bluuebunny/crossref_metadata_2025 huggingface dataset:
Polarization-dependent exciton dynamics in tetracene single crystals
Authors: Zhang Bo , Zhang Chunfeng , Xu Yanqing , Wang Rui , He Bin , Liu Yunlong , Zhang Shimeng , Wang Xiaoyong , Xiao Min
Published: December 2014

We conduct polarization-dependent ultrafast spectroscopy to study the dynamics of singlet fission (SF) in tetracene single crystals. The spectrotemporal species for singlet and triplet excitons in transient absorption spectra are found to be strongly dependent on probe polarization. By carefully analyzing the polarization dependence, the signals contributed by different transitions related to singlet excitons have been disentangled, which is further applied to construct the correlation between dynamics of singlet and triplet excitons. The anisotropy of exciton dynamics provides an alternative approach to tackle the long-standing challenge in understanding the mechanism of singlet fission in organic semiconductors.
Effects of low-temperature (120 °C) annealing on the carrier concentration and trap density in amorphous indium gallium zinc oxide thin film transistors
Authors: Kim Jae-sung , Oh Byung Su , Piao Mingxing , Joo Min-Kyu , Jang Ho-Kyun , Ahn Seung-Eon , Kim Gyu-Tae
Published: December 2014

We report an investigation of the effects of low-temperature annealing on the electrical properties of amorphous indium gallium zinc oxide (a-IGZO) thin-film transistors (TFTs). X-ray photoelectron spectroscopy was used to characterize the charge carrier concentration, which is related to the density of oxygen vacancies. The field-effect mobility was found to decrease as a function of the charge carrier concentration, owing to the presence of band-tail states. By employing the transmission line method, we show that the contact resistance did not significantly contribute to the changes in device performance after annealing. In addition, using low-frequency noise analyses, we found that the trap density decreased by a factor of 10 following annealing at 120 °C. The switching operation and on/off ratio of the a-IGZO TFTs improved considerably after low-temperature annealing.
Dissipative properties and chain evolution of highly strained nanocomposite hydrogel
Authors: Tang Jingda , Xu Gao , Sun Youyi , Pei Yongmao , Fang Daining
Published: December 2014

The dissipative property is crucial to the toughness and recovery of hydrogels. In our investigation, systematic uniaxial tension tests were conducted to evaluate the dissipative properties of poly (N-isopropylacrylamide) nanocomposite hydrogels. Two dissipative mechanisms are presented for both small and large stretches. Before yielding, most dissipation results from the orientation of clay platelets along the tensile direction; after yielding, polymer chains peel off from clay platelets to induce hysteresis. For the first time, a quadratic power law between the hysteresis work and the maximum stretch is obtained. The hysteresis work is irrelevant to the detailed loading history. When the hydrogel is unloaded to a critical displacement, polymer chains can re-adsorb to the surfaces of clay platelets. The quantity of re-ruptured physical bonds is proportional to the product of re-adsorption ratio and that of initially ruptured bonds. These results may be useful for the toughening design of hydrogels.
Tuning the polarization of transmitted light through a double-layered gold film of U-shaped apertures by changing the chiral configuration
Authors: Bao Yongjun , Hou Dongjie , Tang Xinyu , Zhao Bin , Peng Ruwen , Lu Xiang , Shao Jun , Cui Tian , Wang Mu
Published: December 2014

We propose a double-layered gold film structured with U-shaped aperture in chiral configuration to manipulate the polarization of transmitted light. Two U-shaped aperture arrays are fabricated on both gold films separated by a spacing film, where each face-to-face pair of apertures is arranged perpendicularly to each other in counterclockwise or clockwise. Due to the coupling of the pairs, surface plasmon polariton resonances in the double-layered films in phase and out of phase at two frequencies, respectively. The polarization of transmitted light is rotated 90° by switching the chiral configuration of the doubled-layered gold film between counterclockwise and clockwise. The double-layered gold film structured with apertures tailors the polarization state of the transmitted light at their resonance peaks relative to their complementary structures. These results provide us an effective way to realize an extraordinary transmission and manipulate the polarization state of a double-layered films in chiral configuration.
Effects of income supplementation on health of the poor elderly: The case of Mexico
Authors: Aguila Emma , Kapteyn Arie , Smith James P.
Published: December 2014

Significance

Effects of income support on well-being and health of the poor elderly especially in low-income country settings is uncertain as experiments that increase incomes and evaluate their impacts on health among the elderly population are almost nonexistent around the world. In our experiment in the Mexican state of Yucatan, we find strong evidence that income supplements for the poor elderly in low- and middle-income settings can have significant health benefits even in the short run. Additional experiments should be conducted around the world as our experience indicates that these experiments are operationally feasible.
Superresolution microscopy reveals spatial separation of UCP4 and F
0
F
1
-ATP synthase in neuronal mitochondria
Authors: Klotzsch Enrico , Smorodchenko Alina , Löfler Lukas , Moldzio Rudolf , Parkinson Elena , Schütz Gerhard J. , Pohl Elena E.
Published: December 2014

