bluuebunny/crossref_metadata_2025_split huggingface dataset:
An anisotropic elastoplastic model for soft clays based on logarithmic contractancy
Authors: Sivasithamparam Nallathamby , Castro Jorge 
Published: August 2015

SummaryA new constitutive model for soft structured clays is developed based on an existing model called S‐CLAY1S, which is a Cam clay type model that accounts for anisotropy and destructuration. The new model (E‐SCLAY1S) uses the framework of logarithmic contractancy to introduce a new parameter that controls the shape of the yield surface as well as the plastic potential (as an assumed associated flow rule is applied). This new parameter can be used to fit the coefficient of earth pressure at rest, the undrained shear strength or the stiffness under shearing stress paths predicted by the model. The improvement to previous constitutive models that account for soil fabric and bonding is formulated within the contractancy framework such that the model predicts the uniqueness of the critical state line and its slope is independent of the contractancy parameter. Good agreement has been found between the model predictions and published laboratory results for triaxial compression tests. An important finding is that the contractancy parameter, and consequently the shape of the yield surface, seems to change with the degree of anisotropy; however, further study is required to investigate this response. From published data, the yield surface for isotropically consolidated clays seems ‘bullet’ or ‘almond’ shaped, similar to that of the Cam clay model; while for anisotropically consolidated clays, the yield surface is more elliptical, like a rotated and distorted modified Cam clay yield surface. © 2015 The Authors. International Journal for Numerical and Analytical Methods in Geomechanics published by John Wiley & Sons Ltd.
Conformational stability of the RNP domain controls fibril formation of PABPN1
Authors: Liebold Jens , Winter Reno , Golbik Ralph , Hause Gerd , Parthier Christoph , Schwarz Elisabeth 
Published: August 2015

AbstractThe disease oculopharyngeal muscular dystrophy is caused by alanine codon trinucleotide expansions in the N‐terminal segment of the nuclear poly(A) binding protein PABPN1. As histochemical features of the disease, intranuclear inclusions of PABPN1 have been reported. Whereas the purified N‐terminal domain of PABPN1 forms fibrils in an alanine‐dependent way, fibril formation of the full‐length protein occurs also in the absence of alanines. Here, we addressed the question whether the stability of the RNP domain or domain swapping within the RNP domain may add to fibril formation. A variant of full‐length PABPN1 with a stabilizing disulfide bond at position 185/201 in the RNP domain fibrillized in a redox‐sensitive manner suggesting that the integrity of the RNP domain may contribute to fibril formation. Thermodynamic analysis of the isolated wild‐type and the disulfide‐linked RNP domain showed two state unfolding/refolding characteristics without detectable intermediates. Quantification of the thermodynamic stability of the mutant RNP domain pointed to an inverse correlation between fibril formation of full‐length PABPN1 and the stability of the RNP domain.
Thermodynamics of Aβ16–21 dissociation from a fibril: Enthalpy, entropy, and volumetric properties
Authors: Rao Jampani Srinivasa , Mahmoudinobar Farbod , Su Zhaoqian , Dias Cristiano L. 
Published: August 2015

ABSTRACTHere, we provide insights into the thermodynamic properties of A
dissociation from an amyloid fibril using all‐atom molecular dynamics simulations in explicit water. An umbrella sampling protocol is used to compute potentials of mean force (PMF) as a function of the distance ξ between centers‐of‐mass of the A
peptide and the preformed fibril at nine temperatures. Changes in the enthalpy and the entropic energy are determined from the temperature dependence of these PMF(s) and the average volume of the simulation box is computed as a function of ξ. We find that the PMF at 310 K is dominated by enthalpy while the entropic energy does not change significantly during dissociation. The volume of the system decreases during dissociation. Moreover, the magnitude of this volume change also decreases with increasing temperature. By defining dock and lock states using the solvent accessible surface area (SASA), we find that the behavior of the electrostatic energy is different in these two states. It increases (unfavorable) and decreases (favorable) during dissociation in lock and dock states, respectively, while the energy due to Lennard‐Jones interactions increases continuously in these states. Our simulations also highlight the importance of hydrophobic interactions in accounting for the stability of A
. Proteins 2015; 83:1963–1972. © 2015 Wiley Periodicals, Inc.
The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis
Authors: Improta Roberto , Vitagliano Luigi , Esposito Luciana 
Published: August 2015

