bluuebunny/crossref_metadata_2025 huggingface dataset:
Site occupancy and luminescence properties of Ca3Ln(AlO)3(BO3)4:Ce3+,Tb3+,Mn2+ (Ln = Y, Gd)
Authors: Wen Dawei , Kato Hideki , Kobayashi Makoto , Yamamoto Shunsuke , Mitsuishi Masaya , Kakihana Masato
Published: April 2017

In Ca3Ln(AlO)3(BO3)4, ions with larger radii tend to occupy the lower coordination site, while smaller ions prefer to occupy the higher coordination site. This phenomenon is explained by the spatial hindrance Ca3Ln(AlO)3(BO3)4:Ce3+,Tb3+,Mn2+ phosphors exhibit white emission.
Vacuum deposition of high-quality thin films displaying spin transition near room temperature
Authors: Shalabaeva Victoria , Rat Sylvain , Manrique-Juarez Maria Dolores , Bas Alin-Ciprian , Vendier Laure , Salmon Lionel , Molnár Gábor , Bousseksou Azzedine
Published: April 2017

We report on thermally evaporated, crystalline films of [Fe(HB(tz)3)2] (tz = triazolyl), which display spin transition around 338 K.
Patterned photonic crystals for hiding information
Authors: Li Yanan , Zhou Xue , Yang Qiang , Li Yudong , Li Wenbo , Li Huizeng , Chen Shuoran , Li Mingzhu , Song Yanlin
Published: April 2017

A prototype design for hiding messages in photonic crystals was developed by building a coding relationship between optical stopbands and information units.
AAV-iRFP labelling of human mesenchymal stem cells for near-infrared fluorescence imaging
Authors: Huang Can , Lan Wenjun , Wang Feifei , Zhang Chun , Liu Xiaomei , Chen Qin
Published: April 2017

Near-IR fluorescence (NIRF) imaging is a new technology using IR fluorescent protein (iRFP) gene labelling and is potentially useful for in vivo applications. In the present study, we expressed iRFP and the TNF-related apoptosis inducing ligand gene in mesenchymal stem cells (MSCs) using adeno-associated virus (AAV) and showed that iRFP-labelled MSCs can be detected by fluorescence microscopy. We injected mice with MSCs labelled with AAV-iRFP, which we were then able to detect by whole-animal NIRF imaging. Our technique provides a visualizable, convenient and sensitive platform for research on tracking the fate of transplanted MSC cells in vivo.
Experimental operation of drone micro‐SAR with efficient time‐varying velocity compensation
Authors: Lee W.K. , Lee K.W.
Published: April 2017

Drone platform for synthetic aperture radar (SAR) operation has been little publicised due to the technical constraint of the payload implementation. Multi‐rotor drone based SAR is distinguished from the conventional airborne system by the increased sensitivity to turbulences and poor motion stability. Extremely limited power and mass budgets may prevent the use of extra hardware for motion compensation and the difficulty of SAR focusing is aggravated. Feasibility of micro‐SAR drone operation is investigated through field tests, where experimental SAR images are acquired over ground targets. Attempts have been made to implement near‐real‐time compensation for non‐uniform motion disturbance. Finally, experimental drone SAR operation is validated through calibrated SAR images.
Temperature dependent evolution of dynamic heterogeneity in metallic glass
Authors: Luo P. , Li M. X. , Jiang H. Y. , Wen P. , Bai H. Y. , Wang W. H.
Published: April 2017

Substantial efforts in theoretical and experimental studies have demonstrated that the dynamics in supercooled liquids is spatially heterogeneous. However, a complete description concerning the dynamic heterogeneity evolution from liquid to rigid glass is still lacking. Here, by a combining study of the dynamic and static mechanical responses, we quantify the characterization of dynamic heterogeneity and its temperature evolution spanning an unprecedented broad temperature range in metallic glass. We show that the dynamic heterogeneity persists from the warm liquid state into the rigid glassy state and becomes progressively pronounced with cooling, accompanied by increasing breadth of the relaxation rate dispersion.
New density profile reconstruction methods in X-mode reflectometry
Authors: B. Morales R. , Hacquin S. , Heuraux S. , Sabot R.
Published: April 2017

The reconstruction method published by Bottollier-Curtet and Ichtchenko in 1987 has been the standard method of density profile reconstruction for X-mode reflectometry ever since, with only minor revision. Envisaging improved accuracy and stability of the reconstruction method, functions more complex than the linear are evaluated here to describe the refractive index shape in each integration step. The stability and accuracy obtained when using parabolic and fixed or adaptative fractional power functions are compared to the previous method and tested against spurious events and phase noise. The developed relation from the plasma parameters to the best integration shapes allows for the optimization of the reconstruction for any profile shape. In addition, the density profiles can be reconstructed using less probing frequencies without accuracy loss, which speed up the reconstruction algorithm and enable real-time monitoring of faster density profile evolution.
Hydrogenated amorphous silicon oxide (a-SiOx:H) single junction solar cell with 8.8% initial efficiency by reducing parasitic absorptions
Authors: Kim Do Yun , Guijt Erwin , van Swaaij René A. C. M. M. , Zeman Miro
Published: April 2017