Significance

The question as to how the proton motive force in mitochondria is distributed among the proteins that require a proton gradient for their work is one of the central unresolved questions in mitochondrial physiology and important for the mechanistic insight in the function of mitochondrial proteins. Our results suggest that the local separation of the proteins on the inner mitochondrial membrane makes it impossible for uncoupling protein 4 (UCP4) to uncouple phosphorylation from proton pumping. Nonetheless, UCP4 should be well able to shortcut excessive transmembrane proton gradients to thereby regulate reactive oxygen species production. It explains how the proton transporter may fulfill that function without being a real UCP like UCP1.
Free-energy landscape of ion-channel voltage-sensor–domain activation
Authors: Delemotte Lucie , Kasimova Marina A. , Klein Michael L. , Tarek Mounir , Carnevale Vincenzo
Published: December 2014

Significance

Voltage-gated cation channels (VGCCs) shape cellular excitability. Their working cycle involves the complex conformational change of modular protein units called voltage sensor domains (VSDs). For over 40 y, these rearrangements have been recorded as “gating” currents, the intensities and kinetics of which are unique signatures of VGCC function. We show that the atomistic description of VSD activation obtained by molecular dynamics simulations and free-energy calculations is consistent with the phenomenological models adopted to account for the macroscopic observables measured by electrophysiology. Our findings pave the way for in silico studies of the VGCC electrophysiological response and hold promise to uncover the molecular underpinnings of inherited channelopathies and modulation of VGCCs by drugs and toxins.
Autophagic flux without a block differentiates varicella-zoster virus infection from herpes simplex virus infection
Authors: Buckingham Erin M. , Carpenter John E. , Jackson Wallen , Zerboni Leigh , Arvin Ann M. , Grose Charles
Published: December 2014

Significance

Varicella-zoster virus (VZV) is an important pathogen, which causes varicella and herpes zoster in humans. In general, there are similarities in virus-host interactions between the alphaherpesviruses. One notable exception is the response to autophagy. VZV infection induces autophagy. This is in contrast to herpes simplex virus (HSV), which has two genes that inhibit autophagy, ICP34.5 and US11; neither is present in the smaller VZV genome. In this study, we found that VZV-induced autophagic flux was not blocked. These results reinforce prior observations showing a proviral effect of autophagy on VZV infectivity and spread. These VZV findings also exhibit similarities with recent data about a requirement for early phase autophagy during Epstein–Barr virus infection, a phylogenetically distant gammaherpesvirus.
Measuring the effectiveness of scientific gatekeeping
Authors: Siler Kyle , Lee Kirby , Bero Lisa
Published: December 2014

Significance

Peer review is an institution of enormous importance for the careers of scientists and the content of published science. The decisions of gatekeepers—editors and peer reviewers—legitimize scientific findings, distribute professional rewards, and influence future research. However, appropriate data to gauge the quality of gatekeeper decision-making in science has rarely been made publicly available. Our research tracks the popularity of rejected and accepted manuscripts at three elite medical journals. We found that editors and reviewers generally made good decisions regarding which manuscripts to promote and reject. However, many highly cited articles were surprisingly rejected. Our research suggests that evaluative strategies that increase the mean quality of published science may also increase the risk of rejecting unconventional or outstanding work.
Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle
Authors: He Xuesong , McLean Jeffrey S. , Edlund Anna , Yooseph Shibu , Hall Adam P. , Liu Su-Yang , Dorrestein Pieter C. , Esquenazi Eduardo , Hunter Ryan C. , Cheng Genhong , Nelson Karen E. , Lux Renate , Shi Wenyuan
Published: December 2014

Significance

TM7 is one of the most enigmatic bacterial phyla among the uncultivated candidate phyla referred to as “microbial dark matter,” and it has potential pathogenic associations. We revealed molecular insights into its uncultivability and pathogenicity, as well its unique epibiotic and parasitic lifestyle phases. These novel discoveries shed significant light on the biological, ecological, and medical importance of TM7, as well as providing useful information for culturing other TM7 and currently uncultivable bacteria that may evade standard cultivation approaches.
Deep conservation of wrist and digit enhancers in fish
Authors: Gehrke Andrew R. , Schneider Igor , de la Calle-Mustienes Elisa , Tena Juan J. , Gomez-Marin Carlos , Chandran Mayuri , Nakamura Tetsuya , Braasch Ingo , Postlethwait John H. , Gómez-Skarmeta José Luis , Shubin Neil H.
Published: December 2014

Significance

The fossil record shows that the wrist and digits have an aquatic origin, becoming recognizable in a group of (mostly extinct) fish that contained robust fins. Do the fins of living fishes have the equivalent of these structures? Because comparisons of fin and limb morphology have been inconclusive, we sought to investigate this question using developmental and molecular data. By utilizing a nonmodel fish (the spotted gar), we find that the regulatory networks that control “wrist and digit”-building genes (
Hox
) are deeply conserved between fish and tetrapods. The genomic architecture described here defines
Hox
gene activity in fins and limbs as equivalent, in turn suggesting equivalence between the distal bones of fish fins and the wrist and/or digits of tetrapods.
Iron stable isotopes track pelagic iron cycling during a subtropical phytoplankton bloom
Authors: Ellwood Michael J. , Hutchins David A. , Lohan Maeve C. , Milne Angela , Nasemann Philipp , Nodder Scott D. , Sander Sylvia G. , Strzepek Robert , Wilhelm Steven W. , Boyd Philip W.
Published: December 2014

