institutions in Context: The Case of Regional Water Management in Southern California
Authors: Hughes Sara , Pincetl Stephanie
Published: October 2013

Regional collaborative institutions are seen as tools for improving collaboration and for reducing the inefficiency of fragmented management and planning. However, recent research has shown that the ability of new regional institutions to achieve these aims is contingent upon their relationship to the existing institutional landscape. This paper uses network analyses of six newly created Integrated Regional Water Management (IRWM) subregions in southern California to examine how their introduction intersects existing water management systems and whether the patterns of interaction in water planning have changed as a result. The results further our understanding of collaborative governance and regionalism by showing that the ability of regional institutions to facilitate new interactions can vary widely across a given institutional landscape. Further, while IRWM has helped to strengthen the water management network in southern California, it has not replaced existing watershed planning efforts. Interviews with water managers reveal there is support for IRWM but it is still too early to evaluate its effectiveness. Further research should explore the drivers and consequences of heterogeneity in IRWM and whether the incentives for participation are sufficient.
Seasonal water-quality sampling in estuaries, what can it tell us? A case example of eastern Australian subtropical estuaries
Authors: Logan Brendan , Taffs Kathryn H.
Published: October 2013

Point-sampling of water is often referred to as an inaccurate and crude method for use in estuaries; however, budgetary, spatial and time constraints often leave it as the only feasible option. The present paper investigates the relationship between spring water quality and diatom sampling of 52 eastern Australian subtropical estuaries and the OzCoasts determined classification of estuarine condition. In general, estuarine health decreases along the total phosphorus (TP), total nitrogen (TN) and the centric to pennate diatom ratio gradients. However, although there is a general trend, results are varied within each class, with some estuaries classed as extensively modified, recording low nutrient conditions. Principal components analysis (PCA) indicated that 55% of the variance among sites is explained by the first and second axes, with TN, TP, TN : TP, latitude and pH having high correlation with PCA Axis 1, and temperature, conductivity and the centric to pennate diatom ratio being correlated with Axis 2. Two diatom species that may have bioindicator value for estuary conditions were identified. We concluded that even though natural variability and accurate characterisation of estuaries is not possible with point-sampling, it can still identify important information on the status of estuarine condition, particularly in relation to total nutrient concentrations where budget and/or time constraints limit environmental monitoring.
How do young black men having sex with only women differ from those also having sex with men?
Authors: Crosby Richard , Pasternak Ryan , Salazar Laura F. , Terrell Ivy
Published: October 2013

In the US, young Black men (YBM) disproportionately acquire sexually transmissible infections (STI), including infection with HIV. This secondary analysis compared sexual behaviours of YBM (n = 568) not reporting sex with men with those of YBM who have sex with men (YBMSM). In the present study YBMSM were generally less likely to report engagement in sexual risk behaviours, less likely to report incarceration and more likely to ever be tested for HIV. The findings suggest that elevated rates of HIV and/or STI among YBMSM may be a product of higher prevalence rates in sexual networks.
Aryl hydrocarbon receptor deficiency causes dysregulated cellular matrix metabolism and age-related macular degeneration-like pathology
Authors: Hu Peng , Herrmann Rolf , Bednar Amanda , Saloupis Peter , Dwyer Mary A. , Yang Ping , Qi Xiaoping , Thomas Russell S. , Jaffe Glenn J. , Boulton Michael E. , McDonnell Donald P. , Malek Goldis
Published: October 2013

Significance

Age-related Macular Degeneration (AMD) is the leading cause of vision loss. In its early stage, extracellular deposits accumulate below the retinal pigment epithelial layer (RPE), nurse cells to the retina. Identification of therapeutic treatments targeting deposit removal, which when left untreated exacerbate RPE and retinal damage, necessitates the discovery of pathways regulating deposit formation. We show that the activity of a nuclear receptor, essential to xenobiotic/toxin metabolism and cellular debris clearance, is critical to maintaining RPE cell health and that its deficiency in mice causes AMD pathology. This model provides a better understanding of AMD pathogenic mechanisms and a platform for testing novel therapeutics.
Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants
Authors: Parker Stephen C. J. , Stitzel Michael L. , Taylor D. Leland , Orozco Jose Miguel , Erdos Michael R. , Akiyama Jennifer A. , van Bueren Kelly Lammerts , Chines Peter S. , Narisu Narisu ,   NISC Comparative Sequencing Program, Black Brian L. , Visel Axel , Pennacchio Len A. , Collins Francis S. ,   National Institutes of Health Intramural Sequencing Center Comparative Sequencing Program Authors,   NISC Comparative Sequencing Program Authors., Becker Jesse , Benjamin Betty , Blakesley Robert , Bouffard Gerry , Brooks Shelise , Coleman Holly , Dekhtyar Mila , Gregory Michael , Guan Xiaobin , Gupta Jyoti , Han Joel , Hargrove April , Ho Shi-ling , Johnson Taccara , Legaspi Richelle , Lovett Sean , Maduro Quino , Masiello Cathy , Maskeri Baishali , McDowell Jenny , Montemayor Casandra , Mullikin James , Park Morgan , Riebow Nancy , Schandler Karen , Schmidt Brian , Sison Christina , Stantripop Mal , Thomas James , Thomas Pam , Vemulapalli Meg , Young Alice
Published: October 2013

