bluuebunny/crossref_metadata_2025 huggingface dataset:
Dual‐broadband dielectric resonator antenna based on modified Sierpinski fractal geometry
Authors: Liu Hu , Liu Ying , Wei Ming , Gong Shuxi
Published: May 2015

A novel dual‐broadband dielectric resonator antenna (DRA) is presented. The proposed antenna has realised both dual‐band and wideband features by applying the modified Sierpinski structure to the antenna design of the proposed DRA. The measured impedance bandwidths for │S11│ < −10 dB are 2.25–2.6 GHz (14.46%) and 3.1–4.1 GHz (27.78%), which can cover the wireless local area network (WLAN, 2.4–2.484 GHz) and the worldwide interoperability for microwave access (WiMAX, 3.4–3.69 GHz) bands. Meanwhile, stable radiation patterns and gains of about 5 and 3.8 dBi at 2.4 and 3.5 GHz, respectively, have been observed.
Spectral characterisation of offset pulse position modulation
Authors: Ray Indrani , Sibley Martin J. N. , Mather Peter J.
Published: May 2015

Offset pulse position modulation (PPM) has been shown to be more attractive for use in optical fibre channels than on–off keying, digital PPM and in some respects multiple PPM in some applications. However the spectral analysis of this coding scheme has not yet been addressed. In this study the authors present, for the first time, the spectral characteristics of an offset PPM sequence. The results show strong frequency components at the frame rate and, if return‐to‐zero pulses are used, the slot rate.
Implementation of a new medium voltage asymmetric pulse‐width modulation converter with balanced input capacitor voltages
Authors: Lin Bor‐Ren , Zhang Sheng‐Zhi
Published: May 2015

A 1.44 kW DC/DC converter with zero voltage switching (ZVS) for medium voltage applications is proposed in this study. Two half‐bridge circuits with split capacitors are connected in series at high voltage side to limit voltage stresses of power switches at Vin/2. Three DC/DC circuits are adopted to share load current and reduce the current stress of rectifier diodes, transformers and output filter inductors. Two balance capacitors are used in the proposed circuit to automatically balance input split capacitor voltages in every switching cycle. The current doubler rectifier is adopted at low voltage side to partially cancel ripple current so that the root‐mean‐square current at output capacitor is reduced. Asymmetric pulse‐width modulation is used to adjust the duty cycle of power switches and regulate output voltage. The output capacitance of power switches and the external resonant inductance are resonant at the transition interval and power metal‐oxide‐semiconductor field‐effect transistors can be turned on under ZVS. The proposed converter can be applied for high input voltage applications such as a three‐phase 380 V/480 V utility system. Experimental results from a 750–800 V input and 24 V/60 A output are provided to demonstrate the performance of proposed converter.
Distributed fuzzy maximum‐censored mean level detector‐constant false alarm rate detector based on voting fuzzy fusion rule
Authors: Gong Shufeng , Pan Minghai , Long Weijun , Huang Hao
Published: May 2015

In this study, a new distributed fuzzy maximum‐censored mean level detector (MX‐CMLD) constant false alarm rate (CFAR) detection based on fuzzy space and voting fuzzy fusion rule is presented. In the distributed fuzzy MX‐CMLD CFAR detector, each sensor computes the value of the membership function to the false alarm space from the samples of the reference cells and transmits it to the fusion centre. The values are combined according to the voting fuzzy fusion rule and the credibility measure of each sensor to produce a global membership function to the false alarm space in the fusion centre. The simulation results show that the detection performance of the distributed fuzzy MX‐CMLD CFAR detector is better than the other fuzzy distributed detectors in homogeneous and non‐homogeneous background. Furthermore, the simulation results indicate that the fuzzy algebraic product operator rule gives better performance than the binary AND and the binary OR fusion rules.
Processes for design, construction and utilisation of arrays of light‐emitting diodes and light‐emitting diode‐coupled optical fibres for multi‐site brain light delivery
Authors: Bernstein Jacob Gold , Allen Brian Douglas , Guerra Alexander A. , Boyden Edward Stuart
Published: May 2015

Optogenetics enables light to be used to control the activity of genetically targeted cells in the living brain. Optical fibres can be used to deliver light to deep targets, and light‐emitting diodes (LEDs) can be spatially arranged to enable patterned light delivery. In combination, arrays of LED‐coupled optical fibres can enable patterned light delivery to deep targets in the brain. Here the authors describe the process flow for making LED arrays and LED‐coupled optical fibre arrays, explaining key optical, electrical, thermal and mechanical design principles to enable the manufacturing, assembly and testing of such multi‐site targetable optical devices. They also explore accessory strategies such as surgical automation approaches as well as innovations to enable low‐noise concurrent electrophysiology.
First-principles investigation of the dissociation and coupling of methane on small copper clusters: Interplay of collision dynamics and geometric and electronic effects
Authors: Varghese Jithin J. , Mushrif Samir H.
Published: May 2015

