30 Years of Impact:President’s Postdoctoral Fellowship Program

Aquatic Sciences

Andres Aguilar

Weak phylogeographic structure in the endemic western North American fairy shrimp Branchinecta lynchi (Eng, Belk and Erickson 1990)

The vernal pool fairy shrimp (Branchinecta lynchi) (Eng et al. in J Crustac Biol 10:247–277, 1990) is broadly distributed throughout California’s Central Valley with disjunct populations in southern California and southern Oregon. A survey of genetic variation at the mitochondrial cytochrome c oxidase subunit I (COI) gene was conducted from individuals collected throughout the range of the species. Phylogenetic analysis of unique haplotypes could not resolve any significant genetic partitions below the species level. A detailed analysis of samples from two pools indicates that sample sizes underestimate overall variation, but that the general phylogeographic pattern still holds. Evidence was found for a putative long-distance dispersal event between Central Valley sites and the Oregon site. These results indicate that geographically limiting stochastic colonization followed by local diversification may be important in governing current genetic structure for this species. Future and current conservation/restoration efforts should recognize the geographic limitations to population structure for this species and focus on local endemic genetic variation.

Physical Review A

Dorit Aharonov

Quantum to classical phase transition in noisy quantum computers

The fundamental problem of the transition from quantum to classical physics is usually explained by decoherence, and viewed as a gradual process. The study of entanglement, or quantum correlations, in noisy quantum computers implies that in some cases the transition from quantum to classical is actually a phase transition. We define the notion of entanglement length in d-dimensional noisy quantum computers, and show that a phase transition in entanglement occurs at a critical noise rate where the entanglement length transforms from infinite to finite. Above the critical noise rate, macroscopic classical behavior is expected, whereas, below the critical noise rate, subsystems that are macroscopically distant one from another can be entangled. The macroscopic classical behavior in the supercritical phase is shown to hold not only for quantum computers but for any quantum system composed of macroscopically many finite state particles, with local interactions and local decoherence, subjected to some additional conditions. This phenomenon provides a possible explanation for the emergence of classical behavior in such systems. A simple formula for an upper bound on the entanglement length of any such system in the supercritical phase is given, and in principle can be tested experimentally.

Cell

Joy Alcedo, Marina Ayzenzon, Tonia Von Ohlen,Markus Noll, & Joan E. Hoope

The Drosophila smoothened Gene Encodes a Seven-Pass Membrane Protein, a Putative Receptor for the Hedgehog Signal

smoothened (smo) is a segment polarity gene required for correct patterning of every segment in Drosophila. The earliest defect in smomutant embryos is loss of expression of the Hedgehog- responsive gene wingless between 1 and 2 hr after gastrulation. Since smomutant embryos cannot respond to exogenous Hedgehog (Hh) but can respond to exogenous Wingless, the Smo product functions in Hh signaling. Smo acts downstream of or in parallel to Patched, an antagonist of the Hh signal. The smo gene encodes an integral membrane protein with characteristics of G protein–coupled receptors and shows homology to the Drosophila Frizzled protein. Based on its predicted physical characteristics and on its position in the Hh signaling pathway, we suggest that smo encodes a receptor for the Hh signal.

Journal of Computational Physics

Ralph C. Aldredge

Semi-Lagrangian advection–propagation (SLAP) scheme for three-dimensional interface tracking

A fully three-dimensional semi-Lagrangian scheme is developed for computing the evolution of advected self-propagating surfaces (e.g., premixed flames) governed by a level-set advection– propagation equation. The scheme provides third-order spatial accuracy and shape preservation. Example numerical simulations of three-dimensional front propagation are presented to illustrate the capability of the scheme of capturing cusp formation and associated surface-area annihilation as well as the formation and consumption of detached closed-surface pockets behind fronts propagating in highly vortical flow.

Applied Physics Letters

Sarah E. Baker, Michael D. Pocha, Allan S. P. Chang, Donald J. Sirbuly, Stefano Cabrini, Scott D. Dhuey, Tiziana C. Bond & Sonia E. Létant

Detection of bio-organism simulants using random binding on a defect-free photonic crystal

The defect-free photonic crystal(PC) slab geometry was explored for size-selective detection of bio-organism simulants. Through feedback between finite-difference time-domain simulations and experiments, we generated a conservative limit of detection estimate for randomized pore filling of a two-dimensional PC slab, and predict that random binding affords the label-free PC- based optical detection of low numbers (of the order of 10) of biological particles.

Cardiovascular Toxicology

Hargrave, B., Tiangco, D., Lattanzio, F., & Beebe, S. J. (2003).

Cocaine but not morphine causes the generation of reactive oxygen species and activation of NFκB in transiently co-transfected heart and renal epithelial cells.

This study was designed to determine levels of NF-κB reporter gene activity and free radical generation in cultured striated myocytes (H9C2 cells) exposed to cocaine or morphine in the presence of free radical scavengers. Cells were transiently transfected with a NF-κB reporter gene and changes in luciferase activity were detected, by bioluminescence. Using confocal microscopy and 2 ,7 -dichlorofluorescin diacetate, cocaine-induced or morphine-induced free ′ ′radicals were quantified in H9C2 cells. Cocaine and morphine (0–1×10−2 M) were tested separately. Cocaine but not morphine significantly activated Nf-κB reporter gene, activity in H9C2 cells. Overexpression of IκB inhibited NF-κB reporter activity at low (1×10−4 M) but not high (1×10−2 M) cocaine concentrations. Free radicals were generated in H9C2 cells stimulated with cocaine but not with morphine. The production of free radicals and NF-κB reporter gene activity could be blocked with N-acetylcysteine, glutathione, and to a lesser extent, lipoic acid. The results suggest that cocaine induces free radical production, which leads to the activation of NF-κB signal transduction and possible inflammatory responses.

Nature

K. Barbeau , E. L. Rue, K. W. Bruland & A. Butler

Photochemical cycling of iron in the surface ocean mediated by microbial iron(III)-binding ligands

Iron is a limiting nutrient for primary production in large areas of the oceans. Dissolved iron(III) in the upper oceans occurs almost entirely in the form of complexes with strong organic ligands presumed to be of biological origin. Although the importance of organic ligands to aquatic iron cycling is becoming clear, the mechanism by which they are involved in this process remains uncertain. Here we report observations of photochemical reactions involving Fe(III) bound to siderophores—high-affinity iron(III) ligands produced by bacteria to facilitate iron acquisition. We show that photolysis of Fe(III)–siderophore complexes leads to the formation of lower-affinity Fe(III) ligands and the reduction of Fe(III), increasing the availability of siderophore-bound iron for uptake by planktonic assemblages. These photochemical reactions are mediated by the -hydroxy acid moiety, a group which has generally been found to be present in the marine siderophores that have been characterized. We suggest that Fe(III)-binding ligands can enhance the photolytic production of reactive iron species in the euphotic zone and so influence iron availability in aquatic systems.

International Journal of Mathematics

Katrina Barron & Nathan Vander Werf

Permutation-twisted modules for even order cycles acting on tensor product vertex operator superalgebras

We construct and classify (1 2 k)-twisted V k-modules for k even and V a vertex operator ⋯ ⊗superalgebra. In particular, we show that the category of weak (1 2 k)-twisted V k-⋯ ⊗modules for k even is isomorphic to the category of weak parity-twisted V-modules. This result shows that in the case of a cyclic permutation of even order, the construction and classification of permutation-twisted modules for tensor product vertex operator superalgebras are fundamentally different than in the case of a cyclic permutation of odd order, as previously constructed and classified by the first author. In particular, in the even order case it is the parity-twisted V-modules that play the significant role in place of the untwisted V-modules that play the significant role in the odd order case.

ZAAC (Journal of Inorganic and General Chemistry)

Bart M. Bartlett, T. David Harris,Marty W. DeGroot & Jeffrey R. Long Prof.*

High-Spin Ni3Fe2(CN)6 and Cu3Cr2(CN)6 Clusters Based on a Trigonal Bipyramidal Geometry

The synthesis and characterization of two new cyano-bridged cluster compounds, [Tp2(cyclen)3NiII3FeIII2(CN)6](BF4)4 (1) and [(Me3tacn)5CuII3CrIII2(CN)6](ClO4)6 (2), are reported. The structure of each cluster is based upon a trigonal bipyramidal geometry, and ferromagnetic coupling between constituent metal ions is shown to give rise to S = 4 and S = equation image ground states, respectively. A room-temperature assembly reaction generates a purple form of compound 2, wherein two cyanide stretching frequencies in the infrared spectrum (νCN = 2094, 2156 cm−1) indicate partial isomerism of the cyanide bridging ligands. The X-ray crystal structure confirms this isomerism via examination of the C and N thermal parameters. At −40 °C, a metastable green form of the compound is instead isolated, for which a single cyanide stretch at νCN = 2156 cm−1 is consistent with an unisomerized cluster. The temperature-dependence of the magnetization under varying applied field reveals significant axial anisotropy in compound 1, with a significant axial zero-field splitting while compound 2 shows no zero-field splitting in either isolated form. In line with the observed anisotropy, AC magnetic susceptibility measurements performed on compound 1 reveal a frequency- dependent out-of-phase signal suggestive of single-molecule magnet behavior.

Plant Physiology

Bartley LE, Peck ML, Kim SR, Ebert B, Manisseri C, Chiniquy DM, Sykes R, Gao L, Rautengarten C, Vega-Sánchez ME, Benke PI, Canlas PE, Cao P, Brewer S, Lin F,

Smith WL, Zhang X, Keasling JD, Jentoff RE, Foster SB, Zhou J, Ziebell A, An G, Scheller HV, Ronald PC.

Overexpression of a BAHD acyltransferase, OsAt10, alters rice cell wall hydroxycinnamic acid content and saccharification.

Grass cell wall properties influence food, feed, and biofuel feedstock usage efficiency. The glucuronoarabinoxylan of grass cell walls is esterified with the phenylpropanoid-derived hydroxycinnamic acids ferulic acid (FA) and para-coumaric acid (p-CA). Feruloyl esters undergo oxidative coupling with neighboring phenylpropanoids on glucuronoarabinoxylan and lignin.

Examination of rice (Oryza sativa) mutants in a grass-expanded and -diverged clade of BAHD acyl-coenzyme A-utilizing transferases identified four mutants with altered cell wall FA or p-CA contents. Here, we report on the effects of overexpressing one of these genes, OsAt10 (LOC_Os06g39390), in rice. An activation-tagged line, OsAT10-D1, shows a 60% reduction in matrix polysaccharide-bound FA and an approximately 300% increase in p-CA in young leaf tissue but no discernible phenotypic alterations in vegetative development, lignin content, or lignin composition. Two additional independent OsAt10 overexpression lines show similar changes in FA and p-CA content. Cell wall fractionation and liquid chromatography-mass spectrometry experiments isolate the cell wall alterations in the mutant to ester conjugates of a five-carbon sugar with p-CA and FA. These results suggest that OsAT10 is a p-coumaroyl coenzyme A transferase involved in glucuronoarabinoxylan modification. Biomass from OsAT10-D1 exhibits a 20% to 40% increase in saccharification yield depending on the assay. Thus, OsAt10 is an attractive target for improving grass cell wall quality for fuel and animal feed.

National Institute of Health

Kuen-Phon Wu & Jean Baum

“Backbone assignment and dynamics of human α-synuclein in viscous 2 M glucose solution”, We present 1HN, 15N, 13Cα, 13Cβ and 13C assignments and 15N transverse relaxation rates ′(R2) of a Parkinson’s disease-related intrinsically disordered protein, α-synuclein, in the presence of 2 M (360 g/liter) glucose solution.

