bluuebunny/crossref_metadata_2025 huggingface dataset:
Nanometer collimation enhancement of ion beams using channeling effects in track-etched mica capillaries
Authors: Scheuner Clemens , Jankuhn Steffen , Vogt Jürgen , Pezzagna Sébastien , Trautmann Christina , Meijer Jan
Published: November 2017

Long channels with diameter of few tens of nanometer are produced by chemical track etching of swift heavy ion irradiated muscovite sheets. Such small apertures are most suitable e.g. as beam defining apertures for focusing systems in ion beam facilities enabling beam diameters down to a few nanometers. One of the most important parameters to consider is the interaction of the ion beam with the walls of the aperture. We report angle-resolved transmission and energy-loss measurements of MeV ion beams through ion-track-etched capillaries with very high aspect ratio of about 60. For all ion energies, the angle-resolved transmission curves measured through the channels show a significant enhancement with respect to the expected pure geometrical considerations. This broadening of the acceptance angle increases further when the kinetic energy is reduced. This effect is ascribed to low-angle scattering of the ions at the surface of the muscovite capillary walls. These results are well described by simulations applying a similar approach as used for ion beam channeling in crystals.
Evaluation of short interval cortical inhibition and intracortical facilitation from the dorsolateral prefrontal cortex in patients with schizophrenia
Authors: Noda Yoshihiro , Barr Mera S. , Zomorrodi Reza , Cash Robin F. H. , Farzan Faranak , Rajji Tarek K. , Chen Robert , Daskalakis Zafiris J. , Blumberger Daniel M.
Published: November 2017

GABAergic and glutamatergic dysfunction in the dorsolateral prefrontal cortex (DLPFC) are thought to be the core pathophysiological mechanisms of schizophrenia. Recently, we have established a method to index these functions from the DLPFC using the paired transcranial magnetic stimulation (TMS) paradigms of short interval intracortical inhibition (SICI) and facilitation (ICF) combined with electroencephalography (EEG). In this study, we aimed to evaluate neurophysiological indicators related to GABAA and glutamate receptor-mediated functions respectively from the DLPFC in patients with schizophrenia using these paradigms, compared to healthy controls. Given that these activities contribute to cognitive functions, the relationship between the TMS-evoked potential (TEP) modulations by SICI/ICF and cognitive/clinical measures were explored. Compared to controls, patients showed reduced inhibition in P60 (t22 = −4.961, p < 0.0001) by SICI and reduced facilitation in P60 (t22 = 5.174, p < 0.0001) and N100 (t22 = 3.273, p = 0.003) by ICF. In patients, the modulation of P60 by SICI was correlated with the longest span of the Letter-Number Span Test (r = −0.775, p = 0.003), while the modulation of N100 by ICF was correlated with the total score of the Positive and Negative. Syndrome Scale (r = 0.817, p = 0.002). These findings may represent the pathophysiology, which may be associated with prefrontal GABAA and glutamatergic dysfunctions, in the expression of symptoms of schizophrenia.
A Comprehensive Assessment of the Genetic Determinants in Salmonella Typhimurium for Resistance to Hydrogen Peroxide Using Proteogenomics
Authors: Karash Sardar , Liyanage Rohana , Qassab Abdullah , Lay Jackson O. , Kwon Young Min
Published: November 2017

Salmonella is an intracellular pathogen infecting a wide range of hosts and can survive in macrophages. An essential mechanism used by macrophages to eradicate Salmonella is production of reactive oxygen species. Here, we used proteogenomics to determine the candidate genes and proteins that have a role in resistance of S. Typhimurium to H2O2. For Tn-seq, a saturated Tn5 insertion library was grown in vitro under either 2.5 (H2O2L) or 3.5 mM H2O2 (H2O2H). We identified two sets of overlapping genes required for resistance of S. Typhimurium to H2O2L and H2O2H, and the results were validated via phenotypic evaluation of 50 selected mutants. The enriched pathways for H2O2 resistance included DNA repair, aromatic amino acid biosynthesis (aroBK), Fe-S cluster biosynthesis, iron homeostasis and a putative iron transporter system (ybbKLM), and H2O2 scavenging enzymes. Proteomics revealed that the majority of essential proteins, including ribosomal proteins, were downregulated upon exposure to H2O2. On the contrary, a subset of conditionally essential proteins identified by Tn-seq were analyzed by targeted proteomics, and 70% of them were upregulated by H2O2. The identified genes will deepen our understanding on S. Typhimurium survival mechanisms in macrophages, and can be exploited to develop new antimicrobial drugs.
The tight-binding formulation of the Kronig-Penney model
Authors: Marsiglio F. , Pavelich R. L.
Published: November 2017

Electronic band structure calculations are frequently parametrized in tight-binding form; the latter representation is then often used to study electron correlations. In this paper we provide a derivation of the tight-binding model that emerges from the exact solution of a particle bound in a periodic one-dimensional array of square well potentials. We derive the dispersion for such a model, and show that an effective next-nearest-neighbour hopping parameter is required for an accurate description. An electron-hole asymmetry is prevalent except in the extreme tight-binding limit, and emerges through a “next-nearest-neighbour” hopping term in the dispersion. We argue that this does not necessarily imply next-nearest-neighbour tunneling; this assertion is demonstrated by deriving the transition amplitudes for a two-state effective model that describes a double-well potential, which is a simplified precursor to the problem of a periodic array of potential wells. A next-nearest-neighbour tunneling parameter is required for an accurate description even though there are no such neighbours.
Comment on “Thermal compaction of the intrinsically disordered protein tau: entropic, structural, and hydrophobic factors” by A. Battisti, G. Ciasca, A. Grottesi and A. Tenenbaum, Phys. Chem. Chem. Phys., 2017, 19, 8435
Authors: Graziano Giuseppe
Published: November 2017

