bluuebunny/crossref_metadata_2025 huggingface dataset:
Wavelength-scale light concentrator made by direct 3D laser writing of polymer metamaterials
Authors: Moughames J. , Jradi S. , Chan T. M. , Akil S. , Battie Y. , Naciri A. En , Herro Z. , Guenneau S. , Enoch S. , Joly L. , Cousin J. , Bruyant A.
Published: October 2016

We report on the realization of functional infrared light concentrators based on a thick layer of air-polymer metamaterial with controlled pore size gradients. The design features an optimum gradient index profile leading to light focusing in the Fresnel zone of the structures for two selected operating wavelength domains near 5.6 and 10.4 μm. The metamaterial which consists in a thick polymer containing air holes with diameters ranging from λ/20 to λ/8 is made using a 3D lithography technique based on the two-photon polymerization of a homemade photopolymer. Infrared imaging of the structures reveals a tight focusing for both structures with a maximum local intensity increase by a factor of 2.5 for a concentrator volume of 1.5 λ3, slightly limited by the residual absorption of the selected polymer. Such porous and flat metamaterial structures offer interesting perspectives to increase infrared detector performance at the pixel level for imaging or sensing applications.
What determines the interfacial configuration of Nb/Al2O3 and Nb/MgO interface
Authors: Du J. L. , Fang Y. , Fu E. G. , Ding X. , Yu K. Y. , Wang Y. G. , Wang Y. Q. , Baldwin J. K. , Wang P. P. , Bai Q.
Published: October 2016

Nb films are deposited on single crystal Al2O3 (11"Equation missing"0) and MgO(111) substrates by e-beam evaporation technique. Structure of Nb films and orientation relationships (ORs) of Nb/Al2O3 and Nb/MgO interface are studied and compared by the combination of experiments and simulations. The experiments show that the Nb films obtain strong (110) texture, and the Nb film on Al2O3(11"Equation missing"0) substrate shows a higher crystalline quality than that on MgO(111) substrate. First principle calculations show that both the lattice mismatch and the strength of interface bonding play major roles in determining the crystalline perfection of Nb films and ORs between Nb films and single crystal ceramic substrates. The fundamental mechanisms for forming the interfacial configuration in terms of the lattice mismatch and the strength of interface bonding are discussed.
Tunable Surface Plasmon and Phonon Polariton Interactions for Moderately Doped Semiconductor Surfaces
Authors: Janipour Mohsen , Misirlioglu Ibrahim Burc , Sendur Kursat
Published: October 2016

Spatial charge distribution for biased semiconductors fundamentally differs from metals since they can allow inhomogeneous charge distributions due to penetration of the electric field, as observed in the classical Schottky junctions. Similarly, the electrostatics of the dielectric/semiconductor interface can lead to a carrier depletion or accumulation in the semiconductor side when under applied bias. In this study, we demonstrate that the inhomogeneous carrier accumulation in a moderately p-doped GaAs–dielectric interface can be tailored for tunable plasmonics by an external voltage. Solving Maxwell’s equations in the doped GaAs-dielectric stack, we investigate the tunability of the surface plasmon and phonon polaritons’ interaction via an external bias. The plasmonic mode analysis of such an interface reveals interesting dispersion curves for surface plasmon and phonon polariton interactions that are not possible in metals. We show that the plasmon dispersion curve can be engineered through an external bias using the inherent properties of the p-doped GaAs– dielectric interface.
Three representations of the Ising model
Authors: Kruis Joost , Maris Gunter
Published: October 2016

Statistical models that analyse (pairwise) relations between variables encompass assumptions about the underlying mechanism that generated the associations in the observed data. In the present paper we demonstrate that three Ising model representations exist that, although each proposes a distinct theoretical explanation for the observed associations, are mathematically equivalent. This equivalence allows the researcher to interpret the results of one model in three different ways. We illustrate the ramifications of this by discussing concepts that are conceived as problematic in their traditional explanation, yet when interpreted in the context of another explanation make immediate sense.
Intravital imaging reveals improved Kupffer cell-mediated phagocytosis as a mode of action of glycoengineered anti-CD20 antibodies
Authors: Grandjean Capucine L. , Montalvao Fabricio , Celli Susanna , Michonneau David , Breart Beatrice , Garcia Zacarias , Perro Mario , Freytag Olivier , Gerdes Christian A. , Bousso Philippe
Published: October 2016

Anti-CD20 monoclonal antibodies (mAbs) represent an effective treatment for a number of B cell malignancies and autoimmune disorders. Glycoengineering of anti-CD20mAb may contribute to increased anti-tumor efficacy through enhanced antibody-dependent cellular cytotoxicity (ADCC) and phagocytosis (ADP) as reported by in vitro studies. However, where and how glycoengineered Ab may potentiate therapeutic responses in vivo is yet to be elucidated. Here, we have performed mouse liver transplants to demonstrate that the liver is sufficient to mediate systemic B cells depletion after anti-CD20 treatment. Relying on intravital two-photon imaging of human CD20-expressing mice, we provide evidence that ADP by Kupffer cells (KC) is a major mechanism for rituximab-mediated B cell depletion. Notably, a glycoengineered anti-mouse CD20 Ab but not its wild-type counterpart triggered potent KC-mediated B cell depletion at low doses. Finally, distinct thresholds for KC phagocytosis were also observed for GA101 (obinutuzumab), a humanized glycoengineered type II anti-CD20 Ab and rituximab. Thus, we propose that enhanced phagocytosis of circulating B cells by KC represents an important in vivo mechanism underlying the improved activity of glycoengineered anti-CD20 mAbs.
Photodynamic N-TiO2 Nanoparticle Treatment Induces Controlled ROS-mediated Autophagy and Terminal Differentiation of Leukemia Cells
Authors: Moosavi Mohammad Amin , Sharifi Maryam , Ghafary Soroush Moasses , Mohammadalipour Zahra , Khataee Alireza , Rahmati Marveh , Hajjaran Sadaf , Łos Marek J. , Klonisch Thomas , Ghavami Saeid
Published: October 2016