Journal of Geophysical Research – Biogeosciences

Asmeret Asefaw Berhe, Jennifer W. Harden, Margaret S. Torn,Markus Kleber, Sarah D. Burton & John Harte

Persistence of soil organic matter in eroding versus depositional landform positions

Soil organic matter (SOM) processes in dynamic landscapes are strongly influenced by soil erosion and sedimentation. We determined the contribution of physical isolation of organic matter (OM) inside aggregates, chemical interaction of OM with soil minerals, and molecular structure of SOM in controlling storage and persistence of SOM in different types of eroding and depositional landform positions. By combining density fractionation with elemental and spectroscopic analyses, we showed that SOM in depositional settings is less transformed and better preserved than SOM in eroding landform positions. However, which environmental factors exert primary control on storage and persistence of SOM depended on the nature of the landform position considered. In an annual grassland watershed, protection of SOM by physical isolation inside aggregates and chemical association of organic matter (complexation) with soil minerals, as assessed by correlation with radiocarbon concentration, were more effective in the poorly drained, lowest-lying depositional landform positions, compared to well-drained landform positions in the upper parts of the watershed. Results of this study demonstrated that processes of soil erosion and deposition are important mechanisms of long-term OM stabilization.

Combinatorics

Sara Billey, Zachary Hamaker, Austin Roberts, Benjamin Young

Coxeter-Knuth graphs and a signed Little map for type B reduced words

We define an analog of David Little's algorithm for reduced words in type B, and investigate its main properties. In particular, we show that our algorithm preserves the recording tableau of Kra\'{s}kiewicz insertion, and that it provides a bijective realization of the Type B transition equations in Schubert calculus. Many other aspects of type A theory carry over to this new setting. Our primary tool is a shifted version of the dual equivalence graphs defined by Assaf and further developed by Roberts. We provide an axiomatic characterization of shifted dual equivalence graphs, and use them to prove a structure theorem for the graph of Type B Coxeter-Knuth relations.

The Ohio Journal of Science

Blair, Brent C. & Stowasser, Annette

Impact of Lonicera maackii on Decomposition Rates of Native Leaf Litter in a Southwestern Ohio Woodland

The potential for invasive non-native plant species to alter forest ecosystem dynamics is an increasing concern among ecologists. However, while it is clear that invasives have a detrimental impact on native plant species, less is known about how the invasives affect the host habitat. One hypothesis suggests nutrient dynamics at and below the soil surface may be critical. This study investigated the differences in leaf litter decomposition between Lonicera maackii (an invasive shrub) and two native woody species (A. saccharum and Q. rubra). We evaluated mass loss rates from each of the species examined as well as two-species combinations of litter (six treatment combinations) in L. maackii invaded and uninvaded areas of urban woodland in Cincinnati, Ohio. We found that L. maackii decomposed significantly faster than the two native species (e.g., 21 times faster than Q. rubra). Overall, there was a trend of faster decomposition in plots located in the invaded areas although this was statistically significant in only two of the six species combinations. The impact the observed differences in decomposition rates may have on nutrient dynamics and the advantages of accelerated nutrient turnover to L. maackii is discussed.

Geochemistry, Geophysics, Geosystems

Wendy A. Bohrson & Frank J. Spera

Energy-Constrained Recharge, Assimilation, and Fractional Crystallization (EC-RAXFC): A Visual Basic computer code for calculating trace element and isotope variations of open-system magmatic systems

[1] Volcanic and plutonic rocks provide abundant evidence for complex processes that occur in magma storage and transport systems. The fingerprint of these processes, which include fractional crystallization, assimilation, and magma recharge, is captured in petrologic and geochemical characteristics of suites of cogenetic rocks. Quantitatively evaluating the relative contributions of each process requires integration of mass, species, and energy constraints, applied in a self-consistent way. The energy-constrained model Energy-Constrained Recharge, Assimilation, and Fractional Crystallization (EC-RaχFC) tracks the trace element and isotopic evolution of a magmatic system (melt + solids) undergoing simultaneous fractional crystallization, recharge, and assimilation. Mass, thermal, and compositional (trace element and isotope) output is provided for melt in the magma body, cumulates, enclaves, and anatectic (i.e., country rock) melt. Theory of the EC computational method has been presented by Spera and Bohrson (2001, 2002, 2004), and applications to natural systems have been elucidated by Bohrson and Spera (2001, 2003) and Fowler et al. (2004). The purpose of this contribution is to make the final version of the EC-RAχFC computer code available and to provide instructions for code implementation, description of input and output parameters, and estimates of typical values for some input parameters. A brief discussion highlights measures by which the user may evaluate the quality of the output and also provides some guidelines for implementing nonlinear productivity functions. The EC-RAχFC computer code is written in Visual Basic, the programming language of Excel. The code therefore launches in Excel and is compatible with both PC and MAC platforms. The code is available on the authors' Web sites http://magma.geol.ucsb.edu/and http://www.geology.cwu.edu/ecrafc) as well as in the auxiliary material.

The Journal of Experimental Biology

J. M. Burns, N. Skomp, N. Bishop, K. Lestyk & M. Hammill

Development of aerobic and anaerobic metabolism in cardiac and skeletal muscles from harp and hooded seals (2009)

In diving animals, skeletal muscle adaptations to extend underwater time despite selective vasoconstriction include elevated myoglobin (Mb) concentrations, high acid buffering ability (β) and high aerobic and anaerobic enzyme activities. However, because cardiac muscle is perfused during dives, it may rely less heavily on Mb, β and anaerobic pathways to support contractile activity. In addition, because cardiac tissue must sustain contractile activity even before birth, it may be more physiologically mature at birth and/or develop faster than skeletal muscles. To test these hypotheses, we measured Mb levels, β and the activities of citrate synthase (CS), β- hydroxyacyl-CoA dehydrogenase (HOAD) and lactate dehydrogenase (LDH) in cardiac and skeletal muscle samples from 72 harp and hooded seals, ranging in age from fetuses to adults. Results indicate that in adults cardiac muscle had lower Mb levels (14.7%), β (55.5%) and LDH activity (36.2%) but higher CS (459.6%) and HOAD (371.3%) activities (all P<0.05) than skeletal muscle. In addition, while the cardiac muscle of young seals had significantly lower [Mb] (44.7%) β (80.7%) and LDH activity (89.5%) than adults (all P<0.05), it was relatively more mature at birth and weaning than skeletal muscle. These patterns are similar to those in terrestrial species, suggesting that seal hearts do not exhibit unique adaptations to the challenges of an aquatic existence.

Journal of Nanomaterials

Marcos A. Cheney, Robin Jose, Arghya Banerjee,Pradip K. Bhowmik, Shizhi Qian, & Joseph M. Okoh

Synthesis and Characterization of Birnessite and Cryptomelane Nanostructures in Presence of Hoffmeister Anions

The effect of Hoffmeister anions, and on the structure and morphology of birnessite and cryptomelane-type manganese dioxide nanostructures, produced by the reduction reaction of and in aqueous acidic media, was studied. The syntheses were based on the decomposition of aqueous in presence of HCl for birnessite-type and acidified for cryptomelane-type manganese dioxide under soft hydrothermal conditions. They were characterized using X-ray diffraction (XRD), transmission electron microscopy (TEM), and high-resolution transmission electron microscopy (HRTEM) techniques. XRD patterns show the formation of birnessite for the first synthesis and a mixture of cryptomelane and birnessite-types for the second synthesis. XRD data revealed that the Hoffmeister anions have a significant effect on the nanostructures of birnessite. The sulphate ion-treated birnessite has the smallest crystals, whereas the chloride ion-treated birnessite has the largest crystals. Their TEM and HRTEM studies revealed a transformation from nanoplatelet morphology for chloride-treated samples to nanofibrous morphology for sulphate-treated birnessite. For the cryptomelane nanostructures, Hoffmeister anions also show a profound effect on their crystalline structures as determined by XRD analyses revealing a transformation of the cryptomelane phase to birnessite phase of. This transformation is also supported by TEM and HRTEM studies.

Journal of Polymer SciencePart A: Polymer Chemistry

Morgan JR, Cloninger MJ

Synthesis of Carbohydrate-linked Poly(polyoxometalate) PAMAM Dendrimers

Mannose functionalized and ethoxyethanol functionalized poly(amido)amine (PAMAM) dendrimers bound multiple vanadate substituted polyoxotungstate Wells-Dawson type polyoxometalates (POMs). Dendrimers incorporating ten to thirty POMs were characterized using NMR, TEM, and MALDI-TOF MS techniques. The number of metal clusters per dendrimer molecule varied according to dendrimer generation and nature of surface functional groups.

Efforts aimed at using the poly(polyoxometalate) dendrimers as oxidation catalysts are also described.

ScienceAlison N. Olcott, Alex L. Sessions, Frank A. Corsetti,

Alan J. Kaufman, & Tolentino Flavio de Oliviera

Biomarker Evidence for Photosynthesis During Neoproterozoic Glaciation

Laterally extensive black shales were deposited on the São Francisco craton in southeastern Brazil during low-latitude Neoproterozoic glaciation 740 to 700 million years ago. These ∼rocks contain up to 3.0 weight % organic carbon, which we interpret as representing the preserved record of abundant marine primary productivity from glacial times. Extractable biomarkers reflect a complex and productive microbial ecosystem, including both phototrophic bacteria and eukaryotes, living in a stratified ocean with thin or absent sea ice, oxic surface waters, and euxinic conditions within the photic zone. Such an environment provides important constraints for parts of the “Snowball Earth” hypothesis.

Nature

Alberto Cruz-Martín, Rana N. El-Danaf, Fumitaka Osakada,Balaji Sriram, Onkar S. Dhande, Phong L. Nguyen,

Edward M. Callaway, Anirvan Ghosh & Andrew D. Huberman

A dedicated circuit links direction-selective retinal ganglion cells to the primary visual cortex

How specific features in the environment are represented within the brain is an important unanswered question in neuroscience. A subset of retinal neurons, called direction-selective ganglion cells (DSGCs), are specialized for detecting motion along specific axes of the visual field. Despite extensive study of the retinal circuitry that endows DSGCs with their unique tuning properties, their downstream circuitry in the brain and thus their contribution to visual processing has remained unclear. In mice, several different types of DSGCs connect to the dorsal lateral geniculate nucleus (dLGN), the visual thalamic structure that harbours cortical relay neurons. Whether direction-selective information computed at the level of the retina is routed to cortical circuits and integrated with other visual channels, however, is unknown. Here we show that there is a di-synaptic circuit linking DSGCs with the superficial layers of the primary visual cortex (V1) by using viral trans-synaptic circuit mapping and functional imaging of visually driven calcium signals in thalamocortical axons. This circuit pools information from several types of DSGCs, converges in a specialized subdivision of the dLGN, and delivers direction-tuned and orientation-tuned signals to superficial V1. Notably, this circuit is anatomically segregated from the retino-geniculo-cortical pathway carrying non-direction- tuned visual information to deeper layers of V1, such as layer 4. Thus, the mouse harbours several functionally specialized, parallel retino-geniculo-cortical pathways, one of which originates with retinal DSGCs and delivers direction- and orientation-tuned information specifically to the superficial layers of the primary visual cortex. These data provide evidence that direction and orientation selectivity of some V1 neurons may be influenced by the activation of DSGCs.