Hydrogenated amorphous silicon oxide (a-SiOx:H) solar cells have been successfully implemented to multi-junction thin film silicon solar cells. The efficiency of these solar cells, however, has still been below that of state-of-the-art solar cells mainly due to the low Jsc of the a-SiOx:H solar cells and the unbalanced current matching between sub-cells. In this study, we carry out optical simulations to find the main optical losses for the a-SiOx:H solar cell, which so far was mainly optimized for Voc and fill-factor (FF). It is observed that a large portion of the incident light is absorbed parasitically by the p-a-SiOx:H and n-a-SiOx:H layers, although the use of these layers leads to the highest Voc × FF product. When a more transparent and conductive p-nc-SiOx:H layer is substituted for the p-a-SiOx:H layer, the parasitic absorption loss at short wavelengths is notably reduced, leading to higher Jsc. However, this gain in Jsc by the use of the p-nc-SiOx:H compromises the Voc. When replacing the n-a-SiOx:H layer for an n-nc-SiOx:H layer that has low n and k values, the plasmonic absorption loss at the n-nc-SiOx:H/Ag interfaces and the parasitic absorption in the n-nc-SiOx:H are substantially reduced. Implementation of this n-nc-SiOx:H leads to an increase of the Jsc without a drop of the Voc and FF. When implementing a thinner p-a-SiOx:H layer, a thicker i-a-SiOx:H layer, and an n-nc-SiOx:H layer, a-SiOx:H solar cells with not only high Jsc but also high Voc and FF can be fabricated. As a result, an 8.8% a-SiOx:H single junction solar cell is successfully fabricated with a Voc of 1.02 V, a FF of 0.70, and a Jsc of 12.3 mA/cm2, which is the highest efficiency ever reported for this type of solar cell.
Improvement of electrical-resistivity model for polycrystalline films of metals with non-spherical Fermi surface: A case for Os films
Authors: Li S. L. , Zhang Q. Y. , Ma C. Y. , Zhang C. , Yi Z. , Pan L. J.
Published: April 2017

Osmium (Os) is a hexagonal-close-packed metal with a non-spherical Fermi surface that seriously deviates from the assumption in the Mayadas-Shatzkes electrical-resistivity model (MS model) for the size effects of polycrystalline films of metals due to electron scattering by grain boundaries. In this work, we studied the resistivity of the Os films with different thicknesses as a function of temperature in the range of 20 to 296 K. The electron scattering by the surface was found to be unimportant in the contributions to the size effects of resistivity of Os films with a sufficient thickness. Based on the first-principles calculations, an analytical equation was suggested for correction to the MS model and used for fitting the temperature-dependent resistivity of the Os films. The results show that correction to the MS model is necessary and the residual resistivity caused by the defects and impurities cannot be neglected. In addition, the inhomogeneity of resistivity in the direction perpendicular to the film surface was discussed under an assumption of parallel circuits.
Bismuth iron garnet Bi3Fe5O12: A room temperature magnetoelectric material
Authors: Popova Elena , Shengelaya Alexander , Daraselia Dimitri , Japaridze David , Cherifi-Hertel Salia , Bocher Laura , Gloter Alexandre , Stéphan Odile , Dumont Yves , Keller Niels
Published: April 2017

The possibility to control the magnetic properties of a material with an electric field at room temperature via magnetoelectric (ME) coupling is highly desirable for modern applications. Here, we report the unambiguous observation of ME coupling above 300 K that is linear with respect to the electric field in a bismuth iron garnet (BIG). The ferromagnetic resonance technique with electric field modulation was used to quantify ME coupling in Bi3Fe5O12 thin films and patterned structures grown on garnet substrates. The measured coupling value is comparable with that observed for prototypal magnetoelectric Cr2O3. On the basis of our experimental results, the strength of this linear ME coupling is directly linked to the presence of bismuth ions inducing strong spin orbit coupling and to the appearance of local magnetic inhomogeneities related to the magnetic domain structure. The unprecedented combination of magnetic, optical, and magnetoelectrical properties in the BIG is expected to trigger significant interest for technological applications as well as for theoretical studies.
Photoresponse in gate-tunable atomically thin lateral MoS2 Schottky junction patterned by electron beam
Authors: Katagiri Y. , Nakamura T. , Ohata C. , Katsumoto S. , Haruyama J.
Published: April 2017

Among various atomically thin two-dimensional materials, molybdenum disulphide (MoS2) is attracting considerable attention because of its direct energy bandgap in the 2H-semiconducting phase. On the other hand, a 1T-metallic phase, which is very important for unique applications, has been created by various methods. Recently, we demonstrated the creation of in-plane 1T-metal/2H-semiconductor MoS2 lateral Schottky junctions by using electron beam irradiation techniques and revealed their unique electrical properties. Here, we report the optoelectronic measurements proving the formation of this few-layer MoS2 lateral Schottky junction. A large photocurrent is confirmed in the reverse bias voltage regime, while it decreases with increasing distance between an electrode placed on the 2H region and the 2H/1T junction. These results suggest a concentration of high electric field and rapid dissociation of photogenerated excitons at the few-layer lateral Schottky junction, which are beneficial for highly efficient photodetectors.
Temperature-dependent frictional properties of ultra-thin boron nitride nanosheets
Authors: Qu Wenyang , Chen Xiaoming , Ke Changhong
Published: April 2017

