bluuebunny/crossref_metadata_2025 huggingface dataset:
Time-dependent inhibition of PHD2
Authors: Tcholakov Isabelle , Grimshaw Charles E. , Shi Lihong , Kiryanov Andre , Murphy Sean T. , Larson Christopher J. , Plonowski Artur , Ermolieff Jacques
Published: June 2017

Prolyl hydroxylases (PHDs) down-regulate the level of hypoxia-inducible factors (HIFs) by hydroxylating key proline residues that trigger the degradation of the protein and affect the cell and its ability to respond to hypoxic stress. Several small molecule PHD inhibitors are now in various preclinical and clinical stages for the treatment of anemia. The present study provides a detail kinetic analysis for some of these inhibitors. The data generated in the present study suggest that these compounds are reversible and compete directly with the co-substrate, 2-oxoglutarate (2-OG) for binding at the enzyme active site. Most of these compounds are pan PHD inhibitors and exhibit a time-dependent inhibition (TDI) mechanism due to an extremely slow dissociation rate constant, koff, and a long residence time.
Thrombosis in diabetes: a shear flow effect?
Authors: Westein Erik , Hoefer Thomas , Calkin Anna C.
Published: June 2017

Cardiovascular events are the major cause of morbidity and mortality in Type 2 diabetes (T2D). This condition is associated with heightened platelet reactivity, contributing to increased atherothrombotic risk. Indeed, individuals with diabetes respond inadequately to standard antiplatelet therapy. Furthermore, they often experience recurrent events as well as side effects that include excess bleeding. This highlights the need for identification of novel regulators of diabetes-associated thrombosis to target for therapeutic intervention. It is well established that platelet aggregation, a process essential for thrombus formation, is tightly regulated by shear stress; however, the mechanisms underlying shear activation of platelets, particularly in the setting of diabetes, are still poorly understood. This review will address the limitations of current diagnostic systems to assess the importance of shear stress in the regulation of thrombus formation in T2D, and the inability to recapitulate the pro-thrombotic phenotype seen clinically in the setting of T2D. Moreover, we will discuss recent findings utilizing new technologies to define the importance of shear stress in thrombus formation and their potential application to the setting of diabetes. Finally, we will discuss the potential of targeting shear-dependent mechanisms of thrombus formation as a novel therapeutic approach in the setting of T2D.
Speech-Processing Fatigue in Children: Auditory Event-Related Potential and Behavioral Measures
Authors: Key Alexandra P. , Gustafson Samantha J. , Rentmeester Lindsey , Hornsby Benjamin W. Y. , Bess Fred H.
Published: June 2017

Purpose

Fatigue related to speech processing is an understudied area that may have significant negative effects, especially in children who spend the majority of their school days listening to classroom instruction.

Method

This study examined the feasibility of using auditory P300 responses and behavioral indices (lapses of attention and self-report) to measure fatigue resulting from sustained listening demands in 27 children (M= 9.28 years).

Results

Consistent with predictions, increased lapses of attention, longer reaction times, reduced P300 amplitudes to infrequent target stimuli, and self-report of greater fatigue were observed after the completion of a series of demanding listening tasks compared with the baseline values. The event-related potential responses correlated with the behavioral measures of performance.

Conclusion

These findings suggest that neural and behavioral responses indexing attention and processing resources show promise as effective markers of fatigue in children.
Relative Fundamental Frequency Distinguishes Between Phonotraumatic and Non-Phonotraumatic Vocal Hyperfunction
Authors: Heller Murray Elizabeth S. , Lien Yu-An S. , Van Stan Jarrad H. , Mehta Daryush D. , Hillman Robert E. , Pieter Noordzij J. , Stepp Cara E.
Published: June 2017

Purpose

The purpose of this article is to examine the ability of an acoustic measure, relative fundamental frequency (RFF), to distinguish between two subtypes of vocal hyperfunction (VH): phonotraumatic (PVH) and non-phonotraumatic (NPVH).

Method

RFF values were compared among control individuals with typical voices (
N
= 49), individuals with PVH (
N
= 54), and individuals with NPVH (
N
= 35).

Results

Offset Cycle 10 RFF differed significantly among all 3 groups with values progressively decreasing for controls, individuals with NPVH, and individuals with PVH. Individuals with PVH also had lower Offset Cycles 8 and 9 relative to the other 2 groups and lower RFF values for Offset Cycle 7 relative to controls. There was also a trend for lower Onset Cycle 1 RFF values for the PVH group compared with the NPVH group.

Conclusions

RFF values were significantly different between controls and individuals with VH and also between the two subtypes of VH. This study adds further support to the notion that the differences between these two subsets of VH may be functional as well as structural.
Multi‐site European framework for real‐time co‐simulation of power systems
Authors: Stevic Marija , Estebsari Abouzar , Vogel Steffen , Pons Enrico , Bompard Ettore , Masera Marcelo , Monti Antonello
Published: June 2017

The framework for virtual integration of laboratories enables co‐simulation and joint experiments that include hardware and software resources hosted at geographically distributed laboratories. The underlying concept of such framework is geographically distributed real‐time (RT) co‐simulation. To this end, digital RT simulators are interfaced over long distances via shared communication network such as the Internet. This study proposes an architecture for a modular framework supporting virtual integration of laboratories that enable flexible integration of digital RT simulators across Europe. In addition, the framework includes an interface that enables access for third parties via a web browser. A co‐simulation interface algorithm adopted in this study is based on representation of interface quantities in form of dynamic phasors. Time delay between RT digital simulators is compensated by means of phase shift that enables simulation fidelity for slow transients. The proposed architecture is realised for the integration of laboratories across Europe that are located at RWTH Aachen University in Germany, Politecnico di Torino in Italy and at European Commission Joint Research Centres in Petten, Netherland and in Ispra, Italy. The framework for virtual integration of laboratories presented in this study is applied for co‐simulation of transmission and distribution systems.
Near-degeneracy effects on the frequencies of rotationally-split mixed modes in red giants
Authors: Deheuvels S. , Ouazzani R. M. , Basu S.
Published: June 2017

Context. The Kepler space mission has made it possible to measure the rotational splittings of mixed modes in red giants, thereby providing an unprecedented opportunity to probe the internal rotation of these stars.

