bluuebunny/crossref_metadata_2025 huggingface dataset:
The Prevalence of Cruciate Ligament and Meniscus Knee Injury in Young Adults and Associations with Gender, Body Mass Index, and Height a Large Cross-Sectional Study
Authors: Thein Ran , Gordon Barak , Burstein Gideon , Tenenbaum Shay , Derazne Estela , Tzur Dorit , Shamis Ari , Afek Arnon , Kreiss Yitshak , Hershkovich Oded
Published: November 2016

Anterior cruciate ligament and meniscal injuries are associated with secondary osteoarthrosis which may lead to functional impairment and economic burden. The prevalence of knee injury has not been studied in depth. Our purpose was to report the prevalence of knee ligament and meniscal injuries and their associations with gender, body mass index (BMI), and height in young adults and to characterize individuals with meniscal injuries who gained full recovery. A cross-sectional, population-based study was conducted. Information on the disability codes of knee ligament and meniscal injury according to the Regulations of Medical Fitness Determination was retrieved from a medical database containing records of young prerecruits into mandatory service. Logistic regression assessed the association between genders, BMI, and body height to knee injuries. A total of 825,187 subjects were included. Prevalence of knee injuries was 0.35%. Males had 2.2-fold more knee injuries than females. Increased BMI was associated with increased prevalence of knee injury in both genders, more significantly in females (overweight and obese females had an odds ratio of 1.406 and 1.519, respectively, to suffer from concomitant meniscal and ligamentous knee injury). Being underweight was associated with a lower prevalence of knee injury. An above normal BMI was more significantly associated with meniscal and/or ligament injuries that did not fully recover (females > males). Body height was associated with isolated meniscal injury in both genders. We found an association between BMI, body height, and knee injury in both males and females. Higher body height and higher BMI might be risk factors for knee injuries. Higher BMI was associated with greater probability of disability coding. Meniscal and ligament injuries are more common among males.
Dual hydrogen-bonding motifs in complexes formed between tropolone and formic acid
Authors: Nemchick Deacon J. , Cohen Michael K. , Vaccaro Patrick H.
Published: November 2016

The near-ultraviolet π*←π absorption system of weakly bound complexes formed between tropolone (TrOH) and formic acid (FA) under cryogenic free-jet expansion conditions has been interrogated by exploiting a variety of fluorescence-based laser-spectroscopic probes, with synergistic quantum-chemical calculations built upon diverse model chemistries being enlisted to unravel the structural and dynamical properties of the pertinent ground [X̃1A′] and excited [Ã1A′π*π] electronic states. For binary TrOH ⋅ FA adducts, the presence of dual hydrogen-bond linkages gives rise to three low-lying isomers designated (in relative energy order) as INT, EXT1, and EXT2 depending on whether docking of the FA ligand to the TrOH substrate takes place internal or external to the five-membered reaction cleft of tropolone. While the symmetric double-minimum topography predicted for the INT potential surface mediates an intermolecular double proton-transfer event, the EXT1 and EXT2 structures are interconverted by an asymmetric single proton-transfer process that is TrOH-centric in nature. The Ã−X̃ origin of TrOH ⋅ FA at ν̃00=27 484.45cm−1 is displaced by δν̃00=+466.76cm−1 with respect to the analogous feature for bare tropolone and displays a hybrid type − a/b rotational contour that reflects the configuration of binding. A comprehensive analysis of vibrational landscapes supported by the optically connected X̃1A′ and Ã1A′π*π manifolds, including the characteristic isotopic shifts incurred by partial deuteration of the labile TrOH and FA protons, has been performed leading to the uniform assignment of numerous intermolecular (viz., modulating hydrogen-bond linkages) and intramolecular (viz., localized on monomer subunits) degrees of freedom. The holistic interpretation of all experimental and computational findings affords compelling evidence that an external-binding motif (attributed to EXT1), rather than the thermodynamically more stable cleft-bound (INT) form, was the carrier of fluorescence signals observed during the present work.
Copper dry etching by sub-atmospheric-pressure pure hydrogen glow plasma
Authors: Ohmi Hiromasa , Sato Jumpei , Hirano Tatsuya , Kubota Yusuke , Kakiuchi Hiroaki , Yasutake Kiyoshi
Published: November 2016

Copper (Cu) dry etching is demonstrated using a narrow-gap hydrogen plasma generated at 13.3 kPa (100 Torr) for applications in the Cu wiring technology of integrated circuits. A localized hydrogen plasma is generated around the apex of a fine pipe electrode. The Cu etching can be observed only when the process gas contains hydrogen, and the etching rates decrease with decreased hydrogen concentration. The plasma heating effect owing to plasma localization is negligible for the Cu etching because no etching occurs in the presence of pure N2 plasma whose volume is almost equal to that of the pure H2 plasma. Furthermore, the influences of physical sputtering and vacuum ultraviolet irradiation on the Cu etching are confirmed to be insignificant by exposing the samples to rare-gas plasma. The maximum Cu etching rate of 500 nm/min can be achieved at a stage temperature of 0 °C. However, the Cu etching rate has no obvious dependence on the stage temperature in a range from −20 to 330 °C. In contrast, the etching rates for Si and SiO2 at a stage temperature of 0 °C are 100 μm/min and 50 nm/min, respectively. The Cu etching rate is 10 times higher than that of SiO2, which implies that this etching technique has potential applications for Cu wiring on an SiO2 layer. The Cu surface etched by the hydrogen plasma is roughened and exhibits many round pits and bumps, which seems to be owing to excessive incorporation of the diffused hydrogen in the Cu bulk.
Coherent absorption of light by graphene and other optically conducting
surfaces in realistic on-substrate configurations
Authors: Zanotto S. , Bianco F. , Miseikis V. , Convertino D. , Coletti C. , Tredicucci A.
Published: November 2016

