bluuebunny/crossref_metadata_2025 huggingface dataset:
Species distributions represent intraspecific genetic diversity of freshwater fish in conservation assessments
Authors: Hermoso Virgilio , Kennard Mark J. , Schmidt Daniel J. , Bond Nick , Huey Joel A. , Mondol Rashedul K. , Jamandre Brian W. , Hughes Jane M.
Published: July 2016

Accounting for genetic diversity and evolutionary processes has long been recognised as an important goal in conservation planning. However, because genetic data are often lacking, surrogate approaches are widely used. Few studies have, however, assessed the capacity of surrogate data, such as higher taxonomic levels (e.g. species distributions) to portray intraspecific genetic diversity.

Here, we contrast conservation plans based on traditional species distribution data, with those derived from intraspecific genetic data for a smaller subset of species, both using freshwater fish in northern Australia. We modelled the spatial distribution of 46 species and intraspecific genetic diversity within four common species. We then identified priority areas for conservation using both data sets and evaluated the extent to which solutions obtained from species distribution data portrayed genetic diversity.

We found that genetic diversity could be adequately represented within priority areas identified using species distribution data, even at low conservation targets and for species with complex genetic structure. However, this was only true when using the entire fish community (i.e. all 46 species). In contrast, a substantial component of the genetic structure would not be represented in conservation priority areas when using a subset of species.

Our results have important implications for the use of surrogates for genetic diversity in conservation planning. Sufficient genetic diversity might be represented in conservation priority areas by including a broad range of species with distributions ranging from common to rare elements in the community in the prioritisation analyses. We recommend focusing on improving accuracy of data on species distributions to reduce uncertainties in conservation recommendations derived from commission and omission errors, to avoid misuse of limited conservation funds and potential failure of conservation practice.
High‐temperature Bending Strength of Self‐Healing Ni/Al2O3 Nanocomposites
Authors: Pham Hai Vu , Nanko Makoto , Nakao Wataru
Published: July 2016

Bending strength of 5 vol.% Ni/Al2O3 composites as a function of testing temperature is investigated at temperatures ranging from room temperature to 1200°C. Self‐healing performance at high temperatures of the composites is evaluated by conducting high‐temperature bending tests for as‐sintered, as‐cracked, and as‐healed specimens. Bending strength of as‐sintered specimens dramatically decreases from 995 MPa at room temperature to 205 MPa at 1200°C. Additionally, the plastic deformation of the as‐sintered specimens occurs when the testing temperature reaches to 1200°C. The values of high‐temperature bending strength of as‐healed specimens are comparable with those of as‐sintered specimens. Similar to that of as‐sintered specimens, bending strength of as‐healed specimens degrades when the testing temperature increases. Results of the present study indicate that the recovery of bending strength by the self‐healing function is able to achieve at temperatures as high as 1200°C. Unlike the mechanical behaviors at high temperatures of as‐sintered and as‐healed specimens, the bending strength of as‐cracked specimens slightly increases with the increase of testing temperature. This phenomenon is attributed to the effect of the self‐healing mechanism during high‐temperature bending tests.
Optimization of fixation methods for image analysis of the hepatopancreas in whiteleg shrimp, Penaeus vannamei (Boone)
Authors: Cervellione F , McGurk C , Silva P , Owen M A G , Van den Broeck W
Published: July 2016

Pathology in penaeid shrimps relies on histology, which is subjective, time‐consuming and difficult to grade in a reproducible manner. Automated image analysis is faster, objective and suitable for routine screening; however, it requires standardized protocols. The first critical step is proper fixation of the target tissue. Bell & Lightner's (A Handbook of Normal Penaeid Shrimp Histology, 1988, The World Aquaculture Society, Baton Rouge) fixation protocol, widely used for routine histology of paraffin sections, is not optimized for image analysis, and no protocol for frozen sections is described in the available literature. Therefore, the aim of this study was to optimize fixation of the hepatopancreas (HP) from whiteleg shrimp (Penaeus vannamei) for both paraffin and frozen sections using a semiquantitative scoring system. For paraffin sections, four injection volumes and three injection methods were compared, for frozen sections, four freezing methods and four fixation methods. For paraffin sections, optimal fixation was achieved by increasing threefold the fixative volume recommended by Bell and Lightner, from 10% to 30% of the shrimp body weight, combined with single injection into the HP. Optimal fixation for frozen sections was achieved by freezing the cephalothorax with liquid nitrogen, followed by fixation of the section with 60% isopropanol. These optimized methods enable the future use of image analysis and improve classical histology.
Characterization of mesostasis regions in lunar basalts: Understanding late‐stage melt evolution and its influence on apatite formation
Authors: Potts Nicola J. , Tartèse Romain , Anand Mahesh , van Westrenen Wim , Griffiths Alexandra A. , Barrett Thomas J. , Franchi Ian A.
Published: July 2016

