bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of calcium ions on the interactions between surfaces end-grafted with weak polyelectrolytes
Authors: Nap Rikkert J. , Szleifer Igal
Published: July 2018

We study the interactions between two planar surfaces end-tethered with poly(acrylic acid) polymers in electrolyte solutions containing calcium ions, using a molecular theory. We found that by adding divalent calcium ions to an aqueous solution of monovalent ions leads to a dramatic reduction in the size and range of effective interactions between the two polymer layers. This is caused by the formation of favorable calcium bridges, i.e., complexes of one calcium ion and two carboxylic acid monomers, that reduce the effective charge of the polymer layers and, at sufficient calcium ion concentrations, can cause the polymer layers to collapse. For calcium ion concentrations above approximately 1 mM, the repulsions between the opposing end-grafted surfaces disappear and attractions occur. These attractions are correlated with the occurrence of interlayer divalent calcium bridges and do not occur for poly(acrylic acid) layers in contact with reservoir solutions containing only monovalent ions. This result indicates the suitability of divalent calcium ions to control and change the interaction range and strength, which is a useful property that is desirable in the design of stimuli-responsive nanomaterials.
Investigations on the plasma enabled growth of vertical graphene sheets on CNT surface
Authors: Gupta Neha , Sharma Suresh C.
Published: July 2018

A theoretical model is developed to describe the plasma-assisted nucleation and growth kinetics of a vertical graphene (VG) sheet on a carbon nanotube (CNT) surface. The present model accounts the formalization of a charge separation region, i.e., plasma sheath between the bulk plasma and substrate surface in one-dimension along with the kinetics of all the plasma species (neutrals, positively charged species, and electrons), rate of charge accumulation on the graphene sheet surface, and growth of the VG sheet on the CNT surface owing to defect generation and various processes on the CNT surface. Using the model, we demonstrated that variations in the plasma enhanced chemical vapor deposition process control parameters such as the total gas pressure, input power, and substrate bias can be used for significant variation in the plasma composition and characteristics that in turn control the ion bombardment and generation of carbon species on the CNT surface and consequently tune the VG sheet growth characteristics such as height, thickness, and number density profiles of the VG sheet on the CNT surface. The results of the present study indicate that as the total gas pressure is lowered and the input power and substrate bias are enhanced, the number densities and height of the VG sheet on the CNT surface are increased; however, the thickness of the VG sheet is reduced. Some of our theoretical findings are in good agreement with the existing experimental results.
Development and distribution of surface charge on epoxy resin under dc electric field in different gases
Authors: Sima Wenxia , Xu Hang , Sun Potao , Shao Qianqiu , Yin Ze
Published: July 2018

Under DC voltage, charge accumulates on the break insulation of mechanical DC circuit breakers, distorting the local electric field, which increases the risk of break insulation failure. Glass-fiber vacuum-impregnated epoxy resin can be used as an insulation material for DC circuit breakers owing to its excellent mechanical and electrical properties. We have created a system to measure the surface potential of an epoxy resin in different gases. The accumulation and dissipation of the surface charge in air and SF6 are determined, and the effects of air and SF6 are compared. The results show that the polarity of the surface charge is the same as that of the applied DC voltage, and that the main source of the charge is from Schottky charge injection. In SF6, the charge density is higher than that in air, and its decay rate is slower. The decay law of the surface potential in SF6 can be characterized by two exponential superposition formulas. In the early stage, surface charge is attenuated mainly by being transferred along the surface of the insulator and neutralized by gas ions. In the late stage, surface charge is attenuated mainly by transferring through the volume of the insulator.
Early-stage human islet amyloid polypeptide aggregation: Mechanisms behind dimer formation
Authors: Guo Ashley Z. , Fluitt Aaron M. , de Pablo Juan J.
Published: July 2018

Amyloid aggregates of human islet amyloid polypeptide (hIAPP or human amylin) have long been implicated in the development of type II diabetes. While hIAPP is known to aggregate into amyloid fibrils, it is the early-stage prefibrillar species that have been proposed to be cytotoxic. A detailed picture of the early-stage aggregation process and relevant intermediates would be valuable in the development of effective therapeutics. Here, we use atomistic molecular dynamics simulations with a combination of enhanced sampling methods to examine the formation of the hIAPP dimer in water. Bias-exchange metadynamics calculations reveal relative conformational stabilities of the hIAPP dimer. Finite temperature string method calculations identify pathways for dimer formation, along with relevant free energy barriers and intermediate structures. We show that the initial stages of dimerization involve crossing a substantial free energy barrier to form an intermediate structure exhibiting transient β-sheet character, before proceeding to form an entropically stabilized dimer structure.
Relativistic-amplitude electromagnetic waves—Beating the “magnetic” barrier
Authors: Mahajan Swadesh , Lingam Manasvi
Published: July 2018

