bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk Perception
Authors: Everitt Brian S.
Published: December 2014

Life is a risky business, and deciding which risks are worth taking and which should be avoided has important implications both for an individual's lifestyle, and the way society operates. The benefits gained from taking a risk need to be weighed against the possible disadvantages. Acceptable risk is proportional to the amount of benefits. For the individual, living life to the fullest means achieving a balance between reasonable and unreasonable risk, and this will often be a matter of judgement depending largely on the individual's personality. However, in society as a whole, where the same balancing act is required, it has to be achieved through political action and legislation.
Compartmental Analysis
Authors: Becka Michael
Published: December 2014

Ecological, toxicological, and pharmacological research is often concerned with the answer to the question of how a substance is processed within a biological system. The exact knowledge of the corresponding kinetic pattern forms the basis for a useful answer. In order to understand and to characterize kinetic processes, as well as to identify nonlinear kinetics, compartmental analysis yields a useful approach.
Extremes: Spatial Parametric Modeling
Authors: Davison Anthony C.
Published: December 2014

Statistics of spatial extremes is developing very rapidly, owing to the demands of applications in the environmental sciences and the insurance and risk industries. This article sketches the main ideas, based on classical extreme value statistics. The two main threads of work are the fitting of max‐stable models to spatial extremes, and the use of latent variable models, the latter typically in a Bayesian context.
Markov Random Field Models
Authors: Kaiser Mark S.
Published: December 2014

Statistical models formulated on the basis of Markov random fields (MRFs) constitute an appealing approach to the analysis of data that exhibit complex dependence structures. Such data arise commonly in problems of a spatial or spatiotemporal nature, although MRFs are a general mathematical construct that may be used in other situations such as, for example, the representation of genetic dependence among organisms. Within the context of statistical modeling, a MRF may be defined for any set of random variables defined at a discrete point.
Point Processes, Dynamic
Authors: Ensor Katherine Bennett
Published: December 2014

This article deals with the specification and estimation of the intensity rate of point processes. The dynamics can include an arbitrary number of changes of level or modeling the intensity rate as a continuous function of exogenous variables. For discrete change points, the change points can be specified online as the process is observed or in advance with techniques that allow for the estimation of number and time location of changes. The classes of conditional duration models or autoregressive conditional duration models allow direct modeling of the intensity rate of a point process. In spatial dynamic point processes, changes may be governed by topology of the region.
Stochastic Models
Authors: Preisler Haiganoush K.
Published: December 2014

Environmental scientists use models – a system of assumptions presented in a mathematical framework – to study complex interrelationships in ecological processes and to assess and predict the impact of our actions on the environment, among other things. There are a variety of model types: stochastic, deterministic, numerical, to name a few. A major concept that distinguishes stochastic models from other models is the idea of probability, or randomness, that is explicit in all stochastic models.
Exceedance Probability
Authors: Drees Holger
Published: December 2014

The probability that a future observation exceeds a high threshold is approximated and estimated using an extreme value approach.
Synthesis of Secondary Amides from N‐Substituted Amidines by Tandem Oxidative Rearrangement and Isocyanate Elimination
Authors: Debnath Pradip , Baeten Mattijs , Lefèvre Nicolas , Daele Stijn Van , Maes Bert U. W.
Published: December 2014

In this work an efficient tandem process transforming N‐substituted amidines into secondary amides has been described. The process involves N‐acylurea formation by reaction of the substrate with bis(acyloxy)(phenyl)‐λ3‐iodane followed by isocyanate elimination. The periodinane reagents are obtained from the commercially available phenyliodine(III) diacetate [PhI(OAc)2, (PIDA)] by ligand exchange with carboxylic acids. The N‐substituted amidine substrates are easily synthesized from readily available nitriles. The method is applicable for secondary amide synthesis, based on both aliphatic and (hetero)aromatic amines, including challenging amides consisting of sterically hindered acids and amines. Moreover, the protocol allows one to combine steric bulk with electron deficiency in the target amides (aniline based). Such compounds are difficult to synthesize efficiently based on classical condensation reactions involving carboxylic acids and amines. Overall, the synthetic protocol transforms a nitrile into a secondary amide in both aliphatic and (hetero)aromatic systems.

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Supramolecular Catalysis in the Synthesis of Substituted 1 H‐Tetrazoles from Isonitriles by a Self‐Assembled Hexameric Capsule
Authors: Giust Sonia , La Sorella Giorgio , Sperni Laura , Fabris Fabrizio , Strukul Giorgio , Scarso Alessandro
Published: December 2014

The synthesis of substituted 1H‐tetrazoles from aliphatic or aromatic isonitriles and trimethylsilyl azide can be efficiently promoted by the hexameric capsule of resorcin[4]arene as a supramolecular self‐assembled catalyst. The reaction is sensitive to the size and nature of the substrate and is driven by encapsulation of the reagents within the cavity of the supramolecular catalyst.
Oscillations in the Stability of Consecutive Chemical Bonds Revealed by Ion‐Induced Desorption
Authors: Ossowski Jakub , Rysz Jakub , Krawiec Mariusz , Maciazek Dawid , Postawa Zbigniew , Terfort Andreas , Cyganik Piotr
Published: December 2014

