bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inference of Episodic Changes in Natural Selection Acting on Protein Coding Sequences via CODEML
Authors: Bielawski Joseph P. , Baker Jennifer L. , Mingrone Joseph 
Published: June 2016

AbstractThis unit provides protocols for using the CODEML program from the PAML package to make inferences about episodic natural selection in protein‐coding sequences. The protocols cover inference tasks such as maximum likelihood estimation of selection intensity, testing the hypothesis of episodic positive selection, and identifying sites with a history of episodic evolution. We provide protocols for using the rich set of models implemented in CODEML to assess robustness, and for using bootstrapping to assess if the requirements for reliable statistical inference have been met. An example dataset is used to illustrate how the protocols are used with real protein‐coding sequences. The workflow of this design, through automation, is readily extendable to a larger‐scale evolutionary survey. © 2016 by John Wiley & Sons, Inc.
Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families
Authors: Barquist Lars , Burge Sarah W. , Gardner Paul P. 
Published: June 2016

AbstractEmerging high‐throughput technologies have led to a deluge of putative non‐coding RNA (ncRNA) sequences identified in a wide variety of organisms. Systematic characterization of these transcripts will be a tremendous challenge. Homology detection is critical to making maximal use of functional information gathered about ncRNAs: identifying homologous sequence allows us to transfer information gathered in one organism to another quickly and with a high degree of confidence. ncRNA presents a challenge for homology detection, as the primary sequence is often poorly conserved and de novo secondary structure prediction and search remain difficult. This unit introduces methods developed by the Rfam database for identifying “families” of homologous ncRNAs starting from single “seed” sequences, using manually curated sequence alignments to build powerful statistical models of sequence and structure conservation known as covariance models (CMs), implemented in the Infernal software package. We provide a step‐by‐step iterative protocol for identifying ncRNA homologs and then constructing an alignment and corresponding CM. We also work through an example for the bacterial small RNA MicA, discovering a previously unreported family of divergent MicA homologs in genus Xenorhabdus in the process. © 2016 by John Wiley & Sons, Inc.
Size‐Dependence of the Activity of Gold Nanoparticle‐Loaded Titanium(IV) Oxide Plasmonic Photocatalyst for Water Oxidation
Authors: Teranishi Miwako , Wada Masataka , Naya Shin‐ichi , Tada Hiroaki 
Published: June 2016

AbstractMesoporous TiO2 nanocrystalline film was formed on fluorine‐doped tin oxide electrode (TiO2/FTO) and gold nanoparticles (NPs) of different sizes were loaded onto the surface with the loading amount kept constant (Au/TiO2/FTO). Visible‐light irradiation (λ>430 nm) of the Au/TiO2/FTO photoanode in a photoelectrochemical cell with the structure of photoanode|0.1 m NaClO4 aqueous solution|Ag/AgCl (reference electrode)|glassy carbon (cathode) leads to the oxidation of water to oxygen (O2). We show that the visible‐light activity of the Au/TiO2/FTO anode increases with a decrease in Au particle size (d) at 2.9≤d≤11.9 nm due to the enhancement of the charge separation and increasing photoelectrocatalytic activity.
Metal‐Dependent Nucleobase Recognition by Picolinamide
Authors: Dengale Rohit A. , Thopate Shankar R. , Lönnberg Tuomas 
Published: June 2016

AbstractA C‐nucleoside featuring picolinamide as the base moiety has been synthesized and incorporated in the middle of a DNA oligonucleotide. The melting temperatures of duplexes formed by this modified oligonucleotide with its unmodified counterparts placing either adenine, cytosine, guanine or thymine opposite to the picolinamide residue were found to be highly dependent on the identity and concentration of transition metal ions in the samples. For example, AgI uniquely promoted pairing with adenine and PdII with guanine. Pairing with cytosine, on the other hand, was retarded by all of the metal ions studied (AgI, CuII, HgII, NiII, PdII and ZnII).
Surfactant directed synthesis of mesoporous alumina and α‐alumina single crystal
Authors: Mishra Geetanjali , Dash Barsha , Dash Ajit , Bhattacharya I.N. 
Published: June 2016

