bluuebunny/crossref_metadata_2025 huggingface dataset:
A framework for evaluating the effectiveness of conservation attention at the species level
Authors: Washington Harriet , Baillie Jonathan , Waterman Carly , Milner-Gulland E.J.
Published: November 2014

It is essential to understand whether conservation interventions are having the desired effect, particularly in light of increasing pressures on biodiversity and because of requirements by donors that project success be demonstrated. Whilst most evaluations look at effectiveness at a project or organizational level, local efforts need to be connected to an understanding of the effectiveness of conservation directed at a species as a whole, particularly as most metrics of conservation success are at the level of species. We present a framework for measuring the effectiveness of conservation attention at a species level over time, based on scoring eight factors essential for species conservation (engaging stakeholders, management programme, education and awareness, funding and resource mobilization, addressing threats, communication, capacity building and status knowledge), across input, output and outcome stages, in relation to the proportion of the species’ range where each factor attains its highest score. The framework was tested using expert elicitation for 35 mammal and amphibian species on the Zoological Society of London's list of Evolutionarily Distinct and Globally Endangered species. Broad patterns in the index produced by the framework could suggest potential mechanisms underlying change in species status. Assigning an uncertainty score to information demonstrates not only where gaps in knowledge exist, but discrepancies in knowledge between experts. This framework could be a useful tool to link local and global scales of impact on species conservation, and could provide a simple and visually appealing way of tracking conservation over time.
X-ray powder diffraction study of La2LiTaO6
Authors: Rodriguez Mark A. , Griego James J. M. , Brown-Shaklee Harlan J. , Blea-Kirby Mia A. , Ihlefeld John F. , Spoerke Erik D.
Published: November 2014

The structure of La2LiTaO6 has been derived from the powder X-ray powder diffraction (XRD) data. La2LiTaO6 is monoclinic with unit-cell parameters a = 5.621(1) Å, b = 5.776(1) Å, c = 7.954(2) Å, β = 90.34(2)°, space group P21/n (14), and Z = 2. The structure of La2LiTaO6 is an ordered perovskite with alternating Li and Ta octahedra. A new set of powder XRD data (d-spacing and intensity listing) has been generated to replace entry 00-039-0897 within the Powder Diffraction File. The newly elucidated structural data for La2LiTaO6 shall facilitate quantitative analysis of this impurity phase which is often observed during synthesis of the fast-ion conductor phase Li5La3Ta2O12.
Volumetric modulated arc therapy versus 3D conformal radiotherapy for selected childhood neoplasms
Authors: Chojnacka Marzanna , Zygmuntowicz-Piętka Anna , Semaniak Anna , Pędziwiatr Katarzyna , Dąbrowski Ryszard , Skowrońska-Gardas Anna
Published: November 2014

Aim

The comparative study of the plan quality between volumetric modulated arc therapy (VMAT) and 3D conformal therapy (3DCRT) for the treatment of selected representative childhood neoplasms was performed.

Materials and methods

During the year 2013, 44 children with neoplasms were irradiated using VMAT. The 3DCRT plans were created retrospectively and compared with the VMAT plans for four tumour locations. The conformity parameters, dose volume histograms for target volume and organs at risk, number of monitor units and time used to deliver the single fraction were evaluated and compared for each plan. Additionally, for patients with brain tumour the comparison of different arcs configuration was made.

Results

VMAT modality presented the superiority over older conformal methods with regard to the improvement in the dose conformity and normal tissue sparing. The noncoplanar arcs arrangement was beneficial in the decrease of high-dose volume and the protection of the organs at risk located oppositely to the target volume.

Findings

VMAT could be preferred technique for treating childhood neoplasms, especially when the complex-shaped target volume is localised close to the critical structures. The noncoplanar arcs arrangement could be the method of choice in the reirradiated patients and in these with laterally located brain tumours.
Control of cotton fibre elongation by a homeodomain transcription factor GhHOX3
Authors: Shan Chun-Min , Shangguan Xiao-Xia , Zhao Bo , Zhang Xiu-Fang , Chao Lu-men , Yang Chang-Qing , Wang Ling-Jian , Zhu Hua-Yu , Zeng Yan-Da , Guo Wang-Zhen , Zhou Bao-Liang , Hu Guan-Jing , Guan Xue-Ying , Chen Z. Jeffrey , Wendel Jonathan F. , Zhang Tian-Zhen , Chen Xiao-Ya
Published: November 2014

Cotton fibres are unusually long, single-celled epidermal seed trichomes and a model for plant cell growth, but little is known about the regulation of fibre cell elongation. Here we report that a homeodomain-leucine zipper (HD-ZIP) transcription factor, GhHOX3, controls cotton fibre elongation.GhHOX3genes are localized to the 12th homoeologous chromosome set of allotetraploid cotton cultivars, associated with quantitative trait loci (QTLs) for fibre length. Silencing ofGhHOX3greatly reduces (>80%) fibre length, whereas its overexpression leads to longer fibre. Combined transcriptomic and biochemical analyses identify target genes of GhHOX3 that also contain the L1-boxcis-element, including two cell wall loosening protein genesGhRDL1andGhEXPA1. GhHOX3 interacts with GhHD1, another homeodomain protein, resulting in enhanced transcriptional activity, and with cotton DELLA, GhSLR1, repressor of the growth hormone gibberellin (GA). GhSLR1 interferes with the GhHOX3–GhHD1 interaction and represses target gene transcription. Our results uncover a novel mechanism whereby a homeodomain protein transduces GA signal to promote fibre cell elongation.
Glycine-functionalized carbon quantum dots as chemiluminescence sensitization for detection of m-phenylenediamine
Authors: Yan Zhengyu , Yu Yan , Chen Jianqiu
Published: November 2014

