bluuebunny/crossref_metadata_2025 huggingface dataset:
Communication: Slab thickness dependence of the surface tension: Toward a criterion of liquid sheets stability
Authors: Filippini G. , Bourasseau E. , Ghoufi A. , Goujon F. , Malfreyt P.
Published: September 2014

Microscopic Monte Carlo simulations of liquid sheets of copper and tin have been performed in order to study the dependence of the surface tension on the thickness of the sheet. It results that the surface tension is constant with the thickness as long as the sheet remains in one piece. When the sheet is getting thinner, holes start to appear, and the calculated surface tension rapidly decreases with thickness until the sheet becomes totally unstable and forms a cylinder. We assume here that this decrease is not due to a confinement effect as proposed by Werth et al. [Physica A 392, 2359 (2013)] on Lennard-Jones systems, but to the appearance of holes that reduces the energy cost of the surface modification. We also show in this work that a link can be established between the stability of the sheet and the local fluctuations of the surface position, which directly depends on the value of the surface tension. Finally, we complete this study by investigating systems interacting through different forms of Lennard-Jones potentials to check if similar conclusions can be drawn.
Effect of nanohole structure on pyramid textured surface on photo-voltaic performance of silicon solar cell
Authors: Baek Seung-Wook , Lee Gon-Sub , Park Jea-Gun
Published: September 2014

We investigated how the nanohole structure on a {111} pyramid textured surface affected the photovoltaic performance of silicon solar cells by varying nanohole depth. During the effective minority carrier recombination lifetime, the surface reflectance decreased with increasing nanohole depth, showing a trade-off relationship. The power conversion efficiency (PCE) of silicon solar cells with the {111} pyramid textured surface peaked at a specific nanohole depth, i.e., 0.43% PCE enhancement (3.32% enhancement relative to a reference cell) was obtained at the nanohole depth of 94.8 nm.
High-Q filters with complete transports using quasiperiodic rings with spin-orbit interaction
Authors: Qiu R. Z. , Chen C. H. , Tsao C. W. , Hsueh W. J.
Published: September 2014

A high Q filter with complete transports is achieved using a quasiperiodic Thue-Morse array of mesoscopic rings with spin-orbit interaction. As the generation order of the Thue-Morse array increases, not only does the Q factor of the resonance peak increase exponentially, but the number of sharp resonance peaks also increases. The maximum Q factor for the electronic filter of a Thue-Morse array is much greater than that in a periodic array, for the same number of the rings.
Plasma-satellite interaction driven magnetic field perturbations
Authors: Saeed-ur-Rehman  , Marchand Richard
Published: September 2014

We report the first fully kinetic quantitative estimate of magnetic field perturbations caused by the interaction of a spacecraft with space environment. Such perturbations could affect measurements of geophysical magnetic fields made with very sensitive magnetometers on-board satellites. Our approach is illustrated with a calculation of perturbed magnetic fields near the recently launched Swarm satellites. In this case, magnetic field perturbations do not exceed 20 pT, and they are below the sensitivity threshold of the on-board magnetometers. Anticipating future missions in which satellites and instruments would be subject to more intense solar UV radiation, however, it appears that magnetic field perturbations associated with satellite interaction with space environment, might approach or exceed instruments' sensitivity thresholds.
Blue phase liquid crystals stabilized by linear photo-polymerization
Authors: Xu Daming , Yuan Jiamin , Schadt Martin , Wu Shin-Tson
Published: September 2014

Stabilizing a photopolymer-embedded blue phase liquid crystal precursor with linearly polarized UV light is investigated experimentally. When the UV polarization axis is perpendicular to the stripe electrodes of an in-plane-switching cell, anisotropic polymer networks are formed through the linear photo-polymerization process and the electrostriction effect is suppressed. As a result, the measured hysteresis is dramatically reduced from 6.95% to 0.36% and the response time shortened by ∼2× compared to unpolarized UV exposure. To induce larger anisotropy in polymer networks for mitigating the electrostriction effect, high-intensity linearly polarized UV exposure is preferred.
Half of Portugal’s research centers could see their funding plunge
Authors: Feder Toni
Published: September 2014

New policies intended to promote excellence could have the opposite effect and possibly undermine decades of investment in R&D.
White House offers encouragement for cyberphysical systems
Authors: Kramer David
Published: September 2014

SmartAmerica Challenge catalyzes two dozen projects that add further functionality to the Internet of Things.
Chelyabinsk: Portrait of an asteroid airburst
Authors: Kring David A. , Boslough Mark
Published: September 2014

Video and audio from hundreds of smartphones and dashboard cameras combined with seismic, acoustic, and satellite measurements provide the first precise documentation of a 10 000-ton asteroid explosion.
Prediction of nitrogen use in dairy cattle: a multivariate Bayesian approach
Authors: Reed K. F. , Moraes L. E. , Fadel J. G. , Casper D. P. , Dijkstra J. , France J. , Kebreab E.
Published: September 2014

