bluuebunny/crossref_metadata_2025 huggingface dataset:
Facile chemoenzymatic synthesis of biotinylated heparosan hexasaccharide
Authors: Wu Baolin , Wei Na , Thon Vireak , Wei Mohui , Yu Zaikuan , Xu Yongmei , Chen Xi , Liu Jian , Wang Peng George , Li Tiehai
Published: April 2015

A biotinylated heparosan hexasaccharide was synthesized by a facile chemoenzymatic approach in a one-pot multi-enzyme fashion.
Iron- or silver-catalyzed oxidative fluorination of cyclopropanols for the synthesis of β-fluoroketones
Authors: Ren Shichao , Feng Chao , Loh Teck-Peng
Published: April 2015

The FeIII- or AgI-catalyzed oxidative fluorination of cyclopropanols via radical rearrangement is disclosed.
Simulation of radical polymerization of methyl methacrylate at room temperature using a tertiary amine/BPO initiating system
Authors: Zoller Alexander , Gigmes Didier , Guillaneuf Yohann
Published: April 2015

A model was developed for the polymerization of methyl methacrylate at room temperature. The model used both free volume and empirical models for propagation, termination and several side reactions.
Antidiabetic effects of isolated sterols from Ficus racemosa leaves
Authors: Kushwaha Priya Singh , Raj Vinit , Singh Ashok K. , Keshari Amit K. , Saraf Shubhini A. , Mandal Subhash C. , Yadav Rajnish Kumar , Saha Sudipta
Published: April 2015

Isolation and structure confirmation through NMR and MS. Antidiabetic and hypolipidemic activities using streptozotocin induced albino rats. Toxicological assessments. Mechanistic study to PPARγ through molecular docking.
Self-assembled synthesis of urchin-like AlOOH microspheres with large surface area for removal of pollutants
Authors: Song Xueling , Yang Ping , Jia Changchao , Chen Ling , Matras-Postolek Katarzyna
Published: April 2015

Urchin-like AlOOH microspheres synthesized by a chemical induced solvothermal method revealed high efficiency for the removal of Congo red pollutant.
Superhydrophobic Ti6Al4V surfaces with regular array patterns for anti-icing applications
Authors: Shen Yizhou , Tao Jie , Tao Haijun , Chen Shanlong , Pan Lei , Wang Tao
Published: April 2015

We present a route to fabricate a robust anti-icing superhydrophobic surface containing the hierarchical structures of microscale array patterns (built by micromachining) and nanohairs (prepared via hydrothermal growth) on a Ti6Al4V substrate.
The determination of ligand shell composition of bifunctional alkanethiol-capped gold nanoparticles using GC/MS/MS
Authors: Fisher Elizabeth A. , Duffy Stephen J. , Meli M.-Vicki
Published: April 2015

A straightforward calibration is shown to provide effective quantitation of relative amounts of thiol in mixed ligand shells of gold nanoparticles by GC/MS/MS.
Cholesterol-tethered AIEE fluorogens: formation of self-assembled nanostructures
Authors: Palakollu Veerabhadraiah , Kanvah Sriram
Published: April 2015

Design and synthesis of cholesterol conjugated chromophores exhibiting intramolecular charge transfer (ICT) and Aggregation Induced Enhanced Emission (AIEE) and their self-assembling behavior is described.
Aggregation-induced emission and aggregation-promoted photochromism of bis(diphenylmethylene)dihydroacenes
Authors: He Zikai , Shan Liang , Mei Ju , Wang Hong , Lam Jacky W. Y. , Sung Herman H. Y. , Williams Ian D. , Gu Xiao , Miao Qian , Tang Ben Zhong
Published: April 2015

Solid-state photochromism was found in bis(diphenylmethylene)dihydrotetracene, caused by photocyclization of the embeddedcis-stilbene motifs.
Mesoscopic simulation of the self-assembly of the weak polyelectrolyte poly(ethylene oxide)-block-poly(methyl methacrylate) diblock copolymers
Authors: Mu Dan , Li Jian-Quan , Feng Sheng-Yu
Published: April 2015

We designed twelve types of weak polyelectrolytes (i.e., PEO-b-PMMA copolymers (BCP) in multi-arm structures, where six include EO blocks as joint points and the other six have MMA blocks as joint points). Of these, six are displayed; structures with EO blocks as joint points on the left, and those with MMA blocks as joint points on the right.
Correlation between cellulose thin film supramolecular structures and interactions with water
Authors: Tammelin Tekla , Abburi Ramarao , Gestranius Marie , Laine Christiane , Setälä Harri , Österberg Monika
Published: April 2015

Influence of the supramolecular structure of thin films of more crystalline cellulose (left) and highly amorphous cellulose (middle) on water vapour induced behaviour (right).
High performance H2 evolution realized in 20 μm-thin silicon nanostructured photocathodes
Authors: Jung Jin-Young , Park Min-Joon , Li Xiaopeng , Kim Jong-Ho , Wehrspohn Ralf B. , Lee Jung-Ho
Published: April 2015

