bluuebunny/crossref_metadata_2025 huggingface dataset:
Rate-independent and ultra-stable low-temperature sodium storage in pseudocapacitive TiO2nanowires
Authors: Lin Dongmei , Li Kaikai , Wang Qian , Lyu Linlong , Li Baohua , Zhou Limin
Published: July 2019

Low-temperature induced pseudocapacitance results in rate-independent and ultra-stable sodium storage in dual-phase TiO2nanowires.
First-principles study of alkali-metal intercalation in disordered carbon anode materials
Authors: Huang Jian-Xing , Csányi Gábor , Zhao Jin-Bao , Cheng Jun , Deringer Volker L.
Published: July 2019

The intercalation of alkali metals in disordered carbon anode materials is studied by a combination of first-principles and machine-learning methods.
Bimetallic nanoparticle decorated perovskite oxide for state-of-the-art trifunctional electrocatalysis
Authors: Islam Quazi Arif , Majee Rahul , Bhattacharyya Sayan
Published: July 2019

B-site cation exsolution in perovskite oxide (ABO3) catalyst to surface decorated bimetallic nanoparticles facilitates the usually arduous trifunctional electrocatalytic activity towards oxygen reduction and water oxidation cum reduction reactions.
Understanding the characteristics of conducting polymer-redox biopolymer supercapacitors
Authors: Bamgbopa Musbaudeen O. , Edberg Jesper , Engquist Isak , Berggren Magnus , Tybrandt Klas
Published: July 2019

A model is developed to explain and predict the characteristics of conducting polymer-redox biopolymer supercapacitors.
Migration of endothelial cells and mesenchymal stem cells into hyaluronic acid hydrogels with different moduli under induction of pro-inflammatory macrophages
Authors: Duan Yiyuan , Li Xuguang , Zuo Xingang , Shen Tao , Yu Shan , Deng Linhong , Gao Changyou
Published: July 2019

Endothelial cells and mesenchymal stem cells migrate easily into double-network hydrogels with smaller and larger moduli, respectively.
Baseline designing and implementation approach for a Geo‐SAR tomography system
Authors: Bingji Zhao , Qingun Zhang , Chao Dai , Weiping Shu , MingMing Xu
Published: July 2019

This study proposes a new method to design and implement the baseline of a geosynchronous Earth orbit synthetic aperture radar (Geo‐SAR) tomography system. Due to the satellite's orbital property, its ideal revisit cycle is 1 day, and it could be changed through raising or lowering the orbital height. As a result, the local ascending node longitude would move because of the orbital shifting, and all the passes' trajectories are nearly parallel. A baseline designing and implementation approach is advanced according to this characteristic. The cell array configuration and baseline length are illustrated by considering the demand of cross‐range resolution and ambiguity. This study analyses and simulates the Geo‐SAR tomography system baseline properties. Furthermore, a series of parallel trajectories are implemented by controlling orbital altitude as demanding during each cycle. A simulation experiment is performed to verify the efficiency and superiority of this approach, and the results show that it has a good effect on an L‐band mode Geo‐SAR tomography system with three‐dimensional resolution ∼10 m.
Corner target positioning with unknown walls' positions
Authors: Fan Shihao , Cui Guolong , Guo Shisheng , Kong Lingjiang , Yang Xiaobo , Yuan Xingsheng
Published: July 2019

Here we consider a corner target positioning problem under the condition of unknown walls' positions using time‐division multiple‐input‐multiple‐output (MIMO) radar. Firstly, we propose an estimation algorithm for the walls' positions using the Back‐Projection (BP) imaging algorithm. Then, after obtaining the BP image of target, we extract the focus regions produced by different multipaths. Finally, we obtain the position of the target based on the extracted walls' positions and the focus regions. Simulations and experiments results validate the proposed algorithm.
Accuracy analysis of multi‐base InSAR altimeter in ocean surface relative elevation measurement
Authors: Liu Bo , Zhang Running , Wan Xiaoyun , Li Yang , Yuan Shigeng
Published: July 2019

A new sea‐level elevation measurement system was introduced, which uses a distributed multi‐base forward‐scattering mechanism. After introducing the working principle of the system, this study analyses the main influencing factors of relative elevation measurement in detail. It is proved through quantitative expression that the interferometric phase error is the main error source affecting relative elevation measurement. In order to evaluate the system capability and prove that the multi‐base InSAR ( MbInSAR) can meet the application requirements of gravity field inversion through relative ocean surface elevation measurement, three aspects of decorrelation, geometric decorrelation, volumetric decorrelation, and SNR decorrelation, are analysed as the interferometric phase error sources.
Modulation classification based on denoising autoencoder and convolutional neural network with GNU radio
Authors: Wang Jun , Wang Wenfeng , Luo Feixiang , Wei Shaoming
Published: July 2019

In this article, a machine learning method to classify signal with Gaussian noise based on denoising auto encoder (DAE) and convolutional neural network (CNN) is proposed. We combine denoising autoencoder's denoising ability with CNN's feature extraction capability. First, a six‐layer neural network is built, including three CNN layers. Then a dataset containing noiseless signal of 11 modulation is generated. In the simulation, we apply this dataset to train neural network and achieve an accuracy of 94%, which is much higher than performance with noisy signal, meaning that noise can greatly influence the accuracy of neural network. Next, we build a denoising autoencoder and train it with signal of 5 dB signal‐to‐noise ratio (SNR). Compared with neural network without denoising autoencoder, adding a denoising autoencoder can achieve an accuracy of 84% at signal of 18 dB SNR, improved by 58%.
SAR image compression using optronic processing
Authors: Ma Jiacheng , Yang Baozhang , Gao Yesheng , Tao Lei , Liu Xingzhao
Published: July 2019

