bluuebunny/crossref_metadata_2025 huggingface dataset:
Three-dimensional time-domain scattering of waves in the marginal ice zone
Authors: Meylan M. H. , Bennetts L. G.
Published: August 2018

Three-dimensional scattering of ocean surface waves in the marginal ice zone (MIZ) is determined in the time domain. The solution is found using spectral analysis of the linear operator for the Boltzmann equation. The method to calculate the scattering kernel that arises in the Boltzmann model from the single-floe solution is also presented along with new identities for the far-field scattering, which can be used to validate the single-floe solution. The spectrum of the operator is computed, and it is shown to have a universal structure under a special non-dimensionalization. This universal structure implies that under a scaling wave scattering in the MIZ has similar properties for a large range of ice types and wave periods. A scattering theory solution using fast Fourier transforms is given to find the solution for directional incident wave packets. A numerical solution method is also given using the split-step method and this is used to validate the spectral solution. Numerical calculations of the evolution of a typical wave field are presented.

This article is part of the theme issue ‘Modelling of sea-ice phenomena’.
Friction of sea ice
Authors: Schulson Erland M.
Published: August 2018

Static and kinetic friction play a fundamental role in sea-ice mechanics. The coefficient of static friction increases with hold time under normal load and is modelled in terms of creep and fracture of asperities in contact. The coefficient of kinetic friction exhibits velocity strengthening at lower speeds and velocity weakening at intermediate speeds. Strengthening is modelled in terms of asperity creep and hardness; weakening is modelled in terms of a progressive increase in the true area of contact wetted by meltwater produced through frictional heating. The concept is introduced of contact size distribution in which the smallest contacts melt first, leading to the onset of weakening; the largest melt last, leading to a third regime of kinetic friction and again to strengthening where hydrodynamics governs. Neither the static nor the kinetic coefficient is significantly affected by the presence of sea water. The paper closes with a few implications for sea-ice mechanics. The paper is based largely upon a critical review of the literature, but includes a more quantitative, physics-based analysis of velocity strengthening and a new analysis of velocity weakening that incorporates parameters that describe the (proposed) fractal character of the sliding interface.

This article is part of the theme issue ‘Modelling of sea-ice phenomena’.
Ice edge failure process and modelling ice pressure
Authors: Riska Kaj
Published: August 2018

Ice action on ships and offshore structures is commonly determined by calculating the contact ice pressure. The aim of this paper is to describe the empirical background for determining the ice pressure. This review article describes six different test series where ice edge indentation and contact ice pressure have been investigated. These test series are ice pressure measurements onboard IB Sisu in the Baltic in 1977, pendulum tests carried out at Arctec in Ottawa, Canada, in 1979, laboratory and full scale ice crushing tests at WARC in 1988 and onboard IB Sampo 1989, medium scale indentation tests on Hobson's Choice Ice Island 1990, ice crushing tests at NRC, Ottawa 1992 and the JOIA tests in Hokkaido 1996–1999. These tests were selected as at each series a new phenomenon was observed. The aim of the paper is to introduce the main features for ice–structure contact empirically through the description of tests. The paper is concluded with a short description of the existing models for ice pressure, especially to gain an insight and highlight the main observations in each test series and how the models for ice pressure have developed based on the observations.

This article is part of the theme issue ‘Modelling of sea-ice phenomena’.
Thermo-mechanical loads of confined sea ice on structures
Authors: Marchenko Aleksey
Published: August 2018

Records of the ice pressures on the joggle skirt of the coal quay in Spitsbergen were performed over winter seasons in 2013 and 2015. The ice thickness below the quay was above 2 m. Ice temperature over the ice thickness and water pressure at the sea bed were measured synchronously. It was discovered that sea water migrates through the ice confined inside the joggle skirt under the influence of tidal changes of the water pressure below the ice. It leads to the formation of floods on the ice surface during high tide. The ice surface becomes dry during low tide. Ice temperature and ice pressure on the joggle skirt are changed according to the semidiurnal cycle. Spectral analysis and correlation analysis are performed to analyse the loads caused by thermal expansion of the ice. A thermo-mechanical model of ice based on elastic-plastic rheology with thermal effect is used in numerical simulations of the observed phenomena. Numerical simulations are performed with finite element software.

This article is part of the theme issue ‘Modelling of sea-ice phenomena’.
Solitary flexural–gravity waves in three dimensions
Authors: Trichtchenko Olga , Părău Emilian I. , Vanden-Broeck Jean-Marc , Milewski Paul
Published: August 2018

The focus of this work is on three-dimensional nonlinear flexural–gravity waves, propagating at the interface between a fluid and an ice sheet. The ice sheet is modelled using the special Cosserat theory of hyperelastic shells satisfying Kirchhoff's hypothesis, presented in (Plotnikov & Toland. 2011
Phil. Trans. R. Soc. A
369
, 2942–2956 (
doi:10.1098/rsta.2011.0104
)). The fluid is assumed inviscid and incompressible, and the flow irrotational. A numerical method based on boundary integral equation techniques is used to compute solitary waves and forced waves to Euler's equations.