Pt nanoparticles (NPs) are coated on the tapered nanoholes (NHs) integrated using a 20 μm-thin Si wafer. This photocathode significantly improves H2 production via efficient light absorption and suppression of surface recombination for obtaining a high photocurrent value of 23 mA cm−2 at 0 V vs. RHE.
Direct deposition of proton exchange membranes enabling high performance hydrogen fuel cells
Authors: Klingele Matthias , Breitwieser Matthias , Zengerle Roland , Thiele Simon
Published: April 2015

Fuel cells with directly deposited membrane (DDM) reveal an ultra low membrane resistance and outperform conventional catalyst coated membranes (CCM).
Recent developments in multilayered polymeric particles – from fabrication techniques to therapeutic formulations
Authors: Saha Sampa , Loo Say Chye Joachim
Published: April 2015

Multilayered particles are emerging as a powerful platform in pharmaceutics, especially for targeted, triggered and sustained drug delivery.
Peptide-directed crystal growth modification in the formation of ZnO
Authors: Sola-Rabada Anna , Liang Mei-Keat , Roe Martin J. , Perry Carole C.
Published: April 2015

ZnO-binding peptides, differing only by Met or Cys at position 5 modify the mechanism of ZnO crystal growth.
3D conducting polymer platforms for electrical control of protein conformation and cellular functions
Authors: Wan Alwin Ming-Doug , Inal Sahika , Williams Tiffany , Wang Karin , Leleux Pierre , Estevez Luis , Giannelis Emmanuel P. , Fischbach Claudia , Malliaras George G. , Gourdon Delphine
Published: April 2015

Ice-templating of the conducting polymer PEDOT:PSS yields 3D tissue-mimicking scaffolds that can electrically control protein conformation and various cell functions.
Intercalation of coumaric acids into layered rare-earth hydroxides: controllable structure and photoluminescence properties
Authors: Gu Qingyang , Su Feifei , Ma Lijiao , Ma Shulan , Sun Genban , Yang Xiaojing
Published: April 2015

The intercalation of two coumaric acids into LRHs forms composites, which showed tunable luminescence depending on the state and layer ions.
Fathers' and Mothers' Verbal Responsiveness and the Language Skills of Young Children With Autism Spectrum Disorder
Authors: Flippin Michelle , Watson Linda R.
Published: April 2015

Purpose

In this observational study, we examined the interactions of 16 young children with autism spectrum disorder (ASD) and their parents to investigate (a) differences in verbal responsiveness used by fathers and mothers in interactions with their children with ASD and (b) concurrent associations between the language skills of children with ASD and the verbal responsiveness of both fathers and mothers.

Method

Parent verbal responsiveness was coded from video recordings of naturalistic parent–child play sessions using interval-based coding. Child language skills were measured by the Preschool Language Scale–Fourth Edition (Zimmerman, Steiner, & Pond, 2002).

Results

For both fathers and mothers, parent verbal responsiveness was positively associated with child language skills. Mothers' responsiveness was also significantly associated with child cognition. After controlling for child cognition, fathers' verbal responsiveness continued to be significantly related to child language skills.

Conclusions

Although other studies have documented associations between mothers' responsiveness and child language, this is the 1st study to document a significant concurrent association between child language skills of children with ASD and the verbal responsiveness of fathers. Findings of this study warrant the inclusion of fathers in future research on language development and intervention to better understand the potential contributions fathers may make to language growth for children with ASD over time as well as to determine whether coaching fathers to use responsive verbal strategies can improve language outcomes for children with ASD.
Assessment of Reliable Change Using 95% Credible Intervals for the Differences in Proportions: A Statistical Analysis for Case-Study Methodology
Authors: Unicomb Rachael , Colyvas Kim , Harrison Elisabeth , Hewat Sally
Published: April 2015

Purpose

Case-study methodology studying change is often used in the field of speech-language pathology, but it can be criticized for not being statistically robust. Yet with the heterogeneous nature of many communication disorders, case studies allow clinicians and researchers to closely observe and report on change. Such information is valuable and can further inform large-scale experimental designs. In this research note, a statistical analysis for case-study data is outlined that employs a modification to the Reliable Change Index (Jacobson & Truax, 1991). The relationship between reliable change and clinical significance is discussed. Example data are used to guide the reader through the use and application of this analysis.

Method

A method of analysis is detailed that is suitable for assessing change in measures with binary categorical outcomes. The analysis is illustrated using data from one individual, measured before and after treatment for stuttering.

Conclusions

The application of this approach to assess change in categorical, binary data has potential application in speech-language pathology. It enables clinicians and researchers to analyze results from case studies for their statistical and clinical significance. This new method addresses a gap in the research design literature, that is, the lack of analysis methods for noncontinuous data (such as counts, rates, proportions of events) that may be used in case-study designs.
Thermodynamics of the polaron master equation at finite bias
Authors: Krause Thilo , Brandes Tobias , Esposito Massimiliano , Schaller Gernot
Published: April 2015

We study coherent transport through a double quantum dot. Its two electronic leads induce electronic matter and energy transport and a phonon reservoir contributes further energy exchanges. By treating the system-lead couplings perturbatively, whereas the coupling to vibrations is treated non-perturbatively in a polaron-transformed frame, we derive a thermodynamic consistent low-dimensional master equation. When the number of phonon modes is finite, a Markovian description is only possible when these couple symmetrically to both quantum dots. For a continuum of phonon modes however, also asymmetric couplings can be described with a Markovian master equation. We compute the electronic current and dephasing rate. The electronic current enables transport spectroscopy of the phonon frequency and displays signatures of Franck-Condon blockade. For infinite external bias but finite tunneling bandwidths, we find oscillations in the current as a function of the internal bias due to the electron-phonon coupling. Furthermore, we derive the full fluctuation theorem and show its identity to the entropy production in the system.
Lattice cluster theory for dense, thin polymer films
Authors: Freed Karl F.
Published: April 2015

