bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Common Carp on Trophic Dynamics of Sport Fishes in Shallow South Dakota Water Bodies
Authors: Letvin Alexander P. , Brown Michael L. , Bertrand Katie N. , Weber Michael J.
Published: February 2017

The Common Carp Cyprinus carpio is one of the most common freshwater fish invaders worldwide, creating adverse effects on water quality and impacting ecosystem structure and function. To assess how Common Carp impact food web dynamics, we compared the trophic dynamics of Bluegills Lepomis macrochirus and Largemouth Bass Micropterus salmoides in three lakes containing Common Carp populations with the trophic dynamics in three lakes without Common Carp. All six lakes were located in eastern South Dakota. Stable isotope analysis was used to estimate trophic positions and indicate energy sources utilized by adult and age‐0 fish. Additionally, diets of age‐0 Bluegills were analyzed to assess whether Common Carp were inhibiting ontogenetic diet shifts, and bomb calorimetry was used to evaluate differences in energy density of age‐0 fish prior to winter. Age‐0 fish and adult Bluegills derived significantly more energy from pelagic sources in the systems populated with Common Carp. Adult Bluegills in Common Carp systems remained at a relatively constant trophic position across their entire size range, whereas in non–Common Carp systems, the trophic positions of adult Bluegills tended to increase with size. Even though age‐0 fish relied more heavily on pelagic‐derived energy in the systems with Common Carp, significant differences were not observed in the autumn energy densities of age‐0 fish or in the age‐0 Bluegills’ diet. Given our results, Common Carp are unlikely to impact overwinter survival of age‐0 fish in these shallow systems. The present study illustrates the value of using stable isotopes for food web investigations and demonstrates that Common Carp do alter trophic dynamics of other fishes in the systems they invade, but responses differ depending upon the species and life stage.

Received February 11, 2016; accepted November 28, 2016 Published online February 21, 2017
Feeding by Bluefish and Weakfish along Riprap‐Hardened Shorelines: Comparisons with Adjacent Sandy Beach in Delaware Bay, USA
Authors: Torre Michael P. , Targett Timothy E.
Published: February 2017

Shoreline hardening alters the morphology of the intertidal zone and has been shown to impact various measures of shore zone habitat quality. Diet composition and stomach fullness of two predatory fishes, the Bluefish Pomatomus saltatrix and Weakfish Cynoscion regalis, were compared between natural (beach) shorelines and adjacent hardened (riprap) shorelines at three sites in Delaware Bay during July and August 2013 to assess differences in shore zone habitat function. Young Bluefish were available from one site, and their diet consisted primarily of Bay Anchovy Anchoa mitchilli, Atlantic Silversides Menidia menidia, and the mysid shrimp Neomysis americana. Bluefish diet composition differed significantly between beach and riprap during July, with Atlantic Silversides predominating in beach samples and mysids dominating riprap samples. Bluefish also had significantly higher feeding activity (stomach fullness) along beach shorelines than along riprap during August. For young Weakfish, diets were dominated by mysid shrimp, Bay Anchovy, polychaetes, and larval horseshoe crabs Limulus polyphemus and were similar between beach and riprap shorelines at all three sites. The presence of riprap appears to affect foraging by Bluefish, perhaps through alterations in prey fields, capture efficiencies, or both. Results reported here for both species demonstrate the need for further research to assess the effects of shoreline hardening on foraging by dominant species along the U.S. mid‐Atlantic coast.

Received November 16, 2016; accepted December 2, 2016 Published online February 21, 2017
Relationships between Chinook Salmon Swimming Performance and Water Quality in the San Joaquin River, California
Authors: Lehman Brendan , Huff David D. , Hayes Sean A. , Lindley Steven T.
Published: February 2017

There is currently only a limited understanding of the relationship between water quality and predation on Pacific salmon Oncorhynchus spp. smolts. We addressed the hypothesis that poor water quality will decrease a smolt's swimming performance and presumably its predator evasion capabilities. Predation is a major factor affecting salmon smolt survival throughout the San Joaquin River and the Sacramento–San Joaquin Delta of California. Prior studies have quantified predation rates, but the effect of water quality on predator evasion capability has not previously been evaluated. We quantified the swimming performance of juvenile Chinook Salmon O. tshawytscha in relation to water quality variables. The maximum swim speeds (Umax) of 45 hatchery‐reared smolts (7.1–9.9 cm FL) were measured in controlled (laboratory) and field environments by using a mobile swim tunnel respirometer; measurements were obtained before and after the fish received a 2‐d exposure to the lower San Joaquin River while being held in flow‐through cages. To sample across a diversity of environmental conditions, we conducted trials during a 6‐week period that coincided with the peak smolt out‐migration. Regression models were constructed to evaluate relationships between swimming performance and four water quality covariates (water temperature, turbidity, dissolved oxygen, and conductivity). We found negative relationships between Umax and both temperature and turbidity, and we described these relationships graphically. Our findings suggest that water quality management strategies with the potential to improve salmon smolt survival include managing temperatures and suspended sediment concentrations to optimize the swimming capacity of migrating smolts and possibly improve their ability to evade predators.