Small metal clusters exhibit unique size and morphology dependent catalytic activity. The search for alternate minimum energy pathways and catalysts to transform methane to more useful chemicals and carbon nanomaterials led us to investigate collision induced dissociation of methane on small Cu clusters. We report here for the first time, the free energy barriers for the collision induced activation, dissociation, and coupling of methane on small Cu clusters (Cun where n = 2–12) using ab initio molecular dynamics and metadynamics simulations. The collision induced activation of the stretching and bending vibrations of methane significantly reduces the free energy barrier for its dissociation. Increase in the cluster size reduces the barrier for dissociation of methane due to the corresponding increase in delocalisation of electron density within the cluster, as demonstrated using the electron localisation function topology analysis. This enables higher probability of favourable alignment of the C–H stretching vibration of methane towards regions of high electron density within the cluster and makes higher number of sites available for the chemisorption of CH3 and H upon dissociation. These characteristics contribute in lowering the barrier for dissociation of methane. Distortion and reorganisation of cluster geometry due to high temperature collision dynamics disturb electron delocalisation within them and increase the barrier for dissociation. Coupling reactions of CHx (x = 1–3) species and recombination of H with CHx have free energy barriers significantly lower than complete dehydrogenation of methane to carbon. Thus, competition favours the former reactions at high hydrogen saturation on the clusters.
Split octonion reformulation of generalized linear gravitational field equations
Authors: Chanyal B. C.
Published: May 2015

In this paper, we describe the properties of split octonions and their connection with the 2 × 2 Zorn vector matrix containing both scalar and vector components. Starting with a brief description of gravito-dyons, we reformulate the generalized linear gravitational field equations of gravito-dyons in terms of split octonion. We express the generalized gravito-Heavisidian (GH) potentials, fields, and various wave equations of gravito-dyons in terms of split octonions variables. Accordingly, we demonstrate the work-energy theorem of classical mechanics reproducing the continuity equation for the case of gravito-dyons in terms of split octonions. Further, we discuss the split octonionic form of linear momentum conservation law for gravito-dyons in the case of linear gravitational theory. We have summarized the various split octonion equations for the case of the generalized GH-field of gravito-dyons and the generalized electromagnetic field of dyons. The unified fields of dyons and gravito-dyons have been demonstrated and corresponding field equations are discussed in unique and consistent manner in terms of split octonions.
Boundary layer flow of three-dimensional viscoelastic nanofluid past a bi-directional stretching sheet with Newtonian heating
Authors: Ramzan M. , Yousaf Farhan
Published: May 2015

This paper deals with steady three dimensional boundary layer flow of an incompressible viscoelastic nanofluid flow in the presence of Newtonian heating. An appropriate transformation is employed to convert the highly non linear partial differential equations into ordinary differential equations. Homotopy Analysis method (HAM) is used to find series solution of the obtained coupled highly non linear differential equations. The convergence of HAM solutions is discussed via h-curves. Graphical illustrations displaying the influence of emerging parameters on velocity, temperature and concentration profiles are given. It is observed that γ the conjugate parameter for Newtonian heating show increasing behavior on both temperature and concentration profiles. However, the temperature and concentration profiles are increasing and decreasing functions of Brownian motion parameter Nb respectively.
Band-like transport down to 20 K in organic single-crystal transistors based on dioctylbenzothienobenzothiophene
Authors: Cho Joung-min , Higashino Toshiki , Mori Takehiko
Published: May 2015

Band-like transport has been realized down to 20 K in solution-processed single-crystal transistors based on dioctylbenzothienobenzothiophene. The mobility increases from 16 to 52 cm2/V s as the temperature is lowered from 300 to 80 K. An abrupt mobility drop is observed around 80 K, but even below 80 K, gradually increasing mobility is restored again down to 20 K instead of thermally activated transport. From the observation of a shoulder structure in the transfer curve, the mobility drop is attributed to a discrete trap state.
Assembly and Properties of Four New Metal–Organic Complexes Based on 1,4-Naphthalenedicarboxylate: Effect of Four Bis-pyridyl-bis-amide Ligands with Diverse Spacers in the Structures
Authors: Lin Hong-Yan , Zhao Xun-Zhang , Zeng Ling , Wang Qing-Lin , Wang Xiu-Li , Liu Guo-Cheng
Published: May 2015

