bluuebunny/crossref_metadata_2025 huggingface dataset:
Extreme ultraviolet emission and confinement of tin plasmas in the presence of a magnetic field
Authors: Roy Amitava , Murtaza Hassan Syed , Harilal Sivanandan S. , Endo Akira , Mocek Tomas , Hassanein Ahmed
Published: May 2014

We investigated the role of a guiding magnetic field on extreme ultraviolet (EUV) and ion emission from a laser produced Sn plasma for various laser pulse duration and intensity. For producing plasmas, planar slabs of pure Sn were irradiated with 1064 nm, Nd:YAG laser pulses with varying pulse duration (5–15 ns) and intensity. A magnetic trap was fabricated with the use of two neodymium permanent magnets which provided a magnetic field strength ∼0.5 T along the plume expansion direction. Our results indicate that the EUV conversion efficiency do not depend significantly on applied axial magnetic field. Faraday Cup ion analysis of Sn plasma show that the ion flux reduces by a factor of ∼5 with the application of an axial magnetic field. It was found that the plasma plume expand in the lateral direction with peak velocity measured to be ∼1.2 cm/μs and reduced to ∼0.75 cm/μs with the application of an axial magnetic field. The plume expansion features recorded using fast photography in the presence and absence of 0.5 T axial magnetic field are simulated using particle-in-cell code. Our simulation results qualitatively predict the plasma behavior.
Binding conditions for nonlinear ultrasonic generation unifying wave propagation and vibration
Authors: Jin Lim Hyung , Sohn Hoon , Liu Peipei
Published: May 2014

This study provides a physical insight into binding conditions (BCs) for nonlinear ultrasonic generation considering both propagating waves and stationary vibrations. First, the BCs are theoretically formulated for both propagating waves and stationary vibrations. Then, the BCs are experimentally validated with a special focus on nonlinear modulation. Finally, the advantages and disadvantages for using propagating waves or stationary vibrations are discussed.
Enhanced electrical current densities in electrochemical systems through the use of nanostructured electrodes
Authors: Yamada Hidenori , Bandaru Prabhakar R.
Published: May 2014

A model is proposed regarding electrical current from an electrochemical device. The current density, J is explained through electric field induced ion drift in the electrolyte bulk. The resulting equation is largely consistent with, but not identical to, the conventional equation based on ion diffusion at the electrode surface. Experiments using nanostructured electrodes display larger J than conventionally thought possible, which can be explained through the drift-based equation. Our study points to the consequent utility of electrodes comprised closely spaced nanostructures.
Reaping the potentials of nonlinear energy harvesting with tunable damping and modulation of the forcing functions
Authors: Ma T. , Zhang H.
Published: May 2014

The fundamental features of nonlinear dynamical systems are investigated in the context of vibration-based energy harvesting. A generalized, global, multi-frequency resonance condition is shown to exist in nonlinear systems where the energy harvesting efficiency has been maximized. Results show that damping and modulation of the excitation play critical roles in facilitating the frequency match required for resonance by tuning the frequencies of the system and modifying the frequency content of the excitation.
Excess noise in GaAs and AlGaAs avalanche photodiodes with GaSb absorption regions—composite structures grown using interfacial misfit arrays
Authors: Craig A. P. , Reyner C. J. , Marshall A. R. J. , Huffaker D. L.
Published: May 2014

Interfacial misfit arrays were embedded within two avalanche photodiode (APD) structures. This allowed GaSb absorption layers to be combined with wide-bandgap multiplication regions, consisting of GaAs and Al0.8Ga0.2As, respectively. The GaAs APD represents the simplest case. The Al0.8Ga0.2As APD shows reduced dark currents of 5.07 μAcm−2 at 90% of the breakdown voltage, and values for effective k=β/α below 0.2. Random-path-length modeled excess noise is compared with experimental data, for both samples. The designs could be developed further, allowing operation to be extended to longer wavelengths, using other established absorber materials which are lattice matched to GaSb.
Enhanced spin polarization in graphene with spin energy gap induced by spin-orbit coupling and strain
Authors: Liu Zheng-Fang , Wu Qing-Ping , Chen Ai-Xi , Xiao Xian-Bo , Liu Nian-Hua
Published: May 2014

We investigate the possibility of spin polarization in graphene. The result shows that a spin energy gap can be opened in the presence of both spin-orbit coupling and strain. We find that high spin polarization with large spin-polarized current is achieved in the spin energy gap. However, only one of the two modulations is present, no spin polarization can be generated. So the combination of the two modulations provides a way to design tunable spin polarization without need for a magnetic element or an external magnetic field.
Optimization of process parameters for biodiesel extraction from tamanu oil using design of experiments
Authors: Antony Miraculas G. , Bose N. , Edwin Raj R.
Published: May 2014

Petroleum reserves are diminishing at a faster rate and the world is facing twin crisis in fossil fuel depletion and environmental degradation owing to extensive use of fossil fuel. Finding viable and sustainable alternative fuel is crucial for the world at large and especially for oil importing countries like India. In the present work, biodiesel is produced from tamanu oil, which is non-edible, plentiful, and cost effective. However, the viscosity is high which demands a two stage esterification to reduce its fatty acid content within the limits for automotive applications. Due to interactive effects among the process parameters, design of experiments is employed for optimization. It was observed that methanol and catalyst concentration are the major influencing process parameters, whereas time and temperature have insignificant role on acid value reduction and percentage of oil yield. The extracted biodiesel was tested for fuel properties with standard test procedures and found to be in compliance with ASTM standards.
Nonlinear simulation of a spar buoy floating wind turbine under extreme ocean conditions
Authors: Nematbakhsh Ali , Olinger David J. , Tryggvason Gretar
Published: May 2014

