bluuebunny/crossref_metadata_2025 huggingface dataset:
Lebensqualität und funktionelles Ergebnis nach mikrochirurgischer Dekompression bei lumbaler Spinalkanalstenose – eine Registerstudie
Authors: Zarghooni Kourosh , Beyer Frank , Papadaki Joanna , Boese Christoph , Siewe Jan , Schiffer Gereon , Eysel Peer , Bredow Jan
Published: April 2017

Einleitung Die lumbale Spinalkanalstenose (SKS) hat sich in den letzten Jahren durch die gestiegene Lebenserwartung und die höheren Ansprüche an die Lebensqualität zu einer der häufigsten degenerativen Wirbelsäulenveränderungen entwickelt. Bei therapierefraktären Patienten der konservativen Therapie ist die mikrochirurgische Dekompression der Goldstandard in der operativen Behandlung der degenerativen lumbalen Spinalkanalstenose. Ziel der vorgelegten Studie ist die Bewertung der Lebensqualität nach mikrochirurgischer Dekompression bei lumbaler Spinalkanalstenose anhand der Instrumente des DWG-Registers (vorher Spine Tango).

Methode 36 Patienten wurden in diese monozentrische prospektive Beobachtungsstudie von Januar 2013 bis Juni 2014 eingeschlossen. Die Datenerhebung erfolgte über das Spine Tango- bzw. DWG-Register. Es wurden der Core Outcome Measure Index (COMI), Oswestry Disability Index (ODI) und der Lebensqualitätsfragebogen EuroQoL-5D erhoben. Dies erfolgte vor der Operation sowie 6 Wochen, 6 Monate und 12 Monate nach der Operation.

Ergebnisse Im untersuchten Kollektiv fanden sich 13 weibliche und 23 männliche Patienten (36,1 vs. 63,9 %). Für 21 Patienten konnte ein vollständiges Follow-up über den 12-Monats-Zeitraum erhoben werden. Der COMI-Score besserte sich von 8,1 ± 1,5 präoperativ signifikant über das gesamte Follow-up (6 Wochen: 4,5 ± 3,1 (p < 0,001), 6 Monate: 4,8 ± 3,1, 12 Monate: 3,8 ± 3,2). Auch die Beeinträchtigung der Rückenfunktion gemessen im ODI-Score war gegenüber den präoperativen Werten (47,5 ± 17,3) nach 6 Wochen (29,1 ± 22,4; p < 0,005), 6 Monaten (30,0 ± 19,3) und 12 Monaten (23,8 ± 18,2) signifikant besser. Gleichermaßen verhielt es sich mit der Lebensqualität (präoperativ: 0,36 ± 0,38; 6 Wochen: 0,57 ± 0,34 (p < 0,019), 6 Monate: 0,62 ± 0,28, 12 Monate: 0,67 ± 0,31).

Schlussfolgerung Unsere Untersuchung zeigt, dass Patienten ohne Voroperationen und neurologisches Defizit mit lumbaler Spinalkanalstenose eine erhebliche Linderung von Schmerzen und eine Steigerung der Lebensqualität bereits nach 6 Wochen nach stabilitätserhaltender Dekompression erwarten dürfen. Dieser positive postoperative Effekt zeigt sich über 12 Monate weiter progredient. Das DWG-Register bietet eine standardisierte und validierte Möglichkeit, konservative wie operative Behandlungen an der Wirbelsäule langfristig vergleichbar zu machen.
Assessment of Early Cardiovascular Risk in Children and Adolescents with Essential Hypertension
Authors: Stelcar Andreja , Homsak Evgenija , Marcun Varda Natasa
Published: April 2017

The aim of our study was to investigate some early markers of hypertensive target organ damage in hypertensive children and adolescents, and to detect those showing most prominent clinical significance.

We included 100 children with essential hypertension (EH) and 50 age-matched healthy control children, and evaluated left ventricular mass (LVM), intima-media thickness in the carotid arteries (IMT), pulse wave velocity (PWV), microalbuminuria, biochemical parameters and some adipokines.

Statistically significant differences between the 2 groups were observed for HDL-cholesterol, LDL-cholesterol, triglycerides, insulin, uric acid, glucose, apolipoprotein A1, and total adiponectin. The mean values of IMT, PWV and LVM were greater in hypertensive children, but only the differences in IMT and LVM were statistically significant. In addition, hypertensive children showed significantly higher values of AoSP (aortic systolic pressure), AoPP (aortic pulse pressure) and AIx@75 (augmentation index corrected for heart rate of 75 b.p.m.). Metabolic syndrome was diagnosed in 31% of hypertensive children.

A significant number of children with EH have early target organ changes as well as other risk factors, including metabolic syndrome, especially obese ones. However, IMT, LVM and some parameters of arterial stiffness have been found to be early markers in both obese and non-obese hypertensives. In addition, adipokines and coagulation factors seem to be important in obese hypertensives.
Hyperprolactinemia and the Association with All-Cause Mortality and Cardiovascular Mortality
Authors: Krogh Jesper , Selmer Christian , Torp-Pedersen Christian , Gislason Gunnar , Kistorp Caroline
Published: April 2017