We investigate the temperature-dependent frictional properties of mono- and few-layer hexagonal boron nitride nanosheets (BNNSs) by using atomic force microscopy (AFM). The measurements reveal that a modest increase in sample temperature results in a substantial decrease of the frictional force between a silicon AFM tip and a BNNS, and the frictional force change is modulated by the scan velocity of the AFM tip and the number of layers in the BNNS. The activation energy of the contact rupture for the examined BNNSs is found to be around 0.35 eV, which is substantially higher than the reported values for graphene. The observed high activation energy for the BNNS is ascribed to its electronically and topographically corrugated surface, which originates from the polarized nature of B-N bonds and the size difference of B and N atoms. The findings are useful to better understand the physical properties of hexagonal BNNS materials and in the pursuit of their applications, such as substrate materials in nano electronic devices.
Comparison of different bonding techniques for efficient strain transfer using piezoelectric actuators
Authors: Ziss Dorian , Martín-Sánchez Javier , Lettner Thomas , Halilovic Alma , Trevisi Giovanna , Trotta Rinaldo , Rastelli Armando , Stangl Julian
Published: April 2017

In this paper, strain transfer efficiencies from a single crystalline piezoelectric lead magnesium niobate-lead titanate substrate to a GaAs semiconductor membrane bonded on top are investigated using state-of-the-art x-ray diffraction (XRD) techniques and finite-element-method (FEM) simulations. Two different bonding techniques are studied, namely, gold-thermo-compression and polymer-based SU8 bonding. Our results show a much higher strain-transfer for the “soft” SU8 bonding in comparison to the “hard” bonding via gold-thermo-compression. A comparison between the XRD results and FEM simulations allows us to explain this unexpected result with the presence of complex interface structures between the different layers.
Investigation of an anomalous hump phenomenon in via-type amorphous In-Ga-Zn-O thin-film transistors under positive bias temperature stress
Authors: Yang Jianwen , Liao Po-Yung , Chang Ting-Chang , Chen Bo-Wei , Huang Hui-Chun , Su Wan-Ching , Chiang Hsiao-Cheng , Zhang Qun
Published: April 2017

Amorphous InGaZnO thin film transistors (a-IGZO TFTs) with an etching-stop layer (ESL) exhibit an anomalous negative shift of threshold voltage (Vth) under positive bias temperature stress. TFTs with wider and shorter channels show a clear hump phenomenon, resulting from the existence of both main channels and parasitic channels. The electrons trapped in the gate insulator are responsible for the positive shift in the main channel characteristics. The electrons trapped near the IGZO edges and the holes injected into the ESL layer above InGaZnO (IGZO) jointly determine the shift of the parasitic TFT performance.
Human health alters the sustainability of fishing practices in East Africa
Authors: Fiorella Kathryn J. , Milner Erin M. , Salmen Charles R. , Hickey Matthew D. , Omollo Dan O. , Odhiambo Abdi , Mattah Brian , Bukusi Elizabeth A. , Fernald Lia C. H. , Brashares Justin S.
Published: April 2017

Significance

We accept that the environment influences human health, but we know little about how human health affects the environment. However, millions of people around the world rely on natural resources for food and livelihoods and confront a high burden of illness. Experience of illness may change people’s physical capacities, outlook, and planning horizons and shape how they engage with the environment. We analyze these impacts in fishing communities of Lake Victoria, Kenya. Although illness may cause the sickest individuals not to fish, many fishers continue fishing but shift their methods. When sick, fishers use methods that are less physically demanding but illegal and environmentally destructive. Our findings suggest that environmental sustainability may be integrally shaped by the health of resource users.
Anomalous Anderson localization behaviors in disordered pseudospin systems
Authors: Fang A. , Zhang Z. Q. , Louie Steven G. , Chan C. T.
Published: April 2017

Significance

Wave propagation through a 1D disordered potential is always confined spatially due to the constructive interference in the backward direction. This “Anderson localization” behavior applies to all previously known 1D disordered systems in nature. Here, we show that wave propagating in 2D pseudospin-1 systems with 1D disorder has unique localization behaviors. In all conventional materials, stronger disorder always induces stronger localization. However, the localization in pseudospin-1 systems actually becomes weaker after the randomness increases beyond a critical value and a sharp transition separates the localization behavior into two regimes with different localization characteristics. Pseudospin-1 systems have been achieved in artificial crystals such as metamaterials and ultracold atom systems, which would be interesting platforms to observe the anomalous localization behaviors.
SMARCE1 is required for the invasive progression of in situ cancers
Authors: Sokol Ethan S. , Feng Yu-Xiong , Jin Dexter X. , Tizabi Minu D. , Miller Daniel H. , Cohen Malkiel A. , Sanduja Sandhya , Reinhardt Ferenc , Pandey Jai , Superville Daphne A. , Jaenisch Rudolf , Gupta Piyush B.
Published: April 2017