Received July 12, 2016; accepted December 6, 2016 Published online February 21, 2017
Polyphenols from flowers of Magnolia coco and their anti-glycation effects
Authors: Kato Nana , Kawabe Satoko , Ganeko Natsuki , Yoshimura Morio , Amakura Yoshiaki , Ito Hideyuki
Published: February 2017

We investigated the inhibitory effects of several plant extracts on advanced glycation end-products (AGEs) formation. Among tested samples, the flower extract of Magnolia coco showed significant inhibition of AGE formation. We isolated and characterized procyanidin oligomer and four other compounds from the flowers, and evaluated their inhibitory effects on AGE formation and the AGE-derived crosslink-cleaving activity of the isolated compounds.
Influence of AHRR Pro189Ala polymorphism on kidney functions
Authors: Nakayama Kazuhiro , Saito Shinichi , Watanabe Kazuhisa , Miyashita Hiroshi , Nishijima Fuyuhiko , Kamo Yoshie , Tada Koji , Ishizuka Satoshi , Niwa Toshimitsu , Iwamoto Sadahiko , Shimizu Hidehisa
Published: February 2017

The function of aryl hydrocarbon receptor repressor (AHRR) in the kidney is unclear. The present study investigated associations between AHRR Pro189Ala polymorphism and estimated glomerular filtration rates (eGFR), serum creatinine, and hemoglobin levels in 2775 Japanese adults without diabetes. In addition, we examined whether AHRR expression levels in the kidney of control and chronic kidney disease (CKD) rats were changed. Multiple linear regression analyses showed that carriers of the Ala allele had increased eGFR and lower concentrations of serum creatinine and hemoglobin (p < 0.05). Immunohistochemical analysis showed that the expression of AHRR was upregulated in the kidneys of rats with CKD. These findings suggest that AHRR plays distinct roles in kidney functions and hemoglobin values. The effects of the AHRR polymorphism might be intensified in the kidneys of patients with CKD.
A rapid method for analysis of fermentatively produced d-xylonate using ultra-high performance liquid chromatography and evaporative light scattering detection
Authors: Almqvist Henrik , Sandahl Margareta , Lidén Gunnar
Published: February 2017

An ultra-high performance liquid chromatography (UHPLC) based method for the analysis of d-xylonate was developed using an amide column in combination with an evaporative light scattering (ELS) detector. Separation of d-xylonate from other components of the fermentation medium was achieved. The dynamic range of the method was 0.2–7.0 g/L.
Microstructure of diffusion-brazing repaired IN738LC superalloy with uneven surface defect gap width
Authors: Ye Y. , Wei J. , Zou G. , Long W. , Bai H. , Wu A. , Liu L.
Published: February 2017

Slots with uneven width were cut by femtosecond laser in small plates of IN738LC superalloy to imitate service cracks. The ‘cracks’ were repaired by diffusion brazing using BNi-1a or a mixed filler alloy at 1100°C. The joint region was composed of isothermal solidification zone (ISZ), diffusion affected zone (DAZ) and precipitate zone (PZ). The compositions were different between the upper and lower ISZ due to the variation of gap width. The sample, repaired with two kinds of filler metals, had similar DAZ microstructure. PZ of mixed filler alloy bonded sample had a similar microstructure with that of BNi-1a, but less borides. The maximum gap sizes of complete isothermal solidification were almost the same for different filler alloys, followed a square root relationship with time. However, PZ of BNi-1a bonded was larger, resulting from a more base metal dissolution. The relationship between the PZ, ISZ and crack width is discussed.
Women's work–life preferences: reconceptualization and cross-country description over time
Authors: Schleutker Elina
Published: February 2017

According to Hakim's preference theory, women can be divided into three groups based on their work–family preferences: home-centered, adaptive and work-centered. Here it is argued that Hakim's conceptualization of the adaptive women is unsatisfactory, as it does not take into consideration how the adaptive women want to combine work and family. The paper offers a reconceptualization of the adaptive group. Based on when women want to return to employment after childbirth, and how many hours they would like to work, three types of adaptive women are distinguished: the home-oriented adaptive women, the truly adaptive women and the work-oriented adaptive women. To demonstrate the fruitfulness of the reconceptualization, a cross-sectional descriptive study of women's preferences over time is conducted by employing data from International Social Survey Programme.
Evaluation of Various Combinations of Alternative Protein Feedstuffs to Replace Soybean Meal in Diets for Pond-Raised Channel Catfish
Authors: Li Menghe H , Bosworth Brian G , Lucas Penelope M
Published: February 2017

A study was conducted in earthen ponds to evaluate the use of combinations of two or three alternative protein sources to replace soybean meal in diets for Channel Catfish Ictalurus punctatus. Six 28% protein diets containing various combinations of alternative protein feedstuffs—cottonseed meal, corn distillers dried grains with solubles, corn germ meal, peanut meal, and porcine meat and bone meal—were evaluated. Channel Catfish stockers (mean initial weight = 87 g/fish) were stocked into 30 earthen ponds (0.04 ha) at a density of 14,826 fish/ha with five ponds per dietary treatment. They were fed once a day to apparent satiation for a 183-d growing season. There were no significant differences in total diet fed, net yield, weight gain, survival, processing yield, and fillet proximate composition among dietary treatments. Results from the present study show that all soybean meal could be replaced by two or three moderate- and high-protein alternative feedstuffs without significantly affecting growth performance, processing yield, and fillet proximate composition of pond-raised Channel Catfish during food fish grow out.
DeepBlueR: large-scale epigenomic analysis in R
Authors: Albrecht Felipe , List Markus , Bock Christoph , Lengauer Thomas
Published: February 2017

Motivation

While large amounts of epigenomic data are publicly available, their retrieval in a form suitable for downstream analysis is a bottleneck in current research. The DeepBlue Epigenomic Data Server provides a powerful interface and API for filtering, transforming, aggregating and downloading data from several epigenomic consortia.

