bluuebunny/crossref_metadata_2025_split huggingface dataset:
Power calculations and placebo effect for future clinical trials in progressive supranuclear palsy
Authors: Stamelou Maria , Schöpe Jakob , Wagenpfeil Stefan , Del Ser Teodoro , Bang Jee , Lobach Iryna Y. , Luong Phi , Respondek Gesine , Oertel Wolfgang H. , Boxer AdamL. , Höglinger Günter U. ,   for the AL‐108‐231 Investigators, Tauros Investigators, and MDS‐Endorsed PSP Study Group
Published: March 2016

ABSTRACTBackgroundTwo recent randomized, placebo‐controlled trials of putative disease‐modifying agents (davunetide, tideglusib) in progressive supranuclear palsy (PSP) failed to show efficacy, but generated data relevant for future trials.MethodsWe provide sample size calculations based on data collected in 187 PSP patients assigned to placebo in these trials. A placebo effect was calculated.ResultsThe total PSP‐Rating Scale required the least number of patients per group (N = 51) to detect a 50% change in the 1‐year progression and 39 when including patients with ≤ 5 years disease duration. The Schwab and England Activities of Daily Living required 70 patients per group and was highly correlated with the PSP‐Rating Scale. A placebo effect was not detected in these scales.ConclusionsWe propose the 1‐year PSP‐Rating Scale score change as the single primary readout in clinical neuroprotective or disease‐modifying trials. The Schwab and England Activities of Daily Living could be used as a secondary outcome. © 2016 International Parkinson and Movement Disorder Society
The 1H NMR spectrum of pyrazole in a nematic phase
Authors: Provasi Patricio , Jimeno María Luisa , Alkorta Ibon , Reviriego Felipe , Elguero José , Jokisaari Jukka 
Published: March 2016

AbstractThe experimental 1H nuclear magnetic resonance (NMR) spectrum of 1H‐pyrazole was recorded in thermotropic nematic liquid crystal N‐(p‐ethoxybenzylidene)‐p‐butylaniline (EBBA) within the temperature range of 299–308 K. Two of three observable dipolar DHH‐couplings appeared to be equal at each temperature because of fast prototropic tautomerism. Analysis of the Saupe orientational order parameters using fixed geometry determined by computations and experimental dipolar couplings results in a situation in which the molecular orientation relative to the magnetic field (and the liquid crystal director) can be described exceptionally by a single parameter. Copyright © 2016 John Wiley & Sons, Ltd.
Model‐based reconstruction for real‐time phase‐contrast flow MRI: Improved spatiotemporal accuracy
Authors: Tan Zhengguo , Roeloffs Volkert , Voit Dirk , Joseph Arun A. , Untenberger Markus , Merboldt K. Dietmar , Frahm Jens 
Published: March 2016

PurposeTo develop a model‐based reconstruction technique for real‐time phase‐contrast flow MRI with improved spatiotemporal accuracy in comparison to methods using phase differences of two separately reconstructed images with differential flow encodings.MethodsThe proposed method jointly computes a common image, a phase‐contrast map, and a set of coil sensitivities from every pair of flow‐compensated and flow‐encoded datasets obtained by highly undersampled radial FLASH. Real‐time acquisitions with five and seven radial spokes per image resulted in 25.6 and 35.7 ms measuring time per phase‐contrast map, respectively. The signal model for phase‐contrast flow MRI requires the solution of a nonlinear inverse problem, which is accomplished by an iteratively regularized Gauss‐Newton method. Aspects of regularization and scaling are discussed. The model‐based reconstruction was validated for a numerical and experimental flow phantom and applied to real‐time phase‐contrast MRI of the human aorta for 10 healthy subjects and 2 patients.ResultsUnder all conditions, and compared with a previously developed real‐time flow MRI method, the proposed method yields quantitatively accurate phase‐contrast maps (i.e., flow velocities) with improved spatial acuity, reduced phase noise and reduced streaking artifacts.ConclusionThis novel model‐based reconstruction technique may become a new tool for clinical flow MRI in real time. Magn Reson Med 77:1082–1093, 2017. © 2016 International Society for Magnetic Resonance in Medicine
Allyl ethers as combined plasticizing and crosslinkable side groups in polycarbonate‐based polymer electrolytes for solid‐state Li batteries
Authors: Mindemark Jonas , Imholt Laura , Montero José , Brandell Daniel 
Published: March 2016