Significance

More than half of ductal carcinoma in situ (DCIS) lesions will never progress to invasive breast cancers. However, the factors that drive invasion are not well understood. Our findings establish SMARCE1 as a clinically relevant factor that promotes the invasive progression of early-stage breast cancers. SMARCE1 drives invasion by serving as a master regulator of genes encoding proinvasive ECM and proteases required to degrade basement membrane. In functional studies in 3D cultures and animal models, SMARCE1 is dispensable for tumor growth but is required for the invasive and metastatic progression of cancers. In patients, SMARCE1 expression specifically identifies early-stage breast, lung, and ovarian cancers that are likely to eventually progress and metastasize.
Optimization of a Plaque Neutralization Test (PNT) to Identify the Exposure History of Pacific Herring to Viral Hemorrhagic Septicemia Virus (VHSV)
Authors: Hart Lucas M. , MacKenzie Ashley , Purcell Maureen K. , Powers Rachel L. , Hershberger Paul K.
Published: April 2017

Methods for a plaque neutralization test (PNT) were optimized for the detection and quantification of viral hemorrhagic septicemia virus (VHSV) neutralizing activity in the plasma of Pacific Herring Clupea pallasii. The PNT was complement dependent, as neutralizing activity was attenuated by heat inactivation; further, neutralizing activity was mostly restored by the addition of exogenous complement from specific-pathogen-free Pacific Herring. Optimal methods included the overnight incubation of VHSV aliquots in serial dilutions (starting at 1:16) of whole test plasma containing endogenous complement. The resulting viral titers were then enumerated using a viral plaque assay in 96-well microplates. Serum neutralizing activity was virus-specific as plasma from viral hemorrhagic septicemia (VHS) survivors demonstrated only negligible reactivity to infectious hematopoietic necrosis virus, a closely related rhabdovirus. Among Pacific Herring that survived VHSV exposure, neutralizing activity was detected in the plasma as early as 37 d postexposure and peaked at approximately 64 d postexposure. The onset of neutralizing activity was slightly delayed in fish reared at 7.4°C relative to those in warmer temperatures (9.9°C and 13.1°C); however, neutralizing activity persisted for at least 345 d postexposure in all temperature treatments. It is anticipated that this novel ability to assess VHSV neutralizing activity in Pacific Herring will enable retrospective comparisons between prior VHS infections and year-class recruitment failures. Additionally, the optimized PNT could be employed as a forecasting tool capable of identifying the potential for future VHS epizootics in wild Pacific Herring populations.

Received November 7, 2016; accepted January 14, 2017 Published online April 4, 2017
Inhibition of Grass Carp Reovirus Infection by DNA Aptamers against S10 Protein
Authors: Liang Hongru , Fu Xiaozhe , Liu Lihui , Lin Qiang , Guo Huizhi , Li Yonggang , Liu JiaXu , Huang Zhibin , Li Ningqiu
Published: April 2017

Grass Carp reovirus (GCRV) is one of the most pathogenic agents among aquareovirus isolates and has the ability to cause a severe epidemic outbreak of hemorrhagic disease, thus resulting in both a high mortality rate during the culture of Grass Carp Ctenopharyngodon idella and an enormous economic loss. Aptamers have been demonstrated to have strong promising applications in antiviral drug development. In the present study, a complementary DNA fragment encoding the S10 gene of GCRV was cloned. The S10 protein was expressed and purified. Aptamers for S10 protein were selected by the method of selective evolution of ligands by exponential enrichment (SELEX), and their characteristics and antiviral actions were examined. All targeting-selected aptamers formed a similar structure, forming a 5–7 base loop at the terminus. The results show that the aptamers could inhibit the GCRV infection. The most significant inhibitory effect was obsereved when the aptamers were added to the cell culture for 1 h before the cells were infected by GCRV. Our data showed that these novel molecular agents could be considered suitable candidates for anti-GCRV therapy.

Received August 23, 2016; accepted February 5, 2017Published online April 5, 2017
Oculomotor capture is influenced by expected reward value but (maybe) not predictiveness
Authors: Le Pelley Mike E , Pearson Daniel , Porter Alexis , Yee Hannah , Luque David
Published: April 2017

A large body of research has shown that learning about relationships between neutral stimuli and events of significance – rewards or punishments – influences the extent to which people attend to those stimuli in the future. However, different accounts of this influence differ in terms of the critical variable that is proposed to determine learned changes in attention. We describe two experiments using eye-tracking with a rewarded visual search procedure to investigate whether attentional capture is influenced by the predictiveness of stimuli (i.e., the extent to which they provide information about upcoming events) or by their absolute associative value (i.e., the expected incentive value of the outcome that a stimulus predicts). Results demonstrated a clear influence of associative value on the likelihood that stimuli will capture eye-movements, but the evidence for a distinct influence of predictiveness was less compelling. The results of these experiments can be reconciled within a simple account under which attentional prioritization is a monotonic function of the expected, subjective value of the reward that is signalled by a stimulus.
On the mesh nonsingularity of the moving mesh PDE method
Authors: Huang Weizhang , Kamenski Lennard
Published: April 2017

