bluuebunny/crossref_metadata_2025 huggingface dataset:
Randomly arranged cation-ordered nanoregions in lead-free relaxor ferroelectric K1/2Bi1/2TiO3: Prediction from first-principles study
Authors: Niranjan Manish K. , Karuna Kumari P. , Banerjee Krishnarjun , Asthana Saket
Published: June 2018

First-principles density functional calculations are performed to investigate the lattice dynamics, Infrared reflectivity, and Raman intensity spectra of a lead-free ferroelectric K1/2Bi1/2TiO3 system. In particular, the A-site cation ordering in K1/2Bi1/2TiO3 and its effects on lattice dynamics and the Raman spectrum are explored. The results suggest that the cation ordering at the A-site in K1/2Bi1/2TiO3 significantly influences its Raman spectra. From the analysis of theoretical and experimental Raman spectra, it is suggested that randomly arranged cation ordered nanoregions with different A-site orderings are formed in K1/2Bi1/2TiO3 samples. The random arrangement is favored by entropy contributions to free energy and may explain the lack of observed long-range A-site cation ordering in K1/2Bi1/2TiO3. Further, it is suggested that partial A-site cation ordering may also occur in K1/2Bi1/2TiO3 favored by kinetic factors during sample preparation. The Born effective charges of K and Bi ions at the A-site are computed and found to be significantly disparate, thereby suggesting hetero-polar activity at the A-site in K1/2Bi1/2TiO3. The formation of A-site hetero-polar cation ordered nanoregions and their random or/and partially ordered arrangement in K1/2Bi1/2TiO3 may play an important role in the determination of its relaxor properties apart from the dominant role played by polar nanoregions. The computed Infrared reflectivity and Raman intensity spectra are expected to provide benchmark first-principles results for further analysis of experimental spectra and results.
Is human atrial fibrillation stochastic or deterministic?—Insights from missing ordinal patterns and causal entropy-complexity plane analysis
Authors: Aronis Konstantinos N. , Berger Ronald D. , Calkins Hugh , Chrispin Jonathan , Marine Joseph E. , Spragg David D. , Tao Susumu , Tandri Harikrishna , Ashikaga Hiroshi
Published: June 2018

The mechanism of atrial fibrillation (AF) maintenance in humans is yet to be determined. It remains controversial whether cardiac fibrillatory dynamics are the result of a deterministic or a stochastic process. Traditional methods to differentiate deterministic from stochastic processes have several limitations and are not reliably applied to short and noisy data obtained during clinical studies. The appearance of missing ordinal patterns (MOPs) using the Bandt-Pompe (BP) symbolization is indicative of deterministic dynamics and is robust to brief time series and experimental noise. Our aim was to evaluate whether human AF dynamics is the result of a stochastic or a deterministic process. We used 38 intracardiac atrial electrograms during AF from the coronary sinus of 10 patients undergoing catheter ablation of AF. We extracted the intervals between consecutive atrial depolarizations (AA interval) and converted the AA interval time series to their BP symbolic representation (embedding dimension 5, time delay 1). We generated 40 iterative amplitude-adjusted, Fourier-transform (IAAFT) surrogate data for each of the AA time series. IAAFT surrogates have the same frequency spectrum, autocorrelation, and probability distribution with the original time series. Using the BP symbolization, we compared the number of MOPs and the rate of MOP decay in the first 1000 timepoints of the original time series with that of the surrogate data. We calculated permutation entropy and permutation statistical complexity and represented each time series on the causal entropy-complexity plane. We demonstrated that (a) the number of MOPs in human AF is significantly higher compared to the surrogate data (2.7 ± 1.18 vs. 0.39 ± 0.28, p < 0.001); (b) the median rate of MOP decay in human AF was significantly lower compared with the surrogate data (6.58 × 10−3 vs. 7.79 × 10−3, p < 0.001); and (c) 81.6% of the individual recordings had a rate of decay lower than the 95% confidence intervals of their corresponding surrogates. On the causal entropy-complexity plane, human AF lay on the deterministic part of the plane that was located above the trajectory of fractional Brownian motion with different Hurst exponents on the plane. This analysis demonstrates that human AF dynamics does not arise from a rescaled linear stochastic process or a fractional noise, but either a deterministic or a nonlinear stochastic process. Our results justify the development and application of mathematical analysis and modeling tools to enable predictive control of human AF.
Application of photon Doppler velocimetry for characterization of ejecta from shock-loaded samples
Authors: Andriyash A. V. , Astashkin M. V. , Baranov V. K. , Golubinskii A. G. , Irinichev D. A. , Khatunkin V. Yu. , Kondratev A. N. , Kuratov S. E. , Mazanov V. A. , Rogozkin D. B. , Stepushkin S. N.
Published: June 2018

