bluuebunny/crossref_metadata_2025_split huggingface dataset:
Saturation of Zeldovich stretch–twist–fold map dynamos
Authors: Seta Amit , Bhat Pallavi , Subramanian Kandaswamy 
Published: July 2015

Zeldovich’s stretch–twist–fold (STF) dynamo provided a breakthrough in conceptual understanding of fast dynamos, including the small-scale fluctuation dynamos. We study the evolution and saturation behaviour of two types of generalized Baker’s map dynamos, which have been used to model Zeldovich’s STF dynamo process. Using such maps allows one to analyse dynamos at much higher magnetic Reynolds numbers $\mathit{Re}_{M}$ as compared to direct numerical simulations. In the two-strip map dynamo there is constant constructive folding, while the four-strip map dynamo also allows the possibility of a destructive reversal of the field. Incorporating a diffusive step parametrized by $\mathit{Re}_{M}$ into the map, we find that the magnetic field $B(x)$ is amplified only above a critical $\mathit{Re}_{M}=R_{\mathit{crit}}\sim 4$ for both types of dynamos. The growing $B(x)$ approaches a shape-invariant eigenfunction independent of initial conditions, whose fine structure increases with increasing $\mathit{Re}_{M}$. Its power spectrum $M(k)$ displays sharp peaks reflecting the fractal nature of $B(x)$ above the diffusive scale. We explore the saturation of these dynamos in three ways: via a renormalized reduced effective $\mathit{Re}_{M}$ (case I) or due to a decrease in the efficiency of the field amplification by stretching, without changing the map (case IIa), or changing the map (case IIb), and a combination of both effects (case III). For case I, we show that $B(x)$ in the saturated state, for both types of maps, approaches the marginal eigenfunction, which is obtained for $\mathit{Re}_{M}=R_{\mathit{crit}}$ independent of the initial $\mathit{Re}_{M}=R_{M0}$. On the other hand, in case II, for the two-strip map, we show that $B(x)$ saturates, preserving the structure of the kinematic eigenfunction. Thus the energy is transferred to larger scales in case I but remains at the smallest resistive scales in case II, as can be seen from both $B(x)$ and $M(k)$. For the four-strip map, $B(x)$ oscillates with time, although with a structure similar to the kinematic eigenfunction. Interestingly, the saturated state in case III shows an intermediate behaviour, with $B(x)$ similar to the kinematic eigenfunction at an intermediate $\mathit{Re}_{M}=R_{\mathit{sat}}$, with $R_{M0}>R_{\mathit{sat}}>R_{\mathit{crit}}$. The $R_{\mathit{sat}}$ value is determined by the relative importance of the increased diffusion versus the reduced stretching. These saturation properties are akin to the range of possibilities that have been discussed in the context of fluctuation dynamos.
Low-power radio-frequency excitation as a plasma source in a Penning–Malmberg trap: a systematic study
Authors: Maero G. , Chen S. , Pozzoli R. , Romé M. 
Published: July 2015

A novel method was experimentally demonstrated to produce a low-density electron plasma in a Penning–Malmberg trap, exploiting the static electric and magnetic confinement fields together with a periodic excitation with amplitudes as low as 0.5–5 V and frequencies in the MHz range. This unusual technique proved to be applicable as a replacement for conventional electron sources in Penning devices and presents interesting aspects both in terms of basic science and technological applications. Nevertheless, the experimental observations demonstrate the high sensitivity of plasma features of interest (charge, mean density and density distribution) to the experimental conditions, namely trap configuration and excitation parameters, and as a consequence clear trends have not been identified so far. We present an experimental campaign of measurements where several parameters were systematically changed leading to a better assessment of the plasma production mechanism and to the identification of common trends.
Lagrangian coherent structures and plasma transport processes
Authors: Falessi M. V. , Pegoraro F. , Schep T. J. 
Published: July 2015