ABSTRACTAllyl ether‐functional polycarbonates, synthesized by organocatalytic ring‐opening polymerization of the six‐membered cyclic carbonate monomer 2‐allyloxymethyl‐2‐ethyltrimethylene carbonate, were used to prepare non‐polyether polymer electrolytes. UV‐crosslinking of the allyl side groups provided mechanically stable electrolytes with improved molecular flexibility—Tg below −20 °C—and higher ionic conductivity—up to 4.3 × 10−7 S/cm at 25 °C and 5.2 × 10−6 S/cm at 60 °C—due to the plasticizing properties of the allyl ether side groups. The electrolyte function was additionally demonstrated in thin‐film Li battery cells. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 2128–2135
Spa47 is an oligomerization‐activated type three secretion system (T3SS) ATPase from Shigella flexneri
Authors: Burgess Jamie L. , Jones Heather B. , Kumar Prashant , Toth Ronald T. , Middaugh C. Russell , Antony Edwin , Dickenson Nicholas E. 
Published: March 2016

AbstractGram‐negative pathogens often use conserved type three secretion systems (T3SS) for virulence. The Shigella type three secretion apparatus (T3SA) penetrates the host cell membrane and provides a unidirectional conduit for injection of effectors into host cells. The protein Spa47 localizes to the base of the apparatus and is speculated to be an ATPase that provides the energy for T3SA formation and secretion. Here, we developed an expression and purification protocol, producing active Spa47 and providing the first direct evidence that Spa47 is a bona fide ATPase. Additionally, size exclusion chromatography and analytical ultracentrifugation identified multiple oligomeric species of Spa47 with the largest greater than 8 fold more active for ATP hydrolysis than the monomer. An ATPase inactive Spa47 point mutant was then engineered by targeting a conserved Lysine within the predicted Walker A motif of Spa47. Interestingly, the mutant maintained a similar oligomerization pattern as active Spa47, but was unable to restore invasion phenotype when used to complement a spa47 null S. flexneri strain. Together, these results identify Spa47 as a Shigella T3SS ATPase and suggest that its activity is linked to oligomerization, perhaps as a regulatory mechanism as seen in some related pathogens. Additionally, Spa47 catalyzed ATP hydrolysis appears to be essential for host cell invasion, providing a strong platform for additional studies dissecting its role in virulence and providing an attractive target for anti‐infective agents.
Protein side chain conformation predictions with an MMGBSA energy function
Authors: Gaillard Thomas , Panel Nicolas , Simonson Thomas 
Published: March 2016

ABSTRACTThe prediction of protein side chain conformations from backbone coordinates is an important task in structural biology, with applications in structure prediction and protein design. It is a difficult problem due to its combinatorial nature. We study the performance of an “MMGBSA” energy function, implemented in our protein design program Proteus, which combines molecular mechanics terms, a Generalized Born and Surface Area (GBSA) solvent model, with approximations that make the model pairwise additive. Proteus is not a competitor to specialized side chain prediction programs due to its cost, but it allows protein design applications, where side chain prediction is an important step and MMGBSA an effective energy model. We predict the side chain conformations for 18 proteins. The side chains are first predicted individually, with the rest of the protein in its crystallographic conformation. Next, all side chains are predicted together. The contributions of individual energy terms are evaluated and various parameterizations are compared. We find that the GB and SA terms, with an appropriate choice of the dielectric constant and surface energy coefficients, are beneficial for single side chain predictions. For the prediction of all side chains, however, errors due to the pairwise additive approximation overcome the improvement brought by these terms. We also show the crucial contribution of side chain minimization to alleviate the rigid rotamer approximation. Even without GB and SA terms, we obtain accuracies comparable to SCWRL4, a specialized side chain prediction program. In particular, we obtain a better RMSD than SCWRL4 for core residues (at a higher cost), despite our simpler rotamer library. Proteins 2016; 84:803–819. © 2016 Wiley Periodicals, Inc.
Optimization of the immobilization of bacterial spores on glass substrates with organosilanes
Authors: Arreola Julio , Mätzkow Malte , Durán Marlena Palomar , Greeff Anton , Keusgen Michael , Schöning Michael J. 
Published: March 2016