Quantification of dairy cattle nitrogen (N) excretion and secretion is necessary to improve the efficiency with which feed N is converted to milk N (ENU). Faecal and urinary N excretion and milk N secretion are correlated with each other and thus are more accurately described by a multivariate model that can accommodate the covariance between the three observations than by three separate univariate models. Further, by simultaneously predicting the three routes of excretion and taking advantage of the mass balance relationships between them, covariate effects on N partitioning from feed to faeces and absorbed N and from absorbed N to milk and urine N and animal ENU can be estimated. A database containing 1094 lactating dairy cow observations collated from indirect calorimetry experiments was used for model development. Dietary metabolisable energy content (ME, MJ/kg DM) increased ENU at a decreasing rate, increased the efficiency with which feed N was converted to absorbed N and decreased the efficiency with which absorbed N was converted to milk N. However, the parameter estimate of the effect of ME on post-absorption efficiency was not different from zero when the model was fitted to a data subset in which net energy and metabolisable protein were at or above requirement. This suggests the effect of ME on post-absorption N use is dependent on the energy status of the animal.
Niche displacement of human leukemic stem cells uniquely allows their competitive replacement with healthy HSPCs
Authors: Boyd Allison L. , Campbell Clinton J.V. , Hopkins Claudia I. , Fiebig-Comyn Aline , Russell Jennifer , Ulemek Jelena , Foley Ronan , Leber Brian , Xenocostas Anargyros , Collins Tony J. , Bhatia Mickie
Published: September 2014

Allogeneic hematopoietic stem cell (HSC) transplantation (HSCT) is currently the leading strategy to manage acute myeloid leukemia (AML). However, treatment-related morbidity limits the patient generalizability of HSCT use, and the survival of leukemic stem cells (LSCs) within protective areas of the bone marrow (BM) continues to lead to high relapse rates. Despite growing appreciation for the significance of the LSC microenvironment, it has remained unresolved whether LSCs preferentially situate within normal HSC niches or whether their niche requirements are more promiscuous. Here, we provide functional evidence that the spatial localization of phenotypically primitive human AML cells is restricted to niche elements shared with their normal counterparts, and that their intrinsic ability to initiate and retain occupancy of these niches can be rivaled by healthy hematopoietic stem and progenitor cells (HSPCs). When challenged in competitive BM repopulation assays, primary human leukemia-initiating cells (L-ICs) can be consistently outperformed by HSPCs for BM niche occupancy in a cell dose-dependent manner that ultimately compromises long-term L-IC renewal and subsequent leukemia-initiating capacity. The effectiveness of this approach could be demonstrated using cytokine-induced mobilization of established leukemia from the BM that facilitated the replacement of BM niches with transplanted HSPCs. These findings identify a functional vulnerability of primitive leukemia cells, and suggest that clinical development of these novel transplantation techniques should focus on the dissociation of L-IC–niche interactions to improve competitive replacement with healthy HSPCs during HSCT toward increased survival of patients.
Survival Time of Methicillin-Resistant Staphylococcus aureus–Free Status after Institutional Clearance
Authors: Valencia-Rey Paula A. , Strymish Judith , Robillard Ernest , Evans Martin , Weinberg Janice , Gupta Kalpana
Published: September 2014

Objective.

To determine the durability of methicillin-resistant Staphylococcus aureus (MRSA)–free status after patients are removed from contact precautions and the association of specific clearance policy variables with survival

Design.

Retrospective cohort study from October 2007 to April 2013.

Setting.

Veteran Affairs Boston Healthcare System.

Participants.

Patients with a prior history of MRSA who were removed from contact precautions after deemed cleared of their MRSA status by infection prevention.

Methods.

Active nasal screening results and clinical data from acute, long-term, and outpatient care facilities were evaluated to determine survival of MRSA-free status in a time-to-event analysis.

Results.

A total of 351 unique patients were followed for 107,112 patient-days. The median age was 68 years. Overall, 249 (71%) of patients remained MRSA-free, and 102 (29%) reverted to MRSA positive. The median MRSA-free survival was 880 days. Comorbidities, presence of indwelling devices, and the use of systemic antibiotics at the time of clearance screening were not associated with MRSA-free survival. More than 21,000 days of inpatient isolation days were avoided during the study period.

Conclusions.

The majority of patients removed from contact precautions remained MRSA-free for more than 2 years. Antibiotic use at the time of clearance was not associated with reductions in MRSA-free survival. These findings can be used to simplify clearance criteria, promote clearance policies, and reduce patient isolation days.
Dealing with Uncertainty in Agent‐Based Simulation: Farm‐Level Modeling of Adaptation to Climate Change in Southwest Germany
Authors: Troost Christian , Berger Thomas
Published: September 2014

Climate change will most likely confront agricultural producers with natural, economic, and political conditions that have not previously been observed and are largely uncertain. As a consequence, extrapolation from past data reaches its limits, and a process‐based analysis of farmer adaptation is required. Simulation of changes in crop yields using crop growth models is a first step in that direction. However, changes in crop yields are only one pathway through which climate change affects agricultural production. A meaningful process‐based analysis of farmer adaptation requires a whole‐farm analysis at the farm level. We use a highly disaggregated mathematical programming model to analyze farm‐level climate change adaptation for a mountainous area in southwest Germany. Regional‐level results are obtained by simulating each full‐time farm holding in the study area. We address parameter uncertainty and model underdetermination using a cautious calibration approach and a comprehensive uncertainty analysis. We deal with the resulting computational burden using efficient experimental designs and high‐performance computing. We show that in our study area, shifted crop management time slots can have potentially significant effects on agricultural supply, incomes, and various policy objectives promoted under German and European environmental policy schemes. The simulated effects are robust against model uncertainty and underline the importance of a comprehensive assessment of climate change impacts beyond merely looking at crop yield changes. Our simulations demonstrate how farm‐level models can contribute to a process‐based analysis of climate change adaptation if they are embedded into a systematic framework for treating inherent model uncertainty.
Prediction of Indel flanking regions in protein sequences using a variable-order Markov model
Authors: Al-Shatnawi Mufleh , Ahmad M. Omair , Swamy M.N.S.
Published: September 2014

