bluuebunny/crossref_metadata_2025 huggingface dataset:
On the geometric dependence of the molecular dipole polarizability in water: A benchmark study of higher-order electron correlation, basis set incompleteness error, core electron effects, and zero-point vibrational contributions
Authors: Lao Ka Un , Jia Junteng , Maitra Rahul , DiStasio Robert A.
Published: November 2018

In this work, we investigate how geometric changes influence the static dipole polarizability (α) of a water molecule by explicitly computing the corresponding dipole polarizability surface (DPS) across 3125 total (1625 symmetry-unique) geometries using linear response coupled cluster theory including single, double, and triple excitations (LR-CCSDT) and the doubly augmented triple-ζ basis set (d-aug-cc-pVTZ). Analytical formulae based on power series expansions of this ab initio surface are generated using linear least-squares analysis and provide highly accurate estimates of this quantity as a function of molecular geometry (i.e., bond and angle variations) in a computationally tractable manner. An additional database, which consists of 25 representative molecular geometries and incorporates a more thorough treatment of both basis sets and core electron effects, is provided as a current benchmark for this quantity and the corresponding leading-order C6 dispersion coefficient. This database has been utilized to assess the importance of these effects as well as the relative accuracy that can be obtained using several quantum chemical methods and a library of density functional approximations. In addition to high-level electron correlation methods (like CCSD) and our analytical least-squares formulae, we find that the SCAN0, PBE0, MN15, and B97-2 hybrid functionals yield the most accurate descriptions of the molecular polarizability tensor in H2O. Using first-order perturbation theory, we compute the zero-point vibrational correction to α at the CCSDT/d-aug-cc-pVTZ level and find that this correction contributes approximately 3% to the isotropic (αiso) and nearly 50% to the anisotropic (αaniso) polarizability values. In doing so, we find that αiso = 9.8307 bohr3, which is in excellent agreement with the experimental value of 9.83 ± 0.02 bohr3 provided by Russell and Spackman. The DPS reported herein provides a benchmark-quality quantum mechanical estimate of this fundamental quantity of interest and should find extensive use in the development (and assessment) of next-generation force fields and machine-learning based approaches for modeling water in complex condensed-phase environments.
Flow-induced oscillations of three tandem rotating cylinders
Authors: Behara Suresh , Ravikanth B. , Chandra Venu
Published: November 2018

The oscillation responses and the associated wake structures of three rotating tandem cylinders, mounted on elastic supports in both the streamwise (x-) and transverse (y-) directions, are numerically studied. Finite element computations are carried out at Reynolds number Re = 150, where the flow is two-dimensional (2-D), and at Re = 2000 (3-D flow), varying the reduced velocity (U*) in the range U* = 2–14. Each cylinder is placed at a distance of 5 diameters (5D) from its immediate neighbor. In the two-dimensional flow, the upstream and the second downstream cylinders are rotated at the rotation rate (α) of 1, while for the first downstream cylinder, α = 0, 0.5, and 1 are employed. In the 3-D computations, α = 1 is considered for the three bodies. It is observed that at Re = 150, all the cylinders exhibit three distinct lock-in modes, namely, modes I, II, and III. Depending on the rotation configuration, 2S, P + S, and 2P shedding patterns appear in the wake of upstream cylinder, while the downstream cylinders shed 2S, P, P + S, 2P, and T + P modes of primary vortices. In the 3-D flow (at Re = 2000), the upstream cylinder exhibits a bell-shaped profile in the variation of amplitude response as a function of U*. Oscillation responses of the two downstream bodies appear in three distinct regions. During high amplitude oscillations, the upstream cylinder sheds the 2P mode of primary vortices, while in the near wakes of the two downstream bodies, small and incoherent primary vortical structures form due to the presence of three-dimensional instability. Low and high amplitude responses are associated with weak and strong 3-D flow instabilities, respectively.
Intensified proton and carbon ion flux from femtosecond laser driven plasma source
Authors: Singh P. K. , Andreev A. A. , Kakolee K. F. , Ter-Avetisyan S.
Published: November 2018

Ion acceleration from aluminium foils irradiated with a 30 fs laser pulse of ∼1020 W/cm2 intensity at an incidence angle of 45° was investigated. Laser intensity contrast enhancement by a factor of 100 resulted in a nearly 7 and 30 times increase in proton and carbon ion flux, respectively, while their maximum energy remains almost unchanged. More than 1013 protons and 1014 carbon C4+ ions per MeV bandwidth per steradian solid angle were measured. Simulations, being in a good agreement with the experimental findings, have revealed that the difference in proton emission between the low and high contrast cases is a narrower angular distribution of protons at high laser pulse contrast. In the low contrast scenario, the plasma density gradient increases the hot electron divergence, leading to the reduction of particle flux in a fixed solid angle. The analytical model verifies the concept of the theoretical limit of particle flux. These results open up the possibility for further optimization of the laser driven bright source of energetic particles.
Near-ultraviolet Raman and micro-Raman analysis of electronic materials
Authors: Nazari Mohammad , Holtz Mark W.
Published: November 2018

