bluuebunny/crossref_metadata_2025 huggingface dataset:
Improvement of the quasi-continuous-wave lasing properties in organic semiconductor lasers using oxygen as triplet quencher
Authors: Sandanayaka Atula S. D. , Zhao Li , Pitrat Delphine , Mulatier Jean-Christophe , Matsushima Toshinori , Andraud Chantal , Kim Ju-Hyung , Ribierre Jean-Charles , Adachi Chihaya
Published: May 2016

We demonstrate quasi-continuous-wave lasing in solvent-free liquid organic semiconductor distributed feedback lasers based on a blend containing a liquid 9-(2-ethylhexyl)carbazole host doped with a blue-emitting heptafluorene derivative. The liquid gain medium is bubbled with either oxygen or nitrogen in order to investigate the role of a triplet quencher such as molecular oxygen on the quasi-continuous-wave lasing properties of organic semiconductor lasers. The oxygenated laser device exhibits a low threshold of 2 μJ cm−2, which is lower than that measured in the nitrogenated device and is independent of the repetition rate in a range between 0.01 and 4 MHz.
Note: Development of leg size sensors for fluid accumulation monitoring
Authors: Zhang Song , Rajamani Rajesh , Alexander Lee , Serdar Sezen A.
Published: May 2016

A number of diseases can lead to fluid accumulation and swelling in the lower leg. Early detection of leg swelling can be used to effectively predict potential health risks and allows for early intervention from medical providers. Hence this note develops a novel leg size sensor based on the use of magnetic field measurement. An electromagnet is combined with two magnetic field transducers to provide a drift-free leg size estimation technique immune to environmental disturbances. The sensor can measure changes as small as 1 mm in diameter reliably during in vitro tests. Its performance is compared with that of other size measurement techniques.
Experimental realisation of all-dielectric bianisotropic metasurfaces
Authors: Odit Mikhail , Kapitanova Polina , Belov Pavel , Alaee Rasoul , Rockstuhl Carsten , Kivshar Yuri S.
Published: May 2016

All-dielectric reciprocal metasurface based on bianisotropic scatterers operating at microwave frequencies is demonstrated experimentally. Experimental studies of a single bianisotropic particle supporting both electric and magnetic Mie-type resonances are performed, and reveal that the particle with a broken symmetry exhibits different back-scattering for the opposite excitation directions. A metasurface composed of the all-dielectric bianisotropic particles is fabricated and experimentally investigated in the frequency range of 4–9 GHz. The measured data demonstrate that the metasurface is characterized by different reflection phases when being excited from the opposite directions. At the frequency 6.8 GHz, the metasurface provides a 2π phase change in the reflection spectrum with the amplitude close to 1.
Longitudinally polarized single-cycle terahertz pulses generated with high electric field strengths
Authors: Cliffe M. J. , Graham D. M. , Jamison S. P.
Published: May 2016

We demonstrate the generation of single-cycle longitudinally polarized terahertz pulses with field amplitudes in excess of 11 kV/cm using the interferometric recombination of two linearly polarized terahertz beams. High field strength transversely polarized pulses were generated by optical rectification in a matched pair of magnesium-oxide doped stoichiometric lithium niobate (MgO:SLN) crystals with a reversal in the χ333(2) orientation. The discontinuity in χ333(2) produces a polarity flip in the transverse field; the longitudinal field produced as a consequence of the transverse field discontinuity was measured in the far-field. Both the spatial and temporal profiles of the measured longitudinally polarized terahertz radiation were consistent with the propagation of the transverse discontinuity.
Comparative performance of broiler chickens offered nutritionally equivalent diets based on six diverse, ‘tannin-free’ sorghum varieties with quantified concentrations of phenolic compounds, kafirin, and phytate
Authors: Truong Ha H. , Neilson Karlie A. , McInerney Bernard V. , Khoddami Ali , Roberts Thomas H. , Cadogan David J. , Liu Sonia Yun , Selle Peter H.
Published: May 2016