Analytical formulas are derived describing the coherent absorption of light from a realistic multilayer structure composed by an optically conducting surface on a supporting substrate. The model predicts two fundamental results. First, the absorption regime named coherent perfect transparency theoretically can always be reached. Second, the optical conductance of the surface can be extrapolated from absorption experimental data even when the substrate thickness is unknown. The theoretical predictions are experimentally verified by analyzing a multilayer graphene structure grown on a silicon carbide substrate. The graphene thickness estimated through the coherent absorption technique resulted in good agreement with the values obtained by two other spectroscopic techniques. Thanks to the high spatial resolution that can be reached and high sensitivity to the probed structure thickness, coherent absorption spectroscopy represents an accurate and non-destructive diagnostic method for the spatial mapping of the optical properties of two-dimensional materials and of metasurfaces on a wafer scale.
Dynamic simulations show repeated narrowing maximizes DNA linearization in elastomeric nanochannels
Authors: Han Minsub , Kim Byoung Choul , Matsuoka Toshiki , Thouless M. D. , Takayama Shuichi
Published: November 2016

This paper uses computer simulations to reveal unprecedented details about linearization of deoxyribonucleic acid (DNA) inside dynamic nanochannels that can be repeatedly widened and narrowed. We first analyze the effect of rate of channel narrowing on DNA linearization dynamics. Quick (∼0.1 s) narrowing of nanoscale channels results in rapid overstretching of the semi-flexible chain followed by a slower (∼0.1–10 s) relaxation to an equilibrium extension. Two phenomena that induce linearization during channel narrowing, namely, elongational-flow and confinement, occur simultaneously, regardless of narrowing speed. Interestingly, although elongational flow is a minimum at the mid-point of the channel and increases towards the two ends, neither the linearization dynamics nor the degree of DNA extension varies significantly with the center-of-mass of the polymer projected on the channel axis. We also noticed that there was a significant difference in time to reach the equilibrium length, as well as the degree of DNA linearization at short times, depending on the initial conformation of the biopolymer. Based on these observations, we tested a novel linearization protocol where the channels are narrowed and widened repeatedly, allowing DNA to explore multiple conformations. Repeated narrowing and widening, something uniquely enabled by the elastomeric nanochannels, significantly decrease the time to reach the equilibrium-level of stretch when performed within periods comparable to the chain relaxation time and more effectively untangle chains into more linearized biopolymers.
Note: Attenuation motion of acoustically levitated spherical rotor
Authors: Lü P. , Hong Z. Y. , Yin J. F. , Yan N. , Zhai W. , Wang H. P.
Published: November 2016

Here we observe the attenuation motion of spherical rotors levitated by near-field acoustic radiation force and analyze the factors that affect the duration time of free rotation. It is found that the rotating speed of freely rotating rotor decreases exponentially with respect to time. The time constant of exponential attenuation motion depends mainly on the levitation height, the mass of rotor, and the depth of concave ultrasound emitter. Large levitation height, large mass of rotor, and small depth of concave emitter are beneficial to increase the time constant and hence extend the duration time of free rotation.
Role of sharp avoided crossings in short hyper-radial range in recombination of the cold 4He3 system
Authors: Wang Bin-Bin , Han Yong-Chang , Cong Shu-Lin
Published: November 2016

The role of sharp avoided crossings (SACs) in a short hyper-radial range R≤ 50 a.u. in the calculation of recombination for a cold 4He3 system is investigated in the adiabatic hyperspherical representation by “turning off and on” the relevant nonadiabatic couplings. The influence of SACs on the recombination is related with the channels of the system and with the scattering energy. For JΠ = 0+ symmetry, the two-body recombination channel has an attractive potential well, which makes radial wave functions of both two-body recombination channel and three-body continuum channels accessible in the short hyper-radial range where SACs are located. The SACs consequently play an important role in coupled-channel calculations and this is particularly the case for lower scattering energies. However, for excited nuclear orbital momenta, i.e., JΠ = 1−, 2+,…, 7− symmetries, the two-body recombination channel has a repulsive interaction and the radial wave functions are not accessible in the short hyper-radial range. Therefore, omission of SACs in the short range for these symmetries has no effect on the numerical results, which leads to great savings on hyper-radial grid points in the practical numerical calculations. Moreover, to make the nonadiabatic couplings among channels to be continuous in the hyper-radius, different methods associated with the application of consistent phase convention are discussed.
High-efficiency integrated readout circuit for single photon avalanche diode arrays in fluorescence lifetime imaging
Authors: Acconcia G. , Cominelli A. , Rech I. , Ghioni M.
Published: November 2016

