bluuebunny/crossref_metadata_2025 huggingface dataset:
Benchmarking of flux-driven full-F gyrokinetic simulations
Authors: Asahi Yuuichi , Grandgirard Virginie , Idomura Yasuhiro , Garbet Xavier , Latu Guillaume , Sarazin Yanick , Dif-Pradalier Guilhem , Donnel Peter , Ehrlacher Charles
Published: October 2017

Two full-F global gyrokinetic codes are benchmarked to compute flux-driven ion temperature gradient (ITG) turbulence in tokamak plasmas. For this purpose, the Semi-Lagrangian code GYrokinetic SEmi-LAgrangian and the Eulerian code GT5D are employed, which solve the full-F gyrokinetic equation with a realistic fixed flux condition. The equilibrium poloidal flow profile formation processes are benchmarked and compared against the local neoclassical theory. The simulations above are carried out without turbulence, which agree well with each other and with the theoretical estimates. Here, a lot of attention has been paid to the boundary conditions, which have huge impacts on the global shape of radial electric field. The behaviors of micro-instabilities are benchmarked for linear and nonlinear cases without a heat source, where we found good agreements in the linear growth rates and nonlinear critical gradient level. In the nonlinear case, initial conditions are chosen to be identical since they dominate the transient turbulence behavior. Using the appropriate settings for the boundary and initial conditions obtained in the benchmarks above, a flux-driven ITG turbulence simulation is carried out. The avalanche-like transport is assessed with a focus on spatio-temporal properties. A statistical analysis is performed to discuss this self-organized criticality (SOC) like behaviors, where we found a 1/f spectra and a transition to 1/f3 spectra at high-frequency side in both codes. Based on these benchmarks, it is verified that the SOC-like behavior is robust and not dependent on numerics.
A numerical model of acoustic wave caused by a single positive corona source
Authors: Zhang Bo , Li Zhen , He Jinliang
Published: October 2017

Audible noise accompanies corona discharge, which is one of the most important electromagnetic environment issues of high voltage transmission lines. Most of the studies on the audible noise generated by corona discharge focused on statistical analysis of the experimental results and a series of empirical formulas were derived to predict the audible noise. However, few of them interpreted the generating mechanism of the audible noise. Sound wave in the air is actually the fluctuation of the air, which lead to the hypothesis that the sound wave is generated by the interaction of the charged particles and the air molecules in the discharge progress. To validate this hypothesis, experiments were carried out in this paper to study the relationship between the audible noise and the corona current, including the correlation both in time domain and in frequency domain. Based on the experimental results, the fluid equations of the particles in the air were introduced to study the interactions among the electrons, ions, and neutral molecules in the discharge, and a numerical model for the amplitude of corona acoustic emission was developed and validated.
Nanoscale insight into the giant piezoelectric response in lead-free Fe-doped 0.95(Na1/2Bi1/2)TiO3-0.05BaTiO3 single crystal
Authors: Xue Saidong , Ma Jinpeng , Zhao Xiangyong , Wang Feifei , Sun Dazhi , Wang Tao , Shi Wangzhou , Fu Zhengqian , Zhou Huifang , Luo Haosu
Published: October 2017

The Fe-doped lead-free 0.95(Na1/2Bi1/2)TiO3-0.05BaTiO3 single crystal, reported in the previous work, which exhibited giant piezoelectric strain response (normalized strain constant up to ∼1300 pm/V) and a large quasi-static piezoelectric constant d33 of ∼600 pC/N, was investigated here with the emphasis on the domain structure so as to understand the nanoscale mechanism responsible for the giant strain response. Based on in-plane and out-of-plane piezoresponse force microscopy, it was found that Fe ion doping induced domain evolution from macrodomains of several micrometers to nanodomains of tens of nanometers. High-resolution transmission electron microscopy was adopted to give an insight into the fine domain structure after Fe doping. The domain evolution under an in situ electric field was further studied, and the results indicated that the giant strain response originated not only from the polarization rotation around the morphotropic phase boundary but also from the domain contribution.
Hybrid laminated Timoshenko beam
Authors: Raposo C. A. , Villagrán O. V. , Muñoz Rivera J. E. , Alves M. S.
Published: October 2017

We consider the hybrid laminated Timoshenko beam model. This structure is given by two identical layers uniform on top of each other, taking into account that an adhesive of small thickness is bonding the two surfaces and produces an interfacial slip. We suppose that the beam is fastened securely on the left while on the right it’s free and has an attached container. Using the semigroup approach and a result of Borichev and Tomilov, we prove that the solution is polynomially stable.
Tuning chemical potential in the dirac cone by compositional engineering
Authors: Gopal R. K. , Singh Sourabh , Sarkar Jit , Mitra Chiranjib
Published: October 2017

To realize fully topological transport for any device applications it is essential to tune the chemical potential in the bulk gap of the Dirac cone. Bi2Se3 (BS) and Bi2Te3 (BT) thin films do not show in general topological transport as the chemical potential doesn’t lie entirely in the bulk gap. We report the successful formation of bulk insulating ternary topological insulators Bi2Se2Te (BST) by double target pulsed laser deposition technique. The films were deposited with sequential ablation of separate BS and BT targets. From the X-ray diffraction analysis and temperature dependent resistivity, we were able to conclude that the as-grown thin films have ordered chalcogen layers and the chemical potential in these thin films lie in the bulk gap. We have been able to achieve this fully topological transport in our sample grown by this technique. Our Magnetotransport data exhibits pronounced two-dimensional weak-antilocalization behavior (WAL) at low temperatures. It was possible to tune the chemical potential at will in the gap by depositing thin films through pulsed laser deposition technique using this simple and cost effective double target approach to grow quaternary TI thin films.
A multi-purpose reaction cell for the investigation of reactions under solvothermal conditions
Authors: Heidenreich N. , Rütt U. , Köppen M. , Inge A. Ken , Beier S. , Dippel A.-C. , Suren R. , Stock N.
Published: October 2017