Starch is the main source of energy in sorghum-based diets but starch/energy utilisation by broiler chickens offered these diets may be substandard. Both in vitro and in vivo data indicate that the digestibility of sorghum starch is inferior to that of other feed grains, especially maize. Three ‘starch-extrinsic’ factors in grain sorghum, namely ‘non-tannin’ phenolic compounds, kafirin and phytate may negatively influence starch/energy utilisation in sorghum-based broiler diets. To test this hypothesis, concentrations of polyphenols, free, bound and conjugated phenolic acids, kafirin and phytate were quantified in six diverse ‘tannin-free’ (Type I) grain sorghum varieties. These sorghums were incorporated into nutritionally equivalent diets at 620 g/kg and offered to male broiler chickens from 7 to 28 days post-hatch. Growth performance, nutrient utilisation (AME, ME : GE ratios, N retention, AMEn) and starch and protein (N) digestibility coefficients and disappearance rates in four small intestinal segments were determined. Numerous relationships that were either significant (P < 0.05), or approached significance (P < 0.10), were detected that indicated various ‘non-tannin’ phenolic compounds, kafirin and phytate in sorghums negatively influenced nutrient utilisation parameters in broiler chickens. ME : GE ratios are sensitive indicators of efficiency of energy utilisation and were most negatively influenced by flavan-4-ols (r = –0.919; P < 0.015), which are polyphenolic compounds. Moreover, flavan-4-ols in tandem with conjugated vanillic acid negatively influenced (r = –0.993; P < 0.005) ME : GE ratios on the basis of a valid multiple linear regression. Similarly, conjugated vanillic and bound ferulic acids in tandem negatively influenced AME (r = –0.990; P < 0.005). N retention was most negatively influenced by kafirin (r = –0.887; P < 0.025). Thus, it appears that both phenolic compounds and kafirin may have deleterious effects on nutrient utilisation of sorghum-based broiler diets and recommendations are made that should enhance the quality of sorghum as a feedstuff for chicken-meat production based on these findings.
Modelling the spatial patterns of ignition causes and fire regime features in southern France: implications for fire prevention policy
Authors: Curt Thomas , Fréjaville Thibaut , Lahaye Sébastien
Published: May 2016

A good knowledge of the spatiotemporal patterns of the causes of wildfire ignition is crucial to an effective fire policy. However, little is known about the situation in south-eastern France because the fire database contains unreliable data. We used data for cases with well-established causes from 1973–2013 to determine the location of spatial hotspots, the seasonal distribution, the underlying anthropogenic and environmental drivers and the tendency of five main causes to generate large fires. Anthropogenic ignitions were predominant (88%) near human settlements and infrastructures in the lowlands, whilst lightning-induced fires were more common in the coastal mountains. In densely populated urban areas, small summer fires were predominating, due to the negligence of private individuals around their homes or accidental ignitions near infrastructures. In rural hinterlands, ignitions due to negligence by professionals generate many medium-sized fires from autumn to spring. Intentional and accidental ignitions contribute the most to the total burned area and to large fires. We conclude that socioeconomic factors partially control the fire regime, influencing the timing, spatial distribution and potential size of fires. This improved understanding of why, where and when ignitions occur provides the opportunity for controlling certain causes of ignitions and adapting French policy to global changes.
Local spatial distortion caused by simple geometrical figures
Authors: Aksentijevic Aleksandar , Elliott Mark A.
Published: May 2016

Dynamic distortion of the visual field has been shown to affect perceptual judgment of visual dimensions such as size, length, and distance. Here, we report four experiments demonstrating that the different aspects of a triangle differently influence judgments of distance. Specifically, when the base of the triangle faces the centre of the display, participants consistently underestimate and overestimate the distance of a small dot from the unmarked centre of the display relative to conditions in which the vertex of the triangle faces the centre. When the dot is close to the figure, the distance of the dot to the centre is underestimated. Conversely, when the dot is close to the figure, the distance to the centre is overestimated. The effect is replicated when the internal distances are equalized and when ellipses are used instead of triangles. These results support a ripple model of spatial distortion in which local curvature acts to attract or repel objects. In conclusion, we suggest some implications of our findings for theories of perceptual organization.
Does translation involve structural priming?
Authors: Maier Robert M. , Pickering Martin J. , Hartsuiker Robert J.
Published: May 2016

When asked to translate utterances, people might merely make sure that their translations have the same meaning as the source, but they might also maintain aspects of sentence form across languages. We report two experiments in which English–German and German–English bilinguals (without specialist translator training) repeated German ditransitive sentences whose meaning was compatible with more than one grammatical form or translated them into English. Participants almost invariably repeated the sentences accurately, thereby retaining the grammatical structure. Importantly, Experiment 1 found that they tended to repeat grammatical form across languages. Experiment 2 included a condition with sentences that had no grammatical equivalent form in English; here participants tended to persist in the order of thematic roles. We argue that cross-linguistic structural priming plays a major role in the act of translation.
methylFlow: cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing
Authors: Dorri Faezeh , Mendelowitz Lee , Corrada Bravo Héctor
Published: May 2016

Motivation: DNA methylation aberrations are now known to, almost universally, accompany the initiation and progression of cancers. In particular, the colon cancer epigenome contains specific genomic regions that, along with differences in methylation levels with respect to normal colon tissue, also show increased epigenetic and gene expression heterogeneity at the population level, i.e. across tumor samples, in comparison with other regions in the genome. Tumors are highly heterogeneous at the clonal level as well, and the relationship between clonal and population heterogeneity is poorly understood.

Results: We present an approach that uses sequencing reads from high-throughput sequencing of bisulfite-converted DNA to reconstruct heterogeneous cell populations by assembling cell-specific methylation patterns. Our methodology is based on the solution of a specific class of minimum cost network flow problems. We use our methods to analyze the relationship between clonal heterogeneity and population heterogeneity in high-coverage data from multiple samples of colon tumor and matched normal tissues.

Availability and implementation: http://github.com/hcorrada/methylFlow.