Chain compaction is favoured on raising the temperature because the entropy gain of water molecules due to the decrease in solvent-excluded volume increases with temperature.
Shapes matter: examining the optical response evolution in stretched aluminium nanoparticles via time-dependent density functional theory
Authors: Mokkath Junais Habeeb
Published: November 2017

Using first-principles time-dependent density functional theory calculations, we investigate the shape-anisotropy effects on the optical response of a spherical aluminium nanoparticle subjected to a stretching process in different directions.
A bonding evolution analysis for the thermal Claisen rearrangement: an experimental and theoretical exercise for testing the electron density flow
Authors: González-Navarrete Patricio , Andrés Juan , Safont V. Sixte
Published: November 2017

The BET analysis brings about the natural appearance of curly arrows representing thus the electronic flow in molecular rearrangements.
Ultrafast interfacial charge transfer from the LUMO+1 in ruthenium(ii) polypyridyl quinoxaline-sensitized solar cells
Authors: Shahroosvand Hashem , Eskandari Mortaza
Published: November 2017

This paper describes the implementation of robust and modular sensitizers containing aromatic–amphiphilic ligands to provide new insights into the relationship between the molecular structure and electron injection process governing the efficiency of dye-sensitized solar cells (DSSCs).
A new heptadentate picolinate-based ligand and its corresponding Gd(iii) complex: the effect of pendant picolinate versus acetate on complex properties
Authors: Phukan Bedika , Mukherjee Chandan , Varshney Raunak
Published: November 2017

Replacing one picolinate pendant by acetate group in H4bpeda ligand, the synthesised bis(aquated) Gd(iii) complex of ligand H4peada showed better stability and r1 relaxivity for its potential use as MRI contrast agent.
Water promoted allylic nucleophilic substitution reactions of (E)-1,3 diphenylallyl acetate
Authors: Ghorpade Seema A. , Sawant Dinesh N. , Makki Arwa , Sekar Nagaiyan , Eppinger Jörg
Published: November 2017

A transition metal free, reagent free, only water based, greener protocol for the allylic alkylation, allylic amination, and O-allylation of (E)-1,3-diphenylallyl acetate is described.
Correction: Design of a thermoregulated phase-separable system for homogeneous enzymolysis of cellulose
Authors: Li Lu , Liu Xianhong , Yu Shitao , Liu Shiwei , Liu Fusheng , Xie Congxia
Published: November 2017

Correction for ‘Design of a thermoregulated phase-separable system for homogeneous enzymolysis of cellulose’ by Lu Li et al., Green Chem., 2015, 17, 3067–3074.
Magnetic nanoparticles as double-edged swords: concentration-dependent ordering or disordering effects on lysozyme
Authors: Kashanian F. , Habibi-Rezaei M. , Bagherpour A. R. , Seyedarabi A. , Moosavi-Movahedi A. A.
Published: November 2017

The study of the interaction of nanoparticles (NPs) with proteins is of great importance due to its relevance in several fields including nano-biosafety, nano-bioscience, nano-biomedicine, and nano-biotechnology.
Synergistic catalysis of nano-Pd and nano rare-earth oxide/AC: complex nanostructured catalysts fabricated by a photochemical route for selective hydrogenation of phenol
Authors: Zhang Yanji , Zhou Jicheng , Si Jiaqi
Published: November 2017

Cyclohexanone is an important industrial intermediate in the chemical industry, but direct selective hydrogenation of phenol to cyclohexanone under mild conditions to achieve both high conversion and selectivity is a challenge.
Natural sliced wood veneer as a universal porous lightweight substrate for supercapacitor electrode materials
Authors: Lyu Shaoyi , Chen Yanping , Han Shenjie , Guo Limin , Yang Na , Wang Siqun
Published: November 2017

We herein report the use of natural sliced wood veneer as a porous lightweight substrate for supercapacitor electrodes, where PANI/RGO and PPy/RGO were employed as active materials, and both wood electrodes showed good electrochemical performance.
Nickel containing ionic liquid based ordered nanoporous organosilica: a powerful and recoverable catalyst for synthesis of polyhydroquinolines
Authors: Elhamifar Dawood , Khanmohammadi Hamideh , Elhamifar Davar
Published: November 2017

The synthesis, characterization and catalytic application of a novel nickel containing ionic liquid based ordered mesoporous organosilica are demonstrated.
Chondrogenic potential of macroporous biodegradable cryogels based on synthetic poly(α-amino acids)
Authors: Sedlačík T. , K. Acar O. , Studenovská H. , Kotelnikov I. , Kučka J. , Konečná Z. , Zikmund T. , Kaiser J. , Kose G. T. , Rypáček F.
Published: November 2017

Macroporous cryogels of synthetic poly(α-amino acids) modified with RGDS peptides show increased potential for chondrogenesis of hDPSCs.
Methodology for understanding interactions between electrolyte additives and cathodes: a case of the tris(2,2,2-trifluoroethyl)phosphite additive
Authors: Sahore Ritu , Tornheim Adam , Peebles Cameron , Garcia Juan , Dogan Fulya , O'Hanlon Daniel C. , Liao Chen , Iddir Hakim , Zhang Zhengcheng , Bareño Javier , Bloom Ira
Published: November 2017