This article is part of the theme issue ‘Modelling of sea-ice phenomena’.
Tensile fracture of a single crack in first-year sea ice
Authors: Dempsey J. P. , Cole D. M. , Wang S.
Published: August 2018

The break-up of sea ice in the Arctic and Antarctic has been studied during three field trips in the spring of 1993 at Resolute, NWT, and the fall of 2001 and 2004 on McMurdo Sound via
in situ
cyclic loading and fracture experiments. In this paper, the back-calculated fracture information necessary to the specification of an accurate viscoelastic fictitious (cohesive) crack model is presented. In particular, the changing shape of the stress separation curve with varying conditions and loading scenarios is revealed.

This article is part of the theme issue ‘Modelling of sea-ice phenomena’.
Interaction of flexural-gravity waves in ice cover with vertical walls
Authors: Korobkin A. A. , Malenica S. , Khabakhpasheva T.
Published: August 2018

Diffraction of flexural-gravity waves in an ice cover by a bottom mounted structure with vertical walls is studied. The problem is solved by using the so-called vertical modes corresponding to the roots of the dispersion relation for flexural-gravity waves. These modes reduce the original three-dimensional problem to a set of two-dimensional diffraction problems with non-homogeneous boundary conditions on the rigid walls. Two unknown functions presenting in the boundary conditions for each mode are determined using the conditions at the contact line between the ice cover and the vertical walls. The clamped conditions at the contact line, where the ice cover is frozen to the wall, are considered in this study. The solution of the problem is obtained for a single vertical circular cylinder frozen in the ice cover. A general approach to the problem for vertical cylinders of any shapes is presented. The diffraction problems with vertical walls extended to infinity are discussed.

This article is part of the theme issue ‘Modelling of sea-ice phenomena’.
Stress and deformation characteristics of sea ice in a high-resolution, anisotropic sea ice model
Authors: Heorton H. D. B. S. , Feltham D. L. , Tsamados M.
Published: August 2018

The drift and deformation of sea ice floating on the polar oceans is caused by the applied wind and ocean currents. Over ocean basin length scales the internal stresses and boundary conditions of the sea ice pack result in observable deformation patterns. Cracks and leads can be observed in satellite images and within the velocity fields generated from floe tracking. In a climate sea ice model the deformation of sea ice over ocean basin length scales is modelled using a rheology that represents the relationship between stresses and deformation within the sea ice cover. Here we investigate the link between emergent deformation characteristics and the underlying internal sea ice stresses using the Los Alamos numerical sea ice climate model. We have developed an idealized square domain, focusing on the role of sea ice rheologies in producing deformation at spatial resolutions of up to 500 m. We use the elastic anisotropic plastic (EAP) and elastic viscous plastic (EVP) rheologies, comparing their stability, with the EAP rheology producing sharper deformation features than EVP at all space and time resolutions. Sea ice within the domain is forced by idealized winds, allowing for the emergence of five distinct deformation types. Two for a low confinement ratio: convergent and expansive stresses. Two about a critical confinement ratio: isotropic and anisotropic conditions. One for a high confinement ratio and isotropic sea ice. Using the EAP rheology and through the modification of initial conditions and forcing, we show the emergence of the power law of strain rate, in accordance with observations.

This article is part of the theme issue ‘Modelling of sea-ice phenomena’.
Guillain Barré syndrome associated with bladder instillation of Bacille Calmette Guérin (BCG)
Authors: Webb Karmel , Venkatesan Pradhib
Published: August 2018

Introduction. Guillain Barré Syndrome (GBS) has rarely been associated with tuberculosis and has been previously reported after Bacille Calmette Guérin (BCG) vaccination, but we report an association of GBS with intra-vesical BCG instillations followed by the clinical picture of disseminated BCGosis.

Case presentation. A 68-year-old man with bladder carcinoma had a transurethral tumour resection followed by repeated BCG instillations. Catheterization for his eighth dose was traumatic, causing frank haematuria. Ten days later he presented with fevers, myalgia and dyspnoea. Chest X-ray on admission showed micronodular shadowing and a computed tomography scan showed miliary changes in the lungs. Disseminated BCGosis infection was suspected and his symptoms did improve after starting rifamipicin, isoniazid and ethambutol. Over 2 weeks post-admission he developed an unsteady gait, reduced pin-prick sensation below both knees and fingertips, reduced proprioception in both toes and ankles, with absent reflexes in his lower limbs and diminished reflexes in his upper limbs. Nerve conduction studies showed a purely demyelinating sensori-motor peripheral neuropathy in upper and lower limbs, characteristic of GBS.