Genome Research

Christina A. Cuomo, Christopher A. Desjardins, Malina A. Bakowski,Jonathan Goldberg, Amy T. Ma, James J. Becnel, Elizabeth S. Didier, Lin Fan,

David I. Heiman, Joshua Z. Levin, Sarah Young, Qiandong Zeng, & Emily R. Troemel

Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth

Microsporidia comprise a large phylum of obligate intracellular eukaryotes that are fungal- related parasites responsible for widespread disease, and here we address questions about microsporidia biology and evolution. We sequenced three microsporidian genomes from two species, Nematocida parisii and Nematocida sp1, which are natural pathogens of Caenorhabditis nematodes and provide model systems for studying microsporidian pathogenesis. We performed deep sequencing of transcripts from a time course of N. parisiiinfection. Examination of pathogen gene expression revealed compact transcripts and a dramatic takeover of host cells by Nematocida. We also performed phylogenomic analyses ofNematocida and other microsporidian genomes to refine microsporidian phylogeny and identify evolutionary events of gene loss, acquisition, and modification. In particular, we found that all microsporidia lost the tumor-suppressor gene retinoblastoma, which we speculate could accelerate the parasite cell cycle and increase the mutation rate. We also found that microsporidia acquired transporters that could import nucleosides to fuel rapid growth. In addition, microsporidian hexokinases gained secretion signal sequences, and in a functional assay these were sufficient to export proteins out of the cell; thus hexokinase may be targeted into the host cell to reprogram it toward biosynthesis. Similar molecular changes appear during formation of cancer cells and may be evolutionary strategies adopted independently by microsporidia to proliferate rapidly within host cells. Finally, analysis of genome polymorphisms revealed evidence for a sexual cycle that may provide genetic diversity to alleviate problems caused by clonal growth. Together these events may explain the emergence and success of these diverse intracellular parasites.

Scripta Materialia

Lilian P. Dávila, Valerie J. Leppert, Eduardo M. Bringa

The mechanical behavior and nanostructure of silica nanowires via simulations

Atomistic simulations of vitreous silica nanowires under compression were evaluated for size effects on stiffness and for structural transformations using ring distributions. Results from nanowires (diameters 1.4–20.0 nm) bridge the gap between experiments and simulations. Ultrathin nanowires (diameter 4.3 nm, length 14.3 nm) show no change in structure through 25% strain. Thicker nanowires resemble bulk glass in structure and Young’s modulus while longer nanowires (length 57 nm) display buckling modes. Ultrathin nanowire results are ∼consistent with predictions using elasticity calculations.

Nature

Gerardo Dominguez, Gautam Wilkins & Mark H. Thiemens

The Soret effect and isotopic fractionation in high-temperature silicate melts

Diffusion in condensed phases is a ubiquitous but poorly understood phenomenon. For example, chemical diffusion, which is the transport of matter associated with chemical concentration gradients (Fick’s law), is treated as a separate process from thermal transport (the Soret effect), which is mass transport induced by temperature gradients. In the past few years, large variations in the proportions of isotopes of Mg, Ca, Fe, Si and O found in silicate melts subject to thermal gradients have been found, but no physical mechanism has been proposed. Here we present a model of diffusion in natural condensed systems that explains both the chemical and isotopic fractionation of Mg, Ca and Fe in high-temperature geochemical melts. Despite the high temperatures associated with these melts (T > 1,000 °C), we find that consideration of the quantum-mechanical zero-point energy of diffusing species is essential for understanding diffusion at the isotopic level. Our model explains thermal and chemical mass transport as manifestations of the same underlying diffusion mechanism. This work promises to provide insights into mass-transport phenomena (diffusion and evaporation) and associated isotopic fractionations in a wide range of natural condensed systems, including the atmospheric water cycle, geological and geochemical systems and the early Solar System. This work might also be relevant to studies of mass transport in biological and nanotechnological condensed systems.

Advances in Neural InformationProcessing Systems 22 (NIPS 2009)

Alyson K. Fletcher, Sundeep Rangan

Orthogonal Matching Pursuit from Noisy Random Measurements: A New Analysis Orthogonal matching pursuit (OMP) is a widely used greedy algorithm for recovering sparse vectors from linear measurements. A well-known analysis of Tropp and Gilbert shows that OMP can recover a k-sparse n-dimensional real vector from m = 4k log(n) noise-free random linear measurements with a probability that goes to one as n goes to infinity. This work shows strengthens this result by showing that a lower number of measurements, m = 2k log(n-k), is in fact sufficient for asymptotic recovery. Moreover, this number of measurements is also sufficient for detection of the sparsity pattern (support) of the vector with measurement errors provided the signal-to-noise ratio (SNR) scales to infinity. The scaling m = 2k log(n-k) exactly matches the number of measurements required by the more complex lasso for signal recovery.

Nature Physics

T. E. Glover, M. P. Hertlein, S. H. Southworth, T. K. Allison,J. van Tilborg, E. P. Kanter, B. Krässig, H. R. Varma,

B. Rude, R. Santra, A. Belkacem & L. Young

Controlling X-rays with light

Ultrafast X-ray science is an exciting frontier that promises the visualization of electronic, atomic and molecular dynamics on atomic time and length scales. A largely unexplored area of ultrafast X-ray science is the use of light to control how X-rays interact with matter. To extend control concepts established for long-wavelength probes to the X-ray regime, the optical control field must drive a coherent electronic response on a timescale comparable to femtosecond core-hole lifetimes. An intense field is required to achieve this rapid response.

Here, an intense optical control pulse is observed to efficiently modulate photoelectric absorption for X-rays and to create an ultrafast transparency window. We demonstrate an application of X-ray transparency relevant to ultrafast X-ray sources: an all-photonic temporal cross-correlation measurement of a femtosecond X-ray pulse. The ability to control X-ray– matter interactions with light will create new opportunities for present and next-generation X- ray light sources.

Nature

Alyssa A. Goodman, Erik W. Rosolowsky, Michelle A. Borkin,Jonathan B. Foster, Michael Halle, Jens Kauffmann & Jaime E. Pineda

A role for self-gravity at multiple length scales in the process of star formation

Self-gravity plays a decisive role in the final stages of star formation, where dense cores (size approx0.1 parsecs) inside molecular clouds collapse to form star-plus-disk systems. But self- gravity's role at earlier times (and on larger length scales, such as approx1 parsec) is unclear; some molecular cloud simulations that do not include self-gravity suggest that 'turbulent fragmentation' alone is sufficient to create a mass distribution of dense cores that resembles, and sets, the stellar initial mass function. Here we report a 'dendrogram' (hierarchical tree- diagram) analysis that reveals that self-gravity plays a significant role over the full range of possible scales traced by 13CO observations in the L1448 molecular cloud, but not everywhere in the observed region. In particular, more than 90 per cent of the compact 'pre-stellar cores' traced by peaks of dust emission are projected on the sky within one of the dendrogram's self- gravitating 'leaves'. As these peaks mark the locations of already-forming stars, or of those probably about to form, a self-gravitating cocoon seems a critical condition for their existence. Turbulent fragmentation simulations without self-gravity—even of unmagnetized isothermal material—can yield mass and velocity power spectra very similar to what is observed in clouds like L1448. But a dendrogram of such a simulation4 shows that nearly all the gas in it (much more than in the observations) appears to be self-gravitating. A potentially significant role for gravity in 'non-self-gravitating' simulations suggests inconsistency in simulation assumptions and output, and that it is necessary to include self-gravity in any realistic simulation of the star- formation process on subparsec scales.

PALEOCEANOGRAPHY

Tessa M. Hill, Michele LaVigne, Howard J. Spero,Thomas P. Guilderson, Brian Gaylord

Variations in seawater Sr/Ca recorded in deep-sea bamboo corals

A depth transect of deep-sea bamboo corals along the California margin provides evidence that coral strontium to calcium ratios (Sr/Cacoral) record seawater Sr/Ca ratios (Sr/Casw). A calibration was constructed utilizing Sr/Cacoral ratios and previously published Pacific Sr/Casw data (R2 = 0.53, n=12, p<0.01): Sr/Cacoral (mmol/mol) = 4.62*Sr/Casw (mmol/mol) - 36.64 Sr/Casw is ultimately governed by the remineralization of Sr-containing shells of surface water- derived marine organisms (e.g., Acantharia) at intermediate water depths. California margin Sr/Cacoral records from 792 and 1295 m document fluctuations in Sr/Casw that appear decadal-scale. These results suggest that Sr/Casw may not be as stable as previously assumed, and may be influenced by surface productivity on short timescales.

Journal of Mathematical Physics

Sandra Irani

Ground State Entanglement in One Dimensional Translationally Invariant Quantum Systems

We examine whether it is possible for one-dimensional translationally-invariant Hamiltonians to have ground states with a high degree of entanglement. We present a family of translationally invariant Hamiltonians {H_n} for the infinite chain. The spectral gap of H_n is Omega(1/poly(n)). Moreover, for any state in the ground space of H_n and any m, there are regions of size m with entanglement entropy Omega(min{m,n}). A similar construction yields translationally-invariant Hamiltonians for finite chains that have unique ground states exhibiting high entanglement.

The area law proven by Hastings gives a constant upper bound on the entanglement entropy for 1D ground states that is independent of the size of the region but exponentially dependent on 1/Delta, where Delta is the spectral gap. This paper provides a lower bound, showing a family of Hamiltonians for which the entanglement entropy scales polynomially with 1/Delta. Previously, the best known such bound was logarithmic in 1/Delta.

Paleobiology

James W. Valentine

Two genomic paths to the evolution of complexity in bodyplans

Morphologically complex metazoans appear abruptly during the Cambrian explosion. Suggested measures of metazoan complexity include number of cell morphotypes and aspects of the genome such as the amount of DNA, the number of genes, and the information content of the genome or egg. Estimates of gene numbers are now available for metazoan species belonging to five different phyla or subphyla. There is little correlation between gene number and morphological complexity in the invertebrates: relatively complex forms can have fewer genes than relatively simple forms. Presumably, the more complex forms use more gene-expression events during development, implying that, on average, cis-regulatory elements of more complex invertebrates are richer in binding sites than are those of simpler forms. Vertebrates have many more genes than invertebrates and therefore have more total gene-expression events during development, although they may have, on average, fewer expression events per gene than the invertebrates. There are thus two genomic pathways in the evolution of metazoan complexity: one involves increasing the number of genes, the other involves increasing the number of cis-regulatory binding sites. Both modes were associated with the origin of bodyplans that first appear as fossils during the Cambrian explosion.

Plant Physiology

Joseph K. E. Ortega

Plant Cell Growth in Tissue

Cell walls are part of the apoplasm pathway that transports water, solutes, and nutrients to cells within plant tissue. Pressures within the apoplasm (cell walls and xylem) are often different from atmospheric pressure during expansive growth of plant cells in tissue. The previously established Augmented Growth Equations are modified to evaluate the turgor pressure, water uptake, and expansive growth of plant cells in tissue when pressures within the apoplasm are lower and higher than atmospheric pressure. Analyses indicate that a step-down and step-up in pressure within the apoplasm will cause an exponential decrease and increase in turgor pressure, respectively, and the rates of water uptake and expansive growth each undergo a rapid decrease and increase, respectively, followed by an exponential return to their initial magnitude. Other analyses indicate that pressure within the apoplasm decreases exponentially to a lower value after a step-down in turgor pressure, which simulates its behavior after an increase in expansive growth rate. Also, analyses indicate that the turgor pressure decays exponentially to a constant value that is the sum of the critical turgor pressure and pressure within the apoplasm during stress relaxation experiments in which pressures within the apoplasm are not atmospheric pressure. Additional analyses indicate that when the turgor pressure is constant (clamped), a decrease in pressure within the apoplasm elicits an increase in elastic expansion followed by an increase in irreversible expansion rate. Some analytical results are supported by prior experimental research, and other analytical results can be verified with existing experimental methods.