The moving mesh PDE (MMPDE) method for variational mesh generation and adaptation is studied theoretically at the discrete level, in particular the nonsingularity of the obtained meshes. Meshing functionals are discretized geometrically and the MMPDE is formulated as a modified gradient system of the corresponding discrete functionals for the location of mesh vertices. It is shown that if the meshing functional satisfies a coercivity condition, then the mesh of the semi-discrete MMPDE is nonsingular for all time if it is nonsingular initially. Moreover, the altitudes and volumes of its elements are bounded below by positive numbers depending only on the number of elements, the metric tensor, and the initial mesh. Furthermore, the value of the discrete meshing functional is convergent as time increases, which can be used as a stopping criterion in computation. Finally, the mesh trajectory has limiting meshes which are critical points of the discrete functional. The convergence of the mesh trajectory can be guaranteed when a stronger condition is placed on the meshing functional. Two meshing functionals based on alignment and equidistribution are known to satisfy the coercivity condition. The results also hold for fully discrete systems of the MMPDE provided that the time step is sufficiently small and a numerical scheme preserving the property of monotonically decreasing energy is used for the temporal discretization of the semi-discrete MMPDE. Numerical examples are presented.
Sex, Obesity, and Blood Pressure Among African American Adolescents: The Jackson Heart KIDS Pilot Study
Authors: Bruce Marino A , Beech Bettina M , Norris Keith C , Griffith Derek M , Sims Mario , Thorpe Roland J
Published: April 2017

BACKGROUND

This study examined the degree to which sex, weight status, and the presence of hypertension and obesity in parents/grandparents were associated with systolic (SBP) and diastolic (DBP) blood pressure (BP) among African American youth in a pilot offspring study examining obesity-related cardiovascular disease (CVD) risks among adolescents.

METHODS

Data for this study were drawn from 212 adolescents (mean age 15.2 ± 2.2 years, 50.5% female) participating in the Jackson Heart Kids Pilot Study – an offspring cohort study examining cardiovascular disease risks among descendants of Jackson Heart Study participants. SBP (mean 114.4 ± 11.8 mm Hg) and DBP (mean 66.8 ± 9.0 mm Hg) were the primary outcomes. Weight status (46.1% normal weight, 30.1% overweight, 23.6% obese) was the key independent variable. Other covariates were attempts to lose weight, fruit and vegetable consumption, physical activity, and spirituality.

RESULTS

Fully adjusted linear regression models of the total sample produced results indicating that obesity was associated with BP (SBP: β = 7.08, P < 0.01; DBP: β = 8.14, P < 0.001). Sex-stratified analyses indicated that overweight and obesity were associated with SBP (overweight: β = 6.77, P < 0.01; obese: β = 11.65, P < 0.001) and obesity was correlated with DBP (β = 9.86, P < 0.001) among males. For females, overweight was correlated with SBP (β = 4.11, P < 0.05) while obesity was associated with DBP (β = 6.98, P < 0.01). Attempting to lose weight was inversely related to SBP (β = −4.01, P < 0.05) in the full sample and among males (β = −11.94, P < 0.001). Familial presence of hypertension and/or obesity was significantly associated with SBP among adolescent females but not males.

CONCLUSIONS

The relationship between weight status, familial hypertension and obesity status, and BP among adolescents vary by sex. This study underscores the need for additional research investigating the relationship between individual sex, weight status, BP and familial BP, and obesity status on risk among African American adolescents.
StrandScript: evaluation of Illumina genotyping array design and strand correction
Authors: Wang Jing , Samuels David C , Shyr Yu , Guo Yan
Published: April 2017

After the introduction of high-throughput sequencing, genotyping arrays continue to be a viable source for conducting large-scale genetic studies. Currently, Illumina is one of the largest genotyping array manufacturers. One technical issue that has always plagued the post-processing of Illumina genotyping array data is the strand definition. Against convention, Illumina uses their own definition of strand, which is inconsistent with the standard reference forward and reverse definition. This issue has been a major obstacle in the consistency of reporting, meta-analysis and correct interpretation of phenotype association results. To date, the strand issue has not been adequately addressed, prompting us to develop StrandScript, a tool that can convert all genotyping data generated from Illumina genotyping arrays to the reference forward strand. StrandScript works independently of the Illumina array version and is future proof for newer Illumina array designs. Furthermore, StrandScript can examine an Illumina genotyping array manifest file and can detect all problematic SNPs, including SNPs with wrong RS ID and SNPs with mismatched probe sequences. Here, we introduce StrandScript’s design and development, and demonstrate its effectiveness using real genotyping data.

Availability and Implementation

https://github.com/seasky002002/Strandscript

Supplementary information

Supplementary data are available at Bioinformatics online.
Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data
Authors: Alzahrani Majed , Kuwahara Hiroyuki , Wang Wei , Gao Xin
Published: April 2017

Motivation

Growth phenotype profiling of genome-wide gene-deletion strains over stress conditions can offer a clear picture that the essentiality of genes depends on environmental conditions. Systematically identifying groups of genes from such high-throughput data that share similar patterns of conditional essentiality and dispensability under various environmental conditions can elucidate how genetic interactions of the growth phenotype are regulated in response to the environment.

Results

We first demonstrate that detecting such ‘co-fit’ gene groups can be cast as a less well-studied problem in biclustering, i.e. constant-column biclustering. Despite significant advances in biclustering techniques, very few were designed for mining in growth phenotype data. Here, we propose Gracob, a novel, efficient graph-based method that casts and solves the constant-column biclustering problem as a maximal clique finding problem in a multipartite graph. We compared Gracob with a large collection of widely used biclustering methods that cover different types of algorithms designed to detect different types of biclusters. Gracob showed superior performance on finding co-fit genes over all the existing methods on both a variety of synthetic data sets with a wide range of settings, and three real growth phenotype datasets for E. coli, proteobacteria and yeast.