Conclusion. To our knowledge this is the first case report of GBS following bladder instillation of BCG. Given the millions of cases of tuberculosis and millions of doses of administered BCG, GBS must be a very rare adverse effect.
Proprioceptive Sonomyographic Control: A novel method of intuitive proportional control of multiple degrees of freedom for upper-extremity amputees
Authors: Dhawan Ananya S. , Mukherjee Biswarup , Patwardhan Shriniwas , Akhlaghi Nima , Levay Gyorgy , Holley Rahsaan , Joiner Wilsaan , Harris-Love Michelle , Sikdar Siddhartha
Published: August 2018

Technological advances in multi-articulated prosthetic hands have outpaced the methods available to amputees to intuitively control these devices. Amputees often cite difficulty of use as a key contributing factor for abandoning their prosthesis, creating a pressing need for improved control technology. A major challenge of traditional myoelectric control strategies using surface electromyography electrodes has been the difficulty in achieving intuitive and robust proportional control of multiple degrees of freedom. In this paper, we describe a new control method, proprioceptive sonomyographic control that overcomes several limitations of myoelectric control. In sonomyography, muscle mechanical deformation is sensed using ultrasound, as compared to electrical activation, and therefore the resulting control signals can directly control the position of the end effector. Compared to myoelectric control which controls the velocity of the end-effector device, sonomyographic control is more congruent with residual proprioception in the residual limb. We tested our approach with 5 upper-extremity amputees and able-bodied subjects using a virtual target achievement and holding task. Amputees and able-bodied participants demonstrated the ability to achieve positional control for 5 degrees of freedom with an hour of training. Our results demonstrate the potential of proprioceptive sonomyographic control for intuitive dexterous control of multiarticulated prostheses.
CryoEM reveals how the complement membrane attack complex ruptures lipid bilayers
Authors: Menny Anaïs , Serna Marina , Boyd Courtney M. , Gardner Scott , Joseph Agnel Praveen , Morgan B. Paul , Topf Maya , Brooks Nicholas J. , Bubeck Doryen
Published: August 2018

The membrane attack complex (MAC) is one of the immune system’s first responders. Complement proteins assemble on target membranes to form pores that lyse pathogens and impact tissue homeostasis of self-cells. How MAC disrupts the membrane barrier remains unclear. Here we use electron cryo-microscopy and flicker spectroscopy to show that MAC interacts with lipid bilayers in two distinct ways. Whereas C6 and C7 associate with the outer leaflet and reduce the energy for membrane bending, C8 and C9 traverse the bilayer increasing membrane rigidity. CryoEM reconstructions reveal plasticity of the MAC pore and demonstrate how C5b6 acts as a platform, directing assembly of a giant β-barrel whose structure is supported by a glycan scaffold. Our work provides a structural basis for understanding how β-pore forming proteins breach the membrane and reveals a mechanism for how MAC kills pathogens and regulates cell functions.
SureTypeSC - A Random Forest and Gaussian Mixture predictor of high confidence genotypes in single cell data
Authors: Vogel Ivan , Blanshard Robert C. , Hoffmann Eva R.
Published: August 2018

Motivation

Accurate genotyping of DNA from a single cell is required for applications such asde novomutation detection, linkage analysis and lineage tracing. However, achieving high precision genotyping in the single cell environment is challenging due to the errors caused by whole genome amplification. Two factors make genotyping from single cells using single nucleotide polymorphism (SNP) arrays challenging. The lack of a comprehensive single cell dataset with a reference genotype and the absence of genotyping tools specifically designed to detect noise from the whole genome amplification step. Algorithms designed for bulk DNA genotyping cause significant data loss when used for single cell applications.

Results

In this study, we have created a resource of 28.7 million SNPs, typed at high confidence from whole genome amplified DNA from single cells using the Illumina SNP bead array technology. The resource is generated from 104 single cells from two cell lines that are available from the Coriell repository. We used mother-father-proband (trio) information from multiple technical replicates of bulk DNA to establish a high quality reference genotype for the two cell lines on the SNP array. This enabled us to develop SureTypeSC - a two-stage machine learning algorithm that filters a substantial part of the noise, thereby retaining the majority of the high quality SNPs. SureTypeSC also provides a simple statistical output to show the confidence of a particular single cell genotype using Bayesian statistics.

Contact

eva@sund.ku.dk
A novel Versatile Peroxidase from Lentinus squarrosulus (MH172167)towards enhanced delignification and digestibility of crop residues
Authors: Aarthi R , Rao Ramya G , Thammaiah Vandana , Gopinath SM , Sridhar Manpal
Published: August 2018

Scarcity of quality feed is a major constraint concerning livestock productivity with recalcitrant lignin hindering utilization of crop residues as quality animal feed. Degradation of lignin in nature is contributed by white-rot fungi through their enriched ligninolytic system. Versatile Peroxidase plays a key role in ligninolysis through its capability to oxidize diverse class of aromatics without mediators. In this study, wild isolates of wood rotting fungi were screened for potential peroxidases oxidizing manganese and aromatic compounds. The strain identified asLentinus squarrosulus(TAMI004, BankIt2098576 MH172167) was monitored for enzyme activity in solid state and submerged fermentation.L. squarrosulusdemonstrated predominant Versatile Peroxidase activity amongst the screened wild isolates displaying hybrid characteristic of manganese oxidation and manganese independent reactions on aromatic compounds. The manganese oxidizing peroxidase activity evidenced in submerged fermentation was 12 IU/L whereas in solid state fermentation it was 131 IU/L. This ability to act through manganese mediated and independent reactions on phenolics reveals its biotechnological and industrial significance. Treatment of common crop residues with crude extract ofL. squarrosulusrich in Versatile Peroxidase obtained from both Solid state and submerged fermentations showed a decrease in their Neutral Detergent Fiber, Acid Detergent Fiber and Acid Detergent Lignin content showing biodegradation, substantiating the ligninolytic ability and more prominently increase in their digestibility. To the best of our knowledge, this is the first report describing Versatile Peroxidase fromLentinus squarrosuluswith potential to augment the ruminant digestibility of crop residues.