Significance

Using high-throughput experiments, we determined the functional epigenomic landscape in pancreatic islet cells. Computational integration of these data along with similar data from the ENCODE project revealed the presence of large gene control elements across diverse cell types that we refer to as “stretch enhancers.” Stretch enhancers are cell type specific and are associated with increased expression of genes involved in cell-specific processes. We find that genetic variations associated with common disease are highly enriched in stretch enhancers; notably, stretch enhancers specific to pancreatic islets harbor variants linked to type 2 diabetes and related traits. We propose that stretch enhancers form as pluripotent cells differentiate into committed lineages, to program important cell-specific gene expression.
Land reform in the 1950s in Italy and the United States: the thinking of Mario Einaudi
Authors: Mariuzzo Andrea
Published: October 2013

The article discusses the thinking of Mario Einaudi in relation to the ambitious measures with which the Italian government sought to move towards land reform in the immediate post–war period. Einaudi, an intellectual and academic, was by birth Italian but moved to the United States during the Fascist period. Like his father Luigi, the noted economist, he was convinced of the need to stimulate the free market in land in order to increase productivity and modernise cultivation methods; in his writings he repeatedly sought to develop a plan of action that would facilitate collaboration between Rome and Washington in this field, identifying the Tennessee Valley Authority approach as especially suited to the Italian case. However, while his ideas achieved a good public airing, they had a limited impact: on the political front, Cold War priorities pushed Italian and US Marshall Plan experts more towards the redistribution of landownership than towards stimulating the productivity of agricultural businesses, in the attempt to rapidly build a consensus behind the government; and on the cultural front, at the end of the 1950s the issue of backwardness in the rural South started to be interpreted in terms of cultural and social anthropology, an approach which did not directly relate to the development of political programmes.
Cellular and molecular mechanisms underlying presynapse formation
Authors: Chia Poh Hui , Li Pengpeng , Shen Kang
Published: October 2013

Synapse formation is a highly regulated process that requires the coordination of many cell biological events. Decades of research have identified a long list of molecular components involved in assembling a functioning synapse. Yet how the various steps, from transporting synaptic components to adhering synaptic partners and assembling the synaptic structure, are regulated and precisely executed during development and maintenance is still unclear. With the improvement of imaging and molecular tools, recent work in vertebrate and invertebrate systems has provided important insight into various aspects of presynaptic development, maintenance, and trans-synaptic signals, thereby increasing our understanding of how extrinsic organizers and intracellular mechanisms contribute to presynapse formation.
DNA methyltransferase-3–dependent nonrandom template segregation in differentiating embryonic stem cells
Authors: Elabd Christian , Cousin Wendy , Chen Robert Y. , Chooljian Marc S. , Pham Joey T. , Conboy Irina M. , Conboy Michael J.
Published: October 2013

Asymmetry of cell fate is one fundamental property of stem cells, in which one daughter cell self-renews, whereas the other differentiates. Evidence of nonrandom template segregation (NRTS) of chromosomes during asymmetric cell divisions in phylogenetically divergent organisms, such as plants, fungi, and mammals, has already been shown. However, before this current work, asymmetric inheritance of chromatids has never been demonstrated in differentiating embryonic stem cells (ESCs), and its molecular mechanism has remained unknown. Our results unambiguously demonstrate NRTS in asymmetrically dividing, differentiating human and mouse ESCs. Moreover, we show that NRTS is dependent on DNA methylation and on Dnmt3 (DNA methyltransferase-3), indicating a molecular mechanism that regulates this phenomenon. Furthermore, our data support the hypothesis that retention of chromatids with the “old” template DNA preserves the epigenetic memory of cell fate, whereas localization of “new” DNA strands and de novo DNA methyltransferase to the lineage-destined daughter cell facilitates epigenetic adaptation to a new cell fate.
Spatio-temporal overlap of oil spills and early life stages of fish
Authors: Vikebø Frode B. , Rønningen Petter , Lien Vidar S. , Meier Sonnich , Reed Mark , Ådlandsvik Bjørn , Kristiansen Trond
Published: October 2013