Aims. Asymmetries have been detected in the rotational multiplets of several red giants. This is unexpected since all the red giants whose rotation profiles have been measured thus far are found to rotate slowly, and low rotation, in principle, produces symmetrical multiplets. Our aim here is to explain these asymmetries and find a way of exploiting them to probe the internal rotation of red giants.

Methods. We show that in the cases where asymmetrical multiplets were detected, near-degeneracy effects are expected to occur, because of the combined effects of rotation and mode mixing. Such effects have not been taken into account so far. By using both perturbative and non-perturbative approaches, we show that near-degeneracy effects produce multiplet asymmetries that are very similar to the observations. We then propose and validate a method based on the perturbative approach to probe the internal rotation of red giants using multiplet asymmetries.

Results. We successfully apply our method to the asymmetrical l = 2 multiplets of the Kepler young red giant KIC 7341231 and obtain precise estimates of its mean rotation in the core and the envelope. The observed asymmetries are reproduced with a good statistical agreement, which confirms that near-degeneracy effects are very likely the cause of the detected multiplet asymmetries.

Conclusions. We expect near-degeneracy effects to be important for l = 2 mixed modes all along the red giant branch (RGB). For l = 1 modes, these effects can be neglected only at the base of the RGB. They must therefore be taken into account when interpreting rotational splittings and as shown here, they can bring valuable information about the internal rotation of red giants.
Vergleich von klinischem und histopathologischem Staging bei Patienten mit Oropharynxkarzinom
Authors: Knipping Stephan , Theunert Anika , Stock Karsten , Wienke Andreas
Published: June 2017

Hintergrund Trotz der Fortschritte in Diagnostik und Therapie ist die Prognose von Oropharynxkarzinomen weiterhin ungünstig. Deshalb ist es entscheidend, das klinische Staging weiter zu verbessern, um darauf basierend Therapiemodalitäten festzulegen.

Material und Methoden In einer retrospektiven, pseudonymisierten Untersuchung aus einem 13 Jahreszeitraum wurde bei 84 primär operierten Patienten mit einem Oropharynxkarzinom die klinische Klassifikation (cTNM) mit der histopathologischen Beurteilung (pTNM) verglichen. Auch das Vorhandensein von okkulten Metastasen sowie das Gesamtüberleben in Abhängigkeit von der histopathologischen Tumorausdehnung und des regionären Lymphknotenbefalls wurden betrachtet.

Ergebnisse Die höchste Übereinstimmung zwischen cTNM und pTNM konnte bei der Computertomografie erreicht werden. Eine definitive Bewertung mit histopathologischer Zuverlässigkeit ist durch das cTNM nicht möglich. Die MRT-Untersuchungen zeigten die Tendenz, die T- und N-Kategorien und das UICC-Tumorstadium klinisch ausgedehnter einzuschätzen als durch die definitve histopathologische Beurteilung nachgewiesen. Im Rahmen der Untersuchung des Überlebens getrennt nach Geschlecht, histopathologischer T- und N-Kategorien zeigte sich bei den höheren T- bzw. N-Kategorien ein geringeres Gesamtüberleben.

Schlussfolgerungen Trotz aller Fortschritte in der bildgebenden Diagnostik bei Patienten mit Oropharynxkarzinomen ist das cTNM im Vergleich zum pTNM nur partiell in der Lage, mit klinisch geforderter Akkuratesse die TNM-Klassifikation der Tumorerkrankung zu bestimmen. Bei tendenziell sinkenden Prognosen ist es trotz moderner Therapieverfahren entscheidend, das prätherapeutische klinische Staging weiter zu verbessern und zu optimieren.
Aktueller Stand Salvage-chirurgischer Therapiekonzepte bei Rezidivtumoren des Larynx und Pharynx
Authors: Stuck B. , Rothmeier N. , Mattheis S. , Dominas N. , Lang S.
Published: June 2017

