bluuebunny/crossref_metadata_2025 huggingface dataset:
Engaging non-state armed actors in state- and peace-building: options and strategies
Authors: Hofmann Claudia , Schneckener Ulrich
Published: June 2012

Armed actors dominate contemporary conflict environments dramatically. Their degree of dispersion, influence, and effect on international politics make it necessary to establish strategies for interaction with them. This article makes a contribution by assessing particular strategies and their suitability and applicability with regard to specific actors. First, it delineates options for dealing with armed actors based on three perspectives from international relations theory: realist, institutionalist, and constructivist. Second, it matches these perspectives to the capabilities of international actors. Finally, it offers an assessment of the difficulties that arise from the plurality of forms of armed actors, as well as of external actors.
Dependency of the North Pacific winter storm tracks on the zonal distribution of MJO convection
Authors: Lee Yun‐Young , Lim Gyu‐Ho
Published: June 2012

We investigate the effects of the tropical Madden Julian Oscillation (MJO) convection on the zonal location and intensity of storm activity during the boreal cool season (Nov. 1 to Feb. 28, 120 days) over the Pacific Ocean. As tropical convection shifts eastward from the eastern Indian Ocean to the western North Pacific, MJO‐induced local Hadley circulation leads to an eastward displacement of extratropical Rossby Wave Source (RWS). Consequently, this influence leads to an eastward shift of the peak area of the storm track. The storm track is strongest with the MJO convection over the eastern Indian Ocean (phase 3), and it experiences the suppression when MJO convection is located over the Maritime continents (phase 4), and it increases again when the MJO propagates to the western Pacific (phase 5), after which it weakens again (phase 6). The intensity of the storm track, particularly over the western North Pacific (120°E–180°), is determined by the integrated effects of three factors: the midlatitude convective forcing (MCF), the jet stream, and RWS. These factors are associated with the locations of MJO convections. It is estimated that MJO‐induced suppression accounts for only 2.5% of the total observed midwinter suppression (MWS). However, the pattern generated by the MJO is remarkably similar to the observed meridional displacement of North Pacific storm track associated with sub‐seasonal variation. We conclude that the spatial distribution of MJO affects the variation of the Pacific storm track, but is not a cause of the MWS.
Oxidant Production over Antarctic Land and its Export (OPALE) project: An overview of the 2010–2011 summer campaign
Authors: Preunkert Susanne , Ancellet Gérard , Legrand Michel , Kukui Alexandre , Kerbrat Michael , Sarda‐Estève Roland , Gros Valérie , Jourdain Bruno
Published: June 2012

This paper summarizes the objectives and setting of the OPALE (Oxidant Production over Antarctic Land and its Export) project during summer 2010/2011 at Dumont d'Urville. The primary goal of the campaign is to characterize the oxidizing environment of the atmospheric boundary layer along the coast of East Antarctica. A summary of the relevant field chemical measurements is presented including the carbon monoxide and ammonia records that are used here to identify local influences due to station activities and penguin emissions. An overview of the basic meteorological conditions experienced by the site is presented including the results from the trajectory/dispersion model FLEXPART to highlight which types of air mass were sampled (marine boundary layer versus continental Antarctic air). The results of the FLEXPART analysis demonstrate that high ozone levels and related changes in the OH concentrations are associated with the transport of continental air to DDU. Finally, three companion papers are introduced. A first paper is dedicated to the impact of local penguin emissions on the atmospheric budget of several oxygenated volatile organic compounds. The second paper reports on HONO levels that were measured for the first time in Antarctica by using the long path absorption photometer (LOPAP) technique. Finally, in a third paper, major findings on the HOx levels are detailed, leading to the overall conclusion that the photochemistry at coastal East Antarctica is strongly driven by an efficient HOx chemistry compared to the situation at other coastal Antarctic regions.
Drought indicators based on model‐assimilated Gravity Recovery and Climate Experiment (GRACE) terrestrial water storage observations
Authors: Houborg Rasmus , Rodell Matthew , Li Bailing , Reichle Rolf , Zaitchik Benjamin F.
Published: June 2012

The Gravity Recovery and Climate Experiment (GRACE) twin satellites observe time variations in Earth's gravity field which yield valuable information about changes in terrestrial water storage (TWS). GRACE is characterized by low spatial (>150,000 km2) and temporal (>10 days) resolution but has the unique ability to sense water stored at all levels (including groundwater) systematically and continuously. The GRACE Data Assimilation System (DAS), based on the Catchment Land Surface Model (CLSM), enhances the value of the GRACE water storage data by enabling spatial and temporal downscaling and vertical decomposition into moisture components (i.e., groundwater, soil moisture, and snow), which individually are more useful for scientific applications. In this study, GRACE DAS was applied to North America, and GRACE‐based drought indicators were developed as part of a larger effort to investigate the possibility of more comprehensive and objective identification of drought conditions by integrating spatially, temporally, and vertically disaggregated GRACE data into the U.S. and North American Drought Monitors. Previously, the drought monitors lacked objective information on deep soil moisture and groundwater conditions, which are useful indicators of drought. Extensive data sets of groundwater storage from U.S. Geological Survey monitoring wells and soil moisture from the Soil Climate Analysis Network were used to assess improvements in the hydrological modeling skill resulting from the assimilation of GRACE TWS data. The results point toward modest, but statistically significant, improvements in the hydrological modeling skill across major parts of the United States, highlighting the potential value of a GRACE‐assimilated water storage field for improving drought detection.
The planetary water drama: Dual task of feeding humanity and curbing climate change
Authors: Rockström J. , Falkenmark M. , Lannerstad M. , Karlberg L.
Published: June 2012