Results

To make public epigenomic data conveniently available for analysis in R, we developed an R/Bioconductor package that connects to the DeepBlue Epigenomic Data Server, enabling users to quickly gather and transform epigenomic data from selected experiments for analysis in the Bioconductor ecosystem.

Availability and Implementation

http://deepblue.mpi-inf.mpg.de/R.

Requirements

R 3.3, Bioconductor 3.4.

Supplementary information

Supplementary data are available at Bioinformatics online.
RefBool: a reference-based algorithm for discretizing gene expression data
Authors: Jung Sascha , Hartmann Andras , del Sol Antonio
Published: February 2017

Motivation

The identification of genes or molecular regulatory mechanisms implicated in biological processes often requires the discretization, and in particular booleanization, of gene expression measurements. However, currently used methods mostly classify each measurement into an active or inactive state regardless of its statistical support possibly leading to downstream analysis conclusions based on spurious booleanization results.

Results

In order to overcome the lack of certainty inherent in current methodologies and to improve the process of discretization, we introduce RefBool, a reference-based algorithm for discretizing gene expression data. Instead of requiring each measurement to be classified as active or inactive, RefBool allows for the classification of a third state that can be interpreted as an intermediate expression of genes. Furthermore, each measurement is associated to a p- and q-value indicating the significance of each classification. Validation of RefBool on a neuroepithelial differentiation study and subsequent qualitative and quantitative comparison against 10 currently used methods supports its advantages and shows clear improvements of resulting clusterings.

Availability and Implementation

The software is available as MATLAB files in the Supplementary Information and as an online repository (https://github.com/saschajung/RefBool).

Supplementary information

Supplementary data are available at Bioinformatics online.
Readmission After Craniotomy for Tumor: A National Surgical Quality Improvement Program Analysis
Authors: Dasenbrock Hormuzdiyar H. , Yan Sandra C. , Smith Timothy R. , Valdes Pablo A. , Gormley William B. , Claus Elizabeth B. , Dunn Ian F.
Published: February 2017

BACKGROUND: Although readmission has become a common quality indicator, few national studies have examined this metric in patients undergoing cranial surgery.

OBJECTIVE: To utilize the prospective National Surgical Quality Improvement Program 2011-2013 registry to evaluate the predictors of unplanned 30-d readmission and postdischarge mortality after cranial tumor resection.

METHODS: Multivariable logistic regression was applied to screen predictors, which included patient age, sex, tumor location and histology, American Society of Anesthesiologists class, functional status, comorbidities, and complications from the index hospitalization.

RESULTS: Of the 9565 patients included, 10.7% (n = 1026) had an unplanned readmission. Independent predictors of unplanned readmission were male sex, infratentorial location, American Society of Anesthesiologists class 3 designation, dependent functional status, a bleeding disorder, and morbid obesity (all P ≤ .03). Readmission was not associated with operative time, length of hospitalization, discharge disposition, or complications from the index admission. The most common reasons for readmission were surgical site infections (17.0%), infectious complications (11.0%), venous thromboembolism (10.0%), and seizures (9.4%). The 30-d mortality rate was 3.2% (n = 367), of which the majority (69.7%, n = 223) occurred postdischarge. Independent predictors of postdischarge mortality were greater age, metastatic histology, dependent functional status, hypertension, discharge to institutional care, and postdischarge neurological or cardiopulmonary complications (all P < .05).

CONCLUSION: Readmissions were common after cranial tumor resection and often attributable to new postdischarge complications rather than exacerbations of complications from the initial hospitalization. Moreover, the majority of 30-d deaths occurred after discharge from the index hospitalization. The preponderance of postdischarge mortality and complications requiring readmission highlights the importance of posthospitalization management.
National Rates, Causes, Risk Factors, and Outcomes Associated With 30-Day and 90-Day Readmissions Following Degenerative Posterior Cervical Spine Surgery Utilizing the Nationwide Readmissions Database
Authors: Rumalla Kavelin , Smith Kyle A , Arnold Paul M
Published: February 2017

BACKGROUND

Hospital readmissions have profound financial and clinical impacts. Analyses of 30-day readmissions following spine surgery have been previously reported utilizing administrative databases. However, time periods outside the initial 30 days have not been well studied. Furthermore, these databases have limitations regarding coding and institutional crossover.

OBJECTIVE

The authors sought to analyze 30-day and 90-day readmission rates and risk factors using the Nationwide Readmissions Database (NRD) in a retrospective cohort receiving elective, posterior cervical spine surgery for degenerative conditions.

METHODS

NRD is a new source containing approximately 50% of US hospitalizations, with patient-linkage numbers to longitudinally track patients. Patients 18 years of age or older were identified. Preoperative characteristics, demographics, and surgical characteristics were chosen for predictor variables. Thirty-day and 90-day readmission rates were calculated. Statistical analysis was completed using SPSS v.23 software via univariate and multivariate analyses.