Die therapeutischen Konzepte bei Kopf-Hals-Malignomen haben in den letzten 20 Jahren einen erheblichen Wandel erfahren, der mit einer zunehmenden Bedeutung nicht-chirurgischer Therapieverfahren einhergeht. Auch unter den Organerhaltungsprotokollen bzw. nach primärer Radiochemotherapie kommt es jedoch in erheblichem Umfang zum Auftreten von Tumorrezidiven. In dieser Situation stellt die Salvage- bzw. Rettungschirurgie im Kopf-Hals-Bereich häufig die einzig noch verbliebene kurative Option dar. Die Etablierung plastisch-rekonstruktiver Maßnahmen vor ca. 30 Jahren hat das operative Spektrum im Kopf-Hals-Bereich signifikant erweitert und neue Möglichkeiten der Salvage-Chirurgie bei rezidivierenden Karzinomen des Pharynx und Larynx eröffnet. Die Überlebensraten nach Salvage-Chirurgie hängen hierbei im Wesentlichen von der Art der Primärtherapie, der Lokalisation und dem Tumorstadium sowohl bei Erstdiagnose als auch zum Zeitpunkt des Rezidivs ab. Zur plastisch-rekonstruktiven Deckung kommen gestielte Lappen oder mikrovaskulär-anastomosierte Transplantate zum Einsatz. Die am häufigsten angewandten gestielten Lappen sind der M. pectoralis-major- und der Latissimus-dorsi-Lappen. Als freie Transplantate kommt meist das Radialis- oder ALT-Transplantat zum Einsatz. Durch Verwendung dieser Lappen und Transplantate wird nicht-bestrahltes Gewebe in die vorgeschädigten Regionen verlagert, um neben der Wiederherstellung der ursprünglichen Organfunktion auch gefürchtete postoperative Komplikationen, wie z. B. Speichelfisteln, zu reduzieren. Die Indikation zur Salvage-Chirurgie muss auch weiterhin in jedem Einzelfall vor dem Hintergrund der zu erwartenden Morbidität und einer realistischen Einschätzung der Erfolgsaussichten abgewogen werden. Die vorliegende Publikation möchte hierzu entsprechende Empfehlungen geben.
Systemic risk and hierarchical transitions of financial networks
Authors: Nobi Ashadun , Lee Jae Woo
Published: June 2017

In this paper, the change in topological hierarchy, which is measured by the minimum spanning tree constructed from the cross-correlations between the stock indices from the S & P 500 for 1998–2012 in a one year moving time window, was used to analyze a financial crisis. The hierarchy increased in all minor crises in the observation time window except for the sharp crisis of 2007–2008 when the global financial crisis occurred. The sudden increase in hierarchy just before the global financial crisis can be used for the early detection of an upcoming crisis. Clearly, the higher the hierarchy, the higher the threats to financial stability. The scaling relations were developed to observe the changes in hierarchy with the network topology. These scaling relations can also identify and quantify the financial crisis periods, and appear to contain the predictive power of an upcoming crisis.
Functionality and versatility of aggregation-induced emission luminogens
Authors: Feng Guangxue , Kwok Ryan T. K. , Tang Ben Zhong , Liu Bin
Published: June 2017

Breakthrough innovations in light-emitting materials have opened new exciting avenues for science and technology over the last few decades. Aggregation-induced emission (AIE) represents one of such innovations. It refers to a unique light-emitting phenomenon, in which luminescent materials that are non-emissive in molecular state can be induced to emit efficiently in aggregated state. The design and development of AIE luminogens (AIEgens) have overcome technical and fundamental limitations that exist in conventional light-emitting materials, and thus generate great opportunities for various applications. In this review, we aim to introduce the wonderful world of AIE to scientists from different disciplines by summarizing the recent progress made in this exciting research field. The mechanistic analyses and the working principles of the AIE processes are first elaborated, which reveal the restriction of intramolecular motions as the main cause for the AIE effect. The different molecular engineering strategies for the design of new AIEgens are subsequently discussed with examples of various AIEgen systems. The recent high-tech applications of AIEgens as optoelectronic materials, chemical sensors, and biomedical probes are presented and discussed. We hope that this review will stimulate more research interest from physics, chemistry, life science, and biomedical fields to this wonderland of AIE.
Nanometer scale composition study of MBE grown BGaN performed by atom probe tomography
Authors: Bonef Bastien , Cramer Richard , Speck James S.
Published: June 2017

Laser assisted atom probe tomography is used to characterize the alloy distribution in BGaN. The effect of the evaporation conditions applied on the atom probe specimens on the mass spectrum and the quantification of the III site atoms is first evaluated. The evolution of the Ga++/Ga+ charge state ratio is used to monitor the strength of the applied field. Experiments revealed that applying high electric fields on the specimen results in the loss of gallium atoms, leading to the over-estimation of boron concentration. Moreover, spatial analysis of the surface field revealed a significant loss of atoms at the center of the specimen where high fields are applied. A good agreement between X-ray diffraction and atom probe tomography concentration measurements is obtained when low fields are applied on the tip. A random distribution of boron in the BGaN layer grown by molecular beam epitaxy is obtained by performing accurate and site specific statistical distribution analysis.
Investigation of the plasma shaping effects on the H-mode pedestal structure using coupled kinetic neoclassical/MHD stability simulations
Authors: Pankin A. Y. , Rafiq T. , Kritz A. H. , Park G. Y. , Snyder P. B. , Chang C. S.
Published: June 2017

