bluuebunny/crossref_metadata_2025 huggingface dataset:
Accelerated corrosion performance of AISI 316L stainless steel concrete reinforcement used in restoration works of ancient monuments
Authors: Tsouli Sofia , Lekatou Angeliki G. , Siozos Evangelos , Kleftakis Spyridon
Published: August 2018

The accelerated corrosion performance of AISI type 316L stainless steel rebars in solutions simulating concrete exposed to various environments was studied by means of cyclic polarization, before and after a four month salt spray test. B500A structural steel rebars were also tested for comparison reasons. Although 316L showed some susceptibility to localized corrosion during polarization in saturated Ca(OH)2containing 3.5 wt.% NaCl, four months of salt spraying did not significantly affect its polarization behavior. Salt spraying for 4 m did not have any significant effect on the macrostructural state of 316L reinforced concrete.
The size effect of rebars, on the structural integrity of reinforced concrete structures, which are exposed to corrosive environments
Authors: Drakakaki Argyro , Apostolopoulos Charis
Published: August 2018

The goal of the present study is to mention the importance of underestimation of the corrosion damage developed in critical load bearing areas, on the column bases, where formation of plastic hinges is attended, mainly during strong seismic events (Figure 1). In such cases, plastic hinges are expected to absorb the seismic energy, owed to seismic vibration. However, chloride induced corrosion is responsible for significant degradation of concrete infrastructures located in coastal areas. Forecasting the life expectancy of such structures, in corrosive environments, is a challenge in engineering, given the fact that existing internal, external, as well as subcutaneous defects, in combination with the aggressive environmental factors, may be responsible for the development of subcutaneous damage on steel reinforcement [1], which may diminish the tolerance of the critical regions of the structures. Moreover, it is widely known that penetration of chloride ions into reinforced concrete varies according to its porosity and its permeability, however, the major factor for corrosion initiation is the threshold of chloride concentration, which strongly depends on the exposed surface area of steel. In the present experimental study, the variation of corrosion damage, on bare specimens, was evaluated and correlated with the geometry of the exposed surface of steel in corrosion [2]. Finally, a correlation between short bare specimens and the “injured” areas of the long embedded specimens is estimated as well.
The footprint of surface modification treatments on the corrosion-fatigue of AA7075-T651
Authors: Michailidis Nikolaos , Ragousis Antonios , Stergioudi Fani , Castaneda Homero
Published: August 2018

Different manufacturing and surface modification treatments distinctively affect the surface characteristics and microstructure of the workpiece, having a different impact on their effective life-span. The corrosion-fatigue behavior of as-machined (wire-EDM), blasted and anodized aluminum alloy 7075-T651 was investigated using 3.5wt% NaCl aqueous solution and distilled water as corrosive media. An in-situ corrosion-fatigue device capable of producing cyclic loads in a corrosive solution was employed, coupled with FEM analysis. Blasting process offered a prolongation of the corrosion-fatigue life-span in both corrosive media, when compared to the as-machined samples under identical conditions. Anodizing had a deleterious effect in all the examined cases.
Design Right Once for Additive Manufacturing
Authors: Tsakiris Antonios , Salpistis Christos , Mihailidis Athanassios
Published: August 2018

Additive Manufacturing (AM) has been widely considered a key factor for innovative design. However, the utilization of AM has not been as high as expected, although the technology offers key innovative design capabilities, weight reduction, parts count and assembly consolidation as well as material saving. This low utilization is attributed to the lack of AM understanding, mature CAE/CAM software tools addressing AM specific issues such as design support structure generation and removal, residual stresses, surface quality. In most cases, Design for AM (DfAM) is a crucial requisite for a “Design Right Once” approach. Such an approach is shown in the current study using three parts as example: an arthropod’s leg, a gearshift drum and an electric motor mounting frame. The implementation of geometrical conformal lattice structures and lattices with variable density are discussed. A structured design approach is presented and design dilemmas are solved in terms of a DfAM approach. Primary design optimizations are evaluated. Weight reduction is considered throughout the design and free form surfaces are being used. “Freedom to Design” principle is also portrayed and assembly parts consolidation occurs as a natural process of DfAM in comparison with previous design practices. It is concluded that, even from the primary design phase the design engineer can reveal his creativity because of the absence of constraints set by the traditional manufacturing technologies.
Strengthening and ductilizing of magnesium alloying with heavy rare earth elements
Authors: Huang Yuanding , Xu Yulin , You Sihang , Gan Weimin , Karl Karl Ulrich , Hort Norbert
Published: August 2018

Among all alloying elements the rare earth elements (RE) play a key role in improving the ductility, high temperature strength and corrosion resistance effectively for magnesium and its alloys. The present work investigated the influences of single alloying or multi heavy REs (Gd, Dy and Y) alloying on the strengthening and ductilizing of magnesium. These heavy REs have a higher solid solubility in magnesium than that the light REs such as Nd and Ce. It is found that the solid solution strengthening caused by Gd follows the linear relationship with the exponent n value of 1/2 or 2/3. When adding two or more heavy REs in Mg, owing to their interactions and resultant synergetic effects, the effectiveness of strengthening and ductilizing caused by multiple RE addition is much better than that by single RE addition.
Design and Analysis of a Novel Mechanism for the Morphing of Trailing Edge of an Aircraft Wing
Authors: Şahin Harun Levent , Yaman Yavuz
Published: August 2018

