bluuebunny/crossref_metadata_2025 huggingface dataset:
Semiflexible macromolecules in quasi-one-dimensional confinement: Discrete versus continuous bond angles
Authors: Huang Aiqun , Hsu Hsiao-Ping , Bhattacharya Aniket , Binder Kurt
Published: August 2015

The conformations of semiflexible polymers in two dimensions confined in a strip of width D are studied by computer simulations, investigating two different models for the mechanism by which chain stiffness is realized. One model (studied by molecular dynamics) is a bead-spring model in the continuum, where stiffness is controlled by a bond angle potential allowing for arbitrary bond angles. The other model (studied by Monte Carlo) is a self-avoiding walk chain on the square lattice, where only discrete bond angles (0° and ±90°) are possible, and the bond angle potential then controls the density of kinks along the chain contour. The first model is a crude description of DNA-like biopolymers, while the second model (roughly) describes synthetic polymers like alkane chains. It is first demonstrated that in the bulk the crossover from rods to self-avoiding walks for both models is very similar, when one studies average chain linear dimensions, transverse fluctuations, etc., despite their differences in local conformations. However, in quasi-one-dimensional confinement two significant differences between both models occur: (i) The persistence length (extracted from the average cosine of the bond angle) gets renormalized for the lattice model when D gets less than the bulk persistence length, while in the continuum model it stays unchanged. (ii) The monomer density near the repulsive walls for semiflexible polymers is compatible with a power law predicted for the Kratky-Porod model in the case of the bead-spring model, while for the lattice case it tends to a nonzero constant across the strip. However, for the density of chain ends, such a constant behavior seems to occur for both models, unlike the power law observed for flexible polymers. In the regime where the bulk persistence length ℓp is comparable to D, hairpin conformations are detected, and the chain linear dimensions are discussed in terms of a crossover from the Daoud/De Gennes “string of blobs”-picture to the flexible rod picture when D decreases and/or the chain stiffness increases. Introducing a suitable further coarse-graining of the chain contours of the continuum model, direct estimates for the deflection length and its distribution could be obtained.
Room-temperature ferroelectricity of SrTiO3 films modulated by cation concentration
Authors: Yang Fang , Zhang Qinghua , Yang Zhenzhong , Gu Junxing , Liang Yan , Li Wentao , Wang Weihua , Jin Kuijuan , Gu Lin , Guo Jiandong
Published: August 2015

The room-temperature ferroelectricity of SrTiO3 is promising for oxide electronic devices controlled by multiple fields. An effective way to control the ferroelectricity is highly demanded. Here, we show that the off-centered antisite-like defects in SrTiO3 films epitaxially grown on Si (001) play the determinative role in the emergence of room-temperature ferroelectricity. The density of these defects changes with the film cation concentration sensitively, resulting in a varied coercive field of the ferroelectric behavior. Consequently, the room-temperature ferroelectricity of SrTiO3 films can be effectively modulated by tuning the temperature of metal sources during the molecular beam epitaxy growth. Such an easy and reliable modulation of the ferroelectricity enables the flexible engineering of multifunctional oxide electronic devices.
Effects of additional multiwall carbon nanotubes on impact behaviors of LiNi0.5Mn0.3Co0.2O2 battery electrodes
Authors: Le Anh V. , Wang Meng , Shi Yang , Noelle Daniel , Qiao Yu , Lu Weiyi
Published: August 2015

This work introduces a new mechanically triggered thermal runaway mitigation mechanism. The homogenizer of electrode failure (HEF), multiwall carbon nanotube (MWCNT), was added into LiNi0.5Mn0.3Co0.2O2 (NMC532) battery electrodes. We have studied the effect of the HEF additive on the internal electrical resistance and the mechanical impact resistance of the electrodes. The additional MWCNTs reduced the internal electrical resistance of electrodes before mechanical abuse. Upon mechanical abuse, they could mitigate internal shorting and thermal runaway at normal battery working temperature.
Tunnel anisotropic magnetoresistance in CoFeB|MgO|Ta junctions
Authors: Hatanaka S. , Miwa S. , Matsuda K. , Nawaoka K. , Tanaka K. , Morishita H. , Goto M. , Mizuochi N. , Shinjo T. , Suzuki Y.
Published: August 2015

We found that CoFeB|MgO|Ta tunnel junctions exhibit tunnel anisotropic magnetoresistance (TAMR) at room temperature. The tunnel junctions exhibit positive magnetoresistance with the application of a magnetic field normal to the film plane. The dependencies on the applied magnetic field angle and MgO thickness reveal that the magnetoresistance originates from the TAMR, caused by the spin polarization and the spin-orbit interaction at the CoFeB|MgO interface. We also found that the TAMR can be used to detect ferromagnetic resonance in the CoFeB. This detection method could be useful for the characterization of nanomagnets that are free from the spin-transfer effect and the stray field of a reference layer, unlike conventional magnetic tunnel junctions.
Barkhausen-like antiferromagnetic to ferromagnetic phase transition driven by spin polarized current
Authors: Suzuki Ippei , Naito Tomoyuki , Itoh Mitsuru , Taniyama Tomoyasu
Published: August 2015