Motivation : Insertion/deletion (indel) and amino acid substitution are two common events that lead to the evolution of and variations in protein sequences. Further, many of the human diseases and functional divergence between homologous proteins are more related to indel mutations, even though they occur less often than the substitution mutations do. A reliable identification of indels and their flanking regions is a major challenge in research related to protein evolution, structures and functions.

Results : In this article, we propose a novel scheme to predict indel flanking regions in a protein sequence for a given protein fold, based on a variable-order Markov model. The proposed indel flanking region (IndelFR) predictors are designed based on prediction by partial match (PPM) and probabilistic suffix tree (PST), which are referred to as the PPM IndelFR and PST IndelFR predictors, respectively. The overall performance evaluation results show that the proposed predictors are able to predict IndelFRs in the protein sequences with a high accuracy and F1 measure. In addition, the results show that if one is interested only in predicting IndelFRs in protein sequences, it would be preferable to use the proposed predictors instead of HMMER 3.0 in view of the substantially superior performance of the former.

Contact : m_alshat@ece.concordia.ca or omair@ece.concordia.ca or swamy@ece.concordia.ca .

Supplementary information:  Supplementary data are available at Bioinformatics online.
PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data
Authors: Frankhouser David E. , Murphy Mark , Blachly James S. , Park Jincheol , Zoller Mike W. , Ganbat Javkhlan-Ochir , Curfman John , Byrd John C. , Lin Shili , Marcucci Guido , Yan Pearlly , Bundschuh Ralf
Published: September 2014

Motivation : DNA methylation is an epigenetic change occurring in genomic CpG sequences that contribute to the regulation of gene transcription both in normal and malignant cells. Next-generation sequencing has been used to characterize DNA methylation status at the genome scale, but suffers from high sequencing cost in the case of whole-genome bisulfite sequencing, or from reduced resolution (inability to precisely define which of the CpGs are methylated) with capture-based techniques.

Results : Here we present a computational method that computes nucleotide-resolution methylation values from capture-based data by incorporating fragment length profiles into a model of methylation analysis. We demonstrate that it compares favorably with nucleotide-resolution bisulfite sequencing and has better predictive power with respect to a reference than window-based methods, often used for enrichment data. The described method was used to produce the methylation data used in tandem with gene expression to produce a novel and clinically significant gene signature in acute myeloid leukemia. In addition, we introduce a complementary statistical method that uses this nucleotide-resolution methylation data for detection of differentially methylated features.

Availability : Software in the form of Python and R scripts is available at http://bioserv.mps.ohio-state.edu/ premer and is free for non-commercial use.

Contact : pearlly.yan@osumc.edu ; bundschuh@mps.ohio-state.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering
Authors: Verbist Bie M.P. , Thys Kim , Reumers Joke , Wetzels Yves , Van der Borght Koen , Talloen Willem , Aerssens Jeroen , Clement Lieven , Thas Olivier
Published: September 2014

Motivation : In virology, massively parallel sequencing (MPS) opens many opportunities for studying viral quasi-species, e.g. in HIV-1- and HCV-infected patients. This is essential for understanding pathways to resistance, which can substantially improve treatment. Although MPS platforms allow in-depth characterization of sequence variation, their measurements still involve substantial technical noise. For Illumina sequencing, single base substitutions are the main error source and impede powerful assessment of low-frequency mutations. Fortunately, base calls are complemented with quality scores (Qs) that are useful for differentiating errors from the real low-frequency mutations.

Results : A variant calling tool, Q-cpileup, is proposed, which exploits the Qs of nucleotides in a filtering strategy to increase specificity. The tool is imbedded in an open-source pipeline, VirVarSeq, which allows variant calling starting from fastq files. Using both plasmid mixtures and clinical samples, we show that Q-cpileup is able to reduce the number of false-positive findings. The filtering strategy is adaptive and provides an optimized threshold for individual samples in each sequencing run. Additionally, linkage information is kept between single-nucleotide polymorphisms as variants are called at the codon level. This enables virologists to have an immediate biological interpretation of the reported variants with respect to their antiviral drug responses. A comparison with existing SNP caller tools reveals that calling variants at the codon level with Q-cpileup results in an outstanding sensitivity while maintaining a good specificity for variants with frequencies down to 0.5%.

