bluuebunny/crossref_metadata_2025 huggingface dataset:
The Advocacy Coalition Framework Research Program: An Overview
Authors: Cisneros Paúl
Published: September 2016

Paul Sabatier and Hank Jenkins-Smith introduced the Advocacy Coalition Framework (ACF) in the late 1980s to refine the theoretical and methodological tools available for the study of the policy process. Since the late 1990s, the use of the framework has grown in use outside the United States and it is now applied to study a broad range of policy arenas in all continents. ACF scholars have created a core community that regularly synthetizes findings from applications of the framework, giving the ACF the form of a true research program.

The ACF has three principal theoretical domains: advocacy coalitions, policy subsystems, and policy change. The ACF posits that advocacy coalitions and policy subsystems are the most efficient ways to organize actors interested in the policy process for empirical research. The policy subsystem is the main unit of analysis in the ACF, and there are four paths leading to policy change. Expectations about the interactions between and within the three theoretical domains are contained in 15 main hypotheses which have received different degrees of confirmation since the late 1980s. The aspect that has received more attention in existing applications is the effect that external events have on policy change.

The development of the ACF is supported by an active community of scholars that constantly reviews venerable as well as emerging criticisms, introducing adjustments that expand the heuristic power of the ACF in a controlled way. However, some areas in need of further refinement relate to: policy-oriented learning, interactions across subsystems, the theoretical foundations to identification of belief systems, and how the interactions between beliefs and interests affect coalition behavior.
Foreign-Imposed Regime Change
Authors: Reiter Dan
Published: September 2016

International actors sometimes force targeted states to change their governments, a process known
as Foreign-Imposed Regime Change (FIRC). This foreign policy tool serves as a surprisingly active
locus for several theoretical debates in international relations and comparative politics. On the
international relations side, evaluation of FIRC as a policy tool has implications for the following
debates: whether foreign policy decisions are affected by individual leaders or are determined by
structural conditions; whether democracies are more peaceful in their relations with other states;
how belligerents choose their war aims; what factors make for successful military occupation; what
motivates states to go on ideological crusades; whether international actors can successfully
install democracy in postconflict settings; determinants of international trade; and others. On the
comparative politics side, FIRC speaks to what may be the two most important questions in all of
comparative politics: what factors help a state maintain internal order, and what factors help a
state make the transition to democracy?

FIRC also plays an absolutely central role in foreign policy debates, especially for the United
States. FIRC is arguably responsible for both the greatest success in the history of American
foreign policy, the post-1945 pacification of Germany and Japan, and one of the greatest disasters
in U.S. foreign policy history, the 2003 invasion of Iraq and its catastrophic aftermath. Further,
FIRC has played a ubiquitous role in American foreign policy since America’s emergence as a great
power, as the United States has frequently used both overt and covert means to impose regime change
in other countries, especially in Latin America. FIRC has also been a tool used by other major
powers, especially the Soviet Union after 1945 in Eastern Europe and elsewhere. Into the second
decade of the 21st century FIRC remains a controversial foreign policy tool, as some debate the
wisdom of pursuing FIRC in Libya in 2011, and others consider the possibility of pursuing FIRC in
countries such as Syria.

FIRC can be discussed as a theoretical phenomenon and as the subject of empirical research,
focusing on its nature, causes, and effects. The article contains five sections. The first section
discusses the definition and frequency of FIRC. The second section describes the causes of FIRC, why
actors sometimes seek to impose regime change on other states. The third section covers the
international consequences of FIRC, especially whether FIRC reduces conflict between states. The
fourth section addresses the domestic consequences of FIRC, especially whether FIRC is usually
followed by stability and/or democracy. The final section concludes.
Comparative Foreign Policy Analysis
Authors: Lantis Jeffrey S. , Beasley Ryan
Published: September 2016

Comparative foreign policy analysis (CFP) is a vibrant and dynamic subfield of international relations. It examines foreign policy decision making processes related to momentous events as well as patterns in day-to-day foreign interactions of nearly 200 different states (along with thousands of international and nongovernmental organizations). Scholars explore the causes of these behaviors as well as their implications by constructing, testing, and refining theories of foreign policy decision making in comparative perspective. In turn, CFP also offers valuable lessons to government leaders.