A new versatile and easy-to-use remote-controlled reactor setup aimed at the analysis of chemical reactions under solvothermal conditions has been constructed. The reactor includes a heating system that can precisely control the temperature inside the reaction vessels in a range between ambient temperature and 180 °C. As reaction vessels, two sizes of commercially available borosilicate vessels (Vmax = 5 and 11 ml) can be used. The setup furthermore includes the option of stirring and injecting of up to two liquid additives or one solid during the reaction to initiate very fast reactions, quench reactions, or alter chemical parameters. In addition to a detailed description of the general setup and its functionality, three examples of studies conducted using this setup are presented.
Rarefaction cloaking: Influence of the fractal rough surface in gas slider bearings
Authors: Su Wei , Liu Haihu , Zhang Yonghao , Wu Lei
Published: October 2017

For ultra-thin gas lubrication, the surface-to-volume ratio increases dramatically when the flow geometry is scaled down to the micro/nano-meter scale, where surface roughness, albeit small, may play an important role in gas slider bearings. However, the effect of surface roughness on the pressure and load capacity (force) in gas slider bearings has been overlooked. In this paper, on the basis of the generalized Reynolds equation, we investigate the behavior of a gas slider bearing, where the roughness of the slider surface is characterized by the Weierstrass-Mandelbrot fractal function, and the mass flow rates of Couette and Poiseuille flows are obtained by deterministic solutions to the linearized Bhatnager-Gross-Krook equation. Our results show that the surface roughness reduces the local mass flow rate as compared to the smooth channel, but the amount of reduction varies for Couette and Poiseuille flows of different Knudsen numbers. As a consequence, the pressure rise and load capacity in the rough bearing become larger than the ones in the smooth bearing in the slip and early transition flow regimes, e.g., a 6% roughness could lead to an increase of 20% more bearing load capacity. However, this situation is reversed in the free-molecular flow regime, as the ratio of the mass flow rates between Couette and Poiseuille flows is smaller than that in the smooth channel. Interestingly, between the two extremes, we have found a novel “rarefaction cloaking” effect, where the load capacity of a rough bearing equals to that of a smooth bearing at a certain range of Knudsen numbers, as if the roughness does not exist.
Examining transition metal hydrosulfides: The pure rotational spectrum of ZnSH (X̃2A′)
Authors: Bucchino M. P. , Adande G. R. , Halfen D. T. , Ziurys L. M.
Published: October 2017

The pure rotational spectrum of the ZnSH (X̃2A′) radical has been measured using millimeter-wave direct absorption and Fourier transform microwave (FTMW) methods across the frequency range 18–468 GHz. This work is the first gas-phase detection of ZnSH by any spectroscopic technique. Spectra of the 66ZnSH, 68ZnSH, and 64ZnSD isotopologues were also recorded. In the mm-wave study, ZnSH was synthesized in a DC discharge by the reaction of zinc vapor, generated by a Broida-type oven, with H2S; for FTMW measurements, the radical was made in a supersonic jet expansion by the same reactants but utilizing a discharge-assisted laser ablation source. Between 7 and 9 rotational transitions were recorded for each isotopologue. Asymmetry components with Ka = 0 through 6 were typically measured in the mm-wave region, each split into spin-rotation doublets. In the FTMW spectra, hyperfine interactions were also resolved, arising from the hydrogen or deuterium nuclear spins of I = 1/2 or I = 1, respectively. The data were analyzed using an asymmetric top Hamiltonian, and rotational, spin-rotation, and magnetic hyperfine parameters were determined for ZnSH, as well as the quadrupole coupling constant for ZnSD. The observed spectra clearly indicate that ZnSH has a bent geometry. The rm(1) structure was determined to be rZn–S = 2.213(5) Å, rS–H = 1.351(3) Å, and θZn–S–H = 90.6(1)°, suggesting that the bonding occurs primarily through sulfur p orbitals, analogous to H2S. The hyperfine constants indicate that the unpaired electron in ZnSH primarily resides on the zinc nucleus.
Highly coherent visible dispersive wave radiation in suspended core fibers
Authors: Bi Wanjun , Liao Meisong , Liu Yinyao , Wu Dakun , Li Xia , Fang Yongzheng , Zhao Guoying , Li Yigui , Wang Meng , Zhang Longping , Gao Weiqing , Hu Lili
Published: October 2017