We consider the problem of recovering the physical parameters of ejecta from data of photon Doppler velocimetry (PDV). The results of PDV measurements of ejecta production from shock-loaded Pb samples are presented. Shockwaves in the samples were generated by an accelerated flyer-plate. Depending on the sample thickness, the shock-breakout pressure varied from 27.5 to 43 GPa. The ejecta transport occurred in the air. The spectral profile J(ω) of heterodyne beats underlies our analysis of the experiments. The noise-free component of |J(ω)|2 is shown to obey the transport equation which accounts for multiple scattering and absorption of the probing beam in the cloud of moving particles. This provides a means for theoretical modeling of PDV data. Varying the values of the free-surface velocity and the parameters of the velocity distribution of ejecta, we fit the calculated spectrum to the PDV-measured one. We apply this method to time-resolved PDV spectra and, based on the ejecta optical model, recover the values of the free-surface velocity, the areal density, and the density-velocity distribution of ejecta.
Stress-controlled dynamic susceptibility in FeGa stripes
Authors: Dai Guohong , Xing Xiangjun , Shen Yun , Deng Xiaohua
Published: June 2018

Knowledge of the dynamic magnetic susceptibility of patterned films is of great importance for exploring future data-storage applications and microwave devices. Since ferromagnetic resonance frequency is a function of the geometric parameters of a certain magnetic system, in this work, we investigate by micromagnetic simulations a set of stripe-patterned FeGa films, which have an identical thickness of 10 nm but a varying width in the range of 30–80 nm and a varying length in the range of 200–1000 nm. Fast-Fourier transform analysis of the simulation results for ferromagnetic resonance calculation identifies two distinct resonance peaks, which are assigned to a “bulk” mode and an “edge” mode. The presence of stress-induced anisotropy significantly affects both the two resonant modes. The occupation area of the spreading magnetization near the stripe ends is controllable by a tensile or compressive stress applied along the strip width. Consequently, the dynamic susceptibility of FeGa can be adjusted by an applied stress.
Structural surface wave properties of amorphous Bi2Te3 by pulsed laser deposition in the visible and near-infrared regions
Authors: Chai Zhen , Hu Xiaoyong , Zhao Yifan , Wu You , Wang Shufang , Yang Hong , Gong Qihuang
Published: June 2018

Owing to the unique properties of evanescent fields, surface waves show great applications in near field enhancement and in breaking the resolution limit. In this work, we found the amorphous-state Bi2Te3 film deposited by pulsed laser deposition exhibits surface wave properties in an ultrawide waveband ranging from the visible to near-infrared regions. We analyze the surface wave in three ways: the propagation form, localized form, and coupling with a gold nanobar. This work not only breaks the strict limit of a Bi2Te3 topological crystalline insulator but also widens the wavelength region of surface waves compared with a previous report.
Scattering of CO with H2O: Statistical and classical alternatives to close-coupling calculations
Authors: Loreau J. , Faure A. , Lique F.
Published: June 2018

Energy transfer in inelastic atom-molecule and molecule-molecule collisions can be described theoretically using the quantum-mechanical close-coupling method. Unfortunately, for bimolecular collisions implying heavy colliders and/or for which the potential energy surface has a deep well, the resulting coupled equations become numerically intractable and approximate methods have to be employed. H2O—CO collisions provide an important example for which close-coupling calculations are not feasible. In this paper, we investigate the accuracy of three approximate methods (the coupled states method, the quasi-classical trajectory method, and the statistical adiabatic channel model) to describe inelastic collisions of H2O with CO. We perform scattering calculations on a recent 5D potential energy surface, and we compare the results of the three approximate methods to fully converged close-coupling calculations at energies below 300 cm−1 and at low values of the total angular momentum. We show that the statistical method provides an attractive alternative to fully quantum mechanical close-coupling calculations at low collision energies, while the quasi-classical method is more advantageous at high energies.
Bipolar resistive switching behavior in MoS2 nanosheets fabricated on ferromagnetic shape memory alloy
Authors: Kumar Anuj , Pawar Shuvam , Sharma Shubham , Kaur Davinder
Published: June 2018

The present study explores the systematic investigation of resistive switching response of magnetron sputtered MoS2 thin films sandwiched between a Ni-Mn-In ferromagnetic shape memory alloy (bottom) and copper (top) electrodes. The Cu/MoS2/Ni-Mn-In device exhibits stable and reproducible bipolar resistive switching behavior. The current-voltage (I-V) analysis suggests that the device shows ohmic conduction behavior in the low resistance state (LRS) while space charge limited conduction is the dominating conduction mechanism in the high resistance state (HRS). The compliance current vs reset current measurements were also performed which reveals that the power consumption of the device can be suppressed by decreasing the compliance current. To explain the resistive switching behavior in the Cu/MoS2/Ni-Mn-In device, a conceptual model based on copper ion migration, is proposed and well explained. The resistive switching parameters such as the set voltage, LRS and HRS resistances, are also investigated in a temperature range overlapping with the martensite phase transformation temperatures of the bottom ferromagnetic shape memory alloy (Ni-Mn-In) electrode. It provides temperature as an extra degree of freedom to modulate the resistive switching characteristics of the fabricated device. The Cu/MoS2/Ni-Mn-In device shows a decent endurance of 500 and a long retention of 103. These results demonstrate the feasibility of the MoS2 based devices for futuristic tunable nonvolatile resistive random access memory applications.
Solutes from extreme bacteria protect protein-coated devices from drying
Authors: Liebendorfer Adam
Published: June 2018