Significance

The supply and bioavailability of dissolved iron sets the magnitude of surface productivity for approximately 40% of the global ocean; however, our knowledge of how it is transferred between chemical states and pools is poorly constrained. Here we utilize the isotopic composition of dissolved and particulate iron to fingerprint its transformation in the surface ocean by abiotic and biotic processes. Photochemical and biological reduction and dissolution of particulate iron in the surface ocean appear to be key processes in regulating its supply and bioavailability to marine biota. Iron isotopes offer a new window into our understanding of the internal cycling of Fe, thereby allowing us to follow its biogeochemical transformations in the surface ocean.
Remembering the past and imagining the future: Selective effects of an episodic specificity induction on detail generation
Authors: Madore Kevin P. , Schacter Daniel L.
Published: December 2014

According to the constructive episodic simulation hypothesis, remembering past experiences and imagining future experiences both rely heavily on episodic memory. However, recent research indicates that nonepisodic processes such as descriptive ability also influence memory and imagination. We recently found that an episodic specificity induction—brief training in recollecting details of past experiences—enhanced detail generation on memory and imagination tasks but not a picture description task and thereby concluded that the induction can dissociate episodic processes involved in remembering the past and imagining the future from those nonepisodic processes involved in description. To evaluate the generality of our previous findings and to examine the role of generative search in producing those findings, we modified our paradigm so that word cues replaced picture cues, and a word comparison task that requires generation of sentences and word definitions replaced picture description. Young adult participants received either a specificity induction or one of two control inductions before completing the memory, imagination, and word comparison tasks. Replicating and extending our previous work, we found that the specificity induction increased detail generation in memory and imagination without having an effect on word comparison. The induction's selective effect on memory and imagination stemmed from an increase in internal (i.e., on-topic and episodic) details and had no effect on external (e.g., off-topic or semantic) details. The results point to the efficacy of the specificity induction for isolating episodic processes involved in remembering the past and imagining the future even when a nonepisodic task requires generative search.
Self‐Protection, Strategic Interactions, and the Relative Endogeneity of Disease Risks
Authors: Reeling Carson J. , Horan Richard D.
Published: December 2014

Self‐protection is a key behavior that influences infectious disease risks. Spillovers in disease protection create different types of strategic interactions. Under certain conditions, multiple Nash equilibria may arise with the possibility of coordination failure involving excessively low self‐protection, in which case individuals’ expectations of others’ efforts determine which outcome arises. In prior studies, assumed technical relations between self‐protection and infection probabilities drove the strategic interactions. We demonstrate that strategic relations can be endogenously determined and depend on the relative endogeneity of risk (RER), defined here as the degree to which individuals can take control of their own risks in a strategic setting. The potential for coordination failure may arise when RER is sufficiently small, whereas larger levels of RER may eliminate this possibility to ensure larger levels of self‐protection. We find that imposing a behaviorally‐dependent indemnity may increase RER to eliminate the possibility of coordination failure. We apply our analysis to the problem of livestock disease and illustrate the theory using a numerical example of the 2001 United Kingdom foot‐and‐mouth disease epidemic.
Stock assessment methods for sustainable fisheries
Authors: Cadrin Steven X. , Dickey-Collas Mark
Published: December 2014

This special volume of the ICES Journal compiles contributions from the World Conference on Stock Assessment Methods for Sustainable Fisheries (July 2013, Boston, USA). The conference was the product of a strategic initiative on stock assessment methods that engaged many national and regional fishery management organizations to assure that scientists can apply the most appropriate methods when developing management advice. An inclusive workshop was designed to evaluate the performance of a variety of model categories by applying multiple models to selected case study data as well as simulated pseudo-data that had realistic measurement error. All model applications had difficulties in recovering the simulated stock and fishing mortality trends, particularly at the end of the assessment time series, when they are most important for informing fishery management. This general result suggests that the next steps in evaluating the performance of stock assessment methods should include stock status relative to sustainable reference points, catch advice, multi-model consideration, and alternative management procedures. Recognition of the limitations of conventional stock assessment methods should promote further development of data-limited approaches, methods with time-varying parameters, or spatial complexity, and a more revolutionary shift towards the application of multispecies and ecosystem models. The contributions in this volume address methodological themes that are expected to improve the scientific basis of fishery management. Furthermore, the limitations of stock assessment methods and associated uncertainty should be more extensively considered in fishery management strategies and tactical decisions. Recommendations developed during the conference called for the establishment of a global initiative to synthesize regional advances, form guidance on best practices, promote strategic investments, and highlight research needs for fish stock assessments.
An international cross-sectional survey of antimicrobial stewardship programmes in hospitals
Authors: Howard P. , Pulcini C. , Levy Hara G. , West R. M. , Gould I. M. , Harbarth S. , Nathwani D.
Published: December 2014

Objectives

To report the extent and components of global efforts in antimicrobial stewardship (AMS) in hospitals.

Methods

An Internet-based survey comprising 43 questions was disseminated worldwide in 2012.