ABSTRACTThe elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of ψ and/or φ. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the Hα hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen‐bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations. Proteins 2015; 83:1973–1986. © 2015 Wiley Periodicals, Inc.
On the relation between multimarket contact and service quality: Mutual forbearance or network coordination?
Authors: van Reeven Peran , Pennings Enrico 
Published: August 2015

Research summary: We reconsider the relationship between multimarket contact and product quality in the airline industry by arguing that multimarket contact has both a negative mutual forbearance effect on quality and a positive network coordination effect on quality. Multimarket contact increases the frequency of contact between firms, and this anticipated future interaction promotes cooperation. In network industries, especially small firms may want to cooperate in order to increase the attractiveness of the composite product. By using size as a moderating variable, we indeed find a consistent positive effect of multimarket contact on product quality for small airlines. We show that this effect can be attributed to network coordination and that this effect generally dominates the negative mutual forbearance effect in a recent period.Managerial summary: Firms with sales in multiple geographical markets likely encounter each other with mutual respect (i.e., live and let live) because aggressive behavior in one market may lead to retaliatory responses in other markets. Such responses weaken competitive pressures on price and quality. Insofar these firms sell complementary products, they may however also coordinate and improve their joint product offering, resulting in better quality for the consumer. This paper shows that this positive effect of cooperation may dominate the negative competition‐reducing effect, depending on the size distribution of firms. The reason is that small or nondominant firms have a stronger incentive to produce compatible products than large or dominant firms with already a strong position in the (global) market. Copyright © 2015 John Wiley & Sons, Ltd.
Use of higher severity fire areas by female Pacific fishers on the Kern Plateau, Sierra Nevada, California, USA
Authors: Hanson Chad T. 
Published: August 2015

ABSTRACTThe Pacific fisher (Pekania pennanti) is a rare and imperiled forest carnivore, with a genetically distinct and isolated population living in the southern Sierra Nevada mountains of California, USA. Female fishers are of special interest and concern, given their very small numbers and their disproportionately important role in the potential recovery of the population. Using fisher scat detection to assess patterns of habitat use, I conducted analyses regarding use by fishers of unlogged higher severity fire areas at 10–11 years postfire in the 2002 McNally fire area. Contrary to the prevailing current hypothesis regarding fisher postfire habitat use, fishers did not use higher severity fire areas less than low–moderate‐severity areas or unburned forest (n = 77 scats), and female fishers used the large, intense McNally fire area significantly more than unburned forest (n = 12 scats). Female fishers were detected at multiple locations >250 m into the interior of a very large (>5,000 ha), unlogged higher severity fire patch. These results indicate unlogged higher severity fire areas are suitable habitat for fishers, especially female fishers, and suggest a need to revisit current management direction, which emphasizes extensive commercial thinning and postfire logging to reduce fuels and control fire. © 2015 The Wildlife Society.
Habitat‐specific responses of shoot growth and distribution of alpine dwarf‐pine (Pinus pumila) to climate variation
Authors: Amagai Yukihiro , Kaneko Masami , Kudo Gaku 
Published: August 2015

