bluuebunny/crossref_metadata_2025 huggingface dataset:
Exact density functional and wave function embedding schemes based on orbital localization
Authors: Hégely Bence , Nagy Péter R. , Ferenczy György G. , Kállay Mihály
Published: August 2016

Exact schemes for the embedding of density functional theory (DFT) and wave function theory (WFT) methods into lower-level DFT or WFT approaches are introduced utilizing orbital localization. First, a simple modification of the projector-based embedding scheme of Manby and co-workers [J. Chem. Phys. 140, 18A507 (2014)] is proposed. We also use localized orbitals to partition the system, but instead of augmenting the Fock operator with a somewhat arbitrary level-shift projector we solve the Huzinaga-equation, which strictly enforces the Pauli exclusion principle. Second, the embedding of WFT methods in local correlation approaches is studied. Since the latter methods split up the system into local domains, very simple embedding theories can be defined if the domains of the active subsystem and the environment are treated at a different level. The considered embedding schemes are benchmarked for reaction energies and compared to quantum mechanics (QM)/molecular mechanics (MM) and vacuum embedding. We conclude that for DFT-in-DFT embedding, the Huzinaga-equation-based scheme is more efficient than the other approaches, but QM/MM or even simple vacuum embedding is still competitive in particular cases. Concerning the embedding of wave function methods, the clear winner is the embedding of WFT into low-level local correlation approaches, and WFT-in-DFT embedding can only be more advantageous if a non-hybrid density functional is employed.
Non-Condon nonequilibrium Fermi’s golden rule rates from the linearized semiclassical method
Authors: Sun Xiang , Geva Eitan
Published: August 2016

The nonequilibrium Fermi’s golden rule describes the transition between a photoexcited bright donor electronic state and a dark acceptor electronic state, when the nuclear degrees of freedom start out in a nonequilibrium state. In a previous paper [X. Sun and E. Geva, J. Chem. Theory Comput. 12, 2926 (2016)], we proposed a new expression for the nonequilibrium Fermi’s golden rule within the framework of the linearized semiclassical approximation and based on the Condon approximation, according to which the electronic coupling between donor and acceptor is assumed constant. In this paper we propose a more general expression, which is applicable to the case of non-Condon electronic coupling. We test the accuracy of the new non-Condon nonequilibrium Fermi’s golden rule linearized semiclassical expression on a model where the donor and acceptor potential energy surfaces are parabolic and identical except for shifts in the equilibrium energy and geometry, and the coupling between them is linear in the nuclear coordinates. Since non-Condon effects may or may not give rise to conical intersections, both possibilities are examined by considering the following: (1) A modified Garg-Onuchic-Ambegaokar model for charge transfer in the condensed phase, where the donor-acceptor coupling is linear in the primary-mode coordinate, and for which non-Condon effects do not give rise to a conical intersection; (2) the linear vibronic coupling model for electronic transitions in gas phase molecules, where non-Condon effects give rise to conical intersections. We also present a comprehensive comparison between the linearized semiclassical expression and a progression of more approximate expressions, in both normal and inverted regions, and over a wide range of initial nonequilibrium states, temperatures, and frictions.
Probing the electronic structure and Au—C chemical bonding in AuCn− and AuCnH− (n = 2, 4, and 6) using high-resolution photoelectron spectroscopy
Authors: León Iker , Ruipérez Fernando , Ugalde Jesus M. , Wang Lai-Sheng
Published: August 2016

We report a joint photoelectron spectroscopy and theoretical study on AuC4−, AuC6−, and AuCnH− (n = 2, 4, and 6) using high-resolution photoelectron imaging and ab initio calculations. The ground state of AuC2H−, AuC4H−, and AuC6H− is found to be linear, while that of AuC4− and AuC6− is bent. All the species are found to be linear in their neutral ground states. The electron affinities (EAs) are measured to be 3.366(1) and 3.593(1) eV for AuC4 and AuC6, respectively. Both bending and stretching frequencies are resolved in the spectra of AuC4− and AuC6−. High-resolution data of AuCnH− reveal major vibrational progressions in the Au—C stretching and bending modes. AuC2H− has a ground state stretching frequency of 445(10) cm−1 and a bending frequency of 260(10) cm−1; AuC4H− has a ground state stretching frequency of 340(10) cm−1; AuC6H− has a ground state stretching frequency of 260(10) cm−1 and a bending frequency of 55(10) cm−1. The EAs are measured to be 1.475(1), 1.778(1), and 1.962(1) eV for AuC2H, AuC4H, and AuC6H, respectively. The strength of the Au—C bond decreases as the number of carbon atoms increases. The current study provides a wealth of electronic structure information about AuC4−, AuC6−, and AuCnH− (n = 2, 4, and 6) and their corresponding neutrals.
Generalized adsorption isotherms for molecular and dissociative adsorption of a polar molecular species on two polar surface geometries: Perovskite (100) (Pm-3m) and fluorite (111) (Fm-3m)
Authors: Danielson Thomas , Hin Celine , Savara Aditya
Published: August 2016

