bluuebunny/crossref_metadata_2025 huggingface dataset:
A new compact soft x-ray spectrometer for resonant inelastic x-ray scattering studies at PETRA III
Authors: Yin Z. , Peters H. B. , Hahn U. , Agåker M. , Hage A. , Reininger R. , Siewert F. , Nordgren J. , Viefhaus J. , Techert S.
Published: September 2015

We present a newly designed compact grating spectrometer for the energy range from 210 eV to 1250 eV, which would include the Kα1,2 emission lines of vital elements like C, N, and O. The spectrometer is based on a grazing incidence spherical varied line spacing grating with 2400 l/mm at its center and a radius of curvature of 58 542 mm. First, results show a resolving power of around 1000 at an energy of 550 eV and a working spectrometer for high vacuum (10−4 mbar) environment without losing photon intensity.
Uncertainty in a Markov state model with missing states and rates: Application to a room temperature kinetic model obtained using high temperature molecular dynamics
Authors: Chatterjee Abhijit , Bhattacharya Swati
Published: September 2015

Several studies in the past have generated Markov State Models (MSMs), i.e., kinetic models, of biomolecular systems by post-analyzing long standard molecular dynamics (MD) calculations at the temperature of interest and focusing on the maximally ergodic subset of states. Questions related to goodness of these models, namely, importance of the missing states and kinetic pathways, and the time for which the kinetic model is valid, are generally left unanswered. We show that similar questions arise when we generate a room-temperature MSM (denoted MSM-A) for solvated alanine dipeptide using state-constrained MD calculations at higher temperatures and Arrhenius relation — the main advantage of such a procedure being a speed-up of several thousand times over standard MD-based MSM building procedures. Bounds for rate constants calculated using probability theory from state-constrained MD at room temperature help validate MSM-A. However, bounds for pathways possibly missing in MSM-A show that alternate kinetic models exist that produce the same dynamical behaviour at short time scales as MSM-A but diverge later. Even in the worst case scenario, MSM-A is found to be valid longer than the time required to generate it. Concepts introduced here can be straightforwardly extended to other MSM building techniques.
Modifying magnetic properties of ultra-thin magnetite films by growth on Fe pre-covered MgO(001)
Authors: Schemme T. , Krampf A. , Bertram F. , Kuschel T. , Kuepper K. , Wollschläger J.
Published: September 2015

Iron oxide films were reactively grown on iron buffer films, which were deposited before on MgO(001) substrates to analyze the influence of the initial iron buffer layers on the magnetic properties of the magnetite films. X-ray photoelectron spectroscopy and low energy electron diffraction showed that magnetite films of high crystalline quality in the surface near region were formed by this two-step deposition procedure. The underlying iron film, however, was completely oxidized as proved by x-ray reflectometry and diffraction. The structural bulk quality of the iron oxide film is poor compared to magnetite films directly grown on MgO(001). Although the iron film was completely oxidized, we found drastically modified magnetic properties for these films using the magnetooptic Kerr effect. The magnetite films had strongly increased coercive fields, and their magnetic in-plane anisotropy is in-plane rotated by 45∘ compared to magnetite films formed directly by one step reactive growth on MgO(001).
Investigation of the effect of a power feed vacuum gap in solid liner experiments at 1 MA
Authors: Bott-Suzuki S. C. , Cordaro S. W. , Caballero Bendixsen L. S. , Blesener I. C. , Atoyan L. , Byvank T. , Potter W. , Bell K. S. , Kusse B. R. , Greenly J. B. , Hammer D. A.
Published: September 2015

We present an experimental study of plasma initiation of a solid metal liner at the 1 MA level. In contrast to previous work, we introduce a vacuum gap at one of the liner connections to the power feed to investigate how this affects plasma initiation and to infer how this may affect the symmetry of the liner in compression experiments. We observed that the vacuum gap causes non-uniform plasma initiation both azimuthally and axially in liners, diagnosed by gated optical imaging. Using magnetic field probes external to the liner, we also determined that the optical emission is strongly linked to the current distribution in the liner. The apparent persistent of azimuthal non-uniformities may have implications for fusion-scale liner experiments.
Double fishbone instability excited by energetic ions with m = n = 1 in a reversed magnetic shear tokamak plasmas
Authors: Meng Guo , Wang Xian-Qu , Wang Xiaogang , Zhang Rui-Bin
Published: September 2015

Double fishbone mode excited by energetic particles at q = 1 rational surfaces is studied, with the minimum of the safety factor qmin<1. The dispersion relation of the mode is derived based on energy principle and the radial displacement structure is calculated by an iterative method self-consistently. It is found that the double fishbone mode has a two-step mode structure similar to that of double kink modes. For qmin→1, the sharp slope of the ξr distribution at the rational surfaces is smoothened. The effects of the magnetic shear, the minimum of safety factor, the fast ion beta, and the precession frequency on the plasma displacement and growth rate are also analyzed, respectively.
Numerical study on Rayleigh-Taylor instabilities in the lightning return stroke
Authors: Chen Qiang , Chen Bin , Shi Lihua , Yi Yun , Wang Yangyang
Published: September 2015