Availability : The VirVarSeq is available, together with a user’s guide and test data, at sourceforge: http://sourceforge.net/projects/virtools/?source=directory

Contact : bie.verbist@ugent.be

Supplementary information:  Supplementary data are available at Bioinformatics online.
Trans-dimensional finite-fault inversion
Authors: Dettmer Jan , Benavente Roberto , Cummins Phil R. , Sambridge Malcolm
Published: September 2014

This paper develops a probabilistic Bayesian approach to the problem of inferring the spatiotemporal evolution of earthquake rupture on a fault surface from seismic data with rigorous uncertainty estimation. To date, uncertainties of rupture parameters are poorly understood, and the effect of choices such as fault discretization on uncertainties has not been studied. We show that model choice is fundamentally linked to uncertainty estimation and can have profound effects on results. The approach developed here is based on a trans-dimensional self-parametrization of the fault, avoids regularization constraints and provides rigorous uncertainty estimation that accounts for model-selection ambiguity associated with the fault discretization. In particular, the fault is parametrized using self-adapting irregular grids which intrinsically match the local resolving power of the data and provide parsimonious solutions requiring few parameters to capture complex rupture characteristics. Rupture causality is ensured by parametrizing rupture-onset time by a rupture-velocity field and obtaining first rupture times from the eikonal equation. The Bayesian sampling of the parameter space is implemented on a computer cluster with a highly efficient parallel tempering algorithm.

The inversion is applied to simulated and observed W-phase waveforms from the 2010 Maule (Chile) earthquake. Simulation results show that our approach avoids both over- and underparametrization to ensure unbiased inversion results with uncertainty estimates that are consistent with data information. The simulation results also show the ability of W-phase data to resolve the spatial variability of slip magnitude and rake angles. In addition, sensitivity to spatially dependent rupture velocities exists for kinematic slip models.

Application to the observed data indicates that residual errors are highly correlated and likely dominated by theory error, necessitating the iterative estimation of a non-stationary data covariance matrix. The moment magnitude for the Maule earthquake is estimated to be ∼8.9, with slip concentrated in two zones updip of and north and south of the hypocentre, respectively. While this aspect of the slip distribution is similar to previous studies, we show that the slip maximum in the southern zone is poorly resolved compared to the northern zone. Both slip maxima are higher than reported in previous studies, which we speculate may be due to the lack of bias caused by the regularization used in other studies.
Xanthomonas citri subsp. citri Type IV Pilus Is Required for Twitching Motility, Biofilm Development, and Adherence
Authors: Dunger German , Guzzo Cristiane R. , Andrade Maxuel O. , Jones Jeffrey B. , Farah Chuck S.
Published: September 2014

Bacterial type IV pili (T4P) are long, flexible surface filaments that consist of helical polymers of mostly pilin subunits. Cycles of polymerization, attachment, and depolymerization mediate several pilus-dependent bacterial behaviors, including twitching motility, surface adhesion, pathogenicity, natural transformation, escape from immune system defense mechanisms, and biofilm formation. The Xanthomonas citri subsp. citri strain 306 genome codes for a large set of genes involved in T4P biogenesis and regulation and includes several pilin homologs. We show that X. citri subsp. citri can exhibit twitching motility in a manner similar to that observed in other bacteria such as Pseudomonas aeruginosa and Xylella fastidiosa and that this motility is abolished in Xanthomonas citri subsp. citri knockout strains in the genes coding for the major pilin subunit PilAXAC3241, the ATPases PilBXAC3239 and PilTXAC2924, and the T4P biogenesis regulators PilZXAC1133 and FimXXAC2398. Microscopy analyses were performed to compare patterns of bacterial migration in the wild-type and knockout strains and we observed that the formation of mushroom-like structures in X. citri subsp. citri biofilm requires a functional T4P. Finally, infection of X. citri subsp. citri cells by the bacteriophage (ΦXacm4-11 is T4P dependent. The results of this study improve our understanding of how T4P influence Xanthomonas motility, biofilm formation, and susceptibility to phage infection.
Wickerhamiella allomyrinae f.a., sp. nov., a yeast species isolated from the gut of the rhinoceros beetle Allomyrina dichotoma
Authors: Ren Yong-Cheng , Wang Yun , Chen Liang , Ke Tao , Hui Feng-Li
Published: September 2014

Two strains representing Wickerhamiella allomyrinae f.a., sp. nov. were isolated from the gut of Allomyrina dichotoma (Coleoptera: Scarabeidae) collected from the Baotianman National Nature Reserve, Nanyan, Henan Province, China. Sequence analyses of the D1/D2 domains of the LSU rRNA gene revealed that this novel species was located in the Wickerhamiella clade (Saccharomycetes, Saccharomycetales), with three described species of the genus Candida, namely Candida musiphila, Candida spandovensis and Candida sergipensis, as the most closely related species. The novel species differed from these three species by 9.3–9.8 % sequence divergence (35–45 nt substitutions) in the D1/D2 sequences. The species could also be distinguished from the closely related species, C. musiphila, C. spandovensis and C. sergipensis, by growth on vitamin-free medium and at 37 °C. The type strain is Wickerhamiella allomyrinae sp. nov. NYNU 13920T ( = CICC 33031T = CBS 13167T).
Pax6-dependent, but β-catenin-independent, function of Bcl9 proteins in mouse lens development
Authors: Cantù Claudio , Zimmerli Dario , Hausmann George , Valenta Tomas , Moor Andreas , Aguet Michel , Basler Konrad
Published: September 2014

