bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi‐dimensional data representation using linear tensor coding
Authors: Qiao Xu , Liu Xiaoqing , Chen Yen‐wei , Liu Zhi‐Ping
Published: April 2017

Linear coding is widely used to concisely represent data sets by discovering basis functions of capturing high‐level features. However, the efficient identification of linear codes for representing multi‐dimensional data remains very challenging. In this study, the authors address the problem by proposing a linear tensor coding algorithm to represent multi‐dimensional data succinctly via a linear combination of tensor‐formed bases without data expansion. Motivated by the amalgamation of linear image coding and multi‐linear algebra, each basis function in the authors’ algorithm captures some specific variabilities. The basis‐associated coefficients can be used for data representation, compression and classification. When the authors apply the algorithm on both simulated phantom data and real facial data, the experimental results demonstrate their algorithm not only preserves the original information of input data, but also produces localised bases with concrete physical meanings.
Novel image inpainting algorithm based on adaptive fourth‐order partial differential equation
Authors: Li Shuaijie , Yang Xiaohui
Published: April 2017

Image inpainting is used to restore some damaged or missing information regions of an image based on the surrounding information. Inspired by the fourth‐order partial differential equation (PDE), this study presents two adaptive variational functionals for image inpainting, shows a stable variational scheme and investigates existence and uniqueness of solution for the minimising functionals. A consistent numerical discretisation scheme is also constructed for the derived fourth‐order PDEs. The proposed models can simultaneously restore the missing, corrupted or undesirable regions and remove noise. Some successful image inpainting experiments and method comparisons are also provided in this study.
Text segmentation using superpixel clustering
Authors: Zhu Yuanping , Zhang Kuang
Published: April 2017

Text segmentation is important for text image analysis and recognition; however, it is challenging due to noise and complex background in natural scenes. Superpixel‐based image representation can enhance robustness to noise and local disturbances, but conventional superpixel algorithms are difficult to obtain the complete stroke regions and accurate boundaries for text images. In this study, a text segmentation method based on superpixel clustering is proposed. First, to generate accurate superpixels for text images, an adaptive simple linear iterative clustering‐based text superpixel generation algorithm is proposed. The adaptive superpixel size and compactness are calculated to enhance boundary adherence. Second, to increase the complete coverage of strokes from superpixels, superpixel clustering merges homogeneous superpixels into larger regions for both strokes and the background. A modified density‐based spatial clustering of applications with noise is proposed. Finally, stroke superpixel verification assigns each region to a stroke or to the background and the text segmentation result is obtained. The proposed method shows promising robustness to noise and complex background textures. Experimental results on the Korea Advanced Institute of Science and Technology (KAIST) scene text dataset, International Conference on Document Analysis and Recognition (ICDAR) 2003 natural scene text image dataset and Street View Text dataset verify that this method is effective and significantly outperforms existing methods.
Non‐close packaged monolayer of silica nanoparticles on silicon substrate using HF vapour etching
Authors: Van Minh Nguyen , Son Nguyen Ngoc , Lien Nghiem Thi Ha , Hoang Chu Manh
Published: April 2017

Ordered monolayer of silica nanoparticles assembled on solid substrates is useful for a variety of promising applications in photonics, plasmonics, and solar cell. Nanoparticles are usually assembled into close‐ or non‐close‐packed monolayer (CPM) form. The non‐close packed monolayer can be directly deposited from mono‐dispersed colloidal suspension onto a solid substrate in terms of using complicated techniques or tuning the size of nanoparticles in the CPM. An effective method for forming the non‐close packed monolayer of silica nanoparticles is reported. Silica nanoparticles are self‐assembled into the CPM on silicon substrate. The size of silica nanoparticles is tuned by high frequency vapour etching. The dependence of the size and shape of silica nanoparticles on etching time is presented. The effect of sintering conditions on the etching process is also investigated.
Voltage and current conditions for nanoparticle chain formation using dielectrophoresis
Authors: Koshi Tomoya , Nakajima Yuta , Iwase Eiji
Published: April 2017

Here, the voltage and current conditions required to form a nanoparticle chain bridging a gap between electrodes that is several tens of micrometres wide have been examined. When a voltage is applied to a gap between electrodes covered with a dispersion of nanoparticles, the nanoparticles are trapped in the gap by dielectrophoresis, forming a nanoparticle chain. It has been considered that a nanoparticle chain is formed in a gap only when a voltage higher than a certain value with a current lower than a certain value is applied to the gap. In this work, certain voltages were first applied with changing current to a 10 µm‐wide gap between electrodes covered with a dispersion of 150 nm‐diameter gold nanoparticles, and they found that a nanoparticle chain was formed only when 6.1 Vrms or more with 15 mArms or less was applied. Next, the process of nanoparticle chain formation in a 10 µm‐wide gap was directly observed with high‐magnification and high‐speed microscopy, and they clarified the behaviour of nanoparticle chain formation when a low voltage, high voltage with high current, and high voltage with low current were applied. Finally, they measured the critical value of current for nanoparticle chain formation in a gap several tens of micrometres wide.
A new method for calibrating hygrometers
Authors: Huang Jianhua
Published: April 2017