In recent years, lifetime measurements by means of the Time Correlated Single Photon Counting (TCSPC) technique have led to a significant breakthrough in medical and biological fields. Unfortunately, the many advantages of TCSPC-based approaches come along with the major drawback of a relatively long acquisition time. The exploitation of multiple channels in parallel could in principle mitigate this issue, and at the same time it opens the way to a multi-parameter analysis of the optical signals, e.g., as a function of wavelength or spatial coordinates. The TCSPC multichannel solutions proposed so far, though, suffer from a tradeoff between number of channels and performance, and the overall measurement speed has not been increased according to the number of channels, thus reducing the advantages of having a multichannel system. In this paper, we present a novel readout architecture for bi-dimensional, high-density Single Photon Avalanche Diode (SPAD) arrays, specifically designed to maximize the throughput of the whole system and able to guarantee an efficient use of resources. The core of the system is a routing logic that can provide a dynamic connection between a large number of SPAD detectors and a much lower number of high-performance acquisition channels. A key feature of our smart router is its ability to guarantee high efficiency under any operating condition.
Modulation and filamentation instability of ultrarelativistic electromagnetic waves in electron-positron-ion plasma
Authors: Rozina Ch. , Tsintsade N. L. , Maryam N. , Komal S.
Published: November 2016

In this study, we have analytically investigated the effects of nonlinear Landau damping on the temporal growth rate of modulation and filamentation instabilities. Here, the nonlocal nonlinear Landau damping phenomena is appearing due to the nonlinear interaction between ultrarelativistic electromagnetic (UREM) wave (having wave vector normal to the beam) and electron-positron-ion plasma. We found that the ultrarelativistic ponderomotive force is linear, while usually it is nonlinear in relativistic case. We construct three dimensional kinetic nonlinear Schrödinger equation for a slowly varying spatio and temporal amplitude of UREM waves. The equations are then Fourier analyzed to obtain dispersion relation, which admit both modulation and filamentation instabilities. It is shown that nonlinear Landau damping is the main source of modulation instability, for a particular condition taking into account later one the maximum growth rate of modulation instability obtained as a function of amplitude of UREM waves and is displayed graphically. Further, it is shown that for an oscillating density profile, plane wave of uniform intensity becomes unstable and gets filamented. Growth rate of stationary state filament is found to be a function of amplitude of UREM waves and is emphasized that the maximum value of growth rate of filamentation instability is further increased in the presence of nonlinear Landau damping term. Finally, the growth rate of non stationary state filamentation instability is calculated and is shown that the characteristic growth length increases both with perpendicular wave vector and the amplitude of UREM waves.
Use of a probing pulsed magnetic field for determining plasma parameters
Authors: Rousskikh A. G. , Oreshkin V. I. , Zhigalin A. S. , Yushkov G. Yu.
Published: November 2016

A novel, simple, and readily usable method is proposed for measuring the electrical conductivity and temperature of a plasma. The method is based on the interaction of the test plasma with a pulsed magnetic field. The electric signals induced by the magnetic field in the circuits of two probes (miniature solenoids), one immersed in the test plasma and the other placed outside the plasma, provide data for estimating the plasma parameters. The method was verified experimentally by determining the parameters of the plasma flows generated in the cathode spots high-current pulsed vacuum arcs that were used to form cylindrical shells of bismuth Z-pinch plasma.
The impacts of magnetic field on repetitive nanosecond pulsed dielectric barrier discharge in air
Authors: Liu Yidi , Qi Haicheng , Fan Zhihui , Yan Huijie , Ren ChunSheng
Published: November 2016

In this paper, the impacts of the parallel magnetic field on the repetitive nanosecond pulsed dielectric barrier discharge (DBD) are experimentally investigated by optical and electrical measurements. The DBD is generated between two parallel-plate electrodes in the ambient air with the stationary magnetic field on the order of 1 T. The experimental results show that additional microdischarge channels are generated and the photocurrent intensity of the plasma is increased by the magnetic field. The microdischarge channels develop along the magnetic field lines and the diffuse background emission of the discharge is stronger in the DBD with the magnetic field. As the pulse repetition frequency decreases from 1200 Hz to 100 Hz, only the photocurrent intensity of the third discharge that occurred at about 500 ns is noticeably increased by the additional magnetic field. It is believed that the enhancement of the memory effect and the confinement of the magnetic field on electrons are the main reasons.
Experimental evidence of the anti-parallel arrangement of methylammonium ions in perovskites
Authors: Chen Yan-Fang , Tsai Yu-Tang , Bassani Dario M. , Hirsch Lionel
Published: November 2016

Orientation arrangement of methylammonium ions in hybrid organic−inorganic perovskite is still under debate because their tendency for alignment is expected to give rise to either ferroelectric or anti-ferroelectric behavior, which may influence the perovskite device performance. To resolve the debate surrounding the alignment of the organic cations in perovskite materials, we studied the dipole orientation by analysing the dielectric properties of the material. The dielectric permittivity has been investigated as a function of temperature with the data analysed using the Kirkwood–Fröhlich–Onsager theory. From these results, we provide experimental evidence of the anti-parallel arrangement of methylammonium ions in hybrid organic−inorganic perovskite.
Electronic properties and native point defects of high efficient NO oxidation catalysts SmMn2O5
Authors: Li Hao-Bo , Yang Zhi , Liu Jieyu , Yao Xiaolong , Xiong Ka , Liu Hui , Wang Wei-Hua , Lu Feng , Wang Weichao
Published: November 2016