Bcl9andBcl9l(Bcl9/9l) encode Wnt signaling components that mediate the interaction between β-catenin and Pygopus (Pygo) via two evolutionarily conserved domains, HD1 and HD2, respectively. We generated mouse strains lacking these domains to probe the β-catenin-dependent and β-catenin-independent roles of Bcl9/9l and Pygo during mouse development. While lens development is critically dependent on the presence of the HD1 domain, it is not affected by the lack of the HD2 domain, indicating that Bcl9/9l act in this context in a β-catenin-independent manner. Furthermore, we uncover a new regulatory circuit in which Pax6, the master regulator of eye development, directly activatesBcl9/9ltranscription.
Preparation and Use of Sea Urchin Egg Homogenates for Studying NAADP-Mediated Ca2+ Release
Authors: Galione Antony , Chuang Kai-Ting , Funnell Tim M. , Davis Lianne C. , Morgan Anthony J. , Ruas Margarida , Parrington John , Churchill Grant C.
Published: September 2014

NAADP and other Ca2+-mobilizing messengers are membrane impermeant and thus must be added directly to cell-free or broken-cell preparations to effect Ca2+ release. The sea urchin egg homogenate, where the biological activity of NAADP was first reported, remains the gold standard cell-free system for studying NAADP-mediated Ca2+ release. Here we describe how to prepare sea urchin egg homogenate and use it to measure NAADP-mediated Ca2+ release.
Monitoring Autophagic Flux Using Ref(2)P, the Drosophila p62 Ortholog
Authors: DeVorkin Lindsay , Gorski Sharon M.
Published: September 2014

Human p62, also known as Sequestome-1 (SQSTM1), is a multifunctional scaffold protein that contains many domains, including a Phox/Bem1P (PB1) multimerization domain, an ubiquitin-associated (UBA) domain, and a light chain 3 (LC3) recognition sequence. p62 binds ubiquitinated proteins and targets them for degradation by the proteasome. In addition, p62 directly binds LC3; this may serve as a mechanism to deliver ubiquitinated proteins for degradation by autophagy. During this process, p62 itself is degraded. The inhibition of autophagy leads to the accumulation of p62, indicating that it can be used as a marker of autophagic flux. Ref(2)P (refractory to sigma P), the Drosophila ortholog of p62, is also required for the formation of ubiquitinated protein aggregates. Ref(2)P contains a putative LC3-interacting region, and genetic inhibition of autophagy in Drosophila leads to the accumulation of Ref(2)P protein levels. Thus, like p62, Ref(2)P may serve as a marker of autophagic flux. Here we provide two procedures to examine Ref(2)P protein levels in Drosophila ovaries.
Genetic Manipulation of Autophagy in the Drosophila Ovary
Authors: DeVorkin Lindsay , Gorski Sharon M.
Published: September 2014

Flies with mutations in Atg7 or Atg8a are homozygous viable and develop to adulthood, whereas mutations in other autophagy genes, including Atg1, are homozygous lethal. Clonal analysis has been instrumental in examining the role and regulation of lethal Atg genes in many aspects of Drosophila development and survival. The generation of homozygous mutant clones in an otherwise heterozygous mutant background is possible in mitotically active tissues, and is highly beneficial in that the control cells and experimental cells are subjected to the same developmental and nutritional cues allowing for a side-by-side comparison. Several methods are now available to examine the contribution of lethal autophagy genes during Drosophila oogenesis. Here we describe how to generate a homozygous mutant germline using the FLP-DFS (dominant female sterile) technique, how to generate somatic clones, and how to induce targeted gene knockdown in the germline using RNAi.
Detecting RNA–RNA Interactions Using Psoralen Derivatives
Authors: Nilsen Timothy W.
Published: September 2014

Psoralens are tricyclic compounds that intercalate into double-stranded DNA or RNA and, on irradiation with long-wavelength (365-nm) UV light, covalently link pyrimidines on adjacent strands. More rarely, psoralen cross-links can be observed at the ends of helices (i.e., double-stranded–single-stranded boundaries). Although psoralens can, in some instances, cross-link protein to RNA, their primary application is to detect RNA–RNA base-pairing interactions. The most useful psoralen derivative is 4′-aminomethyl trioxsalen (AMT), which is soluble in H2O. This protocol describes the use of AMT to detect RNA–RNA interactions in tissue culture cells or in extracts. Cross-linked RNAs are detectable by their reduced mobility in polyacrylamide gels. Cross-links can be reversed by exposure to short-wavelength (254 nm) UV light.
In Vivo Local Dye Electroporation for Ca2+ Imaging and Neuronal-Circuit Tracing
Authors: Nagayama Shin , Fletcher Max L. , Xiong Wenhui , Lu Xiaohua , Zeng Shaoqun , Chen Wei R.
Published: September 2014

