bluuebunny/crossref_metadata_2025 huggingface dataset:
Reduction of HbA1c and diabetes-related distress after intervention in a diabetes day care clinic in people with type 2 diabetes but not with type 1 diabetes
Authors: Kuniss Nadine , Müller Ulrich , Kloos Christof , Wolf Gunter , Kramer Guido
Published: July 2017

Objective The aim of this prospective, longitudinal study was to assess diabetes-related distress in people with diabetes mellitus type 1 (DM1) and type 2 (DM2) treated for diabetes-related problems and to evaluate, whether distress by diabetes are reduced after intervention in a diabetes day care clinic (DDC).

Methods Diabetes-related burden was assessed with the “Problem Area In Diabetes” (PAID) questionnaire before (T0), directly after (T1) and 6 months after intervention (T2) in the DDC in 72 people (18 DM1, 54 DM2) admitted with a diabetes-specific problem to a DDC in a University department for metabolic diseases. A PAID score of ≥40 was considered as high diabetes-related distress.

Results The PAID score in people with DM1 was not significantly different between T0, T1 and T2. Furthermore, neither HbA1c nor insulin dose did change at T2. In participants with DM2, the PAID score decreased significantly from T0 to T1 (18.4±15.9 vs. 15.4+± 13.0, p=0.042) and preserved the benefit at T2 (15.0±13.3). In addition, there was a significant reduction in HbA1c (−1.2%, p<0.001) and body weight (−1.3 kg, p=0.038) between T0 and T2. Insulin dose per day was 15.0 IU/day lower at T1 (p=0.006) and 9.0 IU/day lower at T2 (p=0.212) in comparison to T0.

Conclusions Diabetes-related distress was reduced after a problem-oriented intervention in a DDC in people with DM2 but not with DM1. Although, all participants at tertiary care level had serious diabetes-specific problems before intervention, mean PAID score was far under the threshold of 40 points thus distress was low.
Hybrid dielectric waveguide spectroscopy of individual plasmonic nanoparticles
Authors: Cuadra J. , Verre R. , Wersäll M. , Krückel C. , Torres-Company V. , Antosiewicz T. J. , Shegai T.
Published: July 2017

Plasmonics is a mature scientific discipline which is now entering the realm of practical applications. Recently, significant attention has been devoted to on-chip hybrid devices where plasmonic nanoantennas are integrated in standard Si3N4 photonic waveguides. Light in these systems is usually coupled at the waveguide apexes by using multiple objectives and/or tapered optical fibers, rendering the analysis of spectroscopic signals a complicated task. Here, we show how by using a grating coupler and a low NA objective, quantitative spectroscopic information similar to standard dark-field spectroscopy can be obtained at the single-nanoparticle level. This technology may be useful for enabling single-nanoparticle studies in non-linear excitation regimes and/or in complex experimental environments, thus enriching the toolbox of nanophotonic methods.
Thermal effects on 3D crater shape during IR laser ablation of monocrystalline silicon: From femtoseconds to microseconds
Authors: Buratin Stefano , Bashtova Kateryna , Kong Ming Chu
Published: July 2017

Analyzing the thermal effects (e.g., heat affected zone and debris analysis) on a laser-ablated crater using electron or atomic force microscopy is a time-consuming process while optical microscopy is limited to providing 2D information. The current work details an alternative method to identify and quantify the thermal effects based on an analysis of the 3D shape of craters. Starting from a thermal diffusion model, an iso-thermal function was developed and an iso-energetic function was defined based on the energy beam distribution. A systematic study of the 3D craters ablated on silicon was carried out at the four temporal regimes that are applicable in the industry: the femtosecond regime at 330 fs, the picosecond regime at 10 ps, the nanosecond regime in the range of 25–220 ns, and the microsecond regime in the range of 2–20 μs. It was shown that the defined Percentage Difference (PD) between the residual sum of squares (RSS) of the ellipsoid function and the RSS of the paraboloid function against the experimental crater, respectively, can be used to evaluate the presence of thermal effects. This corresponded with the results obtained using scanning electron microscope analysis. The analysis of the PD indicated how the crater shape was affected by the pulse duration while the non-thermal/thermal cutoff starting from the ps regime was studied. In addition, the crater shape was found to be affected by the laser beam fluence: for time regimes below the microsecond level, the thermal effects were seen to increase with higher laser beam fluence.
Atomistic mechanisms of copper filament formation and composition in Al2O3-based conductive bridge random access memory
Authors: Nail C. , Blaise P. , Molas G. , Bernard M. , Roule A. , Toffoli A. , Perniola L. , Vallée C.
Published: July 2017