Lattice based kinetic Monte Carlo simulations have been used to determine a functional form for the second order adsorption isotherms on two commonly investigated crystal surfaces: the (111) fluorite surface and the (100) perovskite surface which has the same geometric symmetry as the NaCl (100) surface. The functional form is generalized to be applicable to all values of the equilibrium constant by a shift along the pressure axis. Functions have been determined for estimating the pressure at which a desired coverage would be achieved and, conversely, for estimating the coverage at a certain pressure. The generalized form has been calculated by investigating the surface adsorbate coverage across a range of thermodynamic equilibrium constants that span the range 10−26 to 1013. The equations have been shown to be general for any value of the adsorption equilibrium constant.
Red and blue shift of liquid water’s excited states: A many body perturbation study
Authors: Ziaei Vafa , Bredow Thomas
Published: August 2016

In the present paper, accurate optical absorption spectrum of liquid H2O is calculated in the energy range of 5–20 eV to probe the nature of water’s excited states by means of many body perturbation approach. Main features of recent inelastic X-ray measurements are well reproduced, such as a bound excitonic peak at 7.9 eV with a shoulder at 9.4 eV as well as the absorption maximum at 13.9 eV, followed by a broad shoulder at 18.4 eV. The spectrum is dominated by excitonic effects impacting the structures of the spectrum at low and higher energy regimes mixed by single particle effects at high energies. The exciton distribution of the low-energy states, in particular of S1, is highly anisotropic and localized mostly on one water molecule. The S1 state is essentially a HOCO-LUCO (highest occupied crystal orbital - lowest unoccupied crystal orbital) transition and of intra-molecular type, showing a localized valence character. Once the excitation energy is increased, a significant change in the character of the electronically excited states occurs, characterized through emergence of multiple quasi-particle peaks at 7.9 eV in the quasi-particle (QP) transition profile and in the occurring delocalized exciton density distribution, spread over many more water molecules. The exciton delocalization following a change of the character of excited states at around 7.9 eV causes the blue shift of the first absorption band with respect to water monomer S1. However, due to reduction of the electronic band gap from gas to liquid phase, following enhanced screening upon condensation, the localized S1 state of liquid water is red-shifted with respect to S1 state of water monomer. For higher excitations, near vertical ionization energy (11 eV), quasi-free electrons emerge, in agreement with the conduction band electron picture. Furthermore, the occurring red and blue shift of the excited states are independent of the coupling of resonant and anti-resonant contributions to the spectrum.
A magnetically actuated cellular strain assessment tool for quantitative analysis of strain induced cellular reorientation and actin alignment
Authors: Khademolhosseini F. , Liu C.-C. , Lim C. J. , Chiao M.
Published: August 2016

Commercially available cell strain tools, such as pneumatically actuated elastomer substrates, require special culture plates, pumps, and incubator setups. In this work, we present a magnetically actuated cellular strain assessment tool (MACSAT) that can be implemented using off-the-shelf components and conventional incubators. We determine the strain field on the MACSAT elastomer substrate using numerical models and experimental measurements and show that a specific region of the elastomer substrate undergoes a quasi-uniaxial 2D stretch, and that cells confined to this region of the MACSAT elastomer substrate undergo tensile, compressive, or zero axial strain depending on their angle of orientation. Using the MACSAT to apply cyclic strain on endothelial cells, we demonstrate that actin filaments within the cells reorient away from the stretching direction, towards the directions of minimum axial strain. We show that the final actin orientation angles in strained cells are spread over a region of compressive axial strain, confirming previous findings on the existence of a varied pre-tension in the actin filaments of the cytoskeleton. We also demonstrate that strained cells exhibit distinctly different values of actin alignment coherency compared to unstrained cells and therefore propose that this parameter, i.e., the coherency of actin alignment, can be used as a new readout to determine the occurrence/extent of actin alignment in cell strain experiments. The tools and methods demonstrated in this study are simple and accessible and can be easily replicated by other researchers to study the strain response of other adherent cells.
Direct numerical simulation of a particle attachment to an immersed bubble
Authors: Lecrivain Gregory , Yamamoto Ryoichi , Hampel Uwe , Taniguchi Takashi
Published: August 2016

A numerical extension of the “smooth profile method” is presently suggested to simulate the attachment of a colloidal particle to the surface of an immersed bubble. In this approach, the two fluid-particle boundaries and the fluidic boundary are replaced with diffuse interfaces. The method is tested under various capillary numbers. Upon attachment to a stable bubble, it is found that the method is capable of reproducing the three microprocesses associated with the particle attachment. The change in the trajectory as the particle approaches the fluidic interface, the collision process, and the sliding down the bubble surface are all captured. Potential application of the present method shows great promise in the field of froth flotation, where the capture of hydrophobic particles by rising bubbles is of primary importance.
Propagation characteristics of dust–acoustic waves in presence of a floating cylindrical object in the DC discharge plasma
Authors: Choudhary Mangilal , Mukherjee S. , Bandyopadhyay P.
Published: August 2016

