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Molecular Analysis Of The In Situ Growth Rate Of Subsurface Geobacter Species, Dawn E. Holmes, Ludovic Giloteaux, Melissa Barlett, Milind A. Chavan, Jessica A. Smith, Kenneth H. Williams, Michael Wilkins, Philip Long, Derek Lovley

Derek Lovley

Molecular tools that can provide an estimate of the in situ growth rate of Geobacter species could improve understanding of dissimilatory metal reduction in a diversity of environments. Whole genome microarray analyses of the subsurface isolate, Geobacter uraniireducens, grown under a variety of conditions identified a number of genes that are differentially expressed at different specific growth rates. Expression of two genes encoding ribosomal proteins, rpsC and rplL, were further evaluated with quantitative reverse transcription PCR (qRT-PCR) in cells with doubling times ranging from 6.56 h to 89.28 h. Transcript abundance of rpsC correlated best (r2= 0.90) with specific growth …

A Bayesian Model For Pooling Gene Expression Studies That Incorporates Co-Regulation Information, Erin M. Conlon, Bradley L. L. Postier, Barbara A. Methé, Kelly P. Nevin, Derek R. Lovley

Erin M. Conlon

Current Bayesian microarray models that pool multiple studies assume gene expression is independent of other genes. However, in prokaryotic organisms, genes are arranged in units that are co-regulated (called operons). Here, we introduce a new Bayesian model for pooling gene expression studies that incorporates operon information into the model. Our Bayesian model borrows information from other genes within the same operon to improve estimation of gene expression. The model produces the gene-specific posterior probability of differential expression, which is the basis for inference. We found in simulations and in biological studies that incorporating co-regulation information improves upon the independence model. …

The Rnf Complex Of Clostridium Ljungdahlii Is A Proton-Translocating Ferredoxin: Nad+ Oxidoreductase Essential For Autotrophic Growth, Pier-Luc Tremblay, Tian Zhang, Shabir A. Dar, Ching Leang, Derek Lovley

Derek Lovley

It has been predicted that the Rnf complex of Clostridium ljungdahlii is a proton-translocating ferredoxin:NAD+ oxidoreductase which contributes to ATP synthesis by an H+-translocating ATPase under both autotrophic and heterotrophic growth conditions. The recent development of methods for genetic manipulation of C. ljungdahlii made it possible to evaluate the possible role of the Rnf complex in energy conservation. Disruption of the C. ljungdahlii rnf operon inhibited autotrophic growth. ATP synthesis, proton gradient, membrane potential, and proton motive force collapsed in the Rnf-deficient mutant with H2 as the electron source and CO2 as the electron acceptor. Heterotrophic growth was hindered in …

Assessment Of Regional Climate Model Simulation Estimates Over The Northeast United States, M. A. Rawlins, Raymond S. Bradley, H. F. Diaz

Raymond S Bradley

Given the coarse scales of coupled atmosphere-ocean global climate models, regional climate models (RCMs) are increasingly relied upon for studies at scales appropriate for many impacts studies. We use outputs from an ensemble of RCMs participating in the North American Regional Climate Change Assessment Program (NARCCAP) to investigate potential changes in seasonal air temperature and precipitation between present (1971–2000) and future (2041–2070) time periods across the northeast United States. The models show a consistent modest cold bias each season and are wetter than observations in winter, spring, and summer. Agreement in spatial variability and pattern correlation is good for air …

The Shape And Mechanics Of Curved Fold Origami Structures, Marcelo A. Dias, Christian Santangelo

Christian Santangelo

We develop recursion equations to describe the three-dimensional shape of a sheet upon which a series of concentric curved folds have been inscribed. In the case of no stretching outside the fold, the three-dimensional shape of a single fold prescribes the shape of the entire origami structure. To better explore these structures, we derive continuum equations, valid in the limit of vanishing spacing between folds, to describe the smooth surface intersecting all the mountain folds. We find that this surface has negative Gaussian curvature with magnitude equal to the square of the fold's torsion. A series of open folds with …

The Genome Of Pelobacter Carbinolicus Reveals Surprising Metabolic Capabilities And Physiological Features, Muktak Aklujkar, Shelley A. Haveman, Raymond Didonato, Olga Chertkov, Cliff S. Han, Miriam L. Land, Peter Brown, Derek Lovley