Spores can be immobilized on biosensors to function as sensitive recognition elements. However, the immobilization can affect the sensitivity and reproducibility of the sensor signal. In this work, three different immobilization strategies with organosilanes were optimized and characterized to immobilize Bacillus atrophaeus spores on glass substrates. Five different silanization parameters were investigated: nature of the solvent, concentration of the silane, silanization time, curing process, and silanization temperature. The resulting silane layers were resistant to a buffer solution (e.g., Ringer solution) with a polysorbate (e.g., Tween®80) and sonication.AFM image of silanization on a glass substrate with an organosilane (e.g., APTES).
Excitonic and Photonic Processes in Condensed Matter and Nano Materials
Authors: Silva Carlos , Kashyap Raman 
Published: March 2016

AbstractThis issue contains a collection of papers presented at the 11th International Conference on Excitonic and Photonic Processes in Condensed Matter and Nano Materials (EXCON'15) which was held in Montreal, Canada on 18–22 May 2015. Prof. Jai Singh initiated this conference series in 1994. The venue has wandered around the world, appropriately starting in Darwin (Australia). We were delighted to see the momentum prevailing for the 11th time in Canada, where there is vigorous activity in condensed‐matter physics, nanoscience, and photonics.The EXCON series of conferences focuses on multidisciplinary activities related to exciton physics, providing a forum for research communication amongst condensed‐matter physicists, physical chemists, biophysicists, and materials scientists. EXCON'15 hosted exciting discussions within the following topics:– Molecular crystals, aggregates, and polymers– Inorganic materials, organic/inorganic hybrids– Quantum wells, wires, and dots– Biological systems– Opto‐electronic devices; light‐emitting diodes and solar cells– Nonlinear phenomena, biexcitons, and multi‐excitons– Exciton–exciton interactions and Bose–Einstein condensation– Ultrafast dynamics of excitons; relaxation, energy transport, charge transfer– Strong exciton–light interaction; polaritons– Strong exciton–lattice interactions; photo‐induced phase transitions– New experimental techniques applied to studies of excitons– New theoretical and computational techniques applied to excitonic systemsTo underline the international nature of research on excitonic processes and to reflect the diversity of this community, the conference venue has rotated between Australia, Europe, North America, and Japan. EXCON conferences have been held in Darwin (Australia, 1994), Kurort Gohrisch (Germany, 1996), Boston (USA, 1998), Osaka (Japan, 2000), Darwin again (2002), Cracow (Poland, 2004), Winston‐Salem (USA, 2006), Kyoto (Japan, 2008), Groningen (Netherlands, 2012). The 2015 edition was held in the campus of Polytechnique Montréal. The logo of the conference incorporates an iconic symbol of Montreal – the Olympic stadium, whose dome is a valence band associated with an excitonic system.The EXCON'15 conference was attended by 110 participants including 16 Invited Speakers, amongst whom 7 were female. In 2015, EXCON had a particularly privileged role in joining the world in celebrating the International Year of Light, with special invited speakers as an addition to the pool of the regular program.It is a pleasure to announce that the next conference of the EXCON series will be held in 2018 in Japan, which hosts key players in fields associated with excitonic processes in condensed matter. We believe that we represent the community when we express that we are looking very much forward to the 2018 meeting. (© 2016 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An ARL‐unbiased c‐chart
Authors: Paulino Sofia , Morais Manuel Cabral , Knoth Sven 
Published: March 2016

