bluuebunny/crossref_metadata_2025 huggingface dataset:
Transitions between Major Classes: Vertebrates
Authors: Sumida Stuart S , Devlin Kathleen R
Published: September 2013

The advent of cladistic analyses of relationships between organisms has provided more rigorous means of defining lineages, although fossil records suggest that boundaries between vertebrate clades are not always distinct. At the beginning of the transition from water to land, the earliest tetrapods retain many fish‐like features, and at the end of this continuum numerous terrestrial adaptations may be seen in groups not traditionally classified as amniotes. Characters of the jaw and middle ear, classically associated with Mammalia, differentiated as a functional complex that developed across the therapsid–mammal transition. Feathers and features associated with lightening the skeleton are also found in terrestrial dromaeosaurid dinosaurs, and are not exclusive to birds. That each of these transitions took place through a series of graded steps suggests that they should be considered more as a process than as a point in time or geologic history.

Key Concepts:

The transitions between what are considered major taxonomic groups of vertebrates are not distinct, but rather are ‘blurry’ as they reflect processes and the gradual accumulation of suites functional anatomical and physiological complexes.

The water‐to‐land transition is not a single event. It is a continuum ranging across nearly 50 My from the first tetrapods to the first amniotes.

With new information including the details of transitional forms such as
Tiktaalik
and
Ventastega
, understanding of the changes in the limb skeleton from sarcopterygian fishes to the earliest tetrapods has been refined significantly.

The Late Carboniferous to Early Permian Diadectomorpha have emerged as the closest relatives of crown‐group amniotes, sharing numerous anatomical features with them.

Dromaeosaurid dinosaurs demonstrate a variety of experiments in feather distribution and potential flight adaptations as the group from which Aves evolved.

The lineage leading to extant mammals began the process of transformation of the feeding apparatus, associated modifications of the middle ear and (probable) soft tissue associations in groups generally considered to be closely related but outside of traditionally defined mammals.
Cornales (Dogwood)
Authors: Xiang Qiu‐Yun (Jenny)
Published: September 2013

Cornales, a relatively small, but morphologically diverse, order of flowering plants, consist of trees, shrubs, lianas, rhizomatous herbs and rarely aquatic herbs. The order represents an early divergent lineage in the Asterid clade and has a cosmopolitan distribution, occurring from cold temperate regions to the tropics, rarely in subarctic zones. Four to ten families, depending on how Cornaceae are circumscribed, comprise the order. Recent molecular phylogenetic studies supported a classification of 10 families that diverged during the late Cretaceous and early Tertiary. Many of the 10 families are small and with restricted, modern distributions, but have fossils occurring in areas outside their present distribution. Common representatives include the dogwoods (e.g.,

Cornus florida

(flowering dogwood),

Cornus kousa

(kousa dogwood),

Cornus canadensis

(bunchberry),

Cornus mas

(European cornelian cherry),

Cornus sericea

(red‐osier dogwood),

Nyssa sylvatica

(black gum),

Davidia involucrata

(dove tree),

Hydrangea macrophylla

(Hydrangea),
Deutzia
spp. (deutzias) and
Philadelphus
spp. (mock oranges)), which are widely cultivated as ornamentals. Several species are medicinally important, including

Cornus officinalis

(cornelian cherry),

Camptotheca acuminata

(Happy tree),

Curtisia dentata

(assegai tree) and

Alangium salvifolium

(sage‐leaved alangium).

Key Concepts:

Phylogenetic studies are essential to understanding and conserving biodiversity.

Phylogeny depicts evolutionary relationships of species and speciation events, providing the basis for classification and understanding macro‐ and microevolution.

Including more species and molecular data in phylogenetic studies can help to clarify relationships that were obscured by morphology and difficult to resolve due to rapid radiation.

The age of a lineage on a phylogeny can be estimated using molecular data with a relaxed molecular clock calibrated from fossils (referred to as divergence time estimation).

Time estimation for a given lineage is substantially affected by molecular data, taxon sampling and the phylogenetic nodes calibrated by the fossils.

Dated phylogeny provides the temporal framework to understand diversification patterns and speciation events in absolute historical time that can be linked to specific events in the Earth's history.

