bluuebunny/crossref_metadata_2025 huggingface dataset:
Normal Mode Analysis Techniques in Structural Biology
Authors: López‐Blanco José Ramón , Miyashita Osamu , Tama Florence , Chacón Pablo
Published: October 2014

The dynamic simulation of macromolecular systems with biologically relevant sizes and time scales is critical for understanding macromolecular function. In this context, normal mode analysis (NMA) approximates the complex dynamical behaviour of a macromolecule as a simple set of harmonic oscillators vibrating around a given equilibrium conformation. This technique, originated from classical mechanics, was first applied to investigate the dynamical properties of small biological systems more than 30 years ago. During this time, a wealth of evidence has accumulated to support NMA as a successful tool for simulating macromolecular motions at extended length scales. Today, NMA combined with coarse‐grained representations has become an efficient alternative to molecular dynamics simulations for studying the slow and large‐amplitude motions of macromolecular machines. Interesting insights into these systems can be obtained very quickly with NMA to characterise their flexibility, to predict the directions of their collective conformational changes, or to help in the interpretation of experimental structural data. The recently developed methods and applications of NMA together with an introduction of the underlying theory will be briefly reviewed here.

Key Concepts:

NMA computes all motions around an equilibrium conformation (normal modes).

Normal modes are orthogonal displacement vectors with an associated frequency.

The collective functional motions of the macromolecules are well described by lowest frequency modes.

NMA inexpensive and accurately simulates the slow and large‐amplitude motions of biomolecules, but local reorganisations and the absolute time scale or amplitude of the motions are poorly predicted.

NMA can be used to characterise macromolecular flexibility, to predict the directions of collective conformational changes, and to interpret structural experimental data.
Vagus Nerve Stimulation for Epilepsy
Authors: Haas Alexander M , Benbadis Selim R , Vale Fernando
Published: October 2014

Epilepsy refractory to medical management with antiepileptic drugs continues to pose a problem to clinicians as well as to patients struggling with the limitations imposed on them by their condition. Vagus nerve stimulation (VNS) is a safe and effective surgical treatment for patients with refractory epilepsy who are not candidates for surgery involving resection of temporal lobe structures or epileptogenic foci. Even in those with failed surgical resection, VNS may still provide some benefit, though this must be elucidated. Although the mechanism is still poorly understood, several theories exist as to how VNS exerts its antiepileptic effects and several clinical trials have demonstrated its efficacy and safety. VNS has become the most widely used nonpharmacological therapy for the treatment of drug‐resistant epilepsy.

Key Concepts:

VNS is a safe and effective treatment for patients with refractory epilepsy who are not candidates for surgery involving resection of temporal lobe structures or epileptogenic foci and possibly those that have failed to respond to surgical correction.

Increased reduction of seizure frequency with VNS occurs over time resulting in decreased need for antiepileptic drugs with increased duration of stimulation.

In addition to the benefit of seizure reduction, data exists to support improved subjective quality of life scores with use of VNS.

Although the insertion of the VNS unit is a surgical procedure, it can often be performed as an outpatient surgery and thus does not require inpatient hospitalization as resection‐based epilepsy surgery does.

VNS is generally well tolerated with side effects including mild and including voice alteration and throat pain.
Biochemistry of Toll‐Like Receptors
Authors: Bonham Kevin Scott , Kagan Jonathan C
Published: October 2014

Recognition of potentially pathogenic organisms is a critical first step in an immune response. To prevent pathogen outgrowth, this detection must be rapid and initiate a robust inflammatory response. However, inflammation is dangerous, and spurious activation in response to nonthreatening stimuli has the potential to cause autoimmunity and other inflammatory disorders. For this reason, the pattern recognition receptors (PRRs) of the innate immune system have evolved to recognise pathogen‐associated molecular patterns to distinguish between self and potentially infectious nonself. The first discovered and most well‐studied PRRs are the toll‐like receptors (TLRs), which are transmembrane receptors that detect a diverse set of microbe‐specific products. Extensive work has uncovered the proteins required in TLR signalling, but a more complete understanding of the biochemistry of signalling molecules in their cellular context is required to understand the role of TLRs in pathogen detection and clearance.

Key Concepts:

Pathogen‐associated molecular patterns are molecular patterns unique to potentially pathogenic microbes, conserved among many species, and essential to the fitness of the microbes that use them.

Pattern recognition receptors distinguish self from nonself.

Toll‐like receptor ‘sorting adaptors’ define the subcellular location of signal transduction.

Toll‐like receptor ‘signalling adaptors’ link the cytosolic TIR domain of the receptor to signalling enzymes.
Generalized Linear Mixed Models
Authors: Mcculloch Charles E. , Neuhaus John M.
Published: October 2014

Generalized linear mixed models (GLMMs) are a class of models that incorporates random effects into the linear predictor of a generalized linear model (GLM). This allows the modeling of correlated data within the context of GLMs and greatly extends their breadth of applicability. They thus include both linear mixed models (LMMs) and GLMs as special cases.
Navigating Comics II: Constraints on the Reading Order of Comic Page Layouts
Authors: Cohn Neil , Campbell Hannah
Published: October 2014