A major technical challenge for using optical imaging to analyze neuronal circuit functions is how to effectively load synthetic Ca2+ dyes or neural tracers into the brain. We introduce here a simple but versatile approach to label many neurons and clearly visualize their axonal and dendritic morphology. The method uses a large-tip patch pipette filled with dextran-conjugated Ca2+ dyes or fluorescent tracers. By inserting the pipette into a targeted brain area and passing microampere current pulses, dyes or tracers are electroporated into dendrites and axons near the pipette tip. The dyes are then transported to reveal the entire cell morphology, suitable for both functional Ca2+ imaging and neuronal circuit tracing. This process requires basic physiological equipment normally available in a physiological laboratory.
Transformation of vanadinite [Pb5(VO4)3Cl] by fungi
Authors: Ceci Andrea , Rhee Young Joon , Kierans Martin , Hillier Stephen , Pendlowski Helen , Gray Nia , Persiani Anna Maria , Gadd Geoffrey Michael
Published: September 2014

Saprotrophic fungi were investigated for their bioweathering effects on the vanadium‐ and lead‐containing insoluble apatite group mineral, vanadinite [Pb5(VO4)3Cl]. Despite the insolubility of vanadinite, fungi exerted both biochemical and biophysical effects on the mineral including etching, penetration and formation of new biominerals. Lead oxalate was precipitated by Aspergillus niger during bioleaching of natural and synthetic vanadinite. Some calcium oxalate monohydrate (whewellite) was formed with natural vanadinite because of the presence of associated ankerite [Ca(Fe2+,Mg)(CO3)2]. Aspergillus niger also precipitated lead oxalate during growth in the presence of lead carbonate, vanadium(V) oxide and ammonium metavanadate, while abiotic tests confirmed the efficacy of oxalic acid in solubilizing vanadinite and precipitating lead as oxalate. Geochemical modelling confirmed the complexity of vanadium speciation, and the significant effect of oxalate. Oxalate–vanadium complexes markedly reduced the vanadinite stability field, with cationic lead(II) and lead oxalate also occurring. In all treatments and geochemical simulations, no other lead vanadate, or vanadium minerals were detected. This research highlights the importance of oxalate in vanadinite bioweathering and suggests a general fungal transformation of lead‐containing apatite group minerals (e.g. vanadinite, pyromorphite, mimetite) by this mechanism. The findings are also relevant to remedial treatments for lead/vanadium contamination, and novel approaches for vanadium recovery.
Plant methyl salicylate induces defense responses in the rhizobacterium Bacillus subtilis
Authors: Kobayashi Kazuo
Published: September 2014

Bacillus subtilis is a rhizobacterium that promotes plant growth and health. Cultivation of B. subtilis with an uprooted weed on solid medium produced pleat‐like architectures on colonies near the plant. To test whether plants emit signals that affect B. subtilis colony morphology, we examined the effect of plant‐related compounds on colony morphology. Bacillus subtilis formed mucoid colonies specifically in response to methyl salicylate, which is a plant‐defense signal released in response to pathogen infection. Methyl salicylate induced mucoid colony formation by stimulating poly‐γ‐glutamic acid biosynthesis, which formed enclosing capsules that protected the cells from exposure to antimicrobial compounds. Poly‐γ‐glutamic acid synthesis depended on the DegS‐DegU two‐component regulatory system, which activated DegSU‐dependent gene transcription in response to methyl salicylate. Bacillus subtilis did not induce plant methyl salicylate production, indicating that the most probable source of methyl salicylate in the rhizosphere is pathogen‐infected plants. Methyl salicylate induced B. subtilis biosynthesis of the antibiotics bacilysin and fengycin, the latter of which exhibited inhibitory activity against the plant pathogenic fungus Fusarium oxysporum. We propose that B. subtilis may sense plants under pathogen attack via methyl salicylate, and express defense responses that protect both B. subtilis and host plants in the rhizosphere.
The Impact of Ozone Treatment on Changes in Biologically Active Substances of Cardamom Seeds
Authors: Joanna Brodowska Agnieszka , Śmigielski Krzysztof , Nowak Agnieszka , Brodowska Katarzyna , Catthoor Rik , Czyżowska Agata
Published: September 2014

The overall objective of this study was to develop a decontamination method against microorganisms in cardamom (Elettaria cardamomum (L.) Maton) seeds using ozone as a decontaminating agent. Ozone treatment was conducted 3 times, at 24‐h intervals, and the parameters of the process were determined assuring the least possible losses of biologically active substances (essential oils and polyphenols): ozone concentration 160 to 165.0 g/m3; flow rate 0.1 L/min; pressure 0.5 atm; time 30 min. After each step of decontamination, the microbiological profile of the cardamom seeds was studied, and the contaminating microflora was identified. Next to the microbiological profile, the total polyphenol content (TPC), composition of essential oils, free radical‐scavenging capacity, total antioxidant capacity, ferric‐reducing antioxidant power (FRAP), and LC–MS polyphenol analysis were determined. This study shows that extract from cardamom seeds after ozone treatment is characterized by a better radical scavenging activity (IC50 = 24.18 ± 0.04 mg/mL) than the control sample (IC50 = 31.94 ± 0.05 mg/mL). The extract from cardamom seeds after ozone treatment showed an improved FRAP activity as well (613.64 ± 49.79 mmol TE/g compared to 480.29 ± 30.91 mmol TE/g of control sample). The TPC and the total antioxidant capacity were negatively affected, respectively, 41.2% and 16.2%, compared to the control sample.
Neostigmine vs. sugammadex: observational cohort study comparing the quality of recovery using the Postoperative Quality Recovery Scale
Authors: AMORIM P. , LAGARTO F. , GOMES B. , ESTEVES S. , BISMARCK J. , RODRIGUES N. , NOGUEIRA M.
Published: September 2014

Background

Quality of postoperative recovery is an important outcome after surgery. An observational cohort study was designed to assess the quality of postoperative recovery using the Portuguese version of the Postoperative Quality Recovery Scale (PQRS) in patients treated with neostigmine vs. sugammadex as neuromuscular blocking reversal agents.