SAR image compression is important for space‐borne SAR systems. Many compression methods were proposed, conventional methods were based on digital processing. Traditional methods are much computation and storage consumption. A novel SAR image compression method is proposed here. In the method, SAR image compression is based on the discrete cosine transform (DCT), and it is applied using optronic processing. Both the speckle denoising and the processing of cosine spectrum coefficient are presented in authors’ experiments, which are the crucial parts in SAR image compression. The final experimental result verifies the feasibility of the method.
2D scattering centre intensity pre‐estimated method based on matrix pencil method
Authors: Wang Jun , Lu Yao , Wei Shaoming
Published: July 2019

The accuracy of ultra wide band (UWB) scattering centre parameter estimation is the key bases in the study of target classification and identification. A novel 2D scattering centre parameter estimation algorithm for microwave chamber target is presented here. First, by using GTD model, this method constructs the microwave chamber measured data. Second, using matrix pencil method to build Hankel Matrix as a mathematic progress to estimate position parameter of scattering centres. Third, the type parameter and reflection intensity are estimated based on the least square method and principal components analysis. Using pre‐estimated reflection intensity and clean technique to correctly determine scattering centre number and precisely estimate the reflection intensity of every scattering centres even if the intensity gap between the scattering centres is huge. The simulation results show that this novel approach can accurately and effectively determine the number and the parameters of the scattering centres. The Cramer–Rao lower bound (CRLB) is also given.
Aerial target classification based on feature analysis
Authors: Wu Jiaojiao , Li Ming , Zuo Lei , Liu Huimin
Published: July 2019

Aircrafts are widespread used in the modern warfare. A radar therefore should have the capability to classify and identify the aerial targets. In this study, a method based on feature analysis is proposed to classify and identify the aircraft targets. First, multiple features are extracted and analysed for further utilisation, including Doppler shift, relative amplitude, waveform entropy of time and frequency domain, and time–frequency characteristics. Second, the features are employed for classification purpose by means of the support vector machine. Moreover, a method is presented to identify the helicopter with odd or even number of blades, owing to the width of time–frequency distributions of the returned signals. The performance of the discussed method is verified with the experimental results of measured data.
Coherent integration method for random pulse repetition interval radar based on non‐uniform keystone transform and non‐uniform fast Fourier transform
Authors: Liu He , Tian Jing , Ning Chen , Cui Wei , Deng Jingjing
Published: July 2019

In order to achieve weak target detection, the range migration and Doppler frequency spread induced by the target motion within the coherent processing interval should be compensated to focus the target energy in a certain range‐Doppler cell. This article proposes a new integration method based on non‐uniform Keystone transform and non‐uniform fast Fourier transform (NUFFT) for random pulse repetition interval (PRI) radar. In this method, non‐uniform Keystone transform is applied to correct the linear range migration. After that, the acceleration is estimated by dechirp process and the Doppler frequency spread is compensated. Finally, the target energy is accumulated coherently via NUFFT. Compared with the random PRI generalised Radon‐Fourier transform (RPRI‐GRFT) and the moving target detection method for random PRI radar, the proposed algorithm achieves a good balance between the detection performance and the computational cost. Simulation results are provided to demonstrate the effectiveness of the proposed method.
The Hubble PanCET program: an extensive search for metallic ions in the exosphere of GJ 436 b
Authors: dos Santos L. A. , Ehrenreich D. , Bourrier V. , Lecavelier des Etangs A. , López-Morales M. , Sing D. K. , Ballester G. , Ben-Jaffel L. , Buchhave L. A. , García Muñoz A. , Henry G. W. , Kataria T. , Lavie B. , Lavvas P. , Lewis N. K. , Mikal-Evans T. , Sanz-Forcada J. , Wakeford H.
Published: July 2019

Context. The quiet M2.5 star GJ 436 hosts a warm Neptune that displays an extended atmosphere that dwarfs its own host star. Predictions of atmospheric escape in such planets state that H atoms escape from the upper atmosphere in a collisional regime and that the flow can drag heavier atoms to the upper atmosphere. It is unclear, however, what astrophysical mechanisms drive the process.

Aims. Our objective is to leverage the extensive coverage of observations of the far-ultraviolet (FUV) spectrum of GJ 436 obtained with the Cosmic Origins Spectrograph (COS) to search for signals of metallic ions in the upper atmosphere of GJ 436 b, as well as study the activity-induced variability of the star.

Methods. We analyzed flux time-series of species present in the FUV spectrum of GJ 436 and successfully performed geocoronal contamination removal in the COS Lyman-α profiles obtained near the Earth’s night-side.

Results. GJ 436 displays flaring events with a rate of ~10 d−1. There is evidence for a possibly long-lived active region or longitude that modulates the FUV metallic lines of the star with amplitudes up to 20%. Despite the strong geocoronal contamination in the COS spectra, we detected in-transit excess absorption signals of ~50 and ~30% in the blue and red wings, respectively, of the Lyman-α line. We rule out a wide range of excess absorption levels in the metallic lines of the star during transit.

