bluuebunny/crossref_metadata_2025 huggingface dataset:
Measurements of parametric instabilities at laser intensities relevant to strong shock generation
Authors: Cristoforetti G. , Antonelli L. , Atzeni S. , Baffigi F. , Barbato F. , Batani D. , Boutoux G. , Colaitis A. , Dostal J. , Dudzak R. , Juha L. , Koester P. , Marocchino A. , Mancelli D. , Nicolai Ph. , Renner O. , Santos J. J. , Schiavi A. , Skoric M. M. , Smid M. , Straka P. , Gizzi L. A.
Published: January 2018

Parametric instabilities at laser intensities in the range (2–6) × 1015 W/cm2 (438 nm, 250 ps, 100–300 J) have been investigated in planar geometry at the Prague Asterix Laser System facility via calorimetry and spectroscopy. The density scalelength of the plasma was varied by using an auxiliary pulse to form a preplasma before the arrival of the main laser beam and by changing the delay between the two pulses. Experimental data show that Stimulated Brillouin Scattering (SBS) is more effective than Stimulated Raman Scattering (SRS) in degrading laser-plasma coupling, therefore reducing the energy available for the generation of the shock wave. The level of the SBS backscatter and laser reflection is found to be in the range between 3% and 15% of the incident laser energy, while Backward SRS (BRS) reflectivity ranges between 0.02% and 0.2%, depending on the delay between the pulses. Half-integer harmonic emission is observed and provides a signature of Two Plasmon Decay (TPD) occurring around the quarter of the critical density. Data analysis suggests that SRS is driven in beam speckles with high local intensity and occurs in bursts, particularly at higher laser intensities, due to the presence of kinetic mechanisms saturating the SRS growth in the speckles. Time-resolved measurements also show that BRS occurs in the trailing part of the laser pulse, when the plasma has a longer density scalelength. Our measurements also indicate that hot electrons are predominantly produced by SRS rather than TPD.
X-ray magnetic circular dichroism discloses surface spins correlation in maghemite hollow nanoparticles
Authors: Bonanni Valentina , Basini Martina , Peddis Davide , Lascialfari Alessandro , Rossi Giorgio , Torelli Piero
Published: January 2018

The spin-spin correlations in hollow (H) and full (F) maghemite nanoparticles (NPs) have been studied by X-ray magnetic circular dichroism (XMCD). An unexpected XMCD signal was detected and analyzed under the application of a small field (μ0H = 160 Oe) and at remanence for both F and H NPs. Clear differences in the magnitude and in the lineshape of the XMCD spectra between F and H NPs emerged. By comparing XMCD measurements performed with a variable degree of surface sensitivity, we were able to address the specific role played by the surface spins in the magnetism of the NPs.
Radiation pressure injection in laser-wakefield acceleration
Authors: Liu Y. L. , Kuramitsu Y. , Isayama S. , Chen S. H.
Published: January 2018

We investigated the injection of electrons in laser-wakefield acceleration induced by a self-modulated laser pulse by a two dimensional particle-in-cell simulation. The localized electric fields and magnetic fields are excited by the counter-streaming flows on the surface of the ion bubble, owing to the Weibel or two stream like instability. The electrons are injected into the ion bubble from the sides of it and then accelerated by the wakefield. Contrary to the conventional wave breaking model, the injection of monoenergetic electrons are mainly caused by the electromagnetic process. A simple model was proposed to address the instability, and the growth rate was verified numerically and theoretically.
Zero refractive index in time-Floquet acoustic metamaterials
Authors: Koutserimpas Theodoros T. , Fleury Romain
Published: January 2018

New scientific investigations of artificially structured materials and experiments have exhibited wave manipulation to the extreme. In particular, zero refractive index metamaterials have been on the front line of wave physics research for their unique wave manipulation properties and application potentials. Remarkably, in such exotic materials, time-harmonic fields have an infinite wavelength and do not exhibit any spatial variations in their phase distribution. This unique feature can be achieved by forcing a Dirac cone to the center of the Brillouin zone (Γ point), as previously predicted and experimentally demonstrated in time-invariant metamaterials by means of accidental degeneracy between three different modes. In this article, we propose a different approach that enables true conical dispersion at Γ with twofold degeneracy and generates zero index properties. We break time-reversal symmetry and exploit a time-Floquet modulation scheme to demonstrate a time-Floquet acoustic metamaterial with zero refractive index. This behavior, predicted using stroboscopic analysis, is confirmed by full-wave finite element simulations. Our results establish the relevance of time-Floquet metamaterials as a novel reconfigurable platform for wave control.
Macroscopic equivalence for microscopic motion in a turbulence driven three-dimensional self-assembly reactor
Authors: Hageman T. A. G. , Löthman P. A. , Dirnberger M. , Elwenspoek M. C. , Manz A. , Abelmann L.
Published: January 2018

We built and characterised a macroscopic self-assembly reactor that agitates magnetic, centimeter-sized particles with a turbulent water flow. By scaling up the self-assembly processes to the centimeter-scale, the characteristic time constants also drastically increase. This makes the system a physical simulator of microscopic self-assembly, where the interaction of inserted particles is easily observable. Trajectory analysis of single particles reveals their velocity to be a Maxwell-Boltzmann distribution and it shows that their average squared displacement over time can be modelled by a confined random walk model, demonstrating a high level of similarity to the Brownian motion. The interaction of two particles has been modelled and verified experimentally by observing the distance between two particles over time. The disturbing energy (analogue to temperature) that was obtained experimentally increases with sphere size and differs by an order of magnitude between single-sphere and two-sphere systems (approximately 80 µJ versus 6.5 µJ, respectively).
Systematic design of broadband path-coiling acoustic metamaterials
Authors: Jia Zhetao , Li Junfei , Shen Chen , Xie Yangbo , Cummer Steven A.
Published: January 2018