Derek Lovley

BackgroundThe bacterium Pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically. The genome of P. carbinolicus was sequenced in order to understand its metabolic capabilities and physiological features in comparison with its relatives, acetate-oxidizing Geobacter species.ResultsPathways were predicted for catabolism of known substrates: 2,3-butanediol, acetoin, glycerol, 1,2-ethanediol, ethanolamine, choline and ethanol. Multiple isozymes of 2,3-butanediol dehydrogenase, ATP synthase and [FeFe]-hydrogenase were differentiated and assigned roles according to their structural properties and …

A Genetic System For Clostridium Ljungdahlii: A Chassis For Autotrophic Production Of Biocommodities And A Model Homoacetogen, Ching Leang, Toshiyuki Ueki, Kelly Nevin, Derek R. Lovley

Kelly Nevin

Methods for genetic manipulation of Clostridium ljungdahlii are of interest because of the potential for production of fuels and other biocommodities from carbon dioxide via microbial electrosynthesis or more traditional modes of autotrophy with hydrogen or carbon monoxide as the electron donor. Furthermore, acetogenesis plays an important role in the global carbon cycle. Gene deletion strategies required for physiological studies of C. ljungdahlii have not previously been demonstrated. An electroporation procedure for introducing plasmids was optimized, and four different replicative origins for plasmid propagation in C. ljungdahlii were identified. Chromosomal gene deletion via double-crossover homologous recombination with a suicide vector …

Copyright Developments In 2012 (Version 1.1), Laura Quilter

Laura Quilter

No abstract provided.

Statics And Dynamics Of Atomic Dark-Bright Solitons In The Presence Of Impurities, V. Achilleos, Panos Kevrekidis, V. M. Rothos, D. J. Frantzeskakis

Panos Kevrekidis

Adopting a mean-field description for a two-component atomic Bose-Einstein condensate, we study the statics and dynamics of dark-bright solitons in the presence of localized impurities. We use adiabatic perturbation theory to derive an equation of motion for the dark-bright soliton center. We show that, counterintuitively, an attractive (repulsive) delta-like impurity, acting solely on the bright-soliton component, induces an effective localized barrier (well) in the effective potential felt by the soliton; this way, dark-bright solitons are reflected from (transmitted through) attractive (repulsive) impurities. Our analytical results for the small-amplitude oscillations of solitons are found to be in good agreement with results …

Transfer And Scattering Of Wave Packets By A Nonlinear Trap, Kai Li, Panos Kevrekidis, Boris A. Malomed, D. J. Frantzeskakis

Panos Kevrekidis

In the framework of a one-dimensional model with a tightly localized self-attractive nonlinearity, we study the formation and transfer (dragging) of a trapped mode by “nonlinear tweezers,” as well as the scattering of coherent linear wave packets on the stationary localized nonlinearity. The use of a nonlinear trap for dragging allows one to pick up and transfer the relevant structures without grabbing surrounding “radiation.” A stability border for the dragged modes is identified by means of analytical estimates and systematic simulations. In the framework of the scattering problem, the shares of trapped, reflected, and transmitted wave fields are found. Quasi-Airy …

Beyond The Plaza: Barcelona’S Okupa Squatters At Work In The Wake Of La Crisis, Justin Helepololei

Justin AK Helepololei

As ongoing, financial crisis has kept millions in precarity - and over 40% of Spain's youth unemployed - mass mobilizations of the country's indignados have continued to fill the country's streets and plazas. Nearly one year after the original 15M demonstrations, city-wide occupations have triggered a profusion of more localized and issue-based assemblies. Beyond the plazas, squatter-activists of Barcelona's decades-old “okupa movement” have helped to facilitate the continuation of these dialogues by offering space within dozens of pre-existing squats and even opening new sites to host such interactions. Leveraging decades of experience and skill in re-appropriating spaces, squatters create room …

On Hilbert Modular Threefolds Of Discriminant 49, Lev A. Borisov, Paul E. Gunnells

Paul Gunnells

Let K be the totally real cubic field of discriminant 49 , let \fancyscriptO be its ring of integers, and let p⊂\fancyscriptO be the prime over 7 . Let Γ(p)⊂Γ=SL2(\fancyscriptO) be the principal congruence subgroup of level p . This paper investigates the geometry of the Hilbert modular threefold attached to Γ(p) and some related varieties. In particular, we discover an octic in P3 with 84 isolated singular points of type A2 .