While the application of the lattice cluster theory (LCT) to study the miscibility of polymer blends has greatly expanded our understanding of the monomer scale molecular details influencing miscibility, the corresponding theory for inhomogeneous systems has not yet emerged because of considerable technical difficulties and much greater complexity. Here, we present a general formulation enabling the extension of the LCT to describe the thermodynamic properties of dense, thin polymer films using a high dimension, high temperature expansion. Whereas the leading order of the LCT for bulk polymer systems is essentially simple Flory-Huggins theory, the highly non-trivial leading order inhomogeneous LCT (ILCT) for a film with L layers already involves the numerical solution of 3(L − 1) coupled, highly nonlinear equations for the various density profiles in the film. The new theory incorporates the essential “transport” constraints of Helfand and focuses on the strict imposition of excluded volume constraints, appropriate to dense polymer systems, rather than the maintenance of chain connectivity as appropriate for lower densities and as implemented in self-consistent theories of polymer adsorption at interfaces. The ILCT is illustrated by presenting examples of the computed profiles of the density, the parallel and perpendicular bonds, and the chain ends for free standing and supported films as a function of average film density, chain length, temperature, interaction with support, and chain stiffness. The results generally agree with expected general trends.
Evolution of plasma loops in a semi-toroidal pinch experiment
Authors: Mackel F. , Ridder S. , Tenfelde J. , Tacke T. , Soltwisch H.
Published: April 2015

The FlareLab experiment is a pulsed-power discharge generating magnetized plasma loops similar to a pinch experiment in a semi-toroidal configuration. After gas breakdown along a circular magnetic guide field, the structure expands in its major radius as the plasma becomes highly conductive and the discharge current rises. Photographs, current and electron density measurements reveal a significant broadening in the lateral direction leading to an increasing departure from radial symmetry of plasma parameters in the cross section. It is shown that the luminosity is related to both high electron density and high current density. Simultaneous measurements of current density and electric field reveal a high parallel resistivity of the plasma leading to fast diffusion across the magnetic field. Indications for anomalous resistivity are found by comparison with the Spitzer formula. As the experiment differs from a z-pinch experiment only by the semi-circular shape of the current path, the observed evolution is unexpected and might be of more fundamental significance.
Focus: Phase-resolved nonlinear terahertz spectroscopy—From charge dynamics in solids to molecular excitations in liquids
Authors: Elsaesser Thomas , Reimann Klaus , Woerner Michael
Published: April 2015

Intense terahertz (THz) electric field transients with amplitudes up to several megavolts/centimeter and novel multidimensional techniques are the key ingredients of nonlinear THz spectroscopy, a new area of basic research. Both nonlinear light-matter interactions including the non-perturbative regime and THz driven charge transport give new insight into the character and dynamics of low-energy excitations of condensed matter and into quantum kinetic phenomena. This article provides an overview of recent progress in this field, combining an account of technological developments with selected prototype results for liquids and solids. The potential of nonlinear THz methods for future studies of low-frequency excitations of condensed-phase molecular systems is discussed as well.
Oscillating two-stream instability in a magnetized electron-positron-ion plasma
Authors: Tinakiche Nouara , Annou R.
Published: April 2015

Oscillating two-stream instability (OTSI) in a magnetized electron-ion plasma has been thoroughly studied, e.g., in ionospheric heating experiments [C. S. Liu and V. K. Tripathi, Interaction of Electromagnetic Waves With Electron Beams and Plasmas (World Scientific, 1994); V. K. Tripathi and P. V. Siva Rama Prasad, J. Plasma Phys. 41, 13 (1989); K. Ramachandran and V. K. Tripathi, IEEE Trans. Plasma Sci. 25, 423 (1997)]. In this paper, OTSI is investigated in a magnetized electron-positron-ion plasma. The dispersion relation of the process is established. The pump field threshold, along with the maximum growth rate of the instability is assessed using the Arecibo and HAARP parameters.
Detection of endotoxin using a photonic crystal nanolaser
Authors: Takahashi Daichi , Hachuda Shoji , Watanabe Takumi , Nishijima Yoshiaki , Baba Toshihiko
Published: April 2015

Fast and reliable detection of endotoxin (ET) in medical equipment and pharmaceutical products is an essential precursor to clinical treatment. In this study, we demonstrate the use of shifts in wavelength of photonic crystal nanolasers for sensing the Limulus amebocyte lysate reaction, which is a standard method for detecting ET. From working curves of wavelength shift vs ET concentration, whose correlation factors were as high as 98%, we detected a required concentration of 0.001 EU/ml within 33 min and detected a low concentration of 0.0001 EU/ml.
Communication: Unraveling the 4He droplet-mediated soft-landing from ab initio-assisted and time-resolved density functional simulations: Au@4He300/TiO2(110)
Authors: de Lara-Castells María Pilar , Aguirre Néstor F. , Stoll Hermann , Mitrushchenkov Alexander O. , Mateo David , Pi Martí
Published: April 2015