In this study, we used nitrogen-doped titanium dioxide (N-TiO2) NPs in conjugation with visible light, and show that both reactive oxygen species (ROS) and autophagy are induced by this novel NP-based photodynamic therapy (PDT) system. While well-dispersed N-TiO2 NPs (≤100 μg/ml) were inert, their photo-activation with visible light led to ROS-mediated autophagy in leukemia K562 cells and normal peripheral lymphocytes, and this increased in parallel with increasing NP concentrations and light doses. At a constant light energy (12 J/cm2), increasing N-TiO2 NP concentrations increased ROS levels to trigger autophagy-dependent megakaryocytic terminal differentiation in K562 cells. By contrast, an ROS challenge induced by high N-TiO2 NP concentrations led to autophagy-associated apoptotic cell death. Using chemical autophagy inhibitors (3-methyladenine and Bafilomycin A1), we confirmed that autophagy is required for both terminal differentiation and apoptosis induced by photo-activated N-TiO2. Pre-incubation of leukemic cells with ROS scavengers muted the effect of N-TiO2 NP-based PDT on cell fate, highlighting the upstream role of ROS in our system. In summary, PDT using N-TiO2 NPs provides an effective method of priming autophagy by ROS induction. The capability of photo-activated N-TiO2 NPs in obtaining desirable cellular outcomes represents a novel therapeutic strategy of cancer cells.
Histone acetylation dependent energy landscapes in tri-nucleosome revealed by residue-resolved molecular simulations
Authors: Chang Le , Takada Shoji
Published: October 2016

Histone tail acetylation is a key epigenetic marker that tends to open chromatin folding and activate transcription. Despite intensive studies, precise roles of individual lysine acetylation in chromatin folding have only been poorly understood. Here, we revealed structural dynamics of tri-nucleosomes with several histone tail acetylation states and analyzed histone tail interactions with DNA by performing molecular simulations at an unprecedentedly high resolution. We found versatile acetylation-dependent landscapes of tri-nucleosome. The H4 and H2A tail acetylation reduced the contact between the first and third nucleosomes mediated by the histone tails. The H3 tail acetylation reduced its interaction with neighboring linker DNAs resulting in increase of the distance between consecutive nucleosomes. Notably, two copies of the same histone in a single nucleosome have markedly asymmetric interactions with DNAs, suggesting specific pattern of nucleosome docking albeit high inherent flexibility. Estimated transcription factor accessibility was significantly high for the H4 tail acetylated structures.
Hierarchical phosphorylation of apical membrane antigen 1 is required for efficient red blood cell invasion by malaria parasites
Authors: Prinz Boris , Harvey Katherine L. , Wilcke Louisa , Ruch Ulrike , Engelberg Klemens , Biller Laura , Lucet Isabelle , Erkelenz Steffen , Heincke Dorothee , Spielmann Tobias , Doerig Christian , Kunick Conrad , Crabb Brendan S. , Gilson Paul R. , Gilberger Tim W.
Published: October 2016

Central to the pathogenesis of malaria is the proliferation of Plasmodium falciparum parasites within human erythrocytes. Parasites invade erythrocytes via a coordinated sequence of receptor-ligand interactions between the parasite and host cell. One key ligand, Apical Membrane Antigen 1 (AMA1), is a leading blood-stage vaccine and previous work indicates that phosphorylation of its cytoplasmic domain (CPD) is important to its function during invasion. Here we investigate the significance of each of the six available phospho-sites in the CPD. We confirm that the cyclic AMP/protein kinase A (PKA) signalling pathway elicits a phospho-priming step upon serine 610 (S610), which enables subsequent phosphorylation in vitro of a conserved, downstream threonine residue (T613) by glycogen synthase kinase 3 (GSK3). Both phosphorylation steps are required for AMA1 to function efficiently during invasion. This provides the first evidence that the functions of key invasion ligands of the malaria parasite are regulated by sequential phosphorylation steps.
TM4 of the glutamate transporter GLT-1 experiences substrate-induced motion during the transport cycle
Authors: Rong Xiuliang , Tan Feng , Wu Xiaojuan , Zhang Xiuping , Lu Lingli , Zou Xiaoming , Qu Shaogang
Published: October 2016

