bluuebunny/crossref_metadata_2025 huggingface dataset:
Therapie des subakromialen Schmerzsyndroms
Authors: Matthijs Anja
Published: March 2019

Im VPTMAGAZIN stellen wir regelmäßig aktuelle Studienergebnisse vor. Diesmal: Chaconas EJ, Kolber MJ, Hanney WJ, Daugherty ML, Wilson SH, Sheets C. Shoulder external rotator eccentric training versus general shoulder exercise for subacromial pain syndrome: a randomized controlled trial. Int J Sports Phys Ther. 2017;12:1121–133.
Studies of radiation effects in Al2O3-based metal-oxide-semiconductor structures induced by Si heavy ions
Authors: Zhang J. , Chen X. , Wang L. , Zheng Z. S. , Zhu H. P. , Li B. , Gao J. T. , Li D. L. , Luo J. J. , Han Z. S. , Song C. , Liu X. Y.
Published: March 2019

The radiation effects of metal-oxide-semiconductor (MOS) capacitors based on an Al2O3 gate dielectric were studied using 30 MeV Si heavy ions. To give insights into the types of defects induced by Si ion irradiation in the gate oxide, synergistic experiments involving γ-ray irradiation and Si ion irradiation were carried out. The results revealed that the defects in the as-grown Al2O3 layer were found to be hole trapping centers, whereas Si ion induced new defects were electron trapping centers. The experimental and simulation data of current density-voltage (J-V) curves confirmed that the transmission mechanism of leakage current in the Al2O3 layer was mainly dominated by the Frenkel-Poole mechanism. In detail, the variations of leakage current were mainly due to the attributions of the local built-in electric field-assisted current leakage and the conductive path-assisted current leakage and were found to be dependent on the irradiation condition and Al2O3 thickness. Lastly, the decrease of the gate oxide capacitance of MOS capacitors was attributed to the increase of the series resistance and leakage current in MOS capacitors.
Dynamic duty cycle control strategy for surface nuclear magnetic resonance sounding system
Authors: Zhu Jinbao , Yang Yujing , Teng Fei , Lin Tingting
Published: March 2019

The surface nuclear magnetic resonance (SNMR) technique exploits the NMR phenomenon to quantitatively determine the subsurface distribution of water. In the SNMR sounding system, deeper regions are probed by increasing the pulse moment (the product of the current amplitude and pulse duration). However, the amplitude of the current in the transmitter coil inevitably decays due to the energy loss in the storage capacitor. In practical application, the maximum amplitude of the current in one transmission process is recorded and used as the current amplitude. However, this approach results in errors in calculating the pulse moment and the sensitivity kernel function. In this paper, we build a simulation of the transmission process and the current decay phenomenon appears. From the simulation results, the current amplitude at the end of the pulse is 83% of the maximum. We present a dynamic duty cycle control strategy for a constant excitation current. We calculate the 1D sensitivity kernel function based on the two cases of constant and decaying excitation current, respectively. We observe that the maximum difference between them is greater than 200 nV/m. The inversion results based on a 1D aquifer model containing two aquifers show that the decaying excitation current results in aquifers deeper than the model and the water content of the second aquifer is 50% of the model. A comparative experiment between the decaying excitation current system and the constant excitation current system was conducted in a field experiment. Compared with traditional SNMR instruments, our new system can effectively avoid the phenomenon of excitation current decay in field experiments, and the new SNMR sounding system enables accurate inversion of aquifers.
Effect of antiphase boundaries on the magnetic properties of La2CoMnO6
Authors: Madhogaria R. P. , Das R. , Clements E. M. , Kalappattil V. , Bingham N. S. , Phan M. H. , Srikanth H.
Published: March 2019

We present a comparative study of structural and magnetic properties of the as-grown and annealed samples of double perovskite, La2CoMnO6. The single monoclinic (P21/n) phase has been achieved for both the samples. Electron microscopy highlights the change in morphology of the as-grown and annealed samples, with the annealed sample having more grain boundaries and bigger particle sizes. The annealing in presence of oxygen leads to increase in the population of antiphase boundaries, which is supported by the decreases in the remanent and saturation magnetizations. An analysis of magnetization dynamics by means of AC susceptibility shows four different magnetic transitions, with two high temperature ferromagnetic transitions and two cluster glass-like states emerging at low temperatures, which appear almost identical in both the as-grown and annealed samples.
Droplet actuation on superhydrophobic substrates via electric field gradients
Authors: Guo H. Alex , Maheshwari Shagun , Patel Maya S. , Bhatt Eeshan C. , Chen Chuan-Hua
Published: March 2019

A superhydrophobic surface is non-sticking to aqueous droplets due to minimized solid-liquid contact, but the small contact area also poses challenges to droplet maneuvering. This letter reports a technique using electric field gradients to actuate aqueous droplets on superhydrophobic surfaces. A pin-ring electrode pair underneath the insulating superhydrophobic surface is used to generate electric field gradient above the surface, with the field focused around the pin. The non-uniform field operates on the electrostatically induced charges on the droplet, producing an actuation force attracting the droplet toward the pin. The actuation force is proportional to the square of the imposed field as shown in both experiments and simulations. This non-contact actuation technique is effective in electrostatically trapping and translating superhydrophobic droplets, despite the small solid-liquid contact. The pin-ring configuration can be readily extended to a pin array between two parallel lines, which essentially form a stretched ring closing at infinity. The pin array is used to demonstrate individual actuation of two droplets leading to their eventual coalescence.
Identifying valency and occupation sites of Ir dopants in antiferromagnetic α-Fe2O3 thin films with X-ray absorption fine structure and Mössbauer spectroscopy
Authors: Nozaki Tomohiro , Pati Satya Prakash , Shiokawa Yohei , Suzuki Motohiro , Ina Toshiaki , Mibu Ko , Al-Mahdawi Muftah , Ye Shujun , Sahashi Masashi
Published: March 2019