Interaction Of Sleep And Emotional Content On The Production Of False Memories, Shannon Mckeon, Edward F. Pace-Schott, Rebecca M. C. Spencer

Rebecca M. C. Spencer

Sleep benefits veridical memories, resulting in superior recall relative to off-line intervals spent awake. Sleep also increases false memory recall in the Deese-Roediger-McDermott (DRM) paradigm. Given the suggestion that emotional veridical memories are prioritized for consolidation over sleep, here we examined whether emotion modulates sleep’s effect on false memory formation. Participants listened to semantically related word lists lacking a critical lure representing each list’s ‘‘gist.’’ Free recall was tested after 12 hours containing sleep or wake. The Sleep group recalled more studied words than the Wake group but only for emotionally neutral lists. False memories of both negative and neutral …

Modular Forms And Elliptic Curves Over The Cubic Field Of Discriminant - 23, Paul E. Gunnells, Dan Yasaki

Paul Gunnells

Let F be the cubic field of discriminant –23 and let O Ϲ F be its ring of integers. By explicitly computing cohomology of congruence subgroups of 〖GL〗_2(O) , we computationally investigate modularity of elliptic curves over F.

Vortex–Bright-Soliton Dipoles: Bifurcations, Symmetry Breaking, And Soliton Tunneling In A Vortex-Induced Double Well, M. Pola, J. Stockhofe, P. Schmelcher, Panos Kevrekidis

Panos Kevrekidis

The emergence of vortex-bright soliton dipoles in two-component Bose-Einstein condensates through bifurcations from suitable eigenstates of the underlying linear system is examined. These dipoles can have their bright solitary structures be in phase (symmetric) or out of phase (anti-symmetric). The dynamical robustness of each of these two possibilities is considered and the out-of-phase case is found to exhibit an intriguing symmetry-breaking instability that can in turn lead to tunneling of the brightwave function between the two vortex “wells.” We interpret this phenomenon by virtue of a vortex-induced double-well system, whose spontaneous symmetry breaking leads to asymmetric vortex-bright dipoles, in addition …

Nanomanufacturing Of Biomaterials, Yoni Engel, Jessica D. Schiffman, Julie M. Goddard, Vincent M. Rotello

Jessica D. Schiffman

In this review, we present a few of the many important objectives in the area of biomedical engineering that could open new pathways for nextgeneration biomaterials. We also provide examples of how materials for these goals can be created in an economically viable means through recent advances in high throughput production. These strategies highlight the potential for nanomanufacturing in a variety of areas of importance for human health and safety.

Improved Cathode Materials For Microbial Electrosynthesis, Tian Zhang, Huarong Nie, Timothy S. Bain, Haiyun Lu, Mengmeng Cui, Oona L. Snoeyenbos-West, Ashley E. Franks, Kelly P. Nevin, Thomas P. Russell, Derek Lovley

Derek Lovley

Microbial electrosynthesis is a promising strategy for the microbial conversion of carbon dioxide to transportation fuels and other organic commodities, but optimization of this process is required for commercialization. Cathodes which enhance electrode–microbe electron transfer might improve rates of product formation. To evaluate this possibility, biofilms of Sporomusa ovata, which are effective in acetate electrosynthesis, were grown on a range of cathode materials and acetate production was monitored over time. Modifications of carbon cloth that resulted in a positive-charge enhanced microbial electrosynthesis. Functionalization with chitosan or cyanuric chloride increased acetate production rates 6–7 fold and modification with 3-aminopropyltriethoxysilane gave rates …

Improved Cathode Materials For Microbial Electrosynthesis, Tian Zhang, Huarong Nie, Timothy S. Bain, Haiyun Lu, Mengmeng Cui, Oona L. Snoeyenbos-West, Ashley E. Franks, Kelly Nevin, Thomas P. Russell, Derek R. Lovley

Kelly Nevin

Microbial electrosynthesis is a promising strategy for the microbial conversion of carbon dioxide to transportation fuels and other organic commodities, but optimization of this process is required for commercialization. Cathodes which enhance electrode–microbe electron transfer might improve rates of product formation. To evaluate this possibility, biofilms of Sporomusa ovata, which are effective in acetate electrosynthesis, were grown on a range of cathode materials and acetate production was monitored over time. Modifications of carbon cloth that resulted in a positive-charge enhanced microbial electrosynthesis. Functionalization with chitosan or cyanuric chloride increased acetate production rates 6–7 fold and modification with 3-aminopropyltriethoxysilane gave rates …

Buying Time: Gendered Patterns In Union Contracts, Dan Clawson, Jillian Crocker

Dan Clawson

As products of negotiations, union contracts provide insight into areas of stress concerning work hours and schedules. Our analysis demonstrates the ways workers in two occupations—nurses and firefighters—use collective bargaining to develop workplace policies that enable them to manage jobs and family. The contracts show significant differences between firefighters and nurses over issues of work scheduling, overtime, and vacations. These differences reflect nurses’ concern with putting boundaries on their work lives in favor of caregiving and firefighters’ concern with bread winning. Nurse contracts specify scheduling rules in detail, heavily restrict mandatory overtime, and outline guidelines for distributing prime time vacations. …

Systemic Bias In Wikipedia : What It Looks Like, And How To Deal With It, Laura Quilter

Laura Quilter

No abstract provided.