In statistical process control (SPC), it is usual to assume that counts have a Poisson distribution. The non‐negative, discrete, and asymmetrical character of a control statistic with such a distribution and the value of its target mean may prevent the quality control practitioner to deal with a c‐chart with a pre‐specified in‐control average run length (ARL) or the ability to control not only increases but also decreases in the mean of those counts in a timely fashion. Furthermore, the c‐charts proposed in the SPC literature tend to be ARL‐biased, in the sense that some out‐of‐control ARL values are larger than the in‐control ARL.In this paper, we explore the notions of randomized and uniformly most powerful unbiased tests to eliminate the bias of the ARL function of the c‐chart. Copyright © 2016 John Wiley & Sons, Ltd.
Measurement of compound‐specific carbon isotope ratios (δ13C values) via direct injection of whole crude oil samples
Authors: Barrie Craig D. , Taylor Kyle W. R. , Zumberge John 
Published: March 2016

RationaleStable isotope analysis is a powerful tool in understanding the generation, history and correlation of hydrocarbons. Compound‐specific δ13C measurements of oils allow detailed comparison of individual compound groupings; however, most studies of these sample materials separate and isolate individual fractions based on the chemistries of particular compound groups, potentially losing considerable valuable isotopic data. Even if all fractions are analyzed, this represents a large increase in the data‐processing burden, effectively multiplying data evaluation time and effort by the number of fractions produced. Gas chromatography/isotope ratio mass spectrometry (GC/IRMS) of untreated, whole crude oils allows the immediate collection of a larger suite of valuable isotopic data for these studies.MethodsUntreated (‘neat’, undiluted), whole crude oils were directly injected and measured on a GC/IRMS system, using split (40:1) injections and a 50 m HP‐PONA column. The GC method, 97 min in duration, was designed to maximize baseline separation of target analyte peaks, while an additional oxygen flow was admitted into the combustion reactor to maximize the lifetime of the combustion chemicals.ResultsThe method and setup utilized allow the measurement of a much greater range of the n‐alkanes (n‐C4 to n‐C25+) than traditional methods, while also retaining important cycloalkane, aromatic and isoprenoid peaks within the same analysis. Carbon isotope (δ13C) evaluation of these additional compound classes reveals trends in maturity and origins which are not identifiable when exclusively assessing the traditional n‐alkane package (>n‐C12).ConclusionsThe described setup and method open up new possibilities for assessing the origins and histories of crude oil samples. The data generated for the whole oil n‐alkanes by this method is equivalent to that reported for isolated n‐alkane studies, while also providing valuable additional data on many other important compounds. The end result of this method is a more complete assessment of the carbon isotopic composition of crude oils. Copyright © 2016 John Wiley & Sons, Ltd.
Characterization of aromatic organosulfur model compounds relevant to fossil fuels by using atmospheric pressure chemical ionization with CS2and high‐resolution tandem mass spectrometry
Authors: Tang Weijuan , Sheng Huaming , Jin Chunfen , Riedeman James S. , Kenttämaa Hilkka I. 
Published: March 2016

RATIONALEThe chemistry of desulfurization involved in processing crude oil is greatly dependent on the forms of sulfur in the oil. Sulfur exists in different chemical bonding environments in fossil fuels, including those in thiophenes and benzothiophenes, thiols, sulfides, and disulfides. In this study, the fragmentation behavior of the molecular ions of 17 aromatic organosulfur compounds with various functionalities was systematically investigated by using high‐resolution tandem mass spectrometry.METHODSMultiple‐stage tandem mass spectrometric experiments were carried out using a linear quadrupole ion trap (LQIT) equipped with an atmospheric pressure chemical ionization (APCI) source. (+)APCI/CS2 was used to generate stable dominant molecular ions for all the compounds studied except for three sulfides that also showed abundant fragment ions. The LQIT coupled with an orbitrap mass spectrometer was used for elemental composition analysis, which facilitated the identification of the neutral molecules lost during fragmentation.RESULTSThe characteristic fragment ions generated in MS2 and MS3 experiments provide clues for the chemical bonding environment of sulfur atoms in the examined compounds. Upon collision‐induced dissociation (CID), the molecular ions can lose the sulfur atom in a variety of ways, including as S (32 Da), HS• (33 Da), H2S (34 Da), CS (44 Da), •CHS (45 Da) and CH2S (46 Da). These neutral fragments are not only indicative of the presence of sulfur, but also of the type of sulfur present in the compound. Generally, losses of HS• and H2S were found to be associated with compounds containing saturated sulfur functionalities, while losses of S, CS and •CHS were more common for heteroaromatic sulfur compounds.CONCLUSIONSHigh‐resolution tandem mass spectrometry with APCI/CS2 ionization is a viable approach to determining the types of organosulfur compounds. It can potentially be applied to analysis of complex mixtures, which is beneficial to improving the desulfurization process of fossil fuels. Copyright © 2016 John Wiley & Sons, Ltd.
Towards fair mutual private set intersection with linear complexity
Authors: Debnath Sumit Kumar , Dutta Ratna 
Published: March 2016