Visible dispersive wave (DW) generation is used in several applications, such as in dispersion measurements, fluorescence microscopy, and biomedicine. The effects of fiber characteristics, pump pulse width, and average pump power on DW generation are investigated in suspended core fiber (SCF) by numerical simulation. The coherence of visible DW is high in all cases. The dynamics behind DW generation are analyzed based on pulse evolution spectrograms. Energy exchange between DW and soliton occurs mainly in the first contraction of the first emitted soliton. Numerical simulations using experimental parameters indicate that the DW can be compressed down to approximately 40 fs. In experiments, under the pump pulse with a pulse width of 50 fs and pump wavelength of 1 μm, an isolated DW is generated at ∼480 nm in SCF1 featuring a large fiber core. Under the same pump conditions, isolated DWs at ∼466 nm and ∼485 nm with full width at half maximum of ∼40 nm and conversion efficiency of ∼10% are achieved in SCF2 with a small fiber core. The coherence of DW is better than that of the infrared component based on the comparisons of the pulse trains of DW and the infrared component in supercontinuum. The influence of OH− content on DW generation is also experimentally analyzed.
Heavy and light hole minority carrier transport properties in low-doped n-InGaAs lattice matched to InP
Authors: Walker Alexandre W. , Denhoff Mike W.
Published: October 2017

Minority carrier diffusion lengths in low-doped n-InGaAs using InP/InGaAs double-heterostructures are reported using a simple electrical technique. The contributions from heavy and light holes are also extracted using this methodology, including minority carrier mobilities and lifetimes. Heavy holes are shown to initially dominate the transport due to their higher valence band density of states, but at large diffusion distances, the light holes begin to dominate due to their larger diffusion length. It is found that heavy holes have a diffusion length of 54.5 ± 0.6 μm for an n-InGaAs doping of 8.4 × 1015 cm–3 at room temperature, whereas light holes have a diffusion length in excess of 140 μm. Heavy holes demonstrate a mobility of 692 ± 63 cm2/Vs and a lifetime of 1.7 ± 0.2 μs, whereas light holes demonstrate a mobility of 6200 ± 960 cm–2/Vs and a slightly longer lifetime of 2.6 ± 1.0 μs. The presented method, which is limited to low injection conditions, is capable of accurately resolving minority carrier transport properties.
Communication: Is a coarse-grained model for water sufficient to compute Kapitza conductance on non-polar surfaces?
Authors: Ardham Vikram Reddy , Leroy Frédéric
Published: October 2017

Coarse-grained models have increasingly been used in large-scale particle-based simulations. However, due to their lack of degrees of freedom, it is a priori unlikely that they straightforwardly represent thermal properties with the same accuracy as their atomistic counterparts. We take a first step in addressing the impact of liquid coarse-graining on interfacial heat conduction by showing that an atomistic and a coarse-grained model of water may yield similar values of the Kapitza conductance on few-layer graphene with interactions ranging from hydrophobic to mildly hydrophilic. By design the water models employed yield similar liquid layer structures on the graphene surfaces. Moreover, they share common vibration properties close to the surfaces and thus couple with the vibrations of graphene in a similar way. These common properties explain why they yield similar Kapitza conductance values despite their bulk thermal conductivity differing by more than a factor of two.
Single atom imaging with an sCMOS camera
Authors: Picken C. J. , Legaie R. , Pritchard J. D.
Published: October 2017

Single atom imaging requires discrimination of weak photon count events above the background and has typically been performed using electron-multiplying charge-coupled device cameras, photomultiplier tubes, or single photon counting modules. A scientific complementary metal-oxide semiconductor (sCMOS) provides a cost effective and highly scalable alternative to other single atom imaging technologies, offering fast readout and larger sensor dimensions. We demonstrate single atom resolved imaging of two site-addressable optical traps separated by 10 μm using an sCMOS camera, offering a competitive signal-to-noise ratio at intermediate count rates to allow high fidelity readout discrimination (error <10−6) and sub-μm spatial resolution for applications in quantum technologies.
Advanced MOKE magnetometry in wide-field Kerr-microscopy
Authors: Soldatov I. V. , Schäfer R.
Published: October 2017

The measurement of MOKE (Magneto-Optical Kerr Effect) magnetization loops in a wide-field Kerr microscope offers the advantage that the relevant domain images along the loop can be readily recorded. As the microscope's objective lens is exposed to the magnetic field, the loops are usually strongly distorted by non-linear Faraday rotations of the polarized light that occur in the objective lens and that are superimposed to the MOKE signal. In this paper, an experimental method, based on a motorized analyzer, is introduced which allows to compensate the Faraday contributions, thus leading to pure MOKE loops. A wide field Kerr microscope, equipped with this technology, works well as a laser-based MOKE magnetometer, additionally offering domain images and thus providing the basis for loop interpretation.
Light, flexible carbon nanotube antennas with copper-like performance
Authors: Kim Mark H.
Published: October 2017

Building on a 2013 breakthrough, researchers manufacture carbon nanotube antennas with high radiation efficiency.
A hybrid method for accurate star tracking using star sensor and gyros
Authors: Lu Jiazhen , Yang Lie , Zhang Hao
Published: October 2017

Star tracking is the primary operating mode of star sensors. To improve tracking accuracy and efficiency, a hybrid method using a star sensor and gyroscopes is proposed in this study. In this method, the dynamic conditions of an aircraft are determined first by the estimated angular acceleration. Under low dynamic conditions, the star sensor is used to measure the star vector and the vector difference method is adopted to estimate the current angular velocity. Under high dynamic conditions, the angular velocity is obtained by the calibrated gyros. The star position is predicted based on the estimated angular velocity and calibrated gyros using the star vector measurements. The results of the semi-physical experiment show that this hybrid method is accurate and feasible. In contrast with the star vector difference and gyro-assisted methods, the star position prediction result of the hybrid method is verified to be more accurate in two different cases under the given random noise of the star centroid.
Quantum dots suppress electron scattering resonances in graphene
Authors: Dowd Deborah
Published: October 2017