Contact:  hcorrada@umiacs.umd.edu

Supplementary information:  Supplementary information is available at Bioinformatics online.
Radiation therapy for nasopharyngeal carcinoma: the predictive value of interim survival assessment
Authors: Toya Ryo , Murakami Ryuji , Saito Tetsuo , Murakami Daizo , Matsuyama Tomohiko , Baba Yuji , Nishimura Ryuichi , Hirai Toshinori , Semba Akiko , Yumoto Eiji , Yamashita Yasuyuki , Oya Natsuo
Published: May 2016

Pretreatment characteristics are suggested as predictive and/or prognostic factors for nasopharyngeal carcinoma (NPC); however, individual tumor radiosensitivities have previously not been considered. As boost planning is recommended for NPC, we performed interim assessments of magnetic resonance (MR) images for boost planning and retrospectively evaluated their predictive value for the survival of NPC patients. Radiation therapy via elective nodal irradiation (median dose: 39.6 Gy) with/without chemotherapy was used to treat 63 NPC patients. Boost irradiation (median total dose: 70 Gy) was performed based on the interim assessment. The largest lymph node (LN) was measured on MR images acquired at the time of interim assessment. The site of first failure was local in 8 (12.7%), regional in 7 (11.1%), and distant in 12 patients (19.0%). All 7 patients with regional failure harbored LNs ≥15 mm at interim assessment. We divided the 63 patients into two groups based on LN size [large (≥15 mm), n = 10 and small (<15 mm), n = 53]. Univariate analysis showed that 5-year overall survival (OS) and cause-specific survival (CSS) rates for large LNs were significantly lower than for small LNs (OS: 12.5% vs 70.5%, P < 0.001 and CSS: 25.0% vs 80.0%, P < 0.001). Multivariate analysis showed that large LNs were a significantly unfavorable factor for both OS (hazard ratio = 4.543, P = 0.002) and CSS (hazard ratio = 6.020, P = 0.001). The results suggest that LN size at interim assessment could predict survival in NPC patients.
Buddhist Theories of Causality (karma, pratītyasamutpāda, hetu, pratyaya)
Authors: Skorupski Tadeusz
Published: May 2016

This entry covers four models of causality: karma, pratītyasamutpāda, hetu, and pratyaya. The English terms causality and causation are used here as generic terms. As Buddhist interpretations of causality are complex and controversial, only general features of causation theories are delineated. Buddhist expositions of causality stem from and corroborate Buddhist doctrines and soteriology. In terms of doctrine, Buddhism rejects the existence of a permanent self (ātman), and denies the existence of a first cause in any form. The nature of existence is interpreted in terms of the two truths: conventional and ultimate. Conventionally, there exist beings and things, but only as conceptual entities (prajñaptisat). Ultimately, they do not exist, because they have no permanent core. So how does the inexistent world function? Conceptual entities are dissected into impersonal phenomena or dharmas as ultimate units. The dharmas are momentary, and they arise and vanish in space and time in conformity with definite principles that regulate their flow and interdependence: karma and dependent origination. The term karma, literally “action” or “deed,” as a technical concept, denotes the principle of ethical causation: there are no agents, but there are actions and their consequences. Karma as action denotes an act of mental volition (cetanā), and the bodily and verbal actions that stem from it. Volitional actions are ethically qualified, depending on whether they stem from the three wholesome roots or the three unwholesome roots. Such actions accumulate and yield their fruits: particular body-mind configurations evolving in cyclic rebirths (saṃsāra). The principle of pratītyasamutpāda (dependent origination), denotes the conditionality or interdependence of existential phenomena. Essentially, it accounts for the conditioned flux of phenomenal existence, in particular the interdependent flow of the five aggregates with no ontological substratum. The terms hetu (cause) and pratyaya (condition), occur as a compound or separately. As a compound, hetupratyaya denotes the principle of causes and conditions applicable to all aspects of existence. When included in lists of conditions, it denotes the first condition, the condition qua cause. Individually, they are virtually synonymous, or form either separate or correlated models of causality. In terms of soteriology, causality is integrated into the four noble truths. The second truth teaches the origin of suffering, identified by the Buddha as craving. Otherwise, the origin is interpreted in terms of karma and dependent origination. The third noble truth, the cessation of suffering, teaches the eradication of karma leading to rebirths, and the cessation of suffering: appeasement of dependent origination.
Public Opinion and the European Union
Authors: Kentmen Çin Çiğdem
Published: May 2016