The dispersion characteristics of a circularly polarized electromagnetic wave of arbitrary amplitude, propagating in a highly (thermally and kinematically) relativistic plasma, are shown to approach those of a linear wave in an unmagnetized, non-relativistic plasma. Further aided by high relativistic temperatures, the cut-off frequency tends to become negligibly small; as a result, waves with frequencies well below the nominal plasma and the cyclotron frequencies find the plasma to be essentially transparent. This relativistic phenomenon may greatly advance our ability to understand and model the dynamics of a large class of astrophysical and laser-produced high energy density systems.
A support vector regression method for efficiently determining neutral profiles from laser induced fluorescence data
Authors: Fisher Dustin M. , Kelly Ralph F. , Patel Deep R. , Gilmore Mark
Published: July 2018

A support vector regression (SVR) method is integrated with a collisional radiative (CR) model of helicon plasmas in the Helicon-Cathode (HelCat) linear plasma device to determine Ar i profiles based on metastable-pumped Laser Induced Fluorescence (LIF) measurements. A machine learning approach to the CR model allows for an efficient exploration of the input parameter space and can inherently incorporate probe and LIF measurement errors in profile inputs to which a CR model would normally be sensitive. A training set is created for mapping CR model outputs to Ar i input profiles using radial points as SVR input features and parameters of a sigmoidal-type function as output features. This SVR method may easily be adapted to other LIF pumping schemes and may even be used in conjunction with a CR model to validate electron temperature and density plasma profiles if neutral or ion profiles are already known.
Simple scaling equations for electron spectra, currents, and bulk heating in ultra-intense short-pulse laser-solid interaction
Authors: Kluge T. , Bussmann M. , Schramm U. , Cowan T. E.
Published: July 2018

Intense and energetic electron currents can be generated by ultra-intense lasers interacting with solid density targets. Specifically, for ultra-short laser pulses, their temporal evolution needs to be taken into account for many non-linear processes as instantaneous values may differ significantly from the average. Hence, a dynamic model including the temporal variation of the electron currents—which goes beyond a simple bunching with twice the laser frequency but otherwise constant current—is needed. Here, we present a time-dependent solution to describe the laser generated currents and obtain simple expressions for the electron spectrum, temporal evolution, and resulting correction of average values. To exemplify the semi-empiric model and its predictive capabilities, we show the impact of temporal evolution, spectral distribution, and spatial modulations on Ohmic heating of the bulk target material.
Parametric decay of oblique whistler waves in the Earth's magnetosphere: 2-D PIC simulations
Authors: Ke Yangguang , Gao Xinliang , Lu Quanming , Hao Yufei , Wang Shui
Published: July 2018

Whistler mode waves in the Earth's magnetosphere have already been widely investigated in the linear or quasi-linear regime, but there is still lack of research on nonlinear physical processes. In this paper, with a 2-D PIC simulation model, we have studied the parametric decay of oblique whistler waves for the first time. The parametric decay of an oblique whistler wave first occurs along its propagating direction, which involves a backward daughter whistler wave and a forward ion acoustic mode. This is quite similar to the parametric decay of parallel whistler waves in 1-D simulations. Interestingly, the parametric decay will then take place along the perpendicular direction, which can generate a family of daughter whistler waves along the perpendicular direction with the nearly same parallel wave number. Meanwhile, the highly oblique whistler waves will also be excited during this perpendicular decay, whose wave normal angle can even reach up to the resonant cone angle. Moreover, the parametric decay tends to be stronger for the pump whistler wave with a larger frequency or larger amplitude. But the growth rate of the parametric decay has little change when the wave normal angle of the pump whistler wave varies within a limited range. Interestingly, parallel whistler waves can also experience the similar decay process, which may suggest that the parametric decay of whistler waves should be a multi-dimensional process in nature. During the decay process, the generated ion acoustic waves can accelerate a part of protons through the Landau resonance. Our simulation results not only uncover the evolution pattern of whistler waves during the parametric decay in a two-dimensional regime but also propose a potential nonlinear physical process related to whistler waves in the Earth's magnetosphere.
Phonon anharmonicity in thermoelectric palladium sulfide by Raman spectroscopy
Authors: Chen Liu-Cheng , Cao Zi-Yu , Yu Hao , Jiang Bin-Bin , Su Lei , Shi Xun , Chen Li-Dong , Chen Xiao-Jia
Published: July 2018

Recent advances in the study of thermoelectric materials mainly focus on the developments or designs of methods to reduce thermal conductivities. The information of phonon scattering processes is the key to the understanding of the thermal transfer and transport of a material. Such information is essential for the understanding of the thermal conductivity of a material itself and for the further improvement to demand the requirements for technological applications. Recently, palladium sulfide has been examined as a potential thermoelectric material. However, the high thermal conductivity limits its thermoelectric performance and technological applications. Here, Raman scattering spectroscopy is used to investigate the thermal transport properties of this material over a wide range of temperatures. The nonlinear temperature-dependent frequencies and linewidths of the Raman modes illustrate the anharmonicity of phonon scattering for thermal transport in this material. Three-phonon scattering processes are found to account for the thermal transport in the temperature range of 10–620 K. The high-energy bands of the Bg mode related to the light atom (S) contribute most to the thermal transport properties. More phonon scattering processes including higher orders are seemingly needed to further reduce the thermal conductivity of this material.
Quantum entanglement helps to beat multiplayer games
Authors: Yiu Yuen
Published: July 2018