Conductive filament formation and composition in Oxide-based Conductive Bridge Random Access Memory (CBRAM) are investigated. To this end, Al2O3/Cu-based CBRAM is electrically characterized and studied. Current-voltage characteristics exhibit different forming behaviors depending on device polarization exposing the charged species involved during the forming process. In order to get more insights at the microscopic level, ion diffusion is investigated in depth by first-principles calculations. We study different point defects in Al2O3 which can come either from the post-process of the material itself or after top electrode deposition or during device operation. Since the role of Oxygen Vacancies (VO) and Copper (Cu) ions is core to the switching mechanism, ab initio calculations focus on their displacements. For different charge states in Al2O3, we extract the thermodynamic and activation energies of Cu, Te, Al, and O related point defects. The results reveal that Cu is not the only ion diffusing in the Al2O3-based CBRAM switching mechanism while Te ions appear unfavorable. A Cu/VO based hybrid filament model is proposed, and the impact of Aluminum Vacancies (VAl) on the forming process is demonstrated.
Exploring the driving forces behind the structural assembly of biphenylthiolates on Au(111)
Authors: Verwüster Elisabeth , Wruss Elisabeth , Zojer Egbert , Hofmann Oliver T.
Published: July 2017

In this contribution, we use dispersion-corrected density functional theory to study inter- and intramolecular interactions in a prototypical self-assembled monolayer (SAM) consisting of biphenylthiolates bonded to Au(111) via thiolate groups. The goal is to identify the nature of the interactions that drive the monolayer into a specific conformation. Particular focus is laid on sampling realistic structures rather than high symmetry model configurations. This is achieved by studying conceptually different local minimum structures of the SAM that are obtained via exploring the potential energy surface from systematically varied starting geometries. The six obtained packing motifs differ in the relative arrangement of the two molecules in the unit cell (co-planar versus herringbone) and in the intramolecular configuration (twisted versus planar rings). We find that van der Waals interactions within the organic adsorbate and between the adsorbate and substrate are the main reason that these molecular assemblies can form stable structures at all. The van der Waals interactions are, however, very similar for all observed motifs; by analyzing various types of interactions in the course of three notional SAM-formation steps, we find that the main driving force stabilizing the actual global minimum structure originates from electrostatic interactions between the molecules.
Investigation of the Dzyaloshinskii-Moriya interaction and room temperature skyrmions in W/CoFeB/MgO thin films and microwires
Authors: Jaiswal S. , Litzius K. , Lemesh I. , Büttner F. , Finizio S. , Raabe J. , Weigand M. , Lee K. , Langer J. , Ocker B. , Jakob G. , Beach G. S. D. , Kläui M.
Published: July 2017

Recent studies have shown that material structures, which lack structural inversion symmetry and have high spin-orbit coupling can exhibit chiral magnetic textures and skyrmions which could be a key component for next generation storage devices. The Dzyaloshinskii-Moriya Interaction (DMI) that stabilizes skyrmions is an anti-symmetric exchange interaction favoring non-collinear orientation of neighboring spins. It has been shown that materials systems with high DMI can lead to very efficient domain wall and skyrmion motion by spin-orbit torques. To engineer such devices, it is important to quantify the DMI for a given material system. Here, we extract the DMI at the Heavy Metal/Ferromagnet interface using two complementary measurement schemes, namely, asymmetric domain wall motion and the magnetic stripe annihilation. By using the two different measurement schemes, we find for W(5 nm)/Co20Fe60B20(0.6 nm)/MgO(2 nm) the DMI to be 0.68 ± 0.05 mJ/m2 and 0.73 ± 0.5 mJ/m2, respectively. Furthermore, we show that this DMI stabilizes skyrmions at room temperature and that there is a strong dependence of the DMI on the relative composition of the CoFeB alloy. Finally, we optimize the layers and the interfaces using different growth conditions and demonstrate that a higher deposition rate leads to a more uniform film with reduced pinning and skyrmions that can be manipulated by spin orbit torques.
Pressure in an exactly solvable model of active fluid
Authors: Marini Bettolo Marconi Umberto , Maggi Claudio , Paoluzzi Matteo
Published: July 2017

We consider the pressure in the steady-state regime of three stochastic models characterized by self-propulsion and persistent motion and widely employed to describe the behavior of active particles, namely, the Active Brownian particle (ABP) model, the Gaussian colored noise (GCN) model, and the unified colored noise approximation (UCNA) model. Whereas in the limit of short but finite persistence time, the pressure in the UCNA model can be obtained by different methods which have an analog in equilibrium systems, in the remaining two models only the virial route is, in general, possible. According to this method, notwithstanding each model obeys its own specific microscopic law of evolution, the pressure displays a certain universal behavior. For generic interparticle and confining potentials, we derive a formula which establishes a correspondence between the GCN and the UCNA pressures. In order to provide explicit formulas and examples, we specialize the discussion to the case of an assembly of elastic dumbbells confined to a parabolic well. By employing the UCNA we find that, for this model, the pressure determined by the thermodynamic method coincides with the pressures obtained by the virial and mechanical methods. The three methods when applied to the GCN give a pressure identical to that obtained via the UCNA. Finally, we find that the ABP virial pressure exactly agrees with the UCNA and GCN results.
Interaction between depolarization effects, interface layer, and fatigue behavior in PZT thin film capacitors
Authors: Böttger U. , Waser R.
Published: July 2017

