bluuebunny/crossref_metadata_2025 huggingface dataset:
Flexible and air-stable perovskite network photodetectors based on CH3NH3PbI3/C8BTBT bulk heterojunction
Authors: Xia Huayan , Tong Sichao , Zhang Chujun , Wang Chunhua , Sun Jia , He Jun , Zhang Jian , Gao Yongli , Yang Junliang
Published: June 2018

Flexible perovskite network photodetectors based on the bulk heterojunction (BHJ) of CH3NH3PbI3 and an organic semiconductor dioctylbenzothieno [2,3-b] benzothiophene (C8BTBT) have been fabricated via a simple, one-step solution process. The responsivity, detectivity, and response time as the critical parameters of CH3NH3PbI3/C8BTBT BHJ network photodetectors reach 8.1 AW−1, 2.17 × 1012 Jones, and 7.1 ms, respectively. Meanwhile, they can maintain over 70% of original performance even when exposed to ambient conditions (humidity ∼ 45%) for 50 days without encapsulation. Furthermore, the CH3NH3PbI3/C8BTBT BHJ network photodetectors fabricated on a polyethylene terephthalate (PET) substrate exhibit superior flexibility at different bending radii and large numbers of bending cycles. The photocurrent just shows a decrease of less than 5% as the devices are bent for 10 000 cycles at a small radius of 7.5 mm. The present research indicates that BHJ networks composed of perovskites and organic semiconductors open up the exciting opportunity for fabricating high-performance, low-cost, flexible electronic and optoelectronic devices.
Force-induced rupture of double-stranded DNA in the absence and presence of covalently bonded anti-tumor drugs: Insights from molecular dynamics simulations
Authors: Upadhyaya Anurag , Nath Shesh , Kumar Sanjay
Published: June 2018

DNA intra-strand cross-link (ICL) agents are widely used in the treatment of cancer. ICLs are thought to form a link between the same strand (intra-strand) or complimentary strand (inter-strand) and thereby increase the stability of DNA, which forbids the processes like replication and transcription. As a result, cell death occurs. In this work, we have studied the enhanced stability of a double stranded DNA in the presence of ICLs and compared our findings with the results obtained in the absence of these links. Using atomistic simulations with explicit solvent, a force is applied along and perpendicular to the direction of the helix and we measured the rupture force and the unzipping force of DNA-ICL complexes. Our results show that the rupture and the unzipping forces increase significantly in the presence of these links. The ICLs bind to the minor groove of DNA, which enhance the DNA stabilisation. Such information may be used to design alternative drugs that can stall replication and transcription that are critical to a growing number of anticancer drug discovery efforts.
Occlusion and rupture of ex vivo capillary bifurcation due to acoustic droplet vaporization
Authors: Feng Yi , Qin Dui , Zhang Jun , Zhang Lei , Bouakaz Ayache , Wan Mingxi
Published: June 2018

Gas embolotherapy (GE) consists in the occlusion of tumor blood vessels using gas emboli induced by acoustic droplet vaporization (ADV), to create tumor starvation and localized drug delivery. Therefore, the occlusion and rupture of capillary bifurcation due to ADV was investigated in an ex vivo rat mesentery model using a confocal acousto-optical high-speed microscope system. Following ADV bubble formation, coalescence, and translational movement, the growing bubbles lodged in and then occluded two different capillary bifurcations. Capillary rupture was induced at the bubble lodging area, immediately followed by gas extravasation and bubble dislodging. Before and after bubble lodgment/occlusion, a local microvessel invagination was observed due to the interactions between ADV bubbles and the microvessel itself, indicating a contribution to the capillary rupture. Understanding the transient dynamics of ADV bubble, the bubble–microvessel interaction and the consequent mechanical bio-effects in GE is of the paramount importance for developing and applying this approach in clinical practice.
Unexpected finite size effects in interfacial systems: Why bigger is not always better—Increase in uncertainty of surface tension with bulk phase width
Authors: Longford Francis G. J. , Essex Jonathan W. , Skylaris Chris-Kriton , Frey Jeremy G.
Published: June 2018

We present an unexpected finite size effect affecting interfacial molecular simulations that is proportional to the width-to-surface-area ratio of the bulk phase Ll/A. This finite size effect has a significant impact on the variance of surface tension values calculated using the virial summation method. A theoretical derivation of the origin of the effect is proposed, giving a new insight into the importance of optimising system dimensions in interfacial simulations. We demonstrate the consequences of this finite size effect via a new way to estimate the surface energetic and entropic properties of simulated air-liquid interfaces. Our method is based on macroscopic thermodynamic theory and involves comparing the internal energies of systems with varying dimensions. We present the testing of these methods using simulations of the TIP4P/2005 water forcefield and a Lennard-Jones fluid model of argon. Finally, we provide suggestions of additional situations, in which this finite size effect is expected to be significant, as well as possible ways to avoid its impact.
Time-resolved optical emission spectroscopic studies of picosecond laser produced Cr plasma
Authors: Rao Kavya H. , Smijesh N. , Klemke N. , Philip R. , Litvinyuk I. V. , Sang R. T.
Published: June 2018