Both experiments and theory show that TTFP does not passivate NMC532 cathode surface towards electrolyte oxidation.
MoS2-covered SnS nanosheets as anode material for lithium-ion batteries with high capacity and long cycle life
Authors: Pan Qichang , Zheng Fenghua , Wu Yanan , Ou Xing , Yang Chenghao , Xiong Xunhui , Liu Meilin
Published: November 2017

A designed hierarchical nanostructure consisting of SnS nanosheets and ultrathin MoS2 nanosheets was achieved, and then evaluated as anode material for LIBs with high capacity and long cycle life.
One-pot synthesis of glutathione-responsive amphiphilic drug self-delivery micelles of doxorubicin–disulfide–methoxy polyethylene glycol for tumor therapy
Authors: Duan Xiao , Bai Ting , Du Junjie , Kong Jie
Published: November 2017

We present a novel glutathione-responsive amphiphilic drug self-delivery (DSD) micelle with one-pot synthesis to synergistically address the problems of controlled drug release, degradability, drug tracing and in vivo accumulated toxicity.
High dielectric constant and low dielectric loss poly(vinylidene fluoride) nanocomposites via a small loading of two-dimensional Bi2Te3@Al2O3 hexagonal nanoplates
Authors: Chen Jianwen , Wang Xiucai , Yu Xinmei , Yao Lingmin , Duan Zhikui , Fan Yun , Jiang Yewen , Zhou Yuexia , Pan Zhongbin
Published: November 2017

Nanocomposite films with a small loading of two-dimensional Bi2Te3@Al2O3 hexagonal nanoplates exhibit a high dielectric constant of 140 and relatively low dielectric loss of 0.05 at 1 kHz.
Glimpses of the past activity of Sgr A★ inferred from X-ray echoes in Sgr C
Authors: Chuard D. , Terrier R. , Goldwurm A. , Clavel M. , Soldi S. , Morris M. R. , Ponti G. , Walls M. , Chernyakova M.
Published: November 2017

Context. For a decade now, evidence has accumulated that giant molecular clouds located within the central molecular zone of our Galaxy reflect X-rays coming from past outbursts of the Galactic supermassive black hole. However, the number of illuminating events as well as their ages and durations are still unresolved questions.

Aims. We aim to reconstruct parts of the history of the supermassive black hole Sgr A★ by studying this reflection phenomenon in the molecular complex Sgr C and by determining the line-of-sight positions of its main bright substructures.

Methods. Using observations made with the X-ray observatories XMM-Newton and Chandra and between 2000 and 2014, we investigated the variability of the reflected emission, which consists of a Fe Kα line at 6.4 keV and a Compton continuum. We carried out an imaging and a spectral analysis. We also used a Monte Carlo model of the reflected spectra to constrain the line-of-sight positions of the brightest clumps, and hence to assign an approximate date to the associated illuminating events.

Results. We show that the Fe Kα emission from Sgr C exhibits significant variability in both space and time, which confirms its reflection origin. The most likely illuminating source is Sgr A★. On the one hand, we report two distinct variability timescales, as one clump undergoes a sudden rise and fall in about 2005, while two others vary smoothly throughout the whole 2000–2014 period. On the other hand, by fitting the Monte Carlo model to the data, we are able to place tight constraints on the 3D positions of the clumps. These two independent approaches provide a consistent picture of the past activity of Sgr A★, since the two slowly varying clumps are located on the same wavefront, while the third (rapidly varying) clump corresponds to a different wavefront, that is, to a different illuminating event.

Conclusions. This work shows that Sgr A★ experienced at least two powerful outbursts in the past 300 yrs, and for the first time, we provide an estimation of their age. Extending this approach to other molecular complexes, such as Sgr A, will allow this two-event scenario to be tested further.
Fluorine in the solar neighborhood: Chemical evolution models
Authors: Spitoni E. , Matteucci F. , Jönsson H. , Ryde N. , Romano D.
Published: November 2017

Context. In light of new observational data related to fluorine abundances in solar neighborhood stars, we present chemical evolution models testing various fluorine nucleosynthesis prescriptions with the aim to best fit those new data.

Aim. We consider chemical evolution models in the solar neighborhood testing various nucleosynthesis prescriptions for fluorine production with the aim of reproducing the observed abundance ratios [F/O] versus [O/H] and [F/Fe] versus [Fe/H]. We study in detail the effects of various stellar yields on fluorine production.

Methods. We adopted two chemical evolution models: the classical two-infall model, which follows the chemical evolution of halo-thick disk and thin disk phases; and the one-infall model, which is designed only for thin disk evolution. We tested the effects on the predicted fluorine abundance ratios of various nucleosynthesis yield sources, that is, asymptotic giant branch (AGB) stars, Wolf–Rayet (W-R) stars, Type II and Type Ia supernovae, and novae.

Results. The fluorine production is dominated by AGB stars but the W-R stars are required to reproduce the trend of the observed data in the solar neighborhood with our chemical evolution models. In particular, the best model both for the two-infall and one-infall cases requires an increase by a factor of 2 of the W-R yields. We also show that the novae, even if their yields are still uncertain, could help to better reproduce the secondary behavior of F in the [F/O] versus [O/H] relation.