A design approach for acoustic metamaterial unit cells based on a coiled path with impedance matching layers (IMLs) is proposed in this paper. A theoretical approach is developed to calculate the transmission of the labyrinthine unit cells with different effective refractive indices. The IML is introduced to broaden the transmission bandwidth and produce a lower envelope boundary of transmission for unit cells of different effective refractive indices. According to the theory, cells of all effective refractive indices can be built to achieve unitary transmission at center working frequencies. The working frequency can be tuned by adjusting the length of the IML. Numerical simulations based on finite element analysis are used to validate the theoretical predictions. The high transmission and low dispersive index nature of our designs are further verified by experiments within a broad frequency band of over 1.4 kHz centered at 2.86 kHz. Our design approach can be useful in various wavefront engineering applications.
Theoretical analysis of the domain-swapped dimerization of cytochrome c: An MD and 3D-RISM approach
Authors: Yoshida Norio , Higashi Masahiro , Motoki Hideyoshi , Hirota Shun
Published: January 2018

The structural stability of a cytochrome c domain-swapped dimer compared with that of the monomer was investigated by molecular dynamics (MD) simulations and by three-dimensional reference interaction site model (3D-RISM) theory. The structural fluctuation and structural energy of cytochrome c were treated by MD simulations, and the solvation thermodynamics was treated by 3D-RISM theory. The domain-swapped dimer state is slightly less stable than the monomer state, which is consistent with experimental observations; the total free energy difference is calculated as 25 kcal mol−1. The conformational change and translational/rotational entropy change contribute to the destabilization of the dimer, whereas the hydration and vibrational entropy contribute to the stabilization. Further analyses on the residues located at the hinge loop for swapping were conducted, and the results reveal details at the molecular level of the structural and interaction changes upon dimerization.
Equation of state and optical properties of warm dense helium
Authors: Preising Martin , Lorenzen Winfried , Becker Andreas , Redmer Ronald , Knudson Marcus D. , Desjarlais Michael P.
Published: January 2018

We used molecular dynamics simulations based on density functional theory to study the thermophysical properties of warm dense helium. The influence of different exchange-correlation (XC) functionals was analyzed. We calculated the equation of state at high pressures up to several Mbar and temperatures up to 100 000 K in order to reconstruct recent static, single shock, and quasi-isentropic compression experiments. Furthermore, we calculated the dynamic electrical conductivity and determined the reflectivity and DC conductivity. We compared our results with experimental data and found good agreement between our calculations and the high-pressure experiments. The different XC functionals give similar results in the equation of state calculations, but have a strong impact on the reflectivity and the DC conductivity.
Localized surface plasmon resonance enhanced magneto-optical Kerr effect in Ni80Fe20 thin films coated with Au nanorods
Authors: Choi B. C. , Xu H. , Hajisalem G. , Gordon R.
Published: January 2018

The influence of the localized surface plasmon resonance on the magneto-optical Kerr effect (MOKE) was investigated in Ni80Fe20 thin films coated with gold nanorods. The nanorods are dimensionally tuned to support localized surface plasmon resonance near the incident laser frequency. A significant enhancement of magneto-optical response is observed, in which the MOKE signal is increased by over 40% compared to the reference Ni80Fe20 films. The spectral dependence of MOKE signals exhibits the maximum magneto-optical response centered around the longitudinal surface plasmon resonance wavelength of gold nanorods. Finite-difference time-domain modeling confirms that the excitation of the localized surface plasmons leads to the enhancement of magneto-optical responses.
Polarization and charge-transfer effect on the transport properties in two-dimensional electron gases/LaNiO3 heterostructure
Authors: Chen M. J. , Ning X. K. , Wang Z. J. , Liu P. , Wang S. F. , Wang J. L. , Fu G. S. , Ma S. , Liu W. , Zhang Z. D.
Published: January 2018

The film thickness dependent transport properties of the LaNiO3 (LNO) layer epitaxially grown on LaAlO3/SrTiO3 (LAO) 2-dimensional electronic gas (2DEG) have been investigated. The ultrathin LNO films grown on the 2DEG have a sheet resistance below the values of h/e2 in all temperature ranges. The electron density is enhanced by more than one order of magnitude by capping LNO films. X-ray photoelectron spectroscopy shows that the interface undergoes unambiguous charge transfer and electronic reconstruction, leading to modulation doping of such atomically engineered complex oxide heterointerfaces. The polar-catastrophe of the 2DEG is directly linked to the electronic structure and transport properties of the LNO. The transport properties can be well modulated by the thickness of the LAO in the 2DEG, and the data can be well fitted with the polar-catastrophe scenario. These results suggest a general approach to tunable functional films in oxide heterostructures with the 2DEG.
Electrical and noise properties of proton irradiated 4H-SiC Schottky diodes
Authors: Kozlovski V. V. , Lebedev A. A. , Levinshtein M. E. , Rumyantsev S. L. , Palmour J. W.
Published: January 2018