Excitatory amino acid transporter 2 (EAAT2), also known as glial glutamate transporter type 1 (GLT-1), plays an important role in maintaining the extracellular glutamate concentrations below neurotoxic levels. The highly conserved TM2 transmembrane domain of GLT-1 maintains a stable position during the transport cycle; however, the effect of the transport cycle on the topology of TM4 in not well established. To further reveal the function of TM4, two cysteine pairs between TM2 and TM4 were introduced using site-directed mutagenesis. A significant decrease of transport activity was observed in the I93C/V241C and I97C/V241C mutants upon application of the oxidative cross-linking reagent, copper (II) (1,10-phenanthroline)3 (CuPh), which suggests that a conformational shift is essential for transporter activity. Furthermore, the decrease in activity by CuPh crosslinking was enhanced in external media with glutamate or potassium, which suggests that TM2 and TM4 assume closer proximity in the inward-facing conformation of the transporter. Our results suggest that the TM4 domain of GLT-1 and potentially other glutamate transporters, undergoes a complex conformational shift during substrate translocation, which involves an increase in the proximity of the TM2 and TM4 domains in the inward-facing conformation.
Smartphone-Based Accurate Analysis of Retinal Vasculature towards Point-of-Care Diagnostics
Authors: Xu Xiayu , Ding Wenxiang , Wang Xuemin , Cao Ruofan , Zhang Maiye , Lv Peilin , Xu Feng
Published: October 2016

Retinal vasculature analysis is important for the early diagnostics of various eye and systemic diseases, making it a potentially useful biomarker, especially for resource-limited regions and countries. Here we developed a smartphone-based retinal image analysis system for point-of-care diagnostics that is able to load a fundus image, segment retinal vessels, analyze individual vessel width, and store or uplink results. The proposed system was not only evaluated on widely used public databases and compared with the state-of-the-art methods, but also validated on clinical images directly acquired with a smartphone. An Android app is also developed to facilitate on-site application of the proposed methods. Both visual assessment and quantitative assessment showed that the proposed methods achieved comparable results to the state-of-the-art methods that require high-standard workstations. The proposed system holds great potential for the early diagnostics of various diseases, such as diabetic retinopathy, for resource-limited regions and countries.
The pioneering role of PRDM9 indel mutations in tarsier evolution
Authors: Heerschop Sacha , Zischler Hans , Merker Stefan , Perwitasari-Farajallah Dyah , Driller Christine
Published: October 2016

PRDM9 is currently the sole speciation gene found in vertebrates causing hybrid sterility probably due to incompatible alleles. Its role in defining the double strand break loci during the meiotic prophase I is crucial for proper chromosome segregation. Therefore, the rapid turnover of the loci determining zinc finger array seems to be causative for incompatibilities. We here investigated the zinc finger domain-containing exon of PRDM9 in 23 tarsiers. Tarsiers, the most basal extant haplorhine primates, exhibit two frameshifting indels at the 5′-end of the array. The first mutation event interrupts the reading frame and function while the second compensates both. The fixation of this allele variant in tarsiers led to hypothesize that de- and reactivation of the zinc finger domain drove the speciation in early haplorhine or tarsiiform primates. Moreover, the high allelic diversity within Tarsius points to multiple effects of genetic drift reflecting their phylogeographic history since the Miocene.
Microbial Degradation of Cellular Kinases Impairs Innate Immune Signaling and Paracrine TNFα Responses
Authors: Barth Kenneth , Genco Caroline Attardo
Published: October 2016

The NFκB and MAPK signaling pathways are critical components of innate immunity that orchestrate appropriate immune responses to control and eradicate pathogens. Their activation results in the induction of proinflammatory mediators, such as TNFα a potent bioactive molecule commonly secreted by recruited inflammatory cells, allowing for paracrine signaling at the site of an infection. In this study we identified a novel mechanism by which the opportunistic pathogen Porphyromonas gingivalis dampens innate immune responses by disruption of kinase signaling and degradation of inflammatory mediators. The intracellular immune kinases RIPK1, TAK1, and AKT were selectively degraded by the P. gingivalis lysine-specific gingipain (Kgp) in human endothelial cells, which correlated with dysregulated innate immune signaling. Kgp was also observed to attenuate endothelial responsiveness to TNFα, resulting in a reduction in signal flux through AKT, ERK and NFκB pathways, as well as a decrease in downstream proinflammatory mRNA induction of cytokines, chemokines and adhesion molecules. A deficiency in Kgp activity negated decreases to host cell kinase protein levels and responsiveness to TNFα. Given the essential role of kinase signaling in immune responses, these findings highlight a unique mechanism of pathogen-induced immune dysregulation through inhibition of cell activation, paracrine signaling, and dampened cellular proinflammatory responses.
A crucial role for spatial distribution in bacterial quorum sensing
Authors: Gao Meng , Zheng Huizhen , Ren Ying , Lou Ruyun , Wu Fan , Yu Weiting , Liu Xiudong , Ma Xiaojun
Published: October 2016

Quorum sensing (QS) is a process that enables bacteria to communicate using secreted signaling molecules, and then makes a population of bacteria to regulate gene expression collectively and control behavior on a community-wide scale. Theoretical studies of efficiency sensing have suggested that both mass-transfer performance in the local environment and the spatial distribution of cells are key factors affecting QS. Here, an experimental model based on hydrogel microcapsules with a three-dimensional structure was established to investigate the influence of the spatial distribution of cells on bacterial QS. Vibrio harveyi cells formed different spatial distributions in the microcapsules, i.e., they formed cell aggregates with different structures and sizes. The cell aggregates displayed stronger QS than did unaggregated cells even when equal numbers of cells were present. Large aggregates (LA) of cells, with a size of approximately 25 μm, restricted many more autoinducers (AIs) than did small aggregates (SA), with a size of approximately 10 μm, thus demonstrating that aggregate size significantly affects QS. These findings provide a powerful demonstration of the fact that the spatial distribution of cells plays a crucial role in bacterial QS.
One-Pot Approach to Prepare Organo-silica Hybrid Capillary Monolithic Column with Intact Mesoporous Silica Nanoparticle as Building Block
Authors: Liu Shengju , Peng Jiaxi , Liu Zheyi , Liu Zhongshan , Zhang Hongyan , Wu Ren’an
Published: October 2016