In this paper, design of a novel deployable scissor-structural mechanism (SSM) for active camber and chord morphing airfoil has been presented. The mechanism is created via combination of one four-bar linkage and various scissor-like elements (SLEs). The theory behind scissor-like elements and hierarchical design procedure are adequately explained. Following that design procedure, a scissor-structural mechanism is created in order to satisfy the desired airfoil shapes, which have different camber lines with minimum structural error. It is also possible to modify the chord length by changing the properties and types of the used SLEs. Modifying the design parameters of used SLEs, without increasing the degree-of-freedom (DOF) of the mechanism, will result in infinite number of results. With the help of error definition and developed computerroutine, the best scissor-structural mechanism which satisfy the required tasks properly can be detected.
The effect of friction force and cavitation on wear in piston-cylinder assemblies
Authors: Dellis Polychronis
Published: August 2018

Both in engines and test rigs, cavitation in piston-ring lubrication is a subject studied by many researchers in the past. Although there is no sufficient evidence of cavitation erosion on the surface of the liner, this phenomenon is studied as part of the lubricant transport process. During the transport process the lubricant enters the combustion chamber. The combustion products of consumed oil might contribute to exhaust gas emissions and with emission legislation becoming more stringent, it is important that oil consumption is reduced to the lowest level possible. The role of the piston-rings is becoming more complex with the imposed requirements for lower oil consumption and friction. The piston-ring pack role on engine performance, durability and wear, is becoming on the other hand, more demanding. Between the piston-ring and cylinder liner, cavitation occurs as a result of two-phase liquid flow. Cavitation has long been recognized to degrade performances in most engineering applications and its effect in piston-ring lubrication is that it alters the oil film pressure profile, generated at the converging-diverging wedge of the piston-ring. An area of the piston-ring surface is void, corresponds to subatmospheric pressures and thus, the piston-ring load capacity is altered. Two experimental rigs were used, a simplified single-ring test rig that simulates the piston-ring liner movement at speeds corresponding to idle but the movement is reversed and a single cylinder diesel engine that was used for visualization results only, after the necessary modifications.
Aufstehen, wenn Stehen nicht möglich ist (Teil 2)
Authors: Muesse André
Published: August 2018

In der vorigen Ausgabe haben wir dargestellt, wie Kinästhetik als Methode eingesetzt werden kann, um komplexe Transfergeschehen zu planen und zu koordinieren.
Das Wissen um die Grundlagen menschlicher Bewegung gibt Orientierung in der durchzuführenden Aktivität. Anhand der Bezugsebenen der körperlichen Orientierung
lässt sich Bewegung zwischen zwei Körperpositionen gestalten. Hierzu dienen die in der Kinästhetik idealtypisch beschriebenen Grundpositionen als Modell: Sie
bilden die Bewegungsentwicklung von der Rückenlage zum aufrechten Stand schematisch ab. Mittels der Bezugsebenen lässt sich menschliche Bewegung zwischen diesen
Positionen beschreiben. So können auch hochkomplexe Transfers mit stark bewegungseingeschränkten Menschen analysiert werden. Einzelne Positionen können dabei
als Zwischenschritte zum Innehalten dienen, was für eine bessere Orientierung im Bewegungsablauf sorgt und Sicherheit schafft.
Neue minimalinvasive Therapieoptionen des benignen Prostatasyndroms
Authors: Magistro Giuseppe , Westhofen Thilo , Stief Christian , Gratzke Christian
Published: August 2018

Neue minimalinvasive Therapieansätze zur Behandlung des benignen Prostatasyndroms verfolgen das Ziel, bei gleichwertiger Wirksamkeit zu den etablierten Referenzverfahren ein günstigeres Sicherheitsprofil zu gewährleisten. Insbesondere der vollständige Erhalt der sexuellen Funktion, einschließlich der antegraden Ejakulation, ist von großem Interesse. Idealerweise lassen sich die neuen Prozeduren im ambulanten Setting unter lokaler Betäubung durchführen. Unter den mechanischen Ansätzen konnte für das Urolift®-Verfahren in der kurz- und langfristigen klinischen Evaluierung eine signifikante Besserung der Symptome des unteren Harntraktes (lower urinary tract symptoms; LUTS) für ein selektives Patientengut ohne prominenten Mittellappen gezeigt werden. Dabei ist Urolift in Bezug auf den Erhalt der antegraden Ejakulation und einer kürzeren Rekonvaleszenz dem Referenzverfahren der transurethralen Resektion der Prostata (TURP) überlegen. In der ersten klinischen Beurteilung des „Temporary Implantable Nitinol Device“ (TIND) wurde die schnelle und einfache Durchführbarkeit der neuen Technik aufgezeigt mit ersten vielversprechenden Ergebnissen im 3-Jahres-Verlauf. Für eine adäquate Bewertung des Verfahrens stehen allerdings noch prospektive, randomisierte und kontrollierte Studien aus. Unter den neuen ablativen Verfahren demonstrierte die Verwendung von konvektivem Wasserdampf-Energietransfer in Form des Rezũm®-Systems eine gute Wirksamkeit und Sicherheit in der 3-Jahres-Beurteilung. Es ist auch bei Vorhandensein eines obstruktiven Mittellappens einsetzbar und schont hierbei die antegrade Ejakulation. Innovative Ablationstechnologien wie die Aquablation (AquaBeam®) stehen noch am Anfang ihrer klinischen Bewertung, doch zeigen bereits initiale klinische Studien vielversprechende Resultate, auch im direkten Vergleich mit der TURP.
Fit Daheim – ein Sturzpräventionsprogramm
Authors: Lautenschläger Sindy , Müller Christian
Published: August 2018