Recent studies geared toward understanding the volatile abundances of the lunar interior have focused on the volatile‐bearing accessory mineral apatite. Translating measurements of volatile abundances in lunar apatite into the volatile inventory of the silicate melts from which they crystallized, and ultimately of the mantle source regions of lunar magmas, however, has proved more difficult than initially thought. In this contribution, we report a detailed characterization of mesostasis regions in four Apollo mare basalts (10044, 12064, 15058, and 70035) in order to ascertain the compositions of the melts from which apatite crystallized. The texture, modal mineralogy, and reconstructed bulk composition of these mesostasis regions vary greatly within and between samples. There is no clear relationship between bulk‐rock basaltic composition and that of bulk‐mesostasis regions, indicating that bulk‐rock composition may have little influence on mesostasis compositions. The development of individual melt pockets, combined with the occurrence of silicate liquid immiscibility, exerts greater control on the composition and texture of mesostasis regions. In general, the reconstructed late‐stage lunar melts have roughly andesitic to dacitic compositions with low alkali contents, displaying much higher SiO2 abundances than the bulk compositions of their host magmatic rocks. Relevant partition coefficients for apatite‐melt volatile partitioning under lunar conditions should, therefore, be derived from experiments conducted using intermediate compositions instead of compositions representing mare basalts.
The impact of skin colour on human photobiological responses
Authors: Fajuyigbe Damilola , Young Antony R.
Published: July 2016

Terrestrial solar ultraviolet radiation (UVR) exerts both beneficial and adverse effects on human skin. Epidemiological studies show a lower incidence of skin cancer in people with pigmented skins compared to fair skins. This is attributed to photoprotection by epidermal melanin, as is the poorer vitamin D status of those with darker skins. We summarize a wide range of photobiological responses across different skin colours including DNA damage and immunosuppression. Some studies show the generally modest photoprotective properties of melanin, but others show little or no effect. DNA photodamage initiates non‐melanoma skin cancer and is reduced by a factor of about 3 in pigmented skin compared with white skin. This suggests that if such a modest reduction in DNA damage can result in the significantly lower skin cancer incidence in black skin, the use of sunscreen protection might be extremely beneficial for susceptible population. Many contradictory results may be explained by protocol differences, including differences in UVR spectra and exposure protocols. We recommend that skin type comparisons be done with solar‐simulated radiation and standard erythema doses or physical doses (J/m2) rather than those based solely on clinical endpoints such as minimal erythema dose (MED).
Assessment of children with vascular ring
Authors: Tola Hasan , Ozturk Erkut , Yildiz Okan , Erek Ersin , Haydin Sertac , Turkvatan Aysel , Ergul Yakup , Guzeltas Alper , Bakir Ihsan
Published: July 2016

Background

Vascular rings may cause pressure on the trachea and/or esophagus of varying degree, resulting in symptoms. This study assessed the presentation symptoms, diagnostic methods and treatment results after surgery in children with vascular ring.

Methods

Symptomatic vascular ring patients undergoing surgery between January 2010 and August 2014 at Mehmet Akif Ersoy Cardiovascular Research and Training Hospital, Istanbul, were retrospectively assessed. The presentation symptoms, demographic characteristics, and diagnostic tests were evaluated. Operative data and postoperative follow up, complications and problems were also examined in detail.

Results

Twenty‐one patients underwent surgery, 13 (63%) of whom were male. Median age was 12 months (range, 1 month–8 years). Among these patients, 62% (n = 13) had double aortic arch, 24% (n = 5) had right‐sided aortic arch + ligamentum arteriosum, 10% (n = 2) had left‐sided aortic arch + aberrant right subclavian artery, and 4% (n = 1) had pulmonary sling abnormality. Computed tomography (CT) angiography was performed in 17/21 patients. All the patients were successfully operated on. In the early postoperative period, two patients had chylothorax and one had nerve paralysis of nervus laryngeus recurrens. One patient died in the early period, and two patients had ongoing stridor on follow up.

Conclusions

CT angiography is effective for the differential diagnosis and visualization of vascular ring abnormality. In such cases, full recovery can be assured with early diagnosis and surgery.
Discovering Collaborative Advantage: The Contributions of Goal Categories and Visual Strategy Mapping
Authors: Bryson John M. , Ackermann Fran , Eden Colin
Published: July 2016

Collaboration can make sense when there is some sort of “collaborative advantage” to be gained, meaning organizations can achieve something together that they cannot easily achieve by themselves. However, the literature is essentially silent on how to identify collaborative advantage. This article addresses this shortcoming in the theory of collaborative advantage for public purposes by proposing a set of goal categories that may be used to help articulate collaborative advantage and introducing the use of visual strategy mapping as part of a facilitated group process to figure out what the collaborative advantage might be. Collaborative advantage, as it is normally understood, consists of shared core goals. Collaborative advantage for public purposes should take into account public values beyond shared core goals.
Genetic and environmental influences on the association between performance‐based self‐esteem and exhaustion: A study of the self‐worth notion of burnout
Authors: Svedberg Pia , Hallsten Lennart , Narusyte Jurgita , Bodin Lennart , Blom Victoria
Published: July 2016