Importance

Versatile Peroxidase of White-rot fungi, a relatively less studied lignolytic enzyme, is very efficient in depolymerization of lignin macromolecule through its multivalent catalytic sites. Lignin degradation is very appealing from the application perspective as attack on lignin exposes the energy affluent polysaccharides for utilization in extensive biotechnological applications. Reports on relevance of Versatile Peroxidase for these purposes are still emerging, however the role of ligninolytic enzymes especially Versatile Peroxidase in enriching ruminant feed is yet unturned. Here, this work demonstrates the potential of Versatile Peroxidase from a novel speciesLentinus squarrosulusin delignification thereby upgrading the digestibility and nutritive value of crop residues. The observations validate the importance of the enzyme in improvement of crop residues for feeding ruminants in the current scenario where, livestock productivity is severely impacted by lack of quality feed and demand for alternate feed resources is intensifying.
Computational drug repositioning of bortezomib to reverse metastatic effect ofGALNT14in lung cancer
Authors: Kwon Ok-Seon , Lee Haeseung , Kong Hyeon-Joon , Park Ji Eun , Lee Wooin , Kang Seungmin , Kim Mirang , Kim Wankyu , Cha Hyuk-Jin
Published: August 2018

Although many molecular targets for cancer therapy have been discovered, they often show poor druggability, which is a major obstacle to develop targeted drugs. As an alternative route to drug discovery, we adopted anin silicodrug repositioning (in silicoDR) approach based on large-scale gene expression signatures, with the goal of identifying inhibitors of lung cancer metastasis. Our analysis of clinicogenomic data identified GALNT14, an enzyme involved in O-linked N-acetyl galactosamine glycosylation, as a putative driver of lung cancer metastasis leading to poor survival. To overcome the poor druggability of GALNT14, we leveraged Connectivity Map approach, anin silicoscreening for drugs that are likely to revert the metastatic expression patterns. It leads to identification of bortezomib (BTZ) as a potent metastatic inhibitor, bypassing direct inhibition of poorly druggable target, GALNT14. The anti-metastatic effect of BTZ was verifiedin vitroandin vivo. Notably, both BTZ treatment andGALNT14knockdown attenuated TGFβ-mediated gene expression and suppressed TGFβ-dependent metastatic genes, suggesting that BTZ acts by modulating TGFβ signalingTaken together, these results demonstrate that ourin silicoDR approach is a viable strategy to identify a candidate drug for undruggable targets, and to uncover its underlying mechanisms.
Systematic domain-based aggregation of protein structures highlights DNA-, RNA-, and other ligand-binding positions
Authors: Kobren Shilpa Nadimpalli , Singh Mona
Published: August 2018

Domains are fundamental subunits of proteins, and while they play major roles in facilitating protein–DNA, protein–RNA and other protein–ligand interactions, a systematic assessment of their various interaction modes is still lacking. A comprehensive resource identifying positions within domains that tend to interact with nucleic acids, small molecules and other ligands would expand our knowledge of domain functionality as well as aid in detecting ligand-binding sites within structurally uncharacterized proteins. Here we introduce an approach to identify per-domain-position interaction “propensities” by aggregating protein co-complex structures by domain and ascertaining how frequently residues mapping to each domain position interact with ligands. We perform this domain-based analysis on ∼82,000 co-complex structures, and infer positions involved in binding DNA, RNA, peptides, ions, or small molecules across 4,120 domains, which we refer to collectively as the InteracDome. Cross-validation testing reveals that ligand-binding positions for 1,327 domains can be confidently modeled and used to identify residues facilitating interactions in ∼60–69% of human genes. Our resource of domain-inferred ligand-binding sites should be a great aid in understanding disease etiology: whereas these sites are enriched in Mendelian-associated and cancer somatic mutations, they are depleted in polymorphisms observed across healthy populations. The InteracDome is available at http://interacdome.princeton.edu.
Characterization of L-serine deaminases, SdaA (PA2448) and SdaB (PA5379), and their potential role inPseudomonas aeruginosapathogenesis
Authors: Leal Sixto M. , Newman Elaine , Mathee Kalai
Published: August 2018