Häusliches Setting Fit Daheim ist ein Sturzpräventionsprogramm für zu Hause lebende Menschen im höheren Lebensalter. Wofür benötigen wir bei der hohen Anzahl an Sturzpräventionsprogrammen noch ein weiteres Angebot? In Deutschland liegen bisher keine evidenzbasierten Sturzpräventionsprogramme für zu Hause lebende Menschen im höheren Lebensalter vor, die körperliche Trainingsprogramme und Maßnahmen zur Wohnraumanalyse, -beratung und -anpassung kombinieren und für das häusliche Setting konzipiert sind.
Die medikamentöse Therapie des BPS
Authors: Westhofen Thilo , Magistro Giuseppe , Stief Christian , Gratzke Christian
Published: August 2018

Die medikamentöse Therapie des BPS ist oftmals das erstes Therapieregime bei symptomatischen BPS-Patienten, die unter zuwartendem Verhalten signifikant beschwerdeprogredient werden. Ziel der medikamentösen Therapie ist eine schnelle Verbesserung der „lower urinary tract symptoms“ (LUTS), die Verbesserung des Harnstrahls sowie die Verminderung der Restharnmenge. Unerwünschte Nebenwirkungen sollten möglichst niedrig sein.

Die häufig primär eingesetzten α1-Adrenorezeptorblocker überzeugen bei guter Verträglichkeit durch schnelle Wirksamkeit und signifikante Verbesserung von LUTS, Qmax und Restharnmengen.

Bei LUTS auf Grund von größeren Prostatavolumina zeigen 5α-Reduktase-Hemmer nach längerer Einnahme signifikante Verbesserung hinsichtlich Qmax, LUTS und Restharn. Zudem wirken sie als einziges Medikament relevant der Krankheitsprogression entgegen.

Bei ausgeprägten irritativen Beschwerden zeigen umfangreiche Studien gute Ergebnisse unter Therapie mit Muskarinrezeptorantagonisten und den seit kurzem zur BPS-Therapie erneut in Deutschland erhältlichen Beta-3-Agonisten. Beide bewirken Verbesserung der LUTS, ein günstigeres Nebenwirkungsprofil zeigt sich unter Therapie mit Beta-3-Agonisten.

Vorrangig als Therapie erektiler Dysfunktion (ED) genutzte PDE-5-Hemmer zeigen ebenfalls eine signifikante Verbesserung von LUTS und Restharnmengen und eignen sich gut für Patienten mit LUTS in Kombination mit ED.

Die zunehmend äußerst beliebten Phytopharmaka bestechen durch geringe Nebenwirkungen, werden jedoch auf Grund fraglicher Wirksamkeit durch keine akute Leitlinie empfohlen.

Neue Substanzgruppen, aber auch neue Therapieansätze mit bewährten Substanzen ergänzen laufend das wachsende Spektrum der medikamentösen Therapie des BPS. So ermöglichen neue Therapie-Algorithmen die individuelle Anpassung der Therapie an das Risikoprofil des Patienten unter Berücksichtigung unerwünschter Nebenwirkungen.
Anti-Inflammatory 18β-Glycyrrhetinin Acid Derivatives Produced by Biocatalysis
Authors: Fan Boyi , Jiang Baocheng , Yan Sensen , Xu Bohui , Huang Huilian , Chen Guangtong
Published: August 2018

In this study, the biocatalysis of 18β-glycyrrhetinic acid by two strains of filamentous fungi, namely Rhizopus arrhizus AS 3.2893 and Circinella muscae AS 3.2695, was investigated. Scaled-up biotransformation reactions yielded 14 metabolites. Their structures were established based on extensive nuclear magnetic resonance and high-resolution electrospray ionization mass spectrometry data analyses, and seven of them are new compounds. The two fungal strains exhibited distinct biocatalytic features. R. arrhizus could catalyze hydroxylation and carbonylation reactions, whereas C. muscae preferred to catalyze hydroxylation and glycosidation reactions. These highly specific reactions are difficult to achieve by chemical synthesis, particularly under mild conditions. Furthermore, we found that most of the metabolites exhibited pronounced inhibitory activities on lipopolysaccharides-induced nitric oxide production in RAW264.7 cells. These biotransformed derivatives of 18β-glycyrrhetinic acid could be potential anti-inflammatory agents.
Thoracoscopic Resection of Fluorodeoxyglucose-Avid Mediastinal Lymph Nodes Associated with Advanced Ovarian Carcinoma
Authors: Hamaji Masatsugu , Yamaguchi Ken , Koyasu Sho , Date Hiroshi
Published: August 2018

