bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ion beam transport: modelling and experimental measurements on a large negative ion source in view of the ITER heating neutral beam
Authors: Veltri P. , Sartori E. , Agostinetti P. , Aprile D. , Brombin M. , Chitarin G. , Fonnesu N. , Ikeda K. , Kisaki M. , Nakano H. , Pimazzoni A. , Tsumori K. , Serianni G. 
Published: November 2016

Abstract
Neutral beam injectors are among the most important methods of plasma heating in magnetic confinement fusion devices. The propagation of the negative ions, prior to their conversion into neutrals, is of fundamental importance in determining the properties of the beam, such as its aiming and focusing at long-distances, so as to deposit the beam power in the proper position inside the confined plasma, as well as to avoid interaction with the material surfaces along the beam path. The final design of the ITER Heating Neutral Beam prototype has been completed at Consorzio RFX (Padova, Italy), in the framework of a close collaboration with European, Japanese and Indian fusion research institutes. The physical and technical rationales on which the design is based were essentially driven by numerical modelling of the relevant physical processes, and the same models and codes will be useful to design the DEMO neutral beam injector in the near future. This contribution presents a benchmark study of the codes used for this purpose, by comparing their results against the measures performed in an existing large-power device, hosted at the National Institute for Fusion Science, Japan. In particular, the negative ion formation and acceleration are investigated. A satisfactory agreement was found between codes and experiments, leading to an improved understanding of beam transport dynamics. The interpretation of the discrepancies identified in previous works, possibly related to the non-uniformity of the extracted negative ion current, is also presented.
Is the higher mortality among men with hip fracture explained by sex-related differences in quality of in-hospital care? A population-based cohort study
Authors: Kristensen Pia Kjær , Johnsen Søren Paaske , Mor Anil , Thillemann Theis Muncholm , Pedersen Alma Becic 
Published: November 2016

AbstractBackgroundmortality after hip fracture is two-fold higher in men compared with women. It is unknown whether sex-related differences in the quality of in-hospital care contribute to the higher mortality among men.Objectiveto examine sex-related differences in quality of in-hospital care, 30-day mortality, length of hospital stay and readmission among patients with hip fracture.Designpopulation-based cohort study.Measuresusing prospectively collected data from the Danish Multidisciplinary Hip Fracture Registry, we identified 25,354 patients ≥65 years (29% were men). Outcome measures included quality of in-hospital care as reflected by seven process performance measures, 30-day mortality, length of stay (LOS) and readmission within 30 days after discharge. Data were analysed using multivariable regression techniques.Resultsin general, there were no substantial sex-related differences in quality of in-hospital care. The relative risk for receiving the individual process performance measure ranged from 0.91 (95% confidence interval (CI) 0.85–0.97) to 0.97 (95% CI 0.94–0.99) for men compared with women. The 30-day mortality was 15.9% for men and 9.3% for women corresponding to an adjusted odds ratio (OR) of 2.30 (95% CI 2.09–2.54). The overall readmission risk within 30 days after discharge was 21.6% for men and 16.4% for women (adjusted OR of 1.38 (95% CI 1.29–1.47)). No difference in LOS was observed between men and women.Conclusionssex differences in the quality of in-hospital care appeared not to explain the higher mortality and risk of readmission among men hospitalised with hip fracture.
Accelerating Bayesian inference for evolutionary biology models
Authors: Meyer Xavier , Chopard Bastien , Salamin Nicolas 
Published: November 2016

Abstract

Motivation
Bayesian inference is widely used nowadays and relies largely on Markov chain Monte Carlo (MCMC) methods. Evolutionary biology has greatly benefited from the developments of MCMC methods, but the design of more complex and realistic models and the ever growing availability of novel data is pushing the limits of the current use of these methods.

Results
We present a parallel Metropolis-Hastings (M-H) framework built with a novel combination of enhancements aimed towards parameter-rich and complex models. We show on a parameter-rich macroevolutionary model increases of the sampling speed up to 35 times with 32 processors when compared to a sequential M-H process. More importantly, our framework achieves up to a twentyfold faster convergence to estimate the posterior probability of phylogenetic trees using 32 processors when compared to the well-known software MrBayes for Bayesian inference of phylogenetic trees.