In the self‐worth model, burnout is considered to be a syndrome of performance‐based self‐esteem (PBSE) and experiences of exhaustion. Studies have shown that PBSE and burnout indices such as Pines’ Burnout Measure (BM) are associated. Whether these variables have overlapping etiologies has however not been studied before. Genetic and environmental components of covariation between PBSE and exhaustion measured with Pines’ BM were examined in a bivariate Cholesky model using data from 14,875 monozygotic and dizygotic Swedish twins. Fifty‐two per cent of the phenotypic correlation (r = 0.41) between PBSE and Pines’ BM was explained by genetics and 48% by environmental factors. The findings of the present study strengthen the assumption that PBSE should be considered in the burnout process as proposed by the self‐worth conception of burnout. The present results extend our understanding of the link between this contingent self‐esteem construct and exhaustion and provide additional information about the underlying mechanisms in terms of genetics and environment. This finding corroborates the assumed syndrome view on burnout, while it also suggests an altered view of how the syndrome emerges and how it can be alleviated.
On semi-G-V-type I concepts for directionally differentiable multiobjective programming problems
Authors: Antczak Tadeusz , Ruiz-Garzón Gabriel
Published: July 2016

In this paper, a new class of nonconvex nonsmooth multiobjective programming problems with directionally differentiable functions is considered. The so-called G-V-type I objective and constraint functions and their generalizations are introduced for such nonsmooth vector optimization problems. Based upon these generalized invex functions, necessary and sufficient optimality conditions are established for directionally differentiable multiobjective programming problems. Thus, new Fritz John type and Karush-Kuhn-Tucker type necessary optimality conditions are proved for the considered directionally differentiable multiobjective programming problem. Further, weak, strong and converse duality theorems are also derived for Mond-Weir type vector dual programs.
Low-Leakage Shaft-End Seals for Utility-Scale Supercritical CO2 Turboexpanders
Authors: Bidkar Rahul A. , Sevincer Edip , Wang Jifeng , Thatte Azam M. , Mann Andrew , Peter Maxwell , Musgrove Grant , Allison Timothy , Moore Jeffrey
Published: July 2016

Supercritical carbon dioxide (sCO2) power cycles could be a more efficient alternative to steam Rankine cycles for power generation from coal. Using existing labyrinth seal technology, shaft-end-seal leakage can result in a 0.55–0.65% points efficiency loss for a nominally 500 MWe sCO2 power cycle plant. Low-leakage hydrodynamic face seals are capable of reducing this leakage loss and are considered a key enabling component technology for achieving 50–52% thermodynamic cycle efficiencies with indirect coal-fired sCO2 power cycles. In this paper, a hydrodynamic face seal concept is presented for utility-scale sCO2 turbines. A 3D computational fluid dynamics (CFD) model with real gas CO2 properties is developed for studying the thin-film physics. These CFD results are also compared with the predictions of a Reynolds-equation-based solver. The 3D CFD model results show large viscous shear and the associated windage heating challenge in sCO2 face seals. Following the CFD model, an axisymmetric finite-element analysis (FEA) model is developed for parametric optimization of the face seal cross section with the goal of minimizing the coning of the stationary ring. A preliminary thermal analysis of the seal is also presented. The fluid, structural, and thermal results show that large-diameter (about 24 in.) face seals with small coning (of the order of 0.0005 in.) are possible. The fluid, structural, and thermal results are used to highlight the design challenges in developing face seals for utility-scale sCO2 turbines.
Using Category Theory to Facilitate Multiple Manufacturing Service Database Integration
Authors: Wisnesky Ryan , Breiner Spencer , Jones Albert , Spivak David I. , Subrahmanian Eswaran
Published: July 2016

The goal of this paper is to illustrate the use of category theory (CT) as a basis for the integration of manufacturing service databases. In this paper, we use as our reference prior work by Kulvatunyou et al. (2013, “An Analysis of OWL-Based Semantic Mediation Approaches to Enhance Manufacturing Service Capability Models,” Int. J. Comput. Integr. Manuf., 27(9), pp. 803–823) on the use of web ontology language (OWL)-based semantic web tools to study the integration of different manufacturing service capability (MSC) databases using a generic-model approach that they propose in their paper. We approach the same task using a different set of tools, specifically CT and FQL, a functorial query language based on categorical mathematics. This work demonstrates the potential utility of category-theoretic information management tools and illustrates some advantages of categorical techniques for the integration and evolution of databases. We conclude by making the case that a category-theoretic approach can provide a more flexible and robust approach to integration of existing and evolving information.
Visualizing Relations Between Grammar Rules, Objectives, and Search Space Exploration in Grammar-Based Computational Design Synthesis1
Authors: Königseder Corinna , Shea Kristina
Published: July 2016

Design grammars have been successfully applied in numerous engineering disciplines, e.g., in electrical engineering, architecture, and mechanical engineering. A successful application of design grammars in computational design synthesis (CDS) requires (a) meaningful representation of designs and the design task at hand, (b) careful formulation of grammar rules to synthesize new designs, (c) problem-specific design evaluation, and (d) selection of an appropriate algorithm to guide the synthesis process. Determining these different components of a CDS method requires not only a detailed understanding of each individual part but also of the interdependencies between them. In this paper, a new method is presented to support both CDS method development and application. The method analyzes the designs generated during the synthesis process and visualizes how the design space is explored with respect to design characteristics and objectives. The search algorithm as well as the grammar rules are analyzed with this approach. Two case studies, the synthesis of gearboxes and of bicycle frames, demonstrate how the method can be used to analyze the different components of CDS methods. The presented research can analyze the interplay between grammar rules and the search process during method development.
A Review of Sustainable Machining Engineering: Optimization Process Through Triple Bottom Line
Authors: Peralta Álvarez María Estela , Marcos Bárcena Mariano , Aguayo González Francisco
Published: July 2016