While it is a common concept in chemistry that strengthening of one bond results in weakening of the adjacent ones, no results have been published on if and how this effect protrudes further into the molecular backbone. By binding molecules to a surface in the form of a self‐assembled monolayer, the strength of a primary bond can be selectively altered. Herein, we report that by using secondary‐ion mass spectrometry, we are able to detect for the first time positional oscillations in the stability of consecutive bonds along the adsorbed molecule, with the amplitudes diminishing with increasing distance from the molecule–metal interface. To explain these observations, we have performed molecular dynamics simulations and DFT calculations. These show that the oscillation effects in chemical‐bond stability have a very general nature and break the translational symmetry in molecules.
Scanning‐Tunneling‐Spectroscopy‐Directed Design of Tailored Deep‐Blue Emitters
Authors: Sanning Jan , Ewen Pascal R. , Stegemann Linda , Schmidt Judith , Daniliuc Constantin G. , Koch Tobias , Doltsinis Nikos L. , Wegner Daniel , Strassert Cristian A.
Published: December 2014

Frontier molecular orbitals can be visualized and selectively set to achieve blue phosphorescent metal complexes. For this purpose, the HOMOs and LUMOs of tridentate PtII complexes were measured using scanning tunneling microscopy and spectroscopy. The introduction of electron‐accepting or ‐donating moieties enables independent tuning of the frontier orbital energies, and the measured HOMO–LUMO gaps are reproduced by DFT calculations. The energy gaps correlate with the measured and the calculated energies of the emissive triplet states and the experimental luminescence wavelengths. This synergetic interplay between synthesis, microscopy, and spectroscopy enabled the design and realization of a deep‐blue triplet emitter. Finding and tuning the electronic “set screws” at molecular level constitutes a useful experimental method towards an in‐depth understanding and rational design of optoelectronic materials with tailored excited state energies and defined frontier‐orbital properties.
Multidimensional De Novo Design Reveals 5‐HT2B Receptor‐Selective Ligands
Authors: Rodrigues Tiago , Hauser Nadine , Reker Daniel , Reutlinger Michael , Wunderlin Tiffany , Hamon Jacques , Koch Guido , Schneider Gisbert
Published: December 2014

We report a multi‐objective de novo design study driven by synthetic tractability and aimed at the prioritization of computer‐generated 5‐HT2B receptor ligands with accurately predicted target‐binding affinities. Relying on quantitative bioactivity models we designed and synthesized structurally novel, selective, nanomolar, and ligand‐efficient 5‐HT2B modulators with sustained cell‐based effects. Our results suggest that seamless amalgamation of computational activity prediction and molecular design with microfluidics‐assisted synthesis enables the swift generation of small molecules with the desired polypharmacology.
Supply Chain Management as Private Sector Regulation: What does it Mean for Business Strategy and Public Policy?
Authors: Fiorino Daniel J. , Bhan Manjyot
Published: December 2014

The growing practice of environmental supply chain management by firms constitutes private sector regulation that is analogous in many ways to public sector regulation. Similarly to their public counterparts, private sector regulators set standards, apply standards, monitor for compliance, apply sanctions and require corrective action. Private sector regulation differs, however, in the source of authority, external oversight, analytical requirements, public participation and available sanctions. This article argues that supply chain management by firms goes beyond business objectives by creating positive environmental externalities for society, and that more systematic study of the similarities and contrasts between the two forms of regulation may provide valuable lessons for both. Further, it may be possible to increase the effectiveness of private sector regulation to achieve both public societal and private business goals. From a business perspective, supply chain management enables firms to strategically redefine their relationships with government, reduce uncertainty and promote goal‐oriented collaboration. Copyright © 2014 John Wiley & Sons, Ltd and ERP Environment
Hydroxy‐Functionalized Imidazolium Bromides as Catalysts for the Cycloaddition of CO2 and Epoxides to Cyclic Carbonates
Authors: Anthofer Michael H. , Wilhelm Michael E. , Cokoja Mirza , Drees Markus , Herrmann Wolfgang A. , Kühn Fritz E.
Published: December 2014

Hydroxy‐functionalized mono‐ and bisimidazolium bromides were synthesized and applied as catalysts for the cycloaddition of CO2 and epoxides to cyclic carbonates. A catalyst screening showed the influence of the number of protic hydrogen atoms at the cation for the activation of epoxides. The most active catalyst operates at very mild reaction conditions (70 °C, 0.4 MPa CO2) and can be easily recycled ten times without loss of activity.
Convenient Synthesis of Quinolines from α‐2‐Nitroaryl Alcohols and Alcohols via a Ruthenium‐catalyzed Hydrogen Transfer Strategy
Authors: Xie Feng , Zhang Min , Chen Mengmeng , Lv Wan , Jiang Huanfeng
Published: December 2014