A dynamical system framework is used to describe transport processes in plasmas embedded in a magnetic field. For periodic systems with one degree of freedom, the Poincaré map provides a splitting of the phase space into regions where particles have different kinds of motion: periodic, quasi-periodic or chaotic. The boundaries of these regions are transport barriers, i.e. a trajectory cannot cross such boundaries throughout the evolution of the system. Lagrangian coherent structures generalize this method to systems with the most general time dependence, splitting the phase space into regions with different qualitative behaviours. This leads to the definition of finite-time transport barriers, i.e. trajectories cannot cross the barrier for a finite amount of time. This methodology can be used to identify fast recirculating regions in the dynamical system and to characterize the transport between them.
Guiding-centre transformation of the radiation–reaction force in a non-uniform magnetic field
Authors: Hirvijoki E. , Decker J. , Brizard A. J. , Embréus O. 
Published: July 2015

In this paper, we present the guiding-centre transformation of the radiation–reaction force of a classical point charge travelling in a non-uniform magnetic field. The transformation is valid as long as the gyroradius of the charged particles is much smaller than the magnetic field non-uniformity length scale, so that the guiding-centre Lie-transform method is applicable. Elimination of the gyromotion time scale from the radiation–reaction force is obtained with the Poisson-bracket formalism originally introduced by Brizard (Phys. Plasmas, vol. 11, 2004, 4429–4438), where it was used to eliminate the fast gyromotion from the Fokker–Planck collision operator. The formalism presented here is applicable to the motion of charged particles in planetary magnetic fields as well as in magnetic confinement fusion plasmas, where the corresponding so-called synchrotron radiation can be detected. Applications of the guiding-centre radiation–reaction force include tracing of charged particle orbits in complex magnetic fields as well as the kinetic description of plasma when the loss of energy and momentum due to radiation plays an important role, e.g. for runaway-electron dynamics in tokamaks.
Measurement of the angle, temperature and flux of fast electrons emitted from intense laser–solid interactions
Authors: Rusby D. R. , Wilson L. A. , Gray R. J. , Dance R. J. , Butler N. M. H. , MacLellan D. A. , Scott G. G. , Bagnoud V. , Zielbauer B. , McKenna P. , Neely D. 
Published: July 2015

High-intensity laser–solid interactions generate relativistic electrons, as well as high-energy (multi-MeV) ions and x-rays. The directionality, spectra and total number of electrons that escape a target-foil is dependent on the absorption, transport and rear-side sheath conditions. Measuring the electrons escaping the target will aid in improving our understanding of these absorption processes and the rear-surface sheath fields that retard the escaping electrons and accelerate ions via the target normal sheath acceleration (TNSA) mechanism. A comprehensive Geant4 study was performed to help analyse measurements made with a wrap-around diagnostic that surrounds the target and uses differential filtering with a FUJI-film image plate detector. The contribution of secondary sources such as x-rays and protons to the measured signal have been taken into account to aid in the retrieval of the electron signal. Angular and spectral data from a high-intensity laser–solid interaction are presented and accompanied by simulations. The total number of emitted electrons has been measured as $2.6\times 10^{13}$ with an estimated total energy of $12\pm 1~\text{J}$ from a $100~{\rm\mu}\text{m}$ Cu target with 140 J of incident laser energy during a $4\times 10^{20}~\text{W}~\text{cm}^{-2}$ interaction.
Conformational kinetics reveals affinities of protein conformational states
Authors: Daniels Kyle G. , Suo Yang , Oas Terrence G. 
Published: July 2015

Significance
Despite 50 years of studies of coupled binding and conformational change reactions in proteins and nucleic acids, there has been no detailed analysis of the affinities of the multiple conformational states involved. The relationship between these affinities and the dynamics of conformational change has also been largely overlooked. We perform rigorous kinetic analysis of protein conformational change coupled to binding to concomitantly determine binding affinities of individual conformational states and rate constants for conformational changes. The results point to an inextricable link between affinities of the individual states and the change in conformational dynamics upon binding. The difference in affinities of conformational states is critical for driving conformational change and has implications in molecular recognition, allostery, and drug development.
SomaticSignatures: inferring mutational signatures from single-nucleotide variants
Authors: Gehring Julian S. , Fischer Bernd , Lawrence Michael , Huber Wolfgang 
Published: July 2015