The studies about sustainable manufacturing engineering (SME) contain an increasing body of knowledge, motivated by the rising interest in the processes lifecycle sustainability. Its continuous improvement and optimization (including sustainability criteria) has become an emerging necessity. For this reason, new clean technologies and proposals of work methods are required; they have to integrate the ecological and social dimensions at an operational level in the manufacturing processes, maintaining the economic and technical feasibility attained up to this moment. However, a unified framework does not exist to orientate the lines of research in optimization when applied to sustainability. In this sense, the article reviews studies from scientific literature about sustainable machining developed in the last 15 years. The review has been carried out from the triple bottom-line (TBL) perspective, defined by the three general sustainability dimensions (economy, ecology, and equity). It contributes to the literature and current machining engineering knowledge, with its involvement in mitigating the metabolic rift. The results from the review have allowed to characterize the investigation effort, with regard to the optimization of the sustainable machining processes; even though numerous studies exist which optimize machining operations (with the aim to find the trade-off between different environmental and equity factors), in general, the technical and economic feasibilities are still the priority. The patterns defined through the analysis of the publications have established the current development trend; furthermore, as a consequence of the review results, we propose an outline of articulated lines of investigation with the aim to mitigate the metabolic rift through triple bottom-line, necessary so that machining engineering assumes the goal of finding the balance to achieve integral sustainability.
Classification of Failure Modes in Friction Stir Blind Riveted Lap-Shear Joints With Dissimilar Materials
Authors: Wang Wei-Ming , Ali Khan Haris , Li Jingjing , Miller Scott F. , Zachary Trimble A
Published: July 2016

In transportation sector, there is an increasing need for joining dissimilar materials for lightweight structures; however, substantial barriers to the joining of dissimilar materials have led to an investigation and development of new joining techniques. Friction stir blind riveting (FSBR), a newly invented method, has shown great promise in joining complex structures with dissimilar materials. The process can be utilized more effectively if knowledge regarding the failure mechanisms of the FSBR joints becomes available. This research focuses on investigating the different mechanisms that lead to a failure in FSBR joints under lap-shear tensile tests. An in situ, nondestructive, acoustic emission (AE) testing method was applied during quasi-static tensile tests to monitor the initiation and evolution of damage in FSBR joints with different combinations of dissimilar materials (including aluminum, magnesium, and a carbon-fiber reinforced polymeric composite). In addition, a fractographic analysis was conducted to characterize the failure modes. Finally, based on the analysis, the distinct failure modes and damage accumulation processes for the joints were identified. An AE accumulative hit history curve was found to be efficient to discriminate the deformation characteristics, such as the deformation zone and failure mode, which cannot be observed through a traditional extensometer measurement method. In addition, the AE accumulative hit history curve can be applied to predict the failure extension or moment of FSBR joints through an identification of the changes in curve slope. Such slope changes usually occur around the middle of Zone II, which is defined in this study.
Relative Significance of Multiple Parameters on the Mechanical Specific Energy and Frictional Responses of Polycrystalline Diamond Compact Cutters
Authors: Akbari Babak , Miska Stefan Z.
Published: July 2016

A high pressure single polycrystalline diamond compact (PDC) cutter testing facility was used to investigate the effect of five factors on PDC cutter performance on Alabama marble. The factors include: depth of cut (DOC), rotary speed, back rake angle, side rake angle, and confining (wellbore) pressure. The performance is quantified by two parameters: mechanical specific energy (MSE) and friction angle. Fractional factorial design of experiments methodology was used to design the experiments, enabling detection of potential interactions between factors. Results show that, in the range tested, the only statistically significant factor affecting the MSE is DOC. In other words, DOC's influence is predominant and it can mask the effect of all the other factors. These results could have applications in real time pore pressure detection. Further, the results show that back rake angle is the most statistically significant factor in friction angle. Side rake angle and depth of cut also affect the friction angle, but in a relatively unimportant manner. The MSE–DOC behavior is explained and modeled by cutter edge–groove friction and the circular cutter shape. It is speculated that high cutter edge friction overwhelms the actual cutting process. A comparison of five currently present models in the literature with these results is presented and the conclusion is that the future PDC cutter models should digress from the traditional shear failure plane models.
Experimental Measurements of Forces on Loose Particle in Motion Over Rough Bed Under Waves Using Oblique Particle Image Velocimetry
Authors: Havaldar Sanjay N. , Ting Francis C. K.
Published: July 2016