Nanopatterning with quantum dots holds promise as a tool for tuning optoelectronic properties of graphene-like two-dimensional materials.
Response of demersal fish assemblages to an extreme flood event in a freshwater-deprived estuary in South Africa
Authors: Nodo P. , James N. C. , Childs A.-R. , Nakin M. D. V.
Published: October 2017

The Kariega Estuary in South Africa, is an example of a freshwater-deprived estuary. Large-scale water abstraction and droughts have resulted in this estuary either being uniformly marine or hypersaline. A major episodic flood event in October 2012, the largest ever recorded in this system, provided us with an opportunity to investigate the prolonged effect of an episodic flood on the demersal fish assemblage of a freshwater-deprived estuary. A beam trawl net was used for sampling the fish assemblages from December 2013 to November 2014. The flood event before the sampling period ‘reset’ the system, such that there was a longitudinal salinity gradient from the head to the mouth, which resulted in ‘normal’ estuarine conditions, typical of most estuaries. There was an increase in the abundance of benthopelagic marine migrant species, particularly early juveniles of important fishery species, in the middle and upper reaches during the present study relative to previous studies conducted in this freshwater-deprived system. This suggests increased recruitment of these species into their estuarine nursery habitat. The present study highlights the importance of understanding the effect of freshwater inflow on the demersal estuarine fish assemblage and the nursery role of this and other estuarine systems and their management.
Inferring phase diagrams from X-ray data with background signals using graph segmentation
Authors: Li Shaobo , Xiong Zheng , Hu Jianjun
Published: October 2017

Automated composition-structure-processing phase diagram creation is critical for high-throughput experimental material studies. In particular, diffractogram datasets with large background signals are especially difficult to identify the phase regions. In this work, we proposed a novel graph segmentation algorithm from computer vision to solve the phase diagram prediction problem from X-ray diffraction data with large background signals. We introduced a novel background subtraction algorithm with graph-based clustering/segmentation to build the BGPhase algorithm. Experiments on three datasets with the Al–Cu–Mo material family showed that our phase attribution algorithm can achieve high prediction accuracy ranging from 88.6 to 94.8% or with MCC scores ranging from 0.715 to 0.890. The algorithm can be accessed online at http://mleg.cse.sc.edu/bgphase .
Modulation of microstructure and magnetic properties of Sr-doped CdO films
Authors: Antosoly D. , Ilangovan S. , Nagarethinam V. S. , Balu A. R.
Published: October 2017

Pure and Sr2+-doped CdO (SCO) thin films were deposited on glass substrates by the spray technique using perfume atomiser. The effect of Sr doping concentration on the structural, morphological, optical and magnetic properties was studied and the results obtained are reported in this paper. Pure and Sr-doped CdO thin films exhibit a strong (1 1 1) preferential growth. Nanosized grains are evinced from the TEM images for all the samples. Increased transparency and band gap bowing are observed for the doped films. All the films have an electrical resistivity in the order of 10−2 ohm cm. Photoluminescence studies confirm the presence of intrinsic defects on the films. Defects mediated ferromagnetic behaviour is observed for the doped films. The obtained results infer that Sr doping strongly influenced the physical properties of spray deposited CdO thin films.
Demographics and Interstate Management Implications for Flathead Catfish in the Lower Wabash River, Illinois and Indiana
Authors: Moody-Carpenter Cassi J. , Sass Greg G. , Frankland Leslie D. , Bollinger Eric K. , Colombo Robert E.
Published: October 2017

Flathead Catfish Pylodictis olivaris in the lower Wabash River, Illinois and Indiana, are currently exploited by anglers and commercial fishers under the same fishing regulation; however, the regulations differed between the states prior to 2015. We assessed demographics of Flathead Catfish in this interstate river to gain baseline information to create models to test for sustainable exploitation rates under the new regulation and several hypothetical scenarios. During 2010–2012, we sampled 951 Flathead Catfish (length = 343 ± 5.6 mm [mean ± SE], weight = 914.5 ± 55.6 g, age = 3.5 ± 0.07 years) using pulsed-DC electrofishing, AC electrofishing, commercial harvest, and hoop nets. Mean relative weight of Flathead Catfish was greater than 100%, and proportional size distribution indices (electrofishing = 35, hoop netting = 54) suggested a quality fishery. Total annual mortality (electrofishing = 0.48, hoop netting = 0.54) was similar to estimates in other Midwestern rivers. Yield-per-recruit models predicted that growth overfishing may occur over time under the current regulation; however, demographic metrics relate to recreational and commercial creel assessments. Our results suggest that the current minimum length limit could be raised to increase yield and reduce exploitation. Our findings also demonstrate several useful field and modeling techniques to assess catfish (family Ictaluridae) populations in environments that are difficult to sample and that lack fishery-independent information.