Time-resolved optical emission spectroscopic measurements of a plasma generated by irradiating a Cr target using 60 picosecond (ps) and 300 ps laser pulses are carried out to investigate the variation in the line width (δλ) of emission from neutrals and ions for increasing ambient pressures. Measurements ranging from 10−6 Torr to 102 Torr show a distinctly different variation in the δλ of neutrals (Cr I) compared to that of singly ionized Cr (Cr II), for both irradiations. δλ increases monotonously with pressure for Cr II, but an oscillation is evident at intermediate pressures for Cr I. This oscillation does not depend on the laser pulse widths used. In spite of the differences in the plasma formation mechanisms, it is experimentally found that there is an optimum intermediate background pressure for which δλ of neutrals drops to a minimum. Importantly, these results underline the fact that for intermediate pressures, the usual practice of calculating the plasma number density from the δλ of neutrals needs to be judiciously done, to avoid reaching inaccurate conclusions.
A multiscale model for charge inversion in electric double layers
Authors: Mashayak S. Y. , Aluru N. R.
Published: June 2018

Charge inversion is a widely observed phenomenon. It is a result of the rich statistical mechanics of the molecular interactions between ions, solvent, and charged surfaces near electric double layers (EDLs). Electrostatic correlations between ions and hydration interactions between ions and water molecules play a dominant role in determining the distribution of ions in EDLs. Due to highly polar nature of water, near a surface, an inhomogeneous and anisotropic arrangement of water molecules gives rise to pronounced variations in the electrostatic and hydration energies of ions. Classical continuum theories fail to accurately describe electrostatic correlations and molecular effects of water in EDLs. In this work, we present an empirical potential based quasi-continuum theory (EQT) to accurately predict the molecular-level properties of aqueous electrolytes. In EQT, we employ rigorous statistical mechanics tools to incorporate interatomic interactions, long-range electrostatics, correlations, and orientation polarization effects at a continuum-level. Explicit consideration of atomic interactions of water molecules is both theoretically and numerically challenging. We develop a systematic coarse-graining approach to coarse-grain interactions of water molecules and electrolyte ions from a high-resolution atomistic scale to the continuum scale. To demonstrate the ability of EQT to incorporate the water orientation polarization, ion hydration, and electrostatic correlations effects, we simulate confined KCl aqueous electrolyte and show that EQT can accurately predict the distribution of ions in a thin EDL and also predict the complex phenomenon of charge inversion.
Partial compensation interferometry measurement system for parameter errors of conicoid surface
Authors: Hao Qun , Li Tengfei , Hu Yao , Wang Shaopu , Ning Yan , Chen Zhuo
Published: June 2018

Surface parameters, such as vertex radius of curvature and conic constant, are used to describe the shape of an aspheric surface. Surface parameter errors (SPEs) are deviations affecting the optical characteristics of an aspheric surface. Precise measurement of SPEs is critical in the evaluation of optical surfaces. In this paper, a partial compensation interferometry measurement system for SPE of a conicoid surface is proposed based on the theory of slope asphericity and the best compensation distance. The system is developed to measure the SPE-caused best compensation distance change and SPE-caused surface shape change and then calculate the SPEs with the iteration algorithm for accuracy improvement. Experimental results indicate that the average relative measurement accuracy of the proposed system could be better than 0.02% for the vertex radius of curvature error and 2% for the conic constant error.
A fast response, low heat generating activation method for LHe level sensors
Authors: Choudhury Anup , Sahu Santosh , Kanjilal Dinakar
Published: June 2018

A superconducting liquid helium (LHe) level sensor of length 300 mm has been fabricated based on the principle of differential heat transfer characteristic in helium gas compared to that in liquid. The sensor wire used has a diameter of 38 μm, and the wire was obtained from a pack of multifilament wires. A full thermo-electrical characterisation of the sensor was carried out in a dedicated setup. Its dynamic thermal response was also studied to understand its timing characteristics at different liquid levels and excitation currents. Based on the sensor characterisation, a new level measurement technique is evaluated which can reduce the heat load going to LHe during sensor activation without compromising on its sensitivity or accuracy. The timing response with this technique will make the level detection faster compared to the conventional techniques.
Determining the confined optical length of high index vertical Si nanoforest arrays for photonic applications
Authors: Chaliyawala Harsh A. , Purohit Zeel , Khanna Sakshum , Ray Abhijit , Pati Ranjan K. , Mukhopadhyay Indrajit
Published: June 2018

The structural and the optical properties of different Si nanostructures have been compared. Detailed optical properties of Si nanowires arrays of different optical lengths, fabricated by facile electroless etching technique, have been reported. The theoretical calculation of exponential sine profile at constant λ = 600 nm shows a better explanation in terms of gradient index with optical length for vertical nanowires. The observations signify the possibility of strong light trapping due to an exponential gradient towards the high index along the nanowires and the existence of dense subwavelength features. The optical admittance (Ƶ) shows a strong impact on optical distance (Z) for Z < H, owing to the electromagnetic wave interaction with the nanowires that perceive a different Ƶ at the oblique angle of incidence (AOI). In addition, the experimental reflectance data and the theoretical model for transverse electric and transverse magnetic modes predict that an optical length of 5 μm can exhibit a very low reflectance value. This indicates that the Si nanowires are polarization insensitive over a wide range of AOI (0°–80°). Moreover, Raman spectra showed a very strong light confinement effect in the first order transverse optical band with increasing etching depths. The morphological dependent resonance theory predicts a strong localized light field confinement in the lower wavelength regime for SiNWs. The effect on the strong resonant absorption modes was further correlated with the simulation results obtained by using COMSOL. The obtained results are likely to enhance the maximum absorption of SiNWs for various photonic applications.
Excited states of neutral donor bound excitons in GaN
Authors: Callsen G. , Kure T. , Wagner M. R. , Butté R. , Grandjean N.
Published: June 2018