RESULTS

Between January and September 2013, a total of 29 990 patients were identified. Readmission rates for 30- and 90-days were 5.4% and 10.0%, respectively. The most common reason for readmission during 30-day and 90-day periods was complications of surgical and/or medical care (31.0% vs 21.9%, respectively). The strongest risk factors for 30-day readmission included wound dehiscence, weekend admission at index hospitalization, coagulopathy, and incidental durotomy. The strongest risk factors for 90-day readmission included thromboembolic complications, postoperative hemorrhage, and comorbidities.

CONCLUSION

Identification of predictors of readmission is important to allow for changes in perioperative management to potentially reduce readmissions and improve outcomes. Additionally, knowledge about readmission risk factors allows for preoperative counseling.
Relationships Between Standing Frontal-Plane Knee Alignment and Dynamic Knee Joint Loading During Walking and Jogging in Youth Who Are Obese
Authors: Briggs Matthew S. , Bout-Tabaku Sharon , McNally Michael P. , Chaudhari Ajit M.W. , Best Thomas M. , Schmitt Laura C.
Published: February 2017

Background. Youth who are obese have high risk of poor knee health and cartilage damage. Understanding factors which may affect knee health in youth who are obese is critical for preservation of knee integrity and function.

Objective. This study compared standing frontal-plane knee alignment and knee loading patterns between youth who are obese and those of healthy weight and determine the association between knee alignment and knee loading patterns during walking and jogging.

Design. This study used a cross-sectional matched pair design.

Methods. Twenty youth who were obese and 20 youth who were healthy-weight (ages 11–18 years) were recruited. Three-dimensional motion analysis quantified standing frontal-plane knee alignment as well as frontal- and sagittal-plane knee moments during walking and jogging. Paired t-tests, multiple analysis of covariance, and Spearman's rank correlation coefficients were used for analysis.

Results. The youth who were obese demonstrated greater knee valgus in standing (P = 0.02), lower normalized peak external knee adduction moments during walking (P = 0.003), and greater normalized peak external knee extension moments during jogging (P = 0.003) compared with the youth who were healthy-weight. Standing knee alignment did not correlate with knee moments in the youth who were obese.

Limitations. Results are limited to small, homogeneous cohorts. The standing alignment methodology is not validated in this population and may limit interpretation of results.

Conclusion. Youth who are obese stand in more knee valgus and have altered knee loading patterns during walking and jogging compared with youth who are healthy-weight. Frontal-plane knee alignment does not correlate with frontal-plane knee loading patterns in youth who are obese. A better understanding of other mechanisms related to joint loading in youth who are obese is necessary to maintain long-term joint integrity in this population.
Population Genetic Structure of Venturia effusa, Cause of Pecan Scab, in the Southeastern United States
Authors: Bock Clive H. , Hotchkiss Michael W. , Young Carolyn A. , Charlton Nikki D. , Chakradhar Mattupalli , Stevenson Katherine L. , Wood Bruce W.
Published: February 2017

Venturia effusa is the most important pathogen of pecan in the southeastern United States. Little information exists on the population biology and genetic diversity of the pathogen. A hierarchical sampling of 784 isolates from 63 trees in 11 pecan orchards in the southeastern United States were screened against a set of 30 previously characterized microsatellite markers. Populations were collected from Georgia (n = 2), Florida (n = 1), Alabama (n = 2), Mississippi (n = 1), Louisiana (n = 1), Illinois (n = 1), Oklahoma (n = 1), Texas (n = 1), and Kansas (n = 1). Clonality was low in all orchard populations (≤10.1% of isolates), and there were consistently high levels of genotypic diversity (Shannon-Weiner’s index = 3.49 to 4.59) and gene diversity (Nei’s measure = 0.513 to 0.713). Analysis of molecular variance showed that, although 81% of genetic diversity occurred at the scale of the individual tree, 16% occurred between orchards and only 3% between trees within orchards. All populations could be differentiated from each other (P = 0.01), and various cluster analyses indicated that some populations were more closely related compared with other pairs of populations. This is indicative of some limited population differentiation in V. effusa in the southeastern United States. Bayesian and nearest-neighbor methods suggested eight clusters, with orchards from Georgia and Florida being grouped together. A minimum spanning tree of all 784 isolates also indicated some isolate identification with source population. Linkage disequilibrium was detected in all but one population (Kansas), although 8 of the 11 populations had <20% of loci at disequilibrium. A Mantel test demonstrated a relationship between physical and genetic distance between populations (Z = 11.9, r = 0.559, P = 0.001). None of the populations were at mutation-drift equilibrium. All but 3 of the 11 populations had a deficiency of gene diversity compared with that expected at mutation-drift equilibrium (indicating population expansion); the remaining populations had an excess of gene diversity compared with that expected at mutation-drift equilibrium (indicating a recent bottleneck). These observations are consistent with the known history of pecan and pecan scab, which is that V. effusa became an issue on cultivated pecan in the last approximately 120 years (recent population expansion). Recently reported mating type genes and the sexual stage of this fungus may help explain the observed population characteristics, which bear a strong resemblance to those of other well-characterized sexually reproducing ascomycete pathogens.
Magnetic field concentration assisted by epsilon-near-zero media
Authors: Liberal Iñigo , Li Yue , Engheta Nader
Published: February 2017