Conclusions. The inclusion of the fluorine production by W-R stars seems to be essential to reproduce the new observed ratio [F/O] versus [O/H] in the solar neighborhood. Moreover, the inclusion of novae helps to reproduce the observed fluorine secondary behavior substantially.
Using Organic Synthesis and Chemical Analysis to Understand the Photochemistry of Spore Photoproduct and Other Pyrimidine Dimers
Authors: Li Lei
Published: November 2017

Pyrimidine dimerization is the dominant DNA photoreaction occurring in vitro and in vivo. Three types of dimers, cyclobutane pyrimidine dimers (CPDs), pyrimidine (6-4) pyrimidone photoproducts (6-4PPs), and the spore photoproduct (SP), are formed from the direct dimerization process; it is of significance to understand the photochemistry and photobiology of these dimers. Traditionally, pyrimidine dimerization was studied by using the natural pyrimidine residues thymine and cytosine, which share similar chemical structures and similar reactivity, making it sometimes less straightforward for one to identify the key pyrimidine residue that needs to be excited to trigger the photoreaction. We thus adopted synthetic chemistry to selectively modify the pyrimidine residues or to introduce pyrimidine analogs to the selected positions before UV irradiation is applied. By monitoring the subsequent outcomes from the photoreaction, we were able to gain unique mechanistic insights into the photochemistry of SP as well as of CPDs and 6-4PPs. Moreover, our approaches have resulted in several useful “tools” that can facilitate the understanding of lesion photobiology. Our results summarized in this account illustrate what organic synthesis/chemical analysis may allow us to achieve in future DNA lesion biology studies.

 1 Introduction

 2 Using the Deuterium Labeling Strategy to Understand SP Formation

 3 Using Microcrystals to Reveal the Reaction Intermediates in SP Formation

 4 Using a Phosphate Isostere to Understand the SP Structure

 5 Synthesis of SP Phosphoramidite and SP Structural Studies

 6 Using a Thymine Isostere to Understand CPD Formation

 7 Using a Thymine Isostere to Understand 6-4PP Photoreaction

 8 Understanding the Chemical Stability of SP

 9 Understanding the Chemical Stability of 6-4PP

10 Summary and Perspectives for Future Research
Are the Domains Considered by ICF Comprehensive Enough to Conceptualize Participation in the Patient with Hand Injuries?
Authors: Layeghi Fereydoun , Hosseini Seyyed , Hamidreza Khanke , Asgari Ali , Farzad Maryam
Published: November 2017

Background Although participation is a core concept in multiple models of disability, there is no consensus on its definition.

Objective The aim of this study was to extract participation domains based on review of theories, available outcome measures, and interviews with experts and the person with hand injuries to compare with the ICF domains of participation.

Methods A qualitative approach using a deductive content analysis was employed to extend definitions of participation from theories. Later on, inductive qualitative method using semistructured interview with five experts in different fields and 30 patients with different hand injuries was used. Coding was performed with extracted domains from the content of data, and finally, the extracted domains were compared with the ICF domains of participation.

Results Some of the extracted domains were not considered in ICF.

Conclusion Subjective participation is the main forbearance part. Role, leisure, domestic life, environment, and others are also main missing meanings. This limitation can hinder measuring disability and health.
Value of Resistin in Early Onset Neonatal Sepsis
Authors: Ozdemir Abdurrahman , Elgormus Yusuf
Published: November 2017

The diagnosis of neonatal sepsis is usually difficult because the sign and symptoms are nonspecific. Although C-reactive protein (CRP) and procalcitonin (PCT) are the most commonly used auxiliary tests, they are not reliable enough markers to be used for diagnosis of neonatal sepsis. This study aimed to evaluate the efficacy of resistin in diagnosing early onset neonatal sepsis and to compare its effectiveness to CRP and PCT. This prospective study was performed in the neonatal intensive care unit of Medicine Hospital between June and September 2016. Twenty-nine infants in the sepsis group and 33 infants in the control group were recruited. The Töllner scoring system was used for clinical signs. The hematologic parameters were evaluated using the Manroe and Rodwell scoring systems. The blood samples for CRP, PCT, and resistin were collected at admission (T0), and at 72 hours (T3). Mean plasma resistin level at T0 was 54.20 ± 39.3 ng/mL in the sepsis group and 34.92 ± 6.9 ng/mL in the control group. The sensitivity at T0 for resistin was 76%, and the specificity was 67%. The values of area under the curve (AUC) for CRP, PCT, and resistin were 0.84, 0.66, and 0.72, respectively. We found the diagnostic value of resistin to be lower than CRP, although its plasma levels were elevated. Therefore, we propose that resistin has limited value in diagnosis and follow-up of early-onset neonatal sepsis.
BGG complexes in singular infinitesimal character for type A
Authors: Pandžić Pavle , Souček Vladimír
Published: November 2017

We give a geometric construction of the Bernstein-Gel’fand-Gel’fand (BGG) resolutions in singular infinitesimal character in the case of 1-graded complex Lie algebras of type A.
High-performance oxide thin film transistor fully fabricated by a direct rheology-imprinting
Authors: Tue Phan Trong , Fukada Kazuhiro , Shimoda Tatsuya
Published: November 2017

