bluuebunny/crossref_metadata_2025 huggingface dataset:
A mechanistic study of helicases with magnetic traps
Authors: Hodeib Samar , Raj Saurabh , Manosas Maria , Zhang Weiting , Bagchi Debjani , Ducos Bertrand , Fiorini Francesca , Kanaan Joanne , Le Hir Hervé , Allemand Jean‐François , Bensimon David , Croquette Vincent
Published: May 2017

Helicases are a broad family of enzymes that separate nucleic acid double strand structures (DNA/DNA, DNA/RNA, or RNA/RNA) and thus are essential to DNA replication and the maintenance of nucleic acid integrity. We review the picture that has emerged from single molecule studies of the mechanisms of DNA and RNA helicases and their interactions with other proteins. Many features have been uncovered by these studies that were obscured by bulk studies, such as DNA strands switching, mechanical (rather than biochemical) coupling between helicases and polymerases, helicase‐induced re‐hybridization and stalled fork rescue.
A result on output regulation of lower triangular systems with unknown high‐frequency gain sign
Authors: Guo Meichen , Xu Dabo , Liu Lu
Published: May 2017

This paper concerns global robust output regulation of a class of nonlinear lower triangular systems with an unknown high‐frequency gain as well as an unknown exosystem. A novel class of internal model candidates is integrated with the output regulation framework. As a result, stabilization of the augmented system can be performed without parameter estimators. However, the new internal models bring challenges to the stabilization of the augmented system. To overcome these challenges, we propose a new recursive controller design procedure and use it to develop a Nussbaum‐gain‐based controller. This work extends the existing results on nonlinear output regulation of lower triangular systems to the case where both the high‐frequency gain sign and the exosystem are unknown. Copyright © 2017 John Wiley & Sons, Ltd.
Highly Efficient and Recyclable Metal Salt Catalyst for the Production of Biodiesel: Toward Greener Process
Authors: Yang Tao , Cai Bo , Chang Xin , Pan Hui , Huang Yao‐Bing
Published: May 2017

A highly reactive and recyclable metal catalyst was reported for the transesterification of model vegetable oil with methanol to produce fatty acid methyl esters (FAMEs) under microwave condition. Among the screened catalysts, Al2(SO4)3 provided the highest FAME yield of 98.1 % at 130 oC within 30 min. Different reaction parameters were fully investigated which were found to have great influences on the product yields. Microwave energy showed a remarkable accelerated reaction rate as compared to that from the conventional oil heating way. The catalytic system also showed good tolerance to water and free fatty acids. The catalyst can be easily recovered through a simple extraction/evaporation, which still posed good reactivity in the recycling runs. The characters of the obtained biodiesel was also characterized. Mechanistic studies revealed that the hydrolysis of the metal salt to generate the corresponding cationic and acidic species were responsible for the good catalytic activity of the reaction.
Anticorrosion Effect of 4‐Amino‐5‐(4‐pyridyl)‐4H‐1,2,4‐triazole‐3‐thiol for Mild Steel in HCl Solution
Authors: Farsak Murat , Ongun Yüce Ayşe , Kardaş Gülfeza
Published: May 2017

The effect of 4‐amino‐5‐(4‐pyridyl)‐4H‐1,2,4‐triazole‐3‐thiol (4APT) on the corrosion of mild steel in hydrochloric acid solution was investigated as electrochemically, theoretically and qualitatively. Inhibition efficiency of 4APT on mild steel surface was observed and illuminated by EIS, potentiodynamic polarization, SEM and FTIR techniques. All of the experiments show that 4APT provides a good film layer on the surface and inhibits the corrosion of mild steel by adsorbing on a vast scale. The inhibition efficiency of 4APT was found approximately 96 %. It is understood that 4APT is an effective inhibitor for acid corrosion of mild steel.
Ligand‐Field Asymmetry‐Controlled Luminescent Europium (III) and Samarium(III) Tris(β‐diketonate) Complexes of Diphenyl‐(2‐pyridyl‐N‐oxide)‐ Phosphine Oxide
Authors: Vats Bal Govind , Kannan Shanmugaperumal , Kumar Mukesh , Drew Micheal G. B.
Published: May 2017

Eight new complexes of the type Ln(OO)3.2 L1, Ln(OO)3.L2 (where Ln=Eu, Sm; OO=thenoyl trifluroacetonate(TTA) and dibenzoylmethanate(DBM); L1=diphenyl, (2‐pyridyl) phosphine oxide (PON) and diphenyl‐(2‐pyridyl‐N‐oxide)phosphine oxide (PONO)) were synthesized for the first time. Complexes were characterized by FTIR, CHN analyses and Single crystal X‐ray diffraction techniques. Structures of samarium complexes show that the L1 behaves as a monodentate ligand and bonds through P=O group to metal centre, whereas L2 behaves as a bidentate ligand and bonds through P=O as well as N−O groups to metal centre. Photophysical properties of all the complexes were measured in solid as well as solution states. Due to increase in ligand field asymmetry around the metal centre (by changing ligand from L1 to L2), the asymmetry ratio REu in Europium(III) tris( diketonate)‐L2 complexes were increased. This leads to increase in intrinsic quantum yield complexes with ligand L2 as compared to that of complexes of ligand L1.
Broadband Photocatalytic Activity of Mesoporous Cd(II)‐Doped TiO2
Authors: Chen Chia‐Yun , Wei Ta‐Cheng , Li Jheng‐Yi
Published: May 2017