Strengthening the magnetic response of matter at optical frequencies is of fundamental interest, as it provides additional information in spectroscopy, as well as alternative mechanisms to manipulate light at the nanoscale. Here, we demonstrate theoretically that epsilon-near-zero (ENZ) media can enhance the magnetic field concentration capabilities of dielectric resonators. We demonstrate that the magnetic field enhancement factor is unbounded in theory, and it diverges as the size of the ENZ host increases. In practice, the maximal enhancement factor is limited by dissipation losses in the host, and it is found via numerical simulations that ENZ hosts with moderate losses can enhance the performance of a circular dielectric rod resonator by around one order of magnitude. The physical mechanism behind this process is the strongly inhomogeneous magnetic field distributions induced by ENZ media in neighbouring dielectrics. We show that this is an intrinsic property of ENZ media, and that the occurrence of resonant enhancement is independent of the shape of the host. These results might find applications in spectroscopy, in sensing, in light emission and, in general, in investigating light–matter interactions beyond electric dipole transitions.

This article is part of the themed issue ‘New horizons for nanophotonics’.
Electrical tuning of the polarization state of light using graphene-integrated anisotropic metasurfaces
Authors: Dutta-Gupta Shourya , Dabidian Nima , Kholmanov Iskandar , Belkin Mikhail A. , Shvets Gennady
Published: February 2017

Plasmonic metasurfaces have been employed for moulding the flow of transmitted and reflected light, thereby enabling numerous applications that benefit from their ultra-thin sub-wavelength format. Their appeal is further enhanced by the incorporation of active electro-optic elements, paving the way for dynamic control of light's properties. In this paper, we realize a dynamic polarization state generator using a graphene-integrated anisotropic metasurface (GIAM) that converts the linear polarization of the incident light into an elliptical one. This is accomplished by using an anisotropic metasurface with two principal polarization axes, one of which possesses a Fano-type resonance. A gate-controlled single-layer graphene integrated with the metasurface was employed as an electro-optic element controlling the phase and intensity of light polarized along the resonant axis of the GIAM. When the incident light is polarized at an angle to the resonant axis of the metasurface, the ellipticity of the reflected light can be dynamically controlled by the application of a gate voltage. Thus accomplished dynamic polarization control is experimentally demonstrated and characterized by measuring the Stokes polarization parameters. Large changes of the ellipticity and the tilt angle of the polarization ellipse are observed. Our measurements show that the tilt angle can be changed from positive values through zero to negative values while keeping the ellipticity constant, potentially paving the way to rapid ellipsometry and other characterization techniques requiring fast polarization shifting.

This article is part of the themed issue ‘New horizons for nanophotonics’.
Refractive index sensing with Fano resonances in silicon oligomers
Authors: Chong Katie E. , Orton Henry W. , Staude Isabelle , Decker Manuel , Miroshnichenko Andrey E. , Brener Igal , Kivshar Yuri S. , Neshev Dragomir N.
Published: February 2017

We demonstrate experimentally refractive index sensing with localized Fano resonances in silicon oligomers, consisting of six disks surrounding a central one of slightly different diameter. Owing to the low absorption and narrow Fano-resonant spectral features appearing as a result of the interference of the modes of the outer and the central disks, we demonstrate refractive index sensitivity of more than 150 nm RIU
−1
with a figure of merit of 3.8.

This article is part of the themed issue ‘New horizons for nanophotonics’.
Third-harmonic generation from Mie-type resonances of isolated all-dielectric nanoparticles
Authors: Melik-Gaykazyan Elizaveta V. , Shcherbakov Maxim R. , Shorokhov Alexander S. , Staude Isabelle , Brener Igal , Neshev Dragomir N. , Kivshar Yuri S. , Fedyanin Andrey A.
Published: February 2017

Subwavelength silicon nanoparticles are known to support strongly localized Mie-type modes, including those with resonant electric and magnetic dipolar polarizabilities. Here we compare experimentally the efficiency of the third-harmonic generation from isolated silicon nanodiscs for resonant excitation at the two types of dipolar resonances. Using nonlinear spectroscopy, we observe that the magnetic dipolar mode yields more efficient third-harmonic radiation in contrast to the electric dipolar (ED) mode. This is further supported by full-wave numerical simulations, where the volume-integrated local fields and the directly simulated nonlinear response are shown to be negligible at the ED resonance compared with the magnetic one.

This article is part of the themed issue ‘New horizons for nanophotonics’.
Double-resonant enhancement of third-harmonic generation in graphene nanostructures
Authors: You Jian Wei , You Jie , Weismann Martin , Panoiu Nicolae C.
Published: February 2017

Intriguing and unusual physical properties of graphene offer remarkable potential for advanced, photonics-related technological applications, particularly in the area of nonlinear optics at the deep-subwavelength scale. In this study, we use a recently developed numerical method to illustrate an efficient mechanism that can lead to orders of magnitude enhancement of the third-harmonic generation in graphene diffraction gratings. In particular, we demonstrate that by taking advantage of the geometry dependence of the resonance wavelength of localized surface-plasmon polaritons of graphene ribbons and discs one can engineer the spectral response of graphene gratings so that strong plasmonic resonances exist at both the fundamental frequency and third-harmonic (TH). As a result of this double-resonant mechanism for optical near-field enhancement, the intensity of the TH can be increased by more than six orders of magnitude.