Availability and Implementation

Our program is freely available for download at http://sfb.kaust.edu.sa/Pages/Software.aspx.

Supplementary information

Supplementary data are available at Bioinformatics online.
EzMap: a simple pipeline for reproducible analysis of the human virome
Authors: Czeczko Patrick , Greenway Steven C , de Koning A P Jason
Published: April 2017

In solid-organ transplant recipients, a delicate balance between immunosuppression and immunocompetence must be achieved, which can be difficult to monitor in real-time. Shotgun sequencing of cell-free DNA (cfDNA) has been recently proposed as a new way to indirectly assess immune function in transplant recipients through analysis of the status of the human virome. To facilitate exploration of the utility of the human virome as an indicator of immune status, and to enable rapid, straightforward analyses by clinicians, we developed a fully automated computational pipeline, EzMap, for performing metagenomic analysis of the human virome. EzMap combines a number of tools to clean, filter, and subtract WGS reads by mapping to a reference human assembly. The relative abundance of each virus present is estimated using a maximum likelihood approach that accounts for genome size, and results are presented with interactive visualizations and taxonomy-based summaries that enable rapid insights. The pipeline is automated to run on both workstations and computing clusters for all steps. EzMap automates an otherwise tedious and time-consuming protocol and aims to facilitate rapid and reproducible insights from cfDNA.

Availability and Implementation

EzMap is freely available at https://github.com/dekoning-lab/ezmap.

Supplementary information

Supplementary data are available at Bioinformatics online.
ploidyNGS: visually exploring ploidy with Next Generation Sequencing data
Authors: Augusto Corrêa dos Santos Renato , Goldman Gustavo Henrique , Riaño-Pachón Diego Mauricio
Published: April 2017

ploidyNGS is a model-free, open source tool to visualize and explore ploidy levels in a newly sequenced genome, exploiting short read data. We tested ploidyNGS using both simulated and real NGS data of the model yeast Saccharomyces cerevisiae. ploidyNGS allows the identification of the ploidy level of a newly sequenced genome in a visual way.

Availability and Implementation

ploidyNGS is available under the GNU General Public License (GPL) at https://github.com/diriano/ploidyNGS. ploidyNGS is implemented in Python and R.
Machine learning in computational biology to accelerate high-throughput protein expression
Authors: Sastry Anand , Monk Jonathan , Tegel Hanna , Uhlen Mathias , Palsson Bernhard O , Rockberg Johan , Brunk Elizabeth
Published: April 2017

Motivation

The Human Protein Atlas (HPA) enables the simultaneous characterization of thousands of proteins across various tissues to pinpoint their spatial location in the human body. This has been achieved through transcriptomics and high-throughput immunohistochemistry-based approaches, where over 40 000 unique human protein fragments have been expressed in E. coli. These datasets enable quantitative tracking of entire cellular proteomes and present new avenues for understanding molecular-level properties influencing expression and solubility.

Results

Combining computational biology and machine learning identifies protein properties that hinder the HPA high-throughput antibody production pipeline. We predict protein expression and solubility with accuracies of 70% and 80%, respectively, based on a subset of key properties (aromaticity, hydropathy and isoelectric point). We guide the selection of protein fragments based on these characteristics to optimize high-throughput experimentation.

Availability and implementation

We present the machine learning workflow as a series of IPython notebooks hosted on GitHub (https://github.com/SBRG/Protein_ML). The workflow can be used as a template for analysis of further expression and solubility datasets.

Supplementary information

Supplementary data are available at Bioinformatics online.
Incorporating prior information into differential network analysis using non-paranormal graphical models
Authors: Zhang Xiao-Fei , Ou-Yang Le , Yan Hong
Published: April 2017

Motivation

Understanding how gene regulatory networks change under different cellular states is important for revealing insights into network dynamics. Gaussian graphical models, which assume that the data follow a joint normal distribution, have been used recently to infer differential networks. However, the distributions of the omics data are non-normal in general. Furthermore, although much biological knowledge (or prior information) has been accumulated, most existing methods ignore the valuable prior information. Therefore, new statistical methods are needed to relax the normality assumption and make full use of prior information.

Results

We propose a new differential network analysis method to address the above challenges. Instead of using Gaussian graphical models, we employ a non-paranormal graphical model that can relax the normality assumption. We develop a principled model to take into account the following prior information: (i) a differential edge less likely exists between two genes that do not participate together in the same pathway; (ii) changes in the networks are driven by certain regulator genes that are perturbed across different cellular states and (iii) the differential networks estimated from multi-view gene expression data likely share common structures. Simulation studies demonstrate that our method outperforms other graphical model-based algorithms. We apply our method to identify the differential networks between platinum-sensitive and platinum-resistant ovarian tumors, and the differential networks between the proneural and mesenchymal subtypes of glioblastoma. Hub nodes in the estimated differential networks rediscover known cancer-related regulator genes and contain interesting predictions.