Coupling an oil drift and fates model (Oscar) in an offline environment with an individual-based model (IBM) for Northeast Arctic cod (Gadus morhua) eggs and larvae enables us to quantify the exposure of eggs and larvae to oil from various oil spill scenarios. Oscar describes the spatio-temporal dispersal and fate of hydrocarbons, whereas the egg and larval IBM integrates the exposure of each individual. We can thus evaluate the effects of the time and location of an oil spill on the degree of exposure for individuals from different spawning grounds (SGs). In addition, we quantify how this effect is modified by the dynamic vertical positioning of eggs and the vertical behaviour of larvae. The principal findings of the study indicate that the mean egg and larval exposures for individuals from different SGs are highly dependent on the time and location of the spill and the vertical distribution of the offspring. Approximately 9.9, 4.7, 3.5, and 0.4% of the offspring would experience total polycyclic aromatic hydrocarbon (TPAH) concentrations above 1 µg l−1 (parts per billion, ppb) for oil spill scenarios situated at Haltenbanken, Lofoten, and Vesterålen near the coast and near the shelf edge, respectively, based on the maximum TPAH concentrations in the water column along the individual offspring trajectories.
From pup production to quotas: current status of harp seals in the Greenland Sea
Authors: Øigård Tor Arne , Haug Tore , Nilssen Kjell Tormod
Published: October 2013

Harp seals (Pagophilus groenlandicus) have been harvested for centuries in the North Atlantic. Estimating abundance and monitoring changes in population size are critical for the management of the species. In March 2012, the harp seal pup production was estimated from aerial photographic surveys over the whelping areas. A total area of 305 km2 was photographed and 6034 pups were counted on the photos. From this the total pup production estimate was 89 590 ( s.e. = 12 310, CV = 13.7%). The status of the stock was subsequently assessed by fitting a population model to the independent pup production estimate, the historical catch data, and the historical reproduction data. The 2013 total abundance (including pups) was estimated to be 627 410 (95% CI = 470 540–784 280) harp seals. We demonstrate how the model is used in assessment when exploring the effect of various catch scenarios on future predictions.
Comparison of fluctuations in fish communities and trophic structures of ecosystems from three currents around Japan: synchronies and differences
Authors: Tian Yongjun , Uchikawa Kazuhisa , Ueda Yuji , Cheng Jiahua
Published: October 2013

Tian, Y., Uchikawa, K., Ueda, Y., and Cheng, J. Comparison of fluctuations in fish communities and trophic structures of ecosystems from three currents around Japan: synchronies and differences. – ICES Journal of Marine Science, 71: . Features of three marine ecosystems affected by the Tsushima (TWC), Kuroshio (KC), and Oyashio (OC) currents were analysed based on fishery, oceanographic, and climate datasets during 1955–2010. Principal component (PC) analysis for catches of 25 indicator species showed evident decadal variation patterns with a step change in the first principal component (PC1) in the late 1980s, indicating synchronies in the dominant variation mode across the ecosystems. Step changes were also detected in the mid-1970s in PC2 and PC3 in OC, and around 1970 in PCs in KC and TWC. These indicate that the most marked change across the ecosystems occurred in the late 1980s, corresponding to the late 1980s climate regime shift, but OC also responded strongly to the mid-1970s regime shift, indicating different responses to regime shifts. The generalized additive model showed the PCs associated largely with water temperature in each region as well as climate indices, indicating the importance of regional oceanographic conditions. Ecosystem indicators such as the mean trophic level showed similarities between TWC and KC but differences with OC, indicating that trophic structures in TWC and KC were largely dependent on the mid-trophic (small pelagic species) level, while on demersal species in OC.
Ultrarelativistic electromagnetic counterpart to binary neutron star mergers
Authors: Kyutoku Koutarou , Ioka Kunihito , Shibata Masaru
Published: October 2013