A combined analysis of Ir-doped α-Fe2O3 (001) films, which show a drastic enhancement in the Morin transition temperature as a result of Ir doping, was performed by employing X-ray absorption near edge structure (XANES), extended X-ray absorption fine structure (EXAFS), and Mössbauer spectroscopy analyses at room temperature. The Mössbauer spectra reveal that the valency of Fe remains 3+ after Ir doping. The XANES spectra indicate that the valency of the Ir ion in Ir-doped α-Fe2O3 varies from 3+ to 4+. The EXAFS analysis results clarified that the Ir ions occupy the Fe-sites of α-Fe2O3. These findings help elucidate the mechanism for controlling the Morin transition temperature in α-Fe2O3 films toward antiferromagnetic spintronic applications.
Theory of light-activated catalytic Janus particles
Authors: Uspal W. E.
Published: March 2019

We study the dynamics of active Janus particles that self-propel in solution by light-activated catalytic decomposition of chemical “fuel.” We develop an analytical model of a photo-active self-phoretic particle that accounts for “self-shadowing” of the light by the opaque catalytic face of the particle. We find that self-shadowing can drive “phototaxis” (rotation of the catalytic cap toward the light source) or “anti-phototaxis,” depending on the properties of the particle. Incorporating the effect of thermal noise, we show that the distribution of particle orientations is captured by a Boltzmann distribution with a nonequilibrium effective potential. Furthermore, the mean vertical velocity of phototactic (anti-phototactic) particles exhibits a superlinear (sublinear) dependence on intensity. Overall, our findings show that photo-active particles exhibit a rich “tactic” response to light, which could be harnessed to program complex three-dimensional trajectories.
Investigation of the sound transmission through a locally resonant metamaterial cylindrical shell in the ring frequency region
Authors: Liu Zibo , Rumpler Romain , Feng Leping
Published: March 2019

Locally resonant metamaterial flat panels have proved to potentially exhibit extraordinary sound transmission loss properties when the resonance frequency of the resonators is tuned to the coincidence frequency region. Whether this technique is also effective to address the ring frequency effect for curved panels is investigated in this paper. For this purpose, a cylindrical shell, as a representation of curved panels, is studied from a theoretical and numerical point of view, with a specific focus on the transmission loss behaviour around the ring frequency region when the shell is mounted with local resonators. The influence from the resonators is presented and compared with that for a flat panel. An inverse effect of the resonators is observed on the sound transmission loss between the metamaterial cylindrical shell and the metamaterial flat panel when the resonance frequency of the resonators is tuned to be below or above the ring or coincidence frequency, respectively. Rather than the extraordinary improvement observed for the metamaterial flat panel, tuning such conventional resonators to the ring frequency of curved panels generates two side dips despite a sharp improvement at the ring frequency itself. This phenomenon is explained from an effective impedance point of view developed in this paper. The approach proposed and the conclusions provided may subsequently allow for the design of suitable resonators in order to resolve the ring frequency effect for curved panels.
Room temperature operation of n-type Ge/SiGe terahertz quantum cascade lasers predicted by non-equilibrium Green's functions
Authors: Grange Thomas , Stark David , Scalari Giacomo , Faist Jérôme , Persichetti Luca , Di Gaspare Luciana , De Seta Monica , Ortolani Michele , Paul Douglas J. , Capellini Giovanni , Birner Stefan , Virgilio Michele
Published: March 2019

n-type Ge/SiGe terahertz quantum cascade lasers are investigated using non-equilibrium Green's functions calculations. We compare the temperature dependence of the terahertz gain properties with an equivalent GaAs/AlGaAs quantum cascade laser design. In the Ge/SiGe case, the gain is found to be much more robust to temperature increase, enabling operation up to room temperature. The better temperature robustness with respect to III–V is attributed to the much weaker interaction with optical phonons. The effect of lower interface quality is investigated and can be partly overcome by engineering smoother quantum confinement.
General model for mass transport to planar and nanowire biosensor surfaces
Authors: Jin Decarle S. , Brightbill Eleanor L. , Vogel Eric M.
Published: March 2019