Conclusions. The large atmospheric loss of GJ 436 b observed in Lyman-α transmission spectra is stable over the timescale of a few years, and the red wing signal supports the presence of a variable hydrogen absorption source besides the stable exosphere. The previously claimed in-transit absorption in the Si III line is likely an artifact resulting from the stellar magnetic cycle. The non-detection of metallic ions in absorption could indicate that the escape is not hydrodynamic or that the atmospheric mixing is not efficient in dragging metals high enough for sublimation to produce a detectable escape rate of ions to the exosphere.
Osteonecrosis of the Femoral Head: Can Arthroplasty be Avoided—A Brief Review of Common Interventions
Authors: Einhorn Thomas A. , Anoushiravani Afshin A. , Chen Kevin K. , Draper Thomas , Tsismenakis Tony , Iorio Richard
Published: July 2019

Osteonecrosis of the femoral head (ONFH) is a rapidly progressive degenerative disease frequently affecting individuals within their fourth and fifth decade of life. Though often asymptomatic, patients with ONFH may present with a wide range of symptoms, including deep groin pain. There are many classification systems used to stratify disease severity, of which the Association of Research Circulation Osseous (ARCO) classification system is currently the most comprehensive. Once diagnosed, an estimated 75% of patients will experience femoral head collapse within three years of diagnosis if left untreated. Currently, the only definitive intervention available for ONFH is total hip arthroplasty (THA). However, recent advancements have been made with respect to the available treatment modalities. In this article, the author review the management of ONFH, providing clinicians with the necessary information to counsel their patients.
A synopsis of the genus Bazzania (Marchantiophyta: Lepidoziaceae) in Australia
Authors: Meagher David A.
Published: July 2019

Thirty-five species of the liverwort genus Bazzania are recognised from Australia, including eleven endemics. The greatest diversity is in the Australian Wet Tropics bioregion in northern Queensland, where 28 species are known to exist. Keys to northern and southern Australian species are provided, and each species is described and illustrated. Bazzania uncigera (Reinw., Blume & Nees) Trevis. is newly reported for Australia.
Antitumor effects of MutT homolog 1 inhibitors in human bladder cancer cells
Authors: Lee Jeong Woo , Lee Sangchul , Ho Jin-Nyoung , Youn Je-In , Byun Seok-Soo , Lee Eunsik
Published: July 2019

As standard second-line regimen has not been established for patients who are refractory to or relapse with cisplatin-based chemotherapy, an effective class of novel chemotherapeutic agents is needed for cisplatin-resistant bladder cancer. Recent publications reported that MutT homolog 1 (MTH1) inhibitors suppress tumor growth and induce impressive therapeutic responses in a variety of human cancer cells. Few studies investigated the cytotoxic effects of MTH1 inhibitors in human bladder cancer. Accordingly, we investigated the antitumor effects and the possible molecular mechanisms of MTH1 inhibitors in cisplatin-sensitive (T24) and – resistant (T24R2) human bladder cancer cell lines. These results suggest that TH588 or TH287 may induce cancer cell suppression by off-target effects such as alterations in the expression of apoptosis- and cell cycle-related proteins rather than MTH1 inhibition in cisplatin-sensitive and – resistant bladder cancer cells.

Abbreviations: MTH: MutT homolog; ROS: reactive oxygen species; CCK-8: cell counting kit-8; DCFH-DA: dichlorofluorescein diacetate; PARP: poly (ADP-ribose) polymerase
Worlds of last-resort safety nets? A proposed typology of minimum income schemes in Europe
Authors: Natili Marcello
Published: July 2019

Over the past twenty years, minimum income schemes (MIS) have undergone major transformations in their functions and role. From mainly residual instruments that aimed to guarantee minimum income support and to prevent extreme marginality, in most countries they now have an ambiguous function of providing income support and favouring social and labour market inclusion. Against this background, this article provides an analytical grid that allows describing the different features of last-resort safety nets across Europe, building on the definition of key main dimensions of variation of MISs in Europe – generosity, eligibility and conditionality requirements, institutional configuration, active inclusion profiles. Then, it introduces a new typology of MIS in Europe, building on a new dataset with data on expenditures and coverage collected from National Statistical Offices.
The Effect of Temperature on Structural and optical properties of Manganese Oxide Nanoparticles
Authors: Kareem Jassem Esraa , Mustafa Abdul Majeed Aseel , Mossa Umran Nibras
Published: July 2019

Manganse Oxide nanoparticles from different phase have been prepared by simple chemical method with different temperature. The cubic MnO nanoparticles synthesis from 600°C and transformation to tetragonal MnO2nanopaticles and transformation at 800°C to cubic Mn2O3 nanoparticles. X-ray diffraction and FTIR and UV-Visible have been investigated and crystallite size was calculated using Debye-Scherers equation and it is found to be around (23.4-25.66)nm
DOA-estimation methods with superresolution comparison depending on directivity factor of directive elements of conformal and planar antenna arrays on azimuth-elevation planes
Authors: Aalmuttar Atheer Y.O.
Published: July 2019