The European Union (EU) is a sui generis international organization. It started as a common market of six Western European countries intended to bring stability and peace to Europe after the World War II. Today, the EU is a supranational organization of 28 member states with a tremendous impact not only on the economic but also on the political and social lives of Europeans. Not all European citizens, however, appreciate the policies of the EU; some claim that the EU is challenging the traditional roles and authority of nation-states. There are those who view the EU’s multilingual and multinational structure as a threat to their national integrity. Some citizens also believe that their country’s membership in the EU has been costly. A large literature is dedicated to understanding the dynamics and nature of European public opinion, since a disapproving public can influence governmental policies in the international arena and forestall the deepening of integration through referendums, as in the example of the Irish 2008 referendum on the Treaty of Lisbon. Consequently, there is a much greater focus on how the EU public views the European integration in general, their country’s membership to the EU, enlargement to other countries, certain policy areas such as the Common Foreign and Security Policy, and the euro. There is also a growing literature on public opinion on joining the EU in candidate countries. The literature on the EU provides perhaps the most compelling and detailed analysis of public opinion toward an international organization. Furthermore, this large literature sheds light on the relative contributions of economic cost-benefit calculations and soft (identity-related) factors to the explanation of public support for integration efforts between sovereign states.
Postmodern Architecture
Authors: Hays K. Michael
Published: May 2016

The concept of postmodernism finds its definitive articulation in architecture, even though postmodern thought far exceeds the use of the term postmodern in architectural discourse. Modern architecture—with its utopian aspirations, functional rationality, technological determinism, and aesthetic purism—is understood by postmodern thought as a primary expression of the general search for a metaphysics of certainty and universality, which rejects traditional spatial hierarchies and seeks to establish a new homogeneous and continuous space. In practice, the creation of this new space entails the erasure and replacement of old buildings and city fabric as well as old subjectivities and sensibilities. Against the principles of erasure and replacement, a post-modern ethos in architecture emerged in the years just after World War II with a pars destruens, which criticizes the modern movement’s objective and subjective ambitions, and a pars construens which calls for an embrace of heterogeneity and recombination, accommodation, local identity, “vernacular” building, humanistic sensibilities, and disciplinary traditions. A renewed interest in architecture theory accompanied the new architecture; indeed, postmodern architecture was born in the academy and was developed in journals. New epistemological tools, including structuralism and semiotics, helped provide a theoretical infrastructure. Historians and others outside the profession played key roles in the theorization of postmodern architecture. Drawings became important as an experimental tool as well as a means of representation. The development of theory in the United States and Europe enabled the specification of different trends within postmodern architecture—for example, rationalism versus realism, structuralism versus phenomenology, historicism versus deconstructivism, and avant-garde versus neo-avant-garde. Corollary examples and regional inflections can be found in other countries, but most followed Euro-American models. Meanwhile, the larger currents of postmodern thought flowed through post-structuralist theories of language. Inevitably postmodern architecture also developed a post-structuralist dimension. The embrace of post-structuralist theory eventually precipitated the end of historicist postmodernism, though it is arguable that postmodern thought continues to frame recent architectural production.
Evaluation of Effective Dose from CT Scans for Overweight and Obese Adult Patients Using the VirtualDose Software
Authors: Liang Baohui , Gao Yiming , Chen Zhi , Xu X. George
Published: May 2016

This paper evaluates effective dose (ED) of overweight and obese patients who undergo body computed tomography (CT) examinations. ED calculations were based on tissue weight factors in the International Commission on Radiological Protection Publication 103 (ICRP 103). ED per unit dose length product (DLP) are reported as a function of the tube voltage, body mass index (BMI) of patient. The VirtualDose software was used to calculate ED for male and female obese phantoms representing normal weight, overweight, obese 1, obese 2 and obese 3 patients. Five anatomic regions (chest, abdomen, pelvis, abdomen/pelvis and chest/abdomen/pelvis) were investigated for each phantom. The conversion factors were computed from the DLP, and then compared with data previously reported by other groups. It was observed that tube voltage and BMI are the major factors that influence conversion factors of obese patients, and that ED computed using ICRP 103 tissue weight factors were 24% higher for a CT chest examination and 21% lower for a CT pelvis examination than the ED using ICRP 60 factors. For body CT scans, increasing the tube voltage from 80 to 140 kVp would increase the conversion factors by as much as 19–54% depending on the patient's BMI. Conversion factor of female patients was ~7% higher than the factors of male patients. DLP and conversion factors were used to estimate ED, where conversion factors depended on tube voltage, sex, BMI and tissue weight factors. With increasing number of obese individuals, using size-dependence conversion factors will improve accuracy, in estimating patient radiation dose.
Food supplementation mitigates dispersal-dependent differences in nest defence in a passerine bird
Authors: Récapet Charlotte , Daniel Grégory , Taroni Joëlle , Bize Pierre , Doligez Blandine
Published: May 2016

Dispersing and non-dispersing individuals often differ in phenotypic traits (e.g. physiology, behaviour), but to what extent these differences are fixed or driven by external conditions remains elusive. We experimentally tested whether differences in nest-defence behaviour between dispersing and non-dispersing individuals changed with local habitat quality in collared flycatchers, by providing additional food during the nestling rearing period. In control (non-food-supplemented) nests, dispersers were less prone to defend their brood compared with non-dispersers, whereas in food-supplemented nests, dispersing and non-dispersing individuals showed equally strong nest defence. We discuss the importance of dispersal costs versus adaptive flexibility in reproductive investment in shaping these differences in nest-defence behaviour between dispersing and non-dispersing individuals. Irrespective of the underlying mechanisms, our study emphasizes the importance of accounting for environmental effects when comparing traits between dispersing and non-dispersing individuals, and in turn assessing the costs and benefits of dispersal.
Strength and toughness of structural fibres for composite material reinforcement
Authors: Herráez M. , Fernández A. , Lopes C. S. , González C.
Published: May 2016