AbstractAlpine dwarf‐pine (Pinus pumila) in dominant in the alpine regions of Japan, and often forms the krummholz zone of stunted alpine forest. The distribution of P. pumila is strongly related to the distribution of snow, and shoot growth is also sensitive to weather conditions. Changes in temperature and snowmelt regimes may well affect the distribution patterns of the krummholz zone. P. pumila usually occupies the habitat between the fellfield and snowbed communities, and responses to climate change may differ depending on whether plants are close to the fellfield or the snowbed. We compared the distribution and shoot growth patterns of P. pumila close to both surrounding ecosystems in the Taisetsu Mountains, northern Japan. P. pumila has expanded its distribution area by 14 % toward both edges over the last 32 years. Annual shoot growth was positively affected by summer temperature and sunshine duration, but negatively related to spring temperature toward the fellfield side. Shoot growth was greater at the southeastern edge of patches, where snowdrifts were formed. The results indicated that shoot growth and distribution area increased in warm summers. However, warm springs might have a negative influence on shoot growth, probably because the earlier reduction in cold‐resistance enhances the risk of frost damage in spring close to the fellfield side. This study suggests the importance of understanding the site‐specific responses of shrubs to predict the impacts of climate change on alpine ecosystems.
Positron Emission Tomography Computed Tomography: A Guide for the General Radiologist
Authors: Beadsmoore Clare , Newman David , MacIver Duncan , Pawaroo Davina 
Published: August 2015

Cancer remains a leading cause of death in Canada and worldwide. Whilst advances in anatomical imaging to detect and monitor malignant disease have continued over the last few decades, limitations remain. Functional imaging, such as positron emission tomography (PET), has improved the sensitivity and specificity in detecting malignant disease. In combination with computed tomography (CT), PET is now commonly used in the oncology setting and is an integral part of many cancer patients’ pathways. Although initially the CT component of the study was purely for attenuation of the PET imaging and to provide anatomical coregistration, many centers now combine the PET study with a diagnostic quality contrast enhanced CT to provide one stop staging, thus refining the patient's pathway. The commonest tracer used in everyday practice is FDG (F18-fluorodeoxyglucose). There are many more tracers in routine clinical practice and those with emerging roles, such as 11C-choline, useful in the imaging of prostate cancer; 11C-methionine, useful in imaging brain tumours; C11-acetate, used in imaging hepatocellular carcinomas; 18F-FLT, which can be used as a marker of cellular proliferation in various malignancies; and F18-DOPA and various 68Ga-somatostatin analogues, used in patients with neuroendocrine tumours. In this article we concentrate on FDG PETCT as this is the most commonly available and widely utilised tracer now used to routinely stage a number of cancers. PETCT alters the stage in approximately one-third of patients compared to anatomical imaging alone. Increasingly, PETCT is being used to assess early metabolic response to treatment. Metabolic response can be seen much earlier than a change in the size/volume of the disease which is measured by standard CT imaging. This can aid treatment decisions in both in terms of modifying therapy and in addition to providing important prognostic information. Furthermore, it is helpful in patients with distorted anatomy from surgery or radiotherapy when there is suspicion of recurrent or residual disease. FDG PETCT is not specific for malignancy and can also be used for diagnosing and monitoring a number of inflammatory and infectious conditions that can be difficult to diagnose on anatomical imaging, some of which carry significant morbidity. FDG PETCT is increasingly used in patients with pyrexia of unknown origin and in patients with metastatic malignancies of unidentified primary on conventional imaging. This article reviews the uses of PETCT including an overview of the more common incidental lesions and conditions. It also provides guidance of how to approach a PETCT as a nonradionuclide radiologist and how to interpret a study in the multidisciplinary team setting.
Analysis of parageneses of metapelite gneisses of the Okhotsk granulite complex by minimization of Gibbs thermodynamic potential
Authors: Avchenko O.V. , Chudnenko K.V. , Badredinov Z.G. , Sharova O.I. 
Published: August 2015

Abstract
The problem of modeling of real parageneses has been solved by minimization of Gibbs thermodynamic potential for metapelites of the Okhotsk granulite complex. Model mineral assemblages completely reproduce the composition of minerals and their modal contents in the studied rocks. This fundamental fact directly verifies the solution of the problem, proving the validity of the principle of local equilibrium in the studied assemblages and the agreement of all thermodynamic data accepted on the modeling. The pressure and temperature during the metamorphism of granulites of the Okhotsk complex, estimated by modeling, are 5.2–7.0 kbar and 620–770 °C, which corresponds to the near-boundary conditions of the amphibolitic and granulitic facies. Model mineral assemblages similar to real parageneses in the composition of minerals and their modes can be successfully obtained with the Selektor software under conditions of both inert and moving water. The composition of the external metamorphic fluid and the approximate weight ratio of fluid to rock have been determined. The oxidation potential of this fluid is similar to the potential of oxygen at the buffer C–CO–CO2 if the fluid/rock ratio is 0.03–0.30 and the low partial pressure of water varies from 1.80 to 0.35 kbar. The Okhotsk metamorphic complex is not an analog of the granulites of the southern Aldan Shield, because considerably higher pressure and temperature are typical of the latter.
Comparative analysis of megaflood deposits and alluvium of the Chuya and Katun’ river valleys (Gorny Altai)
Authors: Zolnikov I.D. , Deev E.V. , Nazarov D.V. , Kotler S.A. 
Published: August 2015