Mass transport to the sensor surface is a critical step in biosensing, often being the factor determining the limit of detection. Modeling transport of the analyte to a surface under convection and diffusion is a challenging task often requiring complex simulation. Herein, we provide a general model for mass transport to planar and nanowire biosensors under flow that is applicable over a wide range of variables. The model is then used to examine the importance of radial diffusion compared with planar diffusion under flow. Only under diffusive transport nanowires are found to have greatly reduced settling times compared with planar sensors due to radial diffusion. However, the presence of flow restricts the growth of the depletion region, resulting in comparable settling times between nanowires and planar sensors of the same size. Under flow conditions in typical experiments, radial diffusion associated with nanowire sensors is inessential for fast mass transport. Instead, the sensor length in the flow direction is the critical parameter as it limits the concentration drop that can occur as the analyte flows past the sensor. Decreasing the sensor length along the flow direction is found to greatly reduce settling times for both cases of planar and radial diffusion, even approaching the reaction limited case. Similarly, decreasing the channel height decreases the settling time due to restriction of the depletion region, but not as significantly as decreasing the sensor length.
A new approach to vibrational sum frequency generation spectroscopy using near infrared pulse shaping
Authors: Chowdhury Azhad U. , Watson Brianna R. , Ma Ying-Zhong , Sacci Robert L. , Lutterman Daniel A. , Calhoun Tessa R. , Doughty Benjamin
Published: March 2019

We have developed a multipurpose vibrational sum frequency generation (vSFG) spectrometer that is uniquely capable of probing a broad range of chemical species, each requiring different experimental conditions, without optical realignment. Here, we take advantage of arbitrary near infrared (NIR) waveform generation using a 4f-pulse shaper equipped with a 2D spatial light modulator (SLM) to tailor upconversion pulses to meet sample dependent experimental requirements. This report details the experimental layout, details of the SLM calibration and implementation, and the intrinsic benefits/limitations of this new approach to vSFG spectroscopy. We have demonstrated the competency of this spectrometer by achieving an ∼3-fold increase in spectral resolution compared to conventional spectrometers by probing the model dimethyl sulfoxide/air interface. We also show the ability to suppress nonresonant background contributions from electrode interfaces using time delayed asymmetric waveforms that are generated by the NIR pulse shaper. It is expected that this advancement in instrumentation will broaden the types of samples researchers can readily study using nonlinear surface specific spectroscopies.
Effects of alloying on mode-selectivity in H2O dissociation on Cu/Ni bimetallic surfaces
Authors: Ghosh Smita , Ray Dhiman , Tiwari Ashwani K.
Published: March 2019

The influence of alloying on mode-selectivity in H2O dissociation on Cu/Ni bimetallic surfaces has been studied using a fully quantum approach based on reaction path Hamiltonian. Both the metal alloy catalyst surface and the normal modes of H2O impact the chemical reactivity of H2O dissociation. A combination of these two different factors will enhance their influence reasonably. Among all the bimetallic surfaces, one monolayer (Ni4_Cu(111)) and 12 monolayer of Ni on Cu surface (Ni2_Cu(111)) show lowest barrier to the dissociation. Excitation of bending mode and symmetric stretching mode enhances the reactivity remarkably due to a significant decrease in their frequencies near the transition state in the vibrational adiabatic approximation. In the presence of non-adiabatic coupling between the modes, asymmetric stretching also shows similar enhancement in reactivity to that of symmetric stretching for all the systems. Inclusion of lattice motion using a sudden model enhances the dissociation probability at surface temperature 300 K and at lower incident energy, compared to that of the static surface approximation. The mode selective behaviour of H2O molecules is almost similar on all the Cu- and Ni-based surfaces. The excitation of symmetric stretching vibration by one quantum is shown to have largest efficacy for promoting reactions for all the systems. Overall, the dissociation probabilities for all the systems are enhanced by vibrational excitation of normal modes and become more significant with the non-adiabatic coupling effect.
A semi-analytic model of gas-puff liner-on-target magneto-inertial fusion
Authors: Narkis J. , Rahman H. U. , Valenzuela J. C. , Conti F. , McBride R. D. , Venosa D. , Beg F. N.
Published: March 2019

A semi-analytic model is presented for the gas-puff Staged Z-pinch, a magneto-inertial fusion concept in which an annular gas-puff liner implodes onto a deuterium or deuterium-tritium target. The one-dimensional model is a modification of the semi-analytic model for MagLIF (SAMM) [R. D. McBride and S. A. Slutz, Phys. Plasmas 22, 052708 (2015)], that addresses the different set of physics inherent to a Staged Z-pinch implosion: azimuthal magnetic field transport, shock heating of the fuel, separate ion and electron energy equations, and a simplified radiation model that approximates the liner transition from optically thin to optically thick. Following the explanation of the model, three sample problems are presented: first, a Staged Z-pinch implosion on the Zebra driver (1 MA, 100 ns) is modeled and compared with the HYDRA simulation results; second, the MagLIF point design is modeled and compared to the original simulation results [S. A. Slutz et al., Phys. Plasmas 17, 056303 (2010)] and results from SAMM; and third, we conduct a simple parameter scan and scaling study for a Staged Z-pinch implosion on the LTD-III driver (0.8 MA, 160 ns). Some agreement with HYDRA and SAMM is obtained, and deuterium-deuterium (DD) neutron yield scaling with current is consistent with other existing models and HYDRA simulations.
Flying focus: Spatial and temporal control of intensity for laser-based applications
Authors: Froula D. H. , Palastro J. P. , Turnbull D. , Davies A. , Nguyen L. , Howard A. , Ramsey D. , Franke P. , Bahk S.-W. , Begishev I. A. , Boni R. , Bromage J. , Bucht S. , Follett R. K. , Haberberger D. , Jenkins G. W. , Katz J. , Kessler T. J. , Shaw J. L. , Vieira J.
Published: March 2019