Availability and Implementation
https://bitbucket.org/XavMeyer/hogan

Supplementary information
Supplementary data are available at Bioinformatics online.
Expanding the toolkit for membrane protein modeling in Rosetta
Authors: Koehler Leman Julia , Mueller Benjamin K , Gray Jeffrey J 
Published: November 2016

Abstract

Motivation
A range of membrane protein modeling tools has been developed in the past 5–10 years, yet few of these tools are integrated and make use of existing functionality for soluble proteins. To extend existing methods in the Rosetta biomolecular modeling suite for membrane proteins, we recently implemented RosettaMP, a general framework for membrane protein modeling. While RosettaMP facilitates implementation of new methods, addressing real-world biological problems also requires a set of accessory tools that are used to carry out standard modeling tasks.

Results
Here, we present six modeling tools, including de novo prediction of single trans-membrane helices, making mutations and refining the structure with different amounts of flexibility, transforming a protein into membrane coordinates and optimizing its embedding, computing a Rosetta energy score, and visualizing the protein in the membrane bilayer. We present these methods with complete protocol captures that allow non-expert modelers to carry out the computations.

Availability and Implementation
The presented tools are part of the Rosetta software suite, available at www.rosettacommons.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
The asteroseismic surface effect from a grid of 3D convection simulations – I. Frequency shifts from convective expansion of stellar atmospheres
Authors: Trampedach Regner , Aarslev Magnus J. , Houdek Günter , Collet Remo , Christensen-Dalsgaard Jørgen , Stein Robert F. , Asplund Martin 
Published: November 2016

Abstract
We analyse the effect on adiabatic stellar oscillation frequencies of replacing the near-surface layers in 1D stellar structure models with averaged 3D stellar surface convection simulations. The main difference is an expansion of the atmosphere by 3D convection, expected to explain a major part of the asteroseismic surface effect, a systematic overestimation of p-mode frequencies due to inadequate surface physics. We employ pairs of 1D stellar envelope models and 3D simulations from a previous calibration of the mixing-length parameter, α. That calibration constitutes the hitherto most consistent matching of 1D models to 3D simulations, ensuring that their differences are not spurious, but entirely due to the 3D nature of convection. The resulting frequency shift is identified as the structural part of the surface effect. The important, typically non-adiabatic, modal components of the surface effect are not included in this analysis, but relegated to future papers. Evaluating the structural surface effect at the frequency of maximum mode amplitude, νmax , we find shifts from δν = −0.8 μHz for giants at log g = 2.2 to − 35 μHz for a (Teff = 6901 K, log g = 4.29) dwarf. The fractional effect δν(νmax )/νmax , ranges from −0.1 per cent for a cool dwarf (4185 K, 4.74) to −6 per cent for a warm giant (4962 K, 2.20).
Peanut-shaped metallicity distributions in bulges of edge-on galaxies: the case of NGC 4710
Authors: Gonzalez Oscar A. , Debattista Victor P. , Ness Melissa , Erwin Peter , Gadotti Dimitri A. 
Published: November 2016

Abstract
Bulges of edge-on galaxies are often boxy/peanut-shaped (B/PS), and unsharp masks reveal the presence of an X shape. Simulations show that these shapes can be produced by dynamical processes driven by a bar which vertically thickens the centre. In the Milky Way, which contains such a B/PS bulge, the X-shaped structure is traced by the metal-rich stars but not by the metal-poor ones. Recently, Debattista et al. interpreted this property as a result of the varying effect of the bar on stellar populations with different starting kinematics. This kinematic fractionation model predicts that cooler populations at the time of bar formation go on to trace the X shape, whereas hotter populations are more uniformly distributed. As this prediction is not specific to the Milky Way, we test it with Multi Unit Spectroscopic Explorer (MUSE) observations of the B/PS bulge in the nearby galaxy NGC 4710. We show that the metallicity map is more peanut-shaped than the density distribution itself, in good agreement with the prediction. This result indicates that the X-shaped structure in B/PS bulges is formed of relatively metal-rich stars that have been vertically redistributed by the bar, whereas the metal-poor stars have a more uniform, box-shaped distribution.
Impaired Pain Modulation in Fibromyalgia Patients in Response to Social Distress Manipulation
Authors: Canaipa Rita , Castro-Caldas Alexandre , Moreira João Manuel , Pimentel-Santos Fernando , Branco Jaime Cunha , Treister Roi 
Published: November 2016

Objectives:
Fibromyalgia (FM), a chronic pain condition, is associated with abnormalities in pain modulation. A growing body of evidence has shown that social distress modulates pain sensitivity. The current study aimed to assess the effects of social distress manipulation on pain in FM patients compared with positive (rheumatoid arthritis, RA) and negative (pain-free) controls.