Mesoporous Al2O3 were positively synthesized via treatment of the freshly precipitated amorphous alumina gel using aluminium sulphate as aluminium source, and sodium dodecyl sulphate (SDS) as structure‐directing agent (SDAs). The microstructures, morphologies and textural properties of the as‐prepared materials were characterized by X‐ray diffraction (XRD), transmission electron microscopy (TEM) and thermo gravimetric analysis (TG‐DTA). The calcined product at 600 °C was highly porous in nature having a BET surface area of 42 m2/g. These porous Al2O3 exhibits excellent adsorption performance for Congo red and the corresponding decolourisation efficiencies reached 99% in just 15 min at 27 °C. The subsequent calcined product at 1200 °C is the alpha alumina single crystal hexagonal platelets with rhombohedral crystallization.
A Power Output Estimate of Cylindrically Shaped Flexible Photovoltaic Module with Polygonal Approximation
Authors: SHIBASAKI MAMORU , YACHI TOSHIAKI 
Published: June 2016

SUMMARYFlexible photovoltaic (PV) modules have received a great deal of attention for use in PV systems. At present, the most important issue to be resolved is the optimum shape of flexible PV modules for obtaining maximum power output. A design tool specifically tailored for the flexible PV module is required for this purpose. In the present study, a new method is proposed for estimating the power output of a cylindrically shaped flexible PV module, taking into account the uneven irradiation and temperature that occurs for a curved surface. The average irradiation over the area of the entire module is used in the equation of the proposed method. The temperature is calculated based on the root mean square (RMS) of the irradiation over the area of the entire module. The average and RMS of the irradiation are calculated based on the directional dependence of the global horizontal irradiance. The estimated and measured power outputs are compared. The error rate of the total power output is 2.6%, and the mean absolute percentage error of the power output is 6.8%. The proposed method can reduce the amount of calculation to compare with a conventional method having the same mean absolute percentage error.
An Investigation of Size‐Reduction Effects in High Power Density Boost Converters with a Magnetic Coupling
Authors: AOTO SHOGO , KIMURA SHOTA , IMAOKA JUN , YAMAMOTO MASAYOSHI 
Published: June 2016

SUMMARYThe dc–dc converter using integrated magnetic components that may achieve high power density has gained attention in environmentally friendly cars such as electric vehicles and hybrid electric vehicles. This paper focused on interleaved boost converters using close‐coupled inductors (CCIs) and loose‐coupled inductors (LCIs) that are the integrated magnetic components. Following, detailed electromagnetically analysis for these circuit types were conducted in order to calculate volume of inductors and capacitors that are occupied the large part of space in the converters. The total volume of inductors and capacitors in these circuits were demonstrated clearly through comparison with conventional circuits such as an interleaved boost converter and a single‐phase boost converter. As a result, it became clear that interleaved boost converter using LCIs was effective for miniaturization of total volume. Furthermore, duty ratio of the minimum volume of CCI method is different from the duty ratio of the minimum volume of LCI method.
Effects of analgesics on olfactory function and the perception of intranasal trigeminal stimuli
Authors: Mizera L. , Gossrau G. , Hummel T. , Haehner A. 
Published: June 2016