This paper analyses the potential conflict between resilience of the Earth system and global freshwater requirements for the dual task of carbon sequestration to reduce CO2in the atmosphere, and food production to feed humanity by 2050. It makes an attempt to assess the order of magnitude of the increased consumptive water use involved and analyses the implications as seen from two parallel perspectives; the global perspective of human development within a “safe operating space” with regard to the definition of the Planetary Boundary for freshwater; and the social‐ecological implications at the regional river basin scale in terms of sharpening water shortages and threats to aquatic ecosystems. The paper shows that the consumptive water use involved in the dual task would both transgress the proposed planetary boundary range for global consumptive freshwater use and would further exacerbate already severe river depletion, causing societal problems related to water shortage and water allocation. Thus, strategies to rely on sequestration of CO2 as a mitigation strategy must recognize the high freshwater costs involved, implying that the key climate mitigation strategy must be to reduce emissions. The paper finally highlights the need to analyze both water and carbon tradeoffs from anticipated large scale biofuel production climate change mitigation strategy, to reveal gains and impact of this in contrast to carbon sequestration strategies.
A geochemical clock in earliest Paleogene pelagic carbonates based on the impact‐induced Os isotope excursion at the Cretaceous‐Paleogene boundary
Authors: Ravizza Greg , VonderHaar Denys
Published: June 2012

An impact‐induced osmium (Os) isotope excursion provides a unique means of assessing the completeness of marine Cretaceous‐Paleogene (K‐Pg) boundary sections, and surmounting challenges associated with constraining the time scale of the Earth system recovery from this extreme perturbation. A model of the recovery of seawater187Os/188Os following the impact event allows independent estimates of the time elapsed since the impact, which can be directly compared to time estimates derived from biostratigraphy, magnetostratigraphy and cyclostratigraphy. This approach is tested using data from three deep ocean sites cored by the Ocean Drilling Program (ODP). Data from ODP 1262B (South Atlantic) and ODP 690C (Southern Ocean) display the expected 187Os/188Os minimum very close to the biostratigraphically defined K‐Pg boundary and yield Os‐based accumulation rate estimates similar to those obtained from magnetostratigraphy and orbital tuning. In contrast, the187Os/188Os minimum in ODP 1209C (Western Pacific) occurs ≈9 cm below the K‐Pg boundary. Low Os concentrations throughout the boundary interval and an implausibly rapid recovery to higher, pre‐impact187Os/188Os ratios provide strong evidence for a previously unrecognized gap in the K‐Pg interval of Site 1209. Results presented here provide strong empirical evidence that Os isotope data are uniquely valuable in assessing the completeness and accumulation rates of earliest Paleogene sediments from the deep sea. They are of broad interest because they have implications for astronomical tuning of the geologic time scale and illustrate that whole ocean geochemical perturbations can provide an alternative to biostratigraphy for correlation and timekeeping during abrupt biotic events.
Curved fold‐and‐thrust accretion during the extrusion of a synorogenic viscous allochthonous sheet: The Estepa Range (External Zones, Western Betic Cordillera, Spain)
Authors: Pedrera Antonio , Marín‐Lechado Carlos , Martos‐Rosillo Sergio , Roldán Francisco Javier
Published: June 2012

New structural, borehole, and time domain electromagnetic data allow us to reconstruct the 3‐D geometry of the Estepa range (External Zones of the Western Betic Cordillera), which constitutes an isolated curved fold‐and‐thrust range made up of Jurassic shallow marine carbonates and Cretaceous to Paleocene marls and marly limestones. Contraction and rising load linked to the accretion of the Subbetic nappe enhanced the expulsion of Triassic evaporites and overpressured clays during the early and middle Miocene, finally forming part of a highly deformed mélange unit. This plastic extrusion favored the disconnection of External and Middle Subbetic blocks, including the Sierra de Estepa Range. There, deformation is characterized by northwest‐vergent curved folds‐and‐thrusts associated with NE‐SW frontal ramps and NW‐SE lateral transfer faults that segmented the folds active between 18 and 12 Ma. At a local scale, curvature was achieved under a nearly uniform NW/WNW transport direction suggesting a primary arc type. Friction variation across the heterogeneous detached plastic basal Triassic unit mainly controlled the curvature and segmentation of the fold systems. Transport direction is consistent with previously published slip data from the Internal Subbetic and the Campo de Gibraltar units. After the Late Serravallian, accretion slowed down and a shallow marine unit deposited unconformably placed over the main thrust and folds. The sequence of deformation and emplacement of these ranges is interpreted as a continuous process linked to the early Miocene E continental collision of the Iberian margin thin continental crust and subduction of the Flysch trough oceanic crust beneath the Alboran continental domain.
Predicting the accumulation of mercury‐contaminated sediment on riverbanks—An analytical approach
Authors: Pizzuto Jim
Published: June 2012