Fossils are important records of past distributions of a lineage, providing data on extinction, speciation, and morphological evolution through time.
Parsimony Methods
Authors: Ramírez Martín J
Published: September 2013

Parsimony methods of phylogenetic reconstruction use an explicit criterion of optimality, the minimisation of evolutionary transformations. By doing so, parsimony also minimises instances of homoplasy (convergence or parallelisms) and maximises similarity due to a common descent (homology). Tree evaluation is done by an optimisation algorithm that calculates the length of each character over the tree; the global tree length is the sum of the individual character lengths. The Sankoff generalised algorithm allows for the optimisation of characters with any cost matrices; there are faster algorithms specific for unordered and additive characters. A problem with tree searches is the vast number of possible trees. There are exact solutions only for small datasets, but most real datasets require heuristic strategies. Measures of group support show the degree on which the data hold the conclusions, and sensitivity analyses help express the robustness of phylogenetic inferences on changes in parameters and conditions of analysis.

Key Concepts:

Phylogeny is the theoretical background for the classification of living organisms.

Parsimony methods for phylogenetic reconstruction use the minimisation of evolutionary transformations as the optimality criterion.

The parsimony criterion minimises instances of homoplasy (convergence or parallelisms) and maximises similarity due to common descent.

The optimisation of a character on a tree results in states assigned to hypothetical ancestors, implying the minimum number of transformations.

Tree searching is a complex problem, for which exact solutions are limited to the smaller datasets; most real datasets require heuristic solutions.

Differential transformation costs and character weights can be implemented in parsimony methods.

Measures of support and sensitivity can be used to express the robustness of phylogenetic inferences.
Genetic Counselling Communication: A Discourse‐Analytical Approach
Authors: Sarangi Srikant
Published: September 2013

For a long time, the genetic counselling process had remained a blackbox, especially from a discourse‐analytical perspective. Over the last two decades, the rich and complex communication process that constitutes the ‘hybrid’ activity of genetic counselling has been a focus of study using discourse analysis methodology. Thematically, genetic counselling encompasses topics as diverse as the natural history of a genetic disorder, aspects of (non)diagnosis and prognosis, (non)treatability, lay genetic awareness, future risks for a client and other family members, reproduction choices, psychosocial aspects of coping, the ethical and legal consequences of decisions and privacy issues concerning the disclosure/circulation of genetic information. This range of topics does not follow neat and parallel interactional trajectories; instead the topics become interweaved in an overlapping manner and are managed interactionally under given conditions, including the multiparty nature of participation in the counselling encounter. A discourse‐analytical approach is an attempt to uncover the structural, interactional and thematic organisation of genetic counselling as a situated activity.

Key Concepts:

Genetic counselling as a communicative activity is complex and hybrid, which does not follow a simple ritual interactional routine.

The notion of ‘activity type’ (forms of setting) to characterise communicative events with component ‘discourse types’ (forms of talk) is a useful way to capture the dynamic and variable nature of genetic counselling across modes (face‐to‐face versus telephone‐mediated), disease conditions as well as sociocultural settings.

The activity of genetic counselling can be mapped structurally, interactionally and thematically to illustrate the unique nature of the counselling process.

Concepts such as directiveness and nondirectiveness are part of a continuum and are manifest differently at the interactional level.

At a thematic level, risk and uncertainty are two sides of the same coin and the language of probability assumes significance in terms of risk explanation and risk perception.

The concept of risk is far more complex in genetic counselling than in other disease settings as it includes the associated ‘risk of knowing’ and the ‘risk of (non)disclosure’.

Negotiation of what is normal and what is abnormal can be mapped on to risk/uncertainty trajectories in genetic counselling.

The management of ethical and moral issues in genetic counselling requires an interaction‐based situated approach in preference to the principle‐based guidelines.

In discourse analytic terms, it is possible to distinguish between psychological and sociomoral dimensions of genetic counselling, which underpin clients' decision‐making.

The self‐other orientations (e.g. self versus other; self and other and self‐as‐other) are a key feature of genetic counselling.
Genetic Control of Leaf Shape
Authors: Martinez Ciera C , Sinha Neelima R
Published: September 2013

The variability in leaf morphology is vast; therefore, an understanding of how leaves achieve this diversity has captured the attention of many developmental biologists. Genetic mechanisms that regulate leaf shape are repeated throughout both development and between species. Leaves initiate off the shoot apical meristem and development proceeds from cell division to cell elongation. Leaf initiation and the establishment of the three main axes of a leaf are largely directed by the plant hormone auxin. Work across species reveals that adjustments to the repeated interaction of auxin, gene expression changes and small
ribonucleic acid (RNA)
regulation allowed species‐specific leaf shape differences to emerge. Further, genetic interactions leading to patterning in simple leaf development are reiterated during establishment of leaf complexity. To understand leaf development in an evolutionary context, future research must take advantage of the ever‐expanding genomic tools in nonmodel organisms that exhibit leaf shape diversity.