Materials and Methods:
FM, RA patients and pain-free controls (PFC) were recruited. Demographic, medical, and psychological data were collected. Each participant was exposed to 3 study conditions in a random order: the inclusion (positive social effects) and exclusion (negative social effects) conditions of Cyberball, a game that manipulates social distress, and a control condition. Pain sensitivity in response to nociceptive electrical and thermal (cold) stimuli was assessed before and during each study condition.

Results:
In response to electrical stimuli, pain decreased in both the inclusion and exclusion conditions in PFC and RA groups, whereas inclusion conditions significantly increased pain in the FM group. Social manipulation (inclusion or exclusion) did not affect pain sensitivity as measured in response to thermal stimulation.

Discussion:
These results are in line with previous studies demonstrating altered pain inhibition in FM patients, and suggest that unlike PFC or other non-“stress–related” chronic pain conditions, being socially included may increase pain perception in FM patients. Possible underlying mechanisms and clinical relevance are discussed.
Disparity in Outcomes for Adolescent and Young Adult Patients Diagnosed With Pediatric Solid Tumors Across 4 Decades
Authors: Chen Ishita , Pasalic Dario , Fischer-Valuck Benjamin , Frangoul Haydar , DeWees Todd , Shinohara Eric T. , Perkins Stephanie M. 
Published: November 2016

Objective:
Cancer mortality is a leading cause of disease-related death in the adolescent and young adult (AYA) population. Compared with older and younger patients, AYA patients often experience worse cancer-specific outcomes. Here, we compare AYA and pediatric overall survival (OS) in the most common pediatric extracranial solid tumors.

Materials and Methods:
Using the US Surveillance, Epidemiology, and End Results database, we studied patients (age, 0 to 39 y) diagnosed with Ewing sarcoma, neuroblastoma, osteosarcoma, rhabdomyosarcoma, and Wilms tumor.

Results:
A total of 12,375 patients (age, 0 to 39 y) were diagnosed between 1973 and 2010 (8247 pediatric and 4128 AYA patients). AYA patients with rhabdomyosarcoma and Ewing sarcoma were more likely to present with metastatic disease. OS was significantly worse in the AYA cohort for all tumor types (P<0.001) with the exception of osteosarcoma (P=0.29). Across 2 treatment time periods (1973 to 1989 and 1990 to 2010), there was significant improvement in 5-year OS in all tumor types with the exception of rhabdomyosarcoma; however, AYA patients continued to experience worse OS in the modern treatment cohort with the exception of osteosarcoma patients. There was no improvement in OS among AYA patients with Ewing sarcoma, neuroblastoma, rhabdomyosarcoma, or Wilms tumor over the 2 treatment eras.

Conclusions:
For the most common pediatric extracranial solid tumors, AYA patients experience significantly worse OS compared with pediatric patients. Although improvements in therapy have led to gain in survival for pediatric patients, with the exception of osteosarcoma, AYA experienced no increase in survival over the study period. This investigation demonstrates the importance for further research in the AYA population.
Nontraditional Methods to Evaluate Wound Healing
Authors: Hasatsri Sukhontha , Aramwit Pornanong 
Published: November 2016

BACKGROUND
Traditional evaluation of wound healing is sometimes subjective. It is necessary to develop qualitative and quantitative methods to enable more efficient and accurate evaluation of wounds. Recently, new techniques have been introduced and the correspondence between these techniques and clinician judgment is critical.

OBJECTIVE
Some nontraditional techniques that analyze wound healing were reviewed, which include measurements of the wound area, tissue color, skin barrier function, skin humidity, and keratinocyte morphology.