This article surveys the evolution of CFP as a subfield over time, with special attention to its contributions to academic understanding and policymaking. It begins with a review of the characteristics and contributions of CFP, followed by acknowledgment of early works that helped establish this area of study. The next section of the article reviews major thematic focuses of CFP, including theories of international pressures and factors that may drive state foreign policy as well as strong foundations in studies of domestic politics. Key internal actors and conditions that can influence state foreign policies include individual leaders, institutions and legislatures, bureaucratic organizations and government agencies, and public opinion and nongovernmental organizations. Following this survey of actors and contemporary theories of their role in foreign policy decision-making, the article develops two illustrations of new directions in CFP studies focused on political party factions and role theory in comparative perspective.
Emotions in Foreign Policy Decision Making
Authors: McDermott Rose
Published: September 2016

There are lots of ways that emotions have been studied in psychology and various ways that their
use has been examined in the context of foreign policy. Perhaps one of the most useful ways to
examine the influence of emotion on foreign policy is through the lens of risk and threat
assessment. Some approaches to emotion tend to categorize emotions as valence-based, in terms of
broad-based positivity or negativity. Certainly, elements of this kind of approach can be useful,
particularly in terms of thinking about the ways in which political conservatives appear to have a
negativity bias. However, an investigation of discrete emotions allows a more sophisticated and
nuanced exploration of the effect of emotion on risk analysis and threat assessment, in particular
the effect of fear, anger, and disgust on decision-making under conditions of risky threat. Genetic,
as well as environmental, circumstances can influence individual variance in the experience and
expression of such emotions, and any comprehensive approach to understanding the influence of
emotion on decision-making should take all these factors into account.
Habit Formation and Behavior Change
Authors: Gardner Benjamin , Rebar Amanda L.
Published: September 2016

Within psychology, the term habit refers to a process whereby contexts prompt action automatically, through activation of mental context–action associations learned through prior performances. Habitual behavior is regulated by an impulsive process, and so can be elicited with minimal cognitive effort, awareness, control, or intention. When an initially goal-directed behavior becomes habitual, action initiation transfers from conscious motivational processes to context-cued impulse-driven mechanisms. Regulation of action becomes detached from motivational or volitional control. Upon encountering the associated context, the urge to enact the habitual behavior is spontaneously triggered and alternative behavioral responses become less cognitively accessible.

By virtue of its cue-dependent automatic nature, theory proposes that habit strength will predict the likelihood of enactment of habitual behavior, and that strong habitual tendencies will tend to dominate over motivational tendencies. Support for these effects has been found for many health-related behaviors, such as healthy eating, physical activity, and medication adherence. This has stimulated interest in habit formation as a behavior change mechanism: It has been argued that adding habit formation components into behavior change interventions should shield new behaviors against motivational lapses, making them more sustainable in the long-term. Interventions based on the habit-formation model differ from non-habit-based interventions in that they include elements that promote reliable context-dependent repetition of the target behavior, with the aim of establishing learned context–action associations that manifest in automatically cued behavioral responses. Interventions may also seek to harness these processes to displace an existing “bad” habit with a “good” habit.

Research around the application of habit formation to health behavior change interventions is reviewed, drawn from two sources: extant theory and evidence regarding how habit forms, and previous interventions that have used habit formation principles and techniques to change behavior. Behavior change techniques that may facilitate movement through discrete phases in the habit formation trajectory are highlighted, and techniques that have been used in previous interventions are explored based on a habit formation framework. Although these interventions have mostly shown promising effects on behavior, the unique impact on behavior of habit-focused components and the longevity of such effects are not yet known. As an intervention strategy, habit formation has been shown to be acceptable to intervention recipients, who report that through repetition, behaviors gradually become routinized. Whether habit formation interventions truly offer a route to long-lasting behavior change, however, remains unclear.
Bullying in Sport and Performance Psychology
Authors: Fisher Leslee A. , Dzikus Lars
Published: September 2016

Bullying is a growing problem in sport and performance settings. Bullying falls under the umbrella of “athlete maltreatment,” which includes any form of harm and all relationships where harm could occur in sport and performance. Specifically, bullying is defined as repeated hostile and deliberate behavior from one person (the perpetrator) to another (the target) with the intent to harm or threaten harm to the target; it is marked by an imbalance of power. Often, after extreme bullying, the target feels terrorized.

Athlete maltreatment in sport and performance has been categorized into one of two forms: relational maltreatment and nonrelational maltreatment. Bullying is a relational problem. In particular, sport and performance bullying can occur from coach to player, parent to player, or player to player, and often takes the form of (1) making unreasonable performance demands of the target, (2) repeated threats to restrict or remove the target’s privileges or opportunities, (3) screaming or yelling directed at the target that is unwarranted, (4) repeated and continual criticism of the target’s abilities, (5) discounting or denying the target’s accomplishments, (6) blaming the target for his or her mistakes, (7) threats of and/or actual physical violence toward the target, and (8) social media or e-mail messages with threats or insults toward the target.

