bluuebunny/crossref_metadata_2025 huggingface dataset:
Biochemical targets of drugs mitigating oxidative stress via redox-independent mechanisms
Authors: Gesslbauer Bernd , Bochkov Valery
Published: November 2017

Acute or chronic oxidative stress plays an important role in many pathologies. Two opposite approaches are typically used to prevent the damage induced by reactive oxygen and nitrogen species (RONS), namely treatment either with antioxidants or with weak oxidants that up-regulate endogenous antioxidant mechanisms. This review discusses options for the third pharmacological approach, namely amelioration of oxidative stress by ‘redox-inert’ compounds, which do not inactivate RONS but either inhibit the basic mechanisms leading to their formation (i.e. inflammation) or help cells to cope with their toxic action. The present study describes biochemical targets of many drugs mitigating acute oxidative stress in animal models of ischemia–reperfusion injury or N-acetyl-p-aminophenol overdose. In addition to the pro-inflammatory molecules, the targets of mitigating drugs include protein kinases and transcription factors involved in regulation of energy metabolism and cell life/death balance, proteins regulating mitochondrial permeability transition, proteins involved in the endoplasmic reticulum stress and unfolded protein response, nuclear receptors such as peroxisome proliferator-activated receptors, and isoprenoid synthesis. The data may help in identification of oxidative stress mitigators that will be effective in human disease on top of the current standard of care.
SNARE phosphorylation: a control mechanism for insulin-stimulated glucose transport and other regulated exocytic events
Authors: Laidlaw Kamilla M.E. , Livingstone Rachel , Al-Tobi Mohammed , Bryant Nia J. , Gould Gwyn W.
Published: November 2017

Trafficking within eukaryotic cells is a complex and highly regulated process; events such as recycling of plasma membrane receptors, formation of multivesicular bodies, regulated release of hormones and delivery of proteins to membranes all require directionality and specificity. The underpinning processes, including cargo selection, membrane fusion, trafficking flow and timing, are controlled by a variety of molecular mechanisms and engage multiple families of lipids and proteins. Here, we will focus on control of trafficking processes via the action of the SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) family of proteins, in particular their regulation by phosphorylation. We will describe how these proteins are controlled in a range of regulated trafficking events, with particular emphasis on the insulin-stimulated delivery of glucose transporters to the surface of adipose and muscle cells. Here, we focus on a few examples of SNARE phosphorylation which exemplify distinct ways in which SNARE machinery phosphorylation may regulate membrane fusion.
Fragment-based drug discovery and its application to challenging drug targets
Authors: Price Amanda J. , Howard Steven , Cons Benjamin D.
Published: November 2017

Fragment-based drug discovery (FBDD) is a technique for identifying low molecular weight chemical starting points for drug discovery. Since its inception 20 years ago, FBDD has grown in popularity to the point where it is now an established technique in industry and academia. The approach involves the biophysical screening of proteins against collections of low molecular weight compounds (fragments). Although fragments bind to proteins with relatively low affinity, they form efficient, high quality binding interactions with the protein architecture as they have to overcome a significant entropy barrier to bind. Of the biophysical methods available for fragment screening, X-ray protein crystallography is one of the most sensitive and least prone to false positives. It also provides detailed structural information of the protein–fragment complex at the atomic level. Fragment-based screening using X-ray crystallography is therefore an efficient method for identifying binding hotspots on proteins, which can then be exploited by chemists and biologists for the discovery of new drugs. The use of FBDD is illustrated here with a recently published case study of a drug discovery programme targeting the challenging protein–protein interaction Kelch-like ECH-associated protein 1:nuclear factor erythroid 2-related factor 2.
X-ray free electron laser: opportunities for drug discovery
Authors: Cheng Robert K.Y. , Abela Rafael , Hennig Michael
Published: November 2017

Past decades have shown the impact of structural information derived from complexes of drug candidates with their protein targets to facilitate the discovery of safe and effective medicines. Despite recent developments in single particle cryo-electron microscopy, X-ray crystallography has been the main method to derive structural information. The unique properties of X-ray free electron laser (XFEL) with unmet peak brilliance and beam focus allow X-ray diffraction data recording and successful structure determination from smaller and weaker diffracting crystals shortening timelines in crystal optimization. To further capitalize on the XFEL advantage, innovations in crystal sample delivery for the X-ray experiment, data collection and processing methods are required. This development was a key contributor to serial crystallography allowing structure determination at room temperature yielding physiologically more relevant structures. Adding the time resolution provided by the femtosecond X-ray pulse will enable monitoring and capturing of dynamic processes of ligand binding and associated conformational changes with great impact to the design of candidate drug compounds.
Synthetic biology UK: progress, paradigms and prospects
Authors: Clarke Lionel J.
Published: November 2017