The Rayleigh-Taylor (R-T) instabilities are important hydrodynamics and magnetohydrodynamics (MHD) phenomena that are found in systems in high energy density physics and normal fluids. The formation and evolution of the R-T instability at channel boundary during back-flow of the lightning return stroke are analyzed using the linear perturbation theory and normal mode analysis methods, and the linear growth rate of the R-T instability in typical condition for lightning return stroke channel is obtained. Then, the R-T instability phenomena of lightning return stroke are simulated using a two-dimensional Eulerian finite volumes resistive radiation MHD code. The numerical results show that the evolution characteristics of the R-T instability in the early stage of back-flow are consistent with theoretical predictions obtained by linear analysis. The simulation also yields more evolution characteristics for the R-T instability beyond the linear theory. The results of this work apply to some observed features of the return stroke channel and further advance previous theoretical and experimental work.
Field ionization of high-Rydberg fragments produced after inner-shell photoexcitation and photoionization of the methane molecule
Authors: Kivimäki A. , Sankari A. , Kettunen J. A. , Stråhlman C. , Álvarez Ruiz J. , Richter R.
Published: September 2015

We have studied the production of neutral high-Rydberg (HR) fragments from the CH4 molecule at the C 1s → 3p excitation and at the C 1s ionization threshold. Neutral fragments in HR states were ionized using a pulsed electric field and the resulting ions were mass-analyzed using an ion time-of-flight spectrometer. The atomic fragments C(HR) and H(HR) dominated the spectra, but molecular fragments CHx(HR), x = 1-3, and H2(HR) were also observed. The production of HR fragments is attributed to dissociation of CH4+ and CH42+ ions in HR states. Just above the C 1s ionization threshold, such molecular ionic states are created when the C 1s photoelectron is recaptured after single or double Auger decay. Similar HR states may be reached directly following resonant Auger decay at the C 1s → 3p resonance. The energies and geometries of the parent and fragment ions have been calculated in order to gain insight into relevant dissociation pathways.
Estimation of the shear force in transverse dynamic force microscopy using a sliding mode observer
Authors: Nguyen Thang , Hatano Toshiaki , Khan Said G. , Zhang Kaiqiang , Edwards Christopher , Harniman Robert , Burgess Stuart C. , Antognozzi Massimo , Miles Mervyn , Herrmann Guido
Published: September 2015

In this paper, the problem of estimating the shear force affecting the tip of the cantilever in a Transverse Dynamic Force Microscope (TDFM) using a real-time implementable sliding mode observer is addressed. The behaviour of a vertically oriented oscillated cantilever, in close proximity to a specimen surface, facilitates the imaging of the specimen at nano-metre scale. Distance changes between the cantilever tip and the specimen can be inferred from the oscillation amplitudes, but also from the shear force acting at the tip. Thus, the problem of accurately estimating the shear force is of significance when specimen images and mechanical properties need to be obtained at submolecular precision. A low order dynamic model of the cantilever is derived using the method of lines, for the purpose of estimating the shear force. Based on this model, an estimator using sliding mode techniques is presented to reconstruct the unknown shear force, from only tip position measurements and knowledge of the excitation signal applied to the top of the cantilever. Comparisons to methods assuming a quasi-static harmonic balance are made.
Fractional Pyrolysis of Algae and Model Compounds
Authors: Li Lin-ling , Zhang Rui , Tong Dong-mei , Hu Chang-wei
Published: September 2015

Pyrolysis of algae from Taihu Lake water blooms for bio-oil production was conducted from 473 K to 773 K by a fractional way in six steps. Palmitic acid, agarose and egg white were used as model compounds to study the origin of bio-oil ingredients and interaction of the intermediates from the algae components. In the first step at 473 K, the bio-oil obtained was composed of n-heptadecane and some small molecule acids. Quantities of carboxylic acids (mainly palmitic acid) and some amides, hydrocarbons, esters etc. were evolved in the second step at 523 K. For the third step at 573 K, except the carboxylic acids (still mainly palmitic acid), amides, nitriles, and phenols also accounted for a large proportion whereas respectable amount of indoles and alcohol ketones were attained. The main products in the later three steps were nitriles and phenols at 623 K, hydrocarbons and phenols at 673 K, and only phenols at 773 K, respectively. A higher heating value (HHV) of 36.0 MJ/kg of the bio-oil was obtained at 673 K. The hydrocarbons, palmitic acid and esters in the bio-oil were derived from lipids. The phenols, indoles, pyrroles, small molecular acids, amides like acetamide and some nitriles like phenyl-acetonitrile were generated from proteins. Amides and nitriles were also dated from the interaction of pyrolytic intermediates of lipids and proteins. Fewer products directly from the direct pyrolysis of saccharides were detected in the algae bio-oil due to the interaction of pyrolytic intermediates of saccharides and proteins in algae, and those interactions resulted in the formation of oligomers in the bio-oil at 473 and 523 K. Whereas very weak interaction was observed between lipids and saccharides. The process of fractional pyrolysis by varying temperature provided an advisable way for improving the selectivity of bio-oil from direct pyrolysis, and made the bio-oil much more applicable in down streaming utilization.
Tcn and Tcn@C70 Endohedral Metalofullerenes: ab initio Spin-density-functional Calculations
Authors: Zeng Li-jing , Deng Ke
Published: September 2015