Results

Responses were received from 660 hospitals in 67 countries: Africa, 44; Asia, 50; Europe, 361; North America, 72; Oceania, 30; and South and Central America, 103. National AMS standards existed in 52% of countries, 4% were planning them and 58% had an AMS programme. The main barriers to implementing AMS programmes were perceived to be a lack of funding or personnel, a lack of information technology and prescriber opposition. In hospitals with an existing AMS programme, AMS rounds existed in 64%; 81% restricted antimicrobials (carbapenems, 74.3%; quinolones, 64%; and cephalosporins, 58%); and 85% reported antimicrobial usage, with 55% linking data to resistance rates and 49% linking data to infection rates. Only 20% had electronic prescribing for all patients. A total of 89% of programmes educated their medical, nursing and pharmacy staff on AMS. Of the hospitals, 38% had formally reviewed their AMS programme: reductions were reported by 96% of hospitals for inappropriate prescribing, 86% for broad-spectrum antibiotic use, 80% for expenditure, 71% for healthcare-acquired infections, 65% for length of stay or mortality and 58% for bacterial resistance.

Conclusions

The worldwide development and implementation of AMS programmes varies considerably. Our results should inform and encourage the further evaluation of this with a view to promoting a worldwide stewardship framework. The prospective measurement of well-defined outcomes of the impact of these programmes remains a significant challenge.
Prospective evaluation of the cost of diagnosis and treatment of invasive fungal disease in a cohort of adult haematology patients in the UK
Authors: Ceesay M. Mansour , Sadique Zia , Harris Ross , Ehrlich Alice , Adams Elisabeth J. , Pagliuca Antonio
Published: December 2014

Objectives

The direct cost of invasive fungal disease (IFD) includes antifungal drugs as well as diagnostic tests. The aim of this study was to determine these costs.

Methods

A total of 203 haematology patients were enrolled into the study and followed for a median of 556 days. Data were prospectively collected on antifungal drugs, diagnostic tests, length of stay and antibiotic usage.

Results

The overall mean (IQR) cost of care per patient (using UK-based reference costs) was £88 911 (45 339–121 594), £61 509 (39 748–78 383), £50 332 (23 037–72 057) and £34 075 (19 928–43 900) for proven/probable IFD, possible IFD, not classified and no evidence of IFD, respectively (P < 0.001). The attributable cost of IFD was £54 836. Inpatient hospital stay accounted for nearly 74% of costs. In proven/probable IFD inpatient care, antifungals, antibiotics and IFD status accounted for 68%, 25%, 5% and 2%, respectively, compared with 85%, 11%, 2% and 2%, respectively, for no IFD (P < 0.001). Among the allogeneic transplant patients, £36 914 (60%) of the total cost (£60 917) was used during the first 100 days.

Conclusions

IFD was associated with longer length of stay and higher total overall cost of care, with attributable costs greater than £50 000 per case of IFD. Costs for inpatient stay far outstrip the cost of antifungal agents.
Probing the accretion scheme of the dipping X-ray binary 4U 1915−05 with Suzaku
Authors: Zhang Zhongli , Makishima Kazuo , Sakurai Soki , Sasano Makoto , Ono Ko
Published: December 2014

The dipping low-mass X-ray binary 4U 1915−05 was observed by Suzaku on 2007 November 8 for a net exposure of 39 ks. It was detected by the XIS with a 0.8–10 keV signal rate of 9.84 ± 0.01 cts s−1 per camera, and HXD-PIN with a 12–45 keV signal rate of 0.29 ± 0.01 cts s−1. After removing the periodic dips and an X-ray burst, the 0.8–45 keV continuum was successfully described by an optically thick disk emission with an inner-disk temperature ∼ 0.7 keV and a neutron-star blackbody emission with temperature ∼ 1.3 keV, on condition that the blackbody component, or possibly the disk emission too, is significantly Comptonized. This successful model is consistent with 4U 1915−05 being in a high-soft state in this observation, and implies that its broadband spectrum can be interpreted in the same scheme as for many non-dipping low-mass X-ray binaries in the soft state. Its bolometric luminosity (∼ 0.02 times the Eddington limit) is relatively low for the soft state, but within tolerance, if considering the distance and inclination uncertainties. As a high inclination binary, this source exhibited a stronger Comptonization effect, with a larger Comptonizing y-parameter, compared to low and medium inclination binaries. This suggests that the Comptonizing coronae of these objects in the soft state is in an oblate (rather than spherical) shape, extending along the accretion disk plane, because the y-parameter would not depend on the inclination if the corona were spherical.
The pig X and Y chromosomes: structure, sequence and evolution
Authors: Skinner Benjamin M. , Sargent Carole A. , Churcher Carol , Hunt Toby , Herrero Javier , Loveland Jane , Dunn Matt , Louzada Sandra , Fu Beiyuan , Chow William , Gilbert James , Austin-Guest Siobhan , Beal Kathryn , Carvalho-Silva Denise , Cheng William , Gordon Daria , Grafham Darren , Hardy Matt , Harley Jo , Hauser Heidi , Howden Philip , Howe Kerstin , Lachani Kim , Ellis Peter J.I. , Kelly Daniel , Kerry Giselle , Kerwin James , Ng Bee Ling , Threadgold Glen , Wileman Thomas , Wood Jonathan M D , Yang Fengtang , Harrow Jen , Affara Nabeel A. , Tyler-Smith Chris
Published: December 2014