Key Concepts:

Leaves originate from clusters of stem cells called meristems.

The development of leaves occurs along three main axes: (1) adaxial/abaxial, (2) proximal/distal and (3) medial/lateral.

The development of both meristems and leaves involve morphogenetic activity in zones which are defined by distinct gene expression and cell division/elongation patterns.

The transport and concentration of the hormone auxin largely directs many aspects of leaf morphogenesis.

Leaf and leaflet initiation first begin with the formation of auxin maxima.

Recycling of genetic mechanisms is a theme that occurs throughout leaf development.
Evolution of MicrosatelliteDNA
Authors: Jentzsch Iris M Vargas , Bagshaw Andrew TM , Buschiazzo Emmanuel , Merkel Angelika , Gemmell Neil J
Published: September 2013

Microsatellites are highly mutable nucleotide arrays composed of short motifs repeated in tandem. They are ubiquitously distributed in bacterial and eukaryotic genomes and their abundance and mutability has made them a widely used genetic marker for a variety of applications. One aim of the study of microsatellite evolution is to predict their mutational patterns in order to make them more accurate markers of genetic distance between species or individuals. Applications that use microsatellites as markers work under the basic assumption that microsatellite mutations are simple and random. However, this assumption contrasts with the observed variability of mutation rates across microsatellite loci. Several factors such as array size and sequence motif have been shown to influence microsatellite mutation rates, but research into their evolution is also complicated by the fact that some microsatellites function to regulate gene expression and possibly other genomic functions, and may therefore be subject to selective pressure.

Key Concepts:

Microsatellites are arrays of tandemly repeated 1–6 bp sequence motifs. They are highly abundant in all organisms studied, and they are also highly polymorphic as a result of frequent change of length mutations.

The traditional view of microsatellites as neutrally evolving junk DNA is overly simplistic, which sometimes affects the accuracy of studies that use them as genetic markers.

Many complex processes interact to govern the frequency with which microsatellites mutate, including array length, sequence motif and flanking sequence.

Increasing evidence indicates that a subset of microsatellites function to regulate gene expression, and perhaps also interchromosomal recombination, and the evolution of these microsatellites is therefore influenced by selection.

The mutability of microsatellites, the fact that their mutations are easily reversible, and their abundance and conservation in regulatory regions suggest that they may make a significant contribution to the diversity and adaptation of species, but much work remains to establish the extent of their functional importance.
Structural Basis of Disulfide Bond Formation in the Bacterial Periplasm and Mammalian
ER
Authors: Kojima Rieko , Okumura Masaki , Inaba Kenji
Published: September 2013

Cellular quality control systems rely on the maintenance of protein and redox homoeostasis, in which the formation, reduction and isomerisation of protein disulfide bonds play important roles. The biological kingdoms have evolved catalytic systems that greatly promote oxidative protein folding. Remarkable progress in structural biology in this field has provided molecular views on how protein disulfide bonds are generated
de novo
and transferred to downstream folding substrates. Very recently, a novel concept has emerged, proposing that multiple oxidative pathways work redundantly, distinctly and in a complementary manner in the endoplasmic reticulum of mammalian cells to efficiently produce large quantities, and a wide variety, of secretory proteins. Thus, the oxidative protein folding network is even more complicated in higher eukaryotes than previously thought.

Key Concepts:

Almost all organisms, from bacteria to humans, possess catalytic systems that promote protein‐disulfide bond formation.

Disulfide bond formation networks have diversified dramatically, as evidenced by the appearance of a large number of disulfide oxidoreductases in higher eukaryotes.

High‐resolution structures have been solved for an increasing number of disulfide oxidoreductases, thereby revealing the structural and mechanistic basis of cellular disulfide bond formation systems.

Disulfide bonds play an important role in folding, assembly and stabilisation of various proteins.