Direction finding is widely spread and highly researching area. There are lots of methods to estimate spatial positions of radio sources. It is well known that maximum likelihood estimation method gives the highest accuracy and is capable of reaching Cramer-Rao bound. The main task of the paper is to research of direction-of-arrival estimation methods with super resolution such as MUSIC, Capon etc. Also the methods are not researched deeply for 2D (azimuth and elevation planes) scenarios via conformal and planar antenna arrays with directive elements. The root mean square error (RMSE) rate of estimates by the methods with super resolution such as MUSIC, Capon etc. in azimuth-evaluation cases are calculated via simulation depending on directivity ratio of elements as well as the probability of resolution and spatial spectrum bias. Additionally, the values are estimated in various noise environments and for various geometries of antenna arrays. Some features of functioning MUSIC direction-finding method for azimuth and elevation estimation as a part of the conformal and planar with directive elements are determined. One of the most dangerous features is false peaks which prevent exact spatial coordinate estimation and the processing speed of each method under consideration.
Effect of the Applied Pressure on the Essential Characteristics of Sodium Starch Glycolate Tablets
Authors: Mousa Al-Ibraheemi Zahraa A. , Basim Mahdi Ali , Taip F. S. , Anuar M. S.
Published: July 2019

Immediate onset of action in a lot of cases is extensively used than ordinary therapy, however; produce tablets with acceptable features as tensile strength, suitable with acceptable industrial limits, reduced ordered unit segregation tendency, and rapidly or appropriate disintegration time, is a classic problem. Use disintegrant is considered one of corner stone to achieve pharmaceutical tablets that meet requirements of recommended tablet formulation in the markets. Sodium Starch Glycolate as an elastic material (super disintegrant) is the component of compacted tablets by direct compression in current work. Uniaxial compaction process was implemented by utilizing a universal testing machine. The tablets were compacted under applied load ranging from 75 to 375 MPa. A 13 mm diameter cylindrical die was used to characterize the compression behaviour of the 1.0 ± 0.01 g of material. Number of the evidences from this study is, the tabletted powder characteristics and the volume-pressure measurements relationship were investigated. The recommended tablet formulations were evaluated by using elastic relaxation, indirect tensile strength, friability, and disintegration tests.

Applying load higher than 150 Mpa produces compacts with a longer disintegration time, low elastic relaxation, in addition to tensile strength and friability percentage identical to recommended tablets formulation in the markets.
Synthesis of a Novel 4,4’-[1,4-phenylenebis(1,3,4-thiadiazole-5,2-diyl)] bis(azaneylylidene) bis(methaneylylidene) diphenol and Determination of Its pharmacological and antimicrobial Activities
Authors: Saeed Ban M.S. , Al-jadaan Shaker A.N. , Abbas Basil A.
Published: July 2019

The Cytotoxic activity, median lethal dose (LD50) and the biological activity of new Schiff base compound was determined at 100, 150, 200 and 250 mg/ml against four types of bacteria i.e. Bacillus cereus, Staphylococcus aureus, Escherichia coli and Slmonella sp. and its minimum inhibitory concentration (MIC) was 2,5,4,5 mg/ml for Bacillus cereus, Staphylococcus aureus, Escherichia coli and Slmonella sp. respectively. Median lethal dose (LD50) and cytotoxic activity were also investigated. The results showed that this compound did not affect the red blood until the concentration reach 100mg/ml or above. The LD50 for the compound is 0.28278 gm/kg bw.
Water Desalination Using a New Humidification-Dehumidification (HDH) Technology
Authors: Fares Mohamad N. , Al-Mayyahi Mohammad A. , Rida Mustafa M. , Najim Saleh E.
Published: July 2019

The high global population rate has driven the demand for fresh water to increase rapidly. However, the scarcity of fresh water is creating an escalating pressure on the global community to find other alternative water resources such as wastewater reuse and desalination. Desalination is an effective technique for providing fresh water supply. However, most of current desalination technologies consume large amount of energy. Hence, the cost of fresh water produced is strongly depends on the cost of energy used in the desalination processes. For this purpose, a new water desalination system has been developed through theintegration of a thermal pump system, wetting technology and dehumidification. Power consumption in water desalination has been reduced by controlling water and air flow rates in the new system. The results showed that 1.71 kg/h of fresh water could be produced using only 0.726 kWh which is an important achievement in reducing the energy consumed in the water desalination in small capacity units.
Motivational efficacy of lasers on marrow haemopoetic cells
Authors: Ali Kasim O. H. , Ihsan  , Rostum F. , Al-Idani Mohammed S.
Published: July 2019

Lasers has been proved to increase tissue oxygenation, activate marrow progenitor cells, expanse the microcirculation, accelerate the restoration of functions, stimulate adaptation ability and stabilization of the hormonal status. The semisolid tissue present in the epiphysis of the bone where it’s structure is spongy or cancellous is bone marrow and it formed about 4% of body weight, the marrow is composed of hemopoietic cells, however, the structure of the marrow is of both cellular and non – cellular components. The hemopoietic stem cells are responsible of producing white blood cells, red corpuscles, platelets in addition to the fibroblasts, macrophages, adipocytes, osteoblasts, osteocytes and osteoclasts, the current study aimed to detect the effects of lasers on the bone marrow. Twenty four adult New Zealand male rabbits were used in the study, they were divided into two groups with twelve rabbits each; the first group was treated with He-Ne laser for ten days. the second group was treated with diode laser for ten days. Three rabbits from each group underwent bone marrow aspiration to detect the marrow status assessed by special laboratory investigation at the days “1, 7, 14 & 21 “using “18-ga “gauge needle introduced to the marrow cavity through a small hall done in the trochanteric fossa. Samples collected from animals of different groups examined haematollogically using Wright’s stain. Results of the hematological examinations revealed that low level laser application stimulates the bone marrow and induce the infiltration of the tissues with high numbers of blood cells which were formed by increase mitosis and haemopoiesis to great levels. Conclusions can be done that the irradiation of the marrow with the lasers regardless it’s kind was very efficient to make the marrow of the adult rabbits which tend to be yellow in nature motivated and restore it’s capability of producing of the hemopoietic stem cells and mature blood cells
Dressing of superconducting qubits by their interaction with a low frequency photon reservoir
Authors: Gainutdinov R Kh , Nabieva L J , Garifullin A I , Mutygullina A A
Published: July 2019