An advanced focusing scheme, called a “flying focus,” uses a chromatic focusing system combined with a broadband laser pulse with its colors arranged in time to propagate a high intensity focus over a distance that can be much greater than its Rayleigh length while decoupling the speed at which the peak intensity propagates from its group velocity. The flying focus generates a short effective pulse duration with a small diameter focal spot that co- or counter-propagates along the optical axis at any velocity. Experiments validating the concept measured subluminal (−0.09c) to superluminal (39c) focal spot velocities with a nearly constant peak intensity over 4.5 mm. Experiments that increased the peak intensity above the ionization threshold for gas demonstrated ionization waves propagating at the velocity of the flying focus. These ionization waves of any velocity overcome several laser-plasma propagation issues, including ionization-induced refraction. The flying focus presents opportunities to overcome current fundamental limitations in laser-plasma amplifiers, laser wakefield accelerators, photon accelerators, and high-order frequency conversion.
Effect of coating process on the properties of multi-walled carbon nanotubes/waterborne polyurethane anticorrosive and conductive coating
Authors: Wang Fangfang , Feng Lajun , Huang Yingwei , Li Guangzhao , Zhai Zhe
Published: March 2019

A thicker layer of multi-walled carbon nanotubes (MWCNTs)/waterborne polyurethane (WPU) anticorrosive and conductive coating was respectively prepared on the Q235 steel substrate by brushing (Br) and electrostatic spraying (ES) in this work. The effect of coating process on the dispersion of the MWCNTs and the electrical conductivity, corrosion resistance, and bond strength of the coating was investigated. It was shown that the coating prepared by ES (ES coating) had a smooth surface, few defects and evenly dispersed MWCNTs. The coating prepared by Br (Br coating) had a rough surface, some defects and obviously agglomerated MWCNTs. The electrical conductivity, corrosion resistance, and bond strength of the ES coating were higher than those of the Br coating with the same MWCNT content. As the MWCNT content increased, the electrical conductivity of the ES coating increased, however, its corrosion resistance and bond strength first increased and then decreased. The resistivity of ES 0.3 wt% MWCNTs/WPU coating (12808.4 Ω·m) met the standard requirement of the conductive coating. Its corrosion rate was 3.50×10-5 mm/a immersed in 3.5 wt% NaCl solution. Its bond strength to the Q235 steel substrate was higher than that of ES pure WPU coating. As the MWCNT content increased, the electrical conductivity of the Br coating increased, however, its corrosion resistance and bond strength decreased. When the MWCNT content was 0.6 wt%, the Br coating would conduct electricity. Its corrosion rate was 5.24×10-2 mm/a.
Organosulfates in the Midwestern United States: abundance, composition and stability
Authors: Hughes Dagen D. , Stone Elizabeth A.
Published: March 2019

Environmental contextOrganosulfates in the atmosphere are an indicator that particulate matter has formed from gases in the presence of anthropogenic pollution. By characterising organosulfates in atmospheric fine particulate matter from the Midwestern USA, we found that organosulfates account for a significant fraction of organic carbon and that they are associated with both plant-derived and anthropogenic gases. Our results demonstrate that anthropogenic pollution significantly influences atmospheric particle concentrations and composition.
AbstractOrganosulfates are components of secondary organic aerosol resulting from the oxidation of volatile organic compounds in the presence of acidic sulfate. This study characterises organosulfates in the Midwestern United States for the first time. In fine particulate matter (PM2.5) collected in Iowa City, IA, in September 2017, organosulfates were analysed using liquid chromatography coupled to high-resolution and tandem mass spectrometry (MS) to identify and quantify (or semi-quantify) major species. Among the 22 identified species, methyltetrol sulfate (m/z 215; C5H11SO7−) had the largest contribution to the bisulfate (m/z 97) product ion, as determined by precursor-ion MS/MS (59.5% of signal), followed by ten other isoprene-derived organosulfates (15.2%), seven monoterpene-derived organosulfates (5.6%), three anthropogenic organosulfates (4.3%) and one species of unknown origin (0.6%). Among the quantified species were hydroxyacetone sulfate (4.8±1.1ngm−3), glycolic acid sulfate (21.0±1.5ngm−3), 2-methylgyceric acid sulfate (15.1±0.8ngm−3), C5H7SO7− (m/z 211; 17.9±0.9ngm−3), C5H9SO7− (m/z 213; 16.0±1.0ngm−3), and methyltetrol sulfate (214±8ngm−3); together, these species accounted for 4.4% of organic carbon. To further validate the measurement of organic species in PM using filter samples, the stability of organosulfates on filters frozen at −20°C was evaluated over the course of 1 year. The stored samples revealed no degradation of organosulfates, indicating their stability on filters stored frozen for extended periods of time. This study provides new insight into the abundance and identity of organosulfates in the Midwestern US and demonstrates that isoprene-derived organosulfates, in particular, are a significant contributor to PM2.5 organic carbon.
Factors influencing self-management in patients with type 2 diabetes in general practice: a qualitative study
Authors: Dao Julie , Spooner Catherine , Lo Winston , Harris Mark F.
Published: March 2019