The effects of plasma shaping on the H-mode pedestal structure are investigated. High fidelity kinetic simulations of the neoclassical pedestal dynamics are combined with the magnetohydrodynamic (MHD) stability conditions for triggering edge localized mode (ELM) instabilities that limit the pedestal width and height in H-mode plasmas. The neoclassical kinetic XGC0 code [Chang et al., Phys. Plasmas 11, 2649 (2004)] is used in carrying out a scan over plasma elongation and triangularity. As plasma profiles evolve, the MHD stability limits of these profiles are analyzed with the ideal MHD ELITE code [Snyder et al., Phys. Plasmas 9, 2037 (2002)]. Simulations with the XGC0 code, which includes coupled ion-electron dynamics, yield predictions for both ion and electron pedestal profiles. The differences in the predicted H-mode pedestal width and height for the DIII-D discharges with different elongation and triangularities are discussed. For the discharges with higher elongation, it is found that the gradients of the plasma profiles in the H-mode pedestal reach semi-steady states. In these simulations, the pedestal slowly continues to evolve to higher pedestal pressures and bootstrap currents until the peeling-ballooning stability conditions are satisfied. The discharges with lower elongation do not reach the semi-steady state, and ELM crashes are triggered at earlier times. The plasma elongation is found to have a stronger stabilizing effect than the plasma triangularity. For the discharges with lower elongation and lower triangularity, the ELM frequency is large, and the H-mode pedestal evolves rapidly. It is found that the temperature of neutrals in the scrape-off-layer (SOL) region can affect the dynamics of the H-mode pedestal buildup. However, the final pedestal profiles are nearly independent of the neutral temperature. The elongation and triangularity affect the pedestal widths of plasma density and electron temperature profiles differently. This provides a new mechanism of controlling the pedestal bootstrap current and the pedestal stability.
Laplace-transformed multi-reference second-order perturbation theories in the atomic and active molecular orbital basis
Authors: Helmich-Paris Benjamin , Knecht Stefan
Published: June 2017

In the present article, we show how to formulate the partially contracted n-electron valence second-order perturbation theory (NEVPT2) energies in the atomic and active molecular orbital basis by employing the Laplace transformation of orbital-energy denominators (OEDs). As atomic-orbital (AO) basis functions are inherently localized and the number of active orbitals is comparatively small, our formulation is particularly suited for a linearly scaling NEVPT2 implementation. In our formulation, there are two kinds of NEVPT2 energy contributions, which differ in the number of active orbitals in the two-electron integrals involved. Those involving integrals with either no or a single active orbital can be formulated completely in the AO basis as single-reference second-order Møller–Plesset perturbation theory and benefit from sparse active pseudo-density matrices—particularly if the active molecular orbitals are localized only in parts of a molecule. Conversely, energy contributions involving integrals with either two or three active orbitals can be obtained from Coulomb and exchange matrices generalized for pairs of active orbitals. Moreover, we demonstrate that Laplace-transformed partially contracted NEVPT2 is nothing less than time-dependent NEVPT2 [A. Y. Sokolov and G. K.-L. Chan, J. Chem. Phys. 144, 064102 (2016)] iff the all-active intermediates are computed with the internal-contraction approximation. Furthermore, we show that for multi-reference perturbation theories it is particularly challenging to find optimal parameters of the numerical Laplace transformation as the fit range may vary among the 8 different OEDs by many orders of magnitude. Selecting the number of quadrature points for each OED separately according to an accuracy-based criterion allows us to control the errors in the NEVPT2 energies reliably.
Linear problem of the shock wave disturbance in a non-classical case
Authors: Semenko Evgeny V.
Published: June 2017

A linear problem of the shock wave disturbance for a special (non-classical) case, where both pre-shock and post-shock flows are subsonic, is considered. The phase transition for the van der Waals gas is an example of this problem. Isentropic solutions are constructed. In addition, the stability of the problem is investigated and the known result is approved: the only neutral stability case occurs here. A strictly algebraic representation of the solution in the plane of the Fourier transform is obtained. This representation allows the solution to be studied both analytically and numerically. In this way, any solution can be decomposed into a sum of acoustic and vorticity waves and into a sum of initial (generated by initial perturbations), transmitted (through the shock) and reflected (from the shock) waves. Thus, the wave incidence/refraction/reflection is investigated. A principal difference of the refraction/reflection from the classical case is found, namely, the waves generated by initial pre-shock perturbations not only pass through the shock (i.e., generate post-shock transmitted waves) but also are reflected from it (i.e., generate pre-shock reflected waves). In turn, the waves generated by the initial post-shock perturbation are not only reflected from the shock (generate post-shock reflected waves) but also pass through it (generate pre-shock transmitted waves).
Evolution of the transverse and longitudinal energy distributions of electrons emitted from a GaAsP photocathode as a function of its degradation state
Authors: Jones L. B. , Scheibler H. E. , Gorshkov D. V. , Terekhov A. S. , Militsyn B. L. , Noakes T. C. Q.
Published: June 2017

We present measurements of the transverse and longitudinal energy spread of photoelectrons emitted from a GaAsP photocathode as a function of its degradation state. The cathode was initially activated to a state of negative electron affinity in our photocathode preparation facility, achieving a quantum efficiency of 3% at a wavelength of 532 nm. It was then transferred under XHV conditions to our transverse energy spread spectrometer, where energy spread measurements were made while the photocathode was progressively degraded through a controlled exposure to oxygen. Data have been collected under photocathode illumination at 532 nm, and the changing photoelectron energy distribution associated with the changes in the level of electron affinity due to quantum efficiency degradation through an exposure to 0.25 L of oxygen has been demonstrated. Our experiments have shown that GaAsP boasts a significantly higher resilience to degradation under exposure to oxygen than a GaAs photocathode, though it does exhibit a higher level of mean transverse energy. Coupled with the favourable published data on GaAsP photoemission response times, we conclude that GaAsP is a viable candidate material as a particle accelerator electron source.
Enhanced thermoelectric figure-of-merit in Bi-Sb-Te nanocomposites with homogenously dispersed oxide ceramic ZrO2 nanoparticles
Authors: Madavali B. , Kim H. S. , Lee K. H. , Hong S. J.
Published: June 2017