Drawing comparisons with the study of scientific revolutions by Thomas Kuhn over 50 years ago it is possible to frame synthetic biology as a new paradigm, approaching biology and its potential for redesign from an engineering and information management standpoint. This may help relate it to current thinking about potentially revolutionary future developments stemming from the recent and very rapidly progressing convergence of relevant technologies. However, striking differences from Kuhn's historic examples may also be noted – not only a greater awareness today of potential impacts that highlights the importance of explicitly incorporating broader issues of responsibility and governance but also the rapid growth in numbers of new researchers and entrepreneurs to the field globally which could accelerate the paradigm‐shift process. The UK Synthetic Biology Roadmap 2012 and subsequent 2016 Strategy set out to develop a mechanism to respond nationally to this wider perspective, and examples, both UK and global, are drawn upon to help assess current progress towards the realisation of an ‘engineering biology’ paradigm.
Impact of on‐body IMU placement on inertial navigation
Authors: Strozzi Nicolò , Parisi Federico , Ferrari Gianluigi
Published: November 2017

Even though technology‐aided personal navigation is an extensively studied research topic, approaches based on inertial sensors remain challenging. In this study, the authors present a comparison between different inertial systems, investigating the impacts of on‐body placement of Inertial Measurement Units (IMUs) and, consequently, of different algorithms for the estimation of the travelled path on the navigation accuracy. In particular, the system performance is investigated considering two IMU placements: (i) on the feet and (ii) on the lower back. Sensor fusion is then considered in order to take advantage of the strengths of each placement. The results are validated through an extensive data collection in indoor and outdoor environments.
Synthesis of Monofunctionalized Calix[5]arenes
Authors: Lützen Arne , Ingenfeld Björn , Straub Steffen , Frömbgen Christopher
Published: November 2017

Seven OH-free and O-permethylated monofunctionalized calix[5]arenes carrying either additional methyl or tert-butyl groups are prepared following fragment condensation protocols. This strategy proves to be superior to previous approaches. Calix[5]arenes with free OH groups all adopt a cone conformation stabilized by a seam of hydrogen bonds at the lower rim. Post-condensation modifications, i.e., methylation of phenolic OH groups or functional group interconversions can also be achieved. Bulky tert-butyl groups are also found to stabilize the cone conformations of O-methylated compounds. These compounds offer versatile functional groups that make these concave molecules interesting building blocks for the synthesis of more sophisticated molecular architectures.
Selective 7-endo-Cyclization of 3-Aza-5-alkenols through Oxidative Pd(II)-Catalyzed Olefin Oxyarylation
Authors: Broggini Gianluigi , Gazzola Silvia , Beccalli Egle , Borelli Tea , Castellano Carlo , Diamante Daria
Published: November 2017

3-Aza-5-alkenols undergo selective 7-endo-trig cyclization when treated with a catalytic Pd(II) species, CuCl2 and ArSnBu3 giving 7-aryl-substituted oxazepanes. The intramolecular alkoxylation occurs with formation of a seven-membered ring only when associated with an arylating step. Otherwise, 6-exo-trig reactions, providing morpholine derivatives, were observed.
Advanced Intraprocedural Imaging Applications in Hepatobiliary Intervention
Authors: Kapoor Baljendra , Chauhan Nikunj
Published: November 2017

Intraprocedural three-dimensional imaging and guidance tools, such as cone-beam CT (CBCT), provide valuable guidance in navigating through challenging vascular and nonvascular structures while performing complex hepatobiliary and portal venous interventions, especially in patients with unconventional anatomy and technically difficult pathology. With the advent of these tools, many of the procedures that were once considered contraindicated can now be performed due to improved safety profile and operator confidence. This review describes application of these tools in various oncologic and nononcologic hepatobiliary and portal venous interventions.
The Role of Lipids in the Pathogenesis of Metabolic Syndrome in Adolescents
Authors: Taghizadeh Shahnaz , Alizadeh Mohammad
Published: November 2017

The increasing prevalence of childhood obesity is a driving force behind the increase in adolescent’s metabolic syndrome (MetS). Although there is no clear consensus about the pediatric definition for MetS, this syndrome is becoming very common among adolescents. It is characterized by insulin resistance (IR), dyslipidemia, abdominal obesity and hypertension, and is associated with a high risk of type 2 diabetes mellitus and CVD in adulthood. Due to the increasing prevalence of obesity, there is strong incentive to reduce the impact of the adverse health effects associated with MetS. We explored the etiological role of nutrient-derived metabolic stressors, especially fatty acids, in the development of obesity and MetS. We also reviewed the evidence that pro-inﬂammatory stressors may predispose to obesity-induced insulin resistance. This article presents the opinion that reducing the impact of metabolic and inﬂammatory stressors may reduce the adverse health effects of obesity, and slow the progression towards MetS and CVD in adolescents. Evidence so far is limited from pediatric dietary epidemiological and interventional studies investigating the potential preventive and therapeutic effects of dietary fatty acid modiﬁcation. This review will further investigate our understanding of the interaction between fatty acids in the pathogenesis and progression of MetS in adolescents.
Evaluation der augenärztlichen Versorgung ehemaliger früh- und reifgeborener Kinder im Alter von 4 bis 10 Jahren in Deutschland – Ergebnisse der Wiesbaden Prematurity Study (WPS)
Authors: Fieß Achim , Kölb-Keerl Ruth , Elflein Heike Maria , Schuster Alexander K. , Knuf Markus , Kirchhof Bernd , Oberacher-Velten Isabel , Muether Philipp S. , Bauer Jacqueline
Published: November 2017

Hintergrund Ziele der vorliegenden Untersuchung waren die Evaluation ophthalmologischer Nachsorgeuntersuchungen ehemaliger früh- und reifgeborener Kinder im Alter von 4 bis 10 Jahren und der Vergleich mit den deutschen Leitlinien.

