bluuebunny/crossref_metadata_2025_split huggingface dataset:
PDMS Deposition for Optical Devices by Dip‐Pen Nanolithography
Authors: Zohar Moshe , Azulay Almog Refael , Bykhovsky Dima , Fradkin Zeev , Tapuchi Saad , Auslender Mark 
Published: May 2017

Dip‐pen nanolithography (DPN) is a low‐cost, versatile bench‐top method for directly patterning materials on surfaces with sub‐50 nm resolution; it involves the use of a cantilever tip to transfer a selected ink onto various surfaces to create predefined patterns. Many parameters may influence DPN quality, due to the variety of deposited and surface materials and the chemical interactions between them. DPN tip deposition of liquid inks is not yet well understood, due to the lack of thorough study of the various parameters that need to be controlled in order to achieve uniform patterning. In this research, the printing of polydimethylsiloxane (PDMS) lines and the control of their physical dimensions are investigated; the applied parameters are different humidity levels, n‐hexane dilution proportions and different tip velocities. Numerous experiments accompanied by atomic force microscope measurements are conducted in order to derive a recommended recipe for the required dimensions of the printable lines. A practical aspect of the research is to assess the potential of the application of DPN for the fabrication of various optical devices, such as gratings and waveguides. In order to validate the theoretical results, PDMS printing over silicon is used to successfully produce an optical diffraction grating.
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Blinded review of archival radical prostatectomy specimens supports that contemporary Gleason score 6 prostate cancer lacks metastatic potential
Authors: Nunez Bragayrac Luciano A. , Murekeyisoni Christine , Vacchio Michael J. , Attwood Kristopher , Mehedint Diana C. , Mohler James L. , Azabdaftari Gissou , Xu Bo , Kauffman Eric C. 
Published: May 2017

BackgroundRetrospective identification of Gleason pattern 4 in metastatic Gleason score 3 + 3 = 6 (GS6) radical prostatectomy (RP) specimens has suggested true GS6 prostate cancer (CaP) lacks metastatic potential. However, pathologist awareness of study design and metastasis outcomes at the time of RP review might have introduced upgrading bias. We used pathologist‐blinded methodology for unbiased characterization of metastasis rates for contemporarily defined pathologic GS6 (pGS6) CaP.MethodsAn institutional RP database was queried to identify pGS6 patients with metastasis or concern for micrometastasis based on: 1) biochemical failure (BF) despite negative surgical margins or 2) incomplete biochemical response to salvage/adjuvant radiation. RP specimens were regraded independently by two genitourinary pathologists blinded to study aims or clinical outcomes. Additional blinding was performed by random inclusion of pGS6 control specimens from BF‐free patients. Only upgrading identified independently by both pathologists was considered.ResultsAmong 451 pGS6 patients identified, none had synchronous lymph node metastases and 43/451 (10%) suffered BF. Two patients (0.4%) developed metachronous metastasis during a 110‐month median follow‐up for BF patients. Both metastatic cases had Gleason pattern 4 on blinded RP review, as did 88% of cases with concern for micrometastasis versus 38% of control cases (P = 0.02). All BF patients (29/29) undergoing postoperative radiation had a complete biochemical response or Gleason pattern 4 on blinded RP review.ConclusionsUnbiased pathologist review of archival RP specimens supports absent metastatic potential for contemporarily defined GS6 CaP. Reduced postoperative monitoring is appropriate for pGS6, but may require pathology review to confirm absent Gleason pattern 4.
eQE: An open‐source density functional embedding theory code for the condensed phase
Authors: Genova Alessandro , Ceresoli Davide , Krishtal Alisa , Andreussi Oliviero , DiStasio Robert A. , Pavanello Michele 
Published: May 2017