A nonlinear computational model, based on solving the Navier-Stokes equation, is used to study the motion of a 5 MW spar buoy floating wind turbine in moderate and extreme sea states with irregular waves. The main advantages of using the current model are that there is no limitation on the platform motion, the hydrodynamic loads do not rely on experimental data, and nonlinear hydrodynamic loads can be predicted. The current work extends a previously developed Navier-Stokes model for regular periodic waves on a tension leg platform floating wind turbine. Free decay tests are performed, and pitch, heave, and surge natural frequencies are determined. The responses of the spar buoy to operating conditions with significant wave height of 8 m and mean period of 10 s, and an extreme sea states including waves over 17 m height are studied. For the extreme sea state, a nonlinear model is required, since the platform response amplitudes are not small with respect to the spar buoy diameter. Effects not included in linear models, such as platform pitch angles higher than 10°, complete submergence of the platform tank and tether slacking are captured. Finally, a design study on spar buoy aspect ratio is performed for one sea state and it is shown that higher aspect ratio spars generally lead to lower mean pitch and surge responses as expected, but also may lead to a nonlinear trend in the standard deviations in pitch and heave, probably due to the increase in wind and wave moments on the spar.
A first principles analysis of the effect of hydrogen concentration in hydrogenated amorphous silicon on the formation of strained Si-Si bonds and the optical and mobility gaps
Authors: Legesse Merid , Nolan Michael , Fagas Giorgos
Published: May 2014

In this paper, we use a model of hydrogenated amorphous silicon generated from molecular dynamics with density functional theory calculations to examine how the atomic geometry and the optical and mobility gaps are influenced by mild hydrogen oversaturation. The optical and mobility gaps show a volcano curve as the hydrogen content varies from undersaturation to mild oversaturation, with largest gaps obtained at the saturation hydrogen concentration. At the same time, mid-gap states associated with dangling bonds and strained Si-Si bonds disappear at saturation but reappear at mild oversaturation, which is consistent with the evolution of optical gap. The distribution of Si-Si bond distances provides the key to the change in electronic properties. In the undersaturation regime, the new electronic states in the gap arise from the presence of dangling bonds and strained Si-Si bonds, which are longer than the equilibrium Si-Si distance. Increasing hydrogen concentration up to saturation reduces the strained bonds and removes dangling bonds. In the case of mild oversaturation, the mid-gap states arise exclusively from an increase in the density of strained Si-Si bonds. Analysis of our structure shows that the extra hydrogen atoms form a bridge between neighbouring silicon atoms, thus increasing the Si-Si distance and increasing disorder in the sample.
Expanding emergency department capacity: a multisite study
Authors: Crilly Julia L. , Keijzers Gerben B. , Tippett Vivienne C. , O'Dwyer John A. , Wallis Marianne C. , Lind James F. , Bost Nerolie F. , O'Dwyer Marilla A. , Shiels Sue
Published: May 2014

Objectives The aims of the present study were to identify predictors of admission and describe outcomes for patients who arrived via ambulance to three Australian public emergency departments (EDs), before and after the opening of 41 additional ED beds within the area. Methods The present study was a retrospective comparative cohort study using deterministically linked health data collected between 3 September 2006 and 2 September 2008. Data included ambulance offload delay, time to see doctor, ED length of stay (LOS), admission requirement, access block, hospital LOS and in-hospital mortality. Logistic regression analysis was undertaken to identify predictors of hospital admission. Results Almost one-third of all 286 037 ED presentations were via ambulance (n = 79 196) and 40.3% required admission. After increasing emergency capacity, the only outcome measure to improve was in-hospital mortality. Ambulance offload delay, time to see doctor, ED LOS, admission requirement, access block and hospital LOS did not improve. Strong predictors of admission before and after increased capacity included age >65 years, Australian Triage Scale (ATS) Category 1–3, diagnoses of circulatory or respiratory conditions and ED LOS >4 h. With additional capacity, the odds ratios for these predictors increased for age >65 years and ED LOS >4 h, and decreased for ATS category and ED diagnoses. Conclusions Expanding ED capacity from 81 to 122 beds within a health service area impacted favourably on mortality outcomes, but not on time-related service outcomes such as ambulance offload time, time to see doctor and ED LOS. To improve all service outcomes, when altering (increasing or decreasing) ED bed numbers, the whole healthcare system needs to be considered.
Orthopaedic triaging by podiatrists: a prospective study of patient satisfaction and service efficiency
Authors: Walsh Tom P. , Pilkington Dolores C. , Wong Esther J. , Brown Christopher H. , Mercer Graham E.
Published: May 2014