We investigate the excited states of a neutral donor bound exciton (D0X) in bulk GaN by means of high-resolution, polychromatic photoluminescence excitation (PLE) spectroscopy. The optically most prominent donor in our sample is silicon accompanied by only a minor contribution of oxygen—the key for an unambiguous assignment of excited states. Consequently, we can observe a multitude of Si0X-related excitation channels with linewidths down to 200 μeV. Two groups of excitation channels are identified, belonging either to rotational-vibrational or electronic excited states of the hole in the Si0X complex. Such identification is achieved by modeling the excited states based on the equations of motion for a Kratzer potential, taking into account the particularly large anisotropy of effective hole masses in GaN. Furthermore, several ground- and excited states of the exciton-polaritons and the dominant bound exciton are observed in the photoluminescence (PL) and PLE spectra, facilitating an estimate of the associated complex binding energies. Our data clearly show that great care must be taken if only PL spectra of D0X centers in GaN are analyzed. Every PL feature we observe at higher emission energies with regard to the Si0X ground state corresponds to an excited state. Hence, any unambiguous peak identification renders PLE spectra highly valuable, as important spectral features are obscured in common PL spectra. Here, GaN represents a particular case among the wide-bandgap, wurtzite semiconductors, as comparably low localization energies for common D0X centers are usually paired with large emission linewidths and the prominent optical signature of exciton-polaritons, making the sole analysis of PL spectra a challenging task.
Influence of nonlinear detuning at plasma wavebreaking threshold on backward Raman compression of non-relativistic laser pulses
Authors: Balakin A. A. , Fraiman G. M. , Jia Q. , Fisch N. J.
Published: June 2018

Taking into account the nonlinear dispersion of the plasma wave, the fluid equations for the three-wave (Raman) interaction in plasmas are derived. It is found that, in some parameter regimes, the nonlinear detuning resulting from the plasma wave dispersion during Raman compression limits the plasma wave amplitude to noticeably below the generally recognized wavebreaking threshold. Particle-in-cell simulations confirm the theoretical estimates. For weakly nonlinear dispersion, the detuning effect can be counteracted by pump chirping or, equivalently, by upshifting slightly the pump frequency, so that the frequency-upshifted pump interacts with the seed at the point where the plasma wave enters the nonlinear stage.
Dynamic x-ray spectrometry method for determining stoichiometry of thin films during growth
Authors: Strikovski Mikhail D. , Kim Jeonggoo , Garrahan Steven L. , Kolagani Solomon
Published: June 2018

A method and technique of dynamic x-ray spectrometry is presented for real-time, in situ composition determination of multi-element films during pulsed laser deposition. The method, named as Low-Angle X-ray Spectrometry (LAXS), is capable of determining the composition with an uncertainty of ±5% and requires neither theoretical calculations nor multiple calibration standards of known composition and thickness. Algorithm of LAXS is validated by comparing film composition results with Rutherford Backscattering Spectroscopy analyses. LAXS provides an immediate visual feedback on film composition and guidance for optimizations, which is critical for applications. As a material example, compositions of several Y-Ba-Cu-O films were analyzed and it is shown that LAXS can rapidly identify an optimum oxygen pressure for stoichiometric film deposition.
Microwave magnetic field detection based on Cs vapor cell in free space
Authors: Liu Xiaochi , Jiang Zhiyuan , Qu Jifeng , Hou Dong , Huang Xianhe , Sun Fuyu
Published: June 2018

In this study, we demonstrate the direct measurement of a microwave (MW) magnetic field through the detection of atomic Rabi resonances with Cs vapor cells in a free-space low-Q cavity. The line shape (amplitude and linewidth) of detected Rabi resonances is investigated versus several experimental parameters such as the laser intensity, cell buffer gas pressure, and cell length. The specially designed low-Q cavity creates a suitable MW environment allowing easy testing of different vapor cells with distinct properties. Obtained results are analyzed to optimize the performances of a MW magnetic field sensor based on the present atom-based detection technique.
The role of electric field in microfluidic heating induced by standing surface acoustic waves
Authors: Zheng Tengfei , Wang Chaohui , Hu Qiao , Wei Shoupeng
Published: June 2018

The heating mechanism of standing surface acoustic waves (SSAWs) on a LiNbO3 substrate has been experimentally studied. Three devices with different substrates were used to heat the drops with NaCl concentrations ranging from 0 to 1 g/l, respectively. The device with a glass substrate was used to shield acoustic waves. The device with an Au layer between the LiNbO3 substrate and the droplet was used to shield the alternating current field. The results show that the thermal effect induced by SSAWs on the LiNbO3 substrate is composed of the acoustothermal effect due to SSAWs and the electric field thermal effect (Joule heat) due to the alternating current field. The electric field thermal effect which is ignored in SSAW devices previously plays an important role in the thermal effect induced by SSAWs. These results provide a meaningful insight into the mechanism of SSAW-based heating, which is of great help to guide the effective use of the SSAW-based heating technique for various applications.
180°-phase shift of magnetoelastic waves observed by phase-resolved spin-wave tomography
Authors: Hashimoto Yusuke , Johansen Tom H. , Saitoh Eiji
Published: June 2018