Mesoporous Cd(II)‐doped TiO2 nanoparticles are prepared with various Cd contents through a micelle‐mediated hydrothermal method. The as‐prepared 5 %‐Cd(II) doped TiO2 photocatalysts possess highly organized crystallites with large surface area of 389.05 m2/g, and further display the broadband absorption capability extended toward visible region. The involving photocatalytic phenomena of degrading two kinds of non‐biodegradable azo dyes, Remazol Black 5 and Remazol Brilliant Orange 3R, were kinetically modeled, manifesting the fact that the involving photo‐degradation of these different dyes is in accordance with the second‐order kinetic model. With the optimized doping of Cd ions, the photocatalysts possess the tailored mesoporous architectures, leaving the substantially active sites in photocatlytic processs, along with efficient charge separation of photogenerated carriers due to additional trap levels in TiO2 band structures, further provide the improved capability of dye removal.
Facile and Chemically Sustainable Catalyst‐Free Synthesis of Diverse 2‐Aryl‐4‐Alkyl/Aryl‐Pyrano[3,2‐c]chromen‐5(4H)‐Ones by One‐Pot Multicomponent Reactions at Room Temperature
Authors: Brahmachari Goutam , Nurjamal Khondekar
Published: May 2017

A simple, catalyst‐free, straightforward and highly efficient one‐pot synthesis of pharmaceutically‐interesting diverse kind of functionalized 2‐aryl‐4‐alkyl/aryl‐pyrano[3,2‐c]chromen‐5(4H)‐ones (4 a‐4 z′′) and 3‐/4‐(5‐oxo‐2‐aryl‐4,5‐dihydropyrano[3,2‐c]chromen‐4‐yl)benzaldehydes (4′a‐4′j) has been developed based on a multicomponent reaction between alkyl/aryl aldehydes (1/1′), acetophenones (2) and 4‐hydroxycoumarin (3) in aqueous ethanol at room temperature (25‐30 °C). The salient features of this protocol are mild reaction conditions, use of no catalyst, good to excellent yields, high atom‐economy, eco‐friendliness, easy isolation of products, and reusability of reaction media.
An Unequivocal Synthesis of 2‐Aryl Substituted 3‐Amino‐2,4,5,7‐tetrahydro‐6H‐pyrazolo[3,4‐b]pyridin‐6‐ones
Authors: Bou‐Petit Elisabeth , Picas Elsa , Puigjaner Cristina , Font‐Bardia Mercè , Ferrer Nabí , Sempere Julià , Puig de la Bellacasa Raimon , Batllori Xavier , Teixidó Jordi , Estrada‐Tejedor Roger , Ramon y Cajal Santiago , Borrell José I.
Published: May 2017

The reaction between pyridones (1) and substituted hydrazines 4 can afford two different regioisomeric pyrazolo[3,4‐b]pyridin‐6‐ones 2 and 3 depending on the initial substitution of the methoxy group and the direction of the cyclization. In the case of phenylhydrazine 4 (R3 = Ph), we have clearly shown that the treatment of pyridones 1a–d with 4 (R3 = Ph) in MeOH at temperatures below 140°C yields, independently of the nature and position of the substituents present in the pyridone ring, the open intermediates 7a–d. When the reaction is carried at 140°C under microwave irradiation, the corresponding 2‐aryl substituted pyrazolo[3,4‐b]pyridines 3a–d are always formed. We have experimentally determined, using DSC techniques, the activation energies of the two steps involved in the formation of 3: a) substitution of the methoxy group present in pyridones 1 with phenylhydrazine 4 (R3 = Ph) to afford intermediates 7 and b) cyclization of intermediates 7 to yield pyrazolopyridines 3. The results obtained, 15 and 42 kcal⋅mol−1 respectively, are in agreement with the experimental findings.
Iridium‐Catalyzed Cyclization of o‐Aminobenzamides with Unsaturated Aldehydes to Give 2‐Alkylquinazolinones through a Hydrogen Autotransfer Process
Authors: Zhao Wei , Ma Wangjing , Xiao Tiancun , Li Feng
Published: May 2017

The synthesis of 2‐alkylquinazolinones via iridium‐catalyzed cyclization of o‐aminobenzamides with unsaturated aldehydes has been accomplished. In the presence of [Cp*IrCl2]2, a series of desirable products were obtained in 77–91 % yields. This strategy is attractive due to high atom efficiency and the formation of water as the only side product.
An investigation progress toward Be-based ablator materials for the inertial confinement fusion
Authors: Luo Bingchi , Zhang Jiqiang , He Yudan , Chen Long , Luo Jiangshan , Li Kai , Wu Weidong
Published: May 2017

The Be-based materials with many particular properties lead to an important research subject. The investigation progresses in the fabrication technologies are introduced here, including main three kinds of Be-based materials, such as Be–Cu capsule, $\text{Be}_{2}\text{C}$ ablator and high-purity Be material. Compared with the pioneer workgroup on Be-based materials, the differences in Be–Cu target fabrication were described, and a grain refinement technique by an active hydrogen reaction for Be coating was proposed uniquely. $\text{Be}_{2}\text{C}$ coatings were first prepared by the DC reactive magnetron sputtering with a high deposition rate $({\sim}300~\text{nm}/\text{h})$. Pure polycrystalline $\text{Be}_{2}\text{C}$ films with uniform microstructures, smooth surface, high density $({\sim}2.2~\text{g}\cdot \text{cm}^{3})$ and good optical transparency were fabricated. In addition, the high-purity Be materials with metal impurities in a ppm magnitude were fabricated by the pyrolysis of organometallic Be.
Invasive Russian Knapweed (Acroptilon repens) Creates Large Patches Almost Entirely by Rhizomic Growth
Authors: Gaskin John F. , Littlefield Jeffrey L.
Published: May 2017