Magnitude and phase of major forces that act on a loose non-cohesive particle (sediment) on single layer fixed rough bed (longitudinal slope 2%) were determined from experiments in a laboratory flume under waves. The loose particles were glass spheres of diameter 1.58 ± 0.1 mm and specific gravity 2.5. The range of wave-height-to-water-depth (H/h) ratio in the experiments was 0.366 < H/h < 0.521. The measurement plane was parallel to the bed and located at a height of ½ loose particle diameter (ds) above the rough bed. Grayscale morphological image processing methods were used to separate the fluid and loose sediment phases from the same oblique particle image velocimetry (OPIV) image based on their signature sizes. The OPIV calibration method is presented and validated with conventional particle image velocimetry (PIV) method. Loose particle velocity and accelerations along with the associated fluid velocity and fluid total accelerations in the wave direction were determined simultaneously by processing OPIV used to compute magnitude and phase of major forces that act on the loose sediment particle. It was observed that for same wave period (T), an increase in H/h ratio has a dominant effect on sediment displacements onshore. The phase along with magnitude of the major driving force (drag and fluid accelerations) plays an important role at initiation of loose sediment from its rest position. It is suspected that the loose particle overcomes a critical bed friction force with higher H/h ratio as magnitude of drag force is higher. The resultant force then displaces the sediment onshore which experiences sliding and or rolling motions very close to bed, in a thin fluid layer over maximum protrusion of bed sediments. At the instance, the gravitational force plus bed frictions overcomes the lift force the loose particle attains a new position onshore.
Efficiencies of Eu3+ ions and hydrogen atoms as donors in ZnO thin films
Authors: Akazawa Housei
Published: July 2016

The donor efficiencies of Eu3+ ions and hydrogen atoms in ZnO crystalline films were investigated with reference to that of Ga3+ ions. It was found that Eu3+ ions acted as extrinsic donors in ZnO:Eu films, yielding a resistivity of 1.8 × 10−3 Ω cm at a doping level of 1 at. %. This value is comparable to one for intrinsic donors in undoped ZnO films. The conductivity was maintained as the deposition temperature was increased to 200 °C, and this is evidence for the contribution of extrinsic donors. Deposition of Ga-doped and Eu-doped ZnO films in an H2O gas flow produced oxyhydrogenated ZnO:(Ga, H) and ZnO:(Eu, H) films in which the Ga3+ and Eu3+ donors were deactivated by oxidization. Nevertheless, hydrogen donors contributed to electrical conduction yielding a resistivity of 1 × 10−2 Ω cm. Postannealing in an H2 gas ambient alleviated the excessive oxidization of the films and thereby reactivated the donor action of Ga3+ and Eu3+ ions, causing the resistivity to recover to 10−3 Ω cm for ZnO:(Ga, H) and 10−2 Ω cm for ZnO:(Eu, H). In contrast, vacuum annealing of ZnO:(Ga, H) and ZnO:(Eu, H) films increased resistivity through removal of hydrogen donors while not affecting the oxidized condition of the samples.
Wavenumber transform analysis for acoustic black hole design
Authors: Feurtado Philip A. , Conlon Stephen C.
Published: July 2016

Acoustic black holes (ABHs) are effective, passive, lightweight vibration absorbers that have been developed and shown to effectively reduce the structural vibration and radiated sound of beam and plate structures. ABHs employ a local thickness change that reduces the speed of bending waves and increases the transverse vibration amplitude. The vibrational energy can then be effectively focused and dissipated by material losses or through conventional viscoelastic damping treatments. In this work, the measured vibratory response of embedded ABH plates was transformed into the wavenumber domain in order to investigate the use of wavenumber analysis for characterizing, designing, and optimizing practical ABH systems. The results showed that wavenumber transform analysis can be used to simultaneously visualize multiple aspects of ABH performance including changes in bending wave speed, transverse vibration amplitude, and energy dissipation. The analysis was also used to investigate the structural acoustic coupling of the ABH system and determine the radiation efficiency of the embedded ABH plates compared to a uniform plate. The results demonstrated that the ABH effect results in acoustic decoupling as well as vibration reduction. The wavenumber transform based methods and results will be useful for implementing ABHs into real world structures.
Reporting quality of randomised controlled trial abstracts among high-impact general medical journals: a review and analysis
Authors: Hays Meredith , Andrews Mary , Wilson Ramey , Callender David , O'Malley Patrick G , Douglas Kevin
Published: July 2016

Objective

The aim of this study was to assess adherence to the Consolidated Standards of Reporting Trials (CONSORT) for Abstracts by five high-impact general medical journals and to assess whether the quality of reporting was homogeneous across these journals.

Design

This is a descriptive, cross-sectional study.

Setting

Randomised controlled trial (RCT) abstracts in five high-impact general medical journals.

Participants

We used up to 100 RCT abstracts published between 2011 and 2014 from each of the following journals:The New England Journal of Medicine(NEJM),the Annals of Internal Medicine(Annals IM),The Lancet,the British Medical Journal(The BMJ) andthe Journal of the American Medical Association(JAMA).

Main outcome

The primary outcome was per cent overall adherence to the 19-item CONSORT for Abstracts checklist. Secondary outcomes included per cent adherence in checklist subcategories and assessing homogeneity of reporting quality across the individual journals.