Hyperprolactinemia has been suspected to increase mortality risk, but the available data are conflicting. The objective of this study was to estimate the association between hyperprolactinemia and all-cause and cardiovascular mortality among patients referred for assessment of prolactin. For this study, adults with no prio pituitary disease who underwent prolactin assessment at 3 university Hospitals in Denmark between 2001 and 2011 were included in a retrospective cohort study. A total of 3 633 patients with a median follow-up time of 5.3 years (IQR 2.7–5.7) were included. Mean (SD) age 39.7 (15.5) years and 78% female. 373/3 633 (10.3%) had hyperprolactinemia and during follow-up 330/3 633 (9.1%) patients died of any cause, and 113/3 633 (3.1%) patients died of cardiovascular causes. In males, hyperprolactinemia was associated with age-adjusted incidence rate ratio (IRR) of 1.86 for all-cause mortality (95% CI 1.22–2.82) and 2.55 (95% CI 1.43–4.55) for cardiovascular mortality. The IRR for all-cause mortality was reduced to 1.37 (0.90–2.08) when adjusted for the use of antipsychotic medication. The association between hyperprolactinemia and cardiovascular mortality remained after adjusting for confounders, for example, chronic renal failure, diabetes, and antipsychotic medication. In females, hyperprolactinemia was not associated with all-cause mortality (IRR 1.45; CI 0.86–2.47) or cardiovascular mortality (IRR 0.58; CI 0.14–2.39). In conclusion, hyperprolactinemia was associated with increased cardiovascular mortality in male patients. This association was not found in female patients. Focus on increased cardiovascular risk in males with hyperprolactinemia is warranted.
Piezoelectricity of green carp scales
Authors: Jiang H. Y. , Yen F. , Huang C. W. , Mei R. B. , Chen L.
Published: April 2017

Piezoelectricity takes part in multiple important functions and processes in biomaterials often vital to the survival of organisms. Here, we investigate the piezoelectric properties of fish scales of green carp by directly examining their morphology at nanometer levels. Two types of regions are found to comprise the scales, a smooth one and a rough one. The smooth region is comprised of a ridge and trough pattern and the rough region characterized by a flat base with an elevated mosaic of crescents. Piezoelectricity is found on the ridges and base regions of the scales. From clear distinctions between the composition of the inner and outer surfaces of the scales, we identify the piezoelectricity to originate from the presence of hydroxyapatite which only exists on the surface of the fish scales. Our findings reveal a different mechanism of how green carp are sensitive to their surroundings and should be helpful to studies related to the electromechanical properties of marine life and the development of bio-inspired materials.
On the n-symplectic structure of faithful irreducible representations
Authors: Norris L. K.
Published: April 2017

Each faithful irreducible representation of an N-dimensional vector space V1 on an n-dimensional vector space V2 is shown to define a unique irreducible n-symplectic structure on the product manifold V1×V2. The basic details of the associated Poisson algebra are developed for the special case N = n2, and 2n-dimensional symplectic submanifolds are shown to exist.
Observation of subwavelength localization of cavity plasmons induced by ultra-strong exciton coupling
Authors: Balasubrahmaniyam M. , Kar Durgesh , Sen Prabal , Bisht Prem B. , Kasiviswanathan S.
Published: April 2017

In condensed matter systems, there exists a class of exotic localized electronic states wherein the localization is induced, not by a disorder or a defect, but by extremely strong interactions, for example, Kondo-insulator and Mott-insulator. In this work, we investigate and experimentally implement the photonic analog of localization induced by ultra-strong interactions in a coupled three-mode system. We show that the localization of a propagating mode can be achieved without the aid of an underlying spatial disorder, a defect, or even periodicity. We demonstrate the same by realizing ultra-strong coupling between a highly dispersive cavity plasmon mode and dimer excitons of Rhodamine B. Using a photon tunneling arrangement, we map the dispersion of the hybrid modes and provide evidence for the existence of a quasi-dispersionless hybrid mode with the sub-wavelength localization length and cavity plasmon-like characteristics.
Deep-level stereoscopic multiple traps of acoustic vortices
Authors: Li Yuzhi , Guo Gepu , Ma Qingyu , Tu Juan , Zhang Dong
Published: April 2017

Based on the radiation pattern of a planar piston transducer, the mechanisms underlying the generation of axially controllable deep-level stereoscopic multiple traps of acoustic vortices (AV) using sparse directional sources were proposed with explicit formulae. Numerical simulations for the axial and cross-sectional distributions of acoustic pressure and phase were conducted for various ka (product of the wave number and the radius of transducer) values at the frequency of 1 MHz. It was demonstrated that, for bigger ka, besides the main-AV (M-AV) generated by the main lobes of the sources, cone-shaped side-AV (S-AV) produced by the side lobes were closer to the source plane at a relatively lower pressure. Corresponding to the radiation angles of pressure nulls between the main lobe and the side lobes of the sources, vortex valleys with nearly pressure zero could be generated on the central axis to form multiple traps, based on Gor'kov potential theory. The number and locations of vortex valleys could be controlled accurately by the adjustment of ka. With the established eight-source AV generation system, the existence of the axially controllable multiple traps was verified by the measured M-AV and S-AVs as well as the corresponding vortex valleys. The favorable results provided the feasibility of deep-level stereoscopic control of AV and suggested potential application of multiple traps for particle manipulation in the area of biomedical engineering.
Microscopic insight into thermodynamics of conformational changes of SAP-SLAM complex in signal transduction cascade
Authors: Samanta Sudipta , Mukherjee Sanchita
Published: April 2017