Russian knapweed is an outcrossing perennial invasive weed in North America that can spread by both seed and horizontal rhizomic growth leading to new shoots. The predominant mode of spread at the local scale and dispersal at the long-distance scale informs control but has not been quantitatively researched. We used amplified fragment-length polymorphisms (AFLPs) of DNA collected from 174 shoots in two discrete patches of Russian knapweed at each of three locations in Montana. Out of the 174 shoots collected, we found nine AFLP genotypes. Three out of the six patches were monotypic; the other three patches each had one rare genotype. No genotypes were shared between patches. The maximum diameter of a genet (a genetic individual) was 56.5 m. These results indicate that patch expansion at the local scale is almost entirely by rhizomes that spread and develop new shoots. At the long-distance scale, dispersal is by seed. Controlling seed development through biological control and herbicide use may be effective at stopping long-distance dispersal but may not affect expansion of existing patches.
Global instability of low-density jets
Authors: Coenen W. , Lesshafft L. , Garnaud X. , Sevilla A.
Published: May 2017

The global stability of laminar axisymmetric low-density jets is investigated in the low Mach number approximation. The linear modal dynamics is found to be characterised by two features: a stable arc branch of eigenmodes and an isolated eigenmode. Both features are studied in detail, revealing that, whereas the former is highly sensitive to numerical domain size and its existence can be linked to spurious feedback from the outflow boundary, the latter is the physical eigenmode that is responsible for the appearance of self-sustained oscillations in low-density jets observed in experiments at low Mach numbers. In contrast to previous local spatio-temporal stability analyses, the present global analysis permits, for the first time, the determination of the critical conditions for the onset of global instability, as well the frequency of the associated oscillations, without additional hypotheses, yielding predictions in fair agreement with previous experimental observations. It is shown that under the conditions of those experiments, viscosity variation with composition, as well as buoyancy, only have a small effect on the onset of instability.
Particle resuspension by a periodically forced impinging jet
Authors: Wu Wen , Soligo Giovanni , Marchioli Cristian , Soldati Alfredo , Piomelli Ugo
Published: May 2017

When hovering over sandy terrain, the rotor of helicopters generates a downward jet that induces resuspension of dust and debris. We investigate the mechanisms that govern particle resuspension in such flow using an Eulerian–Lagrangian approach based on large-eddy simulation of turbulence. The wake generated by the helicopter is modelled as a vertical impinging jet, to which a sequence of periodically forced azimuthal vortices is superposed. The resulting flow field provides a unique range of flow scales with which the particles can interact. Downstream of the impingement region, layers of negative azimuthal vorticity (secondary vortices) form on the upwash side of the primary azimuthal (large-scale) vortices. These layers then detach from the surface together with the near-wall (small-scale) vortices populating the wall-jet region. We show how the dynamics of sediments is governed by its interaction with these structures. After initial lift off from the impingement surface, particles accumulate in regions where near-wall vortices roll around the impinging azimuthal vortex, forming rib-like structures that either propel particles away from the azimuthal vortex or entrap them in the shear layer between the azimuthal and secondary vortices. We demonstrate that these trapped particles are more likely to reach the outer flow region and generate a persistent cloud of airborne particles. We also show that, in a time-averaged sense, particle resuspension and deposition fluxes balance each other near the impingement surface.
Topology of vortex breakdown in closed polygonal containers
Authors: Naumov Igor V. , Podolskaya Irina Yu.
Published: May 2017

The topology of vortex breakdown in the confined flow generated by a rotating lid in a closed container with a polygonal cross-section geometry has been analysed experimentally and numerically for different height/radius aspect ratios $h$ from 0.5 to 3.0. The locations of stagnation points of the breakdown bubble emergence and corresponding Reynolds numbers were determined experimentally and numerically by STAR-CCM+ computational fluid dynamics software for square, pentagonal, hexagonal and octagonal cross-section configurations. The flow pattern and velocity were observed and measured by combining seeding particle visualization and laser Doppler anemometry. The vortex breakdown size and position on the container axis were identified for Reynolds numbers ranging from 500 to 2800 in steady flow conditions. The obtained results were compared with the flow structure in the closed cylindrical container. The results allowed revealing regularities of formation of the vortex breakdown bubble depending on $Re$ and $h$ and the cross-section geometry of the confined container. It was found in a diagram of $Re$ versus $h$ that reducing the number of cross-section angles from eight to four shifts the breakdown bubble location to higher Reynolds numbers and a smaller aspect ratio. The vortex breakdown bubble area for octagonal cross-section was detected to correspond to the one for the cylindrical container but these areas for square and cylindrical containers do not overlap in the entire range of aspect ratio.
Finite Reynolds number effect on the scaling range behaviour of turbulent longitudinal velocity structure functions
Authors: Tang S. L. , Antonia R. A. , Djenidi L. , Danaila L. , Zhou Y.
Published: May 2017