The experimental observation of the self–excited dust acoustic waves (DAWs) and its propagation characteristics in the absence and presence of a floating cylindrical object is investigated. The experiments are carried out in a direct current (DC) glow discharge dusty plasma in a background of argon gas. Dust particles are found levitated at the interface of plasma and cathode sheath region. The DAWs are spontaneously excited in the dust medium and found to propagate in the direction of ion drift (along the gravity) above a threshold discharge current at low pressure. Excitation of such a low frequency wave is a result of the ion–dust streaming instability in the dust cloud. Characteristics of the propagating dust acoustic wave get modified in the presence of a floating cylindrical object of radius larger than that of the dust Debye length. Instead of propagation in the vertical direction, the DAWs are found to propagate obliquely in the presence of the floating object (kept either vertically or horizontally). In addition, a horizontally aligned floating object forms a wave structure in the cone shaped dust cloud in the sheath region. Such changes in the propagation characteristics of DAWs are explained on the basis of modified potential (or electric field) distribution, which is a consequence of coupling of sheaths formed around the cylindrical object and the cathode.
The influence of the nitrogen admixture on the evolution of a deuterium pinch column
Authors: Kubes P. , Paduch M. , Cikhardtova B. , Cikhardt J. , Klir D. , Kravarik J. , Rezac K. , Kortanek J. , Zielinska E. , Sadowski M. J. , Tomaszewski K.
Published: August 2016

The application of a mixture of nitrogen and deuterium for the gas-puffing along the anode axis in deuterium plasma-focus discharges, as carried out at megaampere-level currents, enabled observations of the filamentary structure, and the decrease in the transformation velocity of the plasma column to be performed. It made possible to investigate the instability evolution during the production of hard X-rays and fast neutrons in more detail. The constriction of a plasma column transforms itself during the final phase of the compression into one or more small dense plasmoid-like structures which are separated by narrow necks. During the next phase, these structures start to decay by an expansion, in which a part of the plasma volume maintains its compactness. This evolution is explained by an increase and later decrease in the internal poloidal current component by reconnections of the associated magnetic lines, which are responsible for the acceleration of electron and ion beams.
Random regression model with heterogeneous residual variance reduces polynomial order fitted for permanent environmental effect but does not affect genetic parameters for milk production in Sahiwal cattle
Authors: Prakash V. , Gupta A. K. , Gupta A. , Gandhi R. S. , Singh A. , Chakravarty A. K.
Published: August 2016

The random regression test-day models can accelerate the genetic improvement of Sahiwal cattle as test-day milk yield models offer a faster, accurate and economical approach of genetic evaluation. First three lactation monthly test-day records of Sahiwal cows calved between 1961 and 2012 at ICAR-National Dairy Research Institute, Karnal were used to fit random regression model (RRM) with various order of legendre polynomial, and a constant (RRM-HOM) or heterogeneous residual variance (RRM-HET). For both RRM-HOM and RRM-HET third order legendre polynomial for modelling additive genetic effects were found best. There was reduction in order of fit for modelling permanent environmental effects due to assumption of heterogeneous residual variance, as legendre polynomial of sixth order for RRM-HOM and fourth or fifth order for RRM-HET was found to be best, for modelling the permanent environmental effect. First two eigenvalues of additive genetic random regression coefficient matrix explained more than 99% of the additive genetic variation, whereas four eigenvalues explained ~98% of the permanent environment variations. First eigenfunction from both the models did not show any large change along lactation, suggesting most variation can be explained by genes that act in same way during lactation. The heritability estimates were generally low but moderate for some test-day milk yields, and it ranged from 0.007 to 0.088 for first, 0.044 to 0.279 for second, and 0.089 to 0.129 for third lactation from RRM-HOM. The values of genetic correlation between test-day milk yields ranged from 0.06 to 0.99 for first, 0.77 to 0.99 for second, and 0.07 to 0.99 for third lactation, from RRM-HOM. The value of permanent environment correlation ranged from 0.30 to 0.98 for first, 0.07 to 0.99 for second, and 0.16 to 0.98 for third lactation. The genetic correlations between two adjacent test-days were high (≥0.90). RRM-HET also gave similar heritability and correlation estimates. The rank correlation between sire breeding values for first, second, and third lactation, estimated using two models were 0.98, 1.00, and 0.99, respectively, indicating there was no difference in the ranking of animals using two models. Thus the random regression model with lower order of polynomial for modelling additive genetic effect and higher order polynomial for modelling animal permanent environmental effect was found suitable for genetic evaluation and both RRM-HOM and RRM-HET can be used for modelling test-day milk yield and breeding value prediction in Sahiwal cattle.
Homogeneous oxidation of SbIII by aqueous O2: the effect of ionic strength, Pb2+ and EDTA
Authors: Ilgen A. G. , Trainor T. P.
Published: August 2016