The indication for surgery is controversial in patients with advanced ovarian cancer and fluorodeoxyglucose (FDG)-avid mediastinal lymph nodes. Herein we report our experience in thoracoscopic resection of FDG-avid mediastinal lymph nodes associated with advanced ovarian cancer in six patients. No perioperative or long-term mortality was noted. FDG-avid mediastinal lymph nodes in advanced ovarian carcinoma may merit thoracoscopic resection with histological confirmation for more precise staging.
Ultrasound-Guided Aspiration Does Not Reduce the Recurrence Rate of Ganglion Cysts of the Wrist
Authors: Kurkis Gregory , Anastasio Albert , DeVos Marijke , Gottschalk Michael
Published: August 2018

Background Ganglion cysts are the most frequent soft tissue tumor encountered in the upper extremity and are commonly treated by aspiration or by surgical excision. Ultrasound is a promising addition to traditional aspiration, as it allows for visualization of the needle within the ganglion before aspiration.

Questions Are ganglion cysts of the wrist less likely to reoccur if they are aspirated under ultrasound guidance versus “blind” aspiration without the use of ultrasound guidance? Does patient functionality change based on whether or not the cyst recurred?

Patients and Methods In total, 52 patients were successfully contacted and recurrence rates were compared between those whose cyst was treated with ultrasound-guided (13 patients) with those whose cyst was treated with blind aspiration (39 patients). Mean follow-up time was 2.9 years.

Results Recurrence rates were 69% (9 patients) and 74% (29 patients) for the ultrasound-guided and blind aspiration groups, respectively (p-value: 0.73), showing no significant difference in recurrences of wrist ganglion between the two groups. A metric of functionality (Quick–DASH [Disabilities of the Arm, Shoulder, and Hand]) revealed worse outcomes in patients who experienced return of ganglion cyst after aspiration versus those who did not.

Conclusion Additional studies with improved sample sizes are needed to demonstrate the superiority of ultrasound-guided aspiration versus blind aspiration. Due to a high recurrence rate following aspiration (both ultrasound-guided and blinded), a lower threshold for surgical intervention is likely reasonable.

Level of Evidence This is a Level IIIb study.
Notfallmedizin abseits schnell erreichbarer medizinischer Infrastruktur
Authors: Leischker Andreas , Holst Fritz
Published: August 2018

For many acute diseases and injuries, treatment does not differ between industrialised environment and wilderness setting. However, for some emergencies, treatment needs to be adapted if advanced medical care facilities cannot be reached within 4 hours.

In these situations, dislocated joints and fractures should be reduced quickly. Contaminated wounds should be cleaned carefully, with drinking water being sufficient when no sterile solution is available. A patient with a contaminated wound should receive a systemic antibiotic coverage within one hour. Keeping an injured patient warm is crucial to prevent disseminated coagulation.

In most cases in the wilderness, cardiopulmonary resuscitation (CPR) should be stopped after 20 minutes; if no return of spontaneous circulation (ROSC) has occurred. However, in case of severe hypothermia, drowning or cardiac arrest due to lightning, prolonged CPR may be feasible.

Handwashing with soap and water and use of alcohol gels are effective measures for the prevention of travellers’ diarrhoea during expeditions.
Simulating the horizontal growth process of silicon ribbon
Authors: Sun Tao , Ding Jianning , Jiang Cunhua , Xu Jiawei , Yuan Ningyi
Published: August 2018

In this paper, we present a solidification growth model that primarily describes the principal components of horizontal ribbon growth process, but also discusses the interaction between fluid flow and heat transfer, crystallization dynamics, and the effects of oxygen impurity distribution in melts, particularly with respect to the morphology of the interface. The effects of the jet cooling rate, pulling speed, and transfer coefficient on solute transport were studied. The results showed that a higher jet velocity produces a sharper temperature gradient at the interface and a stronger Marangoni effect, facilitates solute transport in the silicon melt, and promotes higher oxygen concentration in crystal. The stronger Marangoni convection causes more rapid oxygen transfer in the silicon melt and a higher oxygen concentration. Solidification front increases the downward flow velocity of the eddy current as the pulling speed is increased; this leads to a decrease in solute concentration at the interface. An increase in the downward flow of the vortex confluence facilitates the reduction of solute concentration in the crystal. An increase in the upward flow of the vortex confluence will increase the concentration in the crystal. The oxygen concentration is concentrated at the top and bottom of the silicon ribbon.
3D-printed capillary for hydrogen filled discharge for plasma based experiments in RF-based electron linac accelerator
Authors: Filippi F. , Anania M. P. , Biagioni A. , Chiadroni E. , Cianchi A. , Ferber Y. , Ferrario M. , Zigler A.
Published: August 2018

Plasma-based acceleration experiments require capillaries with a radius of a few hundred microns to confine plasma up to a centimeter scale capillary length. A long and controlled plasma channel allows to sustain high fields which may be used for manipulation of the electron beams or to accelerate electrons. The production of these capillaries is relatively complicated and expensive since they are usually made with hard materials whose manufacturing requires highly specialized industries. Fine variations of the capillary shape may significantly increase the cost and time needed to produce them. In this article, we demonstrate the possibility of using 3D printed polymeric capillaries to drive a hydrogen-filled plasma discharge up to 1 Hz of repetition rate in an RF based electron linac. The plasma density distribution has been measured after several shot intervals, showing the effect of the surface ablation on the plasma density distribution. This effect is almost invisible in the earlier stages of the discharge. After more than 55000 shots (corresponding to more than 16 h of working time), the effects of the ablation on the plasma density distribution are not evident and the capillary can still be used. The use of these capillaries will significantly reduce the cost and time for prototyping, allowing us to easily manipulate their geometry, laying another building block for future cheap and compact particle accelerators.
Quantization of the damped harmonic oscillator
Authors: Serhan M. , Abusini M. , Al-Jamel Ahmed , El-Nasser H. , Rabei Eqab M.
Published: August 2018