Abstract
Summary: Mutational signatures are patterns in the occurrence of somatic single-nucleotide variants that can reflect underlying mutational processes. The SomaticSignatures package provides flexible, interoperable and easy-to-use tools that identify such signatures in cancer sequencing data. It facilitates large-scale, cross-dataset estimation of mutational signatures, implements existing methods for pattern decomposition, supports extension through user-defined approaches and integrates with existing Bioconductor workflows.
Availability and implementation: The R package SomaticSignatures is available as part of the Bioconductor project. Its documentation provides additional details on the methods and demonstrates applications to biological datasets.
Contact: julian.gehring@embl.de, whuber@embl.de
Supplementary information: Supplementary data are available at Bioinformatics online.
C-It-Loci: a knowledge database for tissue-enriched loci
Authors: Weirick Tyler , John David , Dimmeler Stefanie , Uchida Shizuka 
Published: July 2015

Abstract
Motivation: Increasing evidences suggest that most of the genome is transcribed into RNAs, but many of them are not translated into proteins. All those RNAs that do not become proteins are called ‘non-coding RNAs (ncRNAs)’, which outnumbers protein-coding genes. Interestingly, these ncRNAs are shown to be more tissue specifically expressed than protein-coding genes. Given that tissue-specific expressions of transcripts suggest their importance in the expressed tissue, researchers are conducting biological experiments to elucidate the function of such ncRNAs. Owing greatly to the advancement of next-generation techniques, especially RNA-seq, the amount of high-throughput data are increasing rapidly. However, due to the complexity of the data as well as its high volume, it is not easy to re-analyze such data to extract tissue-specific expressions of ncRNAs from published datasets.
Results: Here, we introduce a new knowledge database called ‘C-It-Loci’, which allows a user to screen for tissue-specific transcripts across three organisms: human, mouse and zebrafish. C-It-Loci is intuitive and easy to use to identify not only protein-coding genes but also ncRNAs from various tissues. C-It-Loci defines homology through sequence and positional conservation to allow for the extraction of species-conserved loci. C-It-Loci can be used as a starting point for further biological experiments.
Availability and implementation: C-It-Loci is freely available online without registration at http://c-it-loci.uni-frankfurt.de.
Contact: uchida@med.uni-frankfurt.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Application of learning to rank to protein remote homology detection
Authors: Liu Bin , Chen Junjie , Wang Xiaolong 
Published: July 2015

Abstract
Motivation: Protein remote homology detection is one of the fundamental problems in computational biology, aiming to find protein sequences in a database of known structures that are evolutionarily related to a given query protein. Some computational methods treat this problem as a ranking problem and achieve the state-of-the-art performance, such as PSI-BLAST, HHblits and ProtEmbed. This raises the possibility to combine these methods to improve the predictive performance. In this regard, we are to propose a new computational method called ProtDec-LTR for protein remote homology detection, which is able to combine various ranking methods in a supervised manner via using the Learning to Rank (LTR) algorithm derived from natural language processing.
Results: Experimental results on a widely used benchmark dataset showed that ProtDec-LTR can achieve an ROC1 score of 0.8442 and an ROC50 score of 0.9023 outperforming all the individual predictors and some state-of-the-art methods. These results indicate that it is correct to treat protein remote homology detection as a ranking problem, and predictive performance improvement can be achieved by combining different ranking approaches in a supervised manner via using LTR.
Availability and implementation: For users’ convenience, the software tools of three basic ranking predictors and Learning to Rank algorithm were provided at http://bioinformatics.hitsz.edu.cn/ProtDec-LTR/home/
Contact: bliu@insun.hit.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Qualitative network models in support of ecosystem approaches to bivalve aquaculture
Authors: Reum Jonathan C. P. , McDonald P. Sean , Ferriss Bridget E. , Farrell Dara M. , Harvey Chris J. , Levin Phillip S. 
Published: July 2015