AbstractIn this work, we present the main features and algorithmic details of a novel implementation of the frozen density embedding (FDE) formulation of subsystem density functional theory (DFT) that is specifically designed to enable ab initio molecular dynamics (AIMD) simulations of large‐scale condensed‐phase systems containing 1000s of atoms. This code (available at http://eqe.rutgers.edu) has been given the moniker of embedded Quantum ESPRESSO (eQE) as it is a generalization of the open‐source Quantum ESPRESSO (QE) suite of programs. The strengths of eQE reside in a hierarchical parallelization scheme that allows for an efficient and fully self‐consistent treatment of the electronic structure (via the addition of an additional DIIS extrapolation layer) while simultaneously exploiting the inherent symmetries and periodicities in the system (via sampling of subsystem‐specific first Brillouin zones and utilization of subsystem‐specific basis sets). While bulk liquids and molecular crystals are two classes of systems that exemplify the utility of the FDE approach (as these systems can be partitioned into weakly interacting subunits), we show that eQE has significantly extended this regime of applicability by outperforming standard semilocal Kohn–Sham DFT (KS‐DFT) for large‐scale heterogeneous catalysts with quite different layer‐specific electronic structure and intrinsic periodicities. eQE features very favorable strong parallel scaling for a model system of bulk liquid water composed of 256 water molecules, which allows for a significant decrease in the overall time to solution when compared to KS‐DFT. We show that eQE achieves speedups greater than one order of magnitude (
) when performing AIMD simulations of such large‐scale condensed‐phase systems as: (1) molecular liquids via bulk liquid water represented by 1024 independent water molecules (3072 atoms with a 25.3× speedup over KS‐DFT), (2) polypeptide/biomolecule solvation via (gly)6 solvated in (H2O)395 (1230 atoms with a 38.6× speedup over KS‐DFT), and (3) molecular crystals via a 3 × 3 × 3 periodic supercell of pentacene (1940 atoms with a 12.0× speedup over KS‐DFT). These results represent a significant improvement over the current state‐of‐the‐art and now enable subsystem DFT‐based AIMD simulations of realistically sized condensed‐phase systems of interest throughout chemistry, physics, and materials science.
Identification of stress degradation products of iloperidone using liquid chromatography coupled with an Orbitrap mass spectrometer
Authors: Pandeti Sukanya , Rout Tofan Kumar , Tadigoppula Narender , Thota Jagadeshwar Reddy 
Published: May 2017

RationaleIloperidone (ILOP) is an atypical antipsychotic drug used for the treatment of schizophrenia and related psychotic disorders. Comprehensive stress testing of the ILOP drug was carried out as per ICH guidelines to understand its degradation profile. The presence of degradation products in a drug affects not only the quality, but also the safety and efficacy of drug formulation. Thus, it is essential to develop an efficient analytical method which can be useful for the separation, identification and characterization of all possible degradation products of ILOP.MethodsILOP was subjected to various stress conditions such as acidic, basic, neutral hydrolysis, oxidation, photolysis and thermal conditions; and the resulting degradation products were investigated using LC‐PDA‐HRMS and MS/MS. An efficient and simple ultra‐high‐performance liquid chromatography (UHPLC) method has been developed on Acquity UPLC® BEH C18 column (2.1 × 100mm, 1.7 μm) using a gradient elution of heptafluorobutyric acid (0.1% HFBA) and acetonitrile as mobile phase.ResultsILOP was found to degrade under acidic and basic hydrolysis and oxidative stress conditions, whereas it was stable under neutral hydrolysis, thermal and photolytic conditions. A total of seven degradation products (DP1 to DP7) were identified and characterized by LC/MS/MS in positive ion mode with accurate mass measurements. The hydrolytic degradation under acidic and basic conditions produced two DPs (DP1 and DP2) and four DPs (DP4 to DP7), respectively, whereas DP3 was formed under oxidative conditions. In silico toxicity predictions showed higher probability values for DP4, DP6 and DP7, which indicates these DPs have the potential to mutate DNA.ConclusionsILOP was found to be labile under hydrolytic and oxidative conditions. The structures of the degradation products were rationalized by appropriate mechanisms. The proposed method can be effectively used for the determination and detection of ILOP and its degradation products.
Integrated vehicle control through the coordination of longitudinal/lateral and vertical dynamics controllers: Flatness and LPV/‐based design
Authors: Fergani S. , Menhour L. , Sename O. , Dugard L. , D'Andréa‐Novel B. 
Published: May 2017