Disulfide bond formation networks are closely related to the protein and redox homeostasis in the cell.
A‐to‐I
RNA
Editing and Human Genetic Disease
Authors: Maas Stefan
Published: September 2013

The regulation of when, where and how genomic information is utilised in cells and organisms is just as important for normal physiology as the
deoxyribonucleic acid
sequence itself. One important molecular tool at the disposal of eukaryotic cells is the process of
ribonucleic acid (RNA)
editing, which involves the recoding of genomically specified sequences within primary RNA transcripts. One kind of RNA editing, A‐to‐I modification, turns out to regulate the expression and function of various genes as well as enhance the functional and phenotypic diversity within the transcriptome and proteome. Recent insights on the A‐to‐I RNA‐editing machinery and the discovery of many additional editing targets, especially within mammalian species, underscore the importance of editing for normal physiology and also uncover strong links to human genetic diseases. Harnessing that knowledge could lead to approaches for treating RNA editing‐related disorders or even to the development of RNA‐directed gene therapy technologies.

Key Concepts:

RNA editing regulates protein function.

RNA editing diversifies the transcriptome and proteome.

ADARs mediate A‐to‐I RNA editing.

Important editing sites include many noncoding RNAs.

Some editing events are essential for survival.

Many editing sites await functional characterisation.

Deregulation of RNA editing can lead to disease.
Gene Therapy for Amyotrophic Lateral Sclerosis
Authors: McEachin Zachary , O'Connor Deirdre , Boulis Nicholas
Published: September 2013

Amyotrophic lateral sclerosis (ALS), commonly referred to as Lou Gehrig's disease, is a chronic, neurodegenerative disease with no known cure. ALS is characterised by the loss of both upper and lower motor neurons. On becoming symptomatic, patients with ALS survive between 1–5 years. The aetiology and pathogenesis of ALS is complex and can vary among cases; however, some forms of ALS have been identified to be genetic in origin. In particular, 20% of familial ALS cases have been attributed to a gain‐of‐function mutation in the SOD1 gene. Thus, gene therapy has been an attractive method to potentially treat ALS. The intention of this article is to provide the reader a summary of common gene therapy strategies for ALS.

Key Concepts:

Amyotrophic lateral sclerosis is a progressive neurodegenerative disease with no known cure.

ALS exists in two forms: familial ALS and sporadic ALS.

Twenty per cent of fALS cases are due to a mutation in the SOD1 gene.

SOD1 murine models have been valuable in the advancement of gene therapy for ALS.

Gene therapy is a promising therapeutic option for ALS.
Gene Therapy for Duchenne Muscular Dystrophy
Authors: van Putten Maaike , Aartsma‐Rus Annemieke
Published: September 2013

Duchenne muscular dystrophy is a severe muscle wasting disorder caused by lack of functional dystrophin, due to reading‐frame disrupting mutations in the
DMD
gene. There is no cure, but several genetic therapeutic approaches aiming to delay disease progression by restoring, manipulating or replacing the
DMD
gene are under investigation in (pre)clinical settings. The antisense‐mediated exon skipping approach, which restores the disrupted reading frame allowing synthesis of partly functional dystrophin proteins is closest to clinical application. The first trials with viral vectors to deliver minidystrophin genes and compounds to force readthrough of premature stop codons by the translation machinery have also been undertaken, whereas other approaches, like genome editing, are still in the early development phase. Despite some remaining hurdles that have to be overcome, lessons learned can be used to catalyse the development of potential therapies.

Key Concepts:

Duchenne muscular dystrophy (DMD) is caused by reading‐frame disrupting mutations in the
DMD
gene, resulting in premature termination of dystrophin synthesis.

Inframe mutations allow synthesis of shorter, but partly functional dystrophin proteins, resulting in the milder Becker muscular dystrophy (BMD) phenotype.

Antisense oligonucleotide‐mediated exon skipping aims to restore the reading frame enabling synthesis of BMD‐like dystrophins, thereby converting the severe DMD into the milder BMD disease.

Gene replacement therapy (replacing the dysfunctional dystrophin cDNA) is hampered by the size and complexity of the
DMD
gene and dystrophin cDNA.

AAV vectors have a limited loading capacity of ∼4.5 kb, requiring the use of mini‐, or microdystrophin genes that encode only the most crucial functional domains.

Ataluren can be used to force the translational machinery to ignore premature stop codons enabling synthesis of intact dystrophin.

Endonuclease‐mediated generation of double‐strand breaks can be used to correct the genetic mutation or restore the reading frame.