We have investigated optically excited magnetoelastic waves by phase-resolved spin-wave tomography (PSWaT). PSWaT reconstructs the dispersion relation of spin waves together with their phase information by using time-resolved magneto-optical imaging for spin-wave propagation followed by an analysis based on the convolution theorem and a complex Fourier transform. In PSWaT spectra for a Bi-doped garnet film, we found a 180°-phase shift of magnetoelastic waves at around the crossing of the dispersion relations of spin and elastic waves. The result is explained by a coupling between spin waves and elastic waves through the magnetoelastic interaction. We also propose an efficient way for the phase manipulation of magnetoelastic waves by rotating the orientation of magnetization less than 10°.
Influence of F– on stark splitting of Yb3+ and the thermal expansion of silica glass
Authors: Cao Yabin , Chen Si , Shao Chongyun , Yu Chunlei
Published: June 2018

A local phosphate/fluoride environment of Yb3+ was created in silica glass using a multi-step method. The influence of F- on the Stark splitting of Yb3+ in Al3+/P5+/F- co-doped silica glass was studied at room-temperature, in addition to its effect on the thermal expansion performance of the glass matrix. The results indicate that Yb3+ ions in Al3+/P5+/F- co-doped silica glass have a larger Stark splitting energy of 2F7/2 compared to Al3+/P5+ co-doped silica glass. Moreover, a larger integrated absorption cross-section (34.58 pm2 × nm), stimulated emission cross-section (0.63 pm2), and better thermal expansion performance (1.3062 × 10−6 K- at 100 °C) are achieved in Al3+/P5+/F- co-doped silica glass. Finally, different function mechanisms of F- in silica and phosphate glasses were analyzed and the F-Si bond was used to explain the results in silica glass. The combination of low refractive index, large Stark splitting energy of 2F7/2, and small thermal expansion makes Al3+/P5+/F- co-doped silica glass a preferred material for large mode area fibers for high-power laser applications.
Flow turbulence topology in regular porous media: From macroscopic to microscopic scale with direct numerical simulation
Authors: Chu Xu , Weigand Bernhard , Vaikuntanathan Visakh
Published: June 2018

Microscopic analysis of turbulence topology in a regular porous medium is presented with a series of direct numerical simulation. The regular porous media are comprised of square cylinders in a staggered array. Triply periodic boundary conditions enable efficient investigations in a representative elementary volume. Three flow patterns—channel with sudden contraction, impinging surface, and wake—are observed and studied quantitatively in contrast to the qualitative experimental studies reported in the literature. Among these, shear layers in the channel show the highest turbulence intensity due to a favorable pressure gradient and shed due to an adverse pressure gradient downstream. The turbulent energy budget indicates a strong production rate after the flow contraction and a strong dissipation on both shear and impinging walls. Energy spectra and pre-multiplied spectra detect large scale energetic structures in the shear layer and a breakup of scales in the impinging layer. However, these large scale structures break into less energetic small structures at high Reynolds number conditions. This suggests an absence of coherent structures in densely packed porous media at high Reynolds numbers. Anisotropy analysis with a barycentric map shows that the turbulence in porous media is highly isotropic in the macro-scale, which is not the case in the micro-scale. In the end, proper orthogonal decomposition is employed to distinguish the energy-conserving structures. The results support the pore scale prevalence hypothesis. However, energetic coherent structures are observed in the case with sparsely packed porous media.
Particle directed dual-fluid flow driven by electrowetting for controllable multiway light valves
Authors: Chen Lin , Xie Shuting , Cao Jieping , Yan Zhibin , Jiang Hongwei , Dou Yingying , Deng Yong , Zhou Guofu , Jin Mingliang , Shui Lingling
Published: June 2018

High efficiency and position controllable multiway light valves are achieved by electrowetting-driven and magnetic particle (MP)-directed oil film dewetting in microscale spaces. The non-transparent oil phase can be attracted to oleophilic MPs and repelled from hydrophilic MPs to adjust the oil film distribution in a microwell (valve area). Thus, in an oil-water dual-fluidic system, the dewetting and breakup point of an oil film can be modulated when driven by electrowetting. By introducing a MP, both the switching speed and opening ratio of a light valve (microwell) are increased, and the time of both starting to open and reaching the maximum opening ratio is reduced. Oleophilic MPs with larger size show better controllability than hydrophilic MPs with smaller size. A 16-way spatial valve is achieved by magnetically moving one MP in a single microwell. Such a phenomenon is also demonstrated on a large area device with high-density microwells, suggesting high potential for optical valves or display applications.
Enhancing noise-induced switching times in systems with distributed delays
Authors: Kyrychko Y. N. , Schwartz I. B.
Published: June 2018

The paper addresses the problem of calculating the noise-induced switching rates in systems with delay-distributed kernels and Gaussian noise. A general variational formulation for the switching rate is derived for any distribution kernel, and the obtained equations of motion and boundary conditions represent the most probable, or optimal, path, which maximizes the probability of escape. Explicit analytical results for the switching rates for small mean time delays are obtained for the uniform and bi-modal (or two-peak) distributions. They suggest that increasing the width of the distribution leads to an increase in the switching times even for longer values of mean time delays for both examples of the distribution kernel, and the increase is higher in the case of the two-peak distribution. Analytical predictions are compared to the direct numerical simulations and show excellent agreement between theory and numerical experiment.
Exploring the benefits of an asymmetric monostable potential function in broadband vibration energy harvesting
Authors: Kumar Aravind , Ali Shaikh Faruque , Arockiarajan A.
Published: June 2018