Availability and Implementation

The source code is at https://github.com/Zhangxf-ccnu/pDNA

Supplementary information

Supplementary data are available at Bioinformatics online.
Practical steps toward integrating economic, social and institutional elements in fisheries policy and management
Authors: Stephenson Robert L. , Benson Ashleen J. , Brooks Kate , Charles Anthony , Degnbol Poul , Dichmont Catherine M. , Kraan Marloes , Pascoe Sean , Paul Stacey D. , Rindorf Anna , Wiber Melanie
Published: April 2017

While international agreements and legislation call for incorporation of four pillars of sustainability, the social (including cultural), economic and institutional aspects (the ‘human dimension’) have been relatively neglected to date. Three key impediments have been identified: a relative lack of explicit social, economic and institutional objectives; a general lack of process (frameworks, governance) for routine integration of all four pillars of sustainability; and a bias towards biological considerations. Practical integration requires a ‘systems’ approach with explicit consideration of strategic and operational aspects of management; multidisciplinary or transdisciplinary evaluations; practical objectives for the four pillars of sustainability; appropriate participation; and a governance system that is able to integrate these diverse considerations in management. We challenge all involved in fisheries to immediately take five practical steps toward integrating ecological, economic, social and institutional aspects: (1) Adopt the perspective of the fishery as a ‘system’ with interacting natural, human and management elements; (2) Be aware of both strategic and operational aspects of fisheries assessment and management; (3) Articulate overarching objectives that incorporate all four pillars of sustainability; (4) Encourage appropriate (and diverse) disciplinary participation in all aspects of research, evaluation and management; and (5) Encourage development of (or emulate) participatory governance.
The influence of complex structure on the spatial dynamics of Atlantic cod (Gadus morhua) in the Gulf of Maine
Authors: Guan Lisha , Chen Yong , Staples Kevin W , Cao Jie , Li Bai
Published: April 2017

Atlantic cod (Gadus morhua) in the Gulf of Maine (GOM) is an iconic marine fishery stock that has experienced a substantial distributional shift since the mid-1990s. A geostatistical delta-generalized linear mixed model was utilized to hindcast yearly season-specific distributions of GOM cod. These distributions were calculated using the spring and fall bottom trawl survey data for the stock, along with cell-based bathymetry and bottom temperature data for the study area for the years 1982–2013. The centre of stock distribution (the centre of gravity), spatial extent in latitude and longitude, area occupied and median habitat temperature were estimated annually to quantify changes in the spatial dynamics of GOM cod. Time series of these distributional metrics were then used to evaluate the influences of climate change and density-dependent habitat selection on GOM cod’s distribution. Results showed that the rapid southwestward shift in the stock distribution after the late 1990s could not simply be attributed to decreasing stock abundance or warming bottom temperatures. The observed shift in cod distribution requires further investigation on whether it is possibly a result of other factors, like fluctuating productivity among subpopulations.
Estimating escapement of fish and invertebrates in a Danish anchor seine
Authors: Noack Thomas , Madsen Niels , Mieske Bernd , Frandsen Rikke P , Wieland Kai , Krag Ludvig A
Published: April 2017

The codend is generally presumed to be the place where the main selectivity of fish occurs in towed fishing gears, but other parts of the net have been found to contribute to the selectivity process of several invertebrate species. This means that conventional selectivity or survival studies may ignore the selectivity of net parts other than the codend for certain species. By attaching 12 small meshed collecting bags to different parts of a Danish anchor seine net and conducting normal commercial fishing activities, this study showed that there is a substantial escapement of fish and (especially) invertebrates from the forward parts of the seine net. For seven species of demersal fish, most fish escaped through the lower panel close to the codend. All invertebrate species were found in higher numbers in the collecting bags than in the codend where many organisms escaped in the lower panel of the wings or the belly. Mean levels of visible damage ranged from 1.00 to 3.25 for collected invertebrates and were similar for all gear parts. Common starfish (Asterias rubens), however, showed highest damage in the extension part of the net.
Does Intrawound Vancomycin Application During Spine Surgery Create Vancomycin-Resistant Organism?
Authors: Chotai Silky , Wright Patty W. , Hale Andrew T. , Jones Whitney A. , McGirt Matthew J. , Patt Joshua C. , Devin Clinton J.
Published: April 2017

BACKGROUND: Surgical site infection (SSI) following spine surgery is a morbid and expensive complication. The use of intrawound vancomycin is emerging as a solution to reduce SSI. The development of vancomycin-resistant pathogens is an understandable concern.

OBJECTIVE: To determine the occurrence of vancomycin-resistant SSI in patients with and without use of intrawound vancomycin.

METHODS: Patients undergoing elective spine surgery were dichotomized based on whether intrawound vancomycin was applied. Outcome was occurrence of SSI requiring return to the operating room within postoperative 90 days. The intrawound culture and vancomycin minimal inhibitory concentrations (MIC) were reviewed. Analyses were conducted to compare the pathogen profile and MIC for vancomycin in patients who received vancomycin and those who did not.

RESULTS: Of the total 2802 patients, 43% (n = 1215) had intrawound vancomycin application during the index surgery. The use of vancomycin was associated with significantly lower deep SSI rates (1.6% [n = 20] vs 2.5% [n = 40], P = .02). The occurrence of Staphylococcus aureus SSI was significantly lower in the patients who had application of intrawound vancomycin (32% vs 65%, P = .003). None of the patients who had application of intrawound vancomycin powder, and subsequently developed an S aureus SSI, demonstrated pathogens with resistance to vancomycin. All patients had MIC < 2 μg/mL, the vancomycin susceptibility threshold. The occurrence of gram-negative SSI (28% vs 7%) and culture negative fluid collection (16% vs 5%) was higher in the vancomycin cohort.