Quantum entangled individuals can more efficiently share resources with others than classical ones.
Comparing the height and area of wild and prescribed fire particle plumes in south-east Australia using weather radar
Authors: Price Owen F. , Purdam Phil J. , Williamson Grant J. , Bowman David M. J. S.
Published: July 2018

Smoke pollution from landscape fires is a major health issue. Prescribed burning aims to reduce the area and impact of wildfire, but itself produces smoke pollution. This raises the question as to whether the smoke production and transport from prescribed fires is substantially different compared to wildfires. We examined the maximum height, width and areal footprint of large-particle plumes from 97 wild and 126 prescribed fires in south-eastern Australia using the existing network of weather radars. Radar detects large particles in smoke (probably those >100 μm) and hence is an imperfect proxy for microfine (<2 μm) particles that are known to affect human health. Of the 223 landscape fires, ~45% of plumes were detected, with the probability being >0.8 for large fires (>100 000 ha) regardless of type, closer than 50 km from the radar. Plume height was strongly influenced by fire area, the height of the planetary boundary layer and fire type. Plume heights differed between wildfire (range 1016–12 206 m, median 3260 m) and prescribed fires (range 706–6397 m, median 1669 m), and prescribed fires were predicted to be 800–1200 m lower than wildfires, controlling for other factors. For both wildfires and prescribed fires, the maximum plume footprint was always near the ground.
On-line processing of verb-argument constructions: Visual recognition threshold and naming latency
Authors: Ellis Nick C.
Published: July 2018

Ellis, O’Donnell, and Römer (2014) used free-association tasks to investigate
knowledge of Verb-Argument Constructions (VACs). They demonstrated that
English speakers have independent implicit knowledge of (i) verb frequency in
the VAC, (ii) VAC-verb contingency, and (iii) verb prototypicality in terms of
centrality within the VAC semantic network. They concluded that VAC processing involves rich associations, tuned by verb type and token frequencies and their contingencies of usage, which interface syntax, lexis, and semantics. However, the tasks they used, where respondents had a minute to think of the verbs that fitted in VAC frames like ‘he __ across the….’, ‘it __ of the….’, etc., were quite conscious and explicit. The current experiments therefore investigate the effects of these factors in on-line processing for recognition and naming. Experiment 1 tested the recognition of VAC exemplars from very brief, masked, visual presentations. Recognition threshold was affected by overall verb frequency in the language, by the frequency with which verbs appear in the VAC, and by VACverb contingency (ΔPcw). Experiment 2 had participants successively name VAC arguments as quickly as possible: first the VAC and then the preposition. Preposition naming latency was a function of verb frequency in the VAC. We consider the implications for the representation and processing of VACs.
The challenges and benefits of annotating oral bilingual corpora
Authors: Bullock Barbara E. , Serigos Jacqueline , Toribio Almeida Jacqueline , Wendorf Arthur
Published: July 2018

This article describes efforts to collect, process, and automatically annotate a corpus of Spanish as spoken in Texas. It elaborates the protocols for the development of the corpus and the procedures for automatic annotation, illustrating the common pitfalls to language identification in bilingual corpora and potential methods for circumventing them. The benefits of a comparative corpus approach to contact varieties is illustrated by a case study of a putative verbal calque from the Spanish in Texas data. It is demonstrated that the relative frequency of the verb is much higher than in its source Mexican variety and that the verb selects different complements in Texas than it does in other varieties. The article concludes with a discussion of how computational tools might be fruitfully exploited to resolve long-standing debates about language variation in contact settings.
The influence of linguistic temporal organization on children’s understanding of temporal terms and concepts
Authors: Wagner Laura
Published: July 2018

The Typological Prevalence Hypothesis argues that the cognitive biases that lead to common cross-linguistic patterns also guide language development. Two studies investigated English learning children’s understanding of temporal terms and concepts and how they might be influenced by three typologically common patterns: the use of a deictic center, the asymmetry between past and future times, and the use of temporal remoteness. Using a timeline task, five- and eight-year-old children were asked to locate events with a range of temporal expressions as well as with general event descriptions. The results provided only limited support for the TPH for the temporal domain but do demonstrate the potential for the hypothesis as a research approach.
The possibility of a libertarian Marxism? A reply to Löwy and Besancenot
Authors: Yates Michael D.
Published: July 2018

Löwy and Besancenot (2018) make compelling arguments, with deep and thoughtful reference to infamous revolutionaries Luxemburg, Benjamin, Breton, and Guérin. In this process, they lay out some clear and compelling principles for a libertarian Marxism and a libertarian communism. And these will surely resonate with the large number of people who are forced to experience the limitations of capitalist democracy on a daily basis. These four thinkers remind us that we need is bottom-up democracy and substantive equality in every aspect of life. However, there are limitations to what they can offer that require further discussion and debate. This reply focuses on three of these limitations: the question of spontaneity, the need for radical education, and the concept of individual freedom.
Transcending the nation: a communist strategy in the era of globalization. A reply to Velissariou
Authors: Milios John
Published: July 2018