Although readers typically believe that comic page layouts should be read following the left to right and down ‘Z‐path’ inherited from written language, several spatial arrangements can push readers to deviate from this order. These manipulations include separating panels from each other, overlapping one panel onto another, and using a long vertical panel to the right of a vertical column to ‘block’ a horizontal row. We asked participants to order empty panels in comic page layouts that manipulated these factors. All manipulations caused participants to deviate from the conventional Z‐path, and this departure was modulated by incremental changes to spatial arrangements: The more layouts deviated from a grid, the less likely participants were to use the Z‐path. Overall, these results reinforce that various constraints push comic readers to engage with panels in predictable ways, even when deviating from the traditional Z‐path of written language. Copyright © 2014 John Wiley & Sons, Ltd.
Injectable Silk Foams for Soft Tissue Regeneration
Authors: Bellas Evangelia , Lo Tim J. , Fournier Eric P. , Brown Joseph E. , Abbott Rosalyn D. , Gil Eun S. , Marra Kacey G. , Rubin J. Peter , Leisk Gary G. , Kaplan David L.
Published: October 2014

Soft tissue fillers are needed for restoration of a defect or augmentation of existing tissues. Autografts and lipotransfer have been under study for soft tissue reconstruction but yield inconsistent results, often with considerable resorption of the grafted tissue. A minimally invasive procedure would reduce scarring and recovery time as well as allow the implant and/or grafted tissue to be placed closer to existing vasculature. Here, the feasibility of an injectable silk foam for soft tissue regeneration is demonstrated. Adipose‐derived stem cells survive and migrate through the foam over a 10‐d period in vitro. The silk foams are also successfully injected into the subcutaneous space in a rat and over a 3‐month period integrating with the surrounding native tissue. The injected foams are palpable and soft to the touch through the skin and returning to their original dimensions after pressure is applied and then released. The foams readily absorb lipoaspirate making the foams useful as a scaffold or template for existing soft tissue filler technologies, useful either as a biomaterial alone or in combination with the lipoaspirate.
Synthesis of Dihydroisobenzofurans via Palladium‐Catalyzed Sequential Alkynylation/Annulation of 2‐Bromobenzyl and 2‐Chlorobenzyl Alcohols under Microwave Irradiation
Authors: Buxaderas Eduardo , Alonso Diego A. , Nájera Carmen
Published: October 2014

The palladium‐catalyzed synthesis of dihydroisobenzofurans has been performed by sequential Sonogashira cross‐coupling/cyclization reactions between terminal alkynes and 2‐(hydroxymethyl)bromo‐ and chlorobenzenes in methanol as solvent at 130 °C under microwave irradiation. A 4,4′‐dichlorobenzophenone oxime‐derived chloro‐bridged palladacycle is an efficient pre‐catalyst to perform this tandem process using 2‐dicyclohexylphosphanyl‐2′,4′,6′‐triisopropylbiphenyl (Xphos) as ancillary ligand and potassium hydroxide as base in the absence of a copper cocatalyst. Under these conditions, functionalized 2‐bromo‐ and 2‐chlorobenzaldehydes are also suitable partners in the domino process affording phthalans in good yields. All the reactions can be performed under air and employing reagent‐grade chemicals under low loading conditions (1 mol% Pd).

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Gold‐Catalyzed Regioselective Meyer–Schuster Rearrangement and Ring Expansion Cascade Leading to α‐Hydroxy‐α‐vinylcyclopentanones
Authors: An Jun‐Hyun , Yun Hokeun , Shin Sunwoong , Shin Seunghoon
Published: October 2014

Readily available cyclobutanols having a butyne‐1,4‐diol moiety underwent a sequential regioselective Meyer–Schuster rearrangement and 1,2‐shift, furnishing α‐hydroxy‐α‐vinylcyclopentanones. The reaction mechanism is consistent with the formation of an allenol intermediate that racemizes under the reaction conditions. Subsequent activation of the allenol leads to an enantio‐ and diastereoselective route to this scaffold.

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Synthesis of optimal thermal membrane distillation networks
Authors: González‐Bravo Ramón , Nápoles‐Rivera Fabricio , Ponce‐Ortega José María , Nyapathi Madhav , Elsayed Nesreen , El‐Halwagi Mahmoud M.
Published: October 2014

Thermal membrane distillation (TMD) is an emerging separation method which involves simultaneous heat and mass transfer through a hydrophobic semipermeable membrane. Traditionally, studies of this technology have focused on the performance of individual modules. Because of purity and recovery requirements, multiple TMD modules may be used in various configurations including series, parallel, and combinations. Furthermore, there may be a need to reroute streams from one module to another or to recycle a stream to the same unit. The objective is to develop a systematic approach to synthesize an optimal TMD network. A structural representation is developed to embed potential configurations of interest. A mathematical formulation is developed to transform the design problem into an optimization task that seeks to minimize the cost of the system. Two case studies are presented to illustrate the applicability of the developed approach and its merit over conventional design scenarios. © 2014 American Institute of Chemical Engineers AIChE J, 61: 448–463, 2015
A Ferrocene‐Functionalized Bistable [2]Rotaxane with Switchable Fluorescence
Authors: Liu Li , Wang Qi , Cheng Ming , Hu Xiao‐Yu , Jiang Juli , Wang Leyong
Published: October 2014

A switchable, bistable molecular shuttle based on dialkylammonium ion and urea functional recognition sites, and a macrocycle bearing a ferrocenyl unit has been constructed, in which the ferrocenyl macrocycle can be easily switched along the thread by addition of acid/base or by addition/removal of acetate anions. The shuttling motion of the macrocycle is accompanied with different fluorescence responses via the adjustment of the photoinduced electron transfer (PET) effect between the ferrocene electron donor and the fluorophores.
Toxoplasmose‐Diagnose mithilfe eines synthetisch hergestellten Glycosylphosphatidylinositol‐Glycans
Authors: Götze Sebastian , Azzouz Nahid , Tsai Yu‐Hsuan , Groß Uwe , Reinhardt Anika , Anish Chakkumkal , Seeberger Peter H. , Varón Silva Daniel
Published: October 2014