Methods

A convenience sample of 101 adult patients undergoing elective surgery with general anaesthesia and treated with neostigmine (n = 48) or sugammadex (n = 53) as neuromuscular blocking reversal agents was included. Patients were evaluated using the Portuguese PQRS version at baseline and postoperatively at 15 (T15) and 40 (T40) min and also at days 1 and 3. Recovery was defined as return to baseline values (or better) at each time points.

Results

The PQRS overall recovery rates were similar in both groups, but recoveries in the nociceptive (96.2% vs. 81.3%, P = 0.02) and physiological (96.2% vs. 70.2%, P = 0.001) domains at T40 were higher in the sugammadex group than in the neostigmine group. Also, there was a trend that patients treated with sugammadex reported significantly better global perspective on the impact of surgery on working capacity and daily activities, as well as higher satisfaction with anaesthetic care.

Conclusions

This pilot study suggests that sugammadex may improve physiological and nociceptive postoperative recovery as well as patient satisfaction with anaesthetic care. Although we lack an explanation for a possible favourable impact of sugammadex on quality of recovery, our results may provide sufficient preliminary data to justify a randomised trial to explore this possibility.
Assortative Mating on Ideology Could Operate Through Olfactory Cues
Authors: McDermott Rose , Tingley Dustin , Hatemi Peter K.
Published: September 2014

Mates appear to assort on political attitudes more than any other social, behavioral, or physical trait, besides religion. Yet the process by which ideologically similar mates end up together remains ambiguous. Mates do not appear to consciously select one another based on ideology, nor does similarity result from convergence. Recently, several lines of inquiry have converged on the finding that olfactory processes have an important role in both political ideology and mate selection. Here we integrate extant studies of attraction, ideology, and olfaction and explore the possibility that assortation on political attitudes may result, in part, from greater attraction to the scent of those with shared ideology. We conduct a study in which individuals evaluated the body odor of unknown others, observing that individuals are more attracted to their ideological concomitants.
Causes of Noncompliance with International Law: A Field Experiment on Anonymous Incorporation
Authors: Findley Michael G. , Nielson Daniel L. , Sharman J.C.
Published: September 2014

Using two field experiments, we probe the efficacy of international rules mandating that incorporation services establish their customers’ true identities. The standards were designed to prevent anonymous “shell” corporations central to money laundering, corruption, and other crimes. Posing as consultants seeking confidential incorporation, we randomly assigned six experimental conditions in emails varying information about monetary reward, international and domestic law, and customer risk to 1,793 incorporation services in 177 countries and 1,722 U.S. firms. Firms in tax havens obey the rules significantly more often than in OECD countries, whereas services in poor nations sometimes prove more compliant than those in rich countries. Only the risk of terrorism and specter of the Internal Revenue Service decrease offers for anonymous incorporation, but they also lower compliance. Offers to “pay a premium” reduce compliance. The risk of corruption decreases response rates but, alarmingly, also decreases compliance rates. Raising international law has no significant effect.
Gastric adenocarcinoma in a diamond python (Morelia spilota spilota)
Authors: Baron HR , Allavena R , Melville LM , Doneley RJT
Published: September 2014

Case report

A 5‐year‐old captive male diamond python (Morelia spilota spilota) was presented with a 1‐month history of regurgitation and anorexia and discrete coelomic distention. Physical examination revealed a firm, immobile mass at approximately two‐thirds of the snout–vent length from the front of the head. Ultrasound‐guided fine needle aspirate biopsy of the mass in the region of the stomach showed necrosis with bacterial infiltration and possibly neoplastic changes. A gastroscopy was conducted, but showed grossly normal gastric mucosa, confirmed by biopsy. On exploratory coeliotomy, it was confirmed the mass involved most of the stomach wall and occluded the gastric lumen. The mass was completely excised and based on histopathology, a diagnosis of gastric adenocarcinoma was made. The snake was found dead 12 h postoperatively, but no specific cause of death was found on postmortem examination.

Conclusion

Most cases of adenocarcinoma in snakes go undiagnosed. This case report illustrates that the architecture of gastric masses may lead to false‐negative gastric biopsy results in snakes with neoplasia.
Friendlessness and theory of mind: A prospective longitudinal study
Authors: Fink Elian , Begeer Sander , Peterson Candida C. , Slaughter Virginia , de Rosnay Marc
Published: September 2014