A novel sensing system has been designed for the detection of m-phenylenediamine based on carbon quantum dots (CQDs)-improved chemiluminescence (CL) in a luminol–potassium permanganate (KMnO4) system.
Catalytic, highly enantioselective, direct amination of enecarbamates
Authors: Dumoulin Audrey , Lalli Claudia , Retailleau Pascal , Masson Géraldine
Published: November 2014

Highly enantioselective electrophilic amination reaction of enecarbamates with dibenzylazodicarboxylate and oxygenated nucleophiles catalyzed by chiral phosphoric acids is reported. Subsequent reduction or oxidation of the resulting precursors of α-hydrazinoimines leads to 1,2-diamines or α-amino acid precursors, respectively, in excellent yields and enantioselectivities.
A highly selective and sensitive fluorescent thiol probe through dual-reactive and dual-quenching groups
Authors: Zhang Huatang , Zhang Changyu , Liu Ruochuan , Yi Long , Sun Hongyan
Published: November 2014

A fluorescent probe installed with dual-reactive and dual-quenching groups was rationally designed and synthesized for highly selective and sensitive sensing of biothiols.
Synthetic studies toward penitrem E: enantiocontrolled construction of B–E rings
Authors: Yoshii Yu , Otsu Takanori , Hosokawa Norihiko , Takasu Kiyosei , Okano Kentaro , Tokuyama Hidetoshi
Published: November 2014

Enantiocontrolled construction of B–E rings of penitrem E was accomplished from 4-iodoindole through diastereoselective Tf2NH-catalyzed (2+2)-cycloaddition.
Phase controlled synthesis of SnSe and SnSe2 hierarchical nanostructures made of single crystalline ultrathin nanosheets
Authors: Ramasamy Parthiban , Manivasakan Palanisamy , Kim Jinkwon
Published: November 2014

A simple solvothermal approach for the phase controlled synthesis of SnSe and SnSe2 hierarchical nanostructures (HNs) has been reported.
Nanoscale spinel LiFeTiO4for intercalation pseudocapacitive Li+storage
Authors: Chen Ruiyong , Knapp Michael , Yavuz Murat , Ren Shuhua , Witte Ralf , Heinzmann Ralf , Hahn Horst , Ehrenberg Helmut , Indris Sylvio
Published: November 2014

Nanosized spinel materials were found to allow a large-amount of Li+intercalation storage without compromising kinetics.
Representing the potential-energy surface of protonated water clusters by high-dimensional neural network potentials
Authors: Kondati Natarajan Suresh , Morawietz Tobias , Behler Jörg
Published: November 2014

We report a reactive neural network potential for protonated water clusters that accurately represents the density-functional theory potential-energy surface.
Solid state concentration quenching of organic fluorophores in PMMA
Authors: Green Adam P. , Buckley Alastair R.
Published: November 2014

In this study the concentration quenching phenomenon is explored for seven organic singlet emitters (Rhodamine 6G, Pyridine 2, Lumogen F Red 305, Perylene, Coumarin 102, DCM and DCJTB) in an inert host of poly(methyl methacrylate) (PMMA).
Microwave-induced catalytic degradation of a textile dye using bentonite–poly(o-toluidine) nanohybrid
Authors: Riaz Ufana , Ashraf S. M.
Published: November 2014

The present study highlights the potential use of natural clay based organic–inorganic hybrids as eco-friendly catalysts for the degradation of Malachite Green under microwave irradiation.
Controllable preparation and properties of active functional hybrid materials with different chromophores
Authors: Wang Shizhe , Guang Shanyi , Xu Hongyao , Ke Fuyou
Published: November 2014

POSS-based active functional hybrid materials were controllably prepared and their optical properties were influenced by molecular structure.
Highly stable nano Ce–La catalyst for hydrogen production from bio-ethanol
Authors: Abd El-Hafiz Dalia R. , Ebiad Mohamed A. , Elsalamony Radwa A. , Mohamed Lamia. S.
Published: November 2014

The catalytic activity of a metal free nano-particle, whose size ranged from 1–10 nm, was studied in ethanol steam reforming reaction for hydrogen production.
Recent progress in organic–inorganic halide perovskite solar cells: mechanisms and material design
Authors: Luo Shiqiang , Daoud Walid A.
Published: November 2014

While energy shortage is always an issue, the impending exhaustion of fossil fuel sources makes it an ever increasingly pressing one.
A quantitative proteomics-based signature of platinum sensitivity in ovarian cancer cell lines
Authors: Fan Gaofeng , Wrzeszczynski Kazimierz O. , Fu Cexiong , Su Gang , Pappin Darryl J. , Lucito Robert , Tonks Nicholas K.
Published: November 2014

