bluuebunny/crossref_metadata_2025 huggingface dataset:
Cryptosporidiuminfections: molecular advances
Authors: LENDNER MATTHIAS , DAUGSCHIES ARWID
Published: March 2014

Cryptosporidiumhost cell interaction remains fairly obscure compared with other apicomplexans such asPlasmodiumorToxoplasma. The reason for this is probably the inability of this parasite to complete its life cyclein vitroand the lack of a system to genetically modifyCryptosporidium. However, there is a substantial set of data about the molecules involved in attachment and invasion and about the host cell pathways involved in actin arrangement that are altered by the parasite. Here we summarize the recent advances in research on host cell infection regarding the excystation process, attachment and invasion, survival in the cell, egress and the available data on omics.
Metacognitive group training for schizophrenia spectrum patients with delusions: a randomized controlled trial
Authors: van Oosterhout B. , Krabbendam L. , de Boer K. , Ferwerda J. , van der Helm M. , Stant A. D. , van der Gaag M.
Published: March 2014

Background

Metacognitive training (MCT) for patients with psychosis is a psychological group intervention that aims to educate patients about common cognitive biases underlying delusion formation and maintenance, and to highlight their negative consequences in daily functioning.

Method

In this randomized controlled trial, 154 schizophrenia spectrum patients with delusions were randomly assigned to either MCT + treatment as usual (TAU) or TAU alone. Both groups were assessed at baseline, and again after 8 and 24 weeks. The trial was completed fully by 111 patients. Efficacy was measured with the Psychotic Symptom Rating Scales (PSYRATS) Delusions Rating Scale (DRS), and with specific secondary measures referring to persecutory ideas and ideas of social reference (the Green Paranoid Thoughts Scale, GPTS), cognitive insight (the Beck Cognitive Insight Scale, BCIS), subjective experiences of cognitive biases (the Davos Assessment of Cognitive Biases Scale, DACOBS) and metacognitive beliefs (the 30-item Metacognitions Questionnaire, MCQ-30). Economic analysis focused on the balance between societal costs and health outcomes (quality-adjusted life years, QALYs).

Results

Both conditions showed a decrease of delusions. MCT was not more efficacious in terms of reducing delusions, nor did it change subjective paranoid thinking and ideas of social reference, cognitive insight or subjective experience of cognitive biases and metacognitive beliefs. The results of the economic analysis were not in favour of MCT + TAU.

Conclusions

In the present study, MCT did not affect delusion scores and self-reported cognitive insight, or subjective experience of cognitive biases and metacognitive beliefs. MCT was not cost-effective.
The Louisville Burlesque War: Empire Circuit Company vs. Columbia Amusement
Authors: Gray Karen R. , Yates Sarah R.
Published: March 2014

The Louisville burlesque war began in July of 1908 and ended in late August, 1909, with the opening of the Columbia Amusement Company's Gayety Theatre. In all, there were over ten court cases and thousands of dollars expended by both sides. It was a conflict which, with the help of the press, moved from a private business matter to embroil the whole community. Beyond its local significance, however, the “Gayety Theatre war” foreshadowed a revolution in national burlesque business.
Dramatic Theory and Criticism: A Response
Authors: Carlson Marvin
Published: March 2014

Bernard Dukore's “Clarification” of my review of the Analytical Sourcebook by Brownstein and Daubert raises some questions of sufficient importance to justify, I believe, some further discussion. The Diderot matter is a fairly minor one, though I must maintain that heading a section “Denis Diderot” which is made up of six short pieces, five actually by other writers, is potentially misleading, footnotes or not, the evidence being that Brownstein and Daubert were in fact so misled.
Thermal boundary conductance between Al films and GaN nanowires investigated with molecular dynamics
Authors: Zhou Xiao-wang , Jones Reese E. , Hopkins Patrick E. , Beechem Thomas E.
Published: March 2014

Using molecular dynamics simulations, we studied the thermal boundary conductance between GaN nanowires and Al films and showed how it may be possible to enhance interfacial thermal transport in this important system.
Observation of g/u-symmetry mixing in the high-n Rydberg states of HD
Authors: Sprecher Daniel , Merkt Frédéric
Published: March 2014

The structure and dynamics of high-n Rydberg states belonging to series converging to the (v+ = 0, N+ = 0–2) levels of the \documentclass[12pt]{minimal}\begin{document}$X^+ \, ^2\Sigma _g^+$\end{document}X+Σg+2 electronic ground state of HD+ were studied by high-resolution spectroscopy from the \documentclass[12pt]{minimal}\begin{document}$GK \, ^1\Sigma _g^+$\end{document}GKΣg+1 (v = 1, N = 1) state under field-free conditions. Three effects of g/u-symmetry breaking were detected: (i) Single-photon transitions from the GK (v = 1, N = 1) state of gerade symmetry to the 30d21 and 31g22 Rydberg states of gerade symmetry were observed after careful compensation of the stray electric fields. (ii) The singlet 61p12 Rydberg state of ungerade symmetry was found to autoionize to the N+ = 0, ℓ = 2 ionization continuum of gerade symmetry with a lifetime of 77(10) ns. (iii) Shifts of up to 20 MHz induced by g/u-symmetry mixing were measured for members of the np11 Rydberg series which lie close to nd21 Rydberg states. These observations were analyzed in the framework of multichannel quantum-defect theory. From the observed level shifts, the off-diagonal eigenquantum-defect element \documentclass[12pt]{minimal}\begin{document}$\mu _\text{pd}$\end{document}μpd of singlet-π symmetry was determined to be 0.0023(3) and the corresponding autoionization dynamics could be characterized. The ionization energy of the GK (v = 1, N = 1) state of HD was determined to be 12 710.544 23(10) cm−1.
Singular structures on liquid rims
Authors: Mayer Hans C. , Krechetnikov Rouslan
Published: March 2014