Chronic friendlessness in childhood predicts adverse mental health outcomes throughout life, yet its earliest roots are poorly understood. In theory, developing a theory of mind (ToM) should help children gain mutual friends and one preschool study (Peterson & Siegal, 2002. Br J Dev Psychol, 20, 205) suggested a cross‐sectional connection. We therefore used a 2‐year prospective longitudinal design to explore ToM as a predictor of mutual friendship in 114 children from age 5 to 7 years after controlling potential confounds including language ability and group popularity. Confirming friendship's distinctiveness from group sociometric status, numerous group‐rejected children (53%) had a mutual friend whereas 23% of those highest in group status did not. Five‐year‐olds with a mutual friend significantly outperformed their friendless peers on a comprehensive ToM battery (basic and advanced false belief). Longitudinally, chronically friendless 7‐year‐olds (no friends at either testing time) stood out for their exceptionally poor Time 1 ToM understanding even after controlling for group popularity, age, and language skill. Extending previous evidence of ToM's predictive links with later social and cognitive outcomes, these results for mutual friendship suggest possible interventions to help reduce the lifelong mental health costs of chronic friendlessness.
Whose picture is this? Children's memory for item and source information
Authors: Chalmers Kerry A.
Published: September 2014

Children aged 3½ to 6½ years viewed pictures of common objects presented either once or three times on one of two consecutive days. A different hand puppet was used to present the pictures on each day, providing both perceptual and temporal cues to source. At test, old (studied) and new (non‐studied) pictures were presented for item recognition and source identification. Results showed that both item and source accuracy were higher for older (M = 5; 9 years) than younger children (M = 4; 6 years). Significant interactions between Age and Day of study were found for both item and source accuracy. For younger children, accuracy was higher for pictures studied on Day 1 than Day 2 (significant for source identification but not item recognition), whereas older children showed the opposite pattern: Higher accuracy for Day 2 than Day 1 (significant for item recognition but not source identification). Results are interpreted with respect to proactive interference and response bias. The utility of signal detection theory measures in determining the basis of age differences in performance of source identification is discussed.
The Differential Profiling of Ubiquitin‐Proteasome and Autophagy Systems in Different Tissues before the Onset of Huntington's Disease Models
Authors: Her Lu‐Shiun , Lin Jian‐Yu , Fu Mu‐Hui , Chang Yu‐Fan , Li Chia‐Ling , Tang Ting‐Yu , Jhang Yu‐Ling , Chang Chih‐Yi , Shih Meng‐Chi , Cheng Pei‐Hsun , Yang Shang‐Hsun
Published: September 2014

Huntington's disease (HD) is a genetic and neurodegenerative disease, leading to motor and cognitive dysfunction in HD patients. At cellular level, this disease is caused by the accumulation of mutant huntingtin (HTT) in different cells, and finally results in the dysfunction of different cells. To clean these mutant proteins, ubiquitin‐proteasome system (UPS) and autophagy system are two critical pathways in the brain; however, little is known in other peripheral tissues. As mutant HTT affects different tissues progressively and might influence the UPS and autophagy pathways at early stages, we attempted to examine two clearance systems in HD models before the onset. Here, in vitro results showed that the accumulation of UPS signals with time was observed obviously in neuroblastoma and kidney cells, not in other cells. In HD transgenic mice, we observed the impairment of UPS, but not autophagy, over time in the cortex and striatum. In heart and muscle tissues, disturbance of autophagy was observed, whereas dysfunction of UPS was displayed in liver and lung. These results suggest that two protein clearance pathways are disturbed differentially in different tissues before the onset of HD, and enhancement of protein clearance at early stages might provide a potential stratagem to alleviate the progression of HD.
Long‐term survival and conditional survival of cancer patients in Japan using population‐based cancer registry data
Authors: Ito Yuri , Miyashiro Isao , Ito Hidemi , Hosono Satoyo , Chihara Dai , Nakata‐Yamada Kayo , Nakayama Masashi , Matsuzaka Masashi , Hattori Masakazu , Sugiyama Hiromi , Oze Isao , Tanaka Rina , Nomura Etsuko , Nishino Yoshikazu , Matsuda Tomohiro , Ioka Akiko , Tsukuma Hideaki , Nakayama Tomio ,   the J‐CANSIS Research Group
Published: September 2014

Although we usually report 5‐year cancer survival using population‐based cancer registry data, nowadays many cancer patients survive longer and need to be followed‐up for more than 5 years. Long‐term cancer survival figures are scarce in Japan. Here we report 10‐year cancer survival and conditional survival using an established statistical approach. We received data on 1 387 489 cancer cases from six prefectural population‐based cancer registries in Japan, diagnosed between 1993 and 2009 and followed‐up for at least 5 years. We estimated the 10‐year relative survival of patients who were followed‐up between 2002 and 2006 using period analysis. Using this 10‐year survival, we also calculated the conditional 5‐year survival for cancer survivors who lived for some years after diagnosis. We reported 10‐year survival and conditional survival of 23 types of cancer for 15–99‐year‐old patients and four types of cancer for children (0–14 years old) and adolescent and young adults (15–29 years old) patients by sex. Variation in 10‐year cancer survival by site was wide, from 5% for pancreatic cancer to 95% for female thyroid cancer. Approximately 70–80% of children and adolescent and young adult cancer patients survived for more than 10 years. Conditional 5‐year survival for most cancer sites increased according to years, whereas those for liver cancer and multiple myeloma did not increase. We reported 10‐year cancer survival and conditional survival using population‐based cancer registries in Japan. It is important for patients and clinicians to report these relevant figures using population‐based data.