This article is part of the themed issue ‘New horizons for nanophotonics’.
Chiral optical fields: a unified formulation of helicity scattered from particles and dichroism enhancement
Authors: Nieto-Vesperinas Manuel
Published: February 2017

We establish a general unified formulation which, using the optical theorem of electromagnetic helicity, shows that dichorism is a phenomenon arising in any scattering—or diffraction—process, elastic or not, of chiral electromagnetic fields by objects either chiral or achiral. It is shown how this approach paves the way to overcoming well-known limitations of standard circular dichroism, like its weak signal or the difficulties of using it with magnetodielectric particles. Based on the angular spectrum, representation of optical fields with only right circular or left circular plane waves, we introduce beams with transverse elliptic polarization and possessing a longitudinal component. Then, our formulation for general optical fields shows how to enhance the extinction rate of incident helicity (and therefore the dichroism signal) versus that of energy of the light scattered or emitted by a particle, or vice versa.

This article is part of the themed issue ‘New horizons for nanophotonics’.
Multipolar interference effects in nanophotonics
Authors: Liu Wei , Kivshar Yuri S.
Published: February 2017

Scattering of electromagnetic waves by an arbitrary nanoscale object can be characterized by a multipole decomposition of the electromagnetic field that allows one to describe the scattering intensity and radiation pattern through interferences of dominating multipole modes excited. In modern nanophotonics, both generation and interference of multipole modes start to play an indispensable role, and they enable nanoscale manipulation of light with many related applications. Here, we review the multipolar interference effects in metallic, metal–dielectric and dielectric nanostructures, and suggest a comprehensive view on many phenomena involving the interferences of electric, magnetic and toroidal multipoles, which drive a number of recently discussed effects in nanophotonics such as unidirectional scattering, effective optical antiferromagnetism, generalized Kerker scattering with controlled angular patterns, generalized Brewster angle, and non-radiating optical anapoles. We further discuss other types of possible multipolar interference effects not yet exploited in the literature and envisage the prospect of achieving more flexible and advanced nanoscale control of light relying on the concepts of multipolar interference through full phase and amplitude engineering.

This article is part of the themed issue ‘New horizons for nanophotonics’.
Creating a Community of Data Champions
Authors: Higman Rosie , Teperek Marta , Kingsley Danny
Published: February 2017

Research Data Management (RDM) presents an unusual challenge for service providers in Higher Education. There is increased awareness of the need for training in this area but the nature of discipline-specific practices involved make it difficult to provide training across a multi-disciplinary organisation. Whilst most UK universities now have a research data team of some description, they are often small and rarely have the resources necessary to provide targeted training to the different disciplines and research career stages that they are increasingly expected to support.

This practice paper describes the approach taken at the University of Cambridge to address this problem by creating a community of Data Champions. This collaborative initiative, working with researchers to provide training and advocacy for good RDM practice, allows for more discipline-specific training to be given, researchers to be credited for their expertise and an opportunity for those interested in RDM to exchange knowledge with others. The ‘community of practice’ model has been used in many sectors, including Higher Education, to facilitate collaboration across organisational units and this initiative will adopt some of the same principles to improve communication across a decentralised institution. The Data Champions initiative at Cambridge was launched in September 2016 and this paper reports on the early months, plans for building the community in the future and the possible risks associated with this approach to providing RDM services.
Reason’s Enemy Is Not Emotion: Engagement of Cognitive Control Networks Explains Biases in Gain/Loss Framing
Authors: Li Rosa , Smith David V. , Clithero John A. , Venkatraman Vinod , Carter R. McKell , Huettel Scott A.
Published: February 2017

In the classic gain/loss framing effect, describing a gamble as a potential gain or loss biases people to make risk-averse or risk-seeking decisions, respectively. The canonical explanation for this effect is that frames differentially modulate emotional processes – which in turn leads to irrational choice behavior. Here, we evaluate the source of framing biases by integrating functional magnetic resonance imaging (fMRI) data from 143 human participants performing a gain/loss framing task with meta-analytic data from over 8000 neuroimaging studies. We found that activation during choices consistent with the framing effect were most correlated with activation associated with the resting or default brain, while activation during choices inconsistent with the framing effect most correlated with the task-engaged brain. Our findings argue against the common interpretation of gain/loss framing as a competition between emotion and control. Instead, our study indicates that this effect results from differential cognitive engagement across decision frames.

Significance Statement

The biases frequently exhibited by human decision-makers have often been attributed to the presence of emotion. Using a large fMRI sample and analysis of whole-brain networks defined with the meta-analytic tool Neurosynth, we find that neural activity during frame-biased decisions are more significantly associated with default behaviors (and the absence of executive control) than with emotion. These findings point to a role for neuroscience in shaping longstanding psychological theories in decision science.
On the relationship between tumour growth rate and survival in non-small cell lung cancer
Authors: Mistry Hitesh B.
Published: February 2017