We provide clear evidence for the effect of a spin polarized current on the antiferromagnetic to ferromagnetic phase transition of an FeRh wire at Co/FeRh wire junctions, where the antiferromagnetic ground state of FeRh is suppressed by injecting a spin polarized current. We find a discrete change in the current-voltage characteristics with increasing current density, which we attribute to the Barkhausen-like motion of antiferromagnetic/ferromagnetic interfaces within the FeRh wire. The effect can be understood via spin transfer, which exerts a torque to the antiferromagnetic moments of FeRh, together with non-equilibrium magnetic effective field at the interface. The conclusion is reinforced by the fact that spin unpolarized current injection from a nonmagnetic Cu electrode has no effects on the antiferromagnetic state of FeRh.
A high-Tc intrinsic Josephson junction emitter tunable from 0.5 to 2.4 terahertz
Authors: Kashiwagi Takanari , Sakamoto Kazuki , Kubo Hiroyuki , Shibano Yuuki , Enomoto Takuma , Kitamura Takeo , Asanuma Kentaro , Yasui Takaki , Watanabe Chiharu , Nakade Kurama , Saiwai Yoshihiko , Katsuragawa Takuya , Tsujimoto Manabu , Yoshizaki Ryozo , Yamamoto Takashi , Minami Hidetoshi , Klemm Richard A. , Kadowaki Kazuo
Published: August 2015

Strong, monochromatic, coherent and continuous terahertz (THz) radiation was generated from the intrinsic Josephson junctions in a cylindrical stand-alone mesa sandwich structure fabricated from a single crystal of the high-temperature superconductor Bi2Sr2CaCu2O8+δ. By varying the base temperature and the dc bias current-voltage characteristic (IVC) points, the emission frequency is tunable from 0.5 to a record high 2.4 THz observed on two inner IVC branch points. Strong emission power peaks were observed at 1.0 THz and 1.6 THz. This device is hence an excellent candidate to fill the “THz gap” between ∼1.4 and 2.0 THz.
Density functional studies on edge-contacted single-layer MoS2 piezotronic transistors
Authors: Liu Wei , Zhang Aihua , Zhang Yan , Wang Zhong Lin
Published: August 2015

The piezotronic effect uses strain-induced piezoelectric charges at interfaces and junctions to tune and/or control carrier transport in piezoelectric semiconductor devices. This effect has recently been observed in single-layer 2D MoS2 materials. However, previous work had found that metallic states are generated at the edge of a free-standing MoS2 flat sheet, and these states may screen the piezoelectric charges. Using density functional theory simulations, we found that the metal–MoS2 interface structure plays an important role in enhancing both the piezoelectric and piezotronic effects in MoS2 transistors by breaking the metallic state screening effect at the MoS2 edge. This study not only provides an understanding of the piezoelectric and piezotronic effects based on first principles calculations but also offers guidance for the design of two-dimensional piezotronic devices.
Thermal stability of ferroelectric domain gratings in Rb-doped KTP
Authors: Lindgren Gustav , Peña Alexandra , Zukauskas Andrius , Liljestrand Charlotte , Ménaert Bertrand , Boulanger Benoît , Canalias Carlota
Published: August 2015

We study the thermal stability of domain walls in periodically poled Rb-doped KTP crystals. Domain-wall motion is observed after annealing the crystals above 550 °C. This motion is highly anisotropic along the a- and b- crystallographic axes. Along the b-axis domain wall motion is in the order of tens of micrometers. In the a-direction, it results in either three orders of magnitude smaller domain wall displacement or in domain merging, depending on the initial domain configuration. We show that the thermal stability of the domain gratings depends on their periodicity, resulting in complete backswitching for sub-micrometer domains annealed at 730 °C.
Directional bilateral filters for smoothing fluorescence microscopy images
Authors: Venkatesh Manasij , Mohan Kavya , Seelamantula Chandra Sekhar
Published: August 2015

Images obtained through fluorescence microscopy at low numerical aperture (NA) are noisy and have poor resolution. Images of specimens such as F-actin filaments obtained using confocal or widefield fluorescence microscopes contain directional information and it is important that an image smoothing or filtering technique preserve the directionality. F-actin filaments are widely studied in pathology because the abnormalities in actin dynamics play a key role in diagnosis of cancer, cardiac diseases, vascular diseases, myofibrillar myopathies, neurological disorders, etc. We develop the directional bilateral filter as a means of filtering out the noise in the image without significantly altering the directionality of the F-actin filaments. The bilateral filter is anisotropic to start with, but we add an additional degree of anisotropy by employing an oriented domain kernel for smoothing. The orientation is locally adapted using a structure tensor and the parameters of the bilateral filter are optimized for within the framework of statistical risk minimization. We show that the directional bilateral filter has better denoising performance than the traditional Gaussian bilateral filter and other denoising techniques such as SURE-LET, non-local means, and guided image filtering at various noise levels in terms of peak signal-to-noise ratio (PSNR). We also show quantitative improvements in low NA images of F-actin filaments.
C5orf30 is a negative regulator of tissue damage in rheumatoid arthritis
Authors: Muthana Munitta , Hawtree Sarah , Wilshaw Adam , Linehan Eimear , Roberts Hannah , Khetan Sachin , Adeleke Gbadebo , Wright Fiona , Akil Mohammed , Fearon Ursula , Veale Douglas , Ciani Barbara , Wilson Anthony G.
Published: August 2015