Received January 11, 2017; accepted August 31, 2017 Published online October 20, 2017
Type I interferon enhances necroptosis of Salmonella Typhimurium–infected macrophages by impairing antioxidative stress responses
Authors: Hos Nina Judith , Ganesan Raja , Gutiérrez Saray , Hos Deniz , Klimek Jennifer , Abdullah Zeinab , Krönke Martin , Robinson Nirmal
Published: October 2017

Salmonella enterica serovar Typhimurium exploits the host’s type I interferon (IFN-I) response to induce receptor-interacting protein (RIP) kinase–mediated necroptosis in macrophages. However, the events that drive necroptosis execution downstream of IFN-I and RIP signaling remain elusive. In this study, we demonstrate that S. Typhimurium infection causes IFN-I–mediated up-regulation of the mitochondrial phosphatase Pgam5 through RIP3. Pgam5 subsequently interacts with Nrf2, which sequesters Nrf2 in the cytosol, thereby repressing the transcription of Nrf2-dependent antioxidative genes. The impaired ability to respond to S. Typhimurium–induced oxidative stress results in reactive oxygen species–mediated mitochondrial damage, energy depletion, transient induction of autophagy, and autophagic degradation of p62. Reduced p62 levels impair interaction of p62 with Keap1, which further decreases Nrf2 function and antioxidative responses to S. Typhimurium infection, eventually leading to cell death. Collectively, we identify impaired Nrf2-dependent redox homeostasis as an important mechanism that promotes cell death downstream of IFN-I and RIP3 signaling in S. Typhimurium–infected macrophages.
DEEPre: sequence-based enzyme EC number prediction by deep learning
Authors: Li Yu , Wang Sheng , Umarov Ramzan , Xie Bingqing , Fan Ming , Li Lihua , Gao Xin
Published: October 2017

Motivation

Annotation of enzyme function has a broad range of applications, such as metagenomics, industrial biotechnology, and diagnosis of enzyme deficiency-caused diseases. However, the time and resource required make it prohibitively expensive to experimentally determine the function of every enzyme. Therefore, computational enzyme function prediction has become increasingly important. In this paper, we develop such an approach, determining the enzyme function by predicting the Enzyme Commission number.

Results

We propose an end-to-end feature selection and classification model training approach, as well as an automatic and robust feature dimensionality uniformization method, DEEPre, in the field of enzyme function prediction. Instead of extracting manually crafted features from enzyme sequences, our model takes the raw sequence encoding as inputs, extracting convolutional and sequential features from the raw encoding based on the classification result to directly improve the prediction performance. The thorough cross-fold validation experiments conducted on two large-scale datasets show that DEEPre improves the prediction performance over the previous state-of-the-art methods. In addition, our server outperforms five other servers in determining the main class of enzymes on a separate low-homology dataset. Two case studies demonstrate DEEPre’s ability to capture the functional difference of enzyme isoforms.

Availability and implementation

The server could be accessed freely at http://www.cbrc.kaust.edu.sa/DEEPre.

Supplementary information

Supplementary data are available at Bioinformatics online.
Policing Football Fans in Switzerland—A Case Study Involving Fans, Stadium Security Employees, and Police Officers
Authors: Brechbühl Alain , Schumacher Dimech Annemarie , Seiler Roland
Published: October 2017

This article presents an analysis of the intergroup dynamics leading to violence between ultra football fans and stadium security employees and between these fans and police forces at a Swiss premier league football match. Twelve narrative interviews with these three stakeholders were conducted and analysed using Interpretative Phenomenological Analysis. The findings further support the applicability of the Elaborated Social Identity Model (ESIM) of crowd behaviour. The fans’ perceptions of the out-group behaviour’s illegitimacy led to a vicious circle of negative group interactions. Specifically, behaviours perceived as provocative seemed to lead to violence escalation. However, the escalation dynamics could only be understood in the context of the power dynamics between the different groups involved. We recommend more proactive forms of crowd management to facilitate positive group interactions and to avoid ‘us against them’ attitudes.
Transition to Cancer Survivorship
Authors: Wood Sylvia K.
Published: October 2017

Transition to cancer survivorship is frequent lexicon denoting the posttreatment phase of cancer treatment. The concept of being in transition to survivorship is not well defined. To critically analyze this concept, data sources (n = 63) (from 1985 to 2016) from nursing, sociology, medicine, and psychology were evaluated employing Rodgers evolutionary method. Transition to cancer survivorship is a turning point with a variable time period one passes through after treatment. It is an individualized experience with degrees of liminality, changes, and challenging consequences. Understanding this concept helps identify patient needs for targeted nursing interventions that can bridge safe passage to cancer survivorship.
Histologic Status of Squamous Cell Carcinoma In Situ After Diagnostic Biopsy in Immunocompetent and Immunosuppressed Patients
Authors: Moioli Eduardo K. , Hsieh Clifford , Tisch Angela , Bolotin Diana
Published: October 2017

BACKGROUND

The histologic status of squamous cell carcinoma in situ (SCC-IS) after diagnostic biopsy has not been well described or compared between immunocompetent and immunosuppressed patients. Expression of immunohistochemical (IHC) markers of aggressive SCC has not been compared between SCC-IS that clears or becomes invasive after biopsy.

OBJECTIVE

To determine the histologic status of SCC-IS after diagnostic biopsy in these populations.

METHODS

Retrospective analysis of 129 patients with SCC-IS treated with excision and 55 patients treated with Mohs surgery. Histologic features of SCC in excised tissue after biopsy were recorded. Known SCC markers were evaluated using IHC.