We have generated an improved assembly and gene annotation of the pig X chromosome, and a first draft assembly of the pig Y chromosome, by sequencing BAC and fosmid clones, and incorporating information from optical mapping and fibre-FISH. The X chromosome carries 1,014 annotated genes, 689 of which are protein-coding. Gene order closely matches that found in Primates (including humans) and Carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X chromosome were absent from the pig (e.g. the cancer/testis antigen family) or inactive (e.g.AWAT1), and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y chromosome assembly focussed on two clusters of male-specific low-copy number genes, separated by an ampliconic region including theHSFYgene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. The long arm of the chromosome is almost entirely repetitive, containing previously characterised sequences. Many of the ancestral X-related genes previously reported in at least one mammalian Y chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes - both single copy and amplified - on the pig Y, to compare the pig X and Y chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y chromosome evolution.
Dynamic reorganization of brain functional networks during cognition
Authors: Bola Michał , Sabel Bernhard
Published: December 2014

How cognition emerges from neural dynamics? The dominant hypothesis states that interactions among distributed brain regions through phase synchronization give basis for cognitive processing. Such phase-synchronized networks are transient and dynamic, established on the timescale of milliseconds in order to perform specific cognitive operations. But unlike resting-state networks, the complex organization of transient cognitive networks is typically not characterized within the graph theory framework. Thus, it is not known whether cognitive processing merely changes strength of functional connections or, conversely, requires qualitatively new topological arrangements of functional networks. To address this question, we recorded high-density EEG when subjects performed a visual discrimination task and conducted and event-related network analysis (ERNA) where source-space weighted functional networks were characterized with graph measures. We revealed rapid, transient, and frequency-specific reorganization of the network?s topology during cognition. Specifically, cognitive networks were characterized by strong clustering, low modularity, and strong interactions between hub-nodes. Our findings suggest that dense and clustered connectivity between the hub nodes belonging to different modules is the ?network fingerprint? of cognition. Such reorganization patterns might facilitate global integration of information and provide a substrate for a ?global workspace? necessary for cognition and consciousness to occur. Thus, characterizing topology of the event-related networks opens new vistas to interpret cognitive dynamics in the broader conceptual framework of graph theory.
ViennaNGS: A toolbox for building efficient next-generation sequencing analysis pipelines
Authors: Wolfinger Michael T. , Fallmann Jörg , Eggenhofer Florian , Amman Fabian
Published: December 2014

Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. It comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools.
Real-world Interaction Networks Buffer Impact of Small Evolutionary Shifts On Biodiversity
Authors: Leventhal Gabriel E , Wang Liyu , Kouyos Roger D
Published: December 2014

Biodiversity maintenance and community evolution depend on the species interaction network. The "diversity-stability debate" has revealed that the complex interaction structure within real-world ecosystems determines how ecological communities respond to environmental changes, but can have opposite effects depending on the community type. Here we quantify the influence of shifts on community diversity and stability at both the species level and the community level. We use interaction networks from 19 real-world mutualistic communities and simulate shifts to antagonism. We demonstrate that both the placement of the shifting species in the community, as well as the structure of the interaction network as a whole contribute to stability and diversity maintenance under shifts. Our results suggest that the interaction structure of natural communities generally enhances community robustness against small ecological and evolutionary changes, but exacerbates the consequences of large changes.
Quantifying Cellular Capacity to Identify Gene Expression Designs With Reduced Burden
Authors: Ceroni Francesca , Algar Rhys , Stan Guy-Bart , Ellis Tom
Published: December 2014

Heterologous gene expression can be a significant burden to cells, consuming resources and causing decreased growth and stability. We describe here anin vivomonitor that tracksE. colicapacity changes in real-time and can be used to assay the burden synthetic constructs and their parts impose. By measuring capacity, construct designs with reduced burden can be identifiedand shown to predictably outperform less efficient designs, despite having equivalent expression outputs.
Cleaning protocols for crystallization robots: preventing protease contamination
Authors: Naschberger Andreas , Fürnrohr Barbara G. , Dunzendorfer-Matt Theresia , Bonagura Christopher A. , Wright David , Scheffzek Klaus , Rupp Bernhard
Published: December 2014

The protease in the commonly used commercial low-foam enzyme cleaner Zymit cannot be completely blocked by EDTA, a widely used inhibitor of metalloproteases, at concentrations of up to 5 mM. Severe protein degradation was observed in crystallization drops after EDTA-containing wash steps unless residual Zymit protease was removed with NaOH at a concentration of at least 0.1 M. Wash steps with 0.1% SDS were also ineffective in completely removing the remaining Zymit activity. Protocols including wash steps with at least 0.1 MNaOH, as for example specified in the original ZENM protocol, are recommended to completely deactivate Zymit protease activity.
Crystallization and preliminary X-ray analysis of the NAD+-reducing [NiFe] hydrogenase fromHydrogenophilus thermoluteolusTH-1
Authors: Taketa Midori , Nakagawa Hanae , Habukawa Mao , Osuka Hisao , Kihira Kiyohito , Komori Hirofumi , Shibata Naoki , Ishii Masaharu , Igarashi Yasuo , Nishihara Hirofumi , Yoon Ki-Seok , Ogo Seiji , Shomura Yasuhito , Higuchi Yoshiki
Published: December 2014