In this work, a suitable Hamiltonian that describes the damped harmonic oscillator is constructed. Besides, the Hamilton-Jacobi equation for this dissipative system is written and the action function is obtained. Then, the system is quantized using two methods: the WKB approximation and the canonical quantization. In addition, evolution of the probability density is plotted at different times, and it is observed that the width of these densities decreases with time. The average energy of the system is also calculated and found to decrease with time.
Low-dimensional dynamics in non-Abelian Kuramoto model on the 3-sphere
Authors: Jaćimović Vladimir , Crnkić Aladin
Published: August 2018

This paper deals with the low-dimensional dynamics in the general non-Abelian Kuramoto model of mutually interacting generalized oscillators on the 3-sphere. If all oscillators have identical intrinsic generalized frequencies and the coupling is global, the dynamics is fully determined by several global variables. We state that these generalized oscillators evolve by the action of the group GH of (quaternionic) Möbius transformations that preserve S3. The global variables satisfy a certain system of quaternion-valued ordinary differential equations, that is an extension of the Watanabe-Strogatz system. If the initial distribution of oscillators is uniform on S3, additional symmetries arise and the dynamics can be restricted further to invariant submanifolds of (real) dimension four.
Development of a mathematical model for submarine granular flows
Authors: Si Pengfei , Shi Huabin , Yu Xiping
Published: August 2018

An Eulerian-Eulerian two-phase model based on a collisional-frictional law for the granular stress is proposed for the description of underwater granular flows and is applied to the collapses of immersed granular columns, which can be viewed as an idealized physical model of submarine landslides. In the mathematical model, the kinetic theory for dry granular flows is extended to take into account the particle-fluid interaction when formulating the collisional stress in the granular material, while the frictional stress is modeled based on an existing relation obtained by statistically averaging the individual contact forces among cohesionless particles. The drag force and the virtual-mass force are considered to represent the inter-phase interaction. The two-phase model is then employed to simulate the laboratory experiments of the collapses of granular columns immersed in an ambient liquid with an emphasis on the effect of the initial packing condition of the granular particles. It has been shown that the computed collapsing process of granular columns is in very good agreement with the experimental observations, and the proposed model can well capture the dynamic features of underwater granular flows. The effects of fluid pressure, drag force, and particle and fluid properties on the granular collapse are also discussed. It is demonstrated that the interstitial fluid flow plays a significant role in the collapsing process.
Experimental and computational analysis of the two-step demagnetization behavior of the surface grains of sintered Nd-Fe-B magnets
Authors: Chen Fugang , Zhang Lanting , Jin Yunxue
Published: August 2018

The two-step demagnetization behavior was observed before the coercive field of a sintered Nd-Fe-B magnet with a large specific surface (S/V). The squareness factor of the demagnetization curve and the energy product decreased with the increase in the S/V, while the remanence and the coercivity were relatively independent of the S/V. The magneto-optical Kerr effect was used to study the magnetic properties of the magnet surface. The surface magnetization switched freely, while the bulk magnetization remained unchanged under a low cyclic magnetic field. Micromagnetic simulations revealed that the anti-demagnetization abilities of grains at the polar surface perpendicular to the c-axis were larger than those at the lateral surface parallel to the c-axis. The different anti-demagnetization abilities of the surface grains induced the initial two-step demagnetization behavior.
Enhanced light coupling into periodic arrays of nanoscale semiconducting fins
Authors: Gawlik Andrzej , Bogdanowicz Janusz , Schulze Andreas , Nuytten Thomas , Tarnowski Karol , Misiewicz Jan , Vandervorst Wilfried
Published: August 2018

In this paper, we study experimentally and theoretically the light coupling into periodic arrays of nanoscale semiconducting fins among others to explain its enhancement when increasing the fin pitch, i.e., the spatial periodicity. With Raman spectroscopy on Si fin arrays, we show the enhancement of the light coupling into the fins in arrays of increasing pitch. We prove that this enhancement is due to the excitation of an electromagnetic mode, which is confined and guided inside the fins, and is more efficiently excited as the pitch increases. Finally, we propose a quantitative analytical model describing the physical mechanism responsible for the light coupling into nanoscale semiconducting fins arranged into periodic arrays of narrow sub-60 nm pitch.
Existence and multiplicity of solutions for a quasilinear Choquard equation via perturbation method
Authors: Yang Xianyong , Zhang Wei , Zhao Fukun
Published: August 2018