METHODS
This review article is based on medical research that focuses on the evaluation of wound healing.

RESULTS
Software-based and advanced device-based techniques generally provide more accurate and precise results than traditional ones, such as the ruler-based technique. Measurement of tissue color can also help to identify the type of tissue. Evaluation of skin barrier function can assist clinicians to analyze functional restoration of skin, whereas skin humidity demonstrates the exudate production status of the wound. In addition, keratinocyte morphology in the wound bed indicates quality of wound healing and side effects of treatment.

CONCLUSION
There is no gold standard method for qualitative and quantitative evaluation of wound healing. It is important to understand the type of wound, sample size, results obtained, advantages, and limitations of each technique.
Comprehensive management of hereditary hemorrhagic telangiectasia
Authors: Lupa Michael D. , Wise Sarah K. 
Published: November 2016

Purpose of review
Hereditary hemorrhagic telangiectasia (HHT), or Osler Weber-Rendu disease, is a rare inherited disorder of fibrovascular tissue affecting various organs. Epistaxis is the most common symptom of HHT but as the disease affects multiple organs, a multisystem and multidisciplinary approach to management is required. The purpose of this article is to provide an overview of the multidisciplinary approach to HHT for the otolaryngologist and to discuss the current pharmacologic and procedural treatment options available for HHT-related epistaxis.

Recent findings
Multidisciplinary expert guidelines have better defined what screening tests are advised for the multisystem evaluation of the HHT patient. New pharmacologic therapies including bevacizumab (Avastin) used submucosally or topically have shown promise as in-office treatment modalities. Sclerotherapy of telangiectasia, including in-office applications, has recently proven safe and effective.

Summary
HHT remains a difficult disease to treat. Being aware of the common organ systems involved by the disease will help the practicing otolaryngologist to ensure the patient receives appropriate multidisciplinary care. For HHT-related epistaxis, new medical and surgical options allow for a wider range of treatments than were previously available.
The evidence for olfactory training in treating patients with olfactory loss
Authors: Patel Zara M. 
Published: November 2016

Purpose of review
The purpose of this review is to go over the only therapy for olfactory loss supported by level 1a evidence that is currently available, which is olfactory training. This therapy is widely underutilized and has the potential to help many patients with olfactory dysfunction who are otherwise offered no management options.

Recent findings
We will review the rationale, clinical studies, and quality of the evidence regarding olfactory training, specifically the olfactory system's inherent ability to regenerate, the plasticity of the system, and the multiple protocols and modifications of protocols present in the literature.

Summary
Olfactory training is an effective therapy for some patients suffering from olfactory loss, and, while we do not yet know the optimal duration or number of odorants or exact patient population it may be most beneficial for, as an extremely easy, self-driven therapy with no significant side-effects, it should be consistently offered to this patient population.
Detangling the evolutionary developmental integration of dentate jaws: evidence that a p63 gene network regulates odontogenesis exclusive of mandible morphogenesis
Authors: Raj Muhammad T. , Boughner Julia C. 
Published: November 2016

SUMMARYVertebrate jaws and dentitions fit and function together, yet the genetic processes that coordinate cranial and dental morphogenesis and evolution remain poorly understood. Teeth but not jaws fail to form in the edentate p63−/− mouse mutant, which we used here to identify genes important to odontogenesis, but not jaw morphogenesis, and that may allow dentitions to change during development and evolution without necessarily affecting the jaw skeleton. With the working hypothesis that tooth and jaw development are autonomously controlled by discreet gene regulatory networks, using gene expression microarray assays validated by quantitative reverse‐transcription PCR we contrasted expression in mandibular prominences at embryonic days (E) 10–13 of mice with normal lower jaw development but either normal (p63+/−, p63+/+) or arrested (p63−/−) tooth development. The p63−/− mice showed significantly different expression (fold change ≥2, ≤−2; P ≤ 0.05) of several genes. Some of these are known to help regulate odontogenesis (e.g., p63, Osr2, Cldn3/4) and/or to be targets of p63 (e.g., Jag1/2, Fgfr2); other genes have no previously reported roles in odontogenesis or the p63 pathway (e.g., Fermt1, Cbln1, Pltp, Krt8). As expected, from E10 to E13, few genes known to regulate mandible morphogenesis differed in expression between mouse strains. This study newly links several genes to odontogenesis and/or to the p63 signaling network. We propose that these genes act in a novel odontogenic network that is exclusive of lower jaw morphogenesis, and posit that this network evolved in oral, not pharyngeal, teeth.
Transient Two-Dimensional Heat Conduction Problem With Partial Heating Near Corners
Authors: McMasters Robert L. , de Monte Filippo , Beck James V. , Amos Donald E. 
Published: November 2016