Although DNA encodes the molecular instructions that underlie the control of cell function, it is the proteins that are primarily responsible for implementing those instructions. Therefore quantitative analyses of the proteome would be expected to yield insights into important candidates for the detection and treatment of disease. We present an iTRAQ (isobaric tag for relative and absolute quantification)-based proteomic analysis of ten ovarian cancer cell lines and two normal ovarian surface epithelial cell lines. We profiled the abundance of 2659 cellular proteins of which 1273 were common to all 12 cell lines. Of the 1273, 75 proteins exhibited elevated expression and 164 proteins had diminished expression in the cancerous cells compared with the normal cell lines. The iTRAQ expression profiles allowed us to segregate cell lines based upon sensitivity and resistance to carboplatin. Importantly, we observed no substantial correlation between protein abundance and RNA expression or epigenetic DNA methylation data. Furthermore, we could not discriminate between sensitivity and resistance to carboplatin on the basis of RNA expression and DNA methylation data alone. The present study illustrates the importance of proteomics-based discovery for defining the basis for the carboplatin response in ovarian cancer and highlights candidate proteins, particularly involved in cellular redox regulation, homologous recombination and DNA damage repair, which otherwise could not have been predicted from whole genome and expression data sources alone.
NHR-176 regulates cyp-35d1 to control hydroxylation-dependent metabolism of thiabendazole in Caenorhabditis elegans
Authors: Jones Laura M. , Flemming Anthony J. , Urwin Peter E.
Published: November 2014

Knowledge of how drugs are metabolized and excreted is an essential component of understanding their fate within and among target and non-target organisms. Thiabendazole (TBZ) was the first benzimidazole (BZ) to be commercially available and remains one of the most important anthelmintic drugs for medical and veterinary use. We have characterized how Caenorhabditis elegans metabolizes and excretes TBZ. We have shown that TBZ directly binds to the nuclear hormone receptor (NHR)-176 and that this receptor is required for the induction by TBZ of the cytochrome P450 (CYP) encoded by cyp-35d1. Further, RNAi inhibition of cyp-35d1 in animals exposed to TBZ causes a reduction in the quantity of a hydroxylated TBZ metabolite and its glucose conjugate that is detected in C. elegans tissue by HPLC. This final metabolite is unique to nematodes and we also identify two P-glycoproteins (PGPs) necessary for its excretion. Finally, we have shown that inhibiting the metabolism we describe increases the susceptibility of C. elegans to TBZ in wild-type and in resistant genetic backgrounds.
Reconfigurable and tuneable bandpass prototype networks achieving minimal absolute bandwidth variation
Authors: Fathelbab Wael M.
Published: November 2014

This study presents the synthesis and design of novel bandpass prototype networks with reconfigurable centre frequencies in two distinct states whose absolute bandwidth is maintained constant. The passbands of the prototypes can also be tuned around the centre frequencies of the two distinct states with minimal absolute bandwidth variation. This is achieved by virtue of a new distributed resonator structure which is thoroughly studied and analysed in this work. The presented circuit concepts are validated through the simulation of a stub‐loaded evanescent mode waveguide filter modelled on high frequency structure simulator (HFSS) realising an absolute bandwidth of 242 MHz in two distinct states that are centred at frequencies of 1150 and 1495 MHz. The filter is manually reconfigured between the two distinct states upon terminating stubs within its resonator structures as either open‐circuits or short‐circuits. The filter is also discretely tuned in each of the two states upon manually altering the values of the loading capacitors of its resonators. The absolute bandwidth of the filter exhibited a maximum variation of only ±28 MHz over the frequency tuning range spanning 977.5 to 1667.5 MHz.
The Comprehensive AOCMF Classification System: Orbital Fractures - Level 3 Tutorial
Authors: Kunz Christoph , Audigé Laurent , Cornelius Carl-Peter , Buitrago-Téllez Carlos H. , Rudderman Randal , Prein Joachim
Published: November 2014

The AOCMF Classification Group developed a hierarchical three-level craniomaxillofacial classification system with increasing level of complexity and details. Within the midface (level 1 code 92), the level 2 system describes the location of the fractures within defined regions in the central and lateral midface including the internal orbit. This tutorial outlines the level 3 detailed classification system for fractures of the orbit. It depicts the orbital fractures according to the subregions defined as orbital rims, anterior orbital walls, midorbit, and apex. The system allows documentation of the involvement of specific orbital structures such as inferior orbital fissure, internal orbital buttress, the greater wing of sphenoid, lacrimal bone, superior orbital fissure, and optic canal. The classification system is presented along with rules for fracture location and coding, a series of case examples with clinical imaging and a general discussion on the design of this classification.
The Comprehensive AOCMF Classification System: Fracture Case Collection, Diagnostic Imaging Work Up, AOCOIAC Iconography and Coding
Authors: Cornelius Carl-Peter , Kunz Christoph , Neff Andreas , Kellman Robert M. , Prein Joachim , Audigé Laurent
Published: November 2014