Significance

Recent studies have reported genetic association of chromosome 5 open reading frame 30 (C5orf30) with both rheumatoid arthritis (RA) susceptibility and the severity of radiological damage to joints. The gene is expressed in vertebrate genomes with a high degree of conservation, implying a central function in these organisms. Here, we report that C5orf30 encodes a 206-aa protein that is highly expressed in RA synovial fibroblasts (RASFs), a cell type implicated in causing joint damage. Importantly inhibition of C5orf30 increases the autoaggressive phenotype of RASFs in vitro and increases joint inflammation and damage in murine inflammatory arthritis. Our data reveals C5orf30 to be a negative regulator of tissue breakdown modulating the autoaggressive phenotype that is characteristic of RASFs.
ProtAnt
Authors: Anthony Laurence , Baker Paul
Published: August 2015

Corpus-based researchers and traditional qualitative researchers, such as those interested in critical discourse analysis, are often required to select prototypical texts for close reading that include the language features of interest that are present in a much larger corpus. Traditional approaches to this selection procedure have been largely ad hoc. In this paper, we offer a more principled way of selecting texts for close reading based on a ranking of texts in terms of the number of keywords they contain. To facilitate this analysis, we have developed a multiplatform, freeware software tool called ProtAnt that analyses the texts, generates a ranked list of keywords based on statistical significance and effect size, and then orders the texts by the number of keywords in them. We describe various experiments that demonstrate the ProtAnt analysis is effective not only at identifying prototypical texts, but also identifying outlier texts that may need to be removed from a target corpus.
Acquisition of the imparfait in L2 French in adults and children: The same or different?
Authors: Kihlstedt Maria
Published: August 2015

In this study, we provide a comparison of adult and child L2 acquisition in relation to their use of the imparfait form in L2 French. Previous research on this form shows that it is an area of considerable difficulty, being lexically and functionally restricted in use even in advanced stages of acquisition. In the study presented here, we compare our child and adult learners in an immersion setting, where the adult learners were studying at a French university, while the children were attending a French immersion school. Their use of the imparfait is explored through a longitudinal lens, where we look in particular at its use to mark different aspectual values, as well as its lexical use with different verbs. The findings indicate that, while both groups benefit from the immersion context, the children’s development seems to be more rapid and more stable: once they start using the imparfait productively, they use it for a greater range of its aspectual values and in a more autonomous way than the adults. The results are discussed with regard to age of onset and the development of L1 and L2 discourse capacities.
Feeding and Growth of Larval Pacific Lamprey Reared in Captivity
Authors: Jolley Jeffrey C , Uh Christina T , Silver Gregory S , Whitesel Timothy A
Published: August 2015

Pacific Lampreys Entosphenus tridentatus are declining in the Columbia River basin as well as in much of their broader range. To mitigate for reductions in abundance, strategies such as hatchery propagation and captive rearing of lamprey larvae are currently being considered. We conducted a series of experiments using captive larval Pacific Lampreys at Eagle Creek National Fish Hatchery to investigate the effect of different food types and different food concentrations on the growth of larvae. In our first experiment, we evaluated the growth of larvae (TL range, 59–145 mm) given four different food types (algae, leaves, yeast–larval fish food, and salmon carcass analogs) and a control group that was not fed. Assimilation of food types was evaluated by tracking unique stable isotope signatures of δ13C and δ15N within larval tissues. Results from experiment 1 indicated that lampreys fed a diet of salmon carcass analog or algae had positive growth (up to 0.16 mm/d and 42% proportional change in length) over approximately 6 months. Isotopic analyses of larval tissues showed unique signatures that matched those of their specific food treatment. Based on the results of experiment 1, we conducted a second experiment to evaluate the growth of larvae fed four different quantities of salmon carcass analog. Results from this experiment indicated larval growth rate increased with increasing rations of food, but positive growth was observed in all feeding treatments. The highest dose of salmon carcass analog resulted in the highest growth (up to 0.15 mm/d and 36% proportional change in length) over 6 months. We successfully reared larval Pacific Lampreys in captivity with minimal mortality and positive growth, which highlights the potential to use captive rearing and propagation as a conservation tool for this ecologically and culturally important species.
A small-world network model of facial emotion recognition
Authors: Takehara Takuma , Ochiai Fumio , Suzuki Naoto
Published: August 2015