In this research, p-type BiSbTe/ZrO2 nanocomposite powders were fabricated by high-energy ball milling. Different weight percentages of ZrO2 (2, 4, and 6 wt. %) nanoparticles were incorporated into the bulk (BiSbTe) matrix by consolidation of as-synthesized nanocomposites (NCs) powder by spark plasma sintering at 673 K. The phase and existence of ZrO2 nano-inclusions was confirmed by X-ray diffraction and transmission electron microscopy-selected area electron diffraction analysis. The Seebeck coefficient of the BiSbTe/ZrO2 NCs was significantly improved (∼36% for 4 wt. % added NCs) by a decrease in the carrier concentration and energy filtering effect, whereas the thermal conductivity was much reduced via strong scattering of carriers/phonons. The peak thermoelectric figure-of-merit (1.34 ± 0.06) was obtained for BiSbTe into which 2 wt. % ZrO2 was dispersed, which was approximately 20% greater than that of the undispersed sample. The hardness of the nanocomposites was significantly improved (∼27%) due to grain-boundary hardening and a dispersion strengthening mechanism.
Isospectral Hamiltonian for position-dependent mass for an arbitrary quantum system and coherent states
Authors: Yahiaoui Sid-Ahmed , Bentaiba Mustapha
Published: June 2017

By means of the unitary transformation, a new way for discussing the ordering prescription of the Schrödinger equation with a position-dependent mass (PDM) for isospectral Hamiltonian operators is presented. We show that the ambiguity parameter choices in the kinetic part of the Hamiltonian can be explained through an exact SUSY QM symmetry as well as a consequence of an accidental symmetry under the Z2 action. By making use of the unitary transformation, we construct coherent states for a family of PDM isospectral Hamiltonians from a suitable choice of ladder operators. We show that these states preserve the usual structure of Klauder-Perelomov’s states and thus saturate and minimize the position-momentum uncertainty relation (PMUR) under some special restrictions. We show that PMUR properties can be used to determine the sign of the superpotential.
Implementation and modeling of a femtosecond laser-activated streak camera
Authors: Zandi O. , Wilkin K. J. , Centurion M.
Published: June 2017

A laser-activated streak camera was built to measure the duration of femtosecond electron pulses. The streak velocity of the device is 1.89 mrad/ps, which corresponds to a sensitivity of 34.9 fs/pixels. The streak camera also measures changes in the relative time of arrival between the laser and electron pulses with a resolution of 70 fs RMS. A full circuit analysis of the structure is presented to describe the streaking field and the general behavior of the device. We have developed a general mathematical model to analyze the streaked images. The model provides an accurate method to extract the pulse duration based on the changes of the electron beam profile when the streaking field is applied.
Two constructions of approximately symmetric informationally complete positive operator-valued measures
Authors: Cao Xiwang , Mi Jiafu , Xu Shanding
Published: June 2017

Symmetric informationally complete positive operator-valued measures (SIC-POVMs) have many applications in quantum information. However, it is not easy to construct SIC-POVMs and there are only a few known classes of them, and we do not even know whether there exists an infinite class of them, thus constructing approximately symmetric informationally complete positive operator-valued measures (ASIC-POVMs) has its own meaning. In this paper, we use character sums over finite fields to present two constructions of ASIC-POVMs. We show that there are some classes of infinite families of ASIC-POVMs by using some special functions over finite fields.
Drivers of sulfide intrusion in Zostera muelleri in a moderately affected estuary in south-eastern Australia
Authors: Holmer Marianne , Bennett William W. , Ferguson Angus J. P. , Potts Jaimie , Hasler-Sheetal Harald , Welsh David T.
Published: June 2017

The seagrass Zostera muelleri Irmisch ex Asch. is abundant in estuaries in Australia and is under pressure from coastal developments. We studied sulfide intrusion in Z. muelleri along a gradient of anthropogenic impact at five stations in the Wallis Lake estuary, Australia. Results showed differences in sediment biogeochemical conditions, seagrass metrics as well as nutrient content and sulfide intrusion along the gradient from the lower estuary (affected) to the lagoon (unaffected). Sulfide intrusion was driven by complex interactions and related to changes in seagrass morphology and sediment biogeochemistry and was modified by the exposure to wind and wave action. The sediments in the lower estuary had high contributions from phytoplanktonic detritus, whereas the organic pools in the lagoon were dominated by seagrass detritus. Despite high concentrations of organic matter, sulfide intrusion was lower at stations dominated by seagrass detritus, probably because of lower sulfide pressure from the less labile nature of organic matter. Porewater diffusive gradients in thin-film (DGT) sulfide samplers showed efficient sulfide reoxidation in the rhizosphere, with high sulfur incorporation in the plants from sedimentary sulfides being likely due to sulfate uptake from reoxidised sulfide. This is a unique adaptation of Z. muelleri, which allows high productivity in estuarine sediments.
Role of information and communication technology in promoting oral health at residential aged care facilities
Authors: Adebayo Bola , Durey Angela , Slack-Smith Linda M.
Published: June 2017