Sport and performance organizations should develop and implement antibullying policies. Six potential steps toward policy development and implementation include: (1) defining bullying behaviors, (2) referring to existing “best-practice” bullying policies, (3) specifically outlining the reporting of bullying incidents, (4) outlining clearly investigation and disciplinary actions to be taken, (5) outlining specific assistance for bullying targets, and (6) including prevention and training procedures. In the meantime, coaches as well as parents and players can recognize that they are role models for everyone with whom they come into contact in sport and performance settings. Coaches, parents, and players can also accept responsibility for creating a respectful and safe sport and performance environment, have a pre-season meeting to discuss antibullying policy, foster open and honest communication, accept critical feedback, not engage or allow bullying behavior themselves, create acceptable boundaries between themselves and others, and teach players to trust their instincts when things do not feel right. More advanced bullying prevention and training procedures can then take place.
Surgical Performance From a Psychological Perspective
Authors: Moran Aidan , Sevdalis Nick , Wallace Lauren
Published: September 2016

At first glance, there are certain similarities between performance in surgery and that in competitive sports. Clearly, both require exceptional gross and fine motor ability and effective concentration skills, and both are routinely performed in dynamic environments, often under time constraints. On closer inspection, however, crucial differences emerge between these skilled domains. For example, surgery does not involve directly antagonistic opponents competing for victory. Nevertheless, analogies between surgery and sport have contributed to an upsurge of research interest in the psychological processes that underlie expertise in surgical performance. Of these processes, perhaps the most frequently investigated in recent years is that of motor imagery (MI) or the cognitive simulation skill that enables us to rehearse actions in our imagination without engaging in the physical movements involved. Research on motor imagery training (MIT; also called motor imagery practice, MIP) has important theoretical and practical implications. Specifically, at a theoretical level, hundreds of experimental studies in psychology have demonstrated the efficacy of MIT/MIP in improving skill learning and skilled performance in a variety of fields such as sport and music. The most widely accepted explanation of these effects comes from “simulation theory,” which postulates that executed and imagined actions share some common neural circuits and cognitive mechanisms. Put simply, imagining a skill activates some of the brain areas and neural circuits that are involved in its actual execution. Accordingly, systematic engagement in MI appears to “prime” the brain for optimal skilled performance. At the practical level, as surgical instruction has moved largely from an apprenticeship model (the so-called see one, do one, teach one approach) to one based on simulation technology and practice (e.g., the use of virtual reality equipment), there has been a corresponding growth of interest in the potential of cognitive training techniques (e.g., MIT/MIP) to improve and augment surgical skills and performance. Although these cognitive training techniques suffer both from certain conceptual confusion (e.g., with regard to the clarity of key terms) and inadequate empirical validation, they offer considerable promise in the quest for a cost-effective supplementary training tool in surgical education. Against this background, it is important for researchers and practitioners alike to explore the cognitive psychological factors (such as motor imagery) that underlie surgical skill learning and performance.
Gender, Justice, and Equity in Education
Authors: Öhrn Elisabet , Weiner Gaby
Published: September 2016

The field known as gender and education emerged in the 1970s, and currently addresses a range of issues of equity and justice in education with the widespread incorporation of “intersectionality” (i.e., the interlocking nature of gender and other categorizations such as social class, race, ethnicity, sexualities, disability). The topics and practices constituting the field have changed over the years, as demonstrated in a survey by the authors of Gender and Education, the main journal of choice for those working in the field. Key topics addressed by researchers include patterns of examination achievement, curriculum and school practices, and the variety of femininities and masculinities produced with/in schooling and education. Overarching themes on the conduct of the field include decreased focus on practice and action, increased emphasis on theorization, critique of the dualisms on which the field is based (girl/boy, male/female, masculinity/femininity), and Anglophone and Western bias.
Calibrating Professional Learning Approaches for Teachers in Inclusive Classrooms in the Context of Implementation Science
Authors: Arthur-Kelly Michael
Published: September 2016

In educational systems, schools, and classrooms, the interface among professional learning approaches and the translation and sustained uptake of research-led inclusive practices needs systematic and sustained attention. A range of variables exist with respect to the complexity of adopting leading, evidence-led practices in actual classroom and school settings. These may include teacher effects, diverse student needs, and limited opportunity for the meaningful analysis of relevant research to practice literature. Similarly, in the larger context of educational systems and processes of change, inhibitors and facilitators are encountered when introducing and sustaining innovative professional learning and changed practices in typical diverse schools. An aspirational model of professional learning for inclusive practices that is informed by the tenets of modern implementation science and cross-cultural perspectives will assist in defining future directions in this area from both an empirical and a heuristic perspective.
The Nixon Administration and American Foreign Relations
Authors: Nichter Luke A.
Published: September 2016