The effect of large-scale forcing on the second- and third-order longitudinal velocity structure functions, evaluated at the Taylor microscale $r=\unicode[STIX]{x1D706}$, is assessed in various turbulent flows at small to moderate values of the Taylor microscale Reynolds number $R_{\unicode[STIX]{x1D706}}$. It is found that the contribution of the large-scale terms to the scale by scale energy budget differs from flow to flow. For a fixed $R_{\unicode[STIX]{x1D706}}$, this contribution is largest on the centreline of a fully developed channel flow but smallest for stationary forced periodic box turbulence. For decaying-type flows, the contribution lies between the previous two cases. Because of the difference in the large-scale term between flows, the third-order longitudinal velocity structure function at $r=\unicode[STIX]{x1D706}$ differs from flow to flow at small to moderate $R_{\unicode[STIX]{x1D706}}$. The effect on the second-order velocity structure functions appears to be negligible. More importantly, the effect of $R_{\unicode[STIX]{x1D706}}$ on the scaling range exponent of the longitudinal velocity structure function is assessed using measurements of the streamwise velocity fluctuation $u$, with $R_{\unicode[STIX]{x1D706}}$ in the range 500–1100, on the axis of a plane jet. It is found that the magnitude of the exponent increases as $R_{\unicode[STIX]{x1D706}}$ increases and the rate of increase depends on the order $n$. The trend of published structure function data on the axes of an axisymmetric jet and a two-dimensional wake confirms this dependence. For a fixed $R_{\unicode[STIX]{x1D706}}$, the exponent can vary from flow to flow and for a given flow, the larger $R_{\unicode[STIX]{x1D706}}$ is, the closer the exponent is to the value predicted by Kolmogorov (Dokl. Akad. Nauk SSSR, vol. 30, 1941a, pp. 299–303) (hereafter K41). The major conclusion is that the finite Reynolds number effect, which depends on the flow, needs to be properly accounted for before determining whether corrections to K41, arising from the intermittency of the energy dissipation rate, are needed. We further point out that it is imprudent, if not incorrect, to associate the finite Reynolds number effect with a consequence of the modified similarity hypothesis introduced by Kolmogorov (J. Fluid Mech., vol. 13, 1962, pp. 82–85) (K62); we contend that this association has misled the vast majority of post K62 investigations of the consequences of K62.
Open Access in the USA: A Ridiculously Brief and Hopelessly Incomplete Overview
Authors: Engsberg Mark
Published: May 2017

Open access (OA) in the United States is similar to a crazy quilt. There is a patchwork of OA policy and practice among the many federal, state, and local jurisdictions in the United States, as well as individual policies and practices in individual institutions, whether those are academic, business, or governmental. By way of a reminder, the United States is a federal republic consisting of 50 states, plus Washington, D.C., five major territories, and various possessions. Most readers know that already, but what one should also understand is that each of the states and territories has its own policies with respect to OA, as does the Federal government.
PROTESTANT LEGAL THEORY? APOLOGY AND OBJECTIONS
Authors: Hammond Jeffrey B.
Published: May 2017

The academic interdisciplinary study of law and religion is in a unique place, brimming with hope and promise. This constellation of scholars, conferences, journals, academic centers, books and book series, and public interest law firms has matured considerably since the “path-breaking” commencement of the movement, the publication of Harold Berman's 1974 short book, The Interaction of Law and Religion. No longer can the study of law and religion be solely identified with the study of the First Amendment's religion clauses. Scholars have explored topics both large scale and fine grain in history, church law, the intersection of religious ethics and law, religion and international human rights law, and in other subareas of the field.
Benchmarks for reasoning with syntax trees containing binders and contexts of assumptions
Authors: FELTY AMY , MOMIGLIANO ALBERTO , PIENTKA BRIGITTE
Published: May 2017

A variety of logical frameworks supports the use of higher order abstract syntax in representing formal systems. Although these systems seem superficially the same, they differ in a variety of ways, for example, how they handle acontextof assumptions and which theorems about a given formal system can be concisely expressed and proved. Our contributions in this paper are two-fold: (1) We develop a common infrastructure and language for describing benchmarks for systems supporting reasoning with binders, and (2) we present several concrete benchmarks, which highlight a variety of different aspects of reasoning within a context of assumptions. Our work provides the background for the qualitative comparison of different systems that we have completed in a separate paper. It also allows us to outline future fundamental research questions regarding the design and implementation of meta-reasoning systems.
“THE DEAD MAN COME TO LIFE AGAIN”: EDWARD ALBERT AND THE STRATEGIES OF BLACK ENDURANCE
Authors: Prizel Natalie
Published: May 2017

This essay tells a story of endurance: the endurance of a person and the endurance of an object in an archive, both of which have survived despite their apparent fungibility and ephemerality. It focuses on a Jamaican veteran of the navy and merchant marine – one Edward Albert – who lost his legs while at sea and therefore took to working at various intervals as a crossing sweeper, beggar, shop-owner, and author in London and Glasgow. Albert should have been lost. His shipmates burnt his legs to the point of bursting, and his doctors presumed him to be dead following their amputation. I located Edward Albert initially in the pages of Henry Mayhew's massive, unwieldy, almost unnavigable archive, the four volumes of London Labour and the London Poor. Mayhew interviews Albert in his home and then refers to a small chapbook Albert sells to accompany his begging. A simple WorldCat search led me to a copy of the book, housed at the University of Washington in Seattle. It had endured.
“THE FASHIONS OF THE CURRENT SEASON”: RECENT CRITICAL WORK ON VICTORIAN SENSATION FICTION
Authors: Beller Anne-Marie
Published: May 2017

Henry Mansel, writing in 1863, was confident in his prediction that the current popular vogue for sensation novels was an ephemeral phase, soon to pass into a deserved oblivion. Yet by the end of a decade marked by extensive and frequently hysterical debates over the genre, the future Poet Laureate, Alfred Austin, was still bemoaning the ubiquity of sensation fiction: “the world may congratulate itself when the last sensational novel has been written and forgotten” (424). Mansel and Austin would doubtless have been astounded (and appalled) at the current status of mid-Victorian sensation fiction in the realm of academic scholarship. Far from being a long-forgotten, inconsequential moment in literary history, the sensation novels of authors such as Wilkie Collins, Mary Elizabeth Braddon, Ellen Wood, and Ouida have prompted a plethora of critical studies, which have impacted on our wider understanding of the dynamics and influences of mid-Victorian literary and publishing practices.
Do we Always Act on Maxims?
Authors: Nyholm Sven
Published: May 2017