Geschätzte zwei Milliarden Menschen sind weltweit mit dem apikomplexen Parasiten Toxoplasma gondii infiziert, der die Ursache für eine Reihe gesundheitlicher Probleme ist. So kann eine Primärinfektion während der Schwangerschaft zum Tod des Fötus oder zu einer geistigen Behinderung des Kindes führen. Da die Medikamente gegen eine Infektion mit T. gondii potenziell schädlich für das ungeborene Kind sind, ist eine verlässliche Diagnose akuter Infektionen von schwangeren Frauen unentbehrlich. Bessere, schnellere, zuverlässigere und günstigere Diagnostika, die auf akkuraten serologischen Tests basieren und definierte Antigene verwenden, sind deshalb von großem Interesse. Synthetische pathogenspezifische Glycosylphosphatidylinositol(GPI)‐Glycan‐Antigene sind solche diagnostischen Biomarker, die eine akkurate Unterscheidung verschiedener Toxoplasmose‐Krankheitsstadien in menschlichen Seren ermöglichen.
A Palladium Nanoparticle–Nanomicelle Combination for the Stereoselective Semihydrogenation of Alkynes in Water at Room Temperature
Authors: Slack Eric D. , Gabriel Christopher M. , Lipshutz Bruce H.
Published: October 2014

The addition of NaBH4to Pd(OAc)2in water containing nanomicelles leads to the generation of H2and Pd nanoparticles. Subsequent reduction of disubstituted alkynes affordsZ‐alkenes in high yields. These reactions are general, take place in water at ambient temperatures, and offer recycling of the aqueous reaction mixture along with low overall E Factors.
Isolierung eines dreifach koordinierten Borkations mit einer Bor‐Schwefel‐Doppelbindung
Authors: Franz Daniel , Irran Elisabeth , Inoue Shigeyoshi
Published: October 2014

Die Umsetzung der sterisch anspruchsvollen Bis(imidazolin‐2‐iminato)‐Ligandenvorstufe (1,2‐(LMesNH)2‐C2H4)[OTs]2 (12+ 2[OTs]−; LMes=1,3‐Dimesitylimidazolin‐2‐yliden, OTs=p‐Toluolsulfonat) mit Lithiumborhydrid ergibt das kationische Boroniumdihydrid (1,2‐(LMesN)2‐C2H4)BH2[OTs] (2+ [OTs]−). Dieses reagiert mit gelbem Schwefel zum Thioxoboransalz (1,2‐(LMesN)2‐C2H4)BS[OTs] (3+ [OTs]−). Die bisher unbekannten Verbindungen 12+ 2[OTs]−, 2+ [OTs]− und 3+ [OTs]− wurden durch spektroskopische Methoden und Einkristallröntgenbeugung charakterisiert. Darüber hinaus wurden die Bindungsverhältnisse in 2+ und 3+ durch DFT‐Rechnungen genauer aufgeklärt. Die theoretische und kristallographische Analyse zeigt, dass 3+ das erste Beispiel für einen stabilen kationischen Komplex mit dreifach koordiniertem Bor ist, der eine Bor‐Schwefel‐Doppelbindung aufweist.
Total Synthesis of the Tetracyclic Antimalarial Alkaloid (±)‐Myrioneurinol
Authors: Nocket Anthony J. , Weinreb Steven M.
Published: October 2014

The first total synthesis of the tetracyclic antimalarial Myrioneuron alkaloid (±)‐myrioneurinol has been accomplished using three highly diastereoselective reactions as pivotal steps: 1) an intramolecular Michael addition of a benzyloxycarbonyl‐protected lactam titanium enolate to an α,β‐unsaturated ester for construction of the spirocyclic C5 quaternary center and the a/d rings, 2) a malonate anion conjugate addition to a transient nitrosoalkene to install the requisite functionality and configuration at the C7 position, and 3) an intramolecular sulfonyliminium aza‐Sakurai reaction to form the b ring and the attendant C9/C10 configuration of the natural product.
A Cascade Strategy Enables a Total Synthesis of (−)‐Gephyrotoxin
Authors: Chu Shuyu , Wallace Stephen , Smith Martin D.
Published: October 2014

A concise and efficient synthesis of (−)‐gephyrotoxin from L‐pyroglutaminol has been realized. The key step in this approach is a diastereoselective intramolecular enamine/Michael cascade reaction that forms two rings and two stereocenters and generates a stable tricyclic iminium cation. A hydroxy‐directed reduction of this intermediate plays a key role in establishing the required cis‐decahydroquinoline ring system, enabling the total synthesis of (−)‐gephyrotoxin in nine steps and 14 % overall yield. The absolute configuration of the synthetic material was confirmed by single‐crystal X‐ray diffraction and is consistent with the structure originally proposed for material isolated from the natural source.
Neo‐Fused Hexaphyrin: A Molecular Puzzle Containing an N‐Linked Pentaphyrin
Authors: Wei Pingchun , Zhang Kai , Li Xin , Meng Deying , Ågren Hans , Ou Zhongping , Ng Seikweng , Furuta Hiroyuki , Xie Yongshu
Published: October 2014