Operation of all oxide thin-film transistors fully fabricated by a direct rheology-imprinting technique was demonstrated. In the device, a highly conductive amorphous La-Ru-O (8 × 10−3 Ω cm) was used as the gate and source/drain electrodes. Indium oxide and amorphous La-Zr-O were utilized as the semiconducting channel and gate insulator, respectively. Silsesquioxane-based SiO2 was used both as a mask and as a passivation layer for the channel. The obtained “on/off” current ratio, field-effect mobility, threshold voltage, and subthreshold swing factor were approximately 107, 8.4 cm2 V−1 s−1, −0.18 V, and 80 mV/decade, respectively.
Improved performance of Ta2O5−x resistive switching memory by Gd-doping: Ultralow power operation, good data retention, and multilevel storage
Authors: Shi K. X. , Xu H. Y. , Wang Z. Q. , Zhao X. N. , Liu W. Z. , Ma J. G. , Liu Y. C.
Published: November 2017

Resistive-switching memory with ultralow-power consumption is very promising technology for next-generation data storage and high-energy-efficiency neurosynaptic chips. Herein, Ta2O5−x-based multilevel memories with ultralow-power consumption and good data retention were achieved by simple Gd-doping. The introduction of a Gd ion, as an oxygen trapper, not only suppresses the generation of oxygen vacancy defects and greatly increases the Ta2O5−x resistance but also increases the oxygen-ion migration barrier. As a result, the memory cells can operate at an ultralow current of 1 μA with the extrapolated retention time of >10 years at 85 °C and the high switching speeds of 10 ns/40 ns for SET/RESET processes. The energy consumption of the device is as low as 60 fJ/bit, which is comparable to emerging ultralow-energy consumption (<100 fJ/bit) memory devices.
Band alignment at interfaces of synthetic few-monolayer MoS2 with SiO2 from internal photoemission
Authors: Shlyakhov I. , Chai J. , Yang M. , Wang S. J. , Afanas’ev V. V. , Houssa M. , Stesmans A.
Published: November 2017

Electron band alignment at interfaces of SiO2 with directly synthesized few-monolayer (ML) thin semiconducting MoS2 films is characterized by using field-dependent internal photoemission of electrons from the valence band of MoS2 into the oxide conduction band. We found that reducing the grown MoS2 film thickness from 3 ML to 1 ML leads to ≈400 meV downshift of the valence band top edge as referenced to the common energy level of the SiO2 conduction band bottom. Furthermore, comparison of the MoS2 layers grown by a H-free process (sputtering of Mo in sulfur vapor) to films synthesized by sulfurization of metallic Mo in H2S indicates a significant (≈500 meV) electron barrier increase in the last case. This effect is tentatively ascribed to the formation of an interface dipole due to the interaction of hydrogen with the oxide surface.
Electrical response of Pt/Ru/PbZr0.52Ti0.48O3/Pt capacitor as function of lead precursor excess
Authors: Gueye Ibrahima , Le Rhun Gwenael , Renault Olivier , Defay Emmanuel , Barrett Nicholas
Published: November 2017

We investigated the influence of the surface microstructure and chemistry of sol-gel grown PbZr0.52Ti0.48O3 (PZT) on the electrical performance of PZT-based metal-insulator-metal (MIM) capacitors as a function of Pb precursor excess. Using surface-sensitive, quantitative X-ray photoelectron spectroscopy and scanning electron microscopy, we confirm the presence of ZrOx surface phase. Low Pb excess gives rise to a discontinuous layer of ZrOx on a (100) textured PZT film with a wide band gap reducing the capacitance of PZT-based MIMs whereas the breakdown field is enhanced. At high Pb excess, the nanostructures disappear while the PZT grain size increases and the film texture becomes (111). Concomitantly, the capacitance density is enhanced by 8.7%, and both the loss tangent and breakdown field are reduced by 20 and 25%, respectively. The role of the low permittivity, dielectric interface layer on capacitance and breakdown is discussed.
Coincidence timing of femtosecond optical pulses in an X-ray free electron laser
Authors: Sanchez-Gonzalez Alvaro , Johnson Allan S. , Fitzpatrick Ann , Hutchison Christopher D. M. , Fare Clyde , Cordon-Preciado Violeta , Dorlhiac Gabriel , Ferreira Josie L. , Morgan Rhodri M. , Marangos Jon P. , Owada Shigeki , Nakane Takanori , Tanaka Rie , Tono Kensuke , Iwata So , van Thor Jasper J.
Published: November 2017

Femtosecond resolution pump-probe experiments are now routinely carried out at X-ray Free Electron Lasers, enabled by the development of cross-correlation “time-tools” which correct the picosecond-level jitter between the optical and X-ray pulses. These tools provide very accurate, <10 fs, measurement of the relative arrival time, but do not provide a measure of the absolute coincidence time in the interaction. Cross-correlation experiments using transient reflectivity in a crystal are commonly used for this purpose, and to date no quantitative analysis of the accuracy or stability of absolute coincidence time determination has been performed. We have performed a quantitative analysis of coincidence timing at the SACLA facility through a cross-correlation of 100 ± 10 fs, 400 nm optical pulses with 7 fs, 10.5 keV X-ray pulses via transient reflectivity in a cerium-doped yttrium aluminum garnet crystal. We have modelled and fit the transient reflectivity, which required a convolution with a 226 ± 12 fs uncertainty that was believed to be dominated by X-ray and laser intensity fluctuations, or assuming an extinction depth of 13.3 μm greater than the literature value of 66.7 μm. Despite this, we are able to determine the absolute coincidence time to an accuracy of 30 fs. We discuss the physical contributions to the uncertainty of coincidence time determination, which may include an uncharacterised offset delay in the development of transient reflectivity, including cascading Auger decays, secondary ionisation and cooling processes. Additionally, we present measurements of the intrinsic short-term and long-term drifts between the X-rays and the optical laser timing from time-tool analysis, which is dominated by a thermal expansion of the 25 m optical path between tool and the interaction region, seen to be ∼60 fs over a period of 5 h.
Critical interventions in debates on the Arab revolutions: centring class
Authors: Salem Sara
Published: November 2017