Regardless of the site of infectivity, all pathogens require high energetic influxes. This energy is required to counterattack the host immune system and in the absence the bacterial infections are easily cleared by the immune system. This study is an investigation into one highly bioenergetic pathway inPseudomonas aeruginosainvolving the amino acid L-serine and the enzyme L-serine deaminase (L-SD).P. aeruginosais an opportunistic pathogen causing infections in patients with compromised immune systems as well as patients with cystic fibrosis. L-SD has been linked directly to the pathogenicity of several organisms including but not limited toCampylobacter jejuni, Mycobacterium bovis,Streptococcus pyogenes, andYersinia pestis. We hypothesized thatP. aeruginosaL-SD is likely to be critical for its virulence. The genome sequence analysis revealed the presence of two L-SD homologs encoded bysdaAandsdaB.We analyzed the ability ofP. aeruginosato utilize serine and the role of SdaA and SdaB in serine deamination by comparing mutant strains ofsdaA(PAOsdaA) andsdaB(PAOsdaB) with their isogenic parentP. aeruginosaPAO1. We demonstrate thatP. aeruginosais unable to use serine as a sole carbon source. However, serine utilization is enhanced in the presence of glycine. Both SdaA and SdaB contribute to L-serine deamination, 34 % and 66 %, respectively. Glycine was also shown to increase the L-SD activity especially from SdaB. Glycine-dependent induction requires the inducer serine. The L-SD activity from both SdaA and SdaB is inhibited by the amino acid L-leucine. These results suggest thatP. aeruginosaL-SD is quite different from the characterizedE. coliL-SD that is glycine-independent but leucine-dependent for activation. Growth mutants able to use serine as sole carbon source were isolated. In addition, suicide vectors were constructed which allow for selective mutation of thesdaAandsdaBgenes on anyP. aeruginosastrain of interest. Future studies with a double mutant will reveal the importance of these genes for pathogenicity.
Identity domains in complex behavior: Toward a biology of personality
Authors: Forkosh Oren , Karamihalev Stoyo , Roeh Simone , Engel Mareen , Alon Uri , Anpilov Sergey , Nussbaumer Markus , Flachskamm Cornelia , Kaplick Paul , Shemesh Yair , Chen Alon
Published: August 2018

Personality traits offer considerable insight into the biological basis of individual differences. However, existing approaches toward understanding personality across species rely on subjective criteria and limited sets of behavioral readouts, resulting in noisy and often inconsistent outcomes. Here, we introduce a mathematical framework for studying individual differences along dimensions with maximum consistency and discriminative power. We validate this framework in mice, using data from a system for high-throughput longitudinal monitoring of group-housed mice that yields a variety of readouts from all across an individual’s behavioral repertoire. We describe a set of stable traits that capture variability in behavior and gene expression in the brain, allowing for better informed mechanistic investigations into the biology of individual differences.
Promoting synthetic symbiosis under environmental disturbances
Authors: Denton Jai A. , Gokhale Chaitanya S.
Published: August 2018

By virtue of complex interactions, the behaviour of mutualistic systems is difficult to study and nearly impossible to predict. We have developed a theoretical model of a modifiable experimental yeast system that is amenable to exploring self-organised cooperation while considering the production and use of specific metabolites. Leveraging the simplicity of an artificial yeast system, a simple model of mutualism, we develop and test the assumptions and stability of this theoretical model. We examine how one-off, recurring and permanent changes to an ecological niche affect a cooperative interaction and identify an ecological “Goldilocks zone” in which the mutualism can survive. Moreover, we explore how a factor like the cost of mutualism – the cellular burden of cooperating – influences the stability of mutualism and how environmental changes shape this stability. Our results highlight the fragility of mutualisms and suggest the use of synthetic biology to stave off an ecological collapse.
On the Number of Driver Nodes for Controlling a Boolean Network to Attractors
Authors: Hou Wenpin , Ruan Peiying , Ching Wai-Ki , Akutsu Tatsuya
Published: August 2018

It is known that many driver nodes are required to control complex biological networks. Previous studies imply that O(N) driver nodes are required in both linear complex network and Boolean network models with N nodes if an arbitrary state is specified as the target. In this paper, we mathematically prove under a reasonable assumption that the expected number of driver nodes is only O(log2N + log2M) for controlling Boolean networks if the targets are restricted to attractors, where M is the number of attractors. Since it is expected that M is not very large in many practical networks, this is a significant improvement. This result is based on discovery of novel relationships between control problems on Boolean networks and the coupon collector’s problem, a well-known concept in combinatorics. We also provide lower bounds of the number of driver nodes as well as simulation results using artificial and realistic network data, which support our theoretical findings.
Fitness effects of competition within and between species change across species’ ranges, and reveal limited local adaptation in rainforestDrosophila
Authors: O’Brien Eleanor K. , Higgie Megan , Jeffs Christopher T. , Hoffmann Ary A. , Hrček Jan , Lewis Owen T. , Bridle Jon R.
Published: August 2018