Neoliberalism and austerity are not ‘false policies’, but strategies of increasing profits by reducing labor and welfare costs. In the process of dismantling labor rights and the welfare state, a part of the population is being marginalized. It becomes ‘superfluous’, and its living conditions approach those of the inflowing refugee masses. However, between indigenous and ‘foreign’ (refugee and immigrant) superfluous populations a clear demarcation line is being reproduced by state apparatuses and the ruling ideology: the demarcation line created by the nation, which excludes the non-nationals (refugees and immigrants) from the polity and certain state provisions. In fact, the nation may be regarded as a facet of the state itself: the ‘historically homogenized’ population of a given capitalist state. Marginalized Greek (or other European) ‘nationals’ tend to consider themselves ‘superior’ to (equally marginalized) foreigners. Fighting nationalism and, even more, transcending divisions reproduced by ideologies of particularism (often being reproduced in solidarity movements that focus on ‘the rights of the ethnic other’), is a precondition for shaping of a radical left internationalism, through the consolidation of what is universal in all subaltern classes and communities: the need of proletarian unity, first of all within the country, struggling against capitalism.
Capitalism, imperialism, and modes of exchange: a reply to Karatani
Authors: Wainwright Joel
Published: July 2018

This paper is a response to Kojin Karatani's article, “Neoliberalism as a historical stage”. Wainwright argues that Karatani elucidates the relationship between capitalism, imperialism, and empire by extending the mode of exchange theory Karatani has been developing over his career. Wainwright explains Karatani's radical reinterpretation of Marxist theory of empire and imperialism, distinguished based on their predominant mode of exchange: empire results from plunder/protection, imperialism from market/capital. In other words, empire and imperialism are neither epiphenomenal nor strategies waiting to be mobilized by political leaders. Rather, both are historical derivations of prevailing modes of exchange. Wainwright contends that these argument, though novel, do not reflect a radical break from Marx. Rather they reflect a return to Marx's original intuition that capitalism must be grasped through an analysis of production and exchange, extending Marx's analysis from Capital so as to explain other social relations. The global economic crisis (which neoliberalism has no means to resolve) and the persistent decline of US hegemony (with no clear alternative), coupled with the intensification of racialized, nationalist and religious forms of political difference, suggest that our world is entering a period of prolonged crisis, marked by imperialism and war.
γ-Secretase promotes membrane insertion of the human papillomavirus L2 capsid protein during virus infection
Authors: Inoue Takamasa , Zhang Pengwei , Zhang Wei , Goodner-Bingham Kylia , Dupzyk Allison , DiMaio Daniel , Tsai Billy
Published: July 2018

Despite their importance as human pathogens, entry of human papillomaviruses (HPVs) into cells is poorly understood. The transmembrane protease γ-secretase executes a crucial function during the early stages of HPV infection, but the role of γ-secretase in infection and the identity of its critical substrate are unknown. Here we demonstrate that γ-secretase harbors a previously uncharacterized chaperone function, promoting low pH–dependent insertion of the HPV L2 capsid protein into endosomal membranes. Upon membrane insertion, L2 recruits the cytosolic retromer, which enables the L2 viral genome complex to enter the retrograde transport pathway and traffic to the Golgi en route for infection. Although a small fraction of membrane-inserted L2 is also cleaved by γ-secretase, this proteolytic event appears dispensable for HPV infection. Our findings demonstrate that γ-secretase is endowed with an activity that can promote membrane insertion of L2, thereby targeting the virus to the productive infectious pathway.
A new look for the growing microtubule end?
Authors: Rice Luke M.
Published: July 2018

What does the end of a growing microtubule look like? In this issue, McIntosh et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201802138) use electron tomography to provide state-of-the-art three-dimensional images of microtubule ends in cells and in vitro, yielding an unexpected answer to this fundamental question.
The Peculiar Logic of the Black-Scholes Model
Authors: Weatherall James Owen
Published: July 2018

The Black-Scholes(-Merton) model of options pricing establishes a theoretical relationship between the “fair” price of an option and other parameters characterizing the option and prevailing market conditions. Here I discuss a common application of the model with the following striking feature: the (expected) output of analysis apparently contradicts one of the core assumptions of the model on which the analysis is based. I will present several attitudes one might take toward this situation and argue that it reveals ways in which a “broken” model can nonetheless provide useful (and tradeable) information.
The Efficiency Question in Economics
Authors: Northcott Robert
Published: July 2018

Much philosophical attention has been devoted to whether economic models explain and more generally to how scientific models represent. Yet there is an issue more practically important to economics than either of these, which I label theefficiency question: regardless of how exactly models represent, or of whether their role is explanatory or something else, is current modeling practice an efficient way to achieve these goals or should research efforts be redirected? In addition to showing how the efficiency question has been relatively neglected, I give two examples of the kind of analysis it requires.
The Public Understanding of What? Laypersons’ Epistemic Needs, the Division of Cognitive Labor, and the Demarcation of Science
Authors: Keren Arnon
Published: July 2018

What must laypersons understand about science to allow them to make sound decisions on science-related issues? Relying on recent developments in social epistemology, this article argues that scientific education should have the goal not of bringing laypersons’ understanding of science closer to that of expert insiders but rather of cultivating the kind of competence characteristic of “competent outsiders.” Moreover, it argues that philosophers of science have an important role to play in attempts to promote this kind of understanding but that, to successfully fulfill this role, they will have to approach central questions in the field differently.
Memory and Optogenetic Intervention: Separating the Engram from the Ecphory
Authors: Robins Sarah K.
Published: July 2018

