bluuebunny/crossref_metadata_2025 huggingface dataset:
Controlling the emission properties of solution-processed organic distributed feedback lasers through resonator design
Authors: Bonal Víctor , Quintana José A. , Villalvilla José M. , Boj Pedro G. , Díaz-García María A.
Published: August 2019

Surface-emitting distributed feedback (DFB) lasers with both, resonator and active material based on solution-processable polymers, are attractive light sources for a variety of low-cost applications. Besides, the lasers should have competitive characteristics compared to devices based on high-quality inorganic resonators. Here, we report high performing all-solution-processed organic DFB lasers, consisting of water-processed photoresist layers with surface relief gratings located over the active films, whose emission properties can be finely tuned through resonator design. Their laser threshold and efficiency are simultaneously optimized by proper selection of residual resist thickness and grating depth, d. Lowest thresholds and largest efficiencies are obtained when there is no residual layer, while a trade-off between threshold and efficiency is found in relation to d, because both parameters decrease with decreasing d. This behaviour is successfully explained in terms of an overlap factor r, defined to quantify the interaction strength between the grating and the light emitted by the active film and traveling along it, via the evanescent field. It is found that optimal grating depths are in the range 100–130 nm (r ~ 0.5−0.4). Overall, this study provides comprehensive design rules towards an accurate control of the emission properties of the reported lasers.
Biofilm formation capacity and presence of virulence factors among commensal Enterococcus spp. from wild birds
Authors: Stępień-Pyśniak Dagmara , Hauschild Tomasz , Kosikowska Urszula , Dec Marta , Urban-Chmiel Renata
Published: August 2019

Enterococci are opportunistic pathogens that can form biofilms during infections and many virulence determinants are involved in this process. Although the virulence factors are often analysed in Enterococcus spp. from humans and food animals, little is known about gut enterococcal isolates from wild birds. Therefore, the determination of virulence factors among enterococci isolated from wild birds may provide new information about a possible source of infection for humans and animals or vice versa via the environment. We analysed different phenotypic and genotypic traits in enterococci from wild birds related to potential virulence in humans and animals and to evaluate biofilm formation and its relationship to virulence genes. The E. faecalis isolates were characterised by greater frequency of biofilm formation in BHI than E. faecium. There was a correlation between hydrophobicity and biofilm formation in BHI broth in E. faecalis. None of the isolates was haemolytic. The presence of some adhesion and gelatinase genes was detected in biofilm-positive isolates. The enterococcal pathogenic factors (esp, hyl, and cyl operon genes) did not seem to be necessary or sufficient for production of biofilm by analysed bacteria. Enterococcus species isolated from wild birds should be considered as a possible source of some virulence determinants.
Single cell study of adipose tissue mediated lipid droplet formation and biochemical alterations in breast cancer cells
Authors: Blücher Christina , Zilberfain Carolin , Venus Tom , Spindler Nick , Dietrich Arne , Burkhardt Ralph , Stadler Sonja C. , Estrela-Lopis Irina
Published: August 2019

Combined staining methods for neutral lipids and confocal Raman microspectroscopy detect increased lipid droplet formation in breast cancer cells influenced by adipose tissue.
Arylallenes and the halogeno-B(C6F5)2 reagents: facile formation of 2-borylindenes
Authors: Tao Xin , Daniliuc Constantin G. , Soloviova Kateryna , Strassert Cristian A. , Kehr Gerald , Erker Gerhard
Published: August 2019

Allenylarenes are converted to the respective 2-borylindenes by treatment with chloro- or bromobis(pentafluorophenyl)borane.
Facile synthesis of 1,2-thiobenzonitriles via Cu-catalyzed denitrogenative radical coupling reaction
Authors: Zhou Yao , Wang Ya , Lou Yixian , Song Qiuling
Published: August 2019

The first example of denitrogenative radical coupling with 3-aminoindazoles is presented. A diverse array of 1,2-thiobenzonitriles were obtained in good yields with wide substrate scope via oxidative C–N cleavage of 3-aminoindazoles.
Doubly interpenetrated indium-tricarboxylate frameworks mediated by small molecules with enhanced porosity
Authors: Du Yujing , Zhong Li , Hu Yue , Li Qipeng , Qian Jinjie
Published: August 2019

A synthetic strategy of indium-tricarboxylate frameworks by using small molecule regulators has been proposed to obtain four types of In-based coordination polymers with doubly interpenetrated structures.
Graphene coated gold nanoparticles: an emerging class of nanoagents for photothermal therapy applications
Authors: Farokhnezhad Mohsen , Esmaeilzadeh Mahdi
Published: August 2019

Optical and photothermal properties of graphene coated gold nanoparticles show that these nanoparticles are more suitable candidates for photothermal therapy applications.
Heteroleptic [Os(Cl)(CO)(P^P)(pbi)] complexes bearing bidentate phosphine and 2-(2-pyridyl)benzimidazolate ligands: impact of isomerism on their luminescence properties
Authors: Kamecka Anna , Suwińska Kinga , Kapturkiewicz Andrzej
Published: August 2019

Two isomeric series of osmium(ii) complexes exhibit significant differences in their luminescence properties.
Photocatalytic degradation of naproxen by a H2O2-modified titanate nanomaterial under visible light irradiation
Authors: Fan Gongduan , Zhan Jiajun , Luo Jing , Zhang Jin , Chen Zhong , You Yifan
Published: August 2019