Background The Southern Adelaide Local Health Network is serviced by one orthopaedic surgeon specialising in foot and ankle surgery. In 2011, the waiting list to see the surgeon was expanding and the need for assistance was growing. The Department of Podiatry agreed to provide a podiatrist to assist in the management of the outpatient waiting list. Although patient outcome is an important outcome measure, we were interested in evaluating the service with respect to how satisfied patients were with seeing a podiatrist. Therefore, the primary aim of the study was to evaluate patient satisfaction with podiatry-led clinics for the orthopaedic outpatient waiting list. Secondary outcomes included discharge rate and efficiency of care. Methods We prospectively recruited a consecutive sample discharged from the Department of Podiatry between 1 May and 1 November 2013 to complete the Client Satisfaction Survey (CSQ-8). This survey was used to evaluate the satisfaction of patients following discharge from the Department of Podiatry. Results There were 49 patients (16 men, 33 women) enrolled in the survey during the 6-month period. Of the 49 patients discharged, 21 (43%) were discharged from the outpatient waiting list. Twenty-eight patients (57%) were referred on to the Department of Orthopaedic Surgery for opinion and management. The mean (± s.d.) number of appointments for each patient was 1.3 ± 0.6. Overall, patients were very satisfied with the assessment and/or treatment they received. Conclusion A podiatrist, working at an extended scope of practice and in collaboration with an orthopaedic surgeon, can successfully and efficiently assess and treat patients on an orthopaedic outpatient waiting list. Patients generally reported a high level of satisfaction with the process and would return to the clinic again if necessary. Hospital networks wanting to efficiently reduce waiting lists may endorse task substitution for appropriately skilled podiatrists. What is known about the topic? Allied health professionals have acted in extended scope of practice roles across several professions. These roles are often implemented in response to long waiting lists to see medical specialists. The acceptance of these practitioners by patients and the efficiency of these clinics are yet to be formally evaluated. What does the paper add? This paper should provide confidence in implementing orthopaedic triaging roles for podiatrists. High satisfaction rates were noted, along with an efficient service, both of which may be attractive for hospital networks. What are the implications for practitioners? Extended scope of practice podiatry roles may be implemented to assist in managing orthopaedic outpatient waiting lists.
Two distinct evolutionary lineages of the Astacus leptodactylus species-complex (Decapoda : Astacidae) inferred by phylogenetic analyses
Authors: Maguire Ivana , Podnar Martina , Jelić Mišel , Štambuk Anamaria , Schrimpf Anne , Schulz Holger , Klobučar Goran
Published: May 2014

Narrow-clawed crayfish (Astacus leptodactylus Eschscholtz, 1823 species-complex) is one of five European freshwater crayfish species. Even though widely distributed, it hasn’t been frequently studied and its taxonomy and systematics are unresolved. The results of a recent comparative morphometric character study revealed that morphometry of Asian and European populations differ significantly. In this research, for the first time, mitochondrial molecular markers (16S rRNA and COI) were used with the aim of elucidating the phylogenetic relationship between European and Asian populations of the narrow-clawed crayfish. Analyses included crayfish from Croatia, Bulgaria, Armenia, Russia, Poland and Turkey, and three different optimality criteria were applied. Phylogenetic relationships were reconstructed using the COI dataset, as well as the concatenated one (COI + 16S rRNA). For both datasets, congruent topologies were obtained and trees were characterised by the existence of two well supported phylogroups, one that included European populations, and the other Asian. Results indicate the presence of distinct evolutionary lineages within the A. leptodactylus species-complex, and corroborate previous results obtained using morphometric analyses.
Exposing hidden-value trade-offs: sharing wildfire management responsibility between government and citizens
Authors: McLennan Blythe , Eburn Michael
Published: May 2014

Developing resilient communities and sharing responsibility for hazard management is the key to Australia’s ‘National Strategy for Disaster Resilience’. There are, however, a wide range of conflicting views on the appropriate responsibilities of governments, citizens and communities that are not well recognised in the national policy discourse. What the ideas of resilient communities and shared responsibility mean for wildfire management and how these ideas might shape wildfire safety thinking and practice is therefore unclear and contested. This paper makes explicit some of the necessary, but often hidden, trade-offs between competing values that are implicit in assessments of where responsibility for wildfire management lies, and how it should be shared. After describing different ways in which responsibility is attributed and legitimated through legal and governance systems, this paper compares and contrasts potential legal and governance implications of four hypothetical scenarios for wildfire management, each of which portrays a contrasting set of extreme value trade-offs. The underlying purpose of the exercise is to encourage stakeholders to draw on the frameworks to explicitly acknowledge and debate the value trade-offs that are necessary, but most often unacknowledged, in more moderate decision-making about how to share responsibility for risk management between governments and citizens.
Evaluating the utility of dynamical downscaling in agricultural impacts projections
Authors: Glotter Michael , Elliott Joshua , McInerney David , Best Neil , Foster Ian , Moyer Elisabeth J.
Published: May 2014

Significance

One of the largest concerns about future climate change is its potential effect on food supply. Crop yield projections require climate inputs at higher resolution than typical for global climate models, and the computationally expensive technique of dynamical downscaling is widely used for this translation. We simulate maize yield in the United States to test whether current dynamical downscaling methods add value over simpler downscaling approaches. Our results suggest that they do not. Addressing large-scale systematic biases in climate output may be a higher priority for understanding future climate change impacts.
Ribosomal protein–Mdm2–p53 pathway coordinates nutrient stress with lipid metabolism by regulating MCD and promoting fatty acid oxidation
Authors: Liu Yong , He Yizhou , Jin Aiwen , Tikunov Andrey P. , Zhou Lishi , Tollini Laura A. , Leslie Patrick , Kim Tae-Hyung , Li Lei O. , Coleman Rosalind A. , Gu Zhennan , Chen Yong Q. , Macdonald Jeffrey M. , Graves Lee M. , Zhang Yanping
Published: May 2014