Raman and micro-Raman analysis methods have been extensively investigated for the study of materials used in electronic and photonic devices. Raman studies are used to understand fundamental phonon properties, along with effects related to the crystal structure, disorder, doping, and external factors such as temperature and stress. Micro-Raman extends these investigations to the micron scale. This article reviews diverse benefits of Raman measurements when carried out using laser excitation in the near-ultraviolet wavelength range, nominally 400 to 325 nm. Micro-Raman methods in the near ultraviolet exploit the key advantage of reduced focal spot size, achievable at shorter wavelengths when using diffraction-limited optics, for mapping with high spatial resolution. There are distinct advantages common to Raman and micro-Raman spectroscopy in the near ultraviolet when compared to the widely used visible excitation. One advantage exploits the shallower optical penetration depth in select materials for probing near-surface regions or interfaces. A second advantage is related to tuning of the excitation photon energy relative to the electronic levels of a material for investigating resonance effects. Finally, the application of Raman scattering to materials which exhibit strong fluorescence requires tuning to a wavelength range away from the potentially obscuring emission. This article overviews several examples of these key advantages to study diverse applied physics problems in electronic and photonic materials. Topics covered include stress mapping in silicon and related materials, stress and thermal effects in gallium nitride and other group-III-nitride semiconductors, and carbon materials ranging from graphite and graphene to diamond grown using chemical vapor deposition. The fundamental effects of stress- and temperature-induced shifts in phonon energies and their application to study epitaxy and device-related effects are also briefly reviewed.
Integration of quantum dots with lithium niobate photonics
Authors: Aghaeimeibodi Shahriar , Desiatov Boris , Kim Je-Hyung , Lee Chang-Min , Buyukkaya Mustafa Atabey , Karasahin Aziz , Richardson Christopher J. K. , Leavitt Richard P. , Lončar Marko , Waks Edo
Published: November 2018

The integration of quantum emitters with integrated photonics enables complex quantum photonic circuits that are necessary for photonic implementation of quantum simulators, computers, and networks. Thin-film lithium niobate is an ideal material substrate for quantum photonics because it can tightly confine light in small waveguides and has a strong electro-optic effect that can switch and modulate single photons at low power and high speed. However, lithium niobate lacks efficient single-photon emitters, which are essential for scalable quantum photonic circuits. We demonstrate deterministic coupling of single-photon emitters with a lithium niobate photonic chip. The emitters are composed of InAs quantum dots embedded in an InP nanobeam, which we transfer to a lithium niobate waveguide with nanoscale accuracy using a pick-and-place approach. An adiabatic taper transfers single photons emitted into the nanobeam to the lithium niobate waveguide with high efficiency. We verify the single photon nature of the emission using photon correlation measurements performed with an on-chip beamsplitter. Our results demonstrate an important step toward fast, reconfigurable quantum photonic circuits for quantum information processing.
Epitaxial Mn5Ge3 (100) layer on Ge (100) substrates obtained by flash lamp annealing
Authors: Xie Yufang , Yuan Ye , Wang Mao , Xu Chi , Hübner René , Grenzer Jörg , Zeng Yu-Jia , Helm Manfred , Zhou Shengqiang , Prucnal Slawomir
Published: November 2018

Mn5Ge3 thin films have been demonstrated as promising spin-injector materials for germanium-based spintronic devices. So far, Mn5Ge3 has been grown epitaxially only on Ge (111) substrates. In this letter, we present the growth of epitaxial Mn5Ge3 films on Ge (100) substrates. The Mn5Ge3 film is synthetized via sub-second solid-state reaction between Mn and Ge upon flash lamp annealing for 20 ms at the ambient pressure. The single crystalline Mn5Ge3 is ferromagnetic with a Curie temperature of 283 K. Both the c-axis of hexagonal Mn5Ge3 and the magnetic easy axis are parallel to the Ge (100) surface. The millisecond-range flash epitaxy provides a new avenue for the fabrication of Ge-based spin-injectors fully compatible with CMOS technology.
A detailed chemical examination reveals frogs’ sticky-tongue hunting technique
Authors: Cockbill Louisa
Published: November 2018

Complex techniques used to analyze the surface interface between frog tongue and prey have revealed protein reordering in response to tongue retraction.
Layer-structured Ti doped O3-Na1−xCr1−xTixO2(x=0, 0.03, 0.05) with excellent electrochemical performance as cathode materials for sodium ion batteries
Authors: Shao Yu , Tang Zhong-feng , Liao Jia-ying , Chen Chun-hua
Published: November 2018

Layer-structured O3 type cathode materials Na1−xCr1−xTixO2 (x=0, 0.03, 0.05) are fabricated by a thermo-polymerization method. The structures and morphologies are characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM) respectively. It has been found that the appropriate Ti doping effectively leads to the formation of uniform morphology. As a cathode, the x=0.03 sample delivers a quite high discharge capacity of 110 mAh/g at 32 C in the voltage range from 2.0 V to 3.6 V (vs. Na/Na+) and with a capacity retention of 96% after 100 cycles at 0.2 C. The Na//Na0.97Cr0.97Ti0.03O2 cell exhibits very high coulombic efficiency (above 96%). All these results suggest that Na0.97Cr0.97Ti0.03O2 is very promising for high-rate sodium ion batteries.
Electrochemical study on hydrogen evolution and CO2 reduction on Pt electrode in acid solutions with different pH
Authors: Yang Jing , Wei Jie , Chen Wei , Chen Yan-xia
Published: November 2018