Various models have been proposed to increase understanding of the cognitive basis of facial emotions. Despite those efforts, interactions between facial emotions have received minimal attention. If collective behaviours relating to each facial emotion in the comprehensive cognitive system could be assumed, specific facial emotion relationship patterns might emerge. In this study, we demonstrate that the frameworks of complex networks can effectively capture those patterns. We generate 81 facial emotion images (6 prototypes and 75 morphs) and then ask participants to rate degrees of similarity in 3240 facial emotion pairs in a paired comparison task. A facial emotion network constructed on the basis of similarity clearly forms a small-world network, which features an extremely short average network distance and close connectivity. Further, even if two facial emotions have opposing valences, they are connected within only two steps. In addition, we show that intermediary morphs are crucial for maintaining full network integration, whereas prototypes are not at all important. These results suggest the existence of collective behaviours in the cognitive systems of facial emotions and also describe why people can efficiently recognize facial emotions in terms of information transmission and propagation. For comparison, we construct three simulated networks—one based on the categorical model, one based on the dimensional model, and one random network. The results reveal that small-world connectivity in facial emotion networks is apparently different from those networks, suggesting that a small-world network is the most suitable model for capturing the cognitive basis of facial emotions.
GalPaK3D: A BAYESIAN PARAMETRIC TOOL FOR EXTRACTING MORPHOKINEMATICS OF GALAXIES FROM 3D DATA
Authors: Bouché N. , Carfantan H. , Schroetter I. , Michel-Dansac L. , Contini T.
Published: August 2015

We present a method to constrain galaxy parameters directly from three-dimensional data cubes. The algorithm compares directly the data with a parametric model mapped in

coordinates. It uses the spectral line-spread function and the spatial point-spread function (PSF) to generate a three-dimensional kernel whose characteristics are instrument specific or user generated. The algorithm returns the intrinsic modeled properties along with both an “intrinsic” model data cube and the modeled galaxy convolved with the 3D kernel. The algorithm uses a Markov Chain Monte Carlo approach with a nontraditional proposal distribution in order to efficiently probe the parameter space. We demonstrate the robustness of the algorithm using 1728 mock galaxies and galaxies generated from hydrodynamical simulations in various seeing conditions from 0.″6 to 1.″2. We find that the algorithm can recover the morphological parameters (inclination, position angle) to within 10% and the kinematic parameters (maximum rotation velocity) to within 20%, irrespectively of the PSF in seeing (up to 1.″2) provided that the maximum signal-to-noise ratio (S/N) is greater than ∼3 pixel−1 and that the ratio of galaxy half-light radius to seeing radius is greater than about 1.5. One can use such an algorithm to constrain simultaneously the kinematics and morphological parameters of (nonmerging) galaxies observed in nonoptimal seeing conditions. The algorithm can also be used on adaptive optics data or on high-quality, high-S/N data to look for nonaxisymmetric structures in the residuals.
Fast and accurate approximate inference of transcript expression from RNA-seq data
Authors: Hensman James , Papastamoulis Panagiotis , Glaus Peter , Honkela Antti , Rattray Magnus
Published: August 2015

Motivation: Assigning RNA-seq reads to their transcript of origin is a fundamental task in transcript expression estimation. Where ambiguities in assignments exist due to transcripts sharing sequence, e.g. alternative isoforms or alleles, the problem can be solved through probabilistic inference. Bayesian methods have been shown to provide accurate transcript abundance estimates compared with competing methods. However, exact Bayesian inference is intractable and approximate methods such as Markov chain Monte Carlo and Variational Bayes (VB) are typically used. While providing a high degree of accuracy and modelling flexibility, standard implementations can be prohibitively slow for large datasets and complex transcriptome annotations.

Results: We propose a novel approximate inference scheme based on VB and apply it to an existing model of transcript expression inference from RNA-seq data. Recent advances in VB algorithmics are used to improve the convergence of the algorithm beyond the standard Variational Bayes Expectation Maximization algorithm. We apply our algorithm to simulated and biological datasets, demonstrating a significant increase in speed with only very small loss in accuracy of expression level estimation. We carry out a comparative study against seven popular alternative methods and demonstrate that our new algorithm provides excellent accuracy and inter-replicate consistency while remaining competitive in computation time.

Availability and implementation: The methods were implemented in R and C++, and are available as part of the BitSeq project at github.com/BitSeq. The method is also available through the BitSeq Bioconductor package. The source code to reproduce all simulation results can be accessed via github.com/BitSeq/BitSeqVB_benchmarking.

Contact:  james.hensman@sheffield.ac.uk or panagiotis.papastamoulis@manchester.ac.uk or Magnus.Rattray@manchester.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
LIBRA: LIgand Binding site Recognition Application
Authors: Viet Hung Le , Caprari Silvia , Bizai Massimiliano , Toti Daniele , Polticelli Fabio
Published: August 2015

Motivation: In recent years, structural genomics and ab initio molecular modeling activities are leading to the availability of a large number of structural models of proteins whose biochemical function is not known. The aim of this study was the development of a novel software tool that, given a protein’s structural model, predicts the presence and identity of active sites and/or ligand binding sites.

Results: The algorithm implemented by ligand binding site recognition application (LIBRA) is based on a graph theory approach to find the largest subset of similar residues between an input protein and a collection of known functional sites. The algorithm makes use of two predefined databases for active sites and ligand binding sites, respectively, derived from the Catalytic Site Atlas and the Protein Data Bank. Tests indicate that LIBRA is able to identify the correct binding/active site in 90% of the cases analyzed, 90% of which feature the identified site as ranking first. As far as ligand binding site recognition is concerned, LIBRA outperforms other structure-based ligand binding sites detection tools with which it has been compared.

Availability and implementation: The application, developed in Java SE 7 with a Swing GUI embedding a JMol applet, can be run on any OS equipped with a suitable Java Virtual Machine (JVM), and is available at the following URL: http://www.computationalbiology.it/software/LIBRAv1.zip.