Environmental contextWhy does antimony become mobile faster in shooting range soils than in laboratory settings? We used controlled experiments and found that increased salinity and the presence of lead (which occurs with antimony at shooting ranges because they are both used in bullets) accelerate the change of antimony to a form that moves more easily through the watershed. This work helps explain the behaviour of this important pollutant – antimony – in the environment. AbstractAntimony (Sb) is a recognised contaminant of concern. The oxidation state of antimony controls its mobility in soil and aqueous environments. The predominance of SbV (as compared with SbIII) in shooting range soils and outflows downstream from stibnite deposits indicates the fast oxidation of SbIII to SbV. To better understand chemical controls on SbIII oxidation to SbV, we performed batch experiments, testing the effect of ionic strength, the presence of a complexing agent—the disodium salt of EDTA (Na2EDTA), and the addition of lead (Pb2+), on the apparent oxidation rate of SbIII to SbV. We also tested whether aqueous FeII reduces SbV to SbIII. We found that the rate of SbIII oxidation increased with increasing ionic strength. We proposed that the reactive species is Sb(OH)2+. The rate of SbIII oxidation was also increased owing to the catalytic effect of Pb2+. The complexation by EDTA decreased the rate of SbIII oxidation to SbV; however, the catalytic effect of Pb2+ was also evident in the systems with EDTA. Although thermodynamically favourable, the reduction of SbV by FeII was not observed in our samples reacted for up to 2 months. The results further explain the absence of SbIII in the shooting range soils, where metallic bullets, containing lead and antimony, undergo oxidation. The potential chemical factors contributing to the fast oxidation observed in the field include the presence of high concentrations of Pb2+, which catalyses the oxidation of SbIII to SbV, and potentially high ionic strength of the soil pore waters.
Microtubule–microtubule sliding by kinesin-1 is essential for normal cytoplasmic streaming in
Drosophila
oocytes
Authors: Lu Wen , Winding Michael , Lakonishok Margot , Wildonger Jill , Gelfand Vladimir I.
Published: August 2016

Significance

Generation of mechanical forces by molecular motors is essential for development. Previously, we showed that the microtubule motor kinesin-1 generates forces by sliding microtubules against each other. Here, we show that microtubule sliding by kinesin-1 is important for normal oocyte cytoplasmic rotation, a process required for efficient localization of mRNAs and proteins during oogenesis. Using recently developed imaging technologies (Maple3 photoconversion and SunTag), we discover a previously uncharacterized population of extremely stable microtubules immobilized at the oocyte cortex and demonstrate that free microtubules move against cortically anchored microtubules, generating forces that contribute to cytoplasmic streaming. Because kinesin-1–based sliding is highly conserved from
Drosophila
to humans, we propose that microtubule sliding is also important for cellular force generation in higher organisms.
Coiled-coil destabilizing residues in the group A
Streptococcus
M1 protein are required for functional interaction
Authors: Stewart Chelsea M. , Buffalo Cosmo Z. , Valderrama J. Andrés , Henningham Anna , Cole Jason N. , Nizet Victor , Ghosh Partho
Published: August 2016

Significance

M proteins are major virulence factors of the widespread bacterial pathogen group A
Streptococcus
. The sequences of M proteins are antigenically variable, but have in common the tendency to form α-helical coiled coil structures. Paradoxically, these same sequences also contain a substantial number of amino acids that destabilize coiled coils. We present an explanation for this paradox in finding that destabilizing residues are essential for conformational dynamics in the M protein, and that these dynamics are required for interaction with human fibrinogen. Our work leads to the general conclusion that destabilizing residues are conserved through evolution in M proteins to enable functional interactions that are necessary for pathogenesis.
Faithfulness in translation of children’s literature
Authors: Kwok Virginia
Published: August 2016

Faithfulness as a principle of translation has been upheld for a long time despite many debates among scholars in the field. In the context of translating children’s literature, this poses further challenges and recent studies have yet to reach a conclusion (Epstein 2012; Nikolajeva 2011; Henitiuk 2011; Kruger 2011; Emery 2004; Dai 2001; Hervey 1997). In this article, from the sociological perspective, I shall discuss this issue by examining Klingberg (1986)’s approach of being faithful to the source text and Oittinen (1993)’s strategy of being faithful to the readers respectively. A study of Chinese translations of The Adventures of Huckleberry Finn for children readers will be looked at. Methods of dialogical approach: purification, simplification, rewording and modernization will be compared with equivalence method to find out which one offers a better reader reception. I argued that having an orientation and purpose of translation with a dialogical view will benefit readers more than simply adhering to the original without deviation at linguistic level. The reasons are that the target text will be more comprehensible for children readers’ stage of cognitive and psychological development, life experience, knowledge, cultural tolerance and linguistic development in reading gems of foreign literature in translation.
Interjectional issues in translation
Authors: Masiola Rosanna
Published: August 2016