Evidence Of Non-Mean-Field-Like Low-Temperature Behavior In The Edwards-Anderson Spin-Glass Model, B. Yucesoy, Helmut G. Katzgraber, Jonathan Machta

Jonathan Machta

The three-dimensional Edwards-Anderson and mean-field Sherrington-Kirkpatrick Ising spin glasses are studied via large-scale Monte Carlo simulations at low temperatures, deep within the spin-glass phase. Performing a careful statistical analysis of several thousand independent disorder realizations and using an observable that detects peaks in the overlap distribution, we show that the Sherrington-Kirkpatrick and Edwards-Anderson models have a distinctly different low-temperature behavior. The structure of the spin-glass overlap distribution for the Edwards-Anderson model suggests that its low-temperature phase has only a single pair of pure states.

Nonlinear Pt-Symmetric Plaquettes, Kai Li, Panos Kevrekidis, Boris A. Malomed, Uwe Günther

Panos Kevrekidis

We introduce four basic two-dimensional (2D) plaquette configurations with onsite cubic nonlinearities, which may be used as building blocks for 2D PT -symmetric lattices. For each configuration, we develop a dynamical model and examine its PT symmetry. The corresponding nonlinear modes are analyzed starting from the Hamiltonian limit, with zero value of the gain-loss coefficient, . Once the relevant waveforms have been identified (chiefly, in an analytical form), their stability is examined by means of linearization in the vicinity of stationary points. This reveals diverse and, occasionally, fairly complex bifurcations. The evolution of unstable modes is explored by means of …

Copyright And Fair Use : An Introduction For Faculty, Laura Quilter

Laura Quilter

In this overview of copyright issues for faculty and researchers, we will discuss how copyright affects you: how to protect and get credit for your work, share what you want to share, and use others' work. Special attention will be given to both questions and problems with using other people's work -- relying on fair use, and asking for permission if it's not a fair use -- and the best ways to manage your own copyrights and licenses. Plenty of time for discussion and questions!

Borexino Calibrations: Hardware, Methods, And Results, H. Back, G. Bellini, J. Benziger, D. Bick, G. Bonfini, D. Bravo, M. Buizza Avanzini, B. Caccianiga, L. Cadonati, F. Calaprice, C. Carraro, P. Cavalcante, A. Chavarria, D. D'Angelo, S. Davini, A. Derbin, A. Etenko, F. Von Feilitzsch, G. Fernandes, K. Fomenko, D. Franco, C. Galbiati, S. Gazzana, C. Ghiano, M. Giammarchi, M. Goeger-Neff, A. Goretti, L. Grandi, E. Guardincerri, S. Hardy, Aldo Ianni, Andrea Ianni, A. Kayunov, S. Kidner, V. Kobychev, D. Korablev, G. Korga, Y. Koshio, D. Kryn, M. Laubenstein, T. Lewke, E. Litvinovich, B. Loer, F. Lombardi, P. Lombardi, L. Ludhova, I. Machulin, S. Manecki, W. Maneschg, G. Manuzio, Q. Meindl, E. Meroni, L. Miramonti, M. Misiaszek, D. Montanari, P. Mosteiro, V. Muratova, L. Oberauer, M. Obolensky, F. Ortica, K. Otis, M. Pallavicini, L. Papp, L. Perasso, S. Perasso, Andrea Pocar, R. S. Raghavan, G. Ranucci, A. Razeto, A. Re, A. Romani, N. Rossi, D. Rountree, A. Sabelnikov, R. Saldanha, C. Salvo, S. Schönert, H. Simgen, M. Skorokhvatov, O. Smirnov, A. Sotnikov, S. Sukhotin, Y. Suvorov, R. Tartaglia, G. Testera, D. Vignaud, R. B. Vogelaar, J. Winter, M. Wojcik, A. Wright, M. Wurm, J. Xu, O. Zaimidoroga, S. Zavatarelli, G. Zuzel