Many therapeutic approaches have progressed to clinical trials.
History of the Signal Hypothesis
Authors: Matlin Karl S
Published: September 2013

The signal hypothesis, which describes how secretory and membrane proteins are targeted to the endoplasmic reticulum, was proposed in 1971 by Günter Blobel and David Sabatini and demonstrated by Blobel and Bernhard Dobberstein in 1975. Subsequent research identified the key components of the membrane insertion and translocation machinery, including the signal recognition particle (SRP), the SRP receptor and the protein‐conducting channel. Ultimately, the signal hypothesis was shown to be true for not only eukaryotes but also prokaryotes. Most importantly, the concept of signal‐mediated targeting was expanded into a general hypothesis of cellular topogenesis that helps to explain how proteins are distributed to their correct locations within the cell following their synthesis in the cytoplasm.

Key Concepts:

Modern cell biology was developed in the post‐World War II period.

Cell biological research in the 30 years after World War II was characterised by a multidisciplinary approach that combined electron microscopy, cell fractionation, biochemical analysis and radioactive pulse‐labelling of proteins.

Formulation of the signal hypothesis was an outgrowth of protein synthesis and secretion research carried out at the Rockefeller University beginning in the late 1940s.

The signal hypothesis was originally proposed by Günter Blobel and David Sabatini in 1971, and demonstrated by Blobel and colleagues in 1975.

The signal hypothesis showed that cytoplasmically synthesised proteins targeted to the ER use a signal sequence to direct them to the ER membrane.

A signal sequence is a short peptide that is part of the original translation product of proteins targeted to the ER, often at theN‐terminus of the protein, and is frequently removed proteolytically after translocation of the nascent polypeptide through the ER membrane.

The mechanism of protein translocation was established through the isolation and characterisation of SRP, the SRP‐receptor and the protein‐conducting channel.

The signal hypothesis was found to be applicable to protein translocation in all eukaryotes and prokaryotes.

Although the original signal hypothesis proposed translocation of proteins during the elongation of the polypeptide chain (cotranslational), translocation was found to also occur in some instances after protein synthesis was complete (post‐translational), primarily through studies of bacteria and yeast.

The concept of signal‐mediated targeting of proteins was expanded into a generalised hypothesis of protein topogenesis by Günter Blobel in 1980.
Membrane Dynamics: Fluorescence Spectroscopy
Authors: Subburaj Yamunadevi , Gallego Raquel Salvador , García‐Sáez Ana J.
Published: September 2013

Membranes are dynamic lipophilic structures that constitute a selective barrier essential for the smooth functioning of cellular machinery. Their complex and highly heterogeneous composition, as well as the intricate diffusion patterns that they display, have been intensely studied in the past decades. Several innovative microscopy techniques have recently been developed to gain insight into the basis of membrane dynamics, interactions, and molecular organization. In this article, we introduce four pioneer fluorescence‐based approaches that have substantially broadened our overall understanding of membranes: fluorescence correlation spectroscopy (FCS), single particle tracking (SPT), fluorescence recovery after photobleaching (FRAP), and 6‐lauroyl‐2‐(dimethylamino)‐naphtalene (LAURDAN) microscopy. We discuss each technique in detail, explaining their principles, methodology, and applications in the research of the dynamic processes controlled by membranes.
Probing Membrane Protein Structure and Dynamics by Fluorescence Spectroscopy
Authors: Kang Guipeun , López‐Peña Ignacio , Bhakta Saajan , Kim Judy E.
Published: September 2013

Applications of fluorescence spectroscopy to biomolecules, with focus on membrane proteins, are discussed in this article. A broad range of molecular insights can be gained with this simple technique because the emission properties of a chromophore are typically sensitive to the environment. The intensities and maximum wavelengths of steady‐state fluorescence spectra are used to elucidate the thermodynamics of membrane protein folding, monitor the extent of solvent exposure of chromophores, determine the depths of insertion into synthetic bilayers, probe the degree of rotational freedom in solvent‐exposed and buried regions, and measure the evolution of distances between donor and acceptor moieties. We also address some of the challenges associated with fluorescence measurements of integral membrane proteins. An important goal is to provide a practical guide for laboratory measurements as well as examples of analyses related to membrane protein structure and dynamics.
WHY IS IT SO DIFFICULT TO REFORM SOME ASIAN BUREAUCRACIES? BUILDING THEORY FROM CAMBODIAN EVIDENCE
Authors: Turner Mark
Published: September 2013