The signalling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, associate with SLAM-associated protein (SAP)-related molecules, composed of single SH2 domain architecture. SAP activates Src-family kinase Fyn after SLAM ligation, resulting in a SLAM-SAP-Fyn complex, where, SAP binds the Fyn SH3 domain that does not involve canonical SH3 or SH2 interactions. This demands insight into this SAP mediated signalling cascade. Thermodynamics of the conformational changes are extracted from the histograms of dihedral angles obtained from the all-atom molecular dynamics simulations of this structurally well characterized SAP-SLAM complex. The results incorporate the binding induced thermodynamic changes of individual amino acid as well as the secondary structural elements of the protein and the solvent. Stabilization of the peptide partially comes through a strong hydrogen bonding network with the protein, while hydrophobic interactions also play a significant role where the peptide inserts itself into a hydrophobic cavity of the protein. SLAM binding widens SAP’s second binding site for Fyn, which is the next step in the signal transduction cascade. The higher stabilization and less fluctuation of specific residues of SAP in the Fyn binding site, induced by SAP-SLAM complexation, emerge as the key structural elements to trigger the recognition of SAP by the SH3 domain of Fyn. The thermodynamic quantification of the protein due to complexation not only throws deeper understanding in the established mode of SAP-SLAM interaction but also assists in the recognition of the relevant residues of the protein responsible for alterations in its activity.
Finite magneto-static field effect on the excitation of THz hybrid modes in an elliptical metallic plasma waveguide with two energy sources
Authors: Safari S. , Jazi B.
Published: April 2017

The effect of finite magnetic field on the excitation, generation, and amplification of slow electromagnetic waves at THz frequency in a magnetized plasma waveguide with elliptical cross section is investigated. In configuration mentioned above, there are two electron beams with opposite directions as energy sources, and the role of magnetic field power on the appearance of the number of dispersion branches is analysed. It is shown that with increasing magnetic field, the field profiles of hybrid waves are increased in regions where the interaction of waves and electron beams are optimized. It is also shown that by applying the magnetic field, generation of THz frequencies can be easy to obtain in comparison to the unmagnetized case. In other words, by applying a finite magnetic field, better THz excitation occurs in the absence of high accelerating voltage. Increasing growth rate which can be achieved with increasing static magnetic field is also investigated. In this paper, because of high longitudinal velocity of electron beams, the effect of finite magnetic field on the fluctuations of electron beams is considered negligible.
Magnetic field effect on the self-focusing of an intense laser pulse interacting with a bulk medium of graphite nanoparticles
Authors: Sepehri Javan N. , Rouhi Erdi F. , Najafi M. N.
Published: April 2017

The motivation of the present work is the study of self-focusing of an intense laser beam propagating through a magnetized bulk medium consisting of metallic nanoparticles. Using a perturbative method, the wave equation describing the nonlinear interaction of the intense laser beam with metallic magnetized nanoparticles is derived. Evolution of the laser spot size for the circular polarization with the Gaussian profile is considered. A graphite nanoparticle medium is introduced as a good candidate for self-focusing of electromagnetic waves with the wavelength in the micrometer range where plasmon resonance occurs. In such a frequency area, using a few hundred Tesla external magnetic field can substantially improve the focusing property of the medium. The threshold power for self-focusing at least two orders of magnitude is less than that for the identical case of the plasma medium. In addition, a typical external magnetic field for improving the focusing property of the medium is much lower than other conventional nonlinear media like plasma.
Energy-based truncation of multi-determinant wavefunctions in quantum Monte Carlo
Authors: Per Manolo C. , Cleland Deidre M.
Published: April 2017

We present a method for truncating large multi-determinant expansions for use in diffusion Monte Carlo calculations. Current approaches use wavefunction-based criteria to perform the truncation. Our method is more intuitively based on the contribution each determinant makes to the total energy. We show that this approach gives consistent behaviour across systems with varying correlation character, which leads to effective error cancellation in energy differences. This is demonstrated through accurate calculations of the electron affinity of oxygen and the atomisation energy of the carbon dimer. The approach is simple and easy to implement, requiring only quantities already accessible in standard configuration interaction calculations.
Note: Production of stable colloidal probes for high-temperature atomic force microscopy applications
Authors: Ditscherlein L. , Peuker U. A.
Published: April 2017

For the application of colloidal probe atomic force microscopy at high temperatures (>500 K), stable colloidal probe cantilevers are essential. In this study, two new methods for gluing alumina particles onto temperature stable cantilevers are presented and compared with an existing method for borosilicate particles at elevated temperatures as well as with cp-cantilevers prepared with epoxy resin at room temperature. The durability of the fixing of the particle is quantified with a test method applying high shear forces. The force is calculated with a mechanical model considering both the bending as well as the torsion on the colloidal probe.
Molecular dynamics simulation of nanobubble nucleation on rough surfaces
Authors: Liu Yawei , Zhang Xianren
Published: April 2017

Here, we study how nanobubbles nucleate on rough hydrophobic surfaces, using long-time standard simulations to directly observe the kinetic pathways and using constrained simulations combined with the thermodynamic integration approach to quantitatively evaluate the corresponding free energy changes. Both methods demonstrate that a two-step nucleation route involving the formation of an intermediate state is thermodynamically favorable: at first, the system transforms from the Wenzel state (liquid being in full contact with the solid surface) to the Cassie state (liquid being in contact with the peaks of the rough surface) after gas cavities occur in the grooves (i.e., the Wenzel-to-Cassie transition); then, the gas cavities coalesce and form a stable surface nanobubble with pinned contact lines (i.e., the Cassie-to-nanobubble transition). Additionally, the free energy barriers for the two transitions show opposing dependencies on the degree of surface roughness, indicating that the surfaces with moderate roughness are favorable for forming stable surface nanobubbles. Moreover, the simulation results also reveal the coexistence and transition between the Wenzel, Cassie, and nanobubble states on rough surfaces.
First principles study of bimetallic Ni13−nAgn nano-clusters (n = 0–13): Structural, mixing, electronic, and magnetic properties
Authors: Datta Soumendu , Raychaudhuri A. K. , Saha-Dasgupta Tanusri
Published: April 2017