This paper is trans-cultural approach to the analysis of interjectional and translational issues. ‘Interjection’ is here intended as an umbrella term extended to a range of emotional utterances along a continuum of primary exclamatory remarks (oh, ah), expletives, greetings, and blessings Interjections, however, may feature either as culture-specific items or be universal and international. The present corpus includes a thematic-based selection including written literature, drama, film adaptation, cartoons and sacred texts. The framework of analysis is thematization within a cross-cultural interface.
Acute Effects of Synthetic Cannabinoids: Update 2015
Authors: Tournebize Juliana , Gibaja Valérie , Kahn Jean-Pierre
Published: August 2016

Background

Cannabis is the most widely used illicit drug in the United States and Europe. In recent years, a range of new substances with cannabis-like effects—known as synthetic cannabinoids (SCs)—have suddenly burst on the drug scene. However, there is limited information about the clinical hazards linked to the use of these emerging substances. This review summarizes the literature to date relating the health effects of SCs. Method: A systematic literature review of original case studies was performed using PubMed and Web of Science (January 1980–July 2015). Only articles in which a drug screening was reported were included in this review.

Results

Forty-six articles meeting the inclusion criteria were included in this review, reporting data on 114 patients who went to hospital emergency departments after exposure to SCs. The majority of patients were adolescent or young adult males (14–25 years; 24.5 ± 10.1 years). The most common route of administration was smoking. The SCs most involved were John William Huffman (JWH) derivatives, followed by XRL-11, ADB-PINACA, AM-2201, MAM-2201, and 5F-PB-22. This analysis showed that the use of these substances may cause minor and moderate side effects similar to those of cannabis intoxication, including tachycardia, nausea, somnolence, hallucinations, paranoia, xerostomia, and injected conjunctivae among others. However, atypical cannabis intoxication effects and worse complications (such as renal injuries, aggressiveness, cerebral ischemia, myocardial infarction, etc.) were also observed, which led to a significant morbidity were also observed. Some SCs were highlighted as being involved in 24 cases of deaths.

Conclusions

In this review, the nature and frequency of the signs and symptoms of SC poisoning were estimated in order to inform health professionals about the health risks of these new and emerging substances.
Reliability of the two-point measurement of the spatial correlation length from Gaussian-shaped fluctuating signals in fusion-grade plasmas
Authors: Kim Jaewook , Nam Y.U. , Lampert M. , Ghim Y.-C.
Published: August 2016

A statistical method for the estimation of the spatial correlation lengths of Gaussian-shaped fluctuating signals with two measurement points is examined to quantitatively evaluate its reliability (variance) and accuracy (bias error). The standard deviation of the correlation value is analytically derived for randomly distributed Gaussian shaped fluctuations satisfying stationarity and homogeneity, allowing us to evaluate, as a function of fluctuation-to-noise ratios, the sizes of averaging time windows and the ratios of the distance between the two measurement points to the true correlation length, and the goodness of the two-point measurement for estimating the spatial correlation length. Analytic results are confirmed with numerically generated synthetic data and real experimental data obtained with the KSTAR beam emission spectroscopy diagnostic. Our results can be applied to Gaussian-shaped fluctuating signals where a correlation length must be measured with only two measurement points.
Contrasting patterns of genetic variation in core and peripheral populations
of highly outcrossing and wind pollinated forest tree species
Authors: Wójkiewicz Błażej , Litkowiec Monika , Wachowiak Witold
Published: August 2016

Gene flow tends to have a homogenising effect on a species’ background genetic variation over large geographical areas. However, it is usually unknown to what extent the genetic structure of populations is influenced by gene exchange between core and peripheral populations that may represent stands of different evolutionary and demographic history. In this study, we looked at the patterns of population differentiation in Scots pine—a highly outcrossing and wind pollinated conifer species that forms large ecosystems of great ecological and economic importance in Europe and Asia. A set of 13 polymorphic nuclear microsatellite loci was analysed to infer the genetic relationships among 24 populations (676 individuals) from Europe and Asia Minor. The study included specimens from the primary continuous range and from isolated, marginal stands that are considered to be autochthonous populations representative of the species’ putative refugial areas. Despite their presumably different histories, a similar level of genetic variation and no evidence of a population bottleneck was found across the populations. Differentiation among populations was relatively low (average F  ST  = 0.035); however, the population structure was not homogenous, which was clearly evident from the allelic frequency spectra and Bayesian assignment analysis. Significant differentiation over short geographical distances was observed between isolated populations within the Iberian and Anatolian Peninsulas (Asia Minor), which contrasted with the absence of genetic differentiation observed between distant populations e.g., between central and northern Europe. The analysed populations were assigned to several groups that corresponded to the geographical regions of their occurrence. These results will be useful in genetics studies in Scots pine that aim to link nucleotide and phenotypic variation across the species distribution range and for development of sustainable breeding and management programs.
A two-part mixed-effects model for analyzing longitudinal microbiome compositional data
Authors: Chen Eric Z. , Li Hongzhe
Published: August 2016

Motivation: The human microbial communities are associated with many human diseases such as obesity, diabetes and inflammatory bowel disease. High-throughput sequencing technology has been widely used to quantify the microbial composition in order to understand its impacts on human health. Longitudinal measurements of microbial communities are commonly obtained in many microbiome studies. A key question in such microbiome studies is to identify the microbes that are associated with clinical outcomes or environmental factors. However, microbiome compositional data are highly skewed, bounded in [0,1), and often sparse with many zeros. In addition, the observations from repeated measures in longitudinal studies are correlated. A method that takes into account these features is needed for association analysis in longitudinal microbiome data.