Mercury was introduced into the South River, Virginia, as a result of industrial use from 1929 to 1950. To guide remediation, an analytical model is developed to predict the mercury inventory resulting from deposition of mercury‐contaminated sediment on subhorizontal surfaces adjacent to the river channel from 1930 to 2007. Sediment cores and geomorphic data were obtained from 27 sites. Mercury inventories range from 0.00019 to 0.573 kg m−2. High mercury inventories are associated with frequent inundation by floodwaters, forested riparian vegetation, and (at only four sites) unusually high sediment accumulation. Over the 10 km study reach, mercury inventories do not vary with downstream distance. The frequency of inundation at each coring site is determined from hydrologic data and a streamtube stage‐discharge model. Water levels are exponentially distributed. A simple parameterization represents the enhanced ability of forested vegetation to trap mercury‐contaminated sediments compared to nonforest vegetation. The calibrated model explains 62% of the observed variation in mercury inventories; 15 of the 27 predicted values are within a factor of 1.8 of the observed values. Calibration indicates a mercury deposition rate during inundation of 0.040 kg m−2 yr−1 (95% C.I. 0.032–0.048), that forested areas accumulate mercury‐contaminated sediment 3.05 (95% C.I. 2.43–3.67) times faster than nonforested areas, and that floodwaters deeper than 0.98 (95% C.I. 0.45–1.53) m do not accumulate suspended sediment or mercury. At four sites, floodplain accumulation of 0.8–1.2 m occurred over a period of 39 (95% C.I. 22–56) years, while sedimentation is negligible (mean: 0.1 m, median: 0.03 m) at other sites.
High‐resolution water content estimation from surface‐based ground‐penetrating radar reflection data by impedance inversion
Authors: Schmelzbach C. , Tronicke J. , Dietrich P.
Published: June 2012

Mapping hydrological parameter distributions in high resolution is essential to understand and simulate groundwater flow and contaminant transport. Of particular interest is surface‐based ground‐penetrating radar (GPR) reflection imaging in electrically resistive sediments because of the expected close link between the subsurface water content and the dielectric permittivity, which controls GPR wave velocity and reflectivity. Conventional tools like common midpoint (CMP) velocity analysis provide physical parameter models of limited resolution only. We present a novel reflection amplitude inversion workflow for surface‐based GPR data capable of resolving the subsurface dielectric permittivity and related water content distribution with markedly improved resolution. Our scheme is an adaptation of a seismic reflection impedance inversion scheme to surface‐based GPR data. Key is relative‐amplitude‐preserving data preconditioning including GPR deconvolution, which results in traces with the source‐wavelet distortions and propagation effects largely removed. The subsequent inversion for the underlying dielectric permittivity and water content structure is constrained by in situ dielectric permittivity data obtained by direct‐push logging. After demonstrating the potential of our novel scheme on a realistic synthetic data set, we apply it to two 2‐D 100 MHz GPR profiles acquired over a shallow sedimentary aquifer resulting in water content images of the shallow (3–7 m depth) saturated zone having decimeter resolution.
Sex and gender differences in health
Authors: Regitz‐Zagrosek Vera
Published: June 2012

The new concept of evidence‐based sex and gender medicine—which includes the fundamental differences of biology and behaviour between women and men—should improve health care for both sexes.
Quantitative proteomic analysis of induced pluripotent stem cells derived from a human Huntington's disease patient
Authors: Chae Jung-Il , Kim Dong-Wook , Lee Nayeon , Jeon Young-Joo , Jeon Iksoo , Kwon Jihye , Kim Jumi , Soh Yunjo , Lee Dong-Seok , Seo Kang Seok , Choi Nag-Jin , Park Byoung Chul , Kang Sung Hyun , Ryu Joohyun , Oh Seung-Hun , Shin Dong Ah , Lee Dong Ryul , Do Jeong Tae , Park In-Hyun , Daley George Q. , Song Jihwan
Published: June 2012

HD (Huntington's disease) is a devastating neurodegenerative genetic disorder caused by abnormal expansion of CAG repeats in the HTT (huntingtin) gene. We have recently established two iPSC (induced pluripotent stem cell) lines derived from a HD patient carrying 72 CAG repeats (HD-iPSC). In order to understand the proteomic profiles of HD-iPSCs, we have performed comparative proteomic analysis among normal hESCs (human embryonic stem cells; H9), iPSCs (551-8) and HD-iPSCs at undifferentiated stages, and identified 26 up- and down-regulated proteins. Interestingly, these differentially expressed proteins are known to be involved in different biological processes, such as oxidative stress, programmed cell death and cellular oxygen-associated proteins. Among them, we found that oxidative stress-related proteins, such as SOD1 (superoxide dismutase 1) and Prx (peroxiredoxin) families are particularly affected in HD-iPSCs, implying that HD-iPSCs are highly susceptible to oxidative stress. We also found that BTF3 (basic transcription factor 3) is up-regulated in HD-iPSCs, which leads to the induction of ATM (ataxia telangiectasia mutated), followed by activation of the p53-mediated apoptotic pathway. In addition, we observed that the expression of cytoskeleton-associated proteins was significantly reduced in HD-iPSCs, implying that neuronal differentiation was also affected. Taken together, these results demonstrate that HD-iPSCs can provide a unique cellular disease model system to understand the pathogenesis and neurodegeneration mechanisms in HD, and the identified proteins from the present study may serve as potential targets for developing future HD therapeutics.
The many faces of p38 mitogen-activated protein kinase in progenitor/stem cell differentiation
Authors: Oeztuerk-Winder Feride , Ventura Juan-Jose
Published: June 2012