A new and straightforward method for convenient synthesis of quinolines via a ruthenium‐catalyzed hydrogen‐transfer strategy has been demonstrated. By employing a commercially available ruthenium catalyst system, different α‐2‐nitroaryl alcohols were efficiently converted in combination with a variety of alcohols into various substituted products in reasonable to good yields upon isolation. The synthetic protocol is operationally simple with a broad substrate scope, and there is no need for the use of specialized reducing agents, making it a practical approach for versatile preparation of various quinoline derivatives.
Li[B(OCH2CF3)4]: Synthesis, Characterization and Electrochemical Application as a Conducting Salt for LiSB Batteries
Authors: Rohde Michael , Eiden Philipp , Leppert Verena , Schmidt Michael , Garsuch Arnd , Semrau Guenter , Krossing Ingo
Published: December 2014

A new Li salt with views to success in electrolytes is synthesized in excellent yields from lithium borohydride with excess 2,2,2‐trifluorethanol (HOTfe) in toluene and at least two equivalents of 1,2‐dimethoxyethane (DME). The salt Li[B(OTfe)4] is obtained in multigram scale without impurities, as long as DME is present during the reaction. It is characterized by heteronuclear magnetic resonance and vibrational spectroscopy (IR and Raman), has high thermal stability (Tdecomposition>271 °C, DSC) and shows long‐term stability in water. The concentration‐dependent electrical conductivity of Li[B(OTfe)4] is measured in water, acetone, EC/DMC, EC/DMC/DME, ethyl acetate and THF at RT In DME (0.8 mol L−1) it is 3.9 mS cm−1, which is satisfactory for the use in lithium‐sulfur batteries (LiSB). Cyclic voltammetry confirms the electrochemical stability of Li[B(OTfe)4] in a potential range of 0 to 4.8 V vs. Li/Li+. The performance of Li[B(OTfe)4] as conducting salt in a 0.2 mol L−1 solution in 1:1 wt % DME/DOL is investigated in LiSB test cells. After the 40th cycle, 86 % of the capacity remains, with a coulombic efficiency of around 97 % for each cycle. This indicates a considerable performance improvement for LiSB, if compared to the standard Li[NTf2]/DOL/DME electrolyte system.
Fabrication and Characterisation of Membrane‐Based Gold Electrodes
Authors: Bakmand Tanya , Kwasny Dorota , Dimaki Maria , Svendsen Winnie E.
Published: December 2014

This work presents a versatile, membrane based electrochemical sensor with thin film electrodes fabricated through E‐beam evaporation directly on porous materials (membranes). Here, the fabrication of the electrodes is described along with possible methods for integration in fluidic systems and characterisation of the electrodes through cyclic voltammetry (CV). The continued porous nature of the membranes after metal deposition is documented and its robustness and stability is investigated. Furthermore, amperometric sensing of dopamine is demonstrated as a proof of concept to validate the usability of the membrane sensor.
Petrographic and Geochemical Constraints on the Provenance of Sanidine‐Bearing Temper in Ceramic Potsherds, Four Corners Region, Southwest USA
Authors: Gonzales David A. , Arakawa Fumi , Koenig Alan
Published: December 2014

Previous researchers proposed that trachybasalt temper with “poikilitic” sanidine, found in pottery from the Mesa Verde region of the American Southwest, was procured along the eastern Chuska Mountains. This served as one line of evidence that Chaco Canyon was a regional trade center linked to the Chuska Mountains in the ninth to thirteenth centuries. Recent geologic studies, however, revealed other potential sources for the trachybasalt temper. A comparison of petrographic features and geochemical signatures of poikilitic sanidine in rock samples and potsherds shows no definitive correlation of temper materials and a specific geologic source. Several outcrops of trachybasalt are identified as less viable prospects, but the results do not support the idea that the sanidine‐rich temper was exclusively gathered in the Chuska Mountains. This conclusion opens up the possibility that raw materials were gathered from local sources that were more accessible, reducing the dependence on a regional trade center.
Do College Youth Serve Others? How and Under Which Circumstances? Implications for Promoting Community Service
Authors: Griffith James , Thomas Todd
Published: December 2014

This chapter describes how data on the extent of community service among a national representative sample of young college students were associated with “supports,” including human, social, and cultural capital. This chapter helps fill missing information on estimates of the occurrence and persistence of community service, types of community service performed, and variables associated with performing such services.
Assessing Civic Engagement at Indiana University–Purdue University Indianapolis
Authors: Pike Gary R. , Bringle Robert G. , Hatcher Julie A.
Published: December 2014

Faculty and staff at Indiana University–Purdue University Indianapolis (IUPUI) have developed several tools to assess campus civic engagement initiatives. This chapter describes the IUPUI Faculty Survey and the Civic‐Minded Graduate Scale, and reports on findings from campus‐based assessment and research.
Community‐Based Theater and Adults with Psychiatric Disabilities: Social Activism, Performance and Community Engagement
Authors: Faigin David A. , Stein Catherine H.
Published: December 2014