This experimental note is concerned with a new effect we discovered in the course of studying water hammering phenomena. Namely, the ejecta originating from the solid plate impact on a water surface brings about a liquid rim at its edge with the fluid flowing towards the rim center and forming a singular structure resembling a “pancake.” Here, we present the experimental observations and a qualitative physical explanation for the effect, which proves to be fundamental to the situation when the size and speed of the impacting body are such that the capillary effects become important.
Chemical reactions of conformationally selected 3-aminophenol molecules in a beam with Coulomb-crystallized Ca+ ions
Authors: Rösch Daniel , Willitsch Stefan , Chang Yuan-Pin , Küpper Jochen
Published: March 2014

Many molecules exhibit multiple conformers that often easily interconvert under thermal conditions. Therefore, single conformations are difficult to isolate which renders the study of their distinct chemical reactivities challenging. We have recently reported a new experimental method for the characterization of conformer-specific effects in chemical reactions [Y.-P. Chang, K. Długołęcki, J. Küpper, D. Rösch, D. Wild, and S. Willitsch, “Specific chemical reactivities of spatially separated 3-aminophenol conformers with cold Ca+ ions,” Science 342, 98–101 (2013)]. Different conformers are spatially separated using inhomogeneous electric fields and reacted with a Coulomb crystal of cold, spatially localized ions in a trap. As a first application, we studied reactions between the two conformers of 3-aminophenol and Ca+. We observed a twofold larger rate constant for the cis compared to the trans conformer which was rationalized in terms of the differences in the long-range ion-molecule interactions. The present article provides a detailed description of the new method and a full account of the experimental results as well as the accompanying theoretical calculations.
Laser monitor for non-destructive testing of materials and processes shielded by intensive background lighting
Authors: Evtushenko G. S. , Trigub M. V. , Gubarev F. A. , Evtushenko T. G. , Torgaev S. N. , Shiyanov D. V.
Published: March 2014

A single-pulse imaging laser projection system (laser monitor) is proposed for real-time monitoring high-speed processes shielded by the intensive background lighting. The brightness temperature of the lighting can reach thousands or even tens of thousands of degrees, which makes it difficult to observe the processes with the naked eye. The estimates of limiting temperatures show that the use of the proposed instrument allows to view the objects when the equivalent brightness temperature of the background lighting is up to 45 000 K. The results of visualization of some bright objects and processes using high-speed copper bromide vapor laser monitor are presented.
First-principles predicted low-energy structures of NaSc(BH4)4
Authors: Tran Huan Doan , Amsler Maximilian , Botti Silvana , Marques Miguel A. L. , Goedecker Stefan
Published: March 2014

According to previous interpretations of experimental data, sodium-scandium double-cation borohydride NaSc(BH4)4 crystallizes in the crystallographic space group Cmcm where each sodium (scandium) atom is surrounded by six scandium (sodium) atoms. A careful investigation of this phase based on ab initio calculations indicates that the structure is dynamically unstable and gives rise to an energetically and dynamically more favorable phase with C2221 symmetry and nearly identical x-ray diffraction pattern. By additionally performing extensive structural searches with the minima-hopping method we discover a class of new low-energy structures exhibiting a novel structural motif in which each sodium (scandium) atom is surrounded by four scandium (sodium) atoms arranged at the corners of either a rectangle with nearly equal sides or a tetrahedron. These new phases are all predicted to be insulators with band gaps of 7.9–8.2 eV. Finally, we estimate the influence of these structures on the hydrogen-storage performance of NaSc(BH4)4.
Dopant spin states and magnetism of Sn1−xFexO2 nanoparticles
Authors: Punnoose A. , Dodge Kelsey , Beltrán J. J. , Reddy K. M. , Franco Nevil , Chess Jordan , Eixenberger Josh , Barrero C. A.
Published: March 2014