Using spin polarized density functional theory based calculations, combined with ab initio molecular dynamics simulation, we carry out a systematic investigation of the bimetallic Ni13−nAgn nano-clusters, for all compositions. This includes prediction of the geometry, mixing behavior, and electronic properties. Our study reveals a tendency towards the formation of a core-shell like structure, following the rule of putting Ni in a high coordination site and Ag in a low coordination site. Our calculations predict negative mixing energies for the entire composition range, indicating mixing to be favored for the bimetallic small sized Ni–Ag clusters, irrespective of the compositions. The magic composition with the highest stability is found for the NiAg12 alloy cluster. We investigate the microscopic origin of a core-shell like structure with negative mixing energy, in which the Ni–Ag inter-facial interaction is found to play a role. We also study the magnetic properties of the Ni–Ag alloy clusters. The Ni dominated magnetism consists of parallel alignment of Ni moments while the tiny moments on Ag align in anti-parallel to Ni moments. The hybridization with the Ag environment causes reduction of Ni moment.
New hexagonal boron nitride polytypes with triple-layer periodicity
Authors: Luo Kun , Yuan Xiaohong , Zhao Zhisheng , Yu Dongli , Xu Bo , Liu Zhongyuan , Tian Yongjun , Gao Guoying , He Julong
Published: April 2017

Regular hexagonal boron nitride (h-BN) samples present a few of intrinsic stacking faults, which result in a long-standing controversy about their electronic properties. To resolve this controversy, we designed eight possible BN polytypes with triple-layer periodicity. Under ambient pressure, the energies of all the proposed polytypes are between those of observed AA and Aa (h-BN) structures. Two proposed polytypes with direct bandgaps might be responsible for the direct bandgap observed in the h-BN samples. A model was proposed to show how the proposed structures might exist in the h-BN samples by analyzing the stacking characteristics and the previous experimental micrographs of h-BN samples.
Multimode instability evolution driven by strong, high-energy-density shocks in a rarefaction-reflected geometry
Authors: Di Stefano C. A. , Rasmus A. M. , Doss F. W. , Flippo K. A. , Hager J. D. , Kline J. L. , Bradley P. A.
Published: April 2017

We present an experiment using lasers to produce a shock pressure of >10 Mbar, which we then use to drive Richtmyer–Meshkov and Rayleigh–Taylor growth at a 2D multimode perturbed interface. Key features of this platform are that we can precisely reproduce the perturbation from iteration to iteration of the experiment, facilitating analysis, and that the lasers allow us to produce very strong shocks, creating a plasma state in the system. We also implement a Bayesian technique to analyze the multimode spectra. This technique enables us to draw quantitative conclusions about the spectrum, even in the presence of significant noise. For instance, we measure the signal contained in the seeded modes over time, as well as the transition of the initial growth rate of these modes into the overall saturation behavior of the spectrum.
Structural and electronic properties of Bi2Se3 topological insulator thin films grown by pulsed laser deposition
Authors: Orgiani P. , Bigi C. , Kumar Das P. , Fujii J. , Ciancio R. , Gobaut B. , Galdi A. , Sacco C. , Maritato L. , Torelli P. , Panaccione G. , Vobornik I. , Rossi G.
Published: April 2017

We report on epitaxial growth of Bi2Se3 topological insulator thin films by Pulsed Laser Deposition (PLD). X-ray diffraction investigation confirms that Bi2Se3 with a single (001)-orientation can be obtained on several substrates in a narrow (i.e., 20 °C) range of deposition temperatures and at high deposition pressure (i.e., 0.1 mbar). However, only films grown on (001)-Al2O3 substrates show an almost-unique in-plane orientation. In-situ spin-resolved angular resolved photoemission spectroscopy experiments, performed at the NFFA-APE facility of IOM-CNR and Elettra (Trieste), show a single Dirac cone with the Dirac point at EB∼0.38 eV located in the center of the Brillouin zone and the spin polarization of the topological surface states. These results demonstrate that the topological surface state can be obtained in PLD-grown Bi2Se3 thin films.
Electronic, optical, and thermoelectric properties of Fe2+xV1−xAl
Authors: Rai D. P. , Sandeep  , Shankar A. , Khenata R. , Reshak A. H. , Ekuma C. E. , Thapa R. K. , Ke San-Huang
Published: April 2017

We report the electronic, optical, and thermoelectric properties of full-Heusler alloy Fe2VAl with Fe antisite doping (Fe2+xV1−xAl) as obtained from the first-principles Tran-Blaha modified Becke-Johnson potential. The results are discussed in relation to the available experimental data and show good agreements for the band gap, magnetic moment, and optical spectra. Exploring our transport data for thermoelectric applicability suggest that Fe2+xV1−xAl is a good candidate with a high figure of merit (ZT) 0.75(0.65) for x = 0.25(0.50) at room temperature.
Diversiform hybrid-polarization surface plasmon polaritons in a dielectric–metal metamaterial
Authors: Zhang Q. , Zhou S. , Fu S. F. , Wang X. Z.
Published: April 2017