Abstract
Predicting the effects of aquaculture development for coastal ecosystems remains challenging, particularly for data-limited systems, and tools that account for complex ecological interactions are needed to support ecosystem approaches to aquaculture. Here, we used qualitative network models (QNMs) to examine the potential community effects of increasing bivalve aquaculture in South Puget Sound, a large estuarine system in Washington, United States. QNMs are formalized conceptual models that require only a qualitative understanding of how variables composing a system interact (that is, the sign of interactions: +, –, and 0) and are therefore well-suited to data-limited systems. Specifically, we examined community-wide responses to scenarios in which bivalve cultivation effort increased for three different bivalve species (Manila clam Venerupis philippinarum, Pacific oyster Crassostrea gigas, and geoduck Panopea generosa). Further, we evaluated community-wide responses to the removal of benthic bivalve predators, a future increase in nutrient loadings, and combinations of these scenarios acting simultaneously. The scenarios enabled identification of potential trade-offs between increased aquaculture and shifts in the abundance of community members and assessment of the possible effects of different management actions. We also analysed the QNM to identify key interactions that influence the sign outcome of community responses to press perturbations, highlighting potential points for management intervention and linkages deserving of more focused quantitative study. QNMs are mathematically robust and highly flexible, but remain underutilized. We suggest that they may serve as valuable tools for supporting ecosystem approaches to aquaculture.
A critique of the balanced harvesting approach to fishing
Authors: Froese Rainer , Walters Carl , Pauly Daniel , Winker Henning , Weyl Olaf L. F. , Demirel Nazli , Tsikliras Athanassios C. , Holt Sidney J. 
Published: July 2015

AbstractThe approach to fisheries termed “balanced harvesting” (BH) calls for fishing across the widest possible range of species, stocks, and sizes in an ecosystem, in proportion to their natural productivity, so that the relative size and species composition is maintained. Such fishing is proposed to result in higher catches with less negative impact on exploited populations and ecosystems. This study examines the models and the empirical evidence put forward in support of BH. It finds that the models used unrealistic settings with regard to life history (peak of cohort biomass at small sizes), response to fishing (strong compensation of fishing mortality by reduced natural mortality), and economics (uniform high cost of fishing and same ex-vessel price for all species and sizes), and that empirical evidence of BH is scarce and questionable. It concludes that evolutionary theory, population dynamics theory, ecosystem models with realistic assumptions and settings, and widespread empirical evidence do not support the BH proposal. Rather, this body of evidence suggests that BH will not help but will hinder the policy changes needed for the rebuilding of ecosystems, healthy fish populations, and sustainable fisheries.
Psychiatric Comorbidity Is Associated Prospectively with Diminished Opioid Analgesia and Increased Opioid Misuse in Patients with Chronic Low Back Pain
Authors: Wasan Ajay D. , Michna Edward , Edwards Robert R. , Katz Jeffrey N. , Nedeljkovic Srdjan S. , Dolman Andrew J. , Janfaza David , Isaac Zach , Jamison Robert N. 
Published: July 2015

AbstractAbstract
In 81 patients with chronic low back pain prospectively studied for 6½ months with placebo followed by opioids, those with high negative affect were prescribed larger average daily doses of opioids, had less improvement in pain, and had a greater rate of opioid misuse than those with low negative affect. These prospective data support previous cross-sectional data to suggest that negative affect presents an important risk factor in inadequate analgesia from opioids and opioid misuse.

Background:
Opioids are frequently prescribed for chronic low back pain (CLBP), but there are little prospective data on which patient subgroups may benefit. Psychiatric comorbidity, such as high levels of depression and anxiety symptoms (termed comorbid negative affect [NA]), is a common presentation and may predict diminished opioid analgesia and/or increased opioid misuse.

Methods:
The authors conducted a 6½-month prospective cohort study of oral opioid therapy, with an active drug/placebo run-in period, in 81 CLBP patients with low, moderate, and high levels of NA. Treatment included an opioid titration phase with a prescribing physician blinded to NA group assignment and a 4-month continuation phase, during which subjects recorded daily pain levels using an electronic diary. The primary outcome was the percent improvement in average daily pain, summarized weekly.

Results:
There was an overall 25% dropout rate. Despite the high NA group being prescribed a higher average daily dose of morphine equivalents, linear mixed model analysis revealed that the 24 study completers in each of the high NA and low NA groups had an average 21 versus 39% improvement in pain, respectively (P < 0.01). The high NA group also had a significantly greater rate of opioid misuse (39 vs. 8%, P < 0.05) and significantly more and intense opioid side effects (P < 0.01).