In this paper, we consider the existence and multiplicity of solutions for the following quasilinear Choquard equation: −Δu+V(x)u−uΔ(u2)=(|x|−μ*|u|p)|u|p−2u,   x∈RN, where N ≥ 3, μ∈(0,N+22), p∈(2,4N−4μN−2). Under some assumptions on V, we obtain the existence of positive solutions, negative solutions, and high-energy solutions via perturbation method.
TiC and TiN supported platinum monolayer as high-performance catalysts for CO oxidation: A DFT study
Authors: Wang Yan , Yang Zongxian
Published: August 2018

The reactivity toward CO oxidation of Pt monolayer supported on TiC(001) and TiN(001) is studied by using empirical dispersion-corrected density functional theory calculations. A number of possible reaction pathways for CO oxidation, including the Eley-Rideal (ER) and Langmuir-Hinshelwood (LH) mechanisms, between adsorbed O2 and CO molecules considering the cases that the adsorbed O2 dissociates first or directly reacts with CO. It is found that the dissociation adsorption of O2 molecules as the initial step is more favorable with lower activation barriers compared with the direct reaction mode. Hence the dissociation of adsorbed O2 molecules plays a very key role in the CO oxidation reaction. For both Pt monolayer systems, our analyses also reveal that the reaction is most likely predominant via the initial ER mechanism and the subsequent LH mechanism. Furthermore, by comparing the activation barriers of the rate-limiting steps, CO oxidation on PtML/TiN(001) shows a higher catalytic activity than that on PtML/TiC(001), showing the important role that the support would play in the catalytic reactions. The present results suggest that the TiN supported monolayer Pt catalyst appears to be a good candidate for CO oxidation at low-temperature.
Low field manifestation of spiral ordering in sheet like BiFeO3 nanostructures
Authors: Tomar Ruchi , Wadehra Neha , Gaikwad Vishwajit M. , Chakraverty S.
Published: August 2018

Magnetic phase diagram of a material could be tuned through structural modication. Here we show significant lowering of magnetic field (Hi) required from transition from cycloidal to canted antiferromagnetic state in sheet like nanostructures of BiFeO3 (BFO), in comparison to reported bulk single crystals of BFO. Structural analysis of this sheet like nanostructured BFO suggests that there is more tilting in FeO6 octahedra that reduce Fe-O-Fe distance in comparison to bulk BFO, leading to decrease in Hi through the reduction of exchange interaction strength.
Energy storage characteristics of (Pb,La)(Zr,Sn,Ti)O3 antiferroelectric ceramics with high Sn content
Authors: Dan Yu , Xu Haojie , Zou Kailun , Zhang Qingfeng , Lu Yinmei , Chang Gang , Huang Haitao , He Yunbin
Published: August 2018

(Pb,La)(Zr,Sn,Ti)O3 (PLZST) antiferroelectric (AFE) materials have been widely investigated for advanced pulsed power capacitors because of their fast charge-discharge rates and superior energy-storage capacity. For practical applications, pulsed power capacitors require not only large energy density but also high energy efficiency, which are very difficult to achieve simultaneously. To address this problem, we herein investigate the energy-storage properties of PLZST AFE ceramics with a high Sn content by considering that the introduction of Sn can make the polarization versus electric-field (P-E) hysteresis loops slimmer. The results show that an optimum Sn content leads to the realization of both large recoverable energy density (Wre) and high energy efficiency (η) in a single material. With a Sn content of 46%, the PLZST AFE ceramic exhibits the best room-temperature energy storage properties with a Wre value as large as 3.2 J/cm3 and an η value as high as 86.5%. In addition, both its Wre and η vary very slightly in the wide temperature range of 20–120 °C. The high Wre and η values and their good thermal stability make the Pb0.97La0.02(Zr0.50Sn0.46Ti0.04)O3 AFE ceramic a promising material for making pulsed power capacitors usable in various conditions.
Biodegradation of emerging pollutants: focus on pharmaceuticals
Authors: Ivshina Irina , Tyumina Elena , Vikhareva Elena
Published: August 2018

A priority environmental problem is pollution and disturbance of natural environments by emerging pollutants ‒ substances of various origins and structures and with known and/or potential ecotoxic effects. One of the most dangerous groups of emerging pollutants is pharmaceutical substances due to their highly stable chemical structure and pronounced biological activity. They are found in soil, bottom sediments, surface, sewage, groundwater and drinking water. Uncontrolled release of pharmaceuticals in open ecosystems is potentially dangerous, entailing environmental consequences. Their negative impacts on living organisms are evident. This has driven the search for effective ways to neutralise persistent pollutants. In Russia, pharmaceutical pollution of the environment has commenced recently and is still presented as research with a local focus. In particular, the dynamics and metabolic mechanisms of pharma pollutants by Rhodococcus actinobacteria, outstanding among other microorganisms for their capacity to degrade a great diversity of degradable pollutants, are most intensively investigated. These studies are implemented at the junction of organic chemistry, molecular biology, biotechnology, and pharmacology. They include a set of interrelated fundamental tasks, such as developing drug detection methods in the cultivation media of microorganisms, elucidating the relationships between the systematic affiliation of microorganisms and their ability to degrade chemically different drug substances, as well as studying the degree of biodegradability and toxic effects of new compounds on the degrading microorganisms, and also the features of their decomposition and co-metabolism. Solving these tasks is important to enable understanding of the environmental fate of pharmaceuticals and to create prerequisites for innovative technical solutions in the advanced treatment of pharmaceutical wastewater. It is also essential for the development of environmentally safe approaches to hazardous pharmaceutical waste management.
Microbiotechnologies for steroid production
Authors: Donova Marina
Published: August 2018