A facile “one-pot” approach to prepare organo-silica hybrid capillary monolithic column with intact mesoporous silica nanoparticle (IMSN) as crosslinker and building block was described. An IMSN crosslinked octadecyl-silica hybrid capillary monolithic column (IMSN-C18 monolithic column) was successfully prepared, and the effects of fabrication conditions (e.g. concentration of intact mesoporous silica nanoparticle, polycondensation temperature, content of vinyltrimethoxysilane and stearyl methacrylate) on the structures of the IMSN-C18 monolithic column were studied in detail. The IMSN-C18 hybrid monolithic column possessed uniform morphology, good mechanical and pH stability (pH 1.1–11), which was applied to the separations of alkyl benzenes, polycyclic aromatic hydrocarbons (PAHs), as well as proteins. The minimum plate height of 10.5 μm (corresponding to 95000 N m−1) for butylbenzene and high reproducibility were achieved. The analysis of tryptic digest of bovine serum albumin (BSA) was carried out on the IMSN-C18 monolithic column by cLC coupled mass spectrometry (cLC-MS/MS), with the protein sequence coverage of 87.5% for BSA, demonstrating its potential application in proteomics.
Prediction of phosphothreonine sites in human proteins by fusing different features
Authors: Zhao Ya-Wei , Lai Hong-Yan , Tang Hua , Chen Wei , Lin Hao
Published: October 2016

Phosphorylation is one of the most important protein post-translation modifications. With the rapid development of high-throughput mass spectrometry, phosphorylation site data is rapidly accumulating, which provides us an opportunity to systematically investigate and predict phosphorylation in proteins. The phosphorylation of threonine is the addition of a phosphoryl group to its polar side chains group. In this work, we statistically analyzed the distribution of the different properties including position conservation, secondary structure, accessibility and some other physicochemical properties of the residues surrounding the phosphothreonine site and non-phosphothreonine site. We found that the distributions of those features are non-symmetrical. Based on the distribution of properties, we developed a new model by using optimal window size strategy and feature selection technique. The cross-validated results show that the area under receiver operating characteristic curve reaches to 0.847, suggesting that our model may play a complementary role to other existing methods for predicting phosphothreonine site in proteins.
Water stability of self-assembled peptide nanostructures for sequential formation of two-dimensional interstitial patterns on layered materials
Authors: Sun Linhao , Narimatsu Takuma , Tsuchiya Shohei , Tanaka Tomohiro , Li Peiying , Hayamizu Yuhei
Published: October 2016

Sequential-assembly of LEY and GrBP5 peptides on a graphite surface.
Language of mechanisms: exam analysis reveals students' strengths, strategies, and errors when using the electron-pushing formalism (curved arrows) in new reactions
Authors: Flynn Alison B. , Featherstone Ryan B.
Published: October 2016

This study investigated students' successes, strategies, and common errors in their answers to questions that involved the electron-pushing (curved arrow) formalism (EPF), part of organic chemistry's language. We analyzed students' answers to two question types on midterms and final exams: (1) draw the electron-pushing arrows of a reaction step, given the starting materials and products; and (2) draw the products of a reaction step, given the starting materials and electron-pushing arrows. For both question types, students were given unfamiliar reactions. The goal was for students to gain proficiency—or fluency—using and interpreting the EPF. By first becoming fluent, students should have lower cognitive load demands when learning subsequent concepts and reactions, positioning them to learn more deeply. Students did not typically draw reversed or illogical arrows, but there were many other error types. Scores on arrows questions were significantly higher than on products questions. Four factors correlated with lower question scores, including: compounds bearing implicit atoms, intramolecular reactions, assessment year, and the conformation of reactants drawn on the page. We found little evidence of analysis strategies such as expanding or mapping structures. We also found a new error type that we describe as picking up electrons and setting them down on a different atom. These errors revealed the difficulties that arose even before the students had to consider the chemical meaning and implications of the reactions. Herein, we describe our complete findings and suggestions for instruction, including videos that we created to teach the EPF.
Pervasive assistive technology for people with dementia: a UCD case
Authors: Thorpe Julia Rosemary , R⊘nn‐Andersen Kristoffer V.H. , Bień Paulina , Özkil Ali Gürcan , Forchhammer Birgitte Hysse , Maier Anja M.
Published: October 2016

Smart mobile and wearable technology offers exciting opportunities to support people with dementia (PwD). Its ubiquity and popularity could even benefit user adoption – a great challenge for assistive technology (AT) for PwD that calls for user‐centred design (UCD) methods. This study describes a user‐centred approach to developing and testing AT based on off‐the‐shelf pervasive technologies. A prototype is created by combining a smartphone, smartwatch and various applications to offer six support features. This is tested among five end‐users (PwD) and their caregivers. Controlled usability testing was followed by field testing in a real‐world context. Data is gathered from video recordings, interaction logs, system usability scale questionnaires, logbooks, application usage logs and interviews structured on the unified theory of acceptance and use of technology model. The data is analysed to evaluate usability, usefulness and user acceptance. Results show some promise for user adoption, but highlight challenges to be overcome, emphasising personalisation and familiarity as key considerations. The complete findings regarding usability issues, usefulness of support features and four identified adoption profiles are used to provide a set of recommendations for practitioners and further research. These contribute toward UCD practices for improved smart, pervasive AT for dementia.
Impact of the Ile105Val Polymorphism of the Glutathione S-transferase P1 (GSTP1) Gene on Obesity and Markers of Cardiometabolic Risk in Young Adult Population
Authors: Chielle E. , Trott A. , da Silva Rosa B. , Casarin J. , Fortuna P. , da Cruz I. , Moretto M. , Moresco R.
Published: October 2016