The existence of non-ferroelectric regions in ferroelectric thin films evokes depolarization effects leading to a tilt of the P(E) hysteresis loop. The analysis of measured hysteresis of lead zirconate titanate (PZT) thin films is used to determine a depolarization factor which contains quantitative information about interfacial layers as well as ferroelectrically passive zones in the bulk. The derived interfacial capacitance is smaller than that estimated from conventional extrapolation techniques. In addition, the concept of depolarization is used for the investigation of fatigue behavior of PZT thin films indicating that the mechanism of seed inhibition, which is responsible for the effect, occurs in the entire film.
Leakage currents and Fermi-level shifts in GaN layers upon iron and carbon-doping
Authors: Fariza A. , Lesnik A. , Neugebauer S. , Wieneke M. , Hennig J. , Bläsing J. , Witte H. , Dadgar A. , Strittmatter A.
Published: July 2017

Semi-insulating GaN is a prerequisite for lateral high frequency and high power electronic devices to isolate the device region from parasitic conductive channels. The commonly used dopants for achieving semi-insulating GaN, Fe, and C cause distinct properties of GaN layers since the Fermi-level is located either above (Fe) or below (C) the midgap position. In this study, precursor-based doping of GaN in metalorganic vapor phase epitaxy is used at otherwise identical growth conditions to control the dopant concentrations in the layer. Using electric force microscopy, we have investigated the contact potentials of Fe- and C-doped samples with respect to a cobalt metal probe tip in dependence of on the dopant concentration. While in Fe-doped samples the sign of the contact potential is constant, a change from positive to negative contact potential values is observed at high carbon concentrations, indicating the shift of the Fermi-level below the midgap position. In vertical transport measurements, C-doped GaN layers with a dopant concentration of 4.6 × 1018 cm−3 exhibit up to 5 orders of magnitude lower dark current at room temperature and significantly lower temperature dependence than Fe-doped samples with a similar dopant concentration. Therefore, precursor-based carbon doping is the superior doping technique to achieve semi-insulating GaN.
Comparison of the laser spot movement inside cylindrical and spherical hohlraums
Authors: Li Zhichao , Yang Dong , Li Sanwei , Huo Wen Yi , Lan Ke , Liu Jie , Ren Guoli , Chen Yao-Hua , Yang Zhiwen , Guo Liang , Hou Lifei , Xie Xuefei , Li Yukun , Deng Keli , Yuan Zheng , Zhan Xiayu , Yuan Guanghui , Zhang Haijun , Jiang Baibin , Huang Lizhen , Du Kai , Zhao Runchang , Li Ping , Wang Wei , Su Jingqin , Jiang Shaoen , Ding Yongkun , He Xian-Tu , Zhang Weiyan
Published: July 2017

Compared with cylindrical hohlraums, the octahedral spherical hohlraums have natural superiority in maintaining high radiation symmetry during the whole capsule implosion process in indirect drive inertial confinement fusion. However, the narrow space between laser beams and the hohlraum wall may disturb laser propagation inside the spherical hohlraum. In this work, the laser propagation inside the spherical hohlraum and cylindrical hohlraum is investigated experimentally by measuring laser spot movement at the SGIII-prototype laser facility. The experimental results show that the laser propagations inside the spherical hohlraum and the cylindrical hohlraum are totally different from each other due to different hohlraum structures. For the spherical hohlraum, although the laser energy is mainly deposited in the initial position of the laser spot during the whole laser pulse, some laser energies are absorbed by the ablated plasmas from the hohlraum wall. Because the laser beam is refracted by the thin plasmas near the laser entrance hole (LEH) region, the laser spot in the spherical hohlraum moves toward the opposite LEH. In contrast, the laser spot in the cylindrical hohlraum moves toward the LEH along the laser path due to the plasma expansion. When the laser is to be turned off, the accumulated plasmas near the LEH region in the cylindrical hohlraum absorb a majority of laser energy and hinder the laser arriving at the appointed position on the hohlraum wall.
Effect of gas composition on morphological properties of graphene nanosheet
Authors: Gupta Neha , Sharma Suresh C.
Published: July 2017

A multiscale theoretical model to study the effect of different gas mixtures on the nucleation and growth kinetics of a graphene nanosheet in the reactive low-temperature plasma environment has been developed. The model includes the plasma sheath formalization, kinetics of all the plasma species, charging of the graphene sheet, plasma-surface interaction, clusters and graphene islands nucleation, and vertical growth of a graphene nanosheet. The three different gas mixtures, i.e., C2H2, CH4, and CF4 with hydrogen and argon, are considered in the present investigation to examine the variations in the number densities of carbon and hydrogen species generated on the catalyst surface and their consecutive effects on the dimensions (i.e., height and thickness) and number density profiles of the graphene nanosheet. It is found that the thickness and height of the graphene sheet are maximum for C2H2 gas mixtures and least for CH4 and CF4, respectively. On the basis of the results obtained, the field emission characteristics of the graphene sheet have been analyzed, and it is estimated that C2H2 contained gas mixture enhances the field emission characteristics of the graphene sheet followed by CH4 and CF4. The presented results are in good agreement with the existing experimental observations.
Development of a virtual metrology method using plasma harmonics analysis
Authors: Jun H. , Shin J. , Kim S. , Choi H.
Published: July 2017