Hydrogen evolution reaction (HER) is the major cathodic reaction which competes CO2 reduction reaction (CO2 RR) on Pt electrode. Molecular level understanding on how these two reactions interact with each other and what the key factors are of CO2 RR kinetics and selectivity will be of great help in optimizing electrolysers for CO2 reduction. In this work, we report our results of hydrogen evolution and CO2 reduction on Pt(111) and Pt film electrodes in CO2 saturated acid solution by cyclic voltammetry and infrared spectroscopy. In solution with pH>2, the major process is HER and the interfacial pH increases abruptly during HER; COad is the only adsorbed intermediate detected in CO2 reduction by infrared spectroscopy; the rate for COad formation increases with the coverage of UPD-H and reaches maximum at the onset potential for HER; the decrease of COad formation under HER is attributed to the available limited sites and the limited residence time for the reduction intermediate (Had), which is necessary for CO2 adsorption and reduction.
Single Pt atoms supported on oxidized graphene as a promising catalyst for hydrolysis of ammonia borane
Authors: Wu Hong , Luo Qi-quan , Zhang Rui-qi , Zhang Wen-hua , Yang Jin-long
Published: November 2018

Based on density functional theory calculations, the full hydrolysis of per NH3BH3 molecule to produce three hydrogen molecules on single Pt atoms supported on oxidized graphene (Pt1/Gr-O) is investigated. It is suggested that the first hydrogen molecule is produced by the combination of two hydrogen atoms from two successive B−H bonds breaking. Then one H2O molecule attacks the left *BHNH3 group (* represents adsorbed state) to form *BH(H2O)NH3 and the elongated O−H bond is easily broken to produce *BH(OH)NH3. The second H2O molecule attacks *BH(OH)NH3 to form *BH(OH)(H2O)NH3 and the breaking of O−H bond pointing to the plane of Pt1/Gr-O results in the desorption of BH(OH)2NH3. The second hydrogen molecule is produced from two hydrogen atoms coming from two H2O molecules and Pt1/Gr-O is recovered after the releasing of hydrogen molecule. The third hydrogen molecule is generated by the further hydrolysis of BH(OH)2NH3 in water solution. The rate-limiting step of the whole process is the combination of one H2O molecule and *BHNH3 with an energy barrier of 16.1 kcal/mol. Thus, Pt1/Gr-O is suggested to be a promising catalyst for hydrolysis of NH3BH3 at room temperature.
Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source
Authors: Yang Huaiyu , von der Fecht-Bartenbach Jenny , Friml Jiřř , Lohmann Jan U. , Neuhäuser Benjamin , Ludewig Uwe
Published: November 2018

Ammonium is the major nitrogen source in some plant ecosystems but is toxic at high concentrations, especially when available as the exclusive nitrogen source. Ammonium stress rapidly leads to various metabolic and hormonal imbalances that ultimately inhibit root and shoot growth in many plant species, including Arabidopsis thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with microarrays was used. Substantial transcriptional differences were most pronounced in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent with previous physiological analyses, major differences in the expression modules of photosynthesis-related genes, an altered mitochondrial metabolism, differential expression of the primary NH4+ assimilation, alteration of transporter gene expression and crucial changes in cell wall biosynthesis were found. A major difference in plant hormone responses, particularly of auxin but not cytokinin, was striking. The activity of the DR5::GUS reporter revealed a dramatically decreased auxin response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4 was partially rescued by exogenous auxin or in specific mutants in the auxin pathway. The data suggest that NH4+-induced nutritional and metabolic imbalances can be partially overcome by elevated auxin levels.
'Plasma Emission' without Langmuir Waves
Authors: Melrose DB
Published: November 2018

Recent observations have confirmed that the level of Langmuir waves associated with type III streams of electrons in the interplanetary medium is usually too low to account for the observed radio emission by the accepted 'plasma emission' processes, and it has been suggested that emission mechanisms which do not require Langmuir waves should be explored. Four such mechanisms are discussed. One is a parametric instability leading directly to second-harmonic emission; it is found inapplicable under conditions of interest here. The other three processes all involve ion-sound turbulence. One which is known in a different context is turbulent bremsstrahlung. Turbulent bremsstrahlung of transverse waves is found to compare unfavourably with the other two processes, which are scattering of an ion-sound (s) wave into a transverse (t) wave and double emission of both waves simultaneously. These latter two processes are related by a crossing symmetry and are treated together with the following results: (i) The processes become greatly enhanced when the beat (w�w', k�k') between the t wave and the s wave nearly satisfies the dispersion relation for Langmuir (I) waves. (ii) A bump-in-the-tail instability (due to electrons with dF(v)/dv > 0) can cause the transverse waves to grow due to double emission; this growth has been likened to a freeelectron maser. (iii) The familiar bump-in-the-tail instability for resonant I waves can be suppressed by the ion-sound waves, and the double-emission instability then takes over with about the same growth rate as the original I-wave instability. (iv) The conditions for the double-emission instability to occur are probably satisfied at least some of the time for type III streams. It is concluded that although 'plasma emission' without Langmuir waves may be possible in principle, it is unlikely to play any role in type III bursts.
An Analytic Distorted Wave Approximation for Intermediate Energy Proton Scattering
Authors: Di Marzio F , Amos K
Published: November 2018