Competition within and between species can have large effects on fitness and may therefore drive local adaptation. However, these effects are rarely tested systematically, or considered when predicting species’ responses to environmental change. We used a field transplant experiment to test the effects of intra and interspecific competition on fitness across the ecological niches of two rainforestDrosophilaspecies that replace each other along an elevation gradient. For the species with the broader elevational range, we also tested for adaptation to the local abiotic and biotic environment. In both species, intraspecific competition reduced productivity more than interspecific competition at the centre of its elevational range, while interspecific competition had a stronger effect at the range edge, where the competing species is more abundant. Local adaptation was detected in the centre of the range of the more widespread species, but only in the presence of intraspecific competition. This study is the first to demonstrate that fitness effects of inter-specific competition increase at ecological margins, while intra-specific competition has more pervasive effects at range centres. This is a key assumption of “tangled bank” models of community evolution and has important implications for predicting the resilience of ecological networks to global change.
Neural Correlates of Causal Confounding
Authors: Liljeholm Mimi
Published: August 2018

As scientists, we are keenly aware that if putative causes perfectly co-vary, the independent influence of neither can be discerned – a “no confounding” constraint on inference, fundamental to philosophical and statistical perspectives on causation. Intriguingly, a substantial behavioral literature suggests that naïve human reasoners, adults and children, are tacitly sensitive to causal confounding. Here, a combination of fMRI and cognitive computational modeling was used to investigate neural substrates mediating such sensitivity. While being scanned, participants observed and judged the influences of various putative causes with confounded or non-confounded, deterministic or stochastic, influences. During judgments requiring generalization of causal knowledge from a feedback-based learning context to a transfer probe, activity in the dorsomedial prefrontal cortex (DMPFC) was better accounted for by a Bayesian causal model, sensitive to both confounding and stochasticity, than a purely error-driven algorithm, sensitive only to stochasticity. Implications for the detection and estimation of distinct forms of uncertainty, and for a neural mediation of domain general constraints on causal induction, are discussed.
Enhancing network activation in Natural Killer cells: Predictions from in silico modeling
Authors: Makaryan Sahak Z. , Finley Stacey D.
Published: August 2018

Natural killer (NK) cells are part of the innate immune system and are capable of killing diseased cells. As a result, NK cells are being used for adoptive cell therapies for cancer patients. The activation of NK cell stimulatory receptors leads to a cascade of intracellular phosphorylation reactions, which activates key signaling species that facilitate the secretion of cytolytic molecules required for cell killing. Strategies that maximize the activation of such intracellular species can increase the likelihood of NK cell activation upon contact with a cancer cell, and thereby improve efficacy of NK cell-based therapies. However, due to the complexity of intracellular signaling, it is difficult to deduce a priori which strategies can enhance species activation. Therefore, we constructed a mechanistic model of the CD16, 2B4 and NKG2D signaling pathways in NK cells to simulate strategies that enhance signaling. The model predictions were fit to published data and validated with a separate dataset. Model simulations demonstrate strong network activation when the CD16 pathway is stimulated. The magnitude of species activation is most sensitive to the receptor concentration and the rate at which the receptor is deactivated. Co-stimulation of CD16 and NKG2D in silico required fewer ligands to achieve half-maximal activation than other combinations, suggesting co-stimulating these pathways is most effective in activating the species. We applied the model to predict the effects of perturbing the signaling network and found two strategies that can potently enhance network activation. When the availability of ligands is low, it is more influential to engineer NK cell receptors that are resistant to proteolytic cleavage. In contrast, for high ligand concentrations, inhibiting phosphatase activity leads to more activation. The work presented here establishes a framework for understanding the complex, nonlinear aspects of NK cell signaling and provides detailed strategies for enhancing NK cell activation.
Impact of fruit-tree shade intensity on the growth,yield, and quality of intercropped wheat
Authors: Qiao Xu , Sai Lihan , Chen Xingwu , Xue Lihua , Lei Junjie
Published: August 2018

Agroforestry is a common traditional practice in China-especially in the southern Xinjiang of Northwest China. However, the productivity of many agroforestry systems has been lower than expected in recent years, highlighting the need for an actionably deep mechanistic understanding of the competition between crops and trees. Here, we chose 3 different fruit tree/wheat intercropping agroforestry systems to investigate influence of different fruit tree shade intensity on the growth, yield and quality of intercropping wheat: jujube/wheat, apricot /wheat, and walnut /wheat. We found that compared to the monoculture wheat system, the mean daily shade intensity of the jujube-, apricot-, and walnut-based intercropping systems were, respectively, 23.2%, 57.5%, and 80.7% shade. The photosynthetic rate of wheat in the jujube-, apricot-, and walnut-based intercropping systems decreased by, respectively, 11.3%, 31.9%, and 36.2% compared to monoculture wheat, and the mean number of fertile florets per spike decreased by 26.4%, 37.4%, and 49.5%. Moreover, the apricot- and walnut-based intercropping systems deleteriously affected grain yield (constituent components spike number, grains per spike, and thousand grain weight) and decreased the total N, P, and K content of intercropping wheat. Tree shading intensity strongly enhanced the protein content, wet gluten content, falling number, dough development time, and dough stability time of wheat, but significantly decreased the softening degree. Strong negative linear correlations were observed between tree shade intensity and the number of fertile florets, grain yield (including spike number, grains per spike, and thousand grain weight), nutrient content (N, P and K), and softening degree of wheat. In contrast, we found that daily shade intensity was positively linearly correlated with protein content, wet gluten content, falling number, dough development time, and dough stability time. We conclude that jujube-based intercropping systems can be practical in the region, as they do not decrease the yield and quality of intercropping wheat. Further research should focus on the above-ground/below-ground interspecific interactions and the mechanisms behind the observations that we observed amongst the intercropping systems.
Viruses.STRING: A virus–host protein–protein interaction database
Authors: Cook Helen Victoria , Tsankova Nadezhda , Szklarczyk Damian , Mering Christian von , Jensen Lars Juhl
Published: August 2018