Many Australian adults with type 2 diabetes mellitus (T2DM) do not follow recommended self-management behaviours that could prevent or delay complications. This exploratory study aimed to investigate the factors influencing self-management of T2DM in general practice. Semi-structured qualitative interviews were conducted with patients with T2DM (n = 10) and their GPs (n = 4) and practice nurses (n = 3) in a low socioeconomic area of Sydney, New South Wales, Australia. The interviews were analysed thematically using the socio-ecological model as a framework for coding. Additional themes were derived inductively based on the explicitly stated meaning of the text. Factors influencing self-management occurred on four levels of the socio-ecological model: individual (e-health literacy, motivation, time constraints); interpersonal (family and friends, T2DM education, patient-provider relationship); organisational (affordability, multidisciplinary care); and community levels (culture, self-management resources). Multi-level strategies are needed to address this wide range of factors that are beyond the scope of single services or organisations. These could include tailoring health education and resources to e-health literacy and culture; attention to social networks and the patient–provider relationship; and facilitating access to affordable on-site allied health services.
OR14I1 is a receptor for the human cytomegalovirus pentameric complex and defines viral epithelial cell tropism
Authors: E Xiaofei , Meraner Paul , Lu Ping , Perreira Jill M. , Aker Aaron M. , McDougall William M. , Zhuge Ronghua , Chan Gary C. , Gerstein Rachel M. , Caposio Patrizia , Yurochko Andrew D. , Brass Abraham L. , Kowalik Timothy F.
Published: March 2019

Significance

Identifying cell-surface receptors required for viral infection is important for developing antiviral therapies and effective vaccines. Human cytomegalovirus (HCMV) infects epithelial cells during interhost transmission. The pentameric protein complex (PC) was identified as being required for infection of this clinically relevant cell type. The majority of neutralizing antibody responses are directed against the PC. Here we describe an HCMV receptor, OR14I1, which binds to the PC and defines epithelial tropism. Importantly, we identified a peptide representing the N terminus of OR14I1 that blocks HCMV infection of epithelial cells. Moreover, an adenylate cyclase signaling pathway functioning downstream of OR14I1 contributes to HCMV infection and endocytosis. These findings reveal information useful for the development of new anti-HCMV therapies and vaccines.
Development of highly potent glucocorticoids for steroid-resistant severe asthma
Authors: He Yuanzheng , Shi Jingjing , Nguyen Quang Tam , You Erli , Liu Hongbo , Ren Xin , Wu Zhongshan , Li Jianshuang , Qiu Wenli , Khoo Sok Kean , Yang Tao , Yi Wei , Sun Feng , Xi Zhijian , Huang Xiaozhu , Melcher Karsten , Min Booki , Xu H. Eric
Published: March 2019

Clinical application of inhaled glucocorticoids (GCs) has been hampered in the case of steroid-resistant severe asthma. To overcome this limitation, we have developed a series of highly potent GCs, including VSGC12, VSG158, and VSG159 based on the structural insight into the glucocorticoid receptor (GR). Particularly, VSG158 exhibits a maximal repression of lung inflammation and is 10 times more potent than the currently most potent clinical GC, Fluticasone Furoate (FF), in a murine model of asthma. More importantly, VSG158 displays a unique property to reduce neutrophilic inflammation in a steroid-resistant airway inflammation model, which is refractory to clinically available GCs, including dexamethasone and FF. VSG158 and VSG159 are able to deliver effective treatments with reduced off-target and side effects. In addition, these GCs also display pharmacokinetic properties that are suitable for the inhalation delivery method for asthma treatment. Taken together, the excellent therapeutic and side-effect profile of these highly potent GCs holds promise for treating steroid-resistant severe asthma.
Genome of
Crucihimalaya himalaica
, a close relative of
Arabidopsis
, shows ecological adaptation to high altitude
Authors: Zhang Ticao , Qiao Qin , Novikova Polina Yu. , Wang Qia , Yue Jipei , Guan Yanlong , Ming Shengping , Liu Tianmeng , De Ji , Liu Yixuan , Al-Shehbaz Ihsan A. , Sun Hang , Van Montagu Marc , Huang Jinling , Van de Peer Yves , Qiong La
Published: March 2019

Crucihimalaya himalaica
, a close relative of
Arabidopsis
and
Capsella
, grows on the Qinghai–Tibet Plateau (QTP) about 4,000 m above sea level and represents an attractive model system for studying speciation and ecological adaptation in extreme environments. We assembled a draft genome sequence of 234.72 Mb encoding 27,019 genes and investigated its origin and adaptive evolutionary mechanisms. Phylogenomic analyses based on 4,586 single-copy genes revealed that
C. himalaica
is most closely related to
Capsella
(estimated divergence 8.8 to 12.2 Mya), whereas both species form a sister clade to
Arabidopsis thaliana
and
Arabidopsis lyrata
, from which they diverged between 12.7 and 17.2 Mya. LTR retrotransposons in
C. himalaica
proliferated shortly after the dramatic uplift and climatic change of the Himalayas from the Late Pliocene to Pleistocene. Compared with closely related species,
C. himalaica
showed significant contraction and pseudogenization in gene families associated with disease resistance and also significant expansion in gene families associated with ubiquitin-mediated proteolysis and DNA repair. We identified hundreds of genes involved in DNA repair, ubiquitin-mediated proteolysis, and reproductive processes with signs of positive selection. Gene families showing dramatic changes in size and genes showing signs of positive selection are likely candidates for
C. himalaica
’s adaptation to intense radiation, low temperature, and pathogen-depauperate environments in the QTP. Loss of function at the S-locus, the reason for the transition to self-fertilization of
C. himalaica
, might have enabled its QTP occupation. Overall, the genome sequence of
C. himalaica
provides insights into the mechanisms of plant adaptation to extreme environments.
Growth factor stimulation promotes multivesicular endosome biogenesis by prolonging recruitment of the late-acting ESCRT machinery
Authors: Quinney Kyle B. , Frankel Elisa B. , Shankar Raakhee , Kasberg William , Luong Peter , Audhya Anjon
Published: March 2019