Results

Search results yielded 466 abstracts, 3 of which were later excluded as they were not RCTs. Analysis was performed on 463 abstracts (97 fromNEJM, 66 fromAnnals IM, 100 fromThe Lancet, 100 fromThe BMJ, 100 fromJAMA). Analysis of all scored items showed an overall adherence of 67% (95% CI 66% to 68%) to the CONSORT for Abstracts checklist.The Lancethad the highest overall adherence rate (78%; 95% CI 76% to 80%), whereasNEJMhad the lowest (55%; 95% CI 53% to 57%). Adherence rates to 8 of the checklist items differed by >25% between journals.

Conclusions

Among the five highest impact general medical journals, there is variable and incomplete adherence to the CONSORT for Abstracts reporting checklist of randomised trials, with substantial differences between individual journals. Lack of adherence to the CONSORT for Abstracts reporting checklist by high-impact medical journals impedes critical appraisal of important studies. We recommend diligent assessment of adherence to reporting guidelines by authors, reviewers and editors to promote transparency and unbiased reporting of abstracts.
Working with GM vaccines: engaging the public
Authors: Clark Madeleine
Published: July 2016

The UK Veterinary Vaccinology Network was among the sponsors of this year's Cheltenham Science Festival, which took place from June 7 to 12. During the festival, Adrian Hill and Andrew Pollard, of the Jenner Institute, and Bryan Charleston, of the Pirbright Institute, represented the network and discussed the development of genetically modified vaccines and the issues surrounding them in animal and human health. Madeleine Clark sums up their presentation
A molecular dynamics study of the growth rate of SiC crystal and its dependence on the temperature
Authors: Zhou Naigen , Zhang Chi , Zeng Xiang , Yuan Jiren , Zhou Lang
Published: July 2016

Molecular dynamics simulations of crystal growth of SiC in the reduced temperature range of 0.51–1.02 have been carried out. In particular, the relationship between the growth rate and the reduced temperature has been investigated by the simulations. The results show that the growth rate increases first with the temperature and then decreases dramatically after passing through a maximum. Calculations of the growth rate according to the Wilson–Frenkel model have been applied to the present system, with the required parameters of the activation energy for atomic diffusion and the free energy changes calculated by molecular dynamics simulations. The temperature dependence of the growth rate, calculated by molecular dynamics, agrees with the prediction of Wilson–Frenkel model, indicating that the crystal growth of SiC is a kind of diffusion limited growth.
Breakup of oxygen nucleus on isotopes of hydrogen and nitrogen nuclei in collisions with protons at 3.25A GeV/c
Authors: Olimov Kosim , Olimov Khusniddin K. , Lutpullaev Sagdulla L. , Olimov Alisher K. , Lugovoi Vladimir V. , Navotny Vadim Sh. , Yuldashev Bekhzod S.
Published: July 2016

Phenomenological analysis of breakup of oxygen nuclei on fragments with the charges one and seven in collisions with protons at 3.25[Formula: see text][Formula: see text]GeV/[Formula: see text] was conducted using the Monte Carlo model of isotropic phase space. For the first time, the contributions of mechanism of diffractive breakup of oxygen nucleus and that of quasi-elastic knocking out of one of the protons of oxygen nucleus by a proton target into channel of formation of proton fragment and [Formula: see text]N nucleus with conservation of recoil proton in final state were determined. Cross-section of diffractive breakup of oxygen [Formula: see text]O nucleus on [Formula: see text]N nucleus and proton fragment and that of diffractive breakup of [Formula: see text]O nucleus on nuclei [Formula: see text]N and 2H were estimated for the first time in [Formula: see text]O[Formula: see text] collisions at 3.25[Formula: see text][Formula: see text]GeV/[Formula: see text].
Example-Based Sketch Segmentation and Labeling Using CRFs
Authors: Schneider Rosália G. , Tuytelaars Tinne
Published: July 2016

We introduce a new approach for segmentation and label transfer in sketches that substantially improves the state of the art. We build on successful techniques to find how likely each segment is to belong to a label, and use a Conditional Random Field to find the most probable global configuration. Our method is trained fully on the sketch domain, such that it can handle abstract sketches that are very far from 3D meshes. It also requires a small quantity of annotated data, which makes it easily adaptable to new datasets. The testing phase is completely automatic, and our performance is comparable to state-of-the-art methods that require manual tuning and a considerable amount of previous annotation [Huang et al. 2014].
Whirlpool
Authors: Mukkara Anurag , Beckmann Nathan , Sanchez Daniel
Published: July 2016

Cache hierarchies are increasingly non-uniform and difficult to manage. Several techniques, such as scratchpads or reuse hints, use static information about how programs access data to manage the memory hierarchy. Static techniques are effective on regular programs, but because they set fixed policies, they are vulnerable to changes in program behavior or available cache space. Instead, most systems rely on dynamic caching policies that adapt to observed program behavior. Unfortunately, dynamic policies spend significant resources trying to learn how programs use memory, and yet they often perform worse than a static policy. We present Whirlpool, a novel approach that combines static information with dynamic policies to reap the benefits of each. Whirlpool statically classifies data into pools based on how the program uses memory. Whirlpool then uses dynamic policies to tune the cache to each pool. Hence, rather than setting policies statically, Whirlpool uses static analysis to guide dynamic policies. We present both an API that lets programmers specify pools manually and a profiling tool that discovers pools automatically in unmodified binaries.