The characterization of the strength and fracture toughness of three common structural fibres, E-glass, AS4 carbon and Kevlar KM2, is presented in this work. The notched specimens were prepared by means of selective carving of individual fibres by means of the focused ion beam. A straight-fronted edge notch was introduced in a plane perpendicular to the fibre axis, with the relative notch depth being
a
0
/
D
≈0.1 and the notch radius at the tip approximately 50 nm. The selection of the appropriate beam current during milling operations was performed to avoid to as much as possible any microstructural changes owing to ion impingement. Both notched and un-notched fibres were submitted to uniaxial tensile tests up to failure. The strength of the un-notched fibres was characterized in terms of the Weibull statistics, whereas the residual strength of the notched fibres was used to determine their apparent toughness. To this end, the stress intensity factor of a fronted edge crack was computed by means of the finite-element method for different crack lengths. The experimental results agreed with those reported in the literature for polyacrylonitrile-based carbon fibres obtained by using similar techniques. After mechanical testing, the fracture surface of the fibres was analysed to ascertain the failure mechanisms. It was found that AS4 carbon and E-glass fibres presented the lower toughness with fracture surfaces perpendicular to the fibre axis, emanating from the notch tip. The fractured region of Kevlar KM2 fibres extended along the fibre and showed large permanent deformation, which explains their higher degree of toughness when compared with carbon and glass fibres.

This article is part of the themed issue ‘Multiscale modelling of the structural integrity of composite materials’.
Hierarchical analysis of the degradation of fibre-reinforced polymers under the presence of void imperfections
Authors: Liebig Wilfried V. , Schulte Karl , Fiedler Bodo
Published: May 2016

The subject of this work is the investigation of the influence of voids on the mechanical properties of fibre-reinforced polymers (FRPs) under compression loading. To specify the damage accumulation of FRPs in the presence of voids, the complex three-dimensional structure of the composite including voids was analysed and a reduced mechanical model composite was derived. The hierarchical analysis of the model composite on a micro-scale level implies the description of the stress and strain behaviour of the matrix using the photoelasticity technique and digital image correlation technology. These studies are presented along with an analytical examination of the stability of a single fibre. As a result of the experimental and analytical studies, the stiffness of the matrix and fibre as well as their bonding, the initial fibre orientation and the fibre diameter have the highest impact on the failure initiation. All these facts lead to a premature fibre–matrix debonding with ongoing loss of stability of the fibre and followed by kink-band formation. Additional studies on the meso-scale of transparent glass FRPs including a unique void showed that the experiments carried out on the model composites could be transferred to real composites.

This article is part of the themed issue ‘Multiscale modelling of the structural integrity of composite materials’.
The role of interlayer adhesion in graphene oxide upon its reinforcement of nanocomposites
Authors: Li Zheling , Kinloch Ian A. , Young Robert J.
Published: May 2016

Graphene oxide (GO) has become a well-established reinforcement for polymer-based nanocomposites. It provides stronger interfacial interaction with the matrix when compared with that of graphene, but its intrinsic stiffness and strength are somewhat compromised because of the presence of functional groups damaging the graphene lattice and increasing its thickness, and its tendency to adopt a crumpled structure. Although the micromechanics of graphene reinforcement in nanocomposites has been studied widely, the corresponding micromechanics investigations on GO have not been undertaken in such detail. In this work, it is shown that the deformation micromechanics of GO can be followed using Raman spectroscopy and the observed behaviour can be analysed with continuum mechanics. Furthermore, it is shown that the reinforcement efficiency of GO is independent of its number of layers and stacking configurations, indicating that it is not necessary to ensure a high degree of exfoliation of GO in the polymer matrix. It also demonstrates the possibility of increasing the concentration of GO in nanocomposites without sacrificing mechanical reinforcement efficiency.

This article is part of the themed issue ‘Multiscale modelling of the structural integrity of composite materials’.
Modelling of stiffness degradation due to cracking in laminates subjected to multi-axial loading
Authors: Kashtalyan M. , Soutis C.
Published: May 2016

The paper presents an analytical approach to predicting the effect of intra- and interlaminar cracking on residual stiffness properties of the laminate, which can be used in the post-initial failure analysis, taking full account of damage mode interaction. The approach is based on a two-dimensional shear lag stress analysis and the equivalent constraint model of the laminate with multiple damaged plies. The application of the approach to predicting degraded stiffness properties of multidirectional laminates under multi-axial loading is demonstrated on cross-ply glass/epoxy and carbon/epoxy laminates with transverse and longitudinal matrix cracks and crack-induced transverse and longitudinal delaminations.