Regulation of stem cells is essential for development and adult tissue homoeostasis. The proper control of stem cell self-renewal and differentiation maintains organ physiology, and disruption of such a balance results in disease. There are many mechanisms that have been established as stem cell regulators, such as Wnt or Notch signals. However, the intracellular mechanisms that mediate and integrate these signals are not well understood. A new intracellular pathway that has been reported to be involved in the regulation of many stem cell types is that of p38 MAPK (mitogen-activated protein kinase). In particular, p38α is essential for the proper differentiation of many haematopoietic, mesenchymal and epithelial stem/progenitor cells. Many reports have shown that disruption of this kinase pathway has pathological consequences in many organs. Understanding the extracellular cues and downstream targets of p38α in stem cell regulation may help to tackle some of the pathologies associated with improper differentiation and regulation of stem cell function. In the present review we present a vision of the current knowledge on the roles of the p38α signal as a regulator of stem/progenitor cells in different tissues in physiology and disease.
A physics-based model of the electrical impedance of ionic polymer metal composites
Authors: Cha Youngsu , Aureli Matteo , Porfiri Maurizio
Published: June 2012

In this paper, we analyze the chemoelectrical behavior of ionic polymer metal composites (IPMCs) in the small voltage range with a novel hypothesis on the charge dynamics in proximity of the electrodes. In particular, we homogenize the microscopic properties of the interfacial region through a so-called composite layer which extends between the polymer membrane and the metal electrode. This layer accounts for the dissimilar properties of its constituents by describing the charge distribution via two species of charge carriers, that is, electrons and mobile counterions. We model the charge dynamics in the IPMC by adapting the multiphysics formulation based on the Poisson-Nernst-Planck (PNP) framework, which is enriched through an additional term to capture the electron transport in the composite layer. Under the hypothesis of small voltage input, we use the linearized PNP model to derive an equivalent IPMC circuit model with lumped elements. The equivalent model comprises a resistor connected in series with the parallel of a capacitor and a Warburg impedance element. These elements idealize the phenomena of charge build up in the double layer region and the faradaic impedance related to mass transfer, respectively. We validate the equivalent model through measurements on in-house fabricated samples addressing both IPMC step response and impedance, while assessing the influence of repeated plating cycles on the electrical properties of IPMCs. Experimental results are compared with theoretical findings to identify the equivalent circuit parameters. Findings from this study are compared with alternative impedance models proposed in the literature.
Surface metallic states in ultrathin Bi(001) films studied with terahertz time-domain spectroscopy
Authors: Yokota K. , Takeda J. , Dang C. , Han G. , McCarthy D. N. , Nagao T. , Hishita S. , Kitajima M. , Katayama I.
Published: June 2012

Dynamical response of surface metallic states in single crystalline ultrathin Bi(001) films on Si(111) 7 × 7 surface was investigated at a spectral range of 0.1–12 THz by broadband terahertz time-domain spectroscopy. The observed transmittance increased with a decrease in the thickness, without showing a gap structure. The measured complex dielectric dispersion was analyzed using a Drude model, and the plasma frequency (ωp) and damping constant (γ) were found to be inversely proportional to the thickness. The results strongly indicate the existence of surface metallic states, whose carrier density and damping constant are estimated to be 3.08 × 1019 cm−3 and 4.83 × 102 THz, respectively.
Micromagnetic simulations of sweep-rate dependent coercivity in perpendicular recording media
Authors: Plumer M. L. , Leblanc M. D. , Whitehead J. P. , van Ek J.
Published: June 2012

The results of micromagnetic simulations are presented, which examine the impact of thermal fluctuations on sweep rate dependent coercivities of both single-layer and exchange-coupled-composite (ECC) perpendicular magnetic recording media. M-H loops are calculated at four temperatures and sweep rates spanning five decades with fields applied normal to the plane and at 45°. The impact of interactions between grains is evaluated. The results indicate a significantly weaker sweep-rate dependence for ECC media suggesting more robustness to long-term thermal effects. Fitting the modeled results to Sharrock-like scaling proposed by Feng and Visscher [J. Appl. Phys. 95, 7043 (2004)] is successful only in the case of single-layer media with the field normal to the plane.
A study of phase transition behaviors of chalcogenide layers using in situ alternative-current impedance spectroscopy
Authors: Huang Yin-Hsien , Huang Yu-Jen , Hsieh Tsung-Eong
Published: June 2012