Optogenetics makes possible the control of neural activity with light. In this article, I explore how the development of this experimental tool has brought about methodological and theoretical advances in the neurobiological study of memory. I begin with Semon’s distinction between the engram and the ecphory, explaining how these concepts present a methodological challenge to investigating memory. Optogenetics provides a way to intervene into the engram without the ecphory that, in turn, opens up new means for testing theories of memory error. I focus on a series of experiments where optogenetics is used to study false memory and forgetting.
Cost-Effectiveness of Renal Denervation Therapy for Treatment-Resistant Hypertension: A Best Case Scenario
Authors: Chowdhury Enayet Karim , Reid Christopher M , Zomer Ella , Kelly Darren J , Liew Danny
Published: July 2018

BACKGROUND

Renal denervation (RDN) is effective at reducing blood pressure (BP) among patients with treatment-resistant hypertension (TRH). However, recent findings regarding the effectiveness of RDN for BP reduction compared with standard treatment of care (SoC) has initiated a rigorous debate about its role in TRH management. In this study, we sought to determine the thresholds for cardiovascular risk and costs of RDN which would make RDN cost-effective.

METHODS

A Markov model was constructed to simulate cardiovascular events over a lifetime among TRH subjects aged 60 years at baseline, and without prior cardiovascular disease. The effect on lowering BP was based on results observed in clinical trials of RDN undertaken to date, and the expected subsequent change to cardiovascular risk was drawn from a published meta-regression. Cost and utility data were drawn from published sources. Incremental cost-effectiveness ratios (ICER) in terms of Australian dollars (AUD) per life year and per quality-adjusted life year (QALY) gained were estimated to assess RDN cost-effectiveness relative to SoC from the Australian health care perspective, assuming a willingness-to-pay threshold of AUD 50,000.

RESULTS

Over a lifetime horizon, the model predicted that at the current estimated costs of RDN (AUD 9531/€6573, 1€ = 1.45 AUD), it would be cost-effective only if it was targeted to patients whose 10-year predicted cardiovascular risk was at least 13.2% initially. The ICERs (discounted) were AUD 49,519 per life year gained and AUD 47,130 per QALY gained.

CONCLUSIONS

At current costs and based on currently observed effects on BP reduction, RDN would be cost-effective among patients with TRH.
Prevalence of Self-Reported Hypertension in Deaf Adults Who Use American Sign Language
Authors: Simons Abbi N , Moreland Christopher J , Kushalnagar Poorna
Published: July 2018

BACKGROUND

In the United States, roughly one-third of adults have hypertension; another third have prehypertension. The prevalence of hypertension in deaf American Sign Language (ASL) users is unknown. We address this gap through a descriptive study for the prevalence of hypertension in the American Deaf community and discuss future directions to address this issue.

METHODS

Self-reported data for 1,388 ASL using deaf adults were compared with a secondary data of 2,830 English-speaking hearing adults. Frequency and percentages were used to describe the prevalence of hypertension in the deaf community. Age-weighted analysis was used to compare unmodifiable risk factors and hypertension rate between deaf and hearing adults.

RESULTS

Deaf and hearing samples’ hypertension rates for gender and age were similar. Significant group differences between deaf and hearing samples emerged across race. Compared with the hearing controls, our deaf sample demonstrated a significantly decreased risk for hypertension with a prevalence of 37% (compared with 45% in the hearing sample).

CONCLUSIONS

Although the hypertension rate for gender and age was similar across deaf and hearing samples, between-group disparities exist for race. The lower rate of hypertension in our deaf sample is likely a consequence of underdiagnoses due to lower health literacy and poor patient–physician communication. Furthermore, deaf black Americans’ lower rates compared with hearing black Americans may be due to poor patient–physician communication, not having regular providers or social stressors. It is recommended that modifiable risk factors and social determinants be investigated to determine their effect on hypertension within the deaf community.
GIGSEA: genotype imputed gene set enrichment analysis using GWAS summary level data
Authors: Zhu Shijia , Qian Tongqi , Hoshida Yujin , Shen Yuan , Yu Jing , Hao Ke
Published: July 2018

Summary level data of GWAS becomes increasingly important in post-GWAS data mining. Here, we present GIGSEA (Genotype Imputed Gene Set Enrichment Analysis), a novel method that uses GWAS summary statistics and eQTL to infer differential gene expression and interrogate gene set enrichment for the trait-associated SNPs. By incorporating empirical eQTL of the disease relevant tissue, GIGSEA naturally accounts for factors such as gene size, gene boundary, SNP distal regulation and multiple-marker regulation. The weighted linear regression model was used to perform the enrichment test, properly adjusting for imputation accuracy, model incompleteness and redundancy in different gene sets. The significance level of enrichment is assessed by the permutation test, where matrix operation was employed to dramatically improve computation speed. GIGSEA has appropriate type I error rates, and discovers the plausible biological findings on the real data set.