Abstract
Sedimentary indicators of catastrophic glacial megafloods—plane-bedded angular gravel, cobbles, and boulders—are described in several sections of the high terraces of the Chuya River valley. The principal difference of these sediments from typical alluvium of this area is demonstrated. The clast roundness, grain size of clasts, and sedimentary structures of the high-terrace deposits of the Chuya and Katun’ valleys indicate the same facies originated through megaflood deposition. These results are at odds with ideas of alluvial, glacial, or glaciofluvial genesis of the high-terrace deposits of the Chuya River.
NIVISON AND THE PHILOSOPHICAL STUDY OF CONFUCIAN THOUGHT: IN MEMORY OF DAVID S. NIVISON (1923–2014)
Authors: Shun Kwong-loi 
Published: August 2015

AbstractOne of David S. Nivison's (1923–2014) most important contributions is his work in bridging philological studies and philosophical inquiry. His methodological approach resonates in spirit with an approach to the study of Chinese thought advocated by Confucian thinkers such as Zhu Xi and Tang Junyi, who both emphasize jing toward early thinkers. He pays careful attention to textual details, is respectful of cultural context, and seeks to preserve the distinctive features of Chinese traditions of thought and avoid imposing on them western philosophical conceptions. In doing so, he exemplifies the spirit of jing, a serious and cautious attitude dedicated to a proper understanding of early thinkers in their cultural context.
Muscle fatigue resistance in the rat hindlimbin vivofrom low dietary intakes of tuna fish oil that selectively increase phospholipidn-3 docosahexaenoic acid according to muscle fibre type
Authors: Henry R. , Peoples G. E. , McLennan P. L. 
Published: August 2015

AbstractDietary fish oil (FO) modulates muscle O2consumption and contractile function, predictive of effects on muscle fatigue. High doses unattainable through human diet and muscle stimulation parameters used engender uncertainty in their physiological relevance. We tested the hypothesis that nutritionally relevant FO doses can modulate membrane fatty acid composition and muscle fatigue. Male Sprague–Dawley rats were randomised to control (10 % olive oil (OO) by weight) or low or moderate FO diet (LowFO and ModFO) (HiDHA tuna fish oil) for 15 weeks (LowFO: 0·3 % FO, 9·7 % OO, 0·25 % energy as EPA+DHA; ModFO: 1·25 % FO, 8·75 % OO, 1·0 % energy as EPA+DHA). Hindlimb muscle function was assessed under anaesthesiain vivousing repetitive 5 s burst sciatic nerve stimulation (0·05 ms, 7–12 V, 5 Hz, 10 s duty cycle, 300 s). There were no dietary differences in maximum developed muscle force. Repetitive peak developed force fell to 50 % within 62 (sem10) s in controls and took longer to decline in FO-fed rats (LowFO 110 (sem15) s; ModFO 117 (sem14) s) (P<0·05). Force within bursts was better sustained with FO and maximum rates of force development and relaxation declined more slowly. The FO-fed rats incorporated higher muscle phospholipid DHA-relative percentages than controls (P<0·001). Incorporation of DHA was greater in the fast-twitch gastrocnemius (Control 9·3 (sem0·8) %, LowFO 19·9 (sem0·4), ModFO 24·3 (sem1·0)) than in the slow-twitch soleus muscle (Control 5·1 (sem0·2), LowFO 14·3 (sem0·7), ModFO 18·0 (sem1·4)) (P<0·001), which was comparable with the myocardium, in line with muscle fibre characteristics. The LowFO and ModFO diets, emulating human dietary and therapeutic supplement intake, respectively, both elicited muscle membrane DHA enrichment and fatigue resistance, providing a foundation for translating these physiological effects to humans.
Sensory dysfunction and quality of life after great auricular nerve sacrifice during parotidectomy: our experience
Authors: Galli J , Pandolfini M , Rigante M , Schinaia L , Guidi M L , Almadori G , Paludetti G 
Published: August 2015