The current voltage characteristics and the low-frequency noise in high voltage 4H-SiC junction barrier Schottky diodes irradiated with high energy (15 MeV) protons were studied at different temperatures and irradiation doses Φ from 3 × 1012 cm−2 to 1 × 1014 cm−2. Irradiation led to the increase of the base resistance and the appearance of slow relaxation processes at small, V ≤ 0.2 V, and at rather high, V ≥ 2 V, forward voltages. The characteristic times of these relaxation processes ranged from ∼1 μs to 103 s. The exponential part of the current-voltage characteristic was only weakly affected by irradiation. The temperature dependence of the base resistance changed exponentially with temperature with activation energy Ea ∼ 0.6 eV, indicating that the Z1/2 level plays a dominant role in this process. The temperature increase also led to the increase of the ideality factor from 1.05 at 25 °C to 1.1 at 172 °C. At elevated temperatures and high forward voltages V > 2–4 V, the current voltage characteristics tend to be super-linear. It is concluded that at high voltages, the space charge limited current of majority carriers (electrons) and hole injection from the p-n regions play an important role in the formation of the current voltage characteristic. The frequency dependences of noise spectral density S of proton irradiated Schottky diodes have the unusual form of S ∼ 1/f 0.5.
Serological diversity, molecular characterisation and antimicrobial sensitivity of avian pathogenic Escherichia coli (APEC) isolates from broiler chickens in Kashmir, India
Authors: Magray S. N. , Wani S. A. , Kashoo Z. A. , Bhat M. A. , Adil S. , Farooq S. , Rather M. A. , Kabli Z. A. , Banday M. T. , Nishikawa Y.
Published: January 2018

The present study has determined the serological diversity, virulence-gene profile and in vitro antibiogram of avian pathogenic Escherichia coli (APEC) isolates from broiler chickens in India suspected to have died of colibacillosis. The virulence-gene profile of APEC was compared with that of the Escherichia coli isolates from faeces of apparently healthy chickens, called avian faecal E. coli (AFEC). In total, 90 representative isolates of APEC and 63 isolates of AFEC were investigated in the present study. The APEC were typed into 19 serogroups, while some isolates were rough and could not be typed. Most prevalent serogroup was O2 (24.44%). Among the eight virulence genes studied, the prevalence of seven genes (iss, iucD, tsh, cva/cvi, irp2, papC and vat) was significantly higher in APEC than in AFEC isolates. However, there was no significant difference between APEC and AFEC isolates for possession of astA gene. The most frequent gene detected among the two groups of organisms was iss, which was present in 98.88% and 44.44% of APEC and AFEC isolates respectively. The in vitro antibiogram showed that the majority (96.6%) of APEC isolates were resistant to tetracycline, while 82.2% were resistant to cephalexin, 78.8% to cotrimoxazole, 68.8% to streptomycin and 63.3% to ampicillin. However, most of them (84.45%) were sensitive to gentamicin. Thus, it is concluded that APEC from the broiler chickens carried putative virulence genes that attributed to their pathogenicity. Furthermore, the majority of APEC isolates were found to be multi-drug resistant, which, in addition to leading treatment failures in poultry, poses a public health threat.
GBA1 deficiency negatively affects physiological α-synuclein tetramers and related multimers
Authors: Kim Sangjune , Yun Seung Pil , Lee Saebom , Umanah George Essien , Bandaru Veera Venkata Ratnam , Yin Xiling , Rhee Peter , Karuppagounder Senthilkumar S. , Kwon Seung-Hwan , Lee Hojae , Mao Xiaobo , Kim Donghoon , Pandey Akhilesh , Lee Gabsang , Dawson Valina L. , Dawson Ted M. , Ko Han Seok
Published: January 2018

Significance

Recent studies have identified a helically folded tetramer as the major normal structure of α-synuclein (α-syn) and that the tetramer resists aggregation. However, the underlying mechanisms that regulate the formation of α-syn tetramers remain elusive. Our study shows that mutations in glucocerebrosidase 1 (
GBA1
) and depletion-induced GBA1 deficiency leading to accumulation of glycosphingolipids (GSLs) are sufficient to cause destabilization of α-syn tetramers and increase the susceptibility of human dopaminergic neurons to cytotoxicity due to exposure to pathologic α-syn fibrils. Therefore, maintaining GBA1 activity and reducing GSLs are potentially important in reducing misfolding and pathogenic aggregation of α-syn in Parkinson’s disease.
Unified description of H-atom–induced chemicurrents and inelastic scattering
Authors: Kandratsenka Alexander , Jiang Hongyan , Dorenkamp Yvonne , Janke Svenja M. , Kammler Marvin , Wodtke Alec M. , Bünermann Oliver
Published: January 2018

Significance

Catalytic reactions at surfaces are exceptionally complex, as they require a multitude of elementary steps. It is therefore very difficult to predict which chemical compounds are catalytically effective. In inelastic scattering experiments in ultrahigh vacuum, the first step of most surface reactions, which is the adsorption, can be studied on model systems in great detail. Based on such experiments new theoretical models can be developed that accurately describe the delicate interplay between electronic and nuclear motion in prototypical chemical reactions, a capability that is needed to make accurate predictions of reaction rates in heterogeneous catalysis, to design useful energy-conversion devices based on chemicurrents, and to understand photocatalysis.
Dynamics of charged excitons in electronically and morphologically homogeneous single-walled carbon nanotubes
Authors: Bai Yusong , Olivier Jean-Hubert , Bullard George , Liu Chaoren , Therien Michael J.
Published: January 2018