A H2O2-modified titanate nanomaterial was synthesized to improve catalytic activity. The influencing factors, intermediate product transformation pathways and degradation mechanism of the photodegradation process of NPX by the HTNM were studied.
Syntheses and crystal structures of new dinuclear lanthanide complexes based on 3-(4-hydroxyphenyl)propanoic acid: Hirshfeld surface analyses and photoluminescence sensing
Authors: He Jiangrong , Wang Jun , Xu Qiuxia , Wu Xiren , Dutta Archisman , Kumar Abhinav , Muddassir Mohd. , Alowais Ahmad , Abduh Naaser A. Y.
Published: August 2019

A series of ten new lanthanide complexes, [Ln2(HPA)6(bipy)2·4H2O·2bipy], were synthesized and their photoluminescence sensing and Hirshfeld surface analyses performed.
Chemistry of cysteine assembly on Au(100): electrochemistry, in situ STM and molecular modeling
Authors: Engelbrekt Christian , Nazmutdinov Renat R. , Zinkicheva Tamara T. , Glukhov Dmitrii V. , Yan Jiawei , Mao Bingwei , Ulstrup Jens , Zhang Jingdong
Published: August 2019

Unique two-dimensional super-structures form when cysteine self-assembles on single-crystal Au(100) due to inter-molecular forces and adsorption energetics, addressed through a comprehensive experimental and quantum computational approach.
Retracted Article: Elevation of USP4 antagonizes oxygen glucose deprivation/reoxygenation-evoked microglia activation and neuroinflammation-mediated neurotoxicity via the TRAF6-NF-κB signaling
Authors: Wang Zhaoxia , Li Xinming , Shao Zhixing , ZhengFang  , Zhai Yueping
Published: August 2019

An ischemic stroke is a devastating neurological disease with the typical occurrence of brain ischemia/reperfusion (I/R) injury, and it has high mortality and disability globally.
Algorithms for the self-optimisation of chemical reactions
Authors: Clayton Adam D. , Manson Jamie A. , Taylor Connor J. , Chamberlain Thomas W. , Taylor Brian A. , Clemens Graeme , Bourne Richard A.
Published: August 2019

Self-optimising chemical systems have experienced a growing momentum in recent years. Herein, we review algorithms used for the self-optimisation of chemical reactions in an accessible way for the general chemist.
Photoelectrochemical-voltaic cells consisting of particulate ZnxCd1−xSe photoanodes with photovoltages exceeding 1.23 V
Authors: Kageshima Yosuke , Someno Akihiko , Teshima Katsuya , Domen Kazunari , Nishikiori Hiromasa
Published: August 2019

A photoelectrochemical-voltaic cell consisting of ZnxCd1−xSe photoanodes generates a photovoltage higher than the thermodynamic onset voltage for water splitting, 1.23 V.
Tough but self-healing and 3D printable hydrogels for E-skin, E-noses and laser controlled actuators
Authors: Wang Yitian , Chang Qiang , Zhan Rixing , Xu Kaige , Wang Ying , Zhang Xingying , Li Bingyun , Luo Gaoxing , Xing Malcolm , Zhong Wen
Published: August 2019

A versatile hydrogel with extraordinary mechanical strength and self-healing efficiency was developed by integrating physically crosslinked graphene oxide into a chemically crosslinked polyacrylic acid network.
Quantifying insect migration across Bohai strait using weather radar
Authors: Cui Kai , Hu Cheng , Wang Rui , Li Siwei , Wu Dongli , Ma Shuqing
Published: August 2019

Weather radars provide continuous recording over extensive spatial coverage, which is valuable for biologists who observe and study biological activities over a wide range of temporal and spatial scales. Through the interpretation of weather radar observations, powerful biological inferences can be obtained. However, when it comes to certain biological problems, such as the determination of biological parameters related to airborne biological densities, weather radar data needs to be processed based on certain assumptions before. This article analyses and calculates the impact of the phenomenon of migratory insects gathering into layers on the interpretation of weather radar data and develops a biomass estimation method with known bio‐spatial distribution characteristics. Quantitative research was conducted on the situation of migrating insects across the Bohai Bay in the autumn of 2012.
Anticiper l’avenir des territoires agricoles en Afrique de l’Ouest : le cas des Niayes au Sénégal
Authors: Camara Clémentine , Bourgeois Robin , Jahel Camille
Published: August 2019

En Afrique de l’Ouest, dans le contexte général de changement climatique et de mondialisation, la croissance démographique exerce une pression accrue sur les ressources naturelles par les changements d’affectation des sols qu’elle engendre. L’avenir des territoires agricoles, en particulier en périphérie des grandes villes, est alors questionné face à l’urbanisation croissante, la dégradation des ressources naturelles et les mutations socio-économiques. Afin d’anticiper les changements que pourraient connaître les territoires ruraux, une démarche de prospective territoriale a été réalisée sur la zone sud des Niayes, au Sénégal. Elle a permis aux experts locaux mobilisés à cet effet d’identifier les facteurs de changement et de co-élaborer des scénarios d’évolutions plausibles du territoire. Les réglementations, la gouvernance et la démographie sont les trois facteurs majeurs pouvant infléchir de l’affectation des sols dans le temps. Ces facteurs déterminent le type de partage de l’espace et d’utilisation des ressources naturelles, pouvant être harmonieux ou conflictuel. Une gouvernance inclusive, une société civile fortement structurée et la préservation des ressources naturelles sont apparues comme essentielles à l’atteinte de futurs harmonieux.
Nutzerbefragung als Qualitätssicherungsmaßnahme in psychosozialen Krebsberatungsstellen
Authors: Ihrig Andreas , Maatouk Imad , Wickert Martin , Wünsch Alexander , Bruns Gudrun , Besseler Markus
Published: August 2019

Ziel Ziel der vorliegenden Erhebung ist es, bislang existierende Erfahrungen von Mitarbeitern psychosozialer Krebsberatungsstellen in Deutschland mit der Nachbefragung von Ratsuchenden als Qualitätssicherungsmaßnahme zu beschreiben und zu bewerten.