CONCLUSIONS: The use of intrawound vancomycin during the index spine surgery was protective against SSI following spine surgery. The application of intrawound vancomycin during index surgery does not appear to create vancomycin-resistant organisms in the event of an SSI.
Frontal Keyhole Craniotomy for Resection of Low- and High-Grade Gliomas
Authors: Burks Joshua D , Conner Andrew K , Bonney Phillip A , Glenn Chad A , Smitherman Adam D , Ghafil Cameron A , Briggs Robert G , Baker Cordell M , Kirch Nicholas I , Sughrue Michael E
Published: April 2017

BACKGROUND

Minimally invasive techniques are increasingly being used to access intra-axial brain lesions.

OBJECTIVE

To describe a method of resecting frontal gliomas through a keyhole craniotomy and share the results with these techniques.

METHODS

We performed a retrospective review of data obtained on all patients undergoing resection of frontal gliomas by the senior author between 2012 and 2015. We describe our technique for resecting dominant and nondominant gliomas utilizing both awake and asleep keyhole craniotomy techniques.

RESULTS

After excluding 1 patient who received a biopsy only, 48 patients were included in the study. Twenty-nine patients (60%) had not received prior surgery. Twenty-six patients (54%) were diagnosed with WHO grade II/III tumors, and 22 patients (46%) were diagnosed with glioblastoma. Twenty-five cases (52%) were performed awake. At least 90% of the tumor was resected in 35 cases (73%). Three of 43 patients with clinical follow-up experienced permanent deficits.

CONCLUSION

We provide our experience in using keyhole craniotomies for resecting frontal gliomas. Our data demonstrate the feasibility of using minimally invasive techniques to safely and aggressively treat these tumors.
Endoscopic Endonasal Approach to the Ventral Jugular Foramen: Anatomical Basis, Technical Considerations, and Clinical Series
Authors: Vaz-Guimaraes Francisco , Nakassa Ana Carolina I. , Gardner Paul A. , Wang Eric W. , Snyderman Carl H. , Fernandez-Miranda Juan C.
Published: April 2017

BACKGROUND: Surgical exposure of the jugular foramen (JF) is challenging given its complex regional anatomy and proximity to critical neurovascular structures.

OBJECTIVE: To describe the anatomical basis, surgical technique, and outcomes of a group of patients who underwent the endoscopic endonasal approach to the JF.

METHODS: Five silicon-injected anatomical specimens were prepared for dissection. Additionally, a chart review was conducted through our patient database, searching for endonasal exposure of the JF. Demographic data, clinical presentation, pathological findings, extent of resection in the JF, and occurrence of complications were analyzed.

RESULTS: The endonasal exposure of the JF requires 3 sequential steps: a transpterygoid, a “far-medial,” and an “extreme-medial” approach. Mobilization or transection of the cartilaginous portion of the eustachian tube (ET) is necessary. In the clinical series, cranial neuropathies were the presenting symptoms in 16 patients (89%). Eighteen tumors (10 chondrosarcomas, 7 chordomas, 1 adenocarcinoma) extended secondarily into the JF. Total tumor resection was achieved in 10 patients (56%), near total (≥90%) in 6 (33%), and subtotal (<90%) in 2 (11%). ET dysfunction (75% of cases), transient palatal numbness (17%), cerebrospinal fluid leakage (17%), and lower cranial nerve palsy (17%) were the most common postoperative complications. There were no carotid artery or jugular vein injuries.

CONCLUSION: The endoscopic endonasal approach to the JF requires mobilization or transection of the cartilaginous portion of the ET. This maneuver provides a safe infrapetrosal surgical route to the JF. It may be considered a valid option, in well-selected cases, for resection of malignant and recurrent cranial base tumors.
Surgery After Primary Radiation Treatment for Sporadic Vestibular Schwannomas: Case Series
Authors: Breshears Jonathan D. , Osorio Joseph A. , Cheung Steven W. , Barani Igor J. , Theodosopoulos Philip V.
Published: April 2017

BACKGROUND: As radiation has become an increasingly popular primary treatment option for sporadic vestibular schwannomas, there is a minority of tumors that do not respond favorably to radiation. Data on repeat radiosurgery are emerging, and salvage surgery has been associated with increased technical difficulty and poor facial nerve outcomes.

OBJECTIVE: To review the current literature and report our results with surgical resection of sporadic vestibular schwannomas that have failed primary radiation treatment.

METHODS: This is a retrospective, single-surgeon case series of patients with sporadic vestibular schwannomas who failed primary radiation treatment and underwent subsequent surgical resection. We analyze demographics, clinical information, and intraoperative findings, focusing on facial nerve functional outcomes and extent of resection.

RESULTS: Between 2006 and 2015, 10 patients with sporadic vestibular schwannomas whose only prior treatment was radiation underwent microsurgical resection. Eight of 10 patients had a postoperative House-Brackmann score of 1 at a median follow-up of 14 months, while 2 patients had House-Brackmann score of 4. Gross total resection was achieved in 7 of 10 cases. Near total resection was achieved in 2 cases, and only subtotal resection was achieved in 1 case.

CONCLUSION: Salvage surgery is a safe and effective option after failure of primary radiation and may offer benefits over repeat radiosurgery.