In this study, a new method was proposed for calibrating hygrometers. The moisture permeation cylinder, which was used to measure the water vapor permeability of fabrics, was used to generate various levels of relative humidity. A dry nitrogen stream was employed to sweep the water vapor away. It was deduced that the relative humidity of the outgoing nitrogen stream was negatively correlated to the volumetric flow rate of nitrogen stream, i.e., the lower the volumetric flow rate, the higher the relative humidity. The hygrometer HMT 333 was chosen to measure the relative humidity of the outgoing nitrogen stream at five levels. The test data indicated that good agreement was observed between the measured humidity and the observed humidity from the Vaisala, Inc. Moreover, this method offers high sensitivity and fast response. Therefore, the relative humidity of the outgoing nitrogen stream can be used as a secondary humidity reference.
Cheap but accurate calculation of chemical reaction rate constants from ab initio data, via system-specific, black-box force fields
Authors: Steffen Julien , Hartke Bernd
Published: April 2017

Building on the recently published quantum-mechanically derived force field (QMDFF) and its empirical valence bond extension, EVB-QMDFF, it is now possible to generate a reliable potential energy surface for any given elementary reaction step in an essentially black box manner. This requires a limited and pre-defined set of reference data near the reaction path and generates an accurate approximation of the reference potential energy surface, on and off the reaction path. This intermediate representation can be used to generate reaction rate data, with far better accuracy and reliability than with traditional approaches based on transition state theory (TST) or variational extensions thereof (VTST), even if those include sophisticated tunneling corrections. However, the additional expense at the reference level remains very modest. We demonstrate all this for three arbitrarily chosen example reactions.
Nature of the valence excited states of bromine in the T and P clathrate cages
Authors: Batista-Romero Fidel A. , Gamboa-Suárez Antonio , Hernández-Lamoneda Ramón , Janda Kenneth C.
Published: April 2017

The guest-host intermolecular potentials for the valence excited states of Br2 in the tetrakaidecahedral(T) and pentakaidecahedral(P) clathrate cages have been calculated using ab initio local correlation methods. We find that the excited states are more strongly bound than the corresponding ground states even in the small T cage where bromine has a tight fit. The angular dependence of the interaction energies is quite anisotropic; this reflects in the corresponding electronic shifts where regions of maxima for blue-shifts in the T cage indicate the presence of halogen bonding. We predict a large temperature dependence of the electronic shifts and compare absolute values with recent experimental studies. This stringent test indicates the reliability of local correlation treatments to describe weak intermolecular forces in ground and excited states.
Exploring the broadening and the existence of two glass transitions due to competing interfacial effects in thin, supported polymer films
Authors: Glor Ethan C. , Angrand Gabriel V. , Fakhraai Zahra
Published: April 2017

In this report, we use ellipsometry to characterize the glass transition in ultra-thin films of poly(2-vinyl pyridine) (P2VP) supported on a silicon substrate. P2VP is known to have attractive substrate interactions, which can increase the Tg of ultra-thin films compared to the bulk value. Here, we use an extended temperature range to show that the glass transition can be extremely broad, indicating that a large gradient of the dynamics exists through the film with slow dynamics near the substrate and enhanced dynamics at the free surface. To observe the effect of these two interfaces on the average thin film dynamics, cooling rate-dependent Tg (CR-Tg) measurements were used to indirectly probe the average relaxation times of the films. We demonstrate that ultra-thin films have lower fragility compared to bulk films, and, when cooled at slow cooling rates (<1 K/min), exhibit extreme broadening of the dynamics (<70 nm) and eventually complete decoupling between the free surface and substrate regions to produce films with two distinct Tg’s (<16 nm). Tg,high increases with decreasing thickness in a similar manner to what has been observed in previous studies on P2VP, and Tg,low decreases with decreasing film thickness in a similar manner to what has been observed in polymer films with enhanced free surfaces and neutral substrate interactions. These observations indicate that the dynamics in thin films of P2VP can be strongly coupled over a length scale of ∼10-20 nm, resulting in two co-existing layers with two distinct glass transitions when the range of the dynamical gradients become too large to sustain (breadth of the transition > 50 K).
Statistical properties of fluctuating enzymes with dynamic cooperativity using a first passage time distribution formalism
Authors: Singh Divya , Chaudhury Srabanti
Published: April 2017

We study the temporal fluctuations in catalytic rates for single enzyme reactions undergoing slow transitions between two active states. We use a first passage time distribution formalism to obtain the closed-form analytical expressions of the mean reaction time and the randomness parameter for reaction schemes where conformational fluctuations are present between two free enzyme conformers. Our studies confirm that the sole presence of free enzyme fluctuations yields a non Michaelis-Menten equation and can lead to dynamic cooperativity. The randomness parameter, which is a measure of the dynamic disorder in the system, converges to unity at a high substrate concentration. If slow fluctuations are present between the enzyme-substrate conformers (off-pathway mechanism), dynamic disorder is present at a high substrate concentration. Our results confirm that the dynamic disorder at a high substrate concentration is determined only by the slow fluctuations between the enzyme-substrate conformers and the randomness parameter is greater than unity. Slow conformational fluctuations between free enzymes are responsible for the emergence of dynamic cooperativity in single enzymes. Our theoretical findings are well supported by comparison with experimental data on the single enzyme beta-galactosidase.
Degradation and recovery of iron doped barium titanate single crystals via modulus spectroscopy and thermally stimulated depolarization current
Authors: Carter J. J. , Bayer T. J. M. , Randall C. A.
Published: April 2017