An analytic distorted wave approximation (ADWA) has been developed for use in analyses of intermediate energy inelastic proton scattering from nuclei. Applications are made to analyse 402 and 800 MeV data from the isoscalar and isovector 1 + and 2+ states in 12C and to the 800 MeV data from the excitation of the 2-(8�88 MeV) state in 160. Comparisons of predictions made using different model two-nucleon t matrices and different models of nuclear structure are given.
Flow Distribution in Parallel Connected Manifolds for Evacuated Tubular Solar Collectors
Authors: McPhedran RC , Mackey DJM , McKenzie DR , Collins RE
Published: November 2018

A model is presented for predicting the flow distribution in solar collector manifolds in which risers are connected in parallel between headers. Both frictional and Bernoulli effects are considered. The distributions resulting from flow in the manifold in which header streams are parallel and opposed are calculated and compared with experiment. Parallel flow gives a more uniform distribution. The outlet header is found to be more critical in balancing the flow distribution than the inlet header. Conditions under which thermosiphon effects are important and flow reversal in risers may occur are discussed with reference to experiment.
A Lamp for Cancer Phototherapy
Authors: Jacka F , Blake AJ
Published: November 2018

The lamp described comprises a 1000 W incandescent filament source, long- and short-wave pass filters, and a non-imaging reflector system. The output of 24 W in the 620-720 nm band is delivered through a 53 mm diameter aperture with a maximum divergence half-angle of 60�. Refracting components may be fitted to modify the output angular or intensity distribution. This lamp has been used to irradiate several different types of malignant tumour in human patients, following intravenous injection of the photoactive drug haematoporphyrin derivative, causing selective necrosis of the malignant tissue. The clinical results are regarded as encouraging.
Particle Motion in Longitudinal Waves. II Superluminal and Luminal Waves
Authors: Rowe ET
Published: November 2018

The motion of charged particles in superluminal and luminal longitudinal waves of arbitrary amplitude is considered in detail, including relativistic effects. In particular we discuss the ability of these waves to accelerate particles. Solutions for the particle orbits are given in both closed form and in terms of relevant expansions. The drift velocity of the particles, which describes the motion of the guiding centre, is identified. Two interesting effects are discovered: (i) the ability of large amplitude superluminal waves to drag particles along at a velocity conjugate to the wave phase speed and (ii) the existence of 'phase locking' particle orbits in the luminal case, in which particles can be accelerated to arbitrary energy.
Boson Bound States Near a Kerr-Newman Naked Singularity
Authors: Yuanjie Li
Published: November 2018

We discuss boson bound states near a Kerr-Newman (KN) naked singularity by means of spectroscopic eigenvalue analysis. The results show that in the background of a KN naked singularity, the self-conjugate extension operator of a boson Hamiltonian has and only has discrete eigenvalues. The discrete eigenvalues exist in the interval (-/-�, /-�). Thus, we find that the boson bound states may appear only for /-� i= o. Here /-� is the boson mass.
Clicks as discourse markers in Peninsular Spanish
Authors: Pinto Derrin , Vigil Donny
Published: November 2018

The research on clicks in Spanish has been surprisingly scarce. Using a data corpus of 764 clicks produced by 20 speakers from
Spain, we approach clicks as discourse markers that execute up to five different functions. Since clicks themselves do not possess
any core semantic meaning, their contribution to the discourse depends solely on their placement and the contextual features with
which they occur. In addition to an analysis of their functions, we report on several elements present in the contiguous pre- and
post-click environment, including pauses, fillers and prolonged syllables. The results indicate significant findings regarding how
click functions relate to certain elements in the click environment.
College Degree Attainment by Age of First Marijuana use and Parental Education
Authors: Linden-Carmichael Ashley N. , Kloska Deborah D. , Evans-Polce Rebecca , Lanza Stephanie T. , Patrick Megan E.
Published: November 2018