We propose a possibility of ultrarelativistic electromagnetic counterparts to gravitational waves from binary neutron star mergers at nearly all the viewing angles. Our proposed mechanism relies on the merger-shock propagation accelerating a smaller mass in the outer parts of the neutron star crust to a larger Lorentz factor Γ with smaller energy ∼1047Γ−1 erg. This mechanism is difficult to resolve by current 3D numerical simulations. The outflows emit synchrotron flares for seconds to days by shocking the ambient medium. Ultrarelativistic flares shine at an early time and in high-energy bands, potentially detectable by current X-ray to radio instruments, such as Swift XRT and Pan-STARRS, and even in low ambient density ∼10−2 cm−3 by EVLA. The flares probe the merger position and time, and the merger types as black hole–neutron star outflows would be non-/mildly relativistic.
Partial Aortic Root Remodeling in Case of Ascending Aortic Aneurysms
Authors: Sansone Fabrizio , Zingarelli Edoardo , Ceresa Fabrizio , Patanè Francesco
Published: October 2013

Objective

In degenerative ascending aortic aneurysms (AAAs), the pathological process may extend into the aortic root, causing aortic regurgitation (AR). As often one or two sinuses are involved, ascending aorta replacement should be associated with selected sinus replacement.

Methods

Thirty patients (21 men and 9 women; mean ± SD age, 70.0 ± 10.4) were operated on for ascending aorta and selected sinus replacement. All patients had degenerative AAA with sinotubular junction and partial root dilatation: one or two sinuses of Valsalva were involved. Mild to moderate-severe AR was present in all patients. The mean ± SD logistic EUROscore 1 was 15.4 ± 12.5. Twenty patients had ascending aorta replacement associated with noncoronary sinus replacement; 8 patients, associated with both right and noncoronary sinuses; 1 patient, associated with both left and noncoronary sinuses; and 1 patient, associated with left coronary sinus alone.

Results

There were no hospital or late deaths. No thromboembolic event or bleeding complications were reported. Postoperative echocardiography did not show significant AR, and computed tomographic scanning revealed a normal positioning of the vascular graft in the ascending aorta.

Conclusions

Remodeling of the sinotubular junction with selected sinus replacement in degenerative AAA is a valuable approach for aortic root remodeling, leading to a significant reduction of AR when the aortic leaflets are normal.
Biphasic responses in multi-site phosphorylation systems
Authors: Suwanmajo Thapanar , Krishnan J.
Published: October 2013

Multi-site phosphorylation systems are repeatedly encountered in cellular biology and multi-site modification is a basic building block of post-translational modification. In this paper, we demonstrate how distributive multi-site modification mechanisms by a single kinase/phosphatase pair can lead to biphasic/partial biphasic dose–response characteristics for the maximally phosphorylated substrate at steady state. We use simulations and analysis to uncover a hidden competing effect which is responsible for this and analyse how it may be accentuated. We build on this to analyse different variants of multi-site phosphorylation mechanisms showing that some mechanisms are intrinsically not capable of displaying this behaviour. This provides both a consolidated understanding of how and under what conditions biphasic responses are obtained in multi-site phosphorylation and a basis for discriminating between different mechanisms based on this. We also demonstrate how this behaviour may be combined with other behaviour such as threshold and bistable responses, demonstrating the capacity of multi-site phosphorylation systems to act as complex molecular signal processors.
A reasoned overview on Boussinesq-type models: the interplay between physics, mathematics and numerics
Authors: Brocchini Maurizio
Published: October 2013

This paper, which is largely the fruit of an invited talk on the topic at the latest International Conference on Coastal Engineering, describes the state of the art of modelling by means of Boussinesq-type models (BTMs). Motivations for using BTMs as well as their fundamentals are illustrated, with special attention to the interplay between the physics to be described, the chosen model equations and the numerics in use. The perspective of the analysis is that of a physicist/engineer rather than of an applied mathematician. The chronological progress of the currently available BTMs from the pioneering models of the late 1960s is given. The main applications of BTMs are illustrated, with reference to specific models and methods. The evolution in time of the numerical methods used to solve BTMs (e.g. finite differences, finite elements, finite volumes) is described, with specific focus on finite volumes. Finally, an overview of the most important BTMs currently available is presented, as well as some indications on improvements required and fields of applications that call for attention.
Global warming triggers the loss of a key Arctic refugium
Authors: Rühland K. M. , Paterson A. M. , Keller W. , Michelutti N. , Smol J. P.
Published: October 2013