RESULTS

Invasive SCC was found in 3% to 16% of residual SCC-IS depending on surgical treatment modality. The history of skin cancer increased the odds of having invasive SCC in SCC-IS excisions (odds ratio 7.1, p < .05). Forty-seven percent of SCC-IS in immunosuppressed patients cleared after diagnostic biopsy compared with 70% in immunocompetent patients (p < .05). Inflammatory infiltrate and molecular markers of aggressive SCCs (Ki-67, matrix metalloproteinase [MMP]-9, MMP-7, transforming growth factor-beta (TGFβ)-RI, TGFβ-RII, and Sox-2) were not predictive of residual or invasive SCC at the time of treatment.

CONCLUSION

Up to 16% of SCC-IS showed invasive SCC at the time of surgical treatment. Immunosuppressed patients are more likely to have residual disease after biopsy. IHC markers of invasive SCC may not predict invasion.
Management of Incompletely Excised Skin Tumors: Our Experience
Authors: Robertson Bernard F. , Wokes James E.T. , Siddiqui Haroon
Published: October 2017

BACKGROUND

Current British Association of Dermatologists guidelines recommend that Mohs micrographic surgery should be considered for incompletely excised basal cell carcinomas and squamous cell carcinomas. Units that perform Mohs surgery are limited. In Teesside, the skin cancer multidisciplinary team discusses all incompletely excised skin tumors, considers all treatment options, provides recommendations, and initiates the agreed management plan.

OBJECTIVE

To assess the outcome and appropriateness of local surgical macroexcision for incompletely excised skin tumors.

METHODS

The authors performed a retrospective analysis of the local skin multidisciplinary team notes from July 2010 to July 2012 identifying all incompletely excised skin cancers. A total of 46 basal cell carcinomas and 27 squamous cell carcinomas were incompletely excised. Case note and pathology report review was used to identify the recommended management option and subsequent outcome.

RESULTS

Fifty-four of the 73 incompletely excised tumor identified underwent further surgical excision locally. Fifty-one of 54 patients (94.4%) had successful completion of excision with a single procedure. The remaining 3 patients' required further surgery, performed locally, to completely excise their tumor. Average follow-up was 35 months with 1 (1.9%) recurrence.

CONCLUSION

In the authors' region, local surgical management of incompletely excised skin tumors has yielded results comparable to Mohs surgery. Mohs surgery remains a viable option in specific cases.
Evaluation of Human Corneal Lenticule Quality After SMILE With Different Cap Thicknesses Using Scanning Electron Microscopy
Authors: Weng Shengbei , Liu Manli , Yang Xiaonan , Liu Fang , Zhou Yugui , Lin Haiqin , Liu Quan
Published: October 2017

Purpose:

To evaluate the surface characteristics of lenticules created by small-incision lenticule extraction (SMILE) with different cap thicknesses.

Methods:

This prospective study included 20 consecutive patients who underwent bilateral SMILE. Surface regularity of the extracted corneal lenticule was analyzed using scanning electron microscopy (SEM) combined with 2 methods: qualitative and quantitative regularity. Qualitative regularity of SEM images was graded by masked observers using an established scoring system. Quantitative regularity of SEM images was assessed by counting the total number and areas of tissue bridges using Image-Pro Plus software. Four different cap thickness of 120, 130, 140, and 150 μm were compared. Refractive outcomes of patients were measured at baseline and 1 month after surgery.

Results:

As 10 specimens were not analyzable, only 30 eyes were included. Postoperatively, all eyes had postoperative uncorrected distance visual acuity of 20/20 or better; 43% had an unchanged corrected distance visual acuity; 43% gained 1 line; 10% lost 1 line. Ultrastructurally, surface irregularity was primarily caused by tissue bridges. The average surface regularity score obtained was 10.87 ± 2.40 for 120 μm, 10.78 ± 2.60 for 130 μm, 8.76 ± 2.16 for 140 μm, and 8.70 ± 2.66 for 150 μm (P < 0.001). The total number and areas of tissue bridges of 120 to 130 μm were significantly less than 140 to 150 μm (P < 0.05). Surface regularity decreased as cap thickness increased (P < 0.05).

Conclusions:

There is smoother appearance of the lenticular surface as seen through SEM when a thin cap is created compared with a thick cap qualitatively and quantitatively.
Causes of Childhood Vision Impairment in the School for the Blind in Eritrea
Authors: Gyawali Rajendra , Moodley Vanessa R.
Published: October 2017

SIGNIFICANCE

Our study provides the much-needed evidence on causes of childhood blindness in Eritrea. This will assist authorities to plan appropriate strategies and implement preventive, curative, and rehabilitative services to address these causes of vision loss in children in this resource-limited country.

PURPOSE

This study aims to identify the causes of severe vision impairment and blindness in children attending the only school for the blind in Eritrea.

METHODS

All children enrolled in the school were examined, and the World Health Organization form for the examination of visually impaired children was used to record the data. Examination included visual acuity, refraction, anterior segment, and fundus assessment. Causes of vision loss for children with severe vision impairment (visual acuity <6/60 to 3/60) and blindness (visual acuity <3/60) are reported. Causes were classified by the anatomical site affected and by underlying etiology based on the timing of the insult and causal factor.