Methodik Vertreter verschiedener psychosozialer Krebsberatungsstellen wurden gebeten, einen Erfahrungsbericht über Nutzerbefragungen zur Qualitätssicherung zu erstellen. 9 Erfahrungsberichte werden vorgestellt und zusammenfassend durch die Arbeitsgruppe Krebsberatungsstellen der Arbeitsgemeinschaft Psychoonkologie der Deutschen Krebsgesellschaft (PSO) diskutiert. Besonderes Augenmerk galt dem von der Arbeitsgruppe empfohlenen Kurzfragebogen KBS-N (Krebsberatungsstellen-Nachbefragungsbogen).

Ergebnisse Alle teilnehmenden psychosozialen Krebsberatungsstellen berichten von positiven Erfahrungen mit Nutzerbefragungen, die jedoch einen personellen und logistischen Aufwand darstellen. Neben dem KBS-N kamen auch ausführlichere Fragebögen zum Einsatz. Die Befragungen wurden entweder kontinuierlich oder stichprobenartig über einen begrenzten Zeitraum hinweg durchgeführt. Die Ratsuchenden werden meist zu einem definierten Zeitpunkt direkt nach den Erstgesprächen oder nach Abschluss der Beratungssequenz befragt. Die Rücklaufquote ist bei persönlicher Ausgabe des Fragebogens nach dem Erstgespräch und Abgabe noch in der Beratungsstelle höher (85–95%) als bei postalischer Zustellung und Rücksendung (47–89%). Alle Beratungsstellen berichten übereinstimmend von sehr positiven Rückmeldungen zu den Beratungsleistungen. Vereinzelte Kritikpunkte betreffen insbesondere organisatorische Rahmenbedingungen.

Schlussfolgerung Nach Abwägung von Aufwand und Nutzen erscheint eine aktive Nachbefragung von Ratsuchenden mit dem Kurzfragebogen KBS-N, zumindest über einen begrenzten Zeitraum hinweg, eine praktikable Qualitätssicherungsmaßnahme darzustellen. Ausführlichere Nutzerbefragungen sind mit einem höheren Aufwand verbunden und daher eher für den Einsatz bei über die Qualitätssicherung hinausgehenden Forschungsfragestellungen geeignet.
The Role of Abnormal Hemostasis and Fibrinolysis in Morbidity and Mortality of Acute Promyelocytic Leukemia
Authors: Kwaan Hau C. , Weiss Ivy , Tallman Martin S.
Published: August 2019

Despite the improved therapeutic advances in the management of acute promyelocytic leukemia (APL), a significant early mortality during induction, also referred to as early death (ED), remains an obstacle for further improvement in outcome. Hemorrhagic complications are the most common cause of morbidity and mortality. Perturbed hemostatic dysfunction is present as the result of abnormalities in both the coagulation and the fibrinolytic systems. The activation of coagulation is distinct from the classical disseminated intravascular coagulation. Multiple abnormalities in the fibrinolytic system have recently been identified. The most significant change is increased production of tissue plasminogen activator (tPA) and its receptor annexin A2 by the APL promyelocytes. Among the hemorrhagic complications, intracranial hemorrhage predominates. The pathogenesis of this catastrophic event is elucidated by new evidence of adverse effect of tissue plasminogen activator (tPA) on the brain, including both the plasmin-dependent and plasmin-independent pathways. In order to address the hemorrhagic complications, a thorough understanding of the hemostatic dysfunction is essential. In this article, our current concept of the abnormal hemostasis in APL is reviewed. The failure to reduce the early death rate, despite the introduction of effective therapy, will also be discussed.
All-Trans Retinoic Acid Impairs Platelet Function and Thrombus Formation and Inhibits Protein Kinase CßI/δ Phosphorylation
Authors: Luo Qi , Wei Guangyu , Wang Xiamin , Xu Xiaoqi , Ju Wen , Li Zhenyu , Gardiner Elizabeth E. , Andrews Robert K. , Zeng Lingyu , Xu Kailin , Qiao Jianlin
Published: August 2019