Methodik In der prospektiven Wiesbaden Prematurity Study (WPS) wurden 503 Kinder, davon 239 Frühgeborene (FG) mit Gestationsalter (GA) ≤ 32 Wochen und 264 Reifgeborene (RG) mit GA ≥ 37 Wochen (Kontrollgruppe) im Alter von 4 bis 10 Jahren inklusive Refraktionsmessung und orthoptischem Status untersucht. Anisometropie war definiert als Refraktionsunterschied von ≥ 1 dpt sphärischem Äquivalent. Die Eltern wurden zusätzlich gefragt, ob nach der Entlassung aus dem Krankenhaus eine augenärztliche Untersuchung stattgefunden habe und wie oft eine solche innerhalb der letzten 12 Monate durchgeführt wurde.

Ergebnis Insgesamt zeigten sich ein Strabismus bzw. eine Anisometropie bei 18 bzw. 10% aller FG- und 2 bzw. 5% aller RG-Kinder. Von den 4 bis 6 Jahre alten FG waren 65% und von den 4 bis 6 Jahre alten RG 42% innerhalb der letzten 12 Monate bei einer augenärztlichen Untersuchung (p = 0,002). Bei 15% aller Kinder mit Strabismus war innerhalb der letzten 12 Monate keine augenärztliche Untersuchung erfolgt. Die Eltern von 3 frühgeborenen Kindern berichteten nach der Entlassung aus dem Krankenhaus, nie bei einer augenärztlichen Kontrolluntersuchung gewesen zu sein.

Schlussfolgerung Zwei Drittel der ehemaligen FG nahmen nach Aussage der Eltern im Alter von 4 bis 6 Jahren innerhalb der letzten 12 Monate an einer augenärztlichen Kontrolluntersuchung teil, was in den Leitlinien für die Versorgung ehemaliger frühgeborener Kinder empfohlen wird. Hier zeigt sich noch Verbesserungspotenzial, um diese Risikopopulation, insbesondere für Strabismus und Amblyopie, bestmöglich zu versorgen.
Enhanced photothermal effect in reduced graphene oxide in solid-state
Authors: Sahadev Nishaina , Anappara Aji A.
Published: November 2017

We report on a giant photothermal effect in few-layer Reduced Graphene Oxide (RGO) in powder form. Graphite oxide synthesized following modified Hummer's method was thermally exfoliated and reduced to obtain RGO consisting of ∼8–10 layers. Upon irradiation with an incoherent, broad-band light source (wavelengths ranging from 250 to 450 nm), an enormous photothermal effect was observed. The heat generated by RGO determined from the isothermal differential photocalorimetric technique is as high as ∼319 W/g resulting from the dominant non-radiative de-excitation of photoexcited electrons due to the absence of a radiative pathway. A practical applicability was demonstrated using a commercial thermoelectric generator wherein upon illumination from a solar-simulator, an open voltage in the mV range was developed, giving a direct proof of the exothermic effect in powder RGO upon light illumination. Herewith, we have demonstrated a proof-of-concept of photothermal effects in solid-state RGO.
Novel doping alternatives for single-layer transition metal dichalcogenides
Authors: Onofrio Nicolas , Guzman David , Strachan Alejandro
Published: November 2017

Successful doping of single-layer transition metal dichalcogenides (TMDs) remains a formidable barrier to their incorporation into a range of technologies. We use density functional theory to study doping of molybdenum and tungsten dichalcogenides with a large fraction of the periodic table. An automated analysis of the energetics, atomic and electronic structure of thousands of calculations results in insightful trends across the periodic table and points out promising dopants to be pursued experimentally. Beyond previously studied cases, our predictions suggest promising substitutional dopants that result in p-type transport and reveal interesting physics behind the substitution of the metal site. Doping with early transition metals (TMs) leads to tensile strain and a significant reduction in the bandgap. The bandgap increases and strain is reduced as the d-states are filled into the mid TMs; these trends reverse as we move into the late TMs. Additionally, the Fermi energy increases monotonously as the d-shell is filled from the early to mid TMs and we observe few to no gap states, indicating the possibility of both p- (early TMs) and n- (mid TMs) type doping. Quite surprisingly, the simulations indicate the possibility of interstitial doping of TMDs; the energetics reveal that a significant number of dopants, increasing in number from molybdenum disulfide to diselenide and to ditelluride, favor the interstitial sites over adsorbed ones. Furthermore, calculations of the activation energy associated with capturing the dopants into the interstitial site indicate that the process is kinetically possible. This suggests that interstitial impurities in TMDs are more common than thought to date and we propose a series of potential interstitial dopants for TMDs relevant for application in nanoelectronics based on a detailed analysis of the predicted electronic structures.
Observation of magnons in Mn2Au films by inelastic Brillouin and Raman light scattering
Authors: Arana M. , Estrada F. , Maior D. S. , Mendes J. B. S. , Fernandez-Outon L. E. , Macedo W. A. A. , Barthem V. M. T. S. , Givord D. , Azevedo A. , Rezende S. M.
Published: November 2017