Structural modification of steroids by microorganisms, known since the 1950s, is nowadays a base for industrial production of many steroid hormones and their high-value precursors. Phytosterols, renewable biomaterials of plant origin, are recognised now as most attractive, low-cost and available raw materials for the pharmaceutical industry.
Assessing occupancy of freshwater fishes in urban boat slips of Toronto Harbour
Authors: Veilleux M. A. N. , Midwood J. D. , Boston C.M. , Lapointe N. W. R. , Portiss R. , Wells M. , Doka S. E. , Cooke S. J.
Published: August 2018

Hardening of natural shorelines in urban aquatic ecosystems can result in a loss of fish habitat and productivity. The north shore of Toronto Harbour (Lake Ontario) has been converted to hardened boat slips for commercial, industrial and recreational purposes, but its potential utility as fish habitat has not been evaluated. The objective of this study was to determine whether fish frequented and utilized four slips in the Inner Harbour of Toronto. Two western boat slips are adjacent to some natural features and have undergone some rehabilitation to increase the complexity of aquatic habitat (i.e. addition of large substrate, overhead cover, and in-water structure). In contrast, the two eastern slips are deeper and more influenced by the turbid Don River. We assessed the timing and duration of occupancy within all four slips for seven fish species using acoustic telemetry. In just under a year, tagged fishes spent a limited amount of time in any one slip. However, there was evidence for increased use at the two western slips by Northern Pike (Esox lucius) in spring, which is likely linked to the proximity of these slips to a known spawning area. Overall, there was no reliable evidence that the majority of the seven adult fish species evaluated frequented either the western or eastern slips. Despite efforts to track and tag a variety of species, insufficient detections prevented a detailed assessment of habitat selection for the majority of species of interest. A more detailed study of the spatial ecology of these fishes is therefore needed to understand the scale of their habitat use and inform the design of habitat rehabilitation projects for hardened shorelines.
CABS-flex standalone: a simulation environment for fast modeling of protein flexibility
Authors: Kurcinski Mateusz , Oleniecki Tymoteusz , Ciemny Maciej Pawel , Kuriata Aleksander , Kolinski Andrzej , Kmiecik Sebastian
Published: August 2018

CABS-flex standalone is a Python package for fast simulations of protein structure flexibility. The package combines simulations of protein dynamics using CABS coarse-grained protein model with the reconstruction of selected models to all-atom representation and analysis of modeling results. CABS-flex standalone is designed to allow for command-line access to the CABS computations and complete control over simulation process. CABS-flex standalone is equipped with features such as: modeling of multimeric and large-size protein systems, contact map visualizations, analysis of similarities to the reference structure and configurable modeling protocol. For instance, the user may modify the simulation parameters, distance restraints, structural clustering scheme or all-atom reconstruction parameters. With these features CABS-flex standalone can be easily incorporated into other methodologies of structural biology.

Availability and implementation

CABS-flex standalone is distributed under the MIT license, which is free for academic and non-profit users. It is implemented in Python. CABS-flex source code, wiki with examples of use and installation instructions for Linux, macOS and Windows are available from the CABS-flex standalone repository at https://bitbucket.org/lcbio/cabsflex.
Clustering of temporal gene expression data with mixtures of mixed effects models with a penalized likelihood
Authors: Lu Darlene , Tripodis Yorghos , Gerstenfeld Louis C , Demissie Serkalem
Published: August 2018

Motivation

Clustering algorithms like K-Means and standard Gaussian mixture models (GMM) fail to account for the structure of variability of replicated data or repeated measures over time. Additionally, a priori cluster number assumptions add an additional complexity to the process. Current methods to optimize cluster labels and number can be inaccurate or computationally intensive for temporal gene expression data with this additional variability.

Results

An extension to a model-based clustering algorithm is proposed using mixtures of mixed effects polynomial regression models and the EM algorithm with an entropy penalized log-likelihood function (EPEM). The EPEM is used to cluster temporal gene expression data with this additional variability. The addition of random effects in our model decreased the misclassification error when compared to mixtures of fixed effects models or other methods such as K-Means and GMM. Applying our method to microarray data from a fracture healing study revealed distinct temporal patterns of gene expression.

Availability and Implementation

https://github.com/darlenelu72/EPEM-GMM.

Supplementary information

Supplementary data are available at Bioinformatics online.
Container-based bioinformatics with Pachyderm
Authors: Novella Jon Ander , Emami Khoonsari Payam , Herman Stephanie , Whitenack Daniel , Capuccini Marco , Burman Joachim , Kultima Kim , Spjuth Ola
Published: August 2018

Motivation

Computational biologists face many challenges related to data size, and they need to manage complicated analyses often including multiple stages and multiple tools, all of which must be deployed to modern infrastructures. To address these challenges and maintain reproducibility of results, researchers need (i) a reliable way to run processing stages in any computational environment, (ii) a well-defined way to orchestrate those processing stages and (iii) a data management layer that tracks data as it moves through the processing pipeline.