All-trans retinoic acid (ATRA) is widely used for induction of complete remission in patients with acute promyelocytic leukemia (APL). ATRA also regulates protein kinase C (PKC) activity. Therapeutic use of ATRA reportedly interferes with hemostatic function in APL patients, including effects on coagulation or other vascular cells, although effects of ATRA on platelets remain unclear. This study aims to investigate the effect of therapeutic-relevant doses of ATRA on platelet function. Human platelets were preincubated with ATRA (0–20 μM) for 1 hour at 37°C, followed by analysis of aggregation, granule secretion, receptor expression by flow cytometry, platelet spreading, or clot retraction. Additionally, ATRA (10 mg/kg) was injected intraperitoneally into mice and tail bleeding time and arterial thrombus formation were evaluated. ATRA inhibited platelet aggregation and adenosine triphosphate release induced by collagen (5 μg/mL) or thrombin (0.05 U/mL) in a dose-dependent manner without affecting P-selectin expression or surface levels of glycoprotein (GP) Ibα, GPVI, or αIIbβ3. ATRA-treated platelets demonstrated reduced spreading on immobilized fibrinogen or collagen and reduced thrombin-induced clot retraction together with reduced phosphorylation of Syk and PLCγ2. In addition, ATRA-treated mice displayed significantly impaired hemostasis and arterial thrombus formation in vivo. Further, in platelets stimulated with either collagen-related peptide or thrombin, ATRA selectively inhibited phosphorylation of PKCßI (Ser661) and PKCδ (Thr505), but not PKCα or PKCßII phosphorylation (Thr638/641). In conclusion, ATRA inhibits platelet function and thrombus formation, possibly involving direct or indirect inhibition of PKCßI/δ, indicating that ATRA might be beneficial for the treatment of thrombotic or cardiovascular diseases.
Underlying mechanistic insights into the structural properties of melamine and uric acid complexes with compositional variation under ambient conditions
Authors: Chattaraj Krishna Gopal , Paul Sandip
Published: August 2019

The structural properties of melamine-uric acid complexes (which are responsible for kidney stones) with compositional variations are examined using a series of classical molecular dynamics simulations. The preferential interaction parameters imply that melamine interacts more strongly with uric acid than with other melamine molecules present in the system, whereas uric acid preferentially interacts with other uric acid molecules rather than with melamine. The stronger interactions among uric acid molecules produce higher-order uric acid clusters, which “drag” neighboring melamine molecules to be added to a cluster. Determination of orientational preferences between aromatic planes reveals that π–π stacking is responsible for uric acid self-association but less significant for melamine-melamine and melamine-uric acid accumulation. Cluster structure analyses suggest that higher concentrations of melamine, uric acid, or both result in a large insoluble melamine-uric acid complex cluster. Molecular mechanics-Poisson Boltzmann surface area calculations give a negative binding energy, indicating favorable complexation between melamine and uric acid molecules. Moreover, the overall complexation energy [ΔG0(mel-mel)+ ΔG0(uri-uri)+ ΔG0(mel-uri)] is more negative than ΔG0bind(mel-uri). The lifetime of melamine dimers is quite low compared with those of uric acid-uric acid and melamine-uric acid dimers, resulting in a low percentage of larger clusters for melamine-melamine interaction and a significant percentage of higher-order melamine-uric acid and uric acid-uric acid clusters with longer lifetimes. Furthermore, melamine and uric acid form strong hydrogen bonds, and melamine-melamine interactions are dominated by hydrogen bonding, whereas uric acid forms only a small number of hydrogen bonds with other uric acid molecules.
Diffusivity ratio effect on the onset of the buoyancy-driven instability of an A + B → C chemical reaction system in a Hele-Shaw cell: Numerical simulations and comparison with experiments
Authors: Kim Min Chan , Cardoso Silvana S. S.
Published: August 2019

The effect of different diffusivities on the evolution of buoyancy-driven instability in a reactive-diffusion system is analyzed. For an instantaneous A + B → C chemical reaction in a Hele-Shaw cell, where a less dense phase of A is layered on top of a denser solution of B, the temporal evolution of the instability motion is traced numerically by using the Fourier spectral method. As expected, the evolution of instabilities can be controlled by chemical factors, such as the ratios of diffusivities, reactant concentrations, and densification coefficients. Double diffusive effects accelerate and hinder the evolution of instabilities and induce the onset of instabilities without an adverse density gradient. The present numerical simulation explains the previous experiments for the NH3 + CH3COOH → CH3COONH4 reaction in a Hele-Shaw cell, which was devised to explain the impact of the chemical reaction in geological CO2 sequestration.
Conical micro-structures as a route for achieving super-repellency in surfaces with intrinsic hydrophobic properties
Authors: Ding W. , Fernandino M. , Dorao C. A.
Published: August 2019

Hydrophobic surfaces like Lotus leaves show amazing self-cleaning properties with the apparent water contact angle above 150° and contact angle hysteresis below 10°. Thus, at low inclination angles, millimeter drops can roll-off easily. This effect can be a consequence of the air trapped below the drop, which allows the droplet to reach a superhydrophobic Cassie-Baxter state. However, the superhydrophobic state can be accompanied by very different adhesive properties due to the pinning of the droplet to the microstructures, implying that even in a hydrophobic or superhydrophobic state, the droplet might not roll-off easily. A superhydrophobic state with minimum adhesion to the surface has been the pursuit in many applications where a super-repellent state is highly desired. Many microstructures have been shown to be able to reach a superhydrophobic state, but only a few have been shown to be capable of achieving a super-repellent state without the help of more complex hierarchical structures. Here, we show that conical structures provide a template for designing super-repellent surfaces where the wetting characteristics look to be invariant in the microscale range. The conical structures can maintain a super-repellent state for all intrinsic contact angles larger than 90°, and the transition from the Cassie-Baxter to the Wenzel state is controlled by the apex angle of the conical structures. This finding advances the understanding of why conical structures can show a superhydrophobic state, which will be beneficial for the design of super-repellent surfaces with a wider intrinsic contact angle range.
Optics integrated compact cavity for rubidium atomic frequency standards
Authors: Kaintura Jaydeep , Ghadiya Ambrish , Soni Shilpi , Bandi Thejesh N.
Published: August 2019