Salem contrasts De Smet’s contribution to the debates on revolution and counter-revolution in Egypt with other important materialist readings of the uprisings. Echoing the centrality of class analysis employed in Gramsci on Tahrir, Salem challenges De Smet’s reading of the Nasserist period and situates Nasserism within a broader pattern of coeval political struggles in Africa.
What is the students’ interest in biology after the biology curriculum modification?
Authors: Čipková Elena , Karolčík Štefan , Dudová Natália , Nagyová Soňa
Published: November 2017

Decreasing interest in Science among students, confirmed by several investigations, calls for the need to revise the contents of the curricula for Science subjects, including Biology. Modern Biology curricula should not only contain key biological concepts but also provide a teacher with sufficient space to develop students’ competencies of scientific work and positive attitudes to Science. When preparing the curriculum, it is necessary to consider also students’ interest in selected curriculum topics and their benefit for everyday life. The objective of our research was to identify whether the performed transformation of the Biology curriculum for elementary schools increased the students’ interest in Biology and the contents thereof. We were also investigating students’ preferences in their interest in Biology topics and their interest in selected teaching methods and approaches. Our research confirmed the positive interest in Biology among majority of students who prefer direct, active participation in the process of knowledge acquisition through the study and exploration of living organisms as well as by the execution and assessment of practicals and experiments.
WASP family proteins and formins compete in pseudopod- and bleb-based migration
Authors: Davidson Andrew J. , Amato Clelia , Thomason Peter A. , Insall Robert H.
Published: November 2017

Actin pseudopods induced by SCAR/WAVE drive normal migration and chemotaxis in eukaryotic cells. Cells can also migrate using blebs, in which the edge is driven forward by hydrostatic pressure instead of actin. In Dictyostelium discoideum, loss of SCAR is compensated by WASP moving to the leading edge to generate morphologically normal pseudopods. Here we use an inducible double knockout to show that cells lacking both SCAR and WASP are unable to grow, make pseudopods or, unexpectedly, migrate using blebs. Remarkably, amounts and dynamics of actin polymerization are normal. Pseudopods are replaced in double SCAR/WASP mutants by aberrant filopods, induced by the formin dDia2. Further disruption of the gene for dDia2 restores cells’ ability to initiate blebs and thus migrate, though pseudopods are still lost. Triple knockout cells still contain near-normal F-actin levels. This work shows that SCAR, WASP, and dDia2 compete for actin. Loss of SCAR and WASP causes excessive dDia2 activity, maintaining F-actin levels but blocking pseudopod and bleb formation and migration.
Identifying functionally informative evolutionary sequence profiles
Authors: Gil Nelson , Fiser Andras
Published: November 2017

Motivation

Multiple sequence alignments (MSAs) can provide essential input to many bioinformatics applications, including protein structure prediction and functional annotation. However, the optimal selection of sequences to obtain biologically informative MSAs for such purposes is poorly explored, and has traditionally been performed manually.

Results

We present Selection of Alignment by Maximal Mutual Information (SAMMI), an automated, sequence-based approach to objectively select an optimal MSA from a large set of alternatives sampled from a general sequence database search. The hypothesis of this approach is that the mutual information among MSA columns will be maximal for those MSAs that contain the most diverse set possible of the most structurally and functionally homogeneous protein sequences. SAMMI was tested to select MSAs for functional site residue prediction by analysis of conservation patterns on a set of 435 proteins obtained from protein–ligand (peptides, nucleic acids and small substrates) and protein–protein interaction databases.

Availability and implementation

A freely accessible program, including source code, implementing SAMMI is available at https://github.com/nelsongil92/SAMMI.git.

Supplementary information

Supplementary data are available at Bioinformatics online.
Hormetic Effects of Carbendazim on the Virulence of Botrytis cinerea
Authors: Cong Menglong , He Shun , Ma Hongju , Li Guoqing , Zhu Fuxing
Published: November 2017

The ascomycete plant-pathogenic fungus Botrytis cinerea infects more than 1,400 plant species worldwide. Stimulatory effects of sublethal doses of fungicides on plant pathogens are of close relevance to disease management. In the present study, stimulatory effects of carbendazim on the virulence of B. cinerea to cucumber plants were investigated. Spraying carbendazim on cucumber plants at 3 to 200 μg/ml had stimulatory effects on the virulence of carbendazim-resistant isolates of B. cinerea and the maximum percent stimulations were 16.7 and 13.5% for isolates HBtom451 and HBstr491, respectively. Preconditioned mycelia (i.e., mycelia grown on potato dextrose agar [PDA] amended with carbendazim at concentrations of 10, 50, or 200 μg/ml) also showed increased virulence, and the maximum percent stimulations for isolates HBtom451 and HBstr491 were 7.9 and 9.5%, respectively. Compared with mycelia grown on PDA without carbendazim, virulence stimulation magnitudes of spraying carbendazim on leaves increased moderately but the concentrations of carbendazim that elicited the maximum stimulation increased 20- and 8-fold for preconditioned isolates HBtom451 and HBstr491, respectively. The time course of infection indicated that virulence stimulation was mediated by a direct stimulation mechanism. Studies of the physiological mechanism for stimulation demonstrated that carbendazim had no significant effects on tolerance to hydrogen peroxide, or on oxalic acid production in B. cinerea. These studies will deepen our understanding of quantitative features of hormetic effects of sublethal doses of fungicides on plant pathogens.
Quality of Life of Adult Survivors After Extra Corporeal Membrane Oxygenation (ECMO)
Authors: Galazzi Alessandro , Brambilla Alessandra , Grasselli Giacomo , Pesenti Antonio , Fumagalli Roberto , Lucchini Alberto
Published: November 2017