This work reports detailed investigations of a series of ∼2.6 nm sized, Sn1−xFexO2 crystallites with x = 0–0.10 using Mossbauer spectroscopy, x-ray photoelectron spectroscopy (XPS), electron paramagnetic resonance spectroscopy (EPR), and magnetometry to determine the oxidation state of Fe dopants and their role in the observed magnetic properties. The magnetic moment per Fe ion μ was the largest ∼6.48 × 10−3 μB for the sample with the lowest (0.001%) Fe doping, and it showed a rapid downward trend with increasing Fe doping. Majority of the Fe ions are in 3+ oxidation state occupying octahedral sites. Another significant fraction of Fe dopant ions is in 4+ oxidation state and a still smaller fraction might be existing as Fe2+ ions, both occupying distorted sites, presumably in the surface regions of the nanocrystals, near oxygen vacancies. These studies also suggest that the observed magnetism is not due to exchange coupling between Fe3+ spins. A more probable role for the multi-valent Fe ions may be to act as charge reservoirs, leading to charge transfer ferromagnetism.
A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations
Authors: Shimojo Fuyuki , Hattori Shinnosuke , Kalia Rajiv K. , Kunaseth Manaschai , Mou Weiwei , Nakano Aiichiro , Nomura Ken-ichi , Ohmura Satoshi , Rajak Pankaj , Shimamura Kohei , Vashishta Priya
Published: March 2014

We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 106-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of techniques are employed for efficiently calculating the long-range exact exchange correction and excited-state forces. The NAQMD trajectories are analyzed to extract the rates of various excitonic processes, which are then used in KMC simulation to study the dynamics of the global exciton flow network. This has allowed the study of large-scale photoexcitation dynamics in 6400-atom amorphous molecular solid, reaching the experimental time scales.
Influence of microwave driver coupling design on plasma density at Testbench for Ion sources Plasma Studies, a 2.45 GHz Electron Cyclotron Resonance Plasma Reactor
Authors: Megía-Macías A. , Cortázar O. D. , Vizcaíno-de-Julián A.
Published: March 2014

A comparative study of two microwave driver systems (preliminary and optimized) for a 2.45 GHz hydrogen Electron Cyclotron Resonance plasma generator has been conducted. The influence on plasma behavior and parameters of stationary electric field distribution in vacuum, i.e., just before breakdown, along all the microwave excitation system is analyzed. 3D simulations of resonant stationary electric field distributions, 2D simulations of external magnetic field mapping, experimental measurements of incoming and reflected power, and electron temperature and density along the plasma chamber axis have been carried out. By using these tools, an optimized set of plasma chamber and microwave coupler has been designed paying special attention to the optimization of stationary electric field value in the center of the plasma chamber. This system shows a strong stability on plasma behavior allowing a wider range of operational parameters and even sustaining low density plasma formation without external magnetic field. In addition, the optimized system shows the capability to produce values of plasma density four times higher than the preliminary as a consequence of a deeper penetration of the magnetic resonance surface in relative high electric field zone by keeping plasma stability. The increment of the amount of resonance surface embedded in the plasma under high electric field is suggested as a key factor.
Reentrant low-field magneto-resistance in La0.3Pr0.4Ca0.3MnO3 film due to spatial confinement
Authors: Jeon J. , Alagoz H. S. , Boos R. , Jung J. , Chow K. H.
Published: March 2014

Spatially confined La0.3Pr0.4Ca0.3MnO3 micro-bridge was found to produce two maxima in the temperature dependence of the magneto-resistance (MR) as well as in the temperature dependence of the area of the hysteresis loops that exist in an isothermal magnetic field scan of the resistance. One of the peaks is close to the metal-insulator transition temperature, as expected for a standard manganite film, while the additional peak occurs at lower temperatures where co-existing metallic and insulating domains have sizes comparable to the spatially confined region. The dependence of the MR of these two peaks on magnetic field is also substantially different, i.e., the MR of the latter peak is considerably less sensitive to magnetic field than the former one.
Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins
Authors: Harada Ryuhei , Takano Yu , Shigeta Yasuteru
Published: March 2014

A powerful conformational sampling method for accelerating structural transitions of proteins, “Fluctuation Flooding Method (FFM),” is proposed. In FFM, cycles of the following steps enhance the transitions: (i) extractions of largely fluctuating snapshots along anisotropic modes obtained from trajectories of multiple independent molecular dynamics (MD) simulations and (ii) conformational re-sampling of the snapshots via re-generations of initial velocities when re-starting MD simulations. In an application to bacteriophage T4 lysozyme, FFM successfully accelerated the open-closed transition with the 6 ns simulation starting solely from the open state, although the 1-μs canonical MD simulation failed to sample such a rare event.
Improved association in a classical density functional theory for water
Authors: Krebs Eric J. , Schulte Jeff B. , Roundy David
Published: March 2014

We present a modification to our recently published statistical associating fluid theory-based classical density functional theory for water. We have recently developed and tested a functional for the averaged radial distribution function at contact of the hard-sphere fluid that is dramatically more accurate at interfaces than earlier approximations. We now incorporate this improved functional into the association term of our free energy functional for water, improving its description of hydrogen bonding. We examine the effect of this improvement by studying two hard solutes (a hard hydrophobic rod and a hard sphere) and a Lennard-Jones approximation of a krypton atom solute. The improved functional leads to a moderate change in the density profile and a large decrease in the number of hydrogen bonds broken in the vicinity of the hard solutes. We find an improvement of the partial radial distribution for a krypton atom in water when compared with experiment.
Strain rate-induced phase transitions in an impact-hardening polymer composite
Authors: Jiang Weifeng , Gong Xinglong , Wang Sheng , Chen Qian , Zhou Hong , Jiang Wanquan , Xuan Shouhu
Published: March 2014