The first neo‐confused hexaphyrin(1.1.1.1.1.0) was synthesized by oxidative ring closure of a hexapyrrane bearing two terminal “confused” pyrroles. The new compound displays a folded conformation with a short interpyrrolic C⋅⋅⋅N distance of 3.102 Å, and thus it readily underwent ring fusion to afford a neo‐fused hexaphyrin with an unprecedented 5,5,5,7‐tetracyclic ring structure. Furthermore, coordination of CuII triggered a ring opening/contracting reaction to afford a CuII complex of an N‐linked pentaphyrin derivative. The roles of reactive NC bonds in the porphyrinoid macrocycles were demonstrated.
Iron(III) Located in the Dinuclear Metallo‐β‐Lactamase IMP‐1 by Pseudocontact Shifts
Authors: Carruthers Thomas J. , Carr Paul D. , Loh Choy‐Theng , Jackson Colin J. , Otting Gottfried
Published: October 2014

Heterodinuclear metalloenzymes are an important class of metalloproteins, but determining the location of the different metal ions can be difficult. Herein we present a new NMR spectroscopy method that uses pseudocontact shifts (PCS) to achieve this without assumptions about the coordinating ligands. The approach is illustrated with the dinuclear [FeZn] complex of IMP‐1, which is a prototypical metallo‐β‐lactamase (MβL) that confers resistance to β‐lactam antibiotics. Results from single‐crystal X‐ray diffraction were compromised by degradation during crystallization. With [GaZn]‐IMP‐1 as diamagnetic reference, the PCSs unambiguously identified the iron binding site in fresh samples of [FeZn]‐IMP‐1, even though the two metal centers are less than 3.8 Å apart and the iron is high‐spin Fe3+, which produces only small PCSs. [FeZn]‐MβLs may be important drug targets, as [FeZn]‐IMP‐1 is enzymatically active and readily produced in the presence of small amounts of Fe3+.
C60‐Mediated Molecular Shape Sorting: Separation and Purification of Geometrical Isomers
Authors: Rana Moumita , Reddy R. Bharathanatha , Rath Bibhuti Bhusan , Gautam Ujjal K.
Published: October 2014

A supramolecular crystallization‐based approach has been developed for the shape‐dependent separation of geometrical isomers under near‐ambient conditions. Difficulties to separate such isomers arise because of their very similar physical properties. The present approach relies on the ability of C60 to preferentially form solvate crystals with molecules of a specific geometry. Subsequently, these molecules are released upon mild heating to regenerate pure C60. By taking isomers of xylene and trimethylbenzene (TMB) as examples, we show that one of the isomers can be extracted from the rest with very high purity. To separate TMB isomers, a new C60–1,3,5‐TMB solvate was developed, which led to the isolation of isomer purities greater than 99.6 %. Versatility, a low operating temperature of approximately 100 °C, a separation efficiency of more than 10 weight % of C60 per cycle, and reagent recyclability makes this a promising molecular shape‐sorting approach.
Study of resonances for the restricted 3‐body problem
Authors: Quarles B. , Musielak Z.E. , Cuntz M.
Published: October 2014

Our aim is to identify and classify mean‐motion resonances (MMRs) for the coplanar circular restricted three‐body problem (CR3BP) for mass ratios between 0.10 and 0.50. Our methods include the maximum Lyapunov exponent, which is used as an indicator for the location of the resonances, the Fast Fourier Transform (FFT) used for determining what kind of resonances are present, and the inspection of the orbital elements to classify the periodicity. We show that the 2:1 resonance occurs the most frequently. Among other resonances, the 3:1 resonance is the second most common, and furthermore both 3:2 and 5:3 resonances occur more often than the 4:1 resonance. Moreover, the resonances in the coplanar CR3BP are classified based on the behaviour of the orbits. We show that orbital stability is ensured for high values of resonance (i.e., high ratios) where only a single resonance is present. The resonances attained are consistent with the previously established resonances for the solar system, i.e., specifically, in regards to the asteroid belt. Previous work employed digital filtering and Lyapunov characteristic exponents to determine stochasticity of the eccentricity, which is found to be consistent with our usage of Lyapunov exponents as an alternate approach based on varying the mass ratio instead of the eccentricity. Our results are expected to be of principal interest to future studies, including augmentations to observed or proposed resonances, of extra‐solar planets in binary stellar systems (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Simultaneous UBVRI observations of the cataclysmic variable AE Aquarii: Temperatures and masses of fireballs
Authors: Zamanov R.K. , Latev G.Y. , Stoyanov K.A. , Boeva S. , Spassov B. , Tsvetkov S.V.
Published: October 2014

We report simultaneous multicolour observations in 5 bands (UBVRI) of the flickering variability of the cataclysmic variable AE Aqr. Our aim is to estimate the parameters (colours, temperature, size) of the fireballs that produce the optical flares. The observed rise times of the optical flares are in the interval 220‐440 s. We estimate the dereddened colours of the fireballs as (U ‐B)0∼0.8‐1.4, (B ‐V)0∼0.03‐0.24, and (V ‐I)0∼0.26‐0.78. We find for the fireballs temperatures of 10000‐25000 K, masses of (7‐90)x1019 g, and sizes of (3‐7)x109 cm (using a distance of d = 86 pc). These values refer to the peak of the flares observed in the UBVRI bands. The data are available upon request from the authors (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
No evidence for an early seventeenth‐century Indian sighting of Kepler's supernova (SN1604)
Authors: van Gent R.H.
Published: October 2014