Results: In this paper, we propose a two-part zero-inflated Beta regression model with random effects (ZIBR) for testing the association between microbial abundance and clinical covariates for longitudinal microbiome data. The model includes a logistic regression component to model presence/absence of a microbe in the samples and a Beta regression component to model non-zero microbial abundance, where each component includes a random effect to account for the correlations among the repeated measurements on the same subject. Both simulation studies and the application to real microbiome data have shown that ZIBR model outperformed the previously used methods. The method provides a useful tool for identifying the relevant taxa based on longitudinal or repeated measures in microbiome research.

Availability and Implementation:  https://github.com/chvlyl/ZIBR

Contact:  hongzhe@upenn.edu
Jack Lindsay's Alienation
Authors: Harker Ben
Published: August 2016

Posterity has not been kind to the Australian-born polymath Jack Lindsay (1900–1990), a self-confessed ‘odd man out’ who published over one hundred and seventy books across a range of genres. This article asks what Lindsay wrote, why it has been forgotten and why we should care. It restores to view Lindsay's politico-cultural trajectory from his conversion to Marxism in 1936. It argues that Lindsay's searching and sceptical Marxism was a source of his prolific creativity and that he evolved a distinct and sometimes eccentric Marxist theoretical framework – a system with the concept of alienation at its core – within which his individual works are most legible. It argues that Lindsay's theoretical Marxism is not reducible to that of ‘British Communism’ or the ‘Old Left’, but exceeded and was mostly in tension with the Marxism of his party and its Soviet models, despite his political affiliation. It explains that Lindsay's oeuvre sank gradually from mainstream cultural visibility through the Cold War and that his conflicted but ongoing CP and Soviet-facing alignment alienated him from an emerging New Left with which he actually shared much theoretical ground. Estranged from his own party and largely dismissed by the New Left, his project disappeared through the cracks that opened during the traumatic realignments of the British Left in the post-1956 decade and remains largely absent from accounts of Marxist thought in Britain today. But though in many ways flawed, Lindsay's central project – tracing the processes of alienation through social formations, sifting human history for moments of resistance to that alienation, and attempting to prefigure a society in which values of creative production and communication are generalized across society as a whole – speaks loudly to ever-sharpening problems and deserves revisiting now.
Can less be more? Effects of reduced frequency of surveys and stock assessments
Authors: Zimmermann Fabian , Enberg Katja
Published: August 2016

Uncertain and inaccurate estimates are a prevailing problem in stock assessment, despite increasingly sophisticated estimation methods and substantial usage of scientific and financial resources. Annual scientific surveys and assessment group meetings require frequent use of research vessels and skilled research staff and are, therefore, particularly costly. This data- and work-intensive approach is often considered paramount for reliable stock estimates and risk management. However, it remains an open question whether the benefits of increasing assessment effort outweigh its marginal costs, or whether the potential impacts of investing less in assessments could generate net benefits. In this study, we explore how different scenarios of reduced survey and assessment frequencies affect estimated stock biomass, predicted catch, and uncertainty. Data of two Northeast Atlantic stocks, blue whiting (Micromesistius poutassou) and Norwegian spring-spawning herring (Clupea harengus), and a widely applied stock assessment model are used to compare the impacts of removing surveys and/or annual assessments. The results show that lower survey and/or assessment frequencies tend to result in deviating estimates of spawning-stock biomass and catch and larger confidence intervals, the observed differences being, however, mostly small. While scenarios without a survey datapoint in the assessment year generally produced the largest deviations in estimates, biannual surveys in general did not affect assessment performance substantially. This indicates that a reduced frequency of surveys and assessments could be an acceptable measure to reduce assessment costs and increase the efficiency of fisheries management, particularly when accompanied by thorough management strategy evaluations and risk assessments.
Beyond Neo-Liberalism: The Trade Union Act 2016 and the Authoritarian State
Authors: Bogg Alan
Published: August 2016

The Trade Union Act 2016 marks a historically significant realignment in the ideological politics of trade union regulation. It represents a more authoritarian style of Conservative ideology and statecraft in the sphere of trade union regulation, and this is reflected in three main characteristics: (i) a repressive strategy of de-democratisation, undermining political resistance and stifling dissent in the democratic process; (ii) heavier reliance on direct State coercion, including the techniques of criminalisation, alongside the empowerment of employers to use civil law remedies against trade unions and workers in industrial action situations; and (iii) the elevation of social order in the regulation of strike activity. The article then considers the likely prospects of the legislation, and the wider ideological significance of this turn towards authoritarianism for Conservative political thought ‘beyond neo-liberalism’.
Rice putative methyltransferase gene OsTSD2 is required for root development involving pectin modification
Authors: Qu Lianghuan , Wu Chunyan , Zhang Fei , Wu Yangyang , Fang Chuanying , Jin Cheng , Liu Xianqing , Luo Jie
Published: August 2016