Ab initio spin-density-functional calculations have been performed to study the equilibrium structural, electronic, and magnetic properties of Tcn and Tcn@C70 endohedral metalofullerenes. Our results indicate that C70 can encapsulate Tcn clusters with up to n=9 atoms. Except n=2, the formation of Tcn@C70 endohedral metalofullerenes is predicted to be exothermic when n≤5, while the encapsulation process becomes increasingly endothermic beyond n=5. When encapsulating into the C70 cage, the geometries as well as electronic structures of the Tc cluster undergo comparative changes. Especially, compared to the isolated Tcn clusters, the total magnetic moments of Tcn@C70 reduce significantly. The analyses of the orbital population, Hirshfeld population and density of states show that electrons transfer from the Tc cluster to the carbon cage through the Tc–C efficient hybridization, which is responsible for such reduction of the whole magnetism.
Quasiclassical Trajectory Study of the Reaction of CD4 with O(1D)
Authors: Shao Ke-jie , Fu Bi-na , Zhang Dong H.
Published: September 2015

Extensive quasiclassical trajectory calculations for the O(1D)+CD4 multichannel reaction were carried out on a new global potential energy surface fit by permutationally invariant polynomials. The product branching ratios, translational energy distributions, and angular distributions of OD+CD3, D+CD2OD/CD3O, and D2+DCOD/D2CO product channels were calculated and compared with the available experimental results. Good agreement between theory and experiment has been achieved, indicating small isotope effects for the title reaction. The O(1D)+CD4 reaction mainly proceeds through the CD3OD intermediate via the trapped abstraction mechanism, with initial abstraction of the D atom rather than the direct insertion, followed by decomposition of CD3OD into various products.
Combining two soil property rasters using an adaptive gating approach
Authors: Clifford David , Guo Yi
Published: September 2015

Given the wide variety of ways one can measure and record soil properties, it is not uncommon to have multiple overlapping predictive maps for a particular soil property. One is then faced with the challenge of choosing the best prediction at a particular point, either by selecting one of the maps, or by combining them together in some optimal manner. This question was recently examined in detail when Malone et al. (2014) compared four different methods for combining a digital soil mapping product with a disaggregation product based on legacy data. These authors also examined the issue of how to compute confidence intervals for the resulting map based on confidence intervals associated with the original input products. In this paper, we propose a new method to combine models called adaptive gating, which is inspired by the use of gating functions in mixture of experts, a machine learning approach to forming hierarchical classifiers. We compare it here with two standard approaches – inverse-variance weights and a regression based approach. One of the benefits of the adaptive gating approach is that it allows weights to vary based on covariate information or across geographic space. As such, this presents a method that explicitly takes full advantage of the spatial nature of the maps we are trying to blend. We also suggest a conservative method for combining confidence intervals. We show that the root mean-squared error of predictions from the adaptive gating approach is similar to that of other standard approaches under cross-validation. However under independent validation the adaptive gating approach works better than the alternatives and as such it warrants further study in other areas of application and further development to reduce its computational complexity.
Intra-annual patterns in adult band-tailed pigeon survival estimates
Authors: Casazza Michael L. , Coates Peter S. , Overton Cory T. , Howe Kristy B.
Published: September 2015

Context
The band-tailed pigeon (Patagioenas fasciata) is a migratory species occurring in western North America with low recruitment potential and populations that have declined an average of 2.4% per year since the 1960s. Investigations into band-tailed pigeon demographic rates date back to the early 1900s, and existing annual survival rate estimates were derived in the 1970s using band return data.

Aims
The primary purpose of the paper was to demonstrate that the apparent paradox between band-tailed pigeon population dynamics (long-term steady decline) and breeding season survival rates (very high) can be explained by changes in survival probability during the remainder of the year.

Methods
We trapped Pacific coast band-tailed pigeons during two separate periods: we equipped pigeons with very high frequency (VHF) radio-transmitters in 1999–2000 (1999 = 20; 2000 = 34); and outfitted pigeons with solar powered platform transmitting terminal (PTT) transmitters in 2006–08 (n = 20). We used known fate models to estimate annual survival rates and seasonal survival variation among four periods based on an annual behavioural cycle based on phenological events (nesting, autumn migration, winter and spring migrations). We used model averaged parameter estimates to account for model selection uncertainty.

Key results
Neither body condition nor sex were associated with variation in band-tailed pigeon survival rates. Weekly survival during the nesting season did not differ significantly between VHF-marked (0.996; CI = 0.984–0.999) and PTT-marked pigeons (0.998; CI = 0.990–1.00). Model averaged annual survival of PTT-marked pigeons was 0.682 (95% CI = 0.426–0.861) and was similar to annual survival estimated in previous studies using band return data. Survival probability was lowest during both migration periods and highest during the nesting period.