Electrical properties of chalcogenide thin films, both pristine Ge2Sb2Te5 (GST) and cerium-doped GST, were investigated by in situ alternative-current (AC) impedance spectroscopy. With the aid of brick-layer model and nano-grain composite model, the roles of grain and grain-boundary on the phase transition of chalcogenides were distinguished and the dominance of grain boundary was observed. Tangent loss behaviors deduced by impedance analysis revealed alien-element doping alters the interfacial polarization and delays the phase-transition rate of GST. Analytical results also illustrated that the in situ AC impedance spectroscopy can be an alternative tool for characterizing the phase-change kinetics of chalcogenides thin films with nano-scale grain sizes.
Enhanced thermoelectric properties by Ir doping of PtSb2 with pyrite structure
Authors: Nishikubo Yoshihiro , Nakano Seiya , Kudo Kazutaka , Nohara Minoru
Published: June 2012

The effects of Ir doping on the thermoelectric properties of Pt1–xIrxSb2 (x = 0, 0.01, 0.03, and 0.1) with pyrite structure were studied. Measurements of electrical resistivity ρ, Seebeck coefficient S, and thermal conductivity κ were conducted. The results showed an abrupt change from semiconducting behavior without Ir (x = 0) to metallic behavior at x = 0.01. The sample with x = 0.01 exhibited large S and low ρ, resulting in a maximum power factor (S2/ρ) of 43 μW/cmK2 at 400 K. The peculiar “pudding mold”-type electronic band dispersion could explain the enhanced thermoelectric properties in the metallic state.
Synthesis and characterization of Co2FeAl nanowires
Authors: Sapkota Keshab R. , Gyawali Parshu , Forbes Andrew , Pegg Ian L. , Philip John
Published: June 2012

We report the growth and characterization of Co2FeAl nanowires. Nanowires are grown using electrospinning method and the diameters range from 50 to 500 nm. These nanowires exhibit cubic crystal structure with a lattice constant of a=5.639 Å. The nanowires exhibit ferromagnetic behavior with a very high Curie temperature. The temperature dependent magnetization behavior displays an anomaly in the temperature range 600–850 K, which disappears at higher external magnetic fields.
On the rapidity of antibiotic resistance evolution facilitated by a concentration gradient
Authors: Hermsen Rutger , Deris J. Barrett , Hwa Terence
Published: June 2012

The rapid emergence of bacterial strains resistant to multiple antibiotics is posing a growing public health risk. The mechanisms underlying the rapid evolution of drug resistance are, however, poorly understood. The heterogeneity of the environments in which bacteria encounter antibiotic drugs could play an important role. E.g., in the highly compartmentalized human body, drug levels can vary substantially between different organs and tissues. It has been proposed that this could facilitate the selection of resistant mutants, and recent experiments support this. To study the role of spatial heterogeneity in the evolution of drug resistance, we present a quantitative model describing an environment subdivided into relatively isolated compartments with various antibiotic concentrations, in which bacteria evolve under the stochastic processes of proliferation, migration, mutation and death. Analytical and numerical results demonstrate that concentration gradients can foster a mode of adaptation that is impossible in uniform environments. It allows resistant mutants to evade competition and circumvent the slow process of fixation by invading compartments with higher drug concentrations, where less resistant strains cannot subsist. The speed of this process increases sharply with the sensitivity of the growth rate to the antibiotic concentration, which we argue to be generic. Comparable adaptation rates in uniform environments would require a high selection coefficient (
s
 > 0.1) for each forward mutation. Similar processes can occur if the heterogeneity is more complex than just a linear gradient. The model may also be applicable to other adaptive processes involving environmental heterogeneity and range expansion.
Theory of active transport in filopodia and stereocilia
Authors: Zhuravlev Pavel I. , Lan Yueheng , Minakova Maria S. , Papoian Garegin A.
Published: June 2012

The biological processes in elongated organelles of living cells are often regulated by molecular motor transport. We determined spatial distributions of motors in such organelles, corresponding to a basic scenario when motors only walk along the substrate, bind, unbind, and diffuse. We developed a mean-field model, which quantitatively reproduces elaborate stochastic simulation results as well as provides a physical interpretation of experimentally observed distributions of Myosin IIIa in stereocilia and filopodia. The mean-field model showed that the jamming of the walking motors is conspicuous, and therefore damps the active motor flux. However, when the motor distributions are coupled to the delivery of actin monomers toward the tip, even the concentration bump of G actin that they create before they jam is enough to speed up the diffusion to allow for severalfold longer filopodia. We found that the concentration profile of G actin along the filopodium is rather nontrivial, containing a narrow minimum near the base followed by a broad maximum. For efficient enough actin transport, this nonmonotonous shape is expected to occur under a broad set of conditions. We also find that the stationary motor distribution is universal for the given set of model parameters regardless of the organelle length, which follows from the form of the kinetic equations and the boundary conditions.
Deer, predators, and the emergence of Lyme disease
Authors: Levi Taal , Kilpatrick A. Marm , Mangel Marc , Wilmers Christopher C.
Published: June 2012