The present study is an in‐depth qualitative inquiry with an established theater troupe composed of adults living with psychiatric disabilities known as The Stars of Light. A grounded theory methodology is used to describe dimensions of social activism and characteristics of theater as a medium of engagement at the individual, setting/troupe, and community levels of analysis. Analysis of a broad scope of interview data, performance content, community contacts, and historical data from the troupe’s 19‐year history led to the identification of eight emergent theoretical concepts formulated from 17 supporting associated themes. The theoretical concepts characterize the impacts of community‐based theater in the lives of participants, and theater troupe processes that contribute to community education and positive social change for adults living with psychiatric disabilities. Advantages, limitations, and future directions for research and action in community‐based theater settings are discussed within the context of present research findings.
Right‐sided infective endocarditis as a potentially fatal complication in patients with long‐term refractory severe bradyarrhythmia after cervical spinal cord injury: A case report
Authors: Miura Naoki , Suzuki Hideaki , Maesawa Shota , Koakutsu Tomoaki , Matsumoto Yasuharu , Fukuda Koji , Kagaya Yutaka , Kushimoto Shigeki , Shimokawa Hiroaki
Published: December 2014

Bradyarrhythmia is usually a spontaneously subsiding complication of cervical spinal cord injury. However, in severe cases, it can lead to cardiac arrest. We report a case of cervical spinal cord injury, complicated by right‐sided infective endocarditis after the placement of a temporary pacing catheter in the right ventricle for severe bradyarrhythmia that led to cardiac arrest. Although the patient's condition was successfully treated by pacing catheter removal and pharmacological therapy, right‐sided infective endocarditis would be a fatal complication in cases of cervical spinal cord injury where cardiac pacing is required for long‐term refractory severe bradyarrhythmia.
A Militant Crusade In Africa: The Great Commission And Segregation
Authors: Jordan Richard
Published: December 2014

During the Cold War and in the aftermath of the Brown v. Board of Education decision, the Calvinist and political fundamentalists of North America opposed the integration of American society and the extension of civil rights to African-Americans. Both were viewed as contrary to God's plan for humankind and omens for the end times. At the same time, these militant clerics spread reformed theology and eschatology to non-white societies across the globe. An important missionary field was Africa, where American and British racial mores influenced the cultural and political struggle. western, capitalistic and democratic principles, white minority-rule, and British imperialism faced African nationalism and communist aid to independence movements. Accordingly, the contrast between militant theology and liberal, modernist Protestantism was interjected into the conflict. Two American crusaders, Carl McIntire and Billy James Hargis, made Africa an important battleground to defend segregation and western influence. Both pursued individual ministries and had differing theological agendas towards race. The International Council of Christian Churches, an organization that McIntire led, spread God's word to black Africans, while Hargis' Christian Crusade Against Communism worked with Rhodesia's white minority government. Their efforts provide insight into the militant theological and political crusade in North America and how they projected their Calvinist ideals into the international arena and into Africa.
ON THE COMPLEXITY OF FINDING A NECESSARY AND SUFFICIENT CONDITION FOR BLASCHKE-OSCILLATORY EQUATIONS
Authors: HEITTOKANGAS JANNE , REIJONEN ATTE
Published: December 2014

If A(z) belongs to the Bergman space , then the differential equation f″+A(z)f=0 is Blaschke-oscillatory, meaning that the zero sequence of every nontrivial solution satisfies the Blaschke condition. Conversely, if A(z) is analytic in the unit disc such that the differential equation is Blaschke-oscillatory, then A(z) almost belongs to . It is demonstrated that certain “nice” Blaschke sequences can be zero sequences of solutions in both cases when A ∈ or A ∉ . In addition, no condition regarding only the number of zeros of solutions is sufficient to guarantee that A ∈ .
Malmgrenia louiseae sp. nov., a new scale worm species (Polychaeta: Polynoidae) from southern Europe with a key to European Malmgrenia species
Authors: Jourde Jérôme , Sampaio Leandro , Barnich Ruth , Bonifácio Paulo , Labrune Céline , Quintino Victor , Sauriau Pierre-Guy
Published: December 2014

Malmgrenia louiseae sp. nov. is described from both the western Mediterranean in the Gulf of Lions, and the north-east Atlantic from off Portugal and the Bay of Biscay. The species was found in muddy sediments in shallow water and is possibly associated with echiurids or synaptid holothurians. Malmgrenia louiseae sp. nov. can be clearly distinguished from all other known Malmgrenia species by the presence of an infra-acicular process in addition to the supra-acicular process on the acicular lobe of the neuropodia, the lack of microtubercules on the elytra, two kinds of notochaetae (stout with blunt tip and slender with fine pointed tip), and exclusively unidentate neurochaetae. An identification key to the north-east Atlantic and Mediterranean Malmgrenia species is provided.
Collecting “Tribal Art”—Sacred or Secular?
Authors: Paterson Robert K.
Published: December 2014

This article explores the history of collecting and dealing in non-Western cultural objects—primarily from the Pacific Islands—from the earliest explorers to the modern auction houses. It considers international and domestic laws relating to indigenous cultural material that might be seen as religious or sacred in character and concludes that while these rules clearly influence both private and institutional practices they fall short of legally impacting the functioning of otherwise lawful markets.
Remarks in Honor of the Legal and Public Policy Legacies of John
Henry Merryman: Cultural Property and Human Cells
Authors: Feldman Robin
Published: December 2014

It is an honor to be invited to speak at this symposium, both for the kind
invitation to address this society, and for the opportunity to honor an esteemed
scholar from my alma mater, Stanford.