We document the rapid transformation of one of the Earth's last remaining Arctic refugia, a change that is being driven by global warming. In stark contrast to the amplified warming observed throughout much of the Arctic, the Hudson Bay Lowlands (HBL) of subarctic Canada has maintained cool temperatures, largely due to the counteracting effects of persistent sea ice. However, since the mid-1990s, climate of the HBL has passed a tipping point, the pace and magnitude of which is exceptional even by Arctic standards, exceeding the range of regional long-term variability. Using high-resolution, palaeolimnological records of algal remains in dated lake sediment cores, we report that, within this short period of intense warming, striking biological changes have occurred in the region's freshwater ecosystems. The delayed and intense warming in this remote region provides a natural observatory for testing ecosystem resilience under a rapidly changing climate, in the absence of direct anthropogenic influences. The environmental repercussions of this climate change are of global significance, influencing the huge store of carbon in the region's extensive peatlands, the world's southern-most polar bear population that depends upon Hudson Bay sea ice and permafrost for survival, and native communities who rely on this landscape for sustenance.
What
,
where
and
when
: deconstructing memory
Authors: Marshall Rachael E. S. , Hurly T. Andrew , Sturgeon Jenny , Shuker David M. , Healy Susan D.
Published: October 2013

The ability of animals to remember the
what
,
where
and
when
of a unique past event is used as an animal equivalent to human episodic memory. We currently view episodic memory as reconstructive, with an event being remembered in the context in which it took place. Importantly, this means that the components of a
what
,
where
,
when
memory task should be dissociable (e.g.
what
would be remembered to a different degree than
when
). We tested this hypothesis by training hummingbirds to a memory task, where the location of a reward was specified according to colour (
what
), location (
where
), and order and time of day (
when
). Although hummingbirds remembered these three pieces of information together more often than expected, there was a hierarchy as to how they were remembered.
When
seemed to be the hardest to remember, while errors relating to
what
were more easily corrected. Furthermore,
when
appears to have been encoded as a combination of time of day and sequence information. As hummingbirds solved this task using reconstruction of different memory components (
what
,
where
and
when
), we suggest that similar deconstructive approaches may offer a useful way to compare episodic and episodic-like memories.
Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma
Authors: Nabilsi Nancy H. , Deleyrolle Loic P. , Darst Russell P. , Riva Alberto , Reynolds Brent A. , Kladde Michael P.
Published: October 2013

Human tumors are comprised of heterogeneous cell populations that display diverse molecular and phenotypic features. To examine the extent to which epigenetic differences contribute to intratumoral cellular heterogeneity, we have developed a high-throughput method, termed MAPit-patch. The method uses multiplexed amplification of targeted sequences from submicrogram quantities of genomic DNA followed by next generation bisulfite sequencing. This provides highly scalable and simultaneous mapping of chromatin accessibility and DNA methylation on single molecules at high resolution. Long sequencing reads from targeted regions maintain the structural integrity of epigenetic information and provide substantial depth of coverage, detecting for the first time minority subpopulations of epigenetic configurations formerly obscured by existing genome-wide and population-ensemble methodologies. Analyzing a cohort of 71 promoters of genes with exons commonly mutated in cancer, MAPit-patch uncovered several differentially accessible and methylated promoters that are associated with altered gene expression between neural stem cell (NSC) and glioblastoma (GBM) cell populations. In addition, considering each promoter individually, substantial epigenetic heterogeneity was observed across the sequenced molecules, indicating the presence of epigenetically distinct cellular subpopulations. At the divergentMLH1/EPM2AIP1promoter, a locus with three well-defined, nucleosome-depleted regions (NDRs), a fraction of promoter copies with inaccessible chromatin was detected and enriched upon selection of temozolomide-tolerant GBM cells. These results illustrate the biological relevance of epigenetically distinct subpopulations that in part underlie the phenotypic heterogeneity of tumor cell populations. Furthermore, these findings show that alterations in chromatin accessibility without accompanying changes in DNA methylation may constitute a novel class of epigenetic biomarker.
Effects of biological control on long‐term population dynamics: identifying unexpected outcomes
Authors: Reilly James R. , Elderd Bret D.
Published: October 2013

Attempts to control natural systems through management have often met with success but have also led to unexpected and often undesirable outcomes. Unfortunately, the ultimate result of such management programmes may not be apparent until long after the control efforts have begun. This is particularly true for forest‐defoliating species that exhibit long‐period cycles such as the invasive gypsy moth Lymantria dispar, which causes widespread damage in some years but is rare in other years.

We studied the effects of two commonly employed biocontrol agents on gypsy moth dynamics using a series of field‐tested and empirically parameterized mathematical models, which allowed us to examine various potential control strategies and assess long‐term effects.