Lyme disease is the most prevalent vector-borne disease in North America, and both the annual incidence and geographic range are increasing. The emergence of Lyme disease has been attributed to a century-long recovery of deer, an important reproductive host for adult ticks. However, a growing body of evidence suggests that Lyme disease risk may now be more dynamically linked to fluctuations in the abundance of small-mammal hosts that are thought to infect the majority of ticks. The continuing and rapid increase in Lyme disease over the past two decades, long after the recolonization of deer, suggests that other factors, including changes in the ecology of small-mammal hosts may be responsible for the continuing emergence of Lyme disease. We present a theoretical model that illustrates how reductions in small-mammal predators can sharply increase Lyme disease risk. We then show that increases in Lyme disease in the northeastern and midwestern United States over the past three decades are frequently uncorrelated with deer abundance and instead coincide with a range-wide decline of a key small-mammal predator, the red fox, likely due to expansion of coyote populations. Further, across four states we find poor spatial correlation between deer abundance and Lyme disease incidence, but coyote abundance and fox rarity effectively predict the spatial distribution of Lyme disease in New York. These results suggest that changes in predator communities may have cascading impacts that facilitate the emergence of zoonotic diseases, the vast majority of which rely on hosts that occupy low trophic levels.
Non-Euclidean geometry of twisted filament bundle packing
Authors: Bruss Isaac R. , Grason Gregory M.
Published: June 2012

Densely packed and twisted assemblies of filaments are crucial structural motifs in macroscopic materials (cables, ropes, and textiles) as well as synthetic and biological nanomaterials (fibrous proteins). We study the unique and nontrivial packing geometry of this universal material design from two perspectives. First, we show that the problem of twisted bundle packing can be mapped exactly onto the problem of disc packing on a curved surface, the geometry of which has a positive, spherical curvature close to the center of rotation and approaches the intrinsically flat geometry of a cylinder far from the bundle center. From this mapping, we find the packing of any twisted bundle is geometrically frustrated, as it makes the sixfold geometry of filament close packing impossible at the core of the fiber. This geometrical equivalence leads to a spectrum of close-packed fiber geometries, whose low symmetry (five-, four-, three-, and twofold) reflect non-Euclidean packing constraints at the bundle core. Second, we explore the ground-state structure of twisted filament assemblies formed under the influence of adhesive interactions by a computational model. Here, we find that the underlying non-Euclidean geometry of twisted fiber packing disrupts the regular lattice packing of filaments above a critical radius, proportional to the helical pitch. Above this critical radius, the ground-state packing includes the presence of between one and six excess fivefold disclinations in the cross-sectional order.
Plasma membrane associated transcription of cytoplasmic DNA
Authors: Cheng Julong , Torkamani Ali , Peng Yingjie , Jones Teresa M. , Lerner Richard A.
Published: June 2012

Cytoplasmic membrane-associated DNA (cmDNA) is a species of DNA that attaches to the plasma membrane and has physical and chemical properties that differ from those of bulk chromosomal and mitochondrial DNAs. Here, we used deep sequencing to analyze cmDNA and showed that satellite DNAs consisting of both of simple (CCATT)
N
repeats from the pericentromere regions of the chromosomes and 171-bp α-satellite repeat sequences from centromeres were highly enriched. Importantly, we found there is a special cytoplasmic membrane-associated transcription system in which DNA-dependent RNA polymerase II, which colocalizes with template cmDNA at the plasma membrane, can transcribe the membrane-associated 171-bp α-satellite repeat sequences into RNA. Analysis of phosphorylation patterns indicated that the RNA polymerase II in the plasma membrane is in a different chemical state from its nuclear counterpart.
Structure/function correlations among coupled binuclear copper proteins through spectroscopic and reactivity studies of NspF
Authors: Ginsbach Jake W. , Kieber-Emmons Matthew T. , Nomoto Ryohei , Noguchi Akio , Ohnishi Yasuo , Solomon Edward I.
Published: June 2012

The terminal step of 4-hydroxy-3-nitrosobenzamide biosynthesis in
Streptomyces murayamaensis
is performed by NspF, a mono-oxygenase that converts
o
-aminophenols to the corresponding nitroso product (hydroxyanilinase activity). Previous biochemical characterization of the resting form of NspF suggested that this enzyme belonged to the coupled binuclear copper enzyme (CBC) family. Another member of this enzyme family, tyrosinase, is able to mono-oxygenate monophenols (monophenolase activity) but not
o
-aminophenols. To gain insight into the unique reactivity of NspF, we have generated and characterized the oxy form of its active site. The observation of spectral features identical to those of oxy-tyrosinase indicates that oxy-NspF contains a Cu
2
O
2
core where peroxide is coordinated in a
μ
-
η
2
∶ 
η
2
mode, confirming that NspF is a CBC enzyme. This oxy form is found to react with monophenols, indicating that, like tyrosinase, NspF also possesses monophenolase activity. A comparison of the two electrophilic mechanisms for the monophenolase and hydroxyanilinase activity indicates a large geometric change between their respective transition states. The potential for specific interactions between the protein pocket and the substrate in each transition state is discussed within the context of the differential reactivity of this family of enzymes with equivalent
μ
-
η
2
∶
η
2
peroxy bridged coupled binuclear copper active sites.
Low-Elevation Dams Are Impediments to Adult Pacific Lamprey Spawning Migration in the Umatilla River, Oregon
Authors: Jackson Aaron , Moser Mary
Published: June 2012