Four new complexes based on 1,4-naphthalenedicarboxylic acid (1,4-H2NDC) and four bis-pyridyl-bis-amide ligands with various spacers (3-bpye = N,N′-bis(3-pyridinecarboxamide)-1,2-ethane; 3-bpfp = bis(3-pyridylformyl)piperazine; 3-bpcd = N,N′-bis(pyridin-3-yl)cyclohexane-1,4-dicarboxamide; and 3-bpcb = N,N′-bis(3-pyridinecarboxamide)-1,4-benzene), namely [Cu2(1,4-NDC)2(3-bpye)(H2O)] (1), [Cu(1,4-NDC)(3-bpfp)0.5] (2), [Cu3(1,4-NDC)3(3-bpcd)3]·2H2O (3), and [Cu(1,4-NDC)(3-bpcb)] (4), have been hydrothermally synthesized. Complex 1 is a 3D coordination network and represents an 8-connected {420.68} topology. Complex 2 shows a 2-fold interpenetrating 3D architecture with a 6-connected {412.63} topology. Complexes 3 and 4 possess similar 2D sql layers with the {44.62} topology, but the coordination modes of 1,4-NDC ligands and the conformations of the two bis-pyridyl-bis-amide ligands are different. The adjacent layers for 3 and 4 are further linked by hydrogen bonding interactions to form 3D supramolecular networks. The successful assemblies of complexes 1–4 imply that by using the different bis-pyridyl-bis-amide ligands with diverse spacers can produce diverse metal–organic networks. Furthermore, the fluorescence and photocatalytic properties of complexes 1–4 have been investigated.
Adrien Albert Award: How to Mine Chemistry Space for New Drugs and Biomedical Therapies
Authors: Winkler David
Published: May 2015

It is clear that the sizes of chemical, ‘drug-like’, and materials spaces are enormous. If scientists working in established therapeutic, and newly established regenerative medicine fields are to discover better molecules or materials, they must find better ways of probing these enormous spaces. There are essentially five ways that this can be achieved: combinatorial and high throughput synthesis and screening approaches; fragment-based methods; de novo molecular design, design of experiments, diversity libraries; supramolecular approaches; evolutionary approaches. These methods either synthesise materials and screen them more quickly, or constrain chemical spaces using biology or other types of ‘fitness functions’. High throughput experimental approaches cannot explore more than a minute part of chemical space. We are nevertheless entering into an era that is data dominated. High throughput experiments, robotics, automated crystallographic beam lines, combinatorial and flow synthesis, high content screening, and the ‘omics’ technologies are providing a flood of data, and efficient methods for extracting meaning from it are essential. This paper describes how new developments in mathematics have provided excellent, robust computational modelling tools for exploring large chemical spaces, for extracting meaning from large datasets, for designing new bioactive agents and materials, and for making truly predictive, quantitative models of the properties of molecules and materials for use in therapeutic and regenerative medicine. We describe these broadly applicable modelling tools and provide examples of their application to serum free stem cell culture, pathogen resistant polymers for implantable devices, new markers and biological mechanisms derived from mathematical analyses of gene array data, and pharmacokinetically important physicochemical properties of small molecules. We also discuss biologically conserved peptide motifs as a design framework for small molecule drugs and give examples of the application of this concept to drug design.
Conservation, mismatch and the research–implementation gap
Authors: Jarvis R. M. , Borrelle S. B. , Breen B. Bollard , Towns D. R.
Published: May 2015

Despite calls to better link research and practice, the gap between knowing and doing continues to limit conservation success. Here we report on the outcomes from a workshop at the Society for Conservation Biology Oceania Conference 2014 on bridging the research–implementation gap. The workshop highlighted how the gap is still very real in conservation and the importance of bringing together researchers and practitioners to discuss their work. Workshop participants discussed how the research–implementation gap influenced their conservation efforts, identified five key mismatches between research and practice, and recommended seven ways we can work together to bridge the gap. The outcomes identified by the workshop are highly relevant to conservation efforts around the world.
A natural experiment of the consequences of concentrating former prisoners in the same neighborhoods
Authors: Kirk David S.
Published: May 2015

Significance

There are ∼5 million formerly imprisoned individuals residing in US neighborhoods, yet this population is highly concentrated in a relatively small number of neighborhoods, typically within metropolitan areas. I find that concentrating former prisoners in the same neighborhoods leads to significantly higher recidivism rates than if ex-prisoners were more dispersed across neighborhoods. The reasons why ex-prisoners concentrate in a select few urban neighborhoods include personal factors such as social ties to the neighborhood, but they also include institutional and structural barriers such as parole policies and housing market dynamics. Policy solutions that disperse the geographic concentration of former prisoners, while leading to some geographic displacement of recidivism, would likely yield a net reduction in recidivism in aggregate.
GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions
Authors: Gundersen Gregory W. , Jones Matthew R. , Rouillard Andrew D. , Kou Yan , Monteiro Caroline D. , Feldmann Axel S. , Hu Kevin S. , Ma’ayan Avi
Published: May 2015

Motivation: Identification of differentially expressed genes is an important step in extracting knowledge from gene expression profiling studies. The raw expression data from microarray and other high-throughput technologies is deposited into the Gene Expression Omnibus (GEO) and served as Simple Omnibus Format in Text (SOFT) files. However, to extract and analyze differentially expressed genes from GEO requires significant computational skills.

Results: Here we introduce GEO2Enrichr, a browser extension for extracting differentially expressed gene sets from GEO and analyzing those sets with Enrichr, an independent gene set enrichment analysis tool containing over 70 000 annotated gene sets organized into 75 gene-set libraries. GEO2Enrichr adds JavaScript code to GEO web-pages; this code scrapes user selected accession numbers and metadata, and then, with one click, users can submit this information to a web-server application that downloads the SOFT files, parses, cleans and normalizes the data, identifies the differentially expressed genes, and then pipes the resulting gene lists to Enrichr for downstream functional analysis. GEO2Enrichr opens a new avenue for adding functionality to major bioinformatics resources such GEO by integrating tools and resources without the need for a plug-in architecture. Importantly, GEO2Enrichr helps researchers to quickly explore hypotheses with little technical overhead, lowering the barrier of entry for biologists by automating data processing steps needed for knowledge extraction from the major repository GEO.