Information and communication technology (ICT) can provide knowledge and clinical support to those working in residential aged care facilities (RACFs). This paper aims to: (1) review literature on ICT targeted at residents, staff and external providers in RACFs including general practitioners, dental and allied health professionals on improving residents’ oral health; (2) identify barriers and enablers to using ICT in promoting oral health at RACFs; and (3) investigate evidence of effectiveness of these approaches in promoting oral health. Findings from this narrative literature review indicate that ICT is not widely used in RACFs, with barriers to usage identified as limited training for staff, difficulties accessing the Internet, limited computer literacy particularly in older staff, cost and competing work demands. Residents also faced barriers including impaired cognitive and psychosocial functioning, limited computer literacy and Internet use. Findings suggest that more education and training in ICT to upskill staff and residents is needed to effectively promote oral health through this medium.
The phospho–caveolin-1 scaffolding domain dampens force fluctuations in focal adhesions and promotes cancer cell migration
Authors: Meng Fanrui , Saxena Sandeep , Liu Youtao , Joshi Bharat , Wong Timothy H. , Shankar Jay , Foster Leonard J. , Bernatchez Pascal , Nabi Ivan R.
Published: June 2017

Caveolin-1 (Cav1), a major Src kinase substrate phosphorylated on tyrosine-14 (Y14), contains the highly conserved membrane-proximal caveolin scaffolding domain (CSD; amino acids 82–101). Here we show, using CSD mutants (F92A/V94A) and membrane-permeable CSD-competing peptides, that Src kinase–dependent pY14Cav1 regulation of focal adhesion protein stabilization, focal adhesion tension, and cancer cell migration is CSD dependent. Quantitative proteomic analysis of Cav1-GST (amino acids 1–101) pull downs showed sixfold-increased binding of vinculin and, to a lesser extent, α-actinin, talin, and filamin, to phosphomimetic Cav1Y14D relative to nonphosphorylatable Cav1Y14F. Consistently, pY14Cav1 enhanced CSD-dependent vinculin tension in focal adhesions, dampening force fluctuation and synchronously stabilizing cellular focal adhesions in a high-tension mode, paralleling effects of actin stabilization. This identifies pY14Cav1 as a molecular regulator of focal adhesion tension and suggests that functional interaction between Cav1 Y14 phosphorylation and the CSD promotes focal adhesion traction and, thereby, cancer cell motility.
CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization
Authors: Xu Taosheng , Le Thuc Duy , Liu Lin , Su Ning , Wang Rujing , Sun Bingyu , Colaprico Antonio , Bontempi Gianluca , Li Jiuyong
Published: June 2017

Identifying molecular cancer subtypes from multi-omics data is an important step in the personalized medicine. We introduce CancerSubtypes, an R package for identifying cancer subtypes using multi-omics data, including gene expression, miRNA expression and DNA methylation data. CancerSubtypes integrates four main computational methods which are highly cited for cancer subtype identification and provides a standardized framework for data pre-processing, feature selection, and result follow-up analyses, including results computing, biology validation and visualization. The input and output of each step in the framework are packaged in the same data format, making it convenience to compare different methods. The package is useful for inferring cancer subtypes from an input genomic dataset, comparing the predictions from different well-known methods and testing new subtype discovery methods, as shown with different application scenarios in the Supplementary Material.

Availability and implementation

The package is implemented in R and available under GPL-2 license from the Bioconductor website (http://bioconductor.org/packages/CancerSubtypes/).

Supplementary information

Supplementary data are available at Bioinformatics online.
MotifHyades: expectation maximization for de novo DNA motif pair discovery on paired sequences
Authors: Wong Ka-Chun
Published: June 2017

Motivation

In higher eukaryotes, protein–DNA binding interactions are the central activities in gene regulation. In particular, DNA motifs such as transcription factor binding sites are the key components in gene transcription. Harnessing the recently available chromatin interaction data, computational methods are desired for identifying the coupling DNA motif pairs enriched on long-range chromatin-interacting sequence pairs (e.g. promoter–enhancer pairs) systematically.

Results

To fill the void, a novel probabilistic model (namely, MotifHyades) is proposed and developed for de novo DNA motif pair discovery on paired sequences. In particular, two expectation maximization algorithms are derived for efficient model training with linear computational complexity. Under diverse scenarios, MotifHyades is demonstrated faster and more accurate than the existing ad hoc computational pipeline. In addition, MotifHyades is applied to discover thousands of DNA motif pairs with higher gold standard motif matching ratio, higher DNase accessibility and higher evolutionary conservation than the previous ones in the human K562 cell line. Lastly, it has been run on five other human cell lines (i.e. GM12878, HeLa-S3, HUVEC, IMR90, and NHEK), revealing another thousands of novel DNA motif pairs which are characterized across a broad spectrum of genomic features on long-range promoter–enhancer pairs.

Availability and implementation

The matrix-algebra-optimized versions of MotifHyades and the discovered DNA motif pairs can be found in http://bioinfo.cs.cityu.edu.hk/MotifHyades.

Supplementary information

Supplementary data are available at Bioinformatics online.
A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation
Authors: Sternes Peter R. , Lee Danna , Kutyna Dariusz R. , Borneman Anthony R.
Published: June 2017