AbstractBackgroundThere is some evidence suggesting that analgesics have an impact on human chemosensory function, especially opioids and cannabinoids are known to interfere with olfactory function. However, largely unknown is the effect of a long‐term use of analgesics on the intranasal trigeminal system so far. Here, we investigated olfactory function and the perception of intranasal trigeminal stimuli in pain patients with long‐term use of analgesics compared to age‐matched healthy controls.MethodsFor this purpose, a psychophysical approach was chosen to measure these sensory functions in 100 chronic pain patients and 95 controls. Olfactory testing was performed using the ‘Sniffin’ Sticks’ test kit, which involves tests for odour threshold, odour discrimination and odour identification. Further, participants were asked to rate the intensity of trigeminal stimuli by using a visual analogue scale.ResultsWe observed that the chronic use of pain medication was associated with significantly reduced perception of intranasal trigeminal stimuli and olfactory function compared to age‐matched controls without intake of analgesics. Results indicate that non‐opioid and opioid drugs, or a combination of both did not differ in their effects on chemosensory function. Further, after eliminating the effect of a co‐existing depression and the use of co‐analgesics, the negative influence of analgesics on olfactory function and trigeminal perception was still evident.ConclusionThe observed effect might be mediated due to interaction with opioid receptors in trigeminal ganglia and nuclei or due to trigeminal/olfactory interaction. As a practical consequence, patients should be made aware of a possible impairment of their olfactory and trigeminal function under long‐term analgesic treatment.What does this study add?We observed that the chronic use of pain medication was associated with significantly reduced olfactory function and perception of intranasal trigeminal stimuli compared to age‐matched controls without intake of analgesics. Non‐opioid and opioid drugs did not differ in their effects on chemosensory function.
Copper Oxide Microstructures with Hemisphere Pineapple Morphology for Selective Amperometric Determination of Vitamin C (L‐ascorbic Acid) in Human Fluids
Authors: Khairy Mohamed , Mahmoud Bahaa G. 
Published: June 2016

AbstractControl over morphology, surface composition and porosity of nanostructured metal oxides play a significant role in designing a selective and sensitive electrochemical sensor. Herein, we explore a simple synthesis route for control fabrication of porous CuO hemisphere pineapple‐like morphology without using any structure directing agents. The results show that, CuO hemispheres are consisting of self‐assembled porous nanoneedles. The as‐prepared CuO hemispheres were simply drop‐casted onto graphite screen‐printed electrodes (CuO‐SPEs). Then, it was tested for determination of ascorbic acid in Britton Robinson (B. R.) buffer of pH 7.4. Interestingly, the CuO‐SPE provides robust, sensitive, fast response and selective enzyme‐less ascorbic acid sensor. These superior features allowed eﬃcient, costless, stable, and precise non‐enzymatic detection of ascorbic acid in urine samples avoiding interferences and enhancing the accuracy of urinalysis examination.
Parametric optimization of Cu (II) and Ni (II) adsorption onto coal dust and magnetized sawdust using box‐behnken design of experiments
Authors: Kapur Meghna , Gupta Rishabh , Mondal Monoj Kumar 
Published: June 2016

The simultaneous removal of Cu (II) and Ni (II) ions from aqueous solution was investigated by using two different adsorbents (coal dust and magnetized sawdust). Experiments were made as a function of initial metal concentration (5–100 mg/L), adsorbent dose (2–20 g/L), and temperature (20–40°C) for the adsorption of metals by employing response surface methodology (RSM) based on Box–Behnken surface statistical design. The pH was kept constant at 4 and 5 for coal dust and magnetized sawdust, respectively. The magnetized sawdust showed better results for both Cu (II) and Ni (II) removal as compared with coal dust. The F statistics and ANOVA analysis confirmed that the model chosen to explain the relationship between the factors and the response is correct.For this work, three‐level three‐factorial experimental design has been applied to validate adsorption parameters affecting the combined removal of Cu (II) and Ni (II) onto coal dust and magnetized saw dust. Optimization of process parameters for Cu (II) and Ni (II) ions adsorption onto the adsorbents was done using RSM. The empirical relationship between the response (adsorption percentage of heavy metal) and the independent variables (initial heavy metal concentration, adsorbent dose, and temperature) has been expressed by the quadratic models. These models in turn help to understand and establish the optimized set of conditions without performing the unnecessary experiments at various combinations. © 2016 American Institute of Chemical Engineers Environ Prog, 35: 1597–1604, 2016
Soil production and hillslope transport in mid‐latitudes during the last glacial–interglacial cycle: a combined data and modelling approach in northern Ardennes
Authors: Bovy Benoît , Braun Jean , Demoulin Alain 
Published: June 2016