Conclusions
Our survival estimates are consistent with those of prior studies and suggest that mortality risk is greatest during migration. Weekly survival probability during winter was nearly the same as during the nesting season; however, winter was the longest period and survival throughout winter was lower than other seasons.

Implications
We present the first inter-seasonal analysis of survival probability of the Pacific coast race of band-tailed pigeons and illustrate important temporal patterns that may influence future species management including harvest strategies and disease monitoring.
The preference for yew (Taxus baccata) by a red (Sciurus vulgaris) only squirrel population
Authors: Haigh Amy , O'Riordan Ruth , Butler Fidelma
Published: September 2015

Context
As invasive grey squirrels continue to spread, red only areas are becoming rarer. It has been reported that red squirrels can outcompete greys only in pure coniferous woodland. In areas of sympatry with grey squirrels, there are concerns about red squirrels’ dependence on certain coniferous tree species in light of recent tree diseases.

Aims
This study aimed to investigate tree selection by red squirrels in an area vulnerable to the spread of the grey squirrel, but currently free of this species.

Methods
During 2013–14, squirrels were trapped and monitored on a 315-ha managed island, with a woodland characterised by a mixture of deciduous and coniferous species. Radio-tracking revealed that squirrels clustered their activity along a network of yew trees, a preference they showed throughout the year. Trap success was also higher in traps placed on yew trees. Yew and beech were selected most commonly, but squirrels were also observed foraging on other items, such as sycamore flowers and lichen. Squirrels spent 35% of their time foraging, utilising the greatest number of tree species in June (n = 13). In spring, squirrels foraged to a greater extent on the ground than in the trees, and exploited a lower number of tree species.

Conclusions
There has been little previous data on the use of yew trees by red squirrels, but they have previously been listed as a species that is preferred by red squirrels rather than greys. This study has further emphasised the importance of this tree species to red squirrels.

Implications
The continued spread of the grey squirrel may lead to red squirrels becoming restricted to areas of intense management such as parks and, accordingly, optimum tree planting is required from the onset for the long-term maintenance of red squirrels. With recent concern about the disease vulnerability of other coniferous species, this study emphasises the relative importance of yew and other tree species in the distribution of red squirrels.
Heteronormative love makes a house a home
Authors: Hiramoto Mie , Teo Cherise Shi Ling
Published: September 2015

This study investigates how luxury apartment housing advertisements in Singapore function as meaning-generating institutions through visual and textual discourse. Advertisements are designed to ascribe a set of attitudes, values, and preoccupations to a group and to imbue their audiences with the idea that they belong to that group. Human models in advertisements represent idealized people and lifestyles, displaying aspirational images of men and women as consumers of products. Under the influence of Confucian patriarchal ideology, the Singapore government has promoted a narrow, heteronormative definition of family in its pro-family policies since 1987. In the advertisements for two different types of luxury apartments — one regulated by the government and the other not — we see two different ways of engaging with pro-family policies that suggest what is expected from ideal members of society in Singapore.
Les prédicatsPrep Nfigés adjectivaux et adverbiaux
Authors: Kaliska Agnieszka K.
Published: September 2015

The purpose of this article is to consider syntactic and semantic properties of frozen predicatesPrep Nin Polish, which may express either a state or a property of the subject. Some of them correspond to adjectival interrogative pronouns, while others correspond rather to an adverbial interrogation. We discuss to what extent these and other syntactic features reflect the notional features, defined as a property or as a state and if they justify the division between the adjectivalPrep Nand the adverbialPrep N. Our analysis is based on Polish data but it also contains references to other languages: French, Korean, English. More general issues are also discussed in this paper: identification of the categories called parts of speech and transfer between categories (nounvs. adjectivevs.adverbe).
Component-wise gradient boosting and false discovery control in survival analysis with high-dimensional covariates
Authors: He Kevin , Li Yanming , Zhu Ji , Liu Hongliang , Lee Jeffrey E. , Amos Christopher I. , Hyslop Terry , Jin Jiashun , Lin Huazhen , Wei Qinyi , Li Yi
Published: September 2015

Motivation: Technological advances that allow routine identification of high-dimensional risk factors have led to high demand for statistical techniques that enable full utilization of these rich sources of information for genetics studies. Variable selection for censored outcome data as well as control of false discoveries (i.e. inclusion of irrelevant variables) in the presence of high-dimensional predictors present serious challenges. This article develops a computationally feasible method based on boosting and stability selection. Specifically, we modified the component-wise gradient boosting to improve the computational feasibility and introduced random permutation in stability selection for controlling false discoveries.

Results: We have proposed a high-dimensional variable selection method by incorporating stability selection to control false discovery. Comparisons between the proposed method and the commonly used univariate and Lasso approaches for variable selection reveal that the proposed method yields fewer false discoveries. The proposed method is applied to study the associations of 2339 common single-nucleotide polymorphisms (SNPs) with overall survival among cutaneous melanoma (CM) patients. The results have confirmed that BRCA2 pathway SNPs are likely to be associated with overall survival, as reported by previous literature. Moreover, we have identified several new Fanconi anemia (FA) pathway SNPs that are likely to modulate survival of CM patients.