Assessments of President Richard Nixon’s foreign policy continue to evolve as scholars tap new possibilities for research. Due to the long wait before national security records are declassified by the National Archives and made available to researchers and the public, only in recent decades has the excavation of the Nixon administration’s engagement with the world started to become well documented. As more records are released by the National Archives (including potentially 700 hours of Nixon’s secret White House tapes that remain closed), scholarly understanding of the Nixon presidency is likely to continue changing. Thus far, historians have pointed to four major legacies of Nixon’s foreign policy: tendencies to use American muscle abroad on a more realistic scale, to reorient the focus of American foreign policy to the Pacific, to reduce the chance that the Cold War could turn hot, and, inadvertently, to contribute to the later rise of Ronald Reagan and the Republican right wing—many of whom had been part of Nixon’s “silent majority.” While earlier works focused primarily on subjects like Vietnam, China, and the Soviet Union, the historiography today is much more diverse – now there is at least one work covering most major aspects of Nixon’s foreign policy.
New Women in Early 20th-Century America
Authors: Rabinovitch-Fox Einav
Published: September 2016

In late 19th- and early 20th-century America, a new image of womanhood emerged that began to shape public views and understandings of women’s role in society.

Identified by contemporaries as a Gibson Girl, a suffragist, a Progressive reformer, a bohemian feminist, a college girl, a bicyclist, a flapper, a working-class militant, or a Hollywood vamp, all of these images came to epitomize the New Woman, an umbrella term for modern understandings of femininity. Referring both to real, flesh-and-blood women, and also to an abstract idea or a visual archetype, the New Woman represented a generation of women who came of age between 1890 and 1920 and challenged gender norms and structures by asserting a new public presence through work, education, entertainment, and politics, while also denoting a distinctly modern appearance that contrasted with Victorian ideals. The New Woman became associated with the rise of feminism and the campaign for women’s suffrage, as well as with the rise of consumerism, mass culture, and freer expressions of sexuality that defined the first decades of the 20th century. Emphasizing youth, mobility, freedom, and modernity, the image of the New Woman varied by age, class, race, ethnicity, and geographical region, offering a spectrum of behaviors and appearances with which different women could identify. At times controversial, the New Woman image provided women with opportunities to negotiate new social roles and to promote ideas of equality and freedom that would later become mainstream.
Integrated Pest Management
Authors: Eiben Jesse
Published: September 2016

This is an advance summary of a forthcoming article in the Oxford Research Encyclopedia of Environmental Science. Please check back later for the full article.

Integrated Pest Management (IPM) is an ecosystem management operational framework to make ecologically and economically sound environmental management decisions in ways that are selective for the pest encountered while minimizing effects not related to the problem at hand. The strength of IPM research and use is to constantly adapt methods and applications of the science behind adaptive decision making to ensure that the most modern and comprehensive problem-solving skills and techniques will be used to manage pest issues. Pests are ubiquitous in every human-managed ecosystem, most commonly encountered in production agriculture and forestry. Pests are also encountered by homeowners and in other environmental management regimes related to ecological restoration, just to name a few IPM use situations. IPM has been practiced by humans throughout the development of human agricultural practices, for major stable food and fiber crops since the advent of agriculture. However, the specific scientific discipline of truly integrating multiple management techniques, from pesticide application, to fertilizer regimes, to resistant plant variety selection, to ecological and cultural management, and finally to cost-benefit analyses to ensure the techniques used are comprehensive for the pest and the rest of the agricultural production system is a relatively new science, first rigorously tested and reviewed in the 1940s. The greatest strengths of the discipline are also its weakness; by being pest-taxon, crop specific, and flexible for a given environmental or management situation, there is a constant need for refinement of IPM decision making processes in very specific situations to be the most efficient and useful in a given pest situation. Given the number of sub-discipline inputs into the robust decision-making framework, many specialists need to be invested in the specific IPM program, or a highly trained and dedicated group must be accountable for wrangling diverse disciplines into a cohesive management regime. Finally, given the vast number of pests and pathogens that affect a production system, it is nearly impossible to have an IPM program for every crop, for every pest, in every system; yet this is what is called upon from the farmers or land managers in nearly every situation. Given the modern push to have answers ready at the push of a button, the discipline of IPM will continue to be refined to remain relevant and at the forefront of safe, efficient, environmentally accountable, and ultimately sustainable sciences in modern ever-changing agricultural production systems.
Agricultural Dispersals in Mediterranean and Temperate Europe
Authors: Salavert Aurélie
Published: September 2016