Significance

The formation of multivesicular endosomes (MVEs) enables the sequestration of numerous membrane-associated cargo molecules, including signaling receptors, to downregulate signal transduction pathways initiated by various stimuli. In this work, we demonstrate that the machinery responsible for MVE biogenesis responds to growth factor stimulation by extending its duration of action at endosomes. Specifically, we show that endosomal sorting complex required for transport-I (ESCRT-I) and Vps4 accumulation at MVEs is dramatically prolonged following growth factor stimulation. Additionally, we demonstrate that native ESCRT complexes exhibit an oscillatory behavior on endosomes, which is dependent on the sequential recruitment of downstream components. Our studies strongly suggest that components of the ESCRT machinery act cyclically and in a coordinated manner to enable a rapid response to changing environmental cues.
Host−guest complexation-mediated codelivery of anticancer drug and photosensitizer for cancer photochemotherapy
Authors: Yu Guocan , Zhu Benyue , Shao Li , Zhou Jiong , Saha Manik Lal , Shi Bingbing , Zhang Zibin , Hong Tao , Li Shijun , Chen Xiaoyuan , Stang Peter J.
Published: March 2019

Significance

The combination of chemotherapy and photodynamic therapy opens up a promising way of overcoming drug resistance, incorporating different mechanisms of actions to achieve synergistic efficacy. However, the antitumor outcome of photodynamic therapy is greatly limited due to the unsatisfactory singlet oxygen generation caused by severe aggregation of the photosensitizer. To this end, we utilize a discrete metallacage containing therapeutic organoplatinum(II) to encapsulate a photosensitizer by forming an inclusion host–guest complex, facilitating the codelivery of chemotherapeutic agent and photosensitizer through nanoformulation. Benefiting from the enhanced permeability and retention effect and active targeting, the nanomedicine exhibits satisfactory antitumor performance against drug-resistant tumor. This pioneering work provides a distinct supramolecular methodology to prepare theranostic systems for multimodality imaging and therapy.
Transition from weak to strong turbulence in magnetized plasmas
Authors: Bratanov Vasil , Mahajan Swadesh , Hatch David
Published: March 2019

The scaling of turbulent heat flux with respect to electrostatic potential is examined in the framework of a reduced (4D) kinetic system describing electrostatic turbulence in magnetized plasmas excited by the ion temperature gradient instability. Numerical simulations were instigated by, and tested the predictions of generic renormalized turbulence models like the 2D fluid model for electrostatic turbulence (Zhang and Mahajan 1993 Phys. Fluids B 5 2000). A fundamental, perhaps, universal result of this theory-simulation combination is the demonstration that there exist two distinct asymptotic states (that can be classified as weak turbulence (WT) and strong turbulence (ST) states) where the turbulent diffusivity Q scales quite differently with the strength of turbulence measured by the electrostatic energy

∥
ϕ

∥

2

. In the case of WT

Q
∝
∥
ϕ

∥

2

, while in ST Q has a weaker dependence on the electrostatic energy and scales as

∥
ϕ
∥

.
Deducing Selberg trace formula via Rankin–Selberg method for 𝐺𝐿₂
Authors: Wu Han
Published: March 2019

In the 1980s, Zagier and Jacquet and Zagier tried to derive the Selberg trace formula by applying the Rankin–Selberg method to the automorphic kernel function. Their derivation was incomplete due to a puzzle of the computation of a residue. We solve this puzzle and complete the derivation. The main input is an extension of the theory of regularized integrals invented by Zagier, which is of independent interest.
In vitro BioID: mapping the CENP-A microenvironment with high temporal and spatial resolution
Authors: Remnant Lucy , Booth Daniel G. , Vargiu Giulia , Spanos Christos , Kerr Alastair R. W. , Earnshaw William C.
Published: March 2019

The centromere is located at the primary constriction of condensed chromosomes where it acts as a platform regulating chromosome segregation. The histone H3 variant CENP-A is the foundation for kinetochore formation. CENP-A directs the formation of a highly dynamic molecular neighborhood whose temporal characterization during mitosis remains a challenge due to limitations in available techniques. BioID is a method that exploits a “promiscuous” biotin ligase (BirA118R or BirA*) to identify proteins within close proximity to a fusion protein of interest. As originally described, cells expressing BirA* fusions were exposed to high biotin concentrations for 24 h during which the ligase transferred activated biotin (BioAmp) to other proteins within the immediate vicinity. The protein neighborhood could then be characterized by streptavidin-based purification and mass spectrometry. Here we describe a further development to this technique, allowing CENP-A interactors to be characterized within only a few minutes, in an in vitro reaction in lysed cells whose physiological progression is “frozen.” This approach, termed in vitro BioID (ivBioID), has the potential to study the molecular neighborhood of any structural protein whose interactions change either during the cell cycle or in response to other changes in cell physiology.
The ecology and significance of below-ground bud banks in plants
Authors: Ott Jacqueline P , Klimešová Jitka , Hartnett David C
Published: March 2019

Background

Below-ground bud banks have experienced much recent interest due to discoveries that they (1) account for the majority of seasonal population renewal in many communities, (2) are crucial to regeneration following disturbance, and (3) have important consequences for plant population dynamics and plant and ecosystem function across a number of habitats.