Contact:  polticel@uniroma3.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
InteractiveROSETTA: a graphical user interface for the PyRosetta protein modeling suite
Authors: Schenkelberg Christian D. , Bystroff Christopher
Published: August 2015

Summary: Modern biotechnical research is becoming increasingly reliant on computational structural modeling programs to develop novel solutions to scientific questions. Rosetta is one such protein modeling suite that has already demonstrated wide applicability to a number of diverse research projects. Unfortunately, Rosetta is largely a command-line-driven software package which restricts its use among non-computational researchers. Some graphical interfaces for Rosetta exist, but typically are not as sophisticated as commercial software. Here, we present InteractiveROSETTA, a graphical interface for the PyRosetta framework that presents easy-to-use controls for several of the most widely used Rosetta protocols alongside a sophisticated selection system utilizing PyMOL as a visualizer. InteractiveROSETTA is also capable of interacting with remote Rosetta servers, facilitating sophisticated protocols that are not accessible in PyRosetta or which require greater computational resources.

Availability and implementation: InteractiveROSETTA is freely available at https://github.com/schenc3/InteractiveROSETTA/releases and relies upon a separate download of PyRosetta which is available at http://www.pyrosetta.org after obtaining a license (free for academic use).

Contact:  bystrc@rpi.edu
database.bio: a web application for interpreting human variations
Authors: Ou Min , Ma Ricky , Cheung Jeanno , Lo Katie , Yee Patrick , Luo Tewei , Chan T.L. , Au Chun Hang , Kwong Ava , Luo Ruibang , Lam Tak-Wah
Published: August 2015

Summary: Rapid advances of next-generation sequencing technology have led to the integration of genetic information with clinical care. Genetic basis of diseases and response to drugs provide new ways of disease diagnosis and safer drug usage. This integration reveals the urgent need for effective and accurate tools to analyze genetic variants. Due to the number and diversity of sources for annotation, automating variant analysis is a challenging task. Here, we present database.bio, a web application that combines variant annotation, prioritization and visualization so as to support insight into the individual genetic characteristics. It enhances annotation speed by preprocessing data on a supercomputer, and reduces database space via a unified database representation with compressed fields.

Availability and implementation: Freely available at https://database.bio

Contact:  rb@l3-bioinfo.com or twlam@cs.hku.hk

Supplementary information:  Supplementary data are available at Bioinformatics online.
High-order harmonics in light curves of Kepler planets
Authors: Armstrong Caden , Rein Hanno
Published: August 2015

The Kepler mission was launched in 2009 and has discovered thousands of planet candidates. In a recent paper, Esteves et al. found a periodic signal in the light curves of KOI-13 and HAT-P-7, with a frequency triple the orbital frequency of a transiting planet. We found similar harmonics in many systems with a high occurrence rate. At this time, the origins of the signal are not entirely certain. We look carefully at the possibility of errors being introduced through our data processing routines but conclude that the signal is real. The harmonics on multiples of the orbital frequency are a result of non-sinusoidal periodic signals. We speculate on their origin and generally caution that these harmonics could lead to wrong estimates of planet albedos, beaming mass estimates, and ellipsoidal variations.
Pressure Ulcer-Related Pelvic Osteomyelitis: A Neglected Disease?
Authors: Bodavula Phani , Liang Stephen Y. , Wu Jiami , VanTassell Paige , Marschall Jonas
Published: August 2015

Background.  Decubitus ulcers can become complicated by pelvic osteomyelitis. Little is known about the epidemiology of pressure ulcer-related pelvic osteomyelitis.

Methods.  We performed a retrospective cohort study of adult patients with pressure ulcer and pelvic osteomyelitis admitted to an academic center from 2006 to 2011. Data on clinical presentation, diagnostic evaluation, and treatment during the index admission were collected. Outcome measures included length of hospital stay and number of readmissions in the subsequent year.

Results.  Two hundred twenty patients were included: 163 (74%) were para/quadriplegic and 148 (67%) were male (148; 67%). Mean age was 50 (±18) years. Pelvic osteomyelitis was the primary admission diagnosis for 117 (53%). Fifty-six (26%) patients had concurrent febrile urinary tract infection. Wound cultures collected for 113 patients (51%) were notable for methicillin-resistant Staphylococcus aureus (37; 33%), Streptococci (19; 17%), and Pseudomonas spp (20; 18%). Plain films were obtained in 89 (40%) patients, computed tomography scans were obtained for 81 (37%) patients, and magnetic resonance images were obtained for 40 (18%) patients. Most patients received osteomyelitis-directed antibiotics (153; 70%), 134 of 153 (88%) of which were scheduled to receive ≥6 weeks of treatment. Fifty-five (25%) patients underwent surgery during the index admission; 48 (22%) patients received a combined medical-surgical approach. One third of patients had ≥2 readmissions during the subsequent year. Patients treated with a combined approach were less likely to be readmitted than those who received antibiotics alone (0 [range, 0–4] vs 1 [0–7] readmissions; P = .04).