It is commonly thought that on Kant’s view of action, ‘everyone always acts on maxims’. Call this the ‘descriptive reading’. This reading faces two important problems. First, the idea that people always act on maxims offends against common sense: it clashes with our ordinary ideas about human agency. Second, there are various passages in which Kant says that it is ‘rare’ and ‘admirable’ to firmly adhere to a set of basic principles that we adopt for ourselves. This article offers an alternative: the ‘normative reading’. On this reading, it is a normative ideal to adopt and act on maxims: it is one of the things we would do if our reason were fully in control of our decision-making.
Was Kant a ‘Kantian Constructivist’?
Authors: Schwartz Jeremy
Published: May 2017

Both metaethicists and Kant scholars alike use the phrase ‘Kantian constructivism’ to refer to a kind of austere constructivism that holds that substantive ethical conclusions can be derived from the practical standpoint of rational agency as such. I argue that this widespread understanding of Kant is incompatible with Kant’s claim that the Categorical Imperative is a synthetica prioripractical judgement. Taking this claim about the syntheticity of the Categorical Imperative seriously implies that moral judgements follow from extra-logical but necessary principles. These principles have to do not with the laws of practical thinking but the laws of practical thought about an object. I conclude that historical Kant was not what has come to be called a ‘Kantian constructivist’.
Scalable, ultra-resistant structural colors based on network metamaterials
Authors: Galinski Henning , Favraud Gael , Dong Hao , Gongora Juan S Totero , Favaro Grégory , Döbeli Max , Spolenak Ralph , Fratalocchi Andrea , Capasso Federico
Published: May 2017

Structural colors have drawn wide attention for their potential as a future printing technology for various applications, ranging from biomimetic tissues to adaptive camouflage materials. However, an efficient approach to realize robust colors with a scalable fabrication technique is still lacking, hampering the realization of practical applications with this platform. Here, we develop a new approach based on large-scale network metamaterials that combine dealloyed subwavelength structures at the nanoscale with lossless, ultra-thin dielectric coatings. By using theory and experiments, we show how subwavelength dielectric coatings control a mechanism of resonant light coupling with epsilon-near-zero regions generated in the metallic network, generating the formation of saturated structural colors that cover a wide portion of the spectrum. Ellipsometry measurements support the efficient observation of these colors, even at angles of 70°. The network-like architecture of these nanomaterials allows for high mechanical resistance, which is quantified in a series of nano-scratch tests. With such remarkable properties, these metastructures represent a robust design technology for real-world, large-scale commercial applications.
Tradict enables accurate prediction of eukaryotic transcriptional states from 100 marker genes
Authors: Biswas Surojit , Kerner Konstantin , Teixeira Paulo José Pereira Lima , Dangl Jeffery L. , Jojic Vladimir , Wigge Philip A.
Published: May 2017

Transcript levels are a critical determinant of the proteome and hence cellular function. Because the transcriptome is an outcome of the interactions between genes and their products, it may be accurately represented by a subset of transcript abundances. We develop a method, Tradict (transcriptome predict), capable of learning and using the expression measurements of a small subset of 100 marker genes to predict transcriptome-wide gene abundances and the expression of a comprehensive, but interpretable list of transcriptional programs that represent the major biological processes and pathways of the cell. By analyzing over 23,000 publicly available RNA-Seq data sets, we show that Tradict is robust to noise and accurate. Coupled with targeted RNA sequencing, Tradict may therefore enable simultaneous transcriptome-wide screening and mechanistic investigation at large scales.
Identifying individuals with physician-diagnosed chronic obstructive pulmonary disease in primary care electronic medical records: a retrospective chart abstraction study
Authors: Lee Theresa M. , Tu Karen , Wing Laura L. , Gershon Andrea S.
Published: May 2017

Little is known about using electronic medical records to identify patients with chronic obstructive pulmonary disease to improve quality of care. Our objective was to develop electronic medical record algorithms that can accurately identify patients with obstructive pulmonary disease. A retrospective chart abstraction study was conducted on data from the Electronic Medical Record Administrative data Linked Database (EMRALD®) housed at the Institute for Clinical Evaluative Sciences. Abstracted charts provided the reference standard based on available physician-diagnoses, chronic obstructive pulmonary disease-specific medications, smoking history and pulmonary function testing. Chronic obstructive pulmonary disease electronic medical record algorithms using combinations of terminology in the cumulative patient profile (CPP; problem list/past medical history), physician billing codes (chronic bronchitis/emphysema/other chronic obstructive pulmonary disease), and prescriptions, were tested against the reference standard. Sensitivity, specificity, and positive/negative predictive values (PPV/NPV) were calculated. There were 364 patients with chronic obstructive pulmonary disease identified in a 5889 randomly sampled cohort aged ≥ 35 years (prevalence = 6.2%). The electronic medical record algorithm consisting of ≥ 3 physician billing codes for chronic obstructive pulmonary disease per year; documentation in the CPP; tiotropium prescription; or ipratropium (or its formulations) prescription and a chronic obstructive pulmonary disease billing code had sensitivity of 76.9% (95% CI:72.2–81.2), specificity of 99.7% (99.5–99.8), PPV of 93.6% (90.3–96.1), and NPV of 98.5% (98.1–98.8). Electronic medical record algorithms can accurately identify patients with chronic obstructive pulmonary disease in primary care records. They can be used to enable further studies in practice patterns and chronic obstructive pulmonary disease management in primary care.
Gender Differences in Bile Acids and Microbiota in Relationship with Gender Dissimilarity in Steatosis Induced by Diet and FXR Inactivation
Authors: Sheng Lili , Jena Prasant Kumar , Liu Hui-Xin , Kalanetra Karen M. , Gonzalez Frank J. , French Samuel W. , Krishnan Viswanathan V. , Mills David A. , Wan Yu-Jui Yvonne
Published: May 2017