A virtual metrology technique based on plasma harmonics is developed for predicting semiconductor processes. From a plasma process performed by 300 mm photoresist stripper equipment, a strong correlation is found between optical plasma harmonics intensities and the process results, such as the photoresist strip rate and strip non-uniformity. Based on this finding, a general process prediction model is developed. The developed virtual metrology model shows that the R-squared (R2) values between the measured and predicted process results are 95% and 64% for the photoresist strip rate and photoresist strip non-uniformity, respectively. This is the first research on process prediction based on optical plasma harmonics analysis, and the results can be applied to semiconductor processes such as dry etching and plasma enhanced chemical vapor deposition.
Coexisting synchronous and asynchronous states in locally coupled array of oscillators by partial self-feedback control
Authors: Bera Bidesh K. , Ghosh Dibakar , Parmananda Punit , Osipov G. V. , Dana Syamal K.
Published: July 2017

We report the emergence of coexisting synchronous and asynchronous subpopulations of oscillators in one dimensional arrays of identical oscillators by applying a self-feedback control. When a self-feedback is applied to a subpopulation of the array, similar to chimera states, it splits into two/more sub-subpopulations coexisting in coherent and incoherent states for a range of self-feedback strength. By tuning the coupling between the nearest neighbors and the amount of self-feedback in the perturbed subpopulation, the size of the coherent and the incoherent sub-subpopulations in the array can be controlled, although the exact size of them is unpredictable. We present numerical evidence using the Landau-Stuart system and the Kuramoto-Sakaguchi phase model.
Perspective: The physics, diagnostics, and applications of atmospheric
pressure low temperature plasma sources used in plasma medicine
Authors: Laroussi M. , Lu X. , Keidar M.
Published: July 2017

Low temperature plasmas have been used in various plasma processing applications for several decades. But it is only in the last thirty years or so that sources generating such plasmas at atmospheric pressure in reliable and stable ways have become more prevalent. First, in the late 1980s, the dielectric barrier discharge was used to generate relatively large volume diffuse plasmas at atmospheric pressure. Then, in the early 2000s, plasma jets that can launch cold plasma plumes in ambient air were developed. Extensive experimental and modeling work was carried out on both methods and much of the physics governing such sources was elucidated. Starting in the mid-1990s, low temperature plasma discharges have been used as sources of chemically reactive species that can be transported to interact with biological media, cells, and tissues and induce impactful biological effects. However, many of the biochemical pathways whereby plasma affects cells remain not well understood. This situation is changing rather quickly because the field, known today as “plasma medicine,” has experienced exponential growth in the last few years thanks to a global research community that engaged in fundamental and applied research involving the use of cold plasma for the inactivation of bacteria, dental applications, wound healing, and the destruction of cancer cells/tumors. In this perspective, the authors first review the physics as well as the diagnostics of the principal plasma sources used in plasma medicine. Then, brief descriptions of their biomedical applications are presented. To conclude, the authors' personal assessment of the present status and future outlook of the field is given.
Deep-subwavelength plasmonic-photonic hybrid band gap opening by acoustic Lamb waves
Authors: Hsu Jin-Chen , Shih Jheng-Hong , Lin Tzy-Rong
Published: July 2017

In this letter, the efficient generation of tunable optical band gaps with the help of acousto-optic (AO) interactions in the deep subwavelength regime is proposed. The optical system consists of a thin dielectric slab and a metal surface separated by a nanoscale air gap. This structure allowed for the confinement of hybridized plasmonic-photonic gap modes, which are highly guided within the air gap. The enhanced AO interaction originated from the disturbance of the acoustic Lamb waves of the slab that can strongly boost the AO interface effect and scatter the optical fields. Therefore, wide optical band gaps and forbidden transmissions were observed in hybrid gap modes at telecommunication wavelengths.
Metallic nanorings for broadband, enhanced extraction of light from solid-state emitters
Authors: Trojak Oliver Joe , Park Suk In , Song Jin Dong , Sapienza Luca
Published: July 2017

We report on the increased extraction of light emitted by solid-state sources embedded within high refractive index materials. This is achieved by making use of a local lensing effect by sub-micron metallic rings deposited on the sample surface and centered around single emitters. We show enhancements in the intensity of the light emitted by InAs/GaAs single quantum dot lines into free space as high as a factor of 20. Such a device is intrinsically broadband and therefore compatible with any kind of solid-state light source. We foresee the fabrication of metallic rings via scalable techniques, like nano-imprint, and their implementation to improve the emission of classical and quantum light from solid-state sources. Furthermore, while increasing the brightness of the devices, the metallic rings can also act as top contacts for the local application of electric fields for carrier injection or wavelength tuning.
Quasi-metallic behavior of ZnO grown by atomic layer deposition: The role of hydrogen
Authors: Beh Holger , Hiller Daniel , Bruns Michael , Welle Alexander , Becker Hans-Werner , Berghoff Birger , Sürgers Christoph , Merz Rolf , Zacharias Margit
Published: July 2017