Availability and implementation: GEO2Enrichr is an open source tool, freely available for installation as browser extensions at the Chrome Web Store and FireFox Add-ons. Documentation and a browser independent web application can be found at http://amp.pharm.mssm.edu/g2e/.

Contact:  avi.maayan@mssm.edu
Fast parametric time warping of peak lists
Authors: Wehrens Ron , Bloemberg Tom G. , Eilers Paul H.C.
Published: May 2015

Summary: Alignment of peaks across samples is a difficult but unavoidable step in the data analysis for all analytical techniques containing a separation step like chromatography. Important application examples are the fields of metabolomics and proteomics. Parametric time warping (PTW) has already shown to be very useful in these fields because of the highly restricted form of the warping functions, avoiding overfitting. Here, we describe a new formulation of PTW, working on peak-picked features rather than on complete profiles. Not only does this allow for a much more smooth integration in existing pipelines, it also speeds up the (already among the fastest) algorithm by orders of magnitude. Using two publicly available datasets we show the potential of the new approach. The first set is a LC–DAD dataset of grape samples, and the second an LC–MS dataset of apple extracts.

Availability and implementation: Parametric time warping of peak lists is implemented in the ptw package, version 1.9.1 and onwards, available from Github (https://github.com/rwehrens/ptw) and CRAN (http://cran.r-project.org). The package also contains a vignette, providing more theoretical details and scripts to reproduce the results below.

Contact:  ron.wehrens@wur.nl
Exploring relation types for literature-based discovery
Authors: Preiss Judita , Stevenson Mark , Gaizauskas Robert
Published: May 2015

Objective Literature-based discovery (LBD) aims to identify “hidden knowledge” in the medical literature by: (1) analyzing documents to identify pairs of explicitly related concepts (terms), then (2) hypothesizing novel relations between pairs of unrelated concepts that are implicitly related via a shared concept to which both are explicitly related. Many LBD approaches use simple techniques to identify semantically weak relations between concepts, for example, document co-occurrence. These generate huge numbers of hypotheses, difficult for humans to assess. More complex techniques rely on linguistic analysis, for example, shallow parsing, to identify semantically stronger relations. Such approaches generate fewer hypotheses, but may miss hidden knowledge. The authors investigate this trade-off in detail, comparing techniques for identifying related concepts to discover which are most suitable for LBD.

Materials and methods A generic LBD system that can utilize a range of relation types was developed. Experiments were carried out comparing a number of techniques for identifying relations. Two approaches were used for evaluation: replication of existing discoveries and the “time slicing” approach.1

Results Previous LBD discoveries could be replicated using relations based either on document co-occurrence or linguistic analysis. Using relations based on linguistic analysis generated many fewer hypotheses, but a significantly greater proportion of them were candidates for hidden knowledge.

Discussion and Conclusion The use of linguistic analysis-based relations improves accuracy of LBD without overly damaging coverage. LBD systems often generate huge numbers of hypotheses, which are infeasible to manually review. Improving their accuracy has the potential to make these systems significantly more usable.
Photon underproduction crisis: Are QSOs sufficient to resolve it?
Authors: Khaire Vikram , Srianand Raghunathan
Published: May 2015

We investigate the recent claim of ‘photon underproduction crisis’ by Kollmeier et al. which suggests that the known sources of ultraviolet (UV) radiation may not be sufficient to generate the inferred H i photoionization rate ($\Gamma _{\rm H\,\small {i}}$) in the low-redshift intergalactic medium. Using the updated QSO emissivities from the recent studies and our cosmological radiative transfer code developed to estimate the UV background, we show that the QSO contributions to $\Gamma _{\rm H\,\small {i}}$ is higher by a factor ∼2 as compared to the previous estimates. Using self-consistently computed combinations of star formation rate density and dust attenuation, we show that a typical UV escape fraction of 4 per cent from star-forming galaxies should be sufficient to explain the inferred $\Gamma _{\rm H\,\small {i}}$ by Kollmeier et al. Interestingly, we find that the contribution from QSOs alone can explain the recently inferred $\Gamma _{\rm H\,\small {i}}$ by Shull et al. which used the same observational data but different simulation. Therefore, we conclude that the crisis is not as severe as it was perceived before and there seems no need to look for alternate explanations such as low luminosity hidden QSOs or decaying dark matter particles.
Pratītyasamutpāda
Authors: Suwanvarangkul Chaisit
Published: May 2015