A compact magnetron cavity having integrated optics is designed and realized for a rubidium atomic clock that is being developed for the Indian Regional Navigation Satellite System. This cavity comprises a cylindrical dielectric cell with 25 mm diameter and 25 mm height. The cavity is designed to resonate at the rubidium hyperfine ground-state frequency of 6.8346 GHz with TE011-mode. A loop gap resonator structure is employed to obtain the required uniform mode along the quantization-axis in the cavity. The cutoff frequency of the cavity is designed in such a way that the influence of optics on the cavity mode is negligible and it is well within the tuning range of the cavity. The measured results of the realized cavity match up to 90% with the RF simulation results. The overall volume and mass of the realized cavity are about 86 cm3 and 120 g, respectively, making it suitable for portable space based applications.
Highly confined radial contour modes in phononic crystal plate based on pillars with cap layers
Authors: Moutaouekkil M. , Talbi A. , El Boudouti E. H. , Elmazria O. , Djafari-Rouhani B. , Pernod P. , Bou Matar O.
Published: August 2019

We investigate highly confined and isolated surface modes in a phononic crystal plate based on pillars with cap layers. The structure is made of a thin membrane supporting periodic pillars each composed of one cylinder surmounted by a disk shaped cap layer. An optimal choice of the geometrical parameters and material composition allows the structure to support isolated radial contour modes confined in the cap layer. In this study, we consider diamond and gold (Au) as the pillar and cap layers, respectively, and aluminum nitride as a thin membrane owing to the strong contrast in their elastic and density properties and to their compatibility with the integrated circuit technology and microwave electroacoustic devices. The phononic crystal based on diamond pillars allows us to induce a wide stop band frequency, and the addition of the Au disk shaped layer on diamond pillars enables us to introduce flat modes within the bandgap. We demonstrate that one can optimize the flat mode frequencies by varying the geometrical parameters of the Au cap layer. The quality factor (Q) of a cavity resonator composed of one line gold/diamond pillar surrounded by an array of diamond pillars on both sides has been investigated. These results clearly show that, using this design approach, one can (i) reduce the acoustic energy leakage out of the resonator and (ii) optimize the cavity resonator’s Q factor by varying only the geometrical parameters of the gold cap layer. The proposed design provides a promising solution for advanced signal processing and sensing applications.
Study of energies and radiative properties of He-like ions within a dense plasma
Authors: Chen Zhan-Bin , Ma Kun , Ma Yu-Long , Wang Kai
Published: August 2019

On the basis of the tensor expression for the Breit-Pauli Hamiltonian and the irreducible tensor theory for many-electron atoms, we have proposed a general analytical method for calculating atomic structures of highly charged ions under a dense plasma environment. In this method, the standard ion-sphere (IS) potential is used to represent the interaction between the charge particles. The Racah wave functions are obtained as the linear combinations of the multi-Slater wave functions. The angular interactions and spin sums are worked out using an irreducible theory of complex systems. Analytical formulas for the calculation of relativistic corrections, such as the mass correction, the one-body Darwin correction, the two-body Darwin correction, and the spin-spin contact interaction, are derived. Energy levels and radiative properties of He-like Al11+ and Ni26+ ions are considered for illustrative purposes. Systematic trends with respect to both the nuclear charge Z and the electron density Ne are observed for all calculated quantities. Self-consistent calculations of dense plasma effects on the atomic structure, based on the same IS potential, are also presented using fully relativistic multiconfiguration Dirac-Fock (MCDF) wave functions in the active space approximation with the inclusion of a finite nuclear size, the Breit interaction, self-energy, and vacuum polarization for comparison purposes. Comparison and analysis are made between our two sets of results and the available results in the literature. The effects of relativistic correlations are investigated in detail for the first time and are found to play an important role in the stability of these systems. The results of this study should be of great help in the modeling and diagnostics of astrophysical and laboratory plasmas.
A deep learning enabler for nonintrusive reduced order modeling of fluid flows
Authors: Pawar S. , Rahman S. M. , Vaddireddy H. , San O. , Rasheed A. , Vedula P.
Published: August 2019

In this paper, we introduce a modular deep neural network (DNN) framework for data-driven reduced order modeling of dynamical systems relevant to fluid flows. We propose various DNN architectures which numerically predict evolution of dynamical systems by learning from either using discrete state or slope information of the system. Our approach has been demonstrated using both residual formula and backward difference scheme formulas. However, it can be easily generalized into many different numerical schemes as well. We give a demonstration of our framework for three examples: (i) Kraichnan-Orszag system, an illustrative coupled nonlinear ordinary differential equation, (ii) Lorenz system exhibiting chaotic behavior, and (iii) a nonintrusive model order reduction framework for the two-dimensional Boussinesq equations with a differentially heated cavity flow setup at various Rayleigh numbers. Using only snapshots of state variables at discrete time instances, our data-driven approach can be considered truly nonintrusive since any prior information about the underlying governing equations is not required for generating the reduced order model. Our a posteriori analysis shows that the proposed data-driven approach is remarkably accurate and can be used as a robust predictive tool for nonintrusive model order reduction of complex fluid flows.
Double Rydberg anions with solvated ammonium kernels: Electron binding energies and Dyson orbitals
Authors: Díaz-Tinoco Manuel , Ortiz J. V.
Published: August 2019