Significance

Although progress has been made in the characterization of p53 in regulating metabolism, very little is known about the signaling pathways involved in this regulation in response to stress in vivo. Here we show thatp53controls hepatic fatty acid oxidation in mice in response to fasting. Disruption of ribosome protein (RP)-mouse double minute (Mdm)2 binding inMdm2C305Fmice results in fasting-induced hepatosteatosis. A full-dosage ofp53and an intact RP-Mdm2-p53 pathway are required for the induction of malonyl coA decarboxylase (MCD), a critical regulator of fatty acid oxidation. Thus, the RP-Mdm2-p53 pathway functions as a key regulator of hepatic lipid homeostasis in response to nutrient deprivation stress, a function that has implications in organismal survival and tumor suppression.
Regulation of photosystem I light harvesting by zeaxanthin
Authors: Ballottari Matteo , Alcocer Marcelo J. P. , D’Andrea Cosimo , Viola Daniele , Ahn Tae Kyu , Petrozza Annamaria , Polli Dario , Fleming Graham R. , Cerullo Giulio , Bassi Roberto
Published: May 2014

Significance

Chloroplasts are particularly prone to photooxidative damage, and carotenoids play a key role in photoprotection. Under excess light conditions, plants accumulate a carotenoid, zeaxanthin, involved in multiple photoprotection events. Although the function of zeaxanthin in photosystem II (PSII) has been investigated thoroughly, its role in photosystem I (PSI) had not been identified. In this work we report a zeaxanthin-dependent regulation of PSI functional antenna size inArabidopsis thaliana. We identified a zeaxanthin-dependent quenching process coupled to improved photostability of PSI, as measured in isolated complexes and leaves. We show that, similar to its action in PSII, zeaxanthin binding to components of PSI leads to the formation of carotenoid radical cations, quenching a fraction of the excitation energy absorbed.
An Automated Algorithm to Preselect Patients to Be Assessed Individually in Point Prevalence Surveys for Hospital-Acquired Infections in Surgery
Authors: Streefkerk Roel H. R. A. , Moorman Peter W. , Parlevliet Gerard A. , van der Hoeven Conrad , Verbrugh Henri A. , Vos Margreet C. , Verkooijen Roel P.
Published: May 2014

In this pilot study, we evaluate an algorithm that uses predictive clinical and laboratory parameters to differentiate between patients with hospital-acquired infection (HAI) and patients without HAI. Seventy-four percent of the studied population of surgical patients could be reliably (negative predictive value of 98%) excluded from detailed assessment by the infection control practitioner.

Infect Control Hosp Epidemiol 2014;35(7):886-887
Evaluation of an Algorithm for Electronic Surveillance of Hospital-Acquired Infections Yielding Serial Weekly Point Prevalence Scores
Authors: Streefkerk Roel H. R. A. , Borsboom Gerard J. J. M. , van der Hoeven Conrad P. , Vos Margreet C. , Verkooijen Roel P. , Verbrugh Henri A.
Published: May 2014

Surveillance of hospital-acquired infections can be approximated by repeated surveys that are performed in a standardized, cost-effective manner. We developed an integrated software system for serial electronic hospital-wide point prevalence surveys using algorithms that proved highly sensitive and specific over a 5-year period in a large university medical center.

Infect Control Hosp Epidemiol 2014;35(7):888–890
T-cells play the classics with a different spin
Authors: Dustin Michael L.
Published: May 2014

The immune system uses much of the classic machinery of cell biology, but in ways that put a different spin on organization and function. Striking recent examples include the demonstration of intraflagellar transport protein and hedgehog contributions to the immune synapse, even though immune cells lack a primary cilium that would be the typical setting for this machinery. In a second example, lymphocytes have their own subfamily of integrins, the β2 subfamily, and only integrins in this family form a stable adhesion ring using freely mobile ligands, a key feature of the immunological synapse. Finally, we showed recently that T-cells use endosomal sorting complexes required for transport (ESCRTs) at the plasma membrane to generate T-cell antigen receptor–enriched microvesicles. It is unusual for the ESCRT pathway to operate at the plasma membrane, but this may allow a novel form of cell–cell communication by providing a multivalent ligand for major histocompatibility complex–peptide complexes and perhaps other receptors on the partnering B-cell. Immune cells are thus an exciting system for novel cell biology even with classical pathways that have been studied extensively in other cell types.
FHIP and FTS proteins are critical for dynein-mediated transport of early endosomes inAspergillus
Authors: Yao Xuanli , Wang Xiangfeng , Xiang Xin
Published: May 2014