Understanding resistance degradation during the application of DC bias and recovery after removing the DC bias provides insight into failure mechanisms and defects in dielectric materials. In this experiment, modulus spectroscopy and thermally stimulated depolarization current (TSDC) techniques were used to characterize the degradation and recovery of iron-doped barium titanate single crystals. Modulus spectroscopy is a very powerful analytical tool applied during degradation and recovery to observe changes in the local conductivity distribution. During degradation, oxygen vacancies migrate to the cathode region, and a counter flow of oxygen anions migrates towards the anode. With increasing time during degradation, the distribution of conductivity broadens only slightly exhibiting crucial differences to iron doped strontium titanate. After removing the DC bias, the recovery shows that a second previously unobserved and distinct conductivity maximum arises in the modulus data. This characteristic with two maxima related to different conductivities in the anode and cathode region is what can be expected from the published defect chemistry. It will be concluded that only the absence of an external electric field during recovery measurements permits the observation of local conductivity measurements without the presence of non-equilibrium conditions such as charge injection. Equilibrium conductivity as a function of oxygen vacancy concentration is described schematically. Oxygen vacancy migration during degradation and recovery is verified by TSDC analysis. We establish a self-consistent rationale of the transient changes in the modulus and TSDC for the iron doped barium titanate single crystal system including electron, hole and oxygen vacancy conductivity. During degradation, the sample fractured.
First phase to form during cobalt germanidation
Authors: Rabie Mohamed A. , Mirza Souzan , Jarvis Victoria , Haddara Yaser M.
Published: April 2017

The first systematic study for the first phase to form during cobalt germanidation was conducted. Hexagonal β-Co5Ge3 was the first phase to form in case of cobalt germanidation on (100) Ge. This phase formed at a temperature as low as 227 °C. Monoclinic CoGe was experimentally shown to be the second phase to form at the same temperature. Our results are contrary to the previous reports suggesting monoclinic CoGe to be the first phase to form. This is mainly due to the experimental setup that was designed to detect all forming phases: in-situ XRD monitoring at constant low temperature long time anneals of 24–48 h. We also report for the first time that both β-Co5Ge3 and monoclinic CoGe phases that formed during cobalt germanidation were highly ordered partial epitaxial crystal orientations.
THz spectroscopy on graphene-like materials for bio-compatible devices
Authors: Papari Gian Paolo , Gargiulo Valentina , Alfè Michela , Di Capua Roberto , Pezzella Alessandro , Andreone Antonello
Published: April 2017

Graphene-like (GL) layers and eumelanin-based graphene-like (EUGL) hybrids have been investigated through THz time domain spectroscopy. The interest in these materials lies on their peculiar chemical-physical properties: the former are conductive water stable materials, whereas the latter are biocompatible materials with good conductive and adhesive properties. Both exhibit promising optoelectronic and bioelectronic applications. We measured mixtures of GL layers or EUGL hybrids with KBr, shaped in pellets with uniform thickness, in order to circumvent problems related to sample inhomogeneity and roughness. A mean field theory was applied to extract direct information on permittivity and conductivity. Data have been carefully fitted through the Drude-Smith theory, confirming the conductive nature of the hybrid materials. The results show that EUGL hybrid-based devices can be promising for the next generation of printable bio-circuits.
Tunable negative differential resistance in planar graphene superlattice resonant tunneling diode
Authors: Sattari-Esfahlan S. M. , Fouladi-Oskuei J. , Shojaei S.
Published: April 2017

Here, we study the negative differential resistance (NDR) of Dirac electrons in biased planar graphene superlattice (PGSL) and investigate the transport characteristics by adopted transfer matrix method within Landauer-Buttiker formalism. Our model device is based on one-dimensional Kronig–Penney type electrostatic potential in monolayer graphene deposited on a substrate, where the bias voltage is applied by two electrodes in the left and right. At Low bias voltages, we found that NDR appears due to breaking of minibands to Wannier-Stark ladders (WSLs). At the critical bias voltage, delocalization appeared by WS states leads to tunneling peak current in current-voltage (I-V) characteristics. With increasing bias voltage, crossing of rungs from various WSL results in multi-peak NDR. The results demonstrate that the structure parameters like barrier/well thickness and barrier height have remarkable effect on I-V characteristics of PGSL. In addition, Dirac gap enhances peak to valley (PVR) value due to suppressing Klein tunneling. Our results show that the tunable PVR in PGSL resonant tunneling diode can be achievable by structure parameters engineering. NDR at ultra-low bias voltages, such as 100 mV, with giant PVR of 20 is obtained. In our device, the multiple same NDR peaks with ultra-low bias voltage provide promising prospect for multi-valued memories and the low power nanoelectronic tunneling devices.
Spin-orbit torque induced magnetization anisotropy modulation in Pt/(Co/Ni)4/Co/IrMn heterostructure
Authors: Engel Christian , Goolaup Sarjoosing , Luo Feilong , Gan Weiliang , Lew Wen Siang
Published: April 2017