Along with ceramics production, sedentism, and herding, agriculture is a major component of the Neolithic as it is defined in Europe. Therefore, the agricultural system of the first Neolithic societies and the dispersal of exogenous cultivated plants to Europe are the subject of many scientific studies. To work on these issues, archaeobotanists rely on residual plant remains—crop seeds, weeds, and wild plants—from archaeological structures like detritic pits, and, less often, storage contexts. To date, no plant with an economic value has been identified as domesticated in Western Europe except possibly opium poppy. The earliest seeds identified at archaeological sites dated to about 5500–5200 bc in the Mediterranean and Temperate Europe. The cultivated plants identified were cereals (wheat and barley), oleaginous plant (flax), and pulses (peas, lentils, and chickpeas). This crop package originated in the Fertile Crescent, where it was clearly established around 7500 bc (final Pre-Pottery Neolithic B), after a long, polycentric domestication process. From the middle of the 7th millennium bc, via the Balkan Peninsula, the pioneer Neolithic populations, with their specific economies, rapidly dispersed from east to west, following two main pathways. One was the maritime route over the northwestern basin of the Mediterranean (6200–5300 bc), and the other was the terrestrial and fluvial route in central and northwestern continental Europe (5500–4900 bc). On their trajectory, the agropastoral societies adapted the Neolithic founder crops from the Middle East to new environmental conditions encountered in Western Europe.

The Neolithic pioneers settled in an area that had experienced a long tradition of hunting and gathering. The Neolithization of Europe followed a colonization model. The Mesolithic groups, although exploiting plant resources such as hazelnut more or less intensively, did not significantly change the landscape. The impact of their settlements and their activities are hardly noticeable through palynology, for example. The control of the mode of reproduction of plants has certainly increased the prevalence of Homo sapiens, involving, among others, a demographic increase and the ability to settle down in areas that were not well adapted to year-round occupation up to that point. The characterization of past agricultural systems, such as crop plants, technical processes, and the impact of anthropogenic activities on the landscape, is essential for understanding the interrelation of human societies and the plant environment. This interrelation has undoubtedly changed deeply with the Neolithic Revolution.
Detailed H i kinematics of Tully–Fisher calibrator galaxies
Authors: Ponomareva Anastasia A. , Verheijen Marc A. W. , Bosma Albert
Published: September 2016

We present spatially resolved H i kinematics of 32 spiral galaxies which have Cepheid or/and tip of the red giant branch distances, and define a calibrator sample for the Tully–Fisher relation. The interferometric H i data for this sample were collected from available archives and supplemented with new Giant Metrewave Radio Telescope observations. This paper describes a uniform analysis of the H i kinematics of this inhomogeneous data set. Our main result is an atlas for our calibrator sample that presents global H i profiles, integrated H i column-density maps, H i surface-density profiles and, most importantly, detailed kinematic information in the form of high-quality rotation curves derived from highly resolved, two-dimensional velocity fields and position–velocity diagrams.
Chemo-hydrodynamic patterns in porous media
Authors: De Wit A.
Published: September 2016

Chemical reactions can interplay with hydrodynamic flows to generate chemo-hydrodynamic instabilities affecting the spatio-temporal evolution of the concentration of the chemicals. We review here such instabilities for porous media flows. We describe the influence of chemical reactions on viscous fingering, buoyancy-driven fingering in miscible systems, convective dissolution as well as precipitation patterns. Implications for environmental systems are discussed.

This article is part of the themed issue ‘Energy and the subsurface’.
Elastic and inelastic deformation of fluid-saturated rock
Authors: Makhnenko Roman Y. , Labuz Joseph F.
Published: September 2016

In siturock is often saturated with fluid, the presence of which affects both elastic parameters and inelastic deformation processes. Techniques were developed for testing fluid-saturated porous rock under the limiting conditions of drained (long-term), undrained (short-term) and unjacketed (solid matrix) response in hydrostatic, axisymmetric and plane-strain compression. Drained and undrained poroelastic parameters, including bulk modulus, Biot and Skempton coefficients, of Berea sandstone were found to be stress dependent up to 35 MPa mean stress, and approximately constant at higher levels of loading. The unjacketed bulk modulus was measured to be constant for pressure up to 60 MPa, and it appears to be larger than the unjacketed pore bulk modulus. An elasto-plastic constitutive model calibrated with parameters from drained tests provided a first-order approximation of undrained inelastic deformation: dilatant hardening was observed due to pore pressure decrease during inelastic deformation of rock specimens with constant fluid content.

This article is part of the themed issue ‘Energy and the subsurface’.
A similarity solution for reaction front propagation in a fracture–matrix system
Authors: Rajaram Harihar , Arshadi Masoud
Published: September 2016

We propose a new composite similarity variable, based on which a similarity solution is derived for reaction front propagation in fracture–matrix systems. The similarity solution neglects diffusion/dispersion within the fracture and assumes the existence of a sharp reaction front in the rock matrix. The reaction front location in the rock matrix is shown to follow a linear decrease with distance along the fracture. The reaction front propagation along the fracture is shown to scale like diffusion (i.e. as the square root of time). The similarity solution using the composite similarity variable appears to be applicable to a broad class of reactive transport problems involving mineral reactions in fracture–matrix systems. It also reproduces the solutions for non-reactive solute and heat transport when diffusion/dispersion/conduction are neglected in the fracture. We compared our similarity solution against numerical simulations for nonlinear reactive transport of an aqueous species with a mineral in the rock matrix. The similarity solutions agree very well with the numerical solutions, especially at later times when diffusion limitations are more pronounced.