In a non‐spatial model, addition of either a manufactured version of the same baculovirus involved in natural epizootics, or a general bioinsecticide Bacillus thuringiensis var. kurstaki (Btk), which directly kills a fraction of the population, decreases the amplitude between boom and bust portions of the cycle.

However, ill‐planned biocontrol applications can result in increased gypsy moth densities over the long term. Thus, control efforts may maintain pest populations at unexpectedly high numbers, which could result in constant forest defoliation.

In a spatial two‐patch model, where one patch is sprayed and the other is left untreated, there is also considerable danger that migration between patches may drive the unsprayed population to levels that could result in constant forest defoliation.

Synthesis and applications: Perturbations to host–pathogen systems may have unexpected results, driving and maintaining populations at multiple levels including those far from desired management goals. It is often assumed that any control strategy that decreases pest populations in the short term is beneficial, but our results show that undesirable outcomes may often occur. The mechanisms we describe apply to many systems that undergo population cycles or outbreaks regulated by density‐dependent processes, and in which disease or pesticide application is used for pest control. We suggest that successful management strategies should closely monitor population responses immediately following the control application to ensure that pest populations are not being maintained at artificially high levels compared with historic data.
Accuracy of allele frequency estimation using pooled RNA‐Seq
Authors: Konczal M. , Koteja P. , Stuglik M. T. , Radwan J. , Babik W.
Published: October 2013

For nonmodel organisms, genome‐wide information that describes functionally relevant variation may be obtained by RNA‐Seq following de novo transcriptome assembly. While sequencing has become relatively inexpensive, the preparation of a large number of sequencing libraries remains prohibitively expensive for population genetic analyses of nonmodel species. Pooling samples may be then an attractive alternative. To test whether pooled RNA‐Seq accurately predicts true allele frequencies, we analysed the liver transcriptomes of 10 bank voles. Each sample was sequenced both as an individually barcoded library and as a part of a pool. Equal amounts of total RNA from each vole were pooled prior to mRNA selection and library construction. Reads were mapped onto the de novo assembled reference transcriptome. High‐quality genotypes for individual voles, determined for 23 682 SNPs, provided information on ‘true’ allele frequencies; allele frequencies estimated from the pool were then compared with these values. ‘True’ frequencies and those estimated from the pool were highly correlated. Mean relative estimation error was 21% and did not depend on expression level. However, we also observed a minor effect of interindividual variation in gene expression and allele‐specific gene expression influencing allele frequency estimation accuracy. Moreover, we observed strong negative relationship between minor allele frequency and relative estimation error. Our results indicate that pooled RNA‐Seq exhibits accuracy comparable with pooled genome resequencing, but variation in expression level between individuals should be assessed and accounted for. This should help in taking account the difference in accuracy between conservatively expressed transcripts and these which are variable in expression level.
Meta‐analysis on blood transcriptomic studies identifies consistently coexpressed protein–protein interaction modules as robust markers of human aging
Authors: van den Akker Erik B. , Passtoors Willemijn M. , Jansen Rick , van Zwet Erik W. , Goeman Jelle J. , Hulsman Marc , Emilsson Valur , Perola Markus , Willemsen Gonneke , Penninx Brenda W.J.H. , Heijmans Bas T. , Maier Andrea B. , Boomsma Dorret I. , Kok Joost N. , Slagboom Pieternella E. , Reinders Marcel J.T. , Beekman Marian
Published: October 2013

The bodily decline that occurs with advancing age strongly impacts on the prospects for future health and life expectancy. Despite the profound role of age in disease etiology, knowledge about the molecular mechanisms driving the process of aging in humans is limited. Here, we used an integrative network‐based approach for combining multiple large‐scale expression studies in blood (2539 individuals) with protein–protein Interaction (PPI) data for the detection of consistently coexpressed PPI modules that may reflect key processes that change throughout the course of normative aging. Module detection followed by a meta‐analysis on chronological age identified fifteen consistently coexpressed PPI modules associated with chronological age, including a highly significant module (P = 3.5 × 10−38) enriched for ‘T‐cell activation’ marking age‐associated shifts in lymphocyte blood cell counts (R2 = 0.603; P = 1.9 × 10−10). Adjusting the analysis in the compendium for the ‘T‐cell activation’ module showed five consistently coexpressed PPI modules that robustly associated with chronological age and included modules enriched for ‘Translational elongation’, ‘Cytolysis’ and ‘DNA metabolic process’. In an independent study of 3535 individuals, four of five modules consistently associated with chronological age, underpinning the robustness of the approach. We found three of five modules to be significantly enriched with aging‐related genes, as defined by the GenAge database, and association with prospective survival at high ages for one of the modules including ASF1A. The hereby‐detected age‐associated and consistently coexpressed PPI modules therefore may provide a molecular basis for future research into mechanisms underlying human aging.
Triple monoamine uptake inhibitors demonstrate a pharmacologic association between excessive drinking and impulsivity in high‐alcohol‐preferring (HAP) mice
Authors: O'Tousa David S. , Warnock Kaitlin T. , Matson Liana M. , Namjoshi Ojas A. , Linn Michael Van , Tiruveedhula Veera Venkata , Halcomb Meredith E. , Cook James , Grahame Nicholas J. , June Harry L.
Published: October 2013