I come to this symposium, not as an expert in cultural property, but as an
inhabitant of the field of biotechnology and intellectual property law. Although
the view from a distance can provide different perspectives, it lacks the layers
of understanding and meaning that are accumulated by those who are steeped in
the field. I cannot possibly hope to offer solutions to issues with which many
brilliant minds have spent a lifetime grappling. Thus, I temper my comments with
the caution appropriate for the exercise. What I can do is offer comparisons
from the treatment of human cells, as well as observations I have suggested in
that context.
Immovable Cultural Heritage at Risk: Past – Present – Future
Authors: Siehr Kurt G.
Published: December 2014

Immovable cultural heritage is still at risk of being neglected by the state responsible for heritage sites, by urban planning of big cities, and by armed conflicts around the world. Normally, because it is immovable, the international community cannot do very much. It can ban the trade of items that became movable property when detached from buildings or illegally excavated in certain protected sites. In other cases, it is the responsibility of the national state to care for cultural heritage and cultural objects. International conventions may furnish help and advice and provide for monitoring any risk to the cultural heritage of state parties.
Local Control Mechanisms of Implicit and Explicit Conflicts
Authors: Zhao Liang , Bai Yang , Ma Jie , Wang Yonghui
Published: December 2014

Congruency sequence effects are observed when the congruency effects following incongruent trials are smaller than those following congruent trials. It is typically assumed that such flexible adjustments are evidence of cognitively controlled dynamic modulations. The present study investigated whether cognitive control acts locally or globally when implicit and explicit conflicts exist simultaneously within a system. The implicit SNARC task and explicit Simon task were combined in a single task. The results showed that congruency effects of one type (e.g., SNARC effect) were only smaller following an incongruent trial of the same type (e.g., SNARC effect), but not when following an incongruent trial of the other type (e.g., Simon effect). These results indicate the operation of local control mechanisms triggered by implicit and explicit conflicts.
Applications in Continuous Flow Acoustophoresis
Authors: Lenshof Andreas , Augustsson Per , Laurell Thomas
Published: December 2014

This chapter presents different applications and modes of operation for acoustophoresis in continuous flow. Concentration, clarification, medium exchange, cytometry applications and other techniques and tricks for manipulating cells and particles for special purposes are covered.
Citrate-capped gold nanoparticles for the label-free detection of ubiquitin C-terminal hydrolase-1
Authors: Agarwal Srishti , Mishra Priyanka , Shivange Gururaj , Kodipelli Naveena , Moros María , de la Fuente Jesús M. , Anindya Roy
Published: December 2014

Ubiquitin C-terminal hydrolase-1 (UCH-L1) is a specific neuronal endoprotease that cleaves the peptide bond between ubiquitin molecules.
A perfluorinated moiety-grafted carbon nanotube electrode for the non-aqueous lithium–oxygen battery
Authors: Thomas Morgan L. , Yamanaka Keisuke , Ohta Toshiaki , Byon Hye Ryung
Published: December 2014

A highly localized Li–O2 electrochemical reaction is demonstrated in close proximity to the perfluorinated moiety grafted to the carbon nanotube electrode.
Copper(ii)-catalyzed methoxylation of unactivated (hetero)aryl C–H bonds using a removable bidentate auxiliary
Authors: Yin Xue-Song , Li Yi-Chen , Yuan Jun , Gu Wen-Jia , Shi Bing-Feng
Published: December 2014

A copper-catalyzed methoxylation of unactivated (hetero)aryl C–H bonds has been developed.
Chemoselective hydration of nitriles to amides using hydrated ionic liquid (IL) tetrabutylammonium hydroxide (TBAH) as a green catalyst
Authors: Veisi Hojat , Maleki Behrooz , Hamelian Mona , Ashrafi Samaneh Sedigh
Published: December 2014

A green, chemoselective synthesis of amides, avoiding the use of any base, metal, or Lewis acid catalyst.
Hydrolysis of cellobiose to monosaccharide catalyzed by functional Lanthanum(iii) metallomicelle
Authors: Peng Xiao , Meng Xiang-Guang , Mi Chun , Liao Xiao-Hong
Published: December 2014

Cellobiose could be effectively hydrolyzed to monosaccharide (glucose, fructose and 1,6-anhydroglucose) by the catalysis of metallomicelle La(DMBO)2under mild conditions.
A novel triple-mode fluorescent pH probe from monomer emission to aggregation-induced emission
Authors: Wang Zhenghua , Ye Jia-Hai , Li Jing , Bai Yang , Zhang Wenchao , He Weijiang
Published: December 2014

A tetraphenylenlene (TPE)-based fluorescent probe could selectively monitor pH in THF–H2O media in wide-range pH. From acidic to basic conditions, it displayed monomer emission, ratiometric fluorescence and aggregation-induced emission successively.
Mechanistic analysis of an asymmetric palladium-catalyzed conjugate addition of arylboronic acids to β-substituted cyclic enones
Authors: Boeser Cornelia L. , Holder Jeffrey C. , Taylor Buck L. H. , Houk K. N. , Stoltz Brian M. , Zare Richard N.
Published: December 2014