An impact-hardening polymer composite that is promising as a protective equipment material for its excellent performance and comfortable characteristics is shown. Falling weight impact experiments are performed to characterize its protective behavior, which is realized by absorbing energy and resisting deformation. From the mechanical tests in different strain rate, it is seen to undergo transitions from a viscous-liquid behavior to a rubbery behavior, then to a glassy behavior. These phase transition are found to be essential for their practical applications in the energy absorption and the deformation resistance.
Absorber and gain chip optimization to improve performance from a passively modelocked electrically pumped vertical external cavity surface emitting laser
Authors: Zaugg C. A. , Gronenborn S. , Moench H. , Mangold M. , Miller M. , Weichmann U. , Pallmann W. P. , Golling M. , Tilma B. W. , Keller U.
Published: March 2014

We present an electrically pumped vertical-external-cavity surface-emitting laser (EP-VECSEL) modelocked with a semiconductor saturable absorber mirror (SESAM) with significantly improved performance. In different cavity configurations, we present the shortest pulses (2.5 ps), highest average output power (53.2 mW), highest repetition rate (18.2 GHz), and highest peak power (4.7 W) to date. The simple and low-cost concept of EP-VECSELs is very attractive for mass-market applications such as optical communication and clocking. The improvements result from an optimized gain chip from Philips Technologie GmbH and a SESAM, specifically designed for EP-VECSELs. For the gain chip, we found a better trade-off between electrical and optical losses with an optimized doping scheme in the substrate to increase the average output power. Furthermore, the device's bottom contact diameter (60 μm) is smaller than the oxide aperture diameter (100 μm), which favors electro-optical conversion into a TEM00 mode. Compared to optically pumped VECSELs we have to increase the field enhancement in the active region of an EP-VECSEL which requires a SESAM with lower saturation fluence and higher modulation depth for modelocking. We therefore used a resonant quantum well SESAM with a 3.5-pair dielectric top-coating (SiNx and SiO2) to enhance the field in the absorber at the lasing wavelength of 980 nm. The absorption bandedge at room temperature is detuned (965 nm) compared to the resonance (980 nm), which enables temperature-tuning of the modulation depth and saturation fluence from approximately 2.5% up to 15% and from 20 μJ/cm2 to 1.1 μJ/cm2, respectively.
Dynamic reactions of a free-pitching foil to the reverse Kármán vortices
Authors: Bao Y. , Tao J. J.
Published: March 2014

In order to understand the energy saving mechanism of fish schooling, the dynamic reactions of a free-pitching downstream foil to the oncoming reverse Kármán vortices shed from a flapping leading foil are investigated numerically. When the position of the hindfoil is optimized in a staggered arrangement, a significant augmentation of the thrust efficiency for the whole two-foil system is obtained because of the suction effect of a vortex pair formed at the leading edge of the hindfoil and the guide-plate effect of the hindfoil on the mean-flow jet originated at the trailing edge of the forefoil.
Thermoelectric magnetic flows in melt during directional solidification
Authors: Wang J. , Fautrelle Y. , Ren Z. M. , Nguyen-Thi H. , Salloum Abou Jaoude G. , Reinhart G. , Mangelinck-Noël N. , Li X. , Kaldre I.
Published: March 2014

Thermoelectric magnetic (TEM) flows in melts, which are generated by TEM forces in liquids, were uncovered by the shape evolution of the planar solid/liquid interface during directional solidification. The solid/liquid interface developing from an initially tilted shape to a nearly flat one has been in situ and real-time observed by means of synchrotron X-ray radiography. The corresponding numerical 3D simulations and velocity measurements of flows in the melt confirm that TEM flows exist and respond to this interface shape change. This observation provides visible evidence for TEM flows in melt and their influence on the solid/liquid interface dynamics when directional solidification is conducted in a magnetic field.
Chronology in lesion tolerance gives priority to genetic variability
Authors: Naiman Karel , Philippin Gaëlle , Fuchs Robert P. , Pagès Vincent
Published: March 2014

Significance

When undergoing genotoxic stress, bacteria respond by the induction of their SOS system that promotes the overexpression of several genes. Among these genes are the specialized translesion synthesis (TLS) DNA polymerases that are able to replicate through a DNA lesion with the risk of inserting a mutation. Because these enzymes are expressed late during the SOS response, it has long been believed that TLS was the last recourse used by the cells in response to a genotoxic stress. In this work, we report evidence that TLS occurs before nonmutagenic bypass of a lesion. Thus, by giving priority to mutagenic bypass, cells are able to generate genetic diversity even for mild genotoxic stress.
Angucyclines as signals modulate the behaviors of
Streptomyces coelicolor
Authors: Wang Weishan , Ji Junjie , Li Xiao , Wang Juan , Li Shanshan , Pan Guohui , Fan Keqiang , Yang Keqian
Published: March 2014