Availability and implementation

GIGSEA is implemented in R, and freely available at www.github.com/zhushijia/GIGSEA.

Supplementary information

Supplementary data are available at Bioinformatics online.
A parallel computational framework for ultra-large-scale sequence clustering analysis
Authors: Zheng Wei , Mao Qi , Genco Robert J , Wactawski-Wende Jean , Buck Michael , Cai Yunpeng , Sun Yijun
Published: July 2018

Motivation

The rapid development of sequencing technology has led to an explosive accumulation of genomic data. Clustering is often the first step to be performed in sequence analysis. However, existing methods scale poorly with respect to the unprecedented growth of input data size. As high-performance computing systems are becoming widely accessible, it is highly desired that a clustering method can easily scale to handle large-scale sequence datasets by leveraging the power of parallel computing.

Results

In this paper, we introduce SLAD (Separation via Landmark-based Active Divisive clustering), a generic computational framework that can be used to parallelize various de novo operational taxonomic unit (OTU) picking methods and comes with theoretical guarantees on both accuracy and efficiency. The proposed framework was implemented on Apache Spark, which allows for easy and efficient utilization of parallel computing resources. Experiments performed on various datasets demonstrated that SLAD can significantly speed up a number of popular de novo OTU picking methods and meanwhile maintains the same level of accuracy. In particular, the experiment on the Earth Microbiome Project dataset (∼2.2B reads, 437 GB) demonstrated the excellent scalability of the proposed method.

Availability and implementation

Open-source software for the proposed method is freely available at https://www.acsu.buffalo.edu/~yijunsun/lab/SLAD.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction
Authors: Han Renmin , Wan Xiaohua , Li Lun , Lawrence Albert , Yang Peng , Li Yu , Wang Sheng , Sun Fei , Liu Zhiyong , Gao Xin , Zhang Fa
Published: July 2018

Motivation

Dual-axis electron tomography is an important 3 D macro-molecular structure reconstruction technology, which can reduce artifacts and suppress the effect of missing wedge. However, the fully automatic data process for dual-axis electron tomography still remains a challenge due to three difficulties: (i) how to track the mass of fiducial markers automatically; (ii) how to integrate the information from the two different tilt series; and (iii) how to cope with the inconsistency between the two different tilt series.

Results

Here we develop a toolkit for fully automatic alignment of dual-axis electron tomography, with a simultaneous reconstruction procedure. The proposed toolkit and its workflow carries out the following solutions: (i) fully automatic detection and tracking of fiducial markers under large-field datasets; (ii) automatic combination of two different tilt series and global calibration of projection parameters; and (iii) inconsistency correction based on distortion correction parameters and the consequently simultaneous reconstruction. With all of these features, the presented toolkit can achieve accurate alignment and reconstruction simultaneously and conveniently under a single global coordinate system.

Availability and implementation

The toolkit AuTom-dualx (alignment module dualxmauto and reconstruction module volrec_mltm) are accessible for general application at http://ear.ict.ac.cn, and the key source code is freely available under request.

Supplementary information

Supplementary data are available at Bioinformatics online.
Incorporating teleseismic tomography data into models of upper mantle slab geometry
Authors: Portner Daniel Evan , Hayes Gavin P
Published: July 2018

Earthquake-based models of slab geometry are limited by the distribution of earthquakes within a subducting slab, which is often heterogeneous. The fast seismic velocity signature of slabs in tomography studies is independent of the distribution of earthquakes within the slab, providing a critical constraint on slab geometry when earthquakes are absent. In order to utilize this constraint, researchers typically hand-contour images of subducting slabs in tomography models, leading to a subjective final slab model. With this paper, we present an automated procedure for extracting slab geometry from teleseismic tomography volumes that limits this subjectivity and provides constraints on the structure of aseismic segments of slabs. This procedure is designed as a complement to earthquake-based slab models rather than as a replacement, which can help to broaden the extent of existing subduction zone geometry databases.
Fluoroscopic-Guided Paramedian Approach for Lumbar Catheter Placement in Cerebrospinal Fluid Shunting: Assessment of Safety and Accuracy
Authors: Tucker Adam , Kajimoto Yoshinaga , Ohmura Tomohisa , Ikeda Naokado , Furuse Motomasa , Nonoguchi Naosuke , Kawabata Shinji , Kuroiwa Toshihiko
Published: July 2018

BACKGROUND

Spinal catheter insertion in lumboperitoneal (LP) shunt surgery for idiopathic normal pressure hydrocephalus (iNPH) is frequently associated with technical difficulties especially in patients with obesity and elderly patients with vertebral deformities.

OBJECTIVE

To elucidate the accuracy and safety of image-guided spinal catheter placement using a paramedian approach (PMA).

METHODS

We retrospectively analyzed 39 consecutive iNPH patients treated by LP shunting with spinal catheter insertion via the PMA. The success rate of catheter placement and the number of changes in puncture location were evaluated. Accuracy of catheter insertion was assessed by measuring both vertical and horizontal deviations in the point of catheter dural penetration from the center of the interlaminar space.

