bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Melt‐Castable Energetic Pyrazole: A Pyrazolyl‐Furazan Framework Bearing Five Nitro Groups
Authors: Dalinger Igor L. , Suponitsky Kyrill Yu. , Pivkina Alla N. , Sheremetev Aleksei B. 
Published: October 2016

AbstractContinuing advances in energetic pyrazole construction foster further its rational use. This work establishes an approach for the first synthesis of nitropyrazole that bear both furazan and trinitromethyl moieties. The approach to the installation of the C(NO2)3 group exploits the destructive nitration of N‐acetonyl group. The target 3‐(3,4‐dinitro‐1‐(trinitromethyl)‐1H‐pyrazol‐5‐yl)‐4‐methylfurazan (6) has promising explosive properties.
Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP‐11 structural models
Authors: El Houasli Marwa , Maigret Bernard , Devignes Marie‐Dominique , Ghoorah Anisah W. , Grudinin Sergei , Ritchie David W. 
Published: October 2016

ABSTRACTMany of the modeling targets in the blind CASP‐11/CAPRI‐30 experiment were protein homo‐dimers and homo‐tetramers. Here, we perform a retrospective docking‐based analysis of the perfectly symmetrical CAPRI Round 30 targets whose crystal structures have been published. Starting from the CASP “stage‐2” fold prediction models, we show that using our recently developed “SAM” polar Fourier symmetry docking algorithm combined with NAMD energy minimization often gives acceptable or better 3D models of the target complexes. We also use SAM to analyze the overall quality of all CASP structural models for the selected targets from a docking‐based perspective. We demonstrate that docking only CASP “center” structures for the selected targets provides a fruitful and economical docking strategy. Furthermore, our results show that many of the CASP models are dockable in the sense that they can lead to acceptable or better models of symmetrical complexes. Even though SAM is very fast, using docking and NAMD energy minimization to pull out acceptable docking models from a large ensemble of docked CASP models is computationally expensive. Nonetheless, thanks to our SAM docking algorithm, we expect that applying our docking protocol on a modern computer cluster will give us the ability to routinely model 3D structures of symmetrical protein complexes from CASP‐quality models. Proteins 2017; 85:463–469. © 2016 Wiley Periodicals, Inc.
Modeling complexes of modeled proteins
Authors: Anishchenko Ivan , Kundrotas Petras J. , Vakser Ilya A. 
Published: October 2016

ABSTRACTStructural characterization of proteins is essential for understanding life processes at the molecular level. However, only a fraction of known proteins have experimentally determined structures. This fraction is even smaller for protein–protein complexes. Thus, structural modeling of protein–protein interactions (docking) primarily has to rely on modeled structures of the individual proteins, which typically are less accurate than the experimentally determined ones. Such “double” modeling is the Grand Challenge of structural reconstruction of the interactome. Yet it remains so far largely untested in a systematic way. We present a comprehensive validation of template‐based and free docking on a set of 165 complexes, where each protein model has six levels of structural accuracy, from 1 to 6 Å Cα RMSD. Many template‐based docking predictions fall into acceptable quality category, according to the CAPRI criteria, even for highly inaccurate proteins (5–6 Å RMSD), although the number of such models (and, consequently, the docking success rate) drops significantly for models with RMSD > 4 Å. The results show that the existing docking methodologies can be successfully applied to protein models with a broad range of structural accuracy, and the template‐based docking is much less sensitive to inaccuracies of protein models than the free docking. Proteins 2017; 85:470–478. © 2016 Wiley Periodicals, Inc.
Influence of irradiation by 60Co gamma‐quanta on reliability of IR‐LEDs based upon AlGaAs heterostructures
Authors: Gradoboev Alexander V. , Simonova Anastasiia V. , Orlova Ksenia N. 
Published: October 2016