We evaluate Whirlpool on a state-of-the-art NUCA cache. Whirlpool significantly outperforms prior approaches: on sequential programs, Whirlpool improves performance by up to 38% and reduces data movement energy by up to 53%; on parallel programs, Whirlpool improves performance by up to 67% and reduces data movement energy by up to 2.6x.
High Performance Packet Processing with FlexNIC
Authors: Kaufmann Antoine , Peter SImon , Sharma Naveen Kr. , Anderson Thomas , Krishnamurthy Arvind
Published: July 2016

The recent surge of network I/O performance has put enormous pressure on memory and software I/O processing sub systems. We argue that the primary reason for high memory and processing overheads is the inefficient use of these resources by current commodity network interface cards (NICs). We propose FlexNIC, a flexible network DMA interface that can be used by operating systems and applications alike to reduce packet processing overheads. FlexNIC allows services to install packet processing rules into the NIC, which then executes simple operations on packets while exchanging them with host memory. Thus, our proposal moves some of the packet processing traditionally done in software to the NIC, where it can be done flexibly and at high speed.

We quantify the potential benefits of FlexNIC by emulating the proposed FlexNIC functionality with existing hardware or in software. We show that significant gains in application performance are possible, in terms of both latency and throughput, for several widely used applications, including a key-value store, a stream processing system, and an intrusion detection system.
True IOMMU Protection from DMA Attacks
Authors: Markuze Alex , Morrison Adam , Tsafrir Dan
Published: July 2016

Malicious I/O devices might compromise the OS using DMAs. The OS therefore utilizes the IOMMU to map and unmap every target buffer right before and after its DMA is processed, thereby restricting DMAs to their designated locations. This usage model, however, is not truly secure for two reasons: (1) it provides protection at page granularity only, whereas DMA buffers can reside on the same page as other data; and (2) it delays DMA buffer unmaps due to performance considerations, creating a vulnerability window in which devices can access in-use memory. We propose that OSes utilize the IOMMU differently, in a manner that eliminates these two flaws. Our new usage model restricts device access to a set of shadow DMA buffers that are never unmapped, and it copies DMAed data to/from these buffers, thus providing sub-page protection while eliminating the aforementioned vulnerability window. Our key insight is that the cost of interacting with, and synchronizing access to the slow IOMMU hardware---required for zero-copy protection against devices---make
copying preferable to zero-copying
.

We implement our model in Linux and evaluate it with standard networking benchmarks utilizing a 40,Gb/s NIC. We demonstrate that despite being more secure than the safest preexisting usage model, our approach provides up to 5x higher throughput. Additionally, whereas it is inherently less scalable than an IOMMU-less (unprotected) system, our approach incurs only 0%--25% performance degradation in comparison.
Lifting Assembly to Intermediate Representation
Authors: Hasabnis Niranjan , Sekar R.
Published: July 2016

Translating low-level machine instructions into higher-level intermediate language (IL) is one of the central steps in many binary analysis and instrumentation systems. Existing systems build such translators manually. As a result, it takes a great deal of effort to support new architectures. Even for widely deployed architectures, full instruction sets may not be modeled, e.g., mature systems such as Valgrind still lack support for AVX, FMA4 and SSE4.1 for x86 processors. To overcome these difficulties, we propose a novel approach that leverages knowledge about instruction set semantics that is already embedded into modern compilers such as GCC. In particular, we present a learning-based approach for automating the translation of assembly instructions to a compiler's architecture-neutral IL. We present an experimental evaluation that demonstrates the ability of our approach to easily support many architectures (x86, ARM and AVR), including their advanced instruction sets. Our implementation is available as open-source software.
Taurus
Authors: Maas Martin , Asanović Krste , Harris Tim , Kubiatowicz John
Published: July 2016

Many distributed workloads in today's data centers are written in managed languages such as Java or Ruby. Examples include big data frameworks such as Hadoop, data stores such as Cassandra or applications such as the SOLR search engine. These workloads typically run across many independent language runtime systems on different nodes. This setup represents a source of inefficiency, as these language runtime systems are unaware of each other. For example, they may perform Garbage Collection at times that are locally reasonable but not in a distributed setting.

We address these problems by introducing the concept of a Holistic Runtime System that makes runtime-level decisions for the entire distributed application rather than locally. We then present Taurus, a Holistic Runtime System prototype. Taurus is a JVM drop-in replacement, requires almost no configuration and can run unmodified off-the-shelf Java applications. Taurus enforces user-defined coordination policies and provides a DSL for writing these policies.