Introduction:

Extracorporeal Membrane Oxygenation (ECMO) is a technique used in the treatment of patients with severe respiratory failure. A lot of studies in the literature investigated the survival rate of patients treated with ECMO, but few are those that assess the long-term outcomes and the quality of life (QoL) of survivors.

Materials and Methods:

A retrospective observational study with prospective QoL assessment through administration of the questionnaire EuroQol-5 Dimension was conducted in acute respiratory distress syndrome patients who h ad ECMO as a rescue therapy for reversible refractory hypoxemia from January 2013 until December 2015 in an Italian referral ECMO center.

Results:

Forty patients were enrolled, but the telephone interview was possible only in 17. The interviewed patients presented a reduction in QoL in the items concerning pain (59%), followed by problems regarding mobility (47%) and anxiety (47%). The patients' perceived QoL, showed in a 0 to100 scale (0 being the worst, 100 being the best value), is of 75% (interquartile range, 70-80).

Discussion:

The problems found are in agreement with the literature about this particular type of patients.

Conclusion:

Most ECMO patients have good physical and social functioning after hospital discharge.
A Protective Eye Shield Reduces Limbal Strain and Its Variability During Simulated Sleep in Adults With Glaucoma
Authors: Flatau Alison , Solano Francisco , Jefferys Joan L. , Damion Christopher , Quigley Harry A.
Published: November 2017

Purpose:

To determine the effect of wearing a protective eye shield (mask) on limbal strain magnitude and variability in glaucoma eyes when sleeping with 1 side of the face down (FD) against a pillow.

Methods:

A prospective, randomized, interventional trial was conducted at the Wilmer Eye Institute with 36 glaucoma patients. A contact lens sensor measured limbal strain (output in equivalent millivolts) during intervals of up to 60 minutes in lateral decubitus, FD, and supine positions. Eighteen subjects wore a mask during 1 of 2 FD intervals, with randomized assignment of the interval. Data from additional trials with no mask were included in some analyses. In addition, some facial-feature dimensions from 3D scanned images of 23 subjects were compared with limbal strain data.

Results:

Wearing a mask trends toward a reduced mean change in contact lens sensor output (limbal strain) on moving to a FD positions [+34.1 mVeq, P=0.01 reduced by −22.3 mVeq, P=0.09 (n=36)]. Mask wearing reduced variability in strain while FD [−22.8 mVeq, P=0.04 (n=18)]. In eyes with past progressive visual field loss, the effect of the mask reduced mean strain change when moving to FD [−44.8 mVeq, P=0.02 (n=31)]. Longer corneal apex to nose-tip and to temple lengths were associated with reduced variability while FD [P=0.02 and 0.04, respectively (n=23)]. Treating both lengths as confounding factors increased statistical significance, particularly for analysis of the no-mask change in strain data moving to and from the FD position [P=0.004 to 0.002 and P=0.03 to 0.01 (n=23)].

Conclusion and Relevance:

Wearing a mask reduced limbal strain and variation in limbal strain during simulated FD sleep, particularly in eyes with past field worsening, as did some facial features.
Relationship Between Open-angle Glaucoma and Stroke: A 2010 to 2012 Korea National Health and Nutrition Examination Survey
Authors: Lee Won June , Jeoung Jin Wook , Na Kyeong Ik , Kim Young Kook , Kim Chan Yun , Park Ki Ho
Published: November 2017

Purpose:

To determine the relationship between open-angle glaucoma (OAG) and stroke in the Korean population.

Materials and Methods:

This study was a population-based, cross-sectional study that used data from the Korea National Health and Nutrition Examination Survey (KNHANES), a complex, stratified, multistage, probability-cluster survey. We analyzed a total of 11,959 participants who were above 40 years old and were included in the fifth KNHANES database (2010 to 2012 data). Weighted prevalence of OAG and stroke in various populations were estimated. Univariate and multivariate logistic regressions were performed to examine potential risk factors for stroke, including OAG. Multivariate adjusted odds ratios (OR) for stroke were examined in subjects with and without OAG. Subjects were also examined by hypertension and diabetes status.

Results:

Stroke patients had a significantly higher OAG prevalence (8.5%) than nonstroke patients (3.8%; P<0.001). After adjusting for selected risk factors, the presence of OAG tended to be associated with stroke (adjusted OR=1.629), but this result was not statistically significant (P=0.053). Stroke and OAG were significantly associated with each other in subjects with hypertension (OR=2.059; P=0.010) and diabetes (OR=2.649; P=0.040). In addition, the associations of stroke and other systemic diseases were stronger when OAG was a comorbid condition.