Availability and implementation: The related source code and documents are freely available at https://sites.google.com/site/bestumich/issues.

Contact:  yili@umich.edu
P-SAMS: a web site for plant artificial microRNA and synthetic trans-acting small interfering RNA design
Authors: Fahlgren Noah , Hill Steven T. , Carrington James C. , Carbonell Alberto
Published: September 2015

Summary: The Plant Small RNAMaker Site (P-SAMS) is a web tool for the simple and automated design of artificial miRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs) for efficient and specific targeted gene silencing in plants. P-SAMS includes two applications, P-SAMS amiRNA Designer and P-SAMS syn-tasiRNA Designer. The navigation through both applications is wizard-assisted, and the job runtime is relatively short. Both applications output the sequence of designed small RNA(s), and the sequence of the two oligonucleotides required for cloning into ‘B/c’ compatible vectors.

Availability and implementation: The P-SAMS website is available at http://p-sams.carringtonlab.org.

Contact:  acarbonell@ibmcp.upv.es or nfahlgren@danforthcenter.org
CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data
Authors: Packer Jonathan S. , Maxwell Evan K. , O’Dushlaine Colm , Lopez Alexander E. , Dewey Frederick E. , Chernomorsky Rostislav , Baras Aris , Overton John D. , Habegger Lukas , Reid Jeffrey G.
Published: September 2015

Motivation: Several algorithms exist for detecting copy number variants (CNVs) from human exome sequencing read depth, but previous tools have not been well suited for large population studies on the order of tens or hundreds of thousands of exomes. Their limitations include being difficult to integrate into automated variant-calling pipelines and being ill-suited for detecting common variants. To address these issues, we developed a new algorithm—Copy number estimation using Lattice-Aligned Mixture Models (CLAMMS)—which is highly scalable and suitable for detecting CNVs across the whole allele frequency spectrum.

Results: In this note, we summarize the methods and intended use-case of CLAMMS, compare it to previous algorithms and briefly describe results of validation experiments. We evaluate the adherence of CNV calls from CLAMMS and four other algorithms to Mendelian inheritance patterns on a pedigree; we compare calls from CLAMMS and other algorithms to calls from SNP genotyping arrays for a set of 3164 samples; and we use TaqMan quantitative polymerase chain reaction to validate CNVs predicted by CLAMMS at 39 loci (95% of rare variants validate; across 19 common variant loci, the mean precision and recall are 99% and 94%, respectively). In the Supplementary Materials (available at the CLAMMS Github repository), we present our methods and validation results in greater detail.

Availability and implementation:  https://github.com/rgcgithub/clamms (implemented in C).

Contact:  jeffrey.reid@regeneron.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
ScaffoldScaffolder: solving contig orientation via bidirected to directed graph reduction
Authors: Bodily Paul M. , Fujimoto M. Stanley , Snell Quinn , Ventura Dan , Clement Mark J.
Published: September 2015

Motivation: The contig orientation problem, which we formally define as the MAX-DIR problem, has at times been addressed cursorily and at times using various heuristics. In setting forth a linear-time reduction from the MAX-CUT problem to the MAX-DIR problem, we prove the latter is NP-complete. We compare the relative performance of a novel greedy approach with several other heuristic solutions.

Results: Our results suggest that our greedy heuristic algorithm not only works well but also outperforms the other algorithms due to the nature of scaffold graphs. Our results also demonstrate a novel method for identifying inverted repeats and inversion variants, both of which contradict the basic single-orientation assumption. Such inversions have previously been noted as being difficult to detect and are directly involved in the genetic mechanisms of several diseases.

Availability and implementation:  http://bioresearch.byu.edu/scaffoldscaffolder.

Contact:  paulmbodily@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Transjugular Intrahepatic Portosystemic Shunt for Extrahepatic Portal Venous Obstruction in Children
Authors: Lv Yong , He Chuangye , Guo Wengang , Yin Zhanxin , Wang Jianhong , Zhang Bojing , Meng Xiangchen , Cai Jingzhi , Luo Bohan , Wu Feifei , Niu Jing , Fan Daiming , Han Guohong
Published: September 2015

Objectives:

To evaluate the feasibility and efficacy of transjugular intrahepatic portosystemic shunt (TIPS) for extrahepatic portal venous obstruction with recurrent variceal bleeding in children.

Methods:

From November 2005 to December 2013, 28 consecutive paediatric patients with extrahepatic portal venous obstruction treated with TIPS for recurrent variceal bleeding refractory to medical/endoscopic therapy and/or surgical treatment in a tertiary‐care centre were followed until last clinical evaluation or death. The median follow‐up time was 36.0 months (range 4.0–106.0 months).