In a recent paper in this journal, Sule et al. (2011) argued that an early 17th‐century Indian mural of the constellation Sagittarius with a dragon‐headed tail indicated that the bright supernova of 1604 was also sighted by Indian astronomers. In this paper it will be shown that this identification is based on a misunderstanding of traditional Islamic astrological iconography and that the claim that the mural represents an early 17th‐century Indian sighting of the supernova of 1604 has to be rejected. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The 1.5 meter solar telescope GREGOR
Authors: Schmidt W. , von der Lühe O. , Volkmer R. , Denker C. , Solanki S.K. , Balthasar H. , Bello González N. , Berkefeld Th. , Collados M. , Fischer A. , Halbgewachs C. , Heidecke F. , Hofmann A. , Kneer F. , Lagg A. , Nicklas H. , Popow E. , Puschmann K.G. , Schmidt D. , Sigwarth M. , Sobotka M. , Soltau D. , Staude J. , Strassmeier K.G. , Waldmann T.A.
Published: October 2014

The 1.5 m telescope GREGOR opens a new window to the understanding of solar small‐scale magnetism. The first light instrumentation includes the Gregor Fabry Pérot Interferometer (GFPI), a filter spectro‐polarimeter for the visible wavelength range, the GRating Infrared Spectro‐polarimeter (GRIS) and the Broad‐Band Imager (BBI). The excellent performance of the first two instruments has already been demonstrated at the Vacuum Tower Telescope. GREGOR is Europe’s largest solar telescope and number 3 in the world. Its all‐reflective Gregory design provides a large wavelength coverage from the near UV up to at least 5 microns. The field of view has a diameter of 150″. GREGOR is equipped with a high‐order adaptive optics system, with a subaperture size of 10 cm, and a deformable mirror with 256 actuators. The science goals are focused on, but not limited to, solar magnetism. GREGOR allows us to measure the emergence and disappearance of magnetic flux at the solar surface at spatial scales well below 100 km. Thanks to its spectro‐polarimetric capabilities, GREGOR will measure the interaction between the plasma flows, different kinds of waves, and the magnetic field. This will foster our understanding of the processes that heat the chromosphere and the outer layers of the solar atmosphere. Observations of the surface magnetic field at very small spatial scales will shed light on the variability of the solar brightness (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The GREGOR Fabry‐Pérot Interferometer
Authors: Puschmann K.G. , Denker C. , Kneer F. , Al Erdogan N. , Balthasar H. , Bauer S.M. , Beck C. , Bello González N. , Collados M. , Hahn T. , Hirzberger J. , Hofmann A. , Louis R.E. , Nicklas H. , Okunev O. , Martínez Pillet V. , Popow E. , Seelemann T. , Volkmer R. , Wittmann A.D. , Woche M.
Published: October 2014

The GREGOR Fabry‐Pérot Interferometer (GFPI) is one of three first‐light instruments of the German 1.5‐meter GREGOR solar telescope at the Observatorio del Teide, Tenerife, Spain. The GFPI uses two tunable etalons in collimated mounting. Thanks to its large‐format, high‐cadence CCD detectors with sophisticated computer hard‐ and software it is capable of scanning spectral lines with a cadence that is sufficient to capture the dynamic evolution of the solar atmosphere. The field‐of‐view (FOV) of 50″×38″is well suited for quiet Sun and sunspot observations. However, in the vector spectropolarimetric mode the FOV reduces to 25″×38″. The spectral coverage in the spectroscopic mode extends from 530–860 nm with a theoretical spectral resolution of R ≈250 000, whereas in the vector spectropolarimetric mode the wavelength range is at present limited to 580–660 nm. The combination of fast narrow‐band imaging and post‐factum image restoration has the potential for discovery science concerning the dynamic Sun and its magnetic field at spatial scales down to ∼50 km on the solar surface (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The return of the mummy: Evidence for starlight reflected from the massive hot Jupiter τ Boo b?
Authors: Rodler F. , Kürster M. , López‐Morales M. , Ribas I.
Published: October 2014

Very recently, we were able to measure CO absorption features in the atmosphere of the non‐transiting planet τ Boo b for the very first time. This allowed us to unravel a long‐term mystery in planet atmosphere studies, the determination of the orbital inclination of a non‐transiting planet and the exact planetary mass, respectively being 46° and 5.7 MJup. In light of these new results, we reanalyzed a UVES/VLT data set taken by us with the goal to detect starlight reflected from this hot Jupiter. In the previous analysis of these data, we found a candidate signal of low confidence (2σ), indicating a geometric albedo of the planetary atmosphere lower than 0.4 and an orbital inclination of 41°, which is close to the recently measured value. We reanalyzed these data by adopting updated orbital parameters and find as result that the candidate signal of marginal significance now appears at an orbital inclination of 43°. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Advanced Spectral Library (ASTRAL): Cool stars edition
Authors: Ayres T.R.
Published: October 2014

ASTRAL is a project to create high‐resolution, high‐S/N UV (1150–3200 Å) atlases of bright stars utilizing HST/STIS. During Cycle 18 (2010–2011), eight cool star targets were observed, including key objects like Procyon and Betelgeuse, churning through 146 orbits in the process. The new spectral atlases are publically available through the project website. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nonlinear time series analysis of Kepler Space Telescope data: Mutually beneficial progress
Authors: Jevtić N. , Stine P. , Schweitzer J.S.
Published: October 2014