Background: Age of first marijuana use is a key predictor of later educational outcomes, but limited work has identified demographic factors that impact this association across continuous ages of first use. The purpose of this study was threefold: (1) to identify the age-varying prevalence of later college degree attainment as a function of age of first marijuana use; (2) to examine the age-varying association of gender and college degree attainment as a function of age of first use; and (3) to examine the age-varying association of parent education and college degree attainment as a function of age of first use. Methods: Data were from the panel portion of the Monitoring the Future (MTF) study, an ongoing longitudinal study of adolescents and young adults. Those who used marijuana by age 22 were included in analyses. Among these participants ( N = 2134), 47.0% were male, 67.5% were white, 53.2% reported having at least one parent with a bachelor's degree or higher, and 44.1% attained a bachelor's degree or higher by age 25/26. Results: Intercept-only and logistic time-varying effect models (TVEMs) modeled prevalences and associations as functions of age of first marijuana use. Prevalence of college degree completion was relatively linear across age of first use; such that college degree attainment increased as age of first use increased. Results indicated that college degree attainment varied across age of first use similarly for men and women. Degree attainment differences existed based on parent education. Parental education and degree attainment were most strongly linked at an age of first use between 16 and 19 years. Conclusions: Findings suggest that age of first marijuana use has an association with academic achievement such that earlier ages of first use are associated with lower academic achievement later in adulthood. Parental education serves as a protective factor against college degree attainment in late adolescence.
Structure elucidation of ostreocin-A and ostreocin-E1, novel palytoxin analogs produced by the dinoflagellate Ostreopsis siamensis, using LC/Q-TOF MS
Authors: Terajima Takehito , Uchida Hideaki , Abe Naoki , Yasumoto Takeshi
Published: November 2018

Palytoxin analogs are marine toxins with large complex polyol structures. A benthic dinoflagellate Ostreopsis siamensis produces more than ten palytoxins (ostreocins, OSTs). The limited sample availability of minor OSTs restricts the definition of their chemical structures. The present investigation characterizes structures of two minor OSTs, i.e., ostreocin-A (OSTA) and ostreocin-E1 (OSTE1), using ostreocin-D (OSTD) as a reference compound, by liquid chromatography/quadrupole-time-of-flight mass spectrometry. The molecular formulas of OSTA and OSTE1 were C127H219N3O54 and C127H217N3O52, respectively. Compared to OSTD, OSTA has an extra oxygen atom whereas OSTE1 lacks one oxygen atom and two hydrogen atoms. The MS/MS experiments (precursor ions: [M + H]+ and [M-H]−) suggested a hydroxyl substitution at C82 in OSTA and alteration(s) between C53 and C100 in OSTE1. Further analysis of structural details in OSTE1 was performed through a pseudo-MS3 experiment (precursor ion: m/z 1432.748). Accordingly, the planar structures of OSTA and OSTE1 were assigned to 42,82-dihydroxy-3,26-didemethyl-19,44-dideoxypalytoxin and 42-hydroxy-3,26-didemethyl-19,44,73-trideoxypalytoxin-72-ene, respectively.

Abbreviations:CID: collision induced dissociation; HR-LC/MS/MS: high-resolution liquid chromatography/tandem mass spectrometry; LC/ESI/Q-TOF MS: liquid chromatography/quadrupole time-of-flight mass spectrometry equipped with an electrospray ionization source; NMR: nuclear magnetic resonance; OSTs: ostreocins; OSTA: ostreocin-A; OSTB: ostreocin-B; OSTD: ostreocin-D; OSTE1: ostreocin-E1; OVTX-a: ovatoxin-a; OVTXs: ovatoxins; PLTX: palytoxin
The ocean-atmospheric condition around Pieh Islands – Western Sumatra, Indonesia and its role on coral reef resilience
Authors: Corvianawatie C , Abrar M , Wouthuyzen S , Darmawan  , Kusumo S , Samsuardi  , Yennafri  , Salatalohi A , Hanif A , Permana S , Arrafat M Y , Tanto T A
Published: November 2018

Pieh Islands located at the Western Sumatra is one of the most affected areas by massive coral bleaching during 2015-2016. The persistence warming or cooling of sea surface temperature due to regional climate phenomena such as El Niño Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) put the coral reef into stress condition leading into coral bleaching. However, corals have an ability to recover from such bleaching condition into normal state by reducing its stressors. A suitable oceanographic condition such as normal range of temperature and salinity, low nutrient concentration, and low sedimentation rate could support corals recovery process. This study aims to understand the variability of the ocean and atmospheric data and its role in coral reef recovery. Data gained from in situ measurements of water quality at Pieh Marine Conservation Area (PMCA) on June 2018. Several historical ocean-atmospheric data were collected to analyze their temporal variability. It is confirmed that the bleaching event was caused by positive IOD and El Niño condition in 2015-2016. However, there is the sign of coral reef recovery during 2017-2018 which is suggested due to the relatively normal condition of the ocean and atmospheric parameters in Pieh Islands.
A Case Report of a Breast Implant–Associated Plasmacytoma and Literature Review of Non-ALCL Breast Implant–Associated Neoplasms
Authors: Beydoun Ahmed Sam , Ovalle Fernando , Brannock Kristina , Gobble Ryan M
Published: November 2018

Lymphomas associated with breast implants are rare, with the most common being anaplastic large cell lymphoma (ALCL). Non-ALCL breast implant–associated lymphomas are even more rare, with only a small handful of such neoplasms reported to date. Given the need to better understand these pathologies as well as the increasing clinical and media attention being paid to these diseases, we review the available literature of hematolymphoid neoplasms other than ALCL associated with breast implants and describe the first case of a patient diagnosed with a primary breast implant–associated plasmacytoma.