This article is part of the themed issue ‘Multiscale modelling of the structural integrity of composite materials’.
Damage and failure modelling of hybrid three-dimensional textile composites: a mesh objective multi-scale approach
Authors: Patel Deepak K. , Waas Anthony M.
Published: May 2016

This paper is concerned with predicting the progressive damage and failure of multi-layered hybrid textile composites subjected to uniaxial tensile loading, using a novel two-scale computational mechanics framework. These composites include three-dimensional woven textile composites (3DWTCs) with glass, carbon and Kevlar fibre tows. Progressive damage and failure of 3DWTCs at different length scales are captured in the present model by using a macroscale finite-element (FE) analysis at the representative unit cell (RUC) level, while a closed-form micromechanics analysis is implemented simultaneously at the subscale level using material properties of the constituents (fibre and matrix) as input. The
N
-layers concentric cylinder (NCYL) model (Zhang and Waas 2014
Acta Mech.
225
, 1391–1417; Patel
et al.
submitted
Acta Mech.
) to compute local stress, srain and displacement fields in the fibre and matrix is used at the subscale. The 2-CYL fibre–matrix concentric cylinder model is extended to fibre and (
N
−1) matrix layers, keeping the volume fraction constant, and hence is called the NCYL model where the matrix damage can be captured locally within each discrete layer of the matrix volume. The influence of matrix microdamage at the subscale causes progressive degradation of fibre tow stiffness and matrix stiffness at the macroscale. The global RUC stiffness matrix remains positive definite, until the strain softening response resulting from different failure modes (such as fibre tow breakage, tow splitting in the transverse direction due to matrix cracking inside tow and surrounding matrix tensile failure outside of fibre tows) are initiated. At this stage, the macroscopic post-peak softening response is modelled using the mesh objective smeared crack approach (Rots
et al.
1985
HERON
30
, 1–48; Heinrich and Waas 2012
53rd AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics and Materials Conference, Honolulu, HI, 23–26 April 2012
. AIAA 2012-1537). Manufacturing-induced geometric imperfections are included in the simulation, where the FE mesh of the unit cell is generated directly from micro-computed tomography (MCT) real data using a code S
impleware
. Results from multi-scale analysis for both an idealized perfect geometry and one that includes geometric imperfections are compared with experimental results (Pankow
et al.
2012
53rd AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics and Materials Conference, Honolulu, HI, 23–26 April 2012
. AIAA 2012-1572).

This article is part of the themed issue ‘Multiscale modelling of the structural integrity of composite materials’.
A comparison of different approaches for imaging cracks in composites by X-ray microtomography
Authors: Yu B. , Bradley R. S. , Soutis C. , Withers P. J.
Published: May 2016

X-ray computed tomography (CT) has emerged as a key imaging tool in the characterization of materials, allowing three-dimensional visualization of an object non-destructively as well as enabling the monitoring of damage accumulation over time through time-lapse imaging. However, small defects and cracks can be difficult to detect, particularly in composite materials where low-contrast, plate-like geometries of large area can compromise detectability. Here, we investigate a number of strategies aimed at increasing the capability of X-ray CT to detect composite damage such as transverse ply cracking and delamination, looking specifically at a woven glass fibre-reinforced three-dimensional composite. High-resolution region of interest (ROI) scanning,
in situ
loading, phase contrast and contrast agents are examined systematically as strategies for improving the defect detectability. Spatial resolution, contrast, signal-to-noise ratio, full width at half maximum, user friendliness and measurement time are all considered. Taken together, the results suggest that high-resolution ROI scanning combined with the increased contrast resulting from staining give the highest defect detectability.

This article is part of the themed issue ‘Multiscale modelling of the structural integrity of composite materials’.
Structural integrity of engineering composite materials: a cracking good yarn
Authors: Beaumont Peter W. R. , Soutis Costas
Published: May 2016

Predicting precisely where a crack will develop in a material under stress and exactly when in time catastrophic fracture of the component will occur is one the oldest unsolved mysteries in the design and building of large-scale engineering structures. Where human life depends upon engineering ingenuity, the burden of testing to prove a ‘fracture safe design’ is immense. Fitness considerations for long-life implementation of large composite structures include understanding phenomena such as impact, fatigue, creep and stress corrosion cracking that affect reliability, life expectancy and durability of structure. Structural integrity analysis treats the design, the materials used, and figures out how best components and parts can be joined, and takes service duty into account. However, there are conflicting aims in the complete design process of designing simultaneously for high efficiency and safety assurance throughout an economically viable lifetime with an acceptable level of risk.