Pectin synthesis and modification are vital for plant development, although the underlying mechanisms are still not well understood. Here, we report the functional characterization of the OsTSD2 gene, which encodes a putative methyltransferase in rice. All three independent T-DNA insertion lines of OsTSD2 displayed dwarf phenotypes and serial alterations in different zones of the root. These alterations included abnormal cellular adhesion and schizogenous aerenchyma formation in the meristematic zone, inhibited root elongation in the elongation zone, and higher lateral root density in the mature zone. Immunofluorescence (with LM19) and Ruthenium Red staining of the roots showed that unesterified homogalacturonan (HG) was increased in Ostsd2 mutants. Biochemical analysis of cell wall pectin polysaccharides revealed that both the monosaccharide composition and the uronic acid content were decreased in Ostsd2 mutants. Increased endogenous ABA content and opposite roles performed by ABA and IAA in regulating cellular adhesion in the Ostsd2 mutants suggested that OsTSD2 is required for root development in rice through a pathway involving pectin synthesis/modification. A hypothesis to explain the relationship among OsTSD2 , pectin methylesterification, and root development is proposed, based on pectin’s function in regional cell extension/division in a zone-dependent manner.
ABA is required for the accumulation of APX1 and MBF1c during a combination of water deficit and heat stress
Authors: Zandalinas Sara I. , Balfagón Damián , Arbona Vicent , Gómez-Cadenas Aurelio , Inupakutika Madhuri A. , Mittler Ron
Published: August 2016

Abscisic acid (ABA) plays a key role in plant acclimation to abiotic stress. Although recent studies suggested that ABA could also be important for plant acclimation to a combination of abiotic stresses, its role in this response is currently unknown. Here we studied the response of mutants impaired in ABA signalling ( abi1-1 ) and biosynthesis ( aba1-1 ) to a combination of water deficit and heat stress. Both mutants displayed reduced growth, biomass, and survival when subjected to stress combination. Focusing on abi1-1 , we found that although its stomata had an impaired response to water deficit, remaining significantly more open than wild type, its stomatal aperture was surprisingly reduced when subjected to the stress combination. Stomatal closure during stress combination in abi1-1 was accompanied by higher levels of H 2 O 2 in leaves, suggesting that H 2 O 2 might play a role in this response. In contrast to the almost wild-type stomatal closure phenotype of abi1-1 during stress combination, the accumulation of ascorbate peroxidase 1 and multiprotein bridging factor 1c proteins, required for acclimation to a combination of water deficit and heat stress, was significantly reduced in abi1-1 . Our findings reveal a key function for ABA in regulating the accumulation of essential proteins during a combination of water deficit and heat stress.
Dimensions and Role-Specific Mediators of Surrogate Trust in the ICU
Authors: Hutchison Paul J. , McLaughlin Katie , Corbridge Tom , Michelson Kelly N. , Emanuel Linda , Sporn Peter H. S. , Crowley-Matoka Megan
Published: August 2016

Objective:

In the ICU, discussions between clinicians and surrogate decision makers are often accompanied by conflict about a patient’s prognosis or care plan. Trust plays a role in limiting conflict, but little is known about the determinants of trust in the ICU. We sought to identify the dimensions of trust and clinician behaviors conducive to trust formation in the ICU.

Design:

Prospective qualitative study.

Setting:

Medical ICU of a major urban university hospital.

Subjects:

Surrogate decision makers of intubated, mechanically ventilated patients in the medical ICU.

Measurements and Main Results:

Semistructured interviews focused on surrogates’ general experiences in the ICU and on their trust in the clinicians caring for the patient. Interviews were audio-recorded, transcribed verbatim, and coded by two reviewers. Constant comparison was used to identify themes pertaining to trust. Thirty surrogate interviews revealed five dimensions of trust in ICU clinicians: technical competence, communication, honesty, benevolence, and interpersonal skills. Most surrogates emphasized the role of nurses in trust formation, frequently citing their technical competence. Trust in physicians was most commonly related to honesty and the quality of their communication with surrogates.

Conclusions:

Interventions to improve trust in the ICU should be role-specific, since surrogate expectations are different for physicians and nurses with regard to behaviors relevant to trust. Further research is needed to confirm our findings and explore the impact of trust modification on clinician-family conflict.
Biomechanics of the Levator Aponeurosis
Authors: Repp Daniel J. , Rubinstein Tal J. , Herreid Peter A. , Sires Bryan S.
Published: August 2016

Purpose:

To investigate biomechanical properties of the levator aponeurosis.

Methods:

Patients undergoing external levator resection for primary or revision correction of acquired ptosis were analyzed as primary and revision groups. Immediately postoperatively, the resected segments of the levator aponeurosis were stressed by adding sequential masses to the tissue. Specimen length was recorded at each stress level. Stress–strain diagrams were used to summarize how the tissue elongated in response to the external forces, because these diagrams correct for differences in specimen size. Representative specimens were analyzed histologically.