An ab-initio-based methodological scheme for He-surface interactions and zero-temperature time-dependent density functional theory for superfluid 4He droplets motion are combined to follow the short-time collision dynamics of the Au@4He300 system with the TiO2(110) surface. This composite approach demonstrates the 4He droplet-assisted sticking of the metal species to the surface at low landing energy (below 0.15 eV/atom), thus providing the first theoretical evidence of the experimentally observed 4He droplet-mediated soft-landing deposition of metal nanoparticles on solid surfaces [Mozhayskiy et al., J. Chem. Phys. 127, 094701 (2007) and Loginov et al., J. Phys. Chem. A 115, 7199 (2011)].
An optical tweezer for complex plasmas
Authors: Schablinski Jan , Wieben Frank , Block Dietmar
Published: April 2015

This paper describes the experimental realization of an optical trap for microparticles levitating in the plasma sheath. Single particles can be trapped in a laser beam comparable to optical tweezers known from colloidal suspensions. The trapping mechanism is discussed and two applications of the system are shown.
The ZnO p-n homojunctions modulated by ZnMgO barriers
Authors: Yang Jing-Jing , Fang Qing-Qing , Wang Dan-Dan , Du Wen-Han
Published: April 2015

In this paper, we fabricated the ultrathin ZnO p-n homojunctions, which modulated by ZnMgO asymmetrical double barriers (ADB). The ADB p-n homojunctions displays step-like curve in the absorption spectrums, this is the first time that quantum confinement effect has been observed in the absorption spectrums at room temperature (RT). The Hall-effect data confirm there is 2-dimensional electron gas in the interface of the ZnMgO ADB p-n junctions. The quantum confinement effect enhances the hall-mobility μ to 103 cm2V −1s−1 based on the polarity of the films. There was no rectification property in the ZnO homojunctions with thickness of 250nm, however, when the ADB was added in the n-type layer of the homojunctions, it displays a typical Zener diode rectification property in the I-V curve.
Metaphorical eternity in action
Authors: Bakhtiar Mohsen
Published: April 2015

Conceptual metaphors can be made real in culture and structure many areas of human experience in nonlinguistic ways (Kövecses 2005). In this paper, relying on a cognitive account of metaphor, I attempted to find out in which ways death metaphors manifest themselves in Iranian culture. Analyzing the rituals of death in Iran, it was revealed that Iranians rely on a set of basic concetual metaphors to conceptualize the taboo of death. Heavily motivated by religious instructions, the whole scenario of death is conceptualized in terms of human physical and psychological experiences. In addition to the event of death, which is conceptualized via the highly generic DEATH IS LIFE metaphor, in this culture, an important mapping of this metaphor, that is, THE DEAD ARE EMOTIONAL BEINGS, is extensively realized and enacted, which provides a unique subsystem for making euphemistic reference to death. Furthermore, the paper comes to the conclusion that most of the entailments of the source domains and some of the source domains turn into social-physical reality. The whole system of death rituals as structured by metaphors imply that we metaphorically never die.
Subclasses of Chinese noun phrases and the parallel occurrence ofde的
Authors: Wang Yuanjie
Published: April 2015

Chinese noun phrases are divided into three subclasses, namely, classification phrases, quantification phrases, and identification phrases, to describe and explain the parallel occurrence ofdein the NPs with a single modifier. The parallelism exists not only between the three subclasses of NPs, but also, within the quantification phrases, between the nominal quantification modifiers and the verbal quantification modifiers. The reason for this parallel occurrence is that, the classification phrase tends to occur withoutdewhen its modifier has a higher ability to classify the head noun, so do the quantification phrase when its modifier has a higher ability to count the head noun, and the identification phrase when its modifier has a higher ability to identify the head noun.
Formant frequency characteristics in Palestinian Arabic-speaking aphasics
Authors: Adam Hisham
Published: April 2015

The aim of this paper is to examine the acoustic characteristics of Arabic vowels as produced by Palestinian Arabic-speaking Broca’s aphasics compared to normal speakers. Five subjects diagnosed with Broca’s aphasia and five normal speakers residing in the West Bank participated in this study. The subjects produced 240 vowel tokens of the eight Arabic vowels (/i:/, /i/, /e:/, /a:/, /a/, /o:/, /u:/ and /u/,). The samples were analyzed using PRAAT and the formants F1 and F2 of the eight Arabic vowels were measured. F1 and F2 values were compared to the data in the literature. Comparisons among speakers of Palestinian Arabic indicated that Broca’s aphasics’ formant frequencies were significantly different to those of normal speakers, showing that formant frequencies of F1 and F2 are generally higher among Broca’s aphasics compared to the control group. Furthermore, the findings reveal that the acoustic vowel space of Broca’s aphasics is more centralized compared to the control subjects. The results also indicate that Broca’s aphasics were able to maintain the phonemic contrast between the long and short vowels. In general, the results may contribute to neurolinguistic research across different languages, especially given that Palestinian Arabic is studied significantly less than other Arabic dialects. Furthermore, the results may have clinical applications when evaluating and/or treating Palestinian Arabic-speaking Broca’s aphasics.
Twenty years of historical pragmatics
Authors: Taavitsainen Irma , Jucker Andreas H.
Published: April 2015