A recurrent question within oncology drug development is predicting phase III outcome for a new treatment using early clinical data. One approach to tackle this problem has been to derive metrics from mathematical models that describe tumour size dynamics termed re-growth rate and time to tumour re-growth. They have shown to be strong predictors of overall survival in numerous studies but there is debate about how these metrics are derived and if they are more predictive than empirical end-points. This work explores the issues raised in using model-derived metric as predictors for survival analyses. Re-growth rate and time to tumour re-growth were calculated for three large clinical studies by forward and reverse alignment. The latter involves re-aligning patients to their time of progression. Hence it accounts for the time taken to estimate re-growth rate and time to tumour re-growth but also assesses if these predictors correlate to survival from the time of progression. We found that neither re-growth rate nor time to tumour re-growth correlated to survival using reverse alignment. This suggests that the dynamics of tumours up until disease progression has no relationship to survival post progression. For prediction of a phase III trial we found the metrics performed no better than empirical end-points. These results highlight that care must be taken when relating dynamics of tumour imaging to survival and that bench-marking new approaches to existing ones is essential.
Local interactions lead to spatially correlated gene expression levels in bacterial groups
Authors: Vliet Simon van , Co Alma Dal , R. Winkler Annina , Spriewald Stefanie , Stecher Bärbel , Ackermann Martin
Published: February 2017

Many bacteria live in spatially structured assemblies where the microenvironment of a cell is shaped by the activities of its neighbors. Bacteria regulate their gene expression based on the inferred state of the environment. This raises the question whether the phenotypes of neighboring cells can become correlated through interactions via the shared microenvironment. Here, we addressed this question by following gene expression dynamics inEscherichia colimicrocolonies. We observed strong spatial correlations in the expression dynamics for pathways involved in toxin production, SOS-stress response, and metabolism. These correlations can partly be explained by a combination of shared lineage history and spatial gradients in the colony. Interestingly, we also found evidence for cell-cell interactions in SOS-stress response, methionine biosynthesis and overall metabolic activity. Together our data suggests that intercellular feedbacks can couple the phenotypes of neighboring cells, raising the question whether gene-regulatory networks have evolved to spatially organize biological functions.
Stochastic model of contact inhibition and the proliferation of melanomain situ
Authors: César Cafundó Morais Mauro , Stuhl Izabella , Sabino Alan U , Lautenschlager Willian W , Queiroga Alexandre S , Tortelli Tharcisio Citrangulo , Chammas Roger , Suhov Yuri , Ramos Alexandre F
Published: February 2017

Contact inhibition is a central feature orchestrating cell proliferation in culture experiments; its loss is associated with malignant transformation and tumorigenesis. We performed a co-culture experiment with human metastatic melanoma cell line (SKMEL-147) and immortalized keratinocyte cells (HaCaT). After 8 days a spatial pattern was detected, characterized by the formation of clusters of melanoma cells surrounded by keratinocytes constraining their proliferation. In addition, we observed that the proportion of melanoma cells within the total population has increased. To explain our results we propose a spatial stochastic model (following a philosophy of the Widom-Rowlinson model from Statistical Physics and Molecular Chemistry) which considers cell proliferation, death, migration, and cell-to-cell interaction through contact inhibition. Our numerical simulations demonstrate that loss of contact inhibition is a sufficient mechanism, appropriate for an explanation of the increase in the proportion of tumor cells and generation of spatial patterns established in the conducted experiments.
Effects of organic ligands on Pb absorption and speciation changes inArabidopsisas determined by micro X-ray fluorescence and X-ray absorption near-edge structure analysis
Authors: Shen Ya Ting , Song Yu Fang
Published: February 2017

Pb can pass through the food chainviaplants and threaten human health, which has attracted widespread attention. Changes in Pb speciation affect its bioavailability in soils and water. However, whether organic ligands can change the uptake and mobility of Pb in plants and increase or decrease Pb bioavailability remains uncertain. To reveal the roles of organic and inorganic Pb in Pb metabolism in plants, the localization and speciation changes of Pb inArabidopsis thalianaplants grown in organic and inorganic Pb were characterized by synchrotron radiation micro X-ray fluorescence and X-ray absorption near-edge structure, respectively. These results demonstrated thatArabidopsisabsorbed more Pb from Pb(NO3)2than Pb(CH3COO)2at the same exposure concentration. A higher percentage of Pb-citrate was found inArabidopsisexposed to inorganic Pb solution, which suggested that Pb-citrate was the main complex for root-to-shoot transportation inArabidopsisexposed to inorganic Pb solutions. Pb complexed with the organic ligand CH3COO−significantly inhibited primary root growth and lateral root development, while, at the same time, Pb was blocked by root hairs, which represented another way to reduce Pb absorption and protect the plant from biotoxicity.
Extensive analysis of N—H...O hydrogen bonding in four classes of phosphorus compounds: a combined experimental and database study
Authors: Hamzehee Farahnaz , Pourayoubi Mehrdad , Nečas Marek , Choquesillo-Lazarte Duane
Published: February 2017