AbstractThe relative efficiency of various hillslope processes through Quaternary glacial–interglacial cycles in the mid‐latitudes is not yet well constrained. Based on a unique set of topographic and soil thickness data in the Ardennes (Belgium), we combine the new CLICHE model of climate‐dependent hillslope evolution with an inversion algorithm in order to get deeper insight into the ways and timing of hillslope dynamics under one such climatic cycle. We simulate the evolution of a synthetic hill reproducing the slope, curvature, and contributing area distributions of the hillslopes of a ~ 2500 km2 real area under a simple two‐stage 120‐kyr‐long climatic scenario with linear transitions between cold and warm stages. The inversion method samples a misfit function in the model parameter space, based on estimates of the fit of topographic derivative distributions in classes of soil thickness and of the relative frequencies of the predicted soil thickness classes. Though the inversion results show remarkable convergence patterns for most parameters, no unique solution emerges. We obtain five clusters of good fits, whose centroids are taken as acceptable model solutions. Based on the predicted time series of average denudation rate and soil thickness, plus snapshots of the soil distribution at characteristic times, we discuss these solutions and, comparing them with independent data not involved in the misfit function, we identify the most realistic scenario. Beyond providing first‐order estimates of several parameters that compare well with published data, our results show that denudation rates increase dramatically for a short time at both warm–cold and cold–warm transitions, when the mean annual temperature passes through the [0, −5 °C] range. We also point to the overwhelming importance of solifluction in shaping hillslopes and transporting soil, and the role of depth‐dependent creep (including frost creep) throughout the climatic cycle, whereas the contributions of simple creep and overland flow are minor. Copyright © 2016 John Wiley & Sons, Ltd.
Spillage sedimentation on large river floodplains
Authors: Lewin John , Ashworth Philip J. , Strick Robert J. P. 
Published: June 2016

AbstractActive deposition across the floodplains of large rivers arises through a variety of processes; collectively these are here termed ‘spillage sedimentation’. Three groups of 11 spillage sedimentation styles are identified and their formative processes described. Form presences on large river floodplains show different combinations of active spillage styles. Only some large floodplains have prominent levees; some have coarse splays; many have accessory channel dispersion and reworking, while still‐water sedimentation in lacustrine environments dominates some lower reaches. Infills are also commonly funnelled into prior, and often linear, negative relief forms relating to former migration within the mainstream channel belt.Shuttle Radar Topography Mission (SRTM) and Landsat 8 data are used to map spillage form types and coverage along a 1700 km reach of the Amazon that has an active floodplain width of up to 110 km with a systematic character transformation down‐valley. Spillage forms associated directly with mainstream processes rarely account for more than 5% of the floodplain deposits. There is a marked decrease in floodplain point bar complexes (PBC) over 1700 km downstream (from 34% to 5%), and an increase in the prevalence of large water bodies (2% to 37%) and accompanying internal crevasses and deltas (0% to 5%). Spillage sedimentation is likely within the negative relief associated with these forms, depending on mainstream sediment‐laden floodwater inputs.Spillage style dominance depends on the balance between sediment loadings, hydrological sequencing, and morphological opportunity. Down‐river form sequences are likely to follow gradient change, prior up‐river sediment sequestration and the altered nature of spilled loads, but also crucially, local floodplain relief and incident water levels and velocities at spillage times. Considering style distribution quantitatively, as a spatially distributed set of identifiable forms, emphasizes the global variety to spillage phenomena along and between large rivers. © 2016 The Authors. Earth Surface Processes and Landforms published by John Wiley & Sons Ltd.
Numerical investigation of the influence of the driving frequency during pile installation of tubular piles
Authors: Heins Evelyn , Hamann Thorben , Grabe Jürgen , Hannot Stephan 
Published: June 2016