Significance

This work addresses the molecular basis for interspecies signaling effects of antibiotics, which have been a controversial but potentially significant emerging topic over the last few years. The “pseudo” gamma-butyrolactone (GBL) receptor (i.e., those GBL receptor homologues often found in
Streptomyces
genomes, but apparently not binding or responding to GBLs), ScbR2, was identified as the receptor of JdB. It has an extraordinary ability to bind and respond to exogenous angucyclines, as well as to be able to directly regulate the biosynthesis of different endogenous antibiotics and the morphological development of
Streptomyces
. Our findings significantly extend understanding of antibiotic-mediated signaling mechanisms and the ecological impact of antibiotics.
Parafoveal Preview Benefit in Unspaced and Spaced Chinese Reading
Authors: Cui Lei , Drieghe Denis , Bai Xuejun , Yan Guoli , Liversedge Simon P.
Published: March 2014

In an eye movement experiment during reading, we compared parafoveal preview benefit during the reading of Chinese sentences either in the familiar, unspaced format or with spaces inserted between the words. Single-character words or the first of a two-character word were either presented normally or were replaced by a pseudocharacter in the preview. Results indicate that word spacing increased the parafoveal preview benefit but only for the one-character target words. We hypothesized that the incorrect preview of the first character of the two-character word prevented parafoveal processing of the ensuing character(s), effectively nullifying any benefits from the spacing. Our results suggest that word boundary demarcation allows for more precise focusing of attention.
Access to Research: the experience of implementing a pilot in public libraries
Authors: FAULDER Sarah , CHA Shinwha
Published: March 2014

The Access to Research project is a collaboration between scholarly publishers and librarians to provide free licensed access to research journals via terminals in public libraries. The project is an element of the ‘balanced package’ proposed by the Finch Working Group on how to expand access to published research in the UK, which reported its recommendations to the UK government in June 2012. We describe the setting up of the project and the findings from a three‐month technical pilot prior to the launch of a two‐year national pilot in February 2014. The project has already attracted support from the major scholarly publishers, with about 8,400 journal titles now available. The access platform has been shown to be usable by public librarians and library patrons. We are now addressing the challenge of understanding how the public will make use of the system and exploring how best to provide training and education for librarians and users.
How research funders can finance APCs in full OA and hybrid journals
Authors: BJÖRK Bo‐Christer , SOLOMON David
Published: March 2014

Open access (OA) publishing is steadily growing in both full OA journals and hybrid journals where authors can pay to open up individual articles. Funding for article processing charges (APCs) is still a strong barrier for many authors, particularly for subscription journals where the hybrid option is expensive and an added extra feature after an article is accepted for publication. Many research funders in Europe have started or are considering mechanisms for paying APCs with earmarked funding in order to increase the uptake of OA. At the same time they are well aware that their actions may influence the way the OA market will develop in the near future. This article discusses a number of scenarios for ways in which funders could cover the cost of APCs, while encouraging the development of a competitive and transparent market for APC‐funded OA scholarly publishing. We provide evidence that the current APC‐funded full OA market is sensitive to journal prestige/impact. We present a value‐based cap funding scheme which could help maintain transparency, bringing hybrid market pricing in line with the full OA market. We also consider a scenario that addresses hybrid ‘double dipping’ while limiting the cost of transitioning to full OA for research‐intensive universities as well as cost‐sharing as a mechanism for providing authors with an incentive for considering cost as well as value in choosing where to publish.
Journal author rights and self‐archiving: the case of Spanish journals
Authors: MELERO R. , RODRÍGUEZ‐GAIRÍN J.M. , ABAD‐GARCÍA F. , ABADAL E.
Published: March 2014

Open access (OA) literature is digital, online, free of charge, and free of most copyright and licensing restrictions. The lack of clarity of publisher permissions for archiving in OA repositories affects the adoption of the green OA route. This paper explores editorial policies and self‐archiving conditions in 1,615 Spanish scholarly journals. 48% are published by university and research institutions, 25% by associations/societies, and 17% by commercial publishers; social sciences and humanities (SSH) accounted for 67% of the journals (44.5% and 22.5%, respectively) followed by health sciences (20%); 71% offered gratis access immediately after publication, and 11% after an embargo; 31% provided some mention of author rights. Self‐archiving was specifically allowed by 65% of the journals; 52% were classified as ROMEO‐blue, 12% as green and 15% as white, and 21% could not be classified; 21%, mostly in SSH, used some type of Creative Commons license.
Trust and Authority in Scholarly Communications in the Light of the Digital Transition: setting the scene for a major study
Authors: NICHOLAS David , WATKINSON Anthony , VOLENTINE Rachel , ALLARD Suzie , LEVINE Kenneth , TENOPIR Carol , HERMAN Eti
Published: March 2014

The paper provides the results of the first phase of the research project Trust and Authority in Scholarly Communications in the Light of the Digital Transition. It provides for an examination of the behaviours and attitudes of academic researchers as producers and consumers of scholarly information resources in the digital era in respect to how they determine authority and trustworthiness in the sources they use, cite, and publish in. The first phase of the study utilized focus groups to formulate research questions for the project as a whole. It provided the direction for the literature review, interviews, and questionnaires studies that would follow. Fourteen focus groups were held in the UK and US in order to obtain this information. A total of 66 science and social science researchers participated. The main findings were: (a) researchers play down difficulties of establishing trustworthiness, not because there are none, but because they have well‐developed methods of establishing trust; (b) citation‐derived metrics are becoming more important in regard to where researchers publish; (c) social media are ancillary to research, but are used for promotion of research and idea generation; (d) researchers are suspicious and confused about open access, but less so if produced by a traditional publisher; (e) there was a uniformity of perceptions/behaviour of researchers irrespective of differences in subject, country, and age; (f) although some early career researchers behave the same as their more senior colleagues this is because of a fear of the system: they actually think differently.
Comparison between user affinity with digital libraries and virtual communities
Authors: YAN Yalan , ZHA Xianjin
Published: March 2014