Nonlinear time series analysis, though a powerful tool, has not been used widely in astronomy and astro‐physics because the principle requirements that the data be sampled uniformly and continuous are rarely met. Kepler Space Telescope variable‐star light curves satisfy these and almost all other requirements. These data have allowed a more systematic study of the methodology and yielded new information. Nonlinear noise reduction is the aspect we focus on here. Nonlinear time series power spectra often have relevant information across all the frequencies in a spectrum. As opposed to traditional filtering that results in a loss of information at the high frequencies, nonlinear local projective noise reduction allows us to significantly reduce noise while keeping high‐frequency information. Nonlinear noise reduction is discussed for a number of Kepler Space Telescope targets with different power‐spectral characteristics. The extremely high quality of the Kepler data has also allowed us to explore the novel use of average mutual information (AMI) for distinguishing signal from noise in broadband spectra. We report on noise reduction for targets with power spectra that contain a fundamental and harmonics, power spectra with no such lines and spectra with high‐frequency lines (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
SONG‐OT: The prototype SONG node at Tenerife
Authors: Uytterhoeven K. , Pallé P.L. , Grundahl F. , Frandsen S. , Christensen‐Dalsgaard J. , Triviño Hage A. , the SONG team
Published: October 2014

The prototype SONG node, SONG‐OT, is currently being installed and tested at Observatory del Teide on Tenerife. SONG will be a global network of 1‐m robotic telescopes, equipped with a high‐resolution échelle spectrograph and dual‐colour lucky imaging cameras. The network will be devoted to the seismic study of bright stars and characterisation of low‐mass planets. We present the current status of the network in general and the SONG‐OT node in particular (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
High precision pointing with a multiline spectrometer at the VTT
Authors: Staiger J.
Published: October 2014

We are investigating the pointing quality of the VTT, Tenerife under the aspect of suitability for long‐term heliosesimological observations. Tests have shown that thermal and mechanical loads within the telescope may create spurious image drifts with shift rates of up to 5″ per hour. During daylong recordings this will reduce significantly the effective size of the field‐of‐view and may infer artificial lateral movements into the data. The underlying problem that not all image position offsets developing during a measurement may be compensated for is common to most high‐resolution solar telescopes independently of the type of pointing system used. We are developing new approaches to address this problem which are to be tested in the near future at the VTT. The simulations established so far show that the problem may be reduced by more than 90% (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Differential rotation and meridional flows of K giants: Predictions from mean field theory
Authors: Küker M. , Rüdiger G.
Published: October 2014

We present a mean field model of the differential rotation and meridional flow of the giant star KIC 8366239. The model predicts a solar‐type surface differential rotation with a total shear of 0.03 rad/d. The horizontal shear decreases with depth and vanishes at the lower boundary. No drastic increase of the rotation rate towards the core is found. The surface meridional flow is directed towards the poles and has amplitude of 26 m/s. The return flow at the bottom of the convective envelope has an amplitude of 16 m/s. The results are compared with those for the K giant Arcturus and the Sun (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Stellar characterization of large spectroscopic datasets: A Bayesian approach
Authors: Kaiser A. , Weiss W.W.
Published: October 2014

The task of accurately determining the fundamental parameters of a star from medium or low resolution spectra is time consuming and requires substantial experience. Since the first large‐scale space missions such as CoRoT or Kepler came along, the need for a fast and statistically sound method emerged to cope with the large amount of ground based support data. We present here a fully automated approach for the determination of stellar parameters from low‐resolution stellar spectra using a Bayesian approach and discuss the reliability and limits of the method (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Variability survey in the young open cluster IC 1805
Authors: Moidzierski D.
Published: October 2014

We present preliminary results of the photometric variability survey in the very young open cluster IC 1805. We found more than 70 variable stars in the field, including pulsating stars and a large sample of most likely pre‐main sequence stars (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Acoustic glitches in solar‐type stars from Kepler
Authors: Mazumdar A. , Monteiro M.J.P.F.G. , Ballot J. , Antia H.M. , Basu S. , Houdek G. , Mathur S. , Cunha M.S. , Silva Aguirre V. , García R.A. , Salabert D. , Verner G.A. , Christensen‐Dalsgaard J. , Metcalfe T.S. , Chaplin W.J.
Published: October 2014

We report the measurement of the acoustic locations of layers of sharp variation in sound speed in the interiors of 19 solar‐type stars observed by the Kepler mission. The oscillatory signal in the frequencies arising due to the acoustic glitches at the base of the convection zone and the second helium ionisation zone was utilised to determine their location by four independent methods. Despite the significantly different methods of analysis, remarkable agreement was found between the results of these four methods. Further, the extracted locations of these layers were found to be consistent with representative models of the stars (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Excitation of pulsation modes in B‐type supergiant stars
Authors: Ostrowski J. , Daszyńska‐Daszkiewicz J. , Pamyatnykh A.A.
Published: October 2014

We present results on the instability analysis of the post main sequence massive star models against radial and nonradial pulsations. Both p‐ and g‐modes can be excited by the κ‐mechanism operating in the metal opacity bump. However, as opposed to the previous published results, an intermediate convective zone (ICZ) related to the hydrogen burning shell is not necessary for excitation of g‐modes. Such modes can be reflected at the chemical composition gradient region surrounding the radiative helium core. We investigate properties of instability parameter, kinetic energy density and work integrals of pulsational modes excited in B‐type supergiant models (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the possibility of using seismic probes to study the core composition in pulsating white dwarfs
Authors: Faria J.P. , Monteiro M.J.P.F.G.
Published: October 2014