The N—H...O hydrogen bond is the characteristic interaction in the crystal structures of N-benzyl-P-phenyl-N′-(p-tolyl)phosphonic diamide, C20H21N2OP or (C6H5)P(O)(NHCH2C6H5)(NHC6H4-p-CH3), (I), diphenylphosphinic 1-methylpropylamide, C16H20NOP or (C6H5)2P(O)[NHCH(CH3)(C2H5)], (II), (S)-1-phenylethylammonium N-[(S)-1-phenylethyl]phenylphosphonamidate, C8H12N+·C14H15NO2P− or [S-(C6H5)CH(CH3)NH3][(C6H5)P(O){S-NHCH(CH3)(C6H5)}(O)], (III), and (4-methylbenzyl)ammonium diphenylphosphinate, C8H12N+·C12H10O2P− or [4-CH3-C6H4CH2NH3][(C6H5)2P(O)(O)], (IV). This article focuses on the N—H...O hydrogen bonds by considering the structures of (I), (II), (III) and (IV), and reviewing their analogous compounds, including 43 (C)P(O)(N)2, 102 (C)2P(O)(N), 31 (C)P(O)(N)(O) and 96 (C)2P(O)(O) structures, deposited in the Cambridge Structural Database (CSD). For the structures with a (C)P(O)(N)2 segment, only neutral hydrogen bonds were found in the CSD. The other three classes of compounds included both neutral and `charge-assisted' hydrogen bonds, and the (C)2P(O)(O) structures were particularly noticeable for a high number of cation–anion compounds. The overall tendencies of N...O distances in neutral and cation–anion compounds were compared. The N—H...O hydrogen-bond angles were also analyzed for the four classes of phosphorus compounds.
The crystal structure of mouse LC3B in complex with the FYCO1 LIR reveals the importance of the flanking region of the LIR motif
Authors: Sakurai Shunya , Tomita Taisuke , Shimizu Toshiyuki , Ohto Umeharu
Published: February 2017

FYVE and coiled-coil domain-containing protein 1 (FYCO1), a multidomain autophagy adaptor protein, mediates microtubule plus-end-directed autophagosome transport by interacting with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7 and phosphatidylinositol 3-phosphate (PI3P). To establish the structural basis for the recognition of FYCO1 by LC3, the crystal structure of mouse LC3B in complex with the FYCO1 LC3-interacting region (LIR) motif peptide was determined. Structural analysis showed that the flanking sequences N-terminal and C-terminal to the LIR core sequence of FYCO1, as well as the tetrapeptide core sequence, were specifically recognized by LC3B and contributed to the binding. Moreover, comparisons of related structures revealed a conserved mechanism of FYCO1 recognition by different LC3 isoforms among different species.
The hyperthermophilic cystathionine γ-synthase from the aerobic crenarchaeonSulfolobus tokodaii: expression, purification, crystallization and structural insights
Authors: Sato Dan , Shiba Tomoo , Mizuno Sae , Kawamura Ayaka , Hanada Shoko , Yamada Tetsuya , Shinozaki Mai , Yanagitani Masahiko , Tamura Takashi , Inagaki Kenji , Harada Shigeharu
Published: February 2017

Cystathionine γ-synthase (CGS; EC 2.5.1.48), a pyridoxal 5′-phosphate (PLP)-dependent enzyme, catalyzes the formation of cystathionine from an L-homoserine derivative and L-cysteine in the first step of the transsulfuration pathway. Recombinant CGS from the thermoacidophilic archaeonSulfolobus tokodaii(StCGS) was overexpressed inEscherichia coliand purified to homogeneity by heat treatment followed by hydroxyapatite and gel-filtration column chromatography. The purified enzyme shows higher enzymatic activity at 353 K under basic pH conditions compared with that at 293 K. Crystallization trials yielded three crystal forms from different temperature and pH conditions. Form I crystals (space groupP21; unit-cell parametersa= 58.4,b= 149.3,c= 90.2 Å, β = 108.9°) were obtained at 293 K under acidic pH conditions using 2-methyl-2,4-pentanediol as a precipitant, whereas under basic pH conditions the enzyme crystallized in form II at 293 K (space groupC2221; unit-cell parametersa= 117.7,b= 117.8,c= 251.3 Å) and in form II′ at 313 K (space groupC2221; unit-cell parametersa= 107.5,b= 127.7,c= 251.1 Å) using polyethylene glycol 3350 as a precipitant. X-ray diffraction data were collected to 2.2, 2.9 and 2.7 Å resolution for forms I, II and II′, respectively. Structural analysis of these crystal forms shows that the orientation of the bound PLP in form II is significantly different from that in form II′, suggesting that the change in orientation of PLP with temperature plays a role in the thermophilic enzymatic activity of StCGS.
Proteolysis of truncated hemolysin A yields a stable dimerization interface
Authors: Novak Walter R. P. , Bhattacharyya Basudeb , Grilley Daniel P. , Weaver Todd M.
Published: February 2017

Wild-type and variant forms of HpmA265 (truncated hemolysin A) fromProteus mirabilisreveal a right-handed, parallel β-helix capped and flanked by segments of antiparallel β-strands. The low-salt crystal structures form a dimeric structureviathe implementation of on-edge main-chain hydrogen bonds donated by residues 243–263 of adjacent monomers. Surprisingly, in the high-salt structures of two variants, Y134A and Q125A-Y134A, a new dimeric interface is formedviamain-chain hydrogen bonds donated by residues 203–215 of adjacent monomers, and a previously unobserved tetramer is formed. In addition, an eight-stranded antiparallel β-sheet is formed from the flap regions of crystallographically related monomers in the high-salt structures. This new interface is possible owing to additional proteolysis of these variants after Tyr240. The interface formed in the high-salt crystal forms of hemolysin A variants may mimic the on-edge β-strand positioning used in template-assisted hemolytic activity.