Hybrid-polarization surface plasmon polaritons (HSPPs) at the interface between an isotropic medium and a one-dimensional metal–dielectric metamaterial (MM) were discussed, where the metal-layer permittivity was described with the improved Drude model. From the obtained dispersion equations, we predicated five types of HSPPs. One type is the Dyakonov-like surface polariton and another type is the tradition-like surface polarton. The others are new types of HSPPs. We establish a numerical simulation method of the attenuated total reflection (ATR) measurement to examine these HSPPs. The results from the ATR spectra are consistent with those from the dispersion equations and indicate the different polarization features of these HSPPs. The numerical results also demonstrate that the observation of each type of HSPPs requires different conditions dictated by the material parameters and the polarization direction of incident light used in the ATR spectra. These results may further widen the space of potential applications of surface plasmon polaritons.
Difructose anhydride III decreases body fat as a low-energy substitute or by decreasing energy intake in non-ovariectomized and ovariectomized female rats
Authors: Fujitani Mina , Kishida Taro , Shimizu Emi , Ishikawa Junji
Published: April 2017

We evaluated the effects of difructose anhydride III (DFAIII) on body weights of ovariectomized rats, which are a good model for obesity by estrogen deficiency-induced overeating. Female rats (10 weeks old) were subjected to ovariectomy or sham operation and then fed with or without a diet containing 3% or 6% DFAIII for 33 days or pair-fed control diet during the same period. Rats fed DFAIII showed significantly decreased food intake, energy intake, body weight gain, body energy accumulation, and fat tissue weight than control group, regardless of ovariectomy. DFAIII may decrease body fat dependent of reduced food/energy intake. Compared with the respective pair feeding groups, rats fed DFAIII showed significantly decreased body energy and fat tissue weight, regardless of ovariectomy, suggesting its potential as a low-energy substitute for high-energy sweeteners. The low energy of DFAIII may contribute to decreased body fat, which may not be dependent on obesity.
Natural Resource Conflict Analysis among Pastoralists in Southern Ethiopia
Authors: Beyene Fekadu
Published: April 2017

This paper examines resource-related conflict among pastoralists in southern Ethiopia, specifically the Somali and Oromo ethnic groups. It applies theories of property rights, environmental security and political ecology to discuss the complexity of the conflict, using narrative analysis and conflict mapping. Results reveal that the conflict results from interrelated cultural, ecological and political factors. The systems of governance, including the setting up of regions on an ethnic basis and associated competition for land and control of water-points, have contributed to violent conflict between the two ethnic groups. The creation of new administrative units (kebeles) close to regional boundaries has exacerbated the conflict. Moreover, change in land use, prompted by insecure property rights to communal land, rather than expected increase in economic benefits has caused conflicts among the clans of the Oromo. The findings suggest Ethiopian authorities support the functioning of traditional access options, successful operation of customary courts and penalising opportunistic actors to address inter-ethnic conflicts. Applying land use and administration guidelines and empowering customary authorities would reduce the incidence of inter-clan conflict.
RNAblueprint: flexible multiple target nucleic acid sequence design
Authors: Hammer Stefan , Tschiatschek Birgit , Flamm Christoph , Hofacker Ivo L , Findeiß Sven
Published: April 2017

Motivation

Realizing the value of synthetic biology in biotechnology and medicine requires the design of molecules with specialized functions. Due to its close structure to function relationship, and the availability of good structure prediction methods and energy models, RNA is perfectly suited to be synthetically engineered with predefined properties. However, currently available RNA design tools cannot be easily adapted to accommodate new design specifications. Furthermore, complicated sampling and optimization methods are often developed to suit a specific RNA design goal, adding to their inflexibility.

Results

We developed a C ++  library implementing a graph coloring approach to stochastically sample sequences compatible with structural and sequence constraints from the typically very large solution space. The approach allows to specify and explore the solution space in a well defined way. Our library also guarantees uniform sampling, which makes optimization runs performant by not only avoiding re-evaluation of already found solutions, but also by raising the probability of finding better solutions for long optimization runs. We show that our software can be combined with any other software package to allow diverse RNA design applications. Scripting interfaces allow the easy adaption of existing code to accommodate new scenarios, making the whole design process very flexible. We implemented example design approaches written in Python to demonstrate these advantages.

Availability and implementation

RNAblueprint, Python implementations and benchmark datasets are available at github: https://github.com/ViennaRNA.

Supplementary information

Supplementary data are available at Bioinformatics online.
Fracture connectivity can reduce the velocity anisotropy of seismic waves
Authors: Rubino J. Germán , Caspari Eva , Müller Tobias M. , Holliger Klaus
Published: April 2017

The degree of connectivity of fracture networks is a key parameter that controls the hydraulic properties of fractured rock formations. The current understanding is that this parameter does not alter the effective elastic properties of the probed medium and, hence, cannot be inferred from seismic data. However, this reasoning is based on static elasticity, which neglects dynamic effects related to wave-induced fluid pressure diffusion (FPD). Using a numerical upscaling procedure based on the theory of quasi-static poroelasticity, we provide the first evidence to suggest that fracture connectivity can reduce significantly velocity anisotropy in the seismic frequency band. Analyses of fluid pressure fields in response to the propagation of seismic waves demonstrate that this reduction of velocity anisotropy is not due to changes of the geometrical characteristics of the probed fracture networks, but rather related to variations of the stiffening effect of the fracture fluid in response to FPD. These results suggest that accounting for FPD effects may not only allow for improving estimations of geometrical and mechanical properties of fracture networks, but may also provide information with regard to the effective hydraulic properties.
High fishing intensity reduces females’ sperm reserve and brood fecundity in a eubrachyuran crab subject to sex- and size-biased harvest
Authors: Pardo Luis M , Riveros Marcela P , Fuentes Juan Pablo , Pinochet Ramona , Cárdenas Carla , Sainte-Marie Bernard
Published: April 2017