RESULTS

The success rate of catheter placement was 100% (39/39). The difficulty rate for catheter insertion, measured by the number of changes in puncture location, was 2.6% (1/39). No bloody punctures or surgical infections were observed. Accuracy of catheter insertion, measured as the degree of deviation, was 0.5 ± 1.9 mm horizontally and 0.0 ± 2.4 mm vertically. The rates of minor complications, including caudal catheter insertion, transient low-pressure headache, and root pain, were 5.1% (2/39), 10.4% (4/39), and 0% (0/43), respectively. Subdural hematoma requiring surgical intervention occurred in 1 case (2.6%). During the mean follow-up period of 36 mo, spinal catheter rupture at the level of the spinous processes was not observed.

CONCLUSION

Fluoroscopic-guided spinal catheter placement via the PMA was safe, accurate, and reliable, even for use in geriatric and obese patients.
CE: A Review of the Revised Sepsis Care Bundles
Authors: Lester Donna , Hartjes Tonja , Bennett Amanda
Published: July 2018

Sepsis is an extreme response to infection that can cause tissue damage, organ failure, and death if not treated promptly and appropriately. Each year in the United States, sepsis affects more than 1.5 million people and kills roughly 250,000. Prompt recognition and treatment of sepsis are essential to saving lives, and nurses play a critical role in the early detection of sepsis, as they are often first to recognize the signs and symptoms of infection. Here, the authors review recent revisions to the sepsis care bundles and discuss screening and assessment tools nurses can use to identify sepsis in the ICU, in the ED, on the medical–surgical unit, and outside the hospital.
Temporal and Spatial Changes of μ-Opioid Receptors in the Brain, Spinal Cord and Dorsal Root Ganglion in a Rat Lumbar Disc Herniation Model
Authors: Kaneuchi Yoichi , Sekiguchi Miho , Kameda Takuya , Kobayashi Yoshihiro , Konno Shin-ichi
Published: July 2018

Study Design.

Controlled, interventional, animal study.

Objective.

To investigate the spatial and temporal changes of μ-opioid receptor (MOR) expression in a rat lumbar disc herniation (LDH) model.

Summary of Background Data.

MORs widely express in the peripheral and central nervous systems, and opioid drugs produce an analgesic effect through their activation. However, the efficacy of opioid drugs is sometimes inadequate in several pathological conditions of pain. MORs in the brain as well as the spinal cord (SC) and dorsal root ganglion (DRG) are thought to be associated with pain-related behavior, but the underlying mechanisms are not completely understood.

Methods.

In all, 91 adult female Sprague-Dawley rats were used. Autologous nucleus pulposus (NP) was applied onto the left L5 DRG in the NP group rats. Rats were divided into two surgical groups, the NP and the sham group. The von Frey test of left hind paw was performed before surgery, and 2, 7, 14, 21 and 28 days after surgery. Immunohistochemistry and immunoblotting in the DRG, SC, Caudate putamen, nucleus accumbens (NAc) and periaqueductal grey matter were performed before surgery, and 2, 7, 14, 21 and 28 days after surgery.

Results.

The thresholds in the NP group were significantly lower than those in the sham group from day 2 onwards. At days 7 and 14, MOR expression in the injured-side SC and DRG were significantly lower than those in the sham group. At day 21, MOR in the NAc was significantly decreased compared to that in the sham group.

Conclusion.

Changes of MOR expression in the NAc, SC and DRG were associated with pain-related behavior. This result might show the underling pathogenesis of the resistance to MOR agonists in the patient with LDH.

Level of Evidence: N/A
Expectations for Postoperative Improvement in Health-Related Quality of Life in Young Patients With Lumbosacral Spondylolisthesis
Authors: Bourassa-Moreau Étienne , Labelle Hubert , Parent Stefan , Hresko Micheal Timothy , Sucato Daniel , Lenke Laurence G. , Marks Michelle , Mac-Thiong Jean-Marc
Published: July 2018

Study Design.

Prospective multicenter study of the changes in Scoliosis Research Society Outcome Questionaire 22 (SRS-22) scores for 78 patients younger than 25 years old surgically treated for lumbosacral spondylolisthesis

Objective.

Report the change of health-related quality of life (HRQOL) in patients younger than 25 years after surgical treatment of lumbosacral spondylolisthesis.

Summary of Background Data.

There is a paucity of data with regard to the influence of surgical treatment on the HRQOL of patients with lumbosacral spondylolisthesis. Large prospective studies are needed to clearly define the benefits of surgery in the young patient population.

Methods.

A prospective multicenter cohort of 78 patients younger than 25 years (14.8 ± 2.9, range: 7.9–23.6 yr) undergoing posterior fusion for lumbosacral spondylolisthesis were enrolled. There were 17 patients with low-grade (<50%) and 61 with high-grade (≥50%) slips. SRS-22 scores calculated before surgery and after 2 years of follow-up were compared for all patients using two-tailed paired t tests. Subanalyses for low- and high-grade patients were done using two-tailed Wilcoxon signed ranked and paired t tests, respectively. The level of significance was set at 0.05.

Results.