The intermetallic antiferromagnetic compound Mn2Au has been attracting considerable interest for antiferromagnetic spintronics due to its high Néel temperature and strong spin–orbit coupling. We report on the experimental investigation of the zero-wave number magnon frequencies in Mn2Au films using Brillouin and Raman inelastic light scattering techniques. The derived effective anisotropy field values are in close agreement with theoretical calculations. With the values of the anisotropy and exchange fields, the full magnon dispersion curves in Mn2Au were calculated. Due to the weak in-plane anisotropy, the k ∼ 0 frequency of the lower magnon branch, 121 GHz, is among the lowest for 3D antiferromagnets, suggesting that Mn2Au is a good candidate for realizing the generation of spin currents by antiferromagnetic resonance driven spin-pumping, as proposed theoretically.
Axial magnetic field and toroidally streaming fast ions in the dense plasma focus are natural consequences of conservation laws in the curved axisymmetric geometry of the current sheath. II. Towards a first principles theory
Authors: Auluck S. K. H.
Published: November 2017

This paper continues earlier discussion [S. K. H. Auluck, Phys. Plasmas 21, 102515 (2014)] concerning the formulation of conservation laws of mass, momentum, and energy in a local curvilinear coordinate system in the dense plasma focus. This formulation makes use of the revised Gratton-Vargas snowplow model [S. K. H. Auluck, Phys. Plasmas 20, 112501 (2013)], which provides an analytically defined imaginary surface in three dimensions which resembles the experimentally determined shape of the plasma. Unit vectors along the local tangent to this surface, along the azimuth, and along the local normal define a right-handed orthogonal local curvilinear coordinate system. The simplifying assumption that physical quantities have significant variation only along the normal enables writing laws of conservation of mass, momentum, and energy in the form of effectively one-dimensional hyperbolic conservation law equations using expressions for various differential operators derived for this coordinate system. This formulation demonstrates the highly non-trivial result that the axial magnetic field and toroidally streaming fast ions, experimentally observed by multiple prestigious laboratories, are natural consequences of conservation of mass, momentum, and energy in the curved geometry of the dense plasma focus current sheath. The present paper continues the discussion in the context of a 3-region shock structure similar to the one experimentally observed: an unperturbed region followed by a hydrodynamic shock containing some current followed by a magnetic piston. Rankine-Hugoniot conditions are derived, and expressions are obtained for the specific volumes and pressures using the mass-flux between the hydrodynamic shock and the magnetic piston and current fraction in the hydrodynamic shock as unknown parameters. For the special case of a magnetic piston that remains continuously in contact with the fluid being pushed, the theory gives closed form algebraic results for the fraction of current flowing in the hydrodynamic shock, specific volume, pressure, and fluid velocity of the hydrodynamic shock region, the tangential, normal, and azimuthal components of velocity in the magnetized plasma, the density of the magnetized plasma, the normal and tangential components of the magnetic field, and the tangential, normal, and azimuthal components of the electric field. This explains the occurrence of azimuthally streaming high energy deuterons experimentally observed by Frascati and Stuttgart. The expression derived for the azimuthal component of vector potential can serve as the basis for a proposed experimental test of the theory.
Single-reference coupled cluster theory for multi-reference problems
Authors: Margraf Johannes T. , Perera Ajith , Lutz Jesse J. , Bartlett Rodney J.
Published: November 2017

Coupled cluster (CC) theory is widely accepted as the most accurate and generally applicable approach in quantum chemistry. CC calculations are usually performed with single Slater-determinant references, e.g., canonical Hartree-Fock (HF) wavefunctions, though any single determinant can be used. This is an attractive feature because typical CC calculations are straightforward to apply, as there is no potentially ambiguous user input required. On the other hand, there can be concern that CC approximations give unreliable results when the reference determinant provides a poor description of the system of interest, i.e., when the HF or any other single determinant ground state has a relatively low weight in the full CI expansion. However, in many cases, the reported “failures” of CC can be attributed to an unfortunate choice of reference determinant, rather than intrinsic shortcomings of CC itself. This is connected to well-known effects like spin-contamination, wavefunction instability, and symmetry-breaking. In this contribution, a particularly difficult singlet/triplet splitting problem in two phenyldinitrene molecules is investigated, where CC with singles, doubles and perturbative triples [CCSD(T)] was reported to give poor results. This is analyzed by using different reference determinants for CCSD(T), as well as performing higher level CCSDT-3 and CCSDT calculations. We show that doubly electron attached and doubly ionized equation-of-motion (DEA/DIP-EOM) approaches are powerful alternatives for treating such systems. These are operationally single-determinant methods that adequately take the multi-reference nature of these molecules into account. Our results indicate that CC remains a powerful tool for describing systems with both static correlation and dynamic correlation, when pitfalls associated with the choice of the reference determinant are avoided.
Intersubband absorption of p-type wurtzite GaN/AlN quantum well for fiber-optics telecommunication
Authors: Park Seoung-Hwan , Ahn Doyeol , Park Chan-Yong
Published: November 2017