The Sanskrit term pratītyasamutpāda (Pāli paṭiccasamuppāda; Tib. rten cing ’brel ’byungརྟེན་ཅིང་འབྲེལ་འབྱུང་; Ch. yuán qǐ縁起; Jpn. engi; Kor. yeon-gi; Viet. Duyên khởi), meaning “dependent arising” or “dependent origination”, is the basis for the Buddha’s teaching on the processes of birth and death and appears in the canon of the two major schools of Buddhism, Theravāda and Mahāyāna. Pratītyasamutpāda is one of the terms that illuminate the ultimate truth in Buddhism. Specifically, it is a particular teaching of Buddhism that deals with the phenomenona, or perpetual changes, caused by karma, the vicissitudes of life, all of which come from direct causes (hetu) and indirect causes (pratyaya). The Buddha once said: “Those who perceive ‘dependent origination’ (pratīyasamutpāda) will perceive the dharma; those who perceive the dharma will perceive ‘dependent origination’” (Saṃyutta Nikāya [Samyutta 22, 87]; see Bodhi 2000, cited under Canonical Sources, Vol. 1, p. 102) Underlying the doctrine of pratītyasamutpāda is the notion that “Because this exists, that arises; because this does not exist, that does not arise.” In short, all the Buddha’s other teachings may be seen as founded on the teaching of pratītyasamutpāda. Pratītyasamutpāda can be also connected to other Buddhist philosophy, such as Dharmadhātu, which states that all beings create themselves and that even the universe is self-created. Dharmadhātu has come to represent the universe as universally corelative, generally interdependent, and mutually originating, and it states that no single being exists independently. Dharmadhātu is also an ethical and a psychological transformation that occurs in the modern world: we can escape the bonds of the existence of samsara by cutting the psychological roots of suffering. This is none other than nirvana.
Sea Level Rise
Authors: Cazenave Anny
Published: May 2015

Sea level is the height of the sea surface expressed either in a geocentric reference frame (absolute sea level) or with respect to the moving Earth’s crust (relative sea level). Absolute sea level variations result from changes in the volume of water filling ocean basins (due either to water density or mass changes), while relative sea level variations designate sea surface height changes with respect to the ground (thus accounting both for “absolute” sea level changes and ground motions). Sea level variations spread over a very broad spectrum. On geological time scales, roughly 5–100 million years ago, 330-foot-amplitude sea level changes depend primarily on tectonics processes, such as large-scale changes in the shape of ocean basins associated with seafloor spreading and midocean ridge expansion, as well as on the existence (or not) of polar ice sheets. On a 10,000–100,000-year time scale, glacial/interglacial cycles driven by changes of the Earth’s orbit and obliquity also cause about 330-foot-amplitude sea level variations. On shorter time scales, 3.3-foot-amplitude sea level changes occur in response to natural climate-forcing factors (change in solar irradiance and volcanic eruptions). Humans also influence climate, and associated sea level change is noticeable since about 1900. Sea level is a very sensitive index of climate change and variability. For example, as the ocean warms in response to global warming, seawaters expand and thus sea level rises. When mountain glaciers melt in response to increasing air temperature, sea level rises because of fresh water mass input to the oceans. Similarly, ice mass loss from the ice sheets causes sea level rise. A corresponding increase of fresh water into the oceans changes water salinity; hence, seawater density as well as ocean circulation affects sea level and its spatial variability. Finally, modification of water storage on land in response to climate variability and direct anthropogenic forcing also causes sea level to vary on interannual to multidecadal time scales. Because of the multidisciplinary character of the sea level topic, as well as enormous progress made since the late 20th century owing to new in situ and space-observing systems, the literature on the subject is vast and continually increasing. For that reason, most of the works listed in this article were published after 2000, although a few older works are also mentioned.
American Cinema, 1976 to Present
Authors: Nystrom Derek
Published: May 2015

American cinema has undergone a series of profound transitions since 1976. In many histories of American film, 1976 marks the end of one New Hollywood—the so-called “Hollywood Renaissance” of art cinema-inspired, personal filmmaking driven by young auteurs—and the start of another New Hollywood, this one more oriented toward blockbuster films that, many critics argue, eschew classical principles of narration in order to foreground special effects sequences and to provide opportunities for merchandizing and other product tie-ins. Whether or not one agrees with this characterization of what these critics call “postclassical” film style, it is indisputable that Hollywood’s corporate and industrial structures in this period treat the domestic theatrical release of a narrative feature film as just one moment in the cultural and economic life of a given “property.” Significant developments in exhibition technologies—cable television, home video, and the Internet—created multiple windows of release for a particular film, not to mention the increasingly important foreign markets. Meanwhile, the return of vertical integration by the incorporation of US film studios into multinational corporate parent companies enabled the monetizing of different film-related properties across multiple markets and media streams, thus dispersing our understanding of what constitutes the film “text.” These changes in industrial practice took place during larger shifts in the United States’ position on the world stage, as the Cold War’s end scrambled one set of geopolitical coordinates while the 9/11 attacks and the ensuing wars generated another. American cinema registered these shifts in a number of ways, both in its depiction of political and military conflicts—many of which rerouted contemporary issues through earlier moments in US history (especially the Vietnam War)—and through its reimagination of gender identity, particularly the various forms of masculinity that critics have aligned with the Reagan, Clinton, and Bush eras. Other changes in race, gender, and sexual identity in American life often found their most provocative expression in the rise of a new “independent” American film movement. Critics have explored whether this movement has generated genuinely alternative forms of film narration and aesthetics, as well as whether their “independence” from major studios is better understood as a partial or qualified one. This article outlines the various critical resources that address these developments, as well as related questions, such as the relationship of American cinema to postmodernism and the shifts in film genre that attended the aforementioned developments.
Epigenetics and Behavior
Authors: Jablonka Eva , Bronfman Zohar
Published: May 2015