Zinc oxide (ZnO) fabricated by atomic layer deposition (ALD) is intrinsically well-conductive (∼5 mΩ cm), in contrast to the single-crystalline bulk material or sputtered ZnO thin films. There are generally three groups of candidates for the intrinsic n-type conductivity: intrinsic point defects, elemental impurities other than hydrogen, and incorporated hydrogen itself. In this study, we assess the different candidates concerning their impact on conductivity. In the presence of free electron densities of up to 5 × 1019 cm−3, impurities other than hydrogen are ruled out due to their ultra-low concentrations in the ppm range. Intrinsic point defects are also considered unlikely since the evolution of conductivity with deposition temperature is not reproduced in the Zn/O ratio as measured by Rutherford backscattering spectrometry. Hence, the most promising candidate is hydrogen with a concentration of ∼1 at. %, i.e., more than sufficient to account for the free electron density. In addition, we find a correlation between the deposition-temperature dependence of the carrier concentration and the hydrogen concentration. The formation energy of the conductive, hydrogen-related state is determined to be ∼40 meV. Hall measurements down to liquid helium temperatures revealed that the electron densities are constant over the whole temperature range. This constitutes a quasi-metallic behavior of ALD-ZnO for deposition temperatures of ≥150 °C. We propose that the very high concentration of hydrogen-induced donor states causes a vanishing ionization energy so that the donor band merges energetically with the ZnO conduction band. This model is supported by ultraviolet photoelectron spectroscopy measurements.
Prediction of intracellular exposure bridges the gap between target- and cell-based drug discovery
Authors: Mateus André , Gordon Laurie J. , Wayne Gareth J. , Almqvist Helena , Axelsson Hanna , Seashore-Ludlow Brinton , Treyer Andrea , Matsson Pär , Lundbäck Thomas , West Andy , Hann Michael M. , Artursson Per
Published: July 2017

Significance

Exposure at the site of action has been identified as one of the three most important factors for success in drug discovery and the design of chemical probes. Modern drug discovery programs have, to a great extent, shifted to intracellular targets, but methods to determine intracellular drug concentrations have been lacking. Here, we use a methodology for predicting intracellular exposure of small-molecule drugs to understand their potency toward intracellular targets. We show that our approach is generally applicable to multiple targets, cell types, and therapeutic areas. We expect that routine measurements of intracellular drug concentration will contribute to reducing the high attrition observed in drug discovery and the design of both better chemical probes and medicines.
Reduced orbitofrontal cortical volume is associated with interdependent self-construal
Authors: Kitayama Shinobu , Yanagisawa Kuniaki , Ito Ayahito , Ueda Ryuhei , Uchida Yukiko , Abe Nobuhito
Published: July 2017

Significance

Recent work in cultural neuroscience suggests that sociocultural processes are reciprocally influenced by neural mechanisms that are recruited to support social behaviors. In particular, interdependent orientations (which include a commitment to duties and obligations, and prosocial tendencies) require both the suspension of self-interest and cognitive attunement to social surroundings. Dominant theoretical perspectives suggest that this orientation is achieved through active inhibitory control of egoism. Our results highlight an alternative pathway wherein the suspension of self-interest is achieved through reduced cortical volumes for personal incentives and goals. This reduced cortical volume is linked to interdependence especially for those who are cognitively attuned to the surrounding context. Therefore interdependent tendencies may be automatic and supported by structurally realized inhibition of egoism.
Enhanced coupling of light into a turbid medium through microscopic interface engineering
Authors: Thompson Jonathan V. , Hokr Brett H. , Kim Wihan , Ballmann Charles W. , Applegate Brian E. , Jo Javier , Yamilov Alexey , Cao Hui , Scully Marlan O. , Yakovlev Vladislav V.
Published: July 2017

Significance

Optical scattering severely limits the range and sensitivity of detection techniques within/through turbid media, such as biological samples and security-related materials. In this article, we demonstrate a method to enhance the coupling of light into a highly scattering medium. This enhanced coupling results in higher optical sensitivity to particles within the medium, as well as enhanced optical transmission through the medium. These results pave the way for enhanced spectroscopy in biological and other turbid media.
The role of verbs and verb classes in identifying German search-constructions
Authors: Proost Kristel
Published: July 2017

This chapter describes the German search-construction, an argument structure construction that is virtually unexplored. It focuses on the questions of how instances of the construction may be detected and how the relations between its variants may be described. Verbs relevant to the construction are detected by corpus searches in DeReKo (Deutsches Referenzkorpus) using the preposition nach as an anchor. The main variants of the construction are identified by grouping the verbs found to occur with it in the corpora into semantic classes. While some variants are related to the central pattern by metaphorical extension or stand in a relationship of precondition to it, all of them are additionally related to at least one other variant by family relationships.
Doing Tsukahara and the Epley in a cross-linguistic perspective
Authors: Brdar-Szabó Rita , Brdar Mario
Published: July 2017