Results

Pachyderm is an open-source workflow system and data management framework that fulfils these needs by creating a data pipelining and data versioning layer on top of projects from the container ecosystem, having Kubernetes as the backbone for container orchestration. We adapted Pachyderm and demonstrated its attractive properties in bioinformatics. A Helm Chart was created so that researchers can use Pachyderm in multiple scenarios. The Pachyderm File System was extended to support block storage. A wrapper for initiating Pachyderm on cloud-agnostic virtual infrastructures was created. The benefits of Pachyderm are illustrated via a large metabolomics workflow, demonstrating that Pachyderm enables efficient and sustainable data science workflows while maintaining reproducibility and scalability.

Availability and implementation

Pachyderm is available from https://github.com/pachyderm/pachyderm. The Pachyderm Helm Chart is available from https://github.com/kubernetes/charts/tree/master/stable/pachyderm. Pachyderm is available out-of-the-box from the PhenoMeNal VRE (https://github.com/phnmnl/KubeNow-plugin) and general Kubernetes environments instantiated via KubeNow. The code of the workflow used for the analysis is available on GitHub (https://github.com/pharmbio/LC-MS-Pachyderm).

Supplementary information

Supplementary data are available at Bioinformatics online.
PrimedRPA: primer design for recombinase polymerase amplification assays
Authors: Higgins Matthew , Ravenhall Matt , Ward Daniel , Phelan Jody , Ibrahim Amy , Forrest Matthew S , Clark Taane G , Campino Susana
Published: August 2018

Recombinase polymerase amplification (RPA), an isothermal nucleic acid amplification method, is enhancing our ability to detect a diverse array of pathogens, thereby assisting the diagnosis of infectious diseases and the detection of microorganisms in food and water. However, new bioinformatics tools are needed to automate and improve the design of the primers and probes sets to be used in RPA, particularly to account for the high genetic diversity of circulating pathogens and cross detection of genetically similar organisms. PrimedRPA is a python-based package that automates the creation and filtering of RPA primers and probe sets. It aligns several sequences to identify conserved targets, and filters regions that cross react with possible background organisms.

Availability and implementation

PrimedRPA was implemented in Python 3 and supported on Linux and MacOS and is freely available from http://pathogenseq.lshtm.ac.uk/PrimedRPA.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
It’s All in the Details: Relations Between Young Children’s Developing Pattern Separation Abilities and Hippocampal Subfield Volumes
Authors: Canada Kelsey L , Ngo Chi T , Newcombe Nora S , Geng Fengji , Riggins Tracy
Published: August 2018

The ability to keep similar experiences separate in memory is critical for forming unique and lasting memories, as many events share overlapping features (e.g., birthday parties, holidays). Research on memory in young children suggests their memories often lack high-resolution details, i.e., show impoverished pattern separation (PS). Recently developed assessments of PS suitable for children allow us to relate the formation of distinct, detailed memories for the development of the hippocampus, a neural structure critical for this ability in adults. The hippocampus displays a protracted developmental profile and underlies the ability to form detailed memories. This study examined age-related differences in hippocampal subfield volumes in 4- to 8-year-old children and relations with performance on a mnemonic similarity task (MST) designed to index memory specificity. Results revealed age-moderated associations between MST performance and cornu ammonis 2-4/dentate gyrus subfields. Specifically, age-related differences in the ability to form detailed memories tracked with normative patterns of volume increases followed by reductions over this age range. That is, greater volume correlated with better performance in younger children, whereas smaller volume correlated with better performance in older children. These findings support the hypothesis that developmental differences in hippocampal circuitry contribute to age-related improvements in detailed memory formation during this period.
Integrable Stochastic Dualities and the Deformed Knizhnik–Zamolodchikov Equation
Authors: Chen Zeying , de Gier Jan , Wheeler Michael
Published: August 2018

We present a new method for obtaining duality functions in multi-species asymmetric exclusion processes (mASEP), from solutions of the deformed Knizhnik–Zamolodchikov (KZ) equations. Our method reproduces, as a special case, duality functions for the self-dual single species ASEP on the integer lattice.
Astrophysical radio background cannot explain the EDGES 21-cm signal: constraints from cooling of non-thermal electrons
Authors: Sharma Prateek
Published: August 2018

Recently the EDGES experiment has claimed the detection of an absorption feature centred at 78 MHz. When interpreted as a signature of cosmic dawn, this feature appears at the correct wavelength (corresponding to a redshift range of z ≈ 15–20) but is larger by at least a factor of two in amplitude compared to the standard 21-cm models. One way to explain the excess radio absorption is by the enhancement of the diffuse radio background at ν = 1.42 GHz (λ = 21 cm) in the rest frame of the absorbing neutral hydrogen. Astrophysical scenarios, based on the acceleration of relativistic electrons by accretion on to supermassive black holes (SMBHs) and by supernovae (SN) from first stars, have been proposed to produce the enhanced radio background via synchrotron emission. In this letter, we show that either the synchrotron or the inverse-Compton (IC) cooling time for such electrons is at least three orders of magnitude shorter than the duration of the EDGES signal centred at z ≈ 17, irrespective of the magnetic field strength. The synchrotron radio emission at 1.42 GHz due to rapidly cooling electrons is ∼103 times smaller than the non-cooling estimate. Thus astrophysical scenarios for excess radio background proposed to explain the EDGES signal appear very unlikely.