Behavioral epigenetics is part of the thriving field of epigenetics, which describes the study of developmental processes that lead to persistent changes in the states of organisms, their components, and their lineages. Such developmental, context-sensitive changes are mediated by epigenetic mechanisms that establish and maintain the changes in patterns of gene expression and cellular structures that occur during ontogeny in both nondividing cells, such as most mature neurons, and dividing cells such as stem cells. When information is vertically transmitted to cells during cell division, or horizontally between cells through migrating reproducing molecules (like small RNAs), and when variations in the transmitted information are not determined by variations in DNA sequence (i.e., the same DNA sequence has more than one cell-heritable epigenetic state), epigenetic inheritance is said to occur. Behavioral epigenetics investigates the role of behavior in the shaping of developmental epigenetic states and the reciprocal role of epigenetic factors and mechanisms in the shaping of the behavior of human and nonhuman animals, at the short-, middle-, and long-term (ontogenetic, ecological, and evolutionary) time scales. The focus is on the molecular-epigenetic study of the interactions between environmental factors, such as ecological factors and habitual activities such as lifestyles and learning, with genetic variation and the neurobiological and physiological mechanisms that mediate between the regulation of gene expression and behavior. This range of epigenetic processes therefore includes, but is not limited to, studies involving epigenetic inheritance and the direct and indirect evolutionary effects of epigenetic developmental mechanisms. The neural-behavioral aspects that occur during ontogeny through the mediation of epigenetic mechanisms are central to behavioral epigenetics and are the main focus of neural epigenetics.
Global regulation of heterochromatin spreading by Leo1
Authors: Verrier Laure , Taglini Francesca , Barrales Ramon R. , Webb Shaun , Urano Takeshi , Braun Sigurd , Bayne Elizabeth H.
Published: May 2015

Heterochromatin plays important roles in eukaryotic genome regulation. However, the repressive nature of heterochromatin combined with its propensity to self-propagate necessitates robust mechanisms to contain heterochromatin within defined boundaries and thus prevent silencing of expressed genes. Here we show that loss of the PAF complex (PAFc) component Leo1 compromises chromatin boundaries, resulting in invasion of heterochromatin into flanking euchromatin domains. Similar effects are seen upon deletion of other PAFc components, but not other factors with related functions in transcription-associated chromatin modification, indicating a specific role for PAFc in heterochromatin regulation. Loss of Leo1 results in reduced levels of H4K16 acetylation at boundary regions, while tethering of the H4K16 acetyltransferase Mst1 to boundary chromatin suppresses heterochromatin spreading inleo1Δcells, suggesting that Leo1 antagonises heterochromatin spreading by promoting H4K16 acetylation. Our findings reveal a previously undescribed role for PAFc in regulating global heterochromatin distribution.
Calculating mutual information for spike trains and other data with distances but no coordinates
Authors: Houghton Conor
Published: May 2015

Many important data types, such as the spike trains recorded from neurons in typical electrophysiological experiments, have a natural notion of distance or similarity between data points, even though there is no obvious coordinate system. Here, a simple Kozachenko–Leonenko estimator is derived for calculating the mutual information between datasets of this type.
Phenotypic assortment in wild primate networks: implications for the dissemination of information
Authors: Carter Alecia J. , Lee Alexander E. G. , Marshall Harry H. , Ticó Miquel Torrents , Cowlishaw Guy
Published: May 2015

Individuals' access to social information can depend on their social network. Homophily—a preference to associate with similar phenotypes—may cause assortment within social networks that could preclude information transfer from individuals who generate information to those who would benefit from acquiring it. Thus, understanding phenotypic assortment may lead to a greater understanding of the factors that could limit the transfer of information between individuals. We tested whether there was assortment in wild baboon (
Papio ursinus
) networks, using data collected from two troops over 6 years for six phenotypic traits—boldness, age, dominance rank, sex and the propensity to generate/exploit information—using two methods for defining a connection between individuals—time spent in proximity and grooming. Our analysis indicated that assortment was more common in grooming than proximity networks. In general, there was homophily for boldness, age, rank and the propensity to both generate and exploit information, but heterophily for sex. However, there was considerable variability both between troops and years. The patterns of homophily we observed for these phenotypes may impede information transfer between them. However, the inconsistency in the strength of assortment between troops and years suggests that the limitations to information flow may be quite variable.
Origin of tensile strength of a woven sample cut in bias directions
Authors: Pan Ning , Kovar Radko , Dolatabadi Mehdi Kamali , Wang Ping , Zhang Diantang , Sun Ying , Chen Li
Published: May 2015