In this work, we show that domain wall (DW) dynamics within a system provide an alternative platform to characterizing spin-orbit torque (SOT) effective fields. In perpendicularly magnetized wires with a Pt/(Co/Ni)4/Co/IrMn stack structure, differential Kerr imaging shows that the magnetization switching process is via the nucleation of the embryo state followed by domain wall propagation. By probing the current induced DW motion in the presence of in-plane field, the SOT effective fields are obtained using the harmonic Hall voltage scheme. The effective anisotropy field of the structure decreases by 12% due to the SOT effective fields, as the in-plane current in the wire is increased.
The mechanical and thermal responses of colliding oxide-coated aluminum nanoparticles
Authors: Ma Bo , Zhao Feng , Cheng Xinlu , Miao Feng , Zhang Jidong
Published: April 2017

The aggregation and fracture of oxide-coated metal nanoparticles have a significant influence on their physical and chemical behaviors in synthesis, combustion, or detonation. How does the dynamic loading caused by the impact between nanoparticles affect them? Motivated by this issue, we carried out molecular dynamic simulations of two colliding aluminum nanoparticles to investigate their mechanical and thermal properties and response at impact velocities of 200 m/s, 600 m/s, 1000 m/s, and 2000 m/s. At the relatively low impact velocities (equal to or less than 1000 m/s), it was observed that the particles are mildly deformed and adhere to each other, but the shells do not undergo fracture under the dynamic loading. The metal core and oxide shell behave elastically at 200 m/s and elasto-plastically at 600 m/s. A concentration of dynamic volumetric stress appears but no concentration of shear stress and no formation of a hot spot. Due to the low intensity of the loading and the efficient propagation of the stress wave, the shells fail to fracture. At an impact velocity of 2000 m/s, the impact region of the shell undergoes ductile fracture, and the two particles undergo sintering and form a new particle re-coated with oxide, resulting from the concentration of dynamic shear stress and the formation of a hot spot. At all impact velocities in our simulations, the impact between the nanoparticles improves the aggregation but has a little effect on the fracture of the oxide shell.
Liquid-phase tuning of porous PVDF-TrFE film on flexible substrate for energy harvesting
Authors: Chen Dajing , Chen Kaina , Brown Kristopher , Hang Annie , Zhang John X. J.
Published: April 2017

Emerging wearable and implantable biomedical energy harvesting devices demand efficient power conversion, flexible structures, and lightweight construction. This paper presents Polyvinylidene fluoride-trifluoroethylene (PVDF-TrFE) micro-porous structures, which can be tuned to specific mechanical flexibilities and optimized for piezoelectric power conversion. Specifically, the water vapor phase separation method was developed to control microstructure formation, pore diameter, porosity, and mechanical flexibility. Furthermore, we investigated the effects of the piezoelectric layer to supporting layer Young's modulus ratio, through using both analytical calculation and experimentation. Both structure flexibility and stress-induced voltage were considered in the analyses. Specification of electromechanical coupling efficiency, made possible by carefully designed three-dimensional porous structures, was shown to increase the power output by five-fold relative to uncoupled structures. Therefore, flexible PVDF-TrFE films with tunable microstructures, paired with substrates of different rigidities, provide highly efficient designs of compact piezoelectric energy generating devices.
Interface properties of NO-annealed 4H-SiC (0001), (112¯), and (11¯00) MOS structures with heavily doped p-bodies
Authors: Kobayashi Takuma , Nakazawa Seiya , Okuda Takafumi , Suda Jun , Kimoto Tsunenobu
Published: April 2017

We investigated electrical characteristics of nitric oxide (NO)-annealed silicon carbide (SiC) (0001), (112¯0), and (11¯00) metal-oxide-semiconductor field effect transistors (MOSFETs) with heavily doped p-bodies (NA = 1 × 1017–3 × 1018 cm−3). Regardless of crystal faces or off-direction, the channel mobility decreased for higher acceptor density. We evaluated the interface state density (Dit) very near the bottom edge of 2-dimensional density of states (2D-DOS) in the conduction band of SiC from the low-temperature subthreshold slope of the MOSFETs. When the acceptor density of the p-body of the MOSFET is increased, the energy levels of 2D-DOS increase due to a stronger quantum confinement effect. Accordingly, the carriers in the heavily doped channel are influenced by the interface states located at higher energy levels. In the SiC MOS structures, the Dit values significantly increase near the conduction band edge (EC). Thus, MOSFETs on heavily doped p-bodies are affected by the higher density of Dit, leading to substantially lower mobility.
All-optical control of weak-light transport and Fano-like resonance using control-probe technique in a quantum-dot-pillar microcavity system
Authors: Yu Rong , Ding Chunling , Zhang Duo , Zhang Suzhen
Published: April 2017