SummaryThis paper deals with global chassis control of automotive vehicles. It focuses on the coordination of suspension and steering/braking vehicle controllers based on the interaction between the vertical and lateral behaviors of the vehicle. It is shown that the lateral acceleration and resulting roll motion of the car generate load transfers that considerably affect vehicle stability. A control law is designed in hierarchical way to improve the overall dynamics of the vehicle and cope with coupled driving maneuvers like obstacle avoidance using steering control and stop‐and‐go control using braking or driving wheel torque. This global control strategy includes two types of controllers. The first one is the longitudinal/lateral nonlinear flatness controller. Based on an appropriate choice of flat outputs, the flatness proof of a 3 DOF two‐wheel nonlinear vehicle model is established. Then, the combined longitudinal and lateral vehicle control is designed using algebraic estimation techniques to provide an accurate estimation of the derivatives and filtering of the reference flat outputs. The second part of the proposed strategy consists of a linear parameter‐varying/
suspension controller. This controller uses lateral acceleration as a varying parameter to account for load transfers that directly affect the suspension system. The coordination between the vehicle vertical and lateral dynamics is highlighted in this study, and the linear parameter‐varying/
framework ensures a specific collaborative coordination between the suspension and the steering/braking controllers, to achieve the desired performance. Simulations on a complex full vehicle model have been validated using experimental data obtained on‐board a real Renault Mégane Coupé. Copyright © 2017 John Wiley & Sons, Ltd.
Climate information websites: an evolving landscape
Authors: Hewitson Bruce , Waagsaether Katinka , Wohland Jan , Kloppers Kate , Kara Teizeen 
Published: May 2017

The climate change agenda is populated by actors and agencies with different objectives, values, and motivations, yet many seek decision scale climate information to inform policy and adaptation responses. A central element of this network of activity is the climate information website (CIW) that has seen a rapid and organic growth, yet with variable content and quality, and unfettered by any code of practice. This builds an ethical–epistemic dilemma that warrants assessment as the presence of CIWs contribute to real‐world consequences and commitment. This study considers the context of CIW growth, and reviews a representative sample of CIWs to draw out key issues for consideration in CIW development. We assess content, function, and use‐case value through a dual approach of a typology and user experience narratives to evaluate the general efficacy of a CIW. The typology reveals strong contrasts in content, complicated interfaces, and an overload of choice making it difficult to converge on a stable outcome. The narratives capture user experience and highlight barriers that include navigation difficulties, jargon laden content, minimal or opaque guidance, and inferred information without context about uncertainty and limits to skill. This illuminates four concerns: (1) the ethics of information provision in a context of real‐world consequences; (2) interfaces that present barriers to achieving robust solutions; (3) weak capacity of both users and providers to identify information of value from the multimodel and multimethod data; and (4) inclusion of data that infer skill. Nonetheless, results provide a positive indication of a community of practice that is still maturing. WIREs Clim Change 2017, 8:e470. doi: 10.1002/wcc.470This article is categorized under:

Climate Models and Modeling > Knowledge Generation with Models
Assessing Impacts of Climate Change > Scenario Development and Application
Enhanced antimicrobial and anticancer properties of ZnO and TiO2 nanocomposites
Authors: Chakra CH. Shilpa , Rajendar V. , Rao K. Venkateswara , Kumar Mirgender 
Published: May 2017

Abstract
The study describes the antibacterial and anticancer activities of a nanocomposite prepared by mixing zinc oxide and titanium dioxide nanoparticles. The particle mixtures were analyzed by X-ray diffraction, Field emission scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, and dynamic light scattering techniques. Thus, analyzed samples were subject to disc diffusion method at various concentrations to analyze their antibacterial activities against two Gram-positive and two Gram-negative bacteria. The same samples were then analyzed for their anticancer activities on four different cell lines. The results indicate a synergistic effect of the nanocomposite on both antibacterial and anticancer properties when compared to their individual counterparts.
Atomic-scale age resolution of planetary events
Authors: White L. F. , Darling J. R. , Moser D. E. , Reinhard D. A. , Prosa T. J. , Bullen D. , Olson D. , Larson D. J. , Lawrence D. , Martin I. 
Published: May 2017