Approximately 30% of current drinkers in the United States drink excessively, and are referred to as problem/hazardous drinkers. These individuals, who may not meet criteria for alcohol abuse or dependence, comprise binge, heavy drinkers, or both. Given their high prevalence, interventions that reduce the risk of binge and heavy drinking have important public health implications. Impulsivity has been repeatedly associated with excessive drinking in the clinical literature. As impulsivity is correlated with, and may play a critical role in, the initiation and maintenance of excessive drinking, this behavior may be an important target for therapeutic intervention. Hence, a better understanding of pharmacological treatments capable of attenuating excessive drinking and impulsivity may markedly improve clinical outcomes. The high‐alcohol‐preferring (HAP) mice represent a strong rodent model to study the relationship between impulsivity and excessive alcohol drinking, as recent evidence indicates they consume high levels of alcohol throughout their active cycle and are innately impulsive. Using this model, the present study demonstrates that the triple monoamine uptake inhibitors (TUIs) amitifadine and DOV 102, 677 effectively attenuate binge drinking, heavy drinking assessed via a 24‐hour free‐choice assay, and impulsivity measured by the delay discounting procedure. In contrast, 3‐PBC, a GABA‐A α1 preferring ligand with mixed agonist‐antagonist properties, attenuates excessive drinking without affecting impulsivity. These findings suggest that in HAP mice, monoamine pathways may predominate as a common mechanism underlying impulsivity and excessive drinking, while the GABAergic system may be more salient in regulating excessive drinking. We further propose that TUIs such as amitifadine and DOV 102, 677 may be used to treat the co‐occurrence of impulsivity and excessive drinking.
Pyogenic liver abscess trends in South Australia
Authors: Chang Angela Christine , Ha Ngoc Buu , Satyadas Thomas , Maddern Guy
Published: October 2013

Background

Pyogenic liver abscess (PLA) is an uncommon but potentially life‐threatening condition. Due to advances in diagnostic and treatment methods, the mortality rate has reduced in recent decades. The aim of this study was to gather recent data to examine PLA trends in South Australia.

Methods

The medical records of all patients admitted to The Queen Elizabeth Hospital, South Australia, between November 2000 and November 2009 with a primary or secondary diagnosis of PLA were retrospectively reviewed.

Results

Thirty‐six patients were identified. Twenty (55.6%) were male and 16 (44.4%) female. The mean patient age was 70.2 years. A single PLA was found in 21 (58.3%) patients and multiple abscesses in 15 (41.7%) patients. Segment 7 of the liver was most commonly affected (10 cases). In 12 patients, multiple organisms were identified. Escherichia coli, Klebsiella pneumonia and Streptococcus species were most commonly identified. All patients received antibiotics and 27 (75%) received additional treatment. Nine patients received open abscess drainage. Fourteen received ultrasound‐guided or computed tomography‐guided percutaneous drainage or aspiration. One patient died as a direct result of a PLA.

Discussion

Since its first description, the epidemiology of PLA has changed. Patients diagnosed with PLA are now older, the male predominance is less and the organism more likely to originate from the biliary tract. The approach to PLA has also progressed with more accurate imaging and better treatment methods becoming available, which has resulted in a low mortality rate. This series confirms the described trends in South Australia.
Central Limit Theorems for Reduced U‐Statistics Under Dependence and Their Usefulness
Authors: Kim Tae Yoon , Ha Jeongcheol , Hwang Sun Young , Park Cheolyong , Luo Zhi‐Ming
Published: October 2013