HRQOL was significantly improved 2 years after surgery for all domains and for the total score of the SRS-22 questionnaire. The individual total score was improved in 66 patients (85%), and 52 patients (67%) improved by at least 0.5 point. All domains and the total score of the SRS-22 questionnaire were significantly improved for high-grade patients, whereas only pain, function, and total score were improved for low-grade patients.

Conclusion.

This is the largest study comparing the HRQOL before and after surgery in young patients with low- and high-grade lumbosacral spondylolisthesis. HRQOL significantly improves after surgery for the majority of patients, especially for high-grade patients. This study helps clinicians to better counsel patients with regard to the benefits of surgery for lumbosacral spondylolisthesis.

Level of Evidence: 2
Compromised vitamin D receptor signalling in malignant melanoma is associated with tumour progression and mitogen-activated protein kinase activity
Authors: Hutchinson Peter E. , Halsall John A. , Popovici Silvia , Papadogeorgakis Eftychios , Osborne Joy E. , Powley Ian R. , Dasari Deepthi , Saldanha Gerald , Pringle James H.
Published: July 2018

The aims of this study were to investigate, in cutaneous malignant melanoma (MM), the integrity of nuclear vitamin D receptor (VDR) signalling, as implied by VDR subcellular location; to investigate the relationship between VDR and tumour progression and the inhibitory effect on VDR by mitogen-activated protein kinase (MAPK) overactivity. Archived tissue from 34 benign melanocytic naevi, 149 MMs and 44 matched metastases were stained by immunohistochemistry for VDR and a subset of primary MMs were stained for phosphorylated-extracellular signal-regulated kinase as a marker of MAPK activity. MM cell lines were investigated to show the subcellular location of VDR and cell viability in response to ligand±MAPK inhibitor. Benign melanocytic naevi showed mainly a strong nuclear VDR staining in contrast to MM where decreased nuclear and emergent cytoplasmic VDRs were associated with malignant progression in terms of dermal invasion and metastasis. MMs that retained exclusive nuclear VDR at the tumour base did not metastasize, a potentially important prognostic indicator. Decreased nuclear VDR correlated with increased cytoplasmic staining, suggesting the failure of nuclear entry as a primary cause of defective VDR signalling in MM. The histological subset analysis and MM cell line studies confirmed the inhibitory effect of MAPK activity on VDR signalling, but the pattern of VDR subcellular localization suggested failure of VDR nuclear entry as a primary effect of MAPK activity rather than direct inhibition of VDR-regulated transcription. Furthermore, high MAPK activity in tumours expressing cytoplasmic VDR was associated with worsened prognosis.
Clinical Approach to Community-acquired Pneumonia
Authors: Cillóniz Catia , Rodríguez-Hurtado Diana , Nicolini Antonello , Torres Antoni
Published: July 2018

Community-acquired pneumonia (CAP) remains a major health problem worldwide. The incidence of pneumonia increases with both age and the presence of specific risk factors, which lead to increased health care costs. However, although there is some controversy over the observed trend in CAP mortality over recent decades, it is clear that mortality in CAP patients who require intensive care unit care remains high. The increase in antibiotic resistance is an important global health problem that needs to be addressed, especially for pneumococcus the most frequent pathogen of CAP. The prudent use of current antibiotics will help to limit the spread of antibiotic resistant clones of pneumococcus. Pneumococcal and influenza vaccinations remain the primary strategy for the prevention of CAP, especially in an at-risk population. This article reviews CAP, with a focus on epidemiology, diagnosis, prognostic factors, microbial etiology, therapy, complications, and prevention.
Magnetoencephalographic Recordings in Infants: A Retrospective Analysis of Seizure-Focus Yield and Postsurgical Outcomes
Authors: Garcia-Tarodo Stephanie , Funke Michael , Caballero Lisa , Zhu Liang , Shah Manish N. , Von Allmen Gretchen K.
Published: July 2018

Purpose:

Magnetoencephalography (MEG) is often incorporated into the presurgical work-up of children with pharmacoresistant epilepsy. There is growing literature on its role in improving selection for epilepsy surgery, particularly when brain MRI is “non-lesional” or in patients with recurrence or intractable seizures after epilepsy surgery. There are, however, no reports on the extrapolation of its role in the presurgical decision-making process of infants.

Methods:

We performed a retrospective analysis of infants who underwent MEG over a 10-year period at our center for presurgical work-up. We reviewed medical records to ascertain seizure history, work-up procedures including brain MRI and scalp EEG, and in the case of surgery, intracranial recordings, operative notes, and follow-up outcomes.

Results:

We identified 31 infants (<2 years of age) who underwent MEG recordings. Despite EEG interictal readings showing patterns of generalized dysfunction in 80%, MEG was able to pinpoint the foci of epileptic activity in 45%. In the MRI-negative group, 44% had focal lateralized interictal spikes on MEG. The sensitivity of MEG to detect interictal epileptiform activity was 90%, and its ability to provide additional information was 28%. Among 18 infants who had surgery, 13 became seizure free at follow-up. The percentage of infants with a focal spike volume on MEG studies and a seizure-free outcome was 66%.

Conclusions:

MEG recordings in infants were found to be as sensitive for identifying seizure focus as other age groups, also supplying additional information to the decision-making process and validating its role in the presurgical work-up of infants with intractable epilepsy.