This paper provides an outline of the changes in linguistics that gave rise to historical pragmatics in the 1990s and that have shaped its development over the twenty years of its existence. These changes have affected virtually all aspects of linguistic analyses: the nature of the data, the research questions, the methods and tools that are being used for the analysis, as well as the nature of the generalizations and findings that result from these investigations. We deal with the changes in terms of shifts in thought styles and discuss seven different turns: the pragmatic turn, the socio-cultural turn, the dispersive turn, the empirical turn, the digital turn, the discursive turn and the diachronic turn. We also deal with some long-standing, recent or emerging interfaces where historical pragmatics interacts with other disciplines and we discuss some future challenges, such as the multimodality and fluidity of communication and the problem of combining big data with pragmatic micro analyses.
Grammaticalization or pragmaticalization of discourse markers?
Authors: Degand Liesbeth , Evers-Vermeul Jacqueline
Published: April 2015

Discourse markers are a crucial component of natural language, which is why a description and account of their diachronic evolution must be part of our linguistic models. However, researchers have different views on whether this evolution should be accounted for in terms of grammaticalization and/or pragmaticalization. In this paper, we provide a structured overview of the accounts given for the diachronic evolution of DMs. It is shown that the different positions encountered in the literature can be brought back to diverging views on the conceptualization of grammar, the categorization of discourse markers, and the weight that is put on specific processes involved in the diachronic change. We provide case studies for each of the positions that we present and discuss.
Spelling out the obvious
Authors: Danckaert Lieven
Published: April 2015

In Danckaert (2014), the Latin particlequidemwas analysed as a marker of emphatic affirmative polarity. Building on this proposal, this paper elaborates on the pragmatic properties of this element. I argue thatquidemis not a neutral but a so-called “presuppositional” polarity marker, which confirms a proposition which (i) is already part of the common ground but (ii) was not overtly spelled out in the (immediately) preceding context. In more formal terms, I propose thatquidemgives rise to the conventional implicature that the speaker assumes that the content of his message might already be known to the addressee, or that it conveys information that the latter expects to hear or read.Quidemcan be regarded as a “lexical marker of common ground”, in the sense of Fetzer and Fischer (2007).
The discovery, nature, and implications of a Papiamentu text fragment from 1783
Authors: Jacobs Bart , van der Wal Marijke J.
Published: April 2015

In this paper, we discuss the recent discovery of four letters written in 1783, one of which is written fully in Papiamentu, the other three comprising Papiamentu fragments. The data in these constitute one of the earliest written attestations of Papiamentu. We first provide a brief overview of the earliest attestations of Papiamentu and then present theLetters as Lootresearch programme, to which we owe the discovery of the 1783 letters. Following this, the article discusses the contents of the letters and the socio-historical context in which they were written. To close, we discuss the value of this new source for Papiamentu studies.
Criticality for Schrödinger type operators based on recurrent symmetric stable processes
Authors: Takeda Masayoshi
Published: April 2015

Let

μ
\mu

be a signed Radon measure on

R

1

\mathbb {R}^1

in the Kato class and consider a Schrödinger type operator

H

μ

=
(
−

d
2

/

d

x
2

)

α
2

+
μ

\mathcal {H}^{\mu }=(-d^2/dx^2)^{\frac {\alpha }{2}} + \mu

on

R

1

\mathbb {R}^1

. Let

1
≤
α
>
2

1\leq \alpha >2

and suppose the support of

μ
\mu

is compact. We then construct a bounded

H

μ

\mathcal {H}^{\mu }

-harmonic function uniformly lower-bounded by a positive constant if

H

μ

\mathcal {H}^{\mu }

is critical. Moreover, we show that there exists no bounded positive

H

μ

\mathcal {H}^{\mu }

-harmonic function if

H

μ

\mathcal {H}^{\mu }

is subcritical.
Endomorphism algebras of factors of certain hypergeometric Jacobians
Authors: Xue Jiangwei , Yu Chia-Fu
Published: April 2015

We classify the endomorphism algebras of factors of the Jacobians of certain hypergeometric curves over a field of characteristic zero. Other than a few exceptional cases, the endomorphism algebras turn out to be either a cyclotomic field

E
=

Q

(

ζ
q

)

E=\mathbb {Q}(\zeta _q)

, or a quadratic extension of

E
E

, or

E
⊕
E

E\oplus E

. This result may be viewed as a generalization of the well known results of the classification of endomorphism algebras of elliptic curves over

C

\mathbb {C}

.
Rationality of the moduli spaces of Eisenstein 𝐾3 surfaces
Authors: Ma Shouhei , Ohashi Hisanori , Taki Shingo
Published: April 2015

K
3

K3

surfaces with non-symplectic symmetry of order

3
3

are classified by open sets of twenty-four complex ball quotients associated to Eisenstein lattices. We show that twenty-two of those moduli spaces are rational.
SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics
Authors: Will Sebastian , Otto Christina , Miladi Milad , Möhl Mathias , Backofen Rolf
Published: April 2015

Motivation: RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of O(n6). Subsequently, numerous faster ‘Sankoff-style’ approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity (≥ quartic time).