NAD+-reducing [NiFe] hydrogenases catalyze the oxidoreduction of dihydrogen concomitant with the interconversion of NAD+and NADH. Here, the isolation, purification and crystallization of the NAD+-reducing [NiFe] hydrogenase fromHydrogenophilus thermoluteolusTH-1 are reported. Crystals of the NAD+-reducing [NiFe] hydrogenase were obtained within one week from a solution containing polyethylene glycol using the sitting-drop vapour-diffusion method and micro-seeding. The crystal diffracted to 2.58 Å resolution and belonged to space groupC2, with unit-cell parametersa= 131.43,b= 189.71,c= 124.59 Å, β = 109.42°. Assuming the presence of two NAD+-reducing [NiFe] hydrogenase molecules in the asymmetric unit,VMwas calculated to be 2.2 Å3 Da−1, which corresponds to a solvent content of 43%. Initial phases were determined by the single-wavelength anomalous dispersion method using the anomalous signal from the Fe atoms.
Systematic analysis of protein–detergent complexes applying dynamic light scattering to optimize solutions for crystallization trials
Authors: Meyer Arne , Dierks Karsten , Hussein Rana , Brillet Karl , Brognaro Hevila , Betzel Christian
Published: December 2014

Detergents are widely used for the isolation and solubilization of membrane proteins to support crystallization and structure determination. Detergents are amphiphilic molecules that form micelles once the characteristic critical micelle concentration (CMC) is achieved and can solubilize membrane proteins by the formation of micelles around them. The results are presented of a study of micelle formation observed byin situdynamic light-scattering (DLS) analyses performed on selected detergent solutions using a newly designed advanced hardware device. DLS was initially appliedin situto detergent samples with a total volume of approximately 2 µl. When measured with DLS, pure detergents show a monodisperse radial distribution in water at concentrations exceeding the CMC. A series of all-transn-alkyl-β-D-maltopyranosides, fromn-hexyl ton-tetradecyl, were used in the investigations. The results obtained verify that the application of DLSin situis capable of distinguishing differences in the hydrodynamic radii of micelles formed by detergents differing in length by only a single CH2group in their aliphatic tails. Subsequently, DLS was applied to investigate the distribution of hydrodynamic radii of membrane proteins and selected water-insoluble proteins in presence of detergent micelles. The results confirm that stable protein–detergent complexes were prepared for (i) bacteriorhodopsin and (ii) FetA in complex with a ligand as examples of transmembrane proteins. A fusion of maltose-binding protein and theDuck hepatitis B virusX protein was added to this investigation as an example of a non-membrane-associated protein with low water solubility. The increased solubility of this protein in the presence of detergent could be monitored, as well as the progress of proteolytic cleavage to separate the fusion partners. This study demonstrates the potential ofin situDLS to optimize solutions of protein–detergent complexes for crystallization applications.
Purification, crystallization and preliminary X-ray diffraction analysis of SpaD, a backbone-pilin subunit encoded by the fimbrialspaFEDoperon inLactobacillus rhamnosusGG
Authors: Chaurasia Priyanka , von Ossowski Ingemar , Palva Airi , Krishnan Vengadesan
Published: December 2014

SpaD is the predicted backbone-pilin subunit of the SpaFED pilus, whose loci are encoded by the fimbrialspaFEDoperon inLactobacillus rhamnosusGG, a Gram-positive gut-adapted commensal strain with perceived probiotic benefits. In this study, soluble recombinant SpaD protein was overproduced inEscherichia coliand then purified by Ni2+-chelating affinity and gel-filtration chromatography. After limited proteolysis with α-chymotrypsin, good-quality crystals of SpaD were obtained which diffracted beyond 2.0 Å resolution. These crystals belonged to the orthorhombic space groupP212121, with unit-cell parametersa= 50.11,b= 83.27,c= 149.65 Å. For phasing, sodium iodide-derivatized crystals were prepared using the halide quick-soaking method and diffraction data were collected in-house to a resolution of 2.2 Å. An interpretable electron-density map was successfully obtained using single-wavelength anomalous diffraction (SAD).
The three-dimensional structure of the cellobiohydrolase Cel7A fromAspergillus fumigatusat 1.5 Å resolution
Authors: Moroz Olga V. , Maranta Michelle , Shaghasi Tarana , Harris Paul V. , Wilson Keith S. , Davies Gideon J.
Published: December 2014

The enzymatic degradation of plant cell-wall cellulose is central to many industrial processes, including second-generation biofuel production. Key players in this deconstruction are the fungal cellobiohydrolases (CBHs), notably those from family GH7 of the carbohydrate-active enzymes (CAZY) database, which are generally known as CBHI enzymes. Here, three-dimensional structures are reported of theAspergillus fumigatusCBHI Cel7A solved in uncomplexed and disaccharide-bound forms at resolutions of 1.8 and 1.5 Å, respectively. The product complex with a disaccharide in the +1 and +2 subsites adds to the growing three-dimensional insight into this family of industrially relevant biocatalysts.
Crystal structure of γ-ethyl-L-glutamateN-carboxy anhydride
Authors: Kanazawa Hitoshi , Inada Aya
Published: December 2014

