bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of dimensionality in neuronal network dynamics
Authors: Ulloa Severino Francesco Paolo , Ban Jelena , Song Qin , Tang Mingliang , Bianconi Ginestra , Cheng Guosheng , Torre Vincent 
Published: July 2016

AbstractRecent results from network theory show that complexity affects several dynamical properties of networks that favor synchronization. Here we show that synchronization in 2D and 3D neuronal networks is significantly different. Using dissociated hippocampal neurons we compared properties of cultures grown on a flat 2D substrates with those formed on 3D graphene foam scaffolds. Both 2D and 3D cultures had comparable glia to neuron ratio and the percentage of GABAergic inhibitory neurons. 3D cultures because of their dimension have many connections among distant neurons leading to small-world networks and their characteristic dynamics. After one week, calcium imaging revealed moderately synchronous activity in 2D networks, but the degree of synchrony of 3D networks was higher and had two regimes: a highly synchronized (HS) and a moderately synchronized (MS) regime. The HS regime was never observed in 2D networks. During the MS regime, neuronal assemblies in synchrony changed with time as observed in mammalian brains. After two weeks, the degree of synchrony in 3D networks decreased, as observed in vivo. These results show that dimensionality determines properties of neuronal networks and that several features of brain dynamics are a consequence of its 3D topology.
Mechanism for insulin-like peptide 5 distinguishing the homologous relaxin family peptide receptor 3 and 4
Authors: Hu Meng-Jun , Shao Xiao-Xia , Wang Jia-Hui , Wei Dian , Guo Yu-Qi , Liu Ya-Li , Xu Zeng-Guang , Guo Zhan-Yun 
Published: July 2016

AbstractThe relaxin family peptides play a variety of biological functions by activating four G protein-coupled receptors, RXFP1–4. Among them, insulin-like peptide 5 (INSL5) and relaxin-3 share the highest sequence homology, but they have distinct receptor preference: INSL5 can activate RXFP4 only, while relaxin-3 can activate RXFP3, RXFP4 and RXFP1. Previous studies suggest that the A-chain is responsible for their different selectivity for RXFP1. However, the mechanism by which INSL5 distinguishes the homologous RXFP4 and RXFP3 remains unknown. In the present work, we chemically evolved INSL5 in vitro to a strong agonist of both RXFP4 and RXFP3 through replacement of its five B-chain residues with the corresponding residues of relaxin-3. We identified four determinants (B2Glu, B9Leu, B17Tyr and a rigid B-chain C-terminus) on INSL5 that are responsible for its inactivity at RXFP3. In reverse experiments, we grafted these determinants onto a chimeric R3/I5 peptide, which contains the B-chain of relaxin-3 and the A-chain of INSL5 and retains full activation potency at RXFP3 and RXFP4. All resultant R3/I5 mutants retained high activation potency towards RXFP4, but most displayed significantly decreased or even abolished activation potency towards RXFP3, confirming the role of these four INSL5 determinants in distinguishing RXFP4 from RXFP3.
Atomic structure and oxygen deficiency of the ultrathin aluminium oxide barrier in Al/AlOx/Al Josephson junctions
Authors: Zeng Lunjie , Tran Dung Trung , Tai Cheuk-Wai , Svensson Gunnar , Olsson Eva 
Published: July 2016

AbstractAl/AlOx/Al Josephson junctions are the building blocks of a wide range of superconducting quantum devices that are key elements for quantum computers, extremely sensitive magnetometers and radiation detectors. The properties of the junctions and the superconducting quantum devices are determined by the atomic structure of the tunnel barrier. The nanoscale dimension and disordered nature of the barrier oxide have been challenges for the direct experimental investigation of the atomic structure of the tunnel barrier. Here we show that the miniaturized dimension of the barrier and the interfacial interaction between crystalline Al and amorphous AlOx give rise to oxygen deficiency at the metal/oxide interfaces. In the interior of the barrier, the oxide resembles the atomic structure of bulk aluminium oxide. Atomic defects such as oxygen vacancies at the interfaces can be the origin of the two-level systems and contribute to decoherence and noise in superconducting quantum circuits.
Chronic Glutathione Depletion Confers Protection against Alcohol-induced Steatosis: Implication for Redox Activation of AMP-activated Protein Kinase Pathway
Authors: Chen Ying , Singh Surendra , Matsumoto Akiko , Manna Soumen K. , Abdelmegeed Mohamed A. , Golla Srujana , Murphy Robert C. , Dong Hongbin , Song Byoung-Joon , Gonzalez Frank J. , Thompson David C. , Vasiliou Vasilis 
Published: July 2016