Size-selective male fisheries may result in sperm limitation whereby the number of sperm is insufficient to fertilize all oöcytes produced by females. In eubrachyuran crabs, females have seminal receptacles for sperm storage which may reduce the risk of sperm limitation over their lifetime. In this study on the commercially exploited eubrachyuran Metacarcinus edwardsii, we evaluate the sperm limitation hypothesis by measuring female reproductive success in five Chilean populations subjected to low or high fishing intensity. The quantity and viability of sperm stored by females was measured in each season and population, and related to resulting brood fecundity. Females’ sperm reserve was larger when fishing intensity was low than when it was high—paralleling previously demonstrated differences in males’ sperm reserve—and especially in the season before oviposition. Sperm viability was in general high (92%) and independent of fishing intensity. Mean brood fecundity adjusted to constant female size was about 60% greater under low compared with high fishing intensity. Thus, in M. edwardsii, population reproductive output could be depressed by male-biased fishing in spite of female sperm storage capability.
A simulation study on the dosimetric benefit of real-time motion compensation in spot-scanning proton therapy for prostate
Authors: Fujii Yusuke , Matsuura Taeko , Takao Seishin , Matsuzaki Yuka , Fujii Takaaki , Miyamoto Naoki , Umegaki Kikuo , Nishioka Kentaro , Shimizu Shinichi , Shirato Hiroki
Published: April 2017

For proton spot scanning, use of a real-time-image gating technique incorporating an implanted marker and dual fluoroscopy facilitates mitigation of the dose distribution deterioration caused by interplay effects. This study explored the advantages of using a real-time-image gating technique, with a focus on prostate cancer. Two patient-positioning methods using fiducial markers were compared: (i) patient positioning only before beam delivery, and (ii) patient positioning both before and during beam delivery using a real-time-gating technique. For each scenario, dose distributions were simulated using the CT images of nine prostate cancer patients. Treatment plans were generated using a single-field proton beam with 3-mm and 6-mm lateral margins. During beam delivery, the prostate was assumed to move by 5 mm in four directions that were perpendicular to the beam direction at one of three separate timings (i.e. after the completion of the first, second and third quartiles of the total delivery of spot irradiation). Using a 3-mm margin and second quartile motion timing, the averaged values for ΔD99, ΔD95, ΔD5 and D5–95 were 5.1%, 3.3%, 3.6% and 9.0%, respectively, for Scenario (i) and 2.1%, 1.5%, 0.5% and 4.1%, respectively, for Scenario (ii). The margin expansion from 3 mm to 6 mm reduced the size of ΔD99, ΔD95, ΔD5 and D5–95 only with Scenario (i). These results indicate that patient positioning during beam delivery is an effective way to obtain better target coverage and uniformity while reducing the target margin when the prostate moves during irradiation.
Exploring the IMF of star clusters: a joint SLUG and LEGUS effort
Authors: Ashworth G. , Fumagalli M. , Krumholz M. R. , Adamo A. , Calzetti D. , Chandar R. , Cignoni M. , Dale D. , Elmegreen B. G. , Gallagher J. S. , Gouliermis D. A. , Grasha K. , Grebel E. K. , Johnson K. E. , Lee J. , Tosi M. , Wofford A.
Published: April 2017

We present the implementation of a Bayesian formalism within the Stochastically Lighting Up Galaxies (slug) stellar population synthesis code, which is designed to investigate variations in the initial mass function (IMF) of star clusters. By comparing observed cluster photometry to large libraries of clusters simulated with a continuously varying IMF, our formalism yields the posterior probability distribution function (PDF) of the cluster mass, age and extinction, jointly with the parameters describing the IMF. We apply this formalism to a sample of star clusters from the nearby galaxy NGC 628, for which broad-band photometry in five filters is available as part of the Legacy ExtraGalactic UV Survey (LEGUS). After allowing the upper-end slope of the IMF (α3) to vary, we recover PDFs for the mass, age and extinction that are broadly consistent with what is found when assuming an invariant Kroupa IMF. However, the posterior PDF for α3 is very broad due to a strong degeneracy with the cluster mass, and it is found to be sensitive to the choice of priors, particularly on the cluster mass. We find only a modest improvement in the constraining power of α3 when adding Hα photometry from the companion Hα-LEGUS survey. Conversely, Hα photometry significantly improves the age determination, reducing the frequency of multi-modal PDFs. With the aid of mock clusters, we quantify the degeneracy between physical parameters, showing how constraints on the cluster mass that are independent of photometry can be used to pin down the IMF properties of star clusters.
The Use of Vancomycin Powder for Surgical Prophylaxis Following Craniotomy
Authors: Ravikumar Vinod , Ho Allen L. , Pendharkar Arjun V. , Sussman Eric S. , Kwong-hon Chow Kevin , Li Gordon
Published: April 2017

BACKGROUND: Intrawound vancomycin powder has been studied extensively in spinal fusion surgeries and been found to reduce rates of surgical site infections (SSIs) significantly. Despite its success in spinal surgeries, topical vancomycin has not been extensively studied with respect to cranial neurosurgery.