This study aims to uncover how specific bacteria and bile acids (BAs) contribute to steatosis induced by diet and farnesoid X receptor (FXR) deficiency in both genders. A control diet (CD) and Western diet (WD), which contains high fat and carbohydrate, were used to feed wild type (WT) and FXR knockout (KO) mice followed by phenotyping characterization as well as BA and microbiota profiling. Our data revealed that male WD-fed FXR KO mice had the most severe steatosis and highest hepatic and serum lipids as well as insulin resistance among the eight studied groups. Gender differences in WD-induced steatosis, insulin sensitivity, and predicted microbiota functions were all FXR-dependent. FXR deficiency enriched Desulfovibrionaceae, Deferribacteraceae, and Helicobacteraceae, which were accompanied by increased hepatic taurine-conjugated cholic acid and β-muricholic acid as well as hepatic and serum lipids. Additionally, distinct microbiota profiles were found in WD-fed WT mice harboring simple steatosis and CD-fed FXR KO mice, in which the steatosis had a potential to develop into liver cancer. Together, the presented data revealed FXR-dependent concomitant relationships between gut microbiota, BAs, and metabolic diseases in both genders. Gender differences in BAs and microbiota may account for gender dissimilarity in metabolism and metabolic diseases.
Common Variants in OPG Confer Risk to Bone Mineral Density Variation and Osteoporosis Fractures
Authors: Sheng Xiaoyong , Cai Guangyong , Gong Xingjun , Yao Zouying , Zhu Ye
Published: May 2017

Although many common variants have been identified for bone mineral density (BMD) and osteoporosis fractures, all the identified risk variants could only explain a small portion of heritability of BMD and osteoporosis fractures. OPG belongs to the tumor necrosis factor receptor superfamily, which plays a crucial role in bone remodeling and is thus a promising candidate gene of osteoporosis. Several studies have explored the association of OPG variants with BMD or osteoporosis fractures, however, the results remain inconsistent among different populations. In the study, we first assessed the relationship between OPG variants and BMD or osteoporosis fractures in our sample size (227 subjects with postmenopausal osteoporosis and 189 controls), and then performed a systematic meta-analysis. Among the nine SNPs genotyped, rs6469804 and rs2073618 showed significant associations with both BMD and osteoporotic fractures, while rs3102735 was only associated with BMD in our samples (P < 0.05). For meta-analyses, data for a total of 12 SNPs were pooled (4725 patients and 37804 controls), and five SNPs, including rs6993813, rs6469804, rs3134070, rs2073618 and rs3102734, showed association with osteoporosis fractures (P < 0.05). On light of the above analysis, we believe that OPG is one promising susceptibility gene of BMD or osteoporotic fractures.
Selective doping of Ni2+ in highly transparent glass-ceramics containing nano-spinels ZnGa2O4 and Zn1+x
Ga2−2x
Ge
x
O4 for broadband near-infrared fiber amplifiers
Authors: Gao Zhigang , Liu Yinyao , Ren Jing , Fang Zaijin , Lu Xiaosong , Lewis Elfed , Farrell Gerald , Yang Jun , Wang Pengfei
Published: May 2017

Selective doping of Ni2+ in octahedral sites provided by nanocrystals embedded in glass-ceramics (GCs) is crucial to the enhancement of broadband near-infrared (NIR) emission. In this work, a NIR emission with a full-width-at-half-maximum (FWHM) of 288 nm is first reported from ZnGa2O4: Ni2+ nano-spinels embedded GCs with excellent transparency. A comparison is made of the NIR luminescence properties of Ni2+ doped GCs containing ZnGa2O4, germanium-substituted ZnGa2O4 nano-spinels (Zn1+x
Ga2−2x
Ge
x
O4), and Zn2GeO4/Li2Ge4O9 composite nanocrystals that are free of Ga3+. The results show that ZnGa2O4: Ni2+ GCs exhibit a significantly enhanced NIR emission. The incorporation of the nucleating agent TiO2 is favored in terms of the increased luminescence intensity and prolonged lifetime. The possible causes for the enhancement effect are identified from the crystal structure/defects viewpoint. The newly developed GCs incorporate good reproducibility to allow for a tolerance of thermal treatment temperature and hence hold great potential of fiberization via the recently proposed “melt-in-tube” method. They can be considered as promising candidates for broadband fiber amplifiers.
Effect of Trichoderma harzianum on maize rhizosphere microbiome and biocontrol of Fusarium Stalk rot
Authors: Saravanakumar Kandasamy , Li Yaqian , Yu Chuanjin , Wang Qiang-qiang , Wang Meng , Sun Jianan , Gao Jin-xin , Chen Jie
Published: May 2017