Level of Evidence: 5
An equivariant Bayesian convolutional network predicts recombination hotspots and accurately resolves binding motifs
Authors: Brown Richard C , Lunter Gerton
Published: November 2018

Motivation

Convolutional neural networks (CNNs) have been tremendously successful in many contexts, particularly where training data are abundant and signal-to-noise ratios are large. However, when predicting noisily observed phenotypes from DNA sequence, each training instance is only weakly informative, and the amount of training data is often fundamentally limited, emphasizing the need for methods that make optimal use of training data and any structure inherent in the process.

Results

Here we show how to combine equivariant networks, a general mathematical framework for handling exact symmetries in CNNs, with Bayesian dropout, a version of Monte Carlo dropout suggested by a reinterpretation of dropout as a variational Bayesian approximation, to develop a model that exhibits exact reverse-complement symmetry and is more resistant to overtraining. We find that this model combines improved prediction consistency with better predictive accuracy compared to standard CNN implementations and state-of-art motif finders. We use our network to predict recombination hotspots from sequence, and identify binding motifs for the recombination–initiation protein PRDM9 previously unobserved in this data, which were recently validated by high-resolution assays. The network achieves a predictive accuracy comparable to that attainable by a direct assay of the H3K4me3 histone mark, a proxy for PRDM9 binding.

Availability and implementation

https://github.com/luntergroup/EquivariantNetworks

Supplementary information

Supplementary data are available at Bioinformatics online.
EpistasisRank and EpistasisKatz: interaction network centrality methods that integrate prior knowledge networks
Authors: Parvandeh Saeid , McKinney Brett A
Published: November 2018

Motivation

An important challenge in gene expression analysis is to improve hub gene selection to enrich for biological relevance or improve classification accuracy for a given phenotype. In order to incorporate phenotypic context into co-expression, we recently developed an epistasis-expression network centrality method that blends the importance of gene–gene interactions (epistasis) and main effects of genes. Further blending of prior knowledge from functional interactions has the potential to enrich for relevant genes and stabilize classification.

Results

We develop two new expression-epistasis centrality methods that incorporate interaction prior knowledge. The first extends our SNPrank (EpistasisRank) method by incorporating a gene-wise prior knowledge vector. This prior knowledge vector informs the centrality algorithm of the inclination of a gene to be involved in interactions by incorporating functional interaction information from the Integrative Multi-species Prediction database. The second method extends Katz centrality to expression-epistasis networks (EpistasisKatz), extends the Katz bias to be a gene-wise vector of main effects and extends the Katz attenuation constant prefactor to be a prior-knowledge vector for interactions. Using independent microarray studies of major depressive disorder, we find that including prior knowledge in network centrality feature selection stabilizes the training classification and reduces over-fitting.

Availability and implementation

Methods and examples provided at https://github.com/insilico/Rinbix and https://github.com/insilico/PriorKnowledgeEpistasisRank.

Supplementary information

Supplementary data are available at Bioinformatics online.
“Build Rapport, Otherwise No Screening Tools in the World Are Going to Help”: Frontline Service Providers’ Views on Current Screening Tools for Elder Abuse
Authors: Brijnath Bianca , Gahan Luke , Gaffy Ellen , Dow Briony
Published: November 2018

Background and Objectives

Without an effective screening tool, accompanied by clear guidelines of what to do when elder abuse is suspected, health workers may face challenges when asking questions about elder abuse. This study aimed to find the most effective and acceptable existing elder abuse screening tool and to create guidelines for using the tool.

Research Design and Methods

A rapid review of the literature identified existing validated elder abuse screening tools. Then, 5 tools (Vulnerability to Abuse Screening Scale [VASS], Elder Abuse Suspicion Index [EASI], Elder Assessment Instrument [EAI], Caregiver Abuse Screen [CASE], and Brief Abuse Screen for the Elderly [BASE]), selected based on their internal rigor, were presented to health professionals to assess the tools’ relevance to their practice. Three focus groups were held with 23 health professionals in Victoria, Australia, in 2017. Data were thematically analyzed.

Results

None of the tools were deemed suitable by participants for use in their practice. Criticisms of the tools included: using outdated terminology, asking binary questions, asking multiple questions at once, failure to consider the older person’s cognitive status, failure to consider how culture mediates elder abuse, and failure to outline a referral pathway to those administering the tool. Participants emphasized that the screening tool must promote trust and rapport between the assessor and the older person to solicit a story on this sensitive subject.