Mn-based oxide SmMn2O5 exhibits great catalytic performance in NO oxidation [Wang et al., Science 337, 832 (2012)]. Nevertheless, the fundamental understanding of SmMn2O5 properties is so far not fully accessible. Here, the SmMn2O5 nanoparticles are synthesized through hydrothermal methods, and the pure phase of triclinic SmMn2O5 is characterized by high-resolution tunneling electron microscope and X-ray diffraction. Furthermore, the X-ray photoelectron spectroscopy, absorption, photoluminescence spectra (PL), and density functional theory based first-principles calculations are employed to explore the fundamental electronic structures of pristine and defective SmMn2O5. Combined with band structure calculations, light absorption, and PL spectra, we first show that SmMn2O5 presents an insulating behavior with an indirect band gap of ∼1.0 eV. Between the two types of crystal fields, i.e., octahedral and tetrahedral, the later one contributes to the dz2 of the valence band edge, resulting in superior catalytic performance of NO oxidation. Furthermore, the native point defects in SmMn2O5 are first reported. Among the various native point defects, we demonstrate that oxygen vacancy (VO) shows the lowest formation energy in oxygen poor conditions, while the oxygen interstitial (Oi) and Mn vacancies are energetically favorable in oxygen rich situations. In other words, SmMn2O5 could be potentially utilized as an oxygen storage material.
Edge-state-induced energy splitting of exciton triplet states in graphene nanoflakes
Authors: Lu Yan , Wei Sheng , Jin Jing , Lu Wengang , Wang Li
Published: November 2016

We explore the edge-state-induced exciton effects in graphene nanoflakes with various edges and shapes. The energy degeneracy of the three triplet excitons is preserved in hexagonal armchair-edged graphene nanoflakes and triangle armchair-edged graphene nanoflakes. However, this energy degeneracy is partly broken in hexagonal zigzag-edged graphene nanoflakes, because of the zigzag-edge-induced spin polarization and the antiferromagnetic coupling between nearest-neighboring edges. And the degeneracy is totally broken in triangle zigzag-edged graphene nanoflakes, due to the spin-polarized edge states and the ferromagnetic coupling between nearest neighboring edges in these systems.
Anomalous specific heats of metallic nanocrystals induced by surface oxidation
Authors: Lei Haile , Luo Jiangshan , Li Jun , Dai Fei , Yang Mengsheng , Zhang Jicheng , Zhang Jingmin
Published: November 2016

Although the low-temperature specific heat in metallic nanocrystals has been extensively demonstrated to be always enhanced due to the surface phonon softening, it is revealed here to be anomalously depressed by the surface oxidation so that the excess specific heat can be either positive or negative as a function of temperature with respect to the counterparts of the bulk crystals. The background mechanism has been theoretically deduced to well explain these experimental phenomena by calculating and comparing the vibrational densities of states (VDOS) of face-centered-cubic-aluminum (fcc-Al) and amorphous-alumina (a-Al2O3) nanoparticles. Different from fcc-Al nanocrystals, both the surface and volume VDOSs g(ω) of a-Al2O3 nanoparticles are scaled as g(ω) ∼ ω1.5 at the low-frequency limit (ω). The effective spatial dimension for the a-Al2O3 surfaces and volume as well as the fcc-Al surfaces is thus assumed to be between 2D and 3D while it is 3D for the fcc-Al volume. The specific heat of a-Al2O3@Al nanoparticles is consequently revealed to show a different T-dependent feature from those of both pure metallic nanocrystals and bulk crystals at low temperatures.
Verification of micrometeorologically determined nitrous oxide fluxes following controlled release from pasture
Authors: Harvey M. J. , Nichol S. E. , McMillan A. M. S. , Martin R. J. , Evans M. J. , Bromley A. M.
Published: November 2016

We have developed a high-precision micrometeorological system capable of measuring emissions of nitrous oxide (N2O) from up to four adjacent pasture plots. The system can be used to compare the influence of environmental factors and management practice on N2O emissions at the paddock scale. The system is capable of determining a minimum detectable N2O difference of the order of 40 pmol/mol, with an ability to resolve flux differences among plots of ~26 µg (N2O-N)/m2.h. So as to independently verify the emission estimates of the micrometeorological system, we developed a calibrated N2O-release system and compared known release rates with the micrometeorological flux estimates. Adjustable release rates up to the equivalent average surface flux of ~500 µg (N2O-N)/m2.h were achieved using mass flow-controlled input of pure N2O in a compressed air stream over two 1.5-ha plots upwind of flux-measurement masts. The comparison of network release rate with measured emission rate was quite variable and complicated by a significant and varying background emissions of N2O from the soil. For optimal steady-wind cases, the ratio of uncorrected measured flux to known release, including the estimated background, was of the order of 0.4–0.5; this ratio is likely to be influenced by the turbulent Schmidt number. Flux estimates for uncorrected flux gradient and WindTrax backward Lagrangian Stochastic method (which includes Schmidt correction) agreed well with a ratio of 0.54. The experiment highlighted the need for accurate estimates of gas eddy diffusivity in the micrometeorological gradient or difference-based flux measurement of N2O.
Warming alters the positive impact of elevated CO2 concentration on cotton growth and physiology during soil water deficit
Authors: Broughton Katrina J. , Smith Renee A. , Duursma Remko A. , Tan Daniel K. Y. , Payton Paxton , Bange Michael P. , Tissue David T.
Published: November 2016