As viruses continue to pose risks to global health, having a better un-derstanding of virus–host protein–protein interactions aids in the development of treatments and vaccines. Here, we introduce Viruses.STRING, a protein–protein interaction database specifically catering to virus-virus and virus-host interactions. This database combines evidence from experimental and text-mining channels to provide combined probabilities for interactions between viral and host proteins. The database contains 177,425 interactions between 239 viruses and 319 hosts. The database is publicly available at viruses.string-db.org, and the interaction data can also be accessed through the latest version of the Cytoscape STRING app.
Adaptation of artificial diets for Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) at laboratory rearing
Authors: Truzi Caio C. , Holzhausen Hurian G. , Chamessanga José A. , Laurentis Valéria L. , Vieira Natalia F. , Vacari Alessandra M. , De Bortoli Sergio A.
Published: August 2018

Helicoverpa armigera is an important pest of crops worldwide, and several studies have focused on the development of artificial diets for this species. However, studies evaluating the insect´s performance at nutritionally different diets are scarce. Larval development is dependent on the ratio of protein and carbohydrates. The aim of this study was to evaluate the biology and to compare the consumption and use of food of H. armigera larvae on diets with different protein levels. The nutritional index, the relative consumption rate, the relative metabolic rate, the relative growth rate, and the apparent digestibility were higher in the diet with added protein. On the other hand, the conversion efficiency of digested food was lower, resulting in a higher metabolic cost. In terms of biological aspects, larval survival was higher for the diet with average protein content and lower for the diet with a high protein level. The pupal period was longer for the diet with a higher protein content, while pupal survival was lower. Among the evaluated diets, the diet with an average protein content resulted in a higher net reproductive rate, a shorter time for the population to double in number, and the highest rates of population growth. The results suggest that lower or higher protein contents in the diets of H. armigera negatively affect the biological aspects of this species.
MafK mediates chromatin remodeling to silence IRF8 expression in non-immune cells in a lineage-specific manner
Authors: Fourier Nitsan , Zolty Maya , Azriel Aviva , Tedesco Donato , Levi Ben-Zion
Published: August 2018

The regulation of gene expression is a result of a complex interplay between chromatin remodeling, transcription factors (TFs) and signaling molecules. Cell differentiation is accompanied by chromatin remodeling of specific loci to permanently silence genes that are not essential for the differentiated cell activity. The molecular cues that recruit the chromatin remodeling machinery are not well characterized. IRF8 is an immune-cell specific TF, and thus, serves as a model gene to elucidate the molecular mechanisms governing its silencing in non-immune cells. A high-throughput shRNA library screen in IRF8 expression-restrictive cells enabled the identification of MafK as modulator of IRF8 silencing, affecting chromatin architecture. ChIP-seq analysis revealed three MafK binding-regions (−25kb, −20kb and IRF8 6thintron) in the IRF8 locus. These MafK binding-sites are sufficient to repress a reporter-gene when cloned in genome-integrated lentiviral reporter constructs in expression-restrictive cells only. Conversely, plasmid-based constructs do not demonstrate such repressive effect. These results highlight the role of these MafK binding-sites in mediating repressed chromatin assembly. Furthermore, removal of MafK-int6 binding-region from BAC-IRF8 reporter construct was sufficient to promote accessible chromatin conformation. Taken together, we identified and characterized several MafK binding elements within the IRF8 locus that mediate repressive chromatin conformation resulting in the silencing of IRF8 expression only in non-immune cells.
PARylation regulates stress granule dynamics, phase separation, and neurotoxicity of disease-related RNA-binding proteins
Authors: Duan Yongjia , Du Aiying , Gu Jinge , Duan Gang , Wang Chen , Ma Zhiwei , Sun Le , Qian Beituo , Deng Xue , Zhang Kai , Tian Kuili , Zhang Yaoyang , Jiang Hong , Liu Cong , Fang Yanshan
Published: August 2018