Dressing of states of superconducting qubits by their interaction with low frequency photons is investigated. We show that the derivative of the self-energy function of a qubits state at its eigenenergy is equal to the total probability to find the system in the virtual states where the reservoir degrees of freedom manifest themselves explicitly. This parameter determines the strongness of the qubit-reservoir interaction. The results of calculations of the self-energy function show that contributions to the dressed states of qubits can be very significant.
Fundamentals of the theory of self-injection locking of multi-frequency laser diode to high-Q optical microresonator
Authors: Galiev R. R. , Kondratiev N. M. , Lobanov V. E. , Bilenko I. A.
Published: July 2019

In this work we present a theoretical model describing a phenomenon of self-injection locking of multi-frequency laser to high-Q optical microresonator. Such process allows high-power single-frequency emission with sub-kHz linewidth from the compact multi-frequency diode laser. Elaborated theory takes into account fast optical feedback due to the Rayleigh scattering, mode competition effect and Bogatov asymmetric mode interaction.
Nanoscale probing a glass transition temperature of heterogeneous azo-polymers using atomic force microscopy
Authors: Skvortsova T A , Chernykh E A , Saparina S V , Bikmeeva K R
Published: July 2019

Azo-polymer materials found diverse applications in many interdisciplinary areas, including frequency conversion, surface relief grating and others. In such devices, stratified polymer systems are often used, in which each layer ranges from 5 nm to 100 nm in thickness. One of the key characteristics of the polymer is the glass transition temperature Tg, which indicates the thermal stability of polymer, depending on its thickness and environment. The method for determining Tg that used in this work is based on recording the dependence of the oscillation phase of an atomic-force microscope probe on the sample temperature. To study the possibility of determining the local Tg, a cross section of a multilayer polymer system, polyethylene/polyamide with the layer thicknesses of 50-100 nm, is used. Tg is measured by a change in the phase of oscillation of the cantilever, which is caused by the loss of energy of the cantilever due to the change in Gibbs energy of the polymer during the thermal expansion. It was possible to measure the local temperature within the glass transition points of the sample and for chemical identification methods used different areas of enhanced optical microscopy (nano - Raman and nano-IR).
On the remodeling conjecture for toric Calabi-Yau 3-orbifolds
Authors: Fang Bohan , Liu Chiu-Chu , Zong Zhengyu
Published: July 2019

The Remodeling Conjecture proposed by Bouchard-Klemm-Mariño-Pasquetti (BKMP) relates the A-model open and closed topological string amplitudes (the all genus open and closed Gromov-Witten invariants) of a semiprojective toric Calabi-Yau 3-manifold/3-orbifold to the Eynard-Orantin invariants of its mirror curve. It is an all genus open-closed mirror symmetry for toric Calabi-Yau 3-manifolds/3-orbifolds. In this paper, we present a proof of the BKMP Remodeling Conjecture for all genus open-closed orbifold Gromov-Witten invariants of an arbitrary semiprojective toric Calabi-Yau 3-orbifold relative to an outer framed Aganagic-Vafa Lagrangian brane. We also prove the conjecture in the closed string sector at all genera.
BLANT—fast graphlet sampling tool
Authors: Maharaj Sridevi , Tracy Brennan , Hayes Wayne B
Published: July 2019

BLAST creates local sequence alignments by first building a database of small k-letter sub-sequences called k-mers. Identical k-mers from different regions provide ‘seeds’ for longer local alignments. This seed-and-extend heuristic makes BLAST extremely fast and has led to its almost exclusive use despite the existence of more accurate, but slower, algorithms. In this paper, we introduce the Basic Local Alignment for Networks Tool (BLANT). BLANT is the analog of BLAST, but for networks: given an input graph, it samples small, induced, k-node sub-graphs called k-graphlets. Graphlets have been used to classify networks, quantify structure, align networks both locally and globally, identify topology-function relationships and build taxonomic trees without the use of sequences. Given an input network, BLANT produces millions of graphlet samples in seconds—orders of magnitude faster than existing methods. BLANT offers sampled graphlets in various forms: distributions of graphlets or their orbits; graphlet degree or graphlet orbit degree vectors, the latter being compatible with ORCA; or an index to be used as the basis for seed-and-extend local alignments. We demonstrate BLANT’s usefelness by using its indexing mode to find functional similarity between yeast and human PPI networks.

Availability and implementation

BLANT is written in C and is available at https://github.com/waynebhayes/BLANT/releases.