Two compounds that help bacteria stay hydrated prevent the damaging effects of drying on protein-coated titanium oxide devices for a day or longer.
A first-principles study reveals effects of cation ordered nanoregions in a lead-free relaxor ferroelectric, K1/2Bi1/2TiO3
Authors: Kim Meeri
Published: June 2018

Researchers investigate cation ordering and its effect on Raman intensity spectra for K 1/2 Bi 1/2 TiO 3 , a promising lead-free piezoceramic material.
Locational relationship between corpus luteum and ovulatory follicle on ovaries alters follicular dynamics and progesterone concentrations of Thai indigenous beef cows exhibiting two follicular waves
Authors: Yama P. , Moonmanee T. , Osathanunkul M. , Jitjumnong J. , Karaphuak W.
Published: June 2018

The present study aims to determine the impact of differences in the locational relationship between the previous corpus luteum (CL) and the further ovulatory follicle (OF) on follicular dynamics and progesterone (P4) concentrations in Thai indigenous beef cows (White Lamphun) exhibiting two follicular waves. Twenty-one cows, exhibiting the two-wave follicular pattern, were studied through interovulatory intervals (IOI), and classified according to the relationship between the previous CL and the further OF on the cattle model ovaries. Classifications were outlined as either an ipsilateral (same ovary) relationship (n = 12), or a contralateral (opposite ovaries) relationship (n = 9). Ultrasound monitoring, which evaluated the follicular diameter, and collection of blood for determining the P4 concentration were performed each day throughout the IOI. The IOI was longer (P < 0.05) in the contralateral cows than in the ipsilateral cows (19.7 ± 0.33 days vs 18.5 ± 0.29 days). Cows with an ipsilateral relationship were found to have further OFs with greater (P < 0.05) diameters than were cows with a contralateral relationship (13.9 ± 0.31 mm vs 12.1 ± 0.21 mm). The mean growth rate of the further OF was greater (P = 0.05) in the ipsilateral cows than in the contralateral cows (1.1 ± 0.11 mm/day vs 0.8 ± 0.04 mm/day). On Day 17 of the IOI, the ipsilateral cows demonstrated their lowest concentration of P4 (P < 0.05). On Day 18 of the IOI, the concentrations of P4 tended to be lower (P = 0.09) in the ipsilateral cows than in the contralateral cows (0.6 ± 0.04 ng/mL vs 1.1 ± 0.12 ng/mL). The interval from the luteinisation until the end of the luteolysis was longer (P < 0.05) in the contralateral group than in the ipsilateral group (18.5 ± 0.50 days vs 16.7 ± 0.33 days). Thus, we conclude that in Thai indigenous beef cows, the growth rate and diameter of the further OF during luteolysis increases more in the ipsilateral relationship than in the contralateral relationship.
How functional traits influence plant growth and shade tolerance across the life cycle
Authors: Falster Daniel S. , Duursma Remko A. , FitzJohn Richard G.
Published: June 2018

Significance

Plant species differ in many functional traits—features of specific tissues and allocation of energy among them. While traits have been used in many correlative approaches to describe communities and demography, it has remained unclear how and why traits should influence whole-plant growth. Here, we present a theoretical framework for understanding the effect of traits on plant growth and shade tolerance. This framework captures diverse patterns of growth in relation to size and explains why the effect of traits on growth changes through ontogeny. By disentangling the effects of plant size, light environment, and traits on growth rates, this study provides a theoretical foundation for understanding growth across diverse tree species around the world.
External light activates hair follicle stem cells through eyes via an ipRGC–SCN–sympathetic neural pathway
Authors: Fan Sabrina Mai-Yi , Chang Yi-Ting , Chen Chih-Lung , Wang Wei-Hung , Pan Ming-Kai , Chen Wen-Pin , Huang Wen-Yen , Xu Zijian , Huang Hai-En , Chen Ting , Plikus Maksim V. , Chen Shih-Kuo , Lin Sung-Jan
Published: June 2018

Significance

Intrinsically photosensitive retinal ganglion cells (ipRGCs) exhibit several important functions including the circadian photo entrainment, pupillary light reflex, alertness, and phototaxis. Whether ipRGCs regulate other physiological activities is unknown. We show that external light stimulation can activate hair follicle stem cells through the eyes via an ipRGC–suprachiasmatic nucleus–sympathetic nervous circuit. Immediately after ipRGCs are stimulated by light, the systemic sympathetic activities are activated. In skin, the local release of norepinephrine activates hair follicle stem cells. This neural circuit enables prompt communication between peripheral tissues and the external environment. Due to the systemic activation of sympathetic activities, this circuit can also allow for timely responses to external light in other organs. It also highlights a function of ipRGCs in regulating autonomic nervous activity.
Visual recognition of cognates and interlingual homographs in two non-native languages
Authors: Zhu Yanjiao , Mok Peggy Pik Ki
Published: June 2018