There is ongoing discussion about the value and reliability of information produced by experts and organized by digital libraries in universities versus information produced by the crowd in virtual communities. This study compares users' perceptions of digital libraries and virtual communities in terms of affinity. In this study, affinity with digital libraries or virtual communities is defined as the degree of importance that users place on digital libraries or virtual communities. Data collected from 334 users of digital libraries and virtual communities were used for data analysis. The statistical method of 'compare means' is employed. We find the mean of affinity with digital libraries is significantly larger than that of virtual communities, suggesting users are likely to perceive higher levels of affinity with digital libraries than with virtual communities. More analysis oriented to different groups is also conducted. The findings and their implications are discussed.
Book reviews
Authors: Gunter Darrell W.
Published: March 2014

The Metadata Handbook: A Book Publisher's Guide to Creating and Distributing Metadata for Print and Ebooks Renée Register and Thad McIlroy Columbus, OH, DATACurate, 2012, 133pp. ISBN: 978‐0‐9858288‐1‐3 (PDF), 978‐0‐9858288‐5‐1 (Kindle), 978‐0‐9858288‐2‐0 (epub), 978‐0‐9858288‐0‐6 (pbk), $125.00 (pbk) $95.00 (e‐book) http://themetadatahandbook.com/
Book reviews
Authors: Slater Eric S.
Published: March 2014

Copyright and Mass Digitization Maurizio Borghi and Stavroula Karapapa Oxford, Oxford University Press, 2013, 177pp. ISBN 978‐0‐19‐966455‐9, hbk, c. £70.00, e‐book c. £46.50
Book reviews
Authors: SMART Pippa
Published: March 2014

What Editors Want: An Author's Guide to Scientific Journal Publishing Philippa K. Benson and Susan C. Silver Chicago, University of Chicago Press, 2012, 192pp. ISBN 978‐0226043142, £13.21 pbk
Kähler-Einstein metrics on Fano manifolds. I: Approximation of metrics with cone singularities
Authors: Chen Xiuxiong , Donaldson Simon , Sun Song
Published: March 2014

This is the first of a series of three papers which prove the fact that a K-stable Fano manifold admits a Kähler-Einstein metric. The main result of this paper is that a Kähler-Einstein metric with cone singularities along a divisor can be approximated by a sequence of smooth Kähler metrics with controlled geometry in the Gromov-Hausdorff sense.
Kähler-Einstein metrics on Fano manifolds. II: Limits with cone angle less than \boldmath2𝜋
Authors: Chen Xiuxiong , Donaldson Simon , Sun Song
Published: March 2014

This is the second of a series of three papers which prove the fact that a K-stable Fano manifold admits a Kähler-Einstein metric. In this paper we consider the Gromov-Hausdorff limits of metrics with cone singularities in the case when the limiting cone angle is less than 2

π

{\pi }

. We show that these are in a natrual way projective algebraic varieties. In the case when the limiting variety and the limiting divisor are smooth we show that the limiting metric also has standard cone singularities.
CorMut: an R/Bioconductor package for computing correlated mutations based on selection pressure
Authors: Li Zhenpeng , Huang Yang , Ouyang Yabo , Jiao Yang , Xing Hui , Liao Lingjie , Jiang Shibo , Shao Yiming , Ma Liying
Published: March 2014

Summary: Correlated mutations constitute a fundamental idea in evolutionary biology, and understanding correlated mutations will, in turn, facilitate an understanding of the genetic mechanisms governing evolution. CorMut is an R package designed to compute correlated mutations in the unit of codon or amino acid mutation. Three classical methods were incorporated, and the computation results can be represented as correlation mutation networks. CorMut also enables the comparison of correlated mutations between two different evolutionary conditions.

Availability and implementation: CorMut is released under the GNU General Public License within bioconductor project, and freely available at http://bioconductor.org/packages/release/bioc/html/CorMut.html .

Contact:  mal@chinaaids.cn or yshao08@gmail.com
Motifs tree: a new method for predicting post-translational modifications
Authors: Charpilloz Christophe , Veuthey Anne-Lise , Chopard Bastien , Falcone Jean-Luc
Published: March 2014

Motivation: Post-translational modifications (PTMs) are important steps in the maturation of proteins. Several models exist to predict specific PTMs, from manually detected patterns to machine learning methods. On one hand, the manual detection of patterns does not provide the most efficient classifiers and requires an important workload, and on the other hand, models built by machine learning methods are hard to interpret and do not increase biological knowledge. Therefore, we developed a novel method based on patterns discovery and decision trees to predict PTMs. The proposed algorithm builds a decision tree, by coupling the C4.5 algorithm with genetic algorithms, producing high-performance white box classifiers. Our method was tested on the initiator methionine cleavage (IMC) and N α -terminal acetylation (N-Ac), two of the most common PTMs.