Ab initio electron-propagator calculations on the electron detachment energies and associated Dyson orbitals of NnH3n+1− for n = 1–5 confirm the assignment of low-energy peaks in anion photoelectron spectra to double Rydberg anions, species in which a closed-shell cation binds a diffuse pair of electrons. The most stable double Rydberg anions contain NnH3n+1+ cores, wherein the NH4+ kernel forms n − 1 hydrogen bonds with ammonia molecules. Other low-energy peaks for a given n pertain to double Rydberg anions of lower n that are weakly bound to ammonia molecules. High-energy peaks arise from the most stable isomers which consist of hydrides bound to N–H bonds of coordinating ammonia molecules. Dyson orbitals of electron detachment are distributed over the periphery of the bonding regions of the NnH3n+1+ cores. For n = 2–4, negative charge accumulates mostly outside the N–H bonds of the NH4+ kernels that are not engaged in hydrogen bonds. For the tetrahedral cases, where n = 1, 5, Dyson orbitals are diffuse, symmetric functions that are orthogonalized to occupied a1 orbitals of the cationic core. Shake-up features in spectra have been assigned to doublet states with a single diffuse electron in an s, p, d, or f orbital.
Effect of metal nanoparticle size and titania crystallinity on the performance of Au/TiO2 catalysts for the promotion of carbon monoxide oxidation at cryogenic temperatures
Authors: Lee Ilkeun , Zaera Francisco
Published: August 2019

The ability of Au/TiO2 catalysts to promote the oxidation of carbon monoxide at cryogenic temperatures was probed by using diffuse-reflectance infrared absorption spectroscopy (DRIFTS). The focus of this work was to identify correlations between the catalytic activity and both the nature of the titania support and the size of the Au nanoparticles (NPs). Two key intermediates were identified: an initial CO adsorbed on defect sites within the titania support with a 2175 cm−1 C–O stretching frequency signature, and a second species with a DRIFTS peak at 2163 cm−1 associated with the intermediate at Au–TiO2 interfacial sites that incorporates atomic oxygen to produce CO2. CO adsorption at the low temperatures associated with this process (120 K) appears to require defective sites, possibly titanate-type surface species: an amorphous (and NaOH-treated) support showed higher activity than crystalline titania. In addition, the catalytic activity peaks at an Au NP average size of about 3 nm, which, in turn, correlates with the population of the second CO intermediate mentioned above. The mechanism that explains this cryogenic oxidation reaction is different than that extensively reported for the room-temperature processes, but both appear to display similar dependence on Au NP diameter.
Nonintrusive approach to reduced order modeling of fluid flows is developed
Authors: Mandel Savannah
Published: August 2019

Limitations can be surpassed as deep learning is used to develop nonintrusive methods of modeling fluid flows.
Teleportation for device-scale quantum computing
Authors: Hill Heather M.
Published: August 2019

Trapped ions interact with help from an entangled pair of messengers.
Genotypic determinants of fluoroquinolone and macrolide resistance in Neisseria gonorrhoeae
Authors: Hall Catherine L. , Harrison Mark A. , Pond Marcus J. , Chow Christine , Harding-Esch Emma M. , Sadiq S. Tariq
Published: August 2019

Background
High rates of antimicrobial resistance (AMR) in Neisseria gonorrhoeae hinder effective treatment, but molecular AMR diagnostics may help address the challenge. This study aimed to appraise the literature for resistance-associated genotypic markers linked to fluoroquinolones and macrolides, to identify and review their use in diagnostics. Methods: Medline and EMBASE databases were searched and data pooled to evaluate associations between genotype and phenotypic resistance. The minimum inhibitory concentration (MIC) cut-offs were ≤ 0.06 mg L−1 for non-resistance to ciprofloxacin and ≤ 0.5 mg L−1 for non-resistance to azithromycin. Results: Diagnostic accuracy estimates were limited by data availability and reporting. It was found that: 1) S91 and D95 mutations in the GyrA protein independently predicted ciprofloxacin resistance and, used together, gave 98.6% (95% confidence interval (CI) 98.0–99.0%) sensitivity and 91.4% (95%CI 88.6–93.7%) specificity; 2) the number of 23S rRNA gene alleles with C2611T or A2059G mutations was highly correlated with azithromycin resistance, with mutation in any allele giving a sensitivity and specificity of 66.1% (95%CI 62.1–70.0%) and 98.9% (95%CI 97.5–99.5%) respectively. Estimated negative (NPV) and positive predictive values (PPV) for a 23S rRNA diagnostic were 98.6% (95%CI 96.8–99.4%) and 71.5% (95%CI 68.0–74.8%) respectively; 3) mutation at amino acid position G45 in the MtrR protein independently predicted azithromycin resistance; however, when combined with 23S rRNA, did not improve the PPV or NPV. Conclusions: Viable candidates for markers of resistance detection for incorporation into diagnostics were demonstrated. Such tests may enhance antibiotic stewardship and treatment options.
Leidenfrost effect studied by video analysis
Authors: Zeuner M , Schwark K , Hanisch C , Ziese M
Published: August 2019