A reduced ‐statistic is a ‐statistic with its summands drawn from a restricted but balanced set of pairs. In this article, central limit theorems are derived for reduced ‐statistics under ‐mixing, which significantly extends the work of Brown & Kildea in various aspects. It will be shown and illustrated that reduced ‐statistics are quite useful in deriving test statistics in various nonparametric testing problems.
The Effect of Extracorporeal Membrane Oxygenation Therapy on Systemic Oxidative Stress Injury in a Porcine Model
Authors: Chen Qiyi , Yu Wenkui , Shi Jiangliang , Shen Juanhong , Hu Yimin , Gong Jianfeng , Li Jieshou , Li Ning
Published: October 2013

Extracorporeal membrane oxygenation (ECMO) therapy can result in systemic immune inflammation and trigger a hemolytic response, both of which can lead to oxidative stress injury. However, currently, there are few studies about whether ECMO can lead to oxidative stress injury. The objective of this study was to determine the effect of ECMO therapy on systemic oxidative stress. Twelve pigs were randomly divided into control and ECMO treatment groups. Blood samples were collected at −1, 0, 2, 6, 12, and 24 h during ECMO therapy in order to measure the levels of various oxidative stress markers in plasma. All animals included in the study were euthanized after 24 h of ECMO treatment. Malondialdehyde (MDA) was used as a marker of oxidation, and superoxide dismutase (SOD), glutathione (GSH), and total antioxidant capacity (T‐AOC) were used as indices for antioxidant activity. The plasma levels of each molecule were similar when measured at −1 and 0 h (P > 0.05). In the control group, MDA, SOD, GSH, and T‐AOC remained relatively constant throughout the study period. However, when ECMO was administered for 2 h, plasma levels of MDA increased significantly; conversely, levels of SOD, GSH, and T‐AOC decreased. Maximum MDA levels and minimal SOD, GSH, and T‐AOC levels were observed after 6 h of ECMO treatment. MDA and SOD levels had returned to baseline at 24 h. At this time‐point, levels of MDA and T‐AOC in samples from the right frontal cortex and jejunum differed significantly between the control and ECMO treatment groups. These results show that early ECMO treatment can induce significant oxidative stress injury in plasma. However, in the latter stage of the treatment, the oxidative stress injury can be repaired gradually. ECMO treatment can also result in mild oxidative stress injury in the jejunum and brain tissue.
Adipose afferent reflex: sympathetic activation and obesity hypertension
Authors: Xiong X.‐Q. , Chen W.‐W. , Zhu G.‐Q.
Published: October 2013

Excessive sympathetic activity contributes to the pathogenesis of hypertension and the progression of the related organ damage. Adipose afferent reflex (AAR) is a sympatho‐excitatory reflex that the afferent activity from white adipose tissue (WAT) increases sympathetic outflow and blood pressure. Hypothalamic paraventricular nucleus (PVN or PVH) is one of the central sites in the control of the AAR, and ionotropic glutamate receptors in the nucleus mediate the AAR. The AAR is enhanced in obesity and obesity hypertension. Enhanced WAT afferent activity and AAR contribute to the excessive sympathetic activation and hypertension in obesity. Blockage of the AAR attenuates the excessive sympathetic activity and hypertension. Leptin may be one of sensors in the WAT for the AAR, and is involved in the enhanced AAR in obesity and hypertension. This review focuses on the neuroanatomical basis and physiological functions of the AAR, and the important role of the enhanced AAR in the pathogenesis of obesity hypertension.
In vitro antimicrobial profile of Ureaplasma urealyticum from genital tract of childbearing‐aged women in Northern and Southern Italy
Authors: Pignanelli Salvatore , Pulcrano Giovanna , Iula Vita Dora , Zaccherini Patrizia , Testa Antonio , Catania Maria Rosaria
Published: October 2013

Ureaplasma urealyticum is an opportunistic pathogen during pregnancy and in newborns. Other clinical problems related to U. urealyticum infections are: no susceptibility to cell wall‐active drugs, limits of antibiotic treatment in pregnancy, and spread of antimicrobial resistance. In addition, the results of antimicrobial susceptibility against U. urealyticum from various countries are few and controversial. The antimicrobial susceptibility of U. urealyticum, isolated from cervical swabs and collected from outpatient childbearing‐aged women in Italy from 2009 to 2012, was performed against fluoroquinolones, macrolides, streptogramin and tetracyclines, using an available biochemical commercial kit and a specific solid culture medium, to improve the therapeutic management of these pathogenic agents. Ureaplasma urealyticum was detected in 49.4% of samples, but significant bacterial load was revealed in 29.8%. In vitro tetracyclines showed the best activity against U. urealyticum, followed by streptogramin, macrolides, and fluoroquinolones.