White dwarfs correspond to the final stages of stellar evolution of solar‐type stars. In these objects, production of energy by nuclear burning has ended which means that a white dwarf simply cools down over the course of the next billion years. It is now known that white dwarfs spend some of their cooling history in an instability strip. The pulsating white dwarfs with an hydrogen atmosphere (called DAV or ZZ Ceti stars) show non‐radial oscillation modes with periods in the range 100–1200 s. In this work we try to illustrate how the oscillation p‐mode frequencies of idealized white dwarf models change as the result of a different chemical composition in the core, with the ultimate goal of determining the chemical stratification from seismic observations. The presence of acoustic glitches in the internal structure results in a periodic signal in the frequencies. We find that this signal depends on the chemical stratification/composition of the core in a form that can be analytically modelled (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Is one month of observations enough? A case study on Kepler‐21
Authors: Valliappan S.P. , Karoff C.
Published: October 2014

We present the asteroseismic analysis of Kepler observations of the bright oscillating star Kepler‐21 (KIC 3632418, KOI 975, HD 179070). The pulsation modes exhibited by this star are similar to the acoustic p‐modes seen in our Sun. The analysis of observations covering a time period of 460 days has showed that the star hosts a small planet (Kepler‐21b), which has a mass of ∼10 MEarth, a radius of 1.64±0.04 REarth and a revolving period of 2.8 days (Howell et al. 2012). Our current work deals with the comparison of p‐mode frequency estimation using 1 and 10 months of observations (Quarter 2.3 and Quarters 5 through 7) of this F5 subgiant (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The non‐adiabatic high‐degree f‐mode
Authors: Zhugzhda Y.D. , Roth M.
Published: October 2014

The current theory of the high‐degree solar f‐mode based on an adiabatic approximation is in contradiction with obser‐vations, since the f‐mode is visible in intensity oscillations of the Sun. As a possible solution we present an universal analytical treatment for a non‐adiabatic f‐mode. This non‐adiabatic theory provides the explanation of brightness oscilla‐tions due to the f‐mode. We find that the non‐adiabatic effects do not lead to a damping of the f‐mode since the dispersion relation is the same as in the adiabatic approximation (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
UCAC4: Stellar kinematics with vector spherical functions
Authors: Vityazev V.V. , Tsvetkov A.S.
Published: October 2014

We present a method of kinematic analysis of proper motions by vector spherical functions, and the results of its application to astrometric data. The sets of vector spherical functions which are orthonormal on a full sphere as well as on a latitude zone are constructed. Decomposition of the proper motions into a set of such functions allows model‐independent study of stellar kinematics. If needed, the parameters of the standard (say, Ogorodnikov‐Milne) model may be derived from the coefficients of the decomposition. In contrast to the commonly used least squares estimation of the model's parameters, vector spherical functions identify all systematic components of the velocity field (no matter, whether they are incorporated into the model or not) and give us a possibility to test whether the data are compatible with the model. In this paper, we apply this technique for the first time to the proper motions from the UCAC4 catalog for stars in the 11 to 16 magnitude range. We derive all‐sky solutions and the solutions based on stars in the northern and southern Galactic hemispheres. The all‐sky solution provide evidence for noticeable magnitude‐dependent trends in the coordinates of the solar motion apex, Oort constants, angular speed of the local Galactic rotation, and the slope of the local rotation velocity curve as we go from bright to faint stars. Furthermore, our all‐sky vector spherical function analysis identified strong and reliable extramodel harmonics, whereas the solutions for the northern and southern hemisphere indicate sign reversals for some of the Ogorodnikov‐Milne parameters. We show that both effects appear simultaneously and can be explained by the slowdown of Galactic rotation with increasing distance from the main Galactic plane. We estimate the absolute value of the vertical gradient of the Galactic rotational velocity to be ∼40 km s–1 kpc–1. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The interstellar medium and star formation in nearby galaxies
Authors: Bigiel F. , Cormier D. , Schmidt T.
Published: October 2014

In this overview article we present some of the key projects we pursue in our Emmy Noether group. Our work is focused on nearby galaxies, where we use multi‐wavelength, state‐of‐the‐art survey data to probe distribution, abundance and properties of gas and dust in the interstellar medium (ISM) on ∼ kpc scales. We study the average, radial distributions of atomic (H I) and molecular hydrogen (H2) across the disks of spiral galaxies and assess local (on 1 kpc scales) correlations between H I, H2 and star formation rate (SFR) surface densities across the inner, optical disks of our sample of ∼ 30 spiral galaxies. The short H2 depletion times (∼ 2 Gyr) we find raises the question of if and how star formation is refueled in galactic disks. We look for such signatures of radial gas flows in our H I data and find compelling evidence at least in one case. We extend and compare our gas‐SFR studies to the outer disks of galaxies, where conditions change significantly in the ISM, e.g., low metallicity and dust abundance. We focus on star formation at low‐metallicity further with detailed ISM studies in dwarf galaxies, where we combine spectroscopic observations in the infrared with detailed modelling to learn about composition and detailed physical properties of the ISM. Of particular interest is the question of what drives large scale star formation in galaxies at low metallicity. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
TIGRE: A new robotic spectroscopy telescope at Guanajuato, Mexico
Authors: Schmitt J. H. M. M. , Schröder K.‐P. , Rauw G. , Hempelmann A. , Mittag M. , González‐Pérez J. N. , Czesla S. , Wolter U. , Jack D. , Eenens P. , Trinidad M. A.
Published: October 2014