When liquid droplets touch a sufficiently hot surface the Leidenfrost effect leads to levitation of the droplets on a steam layer. At the same time the heat flux from hot surface to droplet is strongly reduced and the droplet lifetime is increased. The understanding of this effect, which can readily be observed on a standard stove, requires knowledge of fluid dynamics, basic mechanics and thermodynamics. It therefore combines appealing experiments with interdisciplinary physics and is well-suited for teaching physical principles, experimentation, modelling and data analysis in schools and in the early stages of university physics. The aim of this work is to present some guidance for projects in this area. Video analysis was used to quantitatively measure droplet sizes and lifetimes of water and liquid nitrogen droplets placed on a hot plate. A simple model for a levitating droplet was developed and compared to the data. The findings indicate that video analysis is a suitable way to examine the Leidenfrost effect for droplet diameters between about 3 and 10 mm. From the analysis the effective thermal conductivities of the steam layers were determined and were found to be two to three orders of magnitude smaller than the thermal conductivities of the corresponding gases at rest. By measuring several different droplets under varying parameters it was concluded that the precision of the experimental setup is sufficient to provide a practical tool for pupils and undergraduate students to explore this fascinating everyday phenomenon.
The Role of Plant Diversity In Local Community Of Gili Iyang Island, Sumenep, East Java, Indonesia
Authors: Susiarti S , Sihotang VBL , Rugayah
Published: August 2019

Indonesia is known as an archipelago with more than 17,000 islands, one of which is Gili Iyang Island. The island is located in the eastern part of Madura island, including in the region of Sumenep regency, East Java Province, Indonesia. Gili Iyang Island is reported as one of the highest oxygen sites in the world with tourism potency such as various caves with its natural beauty. The research was aimed to discover the plant diversity and local wisdom of the community. Data was collected through direct observation, open ended interview with 20 informants in two villages. The results showed that no less than 94 species utilized as food, medicines and other purposes. The plant species used for food such as taal (Borassus flabellifer L.), bukkol (Zizyphusjujuba Mill.), bille (Aegle marmelos (L.) Correa.) and bintaos (Wrightia pubescens R.Br.). The latter species is still rare to consume as food, while medicinal materials are landhek (Barleria pronitis L), membhe (Azadirachta indica A. Juss.) and tanggeri (Sida rhombifolia L.).
Frailty, hospital use and mortality in the older population: findings from the Newcastle 85+ study
Authors: Keeble Eilis , Parker Stuart G , Arora Sandeepa , Neuburger Jenny , Duncan Rachel , Kingston Andrew , Hanratty Barbara , Jagger Carol , Robinson Louise , Kirkwood Tom
Published: August 2019

Background

Frailty is a significant determinant of health care utilisation and associated costs, both of which also increase with proximity to death. What is not known is how the relationships between frailty, proximity to death, hospital use and costs develop in a population aged 85 years and over.

Methods

This study used data from a prospective observational cohort, the Newcastle 85+ Study, linked with hospital episode statistics and death registrations. Using the Rockwood frailty index (cut off <0.25), we analysed the relationship between frailty and mortality, proximity to death, hospital use and hospital costs over 2, 5 and 7 years using descriptive statistics, Kaplan–Meier survival curves, Cox’s proportional hazards and negative binomial regression models.

Results

Baseline frailty was associated with a more than two-fold increased risk of mortality after 7 years, compared to people who were non-frail. Participants classified as frail spent more time in hospital over 7 years than the non-frail, but this difference declined over time. Baseline frailty was not associated with increased time spent in hospital during the last 90 days of life.

Conclusion

Evidence continues to accrue on the impact of frailty on emergency health care use. Hospital and community services need to adapt to meet the challenge of introducing new proactive and preventative approaches, designed to achieve benefits in clinical and/or cost effectiveness of frailty management.
gwasrapidd: an R package to query, download and wrangle GWAS catalog data
Authors: Magno Ramiro , Maia Ana-Teresa
Published: August 2019

Motivation

The National Human Genome Research Institute Catalog of Published Genome-Wide Association Studies (GWAS) Catalog has collected, curated and made available data from over 7100 studies. The recently developed GWAS Catalog representational state transfer (REST) application programming interface (API) is the only method allowing programmatic access to this resource.

Results

Here, we describe gwasrapidd, an R package that provides the first client interface to the GWAS Catalog REST API, representing an important software counterpart to the server-side component. gwasrapidd enables users to quickly retrieve, filter and integrate data with comprehensive bioinformatics analysis tools, which is particularly critical for those looking into functional characterization of risk loci.

Availability and implementation

gwasrapidd is freely available under an MIT License, and can be accessed from https://github.com/ramiromagno/gwasrapidd.

Supplementary information

Supplementary data are available at Bioinformatics online.
DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data
Authors: Ramirez R N , Bedirian K , Gray S M , Diallo A
Published: August 2019

Motivation

Visualization of multiple genomic data generally requires the use of public or commercially hosted browsers. Flexible visualization of chromatin interaction data as genomic features and network components offer informative insights to gene expression. An open source application for visualizing HiC and chromatin conformation-based data as 2D-arcs accompanied by interactive network analyses is valuable.

Results

DNA Rchitect is a new tool created to visualize HiC and chromatin conformation-based contacts at high (Kb) and low (Mb) genomic resolutions. The user can upload their pre-filtered HiC experiment in bedpe format to the DNA Rchitect web app that we have hosted or to a version they themselves have deployed. Using DNA Rchitect, the uploaded data allows the user to visualize different interactions of their sample, perform simple network analyses, while also offering visualization of other genomic data types. The user can then download their results for additional network functionality offered in network based programs such as Cytoscape.