Alterations in climate factors such as rising CO2 concentration ([CO2]), warming and reduced precipitation may have significant impacts on plant physiology and growth. This research investigated the interactive effects of elevated [CO2], warming and soil water deficit on biomass production, leaf-level physiological responses and whole-plant water use efficiency (WUEP) in cotton (Gossypium hirsutum L.). Cotton was grown in the glasshouse under two [CO2] treatments (CA, 400 µL L–1; CE, 640 µL L–1) and two temperature treatments (TA, 28°C : 17°C day : night; TE, 32°C : 21°C day : night). Plants were subjected to two progressive water deficit cycles, with a 5-day recovery period between the water deficit periods. CE increased vegetative biomass and photosynthetic rates, and decreased stomatal conductance in TA; however, these responses to CE were not evident under TE. CE increased whole-plant water loss under TA, but increased WUEp, whereas increased whole-plant water loss in TE decreased WUEp regardless of atmospheric [CO2]. CE may provide some positive growth and physiological benefits to cotton at TA if sufficient water is available but CE will not mitigate the negative effects of rising temperature on cotton growth and physiology in future environments.
Optically transparent semiconducting polymer nanonetwork for flexible and transparent electronics
Authors: Yu Kilho , Park Byoungwook , Kim Geunjin , Kim Chang-Hyun , Park Sungjun , Kim Jehan , Jung Suhyun , Jeong Soyeong , Kwon Sooncheol , Kang Hongkyu , Kim Junghwan , Yoon Myung-Han , Lee Kwanghee
Published: November 2016

Significance

When various electronic appliances used in everyday life become deformable and transparent, they will provide tremendous versatility in the design and use of see-through, smart mobile applications, exceeding the limitations of the best developed conventional silicon technologies, which are available only in rigid, opaque forms. However, even recently discovered innovative semiconducting components have failed to simultaneously achieve such flexibility and transparency. Thus, the existing options still comprise only hard, planar, or opaque materials, and obtaining a “key” material for creating truly flexible and transparent electronics has presented a formidable challenge. We report an effective means of creating a “truly flexible, perfectly transparent” and high-mobility semiconducting material and demonstrate several high-end flexible and transparent applications based on a polymeric semiconductor system.
Transcriptomics and neuroanatomy of the clonal raider ant implicate an expanded clade of odorant receptors in chemical communication
Authors: McKenzie Sean K. , Fetter-Pruneda Ingrid , Ruta Vanessa , Kronauer Daniel J. C.
Published: November 2016

Significance

Despite the importance of sociality in the evolutionary history of life, its molecular basis is still poorly understood. The role of novel genes vs. conserved genes is particularly hotly debated. Here we present evidence that a group of 180 odorant receptor genes in the clonal raider ant are expressed in neurons that have been shown to detect cuticular hydrocarbons, one of the most important classes of ant chemical signals. We show that these genes underwent a period of rapid gene duplication in the ancestors of ants and now comprise 0.5%–1.5% of all genes in ant genomes. This discovery provides a striking example of the importance of novel genes in social evolution.
Mechanical bounds to transcriptional noise
Authors: Sevier Stuart A. , Kessler David A. , Levine Herbert
Published: November 2016

Significance

A complete understanding of transcription, which is the first process in the central dogma of biology, is of paramount importance for understand the living world. Many genes transcribe in a significantly noisy or bursty manner, and the understanding of this phenomenon has been the subject of much experimental and theoretical research. In this article, we present work that introduces mechanical feedback as the source of bursting through an intrinsically ordered stochastic process. The resulting statistical properties of gene expression contain a number of previously unexplained universal features of the central dogma.
Evaluating the evaluation of cancer driver genes
Authors: Tokheim Collin J. , Papadopoulos Nickolas , Kinzler Kenneth W. , Vogelstein Bert , Karchin Rachel
Published: November 2016

Significance

Modern large-scale sequencing of human cancers seeks to comprehensively discover mutated genes that confer a selective advantage to cancer cells. Key to this effort has been development of computational algorithms to find genes that drive cancer based on their patterns of mutation in large patient cohorts. Because there is no generally accepted gold standard of driver genes, it has been difficult to quantitatively compare these methods. We present a machine-learning–based method for driver gene prediction and a protocol to evaluate and compare prediction methods. Our results suggest that most current methods do not adequately account for heterogeneity in the number of mutations expected by chance and consequently yield many false-positive calls, particularly in cancers with high mutation rate.
Perceived time slows during fleeting fun or fear
Authors: Corke Mike , Bell Jason , Goodhew Stephanie C. , Smithson Michael , Edwards Mark
Published: November 2016

Previous psychophysical studies at durations greater than 1000 ms have confirmed the anecdotal reports of an increase in the perceived duration of both positively and negatively valenced emotive stimuli; however, the results of studies at durations less than 1000 ms have been inconsistent. This study further investigated the effect of valence on the perception of durations less than 1000 ms. We used both positively and negatively valenced stimuli in order to compare their effects on the distortion of duration, and we tested multiple data points within the sub-one-second range. We found an increase in the perceived duration of both positively and negatively valenced emotional stimuli at all data points. This is consistent with studies at durations longer than 1000 ms and also with models of temporal processing. We also confirmed that Weber fractions, within the range tested, followed the generalized form of Weber’s law.
A GPI processing phospholipase A2, PGAP6, modulates Nodal signaling in embryos by shedding CRIPTO
Authors: Lee Gun-Hee , Fujita Morihisa , Takaoka Katsuyoshi , Murakami Yoshiko , Fujihara Yoshitaka , Kanzawa Noriyuki , Murakami Kei-ichi , Kajikawa Eriko , Takada Yoko , Saito Kazunobu , Ikawa Masahito , Hamada Hiroshi , Maeda Yusuke , Kinoshita Taroh
Published: November 2016