AbstractWe consider the influence of preliminary irradiation by 60Co gamma quanta on emission power decrease during the operating time of IR‐LEDs based upon AlGaAs double heterostructures. Irradiation was realized in passive power mode of the LEDs prior to aging. Aging under long operating time conditions was simulated by a step‐stress approach. We have determined that the emissive power decrease of LED during operating time has two stages. On the first stage, decrease of LED emissive power is due to rearrangement of original defect structure. On the second stage, emissive power goes down as the result of inducing new structural defects. We have shown identical multistage mechanisms of emissive power drop are observed during both operating time and influence of ionizing radiation. We have established that preliminary irradiation has increased reliability and operating time of LEDs. (© 2016 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
MeV ion irradiation effects on the luminescence properties of Si‐implanted SiO2‐thin films
Authors: Chulapakorn T. , Sychugov I. , Suvanam S. S. , Linnros J. , Primetzhofer D. , Hallén A. 
Published: October 2016

AbstractThe effects of MeV heavy ion irradiation at varying fluence and flux on excess Si, introduced in SiO2 by keV ion implantation, are investigated by photoluminescence (PL). From the PL peak wavelength (λ) and decay lifetime (τ), two PL sources are distinguished: i) quasi‐direct recombination of excitons of Si‐nanoparticles (SiNPs), appearing after thermal annealing (λ > 720 nm, τ ∼ μs), and ii) fast‐decay PL, possibly due to oxide‐related defects (λ ∼ 575‐690 nm, τ ∼ ns). The fast‐decay PL (ii) observed before and after ion irradiation is induced by ion implantation. It is found that this fast‐decay luminescence decreases for higher irradiation fluence of MeV heavy ions. After thermal annealing (forming SiNPs), the SiNP PL is reduced for samples irradiated by MeV heavy ions but found to stabilize at higher level for higher irradiation flux; the (ii) band vanishes as a result of annealing. The results are discussed in terms of the influence of electronic and nuclear stopping powers. (© 2016 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Share secrets stage by stage with homogeneous linear feedback shift register in the standard model
Authors: Mashhadi Samaneh 
Published: October 2016

AbstractA new multistage secret‐sharing scheme based on the homogeneous linear feedback shift register is proposed. This scheme has few public outputs, a new simple construction, and different techniques for the reconstruction phase. Moreover, based on the semantic security of the underlying encryption scheme, we prove the computational security of our scheme in the standard model. Copyright © 2016 John Wiley & Sons, Ltd.
Bringing the Stages Back in: Social Network Ties and Start‐up firms’ Access to Venture Capital in China
Authors: Wang Yanbo 
Published: October 2016

Research summarySocial networks are believed to help start‐ups access venture capital (VC). However, the causal mechanisms remain unclear because social ties probably influence both a start‐up's likelihood of being screened for evaluation and its likelihood of being funded. Whereas prior studies conceptualize venture financing as a single‐moment event, in this article, it is theorized as a dynamic multistage process in which a screening decision precedes a funding decision. Failure to address the selection effects at each stage could lead to biased findings regarding how social ties confer advantage in venture financing. This study uses a hand‐collected dataset from China to empirically examine these arguments.Managerial summarySocial networks are believed to help start‐ups access venture capital. However, it is unclear whether this is because social ties help venture capitalists (VCs) and start‐ups overcome the problems of information asymmetry and behavioral opportunism in early‐stage financing or whether VCs are more likely to become aware of investment opportunities embedded within social networks. This study divides VC decision making into two stages: awareness generation and venture evaluation. This study finds that socially connected start‐ups have cumulative advantages in the access to venture capital, but this advantage mainly arises in the early stage where information embedded in social ties helps reduce investors’ search costs in deal screening. In contrast, social ties are a secondary consideration in the subsequent stage of VC funding decisions Copyright © 2016 Strategic Management Society.
Neurotrophic Factor-α1: A Key Wnt-β-Catenin Dependent Anti-Proliferation Factor and ERK-Sox9 Activated Inducer of Embryonic Neural Stem Cell Differentiation to Astrocytes in Neurodevelopment
Authors: Selvaraj Prabhuanand , Xiao Lan , Lee Cheol , Murthy Saravana R. K. , Cawley Niamh X. , Lane Malcolm , Merchenthaler Istvan , Ahn Sohyun , Loh Y. Peng 
Published: October 2016