This article demonstrates how theory can be built to explain cases of public administration reform failure in Asia. Drawing on the methodologies of middle range theory and grounded theory, qualitative data are gathered from the case of Cambodia and then analyzed. The result is the proposition that a specific constellation of reform‐inhibiting factors explains the slow progress of public administration reform in Cambodia. At the center of the constellation is patronage. The cluster of surrounding and interrelated factors includes weak accountability, hegemonic political regime, high and legitimate power distance, low wages, and bureaucratic dysfunction. The chances of reform success increase with the removal or absence of these inhibiting factors. The analysis emphasizes the importance of political economy factors in determining the success or failure of public administration reform. Copyright © 2013 John Wiley & Sons, Ltd.
REVISITING CONFUCIAN BUREAUCRACY: ROOTS OF THE KOREAN GOVERNMENT'S CULTURE AND COMPETITIVENESS
Authors: Im Tobin , Campbell Jesse W. , Cha Seyeong
Published: September 2013

This paper looks at Korea's Chosun dynasty bureaucracy and the Neo‐Confucian principles that formed the basis of its governing philosophy. We argue that Korea's traditional bureaucracy had a number of modern characteristics, including a system of formal and informal checks on the powers of the sovereign and a decision‐making system that encouraged deliberation among highly qualified civil servants. On the basis of this exposition, we also argue that there are strong links between the traditional bureaucracy and its current, modern form. We firstly show how the institutionalization of a strong state during the period of rapid development was as much a return to traditional governing principles as it was a revolution and, secondly, how contemporary organizational culture is shaped by Korea's Confucian heritage. In the final section, we argue that the distinctive characteristics of the Korean bureaucracy have played an important role in limiting the success of a number of Western‐oriented reform efforts. Copyright © 2013 John Wiley & Sons, Ltd.
CAN THERE BE AN ASIAN MODEL OF PUBLIC ADMINISTRATION?
Authors: Cheung Anthony B. L.
Published: September 2013

This article examines the conceptual possibilities of an Asian model of public administration, challenging some pre‐established paradigms along the way. There are two basic contentions. First, there is no such thing as one universal model of public administration that satisfies all national political and cultural situations so that each public administration system is also shaped by its own national tradition and historical evolution. The historical process is as important as the horizontal process of policy learning and transfer from others in the world. Second, Asia has its unique administrative civilization that has been under‐studied in the larger context of contemporary public administration theories and practices. The article does not argue for an Asian‐dominated governance model per se. Rather, the point is that the rapid social and economic growth of some emerging Asian nations has cast further doubt on any deterministic ‘good governance’ model driven predominantly by the Western growth experience. No definite thesis is concluded, and this must involve a process of drawing wisdoms from more Asian ‘national’ and local narratives of administrative histories and practices. Copyright © 2013 John Wiley & Sons, Ltd.
KNOWLEDGE ACCUMULATION IN ASIAN PUBLIC ADMINISTRATION RESEARCH: A CRITICAL REVIEW
Authors: Ko Kilkon
Published: September 2013

Given the growing controversy over the relevance of Anglo‐Saxon style public administration to developing countries and a greater demand for more context‐relevant theories of public administration in Asia, we should expect that Asian scholars achieve a certain level of knowledge growth in line with this controversy and demand. On the basis of the review of 8810 articles published in nine major international journals during 1990–2011, the author found that the number of articles on Asian public administration is very small, and there is no strong pattern of growth in this regard. In addition, there are very few studies adopting a comparative approach covering multiple Asian countries. Copyright © 2013 John Wiley & Sons, Ltd.
KNOWLEDGE‐BUILDING IN ASIAN PUBLIC ADMINISTRATION: AN INTRODUCTORY OVERVIEW
Authors: Haque M. Shamsul , Turner Mark
Published: September 2013

In recent years, the re‐emergence of Asia as a global power coincided with the proliferation of Asian studies in diverse disciplines and institutions worldwide. However, although the state and its administrative apparatus have been directly instrumental to this Asian success story, there is still inadequate research on the role of public administration in Asia. Thus, there is a need for exploring major issues related to research and knowledge building in Asian public administration. Copyright © 2013 John Wiley & Sons, Ltd.
Towards a critical understanding of the photosystem II repair mechanism and its regulation during stress conditions
Authors: Nath Krishna , Jajoo Anjana , Poudyal Roshan Sharma , Timilsina Rupak , Park Yu Shin , Aro Eva-Mari , Nam Hong Gil , Lee C.-H.
Published: September 2013