Control of light by light is a current research topic and is important for a variety of fundamental studies and practical applications. Here, we put forward a chip-scale scheme for all-optical control of small-signal photon transport and Fano-like lineshape in a coupled quantum-dot-pillar microcavity system based on a control-probe technique. Specifically, a bichromatic input light field, which consists of a weak probe field and a tunable control field, is applied to simultaneously drive the pillar cavity mode (called the control-probe technique) and both its reflectivity from and transmittivity through the pillar cavity constitute two output channels (i.e., a reflectivity signal channel and a transmittivity signal channel). We derive full analytical expressions for the reflectivity and transmittivity coefficients via a perturbation method. Using experimentally realistic parameters, theoretical analysis shows that the output probe light of the reflectivity and transmittivity channels can be switched on or off by simply turning on or off the control light field. Hence, the present system can be utilized to realize all-optical switching of the probe light by the control light with high switching contrast ∼1 by means of these two output channels. Interestingly, the reflectivity channel and the transmittivity channel are complementary and offer versatile applications in a two-channel switching. In addition, it is shown that the strong asymmetric Fano lineshape can be generated by properly tuning the frequency of the control light field in this control-probe scheme. The present investigation may be used for developing novel all-optical switching and tunable Fano devices on-chip.
Perspective: A toolbox for protein structure determination in physiological
environment through oriented, 2D ordered, site specific immobilization
Authors: Altissimo M. , Kiskinova M. , Mincigrucci R. , Vaccari L. , Guarnaccia C. , Masciovecchio C.
Published: April 2017

Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based X-ray crystallography and cryo-electron microscopy have made major contributions in determining thousands of protein structures even from micro-sized crystals. They suffer from some limitations that have not been overcome, such as radiation damage, the natural inability to crystallize a number of proteins, and experimental conditions for structure determination that are incompatible with the physiological environment. Today, the ultra-short and ultra-bright pulses of X-ray free-electron lasers have made attainable the dream to determine protein structures before radiation damage starts to destroy the samples. However, the signal-to-noise ratio remains a great challenge to obtain usable diffraction patterns from a single protein molecule. With the perspective to overcome these challenges, we describe here a new methodology that has the potential to overcome the signal-to-noise-ratio and protein crystallization limits. Using a multidisciplinary approach, we propose to create ordered, two dimensional protein arrays with defined orientation attached on a self-assembled-monolayer. We develop a literature-based flexible toolbox capable of assembling different kinds of proteins on a functionalized surface and consider using a graphene cover layer that will allow performing experiments with proteins in physiological conditions.
Magneto-optic measurements on uneven magnetic layers on cardboard
Authors: Blachowicz T. , Ehrmann A. , Mahltig B.
Published: April 2017

Measurements of magnetic hysteresis loops by magneto-optic Kerr effect (MOKE) are usually performed on even surfaces which reflect the impinging laser beam without any disturbance. Alternatively, such measurements can be done on regularly structured samples, resulting in the possibility to investigate different diffraction orders who deliver different information about the magnetism in the magnetic particles. Rough magnetic surfaces, however, occur when rough substrates are coated with a magnetic layer, or when large magnetic particles are placed on a base material due to practical reasons. The article depicts the possibility to measure magnetic hysteresis loops on surfaces with a roughness about one order of magnitude higher than the light wavelength. This enables applied measurements of magnetic parameters on biological samples, textiles, irregular magnetic nanofibers etc.
Spatial Heterogeneity, Variable Rewards, Tag Loss, and Tagging Mortality Affect the Performance of Mark–Recapture Designs to Estimate Exploitation: an Example using Red Snapper in the Northern Gulf of Mexico
Authors: Sackett Dana K. , Catalano Matthew
Published: April 2017

Accurate estimates of exploitation rate are essential to the management of exploited fisheries. Tagging studies are often used to estimate exploitation rates, but the performance of these approaches depends strongly on study design characteristics and the magnitude of assumption violations. We simulated a suite of candidate study designs for 1-year high-reward and variable-reward tagging studies, exploring a range of sample sizes (number of tagged fish), exploitation rates, tagging mortality rates, tag loss rates, proportions of double-tagged fish, and spatial variation in fish density, tag releases, and fishing effort. We calculated the uncertainty, biases, and reward costs of these candidate study designs to determine the most cost-effective approach to accurately estimate exploitation rate for Red Snapper Lutjanus campechanus in Alabama waters of the Gulf of Mexico. We also investigated how incorrectly assuming a 100% reporting rate would affect these study results. Our simulations demonstrated that using all high-reward tags provided more accurate and precise exploitation rate estimates than the variable-reward approach but only if 100% reporting could be safely assumed. Further, distributing tags uniformly over the study area when the true spatial distribution of the population and fishing pressure varied over that area drastically biased exploitation rate estimates, suggesting that prior knowledge of the population's true spatial distribution over the study area is needed to ensure accurate estimates of exploitation rate. The most cost-effective study design involved tagging between 400 and 1,600 fish with high-reward tags, with 40% of the fish double-tagged, and the tags spatially distributed in the same proportion as the population. However, violation of the 100% reporting rate assumption resulted in a proportional downward bias in the estimated exploitation rate. Simulation studies such as this are critical to ensure that cost-effective study designs produce accurate and precise estimates of exploitation rate, particularly for high-value species such as Red Snapper.