The intersubband transition of wurtzite (WZ) p-type GaN/AlN quantum well (QW) structures grown on GaN substrate was investigated theoretically using the multiband effective-mass theory. The peak value of the TE-polarization absorption spectrum is found to be similar to that of the TM-polarization absorption spectrum. The absorption coefficients for TE- and TM-polarizations are mainly attributed to the absorption from the ground state (m1 = 1) because holes are mainly confined in ground states near the band-edge in an investigated range of the carrier density. We observe that a transition wavelength of 1.55 μm can be obtained for the QW structure with a relatively thin (∼16 Å) well width. Thus, we expect that a p-type WZ AlN/GaN heterostructure is applicable for a photodetector application for fiber-optic communications with normal incidence of wave.
Performance improvement induced by asymmetric Y2O3-coated device structure to carbon-nanotube-film based photodetectors
Authors: Wang Fanglin , Xu Haitao , Huang Huixin , Ma Ze , Wang Sheng , Peng Lian-Mao
Published: November 2017

Film-based semiconducting carbon nanotube (CNT) photodetectors are promising candidates for industrial applications. However, unintentional doping from the environment such as water/oxygen (H2O/O2) redox, polymers, etc. changes the doping level of the CNT film. Here, we evaluate the performance of film-based barrier-free bipolar diodes (BFBDs), which are basically semiconducting CNT films asymmetrically contacted by perfect n-type ohmic contact (scandium, Sc) and p-type ohmic contact (palladium, Pd) at the two ends of the diode. We show that normal BFBD devices have large variances of forward current, reverse current, and photocurrent for different doping levels of the channel. We propose an asymmetric Y2O3-coated BFBD device in which the channel is covered by a layer of an Y2O3 film and an overlap between the Sc electrode and the Y2O3 film is designed. The Y2O3 film provides p-type doping to the channel. The overlap section increases the length of the base of the pn junction, and the diffusion current of holes is suppressed. In this way, the rectifier factors (current ratio when voltages are at +0.5 V and −0.5 V) of the asymmetric Y2O3-coated BFBD devices are around two orders of magnitude larger and the photocurrent generation is more stable compared to that of normal devices. Our results provide a way to conquer the influence of unintentional doping from the environment and suppress reverse current in pn diodes. This is beneficial to applications of CNT-based photodetectors and of importance for inspiring methods to improve the performances of devices based on other low dimensional materials.
Direct visualization of polarization reversal of organic ferroelectric memory transistor by using charge modulated reflectance imaging
Authors: Otsuka Takako , Taguchi Dai , Manaka Takaaki , Iwamoto Mitsumasa
Published: November 2017

By using the charge modulated reflectance (CMR) imaging technique, charge distribution in the pentacene organic field-effect transistor (OFET) with a ferroelectric gate insulator [P(VDF-TrFE)] was investigated in terms of polarization reversal of the P(VDF-TrFE) layer. We studied the polarization reversal process and the carrier spreading process in the OFET channel. The I-V measurement showed a hysteresis behavior caused by the spontaneous polarization of P(VDF-TrFE), but the hysteresis I-V curve changes depending on the applied drain bias, possibly due to the gradual shift of the polarization reversal position in the OFET channel. CMR imaging visualized the gradual shift of the polarization reversal position and showed that the electrostatic field formed by the polarization of P(VDF-TrFE) contributes to hole and electron injection into the pentacene layer and the carrier distribution is significantly dependent on the direction of the polarization. The polarization reversal position in the channel region is governed by the electrostatic potential, and it happens where the potential reaches the coercive voltage of P(VDF-TrFE). The transmission line model developed on the basis of the Maxwell-Wagner effect element analysis well accounts for this polarization reversal process in the OFET channel.
Stark effect of doped two-dimensional transition metal dichalcogenides
Authors: Lu Xiaobo , Yang Li
Published: November 2017

The bandgap of two-dimensional (2D) semiconductors can be efficiently tuned by a gate electric field, which is the so-called the Stark effect. We report that doping, which is essential in realistic devices, will substantially change the Stark effect of few-layer transition metal dichalcogenides in unexpected ways. Particularly, in bilayer structures, because of the competition between strong quantum confinement and the intrinsic screening length, electron and hole dopings exhibit surprisingly different Stark effects: doped electrons actively screen the external field and result in a nonlinear Stark effect; however, doped holes do not effectively screen the external field, causing a linear Stark effect that is the same as that of undoped materials. Our further analysis shows that this unusual doping effect is not limited within transition metal dichalcogenides but general for 2D structures. Therefore, doping plays a much more crucial role in functional 2D devices, and this unusual Stark effect also provides a new degree of freedom to tune bandgaps and optical properties of 2D materials.
High-temperature intrinsic ferromagnetism in the (In,Fe)Sb semiconductor
Authors: Kudrin A. V. , Danilov Yu. A. , Lesnikov V. P. , Dorokhin M. V. , Vikhrova O. V. , Pavlov D. A. , Usov Yu. V. , Antonov I. N. , Kriukov R. N. , Alaferdov A. V. , Sobolev N. A.
Published: November 2017