This letter explores the benefits offered by an asymmetric monostable potential function over the conventional symmetric linear and bistable potential functions in broadband vibration energy harvesting. Multi-stable harvesters such as the bistable and tristable harvesters provide an order of magnitude higher power than the linear harvesters while undergoing inter-well oscillations. However, when the excitation noise levels are insufficient to trigger inter-well oscillations, such harvesters provide very low power output. We propose a monostable configuration with an asymmetric potential energy function that is capable of providing a high energy output starting from excitation levels as low as 0.005 g2/Hz (g denotes acceleration due to gravity). The superior performance of the proposed asymmetric configuration over the conventional linear and bistable configurations is demonstrated through experiments, considering a band-limited white noise excitation. The experimental results also indicate that the asymmetric configuration delivers higher power at lower strain levels than the bistable configuration, mitigating the burden on the piezoelectric transducer. Thus, the asymmetric configuration offers a two-fold advantage in energy harvesting, leading to an increase in both the power output and the lifetime of the piezoelectric transducer.
Effect of vitamin A restriction on carcass traits and blood metabolites in Korean native steers
Authors: Peng Dong-Qiao , Lee Jae-Sung , Kim Won-Seob , Kim Young-Shin , Bae Mun-Hee , Jo Yong-Ho , Oh Young-Kun , Baek Youl-Chang , Hwang Seong-Gu , Lee Hong-Gu
Published: June 2018

The objective of the present study was to determine the effect of vitamin A restriction on serum metabolites and carcass performance in Korean native steers during a fattening period. In Study 1, 61 steers were divided into three groups and supplied diets with concentrate and roughage containing 890 IU/kg of provitamin A and then supplemented with either 8000 IU (control), 3000 IU (T1) or 0 IU (T2) of premix vitamin A per kilogram of dry matter. In Study 2, 19 steers were divided into two groups and provided with the same basic diets then supplemented with 8000 IU (control) or 0 IU (T) of premix vitamin A per kilogram of dry matter. In Study 1, we found that serum vitamin A concentrations were significantly (P < 0.05) lower in the T2 group, along with significant (P < 0.05) increases in blood urea nitrogen, albumin, creatinine and non-esterified fatty acid concentrations. In Study 2, the T group had a higher (P < 0.05) skeletal muscle mRNA expression levels of myogenic factor 6 and a trend for the greater yield grade (P=0.095). However, marbling scores in the study showed no significant. Therefore, vitamin A restriction with vitamin premix during the fattening period was associated with a trend for a higher yield grade, but marbling scores that were not significantly higher. Metabolic parameters in this stage could be used as indicators in future metabolic studies and as early health status markers in Korean native steers.
Individuality and slow dynamics in bacterial growth homeostasis
Authors: Susman Lee , Kohram Maryam , Vashistha Harsh , Nechleba Jeffrey T. , Salman Hanna , Brenner Naama
Published: June 2018

Significance

Microbial cells go through repeated cycles of growth and division. These cycles are not perfect: the time and size at division can fluctuate from one cycle to the next. Still, cell size is kept tightly controlled, and fluctuations do not accumulate to large deviations. How this control is implemented in single cells is still not fully understood. We performed experiments that follow individual bacteria in microfluidic traps for hundreds of generations. This enables us to identify distinct individual dynamic properties that are maintained over many cycles of growth and division. Surprisingly, we find that each cell suppresses fluctuations with a different strength; this variability defines an “individual” behavior for each cell, which is inherited along many generations.
Small RNA profiling in
Mycobacterium tuberculosis
identifies MrsI as necessary for an anticipatory iron sparing response
Authors: Gerrick Elias R. , Barbier Thibault , Chase Michael R. , Xu Raylin , François Josie , Lin Vincent H. , Szucs Matthew J. , Rock Jeremy M. , Ahmad Rushdy , Tjaden Brian , Livny Jonathan , Fortune Sarah M.
Published: June 2018

Significance

This work describes the most extensive discovery and functional characterization of small regulatory RNAs (sRNAs) in
Mycobacterium tuberculosis
to date. We comprehensively define the sRNAs expressed in
M. tuberculosis
under five host-like stress conditions. This reference dataset comprehensively defines the expression patterns and boundaries of mycobacterial sRNAs. We perform in-depth characterization of one sRNA, mycobacterial regulatory sRNA in iron (MrsI), which is induced in
M. tuberculosis
in multiple stress conditions. MrsI is critical for the iron-sparing response in mycobacteria by binding directly to mRNAs encoding nonessential iron-containing proteins to repress their expression. Interestingly, MrsI acts in an anticipatory manner, in which its induction by a variety of stresses primes
M. tuberculosis
to enter an iron-sparing state more rapidly upon iron deprivation.
Automatically identifying, counting, and describing wild animals in camera-trap images with deep learning
Authors: Norouzzadeh Mohammad Sadegh , Nguyen Anh , Kosmala Margaret , Swanson Alexandra , Palmer Meredith S. , Packer Craig , Clune Jeff
Published: June 2018