Previous studies on bilingual visual word recognition have been mainly based on European participants, while less is understood
about Asian populations. In this study, the recognition of German-English cognates and interlingual homographs in lexical decision
tasks was examined in the two non-native languages of Cantonese-English-German trilinguals. In the L2 English task, cognates were
reacted to faster and more accurately than their matched non-cognates, while in the equivalent L3 German task, no cognate
facilitation effect was found. However, cognate facilitation effects on response time and accuracy were observed in another L3
German task including cognates and interlingual homographs. The study suggests that Asian trilinguals access L2 and L3 in a
language non-selective manner, despite their low proficiency in the recently acquired L3. Meanwhile, lexical processing in a
non-proficient L3 is to a great extent affected by multiple contextual factors.
Pilgrimage trails and routes: the journey from the past to the present.
Authors: Olsen D. H. , Trono A. , Fidgeon P. R.
Published: June 2018

Tourism routes and trails, and in particular religious routes and trails, are explained in this chapter, before introducing the content of the book.
Religious pilgrimage routes and trails as driving forces for sustainable local development.
Authors: Trono A. , Castronuovo V.
Published: June 2018

This chapter analyses religious itineraries and pilgrimage routes as 'glocal' phenomena, characterized that is by a natural interface between the local and the global. It describes them as a driver of sustainable development above all in rural and/or marginal areas. After a short discussion of the value generated by complex cultural products such as religious itineraries and their impact on local and regional economies, the chapter considers the structure of local relations or 'networks' that give rise to them and sustain them.
The European cultural route of Saint Martin of Tours.
Authors: Afferni R. , Ferrario C.
Published: June 2018

This chapter focuses on the history and development of the cultural route of Saint Martin of Tours, which was made a Cultural Route by the Council of Europe in 2005 and runs through 45 different European countries. More specifically, the chapter investigates the activities of this route as a coordinated network, to identify possible strengths and weaknesses of the itinerary and eventually to propose some suggestions to remedy and answer the challenges. A key aspect is the role that the administrative centre and each local actor can play in enriching and developing the Route as a social, cultural and economic network.
The holy grail route: mystic routes and activities to improve local tourism.
Authors: Fidgeon P. R.
Published: June 2018

This chapter examines how the tourism industry has utilized the myths and legends of the Holy Grail to develop and enhance tourism at various destinations. The chapter focuses more specifically on GRAIL, an EU-sponsored project designed to develop and promote a Pan-European tourism route based on the legend of the Holy Grail. The development of the Grail Route is discussed, as well as some of the opportunities and challenges that have arisen in the course of its planning and evolution as a sustainable tourism product.
Religious pilgrimage routes in the baltic countries: history and perspectives.
Authors: Liutikas D.
Published: June 2018

This chapter highlights the main features of historical and contemporary religious pilgrimage routes in the Baltic countries (Lithuania, Latvia and Estonia). It considers the main factors responsible for their creation and seeks to identify the development opportunities they offer. It considers the historical context and the contemporary challenges of religious pilgrimage routes in terms of the preservation of religious heritage and development of tourism.
The ways to Jerusalem: maritime, cultural and pilgrimage routes.
Authors: Trono A. , Imperiale M. L.
Published: June 2018

After a brief overview of the ancient routes towards Jerusalem, this chapter illustrates the current itinerary of 'The Ways to Jerusalem: Maritime, Cultural and Pilgrimage Routes', which, it is hoped, will be recognized as a cultural itinerary by the Council of Europe and become popular with travellers and tourists. The chapter also sets out the logic that prompted the itinerary and the motives behind it. It describes the objectives to be achieved and the desired results. It illustrates the steps that will transform the itinerary into reality and the network of stakeholders that are already supporting it today. It considers the route's weaknesses but also the historical, cultural, ethical, economic and political values that drive it and justify its desire to play a part in guiding the future of the Mediterranean.
Kashi and Cosmos, India: the pilgrimage circuit of the Panchakroshi Yatra.
Authors: Singh R. P. B. , Rana P. S.
Published: June 2018

This chapter examines the Panchakroshi Yatra or pilgrimage circuit to Varanasi (Uttar Pradesh, India) with a particular focus on the historical development of the route, how the route has helped with local development and cultural identity, and environmental issues that have arisen in recent years along the route.
The Talpa de Allende pilgrimage trail.
Authors: Olsen D. H. , Sánchez R. E.
Published: June 2018

The focus of this chapter is the present-day development of the pilgrimage route called the Ruta del Peregrino which winds its way from the town of Ameca to the Catedral Basílica de Nuestra Señora del Rosario in Talpa de Allende, Mexico. The chapter briefly discusses the history of Talpa de Allende and the establishment of the basilica. Attention is then given to the Ruta del Peregrino and present-day issues along the trail related to regional development, environmental concerns and heritage.
Pilgrimage trails and routes: journeys from the present to the future.
Authors: Trono A. , Olsen D. H.
Published: June 2018

This concluding chapter focuses on the importance of religious pilgrimage routes and trails in the development of regional identity and regional economic development. It also considers strategies to promote sustainable faith-based places and routes, and identifies challenges and opportunities generated by linear religious and spiritual tourism for the near future.
The connections between animal and human abuse and neglect.
Authors: Pinillos R. G.
Published: June 2018