Results: Breaking this barrier, we introduce the novel Sankoff-style algorithm ‘sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)’, which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff’s original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics.

Availability and implementation: SPARSE is freely available at http://www.bioinf.uni-freiburg.de/Software/SPARSE.

Contact:  backofen@informatik.uni-freiburg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Pitfalls in stock discrimination by shape analysis of otolith contours
Authors: Harbitz Alf , Albert Ole Thomas
Published: April 2015

This paper focuses on artefacts that may corrupt stock discrimination by shape analysis of otolith contours, how one can examine if such artefacts are important, and how they can be avoided. The scope focuses on Fourier transforms of contour points, the linear Fisher discrimination technique, and success rates based on cross validation by the “leave one out at a time” technique. The “zero-score” technique is introduced as a tool to examine the importance of a possible artefact, based on the theoretical result that the probability of correct classification of any otolith from either of two identical groups is zero. If one of the identical groups is exposed to a possible influential factor, e.g. a different smoothing, a high classification rate will reveal that this factor is an important artefact. The concept of a “lasso contour” is introduced that drastically reduces the impact of smoothing and provides a non-concave shape that enables a one-dimensional representation of the contour without ambiguities. Results are illustrated by comparison between Greenland halibut (Reinhardtius hippoglossoides) otolith contours from southern Greenland and Northeast Arctic waters. The conclusion is that the probability of correct classification of locality based on the original contours is too optimistic (77–79%), while the scores based on lasso contours are insensitive to smoothing and still optimistically high (68–70%).
Natural tracers reveal population structure of albacore (Thunnus alalunga) in the eastern North Pacific
Authors: Wells R. J. David , Kinney Michael J. , Kohin Suzanne , Dewar Heidi , Rooker Jay R. , Snodgrass Owyn E.
Published: April 2015

Chemical signatures in otoliths and muscle tissue of albacore (Thunnus alalunga) from two regions of the North Pacific were characterized to examine population structure. Regions included northern (offshore northwest United States and Canada, >40°N) and southern (offshore southwest United States and Mexico, <40°N) areas where albacore have demonstrated region-specific differences in movement and size at age. Juvenile (ages 1–4 years) albacore were collected from each region through recreational and commercial fisheries over a 5-year period (2009–2013). Three different otolith chemistry assays were performed, including whole otoliths (proxy for lifetime signature), otolith edge (recent signature), and otolith core (nursery signature). Whole otolith δ13C and δ18O showed similar δ13C and enriched δ18O (∼0.5‰) values for juvenile albacore collected in the southern region; classification success to the two regions ranged from 78 to 91% during each year (similar age classes). Otolith edge δ13C and δ18O showed similar results as whole otoliths, but no regional differences were found for otolith core chemistry. Incorporation of trace element concentrations from whole otoliths improved discrimination between regions to 90–100% classification success during each year of the study, with significantly higher Ba:Ca, Mg:Ca, and Mn:Ca in albacore otoliths from the northern region. Albacore from the southern region also displayed enriched muscle δ13C (∼1.21‰) and δ15N (∼0.85‰) values relative to fish of the same size range from the northern region. Discrimination success between the two regions across all years using muscle δ13C and δ15N was 91%. Ultimately, results from this study suggest regional separation of albacore in the eastern North Pacific warranting region-specific vital rates in future modelling efforts.
Worldwide distribution of the NS3 gene 80K polymorphism among circulating hepatitis C genotype 1 viruses: implication for simeprevir usage
Authors: Vidal Luãnna L. , Santos André F. , Soares Marcelo A.
Published: April 2015

Objectives

Several direct-acting agents against the hepatitis C virus (HCV) NS3 protease and NS5b polymerase have been developed in recent years to improve treatment of this viral infection. Of these, simeprevir is currently recommended for HCV genotype 1 and 4 infections, but genotypic assessment for the presence of 80K is required prior to simeprevir administration due to the reduced susceptibility of genotype 1 viruses carrying that polymorphism. Because the prevalence of 80K at baseline in genotype 1 viruses varies between reports, we wanted to assess its worldwide prevalence.

Methods

Over 3000 HCV genotype 1 sequences reported from drug-naive subjects distributed around the world were retrieved from the HCV Los Alamos and GenBank databases. These were categorized into subtypes and geographical provenance (continent and country), and the presence of the 80K and 80R polymorphisms was visually inspected and counted.

Results

Disparate prevalence of 80K was observed depending on the country/continent analysed. While in resource-rich areas (USA, Western Europe and Australia) a high prevalence of 80K was seen in HCV subtype 1a, in emerging countries, such as Brazil, this prevalence was very low (<1%). HCV subtype 1b sequences from France also displayed a significant occurrence of 80K (6.1%). 80R, on the other hand, was negligible worldwide.