Wine is a complex beverage, comprising hundreds of metabolites produced through the action of yeasts and bacteria in fermenting grape must. Commercially, there is now a growing trend away from using wine yeast (Saccharomyces) starter cultures, toward the historic practice of uninoculated or “wild” fermentation, where the yeasts and bacteria associated with the grapes and/or winery perform the fermentation. It is the varied metabolic contributions of these numerous non-Saccharomyces species that are thought to impart complexity and desirable taste and aroma attributes to wild ferments in comparison to their inoculated counterparts. To map the microflora of spontaneous fermentation, metagenomic techniques were employed to characterize and monitor the progression of fungal species in 5 different wild fermentations. Both amplicon-based ribosomal DNA internal transcribed spacer (ITS) phylotyping and shotgun metagenomics were used to assess community structure across different stages of fermentation. While providing a sensitive and highly accurate means of characterizing the wine microbiome, the shotgun metagenomic data also uncovered a significant overabundance bias in the ITS phylotyping abundance estimations for the common non-Saccharomyces wine yeast genus Metschnikowia. By identifying biases such as that observed for Metschnikowia, abundance measurements from future ITS phylotyping datasets can be corrected to provide more accurate species representation. Ultimately, as more shotgun metagenomic and single-strain de novo assemblies for key wine species become available, the accuracy of both ITS-amplicon and shotgun studies will greatly increase, providing a powerful methodology for deciphering the influence of the microbial community on the wine flavor and aroma.
Trust Busting: The Effect of Fraud on Investor Behavior
Authors: Gurun Umit G , Stoffman Noah , Yonker Scott E
Published: June 2017

We study the importance of trust in the investment advisory industry by exploiting the geographic dispersion of victims of the Madoff Ponzi scheme. Residents of communities that were exposed to the fraud subsequently withdrew assets from investment advisers and increased deposits at banks. Additionally, exposed advisers were more likely to close. Advisers who provided services that can build trust, such as financial planning advice, experienced fewer withdrawals. Our evidence suggests that the trust shock was transmitted through social networks. Taken together, our results show that trust plays a critical role in the financial intermediation industry.

Received April 18, 2016; editorial decision March 8, 2017 by Editor Robin Greenwood.
Opioid Use in Pregnancy, Neonatal Abstinence Syndrome, and Childhood Outcomes
Authors: Reddy Uma M. , Davis Jonathan M. , Ren Zhaoxia , Greene Michael F. ,   for the Opioid Use in Pregnancy, Neonatal Abstinence Syndrome, and Childhood Outcomes Workshop Invited Speakers
Published: June 2017

In April 2016, the Eunice Kennedy Shriver National Institute of Child Health and Human Development invited experts to a workshop to address numerous knowledge gaps and to review the evidence for the screening and management of opioid use in pregnancy and neonatal abstinence syndrome. The rising prevalence of opioid use in pregnancy has led to a concomitant dramatic fivefold increase in neonatal abstinence syndrome over the past decade. Experts from diverse disciplines addressed research gaps in the following areas: 1) optimal screening for opioid use in pregnancy; 2) complications of pregnancy associated with opioid use; 3) appropriate treatments for pregnant women with opioid use disorders; 4) the best approaches for detecting, treating, and managing newborns with neonatal abstinence syndrome; and 5) the long-term effects of prenatal opioid exposure on children. Workshop participants identified key scientific opportunities to advance the understanding of opioid use disorders in pregnancy and to improve outcomes for affected women, their children, and their families. This article provides a summary of the workshop presentations and discussions.
Surgical Pain After Transobturator and Retropubic Midurethral Sling Placement
Authors: Thomas Tonya N. , Siff Lauren N. , Jelovsek J. Eric , Barber Matthew
Published: June 2017

OBJECTIVE:

To compare prevalence and severity of any surgical pain between transobturator and retropubic slings; secondary aims were to compare pain at anatomic locations, pain medication use, and pain resolution between transobturator and retropubic slings and to compare pain between types of transobturator slings.

METHODS:

This is a secondary analysis of the Trial of Mid-Urethral Slings, which compared retropubic and transobturator sling outcomes and included 597 participants from 2006 to 2008. Postoperative assessments included body maps, visual analog scales, Surgical Pain Scales, and medication inventories for 30 days, at 6 weeks, and 6, 12, and 24 months. Postoperative pain prevalence and severity were compared. Mixed models compared pain resolution and severity over time. Regression models compared pain prevalence and severity between types of transobturator slings. Eighty percent power was provided for the primary outcome pain prevalence and 95% power was provided for the primary outcome pain severity.

RESULTS:

Postoperative prevalence of any surgical pain, pain severity, and pain medication was not different between retropubic and transobturator slings. Retropubic sling was associated with greater prevalence of suprapubic pain at 2 weeks (proportion difference 10.6%; 95% confidence interval [CI] 4.6–16.4%; P<.001). Transobturator sling was associated with greater prevalence of groin pain at 2 weeks (proportion difference 12.0%; 95% CI 7.1–16.8%; P<.001). There was no difference in pain resolution (odds ratio [OR] 1.11, 95% CI 0.88–1.40; P=.38). Between types of transobturator slings, the odds of surgical pain were similar at 2 (OR 2.39, 95% CI 0.51–11.31; P=.27) and 6 weeks (OR 0.46, 95% CI 0.02–9.20; P=.61).

CONCLUSION:

Transobturator and retropubic slings are associated with low prevalence of any surgical pain. Transobturator sling was associated with greater prevalence of groin pain at 2 weeks, and retropubic sling was associated with greater prevalence of suprapubic pain at 2 weeks. Surgical pain resolved quickly in both groups.
Placental Abruption With Delayed Fetal Compromise in Maternal Acetaminophen Toxicity
Authors: Taney Juliana , Anastasio Hannah , Paternostro Amanda , Berghella Vincenzo , Roman Amanda
Published: June 2017

BACKGROUND:

After maternal acetaminophen overdose, fetal fulminant liver failure, stillbirth, neonatal death, or preterm delivery may occur.