Results:

Twenty-two specimens from 14 patients in the primary group and 10 specimens from 7 patients in the revision group met inclusion criteria. In the primary group, the mean age was 66 years; 8 patients were women. In the revision group, the mean age was 69 years; 6 patients were women. Levator aponeurosis specimens in both the primary and revision group demonstrated proportional increases in length with increasing stress, demonstrating that the levator aponeurosis is extensile. Given the same amount of stress, the levator aponeurosis from primary specimens elongated more than revision specimens. Histologically, revision specimens exhibited increased collagen and haphazard, tangled elastin fibers.

Conclusions:

The levator aponeurosis obtained during surgical correction of acquired ptosis elongates in response to nominal external forces. This biomechanical property is important because the length of the aponeurosis may vary intraoperatively if variable forces are applied to the eyelid. This property might be related to connective tissue architecture and, specifically, fibrosis. Surgeons performing levator aponeurosis resection should be mindful to maintain a consistent amount of force on the levator aponeurosis when performing the resection to maximize intercase consistency.
The effects of 405 nm light on bacterial membrane integrity determined by salt and bile tolerance assays, leakage of UV-absorbing material and SYTOX green labelling
Authors: McKenzie Karen , Maclean Michelle , Grant M. Helen , Ramakrishnan Praveen , MacGregor Scott J. , Anderson John G.
Published: August 2016

Bacterial inactivation by 405 nm light is accredited to the photoexcitation of intracellular porphyrin molecules resulting in energy transfer and the generation of reactive oxygen species that impart cellular oxidative damage. The specific mechanism of cellular damage, however, is not fully understood. Previous work has suggested that destruction of nucleic acids may be responsible for inactivation; however, microscopic imaging has suggested membrane damage as a major constituent of cellular inactivation. This study investigates the membrane integrity of Escherichia coli and Staphylococcus aureus exposed to 405 nm light. Results indicated membrane damage to both species, with loss of salt and bile tolerance by S. aureus and E. coli, respectively, consistent with reduced membrane integrity. Increased nucleic acid release was also demonstrated in 405 nm light-exposed cells, with up to 50 % increase in DNA concentration into the extracellular media in the case of both organisms. SYTOX green fluorometric analysis, however, demonstrated contradictory results between the two test species. With E. coli, increasing permeation of SYTOX green was observed following increased exposure, with >500 % increase in fluorescence, whereas no increase was observed with S. aureus. Overall, this study has provided good evidence that 405 nm light exposure causes loss of bacterial membrane integrity in E. coli, but the results with S. aureus are more difficult to explain. Further work is required to gain greater understanding of the inactivation mechanism in different bacterial species, as there are likely to be other targets within the cell that are also impaired by the oxidative damage from photo-generated reactive oxygen species.
A FLIC motility assay reveals myosin-6 coordination limited by actin filament buckling
Authors: Krenc Agata K. , Rokicka Jagoda J. , Rock Ronald S.
Published: August 2016

Teams of myosin motors carry out intracellular transport and contract the actin cytoskeleton. To fully understand the behavior of multi-myosin ensembles we need to know the properties of individual myosins and the mode of interaction between them. Current models of the interactions within the myosin complex treat the actin filament as a stiff rod, not contributing to the regulation of collective myosin dynamics. Here, we present data suggesting that force transduction through the actin filament is an important element of interaction within myosin-6 ensembles in vitro. Multiple myosin-6s coordinate their steps if they are separated by a short (and therefore high-force bearing) segment of actin. The measurements were performed using Fluorescence Interference Contrast Microscopy (FLIC) to measure small changes in the height of fluorescently labeled actin. Using FLIC, we assign the positions of myosins in a gliding filament assay geometry and measure their attachment time to actin. We also identify actin segments that are buckled or under tension. We show that myosin-6 holds actin about 10 nm above the surface. However, due to asynchronous myosin stepping, frequent buckles up to about 60 nm high appear. The buckle lifetime decreases as the distance between the myosin-6s is reduced, a sign of inter-motor coordination. Our data are consistent with coordinated stepping of closely spaced myosins, but uncoordinated motility with widely separated myosins where buckles can form. These features would be expected to operate on myosins in the cell, where motor spacing may vary considerably depending on the target organelle.

SIGNIFICANCE STATEMENT

Myosins are molecular motors that carry out intracellular transport. Interactions between the myosins are crucial for understanding their function. Using Fluorescence Interference Contrast (FLIC) microscopy we characterized the interaction between multiple myosin-6 motors immobilized to the surface of a slide and pulling the same actin filament. Our results point towards coordination of myosin steps as a mechanism governing the behavior of a multi-myosin complex. We also demonstrated the unique application of FLIC microscopy for highly parallel identification and measurement of single myosin motors in a gliding filament format. These features of FLIC enable a robust study of collective myosin dynamics.