Conclusions.  This is one of the largest cohort studies of pressure ulcer-related pelvic osteomyelitis to date. Significant variations existed in diagnostic approach. Most patients received antibiotics; those treated with a combined medical-surgical approach had fewer hospital readmissions.
Application of HER2 CISH pharmDX for DNA Ploidy Determination
Authors: He Mai , Pasquariello Terese , Steinhoff Margaret
Published: August 2015

Products of conception (POC) are encountered daily in general pathology practice. The molar workup is an important part of POC examination. Ploidy analysis, expressed as DNA index (DI), is part of the pathologic workup of molar pregnancy. For the past decade, chromogenic in situ hybridization (CISH) has become a popular way to detect HER2 gene amplification. Current study aims to determine whether HER2 CISH dual-color assay can be used to determine DI in POCs. Twenty-two POC cases were chosen from the departmental archives, including 6 complete hydatidiform mole (CM), 10 partial mole (PM), and 6 hydropic POC (HP). CISH assay was performed using the HER2 CISH PharmDx Kit (SK109; Dako). This kit generates red (HER2) and blue (CEN-17) chromogenic signals on the same tissue section. In the 10 triploid PM cases, CISH generated HER2 signal value of 2.925±0.19. Nine cases (90%) had values within this range, except 1 case (2.5). In diploid cases, CISH generated HER2 signal value of 2.063±0.19. Results from 11 (91.7%) cases fell within this range, except 1 HP case (2.35). Sensitivity is 90%, specificity 91.6%, and overall accuracy 90.9%. The current study is the first one that demonstrates HER2/CEN-17 dual-color CISH can be used for microscopic analysis of cell ploidy. This technique provides a relatively easy and straight way to access DI using regular bright-field microscope. Concurrent CEN-17 signal and ploidy in both placental and maternal tissue can be used as internal control. This assay can be performed in any laboratory that can perform immunohistochemistry.
Gramella aquimixticola sp. nov., isolated from water of an estuary environment
Authors: Park Sooyeon , Kim Sona , Jung Yong-Taek , Yoon Jung-Hoon
Published: August 2015

A Gram-stain-negative, aerobic, non-spore-forming bacterial strain, motile by gliding and with rod-shaped or ovoid cells, was isolated from water of an estuary environment at Hwajinpo, South Korea. The strain was designated HJM-19T and subjected to a polyphasic taxonomic study. The novel strain grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain HJM-19T belongs to the genus Gramella. It exhibited 16S rRNA gene sequence similarity values of 97.2–98.1 % to the type strains of Gramella portivictoriae, Gramella aestuariivivens, Gramella marina, Gramella echinicola and Gramella aestuarii, and of 93.9–96.5 % to the type strains of the other species of the genus Gramella with validly published names. Strain HJM-19T contained MK-6 as the predominant menaquinone and anteiso-C15 : 0, anteiso-C17 : 1ω9c and C17 : 0 2-OH as the major fatty acids. The major polar lipids of strain HJM-19T were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain HJM-19T was 48.0 mol%, and its DNA–DNA relatedness values with the type strains of the five phylogenetically closely related species of the genus Gramella were 11–23 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain HJM-19T is separated from other species of the genus Gramella. On the basis of the data presented, strain HJM-19T is considered to represent a novel species of the genus Gramella, for which the name Gramella aquimixticola sp. nov. is proposed. The type strain is HJM-19T ( = KCTC 42706T = NBRC 111224T).
Roseivirga marina sp. nov., isolated from seawater
Authors: Pan Jie , Sun Cong , Wang Rui-Jun , Wu Min
Published: August 2015

Strain PSRT was isolated from seawater of the Pacific Ocean. Cells of the strain were Gram-stain-negative, strictly aerobic, rod-shaped and motile by gliding. Growth was observed at 4–40 °C (optimum 25–30 °C), at pH 6.0–9.5 (optimum pH 7.0–7.5) and with 0.5–8 % (w/v) NaCl (optimum 2–3 %). The major fatty acids were iso-C15 : 1 G (18.9 %), iso-C15 : 0 (26.3 %) and iso-C17 : 0 3-OH (17.9 %). The predominant isoprenoid quinone was MK-7, and the DNA G+C content was 49.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PSRT was most closely related to Roseivirga spongicola UST030701-084T (96.9 % 16S rRNA gene sequence similarity), and they formed a distinct clade in neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees with significant bootstrap supports. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, strain PSRT represents a novel species of the genus Roseivirga, for which the name Roseivirga marina sp. nov. is proposed. The type strain is PSRT ( = MCCC 1K00459T = KCTC 42444T).
Resurrection of the island rule – human-driven extinctions have obscured a basic evolutionary pattern
Authors: Faurby Søren , Svenning Jens-Christian
Published: August 2015

Islands are or have been occupied by unusual species, such as dwarf proboscideans and giant rodents. The discussion of the classical but controversial “island rule,” which states that mammalian body sizes converge on intermediate sizes on islands, has been stimulated by these unusual species. In this paper, we use an unprecedented global data set of the distributions and the body sizes of mammals and a novel analytical method to analyze body size evolution on islands; the analyses produced strong support for the island rule. Islands have suffered massive human-driven losses of species, and we found that the support for the island rule was substantially stronger when the many late-Quaternary extinct species were also considered (particularly, the tendency for dwarfing in large taxa). In this study, the decisive support generated for the island rule confirmed that evolution is markedly different on islands and that human impact may obscure even fundamental evolutionary patterns.
Regulation of gene expression dynamics during developmental transitions by the Ikaros transcription factor
Authors: Arenzana Teresita L. , Schjerven Hilde , Smale Stephen T.
Published: August 2015