By applying Taurus to Garbage Collection, we demonstrate the potential of such a system and use it to explore coordination strategies for the runtime systems of real-world distributed applications, to improve application performance and address tail-latencies in latency-sensitive workloads.
A DNA-Based Archival Storage System
Authors: Bornholt James , Lopez Randolph , Carmean Douglas M. , Ceze Luis , Seelig Georg , Strauss Karin
Published: July 2016

Demand for data storage is growing exponentially, but the capacity of existing storage media is not keeping up. Using DNA to archive data is an attractive possibility because it is extremely dense, with a raw limit of 1 exabyte/mm
3
(109 GB/mm
3
), and long-lasting, with observed half-life of over 500 years. This paper presents an architecture for a DNA-based archival storage system. It is structured as a key-value store, and leverages common biochemical techniques to provide random access. We also propose a new encoding scheme that offers controllable redundancy, trading off reliability for density. We demonstrate feasibility, random access, and robustness of the proposed encoding with wet lab experiments involving 151 kB of synthesized DNA and a 42 kB random-access subset, and simulation experiments of larger sets calibrated to the wet lab experiments. Finally, we highlight trends in biotechnology that indicate the impending practicality of DNA storage for much larger datasets.
OpenPiton
Authors: Balkind Jonathan , McKeown Michael , Fu Yaosheng , Nguyen Tri , Zhou Yanqi , Lavrov Alexey , Shahrad Mohammad , Fuchs Adi , Payne Samuel , Liang Xiaohua , Matl Matthew , Wentzlaff David
Published: July 2016

Industry is building larger, more complex, manycore processors on the back of strong institutional knowledge, but academic projects face difficulties in replicating that scale. To alleviate these difficulties and to develop and share knowledge, the community needs open architecture frameworks for simulation, synthesis, and software exploration which support extensibility, scalability, and configurability, alongside an established base of verification tools and supported software. In this paper we present OpenPiton, an open source framework for building scalable architecture research prototypes from 1 core to 500 million cores. OpenPiton is the world's first open source, general-purpose, multithreaded manycore processor and framework. OpenPiton leverages the industry hardened OpenSPARC T1 core with modifications and builds upon it with a scratch-built, scalable uncore creating a flexible, modern manycore design. In addition, OpenPiton provides synthesis and backend scripts for ASIC and FPGA to enable other researchers to bring their designs to implementation. OpenPiton provides a complete verification infrastructure of over 8000 tests, is supported by mature software tools, runs full-stack multiuser Debian Linux, and is written in industry standard Verilog. Multiple implementations of OpenPiton have been created including a taped-out 25-core implementation in IBM's 32nm process and multiple Xilinx FPGA prototypes.
Discharge Patterns of Hypoglossal Motoneurons During Fictive Breathing, Coughing, and Swallowing
Authors: Roda Fabrice , Gestreau Christian , Bianchi Armand Louis
Published: July 2016

We performed a series of experiments to study the intracellular activity of 58 hypoglossal motoneurons (HMs) in decerebrate, paralyzed, and ventilated cats. Changes in membrane potentials (MP) and discharge activities were evaluated during fictive breathing (FB), swallowing (FS), and coughing (FC). FS and FC were elicited by electrical stimulation of the superior laryngeal nerves. FB, FS, and FC all exhibited characteristic discharge patterns of the phrenic, abdominal, pharyngeal branch of the vagus, and hypoglossal nerves. Thirty-nine HMs displayed respiratory modulation, and 19 were nonrespiratory modulated. Nine HMs did not exhibit MP changes during FB, FS, and FC. During FS, 49 HMs exhibited MP changes consisting of depolarization, hyperpolarization or hyperpolarization-depolarization. HMs involved in FS were either respiratory modulated ( n= 38) or not ( n = 11). Only 20 HMs displayed MP changes and/or discharge activity during FC. All but two HMs fired during the expiratory phase of FC or at the end of this reflex. All HMs involved in FC ( n = 20) were also modulated during both FB and FS. Our results suggest that the XII nucleus is functionally divided into common and distinct subsets of HMs based on their spontaneous activities and responses observed during FS and FC. The changes in MP and discharge frequencies observed during the three behaviors also suggest that HMs are driven by specific premotor neurons during FS, whereas a common premotor pathway is involved during FB and FC.
Role of Eye, Head, and Shoulder Geometry in the Planning of Accurate Arm Movements
Authors: Henriques D.Y.P. , Crawford J. D.
Published: July 2016

Eye-hand coordination requires the brain to integrate visual information with the continuous changes in eye, head, and arm positions. This is a geometrically complex process because the eyes, head, and shoulder have different centers of rotation. As a result, head rotation causes the eye to translate with respect to the shoulder. The present study examines the consequences of this geometry for planning accurate arm movements in a pointing task with the head at different orientations. When asked to point at an object, subjects oriented their arm to position the fingertip on the line running from the target to the viewing eye. But this eye-target line shifts when the eyes translate with each new head orientation, thereby requiring a new arm pointing direction. We confirmed that subjects do realign their fingertip with the eye-target line during closed-loop pointing across various horizontal head orientations when gaze is on target. More importantly, subjects also showed this head-position–dependent pattern of pointing responses for the same paradigm performed in complete darkness. However, when gaze was not on target, compensation for these translations in the rotational centers partially broke down. As a result, subjects tended to overshoot the target direction relative to current gaze; perhaps explaining previously reported errors in aiming the arm to retinally peripheral targets. These results suggest that knowledge of head position signals and the resulting relative displacements in the centers of rotation of the eye and shoulder are incorporated using open-loop mechanisms for eye-hand coordination, but these translations are best calibrated for foveated, gaze-on-target movements.