Due to tribal concerns over the recent decline of Pacific lamprey Lampetra tridentata, a restoration program was initiated to establish a self-sustaining, harvestable lamprey population within the ceded lands of the Confederated Tribes of the Umatilla Indian Reservation in Oregon. We hypothesized that low returns of adult lampreys to spawning areas in the Umatilla River were caused by loss of habitat connectivity in this watershed. We conducted a study to determine whether the ubiquitous, low-elevation irrigation diversion dams in the main-stem Umatilla River were obstacles to adult lamprey spawning migration. Radiotelemetry was used to assess lamprey passage efficiency at seven dams located within the lowest 55-km reach of the Umatilla River. During this 4-year study, we tracked 217 adult Pacific lampreys that were implanted with radio transmitters and released downstream from the dams. Logistic regression analysis indicated that dam design, fish size, and temperature had the greatest effects on passage efficiency. Poor performance (<30% fitted passage probability) was recorded at the two lowest dams in the system and resulted in limited escapement to upper sites. During the study, one dam was breached, after which passage efficiency there immediately improved from 32% to 81%. In addition, water augmentation actions at Three Mile Falls Dam apparently contributed to improved mean passage efficiency of migratory-phase fish (from 17% to 50%). Thus, actions to improve adult lamprey access to historical spawning areas are feasible and are key to successful restoration of this species.

Received June 29, 2011; accepted February 13, 2012
Effect of Brook Trout Removal from a Spawning Stream on an Adfluvial Population of Lahontan Cutthroat Trout
Authors: Scoppettone G. Gary , Rissler Peter H. , Shea Sean P. , Somer William
Published: June 2012

Independence Lake (Nevada and Sierra counties, California) harbors the only extant native population of Lahontan cutthroat trout Oncorhynchus clarkii henshawi in the Truckee River system and one of two extant adfluvial populations in the Lahontan basin. The persistence of this population has been precarious for more than 50 years, with spawning runs consisting of only 30–150 fish. It is assumed that this population was much larger prior to the introduction of nonnative brook trout Salvelinus fontinalis. Brook trout overlap with cutthroat trout in upper Independence Creek, where the cutthroat trout spawn and their resulting progeny emigrate to Independence Lake. In 2005, we began removing brook trout from upper Independence Creek using electrofishers and monitored the cutthroat trout population. Stomach analysis of captured brook trout revealed cutthroat trout fry, and cutthroat trout fry survival increased significantly from 4% to 12% with brook trout removal. Prior to brook trout removal, the only Lahontan cutthroat trout progeny emigrating to Independence Lake were fry; with brook trout removal, juveniles were found entering the lake. In 2010, 237 potential spawners passed a prefabricated weir upstream of Independence Lake. Although the results of this study suggest that brook trout removal from upper Independence Creek has had a positive influence on the population dynamics of Independence Lake Lahontan cutthroat trout, additional years of removal are needed to assess the ultimate effect this action will have upon the cutthroat trout population.

Received August 26, 2011; accepted February 29, 2012
Effects of sputter-deposition-induced and post-deposition thermally activated intermixing on the exchange bias properties of [Pt/Co]×3/(Pt)/IrMn films
Authors: Letellier F , Baltz V , Lechevallier L , Lardé R , Jacquot J-F , Rodmacq B , Breton J-M Le , Dieny B
Published: June 2012

The effects of sputter-deposition-induced and post-deposition thermally activated layer intermixing on the exchange bias properties of [Pt/Co]
x3/Pt(t
Pt)/IrMn films with out-of-plane anisotropy and deposited under a perpendicular magnetic field are investigated. The consequences of the intermixing on the magnetic properties are correlated with atom probe structural investigations. We observe that Co–Mn and Co–Pt intermixing are already present in the as-deposited state. The intermixing is more pronounced for Pt on Co (∼50%) than for Mn on Co (∼10%). It is observed that annealing up to 200 °C does not result in noticeable further diffusion of Mn in Co. In contrast, it significantly accentuates the Co–Pt initial intermixing. This enhanced intermixing leads to a 40% reduction in the exchange bias field. We measured that this reduction is not primarily due to changes in effective anisotropy or in saturation magnetization. This is possibly ascribed to a decrease in the mean interfacial moment and exchange stiffness both due to the observed reduction in Co content within the Co sublayers.
Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model
Authors: Abate Francesco , Acquaviva Andrea , Paciello Giulia , Foti Carmelo , Ficarra Elisa , Ferrarini Alberto , Delledonne Massimo , Iacobucci Ilaria , Soverini Simona , Martinelli Giovanni , Macii Enrico
Published: June 2012

Motivation: Next-generation sequencing technology allows the detection of genomic structural variations, novel genes and transcript isoforms from the analysis of high-throughput data. In this work, we propose a new framework for the detection of fusion transcripts through short paired-end reads which integrates splicing-driven alignment and abundance estimation analysis, producing a more accurate set of reads supporting the junction discovery and taking into account also not annotated transcripts. Bellerophontes performs a selection of putative junctions on the basis of a match to an accurate gene fusion model.