Mutations in RNA-binding proteins localized in ribonucleoprotein (RNP) granules, such as hnRNP A1 and TDP-43, promote aberrant protein aggregations, which are pathological hallmarks in neurodegenerative diseases including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Protein posttranslational modifications (PTMs) are known to regulate RNP granules. In this study, we investigate the function of PARylation, an important PTM involved in DNA damage repair and cell death, in RNP-related neurodegeneration. We reveal that PARylation levels are a major regulator of the dynamic assembly-disassembly of RNP granules, and the disease-related RNPs such as hnRNP A1 and TDP-43 can both be PARylated and bind to PARylated proteins. We further identify the PARylation site of hnRNP A1 at K298, which controls the cytoplasmic translocation of hnRNP A1 in response to stress, as well as the PAR-binding motif (PBM) of hnRNP A1, which is required for the delivery and association of hnRNP A1 to stress granules. Moreover, we show that PAR not only dramatically enhances the liquid-liquid phase separation of hnRNP A1, but also promotes the co-phase separation of hnRNP A1 and TDP-43 in vitro and their interaction in vivo. Finally, we establish that both genetic and pharmacological inhibition of PARP mitigates hnRNP A1 and TDP-43-mediated neurotoxicity in cell and Drosophila models of ALS. Together, our findings indicate a novel and crucial role of PARylation in regulating the assembly and the dynamics of RNP granules, and dysregulation of PARylation may contribute to ALS disease pathogenesis.
Information technology barriers in Indian sugar supply chain: an AHP and fuzzy AHP approach
Authors: Kumar Rupesh , Kansara Surendra
Published: August 2018

Purpose

The purpose of this paper is to find out possible barriers of information technology (IT) applications in the supply chain system of sugar industry in India. All these barriers have their strategic importance for serving the supply chain partners in better way and also help in improving the Indian agrarian economy. The study is a blend of theoretical and practical frameworks, which would focus on those key factors or IT barriers leading to implementation of IT in the sugar supply chain.

Design/methodology/approach

The paper is based on theoretical exploration of potential barriers IT applications in the supply chain system of sugar industry in India and prioritizing these barriers by employing multi-criteria decision-making approach.

Findings

The findings of this paper are identification of barriers of IT applications in the supply chain system of sugar industry in India, and ranking of these barriers in terms of its severity.

Research limitations/implications

Potential barriers of IT applications in the supply chain system of sugar industry in India considered in to the study are 11 in total. There can be more barriers of IT applications in the supply chain system.

Originality/value

This study reveals the application of analytic hierarchy process (AHP) and fuzzy AHP to Indian sugar industry for prioritizing the IT barriers which influence the sugar supply chain.
Non-performing assets and technical efficiency of Indian banks: a meta-frontier analysis
Authors: Arora Nitin , Arora Nidhi Grover , Kanwar Kritika
Published: August 2018

Purpose

The issue of mounting non-performing assets (NPAs) in Indian banking industry is serious and attracting attention of academia and policy planners. Thus, the purpose of this paper is to test the hypothesis whether NPAs in Indian commercial banking have reached at alarming state where they start affecting the technical efficiency levels adversely or not.

Design/methodology/approach

The efficiency score have been computed using case model (model with NPAs as bad/undesirable output) vs control model (model without NPAs as bad/undesirable output) methodology under meta-frontier data envelopment analysis framework.

Findings

It has been noticed that the effect of NPAs on overall technical efficiency and its various components is insignificant. The comparison of the case models (i.e. model with NPAs as bad output) with the control models (i.e. model without NPAs) reveals insignificant difference in average efficiency scores and rank distribution of commercial banks. The major source of inefficiency is technology gap (i.e. structure, setup and objectives of banking) among public, domestic private and foreign private categories of banks.

Practical implications

Though NPAs are increasing in Indian banking industry and specifically in Indian public sector banks because of their compulsory lending to priority sector yet the banks have huge scope to extend credit to priority sector as the NPAs have not reached at alarming stage where they start affecting adversely the efficiency performance.

Originality/value

Given the fact that the banking penetrations, structure and objectives differ significantly across ownership, separate frontiers for each ownership (public, private and foreign banks) category has been used to evaluate the technical efficiency levels of 81 commercial banks operating in India over the period 2005 to 2013.
Computationally efficient permanent magnet traction motor loss assessment
Authors: Sarigiannidis Athanasios , Beniakar Minos , Kladas Antonios
Published: August 2018

Purpose

This paper aims to introduce a computationally efficient hybrid analytical–finite element (FE) methodology for loss evaluation in electric vehicle (EV) permanent magnet (PM) traction motor applications. In this class of problems, eddy current losses in PMs and iron laminations constitute an important part of overall drive losses, representing a key design target.

Design/methodology/approach

Both surface mounted permanent magnet (SMPM) and double-layer interior permanent magnet (IPM) motor topologies are considered. The PM eddy losses are calculated by using analytical solutions and Fourier harmonic decomposition. The boundary conditions are based on slot opening magnetic field strength tangential component in the air gap in the SMPM topology case, whereas the numerically evaluated normal flux density variation on the surface of the outer PM is implemented in the IPM case. Combined analytical–loss evaluation technique has been verified by comparing its results to a transient magnetodynamic two-dimensional FE model ones.

Findings

The proposed loss evaluation technique calculated the total power losses for various operating conditions with low computational cost, illustrating the relative advantages and drawbacks of each motor topology along a typical EV operating cycle. The accuracy of the method was comparable to transient FE loss evaluation models, particularly around nominal speed.

Originality/value

The originality of this paper is based on the development of a fast and accurate PM eddy loss model for both SMPM and IPM motor topologies for traction applications, combining effectively both analytical and FE techniques.