Received July 13, 2016; accepted February 24, 2017 Published online April 14, 2017
Centrioles initiate cilia assembly but are dispensable for maturation and maintenance in C. elegans
Authors: Serwas Daniel , Su Tiffany Y. , Roessler Max , Wang Shaohe , Dammermann Alexander
Published: April 2017

Cilia are cellular projections that assemble on centriole-derived basal bodies. While cilia assembly is absolutely dependent on centrioles, it is not known to what extent they contribute to downstream events. The nematode C. elegans provides a unique opportunity to address this question, as centrioles do not persist at the base of mature cilia. Using fluorescence microscopy and electron tomography, we find that centrioles degenerate early during ciliogenesis. The transition zone and axoneme are not completely formed at this time, indicating that cilia maturation does not depend on intact centrioles. The hydrolethalus syndrome protein HYLS-1 is the only centriolar protein known to remain at the base of mature cilia and is required for intraflagellar transport trafficking. Surprisingly, targeted degradation of HYLS-1 after initiation of ciliogenesis does not affect ciliary structures. Taken together, our results indicate that while centrioles are essential to initiate cilia formation, they are dispensable for cilia maturation and maintenance.
Unsuccessfully Treated Hypertension: A Major Public Health Problem With a Potential Solution
Authors: Furberg Curt D , Sealey Jean E , Blumenfeld Jon D
Published: April 2017

BACKGROUND

About one-half of all hypertensive adults do not have their blood pressure controlled. They are often prescribed medications that conform to national guidelines but they continue to have elevated blood pressure. This public health problem might be improved by applying plasma renin guided therapy.

RESULTS

A contributor to the public health problem of unsuccessfully treated hypertension is that the circulating renin–angiotensin system (RAS) is not recognized in treatment guidelines as clinically relevant for the treatment of hypertension or as important as the body salt status for determining blood pressure levels. Another contributor to the problem is the lack of specificity in the package inserts for antihypertensive drugs. They do not specifically state under the heading “Indications” that RAS blockers are primarily most effective in hypertensive subjects with medium and high plasma renin levels; by contrast, natriuretic drugs are most effective in those with low plasma renin levels.

METHODS

Literature review.

CONCLUSIONS

To address the problem of unsuccessfully treated hypertension, we recommend that the “Indications” section of package inserts for antihypertensive drugs be more specific. The primary indication for RAS blockers ought to be hypertension with medium and high plasma renin levels, and natriuretic agents for those with low plasma renin levels. Similar language ought to be added to treatment guidelines. Additionally, 3 other reasons for lack of blood pressure control also need to be addressed—failure to prescribe antihypertensive drugs to hypertensive subjects, failure of patients to fill prescriptions, and low drug adherence.
Deep learning with word embeddings improves biomedical named entity recognition
Authors: Habibi Maryam , Weber Leon , Neves Mariana , Wiegandt David Luis , Leser Ulf
Published: April 2017

Motivation

Text mining has become an important tool for biomedical research. The most fundamental text-mining task is the recognition of biomedical named entities (NER), such as genes, chemicals and diseases. Current NER methods rely on pre-defined features which try to capture the specific surface properties of entity types, properties of the typical local context, background knowledge, and linguistic information. State-of-the-art tools are entity-specific, as dictionaries and empirically optimal feature sets differ between entity types, which makes their development costly. Furthermore, features are often optimized for a specific gold standard corpus, which makes extrapolation of quality measures difficult.

Results

We show that a completely generic method based on deep learning and statistical word embeddings [called long short-term memory network-conditional random field (LSTM-CRF)] outperforms state-of-the-art entity-specific NER tools, and often by a large margin. To this end, we compared the performance of LSTM-CRF on 33 data sets covering five different entity classes with that of best-of-class NER tools and an entity-agnostic CRF implementation. On average, F1-score of LSTM-CRF is 5% above that of the baselines, mostly due to a sharp increase in recall.

Availability and implementation

The source code for LSTM-CRF is available at https://github.com/glample/tagger and the links to the corpora are available at https://corposaurus.github.io/corpora/.
BIOSSES: a semantic sentence similarity estimation system for the biomedical domain
Authors: Soğancıoğlu Gizem , Öztürk Hakime , Özgür Arzucan
Published: April 2017

Motivation

The amount of information available in textual format is rapidly increasing in the biomedical domain. Therefore, natural language processing (NLP) applications are becoming increasingly important to facilitate the retrieval and analysis of these data. Computing the semantic similarity between sentences is an important component in many NLP tasks including text retrieval and summarization. A number of approaches have been proposed for semantic sentence similarity estimation for generic English. However, our experiments showed that such approaches do not effectively cover biomedical knowledge and produce poor results for biomedical text.