This paper provides a solution for two-dimensional heating over a rectangular region on a homogeneous plate. It has application to verification of numerical conduction codes as well as direct application for heating and cooling of electronic equipment. Additionally, it can be applied as a direct solution for the inverse heat conduction problem, most notably used in thermal protection systems for re-entry vehicles. The solutions used in this work are generated using Green’s functions. Two approaches are used which provide solutions for either semi-infinite plates or finite plates with isothermal conditions which are located a long distance from the heating. The methods are both efficient numerically and have extreme accuracy, which can be used to provide additional solution verification. The solutions have components that are shown to have physical significance.
The extremely precise nature of analytical solutions allows them to be used as prime standards for their respective transient conduction cases. This extreme precision also allows an accurate calculation of heat flux by finite differences between two points of very close proximity which would not be possible with numerical solutions. This is particularly useful near heated surfaces and near corners. Similarly, sensitivity coefficients for parameter estimation problems can be calculated with extreme precision using this same technique. Another contribution of these solutions is the insight that they can bring. Important dimensionless groups are identified and their influence can be more readily seen than with numerical results. For linear problems, basic heating elements on plates, for example, can be solved to aid in understanding more complex cases. Furthermore these basic solutions can be superimposed both in time and space to obtain solutions for numerous other problems.
This paper provides an analytical two-dimensional, transient solution for heating over a rectangular region on a homogeneous square plate. Several methods are available for the solution of such problems. One of the most common is the separation of variables (SOV) method. In the standard implementation of the SOV method, convergence can be slow and accuracy lacking. Another method of generating a solution to this problem makes use of time-partitioning which can produce accurate results. However, numerical integration may be required in these cases, which, in some ways, negates the advantages offered by the analytical solutions. The method given herein requires no numerical integration; it also exhibits exponential series convergence and can provide excellent accuracy. The procedure involves the derivation of previously-unknown simpler forms for the summations, in some cases by virtue of the use of algebraic components. Also, a mathematical identity given in this paper can be used for a variety of related problems.
Design of a Magnetic Cooling Device Using Gadolinium Alloy and Permanent Magnets
Authors: Abdelmessih Amanie N. , Bartholomae Paul W. , Casillas Matthew L. , DeLyon Rocky E. , Flaherty Joshua F. , Goolsby Bradley D. , Langley Moriah M. , Livoni Lindsey A. , Logan Trevor W. , Perhach Nicolas J. , Replogle Jonathan J. , Swann Daniel R. , Williams Garrett M. 
Published: November 2016

Traditionally, heat pumps and refrigerators utilize the vapor compression cycle to achieve cooling. These vapor compression cycles use hydrochlorofluorocarbons (R134a) as the cycle’s working fluid. This refrigerant contributes to global warming and is expected to be phased out. Consequently, new refrigerants as well as new refrigeration methods need to be developed.
The research detailed in this article attempts to implement the magnetocaloric effect of gadolinium alloy in a designed apparatus to lower the temperature of air. Gadolinium alloy has a noticeable magnetocaloric effect within a strong magnetic field (5 T). This research is aimed at producing a noticeable temperature change (2–3 °C) in a relatively smaller magnetic field (1 T) produced with permanent magnets. This work tests the feasibility of magnetic cooling by introducing the design of a magnetic cooling apparatus, using Gadolinium alloy (Gd5Si2Ge2). Small pebbles were used as opposed to a solid plate in order to have an increased surface area to enhance the convection heat transfer process. Permanent magnets were used in the apparatus, to decrease the operating cost. The maximum temperature change encountered in the heat exchanger of the apparatus built was 2.3 °C in a 1 T magnetic field.