(In,Fe)Sb layers with a Fe content up to 13 at. % have been grown on (001) GaAs substrates using the pulsed laser deposition. Transmission electron microscopy shows that the layers are epitaxial and free of second-phase inclusions. The observation of hysteretic magnetoresistance curves at temperatures up to 300 K and the investigations of magnetic circular dichroism reveal that the Curie point lies above room temperature. The resonant character of magnetic circular dichroism confirms the intrinsic ferromagnetism in the (In,Fe)Sb matrix. We suggest that the ferromagnetism of the (In,Fe)Sb matrix is not carrier-mediated and is apparently determined by the mechanism of superexchange interaction between Fe atoms.
Insensitivity of synchronization to network structure in chaotic pendulum systems with time-delay coupling
Authors: Yao Chenggui , Zhan Meng , Shuai Jianwei , Ma Jun , Kurths Jürgen
Published: November 2017

It has been generally believed that both time delay and network structure could play a crucial role in determining collective dynamical behaviors in complex systems. In this work, we study the influence of coupling strength, time delay, and network topology on synchronization behavior in delay-coupled networks of chaotic pendulums. Interestingly, we find that the threshold value of the coupling strength for complete synchronization in such networks strongly depends on the time delay in the coupling, but appears to be insensitive to the network structure. This lack of sensitivity was numerically tested in several typical regular networks, such as different locally and globally coupled ones as well as in several complex networks, such as small-world and scale-free networks. Furthermore, we find that the emergence of a synchronous periodic state induced by time delay is of key importance for the complete synchronization.
Batch fabrication of nanopatterned graphene devices via nanoimprint lithography
Authors: Mackenzie David M. A. , Smistrup Kristian , Whelan Patrick R. , Luo Birong , Shivayogimath Abhay , Nielsen Theodor , Petersen Dirch H. , Messina Sara A. , Bøggild Peter
Published: November 2017

Previous attempts to tune the electrical properties of large-scale graphene via nanopatterning have led to serious degradation of the key electrical parameters that make graphene a desirable material for electronic devices. We use thermal nanoimprint lithography to pattern wafer-scale graphene on a 4-in. wafer with prefabricated 25 mm2 devices. The nanopatterning process introduces a modest decrease in carrier mobility and only a minor change in residual doping. Due to the rapid fabrication time of approximately 90 min per wafer, this method has potential for large-scale industrial production. The chemiresistive gas sensing response towards NO2 was assessed in humid synthetic air and dry air, with devices showing a response to 50 ppb of NO2 only when nanopatterned.
Viscoelastic fluid flow through porous media modeled using pillared microchannels
Authors: Kim Meeri
Published: November 2017

Flow instabilities in microfluidic channels that mimic porous rock offer more insight into enhanced oil recovery.
Building a Culture of Life by Embracing the Feminine Genius: A Message to Catholic Women in Health Care
Authors: Caldwell Susan
Published: November 2017

This article is written to encourage women working in various healthcare fields to understand their call and responsibility to help build a culture of life. By using their natural “feminine genius,” women are uniquely gifted to uphold the sacredness of sex and the dignity of human life in every clinical encounter.
Military Withdrawal from Government Responsibility: Indonesia and Mexico
Authors: Gehrmann Richard
Published: November 2017

‘One of the most remarkable trends in Mexico, dating from its entrance into the Second World War, is the professionalization of its army and the removal of militarism as an open element in domestic politics.’
Contesting Consent: Contemporary Democracy and Ecological Crisis
Authors: Curran Giorel
Published: November 2017

This paper argues that ecological problems and potential ecological crises expose serious deficiencies in the procedural and normative contours of liberal democratic practice. The contemporary contexts of globalisation and accelerating ecological depletion put novel and unprecedented pressures on these liberal democratic polities. Democracy's traditional claims to consent and legitimacy are openly challenged and contested in the light of the emergent ecological trajectory. These issues will be explored through three broad sections. Firstly, ‘legitimation crises’ and problems of consent are examined in the context of ecological (and associated social) imperatives. Some parallels are also drawn from feminist theory. Secondly, the changed meaning of bounded territoriality and the implications it exposes are examined in the light of contemporary ecological, economic and political ‘transboundariness’. Finally, a more participative and discursive democratic alternative is sketched. The claim defended is that more (substantive) democracy, not less, is required in order to mediate the development of ecologically unstainable social visions.
Women's Work and the Howard Government
Authors: Ostenfeld Shane , Strachan Glenda
Published: November 2017

This paper undertakes a preliminary exploration of the impact of social conservatism on Australian industrial relations. It posits that contradictions have emerged under the current government in terms of, on the one hand, support for ‘freeing up’ of the labour market, and, on the other hand, the inherent logic of Howard's free-market economic agenda. The contradiction is that freeing up the labour market involves support for a male breadwinner wage so that women do not enter the workplace. This agenda is carried out driven by free market ideas of minimum legislation, including no minimum wage legislation. To explain this agenda, attention is turned to the influence of right-wing pressure groups. Changes in the composition of the Lyons Forum within the Liberal Party of Australia since the 1998 election are then examined. A continuing influence by the forces of moral conservatism during the second term of the Howard coalition government is evident.
From Technocrats to Classical Bureaucrats: The shifting attitudes of New Zealand's health services purchasing agents
Authors: Gauld Robin
Published: November 2017