OBJECTIVE: To evaluate the efficacy of intrawound topical vancomycin for prevention of SSIs following open craniotomies.

METHODS: We retrospectively analyzed a large series of 350 patients from 2011 to 2015 in a pre/postintervention study of use of topical vancomycin to reduce postoperative craniotomy infection rates. We had a preintervention control group of 225 patients and a postintervention group of 125 patients that received intrawound topical vancomycin.

RESULTS: Our preintervention incidence of SSI was 2.2% and this was significantly reduced to 0% following introduction of topical vancomycin (P < .5). An ad hoc cost analysis suggested a cost savings of

59 965 with the use of topical vancomycin for craniotomies.

CONCLUSION: Our study found a significant reduction in SSI rates after introduction of topical vancomycin. Thus, this simple intervention should be considered in all open craniotomy patients as both infection prophylaxis and a potential cost saving intervention.
Sodium Fluorescein Facilitates Guided Sampling of Diagnostic Tumor Tissue in Nonenhancing Gliomas
Authors: Bowden Stephen G , Neira Justin A , Gill Brian J A , Ung Timothy H , Englander Zachary K , Zanazzi George , Chang Peter D , Samanamud Jorge , Grinband Jack , Sheth Sameer A , McKhann Guy M , Sisti Michael B , Canoll Peter , D’Amico Randy S , Bruce Jeffrey N
Published: April 2017

BACKGROUND

Accurate tissue sampling in nonenhancing (NE) gliomas is a unique surgical challenge due to their intratumoral histological heterogeneity and absence of contrast enhancement as a guide for intraoperative stereotactic guidance. Instead, T2/fluid-attenuated inversion-recovery (FLAIR) hyperintensity on MRI is commonly used as an imaging surrogate for pathological tissue, but sampling from this region can yield nondiagnostic or underdiagnostic brain tissue. Sodium fluorescein is an intraoperative fluorescent dye that has a high predictive value for tumor identification in areas of contrast enhancement and NE in glioblastomas. However, the underlying histopathological alterations in fluorescent regions of NE gliomas remain undefined.

OBJECTIVE

To evaluate whether fluorescein can identify diagnostic tissue and differentiate regions with higher malignant potential during surgery for NE gliomas, thus improving sampling accuracy.

METHODS

Thirteen patients who presented with NE, T2/FLAIR hyperintense lesions suspicious for glioma received fluorescein (10%, 3 mg/kg intravenously) during surgical resection.

RESULTS

Patchy fluorescence was identified within the T2/FLAIR hyperintense area in 10 of 13 (77%) patients. Samples taken from fluorescent regions were more likely to demonstrate diagnostic glioma tissue and cytologic atypia (P < .05). Fluorescein demonstrated a 95% positive predictive value for the presence of diagnostic tissue. Samples from areas of fluorescence also demonstrated greater total cell density and higher Ki-67 labeling than nonfluorescent biopsies (P < .05).

CONCLUSION

Fluorescence in NE gliomas is highly predictive of diagnostic tumor tissue and regions of higher cell density and proliferative activity.
Pseudomonas syringae pv. tomato Strains from New York Exhibit Virulence Attributes Intermediate Between Typical Race 0 and Race 1 Strains
Authors: Kraus Christine M. , Mazo-Molina Carolina , Smart Christine D. , Martin Gregory B.
Published: April 2017

Bacterial speck disease, caused by Pseudomonas syringae pv. tomato, is a persistent problem for fresh-market tomato growers in New York. Race 0 strains of this pathogen express either or both of the type III effectors AvrPto or AvrPtoB, which are recognized by tomato varieties expressing the Pto resistance gene. Pto encodes a protein kinase that activates the host immune system, thereby inhibiting bacterial multiplication and preventing disease development. Race 1 P. syringae pv. tomato strains do not express these effectors and are virulent on tomato whether or not the variety expresses Pto. Very few fresh-market tomato varieties have the Pto gene. We collected six P. syringae pv. tomato strains from naturally infected tomato plants across New York in 2015 and characterized them for their virulence and for the presence of specific effectors. In experiments conducted in the greenhouse, all strains reached population sizes in Pto-expressing tomato leaves that were intermediate between typical race 0 and race 1 strains. This phenotype has not been observed previously and suggests that the strains are recognized by Pto but such recognition is compromised by another P. syringae pv. tomato factor. The strains were found to encode avrPto, which is transcribed and translated. They also express avrPtoB although, as reported for other P. syringae pv. tomato strains, protein expression for this effector was not detectable. Deletion of avrPto from a representative New York strain allowed it to reach high populations in Pto-expressing tomato varieties, without compromising its virulence on susceptible tomato plants. Collectively, our data suggest that introgression of the Pto gene into fresh-market tomato varieties could enhance protection against extant P. syringae pv. tomato strains.
Beet curly top virus Strains Associated with Sugar Beet in Idaho, Oregon, and a Western U.S. Collection
Authors: Strausbaugh Carl A. , Eujayl Imad A. , Wintermantel William M.
Published: April 2017