This chapter studies eponymous verb constructions (EVCs) in medical and sports discourse in English, German, Croatian and Hungarian. These are constructions consisting of a light verb such as to do and an eponymic noun phrase denoting events. A cross-linguistic comparison reveals that, unlike in English, the productivity of EVCs containing reduced eponymic constructions is severely constrained in German, Croatian and Hungarian. These contrasts can be related not only to some structural givens of the languages in question, such as the availability of articles in the language in question, the entrenchment of light verbs, the gender system, but also to the fact that languages can more or less easily accommodate complex metonymies.
Motivation behind the extended senses of the Polish ditransitive construction
Authors: Paszenda Joanna
Published: July 2017

This chapter, drawing on Goldberg’s (1992/2006, 1995, 2002) and Croft’s (2003) analyses of the English ditransitive construction, employs Geeraerts’ (1998/2006) multidimensional model of constructional polysemy. Its main aim is to characterize the family of ditransitive expressions in Polish and to identify the cognitive mechanisms that motivate them. Relying on the groundwork laid by Rudzka-Ostyn’s (1996), Dąbrowska’s (1997), and Fried’s (1999, 2004, 2011) studies of the Polish and Czech dative case, the chapter underscores the semantic contribution of overt case marking on the first object as the key factor licensing the wider semantic range of the Polish pattern compared to the English construction, notably its application to the expression of events of ‘pure’ benefaction, malefaction, and reversed transfer.
Try and try again: Post-error boost of an implicit measure of agency
Authors: Di Costa Steven , Théro Héloïse , Chambon Valérian , Haggard Patrick
Published: July 2017

The sense of agency refers to the feeling that we control our actions and, through them, effects in the outside world. Reinforcement learning provides an important theoretical framework for understanding why people choose to make particular actions. Few previous studies have considered how reinforcement and learning might influence the subjective experience of agency over actions and outcomes. In two experiments, participants chose between two action alternatives, which differed in reward probability. Occasional reversals of action–reward mapping required participants to monitor outcomes and adjust action selection processing accordingly. We measured shifts in the perceived times of actions and subsequent outcomes (‘intentional binding’) as an implicit proxy for sense of agency. In the first experiment, negative outcomes showed stronger binding towards the preceding action, compared to positive outcomes. Furthermore, negative outcomes were followed by increased binding of actions towards their outcome on the following trial. Experiment 2 replicated this post-error boost in action binding and showed that it only occurred when people could learn from their errors to improve action choices. We modelled the post-error boost using an established quantitative model of reinforcement learning. The post-error boost in action binding correlated positively with participants’ tendency to learn more from negative outcomes than from positive outcomes. Our results suggest a novel relation between sense of agency and reinforcement learning, in which sense of agency is increased when negative outcomes trigger adaptive changes in subsequent action selection processing.
Hypothesis Competition beyond Mutual Exclusivity
Authors: Schupbach Jonah N. , Glass David H.
Published: July 2017

Competition between scientific hypotheses is not always a matter of mutual exclusivity. Consistent hypotheses can compete to varying degrees either directly or indirectly via a body of evidence. We motivate and defend a particular account of hypothesis competition by showing how it captures these features. Computer simulations of Bayesian inference are used to highlight the limitations of adopting mutual exclusivity as a simplifying assumption to model scientific reasoning, particularly due to the exclusion of hypotheses that may be true. We end with a case study demonstrating the subtleties involved in hypothesis competition in scientific practice.
No Free Lunch Theorem, Inductive Skepticism, and the Optimality of Meta-induction
Authors: Schurz Gerhard
Published: July 2017

The no free lunch theorem is a radicalized version of Hume’s induction skepticism. It asserts that relative to a uniform probability distribution over all possible worlds, all computable prediction algorithms—whether ‘clever’ inductive or ‘stupid’ guessing methods (etc.)—have the same expected predictive success. This theorem seems to be in conflict with results about meta-induction. According to these results, certain meta-inductive prediction strategies may dominate other (non-meta-inductive) methods in their predictive success (in the long run). In this article this conflict is analyzed and dissolved, by means of probabilistic analysis and computer simulation.
Prediction and modeling of pre-analytical sampling errors as a strategy to improve plasma NMR metabolomics data
Authors: Brunius Carl , Pedersen Anders , Malmodin Daniel , Karlsson B Göran , Andersson Lars I , Tybring Gunnel , Landberg Rikard
Published: July 2017

Motivation

Biobanks are important infrastructures for life science research. Optimal sample handling regarding e.g. collection and processing of biological samples is highly complex, with many variables that could alter sample integrity and even more complex when considering multiple study centers or using legacy samples with limited documentation on sample management. Novel means to understand and take into account such variability would enable high-quality research on archived samples.