Mechanistic insight into a Pd-catalyzed conjugate addition reaction was gained using desorption electrospray ionization coupled to mass spectrometry.
Interplay between the structure and dynamics in liquid and undercooled boron: An ab initio molecular dynamics simulation study
Authors: Jakse N. , Pasturel A.
Published: December 2014

In the present work, the structural and dynamic properties of liquid and undercooled boron are investigated by means of ab initio molecular dynamics simulation. Our results show that both liquid and undercooled states present a well pronounced short-range order (SRO) mainly due to the formation of inverted umbrella structural units. Moreover, we observe the development of a medium-range order (MRO) in the undercooling regime related to the increase of inverted umbrella structural units and of their interconnection as the temperature decreases. We also evidence that this MRO leads to a partial crystallization in the β-rhombohedral crystal below T = 1900 K. Finally, we discuss the role played by the SRO and MRO in the nearly Arrhenius evolution of the diffusion and the non-Arrhenius temperature dependence of the shear viscosity, in agreement with the experiment.
Versatile physiological functions of the Nudix hydrolase family in Arabidopsis
Authors: Yoshimura Kazuya , Shigeoka Shigeru
Published: December 2014

Nudix hydrolases are widely distributed in all kingdoms of life and have the potential to hydrolyze a wide range of organic pyrophosphates, including nucleoside di- and triphosphates, nucleotide coenzymes, nucleotide sugars, and RNA caps. However, except for E. coli MutT and its orthologs in other organisms that sanitize oxidized nucleotides to prevent DNA and RNA mutations, the functions of Nudix hydrolases had largely remained unclear until recently, because many members of this enzyme family exhibited broad substrate specificities. There is now increasing evidence to show that their functions extend into many aspects of the regulation of cellular responses. This review summarizes current knowledge on the molecular and enzymatic properties as well as physiological functions of Arabidopsis Nudix hydrolases. The information presented here may provide novel insights into the physiological roles of these enzymes in not only plant species, but also other organisms.
Rapid Communication: The Asymmetry and Temporal Dynamics of Incidental Letter–Location Bindings in Working Memory
Authors: Elsley Jane V. , Parmentier Fabrice B. R.
Published: December 2014

Verbal–spatial bindings are integral to routine cognitive operations (e.g., reading), yet the processes supporting them in working memory are little understood. Campo and colleagues [Campo, P., Poch, C., Parmentier, F. B. R., Moratti, S., Elsley, J. V., Castellanos, N., … Maestú, F. (2010). Oscillatory activity in prefrontal and posterior regions during implicit letter-location binding. Neuroimage, 49, 2807–2815] recently reported data suggesting obligatory letter–location binding when participants were directed to remember the letters in a display (of letters in locations), but no evidence for binding when instructed to remember the filled locations. The present study contrasted two explanations for this binding asymmetry. First, it may result from an obligatory dependence on “where” during the representation of “what” information, while “where” information may be held independently of its contents (the strong asymmetry hypothesis). Second, it may constitute a snapshot of a dynamic feature inhibition process that had partially completed by test: the asymmetrical inhibition hypothesis. Using Campo and colleagues’ task with a variable retention interval between display and test, we presented four consonants in distinct locations and contrasted performance between “remember letters” and “remember locations” instructions. Our data supported the strong asymmetry hypothesis through demonstrating binding in the verbal task, but not in the spatial task. Critically, when present, verbal–spatial bindings were remarkably stable, enduring for at least 15 seconds.
Probabilistic Graphical Models for Next-generation Genomics and Genetics
Authors: Sinoquet Christine
Published: December 2014

The explosion in omics and other types of biological data has increased the demand for solid, large-scale statistical methods. These data can be discrete or continuous, dependent or independent, from many individuals or tissue types. There might be millions of correlated observations from a single individual, observations at different scales and levels, in addition to covariates. The study of living systems encompasses a wide range of concerns, from prospective to predictive and causal questions, reflecting the multiple interests in understanding biological mechanisms, disease etiology, predicting outcome, and deciphering causal relationships in data. Precisely, probabilistic graphical models provide a flexible statistical framework that is suitable to analyze such data. Notably, graphical models are able to handle dependences within data, which is an almost defining feature of cellular and other biological data.
Graphical Models and Multivariate Analysis of Microarray Data
Authors: Kiiveri Harri
Published: December 2014

The usual analysis of gene expression data ignores the correlation between gene expression values. Biologically, this assumption is unreasonable. The approach presented in this chapter allows for correlation between genes through a sparse Gaussian graphical model: sparse inverse covariance matrices and their associated graphical representations are used to capture the notion of gene networks. Existing methods find their limitations in the issue posed by the identification of the pattern of zeroes in such inverse covariance matrices. A workable solution for determining the zero pattern is provided in this chapter. Two other important contributions of this chapter are a method for very high-dimensional model fitting and a distribution-free approach to hypothesis testing. Such tests address assessment of differential expression and of differential connection, a novel notion introduced in this chapter. An example dealing with real data is presented.
Network Inference in Breast Cancer with Gaussian Graphical Models and Extensions
Authors: Jeanmougin Marine , Charbonnier Camille , Guedj Mickaël , Chiquet Julien
Published: December 2014