The AO classification system for fractures in the adult craniomaxillofacial (CMF) skeleton is organized in anatomic modules in a 3 precision-level hierarchy with account for an increasing complexity and details. Level-1 is most elementary and identifies no more than the presence of fractures in 4 separate anatomical units: the mandible (code 91), midface (92), skull base (93) and cranial vault (94). Level-2 relates the detailed topographic location of the fractures within defined regions of the mandible, central and lateral midface, internal orbit, endo- and exocranial skull base, and the cranial vault. Level-3 is based on an even more refined topographic assessment and focuses on the morphology — fragmentation, displacement, and bone defects — within specified subregions. An electronic fracture case collection complements the preceding tutorial papers, which explain the features and options of the AOCMF classification system in this issue of the Journal. The electronic case collection demonstrates a range of representative osseous CMF injuries on the basis of diagnostic images, narrative descriptions of the fracture diagnosis and their classification using the icons for illustration and coding of a dedicated software AOCOIAC (AO Comprehensive Injury Automatic Classifier). Ninety four case examples are listed in two tables for a fast overview of the electronic content. Each case can serve as a guide to getting started with the new AOCMF classification system using AOCOIAC software and to employ it in the own clinical practice.
Shockwave response of two carbon fiber-polymer composites to 50 GPa
Authors: Dattelbaum Dana M. , Coe Joshua D. , Rigg Paulo A. , Scharff R. Jason , Gammel J. Tinka
Published: November 2014

Shock compression of two molded, carbon fiber-filled polymer composites was performed in gas gun-driven plate impact experiments at impact velocities up to ≈5 km/s. Hugoniot states for both composites were obtained from <5 GPa to nearly 50 GPa. The two materials contained a high fill percentage of chopped carbon fibers, bound by either phenolic or cyanate ester polymeric resins. Their dynamic responses were similar, although the 10 wt. % difference of carbon fill produced measureable divergence in shock compressibility. The chopped carbon fibers in the polymer matrix led to moderately anisotropic shocks, particularly when compared with the more commonly encountered filament-wound carbon fiber-epoxy composites. A discontinuity, or cusp, was observed in the principal Hugoniot of both materials near 25 GPa. We attribute the accompanying volume collapse to shock-driven chemical decomposition above this condition. Inert and reacted products equations of state were used to capture the response of the two materials below and above the cusp.
Negative differential resistance in GaN tunneling hot electron transistors
Authors: Yang Zhichao , Nath Digbijoy , Rajan Siddharth
Published: November 2014

Room temperature negative differential resistance is demonstrated in a unipolar GaN-based tunneling hot electron transistor. Such a device employs tunnel-injected electrons to vary the electron energy and change the fraction of reflected electrons, and shows repeatable negative differential resistance with a peak to valley current ratio of 7.2. The device was stable when biased in the negative resistance regime and tunable by changing collector bias. Good repeatability and double-sweep characteristics at room temperature show the potential of such device for high frequency oscillators based on quasi-ballistic transport.
Boron-tuning transition temperature of vanadium dioxide from rutile to monoclinic phase
Authors: Zhang J. J. , He H. Y. , Xie Y. , Pan B. C.
Published: November 2014

The effect of the doped boron on the phase transition temperature between the monoclinic phase and the rutile phase of VO2 has been studied by performing first-principles calculations. It is found that the phase transition temperature decreases linearly with increasing the doping level of B in each system, no matter where the B atom is in the crystal. More importantly, the descent of the transition temperature is predicted to be as large as 83 K/at. % B, indicating that the boron concentration of only 0.5% can cause the phase transition at room temperature. These findings provide a new routine of modulating the phase transition of VO2 and pave a way for the practicality of VO2 as an energy-efficient green material.
Quantum harmonic oscillator with superoscillating initial datum
Authors: Buniy R. V. , Colombo F. , Sabadini I. , Struppa D. C.
Published: November 2014

In this paper, we study the evolution of superoscillating initial data for the quantum driven harmonic oscillator. Our main result shows that superoscillations are amplified by the harmonic potential and that the analytic solution develops a singularity in finite time. We also show that for a large class of solutions of the Schrödinger equation, superoscillating behavior at any given time implies superoscillating behavior at any other time.
Modeling thin-film piezoelectric polymer ultrasonic sensors
Authors: González M. G. , Sorichetti P. A. , Santiago G. D.
Published: November 2014

This paper presents a model suitable to design and characterize broadband thin film sensors based on piezoelectric polymers. The aim is to describe adequately the sensor behavior, with a reasonable number of parameters and based on well-known physical equations. The mechanical variables are described by an acoustic transmission line. The electrical behavior is described by the quasi-static approximation, given the large difference between the velocities of propagation of the electrical and mechanical disturbances. The line parameters include the effects of the elastic and electrical properties of the material. The model was validated with measurements of a poly(vinylidene flouride) sensor designed for short-pulse detection. The model variables were calculated from the properties of the polymer at frequencies between 100 Hz and 30 MHz and at temperatures between 283 K and 313 K, a relevant range for applications in biology and medicine. The simulations agree very well with the experimental data, predicting satisfactorily the influence of temperature and the dielectric properties of the polymer on the behavior of the sensor. Conversely, the model allowed the calculation of the material dielectric properties from the measured response of the sensor, with good agreement with the published values.
Quantification of thermal and contact resistances of scanning thermal probes
Authors: Kim Kyeongtae , Jeong Wonho , Lee Woochul , Sadat Seid , Thompson Dakotah , Meyhofer Edgar , Reddy Pramod
Published: November 2014