This article presents the findings of two surveys conducted in 1993 and 1997 respectively. The surveys are in the tradition of a growing body of international research inquiring into the attitudes of officials in key policy-making and administrative posts toward aspects of their operating environments. The surveys provide comparative ‘snapshots’ of the attitudes of respondents at two very important phases in the existence of the agencies. Moreover, because of the circumstances in which they were conducted, the surveys offer insights into the effect on officials of radical restructuring, and of managing in a politicized and uncertain environment. The findings, limitations and implications of the research for policymakers and public officials are elucidated.
The Quiet Revolution in Australian Higher Education
Authors: Bostock William W
Published: November 2017

Quiet revolution is a term that was used to describe the fundamental transformation of Quebec society in the 1960s: a profound and permanent process that took place with very little violence or other outward signs of resistance. Australia's higher education sector also underwent a profound transformation in the 1990s, also with strangely little protest or even debate, so that it could also reasonably be called a quiet revolution. This paper examines what changed as a result of the revolution, why it occurred, and why it occurred largely in silence. The answers to these questions about the revolution in higher education provide an interesting case study of the complex interaction between policy, organisation and society.
Specialized ribosomes and specific ribosomal protein paralogs control translation of mitochondrial proteins
Authors: Segev Nadav , Gerst Jeffrey E.
Published: November 2017

Genome duplication in eukaryotes created paralog pairs of ribosomal proteins (RPs) that show high sequence similarity/identity. However, individual paralogs can confer vastly different effects upon cellular processes, e.g., specific yeast paralogs regulate actin organization, bud site selection, and mRNA localization, although how specificity is conferred is unknown. Changes in the RP composition of ribosomes might allow for specialized translation of different subsets of mRNAs, yet it is unclear whether specialized ribosomes exist and if paralog specificity controls translation. Using translatome analyses, we show that the translation of mitochondrial proteins is highly down-regulated in yeast lacking RP paralogs required for normal mitochondrial function (e.g., RPL1b). Although RPL1a and RPL1b encode identical proteins, Rpl1b-containing ribosomes confer more efficient translation of respiration-related proteins. Thus, ribosomes varying in RP composition may confer specialized functions, and RP paralog specificity defines a novel means of translational control.
LIBRA-WA: a web application for ligand binding site detection and protein function recognition
Authors: Toti Daniele , Viet Hung Le , Tortosa Valentina , Brandi Valentina , Polticelli Fabio
Published: November 2017

Recently, LIBRA, a tool for active/ligand binding site prediction, was described. LIBRA’s effectiveness was comparable to similar state-of-the-art tools; however, its scoring scheme, output presentation, dependence on local resources and overall convenience were amenable to improvements. To solve these issues, LIBRA-WA, a web application based on an improved LIBRA engine, has been developed, featuring a novel scoring scheme consistently improving LIBRA’s performance, and a refined algorithm that can identify binding sites hosted at the interface between different subunits. LIBRA-WA also sports additional functionalities like ligand clustering and a completely redesigned interface for an easier analysis of the output. Extensive tests on 373 apoprotein structures indicate that LIBRA-WA is able to identify the biologically relevant ligand/ligand binding site in 357 cases (∼96%), with the correct prediction ranking first in 349 cases (∼98% of the latter, ∼94% of the total). The earlier stand-alone tool has also been updated and dubbed LIBRA+, by integrating LIBRA-WA’s improved engine for cross-compatibility purposes.

Availability and implementation

LIBRA-WA and LIBRA+ are available at: http://www.computationalbiology.it/software.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
RepLong: de novo repeat identification using long read sequencing data
Authors: Guo Rui , Li Yan-Ran , He Shan , Ou-Yang Le , Sun Yiwen , Zhu Zexuan
Published: November 2017

Motivation

The identification of repetitive elements is important in genome assembly and phylogenetic analyses. The existing de novo repeat identification methods exploiting the use of short reads are impotent in identifying long repeats. Since long reads are more likely to cover repeat regions completely, using long reads is more favorable for recognizing long repeats.

Results

In this study, we propose a novel de novo repeat elements identification method namely RepLong based on PacBio long reads. Given that the reads mapped to the repeat regions are highly overlapped with each other, the identification of repeat elements is equivalent to the discovery of consensus overlaps between reads, which can be further cast into a community detection problem in the network of read overlaps. In RepLong, we first construct a network of read overlaps based on pair-wise alignment of the reads, where each vertex indicates a read and an edge indicates a substantial overlap between the corresponding two reads. Secondly, the communities whose intra connectivity is greater than the inter connectivity are extracted based on network modularity optimization. Finally, representative reads in each community are extracted to form the repeat library. Comparison studies on Drosophila melanogaster and human long read sequencing data with genome-based and short-read-based methods demonstrate the efficiency of RepLong in identifying long repeats. RepLong can handle lower coverage data and serve as a complementary solution to the existing methods to promote the repeat identification performance on long-read sequencing data.