AbstractThe pathogenesis of alcoholic liver disease (ALD) is not well established. However, oxidative stress and associated decreases in levels of glutathione (GSH) are known to play a central role in ALD. The present study examines the effect of GSH deficiency on alcohol-induced liver steatosis in Gclm knockout (KO) mice that constitutively have ≈15% normal hepatic levels of GSH. Following chronic (6 week) feeding with an ethanol-containing liquid diet, the Gclm KO mice were unexpectedly found to be protected against steatosis despite showing increased oxidative stress (as reflected in elevated levels of CYP2E1 and protein carbonyls). Gclm KO mice also exhibit constitutive activation of liver AMP-activated protein kinase (AMPK) pathway and nuclear factor-erythroid 2–related factor 2 target genes, and show enhanced ethanol clearance, altered hepatic lipid profiles in favor of increased levels of polyunsaturated fatty acids and concordant changes in expression of genes associated with lipogenesis and fatty acid oxidation. In summary, our data implicate a novel mechanism protecting against liver steatosis via an oxidative stress adaptive response that activates the AMPK pathway. We propose redox activation of the AMPK may represent a new therapeutic strategy for preventing ALD.
Effects of chronic variable stress on cognition and Bace1 expression among wild-type mice
Authors: Cordner Z A , Tamashiro K L K 
Published: July 2016

AbstractStressful life events, activation of the hypothalamic–pituitary–adrenal (HPA) axis and glucocorticoids are now thought to have a role in the development of several neurodegenerative and psychiatric disorders including Alzheimer’s disease (AD) through mechanisms that may include exacerbation of cognitive impairment, neuronal loss, and beta-amyloid (Aβ) and tau neuropathology. In the current study, we use a wild-type mouse model to demonstrate that chronic variable stress impairs cognitive function and that aged mice are particularly susceptible. We also find that stress exposure is associated with a 1.5- to 2-fold increase in the expression of Bace1 in the hippocampus of young adult mice and the hippocampus, prefrontal cortex and amygdala of aged mice. Further, the increased expression of Bace1 was associated with decreased methylation of several CpGs in the Bace1 promoter region. In a second series of experiments, exposure to environmental enrichment (EE) prevented the stress-related changes in cognition, gene expression and DNA methylation. Together, these findings re-affirm the adverse effects of stress on cognition and further suggest that aged individuals are especially susceptible. In addition, demonstrating that chronic stress results in decreased DNA methylation and increased expression of Bace1 in the brain may provide a novel link between stress, Aβ pathology and AD. Finally, understanding the mechanisms by which EE prevented the effects of stress on cognition and Bace1 expression will be an important area of future study that may provide insights into novel approaches to the treatment of AD.
Figurative Language Deficits Associated With Right Hemisphere Disorder
Authors: Lundgren Kristine , Brownell Hiram 
Published: July 2016

PurposeTo describe the nonliteral language deficits associated with right hemisphere disorder (RHD), discuss the neuroimaging data associated with the processing of nonliteral language, and to offer some suggestions for treating this type of cognitive-linguistic disorder.MethodIn this discussion, we review literature on comprehension of metaphor, idioms, proverbs, and sarcasm and provide some treatment options.ConclusionThe evidence-based treatment options for the remediation of figurative language deficits are extremely limited, not only for those individuals with RHD, but for all populations of children and adults with figurative language comprehension impairments.
Compact dual polarised V slit, stub and slot embedded circular patch antenna for UMTS/WiMAX/WLAN applications
Authors: Mathew S. , Ameen M. , Jayakrishnan M.P. , Mohanan P. , Vasudevan K. 
Published: July 2016