The minus end–directed microtubule motor cytoplasmic dynein transports various cellular cargoes, including early endosomes, but how dynein binds to its cargo remains unclear. Recently fungal Hook homologues were found to link dynein to early endosomes for their transport. Here we identified FhipA in Aspergillus nidulans as a key player for HookA (A. nidulans Hook) function via a genome-wide screen for mutants defective in early-endosome distribution. The human homologue of FhipA, FHIP, is a protein in the previously discovered FTS/Hook/FHIP (FHF) complex, which contains, besides FHIP and Hook proteins, Fused Toes (FTS). Although this complex was not previously shown to be involved in dynein-mediated transport, we show here that loss of either FhipA or FtsA (A. nidulans FTS homologue) disrupts HookA–early endosome association and inhibits early endosome movement. Both FhipA and FtsA associate with early endosomes, and interestingly, while FtsA–early endosome association requires FhipA and HookA, FhipA–early endosome association is independent of HookA and FtsA. Thus FhipA is more directly linked to early endosomes than HookA and FtsA. However, in the absence of HookA or FtsA, FhipA protein level is significantly reduced. Our results indicate that all three proteins in the FtsA/HookA/FhipA complex are important for dynein-mediated early endosome movement.
MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers
Authors: Jiang Peng , Meyer Susanne , Hou Zhonggang , Propson Nicholas E. , Soh H. Tom , Thomson James A. , Stewart Ron
Published: May 2014

Summary: Aptamers are ‘synthetic antibodies’ that can bind to target molecules with high affinity and specificity. Aptamers are chemically synthesized and their discovery can be performed completely in vitro , rather than relying on in vivo biological processes, making them well-suited for high-throughput discovery. However, a large fraction of the most enriched aptamers in Systematic Evolution of Ligands by EXponential enrichment (SELEX) rounds display poor binding activity. Here, we present MPBind, a M eta-motif-based statistical framework and pipeline to P redict the Bind ing potential of SELEX-derived aptamers. Using human embryonic stem cell SELEX-Seq data, MPBind achieved high prediction accuracy for binding potential. Further analysis showed that MPBind is robust to both polymerase chain reaction amplification bias and incomplete sequencing of aptamer pools. These two biases usually confound aptamer analysis.

Availability and implementation : MPBind software and documents are available at http://www.morgridge.net/MPBind.html . The human embryonic stem cells whole-cell SELEX-Seq data are available at http://www.morgridge.net/Aptamer/ .

Contact : RStewart@morgridge.org

Supplementary information : Supplementary data are available at Bioinformatics online.
MoDPepInt: an interactive web server for prediction of modular domain–peptide interactions
Authors: Kundu Kousik , Mann Martin , Costa Fabrizio , Backofen Rolf
Published: May 2014

Summary : MoDPepInt (Modular Domain Peptide Interaction) is a new easy-to-use web server for the prediction of binding partners for modular protein domains. Currently, we offer models for SH2, SH3 and PDZ domains via the tools SH2PepInt, SH3PepInt and PDZPepInt, respectively. More specifically, our server offers predictions for 51 SH2 human domains and 69 SH3 human domains via single domain models, and predictions for 226 PDZ domains across several species, via 43 multidomain models. All models are based on support vector machines with different kernel functions ranging from polynomial, to Gaussian, to advanced graph kernels. In this way, we model non-linear interactions between amino acid residues. Results were validated on manually curated datasets achieving competitive performance against various state-of-the-art approaches.

Availability and implementation: The MoDPepInt server is available under the URL http://modpepint.informatik.uni-freiburg.de/

Contact : backofen@informatik.uni-freiburg.de

Supplementary information : Supplementary data are available at Bioinformatics online.
Massifquant: open-source Kalman filter-based XC-MS isotope trace feature detection
Authors: Conley Christopher J. , Smith Rob , Torgrip Ralf J. O. , Taylor Ryan M. , Tautenhahn Ralf , Prince John T.
Published: May 2014

Motivation: Isotope trace (IT) detection is a fundamental step for liquid or gas chromatography mass spectrometry (XC-MS) data analysis that faces a multitude of technical challenges on complex samples. The Kalman filter (KF) application to IT detection addresses some of these challenges; it discriminates closely eluting ITs in the m/z dimension, flexibly handles heteroscedastic m/z variances and does not bin the m/z axis. Yet, the behavior of this KF application has not been fully characterized, as no cost-free open-source implementation exists and incomplete evaluation standards for IT detection persist.

Results: Massifquant is an open-source solution for KF IT detection that has been subjected to novel and rigorous methods of performance evaluation. The presented evaluation with accompanying annotations and optimization guide sets a new standard for comparative IT detection. Compared with centWave, matchedFilter and MZMine2—alternative IT detection engines—Massifquant detected more true ITs in a real LC-MS complex sample, especially low-intensity ITs. It also offers competitive specificity and equally effective quantitation accuracy.

Availability and implementation: Massifquant is integrated into XCMS with GPL license ≥ 2.0 and hosted by Bioconductor: http://bioconductor.org . Annotation data are archived at http://hdl.lib.byu.edu/1877/3232 . Parameter optimization code and documentation is hosted at https://github.com/topherconley/optimize-it .