Discussion and Implications

A successful elder abuse screening tool must be concise, easy to use, account for the older person’s health and social vulnerabilities, and outline a referral pathway if elder abuse is suspected.
Protecting the Rights of Children with Intersex Conditions from Nonconsensual Gender-Conforming Medical Interventions: The View from Europe
Authors: Garland Jameson , Slokenberga Santa
Published: November 2018

Nonconsensual gender-conforming interventions on children with intersex conditions have recently come under sharp criticism from human rights authorities within the United Nations, the Council of Europe, and the European Union, which have identified these interventions as violating children’s rights to bodily integrity, privacy, and protection from violence, torture, and degrading treatment. Responding largely to requests for intervention from nongovernmental organizations, these authorities have called upon nations to reform their legal frameworks, both to prevent these rights violations and to redress them. To date, however, few nations have endeavored to prohibit nonconsensual gender-conforming procedures on children with intersex conditions, and none have enacted significant reforms of their frameworks to redress rights violations. This particular ‘compliance gap’ between human rights recommendations and law reform stems from a failure of national legal orders to formally recognize the scope of rights that are threatened by nonconsensual gender-conforming interventions—rights that are well-established as part of states’ positive obligations to prevent physical and psychological harm to children. This article, therefore, analyzes the nature of the rights at stake and the importance of reporting human rights violations to generate direct calls for reform wherever violations occur. The article further analyzes how developments in Europe may have special significance for legal framework reforms—particularly if they facilitate judicial actions against national authorities through the European Convention of Human Rights, which may serve as a model for litigation elsewhere.
Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions
Authors: Kobren Shilpa Nadimpalli , Singh Mona
Published: November 2018

Domains are fundamental subunits of proteins, and while they play major roles in facilitating protein–DNA, protein–RNA and other protein–ligand interactions, a systematic assessment of their various interaction modes is still lacking. A comprehensive resource identifying positions within domains that tend to interact with nucleic acids, small molecules and other ligands would expand our knowledge of domain functionality as well as aid in detecting ligand-binding sites within structurally uncharacterized proteins. Here, we introduce an approach to identify per-domain-position interaction ‘frequencies’ by aggregating protein co-complex structures by domain and ascertaining how often residues mapping to each domain position interact with ligands. We perform this domain-based analysis on ∼91000 co-complex structures, and infer positions involved in binding DNA, RNA, peptides, ions or small molecules across 4128 domains, which we refer to collectively as the InteracDome. Cross-validation testing reveals that ligand-binding positions for 2152 domains are highly consistent and can be used to identify residues facilitating interactions in ∼63–69% of human genes. Our resource of domain-inferred ligand-binding sites should be a great aid in understanding disease etiology: whereas these sites are enriched in Mendelian-associated and cancer somatic mutations, they are depleted in polymorphisms observed across healthy populations. The InteracDome is available at http://interacdome.princeton.edu.
125. eGISP: Enhanced Surveillance of Neisseria gonorrhoeae Antimicrobial Susceptibility in the United States
Authors: Quilter Laura , Cyr Sancta St , Abitria Vincent , Ancharski Andrew , Bautista Ilene , Bazan Jose , Carifo Karen , Ervin Melissa , Harrison Rebecca , Hoogenboom Aaron , Peterson Amy , Pham Cau , Snyder Brandon , Turner Abigail Norris , Torrone Elizabeth
Published: November 2018

Background

The Gonococcal Isolate Surveillance Project (GISP), which monitors trends in N. gonorrhoeae susceptibility among men with gonococcal urethritis in sexually transmitted disease (STD) clinics, has informed treatment recommendations for 3 decades. However, it has been speculated that susceptibility patterns may differ in women, as well as in the pharynx and rectum. We describe preliminary findings from the enhanced GISP (eGISP), which expands surveillance to pharyngeal, rectal, and endocervical isolates.

Methods

In August 2017, select jurisdictions were funded to collect urogenital and extragenital specimens from men and women seen in participating STD clinics. Positive gonorrhea cultures were sent to regional laboratories for antimicrobial susceptibility testing (AST) by agar dilution. Isolates with elevated minimum inhibitory concentration (MIC) to azithromycin (AZI) (MIC ≥2.0 μg/mL), cefixime (CFX) (MIC ≥0.25 μg/mL), and/or ceftriaxone (CRO) (MIC ≥0.125 μg/mL) were designated as Alert isolates. Clinical and epidemiological data were linked to AST results.

Results

From August 2017 to February 2018, 4 clinics in 4 jurisdictions submitted 468 positive gonococcal specimens for AST; 36.1% were from men who have sex with men (MSM), 51.9% from men who have sex with women (MSW), and 12.0% from women. Overall, 71.8% were urethral, 7.9% endocervical, 7.1% rectal, and 13.2% pharyngeal. Seventy-two isolates (15.4%) were Alerts: 97.2% (N = 70) had elevated MICs to AZI, 2.8% (N = 2) had elevated MICs to CFX, and none had elevated MICs to CRO. No isolate had elevated MICs to both AZI and CFX. Among MSM, 15.9% of urogenital isolates and 16.1% of extragenital isolates had an elevated AZI MIC. Among MSW, 11.8% of urogenital isolates and 14.3% of pharyngeal isolates had an elevated AZI MIC. Among women, 24.3% of endocervical isolates and 26.3% of extragenital isolates had an elevated AZI MIC.

Conclusion

Preliminary eGISP data suggest that enhanced surveillance of pharyngeal, rectal, and endocervical isolates is feasible and that elevated MICs to azithromycin are common among males and females. Including isolates from extragenital anatomic sites and women may help strengthen N. gonorrhoeae surveillance capacity.