Scanning thermal probes are widely used for imaging temperature fields with nanoscale resolution, for studying near-field radiative heat transport and for locally heating samples. In all these applications, it is critical to know the thermal resistance to heat flow within the probe and the thermal contact resistance between the probe and the sample. Here, we present an approach for quantifying the aforementioned thermal resistances using picowatt resolution heat flow calorimeters. The measured contact resistance is found to be in good agreement with classical predictions for thermal contact resistance. The techniques developed here are critical for quantitatively probing heat flows at the nanoscale.
Size-dependent magnetic properties of 100–500 nm diameter IrMn/NiFe disks made by a two-step deposition process
Authors: Liu F. , Ross C. A.
Published: November 2014

A two-step etching and deposition process is presented for making nanoscale exchange-biased NiFe/IrMn disks, and their magnetic properties are described as a function of diameter and thickness. The exchange bias in nanodots with diameters of 100–500 nm was reduced and the coercivity enhanced compared to the continuous film. Etching of the NiFe film prior to depositing the IrMn lowered the exchange bias; and the exchange bias also decreased as dot diameter decreased. The results are interpreted in terms of the relation between dot size and the antiferromagnetic domain size in the IrMn. The two-step process will be useful in introducing exchange bias at local regions of a ferromagnetic film.
Plasma wave aided two photon decay of an electromagnetic wave in a plasma
Authors: Kumar K. K. Magesh , Singh Rohtash , Krishan Vinod
Published: November 2014

The presence of a Langmuir wave in an unmagnetized plasma is shown to allow parametric decay of an electromagnetic wave into two electromagnetic waves, which is otherwise not allowed due to wave number mismatch. The decay occurs at plasma densities below one ninth the critical density and the decay waves propagate at finite angles to the pump laser. Above the threshold, the growth rate scales linearly with the amplitude of the Langmuir wave and the amplitude of the pump electromagnetic wave. The frequency ω of the lower frequency decay wave increases with the angle its propagation vector makes with that of the pump. The growth rate, however, decreases with ω.
Importance of Fermi energy for understanding the intermixing behavior at the LaAlO3/SrTiO3 heterointerface
Authors: Yamamoto Takashi , Mizoguchi Teruyasu
Published: November 2014

We investigated the migration energy and vacancy formation energy of La and Sr ions at a LaAlO3/SrTiO3 heterointerface using first-principles calculations. Our study reveal that the migration energies at the p-type interface are lower than those at the n-type interface, and the formation energies of Sr and La vacancies are relatively high when we assume a reduction atmosphere and insulator conditions. To explain the experimental evidence that intermixing is preferentially taking place at the n-type interface, considering the Fermi energy is critical. We find that the presence of electron carriers plays an important role in the intermixing behaviors at the LaAlO3/SrTiO3 heterointerface.
Structure, magnetism, specific heat, and dielectric properties of Eu2Ta2O7
Authors: Kolodiazhnyi T. , Sakurai H. , Matsushita Y.
Published: November 2014

Polycrystalline Eu2Ta2O7 containing layered perovskite slabs was prepared and analyzed. Eu2Ta2O7 crystallizes in the orthorhombic centrosymmetric Cmcm space group (with unit cell: a = 3.95156(9), b = 27.0775(6), and c = 5.68279(13) Å) isomorphous with high-temperature Sr2Ta2O7. Dielectric measurements reveal that, in contrast to Sr2Ta2O7 which is ferroelectric below 166 K, Eu2Ta2O7 remains paraelectric down to at least 0.45 K and shows no magneto-dielectric coupling. Magnetic data in the 2–400 K range indicate an antiferromagnetic phase transition with a sharp susceptibility peak at 2.71(5) K. Further analysis using specific heat measurements reveals that the second magnetic phase transition occurs at 1.10(5) K and dominates the spin entropy of the Eu2+ 4f7 ions. The possible origin of the two successive magnetic phase transitions in Eu2Ta2O7 requires further studies.
Subnanomolar fluorescent-molecule sensing by guided resonances on nanoimprinted silicon-on-insulator substrates
Authors: Choi Bongseok , Iwanaga Masanobu , Ochiai Tetsuyuki , Miyazaki Hideki T. , Sugimoto Yoshimasa , Sakoda Kazuaki
Published: November 2014

We have produced nanoimprinted silicon-on-insulator (SOI) substrates with high precision and applied them for fluorescence (FL) enhancement of typical dye molecules of Rhodamine series. We experimentally found that the FL signals on the nanoimprinted SOI substrates are enhanced by more than 200 fold as compared with the signals on Si wafers. The FL enhancement mechanism was investigated using spectroscopic and theoretical approaches. The results indicated that guided resonances with large density of states significantly contribute to the FL enhancement. We also substantiated that the FL-enhancing substrates well serve as rapid-sensing platforms for a very dilute FL-molecule solution with subnanomolar concentration. The nanoimprinted SOI substrates were repeatedly reused without degradation.
Comparison of the transcriptional landscapes between human and mouse tissues
Authors: Lin Shin , Lin Yiing , Nery Joseph R. , Urich Mark A. , Breschi Alessandra , Davis Carrie A. , Dobin Alexander , Zaleski Christopher , Beer Michael A. , Chapman William C. , Gingeras Thomas R. , Ecker Joseph R. , Snyder Michael P.
Published: November 2014