Conclusions

The genotypic assessment of 80K in HCV subtype 1a prior to simeprevir administration in emerging countries with significant numbers of HCV infection is questionable, while it should be performed for subtype 1b in certain developed countries.
Measuring the equation of state of the high-z intergalactic medium using curvature statistics
Authors: Padmanabhan Hamsa , Srianand R. , Choudhury T. Roy
Published: April 2015

Using hydrodynamical simulations, we explore the use of the mean and percentiles of the curvature distribution function to recover the equation of state of the high-z (2 < z < 4) intergalactic medium (IGM). We find that the mean and percentiles of the absolute curvature distribution exhibit tight correlation with the temperatures measured at respective characteristic overdensities $\bar{\Delta }_i$s at each redshift. Hence, they provide complementary probes of the same underlying temperature–density distribution, and can in principle be used to simultaneously recover both parameters T0 and γ of the IGM effective equation of state. We quantify the associated errors in the recovered parameters T0 and γ from the intrinsic scatter in the characteristic overdensities and the uncertainties in the curvature measurement.
Clinical Predictors Associated With Warfarin Sensitivity
Authors: Saleh Mohammad I.
Published: April 2015

Our study aimed to identify predictors of warfarin sensitivity like demographic, clinical, and genetic data from a previously collected cohort of patients (n = 4272) with a stable warfarin dose who were able to achieve an observed international normalized ratio of 2–3. Predictors of warfarin sensitivity (dose ≤21 mg/wk) were identified using a 2-stage approach. First, bivariate analysis, using analysis of variance for continuous variables and χ2 test for categorical variables, was performed to identify possible predictors of warfarin sensitivity (P < 0.05). Second, logistic regression with backward stepwise selection was then performed using predictors identified in bivariate analysis step to produce final model containing independent predictors at P < 0.05. Increased warfarin sensitivity was associated with increased age; CYP2C9 genotypes 2/3, 1/3, and 3/3; VKORC1 genotypes AA and AG; and amiodarone use. Decreased warfarin sensitivity (ie, weekly warfarin dose of >21 mg) was associated with increased height, increased weight, having diabetes mellitus, VKORC1 genotype GG, and CYP2C9 genotype 1/1. In conclusion, we identified patients' characteristics associated with warfarin sensitivity. This project is expected to improve patient care by identifying patients who need a low warfarin dose before warfarin administration. Early identification of this subset of patients helps minimize the incidence of bleeding.
Endoscopic Incision for the Treatment of Refractory Esophageal Anastomotic Strictures in Children
Authors: Tan Yuyong , Zhang Jie , Zhou Junfeng , Duan Tianying , Liu Deliang
Published: April 2015

Objectives:

The aim of the present study was to assess the safety and efficacy of endoscopic incision (EI) for the treatment of refractory anastomotic esophageal strictures in pediatric patients.

Methods:

We retrospectively reviewed the medical records of pediatric patients with refractory anastomotic strictures after surgical repair of esophageal atresia who underwent ≥3 sessions of endoscopic treatments (dilation and/or stenting). They were treated with EI alone or together with esophageal stenting. Efficacy and safety were evaluated during periodical follow‐up.

Results:

All of the 7 children received the procedure successfully with the operation time of 15 to 60 minutes. Four of them received EI alone, whereas the other 3 received EI with esophageal stenting (EIES). The symptoms remitted in all of the patients, and the dysphagia score decreased from 3–4 to 0–1 during follow‐up from 1 to 21 months. The average diameter of stricture was enlarged from 3 mm (range 2–5 mm) to 10.6 mm (range 8–12 mm). One patient suffered from chest pain, which resolved within 3 days. Patient 1 had recurrence 11 months after EIES, and patient 6 had recurrence 3 months after EI. They all underwent an additional EI to maintain patency. No severe complications were observed during operation and periodical follow‐up.

Conclusions:

EI is safe and appears effective for refractory esophageal anastomotic strictures in children in the short term. Large comparative studies are warranted to further confirm our findings. The long‐term follow‐up is necessary for assessing the long‐term efficacy of the new technique.
Water Load Test in Childhood Functional Abdominal Pain
Authors: Ozaki Roberto Koity Fujihara , Soares Ana Cristina Fontenele , da Graça Leite Speridião Patricia , Batista de Morais Mauro
Published: April 2015

This cross‐sectional study evaluates the relations between the water load test in childhood functional gastrointestinal disorders with food intake and nutritional status. Patients with functional dyspepsia required a lower maximum water intake to produce fullness (n = 11, median = 380 mL) than patients with irritable bowel syndrome (n = 10, median = 695 mL) or functional abdominal pain (n = 10, median = 670 mL) (P < 0.05). Among patients who ingested ≤560 mL (n = 17) or >560 mL (n = 14) in the water load test, there was no relation between the maximum drinking capacity and food intake, body mass index, or height.
Laboratory Errors in a Pediatric Emergency Department Network
Authors: Lichenstein Richard , O’Connell Karen , Funai Tomohiko , Blumberg Stephen , Shaw Kathy , Ruddy Richard , Mahajan Prashant V. , Chamberlain James M.
Published: April 2015

Objectives

To describe the types and severity of reported laboratory errors in pediatric emergency departments.

Methods

Retrospective review of incident reports classified as laboratory errors from July 2007 to June 2008 within the Pediatric Emergency Care Applied Research Network. Laboratory testing errors recorded included: delayed results or lost specimen, unlabeled specimens, wrong patient, failure to label specimen correctly, and other. The severity of laboratory-related incidents was characterized using the National Coordinating Council for Medication Error Reporting and Prevention severity classification system. Contributing factors were classified as environmental, equipment, human (employee), information technology systems, parent or guardian, or systems-based.