This book chapter discusses the One Welfare framework which covers all aspects of the links between people and animal interactions where these may result in abuse, neglect or violence. It supports reduction of incidence of crime and violence, in particular domestic violence and maltreatment of vulnerable populations such as elderly people, children and animals, and increases awareness of these issues.
The social implications of improved animal welfare.
Authors: Pinillos R. G.
Published: June 2018

This book chapter discusses the One Welfare framework which covers the connection between poor states of human and animal welfare. It examines cases involving animal welfare, socioeconomic indicators and offences in different social contexts, including those taking place within underprivileged communities. Improvements in animal welfare can support interventions tackling social issues (such as homelessness, hoarding, dog fighting and separation anxiety). Integrating animal welfare as part of general livelihood improvement programmes, including disaster and war responses, is seen as key to success.
Animal health and welfare, human well-being, food security and sustainability.
Authors: Pinillos R. G.
Published: June 2018

This book chapter discusses the One Welfare framework which includes elements correlating the level of human well-being with animal welfare, farming environment and sustainable production practices. It focuses on farming and food-producing livestock, and includes the links between animal welfare and food safety, as well as the beneficial aspects of farm animal welfare improvements to wider areas of societal concern such as climate change, sustainability and global food security.
Sustainability: connections between biodiversity, the environment, animal welfare and human well-being.
Authors: Pinillos R. G.
Published: June 2018

This book chapter discusses the One Welfare framework which explores the links between environmental and conservation issues, animal welfare and human well-being. It includes compassionate conservation, aesthetics in the landscape, the impacts of decreased biodiversity, animal-environment conflicts and genetic diversity as support for increased global well-being.
A splenic IgM memory subset with antibacterial specificities is sustained from persistent mucosal responses
Authors: Le Gallou Simon , Zhou Zhicheng , Thai Lan-Huong , Fritzen Remi , de los Aires Alba Verge , Mégret Jérôme , Yu Philipp , Kitamura Daisuke , Bille Emmanuelle , Tros Fabiola , Nassif Xavier , Charbit Alain , Weller Sandra , Weill Jean-Claude , Reynaud Claude-Agnès
Published: June 2018

To what extent immune responses against the gut flora are compartmentalized within mucosal tissues in homeostatic conditions remains a much-debated issue. We describe here, based on an inducible AID fate-mapping mouse model, that systemic memory B cell subsets, including mainly IgM+ B cells in spleen, together with IgA+ plasma cells in spleen and bone marrow, are generated in mice in the absence of deliberate immunization. While the IgA component appears dependent on the gut flora, IgM memory B cells are still generated in germ-free mice, albeit to a reduced extent. Clonal relationships and renewal kinetics after anti-CD20 treatment reveal that this long-lasting splenic population is mainly sustained by output of B cell clones persisting in mucosal germinal centers. IgM-secreting hybridomas established from splenic IgM memory B cells showed reactivity against various bacterial isolates and endogenous retroviruses. Ongoing activation of B cells in gut-associated lymphoid tissues thus generates a diversified systemic compartment showing long-lasting clonal persistence and protective capacity against systemic bacterial infections.
Effects of Lifestyle Modifications on Elevated Blood Pressure and Excess Weight in a Population of Italian Children and Adolescents
Authors: Genovesi Simonetta , Orlando Antonina , Rebora Paola , Giussani Marco , Antolini Laura , Nava Elisa , Parati Gianfranco , Valsecchi Maria Grazia
Published: June 2018

BACKGROUND

Children’s excess weight is a common problem due to low-quality diet and poor physical activity and is a risk factor associated with hypertension. Aim of this study was to assess the effect of a nonpharmacological multidisciplinary intervention on blood pressure (BP) and body weight in a population of children with excess weight and/or elevated BP.

METHODS

Children consecutively referred to a Prevention of Cardiovascular Risk Clinic by the primary care pediatrician from 2009 to 2015 were assessed at baseline and followed up over time.

RESULTS

Out of 273 children (median age 11.4 years, 55% male), 61% were excess weight only, 7% had elevated BP only, and 32% showed both conditions. The probability of reaching the clinical target (normal weight and BP values) at 1 year of follow-up was 19% (confidence interval [CI]: 14%; 24%) and increased up to 38% (CI: 28%; 47%) at 3 years. At 1 year of follow-up, in the overall population both body mass index (BMI) and systolic BP z-scores decreased significantly from 1.77 to 1.47 and from 0.99 to 0.52, respectively (P < 0.0001). BP was significantly reduced in both children with elevated BP only (reduction = 0.91, P = 0.0157) and subjects with excess weight and elevated BP (reduction = 0.89, P < 0.0001). Variables significantly related with systolic BP z-score at 1 year of follow-up were baseline systolic BP z-score and BMI z-score reduction during follow-up (P < 0.001 and P = 0.0003, respectively).

CONCLUSION

Our data demonstrate the efficacy of lifestyles modification on weight and BP in children, both when elevated BP and excess weight were present as distinct clinical problems and in the case of their association.
Xolik: finding cross-linked peptides with maximum paired scores in linear time
Authors: Dai Jiaan , Jiang Wei , Yu Fengchao , Yu Weichuan
Published: June 2018

Motivation

Cross-linking technique coupled with mass spectrometry (MS) is widely used in the analysis of protein structures and protein-protein interactions. In order to identify cross-linked peptides from MS data, we need to consider all pairwise combinations of peptides, which is computationally prohibitive when the sequence database is large. To alleviate this problem, some heuristic screening strategies are used to reduce the number of peptide pairs during the identification. However, heuristic screening strategies may miss some true cross-linked peptides.