The Arrows of Time

Katherine Freese, Matthew G. Brown

The Phantom Bounce: A New Proposal for an Oscillating Cosmology

An oscillating universe cycles through a series of expansions and contractions. We propose a model in which “phantom” energy with a supernegative pressure (p < −) grows rapidly and dominates the late-time expanding phase. The universe’s energy density is so large that the effects of quantum gravity are important at both the beginning and the end of each expansion (or contraction). The bounce can be caused by high energy modifications to the Friedmann equation, which make the cosmology nonsingular. The classic black hole overproduction of oscillating universes is resolved due to their destruction by the phantom energy.

International Journal of Engineering Science

Stephen M. Klisch

A mixture of elastic materials with different constituent temperatures and internal constraints

A novel treatment of the 2nd Law of Thermodynamics and the development of general thermomechanical constraints are introduced for a mixture of two elastic materials in which the constituents may have different temperatures. First, a homothermal quasi-static process at a common mixture temperature is introduced. Part I of the 2nd Law of Thermodynamics is invoked to assert that the Clausius integrals are path-independent, which leads to a prescription, or an identification, of the partial entropy functions. Then, two assumptions are introduced that establish the values of the partial entropy functions for general processes, including those for which the constituent temperatures are not equal. Constitutive restrictions are derived for path-independent processes from the mixture energy equation, and further constitutive restrictions are derived for general processes upon invoking the Clausius–Duhem inequality as a statement of Part II of the 2nd Law of Thermodynamics. The complete set of constitutive restrictions are then shown to equal those derived by other authors, a result which supports the adopted assumptions concerning the partial entropy functions for general processes. Then, an internal constraint involving the deformation gradient tensors and the constituent temperatures is represented by a constraint manifold, and an internally constrained mixture of elastic materials is associated with each unique equivalence class of unconstrained mixtures. The examples of a mixture constrained to have a common temperature and a mixture constrained by temperature-dependent intrinsic compressibility are discussed.

Advances in Neural InformationProcessing Systems 24 (NIPS 2011)

Tianshi Gao & Daphne Koller

Active Classification based on Value of Classifier

Modern classification tasks usually involve many class labels and can be informed by a broad range of features. Many of these tasks are tackled by constructing a set of classifiers, which are then applied at test time and then pieced together in a fixed procedure determined in advance or at training time. We present an active classification process at the test time, where each classifier in a large ensemble is viewed as a potential observation that might inform our classification process. Observations are then selected dynamically based on previous observations, using a value-theoretic computation that balances an estimate of the expected classification gain from each observation as well as its computational cost. The expected classification gain is computed using a probabilistic model that uses the outcome from previous observations. This active classification process is applied at test time for each individual test instance, resulting in an efficient instance-specific decision path. We demonstrate the benefit of the active scheme on various real-world datasets, and show that it can achieve comparable or even higher classification accuracy at a fraction of the computational costs of traditional methods.

American Journal of Botany

Susan C. Lambrecht, Louis S. Santiago, Caroline M. DeVan,J. Carlos Cervera, Cara M. Stripe, Lee A. Buckingham, & Sarah C. Pasquini

PLANT WATER STATUS AND HYDRAULIC CONDUCTANCE DURING FLOWERING IN THE SOUTHERN CALIFORNIA COASTAL SAGE SHRUB SALVIA MELLIFERA (LAMIACEAE)

Premise of the Study: Plant water status during flowering is important for plant reproduction, but the physiology of floral water use is not well understood. We investigated plant water status in relation to leaf and floral physiology in naturally occurring individuals of a semiarid shrub, Salvia mellifera E. Greene.

Methods: We measured stomatal (gs) and corolla (gc) conductance to water vapor, transpiration from leaves (Eleaf) and corollas (Ecorolla), leaf-specific hydraulic conductance (KH), bulk shoot water potential (Ψshoot), and shoot water content on irrigated and control plants to analyze whether water was limiting to leaf and floral water use.

Key Results: Experimental irrigation caused a 203% increase in soil moisture content, a 20% increase in predawn Ψshoot, a 29% increase in midday Ψshoot and a 92% increase in KH . Floral and leaf gas exchange did not respond significantly to water addition, indicating that rates were at seasonal maxima and not limited by water availability. Total daily water use by corollas was ~20% of total shoot water use. There were no significant differences in total daily shoot water use with water addition. Mean shoot water content (5.09 g) was close to mean daily shoot water use (6.71 g), indicating that the equivalent of total shoot water content turned over every .76 d.

Conclusions: These results demonstrate that although irrigation improved whole-plant hydraulic conductance, gas exchange was not limited by water availability. Additionally, the high water use of flowers in this species might limit future flowering and reproductive success during dry years.

Nucleic Acids Research

Mark J. Lawson & Liqing Zhang

Sexy gene conversions: locating gene conversions on the X-chromosome

Gene conversion can have a profound impact on both the short- and long-term evolution of genes and genomes. Here, we examined the gene families that are located on the X- chromosomes of human (Homo sapiens), chimpanzee (Pan troglodytes), mouse (Mus musculus) and rat (Rattus norvegicus) for evidence of gene conversion. We identified seven gene families (WD repeat protein family, Ferritin Heavy Chain family, RAS-related Protein RAB-40 family, Diphosphoinositol polyphosphate phosphohydrolase family, Transcription Elongation Factor A family, LDOC1-related family, Zinc Finger Protein ZIC, and GLI family) that show evidence of gene conversion. Through phylogenetic analyses and synteny evidence, we show that gene conversion has played an important role in the evolution of these gene families and that gene conversion has occurred independently in both primates and rodents. Comparing the results with those of two gene conversion prediction programs (GENECONV and Partimatrix), we found that both GENECONV and Partimatrix have very high false negative rates (i.e. failed to predict gene conversions), which leads to many undetected gene conversions. The combination of phylogenetic analyses with physical synteny evidence exhibits high resolution in the detection of gene conversions.

Annual Review of Physical Chemistry

Ka Yee C. Lee

Collapse Mechanisms of Langmuir Monolayers

When a two-dimensional (2D) film is compressed to its stability limit, it explores the third dimension via collapse. Understanding this 2D-to-3D transition is of great importance as it provides insight into the origin of defects in thin films. This review draws attention to a reversible folding collapse first discovered in model lung surfactant systems and explores the driving forces for this mechanism. The mode of collapse can be tuned by varying the mechanical properties of the film. I present a continuum elastic theory that captures the onset of the observed folding instability and use digital image analysis to analyze the folding dynamics. This article further explores factors that determine the maximum surface pressure a mixed monolayer can sustain and explains the observed phenomenon using the principle of rigidity percolation. The folding transition observed in lipid monolayers described here has also been observed in other systems, including monolayers of nanoparticles.

Earth and Planetary Science Letters

Mary L. Leech

Does the Karakoram fault interrupt mid-crustal channel flow in the western Himalaya?

Variations in the volume and age of Miocene granites and in mid-crustal conductance from the northwest Himalaya to southeastern Tibet imply lateral differences in late orogenic processes. The change from west to east occurs near the Gurla Mandhata dome, where the Karakoram fault terminates and merges with the Indus–Yarlung suture zone. The ‘channel flow’ model, developed in southeastern Tibet, predicts that anatectic partial melts beneath the Tibetan plateau are gravitationally-driven south to a topographic erosional front and are exposed as leucogranites in the Greater Himalaya Sequence; upwellings of these channel granites occur as gneiss domes in the Tethyan Himalaya Sequence. Published magnetotelluric profiles show high conductivity 30–40 km deep beneath Tibet from c. 400 km north of the Main Frontal thrust south across the suture zone, beneath the Himalayan gneiss domes, and to the topographic front; this conductive middle crust corresponds to 2–4% partial melt in the northwest Himalaya and 5–12% melt in southeastern Tibet, sufficient in the latter case to weaken rock for flow. East of the Karakoram termination leucogranites are abundant and are as young as 7 Ma; west of the termination, channel granites are less abundant and no younger than 18 Ma. Middle Miocene (16–14 Ma) leucogranites are found in the Karakoram fault zone located north of the suture zone and south of the proposed anatectic melt source. The initiation of motion on the crustal-penetrating Karakoram fault at 25–21 Ma may have created a barrier to the southward flow of mid-crustal melts and acted as a vertical conduit for these same melts.

Physics of the Earth and Planetary Interiors

Höink, Tobias; Lenardic, Adrian; Jellinek, A. Mark

Earth's thermal evolution with multiple convection modes: A Monte-Carlo approach

We present a thermal evolution model, based on the results of recent numerical simulations, in which we consider that different sized oceanic plates are associated with different modes of surface motion (mobile-lid and sluggish-lid tectonics). These different modes are, in turn, associated with different heat loss scalings. Varying initial conditions and system parameters systematically we run several thousand thermal models that we compare with constraints on present-day mantle temperature, present-day Urey ratio and overall minimum core heat flow. The dual heat loss mode approach readily satisfies the Urey ratio constraint that is unexplained by classic thermal evolution models.

Proceedings of the National Academyof Sciences of the United States of America

Lewis AL, Desa N, Hansen EE, Knirel YA, Gordon JI, Gagneux P, Nizet V, Varki A.

Innovations in host and microbial sialic acid biosynthesis revealed by phylogenomic prediction of nonulosonic acid structure.

Sialic acids (Sias) are nonulosonic acid (NulO) sugars prominently displayed on vertebrate cells and occasionally mimicked by bacterial pathogens using homologous biosynthetic pathways. It has been suggested that Sias were an animal innovation and later emerged in pathogens by convergent evolution or horizontal gene transfer. To better illuminate the evolutionary processes underlying the phenomenon of Sia molecular mimicry, we performed phylogenomic analyses of biosynthetic pathways for Sias and related higher sugars derived from 5,7-diamino- 3,5,7,9-tetradeoxynon-2-ulosonic acids. Examination of approximately 1,000 sequenced microbial genomes indicated that such biosynthetic pathways are far more widely distributed than previously realized. Phylogenetic analysis, validated by targeted biochemistry, was used to predict NulO types (i.e., neuraminic, legionaminic, or pseudaminic acids) expressed by various organisms. This approach uncovered previously unreported occurrences of Sia pathways in pathogenic and symbiotic bacteria and identified at least one instance in which a human archaeal symbiont tentatively reported to express Sias in fact expressed the related pseudaminic acid structure. Evaluation of targeted phylogenies and protein domain organization revealed that the "unique" Sia biosynthetic pathway of animals was instead a much more ancient innovation. Pathway phylogenies suggest that bacterial pathogens may have acquired Sia expression via adaptation of pathways for legionaminic acid biosynthesis, one of at least 3 evolutionary paths for de novo Sia synthesis. Together, these data indicate that some of the long-standing paradigms in Sia biology should be reconsidered in a wider evolutionary context of the extended family of NulO sugars.

Symmetry, Integrability and Geometry:Methods and Applications (SIGMA)

Debra Lewis

Relative Critical Points

Relative equilibria of Lagrangian and Hamiltonian systems with symmetry are critical points of appropriate scalar functions parametrized by the Lie algebra (or its dual) of the symmetry group. Setting aside the structures – symplectic, Poisson, or variational – generating dynamical systems from such functions highlights the common features of their construction and analysis, and supports the construction of analogous functions in non-Hamiltonian settings. If the symmetry group is nonabelian, the functions are invariant only with respect to the isotropy subgroup of the given parameter value. Replacing the parametrized family of functions with a single function on the product manifold and extending the action using the (co)adjoint action on the algebra or its dual yields a fully invariant function. An invariant map can be used to reverse the usual perspective: rather than selecting a parametrized family of functions and finding their critical points, conditions under which functions will be critical on specific orbits, typically distinguished by isotropy class, can be derived. This strategy is illustrated using several well-known mechanical systems – the Lagrange top, the double spherical pendulum, the free rigid body, and the Riemann ellipsoids – and generalizations of these systems.