Photosystem II (PSII) is vulnerable to high light (HL) illumination resulting in photoinhibition. In addition to photoprotection mechanisms, plants have developed an efficient PSII repair mechanism to save themselves from irreversible damage to PSII under abiotic stresses including HL illumination. The phosphorylation/dephosphorylation cycle along with subsequent degradation of photodamaged D1 protein to be replaced by the insertion of a newly synthesized copy of D1 into the PSII complex, is the core function of the PSII repair cycle. The exact mechanism of this process is still under discussion. We describe the recent progress in identifying the kinases, phosphatases and proteases, and in understanding their involvement in the maintenance of thylakoid structure and the quality control of proteins by PSII repair cycle during photoinhibition.
Induced Pluripotency for Translational Research
Authors: Wu Menghua , Chen Guilai , Hu Baoyang
Published: September 2013

The advent of induced pluripotent stem cells (iPSCs) has revolutionized the concept of cellular reprogramming and potentially will solve the immunological compatibility issues that have so far hindered the application of human pluripotent stem cells in regenerative medicine. Recent findings showed that pluripotency is defined by a state of balanced lineage potency, which can be artificially instated through various procedures, including the conventional Yamanaka strategy. As a type of pluripotent stem cell, iPSCs are subject to the usual concerns over purity of differentiated derivatives and risks of tumor formation when used for cell-based therapy, though they provide certain advantages in translational research, especially in the areas of personalized medicine, disease modeling and drug screening. iPSC-based technology, human embryonic stem cells (hESCs) and direct lineage conversion each will play distinct roles in specific aspects of translational medicine, and continue yielding surprises for scientists and the public.
Transitional Justice and Changing Memories of the Past in Central Europe
Authors: David Roman
Published: September 2013

Memories of wrongdoings are often viewed as an obstacle to reconciliation in divided societies. Is it due to the past or the present politics of the past? To examine the dilemma of essentialism versus presentism, this article investigates the impact of transitional justice on memories of wrongdoing. It theorizes that using different transitional justice strategies to deal with the same wrongdoing shapes memories in different ways. The theory is tested via vignette-based surveys in the Czech Republic, Hungary and Poland, which adopted distinct lustration laws. The results show that wrongdoing is viewed through lustration laws, reflecting present power constellations, not history.
Particle capture by a circular cylinder in the vortex-shedding regime
Authors: Espinosa-Gayosso Alexis , Ghisalberti Marco , Ivey Gregory N. , Jones Nicole L.
Published: September 2013

Particle capture, whereby suspended particles contact and adhere to a solid surface (a ‘collector’), is an important mechanism for a range of environmental processes including suspension feeding by corals and ‘filtering’ by aquatic vegetation. In this paper, we use two- and three-dimensional direct numerical simulations to quantify the capture efficiency ($\eta $) of low-inertia particles by a circular cylindrical collector at intermediate Reynolds numbers in the vortex-shedding regime (i.e. for$47\lt \mathit{Re}\leq 1000$, where$\mathit{Re}$is the collector Reynolds number). We demonstrate that vortex shedding induces oscillations near the leading face of the collector which greatly affect the quantity and distribution of captured particles. Unlike in steady, low-$\mathit{Re}$flow, particles directly upstream of the collector are not the most likely to be captured. Our results demonstrate the dependence of the time-averaged capture efficiency on$\mathit{Re}$and particle size, improving the predictive capability for the capture of particles by aquatic collectors. The transition to theoretical high-Reynolds-number behaviour (i.e. $\eta \sim {\mathit{Re}}^{1/ 2} $) is complex due to comparatively rapid changes in wake conditions in this Reynolds number range.
Scaling of streamwise boundary layer streaks and their ability to reduce skin-friction drag
Authors: Shahinfar S. , Fransson J. H. M. , Sattarzadeh S. S. , Talamelli A.
Published: September 2013

Spanwise arrays of miniature vortex generators (MVGs) are used to generate energetic transient disturbance growth, which is able to modulate the boundary layer flow with steady and stable streak amplitudes up to 32 % of the free-stream velocity. This type of modulation has previously been shown to act in a stabilizing manner on modal disturbance growth described by classical instability theory. In an attempt to reproduce a more realistic flow configuration, in the present experimental set-up, Tollmien–Schlichting (TS) waves are generated upstream of the MVG array, allowing for a complete interaction of the incoming wave with the array. Fifteen new MVG configurations are investigated and the stabilizing effect on the TS waves is quantified. We show that the streak amplitude definition is very important when trying to relate it to the stabilization, since it may completely bypass information on the mean streamwise velocity gradient in the spanwise direction, which is an essential ingredient of the observed stabilization. Here, we use an integral-based streak amplitude definition along with a streak amplitude scaling relation based on empiricism, which takes the spanwise periodicity of the streaks into account. The results show that, applying the integral definition, the optimal streak amplitude for attenuating TS wave disturbance growth is around 30 % of the free-stream velocity, which corresponds to ${\sim }20\hspace{0.167em} \% $ in the conventional definition when keeping the spanwise wavelength constant. The experiments also show that the disturbance energy level, based on the full velocity signal, is significantly reduced in the controlled case, and that the onset of transition may be inhibited altogether throughout the measured region in the presence of an MVG array.
A bathtub vortex under the influence of a protruding cylinder in a rotating tank
Authors: Chen Yin-Chung , Huang Shih-Lin , Li Zi-Ya , Chang Chien-Cheng , Chu Chin-Chou
Published: September 2013