Textile fabrics are highly anisotropic, so that their mechanical properties including strengths are a function of direction. An extreme case is when a woven fabric sample is cut in such a way where the bias angle and hence the tension loading direction is around 45° relative to the principal directions. Then, once loaded, no yarn in the sample is held at both ends, so the yarns have to build up their internal tension entirely via yarn–yarn friction at the interlacing points. The overall fabric strength in such a sample is a result of contributions from the yarns being pulled out and those broken during the process, and thus becomes a function of the bias direction angle
θ
, sample width
W
and length
L
, along with other factors known to affect fabric strength tested in principal directions. Furthermore, in such a bias sample when the major parameters, e.g. the sample width
W
, change, not only the resultant strengths differ, but also the strength generating mechanisms (or failure types) vary. This is an interesting problem and is analysed in this study. More specifically, the issues examined in this paper include the exact mechanisms and details of how each interlacing point imparts the frictional constraint for a yarn to acquire tension to the level of its strength when both yarn ends were not actively held by the testing grips; the theoretical expression of the critical yarn length for a yarn to be able to break rather than be pulled out, as a function of the related factors; and the general relations between the tensile strength of such a bias sample and its structural properties. At the end, theoretical predictions are compared with our experimental data.
Cortical microcircuit determination through global perturbation and sparse sampling in grid cells
Authors: Widloski John , Fiete Ila R.
Published: May 2015

Under modern interrogation, famously well-studied neural circuits such as that for orientation tuning in V1 are steadily giving up their secrets, but quite basic questions about connectivity and dynamics, including whether most computation is done by lateral processing or by selective feedforward summation, remain unresolved. We show here that grid cells offer a particularly rich opportunity for dissecting the mechanistic underpinnings of a cortical circuit, through a strategy based on global circuit perturbation combined with sparse neural recordings. The strategy is based on the theoretical insight that small perturbations of circuit activity will result in characteristic quantal shifts in the spatial tuning relationships between grid cells, which should be observable from multisingle unit recordings of a small subsample of the population. The predicted shifts differ qualitatively across candidate recurrent network mechanisms, and also distinguish between recurrent versus feedforward mechanisms. More generally, the proposed strategy demonstrates how sparse neural recordings coupled with global perturbation in the grid cell system can reveal much more about circuit mechanism as it relates to function than can full knowledge of network activity or of the synaptic connectivity matrix.
Ecological and evolutionary adaptations shape the gut microbiome of BaAka African rainforest hunter-gatherers
Authors: Gomez Andres , Petrzelkova Klara , Yeoman Carl J. , Burns Michael B. , Amato Katherine R. , Vlckova Klara , Modry David , Todd Angelique , Jost Robinson Carolyn A. , Remis Melissa J. , Torralba Manolito , Nelson Karen E. , Carbonero Franck , Rex Gaskins H. , Wilson Brenda , Stumpf Rebecca M. , White Bryan A. , Leigh Steven R. , Blekhman Ran
Published: May 2015

The gut microbiome provides access to otherwise unavailable metabolic and immune functions, likely affecting mammalian fitness and evolution. To investigate how this microbial ecosystem impacts evolutionary adaptation of humans to particular habitats, we explore the gut microbiome and metabolome of the BaAka rainforest hunter-gatherers from Central Africa. The data demonstrate that the BaAka harbor a colonic ecosystem dominated by Prevotellaceae and other taxa likely related to an increased capacity to metabolize plant structural polysaccharides, phenolics, and lipids. A comparative analysis shows that the BaAka gut microbiome shares similar patterns with that of the Hadza, another hunter-gatherer population from Tanzania. Nevertheless, the BaAka harbor significantly higher bacterial diversity and pathogen load compared to the Hadza, as well as other Western populations. We show that the traits unique to the BaAka microbiome and metabolome likely reflect adaptations to hunter-gatherer lifestyles and particular subsistence patterns. We hypothesize that the observed increase in microbial diversity and potential pathogenicity in the BaAka microbiome has been facilitated by evolutionary adaptations in immunity genes, resulting in a more tolerant immune system.

Significance

Human ecological adaptation requires changes at the genomic level. However, the gut microbiome, the collection of microbes inhabiting the gastrointestinal tract and their functions, also responds significantly to ecological challenge. To determine how the gut microbiome responds to evolutionary adaptations in the host, we profiled gut bacterial communities of the BaAka, rainforest hunter-gatherers from Central Africa. The gut microbiome of the BaAka shows adaptations to metabolize foods rich in fiber, tannins and fats. Similarly, higher bacterial diversity and abundance of pathogenic bacteria, compared to other hunter-gatherers and western populations, suggest that the BaAka immune system evolved to coexist with increased pathogen threats. Accordingly, these results show how the gut microbiome contributes to human ecological plasticity, impacting host adaptation and evolution.
Molecular Fossils from Microorganisms Preserved in Glacial Ice
Authors: Buford Price P. , Jeffrey Morris J. , Bay Ryan C. , Adhikari Ajeeth , Giovannoni Stephen J. , Vergin Kevin L.
Published: May 2015