Results:

Seventeen boys and 11 girls of ages 7.1 to 17.9 years (median 12.3 years) weighing 19.0 to 62.0 kg (median 33.5 kg) were treated. TIPS was successfully placed in 17 of 28 (60.7%) patients via a transjugular approach alone (n = 4), a combined transjugular/transhepatic approach (n = 9), or a combined transjugular/transsplenic approach (n = 4). Shunt dysfunction occurred in 6 of 17 (35.3%) patients. The cumulative 1‐ and 3‐year free‐from‐variceal‐rebleeding rates in TIPS success group were higher than those in TIPS failure group (75.0% and 67.5% vs 45.5% and 18.2%, respectively, P = 0.0075). Compared with the TIPS failure group, the improvements in the height‐for‐age z scores were greater in the TIPS success group (P = 0.017). Procedure‐related complication occurred in 1 patient (3.6%), and no episode of post‐TIPS hepatic encephalopathy occurred in any patient. Except 1 patient in the TIPS success group died at 115 postoperative days, all patients were alive.

Conclusions:

TIPS is feasible and effective in children with extrahepatic portal venous obstruction and recurrent variceal bleeding. TIPS could represent a less‐invasive alternative to traditional surgical portosystemic shunting or a valuable treatment option if surgery and endoscopic treatment failed.
The metabolic cost of changing walking speeds is significant, implies lower optimal speeds for shorter distances, and increases daily energy estimates
Authors: Seethapathi Nidhi , Srinivasan Manoj
Published: September 2015

Humans do not generally walk at constant speed, except perhaps on a treadmill. Normal walking involves starting, stopping and changing speeds, in addition to roughly steady locomotion. Here, we measure the metabolic energy cost of walking when changing speed. Subjects (healthy adults) walked with oscillating speeds on a constant-speed treadmill, alternating between walking slower and faster than the treadmill belt, moving back and forth in the laboratory frame. The metabolic rate for oscillating-speed walking was significantly higher than that for constant-speed walking (6–20% cost increase for ±0.13–0.27 m s
−1
speed fluctuations). The metabolic rate increase was correlated with two models: a model based on kinetic energy fluctuations and an inverted pendulum walking model, optimized for oscillating-speed constraints. The cost of changing speeds may have behavioural implications: we predicted that the energy-optimal walking speed is lower for shorter distances. We measured preferred human walking speeds for different walking distances and found people preferred lower walking speeds for shorter distances as predicted. Further, analysing published daily walking-bout distributions, we estimate that the cost of changing speeds is 4–8% of daily walking energy budget.
Is domestication driven by reduced fear of humans? Boldness, metabolism and serotonin levels in divergently selected red junglefowl (
Gallus gallus
)
Authors: Agnvall Beatrix , Katajamaa Rebecca , Altimiras Jordi , Jensen Per
Published: September 2015

Domesticated animals tend to develop a coherent set of phenotypic traits. Tameness could be a central underlying factor driving this, and we therefore selected red junglefowl, ancestors of all domestic chickens, for high or low fear of humans during six generations. We measured basal metabolic rate (BMR), feed efficiency, boldness in a novel object (NO) test, corticosterone reactivity and basal serotonin levels (related to fearfulness) in birds from the fifth and sixth generation of the high- and low-fear lines, respectively (44–48 individuals). Corticosterone response to physical restraint did not differ between selection lines. However, BMR was higher in low-fear birds, as was feed efficiency. Low-fear males had higher plasma levels of serotonin and both low-fear males and females were bolder in an NO test. The results show that many aspects of the domesticated phenotype may have developed as correlated responses to reduced fear of humans, an essential trait for successful domestication.
Polarized skylight does not calibrate the compass system of a migratory bat
Authors: Lindecke Oliver , Voigt Christian C. , Pētersons Gunārs , Holland Richard A.
Published: September 2015

In a recent study, Greif
et al.
(Greif
et al. Nat Commun
5, 4488. (
doi:10.1038/ncomms5488
)) demonstrated a functional role of polarized light for a bat species confronted with a homing task. These non-migratory bats appeared to calibrate their magnetic compass by using polarized skylight at dusk, yet it is unknown if migratory bats also use these cues for calibration. During autumn migration, we equipped Nathusius' bats,
Pipistrellus nathusii
, with radio transmitters and tested if experimental animals exposed during dusk to a 90° rotated band of polarized light would head in a different direction compared with control animals. After release, bats of both groups continued their journey in the same direction. This observation argues against the use of a polarization-calibrated magnetic compass by this migratory bat and questions that the ability of using polarized light for navigation is a consistent feature in bats. This finding matches with observations in some passerine birds that used polarized light for calibration of their magnetic compass before but not during migration.
Satyrization without evidence of successful insemination from interspecific mating between invasive mosquitoes
Authors: Carrasquilla María C. , Lounibos L. Philip
Published: September 2015

Previous research has documented low frequencies of interspecific mating in nature between the invasive vectors
Aedes aegypti
and
Aedes albopictus
. It is also known that heterospecific male accessory gland substances transferred during mating sterilize
A. aegypti
but not
A. albopictus
females, leading to satyrization, a form of reproductive interference. This paper demonstrates that satyrization of
A. aegypti
by
A. albopictus
may occur without evidence of successful insemination. Our results show that
A. aegypti
females, previously exposed to
A. albopictus
males, are rendered refractory to subsequent conspecific mating even though their spermathecae contain no heterospecific sperm. Additional experiments demonstrating transfer of labelled semen from
A. albopictus
males to
A. aegypti
females and low production of viable eggs of females housed with conspecific males, following exposure to
A. albopictus
males, confirm higher incidences of satyrization than expected, based on heterospecific insemination rates. We conclude that frequencies of satyrization based on detection of interspecific sperm in spermathecae may underestimate the impact of this form of reproductive interference.
Individuals with higher metabolic rates have lower levels of reactive oxygen species
in vivo
Authors: Salin Karine , Auer Sonya K. , Rudolf Agata M. , Anderson Graeme J. , Cairns Andrew G. , Mullen William , Hartley Richard C. , Selman Colin , Metcalfe Neil B.
Published: September 2015