Results

We directly tackle the combination challenge without using any screening strategies. With the data structure of double-ended queue, the proposed algorithm reduces the quadratic time complexity of exhaustive searching down to the linear time complexity. We implement the algorithm in a tool named Xolik. The running time of Xolik is validated using databases with different numbers of proteins. Experiments using synthetic and empirical datasets show that Xolik outperforms existing tools in terms of running time and statistical power.

Availability and implementation

Source code and binaries of Xolik are freely available at http://bioinformatics.ust.hk/Xolik.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
GrandPrix: scaling up the Bayesian GPLVM for single-cell data
Authors: Ahmed Sumon , Rattray Magnus , Boukouvalas Alexis
Published: June 2018

Motivation

The Gaussian Process Latent Variable Model (GPLVM) is a popular approach for dimensionality reduction of single-cell data and has been used for pseudotime estimation with capture time information. However, current implementations are computationally intensive and will not scale up to modern droplet-based single-cell datasets which routinely profile many tens of thousands of cells.

Results

We provide an efficient implementation which allows scaling up this approach to modern single-cell datasets. We also generalize the application of pseudotime inference to cases where there are other sources of variation such as branching dynamics. We apply our method on microarray, nCounter, RNA-seq, qPCR and droplet-based datasets from different organisms. The model converges an order of magnitude faster compared to existing methods whilst achieving similar levels of estimation accuracy. Further, we demonstrate the flexibility of our approach by extending the model to higher-dimensional latent spaces that can be used to simultaneously infer pseudotime and other structure such as branching. Thus, the model has the capability of producing meaningful biological insights about cell ordering as well as cell fate regulation.

Availability and implementation

Software available at github.com/ManchesterBioinference/GrandPrix.

Supplementary information

Supplementary data are available at Bioinformatics online.
PopViz: a webserver for visualizing minor allele frequencies and damage prediction scores of human genetic variations
Authors: Zhang Peng , Bigio Benedetta , Rapaport Franck , Zhang Shen-Ying , Casanova Jean-Laurent , Abel Laurent , Boisson Bertrand , Itan Yuval
Published: June 2018

Next-generation sequencing (NGS) generates large amounts of genomic data and reveals about 20 000 genetic coding variants per individual studied. Several mutation damage prediction scores are available to prioritize variants, but there is currently no application to help investigators to determine the relevance of the candidate genes and variants quickly and visually from population genetics data and deleteriousness scores. Here, we present PopViz, a user-friendly, rapid, interactive, mobile-compatible webserver providing a gene-centric visualization of the variants of any human gene, with (i) population-specific minor allele frequencies from the gnomAD population genetic database; (ii) mutation damage prediction scores from CADD, EIGEN and LINSIGHT and (iii) amino-acid positions and protein domains. This application will be particularly useful in investigations of NGS data for new disease-causing genes and variants, by reinforcing or rejecting the plausibility of the candidate genes, and by selecting and prioritizing, the candidate variants for experimental testing.

Availability and implementation

PopViz webserver is freely accessible from http://shiva.rockefeller.edu/PopViz/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Flux tope analysis: studying the coordination of reaction directions in metabolic networks
Authors: Gerstl Matthias P , Müller Stefan , Regensburger Georg , Zanghellini Jürgen
Published: June 2018

Motivation

Elementary flux mode (EFM) analysis allows an unbiased description of metabolic networks in terms of minimal pathways (involving a minimal set of reactions). To date, the enumeration of EFMs is impracticable in genome-scale metabolic models. In a complementary approach, we introduce the concept of a flux tope (FT), involving a maximal set of reactions (with fixed directions), which allows one to study the coordination of reaction directions in metabolic networks and opens a new way for EFM enumeration.

Results

A FT is a (nontrivial) subset of the flux cone specified by fixing the directions of all reversible reactions. In a consistent metabolic network (without unused reactions), every FT contains a ‘maximal pathway’, carrying flux in all reactions. This decomposition of the flux cone into FTs allows the enumeration of EFMs (of individual FTs) without increasing the problem dimension by reaction splitting. To develop a mathematical framework for FT analysis, we build on the concepts of sign vectors and hyperplane arrangements. Thereby, we observe that FT analysis can be applied also to flux optimization problems involving additional (inhomogeneous) linear constraints. For the enumeration of FTs, we adapt the reverse search algorithm and provide an efficient implementation. We demonstrate that (biomass-optimal) FTs can be enumerated in genome-scale metabolic models of B.cuenoti and E.coli, and we use FTs to enumerate EFMs in models of M.genitalium and B.cuenoti.

Availability and implementation

The source code is freely available at https://github.com/mpgerstl/FTA.