Results

A total of 335 (42.2%) laboratory reports were related to events in the preanalytic phase. Involved staff personnel were identified in 345 of the reports (43.5%). Nurses were identified in 179 (22.6%) and physicians in 38 (4.8%). The majority of laboratory errors [408 (51.5%)] were not associated with harm; 138 (17.4%) patients were harmed by the error; 136 (98.6%) patients were temporarily harmed and required treatment, and 1 (0.7%) patient was hospitalized or had their hospitalization prolonged with the event. Human factors 657 (82.8%) were the most common contributing factor.

Conclusions

Laboratory errors are a common cause of safety events in the pediatric ED. Most events are preanalytic and involve problems with specimens that are improperly collected, mislabeled, or lost. Although most events were not associated with harm, there is potential for significant injury.
Do Written Disclosures of Serious Events Increase Risk of Malpractice Claims? One Health Care System's Experience
Authors: Painter Lisa M. , Kidwell Kelley M. , Kidwell Richard P. , Janov Cheryl , Voinchet Robert G. , Simmons Richard L. , Wu Albert W.
Published: April 2015

Objective

This study aimed to determine whether Pennsylvania ACT 13 of 2002 (Mcare) requiring the written and verbal disclosure of “serious events” was accompanied by increased malpractice claims or compensation costs in a large U.S. health system.

Main Outcomes and Measures

The primary outcome was the rate of malpractice claims. The secondary outcome was the amount paid for compensation of malpractice claims. The analyses tested the relationship between the rate of serious event disclosures and the outcome variables, adjusted for the year of the event, category of claim, and the degree of “harm” related to the event.

Results

There were 15,028 serious event disclosures and 1302 total malpractice claims among 1,587,842 patients admitted to UPMC hospitals from May 17, 2002, to June 30, 2011. As the number of serious event disclosures increased, the number of malpractice claims per 1000 admissions remained between 0.62 and 1.03. Based on a matched analysis of claims that were disclosed and those that were not (195 pairs), disclosure status was significantly associated with increased claim payout (disclosures had 2.71 times the payout; 95% confidence interval, 1.56–4.72). Claims with higher harm levels H and I were independently associated with higher payouts than claims with lower harm levels A to D (11.15 times the payout; 95% confidence interval, 2.30–54.07).

Conclusions and Relevance

Implementation of a mandated serious event disclosure law in Pennsylvania was not associated with an overall increase in malpractice claims filed. Among events of similar degree of harm, disclosed events had higher compensation paid compared with those that had not been disclosed.
Improved Compliance and Comprehension of a Surgical Safety Checklist With Customized Versus Standard Training: A Randomized Trial
Authors: Rakoff David , Akella Krishna , Guruvegowda Chandrashekar , Chhajwani Sunil , Seshadri SriKrishna , Sola Srikanth
Published: April 2015

Objective

This study aimed to determine the effect of customized training versus standard readily available training on surgical safety checklist (SSCL) compliance and comprehension.

Background

The success of the SSCL in reducing surgical mortality and morbidity depends largely on the degree of compliance among health care workers with the checklist's components. We hypothesized that a customized training program would improve comprehension of the SSCL components among health care workers.

Methods

We prospectively evaluated compliance and comprehension of a locally modified SSCL among surgeons, anesthesiologists, nurses, and perfusionists who were randomized to standard versus customized training in the department of cardiac and thoracic surgery. Standard training included videos, posters, and didactic sessions obtained from the World Health Organization. Customized training consisted of a department-specific orientation video (using local staff as actors), locally made posters, and didactic sessions. Comprehension was assessed by a written exam after each training program. Verbal and written compliance with the SSCL was measured within the operating theater by trained observers.

Results

We observed a total of 244 surgeries for SSCL compliance. Comprehension of the didactic material provided in the training programs was higher in the customized versus the standard training group (75% versus 30%; P < 0.0001). Verbal compliance was higher in the customized versus standard training groups (87% versus 49%; P < 0.0001). Written compliance was 100% for both the customized and standard training groups.

Conclusions

A customized training program improves verbal compliance and comprehension among health care workers when implementing an SSCL, compared with standard readily available training.
Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus
Authors: Dunlap Christopher A. , Kim Soo-Jin , Kwon Soon-Wo , Rooney Alejandro P.
Published: April 2015

The rhizosphere-isolated bacteria belonging to the Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These properties have made these strains the focus of commercial interest. Here, we present the draft genome sequence of B. methylotrophicus KACC 13105T ( = CBMB205T). Comparative genomic analysis showed only minor differences between this strain and the genome of the B. amyloliquefaciens subsp. plantarum type strain, with the genomes sharing approximately 95 % of the same genes. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar. In fact, our results show that the type strain of B. amyloliquefaciens subsp. plantarum FZB42T ( = DSM 23117T = BGSC 10A6T) does not cluster with other members of the B. amyloliquefaciens taxon. Instead, it clusters well within a clade of strains that are assigned to B. methylotrophicus, including the type strain of that species. Therefore, we propose that the subspecies B. amyloliquefaciens subsp. plantarum should be reclassified as a later heterotypic synonym of B. methylotrophicus.