Physical Review Letters

Lisa Randall & Matthew Reece

Dark Matter as a Trigger for Periodic Comet Impacts

Although statistical evidence is not overwhelming, possible support for an approximately 35×106 yr periodicity in the crater record on Earth could indicate a nonrandom underlying enhancement of meteorite impacts at regular intervals. A proposed explanation in terms of tidal effects on Oort cloud comet perturbations as the Solar System passes through the galactic midplane is hampered by lack of an underlying cause for sufficiently enhanced gravitational effects over a sufficiently short time interval and by the time frame between such possible enhancements. We show that a smooth dark disk in the galactic midplane would address both these issues and create a periodic enhancement of the sort that has potentially been observed. Such a disk is motivated by a novel dark matter component with dissipative cooling that we considered in earlier work. We show how to evaluate the statistical evidence for periodicity by input of appropriate measured priors from the galactic model, justifying or ruling out periodic cratering with more confidence than by evaluating the data without an underlying model. We find that, marginalizing over astrophysical uncertainties, the likelihood ratio for such a model relative to one with a constant cratering rate is 3.0, which moderately favors the dark disk model. Our analysis furthermore yields a posterior distribution that, based on current crater data, singles out a dark matter disk surface density of approximately 10M /pc2. The geological record thereby motivates a particular model of dark matter that ⊙will be probed in the near future.

Nature

R. C. Liu, B. Odom, Y. Yamamoto & S. Tarucha

Quantum interference in electron collision

The indistinguishability of identical quantum particles can lead to quantum interferences that profoundly affect their scattering. If two particles collide and scatter, the process that results in the detection of the first particle in one direction and the second particle in another direction interferes quantum mechanically with the physically indistinguishable process where the roles of the particles are reversed. For bosons such as photons, a constructive interference between probability amplitudes can enhance the probability, relative to classical expectations, that both are detected in the same direction — this is known as 'bunching'. But for fermions such as electrons, a destructive interference should suppress this probability ('anti-bunching'); this interference is the origin of the Pauli exclusion principle, which states that two electrons can never occupy the same state. Although two-particle interferences have been shown for colliding photons, no similar demonstration for electrons exists. Here we report the realization of this destructive quantum interference in the collision of electrons at a beam splitter. In our experiments, the quantum interference responsible for the Pauli exclusion principle is manifest as the suppression in electron current noise after collision.

Hawaii Medical Journal

Malcolm Schinstine

A brief description of the Bethesda System for reporting thyroid fine needle aspirates.

Fine needle aspiration has become the most prominent, and the easiest way, to morphologically evaluate lesions of the thyroid. When done correctly, the sensitivity and specificity of thyroid aspirates for detecting malignancy is very high. Unfortunately, clinicians are sometimes confused by the terminology used in thyroid cytopathology reports. One way to mitigate confusion is for all pathologists to use the same diagnostic criteria and terminology.

Standardized terminology for thyroid cytopathology reports has recently been proposed. The following article introduces the concept of the Bethesda System for reporting thyroid aspirates. Sample diagnoses are given to illustrate how thyroid cytopathology reports may appear using the Bethesda System.

International Journal of Remote Sensing

H.S. Butterfield; C.M. Malmström

The effects of phenology on indirect measures of aboveground biomass in annual grasses

Remote sensing is increasingly being used to quantify vegetation biomass across large areas, often with algorithms based on calibrated relationships between biomass and indices such as the normalized difference vegetation index (NDVI). To improve capacity to evaluate grassland dynamics over time, we examined the influence of phenological changes on NDVI-biomass relationships in annual grasses. Our findings support the use of NDVI throughout early growth and the beginning stages of canopy maturation, but suggest caution for later stages. In contrast, measurements of fractional photosynthetically active radiation (fAPAR) absorbed by the canopy and leaf area index (LAI) served as good season-long surrogates for canopy biomass. Canopies reached maximum biomass approximately 40 days after maximum greenness, with biomass increasing by approximately 20% during senescence. For multi-year studies of management impact (i) avoid using seasonal comparisons from dates much after the point of maximum greenness or (ii) consider non-NDVI-based approaches.

Nature

Todd Martinez

Physical chemistry: Seaming is believing

Do excited molecules relaxing to their ground state pass through a 'seam' connecting the potential energy profiles of the states? Experimental data suggest the answer to this long- standing question is 'yes'.

Journal of Applied Physics (2009)

Martinez-Miranda, L.J. & Kurihara, L.K.

Interaction and response of a smectic-A liquid crystal to a nanometer particle: Phase transition due to the combined effect of the functionalization compound and particle size.

The interaction of nanometer particles with organic materials is important because of their increased use in many applications and their potential use in biosystems. We found that liquid crystals respond to nanometer particles differently depending on the surface functionalization of the nanoparticles using x rays and developed a phenomenological model to explain the differences that we observed. We found from the analysis of the peaks close to 0.199 Å−1 that the inverse integrated intensity serves as a measure of how well the liquid crystal has reoriented and compared the graph obtained from the phenomenological theory to the graph obtained with the inverse integrated intensity. An analysis of the widths of these peaks (inverse correlation length) shows that the reorientation under the magnetic field can lead to a phase transition of the portion of the liquid crystal that is reorienting.

Elements

Mary Reid

How long does it take to supersize and, eruption?

Along-recognized correlation between the volume of major eruptions and the time interval between them suggests that magma may accumulate for about a million years before a supereruption. However, radiometric ages and time-dependent phenomena like crystal growth and compositional homogenization show that the duration of supervolcano magma accumulation could be significantly shorter than this. Crystals in supervolcano magmas may have protracted growth histories and may grow from chemically different hosts as crystallization progresses. Semisolid crystal mushes rather than liquid-rich magma chambers may be the prevalent state of supervolcano feeder systems and should be the focus of geophysical studies aimed at predicting future supereruptions.

Journal of Latin American Geography

McAfee, Kathleen

CORN CULTURE AND DANGEROUS DNA: Real and Imagined Consequences of Maize Transgene Flow in Oaxaca

"Genetic pollution" in Oaxaca has become Exhibit A for critics of crop genetic engineering and the focus of angry charges and counterclaims by biotechnology researchers. Like many disputes about science and technology, this one is linked to economic and resource-control conflicts. To understand why this controversy is so intense, we need to locate the scientific findings and claims about crop gene flow within the broader frame of international agro-food restructuring and its consequences for agrarian communities. The dispute over maize transgene flow in Mexico has unfolded in the context of U.S. and "life industry" agendas for trade liberalization and worldwide expansion of intellectual property rights. Equally germane is the cultural and economic significance of corn and of small-scale farming in Mexico, where rural livelihoods have been hard hid by neoliberal reforms. Whether or not the contested report in Nature (November 2001) stands up to scientific scrutiny, it is probable that the introgression into Mexican local maize varieties of Bt transgene constructs from genetically engineered U.S. corn has occurred, despite Mexico's ban on GE grain planting. The possible risks posed by traveling transgenes are not well understood, but there are plausible scientific reasons for concern about possible hazards to agricultural biodiversity and agro-ecosystems. More troubling, however, are the likely consequences -for local food security, cultural survival, and national economic sovereignty- of the private ownership of staple-crop genetic resources and of the influence on trade policy, agricultural research, seed and food markets, and farming-system options of a small number of powerful states and transnational firms. Processes at the global level (e.g., in the WTO), regional level (e.g., trade pacts in the Americas) and local level (farmers' successes in agroecology and organizing) suggest that the political space for alternative agendas may be opening. Despite the privatization and narrowed focus of much research funding, genetics, ecology, crop science, and participatory research have much to contribute to widening this space by evaluating sustainable-farming options as well as biotechnology applications.

Proceedings of the National AcademyOf Sciences of the United States of America

Margaret McFall-Ngaia,1, Michael G. Hadfieldb,1, Thomas C. G. Boschc,Hannah V. Careyd, Tomislav Domazet-Lošoe, Angela E. Douglasf,

Nicole Dubilierg, Gerard Eberlh, Tadashi Fukamii, Scott F. Gilbertj,Ute Hentschelk,Nicole Kingl, Staffan Kjellebergm, Andrew H. Knolln, Natacha Kremera,

Sarkis K. Mazmaniano, Jessica L. Metcalfp, Kenneth Nealsonq, Naomi E. Piercer,John F. Rawlss, Ann Reidt, Edward G. Rubya, Mary Rumphou, Jon G. Sandersr,

Diethard Tautzv, & Jennifer J. Wernegreenw

Animals in a bacterial world, a new imperative for the life sciences

In the last two decades, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and diversity. This review examines how a growing knowledge of the vast range of animal–bacterial interactions, whether in shared ecosystems or intimate symbioses, is fundamentally altering our understanding of animal biology. Specifically, we highlight recent technological and intellectual advances that have changed our thinking about five questions: how have bacteria facilitated the origin and evolution of animals; how do animals and bacteria affect each other’s genomes; how does normal animal development depend on bacterial partners; how is homeostasis maintained between animals and their symbionts; and how can ecological approaches deepen our understanding of the multiple levels of animal–bacterial interaction. As answers to these fundamental questions emerge, all biologists will be challenged to broaden their appreciation of these interactions and to include investigations of the relationships between and among bacteria and their animal partners as we seek a better understanding of the natural world.

Nature Geoscience

Stephen J. Mojzsis

Leftover lithosphere

The earliest evolution of our planet is difficult to reconstruct. Ancient rocks in Western Australia show an isotopic signature that links their formation with 4.3-billion-year-old crust.

Environmental Health Journal

Carolina L. Balazs, Rachel Morello-Frosch, Alan E Hubbard & Isha Ray

Environmental justice implications of arsenic contamination in California’s San Joaquin Valley: a cross-sectional, cluster-design examining exposure and compliance in community drinking water systems

Background: Few studies of environmental justice examine inequities in drinking water contamination. Those studies that have done so usually analyze either disparities in exposure/harm or inequitable implementation of environmental policies. The US EPA’s 2001 Revised Arsenic Rule, which tightened the drinking water standard for arsenic from 50 μg/L to 10 μg/L, offers an opportunity to analyze both aspects of environmental justice.

Methods: We hypothesized that Community Water Systems (CWSs) serving a higher proportion of minority residents or residents of lower socioeconomic status (SES) have higher drinking water arsenic levels and higher odds of non-compliance with the revised standard. Using water quality sampling data for arsenic and maximum contaminant level (MCL) violation data for 464 CWSs actively operating from 2005–2007 in California’s San Joaquin Valley we ran bivariate tests and linear regression models.

Results: Higher home ownership rate was associated with lower arsenic levels (ß-coefficient=

−0.27 μg As/L, 95% (CI), -0.5, -0.05). This relationship was stronger in smaller systems (ß-

coefficient= −0.43, CI, -0.84, -0.03). CWSs with higher rates of homeownership had lower odds

of receiving an MCL violation (OR, 0.33; 95% CI, 0.16, 0.67); those serving higher percentages of minorities had higher odds (OR, 2.6; 95% CI, 1.2, 5.4) of an MCL violation.

Conclusions: We found that higher arsenic levels and higher odds of receiving an MCL violation were most common in CWSs serving predominantly socio-economically disadvantaged communities. Our findings suggest that communities with greater proportions of low SES residents not only face disproportionate arsenic exposures, but unequal MCL compliance challenges.

Nature

Margaret M. Murnane & Jianwei Miao

Optics: Ultrafast X-ray photography

A super-fast, lensless microscope has been developed that works by decoding the diffraction patterns of bright, laser-like flashes of X-rays. This advance should enable ultrafast events at the nanoscale to be recorded.