Andrea Pocar

Borexino was the first experiment to detect solar neutrinos in real-time in the sub-MeV region. In order to achieve high precision in the determination of neutrino rates, the detector design includes an internal and an external calibration system. This paper describes both calibration systems and the calibration campaigns that were carried out in the period between 2008 and 2011. We discuss some of the results and show that the calibration procedures preserved the radiopurity of the scintillator. The calibrations provided a detailed understanding of the detector response and led to a significant reduction of the systematic uncertainties in the Borexino …

Capital Flight From Sub-Saharan African Countries: Updated Estimates, 1970 - 2010, James K. Boyce, Léonce Ndikumana

James K. Boyce

The performance of Sub-Saharan African economies over the past decade has inspired optimism on the region’s prospects. But the region still faces major development challenges, and it is now clear that the majority of its countries will not achieve key millennium development goals.

A key constraint to SSA’s growth and development is the shortage of financing. At the same time, the sub-region is a source of large-scale capital flight, which escalated during last decade even as the region experienced growth acceleration. The group of 33 SSA countries covered by this report has lost a total of $814 billion dollars from …

Multiple Imputation And Higher Education Research, Catherine A. Manly, Ryan S. Wells

Ryan S. Wells

Higher education researchers using survey data often face decisions about handling missing data. Multiple imputation (MI) is considered by many statisticians to be the most appropriate technique for addressing missing data in many circumstances. However, our content analysis of a decade of higher education research literature reveals that the field has yet to make substantial use of this technique despite common employment of quantitative analysis, and that many recommended MI reporting practices are not being followed. We conclude that additional information about the technique and recommended reporting practices may help improve the quality of the research involving missing data. In …

Comment On Khan, Li And Weisbrot (Thomas Weisskopf Festschrift Conference Paper), James K. Boyce

James K. Boyce

Boyce comments on Shahrukh Khan's " The Military and Economic Development in Pakistan, Minqi Li's "Socialism: The 20th Century and the 21st Century" and Mark Weisbrot's "Economic Growth: The Great Slowdown (1980-2000) and Recovery (2000-2010)." He adds his own thoughts on the theme running through these papers: the need to take the role of the state, both in terms of state control over the means of production and resource allocation, but also about the core issue of control over the state itself. This means engaging, as Khan, Li and Weisbrot do, with the historic struggle to build and sustain real …

Gene Number Determination And Genetic Polymorphism Of The Gamma Delta T Cell Co-Receptor Wc1 Genes, Chuang Chen, Carolyn Ta Herzig, Leeson J. Alexander, John W. Keele, Tara G. Mcdaneld, Janice C. Telfer, Cynthia Baldwin

Cynthia Baldwin

Background WC1 co-receptors belong to the scavenger receptor cysteine-rich (SRCR) superfamily and are encoded by a multi-gene family. Expression of particular WC1 genes defines functional subpopulations of WC1+ γδ T cells. We have previously identified partial or complete genomic sequences for thirteen different WC1 genes through annotation of the bovine genome Btau_3.1 build. We also identified two WC1 cDNA sequences from other cattle that did not correspond to sequences in the Btau_3.1 build. Their absence in the Btau_3.1 build may have reflected gaps in the genome assembly or polymorphisms among animals. Since the response of γδ T cells to bacterial …

Capital Flight From North African Countries, Léonce Ndikumana, James K. Boyce

James K. Boyce

Ndikumana and Boyce demonstrate that, while the countries of North Africa have achieved high levels of development relative to their sister nations south of the Sahara, they too have suffered from financial hemorrhages through capital flight. The burden on their economies is substantial in terms of lost investment and foregone government revenue, with adverse effects on economic growth and social service delivery. The authors provide estimates of the total amount of capital flight from four North African countries: Algeria, Egypt, Morocco and Tunisia, from 1970 to 2010.

Angular Tension Of Black Holes, David Kastor, Jennie Traschen

David Kastor

Angular tension is an Arnowitt-Deser-Misner charge that contributes a work term to the first law of black hole mechanics when the range of an angular coordinate is varied and leads to a new Smarr formula for stationary black holes. A phase diagram for singly spinning D=5 black holes shows that angular tension resolves the degeneracies between spherical black holes and (dipole) black rings and captures the physics of the black ring balance condition. Angular tension depends on the behavior of the metric at rotational axes and we speculate on its relation to rod/domain structure characterizations of higher-dimensional black holes and …