CASE:

A 27-year-old woman, gravida 2 para 1, presented at 28 weeks of gestation after unintentional acetaminophen overdose. Four days after ingestion, her laboratory values worsened, including serum aspartate aminotransferase of 5,460 units/L, alanine aminotransferase of 4,936 units/L, and international normalized ratio of 2.9. On day 6 after ingestion, fetal monitoring showed minimal variability with repetitive variable and late decelerations, which prompted cesarean delivery when a hematoma was noted on the maternal placental surface, consistent with placental abruption. The neonate showed no evidence of hepatic dysfunction. Review of the literature suggests that maternal acetaminophen overdose in the second and third trimester is associated with a 5% incidence of fetal compromise (mostly the result of nonreassuring fetal status leading to delivery or stillbirth) occurring within 6 days of ingestion.

CONCLUSION:

Maternal acetaminophen overdose can be associated with delayed fetal compromise, suggesting the importance of continued fetal surveillance several days after ingestion.
Long-term Risk of Urinary Adverse Events in Curatively Treated Patients With Rectal Cancer: A Population-Based Analysis
Authors: Kwaan Mary R. , Fan Yunhua , Jarosek Stephanie , Elliott Sean P.
Published: June 2017

BACKGROUND:

Treatment modalities for rectal cancer, including radiation, are associated with urinary adverse effects.

OBJECTIVE:

The purpose of this study was to determine the influence of surgery and radiation therapy for rectal cancer on long-term urinary complications.

DESIGN:

Using the Surveillance Epidemiology and End Results–Medicare data set from the United States, patients with rectal cancer older than 66 years of age who underwent rectal resection between 1992 and 2007 were stratified into treatment groups that accounted for surgical resection and the timing of radiation therapy, if used. A control group of patients who did not have rectal cancer were matched by age, sex, demographics, and comorbidities. The primary outcome was a urinary adverse event defined as a relevant urinary diagnosis with an associated procedure. Patients with rectal cancer in different treatment groups were compared with control patients using a propensity-adjusted, multivariable Cox regression analysis.

SETTINGS:

The study was conducted with the Surveillance Epidemiology and End Results–Medicare data set from the United States at our institution.

RESULTS:

Of the 11,068 patients with rectal cancer, 56.2% had surgical resection alone, 21.7% received preoperative radiation, and 22.1% received postoperative radiation. The median follow-up for all of the groups of patients was >2 years. All of the groups of patients with rectal cancer were more likely to develop a urinary adverse event compared with control subjects. Adjusted HRs were 2.28 (95% CI, 2.02–2.57) for abdominoperineal resection alone, 2.24 (95% CI, 1.79–2.80) for preoperative radiation and surgical resection, 2.04 (95% CI, 1.70–2.44) for surgical resection and postoperative radiation, and 1.69 (95% CI, 1.52–1.89) for low anterior resection alone.

LIMITATIONS:

Treatment patterns are somewhat outdated, with a large proportion of patients receiving postoperative radiation. The data did not allow for accurate assessment of urinary tract infections or mild urinary retention that is not managed with a procedure.

CONCLUSIONS:

Rectal cancer surgery with or without radiation is associated with a higher risk of urinary complications requiring procedures. Patients who undergo low anterior resection without radiation tend toward the lowest risk for a urinary adverse event.
Clinical Relevance of a Grading System for Anastomotic Leakage After Low Anterior Resection: Analysis From a National Cohort Database
Authors: Frouws Martine A. , Snijders Heleen S. , Malm Steve H. , Liefers Gerrit-Jan , Van de Velde Cornelis J.H. , Neijenhuis Peter A. , Kroon Hidde M.
Published: June 2017

BACKGROUND:

Anastomotic leakage is a severe complication after low anterior resection for rectal cancer. With a global increase in registration initiatives, adapting uniform definitions and grading systems is highly relevant.

OBJECTIVE:

This study aimed to provide clinical parameters to categorize anastomotic leakage into subcategories according to the International Study Group of Rectal Cancer.

DESIGN:

All of the patients who underwent a low anterior resection in the Netherlands with primary anastomosis were included using the population-based Dutch Surgical Colorectal Audit.

SETTINGS:

Data were derived from the Dutch Surgical Colorectal Audit.

MAIN OUTCOME MEASURES:

The development of grade B anastomotic leakage (requiring invasive treatment but no surgery) versus grade C anastomotic leakage (requiring reoperation) was measured.

RESULTS:

Overall, 4287 patients underwent low anterior resection with primary anastomosis. A total of 159 patients (4%) were diagnosed with grade B anastomotic leakage versus 259 (6%) with grade C. Hospital stay and intensive care unit visits were significantly higher in patients with grade C anastomotic leakage compared with patients with grade B leakage. Mortality in patients with grade C leakage was higher compared with grade B leakage, although nonsignificant (5.8% vs 2.5%;p= 0.12). Multivariate analysis showed that patients with diverting stomas (n = 2866) had a decreased risk of developing grade C leakage compared with grade B (OR = 0.17 (95% CI, 0.10–0.29)). Male patients had an increased risk of developing grade C anastomotic leakage, and patients receiving neoadjuvant treatment before surgery had an increased risk of developing grade B anastomotic leakage.

LIMITATIONS:

Some possibly relevant variables, such as smoking and nutritional status, were not recorded in the database.

CONCLUSIONS:

Anastomotic leakage after low anterior resection for rectal cancer was a frequent observed complication in this cohort. Differences in clinical outcome suggest that grade B and C leakage should be considered separate entities in future registrations. In patients with a diverting stoma, the chances of experiencing grade C anastomotic leakage were reduced.See Video Abstractat http://links.lww.com/DCR/A315.