There is increasing interest in the effect of energy metabolism on oxidative stress, but much ambiguity over the relationship between the rate of oxygen consumption and the generation of reactive oxygen species (ROS). Production of ROS (such as hydrogen peroxide, H
2
O
2
) in the mitochondria is primarily inferred indirectly from measurements
in vitro
, which may not reflect actual ROS production in living animals. Here, we measured
in vivo
H
2
O
2
content using the recently developed MitoB probe that becomes concentrated in the mitochondria of living organisms, where it is converted by H
2
O
2
into an alternative form termed MitoP; the ratio of MitoP/MitoB indicates the level of mitochondrial H
2
O
2
in vivo
. Using the brown trout
Salmo trutta
, we tested whether this measurement of
in vivo
H
2
O
2
content over a 24 h-period was related to interindividual variation in standard metabolic rate (SMR)
.
We showed that the H
2
O
2
content varied up to 26-fold among fish of the same age and under identical environmental conditions and nutritional states. Interindividual variation in H
2
O
2
content was unrelated to mitochondrial density but was significantly associated with SMR: fish with a higher mass-independent SMR had a lower level of H
2
O
2
. The mechanism underlying this observed relationship between SMR and
in vivo
H
2
O
2
content requires further investigation, but may implicate mitochondrial uncoupling which can simultaneously increase SMR but reduce ROS production. To our knowledge, this is the first study in living organisms to show that individuals with higher oxygen consumption rates can actually have lower levels of H
2
O
2
.
A self-regulating biomolecular comparator for processing oscillatory signals
Authors: Agrawal Deepak K. , Franco Elisa , Schulman Rebecca
Published: September 2015

While many cellular processes are driven by biomolecular oscillators, precise control of a downstream on/off process by a biochemical oscillator signal can be difficult: over an oscillator's period, its output signal varies continuously between its amplitude limits and spends a significant fraction of the time at intermediate values between these limits. Further, the oscillator's output is often noisy, with particularly large variations in the amplitude. In electronic systems, an oscillating signal is generally processed by a downstream device such as a comparator that converts a potentially noisy oscillatory input into a square wave output that is predominantly in one of two well-defined on and off states. The comparator's output then controls downstream processes. We describe a method for constructing a synthetic biochemical device that likewise produces a square-wave-type biomolecular output for a variety of oscillatory inputs. The method relies on a separation of time scales between the slow rate of production of an oscillatory signal molecule and the fast rates of intermolecular binding and conformational changes. We show how to control the characteristics of the output by varying the concentrations of the species and the reaction rates. We then use this control to show how our approach could be applied to process different
in vitro
and
in vivo
biomolecular oscillators, including the p53-Mdm2 transcriptional oscillator and two types of
in vitro
transcriptional oscillators. These results demonstrate how modular biomolecular circuits could, in principle, be combined to build complex dynamical systems. The simplicity of our approach also suggests that natural molecular circuits may process some biomolecular oscillator outputs before they are applied downstream.
A frequency-based hypothesis for mechanically targeting and selectively attacking cancer cells
Authors: Fraldi M. , Cugno A. , Deseri L. , Dayal K. , Pugno N. M.
Published: September 2015

Experimental studies recently performed on single cancer and healthy cells have demonstrated that the former are about 70% softer than the latter, regardless of the cell lines and the measurement technique used for determining the mechanical properties. At least in principle, the difference in cell stiffness might thus be exploited to create mechanical-based targeting strategies for discriminating neoplastic transformations within human cell populations and for designing innovative complementary tools to cell-specific molecular tumour markers, leading to possible applications in the diagnosis and treatment of cancer diseases. With the aim of characterizing and gaining insight into the overall frequency response of single-cell systems to mechanical stimuli (typically low-intensity therapeutic ultrasound), a generalized viscoelastic paradigm, combining classical and spring-pot-based models, is introduced for modelling this problem by neglecting the cascade of mechanobiological events involving the cell nucleus, cytoskeleton, elastic membrane and cytosol. Theoretical results show that differences in stiffness, experimentally observed
ex vivo
and
in vitro
, allow healthy and cancer cells to be discriminated, by highlighting frequencies (from tens to hundreds of kilohertz) associated with resonance-like phenomena—prevailing on thermal fluctuations—that could be helpful in targeting and selectively attacking tumour cells.
Rigidly foldable origami gadgets and tessellations
Authors: Evans Thomas A. , Lang Robert J. , Magleby Spencer P. , Howell Larry L.
Published: September 2015