This article is part of the themed issue ‘Energy and the subsurface’.
Differential Expression Analysis for RNAseq using Poisson Mixed Models
Authors: Sun Shiquan , Hood Michelle , Scott Laura , Peng Qinke , Mukherjee Sayan , Tung Jenny , Zhou Xiang
Published: September 2016

Identifying differentially expressed (DE) genes from RNA sequencing (RNAseq) studies is among the most common analyses in genomics. However, RNAseq DE analysis presents several statistical and computational challenges, including over-dispersed read counts and, in some settings, sample non-independence. Previous count-based methods rely on simple hierarchical Poisson models (e.g., negative binomial) to model independent over-dispersion, but do not account for sample non-independence due to relatedness, population structure and/or hidden confounders. Here, we present a Poisson mixed model with two random effects terms that account for both independent over-dispersion and sample non-independence. We also develop a scalable sampling-based inference algorithm using a latent variable representation of the Poisson distribution. With simulations, we show that our method properly controls for type I error and is generally more powerful than other widely used approaches, except in small samples (n<15) with other unfavorable properties (e.g., small effect sizes). We also apply our method to three real data sets that contain related individuals, population stratification, or hidden confounders. Our results show that our method increases power in all three data compared to other approaches, though the power gain is smallest in the smallest sample (n=6). Our method is implemented in MACAU, freely available atwww.xzlab.org/software.html.
Comparative genomics and metagenomics analyses of endangered Père David’s deer (Elaphurus davidianus) provide insights into population recovery
Authors: Zhang Xuejing , Deng Cao , Ding Jingjing , Ren Yi , Zhao Xiang , Qin Shishang , Zhu Shilin , Wang Zhiwen , Chai Xiaoqiang , Huang Huasheng , Ding Yuhua , Lu Guoqing , Zhu Lifeng
Published: September 2016

The milu (Père David’s deer,Elaphurus davidianus) has become a classic example of how highly endangered animal species can be rescued. However, the mechanisms that underpinned this population recovery remain largely unknown. As part of this study, we sequenced and analyzed whole genomes from multiple captive individuals. Following this analysis, we observed that the milu experienced a prolonged population decline over the last 200,000 years, which led to an elongated history of inbreeding. This protracted inbreeding history facilitated the purging of deleterious recessive alleles, thereby ameliorating associated threats to population viability. Because of this phenomenon, milu are now believed to be less susceptible to future inbreeding depression occurrences. SNP distribution patterns confirmed inbreeding history and also indicated sign of increased and increasing diversity in the recovered milu population. A selective sweep analysis identified two outlier genes (CTSR2andGSG1) that were related to male fertility. Furthermore, we observed strong signatures of selection pertaining to the host immune system, including six genes (SERPINE1, PDIA3, CD302, IGLL1, VPREB3, andCD53 antigen), which are likely to strengthen resistance to pathogens. We also identified several adaptive features including the over-representation of gene families encoding for olfactory receptor activity, a high selection pressure pertaining to DNA repair and host immunity, and tolerance to high-salt swamp diets. Moreover, glycan biosynthesis, lipid metabolism, and cofactor and vitamin metabolism were all significantly enriched in the gut microbiomes of milu. We speculate that these characteristics play an important role in milu energy metabolism, immunity, development, and health. In conclusion, our findings provide a unique insight into animal population recovery strategies.
LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences
Authors: Disdero Eric , Filée Jonathan
Published: September 2016

Motivation

Population genomic analysis of transposable elements has greatly benefited from recent advances of sequencing technologies. However, the propensity of transposable elements to nest in highly repeated regions of genomes limits the efficiency of bioinformatic tools when short read sequences technology is used.

Results

LoRTE is the first tool able to use PacBio long read sequences to identify transposon deletions and insertions between a reference genome and genomes of different strains or populations. Tested against Drosophila melanogaster PacBio datasets, LoRTE appears to be a reliable and broadly applicable tools to study the dynamic and evolutionary impact of transposable elements using low coverage, long read sequences.

Availability and Implementation

LoRTE is available athttp://www.egce.cnrs-gif.fr/?p=6422. It is written in Python 2.7 and only requires the NCBI BLAST + package. LoRTE can be used on standard computer with limited RAM resources and reasonable running time even with large datasets.