Molecular Cell

Lorena Navarro, Antonius Koller, Roland Nordfelth,Hans Wolf-Watz, Susan Taylor, Jack E. Dixon

Identification of a Molecular Target for the Yersinia Protein Kinase A

Pathogenic bacteria of the genus Yersinia employ a type III secretion system to inject bacterial effector proteins directly into the host cytosol. One of these effectors, the Yersinia serine/threonine protein kinase YpkA, is an essential virulence determinant involved in host actin cytoskeletal rearrangements and in inhibition of phagocytosis. Here we report that YpkA inhibits multiple Gαq signaling pathways. The kinase activity of YpkA is required for Gαq inhibition. YpkA phosphorylates Ser47, a key residue located in the highly conserved diphosphate binding loop of the GTPase fold of Gαq. YpkA-mediated phosphorylation of Ser47 impairs guanine nucleotide binding by Gαq. Y. pseudotuberculosis expressing wild-type YpkA, but not a catalytically inactive YpkA mutant, interferes with Gαq-mediated signaling pathways. Identification of a YpkA-mediated phosphorylation site in Gαq sheds light on the contribution of the kinase activity of YpkA to Yersinia pathogenesis.

Entomology

Jiménez-Martínez, E.S. & N.A. Bosque-Pérez

Life history of the bird cherry-oat aphid, Rhopalosiphum padi on transgenic and non- transformed wheat challenged with Wheat streak mosaic virus

The life history of the bird cherry-oat aphid, Rhopalosiphum padi (L.) (Hemiptera: Aphididae), was studied via laboratory assays on Wheat streak mosaic virus (WSMV)-infected and non- infected transgenic and non-transformed wheat [Triticum aestivum L. (Poaceae)]. Although R. padi is not a WSMV vector, it is known to colonize WSMV-infected wheat plants. Two transgenic soft white winter wheat genotypes, 366-D03 and 366-D8, that express the WSMV coat protein gene, and the WSMV-susceptible non-transformed cultivar Daws were tested. All genotypes showed disease symptoms when infected with WSMV. Whereas plant height was significantly reduced on virus-infected compared to non-infected plants of all genotypes, virus- infected transgenic plants exhibited lower virus titer and lower disease rating scores than Daws. No significant effects of WSMV infection or genotypes were observed on the length of R. padi nymphal development period, nor on their pre-, and post-reproductive periods. Rhopalosiphum padi reproductive period was significantly longer on Daws infected with WSMV than on non- infected plants of this cultivar. In contrast, there were no significant differences in length of R. padi reproductive period between virus-infected and non-infected transgenic plants within a genotype. Rhopalosiphum padi daily fecundity was significantly lower and adult longevity significantly longer on virus-infected than on non-infected plants of all genotypes. Total aphid fecundity and intrinsic rate of increase were not significantly different among treatments. The percentage of winged aphids that developed was greater on WSMV-infected compared to non- infected plants within a genotype. Results indicate that both virus infection status of plants and wheat genotype influence the life history of R. padi.

Journal of Algebra

Zajj Daugherty & Rosa Orellana

THE QUASI-PARTITION ALGEBRA

We introduce the quasi-partition algebra QPk(n) as a centralizer algebra of the symmetric group. This algebra is a subalgebra of the partition algebra and inherits many similar combinatorial properties. We construct a basis for QPk(n), give a formula for its dimension in terms of the Bell numbers, and describe a set of generators for QPk(n) as a complex algebra. In addition, we give the dimensions and indexing set of its irreducible representations. We also provide the Bratteli diagram for the tower of quasi-partition algebras (constructed by letting k range over the positive integers).

Marine Mammal Science

Rudy M. Ortiz*, Brett Long, Dave Casper,C. Leo Ortiz & Terrie M. Williams

Biochemical and hormonal changes during acute fasting and re-feeding in bottlenose dolphins (Tursiops truncatus)

Interrupted feeding patterns may be the consequence of changes in resource avail-ability, long distance travel, or migration in many species of cetaceans. In addition to these natural fasting events, marked global depletion of fisheries (Myers and Worm 2003) could also affect natural feeding schedules of wild cetaceans. In contrast to many studies on pinnipeds (Ortiz et al. 1978, 2001a, b; Crocker et al. 1998; Guinet et al. 2004; Champagne et al. 2005), the physiological effects of fasting events in cetaceans have not been well described. In mammals, food deprivation is associated with various phases of metabolic substrate utilization depending on the length of the perturbation. Early periods (minutes to hours) of the cessation of eating are associated with increased glucose metabolism, which may lead to an acute period of hypoglycemia. The next phase (hours to days) of fasting is characterized by increased lipid metabolism, which is important for sparing lean tissue, or protein. This phase of starvation is characterized by increased non-esterified fatty acids (NEFAs) and a decrease in blood urea nitrogen (BUN), which reflects a reduction in lean tissue catabolism (Goodman et al. 1980, Lowell and Goodman 1987, Ortiz et al. 2003b). If the period of food deprivation is extensive (weeks) and fat depots are increasingly diminished, food deprivation promotes phase III of starvation that is characterized by increased lean tissue catabolism (Cahill 1976, Goodman et al. 1980, Lowell and Goodman 1987, Cherel et al. 1988).

LANGMUIR

Hellman KM, Mason P (2012)

Dynamics of a Disturbed Sessile Drop Measured by Atomic Force Microscopy

A new method for studying the dynamics of a sessile drop by atomic force microscopy (AFM) is demonstrated. A hydrophobic microsphere (radius, r similar to 20-30 mu m) is brought into contact with a small sessile water drop resting on a polytetrafluoroethylene (PTFE) surface.

When the microsphere touches the liquid surface, the meniscus rises onto it because of capillary forces. Although the microsphere volume is 6 orders of magnitude smaller than the drop, it excites the normal resonance modes of the liquid interface. The sphere is pinned at the interface, whose small (<100 nm) oscillations are readily measured with AFM. Resonance oscillation frequencies were measured for drop volumes between 5 and 200 mu L. The results for the two lowest normal modes are quantitatively consistent with continuum calculations for the natural frequency of hemispherical drops with no adjustable parameters. The method may enable sensitive measurements of volume, surface tension, and viscosity of small drops.

Journal of Experimental Biology

Marjorie L Patrick, Karlygash Aimanova, Heather R. Sanders, & Sarjeet S. Gill

P-type Na+/K+-ATPase and V-type H+-ATPase expression patterns in the osmoregulatory organs of larval and adult mosquito Aedes aegypti

This study describes the expression patterns of P-type Na(+)/K(+)-ATPase and V-type H(+)- ATPase in the larval and adult forms of the mosquito Aedes aegypti and provides insight into their relative importance in ion transport function of key osmoregulatory organs. RT-PCR assays indicate that, at the level of the gene, both ATPases are expressed in all of the osmoregulatory tissues of larvae (midgut, Malpighian tubules, rectum and anal papillae) and adults (stomach, Malpighian tubules, anterior hindgut and rectum). Immunohistochemical studies determined that both ATPases are present in high levels in all the relevant organs, with the exception of the larval rectum (P-type Na(+)/K(+)-ATPase only). In larval gastric caeca, ATPase location corresponds to the secretory (basal P-type Na(+)/K(+)-ATPase, apical V-type H(+)-ATPase) and ion-transporting (V-type H(+)-ATPase on both membranes) regions as previously described. The two ATPases switch membrane location along the length of the larval midgut, indicating three possible regionalizations, whereas the adult stomach has uniform expression of basolateral P- type Na(+)/K(+)-ATPase and apical V-type H(+)-ATPase in each cell. In both larval and adult Malpighian tubules, the distal principal cells exhibit high expression levels of V-type H(+)- ATPase (apically and cytoplasmically) whereas P-type Na(+)/K(+)-ATPase is highly expressed in stellate cells found only in the distal two-thirds of each tubule. By contrast, the proximal principal cells express both P-type Na(+)/K(+)-ATPase (basal) and V-type H(+)-ATPase (apical).

These results suggest a functional segregation along the length of the Malpighian tubules based on cell type and region. P-type Na(+)/K(+)-ATPase is the only pump apparent in the larval rectum whereas in the larval anal papillae and the adult hindgut (including the anterior hindgut and rectum with rectal pads), P-type Na(+)/K(+)-ATPase and V-type H(+)-ATPase localize to the basal and apical membranes, respectively. We discuss our findings in light of previous physiological and morphological studies and re-examine our current models of ion transport in these two developmental stages of mosquitoes that cope with disparate osmoregulatory challenges.

The Journal of Neuroscience

Hellman K.M., Mason P. (2012)

Opioids disrupt pro-nociceptive modulation mediated by raphe magnus.

In anesthetized rats, opioid analgesia is accompanied by a specific pattern of tonic activity in two neuronal populations within the medullary raphe magnus (RM): opioids silence pain- facilitatory ON cells and produce sustained discharge in pain-inhibitory OFF cells. These tonic activity patterns, hypothesized to generate a tonic analgesic state, have not been observed in recordings made without anesthesia. Therefore, we recorded ON and OFF cell activity before and after an analgesic dose of morphine in unanesthetized mice. The tonic activity of ON and OFF cells was unchanged by morphine. Rather, morphine suppressed the phasic ON cell excitation and OFF cell inhibition evoked by noxious stimulation. Before morphine, the magnitude of the noxious stimulus-evoked burst in ON cells correlated with motor withdrawal magnitude, suggesting that ON cells facilitate nocifensive motor reactions. Contrary to model prediction, OFF cell activity was greater before stimulus trials that evoked withdrawals than those without withdrawals. Since withdrawals only occurred when OFF cell activity was suppressed, a decrease in OFF cell activity appears to serve as a pro-nociceptive signal that synchronizes and therefore strengthens the ensuing motor reaction. We further propose that morphine acts in RM to suppress ON and OFF cell phasic responses and thereby disable RM's pro-nociceptive output. Thus, RM cells produce antinociception by failing to exert the pro- nociceptive effects normally engaged by noxious stimulation. These findings revise the conventional understanding of supraspinal opioid analgesia and demonstrate that RM produces on demand rather than state modulation, allowing RM cells to serve other functions during pain-free periods.

SIAM:Society for Industrial and Applied Mathematics

Toniann Pitassi & Nathan Segerlind

EXPONENTIAL LOWER BOUNDS AND INTEGRALITY GAPS FOR TREE-LIKE LOVASZ–SCHRIJVER PROCEDURES ´

The matrix cuts of Lov´asz and Schrijver are methods for tightening linear relaxations of zero- one programs by the addition of new linear inequalities. We address the question of how many new inequalities are necessary to approximate certain combinatorial problems, and we solve certain instances of Boolean satisfiability. Our first result is a size/rank tradeoff for tree-like Lov´asz– Schrijver refutations, showing that any refutation that has small size also has small rank. This allows us to immediately derive exponential-size lower bounds for tree-like refutations of many unsatisfiable systems of inequalities where, prior to our work, only strong rank bounds were known. Unfortunately, we show that this tradeoff does not hold more generally for derivations of arbitrary inequalities. We give a very simple example showing that derivations can be very small but nonetheless require maximal rank. This rules out a generic argument for obtaining a size-based integrality gap from the corresponding rank-based integrality gap. Our second contribution is to show that a modified argument can often be used to prove size-based integrality gaps from rank-based integrality gaps. We apply this method to prove size-based integrality gaps for several prominent examples where, prior to our work, only rank-based integrality gaps were known. Our third contribution is to prove new separation results. Using our machinery for converting rank-based lower bounds and integrality gaps into size-based lower bounds, we show that tree-like LS+ cannot polynomially simulate tree-like cutting planes, and that tree-like LS+ cannot polynomially simulate resolution.