Glycosylphosphatidylinositol-anchored proteins (GPI-APs) can be shed from the cell membrane by GPI cleavage. In this study, we report a novel GPI-processing enzyme, termed post-glycosylphosphatidylinositol attachment to proteins 6 (PGAP6), which is a GPI-specific phospholipase A2 mainly localized at the cell surface. CRIPTO, a GPI-AP, which plays critical roles in early embryonic development by acting as a Nodal coreceptor, is a highly sensitive substrate of PGAP6, whereas CRYPTIC, a close homologue of CRIPTO, is not sensitive. CRIPTO processed by PGAP6 was released as a lysophosphatidylinositol-bearing form, which is further cleaved by phospholipase D. CRIPTO shed by PGAP6 was active as a coreceptor in Nodal signaling, whereas cell-associated CRIPTO activity was reduced when PGAP6 was expressed. Homozygous Pgap6 knockout mice showed defects in early embryonic development, particularly in the formation of the anterior–posterior axis, which are common features with Cripto knockout embryos. These results suggest PGAP6 plays a critical role in Nodal signaling modulation through CRIPTO shedding.
The Monge-Ampère equation for (𝑛-1)-plurisubharmonic functions on a compact Kähler manifold
Authors: Tosatti Valentino , Weinkove Ben
Published: November 2016

A

C
2

C^2

function on

C

n

\mathbb {C}^n

is called

(
n
−
1
)

(n-1)

-plurisubharmonic in the sense of Harvey-Lawson if the sum of any

n
−
1

n-1

eigenvalues of its complex Hessian is non-negative. We show that the associated Monge-Ampère equation can be solved on any compact Kähler manifold. As a consequence we prove the existence of solutions to an equation of Fu-Wang-Wu, giving Calabi-Yau theorems for balanced, Gauduchon, and strongly Gauduchon metrics on compact Kähler manifolds.
Lipid disequilibrium disrupts ER proteostasis by impairing ERAD substrate glycan trimming and dislocation
Authors: To Milton , Peterson Clark W. H. , Roberts Melissa A. , Counihan Jessica L. , Wu Tiffany T. , Forster Mercedes S. , Nomura Daniel K. , Olzmann James A.
Published: November 2016

The endoplasmic reticulum (ER) mediates the folding, maturation, and deployment of the secretory proteome. Proteins that fail to achieve their native conformation are retained in the ER and targeted for clearance by ER-associated degradation (ERAD), a sophisticated process that mediates the ubiquitin-dependent delivery of substrates to the 26S proteasome for proteolysis. Recent findings indicate that inhibition of long-chain acyl-CoA synthetases with triacsin C, a fatty acid analogue, impairs lipid droplet (LD) biogenesis and ERAD, suggesting a role for LDs in ERAD. However, whether LDs are involved in the ERAD process remains an outstanding question. Using chemical and genetic approaches to disrupt diacylglycerol acyltransferase (DGAT)–dependent LD biogenesis, we provide evidence that LDs are dispensable for ERAD in mammalian cells. Instead, our results suggest that triacsin C causes global alterations in the cellular lipid landscape that disrupt ER proteostasis by interfering with the glycan trimming and dislocation steps of ERAD. Prolonged triacsin C treatment activates both the IRE1 and PERK branches of the unfolded protein response and ultimately leads to IRE1-dependent cell death. These findings identify an intimate relationship between fatty acid metabolism and ER proteostasis that influences cell viability.
The polycystins are modulated by cellular oxygen-sensing pathways and regulate mitochondrial function
Authors: Padovano Valeria , Kuo Ivana Y. , Stavola Lindsey K. , Aerni Hans R. , Flaherty Benjamin J. , Chapin Hannah C. , Ma Ming , Somlo Stefan , Boletta Alessandra , Ehrlich Barbara E. , Rinehart Jesse , Caplan Michael J.
Published: November 2016

Autosomal dominant polycystic kidney disease is caused by mutations in the genes encoding polycystin-1 (PC1) and polycystin-2 (PC2), which form an ion channel complex that may mediate ciliary sensory processes and regulate endoplasmic reticulum (ER) Ca2+ release. Loss of PC1 expression profoundly alters cellular energy metabolism. The mechanisms that control the trafficking of PC1 and PC2, as well as their broader physiological roles, are poorly understood. We found that O2 levels regulate the subcellular localization and channel activity of the polycystin complex through its interaction with the O2-sensing prolyl hydroxylase domain containing protein EGLN3 (or PHD3), which hydroxylates PC1. Moreover, cells lacking PC1 expression use less O2 and show less mitochondrial Ca2+ uptake in response to bradykinin-induced ER Ca2+ release, indicating that PC1 can modulate mitochondrial function. These data suggest a novel role for the polycystins in sensing and responding to cellular O2 levels.
PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS
Authors: Chen Feng , Wang Shuang , Jiang Xiaoqian , Ding Sijie , Lu Yao , Kim Jihoon , Sahinalp S Cenk , Shimizu Chisato , Burns Jane C , Wright Victoria J , Png Eileen , Hibberd Martin L , Lloyd David D , Yang Hai , Telenti Amalio , Bloss Cinnamon S , Fox Dov , Lauter Kristin , Ohno-Machado Lucila
Published: November 2016