Fusarium stalk rot (FSR) caused by Fusarium graminearum (FG) significantly affects the productivity of maize grain crops. Application of agrochemicals to control the disease is harmful to environment. In this regard, use of biocontrol agent (BCA) is an alternative to agrochemicals. Although Trichoderma species are known as BCA, the selection of host-pathogen specific Trichoderma is essential for the successful field application. Hence, we screened a total of 100 Trichoderma isolates against FG, selected Trichoderma harzianum (CCTCC-RW0024) for greenhouse experiments and studied its effect on changes of maize rhizosphere microbiome and biocontrol of FSR. The strain CCTCC-RW0024 displayed high antagonistic activity (96.30%), disease reduction (86.66%), biocontrol-related enzyme and gene expression. The root colonization of the strain was confirmed by eGFP tagging and qRT-PCR analysis. Pyrosequencing revealed that exogenous inoculation of the strain in maize rhizosphere increased the plant growth promoting acidobacteria (18.4%), decreased 66% of FG, and also increased the plant growth. In addition, metabolites of this strain could interact with pathogenicity related transcriptional cofactor FgSWi6, thereby contributing to its inhibition. It is concluded that T. harzianum strain CCTCC-RW0024 is a potential BCA against FSR.
Characterization of off-odours and potentially harmful substances in a fancy dress accessory handbag for children
Authors: Wiedmer Christoph , Velasco-Schön Cristina , Buettner Andrea
Published: May 2017

A fancy dress accessory handbag for children was claimed by consumers to exhibit an offensive smell. Sensory characterization by an expert panel revealed, amongst others, rubber- and car tire - like notes. For elucidation of the molecular reasons of this sensory defect, the volatile fraction of the product was isolated by means of solvent extraction and high vacuum distillation. Identification of the main odorants was accomplished by means of one- and two-dimensional gas chromatography, with parallel mass spectrometric and olfactometric detection. In total more than 60 odorants were detected in the sample and more than 30 of these odour-active substances could be identified. Amongst them were a number of naphthalene derivatives as well as saturated and mono- or di-unsaturated carbonyl compounds. The naphthalene derivatives that were identified in the children’s article appeared to be mainly responsible for the characteristic off-odour. Additionally, a GC-MS-screening for polycyclic aromatic hydrocarbons (PAHs) was performed, which revealed the presence of 15 PAHs in total. However, 14 of them were of no relevance for the smell of the product.
The active site structure and catalytic mechanism of arsenite oxidase
Authors: Warelow Thomas P. , Pushie M. Jake , Cotelesage Julien J. H. , Santini Joanne M. , George Graham N.
Published: May 2017

Arsenite oxidase is thought to be an ancient enzyme, originating before the divergence of the Archaea and the Bacteria. We have investigated the nature of the molybdenum active site of the arsenite oxidase from the Alphaproteobacterium Rhizobium sp. str. NT-26 using a combination of X-ray absorption spectroscopy and computational chemistry. Our analysis indicates an oxidized Mo(VI) active site with a structure that is far from equilibrium. We propose that this is an entatic state imposed by the protein on the active site through relative orientation of the two molybdopterin cofactors, in a variant of the Rây-Dutt twist of classical coordination chemistry, which we call the pterin twist hypothesis. We discuss the implications of this hypothesis for other putatively ancient molybdopterin-based enzymes.
The quantum Zeno and anti-Zeno effects with strong system-environment coupling
Authors: Chaudhry Adam Zaman
Published: May 2017

To date, studies of the quantum Zeno and anti-Zeno effects focus on quantum systems that are weakly interacting with their environment. In this paper, we investigate what happens to a quantum system under the action of repeated measurements if the quantum system is strongly interacting with its environment. We consider as the quantum system a single two-level system coupled strongly to a collection of harmonic oscillators. A so-called polaron transformation is then used to make the problem in the strong system-environment coupling regime tractable. We find that the strong coupling case exhibits quantitative and qualitative differences as compared with the weak coupling case. In particular, the effective decay rate does not depend linearly on the spectral density of the environment. This then means that, in the strong coupling regime that we investigate, increasing the system-environment coupling strength can actually decrease the effective decay rate. We also consider a collection of two-level atoms coupled strongly with a common environment. In this case, we find that there are further differences between the weak and strong coupling cases since the two-level atoms can now indirectly interact with one another due to the common environment.
Preclinical evaluation of PAC1 targeting with radiolabeled Maxadilan
Authors: Joosten Lieke , Brom Maarten , Schäfer Martin K. H. , Boerman Otto C. , Weihe Eberhard , Gotthardt Martin
Published: May 2017

There is an ongoing search for new tracers to optimize imaging of beta cell-derived tumors (insulinomas). The PAC1 receptor, expressed by insulinomas, can be used for targeting of these tumors. Here, we investigated whether radiolabeled maxadilan could be used for insulinoma imaging. Maxadilan was C- or N-terminally conjugated with DTPA (termed maxadilan-DPTA or DTPA-maxadilan respectively). BALB/c nude mice bearing subcutaneous INS-1 tumors were injected with either In-111-labeled maxadilan-DTPA or In-111-DTPA-maxadilan. Biodistribution studies were carried out at 1, 2 and 4 hours after injection and SPECT/CT imaging 1 and 4 hours after injection of maxadilan-DTPA-111In. Radiolabeling of maxadilan-DTPA (680 MBq/nmol) was more efficient than of DTPA-maxadilan (55 MBq/nmol). Conjugation with DTPA slightly reduced receptor binding affinity in vitro: IC50 values were 3.2, 21.0 and 21.0 nM for maxadilan, natIn-DTPA-maxadilan and maxadilan-DTPA-natIn respectively. Upon i.v. injection maxadilan-DTPA-111In accumulated specifically in INS-1 tumors (7.30 ± 1.87%ID/g) and in the pancreas (3.82 ± 0.22%ID/g). INS-1 tumors were clearly visualized by small animal SPECT/CT. In conclusion, this study showed that the high affinity of maxadilan to the PAC1 receptor was maintained after DTPA conjugation. Furthermore, radiolabeled maxadilan-DTPA accumulated specifically in INS-1 tumors and, therefore, may qualify as a useful tracer to image insulinomas.
Hybrid Three-Mode Correlation and Squeezing in a Pr3+:YSO Crystal
Authors: Liu Zongchen , Ahmed Irfan , Abdisa Garuma , Jiang Zihai , Fan Shuwei , Wang Hongxing , Zhang Yanpeng
Published: May 2017