Clustering genes with high correlations will group genes with close expression profiles, defining clusters of co-expressed genes. However, such correlations do not provide any clue on the chain of information going from gene to gene. Partial correlation consists in quantifying the correlation between two genes after excluding the effects of the other genes. Partial correlation thus makes it possible to distinguish between the correlation of two genes due to direct causal relationships from the correlation that originates via intermediate genes. In this chapter, Gaussian graphical model (GGM) learning is set up as a covariate selection problem. Two least absolute shrinkage and selection operator (LASSO)-type techniques are described, the graphical LASSO approach and the neighborhood selection. Then two extensions to the classical GGM are presented. GGMs are extended in structured GGMs, to account for modularity, and more generally heterogeneity in the gene connection features. The extension using a biological prior on the network structure is illustrated on real data.
Utilizing Genotypic Information as a Prior for Learning Gene Networks
Authors: Chipman Kyle , Singh Ambuj
Published: December 2014

The combination of genotypic and genome-wide expression data arising from segregating populations offers an unprecedented opportunity to model and dissect complex phenotypes. Leading studies have augmented Bayesian networks with genotypic data, providing a powerful framework for learning and modeling causal relationships. However, one major drawback of these methods is that they are generally limited to resolving causal orderings for transcripts most proximal to the genomic loci. This chapter reviews two methods where all interactions between genotype and gene transcripts are considered collectively in order to better resolve causal relationships between gene transcripts. The likelihood-based causality model selection (LCMS) of Schadt and collaborators is first described. Then, the stochastic causal tree (SCT) method is depicted. The information provided by such methods is intended to be used as a prior for Bayesian network structure learning, resulting in enhanced performance for gene network reconstruction.
Bayesian, Systems-based, Multilevel Analysis of Associations for Complex Phenotypes: from Interpretation to Decision
Authors: Antal Péter , Millinghoffer András , Hullám Gábor , Hajós Gergely , Sárközy Péter , Gézsi András , Szalai Csaba , Falus András
Published: December 2014

The relative scarcity of the results reported by genetic association studies (GAS) prompted many research directions. Despite the centrality of the concept of association in GASs, refined concepts of association are missing; meanwhile, various feature subset selection methods became de facto standards for defining multivariate relevance. On the other hand, probabilistic graphical models, including Bayesian networks (BNs) are more and more popular, as they can learn nontransitive, multivariate, nonlinear relations between complex phenotypic descriptors and heterogeneous explanatory variables. To integrate the advantages of Bayesian statistics and BNs, the Bayesian network based Bayesian multilevel analysis of relevance (BN-BMLA) was proposed. This approach allows the processing of multiple target variables, while ensuring scalability and providing a multilevel view of the results of multivariate analysis. This chapter discusses the use of Bayesian BN-based analysis of relevance in exploratory data analysis, optimal decision and study design, and knowledge fusion, in the context of GASs.
Andalusi Arabic negators and interrogatives
Authors: Wilmsen David
Published: December 2014

The earliest unambiguous evidence for grammatical šī in Arabic comes in a few instances of an indefinite determiner and negator šī in the vernacular poetry and folk proverbs of Arab Spain (al-Andalus), evidence for a copular interrogative formed with a suffixed -š also appearing in two places. Conventionally and mistakenly interpreted as negators, these would show the operation of a Jespersen’s Cycle in Andalusi Arabic. Considering them in the context of exclamatives and rhetorically negative questions in living Arabic dialects and in their indigenous setting allows us to draw a different conclusion: negating with -š began when interrogatives formed with reflexes of šī were negated with mā, thus permitting their reanalysis as negators, even as they retained the post-positive -š of interrogation.
The Debate over Authority
Authors: Rose Jacqueline
Published: December 2014

This chapter explores the triangular relationship between lay government, ecclesiastical authorities, and the individual Christian. Adiaphora constituted non‐doctrinal matters regarded as ‘indifferent’; mainly rites and ceremonies, but perhaps encompassing church government as well. These issues were central to negotiations over comprehension and were rooted in the theology of Christian liberty. However, the royal supremacy of the civil magistrate in the English Church meant that adiaphora unavoidably raised questions about law and authority. Discussions about the casuistry of obedience brought to the fore the psychological dilemmas of conformity. Debating the aesthetics of worship and their relationship to the remnants of Catholic ‘Popery’ rendered problematic the identity of the English Church. This chapter explores what was distinctive about the Restoration phase of an argument as old as the English Reformation, and how this complicates notions of toleration in the seventeenth century.
Circumstantial Temporary Concessions
Authors: Seaward Paul
Published: December 2014

The Acts passed by the Cavalier Parliament in 1661–5 which prevented many ‘Puritans’ and ‘Presbyterians’ from conforming to the Church of England, and punished those who tried to establish alternative forms of religious worship, have often been known as the ‘Clarendon Code’, after Edward Hyde, Earl of Clarendon. Yet Clarendon's writings, and his attitudes to church matters during the early 1640s, suggest someone who was more concerned to promote religious peace than a determined and rigid advocate of uniformity and persecution; moreover, during 1662 he made strenuous efforts to reduce the severity of some aspects of the uniformity bill. This chapter argues that despite his adiaphorist approach, Clarendon, like many others, was firmly and decisively in favour of uniformity, but that he was nevertheless genuinely concerned about the pace of the change that was being driven on—principally by the hierarchy of the Church.
The Bishops of Ireland and the Beasts at Ephesus
Authors: Armstrong Robert
Published: December 2014