Supplementary information

Supplementary data are available at Bioinformatics online.
Carbon monoxide released by CORM-A1 prevents yeast cell death via autophagy stimulation
Authors: Figueiredo-Pereira Cláudia , Menezes Regina , Ferreira Sofia , Santos Cláudia N , Vieira Helena L A
Published: July 2019

Autophagy is an autodigestive process, promoting cytoprotection by the elimination of dysfunctional organelles, misfolded proteins and toxic aggregates. Carbon monoxide (CO) is an endogenous gasotransmitter that under low concentrations prevents cell death and inflammation. For the first time, the role of autophagy in CO-mediated cytoprotection against oxidative stress was evaluated in the model yeast Saccharomyces cerevisiae. The boron-based CO-releasing molecule, CORM-A1, was used to deliver CO. CORM-A1 partially prevented oxidative stress-induced cell death in yeast. Likewise, CORM-A1 activated autophagy under basal physiological conditions, which were assessed by autophagic flux and the expression of mCherry-Atg8 or GFP-Atg8. Inhibition of autophagy by knocking out key autophagic genes in yeast (ATG8 or ATG11) blocked CORM-A1 cytoprotective effect, indicating the critical role of autophagy in CO-induced cytoprotection. The CO-mediated cytoprotection via autophagy induction observed in yeast was validated in primary cultures of astrocytes, a well-characterized model for CO's cytoprotective functions. As in yeast, CORM-A1 prevented oxidative stress-induced cell death in an autophagy-dependent manner in astrocytes. Overall, our data support the cytoprotective action of CO against oxidative stress. CO promotes cytoprotection in yeast via autophagy, opening new possibilities for the study of molecular mechanisms of CO's biological functions using this powerful eukaryotic model.
A Three-Sample Test for Introgression
Authors: Hahn Matthew W , Hibbins Mark S
Published: July 2019

Many methods exist for detecting introgression between nonsister species, but the most commonly used require either a single sequence from four or more taxa or multiple sequences from each of three taxa. Here, we present a test for introgression that uses only a single sequence from three taxa. This test, denoted D3, uses similar logic as the standard D-test for introgression, but by using pairwise distances instead of site patterns it is able to detect the same signal of introgression with fewer species. We use simulations to show that D3 has statistical power almost equal to D, demonstrating its use on a data set of wild bananas (Musa). The new test is easy to apply and easy to interpret, and should find wide use among currently available data sets.
Comparison of machine perfusion versus cold storage in kidney transplant recipients from expanded criteria donors: a cohort-based study
Authors: Foucher Yohann , Fournier Marie-Cécile , Legendre Christophe , Morelon Emmanuel , Buron Fanny , Girerd Sophie , Ladrière Marc , Mourad Georges , Garrigue Valérie , Glotz Denis , Lefaucheur Carmen , Cassuto Elisabeth , Albano Laetitia , Giral Magali , Dantal Jacques ,   for the DIVAT Consortium, Hériot Lyon E , Badet Lionel , Maria Brunet F B , Cahen Rémi , Daoud Sameh , Fournie Coralie , Grégoire Arnaud , Koenig Alice , Charlène Lévi E M , Pouteil-Noble Claire , Rimmelé Thomas , Thaunat Olivier , Sylvie Delmas V G , Le Quintrec Moglie , Pernin Vincent , Serre Jean-Emmanuel , Eschwege Pascal , Luc Frimat S G , Jacques Hubert M L , Laurain Emmanuelle , Leblanc Louis , Lecoanet Pierre , Lemelle Jean-Louis , Blancho Gilles , Branchereau Julien , Cantarovich Diego , Agnès Chapelet J D , Deltombe Clément , Figueres Lucile , Claire Garandeau M G , Gourraud-Vercel Caroline , Hourmant Maryvonne , Karam Georges , Kerleau Clarisse , Meurette Aurélie , Ville Simon , Kandell Christine , Moreau Anne , Renaudin Karine , Cesbron Anne , Delbos Florent , Walencik Alexandre , Devis Anne , Laeticia Albano E C , Amrouche Lucile , Anglicheau Dany , Aubert Olivier , Lynda Bererhi C L , Loupy Alexandre , Martinez Frank , Sberro-Soussan Rébecca , Scemla Anne , Tinel Claire , Zuber Julien
Published: July 2019

Background

Most studies comparing the efficacy of hypothermic machine perfusion (HMP) versus static cold storage (SCS) are based on short-term outcomes. We aimed to better evaluate the mid-term impact of HMP in patients receiving expanded criteria donor (ECD) kidneys.

Methods

The analyses were based on the French Données Informatisées et VAlidées en Transplantation (DIVAT) observational cohort. Patients aged ≥45 years transplanted for the first or second times from an ECD donor since 2010 were studied. Our study reported the graft and/or patient survivals and the incidence of acute rejection episode. The Cox models and the Kaplan–Meier estimators, weighted on the propensity score, were used to study the times-to-events.

Results

Among the 2019 included patients, 1073 were in the SCS group versus 946 in the HMP group. The mean life expectancy with functioning graft was 5.7 years [95% confidence interval (CI) 5.4–6.1] for the HMP cohort followed-up for 8 years post-transplantation versus 6.0 years (95% CI 5.7–6.2) for the SCS group. These mid-term results were comparable in the patients receiving grafts from donors aged ≥70 years and in the transplantations with cold ischaemia time ≥18 h.