Scope

This review presents an overview of the role of bud banks in plant population renewal, examines bud bank life history, summarizes bud bank traits and their potential ecological implications, synthesizes the response of bud banks to disturbance, and highlights gaps to guide future research. The characteristics and life history of buds, including their natality, dormancy, protection and longevity, provide a useful framework for advancing our understanding of bud banks. The fate of buds depends on their age, size, type, location, and biotic and abiotic factors that collectively regulate bud bank dynamics. A bud bank can provide a demographic storage effect stabilizing population dynamics, and also confer resistance to disturbance and invasion. Regeneration capacity following disturbance is determined by interactions among the rates of bud natality, depletion and dormancy (meristem limitation), and the resources available to support the regeneration process. The resulting response of plants and their bud banks to disturbances such as fire, herbivory and anthropogenic sources determines the community’s regenerative capacity.

Conclusions

Vegetation responses to environmental change may be mediated through changes in bud bank dynamics and phenology. Environmental change that depletes the bud bank or prohibits its formation likely results in a loss of vegetation resilience and plant species diversity. Standardization of bud sampling, examination of bud banks in more ecosystems and their response to environmental variation and disturbance regimes, employment of stage-structured bud bank modelling and evaluation of the cost of bud bank construction and maintenance will benefit this expanding field of research.
Sharing the burden: on the division of parental care and vocalizations during incubation
Authors: Kavelaars Marwa M , Lens Luc , Müller Wendt
Published: March 2019

In species with biparental care, individuals only have to pay the costs for their own parental investment, whereas the contribution of their partner comes for free. Each parent hence benefits if its partner works harder, creating an evolutionary conflict of interest. How parents resolve this conflict and how they achieve the optimal division of parental tasks often remains elusive. In this study, we investigated whether lesser black-backed gulls (Larus fuscus) divide parental care during incubation equally and whether this correlates with the extent of vocalizations between pair-members during incubation. We then investigated whether pairs showing more evenly distributed incubation behavior had a higher reproductive success. To this end, we recorded incubation behavior and vocalizations for 24-h time periods. Subsequently, we experimentally increased or decreased brood sizes in order to manipulate parental effort, and followed offspring development from hatching till fledging. Although incubation bouts were, on average, slightly longer in females, patterns varied strongly between pairs, ranging from primarily female incubation over equal sex contributions to male-biased incubation. Pairs contributing more equally to incubation vocalized more during nest relief and had a higher reproductive output when brood sizes were experimentally increased. Thus, vocalizations and a more equal division of parental care during incubation may facilitate higher levels of care during the nestling period, as suggested by a greater reproductive success when facing high brood demand, or they indicate pair quality.
Invasive shrubs modify rodent activity timing, revealing a consistent behavioral rule governing diel activity
Authors: Guiden Peter W , Orrock John L
Published: March 2019

Animals adjust the timing of their activity to maximize benefits, such as access to resources, and minimize costs, such as exposure to predators. Despite many examples of invasive plants changing animal behavior, the potential for invasive plants to alter the timing of animal activity remains unexplored. In eastern North America, invasive shrubs might have particularly strong effects on animal activity timing during spring and fall, when many invasive shrubs retain their leaves long after native species’ leaves senesce. We experimentally removed an invasive shrub (buckthorn, Rhamnus cathartica) and monitored the activity timing of a ubiquitous small-mammal species (white-footed mouse, Peromyscus leucopus) in spring, summer, and fall. We captured nearly 3 times as many P. leucopus in plots invaded by R. cathartica compared with plots with R. cathartica removed, and P. leucopus were captured 2 h earlier in invaded plots. Regardless of invasion treatment, P. leucopus appear to follow a common rule to set activity timing: P. leucopus were only active below a threshold of ground-level moonlight illuminance (0.038 lux). Diel and monthly lunar cycles play an important role in regulating small-mammal activity, but our data suggest that decreased light penetration dampens the influence of moonlight illuminance in habitats invaded by R. cathartica, allowing P. leucopus to remain active throughout the night. By changing the temporal niche of ubiquitous native animals, invasive shrubs may have unappreciated effects on many ecological interactions, including processes that alter community diversity and affect human health.
BrAPI—an application programming interface for plant breeding applications
Authors: Selby Peter , Abbeloos Rafael , Backlund Jan Erik , Basterrechea Salido Martin , Bauchet Guillaume , Benites-Alfaro Omar E , Birkett Clay , Calaminos Viana C , Carceller Pierre , Cornut Guillaume , Vasques Costa Bruno , Edwards Jeremy D , Finkers Richard , Yanxin Gao Star , Ghaffar Mehmood , Glaser Philip , Guignon Valentin , Hok Puthick , Kilian Andrzej , König Patrick , Lagare Jack Elendil B , Lange Matthias , Laporte Marie-Angélique , Larmande Pierre , LeBauer David S , Lyon David A , Marshall David S , Matthews Dave , Milne Iain , Mistry Naymesh , Morales Nicolas , Mueller Lukas A , Neveu Pascal , Papoutsoglou Evangelia , Pearce Brian , Perez-Masias Ivan , Pommier Cyril , Ramírez-González Ricardo H , Rathore Abhishek , Raquel Angel Manica , Raubach Sebastian , Rife Trevor , Robbins Kelly , Rouard Mathieu , Sarma Chaitanya , Scholz Uwe , Sempéré Guilhem , Shaw Paul D , Simon Reinhard , Soldevilla Nahuel , Stephen Gordon , Sun Qi , Tovar Clarysabel , Uszynski Grzegorz , Verouden Maikel ,   The BrAPI consortium
Published: March 2019