Significance

Formation of quasiparticles, such as excitons, polarons, and trions in semiconductors are the foundation for modern optoelectronics. Unlike the widely investigated exciton and polaron, the trion, a three-body charge-exciton bound state, is less familiar due to its small binding energy in conventional inorganic semiconductors. Here, employing ultrafast spectroscopy and rigorously controlled charge-doping levels, we characterize trion creation and decay in single-walled carbon nanotubes (SWNTs), wherein trions are stable at room temperature. We show that SWNT trions derive exclusively from a precursor exciton state, and importantly, that exciton-to-trion conversion can approach unity under appropriate conditions. Because trions simultaneously carry excitation energy, charge, and spin, our findings may guide design of new SWNT-based optoelectronic devices, including photovoltaics, photodetectors, and spintronics.
Fenofibrate prevents skeletal muscle loss in mice with lung cancer
Authors: Goncalves Marcus D. , Hwang Seo-Kyoung , Pauli Chantal , Murphy Charles J. , Cheng Zhe , Hopkins Benjamin D. , Wu David , Loughran Ryan M. , Emerling Brooke M. , Zhang Guoan , Fearon Douglas T. , Cantley Lewis C.
Published: January 2018

Significance

The cancer anorexia cachexia syndrome (CACS) is a condition characterized by skeletal muscle degradation with no effective treatment. CACS is particularly prevalent in patients with nonsmall cell lung cancer, where it reduces quality of life and increases mortality. Using an inducible lung cancer model, we characterize the changes in intermediary metabolism that occur during CACS in mice. We identify a unique serum metabolite profile consisting of low ketones and increased glucocorticoid levels. Hypoketonemia is associated with reduced expression of hepatic peroxisome proliferator-activated receptor-α (PPARα) targets that regulate fatty acid oxidation and ketogenesis. Replacing ketone production using the PPARα agonist, fenofibrate, reduced glucocorticoid levels, prevented skeletal muscle wasting, and minimized weight loss. These exciting results provide important preclinical data toward a therapeutic strategy.
Pyruvate induces torpor in obese mice
Authors: Soto Marion , Orliaguet Lucie , Reyzer Michelle L. , Manier M. Lisa , Caprioli Richard M. , Kahn C. Ronald
Published: January 2018

Significance

Mice can reduce their body temperature and metabolic rate and enter torpor when they are subjected to cold, calorie deprivation, or administration of some metabolic inhibitors. Here we show that administration of pyruvate, a key metabolic intermediate and substrate for gluconeogenesis, induces torpor in obese mice, resulting in marked hypothermia, decreased activity, and decreased metabolic rate. This is dependent on adenosine signaling and on changes in key brain metabolites, including GABA. Lean mice are protected from pyruvate-induced torpor by activating their brown adipose tissue. Understanding this pathway can help provide new approaches for inducing a hypometabolic state in mammals, which could be beneficial in states of food deprivation or ischemia–reperfusion injury and for organ preservation in surgical situations.
Influence of anterior midcingulate cortex on drinking behavior during thirst and following satiation
Authors: Saker Pascal , Farrell Michael J. , Egan Gary F. , McKinley Michael J. , Denton Derek A.
Published: January 2018

Significance

This study provides important insight into how the human brain regulates fluid intake in response to changes in hydration status. The findings presented here reveal that activity in the anterior midcingulate cortex (aMCC) is associated with drinking responses during a state of thirst, and that this region is likely to contribute to the facilitation of drinking during this state. These results are consistent with a reduction in the influence of the aMCC contributing to the conclusion of drinking during a state of satiation. Because drinking stops before changes in blood volume and chemistry signal the restoration of fluid balance, these results implicate the aMCC in the regulation of drinking behavior before these changes manifest within the circulatory system.
Reverse chemical ecology approach for the identification of an oviposition attractant forCulex quinquefasciatus
Authors: Choo Young-Moo , Xu Pingxi , Hwang Justin K. , Zeng Fangfang , Tan Kaiming , Bhagavathy Ganga , Chauhan Kamlesh R. , Leal Walter S.
Published: January 2018

Significance

Surveillance of mosquito populations is essential for determining the best timing for intervention as well as for monitoring circulation of new and previously detected pathogens. Trapping gravid females is more effective because they are more likely to be infected than nongravid females. However, better gravid trap attractants are sorely needed to replace fermentation recipes, which are cumbersome, have poor quality control, generate an offensive smell, and do not provide a long-term and consistent source of attractants. By using a reverse chemical ecology approach based on odorant receptors from the southern house mosquito, we have identified that acetaldehyde in a wide range of doses both attracts gravid female mosquitoes and stimulates them to lay eggs in oviposition trays.
What’s in a Demonym? A Note on a New and Uplifting Ethnonym
Authors: Tent Jan
Published: January 2018

Ethnicity is all important in Fiji, and labels for the different ethnic groups are a constant source of debate. A significant proportion of Fiji’s population are descendants of indentured laborers from the Indian subcontinent. An appropriate name for these citizens has for a long time been a contentious issue. In 2017 a new name was proposed; one that signals the beginning of a change in attitude. This note reports on the new name.
Preparation of super-hydrophobic surface on Al–Mg alloy substrate by electrochemical etching
Authors: Ma Ning , Chen Yang , Zhao Shuguo , Li Jingchun , Shan Baofeng , Sun Juhe
Published: January 2018