Contact:  cjconley@ucdavis.edu or jtprince@chem.byu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Nonresponse and Mode Effects in Self- and Interviewer-Administered Surveys
Authors: Atkeson Lonna Rae , Adams Alex N. , Alvarez R. Michael
Published: May 2014

We examine the quality of two probability-based polls, one interviewer administered (telephone) and one self-administered (Internet and mail mixed mode survey). The polls use the same sampling frame (registered voters) and the same questions. First, we examine the representativeness of both surveys using information known about the population, and although we find important differences between the two in terms of sampling and nonresponse bias, we also find that both surveys represent the underlying population despite low response rates. We also test for mode effects between surveys due to social desirability and how it influences nondifferentiation or satisficing. Using a variety of methods (t-tests, multivariate regression, and genetic propensity matching), we find evidence that the presence of an interviewer alters response patterns on ego-driven questions. The implications of our work are important, due to the increasing popularity of mixed mode surveys. Researchers need to be methodologically sensitive to these differences when analyzing surveys that allow for different response modes.
Introduction to Political Analysis Mini-Symposium on Advances in Survey Methodology
Authors: Atkeson Lonna Rae , Alvarez R. Michael
Published: May 2014

Over the last decade the survey environment has been rapidly changing, creating new opportunities and new challenges for survey methodologists. These include: relatively low response among all contact modes and designs; the rapid replacement of landline telephones for mobile and smart phones; the integration of new and different types of data for sampling and new sampling methods; the use of different survey interview modes; how to study behaviors and opinions about sensitive topics; and the development of survey designs for experts and opinion leaders. All have implications for data quality and for our ability to consistently and reliably answer substantive and theoretical questions about politics and society.
Cellular buckling in stiffened plates
Authors: Wadee M. Ahmer , Farsi Maryam
Published: May 2014

An analytical model based on variational principles for a thin-walled stiffened plate subjected to axial compression is presented. A system of nonlinear differential and integral equations is derived and solved using numerical continuation. The results show that the system is susceptible to highly unstable local–global mode interaction after an initial instability is triggered. Moreover, snap-backs in the response showing sequential destabilization and restabilization, known as cellular buckling or snaking, arise. The analytical model is compared with static finite element (FE) models for joint conditions between the stiffener and the main plate that have significant rotational restraint. However, it is known from previous studies that the behaviour, where the same joint is insignificantly restrained rotationally, is captured better by an analytical approach than by standard FE methods; the latter being unable to capture cellular buckling behaviour even though the phenomenon is clearly observed in laboratory experiments.
A non-asymptotic homogenization theory for periodic electromagnetic structures
Authors: Tsukerman Igor , Markel Vadim A.
Published: May 2014

Homogenization of electromagnetic periodic composites is treated as a two-scale problem and solved by approximating the fields on both scales with eigenmodes that satisfy Maxwell's equations and boundary conditions as accurately as possible. Built into this homogenization methodology is an error indicator whose value characterizes the accuracy of homogenization. The proposed theory allows one to define not only bulk, but also position-dependent material parameters (e.g. in proximity to a physical boundary) and to quantify the trade-off between the accuracy of homogenization and its range of applicability to various illumination conditions.
Geodermatophilus brasiliensis sp. nov., isolated from Brazilian soil
Authors: Bertazzo Marcelo , Montero-Calasanz Maria del Carmen , Martinez-Garcia Manuel , Spröer Cathrin , Schumann Peter , Kroppenstedt Reiner M. , Stackebrandt Erko , Klenk Hans-Peter , Fiedler Hans-Peter
Published: May 2014

A Gram-reaction-positive bacterial isolate, designated Tü 6233T, with rudimentary, coral-pink vegetative mycelium that formed neither aerial mycelium nor spores, was isolated from a Brazilian soil sample. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus

Geodermatophilus

. Cell-wall hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid and galactose as the diagnostic sugar. The major fatty acids were iso-C16 : 0, iso-C15 : 0 and C17 : 1ω8c and the predominant menaquinone was MK-9(H4). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol, an unknown glycophospholipid and an unknown phospholipid. The DNA G+C content of the strain was 75.4 mol%. The 16S rRNA gene sequence identity with members of the genus

Geodermatophilus

was 94.2–98.7 %. Based on phenotypic, chemotaxonomic and phylogenetic data, strain Tü 6233T is proposed to represent a novel species, Geodermatophilus brasiliensis sp. nov., with the type strain Tü 6233T ( = DSM 44526T = CECT 8402T).
Quantifying the effects of anagenetic and cladogenetic evolution
Authors: Bartoszek Krzysztof
Published: May 2014

An ongoing debate in evolutionary biology is whether phenotypic change occurs predominantly around the time of speciation or whether it instead accumulates gradually over time. In this work I propose a general framework incorporating both types of change, quantify the effects of speciational change via the correlation between species and attribute the proportion of change to each type. I discuss results of parameter estimation of Hominoid body size in this light. I derive mathematical formulae related to this problem, the probability generating functions of the number of speciation events along a randomly drawn lineage and from the most recent common ancestor of two randomly chosen tip species for a conditioned Yule tree. Additionally I obtain in closed form the variance of the distance from the root to the most recent common ancestor of two randomly chosen tip species.
A comparative study of techniques for differential expression analysis on RNA-Seq data
Authors: Zhang Zong Hong , Jhaveri Dhanisha J. , Marshall Vikki M. , Bauer Denis C. , Edson Janette , Narayanan Ramesh K. , Robinson Gregory J. , Lundberg Andreas E. , Bartlett Perry F. , Wray Naomi R. , Zhao Qiong-Yi
Published: May 2014