Conclusions

Our study challenges the utility of using HMP to improve mid-term patient and graft survival. Nevertheless, the improvement of the short-term outcomes is indisputable. It is necessary to continue technological innovations to obtain long-term results.
Diagnosis of CO2 dynamics and fluxes in global coastal oceans
Authors: Cao Zhimian , Yang Wei , Zhao Yangyang , Guo Xianghui , Yin Zhiqiang , Du Chuanjun , Zhao Huade , Dai Minhan
Published: July 2019

Global coastal oceans as a whole represent an important carbon sink but, due to high spatial–temporal variability, a mechanistic conceptualization of the coastal carbon cycle is still under development, hindering the modelling and inclusion of coastal carbon in Earth System Models. Although temperature is considered an important control of sea surface pCO2, we show that the latitudinal distribution of global coastal surface pCO2 does not match that of temperature, and its inter-seasonal changes are substantially regulated by non-thermal factors such as water mass mixing and net primary production. These processes operate in both ocean-dominated and river-dominated margins, with carbon and nutrients sourced from the open ocean and land, respectively. These can be conceptualized by a semi-analytical framework that assesses the consumption of dissolved inorganic carbon relative to nutrients, to determine how a coastal system is a CO2 source or sink. The framework also finds utility in accounting for additional nutrients in organic forms and testing hypotheses such as using Redfield stoichiometry, and is therefore an essential step toward comprehensively understanding and modelling the role of the coastal ocean in the global carbon cycle.
Healing and Religion
Authors: Beeler Dori-Michelle , Jonker Jojan L.
Published: July 2019

The etymology of the term “healing” dates back to 900 ce with references pointing to northwestern Europe. Historically, healing is seen to be embedded in religion. The connection between religion and healing, while emphasizing an anthropological approach, considers categories such as (but not limited to): worldviews, religious beliefs, religious and spiritual practices, rituals, deities, and symbols rather than science. Considered holistically, studies on healing depict “healing-as-practice” (framed as praxis: theory and practice integrated) rather than just a phrase, a concept, a cognitive undertaking or even a discipline in and of itself. Positioned in this way, healing is also situated in practices of global institutions, religions, spiritualties, and indigenous communities alike. In doing so, the nuances of healing used as a phrase or concept, as well as the flexibility it has in terms of understanding what matters to humans are illuminated. Healing embraces all dimensions of human life: the physical, psychological, social, and cultural. This helps position the term “healing,” a popular term within biomedicine, health care, and complementary and alternative medicine (CAM) modalities, as associated with holism. In considering the holistic nature of healing, one process includes the healing of bones, organs, and tissue suggesting an underlying common order for healing that can be influenced by religious or spiritual rituals. At the other end of the spectrum of processes, individuals experience healing without any improvement in bodily function. Rather, they experience a type of subjective transformation as a result of distinct cultural, religious, or spiritual practices. In between the biological mechanisms of healing and the psychosomatic influences on healing, lies healing-as-praxis where something or someone intervenes in a person’s constellation of body, mind, spirit, and environment intent on stimulating healing or reaching a state of healing. This indicates that healing-as-practice has (at least) three domains; process or activity, intervention, and outcome or accomplishment, and relates to tradition, community, and social environment. Furthermore, healing-as-practice implies salutogenesis, an approach that focuses on the processes that support healing and well-being; while a focus on illness has to do with the configuration of one’s social, psychological, and spiritual condition. Thus, a distinction is made between curing and healing. Healing is concerned with meaning in relation to illness and curing is related to disease, albeit the terms illness and disease may be swapped in which case disease is interpreted as dis-ease—to be read as “being not at ease”—where mind and/or spirit are also involved. Therefore, the relation between healing and religion/spirituality is a natural one.
Erianin alleviates diabetic retinopathy by reducing retinal inflammation initiated by microglial cells via inhibiting hyperglycemia‐mediated ERK1/2–NF‐κB signaling pathway
Authors: Zhang Tianyu , Ouyang Hao , Mei Xiyu , Lu Bin , Yu Zengyang , Chen Kaixian , Wang Zhengtao , Ji Lili
Published: July 2019

Blood‐retinal barrier (BRB) breakdown is a typical event in the early stage of diabetic retinopathy (DR). This study aims to elucidate the protection of erianin, a natural compound isolated from Dendrobium chrysotoxum Lindl, against DR development. Erianin alleviated BRB breakdown and rescued the reduced claudin1 and occludin expression in retinas from streptozotocin‐induced diabetic mice. Erianin reduced microglial activation, ERK1/2 phosphorylation, NF‐κB transcriptional activation, and the elevated TNF‐α expression both in vitro and in vivo. ERK1/2 inhibitor U0126 abrogated NF‐κB activation in D‐glucose‐treated BV2 cells. Erianin reduced cellular glucose uptake, and molecular docking analysis indicated the potential interaction of erianin with glucose transporter (GLUT)1. GLUT1 inhibitor (STF31) reduced the activation of the ERK1/2‐NF‐κB signaling pathway. Coculture with D‐glucose‐stimulated microglial BV2 cells and with TNF‐α stimulation both induced inner BRB and outer BRB damage in human retinal endothelial cells and APRE19 cells, but erianin improved all these damages. In summary, erianin attenuated BRB breakdown during DR development by inhibiting microglia‐triggered retinal inflammation via reducing cellular glucose uptake and abrogating the subsequent activation of the downstream ERK1/2‐NF‐κB pathway. Moreover, erianin also alleviated BRB damage induced by TNF‐α released from the activated microglia.—Zhang, T., Ouyang, H., Mei, X., Lu, B., Yu, Z., Chen, K., Wang, Z., Ji, L. Erianin alleviates diabetic retinopathy by reducing retinal inflammation initiated by microglial cells via inhibiting hyperglycemia‐mediated ERK1/2‐NF‐κB signaling pathway. FASEB J. 33, 11776‐11790 (2019). www.fasebj.org
BMP9 directly induces rapid GSK3‐β phosphorylation in a Wnt‐independent manner through class I PI3K‐Akt axis in osteoblasts
Authors: Eiraku Nahoko , Chiba Norika , Nakamura Toshiaki , Amir Muhammad Subhan , Seong Chang‐Hwan , Ohnishi Tomokazu , Kusuyama Joji , Noguchi Kazuyuki , Matsuguchi Tetsuya
Published: July 2019