Availability and implementation

The software of RepLong is freely available at https://github.com/ruiguo-bio/replong.

Supplementary information

Supplementary data are available at Bioinformatics online.
The ICC’s First ‘Forced Pregnancy’ Case in Historical Perspective
Authors: Grey Rosemary
Published: November 2017

Reproductive violence, as distinct from the related issue of sexual violence, is yet to be truly ‘surfaced’ in international criminal law. Yet, this kind of violence has long been a feature of war, and is repugnant to the values that international criminal law protects. The Ongwen case, which commenced trial in the International Criminal Court in December 2016, is a step forward in this regard. Not only is this the first case in any international criminal court to include charges of ‘forced pregnancy’; it is also one of the only cases in which reproductive violence outside the context of genocide or ‘ethnic cleansing’ has been understood as a crime under international law. This article situates this landmark case is its historical contex, and raises some broader concerns about the limited response to reproductive violence in the development and enforcement of international criminal law. Based on an analysis of the law and practice of past and present international criminal courts, it shows that accountability for conflict-related reproductive violence has been patchy at best, and that there has been little recognition of the harms that such violence causes to individual victims, as distinct from the groups to which they ‘belong’. The article concludes by sketching out some steps to remedy these omissions, building on the progress made in the Ongwen case. Underlying the article is a view that reproductive autonomy is a distinct value from sexual autonomy, and that, where possible, conduct which offends this value should be punished as a separate crime.
Nanomaterial libraries and model organisms for rapid high-content analysis of nanosafety
Authors: Li Yiye , Wang Jing , Zhao Feng , Bai Bing , Nie Guangjun , Nel André E , Zhao Yuliang
Published: November 2017

Safety analysis of engineered nanomaterials (ENMs) presents a formidable challenge regarding environmental health and safety, due to their complicated and diverse physicochemical properties. Although large amounts of data have been published regarding the potential hazards of these materials, we still lack a comprehensive strategy for their safety assessment, which generates a huge workload in decision-making. Thus, an integrated approach is urgently required by government, industry, academia and all others who deal with the safe implementation of nanomaterials on their way to the marketplace. The rapid emergence and sheer number of new nanomaterials with novel properties demands rapid and high-content screening (HCS), which could be performed on multiple materials to assess their safety and generate large data sets for integrated decision-making. With this approach, we have to consider reducing and replacing the commonly used rodent models, which are expensive, time-consuming, and not amenable to high-throughput screening and analysis. In this review, we present a ‘Library Integration Approach’ for high-content safety analysis relevant to the ENMs. We propose the integration of compositional and property-based ENM libraries for HCS of cells and biologically relevant organisms to be screened for mechanistic biomarkers that can be used to generate data for HCS and decision analysis. This systematic approach integrates the use of material and biological libraries, automated HCS and high-content data analysis to provide predictions about the environmental impact of large numbers of ENMs in various categories. This integrated approach also allows the safer design of ENMs, which is relevant to the implementation of nanotechnology solutions in the pharmaceutical industry.
The Elusive Search for Reniform Nematode Resistance in Cotton
Authors: Khanal Churamani , McGawley Edward C. , Overstreet Charles , Stetina Salliana R.
Published: November 2017

The reniform nematode (Rotylenchulus reniformis Linford and Oliveira) has emerged as the most important plant-parasitic nematode of cotton in the United States cotton belt. Success in the development of reniform nematode-resistant upland cotton cultivars (Gossypium hirsutum L.) has not been realized despite over three decades of breeding efforts. Research approaches ranging from conventional breeding to triple species hybrids to marker-assisted selection have been employed to introgress reniform nematode resistance from other species of cotton into upland cultivars. Reniform nematode-resistant breeding lines derived from G. longicalyx were developed in 2007. However, these breeding lines displayed stunting symptoms and a hypersensitive response to reniform nematode infection. Subsequent breeding efforts focused on G. barbadense, G. aridum, G. armoreanum, and other species that have a high level of resistance to reniform nematode. Marker-assisted selection has greatly improved screening of reniform nematode-resistant lines. The use of advanced molecular techniques such as CRISPER-Cas9 systems and alternative ways such as delivery of suitable “cry” proteins and specific double-stranded RNA to nematodes will assist in developing resistant cultivars of cotton. In spite of the efforts of cotton breeders and nematologists, successes are limited only to the development of reniform nematode-resistant breeding lines. In this article, we provide an overview of the approaches employed to develop reniform nematode-resistant upland cotton cultivars in the past, progress to date, major obstacles, and some promising future research activity.
The Development of a Clinical Peer Review Tool
Authors: Lundeen John D. , Warr Rebecca J. , Cortes Cynthia G. , Wallis Frankie , Coleman Jennifer J.
Published: November 2017

Faculty evaluation for the purpose of promotion and tenure frequently includes peer review as a part of the process. Faculty review by a peer may provide an assessment of teaching effectiveness and information related to the faculty member’s professional development activities. This article presents an innovative, evidence-based approach using selected National League for Nursing core competencies and International Nursing Association for Clinical Simulation and Learning clinical simulation standards in the development of a faculty peer review tool to gather data on clinical teaching to be used during the promotion and tenure process.