bluuebunny/crossref_metadata_2025_split huggingface dataset:
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’.
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’.
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

ABSTRACTTechnological 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

AbstractThe 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

AbstractMotivationAccurate 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.ResultsIn 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.Contacteva@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

AbstractScarcity 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.ImportanceVersatile 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

AbstractAlthough 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

AbstractDomains 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

ABSTRACTRegardless 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

AbstractPersonality 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.
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

AbstractIt 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

AbstractCompetition 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

AbstractAs 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.