The aim of the study was to investigate the association between Glutathione S-transferase P1 (GSTP1) gene polymorphism with obesity and markers of cardiometabolic risk. A cross-sectional study was carried out in individuals aged≥18 and ≤30 years. The study included 54 normal weight, 27 overweight and 68 obese volunteers. Anthropometric measurements and biochemical parameters were evaluated, the DNA was extracted from blood samples and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to measure GSTP1 Ile105Val gene polymorphism of the study participants. Also, biochemical analysis and hormone assays were carried out. A positive association between GSTP1 polymorphism and obesity was observed on subjects carrying at least one G allele (AG and GG). GG genotype was found only in the obese group. The G allele carriers presented 2.4 times higher chance of obesity when compared to those with the AA genotype. These results were independent of sex and age. We suggest that despite a study in population regional (south of Brazil), the GSTP1 gene polymorphism may play a significant role in the increase of susceptibility of obesity and contribute to identify the cardiovascular risk in young adults.
Drag measurements in laterally confined 2D canopies: Reconfiguration and sheltering effect
Authors: Barsu Sylvie , Doppler Delphine , Jerome J. John Soundar , Rivière Nicolas , Lance Michel
Published: October 2016

Plants in aquatic canopies deform when subjected to a water flow and so, unlike a rigid bluff body, the resulting drag force FD grows sub-quadratically with the flow velocity Ū. In this article, the effect of density on the canopy reconfiguration and the corresponding drag reduction is experimentally investigated for simple 2D synthetic canopies in an inclinable, narrow water channel. The drag acting on the canopy, and also on individual sheets, is systematically measured via two independent techniques. Simultaneous drag and reconfiguration measurements demonstrate that data for different Reynolds numbers (400–2200), irrespective of sheet width (w) and canopy spacing (ℓ), collapse on a unique curve given by a bending beam model which relates the reconfiguration number and a properly rescaled Cauchy number. Strikingly, the measured Vogel exponent V and hence the drag reduction via reconfiguration is found to be independent of the spacing between sheets and the lateral confinement; only the drag coefficient decreases linearly with the sheet spacing since a strong sheltering effect exists as long as the spacing is smaller than a critical value depending on the sheet width.
Spatial instability of viscous double-layer liquid sheets
Authors: Ye Han-Yu , Yang Li-Jun , Fu Qing-Fei
Published: October 2016

This paper investigates the spatial instability of a double-layer viscous liquid sheet moving in a stationary gas medium. A linear stability analysis is conducted and two situations are considered, an inviscid-gas situation and a viscous-gas situation. In the inviscid-gas situation, the basic state of the entire gas phase is stationary and the analytical dispersion relation is derived. Similar to single-layer sheets, the instability of double-layer sheets presents two unstable modes, the sinuous and the varicose modes. However, the result of the base-case double-layer sheet indicates that the cutoff wavenumber of the dispersion curve is larger than that of a single-layer sheet. A decomposition of the growth rate is performed and the result shows that for small wavenumbers, the surface tension of all three interfaces and the aerodynamic forces of both the lower and upper gases contribute significantly to the unstable growth rate. In contrast, for large wavenumbers the major contribution to the unstable growth rate is only the surface tension of the upper interface and the aerodynamic force of the upper gas. In the viscous-gas situation, although the majority of the gas phase is stationary, gas boundary layers exist at the vicinity of the moving liquid sheet, and the stability problem is solved by a spectral collocation method. Compared with the inviscid-gas solution, the growth rate at large wavenumber is significantly suppressed. The decomposition of growth rate indicates that all the aerodynamic and surface tension terms behave consistently throughout the entire unstable wavenumber range. The effects of various parameters are discussed. In addition, the effect of gas viscosity and the gas velocity profile is investigated separately, and the results indicate that both factors affect the maximum growth rate and the dominant wavenumber, although the effect of the gas velocity profile is stronger than that of the gas viscosity.
Structural analysis of liquid aluminum at high pressure and high temperature using the hard sphere model
Authors: Ikuta Daijo , Kono Yoshio , Shen Guoyin
Published: October 2016

The structure of liquid aluminum is measured up to 6.9 GPa and 1773 K using a multi-angle energy-dispersive X-ray diffraction method in a Paris-Edinburgh press. The effect of pressure and temperature on the structure and density of liquid aluminum is analyzed by means of the hard sphere model. Peak positions in the structure factor of liquid aluminum show a nearly constant value with varying temperatures at ∼1–2 GPa and slightly change with varying pressures up to 6.9 GPa at 1173–1773 K. In contrast, the height of the first peak in the structure factor significantly changes with varying pressures and temperatures. Hard sphere model analysis shows that the structure of liquid aluminum in the pressure-temperature range of this study is controlled mostly by the packing fraction with only a minor change in hard sphere diameters. The obtained packing fractions and hard sphere diameters are used to calculate densities of liquid aluminum at high pressure-temperature conditions.
The rheo-Raman microscope: Simultaneous chemical, conformational, mechanical, and microstructural measures of soft materials
Authors: Kotula Anthony P. , Meyer Matthew W. , De Vito Francesca , Plog Jan , Hight Walker Angela R. , Migler Kalman B.
Published: October 2016