The super-hydrophobic surface was successfully prepared on the Al–Mg alloy substrate by electrochemical etching in neutral NaCl solution and low surface energy modification. Complex micro-structures and fluoroalkylsilane played important roles in the formation of super-hydrophobic surfaces. Scanning electron microscopy images, energy dispersive spectroscopy and contact angle measurement were performed to characterise the morphological features, chemical composition and wettability of the prepared surfaces. Surface wetting changes, reaction mechanisms and the effect of current density on morphology were also analysed in detail. The stability, friction and electrochemical tests showed that the prepared surfaces had excellent corrosion resistance and abrasion resistance.
Prenylation enhances the biological activity of dietary flavonoids by altering their bioavailability
Authors: Mukai Rie
Published: January 2018

Flavonoids are distributed across the plant kingdom and have attracted substantial attention owing to their potential benefits for human health. Several studies have demonstrated that flavonoids prenylation enhances various biological activities, suggesting an attractive tool for developing functional foods. This review provides an overview of the current knowledge on how prenylation influences the biological activity and bioavailability of flavonoids. The enhancement effect of prenylation on the biological activities of dietary flavonoids in mammals was demonstrated by comparing the effect of 8-prenyl naringenin (8PN) with that of parent naringenin in the prevention of disuse muscle atrophy in mice. This enhancement results from higher muscular accumulation of 8PN than naringenin. As to bioavailability, despite the lower absorption of 8-prenyl quercetin (8PQ) compared with quercetin, higher 8PQ accumulation was found in the liver and kidney. These data imply that prenylation interferes with the elimination of flavonoids from tissues.
The 1975 Japanese diet has a stress reduction effect in mice: search for physiological effects using metabolome analysis
Authors: Iwagaki Yui , Sugawara Saeko , Huruya Yasuhisa , Sato Miki , Wu Qiming , E Shuang , Yamamoto Kazushi , Tsuduki Tsuyoshi
Published: January 2018

We aimed to find new physiological effects of the Japanese diet. First, to determine the key components in serum from mice fed the 1975 diet, serum from mice fed the 1960, 1975, 1990 or 2005 Japanese diet was analyzed using CE-TOFMS and LC-TOFMS. Based on these results, the key components were determined by principal component analysis. Among the identified compounds, GABA was included. Therefore, a stress reduction effect was inferred as a novel physiological effect of this diet. Next, we tested whether the 1975 diet had an actual stress reduction effect in mice. Mice were given the 1975 diet or a control diet for 4 weeks, after which they were divided into restraint stress and non-stress groups. Mice fed the 1975 diet had significantly decreased stress parameters compared with those fed the control diet. These results provide the first evidence that the 1975 Japanese diet has a stress reduction effect.
TPXL-1 activates Aurora A to clear contractile ring components from the polar cortex during cytokinesis
Authors: Mangal Sriyash , Sacher Jennifer , Kim Taekyung , Osório Daniel Sampaio , Motegi Fumio , Carvalho Ana Xavier , Oegema Karen , Zanin Esther
Published: January 2018

During cytokinesis, a signal from the central spindle that forms between the separating anaphase chromosomes promotes the accumulation of contractile ring components at the cell equator, while a signal from the centrosomal microtubule asters inhibits accumulation of contractile ring components at the cell poles. However, the molecular identity of the inhibitory signal has remained unknown. To identify molecular components of the aster-based inhibitory signal, we developed a means to monitor the removal of contractile ring proteins from the polar cortex after anaphase onset. Using this assay, we show that polar clearing is an active process that requires activation of Aurora A kinase by TPXL-1. TPXL-1 concentrates on astral microtubules coincident with polar clearing in anaphase, and its ability to recruit Aurora A and activate its kinase activity are essential for clearing. In summary, our data identify Aurora A kinase as an aster-based inhibitory signal that restricts contractile ring components to the cell equator during cytokinesis.
Discrete monotonicity of means and its applications
Authors: Nishimura Ryo
Published: January 2018

In this paper, we obtain new inequalities for the logarithmic mean and the complete elliptic integral of the first kind. In order to prove the inequalities, we use the monotonicity property of sequences defined by these functions. Additionally, we apply our approach to previous studies. As a result, we get refinements of known inequalities.
The Temporal Dynamics of Brain Plasticity in Aging
Authors: de Lange Ann-Marie Glasø , Bråthen Anne Cecilie Sjøli , Rohani Darius A , Fjell Anders M , Walhovd Kristine B
Published: January 2018

Cognitive training has been suggested as a possible remediation of decline in brain structure with older age. However, it is unknown whether training effects are transient or enduring, as no studies have examined training-induced plasticity relative to decline in older adults across extended periods with multiple intervention phases. We investigated the temporal dynamics of brain plasticity across periods on and off memory training, hypothesizing that (1) a decline in white matter (WM) microstructure would be observed across the duration of the study and (2) that periods of memory training would moderate the WM microstructural decline. In total, 107 older adults followed a 40-week program, including 2 training periods separated by periods with no intervention. The general decline in WM microstructure observed across the duration of the study was moderated following the training periods, demonstrating that cognitive training may mitigate age-related brain deterioration. The training-related improvements were estimated to subside over time, indicating that continuous training may be a premise for the enduring attenuation of neural decline. Memory improvements were largely maintained after the initial training period, and may thus not rely on continuous training to the same degree as WM microstructure.
SemEHR: A general-purpose semantic search system to surface semantic data from clinical notes for tailored care, trial recruitment, and clinical research*
Authors: Wu Honghan , Toti Giulia , Morley Katherine I , Ibrahim Zina M , Folarin Amos , Jackson Richard , Kartoglu Ismail , Agrawal Asha , Stringer Clive , Gale Darren , Gorrell Genevieve , Roberts Angus , Broadbent Matthew , Stewart Robert , Dobson Richard JB
Published: January 2018

Objective

Unlocking the data contained within both structured and unstructured components of electronic health records (EHRs) has the potential to provide a step change in data available for secondary research use, generation of actionable medical insights, hospital management, and trial recruitment. To achieve this, we implemented SemEHR, an open source semantic search and analytics tool for EHRs.