Conclusions:
These results indicate that the benefit and risk considerations in CLBP patients with high NA versus low NA are distinctly different. Thus, NA is an important phenotypic variable to characterize at baseline, before deciding whether to prescribe opioids for CLBP.
An Anatomic Study of the Greater Trochanter Starting Point for Intramedullary Nailing in the Skeletally Immature
Authors: Park Paul J. , Weinberg Douglas S. , Petro Kathleen F. , Liu Raymond W. 
Published: July 2015

Background:
Trochanteric entry femoral nails have been increasing in popularity in the pediatric population for stabilization in fractures and osteotomies. The proper position for entry point in the coronal plane has been well studied; however, the sagittal plane in the pediatric population has not yet been well characterized.

Methods:
Eighty-eight cadaveric femora aged 8 to 20 years were studied in an apparent neck-shaft angle (ANSA) position, with distal condyles flat on the surface, and a true neck-shaft angle (TNSA) position, with internal rotation to neutralize femoral anteversion. Anterior and lateral offset were measured on lateral and anteroposterior photographs, respectively, as the perpendicular distance from the greater trochanter apex to the center of the intramedullary canal. The effect of rotational position (ANSA vs. TNSA) of the proximal femur was compared using the intraclass correlation coefficient for anterior and lateral offset. Correlations between age, demographics, anteversion, and greater trochanter morphology with anterior and lateral offset were evaluated with multiple regression analysis.

Results:
The mean age was 15.8±3.8 years. The mean anterior displacement of the trochanteric apex was 4.8±3.0 and 4.6±3.2 mm in the ANSA and TNSA positions, respectively. The mean lateral displacement was 10.6±4.2 and 9.7±4.0 mm in the ANSA and TNSA positions, respectively. The intraclass coefficient for anterior offset in the ANSA versus TNSA position was 0.704 and 0.900 for lateral offset. Change was minimal for anterior offset in the ANSA and TNSA positions versus age (standardized beta values 0.240, 0.241, respectively). There was a significant correlation with increasing lateral offset in the ANSA and TNSA positions with increasing age (standardized beta values 0.500, 0.385 respectively).

Conclusions:
In the pediatric population, the tip of the greater trochanter is consistently anterior by approximately 5 mm. The mean lateral displacement was approximately 10 mm and increased with increasing age.

Clinical Relevance:
Nail entry at the pediatric greater trochanter apex would likely result in anterior placement. We recommend inserting the guidewire 5 mm posterior to the apex of the trochanter and confirming coronal and sagittal position with fluoroscopy.
Why Lumbar Artificial Disk Replacements (LADRs) Fail
Authors: Pettine Kenneth , Ryu Robert , Techy Fernando 
Published: July 2015

Study Design:
A retrospective review of prospectively collected data.

Objective:
To determine why artificial disk replacements (ADRs) fail by examining results of 91 patients in FDA studies performed at a single investigational device exemption (IDE) site with minimum 2-year follow-up.

Summary of Background Data:
Patients following lumbar ADR generally achieve their 24-month follow-up results at 3 months postoperatively.

Materials and Methods:
Every patient undergoing ADR at 1 IDE site by 2 surgeons was evaluated for clinical success. Failure was defined as <50% improvement in ODI and VAS or any additional surgery at index or adjacent spine motion segment. Three ADRs were evaluated: Maverick, 25 patients; Charité, 31 patients; and Kineflex, 35 patients. All procedures were 1-level operations performed at L4–L5 or L5–S1. Demographics and inclusion/exclusion criteria were similar and will be discussed.

Results:
Overall clinical failure occurred in 26% (24 of 91 patients) at 2-year follow-up. Clinical failure occurred in: 28% (Maverick) (7 of 25 patients), 39% (Charité) (12 of 31 patients), and 14% (Kineflex) (5 of 35 patients). Causes of failure included facet pathology, 50% of failure patients (12 of 24). Implant complications occurred in 5% of total patients and 21% of failure patients (5 of 24). Only 5 patients went from a success to failure after 3 months. Only 1 patient went from a failure to success after a facet rhizotomy 1 year after ADR.

Conclusions:
Seventy-four percent of patients after ADR met strict clinical success after 2-year follow-up. The clinical success versus failure rate did not change from their 3-month follow-up in 85 of the 91 patients (93%). Overall clinical success may be improved most by patient selection and implant type.