The design and performance of an instrument capable of simultaneous Raman spectroscopy, rheology, and optical microscopy are described. The instrument couples a Raman spectrometer and optical microscope to a rotational rheometer through an optically transparent base, and the resulting simultaneous measurements are particularly advantageous in situations where flow properties vary due to either chemical or conformational changes in molecular structure, such as in crystallization, melting, gelation, or curing processes. Instrument performance is demonstrated on two material systems that show thermal transitions. First, we perform steady state rotational tests, Raman spectroscopy, and polarized reflection microscopy during a melting transition in a cosmetic emulsion. Second, we perform small amplitude oscillatory shear measurements along with Raman spectroscopy and polarized reflection microscopy during crystallization of a high density polyethylene. The instrument can be applied to study structure-property relationships in a variety of soft materials including thermoset resins, liquid crystalline materials, colloidal suspensions undergoing sol-gel processes, and biomacromolecules. Official contribution of the National Institute of Standards and Technology; not subject to copyright in the United States.
Choline and betaine ameliorate liver lipid accumulation induced by vitamin B6 deficiency in rats
Authors: Kitagawa Erina , Yamamoto Tatsuya , Fujishita Mayuko , Ota Yuki , Yamamoto Kohei , Nakagawa Tomoyuki , Hayakawa Takashi
Published: October 2016

We investigated the efficacy of supplementing the diet with choline or betaine in ameliorating lipid accumulation induced by vitamin B6 (B6) deficiency in rat liver. Male Wistar rats were fed a control, B6-deficient, choline-supplemented (2, 4, or 6 g choline bitartrate/kg diet) B6-deficient diet or betaine-supplemented (1, 2, or 4 g betaine anhydrous/kg diet) B6-deficient diet for 35 d; all diets contained 9 g l-methionine (Met)/kg diet. Choline or betaine supplementation attenuated liver lipid deposition and restored plasma lipid profiles to control levels. These treatments restored the disruptions in Met metabolism and the phosphatidylcholine (PC)/phosphatidylethanolamine (PE) ratio induced by B6 deficiency in liver microsomes. These results suggest that choline and betaine ameliorated liver lipid accumulation induced by B6 deficiency via recovery of Met metabolism and very low-density lipoprotein secretion by restoring the supply of PC derived from PE.
PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL
Authors: Janson Giacomo , Zhang Chengxin , Prado Maria Giulia , Paiardini Alessandro
Published: October 2016

Motivation

The recently released PyMod GUI integrates many of the individual steps required for protein sequence-structure analysis and homology modeling within the interactive visualization capabilities of PyMOL. Here we describe the improvements introduced into the version 2.0 of PyMod.

Results

The original code of PyMod has been completely rewritten and improved in version 2.0 to extend PyMOL with packages such as Clustal Omega, PSIPRED and CAMPO. Integration with the popular web services ESPript and WebLogo is also provided. Finally, a number of new MODELLER functionalities have also been implemented, including SALIGN, modeling of quaternary structures, DOPE scores, disulfide bond modeling and choice of heteroatoms to be included in the final model.

Availability and Implementation

PyMod 2.0 installer packages for Windows, Linux and Mac OS X and user guides are available at http://schubert.bio.uniroma1.it/pymod/index.html. The open source code of the project is hosted at https://github.com/pymodproject/pymod.
Distribution characteristics of coronal electric current density as an indicator for the occurrence of a solar flare
Authors: Kang Jihye , Magara Tetsuya , Inoue Satoshi , Kubo Yuki , Nishizuka Naoto
Published: October 2016

In this paper we investigate the distribution characteristics of the coronal electric current density in a flare-producing active region (AR12158; SOL2014-09-10) by reconstructing nonlinear force-free (NLFF) fields from photospheric magnetic field data. A time series of NLFF fields shows the spatial distribution and its temporal development of coronal current density in this active region. A fractal dimensional analysis shows that a concentrated coronal current forms a structure of fractal spatiality. Furthermore, the distribution function of coronal current density is featured with a double power-law profile, and the value of electric current density at the breaking point of a double power-law fitting function shows a noticeable time variation toward the onset of an X-class flare. We discuss that this quantity will be a useful indicator for the occurrence of a flare.
News Shocks in Open Economies: Evidence from Giant Oil Discoveries*
Authors: Arezki Rabah , Ramey Valerie A. , Sheng Liugang
Published: October 2016

This article explores the effect of news shocks in open economies using worldwide giant oil and gas discoveries as a directly observable measure of news shocks about future output—the delay between a discovery and production is on average four to six years. We first analyze the effects of a discovery in a two-sector small open economy model with a resource sector. We then estimate the effects of giant oil and gas discoveries on a large panel of countries. Our empirical estimates are consistent with the predictions of the model. After an oil or gas discovery, the current account and saving rate decline for the first five years and then rise sharply during the ensuing years. Investment rises robustly soon after the news arrives, whereas GDP does not increase until after five years. Employment rates fall slightly and remain low for a sustained period.
Estrogen alone and health outcomes in black women by African ancestry: a secondary analyses of a randomized controlled trial
Authors: Chlebowski Rowan T. , Barrington Wendy , Aragaki Aaron K. , Manson JoAnn E. , Sarto Gloria , O'Sullivan Mary J. , Wu Daniel , Cauley Jane A. , Qi Lihong , Wallace Robert L. , Prentice Ross L.
Published: October 2016

Objective:

In postmenopausal black women in the Women's Health Initiative randomized trial, estrogen alone reduced breast cancers but its comprehensive influence on health outcomes in black women is unknown. Therefore, we examined this issue in the Women's Health Initiative overall and by African ancestry.