AbstractIn this paper, we propose a two‐way oblivious pseudorandom function (mOPRF) secure in standard model against malicious parties under the decisional composite residuosity and decisional Diffie–Hellman assumptions. Using this two‐way OPRF, we construct an optimistic mutual private set intersection (PSI) protocol conserving fairness. In our PSI protocol, fairness is obtained by a semi‐trusted arbiter in the sense that it cannot get access to the private information of the two parties, but we believe that it will follow the protocol. To the best of our knowledge, our PSI protocol is the first fair PSI with linear communication and computation complexities and is proven to be secure in standard model against malicious adversaries under decisional q‐Diffie–Hellman inversion, decisional composite residuosity, and decisional Diffie–Hellman assumptions. Apart from that, we present a modified version of the OPRF that requires less number of communication rounds. Copyright © 2016 John Wiley & Sons, Ltd.
Seeding strategies in search‐based unit test generation
Authors: Rojas José Miguel , Fraser Gordon , Arcuri Andrea 
Published: March 2016

SummarySearch‐based techniques have been applied successfully to the task of generating unit tests for object‐oriented software. However, as for any meta‐heuristic search, the efficiency heavily depends on many factors; seeding, which refers to the use of previous related knowledge to help solve the testing problem at hand, is one such factor that may strongly influence this efficiency. This paper investigates different seeding strategies for unit test generation, in particular seeding of numerical and string constants derived statically and dynamically, seeding of type information and seeding of previously generated tests. To understand the effects of these seeding strategies, the results of a large empirical analysis carried out on a large collection of open‐source projects from the SF110 corpus and the Apache Commons repository are reported. These experiments show with strong statistical confidence that, even for a testing tool already able to achieve high coverage, the use of appropriate seeding strategies can further improve performance. © 2016 The Authors. Software Testing, Verification and Reliability Published by John Wiley & Sons Ltd.
Design procedure for precast fibre‐reinforced concrete segments in tunnel lining construction
Authors: Di Carlo Fabio , Meda Alberto , Rinaldi Zila 
Published: March 2016

AbstractThis paper presents a procedure for designing precast tunnel segments for mechanically excavated tunnel linings in fibre‐ reinforced concrete, without any traditional steel reinforcement. Both ultimate and serviceability limit states are considered as well as structural checks at different construction stages of the segment, including demoulding, positioning on floor, storage, transportation, handling and the final stage concerning the loads due to the ground pressure.The structural checks are performed by means of bending moment‐axial force interaction envelopes for both the considered limit states, once the constitutive relationship of the material is defined for each stage. Traditional interaction envelopes are drawn for the ultimate limit state check, whereas for the serviceability limit state check, envelopes obtained by limiting the maximum crack opening and maximum concrete compressive stress are proposed. The shear action is also accounted for by reducing the bending moment‐axial force envelope. The possibility of having the assistance of a test procedure for particular loading situations is also proposed. Finally, a case study related to a precast steel fibre‐reinforced concrete segment is analysed in order to clarify the procedure and show, practically, how to define the actions and evaluate the interaction envelopes.