Curly top of sugar beet is a serious, yield-limiting disease in semiarid production areas caused by Beet curly top virus (BCTV) and transmitted by the beet leafhopper. One of the primary means of control for BCTV in sugar beet is host resistance but effectiveness of resistance can vary among BCTV strains. Strain prevalence among BCTV populations was last investigated in Idaho and Oregon during a 2006-to-2007 collection but changes in disease severity suggested a need for reevaluation. Therefore, 406 leaf samples symptomatic for curly top were collected from sugar beet plants in commercial sugar beet fields in Idaho and Oregon from 2012 to 2015. DNA was isolated and BCTV strain composition was investigated based on polymerase chain reaction assays with strain-specific primers for the Severe (Svr) and California/Logan (CA/Logan) strains and primers that amplified a group of Worland (Wor)-like strains. The BCTV strain distribution averaged 2% Svr, 30% CA/Logan, and 87% Wor-like (16% had mixed infections), which differed from the previously published 2006-to-2007 collection (87% Svr, 7% CA/Logan, and 60% Wor-like; 59% mixed infections) based on a contingency test (P < 0.0001). Whole-genome sequencing (GenBank accessions KT276895 to KT276920 and KX867015 to KX867057) with overlapping primers found that the Wor-like strains included Wor, Colorado and a previously undescribed strain designated Kimberly1. Results confirm a shift from Svr being one of the dominant BCTV strains in commercial sugar beet fields in 2006 to 2007 to becoming undetectable at times during recent years.
Protection Against Common Bean Rust Conferred by a Gene-Silencing Method
Authors: Cooper Bret , Campbell Kimberly B.
Published: April 2017

Rust disease of the dry bean plant, Phaseolus vulgaris, is caused by the fungus Uromyces appendiculatus. The fungus acquires its nutrients and energy from bean leaves using a specialized cell structure, the haustorium, through which it secretes effector proteins that contribute to pathogenicity by defeating the plant immune system. Candidate effectors have been identified by DNA sequencing and motif analysis, and some candidates have been observed in infected leaves by mass spectrometry. To assess their roles in pathogenicity, we have inserted small fragments of genes for five candidates into Bean pod mottle virus. Plants were infected with recombinant virus and then challenged with U. appendiculatus. Virus-infected plants expressing gene fragments for four of five candidate effectors accumulated lower amounts of rust and had dramatically less rust disease. By contrast, controls that included a fungal gene fragment for a septin protein not expressed in the haustorium died from a synergistic reaction between the virus and the fungus. The results imply that RNA generated in the plant moved across the fungal haustorium to silence effector genes important to fungal pathogenicity. This study shows that four bean rust fungal genes encode pathogenicity determinants and that the expression of fungal RNA in the plant can be an effective method for protecting bean plants from rust.
Cerebral vasculitis and intracranial multiple aneurysms in a child with Lyme neuroborreliosis
Authors: Kortela Elisa , Hytönen Jukka , Numminen Jussi , Overmyer Margit , Saxen Harri , Oksi Jarmo
Published: April 2017

Introduction. Lyme borreliosis is a multisystem tick-borne disease caused by Borrelia burgdo
rferi. Neurological manifestations are reported in up to 15 % of adult patients with Lyme disease, while the frequency among children is higher. The most common manifestations are painful radiculopathy, facial nerve paresis and lymphocytic meningitis. Epileptic seizures and cerebral vasculitis with stroke or aneurysms are very rare complications.

Case presentation. We describe a paediatric patient with sensorineural auditory dysfunction, headache, fatigue and epileptic seizures as sequelae of meningoencephalitis/Lyme neuroborreliosis (LNB) caused by B. burgdo
rferi. Brain magnetic resonance imaging revealed widespread enhancement of the leptomeninges, cranial nerves and artery walls compatible with vasculitis and disturbances in cerebrospinal fluid (CSF) circulation. The patient was treated with ceftriaxone for 2 weeks. Two years later, the patient had an ischemic stroke. Brain magnetic resonance angiography revealed multiple aneurysms, which were not present previously. The largest aneurysm was operated rapidly. The patient was treated with another course of intravenous ceftriaxone for 4 weeks and pulse therapy with corticosteroids. He recovered well.

Conclusion

. This unique case demonstrates complications of LNB that can result in serious morbidity or even mortality. Lumbar puncture and analysis should be considered for paediatric patients with epileptic seizures or cerebrovascular events living in a Lyme borreliosis endemic area.
Gender inequality in the work environment: a study of private research organizations in India
Authors: Gupta Namrata
Published: April 2017

Purpose

Since liberalization in the 1990s, India has witnessed a growth in the number of educated middle-class women in professions. However, there are few women in leadership positions and decision-making bodies. While the earlier notion of the ideal woman as homemaker has been replaced by one which idealizes women of substance, a woman’s role in the family continues to be pivotal and is even viewed as central in defining Indian culture. The purpose of this paper is to analyze how and to what extent gender inequalities are reproduced in the organizations employing educated professionals.

Design/methodology/approach

Based on the perspective that gender is socially constructed, this paper analyzes gender inequality in Indian organizations through semi-structured interviews of men and women scientists in two private pharmaceutical laboratories.

Findings

The findings show reproduction of a gendered normative order through two types of norms and practices: one, norms and practices that favor men and second, socio-cultural norms that devalue women in public spaces which help to maintain masculinity in the workplace. Although these practices might be found elsewhere in the world, the manner in which they are enacted reflects national cultural norms.

Originality/value

The paper highlights how various norms and practices enacted in the specific Indian socio-cultural context construct and maintain masculinity at workplace depriving opportunities to professional women which affect their rise to leadership positions.