A single probe‐fed novel V slit, stub and slot embedded circular microstrip antenna with resonances in the three bands of UMTS, worldwide interoperability for microwave access (WiMAX) and WLAN is presented. The polarisation is circular in the UMTS band and linear in the other two bands. Asymmetrical V slits in the patch boundary along with an embedded circular slot in the patch centre are employed to introduce the perturbation necessary for circular polarisation. Impedance bandwidths (BWs) of 4.2, 2 and 6.2%, respectively, in the three bands centred at 2, 3.5 and 5.6 GHz are obtained. The axial ratio BW is 2.3% in the UMTS band. Moderate gains of 4.4, 3.5 and 2.8 dBi are obtained in the three bands. There is a patch size reduction of about 48% when compared with the conventional circular patch antenna at a fixed operating frequency. The radiation pattern is directional in the WiMAX band and nearly omnidirectional in the WLAN band.
800 years on can Magna Carta still disrupt the executive?
Authors: Moss Michael 
Published: July 2016

AbstractIn June 1215 King John put his seal to Magna Carta, which over the centuries has become an icon of English (British) liberties. Clause 40 about not selling, denying or delaying justice, and Clause 39, that no free man is to be imprisoned or dispossessed “save by the lawful judgment of his peers or by the law of the land” are still in force today. For these reasons Lord Denning described Magna Carta as “the greatest constitutional document of all times—the foundation of the freedom of the individual against the arbitrary authority of the despot”. In other words the executive can never be above the law, but for this principle to be enforced the state must disclose evidence by due process to the public by which it can be held to account. This essay explores the threats to openness of government in the digital age, which runs the risk of undermining this fundamental principle of the British constitution. These range from the intrusiveness of our surveillance society, ill-considered notions of a post-privacy world, misconceived concepts of open data to the immense difficulty of scrutinizing born-digital data released under due process for sensitive content. Such threats are balanced by a much more assertive judiciary under the supreme court, which like its American counterpart strikes down legislation, an unelected second chamber willing to challenge the executive and House of Commons select committees that are increasingly baring their teeth. This article is published as part of a collection entitled ‘IT as a utility’.
Internal strain drives spontaneous periodic buckling in collagen and regulates remodeling
Authors: Dittmore Andrew , Silver Jonathan , Sarkar Susanta K. , Marmer Barry , Goldberg Gregory I. , Neuman Keir C. 
Published: July 2016

Significance
Collagen fibrils resemble nanoscale cables that self-assemble and constitute the most prevalent protein structure in the body. Our experiments reveal unanticipated defects that form along collagen fibrils. These defects are the initiation sites of collagenase activity and represent a strain-sensitive mechanism for regulating tissue remodeling. The emergence of defects, their spatial periodicity, and fluctuations are quantitatively accounted for with a buckling model in which defects spontaneously form, repulsively interact, and self-heal.
Groundwater methane in relation to oil and gas development and shallow coal seams in the Denver-Julesburg Basin of Colorado
Authors: Sherwood Owen A. , Rogers Jessica D. , Lackey Greg , Burke Troy L. , Osborn Stephen G. , Ryan Joseph N. 
Published: July 2016

Significance
The impact of unconventional oil and gas development on groundwater quality remains controversial. We use an archive of public domain data to examine factors influencing the distribution and sources of groundwater methane in the oil- and gas-producing Denver-Julesburg Basin of Colorado. Thermogenic stray gas sourced from deep oil and gas reservoirs impacted 42 water wells in 32 separate cases at a rate of about two cases per year from 2001 to 2014. The rate did not change after the introduction of horizontal drilling combined with high-volume hydraulic fracturing in 2010. The risk of stray gas contamination ranged from 0.12% of 35,000 water wells in the basin (lower estimate) to 4.5% of the 924 water wells that were tested (upper estimate).
Blind tests of RNA nearest-neighbor energy prediction
Authors: Chou Fang-Chieh , Kladwang Wipapat , Kappel Kalli , Das Rhiju 
Published: July 2016

Significance
Understanding RNA machines and how their behavior can be modulated by chemical modification is increasingly recognized as an important biological and bioengineering problem, with continuing discoveries of riboswitches, mRNA regulons, CRISPR-guided editing complexes, and RNA enzymes. Computational strategies for understanding RNA energetics are being proposed, but have not yet faced rigorous tests. We describe a modeling strategy called RECCES–Rosetta (reweighting of energy-function collection with conformational ensemble sampling in Rosetta) that models the full ensemble of motions of RNA in single-stranded form and in helices, including nonstandard nucleotides, such as 2,6-diaminopurine, a variant of adenosine. When compared with experiments, including blind tests, the energetic accuracies of RECCES–Rosetta calculations are at levels close to experimental error, suggesting that computation can now be used to predict and design basic RNA energetics.
Equity and length of lifespan are not the same
Authors: Seligman Benjamin , Greenberg Gabi , Tuljapurkar Shripad 
Published: July 2016