Supplementary information

Supplementary data are available at Bioinformatics online.
Exploring drivers of gene expression in the Cancer Genome Atlas
Authors: Rau Andrea , Flister Michael , Rui Hallgeir , Auer Paul L
Published: June 2018

Motivation

The Cancer Genome Atlas (TCGA) has greatly advanced cancer research by generating, curating and publicly releasing deeply measured molecular data from thousands of tumor samples. In particular, gene expression measures, both within and across cancer types, have been used to determine the genes and proteins that are active in tumor cells.

Results

To more thoroughly investigate the behavior of gene expression in TCGA tumor samples, we introduce a statistical framework for partitioning the variation in gene expression due to a variety of molecular variables including somatic mutations, transcription factors (TFs), microRNAs, copy number alternations, methylation and germ-line genetic variation. As proof-of-principle, we identify and validate specific TFs that influence the expression of PTPN14 in breast cancer cells.

Availability and implementation

We provide a freely available, user-friendly, browseable interactive web-based application for exploring the results of our transcriptome-wide analyses across 17 different cancers in TCGA at http://ls-shiny-prod.uwm.edu/edge_in_tcga. All TCGA Open Access tier data are available at the Broad Institute GDAC Firehose and were downloaded using the TCGA2STAT R package. TCGA Controlled Access tier data are available via controlled access through the Genomic Data Commons (GDC). R scripts used to download, format and analyze the data and produce the interactive R/Shiny web app have been made available on GitHub at https://github.com/andreamrau/EDGE-in-TCGA.
Stakeholder expectations, roles and responsibilities in Dutch health promotion for people with intellectual disabilities
Authors: Kuijken N M J , Vlot-van Anrooij K , van Schrojenstein Lantman-de Valk H M J , Leusink G , Naaldenberg J , Nijhuis-van der Sanden M W
Published: June 2018

This two-phase, qualitative study aims to obtain an overview of stakeholders in the network of people with intellectual disabilities (ID) and their perceived facilitating and hindering factors, expectations, and perceived roles and responsibilities with regard to health promotion. In phase 1, four workshops were conducted to provide insight into involved stakeholders. In phase 2, 29 semi-structured interviews were conducted with stakeholders regarding their views on health promotion. Data were analysed using stakeholder matrices and a combination of domain and thematic analysis. Daily caregivers were identified as the most important and influential stakeholders. Interviewed stakeholders perceived barriers to a healthy lifestyle as relating mainly to the person with ID and, although they stated that people with ID need support to be able to live healthily, there was ambiguity about roles and responsibilities for providing this support. Daily caregivers are not properly facilitated to support a healthy lifestyle. Stakeholders expressed the need for a culture change towards a greater health promotion ethos in care for people with ID. A facilitating context is needed in which the social network supports autonomy and offers opportunities to adapt to physical, social and emotional challenges. Stakeholders see the importance of, and are willing to support, healthy behaviour. They are hindered by a lack of a shared vision and united system in which all stakeholders know their roles and responsibilities. Promotion of a healthy lifestyle should be part of every service provider employee’s job and propagated throughout the organization as part of its mission and vision.
Routing problems in agricultural cooperatives: a model for optimization of transport vehicle logistics
Authors: Guitián de Frutos Roque M , Casas-Méndez Balbina
Published: June 2018

This study considers the problem of optimizing the routes of vehicles used in an agricultural cooperative that distributes animal feed to its customers. Different peculiarities distinguish our problem from the general Vehicle Routing Problem because there exists a type of time window constraint, truck capacity is limited, trucks are compartmentalized, there are access restrictions for trucks to some farms and our problem has the main objective of maximizing the amount of feed distributed every day and an auxiliary criterion of minimizing the transport costs. We present a mathematical programming formulation of the model that represents the logistics management problem. As solving the exact model is computationally expensive, we opt for a hybrid heuristic approach that first uses an insertion heuristic algorithm to obtain an initial solution and then improvement processes are performed using the so-called simulated annealing metaheuristic. We have built a graphical interface that allows easy use of the system and, in particular, efficient post-optimality analysis. Moreover, this interface can easily interface with other management tools. The utility of our model is shown with real and simulated data sets.
The Kodaira Dimension of Contact 3-Manifolds and Geography of Symplectic Fillings
Authors: Li Tian-Jun , Mak Cheuk Yu
Published: June 2018

We introduce the Kodaira dimension of contact 3-manifolds and establish some basic properties. Contact 3-manifolds with distinct Kodaira dimensions behave differently when it comes to the geography of various kinds of symplectic fillings. On the other hand, we also prove that, given any contact 3-manifold, there is a lower bound of $2\chi +3\sigma $ for all of its minimal symplectic fillings. This is motivated by Stipsicz’s result in [38] for Stein fillings. Finally, we discuss various aspects of exact self-cobordisms of fillable contact 3-manifolds.
Evaluating active learning methods for annotating semantic predications
Authors: Vasilakes Jake , Rizvi Rubina , Melton Genevieve B , Pakhomov Serguei , Zhang Rui
Published: June 2018

Objectives

This study evaluated and compared a variety of active learning strategies, including a novel strategy we proposed, as applied to the task of filtering incorrect semantic predications in SemMedDB.