Significance

To date, various studies have found similarities between humans and mice on a molecular level, and indeed, the murine model serves as an important experimental system for biomedical science. In this study of a broad number of tissues between humans and mice, high-throughput sequencing assays on the transcriptome and epigenome reveal that, in general, differences dominate similarities between the two species. These findings provide the basis for understanding the differences in phenotypes and responses to conditions in humans and mice.
SAMNetWeb: identifying condition-specific networks linking signaling and transcription
Authors: Gosline Sara J. C. , Oh Coyin , Fraenkel Ernest
Published: November 2014

Motivation  : High-throughput datasets such as genetic screens, mRNA expression assays and global phospho-proteomic experiments are often difficult to interpret due to inherent noise in each experimental system. Computational tools have improved interpretation of these datasets by enabling the identification of biological processes and pathways that are most likely to explain the measured results. These tools are primarily designed to analyse data from a single experiment (e.g. drug treatment versus control), creating a need for computational algorithms that can handle heterogeneous datasets across multiple experimental conditions at once.

Summary: We introduce SAMNetWeb, a web-based tool that enables functional enrichment analysis and visualization of high-throughput datasets. SAMNetWeb can analyse two distinct data types (e.g. mRNA expression and global proteomics) simultaneously across multiple experimental systems to identify pathways activated in these experiments and then visualize the pathways in a single interaction network. Through the use of a multi-commodity flow based algorithm that requires each experiment ‘share’ underlying protein interactions, SAMNetWeb can identify distinct and common pathways across experiments.

Availability and implementation: SAMNetWeb is freely available at http://fraenkel.mit.edu/samnetweb.

Contact:  fraenkel-admin@mit.edu
Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data
Authors: Kyoda Koji , Tohsato Yukako , Ho Kenneth H. L. , Onami Shuichi
Published: November 2014

Motivation: Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats.

Results: We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis.

Availability and implementation: A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/.

Contact:  sonami@riken.jp

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Looking in the rear-view mirror: bias and retrospective patterns in
integrated, age-structured stock assessment models
Authors: Hurtado-Ferro Felipe , Szuwalski Cody S. , Valero Juan L. , Anderson Sean C. , Cunningham Curry J. , Johnson Kelli F. , Licandeo Roberto , McGilliard Carey R. , Monnahan Cole C. , Muradian Melissa L. , Ono Kotaro , Vert-Pre Katyana A. , Whitten Athol R. , Punt André E.
Published: November 2014

Retrospective patterns are systematic changes in estimates of population size, or other assessment model-derived quantities, that occur as additional years of data are added to, or removed from, a stock assessment. These patterns are an insidious problem, and can lead to severe errors when providing management advice. Here, we use a simulation framework to show that temporal changes in selectivity, natural mortality, and growth can induce retrospective patterns in integrated, age-structured models. We explore the potential effects on retrospective patterns of catch history patterns, as well as model misspecification due to not accounting for time-varying biological parameters and selectivity. We show that non-zero values for Mohn’s ρ (a common measure for retrospective patterns) can be generated even where there is no model misspecification, but the magnitude of Mohn’s ρ tends to be lower when the model is not misspecified. The magnitude and sign of Mohn’s ρ differed among life histories, with different life histories reacting differently from each type of temporal change. The value of Mohn’s ρ is not related to either the sign or magnitude of bias in the estimate of terminal year biomass. We propose a rule of thumb for values of Mohn’s ρ which can be used to determine whether a stock assessment shows a retrospective pattern.
GRASP: Guided Reference-based Assembly of Short Peptides
Authors: Zhong Cuncong , Yang Youngik , Yooseph Shibu
Published: November 2014

Protein sequences predicted from metagenomic datasets are annotated by identifying their homologs via sequence comparisons with reference or curated proteins. However, a majority of metagenomic protein sequences are partial-length, arising as a result of identifying genes on sequencing reads or on assembled nucleotide contigs, which themselves are often very fragmented. The fragmented nature of metagenomic protein predictions adversely impacts homology detection and, therefore, the quality of the overall annotation of the dataset. Here we present a novel algorithm called GRASP that accurately identifies the homologs of a given reference protein sequence from a database consisting of partial-length metagenomic proteins. Our homology detection strategy is guided by the reference sequence, and involves the simultaneous search and assembly of overlapping database sequences. GRASP was compared to three commonly used protein sequence search programs (BLASTP, PSI-BLAST and FASTM). Our evaluations using several simulated and real datasets show that GRASP has a significantly higher sensitivity than these programs while maintaining a very high specificity. GRASP can be a very useful program for detecting and quantifying taxonomic and protein family abundances in metagenomic datasets. GRASP is implemented in GNU C++, and is freely available at http://sourceforge.net/projects/grasp-release.
Does Working from Home Work? Evidence from a Chinese Experiment
*
Authors: Bloom Nicholas , Liang James , Roberts John , Ying Zhichun Jenny
Published: November 2014