AbstractEmbryonic neurodevelopment involves inhibition of proliferation of multipotent neural stem cells (NSCs) followed by differentiation into neurons, astrocytes and oligodendrocytes to form the brain. We have identified a new neurotrophic factor, NF-α1, which inhibits proliferation and promotes differentiation of NSC/progenitors derived from E13.5 mouse cortex. Inhibition of proliferation of these cells was mediated through negatively regulating the Wnt pathway and decreasing β-catenin. NF-α1 induced differentiation of NSCs to astrocytes by enhancing Glial Fibrillary Acidic Protein (GFAP) expression through activating the ERK1/2-Sox9 signaling pathway. Cultured E13.5 cortical stem cells from NF-α1-knockout mice showed decreased astrocyte numbers compared to wild-type mice, which was rescued by treatment with NF-α1. In vivo, immunocytochemistry of brain sections and Western blot analysis of neocortex of mice showed a gradual increase of NF-α1 expression from E14.5 to P1 and a surge of GFAP expression at P1, the time of increase in astrogenesis. Importantly, NF-α1-Knockout mice showed ∼49% fewer GFAP positive astrocytes in the neocortex compared to WT mice at P1. Thus, NF-α1 is critical for regulating antiproliferation and cell fate determination, through differentiating embryonic stem cells to GFAP-positive astrocytes for normal neurodevelopment.
Generation of Functional Human Retinal Ganglion Cells with Target Specificity from Pluripotent Stem Cells by Chemically Defined Recapitulation of Developmental Mechanism
Authors: Teotia Pooja , Chopra Divyan A. , Dravid Shashank Manohar , Van Hook Matthew J. , Qiu Fang , Morrison John , Rizzino Angie , Ahmad Iqbal 
Published: October 2016

Abstract
Glaucoma is a complex group of diseases wherein a selective degeneration of retinal ganglion cells (RGCs) lead to irreversible loss of vision. A comprehensive approach to glaucomatous RGC degeneration may include stem cells to functionally replace dead neurons through transplantation and understand RGCs vulnerability using a disease in a dish stem cell model. Both approaches require the directed generation of stable, functional, and target-specific RGCs from renewable sources of cells, that is, the embryonic stem cells and induced pluripotent stem cells. Here, we demonstrate a rapid and safe, stage-specific, chemically defined protocol that selectively generates RGCs across species, including human, by recapitulating the developmental mechanism. The de novo generated RGCs from pluripotent cells are similar to native RGCs at the molecular, biochemical, functional levels. They also express axon guidance molecules, and discriminate between specific and nonspecific targets, and are nontumorigenic.
Lewis Base Catalyzed Stereo‐ and Regioselective Bromocyclization
Authors: Gieuw Matthew H. , Ke Zhihai , Yeung Ying‐Yeung 
Published: October 2016

AbstractOxygen‐ and nitrogen‐containing heterocyclic compounds are widely recognized as key components in many natural products and biologically relevant molecules, but often the problem comes down to methodologies in synthesizing them. Halocyclization of olefinic substrates is a promising strategy in the construction of O‐ and N‐heterocyclic compounds, which further signifies the development of their asymmetric variants. Over the past years, our group has been devoted to this particular area of asymmetric electrophilic halocyclization with chalcogen‐containing molecules as catalysts. In this account, the main focus is on the development of our novel chiral catalysts and applications derived from the reaction products.
Recent Developments in Coinage Metal Catalyzed Transformations of Stabilized Vinyldiazo Compounds: Beyond Carbenic Pathways
Authors: López Enol , González‐Pelayo Silvia , López Luis A. 
Published: October 2016