Significance

Motion-sensor cameras in natural habitats offer the opportunity to inexpensively and unobtrusively gather vast amounts of data on animals in the wild. A key obstacle to harnessing their potential is the great cost of having humans analyze each image. Here, we demonstrate that a cutting-edge type of artificial intelligence called deep neural networks can automatically extract such invaluable information. For example, we show deep learning can automate animal identification for 99.3% of the 3.2 million-image Snapshot Serengeti dataset while performing at the same 96.6% accuracy of crowdsourced teams of human volunteers. Automatically, accurately, and inexpensively collecting such data could help catalyze the transformation of many fields of ecology, wildlife biology, zoology, conservation biology, and animal behavior into “big data” sciences.
Cell-intrinsic regulation of murine epidermal Langerhans cells by protein S
Authors: Tabib Yaara , Jaber Nora S. , Nassar Maria , Capucha Tal , Mizraji Gabriel , Nir Tsipora , Koren Noam , Aizenbud Itay , Maimon Avraham , Eli-Berchoer Luba , Wilensky Asaf , Burstyn-Cohen Tal , Hovav Avi-Hai
Published: June 2018

Significance

Langerhans cells (LCs) are the exclusive antigen-presenting cells of the epidermis, capable of mounting immunity and tolerance. LCs maintain themselves locally by self-renewing throughout life, a process that is regulated by both LCs and keratinocytes. Nevertheless, the mechanisms underlying this process are not clearly understood. Using targeted genetic ablation, we demonstrate that lack of protein S (PROS1) in keratinocytes, but not in LCs, results in reduced numbers of terminally developed LCs. This is due to increased apoptosis of LCs and associated with altered expression of cytokines involved in tissue homeostasis. Furthermore, PROS1 also down-regulates LC differentiation from bone marrow precursors. Together, these identify PROS1 as a regulator of LC development and homeostasis.
Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance
Authors: Nyerges Ákos , Csörgő Bálint , Draskovits Gábor , Kintses Bálint , Szili Petra , Ferenc Györgyi , Révész Tamás , Ari Eszter , Nagy István , Bálint Balázs , Vásárhelyi Bálint Márk , Bihari Péter , Számel Mónika , Balogh Dávid , Papp Henrietta , Kalapis Dorottya , Papp Balázs , Pál Csaba
Published: June 2018

Significance

Antibiotic development is frequently plagued by the rapid emergence of drug resistance. However, assessing the risk of resistance development in the preclinical stage is difficult. By building on multiplex automated genome engineering, we developed a method that enables precise mutagenesis of multiple, long genomic segments in multiple species without off-target modifications. Thereby, it enables the exploration of vast numbers of combinatorial genetic alterations in their native genomic context. This method is especially well-suited to screen the resistance profiles of antibiotic compounds. It allowed us to predict the evolution of resistance against antibiotics currently in clinical trials. We anticipate that it will be a useful tool to identify resistance-proof antibiotics at an early stage of drug development.
Cellulose synthase complexes display distinct dynamic behaviors during xylem transdifferentiation
Authors: Watanabe Yoichiro , Schneider Rene , Barkwill Sarah , Gonzales-Vigil Eliana , Hill Joseph L. , Samuels A. Lacey , Persson Staffan , Mansfield Shawn D.
Published: June 2018

Significance

Cellulose, the most abundant biopolymer on earth, is the major constituent of plant cell walls and is ubiquitously used by industry. This biopolymer is made by plasma membrane-localized CELLULOSE SYNTHASE (CESA) enzymes. To transit from deposition of a growing primary cell wall to a strong secondary cell wall, xylem cells must remodel the CESA machinery to express a new set of CESA isoforms specific to secondary cell wall synthesis. We outline a detailed framework for how this change in cellulose synthesis occurs. Our work provides the principles for how plants change their capacity to produce cellulose and therefore plant biomass.
Synthesis of trilobatin from naringin via prunin as the key intermediate: acidic hydrolysis of the α-rhamnosidic linkage in naringin under improved conditions
Authors: Kurahayashi Kazuki , Hanaya Kengo , Higashibayashi Shuhei , Sugai Takeshi
Published: June 2018

Trilobatin [4ʹ-(β-D-glucopyranosyloxy)-2ʹ,4”,6ʹ-trihydroxydihydrochalcone] was synthesized from commercially available naringin in three steps with an overall yield of 30%. The key step was the acid-catalyzed site-selective hydrolysis of terminal α-rhamnopyranosidic linkage in neohesperidose involved in naringin under controlled conditions, by applying a high-pressure steam sterilizer.
Microstructure Noise and Realized Variance in the Live Cattle Futures Market
Authors: Couleau Anabelle , Serra Teresa , Garcia Philip
Published: June 2018

Recently, U.S. live cattle futures prices have experienced high levels of intraday price variance, which have raised concerns about the possible impact of microstructure noise from high frequency trading on market instability. This article identifies both the magnitude and the duration of the bias caused by market microstructure noise in measuring efficient price variance in the live cattle futures market from 2011 to 2016, with emphasis on price variance behavior in recent years. Market microstructure noise increases observed price variance, but its effects are not large and do not last more than three to four minutes in response to changing information. Intraday price variance has increased in recent years, but the findings provide little evidence that high frequency traders were responsible for economically meaningful market noise. Informatively, steps taken by the CME and cattle producers to mitigate noise have not been fruitful to date, and signal that the magnitude of noise will likely vary with the magnitude of changes in demand and cyclical supply.
Mental Imagery Follows Similar Cortical Reorganization as Perception: Intra-Modal and Cross-Modal Plasticity in Congenitally Blind
Authors: de Borst A W , de Gelder B
Published: June 2018