RESULTS

A total of 92 children were examined, and 71 (77.2%) of them had severe vision impairment and blindness. The major causes of vision loss were corneal scars (16.9%), cataract (12.7%), phthisis bulbi (11.3%), congenital eye deformities (11.3%), optic atrophy (9.3%), and presumed chorioretinal Toxoplasma scars (7.0%). Hereditary factors were the major known etiological category (15.5%) followed by the sequel of eye injuries (12.7%). Blindness due to vitamin A deficiency was not found, whereas infectious causes such as measles and ophthalmia neonatorum were relatively absent (one case each). Potentially avoidable causes of vision impairment were accounted for in 47.9% of children.

CONCLUSIONS

This study provides the first direct evidence on childhood vision impairment in Eritrea. Despite the limitations, it is clearly shown that nearly half of the vision loss is due to avoidable causes. Thus, preventive public health strategies, specialist pediatric eye care, and rehabilitative services are recommended to address childhood vision impairment in Eritrea.
The Effects of Electroconvulsive Therapy Augmentation of Antipsychotic Treatment on Cognitive Functions in Patients With Treatment-Resistant Schizophrenia
Authors: Vuksan Ćusa Bjanka , Klepac Nataša , Jakšić Nenad , Bradaš Zoran , Božičević Marija , Palac Natalia , Šagud Marina
Published: October 2017

Objectives

Treatment-resistant schizophrenia (TRS) continues to be a challenge in modern psychiatry. Most of these patients have severe neurocognitive deficits. Electroconvulsive therapy (ECT) has proved effective and safe in the treatment of TRS, but because of potential neurocognitive adverse effects, it is associated with many controversies. The aim of this prospective, open study was to evaluate the effects of ECT augmentation of antipsychotics on cognitive functions in patients with TRS.

Methods

Overall, 31 inpatients with TRS were included, 16 men, with an average (SD) age of 34.1 (11.187) years. The evaluation of clinical symptoms and global impression, as well as verbal memory, visual memory, working memory, psychomotor speed, verbal fluency, and executive functioning, was conducted before and after the completion of ECT treatment.

Results

We ran a series of paired-samples t tests, and the Bonferroni adjustment for multiple comparisons reduced the significance level to P = 0.004. The neurocognitive domains that demonstrated statistically significant improvement were immediate and delayed verbal memory, and executive functioning, whereas statistical trend was observed for visual memory and psychomotor speed. None of the neurocognitive functions exhibited significant deterioration after the ECT treatment. Electroconvulsive therapy was effective in reducing general symptoms of schizophrenia, resulting in more than 30% decrease in the overall symptom severity measured by the Positive and Negative Syndrome Scale.

Conclusions

Notwithstanding some limitations of this study, the combination of ECT and antipsychotics has improved several neurocognitive domains, without evidence of worsening of any cognitive functions.
Redox-sensitive reversible self-assembly of amino acid–naphthalene diimide conjugates
Authors: Liyanage Wathsala , Rubeo Paul W. , Nilsson Bradley L.
Published: October 2017

Peptide and low molecular weight amino acid-based materials that self-assemble in response to environmental triggers are highly desirable candidates in forming functional materials with tunable biophysical properties. In this paper, we explore redox-sensitive self-assembly of cationic phenylalanine derivatives conjugated to naphthalene diimide (NDI). Self-assembly of the cationic Phe-NDI conjugates into nanofibrils was induced in aqueous solvent at high ionic strength. Under reducing conditions, these self-assembled Phe-NDI conjugate fibrils underwent a morphological change to non-fibril aggregates. Upon reoxidation, the initially observed fibrils were reformed. The study herein provides an interesting strategy to effect reversible switching of the structure of supramolecular materials that can be applied to the development of sophisticated stimulus-responsive materials.
Peptide-based ambidextrous bifunctional gelator: applications in oil spill recovery and removal of toxic organic dyes for waste water management
Authors: Basu Kingshuk , Nandi Nibedita , Mondal Biplab , Dehsorkhi Ashkan , Hamley Ian W. , Banerjee Arindam
Published: October 2017

A low molecular weight peptide-based ambidextrous gelator molecule has been discovered for efficient control of water pollution. The gelator molecules can gel various organic solvents with diverse polarity, e.g.
n
-hexane,
n
-octane, petroleum ether, petrol, diesel, aromatic solvents like chlorobenzene, toluene, benzene,
o
-xylene and even aqueous phosphate buffer of pH 7.5. These gels have been thoroughly characterized using various techniques including field emission scanning electron microscopy, Fourier transform infrared spectroscopy, X-ray powder diffraction analysis, small angle X-ray scattering and rheological experiments. Interestingly, hydrogel obtained from the gelator molecule has been found to absorb toxic organic dyes (both cationic and anionic dyes) from dye-contaminated water. The gelator molecule can be reused for several cycles, indicating its possible future use in waste water management. Moreover, this gelator can selectively gel petrol, diesel, pump oil from an oil–water mixture in the presence of a carrier solvent, ethyl acetate, suggesting its efficient application for oil spill recovery. These results indicate that the peptide-based ambidextrous gelator produces soft materials (gels) with dual function: (i) removal of toxic organic dyes in waste water treatment and (ii) oil spill recovery.
What can machine learning do for antimicrobial peptides, and what can antimicrobial peptides do for machine learning?
Authors: Lee Ernest Y. , Lee Michelle W. , Fulan Benjamin M. , Ferguson Andrew L. , Wong Gerard C. L.
Published: October 2017