Methods

We propose several approaches for sentence-level semantic similarity computation in the biomedical domain, including string similarity measures and measures based on the distributed vector representations of sentences learned in an unsupervised manner from a large biomedical corpus. In addition, ontology-based approaches are presented that utilize general and domain-specific ontologies. Finally, a supervised regression based model is developed that effectively combines the different similarity computation metrics. A benchmark data set consisting of 100 sentence pairs from the biomedical literature is manually annotated by five human experts and used for evaluating the proposed methods.

Results

The experiments showed that the supervised semantic sentence similarity computation approach obtained the best performance (0.836 correlation with gold standard human annotations) and improved over the state-of-the-art domain-independent systems up to 42.6% in terms of the Pearson correlation metric.

Availability and implementation

A web-based system for biomedical semantic sentence similarity computation, the source code, and the annotated benchmark data set are available at: http://tabilab.cmpe.boun.edu.tr/BIOSSES/.
Large-scale structure prediction by improved contact predictions and model quality assessment
Authors: Michel Mirco , Menéndez Hurtado David , Uziela Karolis , Elofsson Arne
Published: April 2017

Motivation

Accurate contact predictions can be used for predicting the structure of proteins. Until recently these methods were limited to very big protein families, decreasing their utility. However, recent progress by combining direct coupling analysis with machine learning methods has made it possible to predict accurate contact maps for smaller families. To what extent these predictions can be used to produce accurate models of the families is not known.

Results

We present the PconsFold2 pipeline that uses contact predictions from PconsC3, the CONFOLD folding algorithm and model quality estimations to predict the structure of a protein. We show that the model quality estimation significantly increases the number of models that reliably can be identified. Finally, we apply PconsFold2 to 6379 Pfam families of unknown structure and find that PconsFold2 can, with an estimated 90% specificity, predict the structure of up to 558 Pfam families of unknown structure. Out of these, 415 have not been reported before.

Availability and Implementation

Datasets as well as models of all the 558 Pfam families are available at http://c3.pcons.net/. All programs used here are freely available.
A multi-systemic mitochondrial disorder due to a dominant p.Y955H disease variant in DNA polymerase gamma
Authors: Siibak Triinu , Clemente Paula , Bratic Ana , Bruhn Helene , Kauppila Timo E.S. , Macao Bertil , Rosenberger Florian A. , Lesko Nicole , Wibom Rolf , Naess Karin , Nennesmo Inger , Wedell Anna , Peter Bradley , Freyer Christoph , Falkenberg Maria , Wredenberg Anna
Published: April 2017

Mutations in the mitochondrial DNA polymerase, POLG, are associated with a variety of clinical presentations, ranging from early onset fatal brain disease in Alpers syndrome to chronic progressive external ophthalmoplegia. The majority of mutations are linked with disturbances of mitochondrial DNA (mtDNA) integrity and maintenance. On a molecular level, depending on their location within the enzyme, mutations either lead to mtDNA depletion or the accumulation of multiple mtDNA deletions, and in some cases these molecular changes can be correlated to the clinical presentation. We identified a patient with a dominant p.Y955H mutation in POLG, presenting with a severe, early-onset multi-systemic mitochondrial disease with bilateral sensorineural hearing loss, cataract, myopathy, and liver failure. Using a combination of disease models of Drosophila melanogaster and in vitro biochemistry analysis, we compare the molecular consequences of the p.Y955H mutation to the well-documented p.Y955C mutation. We demonstrate that both mutations affect mtDNA replication and display a dominant negative effect, with the p.Y955H allele resulting in a more severe polymerase dysfunction.
Tracking Career Paths of Women in Neurosurgery
Authors: Renfrow Jaclyn J , Rodriguez Analiz , Wilson Taylor A , Germano Isabelle M , Abosch Aviva , Wolfe Stacey Quintero
Published: April 2017

BACKGROUND

Women represent a growing cohort of US neurosurgeons.

OBJECTIVE

To describe postresidency fellowship, practice environment, and updated academic rank among female neurosurgeons.

METHODS

Databases from the American Association of Neurological Surgeons (AANS) and the American Board of Neurological Surgery (ABNS) from 1964 to 2013 were reviewed for female neurosurgery residency graduates. Data on postresidency fellowships, practice environment (private vs academic), academic rank, board certification, and AANS/CNS (Congress of Neurological Surgeons) Joint Section on Women in Neurosurgery (WINS) membership were collected in 2016. Academic rank was verified from program websites and electronic correspondence. Faculty members were asked to report directorships and tenure. The AANS/CNS Joint Section on Women in Neurosurgery verified WINS membership.

RESULTS

A total of 379 female neurosurgery residency graduates were identified in this 50-yr span. Of these, 70% became ABNS certified, and 2.1% left neurosurgery. Twenty-seven percent of women (n = 103) pursued fellowships, with pediatric neurosurgery (33%) the most common. Regarding practice environment, 26% entered academic medicine (n = 91), with 42 at the rank of assistant professor, 33 at the rank of associate professor, and 16 reaching the rank of full professor.