Bone morphogenetic protein (BMP)9 has been reported to be the most potent BMP to induce bone formation. However, the details of BMP9‐transduced intracellular signaling remain ambiguous. Here, we have investigated signal transduction mechanisms of BMP9 in comparison to BMP2, another potent inducer of bone formation, in osteoblasts. In a mouse osteoblast cell line, BMP9 induced higher mRNA levels of alkaline phosphatase (ALP) and runt‐related transcription factor 2 (Runx2) than BMP2 within 2 h. Unlike BMP2, BMP9 induced rapid phosphorylation of glycogen synthase kinase 3‐β (GSK3‐β) and protein kinase B (Akt) and increased the cellular protein content of β‐catenin. BMP9 moderately increased mRNA levels of several canonical Wingless‐related integration site to lower degrees than BMP2. Furthermore, BMP9‐induced GSK3‐β phosphorylation was not inhibited by pretreatment with actinomycin D, cycloheximide, or Brefeldin A, indicating it is independent of Wnt protein secretion. BMP9‐induced GSK3‐β phosphorylation was abrogated by Akt or class I PI3K‐specific inhibitors. Moreover, inactivation of GSK3‐β by LiCl did not further promote ALP and Runx2 mRNA induction by BMP9 as significantly as that by BMP2. Notably, BMP9‐induced GSK3‐β phosphorylation was inhibited by small interfering RNA against endoglin and GIPC PDZ domain‐containing family, member 1. Taken together, our present findings have indicated that BMP9 directly activates GSK3β‐β‐catenin signaling pathway through class I PI3K‐Akt Axis in osteoblasts, which may be essential for the potent osteoinductive activity of BMP9.—Eiraku, N., Chiba, N., Nakamura, T., Amir, M. S., Seong, C.‐H., Ohnishi, T., Kusuyama, J., Noguchi, K., Matsuguchi, T. BMP9 directly induces rapid GSK3‐β phosphorylation in a Wnt‐independent manner through class I PI3K‐Akt axis in osteoblasts. FASEB J. 33, 12124‐12134 (2019). www.fasebj.org
Focal Length Fluidity: Research Questions in Medical Education Research and Scholarship
Authors: Young Meredith , LaDonna Kori , Varpio Lara , Balmer Dorene F.
Published: July 2019

Research and scholarship in health professions education has been shaped by intended audience (i.e., producers vs users) and the purpose of research questions (i.e., curiosity driven or service oriented), but these archetypal dichotomies do not represent the breadth of scholarship in the field. Akin to an array of lenses required by scientists to capture images of a black hole, the authors propose the analogy of lenses with different focal lengths to consider how different kinds of research questions can offer insight into health professions research—a microscope, a magnifying glass, binoculars, and telescopes allow us to ask and answer different kinds of research questions. They argue for the relevance of all of the different kinds of research questions (or focal lengths); each provides important insight into a particular phenomenon and contributes to understanding that phenomenon in a different way. The authors propose that research questions can move fluidly across focal lengths. For example, a theoretical question can be made more pragmatic through asking “how” questions (“How can we observe and measure a phenomenon?”), whereas a pragmatic question can be made more theoretic by asking a series of “why” questions (“Why are these findings relevant to larger issues?”). In summary, only through the combination of lenses with different focal lengths, brought to bear through interdisciplinary work, can we fully comprehend important phenomena in health professions education and scholarship—the same way scientists managed to image a black hole.
Academic Medicine and Science Diplomacy: Medical Education in Iraq
Authors: Kron Michael , Roenius Matthew , Alqortasi Mohammed Abdul Mahdi , Alhaidari Taghreed , Hussein Mohammed , Hameed Ekhlas Khalid , Salih Ibtesam Khalid
Published: July 2019

Physicians are infrequently selected to serve in the yearlong role of Jefferson Science Fellow (JSF) as senior science advisor for the U.S. Department of State or the United States Agency for International Development. The authors discuss the role of a JSF in promoting “science diplomacy” from the perspective of one alumnus, who sites examples of ongoing, long-term collaborative projects including one focusing on medical education reform in Iraq that would not have been possible without the JSF program. More than 3 decades of political and social unrest, terrorism, the internal displacement of millions of Iraqi citizens, the arrival of Syrian refugees, international sanctions, and the effect of fluctuating oil prices that fund education in Iraq have all led to a standstill in modernizing educational systems and the need for reform. In 2016, new opportunities for international collaboration and travel allowed faculty from the Al Kindy College of Medicine, University of Baghdad, Iraq, to visit the United States, explore U.S. medical school teaching methods, interact with U.S. faculty and students, and then implement their vision of a revised medical curriculum. These faculty members shared their observations with the Iraqi Council of Deans, which represents all 30 Iraqi medical schools. Structural changes in curriculum content and teaching methods have been implemented with the goal of restoring quantifiable excellence in education and health care in Iraq. The authors close with lessons learned to encourage other physicians to participate in the JSF program, which offers a unique opportunity to influence foreign policy through science diplomacy.