Antimicrobial peptides (AMPs) are a diverse class of well-studied membrane-permeating peptides with important functions in innate host defense. In this short review, we provide a historical overview of AMPs, summarize previous applications of machine learning to AMPs, and discuss the results of our studies in the context of the latest AMP literature. Much work has been recently done in leveraging computational tools to design new AMP candidates with high therapeutic efficacies for drug-resistant infections. We show that machine learning on AMPs can be used to identify essential physico-chemical determinants of AMP functionality, and identify and design peptide sequences to generate membrane curvature. In a broader scope, we discuss the implications of our findings for the discovery of membrane-active peptides in general, and uncovering membrane activity in new and existing peptide taxonomies.
Self-assembly of mutant huntingtin exon-1 fragments into large complex fibrillar structures involves nucleated branching
Authors: Wagner Anne S. , Politi Antonio Z. , Ast Anne , Bravo-Rodriguez Kenny , Baum Katharina , Buntru Alexander , Strempel Nadine U. , Brusendorf Lydia , Hänig Christian , Boeddrich Annett , Plassmann Stephanie , Klockmeier Konrad , Ramirez-Anguita Juan M. , Sanchez-Garcia Elsa , Wolf Jana , Wanker Erich E.
Published: October 2017

Huntingtin (HTT) fragments with extended polyglutamine (polyQ) tracts self-assemble into amyloid-like fibrillar aggregates. Elucidating the fibril formation mechanism is critical for understanding Huntington’s disease pathology and for developing novel therapeutic strategies. Here, we performed systematic experimental and theoretical studies to examine the self-assembly of an aggregation-prone N-terminal HTT exon-1 fragment with 49 glutamines (Ex1Q49). Using high resolution imaging techniques such as electron microscopy and atomic force microscopy, we show that Ex1Q49 fragments in cell-free assays spontaneously convert into large, highly complex bundles of amyloid fibrils with multiple ends and fibril branching points. Furthermore, we present experimental evidence that two nucleation mechanisms control spontaneous Ex1Q49 fibrillogenesis: (1) a relatively slow primary fibril-independent nucleation process, which involves the spontaneous formation of aggregation-competent fibrillary structures, and (2) a fast secondary fibril-dependent nucleation process, which involves nucleated branching and promotes the rapid assembly of highly complex fibril bundles with multiple ends. The proposed aggregation mechanism is supported by studies with the small molecule O4, which perturbs early events in the aggregation cascade and delays Ex1Q49 fibril assembly, comprehensive mathematical and computational modelling studies, and seeding experiments with small, preformed fibrillar Ex1Q49 aggregates that promote the assembly of amyloid fibrils. Together, our results suggest that nucleated branchingin vitroplays a critical role in the formation of complex fibrillar HTT exon-1 aggregates with multiple ends.
Myosin IIA interacts with the spectrin-actin membrane skeleton to control red blood cell membrane curvature and deformability
Authors: Smith Alyson S. , Nowak Roberta B. , Zhou Sitong , Giannetto Michael , Gokhin David S. , Papoin Julien , Ghiran Ionita C. , Blanc Lionel , Wan Jiandi , Fowler Velia M.
Published: October 2017

The biconcave disc shape and deformability of mammalian red blood cells (RBCs) relies upon the membrane skeleton, a viscoelastic network of short, membrane-associated actin filaments (F-actin) cross-linked by long, flexible spectrin tetramers. Nonmuscle myosin II (NMII) motors exert force on diverse F-actin networks to control cell shapes, but a function for NMII contractility in the 2D spectrin-F-actin network in RBCs has not been tested. Here, we show that RBCs contain membrane skeleton-associated NMIIA puncta, identified as bipolar filaments by super-resolution fluorescence microscopy. NMIIA association with the membrane skeleton is ATP-dependent, consistent with NMIIA motor domains binding to membrane skeleton F-actin and contributing to membrane mechanical stability. In addition, the NMIIA heavy and light chains are phosphorylatedin vivoin RBCs, indicating active regulation of NMIIA motor activity and filament assembly, while reduced heavy chain phosphorylation of membrane skeleton-associated NMIIA indicates assembly of stable filaments at the membrane. Treatment of RBCs with blebbistatin, an inhibitor of NMII motor activity, decreases the number of NMIIA filaments associated with the membrane and enhances local, nanoscale membrane oscillations, suggesting decreased membrane tension. Blebbistatin-treated RBCs also exhibit elongated shapes, loss of membrane curvature, and enhanced deformability, indicating a role for NMIIA contractility in promoting membrane stiffness and maintaining RBC biconcave disc cell shape. As structures similar to the RBC membrane skeleton are conserved in many metazoan cell types, these data demonstrate a general function for NMII in controlling specialized membrane morphology and mechanical properties through contractile interactions with short F-actin in spectrin-F-actin networks.

Significance statement

The biconcave disc shape and deformability of the mammalian RBC is vital to its circulatory function, relying upon a 2D viscoelastic spectrin-F-actin network attached to the membrane. A role for myosin II (NMII) contractility in generating tension in this network and controlling RBC shape has never been tested. We show that NMIIA forms phosphorylated bipolar filaments in RBCs, which associate with F-actin at the membrane. NMIIA motor activity is required for interactions with the spectrin-F-actin network, and regulates RBC biconcave shape and deformability. These results provide a novel mechanism for actomyosin force generation at the plasma membrane, and may be applicable to other cell types such as neurons and polarized epithelial cells with a spectrin-F-actin-based membrane skeleton.