In the title compound (alternative nameN-carboxy-L-glutamic anhydride γ-ethyl ester), C8H11NO5, the oxazolidine ring is essentially planar, with a maximum deviation of 0.019 (2) Å. In the crystal, molecules are linked by N—H...O hydrogen bonds between the imino group and the carbonyl O atom in the ethyl ester group, forming a tape structure along thec-axis direction. The oxazolidine rings of adjacent tapes are arranged into a layer parallel to theacplane. This arrangement is favourable for the polymerization of the title compound in the solid state.
Use of Vitamin D Receptor Activator, Incident Cardiovascular Disease and Death in a Cohort of Hemodialysis Patients
Authors: Shoji Tetsuo , Marubayashi Seiji , Shigematsu Takashi , Iseki Kunitoshi , Tsubakihara Yoshiharu ,   the Committee of Renal Data Registry,   the Japanese Society for Dialysis Therapy
Published: December 2014

The use of vitamin D receptor activators (VDRAs) is an independent predictor of a lower risk of death from cardiovascular disease (CVD) in patients with chronic kidney disease (CKD). We examined whether the use of VDRAs and other CKD‐mineral bone disorder (MBD)‐related factors are associated with incident CVD or death after CVD in hemodialysis patients. This is a historical cohort study of 37 690 prevalent hemodialysis patients without previous history of CVD at the end of 2004 extracted from a nationwide registry in Japan. The key exposure was the use of VDRAs, and the outcomes were incident CVD (myocardial infarction, cerebral infarction, cerebral hemorrhage, and sudden death) and death after CVD during the 1‐year follow‐up. VDRAs were used in 57% of the subjects at baseline. We identified 2433 patients with incident CVD and 397 deaths after the events. In multivariate logistic regression models, independent predictors of incident CVD were non‐use of VDRA, higher intact PTH, non‐use of calcium‐based phosphate‐binder, and non‐use of non‐calcium‐based phosphate binder. Risk of death after CVD was not significantly associated with VDRA, whereas it was lower in those with lower corrected calcium, and the risk was higher in those with higher phosphate and in non‐users of calcium‐based phosphate binders. The use of VDRAs was associated with a lower risk of incident CVD but not with death after CVD in this large cohort of hemodialysis patients. The CKD‐MBD‐related predictors of poor outcomes are associated with the risk of incident CVD, the risk of death after CVD, or both.
The relationship between synovial fluid VEGF and serum leptin with ultrasonographic findings in knee osteoarthritis
Authors: Kim Hae‐Rim , Lee Jung‐Hwa , Kim Kyoung‐Woon , Kim Bo‐Mi , Lee Sang‐Heon
Published: December 2014

Aim

This study aimed to determine synovial fluid and serum biomarkers which could accord with radiological and ultrasonographic findings in knee osteoarthritis.

Methods

Thirty‐four patients with knee osteoarthritis were detected with joint effusion by clinical examination. Both knee joints were examined using plain radiographs and ultrasonography. Questions were obtained for visual analog scale (VAS), Western Ontario McMaster Universities Osteoarthritis Index and Health Assessment Questionnaire (HAQ). Synovial fluid (SF) and serum levels of vascular endothelial growth factor (VEGF), matrix metalloproteinase (MMP)‐13, leptin, resistin and cartilage oligomeric matrix protein (COMP) were measured using enzyme‐linked immunosorbent assay.

Results

Synovial fluid VEGF level was positively correlated with Kellgren–Lawrence (KL) grades and it was higher in patients with KL grade 4 than those with KL grade 2. SF VEGF correlated with ultrasonographic findings, such as the length of medial osteophytes. The amount of effusion was positively correlated with SF resistin. Serum leptin level had positive correlation with HAQ and the length of medial osteophytes. MMP‐13 or COMP levels were not correlated with radiographic or ultrasonographic findings.

Conclusion

Synovial fluid VEGF level was correlated with radiographic grading, ultrasonographic findings and functional statues in knee osteoarthritis, and serum leptin level also correlated with the ultrasonographic findings and functional status of knee osteoarthritis.
Evidence of ERBB3 gene association with rheumatoid arthritis predisposition
Authors: Chatzikyriakidou Anthoula , Voulgari Paraskevi V. , Drosos Alexandros A.
Published: December 2014

Aim

ERBB3 (v‐erb‐b2 erythroblastic leukemia viral oncogene homolog 3) gene was reported to be related with susceptibility to several autoimmune diseases. Taking this into account, we searched, for the first time, the ERBB3 gene association with rheumatoid arthritis liability.

Methods

One hundred and eighty‐six RA patients and 147 controls were enrolled in the study. Polymerase chain reaction – restriction fragment length polymorphism assay was conducted in rs2271189 and rs2292239 genotyping.

Results

A statistically significant difference was observed in rs2271189 allele distribution between RA patients and controls (P = 0.029, odds ratio: 1.460, 95% confidence interval: 1.040–2.050).