Significance
We find that the causes of death that have led to greater equality among lifespans are different from the causes that have led to longer average lifespan, also called life expectancy. Control of leading causes of death, such as heart disease, increased life expectancy, whereas medical interventions on infant mortality led to greater equality. Action to promote health equity will require further mitigation of the killers of young people rather than solely focusing on the most common causes of death.
Early establishment of trees at the alpine treeline: idiosyncratic species responses to temperature-moisture interactions
Authors: Loranger Hannah , Zotz Gerhard , Bader Maaike Y. 
Published: July 2016

AbstractOn a global scale, temperature is the main determinant of arctic and alpine treeline position. However on a local scale, treeline form and position vary considerably due to other climatic factors, tree species ecology and life-stage-dependent responses. For treelines to advance poleward or uphill, the first steps are germination and seedling establishment. These earliest life stages may be major bottlenecks for treeline tree populations and will depend differently on climatic conditions than adult trees. We investigated the effect of soil temperature and moisture on germination and early seedling survival in a field experiment in the French Alps near the local treeline (2100 m a.s.l.) using passive temperature manipulations and two watering regimes. Five European treeline tree species were studied: Larix decidua , Picea abies , Pinus cembra , Pinus uncinata and Sorbus aucuparia . In addition, we monitored the germination response of three of these species to low temperatures under controlled conditions in growth chambers. The early establishment of these trees at the alpine treeline was limited either by temperature or by moisture, the sensitivity to one factor often depending on the intensity of the other. The results showed that the relative importance of the two factors and the direction of the effects are highly species-specific, while both factors tend to have consistent effects on both germination and early seedling survival within each species. We show that temperature and water availability are both important contributors to establishment patterns of treeline trees and hence to species-specific forms and positions of alpine treelines. The observed idiosyncratic species responses highlight the need for studies including several species and life-stages to create predictive power concerning future treeline dynamics.
Towards the knowledge-based design of universal influenza epitope ensemble vaccines
Authors: Sheikh Qamar M. , Gatherer Derek , Reche Pedro A , Flower Darren R. 
Published: July 2016

Abstract
Motivation: Influenza A viral heterogeneity remains a significant threat due to unpredictable antigenic drift in seasonal influenza and antigenic shifts caused by the emergence of novel subtypes. Annual review of multivalent influenza vaccines targets strains of influenza A and B likely to be predominant in future influenza seasons. This does not induce broad, cross protective immunity against emergent subtypes. Better strategies are needed to prevent future pandemics. Cross-protection can be achieved by activating CD8+ and CD4+ T cells against highly conserved regions of the influenza genome. We combine available experimental data with informatics-based immunological predictions to help design vaccines potentially able to induce cross-protective T-cells against multiple influenza subtypes.
Results: To exemplify our approach we designed two epitope ensemble vaccines comprising highly conserved and experimentally verified immunogenic influenza A epitopes as putative non-seasonal influenza vaccines; one specifically targets the US population and the other is a universal vaccine. The USA-specific vaccine comprised 6 CD8+ T cell epitopes (GILGFVFTL, FMYSDFHFI, GMDPRMCSL, SVKEKDMTK, FYIQMCTEL, DTVNRTHQY) and 3 CD4+ epitopes (KGILGFVFTLTVPSE, EYIMKGVYINTALLN, ILGFVFTLTVPSERG). The universal vaccine comprised 8 CD8+ epitopes: (FMYSDFHFI, GILGFVFTL, ILRGSVAHK, FYIQMCTEL, ILKGKFQTA, YYLEKANKI, VSDGGPNLY, YSHGTGTGY) and the same 3 CD4+ epitopes. Our USA-specific vaccine has a population protection coverage (portion of the population potentially responsive to one or more component epitopes of the vaccine, PPC) of over 96 and 95% coverage of observed influenza subtypes. The universal vaccine has a PPC value of over 97 and 88% coverage of observed subtypes.
Availability and Implementation: http://imed.med.ucm.es/Tools/episopt.html .
Contact: d.r.flower@aston.ac.uk
SYNBADm: a tool for optimization-based automated design of synthetic gene circuits
Authors: Otero-Muras Irene , Henriques David , Banga Julio R. 
Published: July 2016