This article is part of the themed issue ‘Multiscale modelling of the structural integrity of composite materials’.
Measurement uncertainty matters: ecological management using POMDPs
Authors: Memarzadeh Milad , Boettiger Carl
Published: May 2016

Over the past 30 years, researchers have used various approximations to address the impact of measurement uncertainty on optimal management policy.This literature has consistently suggested the counter-intuitive proposition that increasing harvest levels in the presence of measurement error is often optimal. Here, we use state-of-the art algorithms for Partially Observed Markov Decision Processes (POMDPs) to provide the first complete solution to this classic problem, and demonstrate that contrary to previous work, the resulting policy is usually more conservative than without measurement error. We demonstrate that management which underestimates the measurement error results in both low economic returns and high frequency of stock collapses, while overestimating the role of measurement error can still result in nearly-optimal economic performance while avoiding stock collapse.
GutCyc: a Multi-Study Collection of Human Gut Microbiome Metabolic Models
Authors: Hahn Aria S. , Altman Tomer , Konwar Kishori M. , Hanson Niels W. , Kim Dongjae , Relman David A. , Dill David L. , Hallam Steven J.
Published: May 2016

Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between studies introduce systematic differences that confound comparative analyses. To overcome these challenges, we developed GUTCYC, a compendium of environmental pathway genome databases constructed from 418 assembled human microbiome datasets using METAPATHWAYS, enabling reproducible functional metagenomic annotation. We also generated metabolic network reconstructions for each metagenome using the PATHWAYTOOLSsoftware, empowering researchers and clinicians interested in visualizing and interpreting metabolic pathways encoded by the human gut microbiome. For the first time, GUTCYCprovides consistent annotations and metabolic pathway predictions, making possible comparative community analyses between health and disease states in inflammatory bowel disease, Crohn’s disease, and type 2 diabetes. GUTCYCdata products are searchable online, or may be downloaded and explored locally using METAPATHWAYSand PATHWAYTOOLS.
A large field of view two-photon mesoscope with subcellular resolution for in vivo imaging
Authors: Sofroniew N. J. , Flickinger D. , King J. , Svoboda K.
Published: May 2016

Imaging is used to map activity across populations of neurons. Microscopes with cellular resolution have small (< 1 millimeter) fields of view and cannot simultaneously image activity distributed across multiple brain areas. Typical large field of view microscopes do not resolve single cells, especially in the axial dimension. We developed a 2-photon random access mesoscope (2p-RAM) that allows high-resolution imaging anywhere within a volume spanning multiple brain areas (Ø 5 mm × 1 mm cylinder). 2p-RAM resolution is near diffraction limited (lateral, 0.66 μm, axial 4.09 μm at the center; excitation wavelength = 970 nm; numerical aperture = 0.6) over a large range of excitation wavelengths. A fast threedimensional scanning system allows efficient sampling of neural activity in arbitrary regions of interest across the entire imaging volume. We illustrate the use of the 2p-RAM by imaging neural activity in multiple, non-contiguous brain areas in transgenic mice expressing protein calcium sensors.
JuPOETs: A Constrained Multiobjective Optimization Approach to Estimate Biochemical Model Ensembles in the Julia Programming Language
Authors: Bassen David , Vilkhovoy Michael , Minot Mason , Butcher Jonathan T , Varner Jeffrey D.
Published: May 2016

Ensemble modeling is a well established approach for obtaining robust predictions and for simulating course grained population behavior in deterministic mathematical models. In this study, we present a multiobjective based technique to estimate model ensembles, the Pareto Optimal Ensemble Technique in the Julia programming language (JuPOETs). JuPOETs integrates simulated annealing with Pareto optimality to estimate parameter ensembles on or near the optimal tradeoff surface between competing training objectives. We demonstrated JuPOETs on a suite of multiobjective problems, including test functions with parameter bounds and system constraints as well as for the identification of a proof-of-concept biochemical model with four conflicting training objectives. JuPOETs identified optimal or near optimal solutions approximately six-fold faster than a corresponding implementation in Octave for the suite of test functions. For the proof-of-concept biochemical model, JuPOETs produced an ensemble of parameters that gave both the mean of the training data for conflicting data sets, while simultaneously estimating parameter sets that performed well on each of the individual objective functions. JuPOETs can be adapted to solve many problem types, including mixed binary and continuous variable types, bilevel optimization problems and constrained problems without altering the base algorithm. JuPOETs can be installed using the Julia package manager from the JuPOETs GitHub repository athttps://github.com/varnerlab/POETs.jl.
Detailed dendritic excitatory/inhibitory balance through heterosynaptic spike-timing-dependent plasticity
Authors: Hiratani Naoki , Fukai Tomoki
Published: May 2016

Balance between excitatory and inhibitory inputs is a key feature of cortical dynamics. Such balance is arguably preserved in dendritic branches, yet its underlying mechanism and functional roles remain unknown. Here, by considering computational models of heterosynaptic spike-timing-dependent plasticity (STDP), we show that the detailed excitatory/inhibitory balance on dendritic branch is robustly achieved through heterosynaptic interaction between excitatory and inhibitory synapses. The model well reproduces experimental results on heterosynaptic STDP, and provides analytical insights. Furthermore, heterosynaptic STDP explains how maturation of inhibitory neurons modulates selectivity of excitatory neurons in critical period plasticity of binocular matching. Our results propose heterosynaptic STDP as a critical factor in synaptic organization and resultant dendritic computation.