Rigidly foldable origami allows for motion where all deflection occurs at the crease lines and facilitates the application of origami in materials other than paper. In this paper, we use a recently discovered method for determining rigid foldability to identify existing flat-foldable rigidly foldable tessellations, which are also categorized. We introduce rigidly foldable origami
gadgets
which may be used to modify existing tessellations or to create new tessellations. Several modified and new rigidly foldable tessellations are presented.
A process of rumour scotching on finite populations
Authors: de Arruda Guilherme Ferraz , Lebensztayn Elcio , Rodrigues Francisco A. , Rodríguez Pablo Martín
Published: September 2015

Rumour spreading is a ubiquitous phenomenon in social and technological networks. Traditional models consider that the rumour is propagated by pairwise interactions between spreaders and ignorants. Only spreaders are active and may become stiflers after contacting spreaders or stiflers. Here we propose a competition-like model in which spreaders try to transmit an information, while stiflers are also active and try to scotch it. We study the influence of transmission/scotching rates and initial conditions on the qualitative behaviour of the process. An analytical treatment based on the theory of convergence of density-dependent Markov chains is developed to analyse how the final proportion of ignorants behaves asymptotically in a finite homogeneously mixing population. We perform Monte Carlo simulations in random graphs and scale-free networks and verify that the results obtained for homogeneously mixing populations can be approximated for random graphs, but are not suitable for scale-free networks. Furthermore, regarding the process on a heterogeneous mixing population, we obtain a set of differential equations that describes the time evolution of the probability that an individual is in each state. Our model can also be applied for studying systems in which informed agents try to stop the rumour propagation, or for describing related susceptible–infected–recovered systems. In addition, our results can be considered to develop optimal information dissemination strategies and approaches to control rumour propagation.
A severe red tide (Tampa Bay, 2005) causes an anomalous decrease in biological sound
Authors: Indeck Katherine L. , Simard Peter , Gowans Shannon , Lowerre-Barbieri Susan , Mann David A.
Published: September 2015

Although harmful algal blooms (HABs) are known to cause morbidity and mortality in marine organisms, their sublethal effects are poorly understood. The purpose of this study was to compare ambient noise levels during a severe HAB event in Tampa Bay, Florida, to those during non-HAB periods. Passive acoustic monitoring was conducted using bottom-mounted autonomous acoustic recorders during a severe HAB in summer 2005, and in summers 2006, 2011 and 2012 (non-severe HAB years). Ambient noise levels were significantly higher during the non-HAB years due to an abundance of snapping shrimp (
Alpheidae
) sounds and fish chorusing. The difference of sound intensity between the study years is most likely attributable to effects of the HAB on the abundance and/or behaviour of fish and snapping shrimp as a result of mortality and stress-induced behavioural modifications.
Elastodynamic image forces on dislocations
Authors: Gurrutxaga-Lerma Beñat , Balint Daniel S. , Dini Daniele , Sutton Adrian P.
Published: September 2015

The elastodynamic image forces on edge and screw dislocations in the presence of a planar-free surface are derived. The explicit form of the elastodynamic fields of an injected, quiescent screw dislocation are also derived. The resulting image forces are affected by retardation effects: the dislocations experience no image force for a period of time defined by the arrival and reflection at the free surface of the dislocation fields. For the case of injected, stationary dislocations, it is shown that the elastodynamic image force tends asymptotically to the elastotatic prediction. For the case of injected, moving dislocations, it is shown that the elastodynamic image force on both the edge and the screw dislocations is magnified by inertial effects, and becomes increasingly divergent with time; this additional effect, missing in the elastostatic description, is shown to be substantial even for slow moving dislocations. Finally, it is shown that the elastodynamic image force of an edge dislocation moving towards the surface at the Rayleigh wave speed becomes repulsive, rather than attractive; this is suggestive of instabilities at the core of the dislocation, and likely resonances with the free surface.
Mitonuclear linkage disequilibrium in human populations
Authors: Sloan Daniel B. , Fields Peter D. , Havird Justin C.
Published: September 2015

There is extensive evidence from model systems that disrupting associations between co-adapted mitochondrial and nuclear genotypes can lead to deleterious and even lethal consequences. While it is tempting to extrapolate from these observations and make inferences about the human-health effects of altering mitonuclear associations, the importance of such associations may vary greatly among species, depending on population genetics, demographic history and other factors. Remarkably, despite the extensive study of human population genetics, the statistical associations between nuclear and mitochondrial alleles remain largely uninvestigated. We analysed published population genomic data to test for signatures of historical selection to maintain mitonuclear associations, particularly those involving nuclear genes that encode mitochondrial-localized proteins (N-mt genes). We found that significant mitonuclear linkage disequilibrium (LD) exists throughout the human genome, but these associations were generally weak, which is consistent with the paucity of population genetic structure in humans. Although mitonuclear LD varied among genomic regions (with especially high levels on the X chromosome), N-mt genes were statistically indistinguishable from background levels, suggesting that selection on mitonuclear epistasis has not preferentially maintained associations involving this set of loci at a species-wide level. We discuss these findings in the context of the ongoing debate over mitochondrial replacement therapy.