Motivation

We introduce PRINCESS, a privacy-preserving international collaboration framework for analyzing rare disease genetic data that are distributed across different continents. PRINCESS leverages Software Guard Extensions (SGX) and hardware for trustworthy computation. Unlike a traditional international collaboration model, where individual-level patient DNA are physically centralized at a single site, PRINCESS performs a secure and distributed computation over encrypted data, fulfilling institutional policies and regulations for protected health information.

Results

To demonstrate PRINCESS’ performance and feasibility, we conducted a family-based allelic association study for Kawasaki Disease, with data hosted in three different continents. The experimental results show that PRINCESS provides secure and accurate analyses much faster than alternative solutions, such as homomorphic encryption and garbled circuits (over 40 000× faster).

Availability and Implementation

https://github.com/achenfengb/PRINCESS_opensource

Supplementary information

Supplementary data are available at Bioinformatics online.
Screening for medication errors using an outlier detection system
Authors: Schiff Gordon D , Volk Lynn A , Volodarskaya Mayya , Williams Deborah H , Walsh Lake , Myers Sara G , Bates David W , Rozenblum Ronen
Published: November 2016

Objective: The study objective was to evaluate the accuracy, validity, and clinical usefulness of medication error alerts generated by an alerting system using outlier detection screening.

Materials and Methods: Five years of clinical data were extracted from an electronic health record system for 747 985 patients who had at least one visit during 2012–2013 at practices affiliated with 2 academic medical centers. Data were screened using the system to detect outliers suggestive of potential medication errors. A sample of 300 charts was selected for review from the 15 693 alerts generated. A coding system was developed and codes assigned based on chart review to reflect the accuracy, validity, and clinical value of the alerts.

Results: Three-quarters of the chart-reviewed alerts generated by the screening system were found to be valid in which potential medication errors were identified. Of these valid alerts, the majority (75.0%) were found to be clinically useful in flagging potential medication errors or issues.

Discussion: A clinical decision support (CDS) system that used a probabilistic, machine-learning approach based on statistically derived outliers to detect medication errors generated potentially useful alerts with a modest rate of false positives. The performance of such a surveillance and alerting system is critically dependent on the quality and completeness of the underlying data.

Conclusion: The screening system was able to generate alerts that might otherwise be missed with existing CDS systems and did so with a reasonably high degree of alert usefulness when subjected to review of patients’ clinical contexts and details.
The Impact of a National Faculty Development Program Embedded Within an Academic Professional Organization
Authors: Baldwin Constance D. , Gusic Maryellen E. , Chandran Latha
Published: November 2016

A sizeable literature describes the effectiveness of institution-based faculty development programs in nurturing faculty educators as scholars, but national programs are less common and seldom evaluated. To fill this role, the Educational Scholars Program (ESP) was created within the Academic Pediatric Association (APA) in 2006. It is a national, three-year, cohort-based certification program focused on fostering educational scholarship. This article describes the development and outcomes of an innovative program embedded within the framework of a national professional organization, and offers a model for potential adaptation by similar organizations to enhance their support of educators.

After 10 years, 171 scholars have enrolled in the ESP, and 50 faculty have participated. Scholars are assigned a faculty advisor and participate in three full-day sessions at a national meeting; online, interactive learning modules; and a mentored, scholarly project. The program receives support from the APA in four organizational frames: structural, human resource, political, and symbolic. The self-perceived scholarly proficiency of the scholars in Cohort 1 increased significantly over time, and their productivity and collaborations increased during and after the program. Scholars wrote enthusiastically about their experience in yearly and postprogram evaluations. In interviews, eight past APA presidents explained that the ESP strengthened the APA’s mission, created new leaders, and provided a new model for other APA programs. Outcomes of the ESP suggest that a longitudinal faculty development program embedded within a national professional organization can create a social enterprise not only within the organization but also within the broader national community of educator–scholars.
B-Type Natriuretic Peptide Predicts Morbidity and Long-Term Mortality in Coronary Artery Bypass Grafting and Valve Surgery
Authors: Endicott Kendal M. , Amdur Richard L. , Greenberg Michael D. , Trachiotis Gregory D.
Published: November 2016

Objective

To assess whether B-type natriuretic peptide (BNP) levels are a useful predictor of morbidity and mortality as well as long-term survival in patients after coronary artery bypass grafting (CABG) and valve surgery.

Methods

A retrospective review of CABG and/or valve surgery patients from 2012 to 2015 at a single center was conducted. A total of 432 patients were identified (CABG, 295 patients; valve, 82 patients; and CABG + valve, 55 patients). B-type natriuretic peptide levels were divided into quartiles (Q1-Q4). Mortality data were available for up to 3.4 years after surgery.