Results

This study investigated whether pre-analytical sample variability could be predicted and reduced by modeling alterations in the plasma metabolome, measured by NMR, as a function of pre-centrifugation conditions (1–36 h pre-centrifugation delay time at 4 °C and 22 °C) in 16 individuals. Pre-centrifugation temperature and delay times were predicted using random forest modeling and performance was validated on independent samples. Alterations in the metabolome were modeled at each temperature using a cluster-based approach, revealing reproducible effects of delay time on energy metabolism intermediates at both temperatures, but more pronounced at 22 °C. Moreover, pre-centrifugation delay at 4 °C resulted in large, specific variability at 3 h, predominantly of lipids. Pre-analytical sample handling error correction resulted in significant improvement of data quality, particularly at 22 °C. This approach offers the possibility to predict pre-centrifugation delay temperature and time in biobanked samples before use in costly downstream applications. Moreover, the results suggest potential to decrease the impact of undesired, delay-induced variability. However, these findings need to be validated in multiple, large sample sets and with analytical techniques covering a wider range of the metabolome, such as LC-MS.

Availability and implementation

The sampleDrift R package is available at https://gitlab.com/CarlBrunius/sampleDrift.

Supplementary information

Supplementary data are available at Bioinformatics online.
Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer
Authors: Baker Simon , Ali Imran , Silins Ilona , Pyysalo Sampo , Guo Yufan , Högberg Johan , Stenius Ulla , Korhonen Anna
Published: July 2017

Motivation

To understand the molecular mechanisms involved in cancer development, significant efforts are being invested in cancer research. This has resulted in millions of scientific articles. An efficient and thorough review of the existing literature is crucially important to drive new research. This time-demanding task can be supported by emerging computational approaches based on text mining which offer a great opportunity to organize and retrieve the desired information efficiently from sizable databases. One way to organize existing knowledge on cancer is to utilize the widely accepted framework of the Hallmarks of Cancer. These hallmarks refer to the alterations in cell behaviour that characterize the cancer cell.

Results

We created an extensive Hallmarks of Cancer taxonomy and developed automatic text mining methodology and a tool (CHAT) capable of retrieving and organizing millions of cancer-related references from PubMed into the taxonomy. The efficiency and accuracy of the tool was evaluated intrinsically as well as extrinsically by case studies. The correlations identified by the tool show that it offers a great potential to organize and correctly classify cancer-related literature. Furthermore, the tool can be useful, for example, in identifying hallmarks associated with extrinsic factors, biomarkers and therapeutics targets.

Availability and implementation

CHAT can be accessed at: http://chat.lionproject.net. The corpus of hallmark-annotated PubMed abstracts and the software are available at: http://chat.lionproject.net/about

Supplementary information

Supplementary data are available at Bioinformatics online.
A robust DF-REML framework for variance components estimation in genetic studies
Authors: Lourenço V M , Rodrigues P C , Pires A M , Piepho H -P
Published: July 2017

Motivation

In genetic association studies, linear mixed models (LMMs) are used to test for associations between phenotypes and candidate single nucleotide polymorphisms (SNPs). These same models are also used to estimate heritability, which is central not only to evolutionary biology but also to the prediction of the response to selection in plant and animal breeding, as well as the prediction of disease risk in humans. However, when one or more of the underlying assumptions are violated, the estimation of variance components may be compromised and therefore so may the estimates of heritability and any other functions of these. Considering that datasets obtained from real life experiments are prone to several sources of contamination, which usually induce the violation of the assumption of the normality of the errors, a robust derivative-free restricted-maximum likelihood framework (DF-REML) together with a robust coefficient of determination are proposed for the LMM in the context of genetic studies of continuous traits.

Results

The proposed approach, in addition to the robust estimation of variance components and robust computation of the coefficient of determination, allows in particular for the robust estimation of SNP-based heritability by reducing the bias and increasing the precision of its estimates. The performance of both classical and robust DF-REML approaches is compared via a Monte Carlo simulation study. Additionally, three examples of application of the methodologies to real datasets are given in order to validate the usefulness of the proposed robust approach. Although the main focus of this article is on plant breeding applications, the proposed methodology is applicable to both human and animal genetic studies.

Availability and implementation

Source code implemented in R is available in the Supplementary Material.

Supplementary information

Supplementary data are available at Bioinformatics online.
Maternal mood in pregnancy: fetal origins of child neurodevelopment
Authors: Glover Vivette , O’Connor Thomas G. , O’Donnell Kieran
Published: July 2017

Women experience as many symptoms of anxiety, depression, and stress during pregnancy as in the postnatal period. This can affect not only the woman herself but also the development of her fetus, and have long-term effects on several different outcomes including the cognitive ability and behaviour of her child, although most children are not affected. The particular outcomes affected may depend on the timing of the exposure, specific genetic vulnerabilities, and the quality of postnatal care provided. Recent research has shown that increased maternal anxiety is associated with altered placental function, and a greater association between maternal and fetal cortisol. This interrelationship of hormonal associations during the fetal stage could potentially impact on fetal/infant outcomes, and supports the need for continuing research in the field. Chapter 3 covers studies on maternal mood in pregnancy and explores the underlying mechanisms and types of stress.
Psycho-oncology and psychosocial aspects of gynaecological cancer
Authors: Onishi Hideki , Ishida Mayumi
Published: July 2017