The study of microbial evolution is hindered by the fact that microbial populations leave few fossils. We hypothesized that bacterial cells preserved in ancient ice could be used as a molecular fossil record if their DNA could be extracted and sequenced. Channels formed along triple junctions of ice crystals contain liquid “veins” in which microbial cells may be preserved intact. Since vertical motion through the ice matrix is impossible, microbes found in ice cores are representative of microbes present at the time the ice was formed. We detected chlorophyll fluorescence in intact ice cores taken from Greenland and Antarctica. Flow cytometric analysis localized at least some of this fluorescence to particles < 1 μm in diameter. Metagenomic analysis of meltwater indeed revealed sequences similar to modern strains of the picocyanobacterial generaSynechococcusandProchlorococcus, and some of these sequences were distinct from any sequences known from modern oceans or glacial environments. Our study is a first proof-of-concept of the use of ice cores as records of microbial evolution, and we suggest that future genetic studies with higher vertical resolution in the cores might shed light on the pace and character of evolution of these ecologically important cells.
FIQT: a simple, powerful method to accurately estimate effect sizes in genome scans
Authors: Bigdeli Tim B. , Lee Donghyung , Riley Brien P. , Vladimirov Vladimir , Fanous Ayman H. , Kendler Kenneth S. , Bacanu Silviu-Alin
Published: May 2015

Genome scans, including both genome-wide association studies and deep sequencing, continue to discover a growing number of significant association signals for various traits. However, often variants meeting genome-wide significance criteria explain far less of the overall trait variance than “sub-threshold” association signals. To extract these sub-threshold signals, there is a need for methods which accurately estimate the mean of all (normally-distributed) test-statistics from a genome scan (i.e., Z-scores). This is currently achieved by the difficult procedures of adjusting all Z-scorestatistics for “winner’s curse” (multiple testing). Given that multiple testing adjustments are much simpler for p-values, we propose a method for estimating Z-scores means by i) first adjusting their p-values for multiple testing and then ii) transforming the adjusted p-values to upper tail Z-scores with the sign of the original statistics. Because a False Discovery Rate (FDR) procedure is used for multiple testing adjustment, we denote this methodFDRInverseQuantile Transformation (FIQT). When compared to competitors, e.g. Empirical Bayes (including proposed improvements), FIQT is more i) accurate and ii) computationally efficient by orders of magnitude. Its accuracy advantage is substantial at larger sample sizes and/or moderate numbers of association signals. Practical application of FIQT to Z-scores from the first Psychiatric Genetic Consortium (PGC) schizophrenia predicts a non-trivial fraction of the significant signal regions from the subsequent published PGC schizophrenia studies. Finally, we suggest that FIQT might be i) used to improve subject level risk prediction and ii) further improved by modelling the noncentrality ofstatistics.
The Multi-allelic Genetic Architecture of a Variance-heterogeneity Locus for Molybdenum Accumulation Acts as a Source of Unexplained Additive Genetic Variance
Authors: Forsberg Simon K.G. , Andreatta Matthew E. , Huang Xin-Yuan , Danku John , Salt David E. , Carlborg Örjan
Published: May 2015

Most biological traits are regulated by both genetic and environmental factors. Individual loci contributing to the phenotypic diversity in a population are generally identified by their contributions to the trait mean. Genome-wide association (GWA) analyses can also detect loci based on variance differences between genotypes and several hypotheses have been proposed regarding the possible genetic mechanisms leading to such signals. Little is, however, known about what causes them and whether this genetic variance-heterogeneity reflects mechanisms of importance in natural populations. Previously, we identified a variance-heterogeneity GWA (vGWA) signal for leaf molybdenum concentrations inArabidopsis thaliana. Here, fine-mapping of this association to a ∼78 kb Linkage Disequilibrium (LD)-block reveals that it emerges from the independent effects of three genetic polymorphisms on the high-variance associated version of this LD-block. By revealing the genetic architecture underlying this vGWA signal, we uncovered the molecular source of a significant amount of hidden additive genetic variation (“missing heritability”). Two of the three polymorphisms on the high-variance LD-block are promoter variants for Molybdate transporter 1 (MOT1), and the third a variant located ∼25 kb downstream of this gene. A fourth independent association was also detected ∼600 kb upstream of the LD-block. Testing of T-DNA knockout alleles for genes in the associated regions suggestAT2G25660(unknown function) andAT2G26975(Copper Transporter 6; COPT6) as the strongest candidates for the associations outsideMOT1. Our results show that multi-allelic genetic architectures within a single LD-block can lead to a variance-heterogeneity between genotypes in natural populations. Further they provide novel insights into the genetic regulation of ion homeostasis inA. thaliana, and empirically confirm that variance-heterogeneity based GWA methods are a valuable tool to detect novel associations of biological importance in natural populations.