Results: The resulting classifiers perform well when compared with existing models. On a set of eukaryotic proteins, they display a cross-validated Matthews correlation coefficient of 0.83 (IMC) and 0.65 (N-Ac). When used to predict potential substrates of N-terminal acetyltransferaseB and N-terminal acetyltransferaseC, our classifiers display better performance than the state of the art. Moreover, we present an analysis of the model predicting IMC for Homo sapiens proteins and demonstrate that we are able to extract experimentally known facts without prior knowledge. Those results validate the fact that our method produces white box models.

Availability and implementation: Predictors for IMC and N-Ac and all datasets are freely available at http://terminus.unige.ch/ .

Contact:  jean-luc.falcone@unige.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
VariantAnnotation
: a
Bioconductor
package for exploration and annotation of genetic variants
Authors: Obenchain Valerie , Lawrence Michael , Carey Vincent , Gogarten Stephanie , Shannon Paul , Morgan Martin
Published: March 2014

Summary:  VariantAnnotation is an R / Bioconductor package for the exploration and annotation of genetic variants. Capabilities exist for reading, writing and filtering variant call format (VCF) files. VariantAnnotation allows ready access to additional R / Bioconductor facilities for advanced statistical analysis, data transformation, visualization and integration with diverse genomic resources.

Availability and implementation: This package is implemented in R and available for download at the Bioconductor Web site ( http://bioconductor.org/packages/2.13/bioc/html/ VariantAnnotation .html ). The package contains extensive help pages for individual functions and a ‘vignette’ outlining typical work flows; it is made available under the open source ‘Artistic-2.0’ license. Version 1.9.38 was used in this article.

Contact:  vobencha@fhcrc.org
molBLOCKS: decomposing small molecule sets and uncovering enriched fragments
Authors: Ghersi Dario , Singh Mona
Published: March 2014

Summary: The chemical structures of biomolecules, whether naturally occurring or synthetic, are composed of functionally important building blocks. Given a set of small molecules—for example, those known to bind a particular protein—computationally decomposing them into chemically meaningful fragments can help elucidate their functional properties, and may be useful for designing novel compounds with similar properties. Here we introduce molBLOCKS , a suite of programs for breaking down sets of small molecules into fragments according to a predefined set of chemical rules, clustering the resulting fragments, and uncovering statistically enriched fragments. Among other applications, our software should be a great aid in large-scale chemical analysis of ligands binding specific targets of interest.

Availability and implementation:  molBLOCKS is available as GPL C++ source code at http://compbio.cs.princeton.edu/molblocks .

Contact:  mona@cs.princeton.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Combined effects of exploitation and temperature on fish stocks in the Northeast Atlantic
Authors: Rouyer Tristan , Fromentin Jean-Marc , Hidalgo Manuel , Stenseth Nils C.
Published: March 2014

Fish stock fluctuations are affected by two potentially confounding forces: the removal of individuals by fisheries and climatic variations affecting the productivity of fish populations. Disentangling the relative importance of these forces has thus been a question of primary importance for fisheries management and conservation. Through the analysis of long-term time-series for 27 fish stocks from the Northeast Atlantic, the present study shows that the sign and intensity of the effect of temperature on biomass are dependent on the geographical location: the stocks located at the southernmost and northernmost latitudes of our study displayed stronger associations with temperature than the stocks located in the middle range of latitudes. As a consequence, the investigation of the combined effects of exploitation and the environment revealed that the stocks at the northern/southern boundaries of the spatial extent of the species were more prone to combined effects. The interplay between geographic location, climate and exploitation thus plays a significant role in fish stock productivity, which is generally ignored during assessment, thus affecting management procedures.
Defining the Role of prolamin-box binding factor1 Gene
During Maize Domestication
Authors: Lang Zhihong , Wills David M , Lemmon Zachary H , Shannon Laura M , Bukowski Robert , Wu Yongrui , Messing Joachim , Doebley John F
Published: March 2014

The prolamin-box binding factor1 (pbf1) gene encodes a transcription factor that controls the expression of seed storage protein (zein) genes in maize. Prior studies show that pbf1 underwent selection during maize domestication although how it affected trait change during domestication is unknown. To assay how pbf1 affects phenotypic differences between maize and teosinte, we compared nearly isogenic lines (NILs) that differ for a maize versus teosinte allele of pbf1. Kernel weight for the teosinte NIL (162mg) is slightly but significantly greater than that for the maize NIL (156mg). RNAseq data for developing kernels show that the teosinte allele of pbf1 is expressed at about twice the level of the maize allele. However, RNA and protein assays showed no difference in zein profile between the two NILs. The lower expression for the maize pbf1 allele suggests that selection may have favored this change; however, how reduced pbf1 expression alters phenotype remains unknown. One possibility is that pbf1 regulates genes other than zeins and thereby is a domestication trait. The observed drop in seed weight associated with the maize allele of pbf1 is counterintuitive but could represent a negative pleiotropic effect of selection on some other aspect of kernel composition.
Relating Latent Class Assignments to External Variables: Standard Errors for Correct Inference
Authors: Bakk Zsuzsa , Oberski Daniel L. , Vermunt Jeroen K.
Published: March 2014