Methods:

A total of 1,616 black women with prior hysterectomy, including 1,061 with percent African ancestry determination, at 40 US centers were randomly assigned to conjugated equine estrogen (0.625 mg/d) or placebo for 7.2 years’ (median) intervention with 13 years’ cumulative follow-up. Coronary heart disease (CHD) and breast cancer were primary efficacy and safety outcomes, respectively. A global index also included stroke, colorectal cancer, hip fracture, pulmonary embolism, and death.

Results:

Black women in the estrogen-alone group compared with black women in the placebo group had fewer breast cancers (17 vs 40, hazard ratio [HR] 0.47, 95% CI 0.26-0.82). In women with more than 80% African ancestry, breast cancer HR was lower (0.32, 95% CI 0.12-0.86, trend P = 0.04 for ancestry effect). Most other outcomes including CHD, stroke, hip fracture, and the global index were null with estrogen use in black women; a global index effect was more favorable in younger black women (HR 0.65, 95% CI 0.43-0.98).

Conclusions:

In black postmenopausal women with prior hysterectomy, estrogen alone significantly reduced breast cancer incidence with no adverse influence on CHD, venous thromboembolism, or all-cause mortality. Favorable estrogen-alone global index effects in younger black women warrant further study.
Increased expression of progesterone receptor membrane component 1 is associated with aggressive phenotype and poor prognosis in ER-positive and negative breast cancer
Authors: Ruan Xiangyan , Zhang Ying , Mueck Alfred O. , Willibald Marina , Seeger Harald , Fehm Tanja , Brucker Sara , Neubauer Hans
Published: October 2016

Objective:

Expression of progesterone receptor membrane component 1 (PGRMC1) has been shown to be higher in breast cancer than normal tissue. We have previously shown that certain progestogens strongly stimulate proliferation of breast cancer cells overexpressing PGRMC1, and therefore hypothesize that PGRMC1 may play a critical role in breast cancer progression. Because little information is available if expression of PGRMC1 is also associated with worse prognosis for breast cancer patients, in this study we investigated the clinicopathologic significance of PGRMC1 expression in breast cancer tissue.

Methods:

Expression of PGRMC1 was analyzed by immunohistochemical staining of primary tumor tissues obtained from 69 breast cancer patients. A labeling score was developed, and results were correlated with tumor size, lymph node metastasis, and clinical outcome.

Results:

Overexpression of PGRMC1 is correlating with larger tumor size and lymph node metastasis. Kaplan-Meier survival curves indicate that patients with PGRMC1hightumors have poorer disease-free and overall survival independent from the estrogen receptor status than breast cancer patients with PGRMC1lowtumors.

Conclusions:

Our findings suggest that the expression of PGRMC1 might be useful for predicting prognosis in patients with breast cancer.
Bioavailable insulin-like growth factor-I as mediator of racial disparity in obesity-relevant breast and colorectal cancer risk among postmenopausal women
Authors: Jung Su Yon , Barrington Wendy E. , Lane Dorothy S. , Chen Chu , Chlebowski Rowan , Corbie-Smith Giselle , Hou Lifang , Zhang Zuo-Feng , Paek Min-So , Crandall Carolyn J.
Published: October 2016

Objective:

Bioavailable insulin-like growth factor-I (IGF-I) interacts with obesity and exogenous estrogen (E) in a racial disparity in obesity-related cancer risk, yet their interconnected pathways are not fully characterized. We investigated whether circulating bioavailable IGF-I acted as a mediator of the racial disparity in obesity-related cancers such as breast and colorectal (CR) cancers and how obesity and E use regulate this relationship.

Methods:

A total of 2,425 white and 164 African American (AA) postmenopausal women from the Women's Health Initiative Observational Study were followed from October 1, 1993 through August 29, 2014. To assess bioactive IGF-I as a mediator of race-cancer relationship, we used the Baron-Kenny method and quantitative estimation of the mediation effect.

Results:

Compared with white women, AA women had higher IGF-I levels; their higher risk of CR cancer, after accounting for IGF-I, was no longer significant. IGF-I was associated with breast and CR cancers even after controlling for race. Among viscerally obese (waist/hip ratio >0.85) and overall nonobese women (body mass index <30), IGF-I was a strong mediator, reducing the racial disparity in both cancers by 30% and 60%, respectively. In E-only users and nonusers, IGF-I explained the racial disparity in CR cancer only modestly.