Abstract
Motivation: The design of de novo circuits with predefined performance specifications is a challenging problem in Synthetic Biology. Computational models and tools have proved to be crucial for a successful wet lab implementation. Natural gene circuits are complex, subject to evolutionary tradeoffs and playing multiple roles. However, most synthetic designs implemented to date are simple and perform a single task. As the field progresses, advanced computational tools are needed in order to handle greater levels of circuit complexity in a more flexible way and considering multiple design criteria.
Results: This works presents SYNBADm (SYNthetic Biology Automated optimal Design in Matlab), a software toolbox for the automatic optimal design of gene circuits with targeted functions from libraries of components. This tool makes use of global optimization to simultaneously search the space of structures and kinetic parameters. SYNBADm can efficiently handle high levels of circuit complexity and can consider multiple design criteria through multiobjective optimization. Further, it provides flexible design capabilities, i.e. the user can define the modeling framework, library of components and target performance function(s).
Availability and Implementation: SYNBADm runs under the popular MATLAB computational environment, and is available under GPLv3 license at https://sites.google.com/site/synbadm
Contact: ireneotero@iim.csic.es or julio@iim.csic.es
PyPanda: a Python package for gene regulatory network reconstruction
Authors: van IJzendoorn David G.P. , Glass Kimberly , Quackenbush John , Kuijjer Marieke L. 
Published: July 2016

Abstract
Summary: PANDA ( P assing A ttributes between N etworks for D ata A ssimilation) is a gene regulatory network inference method that uses message-passing to integrate multiple sources of ‘omics data. PANDA was originally coded in C ++. In this application note we describe PyPanda, the Python version of PANDA. PyPanda runs considerably faster than the C ++ version and includes additional features for network analysis.
Availability and implementation: The open source PyPanda Python package is freely available at http://github.com/davidvi/pypanda .
Contact: mkuijjer@jimmy.harvard.edu or d.g.p.van_ijzendoorn@lumc.nl
Childhood socioeconomic disadvantage is associated with lower mortality in older Japanese men: the JAGES cohort study
Authors: Tani Yukako , Kondo Naoki , Nagamine Yuiko , Shinozaki Tomohiro , Kondo Katsunori , Kawachi Ichiro , Fujiwara Takeo 
Published: July 2016

Abstract
Background: Childhood socioeconomic disadvantage has been previously linked to increased mortality risk in adulthood. However, most previous studies have focused on middle-aged adults in Western contexts. Here, we sought to examine the association between childhood socioeconomic status (SES) and mortality among healthy older Japanese adults.
Methods: We conducted a 3-year follow-up of participants in the Japan Gerontological Evaluation Study (JAGES), a population-based cohort of 65- to 103-year-old Japanese adults. Childhood SES was assessed by survey at baseline. Mortality from 2010 to 2013 was analysed for 15 449 respondents (7143 men and 8306 women). Cox regression models were used to estimate hazard ratios (HR) for risk of death.
Results: A total of 754 deaths occurred during the 3-year follow-up. Lower childhood SES was significantly associated with lower mortality in men, but not in women. Compared with men growing up in more advantaged childhood socioeconomic circumstances, the age-adjusted HR for men from low childhood SES backgrounds was 0.75 [95% confidence interval (CI): 0.56–1.00]. The association remained significant after adjustment for height, education, adult SES, municipalities of residence, health behaviours, disease status and current social relationships (HR = 0.64; 95% CI 0.47–0.87). This association was stronger among men aged 75 years or older, HR = 0.67 (95% CI: 0.47–0.95), compared with men aged 65–74 years, HR = 0.90 (95% CI: 0.54–1.51).
Conclusions: Childhood socioeconomic disadvantage is associated with lower mortality among men aged 75 years or older, which may be due to selective survival, or alternatively to childhood physical training or postwar calorie restriction in this generation of Japanese males.