Cortical plasticity in congenitally blind individuals leads to cross-modal activation of the visual cortex and may lead to superior perceptual processing in the intact sensory domains. Although mental imagery is often defined as a quasi-perceptual experience, it is unknown whether it follows similar cortical reorganization as perception in blind individuals. In this study, we show that auditory versus tactile perception evokes similar intra-modal discriminative patterns in congenitally blind compared with sighted participants. These results indicate that cortical plasticity following visual deprivation does not influence broad intra-modal organization of auditory and tactile perception as measured by our task. Furthermore, not only the blind, but also the sighted participants showed cross-modal discriminative patterns for perception modality in the visual cortex. During mental imagery, both groups showed similar decoding accuracies for imagery modality in the intra-modal primary sensory cortices. However, no cross-modal discriminative information for imagery modality was found in early visual cortex of blind participants, in contrast to the sighted participants. We did find evidence of cross-modal activation of higher visual areas in blind participants, including the representation of specific-imagined auditory features in visual area V4.
Keystone Virus Isolated From a Florida Teenager With Rash and Subjective Fever: Another Endemic Arbovirus in the Southeastern United States?
Authors: Lednicky John A , White Sarah K , Stephenson Caroline J , Cherabuddi Kartikeya , Loeb Julia C , Moussatche Nissin , Lednicky Andrew , Morris J Glenn
Published: June 2018

Keystone virus, a California-serogroup orthobunyavirus, was first isolated in 1964 from mosquitoes in Keystone, Florida. There were no prior reports of isolation from humans, despite studies suggesting that ~20% of persons living in the region are seropositive. We report virus isolation from a Florida teenager with a rash and fever.
Singular value decomposition versus sparse grids: refined complexity estimates
Authors: Griebel Michael , Harbrecht Helmut
Published: June 2018

We compare the cost complexities of two approximation schemes for functions that live on the product domain $\varOmega _1\times \varOmega _2$ of sufficiently smooth domains $\varOmega _1\subset \mathbb{R}^{n_1}$ and $\varOmega _2\subset \mathbb{R}^{n_2}$, namely the singular value / Karhunen–Lòeve decomposition and the sparse grid representation. We assume that appropriate finite element methods with associated orders $r_1$ and $r_2$ of accuracy are given on the domains $\varOmega _1$ and $\varOmega _2$, respectively. This setting reflects practical needs, since often black-box solvers are used in numerical simulation, which restrict the freedom in the choice of the underlying discretization. We compare the cost complexities of the associated singular value decomposition and the associated sparse grid approximation. It turns out that, in this situation, the approximation by the sparse grid is always equal or superior to the approximation by the singular value decomposition. The results in this article improve and generalize those from the study by Griebel & Harbrecht (2014, Approximation of bi-variate functions. Singular value decomposition versus sparse grids. IMA J. Numer. Anal., 34, 28–54). Especially, we consider the approximation of functions from generalized isotropic and anisotropic Sobolev spaces.
Transcriptome Characterization of Matched Primary Breast and Brain Metastatic Tumors to Detect Novel Actionable Targets
Authors: Varešlija Damir , Priedigkeit Nolan , Fagan Ailís , Purcell Siobhan , Cosgrove Nicola , O’Halloran Philip J , Ward Elspeth , Cocchiglia Sinéad , Hartmaier Ryan , Castro Carlos A , Zhu Li , Tseng George C , Lucas Peter C , Puhalla Shannon L , Brufsky Adam M , Hamilton Ronald L , Mathew Aju , Leone Jose P , Basudan Ahmed , Hudson Lance , Dwyer Róisín , Das Sudipto , O’Connor Darran P , Buckley Patrick G , Farrell Michael , Hill Arnold D K , Oesterreich Steffi , Lee Adrian V , Young Leonie S
Published: June 2018

Background

Breast cancer brain metastases (BrMs) are defined by complex adaptations to both adjuvant treatment regimens and the brain microenvironment. Consequences of these alterations remain poorly understood, as does their potential for clinical targeting. We utilized genome-wide molecular profiling to identify therapeutic targets acquired in metastatic disease.

Methods

Gene expression profiling of 21 patient-matched primary breast tumors and their associated brain metastases was performed by TrueSeq RNA-sequencing to determine clinically actionable BrM target genes. Identified targets were functionally validated using small molecule inhibitors in a cohort of resected BrM ex vivo explants (n = 4) and in a patient-derived xenograft (PDX) model of BrM. All statistical tests were two-sided.

Results

Considerable shifts in breast cancer cell-specific gene expression profiles were observed (1314 genes upregulated in BrM; 1702 genes downregulated in BrM; DESeq; fold change > 1.5, Padj < .05). Subsequent bioinformatic analysis for readily druggable targets revealed recurrent gains in RET expression and human epidermal growth factor receptor 2 (HER2) signaling. Small molecule inhibition of RET and HER2 in ex vivo patient BrM models (n = 4) resulted in statistically significantly reduced proliferation (P < .001 in four of four models). Furthermore, RET and HER2 inhibition in a PDX model of BrM led to a statistically significant antitumor response vs control (n = 4, % tumor growth inhibition [mean difference; SD], anti-RET = 86.3% [1176; 258.3], P < .001; anti-HER2 = 91.2% [1114; 257.9], P < .01).