Patients with gynaecological cancer encounter, everyday, various problems in their family lives, jobs, and finances, in addition to the direct effects of the cancer itself. They also face problems concerning a loss of femininity, such as those related to the menopause, their reproductive function, and sexual activity that is brought about by the effects of the disease and its management. Hence, problems are not only limited to the biological aspect of cancer, but also to its impact on psychosocial aspects, thereby increasing the level of stress in these patients. Hence, when considering the problems of patients with gynaecological cancer, its psychosocial impact, and its effect on day-to-day living should be addressed in addition to the physical aspect of the disease. Otherwise, treatment will be inadequate. Chapter 10 addresses this. Recognition of the importance of solving these psychosocial problems, which can be distressing to many patients with gynaecological cancer, and the early identification along with appropriate intervention for these problems, would aid in improving the quality-of-life of these sufferers. Furthermore, the biopsychosocial impact of the cancer extends to close family members who care for the patient, particularly the spouse/ partner, and thus increases their risk of psychosomatic disease besides malignancy. Cancer support services should include the family care-givers. Two vignettes illustrate the complex biopsychosocial issues associated with gynaecological cancer, and one depicts issues after bereavement.
Migration, gender, and cultural issues in healthcare: psychosomatic implications
Authors: Lal Mira
Published: July 2017

Human migration involves moving to a new permanent or semi-permanent location. Whether on an individual basis, in small groups or in large numbers, whether due to economic necessity (emigrants), sociocultural strife or the effects of war (refugees), it can contribute to stress in the mobile along with the settled population. Uncertainty then, increases the risk of psychosomatic disease in those relocating because of the changes in their personal/social support networks. The available healthcare for the displaced may not address their health needs adequately. Chapter 12 deliberates on this. Gender-related issues, with a female preponderance as victims come to the fore in displaced populations. These include the health effects of domestic and sexual violence or gender-based violence. International organisations, including the UN, the WHO, and FIGO, along with organisations from various countries that promote women's and children's health, have developed guidelines, and attempted to engender political will to endeavour to stop this preventable morbidity. Nevertheless, it persists with a biopsychosociocultural impact, and can be fatal. Unwanted pregnancies can result from gender-based violence or failed contraception with the pregnant woman seeking termination (abortion). Annually, about 42 million women resort to illegal methods of abortion, and risk grievous harm due to a lack of legalized services. Female genital mutilation, a form of gender-based violence with genitourinary sequelae that is carried out on girls, has global implications. It prevails due to cultural acceptance, despite major health consequences. It is illegal in the UK, and the RCOG has developed guidelines. Vignettes in this chapter illustrate these gender-related health issues.
Finding the Poor vs. Measuring Their Poverty: Exploring the Drivers of Targeting Effectiveness in Indonesia
Authors: Bah Adama , Bazzi Samuel , Sumarto Sudarno , Tobias Julia
Published: July 2017

Centralized targeting registries are increasingly used to allocate social assistance benefits in developing countries. There are two key design issues that matter for targeting accuracy: (i) which households to survey for inclusion in the registry; and (ii) how to rank surveyed households. We attempt to identify their relative importance by evaluating Indonesia's Unified Database for Social Protection Programs (UDB), among the largest targeting registries in the world, used to provide social assistance to over 25 million households. Linking administrative data with an independent household survey, we find that the UDB system is more progressive than previous, program-specific targeting approaches. However, simulating an alternative targeting system based on enumerating all households, we find a one-third reduction in undercoverage of the poor compared to focusing on households registered in the UDB. Overall, there are large gains in targeting performance from improving the initial registration stage relative to the ranking stage.
Novel Insights into Tat Pathway in Xanthomonas oryzae pv. oryzae Stress Adaption and Virulence: Identification and Characterization of Tat-Dependent Translocation Proteins
Authors: Wu Guichun , Su Panpan , Wang Bo , Zhang Yuqiang , Qian Guoliang , Liu Fengquan
Published: July 2017

Xanthomonas oryzae pv. oryzae, an economically important bacterium, causes a serious disease in rice production worldwide called bacterial leaf blight. How X. oryzae pv. oryzae infects rice and causes symptoms remains incompletely understood. Our earlier works demonstrated that the twin-arginine translocation (Tat) pathway plays an vital role in X. oryzae pv. oryzae fitness and virulence but the underlying mechanism is unknown. In this study, we used strain PXO99A as a working model, and identified 15 potential Tat-dependent translocation proteins (TDTP) by using comparative proteomics and bioinformatics analyses. Combining systematic mutagenesis, phenotypic characterization, and gene expression, we found that multiple TDTP play key roles in X. oryzae pv. oryzae adaption or virulence. In particular, four TDTP (PXO_02203, PXO_03477, PXO_02523, and PXO_02951) were involved in virulence, three TDTP (PXO_02203, PXO_03477, and PXO_02523) contributed to colonization in planta, one TDTP (PXO_02671) had a key role in attachment to leaf surface, four TDTP (PXO_02523, PXO_02951, PXO_03132, and PXO_03841) were involved in tolerance to multiple stresses, and two TDTP (PXO_02523 and PXO_02671) were required for full swarming motility. These findings suggest that multiple TDTP may have differential contributions to involvement of the Tat pathway in X. oryzae pv. oryzae adaption, physiology, and pathogenicity.