Conclusions:

Bioavailable IGF-I is potentially important in racial disparities in obesity-related breast and CR cancer risk between postmenopausal AA and white women. Body fat distribution and E use may be part of the interconnected hormonal pathways related to racial difference in IGF-I levels and obesity-related cancer risk.
A Case of Child Physical Abuse With a Rolling Pin Insertion, Resulting in Bladder and Rectal Perforation
Authors: Kondolot Meda , Doganay Selim , Turan Cüneyt , Asil Hasim , Oztop Didem B. , Ozdemir Caglar
Published: October 2016

Visceral injuries are not uncommon in nonaccidental trauma and often require emergent operative intervention. However, sometimes it can be difficult to assess the extent of injury. In this report, we present a case of child physical abuse resulting in bladder and rectal perforations, which was initially referred to our hospital as acute abdomen with intraperitoneal free fluid on ultrasonography. An exploratory laparotomy revealed the perforations and surgical repair was performed. The patient was evaluated by the Hospital Child Protective team and it was revealed that bladder and rectum perforations were due to insertion of rolling pin into the rectum by the stepmother. The child was discharged home uneventfully with a temporary colostomy. We believe that this is the first reported case in the English literature of inflicted perforation of the rectum and bladder through insertion of a rolling pin.
Prevalence of Abuse Among Young Children With Rib Fractures
Authors: Paine Christine Weirich , Fakeye Oludolapo , Christian Cindy W. , Wood Joanne N.
Published: October 2016

Objectives

We aimed to estimate the prevalence of abuse in young children presenting with rib fractures and to identify demographic, injury, and presentation-related characteristics that affect the probability that rib fractures are secondary to abuse.

Methods

We searched PubMed/MEDLINE and CINAHL databases for articles published in English between January 1, 1990, and June 30, 2014 on rib fracture etiology in children 5 years or younger. Two reviewers independently extracted predefined data elements and assigned quality ratings to included studies. Study-specific abuse prevalences and the sensitivities, specificities, and positive and negative likelihood ratios of patients' demographic and clinical characteristics for abuse were calculated with 95% confidence intervals.

Results

Data for 1396 children 48 months or younger with rib fractures were abstracted from 10 articles. Among infants younger than 12 months, abuse prevalence ranged from 67% to 82%, whereas children 12 to 23 and 24 to 35 months old had study-specific abuse prevalences of 29% and 28%, respectively. Age younger than 12 months was the only characteristic significantly associated with increased likelihood of abuse across multiple studies. Rib fracture location was not associated with likelihood of abuse. The retrospective design of the included studies and variations in ascertainment of cases, inclusion/exclusion criteria, and child abuse assessments prevented further meta-analysis.

Conclusions

Abuse is the most common cause of rib fractures in infants younger than 12 months. Prospective studies with standardized methods are needed to improve accuracy in determining abuse prevalence among children with rib fractures and characteristics associated with abusive rib fractures.
Presentation of Acute Childhood Stroke in a Tertiary Pediatric Emergency Department
Authors: Yock-Corrales Adriana , Varela-Bulgarelli Flory , Barboza Cary , Gutierrez-Mata Alfonso , Mackay Mark T. , Babl Franz
Published: October 2016

Objectives

The aim was to describe clinical presentation, management, and outcomes of stroke in a tertiary emergency department (ED) of a developing country.

Methodology

Retrospective case series of patients aged 1 month to 18 years presenting to an ED with radiological confirmed acute stroke during a 7-year period were studied.

Results

Ninety-five patients were identified. Twenty-five patients were excluded because of incomplete records (8) or not presenting via ED (17). Thirty-four (48.5%) were diagnosed with hemorrhagic stroke (HS), 30 (42.8%) with arterial ischemic stroke (AIS), and 6 (8.5%) with sinus venous thrombosis (SVT). Mean age was 5.3 years, and 55.3% were male. The median time from onset of symptoms to ED presentation was 24 hours (mean, 55 hours; interquartile range [IQR], 14–72) for AIS, 24 hours (mean, 46.9 hours; IQR, 9–48) for HS, and 120 hours (mean,112 hours; IQR, 72–168) for SVT. Congenital cardiac disease was the most common risk factor (9%). For AIS, the most common symptoms were focal numbness 56.6% (95% confidence interval [CI], 37.8%–75.4%), focal weakness 56.6% (95% CI, 37.8%–75.4%), and seizures 50% (95% CI, 31%–68.8%). For HS, the most common symptoms were headache 64.7% (95% CI, 47.7%–81.6%), vomiting 79.4 (95% CI, 65–93.7), and altered mental status 64.7% (95% CI, 47.7–81.6). Computed tomography scan was done in 100% of the patients and magnetic resonance imaging in 54%. Twenty-five (36%) patients were admitted to intensive care unit and required intubation. Long-term deficit was identified in 24 (36%) patients based on medium-term follow-up.

Conclusions

The spectrum of stroke in a developing country was similar to published series from developed countries in terms of final diagnosis, risk factors, and delay to ED presentation, neuroimaging, and long-term neurodeficits. No tropical diseases were identified as risk factors.
Improved insights into protein thermal stability: from the molecular to the structurome scale
Authors: Pucci Fabrizio , Rooman Marianne
Published: October 2016

Despite the intense efforts of the last decades to understand the thermal stability of proteins, the mechanisms responsible for its modulation still remain debated. In this investigation, we tackle this issue by showing how a multiscale perspective can yield new insights. With the help of temperature-dependent statistical potentials, we analysed some amino acid interactions at the molecular level, which are suggested to be relevant for the enhancement of thermal resistance. We then investigated the thermal stability at the protein level by quantifying its modification upon amino acid substitutions. Finally, a large scale analysis of protein stability—at the structurome level—contributed to the clarification of the relation between stability and natural evolution, thereby showing that the mutational profile of proteins differs according to their thermal properties. Some considerations on how the multiscale approach could help in unravelling the protein stability mechanisms are briefly discussed.

This article is part of the themed issue ‘Multiscale modelling at the physics–chemistry–biology interface’.