Results: We report the fusion genes discovered by the proposed framework on experimentally validated biological samples of chronic myelogenous leukemia (CML) and on public NCBI datasets, for which Bellerophontes is able to detect the exact junction sequence. With respect to state-of-art approaches, Bellerophontes detects the same experimentally validated fusions, however, it is more selective on the total number of detected fusions and provides a more accurate set of spanning reads supporting the junctions. We finally report the fusions involving non-annotated transcripts found in CML samples.

Availability and implementation: Bellerophontes JAVA/Perl/Bash software implementation is free and available at http://eda.polito.it/bellerophontes/.

Contact:  francesco.abate@polito.it
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics
Authors: Hoehndorf Robert , Dumontier Michel , Gkoutos Georgios V.
Published: June 2012

Motivation: Many complex diseases are the result of abnormal pathway functions instead of single abnormalities. Disease diagnosis and intervention strategies must target these pathways while minimizing the interference with normal physiological processes. Large-scale identification of disease pathways and chemicals that may be used to perturb them requires the integration of information about drugs, genes, diseases and pathways. This information is currently distributed over several pharmacogenomics databases. An integrated analysis of the information in these databases can reveal disease pathways and facilitate novel biomedical analyses.

Results: We demonstrate how to integrate pharmacogenomics databases through integration of the biomedical ontologies that are used as meta-data in these databases. The additional background knowledge in these ontologies can then be used to enable novel analyses. We identify disease pathways using a novel multi-ontology enrichment analysis over the Human Disease Ontology, and we identify significant associations between chemicals and pathways using an enrichment analysis over a chemical ontology. The drug–pathway and disease–pathway associations are a valuable resource for research in disease and drug mechanisms and can be used to improve computational drug repurposing.

Availability:  http://pharmgkb-owl.googlecode.com

Contact:  rh497@cam.ac.uk
Debt, Deleveraging, and the Liquidity Trap: A Fisher-Minsky-Koo Approach*
Authors: Eggertsson Gauti B. , Krugman Paul
Published: June 2012

In this article we present a simple new Keynesian–style model of debt-driven slumps—that is, situations in which an overhang of debt on the part of some agents, who are forced into rapid deleveraging, is depressing aggregate demand. Making some agents debt-constrained is a surprisingly powerful assumption. Fisherian debt deflation, the possibility of a liquidity trap, the paradox of thrift and toil, a Keynesian-type multiplier, and a rationale for expansionary fiscal policy all emerge naturally from the model. We argue that this approach sheds considerable light both on current economic difficulties and on historical episodes, including Japan’s lost decade (now in its 18th year) and the Great Depression itself.
A thermal analysis of the operation of microscale, inorganic light-emitting diodes
Authors: Lu Chaofeng , Li Yuhang , Song Jizhou , Kim Hoon-Sik , Brueckner Eric , Fang Bo , Hwang Keh-Chih , Huang Yonggang , Nuzzo Ralph G. , Rogers John A.
Published: June 2012

An analytical model is developed to study the thermal properties of microscale, inorganic light-emitting diodes (μ-ILEDs) with ultra-thin geometries and layouts. The predicted surface and μ-ILED temperatures agree well with experiments and finite-element simulations. A simple scaling law is obtained for the normalized μ-ILED temperature versus the normalized μ-ILED size. This study provides a theory to guide the design of layouts that minimize adverse thermal effects on the performance of μ-ILEDs not only for solid-state lighting but also for applications integrating μ-ILED devices on complex/soft substrate as are currently of interest in optogenetics and other emerging areas in biology.
The histone H3 Lys 27 demethylase JMJD3 regulates gene expression by impacting transcriptional elongation
Authors: Chen Shuzhen , Ma Jian , Wu Feizhen , Xiong Li-jun , Ma Honghui , Xu Wenqi , Lv Ruitu , Li Xiaodong , Villen Judit , Gygi Steven P. , Liu Xiaole Shirley , Shi Yang
Published: June 2012

The histone H3 Lys 27 (H3K27) demethylase JMJD3 has been shown to play important roles in transcriptional regulation and cell differentiation. However, the mechanism underlying JMJD3-mediated transcriptional regulation remains incompletely understood. Here we show that JMJD3 is associated with KIAA1718, whose substrates include dimethylated H3K27 (H3K27me2), and proteins involved in transcriptional elongation. JMJD3 and KIAA1718 directly bind to and regulate the expression of a plethora of common target genes in both a demethylase activity-dependent and -independent manner in the human promyelocytic leukemia cell line HL-60. We found that JMJD3 and KIAA1718 collaborate to demethylate trimethylated H3K27 (H3K27me3) on a subset of their target genes, some of which are bivalently marked by H3K4me3 and H3K27me3 and associated with promoter-proximal, paused RNA polymerase II (Pol II) before activation. Reduction of either JMJD3 or KIAA1718 diminishes Pol II traveling along the gene bodies of the affected genes while having no effect on the promoter-proximal Pol II. Furthermore, JMJD3 and KIAA1718 also play a role in localizing elongation factors SPT6 and SPT16 to the target genes. Our results support the model whereby JMJD3 activates bivalent gene transcription by demethylating H3K27me3 and promoting transcriptional elongation. Taken together, these findings provide new insight into the mechanisms by which JMJD3 regulates gene expression.