Availability and implementation

DNA Rchitect is freely available both as a web application written primarily in R available at http://shiny.immgen.org/DNARchitect/ and as an open source released under an MIT license at: https://github.com/alosdiallo/DNA_Rchitect.
VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data
Authors: Kim Kyungsoo , Yang Sunmo , Ha Sang-Jun , Lee Insuk
Published: August 2019

Motivation

The immune system has diverse types of cells that are differentiated or activated via various signaling pathways and transcriptional regulation upon challenging conditions. Immunophenotyping by flow and mass cytometry are the major approaches for identifying key signaling molecules and transcription factors directing the transition between the functional states of immune cells. However, few proteins can be evaluated by flow cytometry in a single experiment, preventing researchers from obtaining a comprehensive picture of the molecular programs involved in immune cell differentiation. Recent advances in single-cell RNA sequencing (scRNA-seq) have enabled unbiased genome-wide quantification of gene expression in individual cells on a large scale, providing a new and versatile analytical pipeline for studying immune cell differentiation.

Results

We present VirtualCytometry, a web-based computational pipeline for evaluating immune cell differentiation by exploiting cell-to-cell variation in gene expression with scRNA-seq data. Differentiating cells often show a continuous spectrum of cellular states rather than distinct populations. VirtualCytometry enables the identification of cellular subsets for different functional states of differentiation based on the expression of marker genes. Case studies have highlighted the usefulness of this subset analysis strategy for discovering signaling molecules and transcription factors for human T-cell exhaustion, a state of T-cell dysfunction, in tumor and mouse dendritic cells activated by pathogens. With more than 226 scRNA-seq datasets precompiled from public repositories covering diverse mouse and human immune cell types in normal and disease tissues, VirtualCytometry is a useful resource for the molecular dissection of immune cell differentiation.

Availability and implementation

www.grnpedia.org/cytometry
ArtiFuse—computational validation of fusion gene detection tools without relying on simulated reads
Authors: Sorn Patrick , Holtsträter Christoph , Löwer Martin , Sahin Ugur , Weber David
Published: August 2019

Motivation

Gene fusions are an important class of transcriptional variants that can influence cancer development and can be predicted from RNA sequencing (RNA-seq) data by multiple existing tools. However, the real-world performance of these tools is unclear due to the lack of known positive and negative events, especially with regard to fusion genes in individual samples. Often simulated reads are used, but these cannot account for all technical biases in RNA-seq data generated from real samples.

Results

Here, we present ArtiFuse, a novel approach that simulates fusion genes by sequence modification to the genomic reference, and therefore, can be applied to any RNA-seq dataset without the need for any simulated reads. We demonstrate our approach on eight RNA-seq datasets for three fusion gene prediction tools: average recall values peak for all three tools between 0.4 and 0.56 for high-quality and high-coverage datasets. As ArtiFuse affords total control over involved genes and breakpoint position, we also assessed performance with regard to gene-related properties, showing a drop-in recall value for low-expressed genes in high-coverage samples and genes with co-expressed paralogues. Overall tool performance assessed from ArtiFusions is lower compared to previously reported estimates on simulated reads. Due to the use of real RNA-seq datasets, we believe that ArtiFuse provides a more realistic benchmark that can be used to develop more accurate fusion gene prediction tools for application in clinical settings.

Availability and implementation

ArtiFuse is implemented in Python. The source code and documentation are available at https://github.com/TRON-Bioinformatics/ArtiFusion.

Supplementary information

Supplementary data are available at Bioinformatics online.
Agenesis of the putamen and globus pallidus caused by recessive mutations in the homeobox gene GSX2
Authors: De Mori Roberta , Severino Mariasavina , Mancardi Maria Margherita , Anello Danila , Tardivo Silvia , Biagini Tommaso , Capra Valeria , Casella Antonella , Cereda Cristina , Copeland Brett R , Gagliardi Stella , Gamucci Alessandra , Ginevrino Monia , Illi Barbara , Lorefice Elisa , Musaev Damir , Stanley Valentina , Micalizzi Alessia , Gleeson Joseph G , Mazza Tommaso , Rossi Andrea , Valente Enza Maria
Published: August 2019

Congenital malformations of the basal ganglia are rare. De Mori et al. describe a novel syndrome of severe dystonic tetraparesis and intellectual impairment, with hypo/agenesis of the basal ganglia. The syndrome is caused by recessive mutations in GSX2, a homeobox gene expressed in ganglionic eminences and essential for basal ganglia development.
The Elimination of Neglected Tropical Diseases: A Case Study Exemplifying How Foreign Assistance Funding Can Be Catalytic in Reducing the Burden of Major Global Health Conditions
Authors: Wainwright Emily , Evans Darin , Rotondo Lisa , Pou Bolivar , Yevstigneyeva Violetta , Zoerhoff Kathryn L , Ottesen Eric A , Reithinger Richard
Published: August 2019

In 2006, following direct advocacy and published rationale, the US Agency for International Development (USAID) established a neglected tropical diseases (NTDs) program to support the scale-up of integrated platforms to target the elimination and control of 5 NTDs—lymphatic filariasis, trachoma, onchocerciasis, schistosomiasis, and soil-transmitted helminthiasis.

By 2017, more than 2.3 billion NTD treatments had been delivered to at-risk populations in 25 countries, leveraging $19 billion in donated drugs—approximately $26 dollars in donated medicine per $1 spent by USAID. As a result, most of the supported countries are on track to achieve their elimination goals (for lymphatic filariasis and trachoma) by 2020 or 2021 and their control goals soon thereafter.

Though “small” when compared to other global health initiatives, this investment proved to be catalytic, and indeed highlights how foreign assistance funding can be transformative, in reducing the burden of major global health conditions such as NTDs.