We report the generation of three-mode hybrid intensity-noise correlation and intensity-difference squeezing of spontaneous parametric four-wave mixing (SP-FWM) and fourth-order fluorescence (FL) signals in the heteronuclear-like (three-level Λ-type) molecular structure of a Pr3+:Y2SiO5 (Pr3+:YSO) crystal using the nonlinear cross-Kerr effect under a polarized dressing effect. In the semi-classical view of a Kerr nonlinear medium, the amplitude of two-mode hybrid correlations of this kind is subject to a limit determined by the hybrid maximally entangled state. Whereas the degree of correlation and squeezing is determined by the dressing effects of the input laser fields participating in the SP-FWM process. We also find that the variations in magnitude of three-mode hybrid intensity-noise correlation and intensity-difference squeezing are consistent with nonlinear cross-Kerr processes. Such a three-mode hybrid signal may have potential applications in long-distance communication, dense coding, all-optical communication and quantum storage on photonic chips.
Light perception in aerial tissues enhances DWF4 accumulation in root tips and induces root growth
Authors: Sakaguchi Jun , Watanabe Yuichiro
Published: May 2017

Many attempts have been made to characterize the activities of brassinosteroids (BRs), which are important plant hormones. The crosstalk between light perception and the BR signalling pathway has been extensively studied regarding its effects on photomorphogenesis, especially in elongating etiolated hypocotyls. In contrast, how and where the light induces BR biosynthesis remain uncharacterized. DWF4 is one of the main enzymes involved in the BR biosynthesis pathway in Arabidopsis thaliana. We established DWF4-GUS A. thaliana lines in a homozygous dwf4-102 genetic background, but functionally complemented with a genomic DWF4 sequence fused in-frame with a β-glucuronidase (GUS) marker gene. The DWF4-GUS plants enabled the visualization of the accumulation of DWF4 under different conditions. We investigated the effects of aboveground light on root and hypocotyl growth. We observed that root length increased when shoots were maintained under light irrespective of whether roots were exposed to light. We also determined that light perception in aerial tissues enhanced DWF4 accumulation in the root tips. Overall, our data indicate that BR biosynthesis is promoted in the root tip regions by an unknown mechanism in distantly located shoot tissues exposed to light, leading to increased root growth.
Anomalous in-plane anisotropic Raman response of monoclinic semimetal 1 T´-MoTe
2
Authors: Song Qingjun , Wang Haifeng , Pan Xingchen , Xu Xiaolong , Wang Yilun , Li Yanping , Song Fengqi , Wan Xiangang , Ye Yu , Dai Lun
Published: May 2017

The recently discovered two-dimensional (2D) semimetal 1 T´-MoTe2 exhibits colossal magnetoresistance and superconductivity, driving a strong research interest in the material’s quantum phenomena. Unlike the typical hexagonal structure found in many 2D materials, the 1 T´-MoTe2 lattice has strong in-plane anisotropy. A full understanding of the anisotropy is necessary for the fabrication of future devices which may exploit these quantum and topological properties, yet a detailed study of the material’s anisotropy is currently lacking. While angle resolved Raman spectroscopy has been used to study anisotropic 2D materials, such as black phosphorus, there has been no in-depth study of the Raman dependence of 1 T´-MoTe2 on different layer numbers and excitation energies. Here, our angle resolved Raman spectroscopy shows intricate Raman anisotropy dependences of 1 T´-MoTe2 on polarization, flake thickness (from single layer to bulk), photon, and phonon energies. Using a Paczek approximation, the anisotropic Raman response can be captured in a classical framework. Quantum mechanically, first-principle calculations and group theory reveal that the anisotropic electron-photon and electron-phonon interactions are nontrivial in the observed responses. This study is a crucial step to enable potential applications of 1 T´-MoTe2 in novel electronic and optoelectronic devices where the anisotropic properties might be utilized for increased functionality and performance.
Stretchable, Twisted Conductive Microtubules for Wearable Computing, Robotics, Electronics, and Healthcare
Authors: Do Thanh Nho , Visell Yon
Published: May 2017

Stretchable and flexible multifunctional electronic components, including sensors and actuators, have received increasing attention in robotics, electronics, wearable, and healthcare applications. Despite advances, it has remained challenging to design analogs of many electronic components to be highly stretchable, to be efficient to fabricate, and to provide control over electronic performance. Here, we describe highly elastic sensors and interconnects formed from thin, twisted conductive microtubules. These devices consist of twisted assemblies of thin, highly stretchable (>400%) elastomer tubules filled with liquid conductor (eutectic gallium indium, EGaIn), and fabricated using a simple roller coating process. As we demonstrate, these devices can operate as multimodal sensors for strain, rotation, contact force, or contact location. We also show that, through twisting, it is possible to control their mechanical performance and electronic sensitivity. In extensive experiments, we have evaluated the capabilities of these devices, and have prototyped an array of applications in several domains of stretchable and wearable electronics. These devices provide a novel, low cost solution for high performance stretchable electronics with broad applications in industry, healthcare, and consumer electronics, to emerging product categories of high potential economic and societal significance.