Journal of Theoretical Probability

Amber L. Puha

A Reversible Nearest Particle System on the Homogeneous Tree

We introduce a modified contact process on the homogeneous tree. The modification is to the death rate: an occupied site becomes vacant at rate one if the number of occupied id neighbors is at most one. This modification leads to a growth model which is reversible, off the empty set, provided the initial set of occupied sites is connected.

Reversibility admits tools for studying the survival properties of the system not available in a nonreversible situation. Four potential phases are considered: extinction, weak survival, strong survival, and complete convergence. The main result of this paper is that there is exactly one phase transition on the binary tree. Furthermore, the value of the birth parameter at which the phase transition occurs is explicitly computed In particulars survival and complete convergence hold if the birth parameter exceeds 1/4. Otherwise, the expected extinction time is finite.

Journal of Medical Genetics

Garcia-Bertrand R., Simms T.M., Cadenas A.M., Herrera R.J.

United Arab Emirates: Phylogenetic relationships and ancestral populations.

In the current report, 109 unrelated individuals from the United Arab Emirates (UAE) were typed across 15 autosomal short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D149S433, vWA, TPOX, D18S51, D5S818 and FGA) routinely employed in population genetics analyses and compared across a set of ethnically and geographically targeted reference collections. UAE, located at the southeastern most portion of the Arabian Peninsula, in the tri-continental crossroads connecting Africa, Europe and Asia, has been influenced by a number of human dispersal waves from a plethora of sources including the Paleolithic "Out of Africa" migrations, the exodus of Neolithic pastoral agriculturalists from the Fertile Crescent and Northern Africa, as well as more recent migrations from Asia and the Middle East. We found that despite the high levels of consanguinity that characterize UAE, this population is genetically highly heterogeneous. When compared to various world-wide biogeographical regions, the Arabian Peninsula exhibits the highest intra- population variance. Admixture analyses indicate that UAE and Bahrain uniquely in Arabia share 23.7% and 22.9%, respectively, of their DNA with Southwest Asian populations. Similar and complex Structure profiles are seen among Arabian Peninsula populations underscoring the high genetic diversity of the region. Although UAE shares a number of genetic characteristics in common with the rest of the populations in the Arabian Peninsula, it is unique in terms of its relative high Asian genetic component, likely the result of geographical proximity to Southwest Asia, west-bound waves of migration and socio-political ties with territories to the east.

The Journal of Physical Chemistry B

Robin L. Blumberg Selinger, Andrew Konya,Alex Travesset, Jonathan V. Selinger

Monte Carlo studies of the XY model on two-dimensional curved surfaces

To explore the interaction between topological defects and curvature in materials with orientational order, we perform Monte Carlo studies of the two-dimensional XY model on the surface of curved substrates. Each curved surface is patterned with a random lattice constructed via random sequential absorption, and an XY spin is positioned at each lattice site. Spins lie in the plane locally tangent to the surface and interact with neighbors defined via a distance cutoff. We demonstrate that the relative phase associated with vortices is significant in curved geometries and plays a role in microstructural evolution. We also observe that any nonuniform curvature, e.g., on the surface of a torus, induces spontaneous segregation of positive and negative vortices and promotes the formation of deeply metastable defect microstructures. Though qualitative in nature, these observations provide novel insights into the patterning of topological defects in curved geometries and suggest that the Kosterlitz– Thouless transition may be altered in geometries with nonuniform curvature.

Integrative and Comparative Biology

Serb J.M., Porath-Krause A.J., Pairett A.N.

Uncovering a gene duplication of the photoreceptive protein, opsin, in scallops (Bivalvia: Pectinidae)

Evolutionary biologists have long been interested in how expansions of the photosensory system might contribute to morphological differentiation of animals. Comparative studies in vertebrate and arthropod lineages have provided considerable insight into how the duplication of opsin, the first gene of the phototransduction pathway, have led to functional differentiation and new ecological opportunities; however, this relationship cannot be examined in many invertebrate groups as we have yet to characterize their opsin content. Scallops (Pectinidae) are a promising molluscan model to study the evolution of opsin and its potential role in speciation. Recently, we discovered a second Gq-coupled, or r-, opsin gene expressed in the eyes of two scallop species. To investigate the evolutionary origin of this opsin, we screened 12 bivalve species from 4 families, representing both mobile and sessile species, with and without eyes.

Although only one ortholog was recovered from the genome of the eyeless, immobile oyster, we found both genes to have been retained in 3 families comprising the order Pectinoida.

Within this clade, non-mobile species of scallops appear to have lost one gene. Phylogeny- based tests of selection indicate different degrees of purifying selection following duplication. These data, in conjunction with highly divergent gene sequences and ortholog-specific retention, suggest functional differences. Our results are congruent with a Gq-opsin gene duplication in an oyster-Pectinoida ancestor, approximately 470 Mya, and suggest the likelihood of retaining both genes is associated with either the presence of eyes and/or degree of mobility. The identification of two highly divergent Gq-opsin genes in scallops is valuable for future functional investigations and provides a foundation for further study of a morphologically and ecologically diverse clade of bivalves that has been understudied with respect to visual ecology and diversification of opsin.

Journal of Community Health

Tarleton, Heather; Smith, Lisa; Zhang, Zuo-Feng; Kuo, Tony

Utility of Anthropometric Measures in a Multiethnic Population: Their Association with Prevalent Diabetes, Hypertension and Other Chronic Disease Comorbidities

Body mass index (BMI) and waist circumference (WC) are two common anthropometric measures of obesity in clinical and public health practice. Consensus, however, remains elusive regarding their utility for predicting cardiovascular disease risk in multiethnic populations. We address this gap in the literature by analyzing cross-sectional data from the first round of the Los Angeles County Health and Nutrition Examination Survey, 2011. We characterized the relationships between BMI, WC, waist-to-hip ratios, waist-to-height ratios, and chronic disease extent, as confirmed by the presence of hypertension, diabetes, and/or two or more other chronic conditions as defined by a composite indicator 'comorbidity'. To account for race/ethnicity, age, gender, and cigarette smoking frequency, adjusted odds ratios (aOR) were generated and reported for each of the regression analyses. Whereas being overweight was associated with hypertension alone (aOR 2.10; 95 % CI 1.12-3.94), obesity was associated with hypertension (aOR 5.04; 95 % CI 2.80-9.06) as well as diabetes (aOR 5.28; 95 % CI 2.25-12.3) and comorbidity (aOR 3.69; 95 % CI 2.02-6.77). In whites and African-Americans, BMI and WC were positively related to diabetes, hypertension and comorbidity. In Hispanics, BMI and WC were also positively related to diabetes and comorbidity, but only the former measure was associated with hypertension ( p < 0.050). In Asians, BMI was not a significant predictor of diabetes, hypertension and/or comorbidity. Collectively, the findings suggest that BMI is not universally informative and waist circumference and its derivatives may represent a viable, more racially/ethnically appropriate alternative for use with selected minority groups.

Reviews of Geophysics

Susan Y. Schwartz & Juliana M. Rokosky

Slow slip events and seismic tremor at circum-Pacific subduction zones

[1] It has been known for a long time that slip accompanying earthquakes accounts for only a fraction of plate tectonic displacements. However, only recently has a fuller spectrum of strain release processes, including normal, slow, and silent earthquakes (or slow slip events) and continuous and episodic slip, been observed and generated by numerical simulations of the earthquake cycle. Despite a profusion of observations and modeling studies the physical mechanism of slow slip events remains elusive. The concurrence of seismic tremor with slow slip episodes in Cascadia and southwestern Japan provides insight into the process of slow slip. A perceived similarity between subduction zone and volcanic tremor has led to suggestions that slow slip involves fluid migration on or near the plate interface. Alternatively, evidence is accumulating to support the notion that tremor results from shear failure during slow slip.

Global observations of the location, spatial extent, magnitude, duration, slip rate, and periodicity of these aseismic slip transients indicate significant variation that may be exploited to better understand their generation. Most slow slip events occur just downdip of the seismogenic zone, consistent with rate- and state-dependent frictional modeling that requires unstable to stable transitional properties for slow slip generation. At a few convergent margins the occurrence of slow slip events within the seismogenic zone makes it highly likely that transitions in frictional properties exist there and are the loci of slow slip nucleation. Slow slip events perturb the surrounding stress field and may either increase or relieve stress on a fault, bringing it closer to or farther from earthquake failure, respectively. This paper presents a review of slow slip events and related seismic tremor observed at plate boundaries worldwide, with a focus on circum-Pacific subduction zones. Trends in global observations of slow slip events suggest that (1) slow slip is a common phenomena observed at almost all subduction zones with instrumentation capable of recording it, (2) different frictional properties likely control fast versus slow slip, (3) the depth range of slow slip may be related to the thermal properties of the plate interface, and (4) the equivalent seismic moment of slow slip events is proportional to their duration (Moατ), different from the Moατ3 scaling observed for earthquakes.

Infection and Immunity

Barbour SE1, Ishihara Y, Fakher M, Al-Darmaki S, Caven TH,Shelburne CP, Best AM, Schenkein HA, Tew JG

Monocyte differentiation in localized juvenile periodontitis is skewed toward the dendritic cell phenotype.

Several lines of evidence indicate that the monocytes of subjects with localized juvenile periodontitis (LJP) are functionally distinct from cells of age- and race-matched nonperiodontitis (NP) subjects. Among the abnormalities are the propensity to secrete large amounts of prostaglandin E(2) and the induction of immunoglobulin G2 (IgG2) antibodies. The experiments described here were performed to further characterize the LJP monocytes and to determine if these cells mature differently than NP monocytes. When adherent monocytes from LJP subjects were cultured in the presence of human serum, both macrophages and cells with the morphology of immature monocyte-derived dendritic cells (MDDC) were observed. Within 4 days the prevalence of the immature MDDC was approximately twofold higher in LJP cultures than in NP cultures. In addition to their dendritic morphology, these cells were CD11c(+) and CD14(-) or CD14(low) and stimulated potent autologous mixed leukocyte reactions, consistent with differentiation to the MDDC phenotype. Like LJP monocytes, cultures of MDDC generated with interleukin-4 and granulocyte-macrophage colony-stimulating factor selectively induced IgG2 in cultures of pokeweed mitogen-stimulated NP leukocytes. Together, these data suggest that the monocytes of LJP subjects have a propensity to differentiate into MDDC and that this differentiation may be related to the high levels of IgG2 that are observed in the sera of LJP subjects. As high levels of circulating IgG2 are correlated with less severe disease, the propensity of LJP monocytes to differentiate into MDDC may have important implications for both the host response against oral pathogens and the progression of LJP.

Science

Heiko O. Jacobs, Andrea R. Tao, Alexander Schwartz,David H. Gracias, George M. Whitesides

Fabrication of a Cylindrical Display by Patterned Assembly

We demonstrate the patterned assembly of integrated semiconductor devices onto planar, flexible, and curved substrates on the basis of capillary interactions involving liquid solder. The substrates presented patterned, solder-coated areas that acted both as receptors for the components of the device during its assembly and as electrical connections during its operation. The components were suspended in water and agitated gently. Minimization of the free energy of the solder-water interface provided the driving force for the assembly. One hundred and thirteen GaAlAs light-emitting diodes with a chip size of 280 micrometers were fabricated into a prototype cylindrical display. It was also possible to assemble 1500 silicon cubes, on an area of 5 square centimeters, in less than 3 minutes, with a defect rate of 2%.∼

BMC Proceedings

Timothy Thornton, Matthew P Conomos, Serge Sverdlov,Elizabeth M Blue, Charles YK Cheung, Christopher G Glazner,

Steven M Lewis and Ellen M Wijsman

Estimating and adjusting for ancestry admixture in statistical methods for relatedness inference, heritability estimation, and association testing

It is well known that genetic association studies are not robust to population stratification. Two widely used approaches for the detection and correction of population structure are principal component analysis and model-based estimation of ancestry. These methods have been shown to give reliable inference on population structure in unrelated samples. We evaluated these two approaches in Mexican American pedigrees provided by the Genetic Analysis Workshop 18. We also estimated identity-by-descent sharing probabilities and kinship coefficients, with adjustment for ancestry admixture, to confirm documented pedigree relationships as well as to identify cryptic relatedness in the sample. We also estimated the heritability of the first simulated replicate of diastolic blood pressure (DBP). Finally, we performed an association analysis with simulated DBP, comparing the performance of an association method that corrects for population structure but does not account for relatedness to a method that adjusts for both population and pedigree structure. Analyses with simulated DBP were performed with knowledge of the underlying trait model.