CONCLUSION

Upon completion of training, 27% of women pursue fellowships. The distribution of women in private vs academic practice environments is proportionate to male neurosurgeons; however, the number women in academic leadership positions remains exceedingly low, with disproportionate representation in higher academic ranks. Women in national organized neurosurgery are increasing. Tracking the career paths of women in neurosurgery is a necessary step to identifying current achievements and opportunities for future progress.
Pediatric Clival Chordoma: A Curable Disease that Conforms to Collins' Law
Authors: Rassi Marcio S , Hulou M Maher , Almefty Kaith , Bi Wenya Linda , Pravdenkova Svetlana , Dunn Ian F , Smith Timothy R , Al-Mefty Ossama
Published: April 2017

BACKGROUND

Skull base chordomas in children are extremely rare. Their course, management, and outcome have not been defined.

OBJECTIVE

To describe the preeminent clinical and radiological features in a series of pediatric patients with skull base chordomas and analyze the outcome of a cohort who underwent uniform treatment. We emphasize predictors of overall survival and progression-free survival, which aligns with Collins’ law for embryonal tumors.

METHODS

Thirty-one patients with a mean age of 10.7 yr (range 0.8-22) harboring skull base chordomas were evaluated. We retrospectively analyzed the outcomes and prognostic factors for 18 patients treated by the senior author, with uniform management of surgery with the aim of gross total resection and adjuvant proton-beam radiotherapy. Mean follow-up was 119.2 mo (range 8-263).

RESULTS

Abducens nerve palsy was the most common presenting symptom. Imaging disclosed large tumors that often involve multiple anatomical compartments. Patients undergoing gross total resection had significantly increased progression-free survival (P = .02) and overall survival (P = .05) compared with those having subtotal resection. Those who lived through the period of risk for recurrence without disease progression had a higher probability of living entirely free of progression (P = .03; odds ratio = 16.0). Age, sex, and histopathological variant did not yield statistical significance in survival.

CONCLUSION

Long-term overall and progression-free survival in children harboring skull base chordomas can be achieved with gross surgical resection and proton-beam radiotherapy, despite an advanced stage at presentation. Collins’ law does apply to pediatric skull base chordomas, and children with this disease have a high hope for cure.
Effectiveness of McKenzie Method–Based Self-Management Approach for the Secondary Prevention of a Recurrence of Low Back Pain (SAFE Trial): Protocol for a Pragmatic Randomized Controlled Trial
Authors: de Campos Tarcisio F. , Maher Chris G. , Clare Helen A. , da Silva Tatiane M. , Hancock Mark J.
Published: April 2017

Background. Although many people recover quickly from an episode of low back pain (LBP), recurrence is very common. There is limited evidence on effective prevention strategies for recurrences of LBP.

Objective. The purpose of this study was to determine the effectiveness of a McKenzie method–based self–management approach in the secondary prevention of LBP.

Design. This will be a pragmatic randomized controlled trial.

Setting. Participants will be recruited from the community and primary care, with the intervention delivered in a number of physical therapist practices in Sydney, Australia.

Participants. The study will have 396 participants, all of whom are at least 18 years old.

Intervention. Participants will be randomly assigned to either the McKenzie method–based self-management approach group or a minimal intervention control group.

Measurements. The primary outcome will be days to first self-reported recurrence of an episode of activity-limiting LBP. The secondary outcomes will include: days to first self–reported recurrence of an episode of LBP, days to first self-reported recurrence of an episode of LBP leading to care seeking, and the impact of LBP over a 12-month period. All participants will be followed up monthly for a minimum of 12 months or until they have a recurrence of activity-limiting LBP. All participants will also be followed-up at 3, 6, 9, and 12 months to assess the impact of back pain, physical activity levels, study program adherence, credibility, and adverse events.

Limitations. Participants and therapists will not be masked to the interventions.

Conclusions. To our knowledge, this will be the first large, high-quality randomized controlled trial investigating the effectiveness of a McKenzie method–based self–management approach for preventing recurrences of LBP. If this approach is found to be effective, it will offer a low-cost, simple method for reducing the personal and societal burdens of LBP.
Out of many, one? U.S. sub-national political-economies in the post-welfare reform era
Authors: Bjorklund Eric
Published: April 2017

Despite increased research on social policy variation among U.S. states, few have examined U.S. state-level political-economies in the wake of welfare reform. This is problematic given the ability of state-level political-economies to solidify patterns of stratification. I address this by analyzing four dimensions of U.S. state-level political-economies in the welfare reform era: labor policy, family/social policy, tax policy, and state imposed fiscal constraint. From this analysis I delineate five state-level political-economic types: (1) progressive; (2) contested progressive; (3) boilerplate; (4) frontier conservative; and (5) Southern conservative. Four determinants of type membership are also evaluated: Democratic Party control, unionization, racial fractionalization and income per capita. While my results demonstrate these as meaningful determinants, patterns of association vary by type, thus suggesting a revision to the assumed progressive/conservative continuum of U.S. social policy and political-economies. I conclude by elaborating how my analysis expands our understanding of U.S., and cross-national, political-economies.