Methods

SemEHR implements a generic information extraction (IE) and retrieval infrastructure by identifying contextualized mentions of a wide range of biomedical concepts within EHRs. Natural language processing annotations are further assembled at the patient level and extended with EHR-specific knowledge to generate a timeline for each patient. The semantic data are serviced via ontology-based search and analytics interfaces.

Results

SemEHR has been deployed at a number of UK hospitals, including the Clinical Record Interactive Search, an anonymized replica of the EHR of the UK South London and Maudsley National Health Service Foundation Trust, one of Europe’s largest providers of mental health services. In 2 Clinical Record Interactive Search–based studies, SemEHR achieved 93% (hepatitis C) and 99% (HIV) F-measure results in identifying true positive patients. At King’s College Hospital in London, as part of the CogStack program (github.com/cogstack), SemEHR is being used to recruit patients into the UK Department of Health 100 000 Genomes Project (genomicsengland.co.uk). The validation study suggests that the tool can validate previously recruited cases and is very fast at searching phenotypes; time for recruitment criteria checking was reduced from days to minutes. Validated on open intensive care EHR data, Medical Information Mart for Intensive Care III, the vital signs extracted by SemEHR can achieve around 97% accuracy.

Conclusion

Results from the multiple case studies demonstrate SemEHR’s efficiency: weeks or months of work can be done within hours or minutes in some cases. SemEHR provides a more comprehensive view of patients, bringing in more and unexpected insight compared to study-oriented bespoke IE systems. SemEHR is open source, available at https://github.com/CogStack/SemEHR.
Revisiting Stephan's Quintet with deep optical images
Authors: Duc Pierre-Alain , Cuillandre Jean-Charles , Renaud Florent
Published: January 2018

Stephan's Quintet, a compact group of galaxies, is often used as a laboratory to study a number of phenomena, including physical processes in the interstellar medium, star formation, galaxy evolution, and the formation of fossil groups. As such, it has been subject to intensive multiwavelength observation campaigns. Yet, models lack constrains to pin down the role of each galaxy in the assembly of the group. We revisit here this system with multiband deep optical images obtained with MegaCam on the Canada–France–Hawaii Telescope (CFHT), focusing on the detection of low surface brightness (LSB) structures. They reveal a number of extended LSB features, some new, and some already visible in published images but not discussed before. An extended diffuse, reddish, lopsided, halo is detected towards the early-type galaxy NGC 7317, the role of which had so far been ignored in models. The presence of this halo made of old stars may indicate that the group formed earlier than previously thought. Finally, a number of additional diffuse filaments are visible, some close to the foreground galaxy NGC 7331 located in the same field. Their structure and association with mid-infrared emission suggest contamination by emission from Galactic cirrus.
Exploring Elicitors of the Beneficial Rhizobacterium Bacillus amyloliquefaciens SQR9 to Induce Plant Systemic Resistance and Their Interactions With Plant Signaling Pathways
Authors: Wu Gengwei , Liu Yunpeng , Xu Yu , Zhang Guishan , Shen Qirong , Zhang Ruifu
Published: January 2018

Beneficial rhizobacteria have been reported to produce various elicitors that induce plant systemic resistance, but there is little knowledge concerning the relative contribution of multiple elicitors from a single beneficial rhizobacterium on the induced systemic resistance in plants and the interactions of these elicitors with plant signaling pathways. In this study, nine mutants of the plant growth–promoting rhizobacterium Bacillus amyloliquefaciens SQR9 deficient in producing the extracellular compounds, including fengycin, bacillomycin D, surfactin, bacillaene, macrolactin, difficidin, bacilysin, 2,3-butandiol, and exopolysaccharides, were tested for the induction of systemic resistance against Pseudomonas syringae pv. tomato DC3000 and Botrytis cinerea and the transcription of the salicylic acid, jasmonic acid, and ethylene signaling pathways in Arabidopsis. Deficiency in producing any of these compounds in SQR9 significantly weakened the induced plant resistance against these phytopathogens. These SQR9-produced elicitors induced different plant defense genes. For instance, the enhancement of 1,3-glucanase (PR2) by SQR9 was impaired by a deficiency of macrolactin but not surfactin. SQR9 mutants deficient in the lipopeptide and polyketide antibiotics remained only 20% functional for the induction of resistance-related gene transcription. Overall, these elicitors of SQR9 could act synergistically to induce plant systemic resistance against different phytopathogens through different signaling pathway genes, and the bacterial antibiotics are major contributors to the induction.
A Case Study of the NCRP 156 Wound Model of Embedded DU Using Data From Urine Uranium Concentrations of Wounded Veterans
Authors: Walkingstick Michael T. , Krage Eric S. , Brey Richard R.
Published: January 2018