Motivation

Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge.

Results

To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases.

Availability and implementation

More information on BrAPI, including links to the specification, test suites, BrAPPs, and sample implementations is available at https://brapi.org/. The BrAPI specification and the developer tools are provided as free and open source.
Enhanced Waddington landscape model with cell–cell communication can explain molecular mechanisms of self-organization
Authors: Fooladi Hosein , Moradi Parsa , Sharifi-Zarchi Ali , Hosein Khalaj Babak
Published: March 2019

Motivation

The molecular mechanisms of self-organization that orchestrate embryonic cells to create astonishing patterns have been among major questions of developmental biology. It is recently shown that embryonic stem cells (ESCs), when cultured in particular micropatterns, can self-organize and mimic the early steps of pre-implantation embryogenesis. A systems-biology model to address this observation from a dynamical systems perspective is essential and can enhance understanding of the phenomenon.

Results

Here, we propose a multicellular mathematical model for pattern formation during in vitro gastrulation of human ESCs. This model enhances the basic principles of Waddington epigenetic landscape with cell–cell communication, in order to enable pattern and tissue formation. We have shown the sufficiency of a simple mechanism by using a minimal number of parameters in the model, in order to address a variety of experimental observations such as the formation of three germ layers and trophectoderm, responses to altered culture conditions and micropattern diameters and unexpected spotted forms of the germ layers under certain conditions. Moreover, we have tested different boundary conditions as well as various shapes, observing that the pattern is initiated from the boundary and gradually spreads towards the center. This model provides a basis for in-silico modeling of self-organization.

Availability and implementation

https://github.com/HFooladi/Self_Organization.

Supplementary information

Supplementary data are available at Bioinformatics online.
IsoCor: isotope correction for high-resolution MS labeling experiments
Authors: Millard Pierre , Delépine Baudoin , Guionnet Matthieu , Heuillet Maud , Bellvert Floriant , Létisse Fabien
Published: March 2019

Mass spectrometry (MS) is widely used for isotopic studies of metabolism and other (bio)chemical processes. Quantitative applications in systems and synthetic biology require to correct the raw MS data for the contribution of naturally occurring isotopes. Several tools are available to correct low-resolution MS data, and recent developments made substantial improvements by introducing resolution-dependent correction methods, hence opening the way to the correction of high-resolution MS (HRMS) data. Nevertheless, current HRMS correction methods partly fail to determine which isotopic species are resolved from the tracer isotopologues and should thus be corrected. We present an updated version of our isotope correction software (IsoCor) with a novel correction algorithm which ensures to accurately exploit any chemical species with any isotopic tracer, at any MS resolution. IsoCor v2 also includes a novel graphical user interface for intuitive use by end-users and a command-line interface to streamline integration into existing pipelines.

Availability and implementation

IsoCor v2 is implemented in Python 3 and was tested on Windows, Unix and MacOS platforms. The source code and the documentation are freely distributed under GPL3 license at https://github.com/MetaSys-LISBP/IsoCor/ and https://isocor.readthedocs.io/.
TISIDB: an integrated repository portal for tumor–immune system interactions
Authors: Ru Beibei , Wong Ching Ngar , Tong Yin , Zhong Jia Yi , Zhong Sophia Shek Wa , Wu Wai Chung , Chu Ka Chi , Wong Choi Yiu , Lau Chit Ying , Chen Ian , Chan Nam Wai , Zhang Jiangwen
Published: March 2019

The interaction between tumor and immune system plays a crucial role in both cancer development and treatment response. To facilitate comprehensive investigation of tumor–immune interactions, we have designed a user-friendly web portal TISIDB, which integrated multiple types of data resources in oncoimmunology. First, we manually curated 4176 records from 2530 publications, which reported 988 genes related to anti-tumor immunity. Second, genes associated with the resistance or sensitivity of tumor cells to T cell-mediated killing and immunotherapy were identified by analyzing high-throughput screening and genomic profiling data. Third, associations between any gene and immune features, such as lymphocytes, immunomodulators and chemokines, were pre-calculated for 30 TCGA cancer types. In TISIDB, biologists can cross-check a gene of interest about its role in tumor–immune interactions through literature mining and high-throughput data analysis, and generate testable hypotheses and high quality figures for publication.

Availability and implementation

http://cis.hku.hk/TISIDB

Supplementary information

Supplementary data are available at Bioinformatics online.