Contact

jonathan.filee@ecge.cnrs-gif.fr
Measuring MEG closer to the brain: Performance of on-scalp sensor arrays
Authors: Iivanainen Joonas , Stenroos Matti , Parkkonen Lauri
Published: September 2016

Optically-pumped magnetometers (OPMs) have recently reached sensitivity levels required for magnetoencephalogra-phy (MEG). OPMs do not need cryogenics and can thus be placed within millimetres from the scalp into an array that adapts to the invidual head size and shape, thereby reducing the distance from cortical sources to the sensors. Here, we quantified the improvement in recording MEG with hypothetical on-scalp OPM arrays compared to a 306-channel state-of-the-art SQUID array (102 magnetometers and 204 planar gradiometers).

We simulated OPM arrays that measured either normal (nOPM; 102 sensors), tangential (tOPM; 204 sensors), or all components (aOPM; 306 sensors) of the magnetic field. We built forward models based on magnetic resonance images of 10 adult heads; we employed a three-compartment boundary element model and distributed current dipoles evenly across the cortical mantle.

Compared to the SQUID magnetometers, nOPM and tOPM yielded 7.5 and 5.3 times higher signal power, while the correlations between the field patterns of source dipoles were reduced by factors of 2.8 and 3.6, respectively. Values of the field-pattern correlations were similar across nOPM, tOPM and SQUID gradiometers. Volume currents reduced the signals of primary currents on average by 10%, 72% and 15% in nOPM, tOPM and SQUID magnetometers, respectively. The information capacities of the OPM arrays were clearly higher than that of the SQUID array. The dipole-localization accuracies of the arrays were similar while the minimum-norm-based point-spread functions were on average 2.4 and 2.5 times more spread for the SQUID array compared to nOPM and tOPM arrays, respectively.
LSD1—a pivotal epigenetic regulator of brown and beige fat differentiation and homeostasis
Authors: Lin Jean Z. , Farmer Stephen R.
Published: September 2016

In this issue of Genes & Development, Zeng and colleagues (pp. 1822–1836) identify lysine-specific demethylase 1 (LSD1) as a pivotal regulator of whole-body energy expenditure by controlling the oxidative and thermogenic activity of brown adipose tissue (BAT). They show that LSD1 interacts with PRDM16 to repress select white adipose tissue (WAT) genes but also represses hydroxysteroid 11-β-dehydrogenase 1 (HSD11B1) independently of PRDM16 to prevent production of glucocorticoids that impair BAT functions. Their study provides important insight into epigenetic mechanisms regulating the function of BAT.
Crystal structure of an aryl cyclohexyl nonanoid, an antiproliferative molecule isolated from the spice Myristica malabarica
Authors: Bauri Ajoy Kumar , Foro Sabine , Do Nhu Quynh Nguyen
Published: September 2016

The title compound, C21H26O5, an aryl cyclohexyl nonanoid {systematic name: 3,5-dihydroxy-2-[9-(4-hydroxyphenyl)nonanoyl]cyclohexa-2,4-dien-1-one}, extracted from the spice plant Myristica malabarica comprises two ring components, a 4-hydroxyphenyl moiety and a 3,5-dihydroxycyclohexa-2,4-dienone moiety linked by a nonanoyl chain. The molecule has an extended essentially planar conformation stabilized by an intramolecular hydroxy O—H...Ocarbonyl hydrogen bond, giving a dihedral angle between the two ring systems of 6.37 (15)°. The C, O and H atoms associated with one of the hydroxy groups of the cyclohexadienone component are disordered over two sets of sites with site occupancies of 0.6972 and 0.3028. In the crystal, hydroxy O—H...O hydrogen bonds to carbonyl O-atom acceptors form large centrosymmetric R
2
2(36) cyclic dimers, which are further extended into supramolecular one-dimensional ribbon structures along [1-11].
Job characteristics, work involvement, and job performance of public servants
Authors: Johari Johanim , Yahya Khulida Kirana
Published: September 2016

Purpose

The primary purpose of this study is to assess the predicting role of job characteristics on job performance. Dimensions in the job characteristics construct are skill variety, task identity, task significance, autonomy and feedback. Further, work involvement is tested as a mediator in the hypothesized link.

Design/methodology/approach

A total of 256 public servants reported on their job characteristics and work involvement while supervisory ratings were used to assess their level of job performance. SPSS version 14 and AMOS 16 were used for statistical analyses of the data. A hypothesized structural equation model was tested to examine both direct and indirect influence of job characteristics on job performance.

Findings

The findings revealed that task significance and feedback significantly influence job performance and the relationships are mediated by work involvement. Skill variety, however, has a significant and direct influence on public servants’ job performance.