Recent advances in next-generation sequencing technology allow high-throughput cDNA sequencing (RNA-Seq) to be widely applied in transcriptomic studies, in particular for detecting differentially expressed genes between groups. Many software packages have been developed for the identification of differentially expressed genes (DEGs) between treatment groups based on RNA-Seq data. However, there is a lack of consensus on how to approach an optimal study design and choice of suitable software for the analysis. In this comparative study we evaluate the performance of three of the most frequently used software tools: Cufflinks-Cuffdiff2, DESeq and edgeR. A number of important parameters of RNA-Seq technology were taken into consideration, including the number of replicates, sequencing depth, and balancedvs.unbalanced sequencing depth within and between groups. We benchmarked results relative to sets of DEGs identified through either quantitative RT-PCR or microarray. We observed that edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives. Overall, DESeq or taking the intersection of DEGs from two or more tools is recommended if the number of false positives is a major concern in the study. In other circumstances, edgeR is slightly preferable for differential expression analysis at the expense of potentially introducing more false positives.
Extensive Regulation of Metabolism and Growth during the Cell Division Cycle
Authors: Slavov Nikolai , Botstein David , Caudy Amy
Published: May 2014

Yeast cells grown in culture can spontaneously synchronize their respiration, metabolism, gene expression and cell division. Such metabolic oscillations in synchronized cultures reflect single-cell oscillations, but the relationship between the oscillations in single cells and synchronized cultures is poorly understood. To understand this relationship and the coordination between metabolism and cell division, we collected and analyzed DNA-content, gene-expression and physiological data, at hundreds of time-points, from cultures metabolically-synchronized at different growth rates, carbon sources and biomass densities. The data enabled us to extend and generalize our mechanistic model, based on ensemble average over phases (EAP), connecting the population-average geneexpression of asynchronous cultures to the gene-expression dynamics in the single-cells comprising the cultures. The extended model explains the carbon-source specific growth-rate responses of hundreds of genes. Our physiological data demonstrate that the frequency of metabolic cycling in synchronized cultures increases with the biomass density, suggesting that this cycling is an emergent behavior, resulting from the entraining of the single-cell metabolic cycle by a quorum-sensing mechanism, and thus underscoring the difference between metabolic cycling in single cells and in synchronized cultures. Measurements of constant levels of residual glucose across metabolically synchronized cultures indicate that storage carbohydrates are required to fuel not only the G1/S transition of the division cycle but also the metabolic cycle. Despite the large variation in profiled conditions and in the scale of their dynamics, most genes preserve invariant dynamics of coordination with each other and with the rate of oxygen consumption. Similarly, the G1/S transition always occurs at the beginning, middle or end of the high oxygen consumption phases, analogous to observations in human and drosophila cells. These results highlight evolutionary conserved coordination among metabolism, cell growth and division.
Artificially Inducing Close Apposition of Endoplasmic Reticulum and Mitochondria Induces Mitochondrial Fragmentation
Authors: Miller Victoria J. , Stephens David J.
Published: May 2014

Cycles of mitochondrial fission and fission are essential for normal cell physiology. Defects in the machinery controlling these processes lead to neurodegenerative disease. While we are beginning to understand the machinery that drives fission, our knowledge of the spatial and temporal control of this event is lacking. Here we use a rapamycin-inducible heterodimerization system comprising both ER and mitochondrial transmembrane components to bring the ER membrane into close physical proximity with mitochondria. We show that this artificial apposition of membranes is sufficient to cause rapid mitochondrial fragmentation. Resulting mitochondrial fragments are shown to be distinct entities using fluorescence recovery after photobleaching. We also show that these fragments retain a mitochondrial membrane potential. In contrast, inducible tethering of the peripheral ER exit site protein TFG does not cause mitochondrial fragmentation suggesting that very close apposition of the two membranes is required.
Cis-regulatory Elements and Human Evolution
Authors: Siepel Adam , Arbiza Leonardo
Published: May 2014

Modification of gene regulation has long been considered an important force in human evolution, particularly through changes tocis-regulatory elements (CREs) that function in transcriptional regulation. For decades, however, the study ofcis-regulatory evolution was severely limited by the available data. New data sets describing the locations of CREs and genetic variation within and between species have now made it possible to study CRE evolution much more directly on a genome-wide scale. Here, we review recent research on the evolution of CREs in humans based on large-scale genomic data sets. We consider inferences based on primate divergence, human polymorphism, and combinations of divergence and polymorphism. We then consider “new frontiers” in this field stemming from recent research on transcriptional regulation.
Lipoate-Protein Ligase and Octanoyltransferase Are Essential for Protein Lipoylation in Mitochondria of Arabidopsis
Authors: Ewald Ralph , Hoffmann Christiane , Florian Alexandra , Neuhaus Ekkehard , Fernie Alisdair R. , Bauwe Hermann
Published: May 2014