AbstractTransition metal‐catalyzed transformations of vinyldiazo compounds have become a versatile tool in organic synthesis. Although several transition metals have been investigated for this purpose, this field has been mainly dominated by dirhodium catalysts. Remarkable levels of chemo‐, regio‐, diastereo‐ and enantioselectivity have been reached in some of these rhodium‐catalyzed transformations. In the last few years coinage metals have also emerged as useful catalysts in transformations involving vinyldiazo compounds. In some cases, highly efficient catalyst‐dependent protocols arising from divergent mechanistic pathways have been reported. In this Personal Account, we aim to showcase recent advances in metal coinage catalyzed transformations of vinyldiazoacetates, an exciting field of research to which our group has actively contributed in the last few years.
Secondary science teachers as curriculum makers: Mapping and designing Scotland's new Curriculum for Excellence
Authors: Wallace Carolyn S. , Priestley Mark R. 
Published: October 2016

AbstractScotland is one of several countries to have recently implemented a new national curriculum to highlight 21st century educational priorities. Teachers have been mandated to follow the new curriculum guidelines, known as Curriculum for Excellence (CfE), since the fall of 2010. The purpose of this study was to use a phenomenological lens to investigate how Scottish secondary science teachers are experiencing their work of curriculum development, including daily lesson design and more broadly, curriculum mapping within the context of reform (Remillard [1999], Curriculum Inquiry, 29: 315–342). We probed seven science teachers’ experiences to create both a composite profile of conscious thoughts about curriculum design and individual profiles that highlight interactions between the curriculum mandates, beliefs, and agentic orientations. The study indicated that changes to curriculum development required accepting new cognitive commitments including: (i) analyzing the CfE document to discern the most significant principles underlying change; (ii) reflecting on the ways that science teacher curriculum development is a problem‐solving endeavor; (iii) undertaking the complex processes of curriculum mapping, from primary school all the way through national qualification exams; and (iv) recognizing that the epistemological frame for students’ science learning has changed and providing opportunities for students to create and apply knowledge. Two significant findings include the unpacking of these cognitive activities as part of a transformation toward a new epistemology of pedagogy, and the assertion that official curriculum documents can promote change, albeit with caveats concerning individual beliefs, agentic orientations, and possibilities for agency within school contexts. © 2016 Wiley Periodicals, Inc. J Res Sci Teach 54: 324–349, 2017
Advances in RNA molecular dynamics: a simulator's guide to RNA force fields
Authors: Vangaveti Sweta , Ranganathan Srivathsan V. , Chen Alan A. 
Published: October 2016

Molecular simulations have become an essential tool for biochemical research. When they work properly, they are able to provide invaluable interpretations of experimental results and ultimately provide novel, experimentally testable predictions. Unfortunately, not all simulation models are created equal, and with inaccurate models it becomes unclear what is a bona fide prediction versus a simulation artifact. RNA models are still in their infancy compared to the many robust protein models that are widely in use, and for that reason the number of RNA force field revisions in recent years has been rapidly increasing. As there is no universally accepted ‘best’ RNA force field at the current time, RNA simulators must decide which one is most suited to their purposes, cognizant of its essential assumptions and their inherent strengths and weaknesses. Hopefully, armed with a better understanding of what goes inside the simulation ‘black box,’ RNA biochemists can devise novel experiments and provide crucial thermodynamic and structural data that will guide the development and testing of improved RNA models. WIREs RNA 2017, 8:e1396. doi: 10.1002/wrna.1396This article is categorized under:

RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry
RNA Evolution and Genomics > Computational Analyses of RNA
RNA Methods > RNA Analyses In Vitro and In Silico
Posttranscriptional regulation of intestinal epithelial integrity by noncoding RNAs
Authors: Wang Jun‐Yao , Xiao Lan , Wang Jian‐Ying 
Published: October 2016