A rising share of employees now regularly engage in working from home (WFH), but there are concerns this can lead to “shirking from home.” We report the results of a WFH experiment at Ctrip, a 16,000-employee, NASDAQ-listed Chinese travel agency. Call center employees who volunteered to WFH were randomly assigned either to work from home or in the office for nine months. Home working led to a 13% performance increase, of which 9% was from working more minutes per shift (fewer breaks and sick days) and 4% from more calls per minute (attributed to a quieter and more convenient working environment). Home workers also reported improved work satisfaction, and their attrition rate halved, but their promotion rate conditional on performance fell. Due to the success of the experiment, Ctrip rolled out the option to WFH to the whole firm and allowed the experimental employees to reselect between the home and office. Interestingly, over half of them switched, which led to the gains from WFH almost doubling to 22%. This highlights the benefits of learning and selection effects when adopting modern management practices like WFH.
Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures
Authors: Pražnikar Jure , Turk Dušan
Published: November 2014

The refinement of a molecular model is a computational procedure by which the atomic model is fitted to the diffraction data. The commonly used target in the refinement of macromolecular structures is the maximum-likelihood (ML) function, which relies on the assessment of model errors. The current ML functions rely on cross-validation. They utilize phase-error estimates that are calculated from a small fraction of diffraction data, called the test set, that are not used to fit the model. An approach has been developed that uses the work set to calculate the phase-error estimates in the ML refinement from simulating the model errorsviathe random displacement of atomic coordinates. It is called ML free-kick refinement as it uses the ML formulation of the target function and is based on the idea of freeing the model from the model bias imposed by the chemical energy restraints used in refinement. This approach for the calculation of error estimates is superior to the cross-validation approach: it reduces the phase error and increases the accuracy of molecular models, is more robust, provides clearer maps and may use a smaller portion of data for the test set for the calculation ofRfreeor may leave it out completely.
X-ray structures of eIF5B and the eIF5B–eIF1A complex: the conformational flexibility of eIF5B is restricted on the ribosome by interaction with eIF1A
Authors: Zheng Aiping , Yu Jian , Yamamoto Reo , Ose Toyoyuki , Tanaka Isao , Yao Min
Published: November 2014

eIF5B and eIF1A are two translation-initiation factors that are universally conserved among all kingdoms. They show a unique interaction in eukaryotes which is important for ribosomal subunit joining. Here, the structures of two isolated forms of yeast eIF5B and of the eIF5B–eIF1A complex (eIF1A and eIF5B do not contain the respective N-terminal domains) are reported. The eIF5B–eIF1A structure shows that the C-terminal tail of eIF1A binds to eIF5B domain IV, while the core domain of eIF1A is invisible in the electron-density map. Although the individual domains in all structures of eIF5B or archaeal IF5B (aIF5B) are similar, their domain arrangements are significantly different, indicating high structural flexibility, which is advantageous for conformational change during ribosomal subunit joining. Based on these structures, models of eIF5B, eIF1A and tRNAiMeton the 80S ribosome were built. The models suggest that the interaction between the eIF1A C-terminal tail and eIF5B helps tRNAiMetto bind to eIF5B domain IV, thus preventing tRNAiMetdissociation, stabilizing the interface for subunit joining and providing a checkpoint for correct ribosome assembly.
Multi-lamellar organization of fully deuterated lipid extracts of yeast membranes
Authors: Gerelli Yuri , de Ghellinck Alexis , Jouhet Juliette , Laux Valérie , Haertlein Michael , Fragneto Giovanna
Published: November 2014

Neutron scattering studies on mimetic biomembranes are currently limited by the low availability of deuterated unsaturated lipid species. In the present work, results from the first neutron diffraction experiments on fully deuterated lipid extracts from the yeastPichia pastorisare presented. The structural features of these fully deuterated lipid stacks are compared with those of their hydrogenous analogues and with other similar synthetic systems. The influence of temperature and humidity on the samples has been investigated by means of small momentum-transfer neutron diffraction. All of the lipid extracts investigated self-assemble into multi-lamellar stacks having different structural periodicities; the stacking distances are affected by temperature and humidity without altering the basic underlying arrangement. At high relative humidity the deuterated and hydrogenous samples are similar in their multi-lamellar arrangement, being characterized by two main periodicities of ∼75 and ∼110 Å reflecting the presence of a large number of polar phospholipid molecules. Larger differences are found at lower relative humidity, where hydrogenous lipids are characterized by a larger single lamellar structure than that observed in the deuterated samples. In both cases the heterogeneity in composition is reflected in a wide structural complexity. The different behaviour upon dehydration can be related to compositional differences in the molecular composition of the two samples, which is attributed to metabolic effects related to the use of perdeuterated growth media.
Crystal structure of ethyl (6-hydroxy-1-benzofuran-3-yl)acetate sesquihydrate
Authors: Krishnaswamy G. , Suchetan P. A. , Sreenivasa S. , Naveen S. , Lokanath N. K. , Aruna Kumar D. B.
Published: November 2014