This chapter assesses the means whereby Protestant Ireland saw the reimposition of a full‐blown ‘Anglican’ order and the exclusion of large numbers of Presbyterian clergymen, ahead of comparable developments in England, and based explicitly on pre‐war norms. That re‐establishment took on regional and ‘national’ dimensions, with the largest expulsions of ministers occurring among the Scottish communities of north‐east and north‐west Ulster, and it generated disorder and communal tension on the ground closer to the Scottish than the English experience of Restoration. Yet while it was in the interests of later denominational historians and apologists, both Anglican and Presbyterian, to emphasize the sharp and decisive break between them in these years, this chapter will also look at evidence of some ambiguities, and some opportunities, which blur such straightforward conclusions, and it will consider how far these offered the possibility of a different, more comprehensive, settlement.
Going Dutch
Authors: Cotter Cory
Published: December 2014

This chapter explores the cross‐cultural connections of a small but tightly‐knit community of ejected ministers who fled to the Dutch Republic in the wake of the Restoration Settlement (1660–2), focusing on the English‐Scottish community in Holland (c.1660–90), with occasional glances further afield. Mapping out their intellectual networks, both home and abroad, first the statistical significance of Leiden University, especially for Britons (who formed one of its largest contingents of foreign students) is quantified. Second, it is argued that contrary to current historiography, national boundaries proved irrelevant to intellectual and social exchanges between English and Scottish dissenters in Dutch exile. Finally, there is a demonstration of how these general patterns of intellectual exchange and movement specifically applied to a tightly‐knit community of preachers, plotters, and physicians (at Leiden, and beyond) during the post‐Restoration period.
Kablammo: an interactive, web-based BLAST results visualizer
Authors: Wintersinger Jeff A. , Wasmuth James D.
Published: December 2014

Motivation: Kablammo is a web-based application that produces interactive, vector-based visualizations of sequence alignments generated by BLAST. These visualizations can illustrate many features, including shared protein domains, chromosome structural modifications and genome misassembly.

Availability and implementation: Kablammo can be used at http://kablammo.wasmuthlab.org. For a local installation, the source code and instructions are available under the MIT license at http://github.com/jwintersinger/kablammo.

Contact:  jeff@wintersinger.org
SMC3 may play an important role in atopic asthma development
Authors: Cheng Qi , Huang Wanjie , Chen Ning , Shang Yunxiao , Zhang Han
Published: December 2014

Introduction

As a common disease with a complex risk, including genetic and environmental factors, atopic asthma is prevalent but treatable. The aim of the study was to predict the underlying mechanism of asthma and identify target genes for the disease.

Methods

The affymetrix chip data, GSE18965, were available from Gene Expression Omnibus and the differentially expressed genes (DEGs) between nine atopic asthmatic specimens and seven healthy nonatopic samples were identified by R. Then Gene Ontology and pathway enrichment analyses were performed to these DEGs. Further, search tool for the retrieval of interacting genes/proteins (STRING) was used to select protein–protein interaction (PPI) for DEGs, and then the network was visualized by Cytoscape. Finally, transcription factor binding site analysis was conducted to the hot gene.

Results

Total 565 DEGs were identified, including 535 upregulated and 30 downregulated genes. The upregulated genes, such as structural maintenance of chromosome (SMC)3, significantly affected cellular component of extracellular matrix (P = 1.56E‐04). Otherwise, DEGs were remarkably enriched in three pathways, including transforming growth factor‐beta signaling pathway (P = 0.005252649). Further, SMC3 was detected as hot gene in PPI network, and NET (Elk3) was predicted as the significant transcription factor for this gene.

Conclusion

SMC3 may play an important role in atopic asthma development; therefore, it has the potential to be the target for the disease. Moreover, our findings provide more knowledge about the mechanism of atopic asthma and help the researchers to explore it in future.
The Ethics of Democratic Deceit
Authors: Edyvane Derek
Published: December 2014

Deception presents a distinctive ethical problem for democratic politicians. This is because there seem in certain situations to be compelling democratic reasons for politicians both to deceive and not to deceive the public. Some philosophers have sought to negotiate this tension by appeal to moral principle, but such efforts may misrepresent the felt ambivalence surrounding dilemmas of public office. A different approach appeals to the moral character of politicians, and to the variety of forms of manipulative communication at their disposal. The public is usually more indulgent of politicians who ‘spin’ the truth than of those who tell bare‐faced lies, but this could be a mistake. Spin expresses disdain for the democratic value of truthfulness, and so democratic ‘spin‐doctors’ ought to trouble us more than they typically do. The cause of confusion here may reside in the failure to appreciate the distinctiveness of public morality, and in the misguided application of private standards of behaviour to a public context in which they are out of place.