Research limitations/implications

The research results have provided support for the key theoretical propositions. Specifically, this study has managed to substantiate some empirical evidences in partial support of the job characteristics theory.

Practical implications

As for practical implication, the significant and positive impact of skill variety, task significance and feedback on job performance suggests the importance of these job characteristics dimensions in promoting high level of job performance among public servants.

Originality/value

This study aims to provide additional empirical evidence in support of the job characteristics theory. The theoretical framework of this study managed to substantiate empirical evidence in partial support of the job characteristics theory.
Promoting self-directed learning in a learning organization: tools and practices
Authors: Rana Sowath , Ardichvili Alexandre , Polesello Daiane
Published: September 2016

Purpose

The purpose of this paper is to examine a set of practices that can help promote self-directed learning (SDL) in congruence with the goals of developing and maintaining a learning organization.

Design/methodology/approach

Findings from this study were derived from an extensive review of the SDL and the learning organization literature, as well as the body of research that examines the connections between the two constructs.

Findings

This paper identifies the following set of practices as integral to promoting SDL in a learning organization: building and communicating a shared vision to employees at all levels; fostering collaboration, interaction and teamwork; empowering employees through participatory work practices; encouraging and providing opportunities for continuous learning; and using relevant technologies in the workplace.

Originality/value

This paper addresses the paucity of research that investigates the connections between SDL and the learning organization and that specifically examines important practicesvis-à-visthe two concepts.
Bare ownership of residential properties: insights on two segments of the Italian market
Authors: Morano Pierluigi , Tajani Francesco
Published: September 2016

Purpose

This paper aims to deal with the sale of the bare ownership subject to the lifetime usufruct to the seller as an alternative channel for housing investments in Italian cities. The first aim of the study is to understand in greater detail the bare ownership market while also stimulating the interest of researchers in this segment of the housing market that up until now has been marginally analyzed so far. The second aim is to make the estimation of the bare ownership easier and more reliable for market investors and institutions. The third aim is to quantify on the markets investigated in this paper, the “actual” appraisal coefficients for the usufructuary presence, as well as compare these coefficients with the ones set for tax purposes to highlight either the concordance or discordance.

Design/methodology/approach

A hedonic price model is developed, with which it is possible to evaluate the market price of the bare ownership as a function of the determinants of value in the market segments in question, in particular the life expectancy of the usufructuary.

Findings

Through the hedonic models defined in this work, it is possible to appraise the market value of the bare ownership of residential flats in a building located in the same districts overcoming the limitations of the procedures currently used. Comparing the appraisal coefficients for the usufructuary presence estimated through the hedonic models defined in this work, with the legally defined coefficients applied countrywide for tax purpose, it is possible to conclude that the latter markedly underestimate the market value of bare ownership, thereby leading to fiscal iniquities and substantial social costs.

Research limitations/implications

It has not been possible to know the gender of the usufructuary. Rather limited size of the apartment sales samples.

Practical implications

The bare ownership market is currently an important sector that deserves greater attention from the institutions, market investors and real estate research. The model developed allows to estimate the “actual” coefficients for the determination of the market value of the bare ownership of residential units.

Originality/value

There are currently no studies nor descriptive investigations relating to either the bare ownership market segments or recent cases of estimates. The present study is the first in current literature that both systematically deals with the quantification of the “actual” appraisal coefficients for the usufructuary presence, as well as compares these coefficients with the ones set for tax purposes.
A psychological perspective on immigration: the reasons and hardships of migrating to Brazil’s capital, Brasília
Authors: Carvalho Alberto Rodrigues , Martins Francisco Catunda
Published: September 2016

Purpose

The purpose of this paper is to seek the inner motivations present in immigrants moving from different regions of Brazil to its capital, Brasília. The goal is to find out the individuals’ stories, not only the macroeconomic aspects usually studied in migration movements. Also, the authors intend to understand how impacting the process of leaving one’s homeland and loved ones behind can be.

Design/methodology/approach

In this study, ten recent immigrants were interviewed about their inner motivations to migrate to Brasília and the difficulties faced. Their answers were categorized and distributed into charts showing the most relevant parts for the study.

Findings

Two main topics stood out: work and love. The search for a meaningful and rewarding job is a strong enough reason to migrate. Love presents itself as a different reason to migrate, especially when economic and political reasons are the most common motivators. Love has to do with wanting to be with a partner or family. Migration is a time for crisis, mourning can be present and the strangeness of the new place may affect some more than others. All interviewees mentioned the hardships of adapting, be it emotionally or psychologically.

Originality/value

It is a response to the lack of clinical psychology studies about migration in Brazil. The importance of having studies carried out with a more qualitative perspective in the field of migration, in which the focus are the inner motivations of the migrants and what their experiences are.