Results

B-type natriuretic peptide quartile was independently associated with any complication on multivariate analysis. Patients in Q4 were at highest risk (adjusted odds ratio, 3.81; P = 0.047 vs Q1). There was a significant association between BNP quartile and time to death (logrank χ2, 8.30; P = 0.04) with greatest association 9 months postoperatively. B-type natriuretic peptide quartile was significantly associated with time to death in Cox regression in Q2 (hazard ratio [HR], 3.73 (1.04–13.44); P = 0.044) and Q4 (HR, 4.33 (1.14–16.44); P = 0.031). Q3 also had a higher risk of death (HR, 3.5 vs Q1); however, this was only significant at a trend level (P = 0.06). Using a risk model generated from logistic regression, we determined that the highest risk group had relative risk of complications 30 times higher than the lowest risk group.

Conclusions

B-type natriuretic peptide levels are an independent predictor of morbidity after CABG and/or valve surgery regardless of type of procedure or on/off bypass usage. B-type natriuretic peptide levels also correlate with time to death, highlighting the need for sustained follow-up and heart failure management to improve survival in patients with elevated BNP levels presenting for all cardiac surgery.
Recurrent Orbital Inflammation Mimicking Orbital Cellulitis Associated With Orbitopalpebral Venous Lymphatic Malformation
Authors: Galindo-Ferreiro Alicia , Alkatan Hind M. , ElKhamary Sahar M. , AlDosairi Saif , Cruz A. Augusto V.
Published: November 2016

An 8-year-old boy initially presented with an orbitopalpebral mass diagnosed clinically and radiologically as a low-flow diffuse venous lymphatic malformation involving the left upper eyelid and orbit. Over 8 months of follow up, he had 2 acute episodes of severe orbital inflammation that warranted hospitalization and treatment with intravenous antibiotic, steroids and surgical debulking. After a third surgical excision, the lesion remained clinically stable.
Bloody Epiphora (Hemolacria) Years After Repair of Orbital Floor Fracture
Authors: Chon Brian H. , Zhang Rui , Bardenstein David S. , Coffey Michael , Collins Atif C.
Published: November 2016

Surgical repair of orbital fractures with implants is a widely used treatment modality. While a variety of established complications are associated with this technique, most are directly understood and treated. Bloody epiphora is a finding with potentially ominous causes. The authors present a unique case of bloody epiphora, accompanied by orbital hemorrhage arising several years after orbital floor fracture repair, due to erosion of the nasolacrimal drainage system by a displaced implant combined with anticoagulation. The collection and evaluation of all protected patient health information was compliant with the regulations and conditions set forth in the Health Insurance Portability and Availability Act of 1996.
Agreement between arterial and venous lactate in emergency department patients: a prospective study of 157 consecutive patients
Authors: Paquet Anne-Laure , Valli Vanina , Philippon Anne-Laure , Devilliers Catherine , Bloom Ben , Hausfater Pierre , Riou Bruno , Freund Yonathan
Published: November 2016

Introduction

In the emergency department (ED), lactate is routinely used for risk stratification. Whether venous or arterial lactate measured on blood gas is interchangeable is not known. We hypothesized that venous lactate can be used instead of arterial lactate for the evaluation of acute patients in the ED.

Patients and methods

This was a prospective single-center study. All patients requiring a lactate measurement were enrolled and we simultaneously drew arterial and venous blood. We followed up all patients to hospital discharge. Our primary aim was to evaluate agreements between the two measurements using Bland and Altman plots with the report of bias (mean difference) and limits of agreements. We also aimed to determine the rate of misclassification (defined as one measurement<1.8 mmol/l and the other>2.2). Our secondary aim was to evaluate their respective prognostic value to predict in-hospital death or admission in the ICU longer than 72 h.

Results

The mean age of the 132 analyzed patients was 62 years (SD: 18 years), and 59% were men. The mean difference (bias) between arterial and venous lactate was −0.6 mmol/l (limits of agreement: −1.7 to 0.6 mmol/l). The rate of misclassification was 8% (95% confidence interval: 3–2%). Both methods present similar performances for the prediction of poor outcomes, with an area under the receiving operator characteristic curves of 0.67 for both. Results were similar when focused only on septic patients.

Conclusion

Venous and arterial lactates do not agree well, and there is a high misclassification rate. Venous lactate does not appear to be interchangeable with arterial sampling.
Clinically Mild Encephalitis/Encephalopathy With a Reversible Splenial Lesion Accompanied by Epstein-Barr Virus Hemophagocytic Lymphohistiocytosis: A Case Report and Review of the Literature
Authors: Yamaguchi Hiroshi , Ishida Toshiaki , Yokoi Takehito , Tanaka Tsukasa , Maruyama Azusa , Nagase Hiroaki , Hasegawa Daiichiro , Imadome Ken-Ichi , Takeda Hiroki , Kosaka Yoshiyuki , Uetani Yoshiyuki
Published: November 2016

Central nervous system involvement in hemophagocytic lymphohistiocytosis (HLH) is associated with a poor outcome. For such patients, it is unknown whether more aggressive therapies, such as intrathecal methotrexate or hydrocortisone, are inevitably required. We present a very rare case of 3-year-old Japanese girl who developed mild encephalitis/encephalopathy with a reversible splenial lesion, accompanied by Epstein-Barr virus–associated HLH, and review previous similar reports. Our case and previous reports suggest that mild encephalitis/encephalopathy with a reversible splenial lesion accompanied by Epstein-Barr virus–associated HLH has a relatively good prognosis, even in the absence of intrathecal treatments.