Materials and methods

We evaluated 8 active learning strategies covering 3 types—uncertainty, representative, and combined—on 2 datasets of 6,000 total semantic predications from SemMedDB covering the domains of substance interactions and clinical medicine, respectively. We also designed a novel combined strategy called dynamic β that does not use hand-tuned hyperparameters. Each strategy was assessed by the Area under the Learning Curve (ALC) and the number of training examples required to achieve a target Area Under the ROC curve. We also visualized and compared the query patterns of the query strategies.

Results

All types of active learning (AL) methods beat the baseline on both datasets. Combined strategies outperformed all other methods in terms of ALC, outperforming the baseline by over 0.05 ALC for both datasets and reducing 58% annotation efforts in the best case. While representative strategies performed well, their performance was matched or outperformed by the combined methods. Our proposed AL method dynamic β shows promising ability to achieve near-optimal performance across 2 datasets.

Discussion

Our visual analysis of query patterns indicates that strategies which efficiently obtain a representative subsample perform better on this task.

Conclusion

Active learning is shown to be effective at reducing annotation costs for filtering incorrect semantic predications from SemMedDB. Our proposed AL method demonstrated promising performance.
Growth and agglomeration in the heterogeneous space: a generalized AK approach
Authors: Boucekkine Raouf , Fabbri Giorgio , Federico Salvatore , Gozzi Fausto
Published: June 2018

We provide an optimal growth spatio-temporal setting with capital accumulation and diffusion across space to study the link between economic growth triggered by capital spatio-temporal dynamics and agglomeration across space. The technology is AK, K being broad capital. The social welfare function is Benthamite. In sharp contrast to the related literature, which considers homogeneous space, we derive optimal location outcomes for any given space distributions for technology and population. Both the transitional spatio-temporal dynamics and the asymptotic spatial distributions are computed in closed form. Concerning the latter, we find, among other results, that: (i) due to inequality aversion, the consumption per capital distribution is much flatter than the distribution of capital per capita; (ii) endogenous spillovers inherent in capital spatio-temporal dynamics occur as capital distribution is much less concentrated than the (pre-specified) technological distribution; (iii) the distance to the center (or to the core) is an essential determinant of the shapes of the asymptotic distributions, that is relative location matters.
Assessment and Treatment of Problem Internet Use
Authors: Young Kimberly
Published: June 2018

Research over the last decade has identified Internet addiction as a new and often unrecognized clinical disorder that impacts a user’s ability to control online use to the extent that it can cause relational, occupational, and social problems. Symptoms of problem Internet use are compared to criteria used to diagnose other addictions. In particular, pathological gambling is compared to problematic Internet use because of overlapping criteria. This chapter describes the diagnostic and treatment implications of the disorder. As technology is used with great frequency, detection and diagnosis of Internet addiction is often difficult. Symptoms may be masked by legitimate use of the Internet, and clinicians may overlook asking questions about technology use because problem Internet use is still a new and often unrecognized condition. This chapter outlines diagnostic conceptualizations of problem Internet use along with assessment and treatment considerations and the newest inclusion in the DSM-5 for Internet Gaming Disorder.
Issues in Arabic Computational Linguistics
Authors: Ditters Everhard
Published: June 2018

This article focuses on the current state of affairs in the field of Arabic computational linguistics. It begins by briefly monitoring relevant trends in phonetics and phonology, morphology, syntax, lexicology, semantics, stylistics, and pragmatics. Then, the chapter describes changes or special accents within formal Arabic syntax. After some evaluative remarks about the approach opted for, it continues with a linguistic description of literary Arabic for analysis purposes as well as an introduction to a formal description, pointing to some early results. The article hints at further perspectives for ongoing research and possible spinoffs such as a formalized description of Arabic syntax in formalized dependency rules as well as a subset thereof for information retrieval purposes.
Political Discussion and Deliberation Online
Authors: Stromer-Galley Jennifer
Published: June 2018

As information and communication technologies have diffused, scholars have turned attention to online informal political discussion and formal deliberation because of the importance of online political talk for constructing society and informing government policy. This chapter examines the research on both formal deliberation and informal discussion online, identifies the importance of this research area, signals its major findings, and examines key unanswered questions. Along the way it argues that more research is needed to understand why women and minorities are less likely to talk politics online; better conceptual clarity is needed about the phenomenon of interest; more experimental work is required to isolate the causes and consequences of channel characteristics and mechanics that produce higher-quality discussion and decisions; and more work is needed that extends across information and communication technologies (ICTs), cross-culturally, and beyond democratically-governed societies.
New Media and Political Campaigns
Authors: Owen Diana
Published: June 2018

New media have been playing an increasingly central role in American elections since they first appeared in 1992. While television remains the main source of election information for a majority of voters, digital communication platforms have become prominent. New media have triggered changes in the campaign strategies of political parties, candidates, and political organizations; reshaped election media coverage; and influenced voter engagement. This chapter examines the stages in the development of new media in elections from the use of rudimentary websites to the rise sophisticated social media. It discusses the ways in which new media differ from traditional media in terms of their form, function, and content; identifies the audiences for new election media; and examines the effects on voter interest, knowledge, engagement, and turnout. Going forward, scholars need to employ creative research methodologies to catalogue and analyze new campaign media as they emerge and develop.