Conclusion

As far as we know, this is the first study which correlates ERBB3 gene with RA susceptibility, adding to a previous report of chromosome 12q13 association with RA liability. Furthermore, we confirmed that polymorphism rs2271189 can predict better ERBB3 gene association with disorders than the previously reported ERBB3 variants. More studies in other ethnic groups of patients are needed so as to reveal the extent of the herein observed genetic association.
Symbiotic bacteria contribute to increasing the population size of a freshwater crustacean, Daphnia magna
Authors: Peerakietkhajorn Saranya , Tsukada Koji , Kato Yasuhiko , Matsuura Tomoaki , Watanabe Hajime
Published: December 2014

The filter‐feeding crustacean Daphnia is a key organism in freshwater ecosystems. Here, we report the effect of symbiotic bacteria on ecologically important life history traits, such as population dynamics and longevity, in Daphnia magna. By disinfection of the daphniid embryos with glutaraldehyde, aposymbiotic daphniids were prepared and cultured under bacteria‐free conditions. Removal of bacteria from the daphniids was monitored by quantitative polymerase chain reaction for bacterial 16S rRNA gene. The population of aposymbiotic daphniids was reduced 10‐folds compared with that of the control daphniids. Importantly, re‐infection with symbiotic bacteria caused daphniids to regain bacteria and increase their fecundity to the level of the control daphniids, suggesting that symbiotic bacteria regulate Daphnia fecundity. To identify the species of symbiotic bacteria, 16S rRNA genes of bacteria in daphniids were sequenced. This revealed that 50% of sequences belonged to the Limnohabitans sp. of the Betaproteobacteria class and that the diversity of bacterial taxa was relatively low. These results suggested that symbiotic bacteria have a beneficial effect on D. magna, and that aposymbiotic Daphnia are useful tools in understanding the role of symbiotic bacteria in the environmental responses and evolution of their hosts.
A survey of etiologic hypotheses among testicular cancer researchers
Authors: Stang A. , Trabert B. , Rusner C. , Poole C. , Almstrup K. , Rajpert‐De Meyts E. , McGlynn K. A.
Published: December 2014

Basic research results can provide new ideas and hypotheses to be examined in epidemiological studies. We conducted a survey among testicular cancer researchers on hypotheses concerning the etiology of this malignancy. All researchers on the mailing list of Copenhagen Testis Cancer Workshops and corresponding authors of PubMed‐indexed articles identified by the search term ‘testicular cancer’ and published within 10 years (in total 2750 recipients) were invited to respond to an e‐mail‐based survey. Participants of the 8th Copenhagen Testis Cancer Workshop in May 2014 were subsequently asked to rate the plausibility of the suggested etiologic hypotheses on a scale of 1 (very implausible) to 10 (very plausible). This report describes the methodology of the survey, the score distributions by individual hypotheses, hypothesis group, and the participants’ major research fields, and discuss the hypotheses that scored as most plausible. We also present plans for improving the survey that may be repeated at a next international meeting of experts in testicular cancer. Overall 52 of 99 (53%) registered participants of the 8th Copenhagen Testis Cancer Workshop submitted the plausibility rating form. Fourteen of 27 hypotheses were related to exposures during pregnancy. Hypotheses with the highest mean plausibility ratings were either related to pre‐natal exposures or exposures that might have an effect during pregnancy and in post‐natal life. The results of the survey may be helpful for triggering more specific etiologic hypotheses that include factors related to endocrine disruption, DNA damage, inflammation, and nutrition during pregnancy. The survey results may stimulate a multidisciplinary discussion about new etiologic hypotheses of testicular cancer.
The idea of ‘Country’: Reframing post‐disaster recovery in Indigenous Taiwan settings
Authors: Hsu Minna , Howitt Richard , Chi Chun‐Chieh
Published: December 2014

In Australian Aboriginal thinking, the idea of ‘Country’ comprises complex ideas about relationships and connection. It simultaneously encompasses territorial affiliation, a social identification and cosmological orientation. It draws attention to what might be glossed as people‐to‐environment, people‐to‐people and people‐to‐cosmos relations. These relations influence disaster responses, but are rarely mobilised explicitly in shaping formal recovery and reconstruction efforts. Colonial disruption of connections to Country imposed new practices and presences into contemporary Indigenous geographies and is often reinforced in disaster settings. This paper considers more recent disruptions arising from post‐disaster recovery in Taiwan, arguing that the idea of Country offers a powerful way of framing cultural and social dimensions of post‐disaster relief and recovery for government agencies, non‐government organisations and research alike.
Decolonising Pacific research, building Pacific research communities and developing Pacific research tools: The case of the talanoa and the faafaletui in Samoa
Authors: Suaalii‐Sauni Tamasailau , Fulu‐Aiolupotea Saunimaa Ma
Published: December 2014

In building Samoan academic researcher capacity in Samoa, we argue that there is a need to first establish the kind of researcher community advocated by Linda Tuhiwai Smith, and to do so through developing research tools, such as the talanoa and faafaletui, in partnership with researcher capacity‐building initiatives such as the applied postgraduate social and health research methods course (coded PUBX731‐HSA505) run by the Centre for International Health, University of Otago, in partnership with the National University of Samoa. This paper offers a commentary on the talanoa and faafaletui as Pacific research methodologies, and asks what its value might be for researchers in Samoa. It reflects on the learning experiences of staff and students of the applied social and health research methods course in relation to the talanoa and faafaletui as Pacific research methodologies or methods. It concludes that developing Pacific research and researcher capacity in Pacific Island countries, such as Samoa, must include opening up spaces within these communities to critically engage what is Pacific or Samoan or indigenous about these research tools, methods or methodologies, and how they might differ in form or substance from other methods or methodologies.