Disclosures

All authors: No reported disclosures.
150. Relative Effectiveness of High-Dose and Standard-Dose Influenza Vaccine Against Influenza-Related Hospitalization Among Older Adults—United States, 2015–2017
Authors: Doyle Joshua , Beacham Lauren , Alyanak Elif , Gaglani Manjusha , Martin Emily T , Middleton Don , Silveira Fernanda P , Talbot H Keipp , Zimmerman Richard , Flannery Brendan , Ferdinands Jill M
Published: November 2018

Background

Seasonal influenza causes substantial morbidity and mortality, and older adults are disproportionately affected. Newer vaccines have been developed for use in people 65 years and older, including a trivalent inactivated vaccine with a 4-fold higher dose of antigen (IIV-HD). In recent years, the use of IIV-HD has increased sufficiently to evaluate its effectiveness compared with standard-dose inactivated influenza vaccines (IIV-SD).

Methods

Hospitalized patients with acute respiratory illness were enrolled in an observational vaccine effectiveness study at 8 hospitals in 4 states participating in the United States Hospitalized Adult Influenza Vaccine Effectiveness Network during the 2015–2016 and 2016–2017 influenza seasons. Predominant influenza A virus subtypes were H1N1 and H3N2, respectively, during these seasons. All enrolled patients were tested for influenza virus with polymerase chain reaction. Receipt and type of influenza vaccine was determined from electronic records and chart review. Odds of laboratory-confirmed influenza were compared among vaccinated and unvaccinated patients. Relative odds of laboratory-confirmed influenza were determined for patients who received IIV-HD or IIV-SD, and adjusted for potential confounding variables via logistic regression.

Results

Among 1,744 enrolled patients aged ≥ 65 years, 1,105 (63%) were vaccinated; among those vaccinated, 621 (56%) received IIV-HD and 484 (44%) received IIV-SD. Overall, 315 (18%) tested positive for influenza, including 97 (6%) who received IIV-HD, 86 (5%) who received IIV-SD, and 132 (8%) who were unvaccinated. Controlling for age, race, sex, enrollment site, date of illness, index of comorbidity, and influenza season, the adjusted odds of influenza among patients vaccinated with IIV-HD vs. IIV-SD were 0.72 (P = 0.06, 95% CI: 0.52 to 1.01).

Conclusion

Comparison of high-dose vs. standard-dose vaccine effectiveness during 2 recent influenza seasons (1 H1N1 and 1 H3N2-predominant) suggested relative benefit (nonsignificant) of high-dose influenza vaccine in protecting against influenza-associated hospitalization among persons aged 65 years and older; additional years of data are needed to confirm this finding.

Disclosures

H. K. Talbot, sanofi pasteur: Investigator, Research grant. Gilead: Investigator, Research grant. MedImmune: Investigator, Research grant. Vaxinnate: Safety Board, none. Seqirus: Safety Board, none.
166. TGF-β Restricts T-cell IFNg Production in Pulmonary Tuberculous Granulomas
Authors: Gern Benjamin , Adams Kristin , Plumlee Courtney , Gerner Michael , Urdahl Kevin
Published: November 2018

Background

IFNg production by CD4 T cells has been thought to be critical for immunity against Mycobacterium tuberculosis (Mtb); however, recent studies show that IFNg-producing CD4 T cells are more effective at preventing dissemination than controlling Mtb in the lung. Because optimal control of Mtb infection requires direct interactions between CD4 T cells and Mtb-infected cells presenting cognate antigen on MHCII, we sought to determine the location of CD4 T-cell antigen recognition and IFNg production in the Mtb-infected lung.

Methods

We infected mice with an ultra-low dose (ULD) of Mtb (1–3 CFU), a model developed in our laboratory which results in well-circumscribed granulomas that recapitulate many features of human Mtb granulomas. Using immunohistochemistry and quantitative imaging, we examined their lungs 35 days later for phenotypic and spatial analysis of T-cell receptor (TCR) signaling (using IRF4) and IFNγ production. We tested the antigen specificity of these responses with an adoptive transfer of both Mtb-specific and OVA-specific control CD4 T cells into ULD Mtb-infected mice. To assess the role of TGFβ signaling on T-cell localization and function, we performed the same analysis in mice lacking the TGFβ receptor (TGFβR) on T cells.

Results

Within Mtb-infected lungs, many T cells localize near Mtb cells and undergo TCR signaling. Despite this, we found very few cells producing IFNγ within the granuloma (Figure 1). In our adoptive transfer experiment, both cell types infiltrated the granuloma. The Mtb-specific, but not OVA-specific, T cells had active TCR engagement though only a small fraction of these cells produced IFNγ, and this IFNγ was diminished near Mtb (Figure 2). Conversely, in the TGFβR conditional knockout, we found increased IFNγ production that was highest within the granuloma (Figure 3).

Conclusion

Despite ongoing TCR stimulation in T cells, IFNγ production is restricted in areas where cognate interactions are most likely to occur. TGFβ plays a critical role in mediating this effect, as T cells lacking the receptor can produce more IFNγ near infected cells. These findings help explain why IFNγ-producing T cells have limited capacity to control pulmonary Mtb infection and could guide new strategies for vaccine and immunotherapeutic development.

Disclosures

All authors: No reported disclosures.