AbstractResolving the timing of crustal processes and meteorite impact events is central to understanding the formation, evolution and habitability of planetary bodies. However, identifying multi-stage events from complex planetary materials is highly challenging at the length scales of current isotopic techniques. Here we show that accurate U-Pb isotopic analysis of nanoscale domains of baddeleyite can be achieved by atom probe tomography. Within individual crystals of highly shocked baddeleyite from the Sudbury impact structure, three discrete nanostructural domains have been isolated yielding average206Pb/238U ages of 2,436±94 Ma (protolith crystallization) from homogenous-Fe domains, 1,852±45 Ma (impact) from clustered-Fe domains and 1,412±56 Ma (tectonic metamorphism) from planar and subgrain boundary structures. Baddeleyite is a common phase in terrestrial, Martian, Lunar and asteroidal materials, meaning this atomic-scale approach holds great potential in establishing a more accurate chronology of the formation and evolution of planetary crusts.
Conformational dynamics of dynamin-like MxA revealed by single-molecule FRET
Authors: Chen Yang , Zhang Lei , Graf Laura , Yu Bing , Liu Yue , Kochs Georg , Zhao Yongfang , Gao Song 
Published: May 2017

AbstractHuman myxovirus resistance protein 1 (MxA) restricts a wide range of viruses and is closely related to the membrane-remodelling GTPase dynamin. The functions of MxA rely on domain rearrangements coupled with GTP hydrolysis cycles. To gain insight into this process, we studied real-time domain dynamics of MxA by single-molecule fluorescence resonance energy transfer. We find that the GTPase domain-bundle-signalling-element (BSE) region can adopt either an ‘open’ or a ‘closed’ conformation in all nucleotide-loading conditions. Whereas the open conformation is preferred in nucleotide-free, GDP·AlF4−-bound and GDP-bound forms, loading of GTP activates the relative movement between the two domains and alters the conformational preference to the ‘closed’ state. Moreover, frequent relative movement was observed between BSE and stalk via hinge 1. On the basis of these results, we suggest how MxA molecules within a helical polymer collectively generate a stable torque through random GTP hydrolysis cycles. Our study provides mechanistic insights into fundamental cellular events such as viral resistance and endocytosis.
A decadal analysis of bioeroding sponge cover on the inshore Great Barrier Reef
Authors: Ramsby Blake D. , Hoogenboom Mia O. , Whalan Steve , Webster Nicole S. , Thompson Angus 
Published: May 2017

AbstractDecreasing coral cover on the Great Barrier Reef (GBR) may provide opportunities for rapid growth and expansion of other taxa. The bioeroding sponges Cliona spp. are strong competitors for space and may take advantage of coral bleaching, damage, and mortality. Benthic surveys of the inshore GBR (2005–2014) revealed that the percent cover of the most abundant bioeroding sponge species, Cliona orientalis, has not increased. However, considerable variation in C. orientalis cover, and change in cover over time, was evident between survey locations. We assessed whether biotic or environmental characteristics were associated with variation in C. orientalis distribution and abundance. The proportion of fine particles in the sediments was negatively associated with the presence-absence and the percent cover of C. orientalis, indicating that the sponge requires exposed habitat. The cover of corals and other sponges explained little variation in C. orientalis cover or distribution. The fastest increases in C. orientalis cover coincided with the lowest macroalgal cover and chlorophyll a concentration, highlighting the importance of macroalgal competition and local environmental conditions for this bioeroding sponge. Given the observed distribution and habitat preferences of C. orientalis, bioeroding sponges likely represent site-specific – rather than regional – threats to corals and reef accretion.
Segmental Duplication of Chromosome 11 and its Implications for Cell Division and Genome-wide Expression in Rice
Authors: Zhang Rong , Xue Chao , Liu Guanqing , Liu Xiaoyu , Zhang Mingliang , Wang Xiao , Zhang Tao , Gong Zhiyun 
Published: May 2017