The DNA-binding protein Ikaros is a potent tumor suppressor and hematopoietic regulator. However, the mechanisms by which Ikaros functions remain poorly understood, due in part to its atypical DNA-binding properties and partnership with the poorly understood Mi-2/NuRD complex. In this study, we analyzed five sequential stages of thymocyte development in a mouse strain containing a targeted deletion of Ikaros zinc finger 4, which exhibits a select subset of abnormalities observed in Ikaros-null mice. By examining thymopoiesis in vivo and in vitro, diverse abnormalities were observed at each developmental stage. RNA sequencing revealed that each stage is characterized by the misregulation of a limited number of genes, with a strong preference for stage-specific rather than lineage-specific genes. Strikingly, individual genes rarely exhibited Ikaros dependence at all stages. Instead, a consistent feature of the aberrantly expressed genes was a reduced magnitude of expression level change during developmental transitions. These results, combined with analyses of the interplay between Ikaros loss of function and Notch signaling, suggest that Ikaros may not be a conventional activator or repressor of defined sets of genes. Instead, a primary function may be to sharpen the dynamic range of gene expression changes during developmental transitions via atypical molecular mechanisms that remain undefined.
Crystal structure ofrac-(3aR,4S,5aR,6S,9R,10aS,10bR)-3a,5a,9-trimethyltetradecahydro-6,9-epoxycyclohepta[e]inden-4-ol monohydrate
Authors: Schäfer Andreas , Golz Christopher , Preut Hans , Strohmann Carsten , Hiersemann Martin
Published: August 2015

The title hydrate, C17H28O2·H2O, was synthesized in order to determine the relative configuration of the tetracyclic framework. The fused 5,6,7-tricarbocyclic core exhibits an entirecis-annulation, featuring a 1,4-cis-relation of the angular methyl groups in the six-membered ring. The oxa bridge of the epoxycycloheptane moiety is oriented towards the concave face of the boat-shaped molecule, whereas the angular methyl groups are directed towards the convex face. The asymmetric unit of the crystal contains two nearly identical formula units, which are relatedviaa pseudo-centre of symmetry. The structure could be solved in the space groupsI-4 andI41/a. The refinement in the acentric space group, however, gave significantly better results and these are used in this paper. O—H...O hydrogen bonds are observed between the organic molecules, between the organic molecules and the water molecules, and between the water molecules, forming a chain along thec-axis direction.
Graduates giving back – a mentoring program for MBA students
Authors: Darwin Ann
Published: August 2015

Purpose

– The purpose of this paper is to discuss the challenges and obstacles encountered in the implementation of a mentoring program for Master of Business Administration (MBA) students at the University of South Australia (UniSA) Business School. The paper starts with an exploration into the need for a mentoring program, the trial and subsequent four years of implementation. The paper also explores the network model of mentoring and the reasons why this, rather than a more traditional model, was chosen for the program’s implementation.

Design/methodology/approach

– This exploratory case study uses data from over 600 students and their alumni mentors over a five-year period to evaluate and improve the program as well as cultivating a critical community of adult learners.

Findings

– Feedback from students indicates that the mentoring program is regarded by most as a value-added feature of their early learning as it offers support, if and when it is required, from those who have been there before.

Research limitations/implications

– Results are limited to one institution. However, as research into mentoring for higher education students is thin on the ground, this study contributes to our understanding of the positive impacts of mentoring on student success.

Practical implications

– This paper emphasizes the importance of business leaders giving back to their alma mater through mentoring current MBA students. It shows how mentoring can support learning and management development.

Originality/value

– This is an original study which explores ways to increase the learning of higher education students for positive social outcomes.
Experimental desktop 3D printing using dual extrusion and water-soluble polyvinyl alcohol
Authors: Duran Chelsea , Subbian Vignesh , Giovanetti Matthew T. , Simkins Jeffrey R. , Beyette Jr Fred R.
Published: August 2015

Purpose

– This paper aims to discuss the use of polyvinyl alcohol (PVA) as a water-soluble support material in desktop three-dimensional (3D) printing. Using a water-soluble material as one of the printing filaments in a dual-extrusion 3D printer provides the flexibility of printing support structures and rafts in complex components and prototypes. This paper focuses on the challenges of acrylonitrile butadiene styrene (ABS)–PVA dual-extrusion printing, and optimal settings and techniques for such hybrid printing.

Design/methodology/approach

– Several hybrid ABS–PVA parts were printed using a commercial desktop 3D printer. An experimental study was designed to examine the solubility of the PVA support in water by varying four different parameters: length of time in water, water temperature, stirring rate and PVA surface area. The rate of PVA solubility in water was then used to examine its relationship with each parameter.