AbstractObjective:This study aimed to investigate the impact on patients' quality of life of great auricular nerve sacrifice during parotidectomy.Methods:A retrospective review was conducted of 191 consecutive patients who underwent parotidectomy with great auricular nerve sacrifice between 2006 and 2011. Residual sensory dysfunction and its impact on quality of life was analysed using an eight-item quality of life survey.Results:In all, 139 out of 191 patients (72.8 per cent) experienced one or more abnormal sensations in the ear or neck region after surgery. There was a moderate inverse correlation between the number of abnormal sensations and time elapsed since surgery. Moreover, the degree of discomfort correlated significantly with the frequency of symptom occurrence (p< 0.001), duration of the abnormal sensation (p< 0.001) and size of the affected area (p< 0.001).Conclusion:Sacrifice of the great auricular nerve has only a small impact on patient quality of life; their daily activities are not significantly affected.
Prevalent emm types and superantigen gene patterns of group A Streptococcus in Thailand
Authors: PAVEENKITTIPORN W. , NOZAWA T. , DEJSIRILERT S. , NAKAGAWA I. , HAMADA S. 
Published: August 2015

SUMMARYGroup A Streptococcus (GAS) are globally distributed bacterial pathogens. We examined the emm genotypes, which are important indicators of virulence, of 349 clinical GAS isolates collected using two surveillance systems, i.e. Invasive Bacterial Infection Surveillance (IBIS) from 2010 to 2011 (234 isolates) and routine surveillance of clinically isolated bacteria from various hospitals during 1996–2011 (115 isolates) in Thailand. The major emm genotypes in IBIS samples were emm44 (12·0%), emm104 (6·8%), emm22 (5·6%), and emm81 (5·6%), whereas only one isolate (0·4%) had the emm1 genotype, which is significantly more common in invasive cases in the Western world. In samples collected during routine surveillance, emm238 (10·4%), emm44 (8·7%), and emm165 (7·0%) were dominant. The major superantigen gene profiles were similar between the groups, and 30·1% of isolates did not possess the phage-encoded superantigens (speA, speC, speH, speI, speK, speL, speM, ssa). Although most isolates exhibited limited gene profiles, emm44 isolates had highly variable gene profiles (15 patterns). We conclude that emm44 is the predominant GAS genotype in Thailand, and isolates varied in superantigen gene profiles.
Reasons for measles cases not being vaccinated with MMR: investigation into parents' and carers' views following a large measles outbreak
Authors: McHALE P. , KEENAN A. , GHEBREHEWET S. 
Published: August 2015

SUMMARYUptake rates for the combined measles, mumps and rubella (MMR) vaccine have been below the required 95% in the UK since a retracted and discredited article linking the MMR vaccine with autism and inflammatory bowel disease was released in 1998. This study undertook semi-structured telephone interviews among parents or carers of 47 unvaccinated measles cases who were aged between 13 months and 9 years, during a large measles outbreak in Merseyside. Results showed that concerns over the specific links with autism remain an important cause of refusal to vaccinate, with over half of respondents stating this as a reason. A quarter stated child illness during scheduled vaccination time, while other reasons included general safety concerns and access issues. Over half of respondents felt that more information or a discussion with a health professional would help the decision-making process, while a third stated improved access. There was clear support for vaccination among respondents when asked about current opinions regarding MMR vaccine. The findings support the hypothesis that safety concerns remain a major barrier to MMR vaccination, and also support previous evidence that experience of measles is an important determinant in the decision to vaccinate.