In the title hydrate, C12H12O4·1.5H2O, one of the water molecules in the asymmetric unit is located on a twofold rotation axis. The molecule of the benzofuran derivative is essentially planar (r.m.s. deviation for the non-H atoms = 0.021 Å), with the ester group adopting a fully extended conformation. In the crystal, O—H...O hydrogen bonds between the water molecules and the hydroxy groups generate a centrosymmetricR66(12) ring motif. TheseR66(12) rings are fused, forming a one-dimensional motif extending along thec-axis direction.
Crystal structure of methyl 2-(2H-1,3-benzodioxol-5-yl)-7,9-dibromo-8-oxo-1-oxaspiro[4.5]deca-2,6,9-triene-3-carboxylate
Authors: Martins Lucimara Julio , Simoni Deborah de Alencar , Aparicio Ricardo , Coelho Fernando
Published: November 2014

The title compound, C18H12Br2O6, was synthesized from Morita–Baylis–Hillman adducts. It incorporates the brominated spiro-hexadienone moiety typically exhibited by compounds of this class that exhibit biological activity. Both the brominated cyclohexadienone and the central five-membered rings are nearly planar (r.m.s. deviations of 0.044 and 0.016 Å, respectively), being almost perpendicularly oriented [interplanar angle = 89.47 (5)°]. With respect to the central five-membered ring, the brominated cyclohexadienone ring, the benzodioxol ring and the carboxylate fragment make C—O—C—C, O—C—C—C and C—C—C—O dihedral angles of −122.11 (8), −27.20 (11) and −8.40 (12)°, respectively. An intramolecular C—H...O hydrogen bond occurs. In the crystal, molecules are linked by non-classical C—H...O and C—H...Br hydrogen bonds resulting in a molecular packing in which the brominated rings are in a head-to-head orientation, forming well marked planes parallel to thebaxis.
Crystal structure of (1S,2R,6R,7R,8S,12S)-4,10,17-triphenyl-15-thia-4,10-diazapentacyclo[5.5.5.01,16.02,6.08,12]heptadeca-13,16-diene-3,5,9,11-tetronep-xylene hemisolvate
Authors: Noland Wayland E. , Kroll Neil J. , Huisenga Matthew P. , Yue Ruixian A. , Lang Simon B. , Klein Nathan D. , Tritch Kenneth J.
Published: November 2014

The title tetrone compound, C32H22N2O4S· 0.5C8H10, is the major product (50% yield) of an attempted Diels–Alder reaction of 2-(α-styryl)thiophene withN-phenylmaleimide (2 equivalents) in toluene. Recrystallization of the resulting powder fromp-xylene gave the title hemisolvate; thep-xylene molecule is located about an inversion center. In the crystal, the primary tetrone contacts are between a carbonyl O atom and the four flagpole H atoms of the bicyclo[2.2.2]octene core, forming chains along [001].
About the polymorphism of [Li(C4H8O)3]I: crystal structures of trigonal and tetragonal polymorphs
Authors: Gärtner Stefanie , Gärtner Tobias , Gschwind Ruth-Maria , Korber Nikolaus
Published: November 2014

Two new trigonal and tetragonal polymorphs of the title compound, iodidotris(tetrahydrofuran-κO)lithium, are presented, which both include the isolated ion pair Li(THF)3+·I−. One Li—I ion contact and three tetrahydrofuran (THF) molecules complete the tetrahedral coordination of the lithium cation. The three-dimensional arrangement in the two polymorphs differs notably. In the trigonal structure, the ion pair is located on a threefold rotation axis of space groupP-3 and only one THF molecule is present in the asymmetric unit. In the crystal, strands of ion pairs parallel to [001] are observed with an eclipsed conformation of the THF molecules relative to the Li...I axis of two adjacent ion pairs. In contrast, the tetragonal polymorph shows a much larger unit cell in which all atoms are located on general positions of the space groupI41cd. The resulting three-dimensional arrangement shows helical chains of ion pairs parallel to [001]. Apart from van der Waals contacts, no remarkable intermolecular forces are present between the isolated ion pairs in both structures.
Are earnings quality attributes reflected in financial strength ratings?
Authors: Ames Daniel , S. Hines Chris , Sankara Jomo
Published: November 2014

Purpose

– The purpose of this paper is to examine whether earnings quality attributes are reflected in AM best's financial strength ratings (FSRs), a measure widely used in the insurance industry to assess financial health.

Design/methodology/approach

– Using a sample of insurance companies during the period 2006-2012, the authors measure the quality of reported earnings using three accounting-based measures: earnings persistence, accrual quality, and earnings smoothness.

Findings

– The authors find that better earnings persistence, higher accrual quality, and less earnings smoothing are reflected in higher FSRs for both public and private insurers, with the magnitude of the effect greater for private insurers.

Originality/value

– This is the first study of which the authors are aware that seeks to understand the impact, if any, of variations in the quality of reported financial information on the perceived financial health of firms by ratings agencies in the insurance industry. The authors also include a novel research design in assessing the determinants of financial health ratings. Users of FSRs should be aware of the impact of ownership structure on ratings agencies’ propensity to incorporate reported earnings attributes in their ratings.