TIGRE is a new robotic spectroscopy telescope located in central Mexico at the La Luz Observatory of the University of Guanajuato. The 1.2 m telescope is fiber‐coupled to an ´echelle spectrograph with a spectral resolving power exceeding 20000 over most of the covered spectral range between 3800 Å and 8800 Å, with a small gap of 130 Å around 5800 Å. TIGRE operates robotically, i.e. it (normally) carries out all observations without any human intervention, including, in particular, the target selection in any given observing night. In this paper we describe the properties of the TIGRE instrumentation and its technical realization, as well as our first operational experience with the performance and efficiency of the overall system. Finally, we present some examples of recent TIGRE observations. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An augmented Lagrangian origin‐based algorithm for link‐capacitated traffic assignment problem
Authors: Shi Feng , Xu Guang‐ming , Huang Helai
Published: October 2014

The origin‐based algorithm is embedded into the augmented Lagrangian method for the link‐capacitated traffic assignment problem. In order to solve the “nonexistence” problem due to the second partial derivatives of the augmented Lagrangian function at some specific points, the approximate expressions of the second partial derivatives are amended in the origin‐based algorithm. The graph of last common nodes is developed on the basis of the restricted single‐origin network. A method is proposed for finding n–1 last common nodes of the restricted single‐origin network, resulting in computational complexity of O(n2) in finding last common nodes. Numerical analysis on the Sioux Falls network and Chicago Sketch network demonstrated the effectiveness and characteristics of the proposed algorithm. Copyright © 2014 John Wiley & Sons, Ltd.
Hydrolysis‐determining substrate characteristics in liquid hot water pretreated hardwood
Authors: Kim Youngmi , Kreke Thomas , Ko Ja Kyong , Ladisch Michael R.
Published: October 2014

Fundamental characterization of pretreated hardwood and its interactions with cellulolytic enzymes has confirmed that a pathway exists for dramatically reducing the loading of cellulase required for hydrolysis of pretreated biomass. We demonstrate that addition of protein effecting a seven‐fold decrease in the specific activity of cellulases enables a ten‐fold reduction in enzyme loading while maintaining a high level of cellulose hydrolysis in pretreated hardwood. While use of protein and other additives that adsorb on lignin have been reported previously, the current work demonstrates the effect in a dramatic manner and brings the rationale for this change into clear focus. The key to this result is recognizing and mitigating the pretreatment conundrum where increasingly severe pretreatment conditions enhance accessibility of the enzymes not only to cellulose, but also to lignin. The lignin adsorbs enzyme protein causing loss of cellulase activity. More enzyme, added to compensate for this lost activity, results in a higher cellulase loading. The addition of a different protein, such as BSA, prevents cellulase adsorption on lignin and enables the enzyme itself to better target its glucan substrate. This effect dramatically reduces the amount of cellulase for a given level of conversion with enzyme loadings of 15 FPU and 1.3 FPU/g solids both achieving 80% conversion. The understanding of this phenomenon reinvigorates motivation for the search for other approaches that prevent cellulase adsorption on lignin in order to achieve high glucose yields at low enzyme loadings for pretreated lignocellulose. Biotechnol. Bioeng. 2015;112: 677–687. © 2014 Wiley Periodicals, Inc.
Oncological outcome of malignant colonic obstruction in the Dutch Stent-In 2 trial
Authors: Sloothaak D A M , van den Berg M W , Dijkgraaf M G W , Fockens P , Tanis P J , van Hooft J E , Bemelman W A , van Hooft J E , Fockens P , Bemelman W A , Dijkgraaf M G , Sprangers M A , Buskens C J , Jansen J M , Gerhards M F , Timmer R , van Ramshorst B , Oldenburg B , van Hilligersberg R , Bakker C M , Sosef M , Witteman P , Kruyt P , ten Hove W R , Tseng L N , van der Linde K , Koopal S A , Marinelli A W , Perk L , Lutke Holzik M F , Grubben M J , Heisterkamp J , Depla A C , Derksen E , Naber A H , van Geloven A A , Breumelhof R , Davids P H , Akol H , van der Zaag E , Schenk E , Patijn G A , Veenendaal R A , Tollenaar R A , van Berkel A , Gilissen L P , Nieuwenhuijzen G A , van der Waaij L A , Baas P C , Cense H , Scholten P , van Wagensveld B , Koornstra J J , Havenga K , van Milligen de Wit M , Rijken A M , Cazemier M , Guicherit O R , Houben M H , Steup W H
Published: October 2014

Background

The Stent-In 2 trial randomized patients with malignant colonic obstruction to emergency surgery or stent placement as a bridge to elective surgery. The aim of this study was to compare the oncological outcomes.

Methods

Disease recurrence, and disease-free, disease-specific and overall survival were evaluated, including a subgroup analysis of patients with a stent- or guidewire-related perforation.

Results

Of 98 patients included in the original Stent-In 2 trial, patients with benign (16) or incurable (23) disease were excluded from this study, along with a patient who had withdrawn from the trial. Of the remaining 58 patients, 32 were randomized to emergency surgery (31 resection, 1 stoma only) and 26 to stenting. Unsuccessful stenting required emergency surgery in six patients owing to wire or stent perforation. Locoregional or distant disease recurrence developed in nine of 32 patients in the emergency surgery group and 13 of 26 in the stent group. Disease-free survival was worse in the subgroup with stent- or guidewire-related perforation. Five of six patients in this subgroup developed a recurrence, compared with nine of 32 in the emergency surgery group and eight of 20 who had unperforated stenting.

Conclusion

Stent placement for malignant colonic obstruction was associated with a risk of recurrence in this trial, but the numbers are small. There is not enough evidence to refute the approach strongly. Registration number: ISRCTN46462267 (http://www.controlled-trials.com).