Latent class analysis is used in the political science literature in both substantive applications and as a tool to estimate measurement error. Many studies in the social and political sciences relate estimated class assignments from a latent class model to external variables. Although common, such a “three-step” procedure effectively ignores classification error in the class assignments; Vermunt (2010, “Latent class modeling with covariates: Two improved three-step approaches,”Political Analysis18:450–69) showed that this leads to inconsistent parameter estimates and proposed a correction. Although this correction for bias is now implemented in standard software, inconsistency is not the only consequence of classification error. We demonstrate that the correction method introduces an additional source of variance in the estimates, so that standard errors and confidence intervals are overly optimistic when not taking this into account. We derive the asymptotic variance of the third-step estimates of interest, as well as several candidate-corrected sample estimators of the standard errors. These corrected standard error estimators are evaluated using a Monte Carlo study, and we provide practical advice to researchers as to which should be used so that valid inferences can be obtained when relating estimated class membership to external variables.
Two novel Saccharomycopsis species isolated from black olive brines and a tropical plant. Description of Saccharomycopsis olivae f. a., sp. nov. and Saccharomycopsis guyanensis f. a., sp. nov. Reassignment of Candida amapae to Saccharomycopsis amapae f. a., comb. nov., Candida lassenensis to Saccharomycopsis lassenensis f. a., comb. nov. and Arthroascus babjevae to Saccharomycopsis babjevae f. a., comb. nov.
Authors: Jacques Noémie , Louis-Mondesir Christelle , Coton Monika , Coton Emmanuel , Casaregola Serge
Published: March 2014

Three yeast strains related to members of the genus Saccharomycopsis were isolated. One strain (CLIB 1310) was isolated from olive brines of fermented black olives in France and two strains (CLIB 1454 and CLIB 1455) were isolated from a plant in French Guiana. Sequence analyses based on the D1/D2 domains of the nuclear large subunit rRNA gene, small-subunit rRNA gene and partial EF-1α gene revealed that the strains represented two novel taxa exhibiting extensive sequence divergence from the previously described species of the genus Saccharomycopsis. Two novel species are described to accommodate these newly isolated strains: Saccharomycopsis olivae sp. nov. (type strain CLIB 1310T = CBS 12701T) and Saccharomycopsis guyanensis sp. nov. (type strain CLIB 1455T = CBS 12914T and strain CLIB 1454). Both strains CLIB 1454 and CLIB 1455T displayed identical sequences but differed in their ability to metabolize sorbitol and in their morphology on agar medium. Candida amapae, Candida lassensensis and Arthroascus babjevae belonging to the Saccharomycopsis clade, are reassigned to Saccharomycopsis as novel combinations.
HDAC-regulated myomiRs control BAF60 variant exchange and direct the functional phenotype of fibro-adipogenic progenitors in dystrophic muscles
Authors: Saccone Valentina , Consalvi Silvia , Giordani Lorenzo , Mozzetta Chiara , Barozzi Iros , Sandoná Martina , Ryan Tammy , Rojas-Muñoz Agustin , Madaro Luca , Fasanaro Pasquale , Borsellino Giovanna , De Bardi Marco , Frigè Gianmaria , Termanini Alberto , Sun Xin , Rossant Janet , Bruneau Benoit G. , Mercola Mark , Minucci Saverio , Puri Pier Lorenzo
Published: March 2014

Fibro-adipogenic progenitors (FAPs) are important components of the skeletal muscle regenerative environment. Whether FAPs support muscle regeneration or promote fibro-adipogenic degeneration is emerging as a key determinant in the pathogenesis of muscular diseases, including Duchenne muscular dystrophy (DMD). However, the molecular mechanism that controls FAP lineage commitment and activity is currently unknown. We show here that an HDAC–myomiR–BAF60 variant network regulates the fate of FAPs in dystrophic muscles of mdx mice. Combinatorial analysis of gene expression microarray, genome-wide chromatin remodeling by nuclease accessibility (NA) combined with next-generation sequencing (NA-seq), small RNA sequencing (RNA-seq), and microRNA (miR) high-throughput screening (HTS) against SWI/SNF BAF60 variants revealed that HDAC inhibitors (HDACis) derepress a “latent” myogenic program in FAPs from dystrophic muscles at early stages of disease. Specifically, HDAC inhibition induces two core components of the myogenic transcriptional machinery, MYOD and BAF60C, and up-regulates the myogenic miRs (myomiRs) (miR-1.2, miR-133, and miR-206), which target the alternative BAF60 variants BAF60A and BAF60B, ultimately directing promyogenic differentiation while suppressing the fibro-adipogenic phenotype. In contrast, FAPs from late stage dystrophic muscles are resistant to HDACi-induced chromatin remodeling at myogenic loci and fail to activate the promyogenic phenotype. These results reveal a previously unappreciated disease stage-specific bipotency of mesenchimal cells within the regenerative environment of dystrophic muscles. Resolution of such bipotency by epigenetic intervention with HDACis provides a molecular rationale for the in situ reprogramming of target cells to promote therapeutic regeneration of dystrophic muscles.