Findings

– Numerous problems were encountered while printing ABS–PVA printing parts, including storing the spool of PVA in a dry environment, determining optimal extrusion and build plate temperatures and ABS–PVA adherence during dual extrusion printing. There is no strong literature to address these challenges. Hence, optimal settings and techniques for effective hybrid ABS–PVA were determined. Print yields were also recorded to examine the reliability of ABS–PVA printing.

Research limitations/implications

– The tendency of PVA to absorb moisture resulted in a number of build fails and prevented build times longer than 40 minutes. Future work can explore how to print PVA directly from a dry environment.

Practical implications

– The optimal settings and techniques for dual-extrusion ABS–PVA printing that are presented in this paper can effectively be used to explore prototyping of geometrically complex parts with PVA as support material.

Originality/value

– In addition to the practical implications, the results from this work are a valuable addition to the literature related to printing using water-soluble polymers such as PVA. The experimental methods and techniques of this paper can be used to assess the reliability of similar 3D printing technologies.
The impact of process parameters on mechanical properties of parts fabricated in PLA with an open-source 3-D printer
Authors: Lanzotti Antonio , Grasso Marzio , Staiano Gabriele , Martorelli Massimo
Published: August 2015

Purpose

– This study aims to quantify the ultimate tensile strength and the nominal strain at break (ɛf) of printed parts made from polylactic acid (PLA) with a Replicating Rapid prototyper (Rep-Rap) 3D printer, by varying three important process parameters: layer thickness, infill orientation and the number of shell perimeters. Little information is currently available about mechanical properties of parts printed using open-source, low-cost 3D printers.

Design/methodology/approach

– A computer-aided design model of a tensile test specimen was created, conforming to the ASTM:D638. Experiments were designed, based on a central composite design. A set of 60 specimens, obtained from combinations of selected parameters, was printed on a Rep-Rap Prusa I3 in PLA. Testing was performed using a JJ Instruments – T5002-type tensile testing machine and the load was measured using a load cell of 1,100 N.

Findings

– This study investigated the main impact of each process parameter on mechanical properties and the effects of interactions. The use of a response surface methodology allowed the proposition of an empirical model which connects process parameters and mechanical properties. Even though results showed a high variability, additional ideas on how to understand the impact of process parameters are suggested in this paper.

Originality/value

– On the basis of experimental results, it is possible to obtain practical suggestions to set common process parameters in relation to mechanical properties. Experiments discussed in the present paper provide a variety of data and insight regarding the relationship among the main process parameters and the stiffness and strength of fused deposition modeling-printed parts made from PLA. In particular, this paper underlines the shortage in existing literature concerning the impact of process parameters on the elastic modulus and the strain to failure for the PLA. The experimental data produced show a good degree of compliance with analytical formulations and other data found in literature.
The Myth of Bondi's Black Sunday
Authors: BOOTH DOUGLAS
Published: August 2015

On 6 February 1938, five bathers drowned while swimming between the flags at Bondi Beach, Sydney, Australia. In surf lifesaving history, the day is known as Black Sunday. The dominant heroic narrative of Black Sunday highlights freak surf conditions and the gallantry, efficiency, and adeptness of Bondi's volunteer surf lifesavers. In this article I analyse this representation as a myth. Here I employ the French philosopher Roland Barthes' concept of myth, not as a falsehood, but as simplistic story, replete with silences and devoid of critical assessment. I argue that the myth of Black Sunday served the interests of Surf Life Saving Australia well in establishing its status as the country's premier safety service. However, the culture that underpinned that myth still persists with ongoing ramifications for risk assessment at the beach.
Biomedical Activity and Related Volatile Compounds of Thai Honeys from 3 Different Honeybee Species
Authors: Pattamayutanon Praetinee , Angeli Sergio , Thakeow Prodpran , Abraham John , Disayathanoowat Terd , Chantawannakul Panuwan
Published: August 2015

This study investigated the effect of 3 factors (floral source, honeybee species, and postcollection processing) that influence the antibacterial activity, free radical reduction, and other biochemical compositions of different honey types typical of Thailand. Honey samples from 3 honeybee species (Apis mellifera, Apis cerana, and Apis dorsata) were obtained from 9 floral sources (longan, wild flower, lychee, coffee, sunflower, sesame, bitter bush, para‐rubber, and manuka as a control) in different regions of Thailand. These samples were evaluated for both their total and nonperoxide antibacterial activity against 10 human pathogens by agar incorporation technique. Honey samples were further analyzed to evaluate the capacity for free radical‐scavenging activity, total phenolic content, and the total flavonoid contents by the 2,2‐diphenyl‐1‐picrylhydrazyl assay, Folin–Ciocalteu method, and aluminum chloride colorimetric assay, respectively. Furthermore, the volatile organic compounds (VOCs) of Thai honey samples were investigated by headspace solid‐phase microextraction and gas chromatography‐mass spectrometry analysis. Findings of this study suggest a strong correlation between floral origin and honeybee species on one hand, and differences in %Brix, total acidity, protein content, antimicrobial activities, free radical reduction, phenolic, and flavonoid contents on the other hand. Moreover, VOCs of wild and coffee honey types were remarkably different, depending on the floral source. Both honeys contained characteristics of VOCs, some of which are involved in antibacterial and antioxidant activities.