Conclusions

RNA-seq profiling of longitudinally collected specimens uncovered recurrent gene expression acquisitions in metastatic tumors, distinct from matched primary tumors. Critically, we identify aberrations in key oncogenic pathways and provide functional evidence for their suitability as therapeutic targets. Altogether, this study establishes recurrent, acquired vulnerabilities in BrM that warrant immediate clinical investigation and suggests paired specimen expression profiling as a compelling and underutilized strategy to identify targetable dependencies in advanced cancers.
Number of Risky Lifestyle Behaviors and Breast Cancer Risk
Authors: Ellingjord-Dale Merete , Vos Linda , Vik Hjerkind Kirsti , Hjartåker Anette , Russnes Hege G , Tretli Steinar , Hofvind Solveig , dos-Santos-Silva Isabel , Ursin Giske
Published: June 2018

Background

Lifestyle factors are associated with overall breast cancer risk, but less is known about their associations, alone or jointly, with risk of specific breast cancer subtypes.

Methods

We conducted a case–control subjects study nested within a cohort of women who participated in the Norwegian Breast Cancer Screening Program during 2006–2014 to examine associations between risky lifestyle factors and breast cancer risk. In all, 4402 breast cancer cases subjects with information on risk factors and hormone receptor status were identified. Conditional logistic regression was used to estimate odds ratios (ORs), with 95% confidence intervals (CIs), in relation to five risky lifestyle factors: body mass index (BMI) of 25 kg/m² or greater, three or more glasses of alcoholic beverages per week, ever smoking, fewer than four hours of physical activity per week, and ever use of menopausal hormone therapy. Analyses were adjusted for education, age at menarche, number of pregnancies, and menopausal status. All statistical tests were two-sided.

Results

Compared with women with no risky lifestyle behaviors, those with five had 85% (OR = 1.85, 95% CI = 1.42 to 2.42, Ptrend < .0001) increased risk of breast cancer overall. This association was limited to luminal A–like (OR = 2.20, 95% CI = 1.55 to 3.12, Ptrend < .0001) and luminal B–like human epidermal growth factor receptor 2 (HER2)–positive (OR = 1.66, 95% CI = 0.61 to 4.54, Ptrend < .004) subtypes. Number of risky lifestyle factors was not associated with increased risk of luminal B–like HER2-negative, HER2-positive, or triple-negative subtypes (Ptrend > .18 for all).

Conclusions

Number of risky lifestyle factors was positively associated with increased risk for luminal A–like and luminal B–like HER2-positive breast cancer.
Family Functioning and Medical Adherence Across Children and Adolescents With Chronic Health Conditions: A Meta-Analysis
Authors: Psihogios Alexandra M , Fellmeth Heather , Schwartz Lisa A , Barakat Lamia P
Published: June 2018

Objectives

A meta-analysis examined family functioning and medical adherence in children and adolescents with chronic health conditions. Family functioning was evaluated at the level of the family unit, as well as parent–child interactions.

Methods

We conducted literature searches using PubMed, PsycINFO, SCOPUS, Web of Science, and Cochrane. After reviewing 764 articles, 62 studies met eligibility criteria. Pearson’s r correlations were the effect size of interest. We conducted both omnibus and domain-specific (e.g., family conflict, cohesion) meta-analyses. Meta-regressions examined whether relevant covariates related to the magnitude of the effect.

Results

The omnibus meta-analysis showed that family functioning was significantly related to medical adherence across a variety of pediatric chronic health conditions. Lower family conflict, greater family cohesion, greater family flexibility, more positive communication, and better family problem-solving were each associated with better adherence. There were no significant differences in the magnitude of the omnibus effect based on child age, measurement features (subjective vs. objective or bioassay adherence; family unit vs. parent–child interactions), or study quality.

Conclusions

Consistent with social–ecological frameworks, findings supported links between family functioning and medical adherence. This study highlights several limitations of the extant research, including absence of a guiding theoretical framework and several methodological weaknesses. We offer clinical and research recommendations for enhancing scientific understanding and promotion of adherence within the family context.
Implications for the missing low-mass galaxies (satellites) problem from cosmic shear
Authors: Jimenez Raul , Verde Licia , Kitching Thomas D
Published: June 2018

The number of observed dwarf galaxies, with dark matter mass ≲1011 M⊙ in the Milky Way or the Andromeda galaxy does not agree with predictions from the successful ΛCDM paradigm. To alleviate this problem, a suppression of dark matter clustering power on very small scales has been conjectured. However, the abundance of dark matter halos outside our immediate neighbourhood (the Local Group) seem to agree with the ΛCDM–expected abundance. Here we connect these problems to observations of weak lensing cosmic shear, pointing out that cosmic shear can make significant statements about the missing satellites problem in a statistical way. As an example and pedagogical application, we use recent constraints on small-scale power suppression from measurements of the CFHTLenS data. We find that, on average, in a region of ∼Gpc3 there is no significant small-scale power suppression. This implies that suppression of small-scale power is not a viable solution to the ‘missing satellites problem’ or, alternatively, that on average in this volume there is no ‘missing satellites problem’ for dark matter masses ≳5 × 109 M⊙. Further analysis of current and future weak lensing surveys will probe much smaller scales, k > 10h Mpc−1 corresponding roughly to masses M < 109M⊙.