Conclusions:

Although there was no overall statistical significance, patients with OAG had an increased risk of stroke, among those with systemic comorbidities, including hypertension and diabetes. Our results may provide insight on the underlying mechanisms of OAG and their association with stroke development.
Concerns of Anophthalmic Patients Wearing Cryolite Glass Prosthetic Eyes
Authors: Rokohl Alexander C. , Koch Konrad R. , Trester Marc , Trester Wolfgang , Pine Keith R. , Heindl Ludwig M.
Published: November 2017

Purpose:

To identify the main concerns of patients experienced in wearing cryolite glass prosthetic eyes and to investigate how these have changed over time.

Methods:

One hundred six patients experienced in wearing prosthetic eyes for at least 2 years were asked to complete an anonymous questionnaire regarding prosthetic eye concerns at the time of initial eye loss and at the present time. Main outcome measures included changes in levels of concern over time.

Results:

Initially, the participants were mainly concerned about their appearance, health of the fellow eye, and coping with monocularity. Over time, there was a significant increase of the level of concern regarding the health of the remaining eye (p < 0.001) and regarding watering, crusting, and discharge (p < 0.001). Loss of balance did not change significantly (p = 0.302). All other concerns decreased significantly over time (p < 0.001), with levels of concern about appearance decreasing the most. The current leading concern was the health of the remaining eye followed by concerns about watering, crusting, and discharge. Length of time since natural eye loss was the most important explanatory variable, with significant impact on the concerns about appearance (p = 0.013), retention of the prosthetic eye (p = 0.002), and eyelid contour (p = 0.004).

Conclusions:

Health of the remaining eye is the most common current concern of anophthalmic patients, acknowledging the need of good ophthalmologic follow up after losing an eye. The second most important concern is with watering, crusting, and discharge, suggesting further research for establishing an evidence-based protocol for cryolite glass prosthetic eye maintenance and supportive treatment.
Polycythemia vera and essential thrombocythemia: algorithmic approach
Authors: Vannucchi Alessandro M. , Guglielmelli Paola , Tefferi Ayalew
Published: November 2017

Purpose of review

To describe an algorithm-based approach, whenever available, to the diagnosis, the risk stratification criteria informing therapy and the current management of polycythemia vera and essential thrombocythemia.

Recent findings

Description of recurrent genetic abnormalities in driver genes, including Janus Kinase 2 (JAK2), myeloproliferative leukemia and calreticulin, a better appreciation of the key diagnostic role of bone marrow features, results of large epidemiologic studies and a few but landmark controlled clinical trials produced in the last decade, all resulted in a reappraisal of the approach to polycythemia vera and essential thrombocythemia.

The revised 2017 WHO classification of polycythemia vera and essential thrombocythemia allows early diagnosis and accurate distinction from other chronic myeloproliferative neoplasms, particulary prefibrotic myelofibrosis. The prognostic value of selected mutations is being appreciated and JAK2V617F mutation is currently incorporated as risk variable in prognostic system for essential thrombocythemia. Risk-adjusted stratification is used to select therapeutic approaches that include target agents. However, there is not yet a curative approach to these hematologic neoplasms, and although their management has much improved in the last decades, the associated morbidity and mortality remains significant and may be worsened by toxicities of therapeutic agents. Therefore, several clinically relevant endpoints remain unmet.
Assessing the Gene Regulatory Landscape in 1,188 Human Tumors
Authors: Calabrese C , Lehmann K , Urban L , Liu F , Erkek S , Fonseca NA , Kahles A , Kilpinen H , Markowski J ,   PCAWG Group 3, Waszak SM , Korbel JO , Zhang Z , Brazma A , Rätsch G , Schwarz RF , Stegle O
Published: November 2017

Cancer is characterised by somatic genetic variation, but the effect of the majority of non-coding somatic variants and the interface with the germline genome are still unknown. We analysed the whole genome and RNA-Seq data from 1,188 human cancer patients as provided by the Pan-cancer Analysis of Whole Genomes (PCAWG) project to map cis expression quantitative trait loci of somatic and germline variation and to uncover the causes of allele-specific expression patterns in human cancers. The availability of the first large-scale dataset with both whole genome and gene expression data enabled us to uncover the effects of the non-coding variation on cancer. In addition to confirming known regulatory effects, we identified novel associations between somatic variation and expression dysregulation, in particular in distal regulatory elements. Finally, we uncovered links between somatic mutational signatures and gene expression changes, including TERT and LMO2, and we explained the inherited risk factors in APOBEC-related mutational processes. This work represents the first large-scale assessment of the effects of both germline and somatic genetic variation on gene expression in cancer and creates a valuable resource cataloguing these effects.
Collapse and rescue of cooperation in evolving dynamic networks
Authors: Akçay Erol
Published: November 2017

The evolutionary dynamics of social traits depend crucially on the social structure of a population, i.e., who interacts with whom. A large body of work studies the effect of social structure on behaviors such as cooperation, but relatively little is known about how social structure itself coevolves with social traits. Here, I use a simple yet realistic model of within-group social structure to study such coevolution. In this model, social connections are either inherited from a parent or made with random individuals. My model shows cooperation can evolve when individuals make few random connections, but the presence of cooperation selects for increased rates of random connections, which leads to the collapse of cooperation. Inherent costs of social connections can prevent this negative feedback, but the more beneficial cooperation is, the higher linking costs have to be maintain it, and linking costs can negate some or all of the aggregate benefits of cooperation. Exogenously maintained social inheritance can mitigate the latter problem and allow cooperation to persist and increase the average fitness of a population. These results illustrate how coevolutionary dynamics can constrain the long-term persistence of cooperation.