AbstractNumerical investigation of the influence of the driving frequency during pile installation of tubular piles: Offshore and nearshore structures are predominantly founded by the use of open‐ended profiles. The installation of open‐ended profiles into the subsoil is usually done using the impact pile driving technique. To make the installation process more efficient, especially when considering the penetration velocity of the pile and the noise level, a new pile driving method was developed by IHC IQIP, formerly known as IHC Hydrohammer B.V. The influence of the standard driving method in comparison to the new driving technique is investigated in this contribution. This is done using the Finite Element Method (FEM) including a two‐phase model for fully saturated soil.Numerische Untersuchung zum Einfluss der Schlagfrequenz beim Einbringen von Rohrpfählen. Für die Gründung von Offshore‐ und Nearshore‐Anlagen werden vorwiegend offene Profile verwendet. Die Einbringung der offenen Profile in den anstehenden Boden erfolgt meist schlagend. Um den Pfahlinstallationsprozess insbesondere hinsichtlich Einbringgeschwindigkeit und Schallemission effizienter zu gestalten, wurde von IHC IQIP, früher bekannt als IHC Hydrohammer B.V., eine neue Schnellschlagramme entwickelt. In diesem Beitrag soll der Einfluss der Standardramme im Vergleich zur Schnellschlagramme untersucht werden. Dies geschieht mithilfe der Finite‐Elemente‐Methode (FEM) unter Berücksichtigung eines Zweiphasenmodells für den wassergesättigten Boden.Dieser Artikel wurde aus technischen Problemen doppelt veröffentlicht 10.1002/gete.201500014.
Zur Rolle der Materialmodelle beim Standsicherheitsnachweis
Authors: Kolymbas Dimitrios , Fellin Wolfgang , Schneider‐Muntau Barbara , Medicus Gertraud , Schranz Fabian 
Published: June 2016

AbstractDie Ansicht, dass für die numerische Simulation von geotechnischem Versagen das Materialmodell keine wesentliche Rolle spielt, wird kritisch erörtert. Aufgrund von Literaturhinweisen und eigenen Untersuchungen wird gezeigt, dass das Materialmodell durchaus eine Rolle spielen kann. Es ist daher fundiertes Fachwissen über die Materialmodelle erforderlich. Eine Außerachtlassung von Materialmodellen bei Standsicherheitsnachweisen a priori sollte vermieden werden.Dieser Artikel wurde aus technischen Problemen doppelt veröffentlicht 10.1002/gete.201500017.On the role of constitutive models in simulation of limit state. This paper challenges the critical perception that constitutive models play no important role in numerical simulation of geotechnical collapses. Contrary to this conventional perception, the role of constitutive models in collapse simulations is investigated and highlighted by means of published results and own research. This shows that application of constitutive models in numerical investigations of limit states demands a profound knowledge of them.
Prüfung der Oxidationsbeständigkeit von Kunststoffdichtungsbahnen im Autoklav
Authors: Koroliuk Stepan , Mähner Dietmar , Schmeing Johanna , Kreyenschmidt Martin 
Published: June 2016

AbstractDas Oxidationsverhalten von chemisch mit Phenolen und Phosphiten stabilisierten Kunststoffdichtungsbahnen aus Polyethylen mit unterschiedlichen Additivkonzentrationen wurde bei hohen und niedrigen Sauerstoffdrücken mittels Autoklaventest untersucht. Dabei zeigte sich, dass der Einfluss der chemischen Stabilisierung bei einem Sauerstoffdruck von 50 bar so stark reduziert wird, dass der Einfluss der Stabilisierung auf die Lebensdauer nicht bestimmt werden kann. Der Einfluss der chemischen Stabilisierung auf das Oxidationsverhalten der Kunststoffdichtungsbahnen bei niedrigeren Sauerstoffdrücken bis zu 5 bar lässt sich dagegen erfassen und evaluieren. Die effektive Geschwindigkeitskonstante des Stabilisatorverbrauchs folgt einem Potenzgesetz über dem Sauerstoffdruck.Dieser Artikel wurde aus technischen Problemen doppelt veröffentlicht 10.1002/gete.201500020.Testing of the oxidation resistance of geomembranes in the autoclave. The oxidation behavior of geomembranes, which are chemically stabilized by phenols and phosphites, with different additive concentrations was studied at high and low oxygen pressures by the autoclave test. It was found that the influence of chemical stabilization at an oxygen pressure of 50 bar is strongly suppressed and the influence of the stabilization regarding the lifetime cannot be determined. However, the influence of chemical stabilization on the oxidation behavior of geomembranes at lower oxygen pressures up to 5 bar can be detected and evaluated. The effective rate constant of the stabilizer depletion obeys a power law in oxygen pressure.