Journal of Computational Physics

Mayya Tokman

A new class of exponential propagation iterative methods of Runge-Kutta type (EPIRK)

We propose a new class of the exponential propagation iterative methods of Runge–Kutta-type (EPIRK). The EPIRK schemes are exponential integrators that can be competitive with explicit and implicit methods for integration of large stiff systems of ODEs. Introducing the new, more general than previously proposed, ansatz for EPIRK schemes allows for more flexibility in deriving computationally efficient high-order integrators. Recent extension of the theory of B- series to exponential integrators [1] is used to derive classical order conditions for schemes up to order five. An algorithm to systematically solve these conditions is presented and several new fifth order schemes are constructed. Several numerical examples are used to verify the order of the methods and to illustrate the performance of the new schemes.

Functional Ecology

Nora Underwood

When herbivores come back: effects of repeated damage on induced resistance

Plants are known to respond to damage with subsequent changes in resistance. The consequences of these changes for plant fitness and herbivore populations will depend on both the response of a plant to a particular attack at a given moment and on how plants respond through time to varying levels of damage and varying numbers of attacks. While a small number of studies document how induced resistance changes with time after attack (time course of induction) and different levels of damage, few studies have examined the cumulative level of resistance after multiple attacks, and little is known about how the plant's response to damage changes with subsequent attacks. Two experiments were conducted to address the consequences of repeated damage for resistance of tomato (Solanum lycopersicum, var Castlemart) to a common pest, the beet armyworm (Spodoptera exigua). The first experiment documented the time course of resistance following a single damage event using both growth and choice bioassays. The second experiment examined whether the plant responded differently to one versus two damage events. Results show that plants were significantly induced by day 1 and remained induced until 15 or 20 days later, suggesting that repeated damage during the response to initial damage is possible. Plants receiving a second bout of damage were able to further increase their resistance level over the level reached in response to a first bout of damage, but the magnitude of response to the second damage event was initially smaller and slower than the response to a single damage event. There was no evidence in this study for immune-like memory in induced resistance. Results of this study suggest that plants can respond to repeated damage, but that there is some limit on responses to repeated damage. Such limits on total plant resistance will affect the influence of induced resistance on herbivore populations and are consistent with assumptions of existing models of induced resistance and herbivore population dynamics, although models have not yet considered the consequences of slower rather than smaller responses to repeated damage.

Journal of Geophysical Research

Sharon L. Vadas, Hidehiko Suzuki, Michael J. Nicolls,Takuji Nakamura, & Robert O. Harmon

Atmospheric gravity waves excited by a fireball

In a companion paper, Suzuki et al. [2013] studied an expanding circular train observed in the Na airglow for 9 minutes above Syowa Station, Antarctica, on 7 June 2008. This train was created by a southwestward-moving fireball meteor. Here, we report on “V”-shaped faint gravity waves (GWs) partially visible in many of the Na airglow images 8 to 43 minutes after the meteor. The GW phase lines appear to originate from the horizontal projection of the meteor path, with angles −42 to −52◦ south and 10 to 20◦ 11 north of the path. The GWs south of the path propagated southwestward with a horizontal phase speed of cH 80 − 100m/s, ∼while those north of the path propagated northwestward with cH 20 − 40m/s. Those south ∼(north) of the path had horizontal wavelengths λH 25 − 35 km (λH 18 km) and periods τr ∼ ∼

5−6 min (τr 7−15 min). We then model the GWs excited by idealized horizontal and ∼ ∼slanted heatings and body forces. We show that the GW phase lines form “V’s”when the heat/force is slanted vertically. If the central altitude of the heat/force is z0 > 92 km, the open ends of the “V”s are mainly directed away from the meteor trajectory. If the heat/force is long enough, two oppositely-directed “V”s are created, forming an “X” at the center of the structure. We find that λH depends sensitively on the width of the heating. We obtain heating parameters which compare reasonably well with the Na observations: z0 120 km, half-∼length half-max of 25 25 − 35 km, and half-width half-max of 2 − 3 km.∼ ∼

American Journal of Botany

Ana I. Vazquez, Gustavo de los Campos, Yann C. Klimentidis,Guilherme J. M. Rosa, Daniel Gianola, Nengjun Yi & David B. Allison

A Comprehensive Genetic Approach for Improving Prediction of Skin Cancer Risk in Humans

Prediction of genetic risk for disease is needed for preventive and personalized medicine. Genome-wide association studies have found unprecedented numbers of variants associated with complex human traits and diseases. However, these variants explain only a small proportion of genetic risk. Mounting evidence suggests that many traits, relevant to public health, are affected by large numbers of small-effect genes and that prediction of genetic risk to those traits and diseases could be improved by incorporating large numbers of markers into whole-genome prediction (WGP) models. We developed a WGP model incorporating thousands of markers for prediction of skin cancer risk in humans. We also considered other ways of incorporating genetic information into prediction models, such as family history or ancestry (using principal components, PCs, of informative markers). Prediction accuracy was evaluated using the area under the receiver operating characteristic curve (AUC) estimated in a cross- validation. Incorporation of genetic information (i.e., familial relationships, PCs, or WGP) yielded a significant increase in prediction accuracy: from an AUC of 0.53 for a baseline model that accounted for nongenetic covariates to AUCs of 0.58 (pedigree), 0.62 (PCs), and 0.64 (WGP). In summary, prediction of skin cancer risk could be improved by considering genetic information and using a large number of single-nucleotide polymorphisms (SNPs) in a WGP model, which allows for the detection of patterns of genetic risk that are above and beyond those that can be captured using family history. We discuss avenues for improving prediction accuracy and speculate on the possible use of WGP to prospectively identify individuals at high risk.

Nature Geoscience

Aaron A. Velasco, Stephen Hernandez, Tom Parsons & Kris Pankow

Global ubiquity of dynamic earthquake triggering

Earthquakes can be triggered by local changes in the stress field (static triggering) due to nearby earthquakes or by stresses caused by the passage of surface (Rayleigh and Love) waves from a remote, large earthquake (dynamic triggering). However, the mechanism, frequency, controlling factors and the global extent of dynamic triggering are yet to be fully understood. Because Rayleigh waves involve compressional and dilatational particle motion (volumetric changes) as well as shearing, whereas Love waves only involve shearing, triggering by either wave type implies fundamentally different physical mechanisms. Here, we analyse broadband seismograms from over 500 globally distributed stations and use an automated approach to systematically identify small triggered earthquakes—the low-amplitude signals of such earthquakes would normally be masked by high-amplitude surface waves. Our analysis reveals that out of 15 earthquakes studied of magnitude (M) greater than 7.0 that occurred after 1990, 12 are associated with significant increases in the detection of smaller earthquakes during the passage of both the Love and Rayleigh waves. We conclude that dynamic triggering is a ubiquitous phenomenon that is independent of the tectonic environment of the main earthquake or the triggered event.

Evolution

Sacha N. Vignieri, Joanna G. Larson, & Hopi E. Hoekstra

The selective advantage of crypsis in mice

The light color of mice that inhabit the sandy dunes of Florida’s coast have served as a textbook example of adaptation for nearly a century, despite the fact that the selective advantage of crypsis has never been directly tested or quantified in nature. Using plasticine mouse models of light and dark color, we demonstrate a strong selective advantage for mice that match their local background substrate. Furthe our data suggest that stabilizing selection maintains color matching within a single habitat, as models that are both lighter and darker than their local environment are selected against. These results provid empirical evidence in support of the hypothesis that visual hunting predators shape color patterning I Peromyscus mice and suggest a mechanism by which selection drives the pronounced color variation among populations.

Oxford Journals – Behavioral Ecology

Kerstin Wasson, & Bruce E. Lyon

Flight or fight: flexible antipredatory strategies in porcelain crabs

Autotomy, the voluntary shedding of limbs or other body parts in the face of predation, is a highly effective escape mechanism that has evolved independently in a variety of taxa. Crabs are unusual in that the limb that is typically sacrificed during autotomy, the anterior clawed cheliped, can also be used to ward off attack. During an encounter with a predator, an individual must thus decide between two mutually exclusive strategies: flight or fight. We used experimental predation encounters with two species of porcelain crabs (genus Petrolisthes) to examine the factors that influence the decision to flee versus fight and to determine the degree to which this decision is context-dependent. We found that autotomy was highly conditional.

The characteristics that best predicted autotomy—smaller body size or female gender—also correlated with a lower escape rate by the alternative escape tactic, struggling and pinching the predator. Variation among individuals in the benefit of autotomy (relative to alternative tactics) appears to drive variation in propensity to autotomize. Porcelain crabs thus demonstrate adaptive flexibility, employing the costly strategy of autotomizing a limb as a last resort, only when their chance at success by struggling is low.

Journal of Knot Theory and Its Ramifications

Robin T. Wilson

KNOTS WITH INFINITELY MANY INCOMPRESSIBLE SEIFERT SURFACES

We show that a knot in S3 with an infinite number of incompressible Seifert surfaces contains a closed non-peripheral incompressible surface in its complement.

Current Opinion in Insect Science

Yang, L.H. & C. Gratton

Insects as drivers of ecosystem processes

Insects and other small invertebrates are ubiquitous components of all terrestrial and freshwater food webs, but their cumulative biomass is small relative to plants and microbes. As a result, it is often assumed that these animals make relatively minor contributions to ecosystem processes. Despite their small sizes and cumulative biomass, we suggest that these animals may commonly have important effects on carbon and nutrient cycling by modulating the quality and quantity of resources that enter the detrital food web, with consequences at the ecosystem level. These effects can occur through multiple pathways, including direct inputs of insect biomass, the transformation of detrital biomass, and the indirect effects of predators on herbivores and detritivores. In virtually all cases, the ecosystem effects of these pathways are ultimately mediated through interactions with plants and soil microbes. Merging our understanding of insect, plant and microbial ecology will offer a valuable way to better integrate community-level interactions with ecosystem processes.

Physical Review B

Roya Zandi, Thorsten Emig, and Umar Mohideen

Quantum and thermal Casimir interaction between a sphere and a plate: Comparison of Drude and plasma models

We calculate the Casimir interaction between a sphere and a plate, both described by the plasma model, the Drude model, or generalizations of the two models. We compare the results at both zero and finite temperatures. At asymptotically large separations we obtain analytical results for the interaction that reveal a nonuniversal, i.e., material-dependent interaction for the plasma model. The latter result contains the asymptotic interaction for Drude metals and perfect reflectors as different but universal limiting cases. This observation is related to the screening of a static magnetic field by a London superconductor. For small separations we find corrections to the proximity force approximation that support correlations between geometry and material properties that are not captured by the Lifshitz theory. Our results at finite temperatures reveal for Drude metals a nonmonotonic temperature dependence of the Casimir free energy and a negative entropy over a sizeable range of separations.

30 Years of Impact:President’s Postdoctoral Fellowship Program