Prosthetic lipoyl groups are required for the function of several essential multienzyme complexes, such as pyruvate dehydrogenase (PDH), α-ketoglutarate dehydrogenase (KGDH), and the glycine cleavage system (glycine decarboxylase [GDC]). How these proteins are lipoylated has been extensively studied in prokaryotes and yeast (Saccharomyces cerevisiae), but little is known for plants. We earlier reported that mitochondrial fatty acid synthesis by ketoacyl-acyl carrier protein synthase is not vital for protein lipoylation in Arabidopsis (Arabidopsis thaliana) and does not play a significant role in roots. Here, we identify Arabidopsis lipoate-protein ligase (AtLPLA) as an essential mitochondrial enzyme that uses octanoyl-nucleoside monophosphate and possibly other donor substrates for the octanoylation of mitochondrial PDH-E2 and GDC H-protein; it shows no reactivity with bacterial and possibly plant KGDH-E2. The octanoate-activating enzyme is unknown, but we assume that it uses octanoyl moieties provided by mitochondrial β-oxidation. AtLPLA is essential for the octanoylation of PDH-E2, whereas GDC H-protein can optionally also be octanoylated by octanoyltransferase (LIP2) using octanoyl chains provided by mitochondrial ketoacyl-acyl carrier protein synthase to meet the high lipoate requirement of leaf mesophyll mitochondria. Similar to protein lipoylation in yeast, LIP2 likely also transfers octanoyl groups attached to the H-protein to KGDH-E2 but not to PDH-E2, which is exclusively octanoylated by LPLA. We suggest that LPLA and LIP2 together provide a basal protein lipoylation network to plants that is similar to that in other eukaryotes.
Ribosomal Protein RPL27a Promotes Female Gametophyte Development in a Dose-Dependent Manner
Authors: Zsögön Agustin , Szakonyi Dóra , Shi Xiuling , Byrne Mary E.
Published: May 2014

Ribosomal protein mutations in Arabidopsis (Arabidopsis thaliana) result in a range of specific developmental phenotypes. Why ribosomal protein mutants have specific phenotypes is not fully known, but such defects potentially result from ribosome insufficiency, ribosome heterogeneity, or extraribosomal functions of ribosomal proteins. Here, we report that ovule development is sensitive to the level of Ribosomal Protein L27a (RPL27a) and is disrupted by mutations in the two paralogs RPL27aC and RPL27aB. Mutations in RPL27aC result in high levels of female sterility, whereas mutations in RPL27aB have a significant but lesser effect on fertility. Progressive reduction in RPL27a function results in increasing sterility, indicating a dose-dependent relationship between RPL27a and female fertility. RPL27a levels in both the sporophyte and gametophyte affect female gametogenesis, with different developmental outcomes determined by the dose of RPL27a. These results demonstrate that RPL27aC and RPL27aB act redundantly and reveal a function for RPL27a in coordinating complex interactions between sporophyte and gametophyte during ovule development.
Structures of inactive CRP species reveal the atomic details of the allosteric transition that discriminates cyclic nucleotide second messengers
Authors: Seok Seung-Hyeon , Im Hookang , Won Hyung-Sik , Seo Min-Duk , Lee Yoo-Sup , Yoon Hye-Jin , Cha Min-Jeong , Park Jin-Young , Lee Bong-Jin
Published: May 2014

The prokaryotic global transcription factor CRP has been considered to be an ideal model for in-depth study of both the allostery of the protein and the differential utilization of the homologous cyclic nucleotide second messengers cAMP and cGMP. Here, atomic details from the crystal structures of two inactive CRP species, an apo form and a cGMP-bound form, in comparison with a known active conformation, the cAMP–CRP complex, provide macroscopic and microscopic insights into CRP allostery, which is coupled to specific discrimination between the two effectors. The cAMP-induced conformational transition, including dynamic fluctuations, can be driven by the fundamental folding forces that cause water-soluble globular proteins to construct an optimized hydrophobic core, including secondary-structure formation. The observed conformational asymmetries underlie a negative cooperativity in the sequential binding of cyclic nucleotides and a stepwise manner of binding with discrimination between the effector molecules. Additionally, the finding that cGMP, which is specifically recognized in asynconformation, induces an inhibitory conformational change, rather than a null effect, on CRP supports the intriguing possibility that cGMP signalling could be widely utilized in prokaryotes, including in aggressive inhibition of CRP-like proteins.
Structural elucidation of the hormonal inhibition mechanism of the bile acid cholate on human carbonic anhydrase II
Authors: Boone Christopher D. , Tu Chingkuang , McKenna Robert
Published: May 2014

The carbonic anhydrases (CAs) are a family of mostly zinc metalloenzymes that catalyze the reversible hydration/dehydration of CO2into bicarbonate and a proton. Human isoform CA II (HCA II) is abundant in the surface epithelial cells of the gastric mucosa, where it serves an important role in cytoprotection through bicarbonate secretion. Physiological inhibition of HCA IIviathe bile acids contributes to mucosal injury in ulcerogenic conditions. This study details the weak biophysical interactions associated with the binding of a primary bile acid, cholate, to HCA II. The X-ray crystallographic structure determined to 1.54 Å resolution revealed that cholate does not make any direct hydrogen-bond interactions with HCA II, but instead reconfigures the well ordered water network within the active site to promote indirect binding to the enzyme. Structural knowledge of the binding interactions of this nonsulfur-containing inhibitor with HCA II could provide the template design for high-affinity, isoform-specific therapeutic agents for a variety of diseases/pathological states, including cancer, glaucoma, epilepsy and osteoporosis.