Depleted uranium (DU) munitions were initially used by the United States (U.S.) military during the first Persian Gulf War in 1991 in order to penetrate heavily armored vehicles. However, as a result of friendly fire, several U.S. military personnel received intakes from DU munitions. One of the ongoing concerns for these wounded veterans is the potential long-term exposure received from DU embedded fragments. The United States Army Institute of Public Health (AIPH) is the first laboratory that analyzes the urine bioassays from Army Soldiers that are injured with DU fragments. The United States Air Force School of Aerospace Medicine also evaluates bioassays from DU injuries. The urine bioassay data collected by AIPH was evaluated using the NCRP 156 wound model coefficients for the DU-Wafer, Fragment, and Particle models. The maximum likelihood method was used in the Integrated Modules for Bioassay Analysis (IMBA-PPAE) to calculate the estimates of intake and tissue doses. Evaluating the three models for wound retention, the DU-Wafer and Fragment model yielded a credible fit to the bioassay data. Comparing the two models, the DU-Wafer model fits the data better than the Fragment model when comparing their autocorrelation coefficient and chi-squared values of (P 1.73 × 10−1, c2 4.83 × 10−1), (P 2.01 × 10−2, c2 1.09), respectively. This evaluation supports the validity of both the DU-wafer model as well as the default fragmentation model proposed by NCRP 156.
Novel EWSR1-SMAD3 Gene Fusions in a Group of Acral Fibroblastic Spindle Cell Neoplasms
Authors: Kao Yu-Chien , Flucke Uta , Eijkelenboom Astrid , Zhang Lei , Sung Yun-Shao , Suurmeijer Albert J.H. , Antonescu Cristina R.
Published: January 2018

Benign/low-grade fibroblastic tumors encompass a broad spectrum of tumors with different morphologies and molecular genetic abnormalities. However, despite significant progress in recent genomic characterization, there are still tumors in this histologic spectrum that are difficult to classify, lacking known molecular characteristics. Triggered by a challenging congenital spindle cell neoplasm arising in the heel of a 1-year-old boy, we applied RNA sequencing for genetic discovery and identified a novel EWSR1-SMAD3 gene fusion. On the basis of the index case superficial acral location and fibroblastic appearance with a nonspecific immunophenotype, we searched our files for similar cases and screened them by fluorescence in situ hybridization for these abnormalities. Thus an identical EWSR1-SMAD3 fusion was identified in 2 additional spindle cell tumors with similar clinicopathologic features. Both cases occurred in the feet of adult women (58 and 61 y old) and were characterized by distinctive nodular growth with zonation pattern of peripheral hypercellular areas arranged in short fascicles, transitioning to hypocellular central areas of hyalinization and infarction. Focal stippled calcification in the collagenous area was present in 1 case. All 3 tumors had similar immunoprofiles, being negative for SMA, CD34, CD31, and S100, but showing consistent ERG positivity of uncertain significance. Follow-up information was available in 2 patients who developed local recurrences after incomplete initial excisions, at 5 and 14 months, respectively. None developed metastatic disease. In summary, we report a group of locally recurrent superficial acral tumors, characterized by bland spindle cell fascicular growth, occasional zonation pattern, ERG positivity, and recurrent EWSR1-SMAD3 gene fusions.
Bone Marrow Involvement in Patients With Nodular Lymphocyte Predominant Hodgkin Lymphoma
Authors: Agbay Rose Lou Marie C. , Loghavi Sanam , Zuo Zhuang , Fayad Luis , Dabaja Bouthaina , Medeiros L. Jeffrey , Khoury Joseph D.
Published: January 2018

The spectrum of bone marrow lesions in patients with nodular lymphocyte predominant Hodgkin lymphoma (NLPHL) has not been evaluated systematically. In this study, we analyzed a cohort of 262 NLPHL patients who underwent staging bone marrow evaluation or targeted bone biopsy as a part of their initial diagnostic workup, among which lymphoma was detected in 24 (9.2%) patients. Eleven patients had bone marrow findings of NLPHL (few large B cells in a background of small B cell and T cell), and 13 patients had either T-cell/histiocyte-rich large B-cell lymphoma (large B cells in a background of T cells and histiocytes) or typical diffuse large B-cell lymphoma (sheets of large B cells). Bone marrow involvement was more common in patients with variant NLPHL histologic patterns in the lymph node as compared with those who had classic patterns (12/18 vs. 4/16; P=0.02). An additional 27 NLPHL patients had bone marrow specimens involved by lymphoid aggregates composed of small T cells and B cells without large B cells; this subgroup had a longer event-free survival than patients with lymphoma in the bone marrow (145 vs. 35 mo). Disease recurrence or progression was more frequent in patients with bone marrow involvement by either NLPHL or LBCL, compared with patients who had lymphoid aggregates (13/21 vs. 8/26; P=0.04). In conclusion, staging bone marrow sampling detects lymphoma in a sizeable subset of NLPHL patients, particularly those with variant histologic patterns. Lymphoid aggregates lacking large B cells in staging bone marrow specimens from NLPHL patients can be regarded as clinically benign without impact on stage, outcome, or risk stratification.
Comparison of Myocyte Enhancer Factor 2B Versus Other Germinal Center-associated Antigens in the Differential Diagnosis of B-Cell Non-Hodgkin Lymphomas
Authors: Moore Erika M. , Swerdlow Steven H. , Gibson Sarah E.
Published: January 2018

Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells. Limited data exists concerning its expression in B-cell lymphomas, and comparison with other GC-associated antigens is lacking. Its role in the differential diagnosis of B-cell lymphomas, particularly in the distinction of follicular lymphoma (FL) versus marginal zone lymphoma (MZL), remains to be determined. We evaluated MEF2B expression, in comparison with additional GC markers, LIM domain-only transcription factor 2 (LMO2), and human GC-associated lymphoma (HGAL), in a variety of B-cell lymphomas, with particular emphasis on their utility in differentiating FL from MZL. MEF2B was positive in all FL and Burkitt lymphomas, 8/9 mantle cell lymphomas, 2/24 splenic MZL, 1/10 chronic lymphocytic leukemia/small lymphocytic lymphomas, and 38/44 diffuse large B-cell lymphoma (DLBCL), but was negative in all extranodal MZL of mucosa-associated lymphoid tissue, nodal MZL, and B-lymphoblastic lymphomas. Focusing on low-grade FL versus MZL, MEF2B was 100% sensitive and 95% specific for FL, which was similar to BCL6, but superior to LMO2 (sensitivity 87%, specificity 86%) and HGAL (sensitivity 97%, specificity 86%). Importantly, MEF2B was positive in 4/4 FL with plasmacytoid differentiation, which were CD10−, only weakly BCL6+, and included 1 case that lacked both LMO2 and HGAL expression. MEF2B was positive in 22/25 (88%) GC-type DLBCL, but was also positive in 16/19 (61%) non–GC-type DLBCL. MEF2B shows superior sensitivity and specificity than LMO2 and HGAL in the differential diagnosis of FL versus MZL and is particularly useful in FL with plasmacytoid differentiation, which may have morphologic and immunophenotypic overlap with MZL. MEF2B, however, is not specific for GC-derived B-cell lymphomas as it is also apparently positive in most mantle cell lymphoma and many non–GC-type DLBCL.
High-grade Endometrioid Carcinoma of the Ovary
Authors: Assem Hisham , Rambau Peter F. , Lee Sandra , Ogilvie Travis , Sienko Anna , Kelemen Linda E. , Köbel Martin
Published: January 2018

Although infrequently encountered, the diagnosis of ovarian high-grade endometrioid carcinoma remains a diagnostic challenge with potential consequences for targeted therapies and genetic counselling. We studied the clinical, morphologic, and immunohistochemical features of ovarian high-grade endometrioid carcinomas and their diagnostic reproducibility compared with tuboovarian high-grade serous carcinomas. Thirty cases confirmed as International Federation of Gynecology and Obstetrics grade 3 endometrioid carcinomas were identified from 182 ovarian endometrioid carcinomas diagnosed in Alberta, Canada, between 1978 and 2010, from the population-based Alberta Ovarian Tumor Types cohort. Cases of lower grade endometrioid and high-grade serous carcinoma served for comparison. Ten immunohistochemical markers were assessed on tissue microarrays. Clinical data were abstracted and survival analyses performed using Cox regression. Interobserver reproducibility for histologic type was assessed using 1 representative hematoxylin and eosin–stained slide from 25 randomly selected grade 3 endometrioid carcinomas and 25 high-grade serous carcinomas. Histotype was independently assigned by 5 pathologists initially blinded to immunohistochemical WT1/p53 status, with subsequent reassessment unblinded to WT1/p53 status. Patients diagnosed with grade 3 endometrioid carcinoma had a significantly longer survival compared with high-grade serous carcinoma in univariate analysis (hazard ratio [HR]=0.34, 95% confidence interval [CI]=0.16-0.67, P=0.0012) but not after adjusting for age, stage, treatment center, and residual tumor (HR=1.01, 95% CI=0.43-2.16, P=0.98). Grade 3 endometrioid carcinoma cases (N=30) were identical to grade 2 endometrioid carcinoma cases (N=23) with respect to survival in univariate analysis (HR=1.07, 95% CI=0.39-3.21, P=0.89) and immunohistochemical profile. Using histomorphology alone, interobserver agreement for the diagnosis of grade 3 endometrioid or high-grade serous carcinoma was 69%, which significantly increased (P<0.0001) to 96% agreement with the knowledge of WT1/p53 status. Our data support the diagnostic value of WT1/p53 status in differentiating between grade 3 endometrioid carcinoma and high-grade serous carcinoma. However, grade 3 and grade 2 endometrioid carcinomas showed no differences in immunophenotype or clinical parameters, suggesting that they could be combined into a single group.
MoB (Measurement of Biodiversity): a method to separate the scale-dependent effects of species abundance distribution, density, and aggregation on diversity change
Authors: McGlinn Daniel J. , Xiao Xiao , May Felix , Gotelli Nicholas J. , Engel Thore , Blowes Shane A. , Knight Tiffany M. , Purschke Oliver , Chase Jonathan M. , McGill Brian J.
Published: January 2018

Little consensus has emerged regarding how proximate and ultimate drivers such as productivity, disturbance, and temperature may affect species richness and other aspects of biodiversity. Part of the confusion is that most studies examine species richness at a single spatial scale and ignore how the underlying components of species richness can vary with spatial scale.

We provide an approach for the measurement of biodiversity (MoB) that decomposes changes in species rarefaction curves into proximate components attributed to: 1) the species abundance distribution, 2) density of individuals, and 3) the spatial arrangement of individuals. We decompose species richness by comparing spatial and nonspatial sample- and individual-based species rarefaction curves that differentially capture the influence of these components to estimate the relative importance of each in driving patterns of species richness change.

We tested the validity of our method on simulated data, and we demonstrate it on empirical data on plant species richness in invaded and uninvaded woodlands. We integrated these methods into a new R package (mobr).

The metrics that mobr provides will allow ecologists to move beyond comparisons of species richness in response to ecological drivers at a single spatial scale towards a dissection of the proximate components that determine species richness across scales.