AbstractSegmental duplication is a major structural variation that occurs in chromosomes. Duplication leads to the production of gene copies with increased numbers of related repeat segments, causing the global genome to be in a state of imbalance. In addition, if the added segment contains a centromeric specific DNA, the duplicated chromosome will have structural multiple centromeres. We identified a segmental duplication containing structurally tricentric regions derived from the short arm of chromosome 11 (11L∙ + 11L∙ + 11S∙11S∙11S∙11S, “∙” represents the centromeric DNA repeat loci), and analyzed its implications for cell division and genome-wide expression. In the variant, only the middle centromere of 11S∙11S∙11S∙11S is functionally active. As a result, the structurally tricentric chromosome was stable in mitosis, because it is actually a functional monocentric chromosome. However, the structurally tricentric chromosome, which usually formed a bivalent, was either arranged on the equatorial plane or was lagging, which affected its separation during meiosis. Furthermore, RNA-seq and RT-qPCR analysis showed that the segmental duplication affected genome-wide expression patterns. 34.60% of genes in repeat region showed positive dosage effect. Thus, the genes on chromosome arm 11S-2 didn’t exhibit obviously dosage compensation, as illustrated by no peak around a ratio of 1.00. However, the gene dosage effect will reduce after sexual reproduction of a generation.
Oscillations in networks of networks stem from adaptive nodes with memory
Authors: Goldental Amir , Uzan Herut , Sardi Shira , Kanter Ido 
Published: May 2017

AbstractWe present an analytical framework that allows the quantitative study of statistical dynamic properties of networks with adaptive nodes that have memory and is used to examine the emergence of oscillations in networks with response failures. The frequency of the oscillations was quantitatively found to increase with the excitability of the nodes and with the average degree of the network and to decrease with delays between nodes. For networks of networks, diverse cluster oscillation modes were found as a function of the topology. Analytical results are in agreement with large-scale simulations and open the horizon for understanding network dynamics composed of finite memory nodes as well as their different phases of activity.
RNA-sequencing Identifies Novel Pathways in Sarcoidosis Monocytes
Authors: Talreja Jaya , Farshi Pershang , Alazizi Adnan , Luca Francesca , Pique-Regi Roger , Samavati Lobelia 
Published: May 2017

AbstractSarcoidosis is a complex systemic granulomatous disorder of unknown etiology. Genome-wide association studies have not been able to explain a causative role for nucleotide variation in its pathogenesis. The goal of the present study was to identify the gene expression profile and the cellular pathways altered in sarcoidosis monocytes via RNA-sequencing. Peripheral blood monocytes play a role in sarcoidosis inflammation. Therefore, we determined and compared the transcriptional signature of monocytes from peripheral blood from sarcoidosis patients and healthy controls via RNA-sequencing. We found 2,446 differentially expressed (DE) genes between sarcoidosis and healthy control monocytes. Analysis of these DE genes showed enrichment for ribosome, phagocytosis, lysosome, proteasome, oxidative phosphorylation and metabolic pathways. RNA-sequencing identified upregulation of genes involved in phagocytosis and lysosomal pathway in sarcoidosis monocytes, whereas genes involved in proteasome degradation and ribosomal pathways were downregulated. Further studies are needed to investigate the role of specific genes involved in the identified pathways and their possible interaction leading to sarcoidosis pathology.
Palaeoclimatic conditions in the Mediterranean explain genetic diversity of Posidonia oceanica seagrass meadows
Authors: Chefaoui Rosa M. , Duarte Carlos M. , Serrão Ester A. 
Published: May 2017

AbstractPast environmental conditions in the Mediterranean Sea have been proposed as main drivers of the current patterns of distribution of genetic structure of the seagrass Posidonia oceanica, the foundation species of one of the most important ecosystems in the Mediterranean Sea. Yet, the location of cold climate refugia (persistence regions) for this species during the Last Glacial Maximum (LGM) is not clear, precluding the understanding of its biogeographical history. We used Ecological Niche Modelling together with existing phylogeographic data to locate Pleistocene refugia in the Mediterranean Sea and to develop a hypothetical past biogeographical distribution able to explain the genetic diversity presently found in P. oceanica meadows. To do that, we used an ensemble approach of six predictive algorithms and two Ocean General Circulation Models. The minimum SST in winter and the maximum SST in summer allowed us to hindcast the species range during the LGM. We found separate glacial refugia in each Mediterranean basin and in the Central region. Altogether, the results suggest that the Central region of the Mediterranean Sea was the most relevant cold climate refugium, supporting the hypothesis that long-term persistence there allowed the region to develop and retain its presently high proportion of the global genetic diversity of P. oceanica.