Maintenance of the gut epithelial integrity under stressful environments requires epithelial cells to rapidly elicit changes in gene expression patterns to regulate their survival, adapt to stress, and keep epithelial homeostasis. Disruption of the intestinal epithelial integrity occurs commonly in patients with various critical illnesses, leading to the translocation of luminal toxic substances and bacteria to the blood stream. Recently, noncoding RNAs (ncRNAs) have emerged as a novel class of master regulators of gene expression and are fundamentally involved in many aspects of gut mucosal regeneration, protection, and epithelial barrier function. Here, we highlight the roles of several intestinal epithelial tissue‐specific microRNAs, including miR‐222, miR‐29b, miR‐503, and miR‐195, and long ncRNAs such as H19 and SPRY4‐IT1 in the regulation of cell proliferation, apoptosis, migration, and cell‐to‐cell interactions and also further analyze the mechanisms through which ncRNAs and their interactions with RNA‐binding proteins modulate the stability and translation of target mRNAs. WIREs RNA 2017, 8:e1399. doi: 10.1002/wrna.1399This article is categorized under:

Translation > Translation Regulation
RNA Turnover and Surveillance > Regulation of RNA Stability
RNA in Disease and Development > RNA in Disease
Triple Antithrombotic Therapy and Outcomes in Post‐PCI Patients Undergoing Non‐cardiac Surgery
Authors: Valle Javier A. , Graham Laura , DeRussy Aerin , Itani Kamal , Hawn Mary T. , Maddox Thomas M. 
Published: October 2016

AbstractBackgroundTriple therapy, or the use of anticoagulants with dual antiplatelet therapy (DAPT), is often used to protect against ischemic events in post‐percutaneous coronary intervention (PCI) patients with indications for anticoagulation, but is associated with increased bleeding. As both ischemic and bleeding risks increase in the perioperative period, the impact of triple therapy may be especially pronounced in patients undergoing surgery. Outcomes in this population are currently unknown.MethodsWe identified patients undergoing non‐cardiac surgeries within 2 years of PCI in Veterans Affairs hospitals from 2004 to 2012. We compared perioperative major adverse cardiovascular and cerebrovascular events (MACCE: mortality, myocardial infarction, stroke, revascularization) and bleeding events (in‐hospital bleeding, transfusion) between surgeries in patients prescribed triple therapy and DAPT, adjusting for clinical, demographic, and operative characteristics.ResultsAmong 7811 surgeries, 391 (5.0 %) occurred in patients receiving triple therapy. 44 (11.3 %) MACCE and 107 (27.4 %) bleeding events occurred with surgeries in triple therapy patients, compared to 366 (4.9 %) MACCE and 980 (13.2 %) bleeding events in DAPT patients. After adjustment, surgery in triple therapy patients was associated with higher rates of MACCE [odds ratio (OR) 1.65, 95 % confidence interval (CI) 1.16–2.34] or bleeding (OR 1.52, 95 % CI 1.17–1.99) as compared to surgery in DAPT patients.ConclusionsOne in twenty post‐PCI patients undergoing non‐cardiac surgery were on triple therapy. Surgery in these patients was associated with higher MACCE and bleeding events compared to surgery in patients on DAPT, independent of clinical and operative characteristics. These findings identify a high‐risk population for surgery, which may warrant increased surveillance for adverse perioperative events.
Pharmacogenomics of Drug Metabolizing Enzymes and Transporters: Relevance to Precision Medicine
Authors: Ahmed Shabbir , Zhou Zhan , Zhou Jie , Chen Shu-Qing 
Published: October 2016

Abstract
The interindividual genetic variations in drug metabolizing enzymes and transporters influence the efficacy and toxicity of numerous drugs. As a fundamental element in precision medicine, pharmacogenomics, the study of responses of individuals to medication based on their genomic information, enables the evaluation of some specific genetic variants responsible for an individual’s particular drug response. In this article, we review the contributions of genetic polymorphisms to major individual variations in drug pharmacotherapy, focusing specifically on the pharmacogenomics of phase-I drug metabolizing enzymes and transporters. Substantial frequency differences in key variants of drug metabolizing enzymes and transporters, as well as their possible functional consequences, have also been discussed across geographic regions. The current effort illustrates the common presence of variability in drug responses among individuals and across all geographic regions. This information will aid health-care professionals in prescribing the most appropriate treatment aimed at achieving the best possible beneficial outcomes while avoiding unwanted effects for a particular patient.