Significance statement

Recent experimental studies have revealed that relative spike timings among neighboring Glutamatergic and GABAergic synapses on a dendritic branch significantly influences changes in synaptic efficiency of these synapses. This heterosynaptic form of spike-timing-dependent plasticity (STDP) is potentially important for shaping the synaptic organization and computation of neurons, but its functional role remains elusive. Here, through computational modeling, we show that heterosynaptic plasticity causes the detailed balance between excitatory and inhibitory inputs on the dendrite, at the parameter regime where previous experimental results are well reproduced. Our result reveals a potential principle of GABA-driven neural circuit formation.
Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears
Authors: Fortes Gloria G. , Grandal-d'Anglade Aurora , Kolbe Ben , Fernandes Daniel , Meleg Ioanna N. , García-Vázquez Ana , Pinto-Llona Ana C. , Constantin Silviu , de Torres Trino J. , Ortiz Jose E. , Frischauf Christine , Rabeder Gernot , Hofreiter Michael , Barlow Axel
Published: May 2016

Ancient DNA studies have revolutionised the study of extinct species and populations, providing insights on phylogeny, phylogeography, admixture and demographic history. However, inferences on behaviour and sociality have been far less frequent. Here, we investigate the complete mitochondrial genomes of extinct Late Pleistocene cave bears and middle Holocene brown bears that each inhabited multiple geographically proximate caves in northern Spain. In cave bears, we find that, although most caves were occupied simultaneously, each cave almost exclusively contains a unique lineage of closely related haplotypes. This remarkable pattern suggests extreme fidelity to their birth site in cave bears, best described as homing behaviour, and that cave bears formed stable maternal social groups at least for hibernation. In contrast, brown bears do not show any strong association of mitochondrial lineage and cave, suggesting that these two closely related species differed in aspects of their behaviour and sociality. This difference is likely to have contributed to cave bear extinction, which occurred at a time in which competition for caves between bears and humans was likely intense and the ability to rapidly colonise new hibernation sites would have been crucial for the survival of a species so dependent on caves for hibernation as cave bears. Our study demonstrates the potential of ancient DNA to uncover patterns of behaviour and sociality in ancient species and populations, even those that went extinct many tens of thousands of years ago.
Rapid dynamics of cell-shape recovery in response to local deformations
Authors: Haase Kristina , Shendruk Tyler N. , Pelling Andrew E.
Published: May 2016

It is vital that cells respond rapidly to mechanical cues within their microenvironment through changes in cell shape and volume, which rely upon the mechanical properties of cells’ highly interconnected cytoskeletal networks and intracellular fluid redistributions. While previous research has largely investigated deformation mechanics, we now focus on the immediate cell-shape recovery response following mechanical perturbation by inducing large, local, and reproducible cellular deformations using AFM. By continuous imaging within the plane of deformation, we characterize the membrane and cortical response of HeLa cells to unloading, and model the recovery via overdamped viscoelastic dynamics. Importantly, the majority (90%) of HeLa cells recover their cell shape in < 1s. Despite actin remodelling on this time scale, we show that cell recovery time is not affected by load duration nor magnitude. To further explore this rapid recovery response, we expose cells to cytoskeletal destabilizers and osmotic shock conditions, which exposes the interplay between actin and osmotic pressure. We show that the rapid dynamics of recovery depend crucially on intracellular pressure, and provide strong evidence that cortical actin is the key regulator in the cell-shape recovery processes, in both cancerous and non-cancerous epithelial cells.
Specimen preparation for cryogenic coherent X-ray diffraction imaging of biological cells and cellular organelles by using the X-ray free-electron laser at SACLA
Authors: Kobayashi Amane , Sekiguchi Yuki , Oroguchi Tomotaka , Okajima Koji , Fukuda Asahi , Oide Mao , Yamamoto Masaki , Nakasako Masayoshi
Published: May 2016

Coherent X-ray diffraction imaging (CXDI) allows internal structures of biological cells and cellular organelles to be analyzed. CXDI experiments have been conducted at 66 K for frozen-hydrated biological specimens at the SPring-8 Angstrom Compact Free-Electron Laser facility (SACLA). In these cryogenic CXDI experiments using X-ray free-electron laser (XFEL) pulses, specimen particles dispersed on thin membranes of specimen disks are transferred into the vacuum chamber of a diffraction apparatus. Because focused single XFEL pulses destroy specimen particles at the atomic level, diffraction patterns are collected through raster scanning the specimen disks to provide fresh specimen particles in the irradiation area. The efficiency of diffraction data collection in cryogenic experiments depends on the quality of the prepared specimens. Here, detailed procedures for preparing frozen-hydrated biological specimens, particularly thin membranes and devices developed in our laboratory, are reported. In addition, the quality of the frozen-hydrated specimens are evaluated by analyzing the characteristics of the collected diffraction patterns. Based on the experimental results, the internal structures of the frozen-hydrated specimens and the future development for efficient diffraction data collection are discussed.