Numerical simulations and laboratory experiments were jointly conducted to investigate a bathtub vortex under the influence of a protruding cylinder in a rotating tank. In the set-up, a central drain hole is placed at the bottom of the tank and a top-down cylinder is suspended from the rigid top lid, with fluid supplied from the sidewall for mass conservation. The cylinder is protruded to produce the Taylor column effect. The flow pattern depends on the Rossby number ($\mathit{Ro}= U/ fR$), the Ekman number ($\mathit{Ek}= \nu / f{R}^{2} )$ and the height ratio, $h/ H$, where $R$ is the radius of the cylinder, $f$ is the Coriolis parameter, $\nu $ is the kinematic viscosity of the fluid, $h$ is the vertical length of the cylinder and $H$ is the height of the tank. It is found appropriate to choose $U$ to be the average inflow velocity of fluid entering the column beneath the cylinder. Steady-state solutions obtained by numerically solving the Navier–Stokes equations in the rotating frame are shown to have a good agreement with flow visualizations and particle tracking velocimetry (PTV) measurements. It is known that at $\mathit{Ro}\sim 1{0}^{- 2} $, the central downward flow surrounded by the neighbouring Ekman pumping forms a classic one-celled bathtub vortex structure when there is no protruding cylinder ($h/ H= 0$). The influence of a suspended cylinder ($h/ H\not = 0$) leads to several findings. The bathtub vortex exhibits an interesting two-celled structure with an inner Ekman pumping (EP) and an outer up-drafting motion, termed Taylor upwelling (TU). The two regions of up-drafting motion are separated by a notable finite-thickness structure, identified as a (thin-walled) Taylor column. The thickness ${ \delta }_{T}^{\ast } $ of the Taylor column is found to be well correlated to the height ratio and the Ekman number by ${\delta }_{T} = { \delta }_{T}^{\ast } / R= {(1- h/ H)}^{- 0. 32} {\mathit{Ek}}^{0. 095} $. The Taylor column presents a barrier to the fluid flow such that the fluid from the inlet may only flow into the inner region through the narrow gaps, one above the Taylor column and one beneath it (conveniently called Ekman gaps). As a result, five types of routes along which the fluid may flow to and exit at the drain hole could be identified for the multi-celled vortex structure. Moreover, the flow rates associated with the five routes were calculated and compared to help understand the relative importance of the component flow structures. The weaker influence of the Taylor column effect on the bathtub vortex at $\mathit{Ro}\sim 1$ or even higher $\mathit{Ro}\sim 1{0}^{2} $ is also discussed.
Characterizing ego-networks using motifs
Authors: CUNNINGHAM PÁDRAIG , HARRIGAN MARTIN , WU GUANGYU , O'CALLAGHAN DEREK
Published: September 2013

We assess the potential of network motif profiles to characterize ego-networks in much the same way that a bag-of-words strategy allows text documents to be compared in a vector space framework. This is potentially valuable as a generic strategy for comparing nodes in a network in terms of the network structure in which they are embedded. In this paper, we consider the computational challenges and model selection decisions involved in network motif profiling. We also present three case studies concerning the analysis of Wikipedia edit networks, YouTube spam campaigns, and peer-to-peer lending in the Prosper marketplace.
Effects of lutein and lycopene on carotid intima–media thickness in Chinese subjects with subclinical atherosclerosis: a randomised, double-blind, placebo-controlled trial
Authors: Zou Zhi-Yong , Xu Xian-Rong , Lin Xiao-Ming , Zhang Hua-Bin , Xiao Xin , Ouyang Li , Huang Yang-Mu , Wang Xun , Liu Ya-Qiong
Published: September 2013

The aim of the present study was to evaluate the effects of lutein and lycopene supplementation on carotid artery intima–media thickness (CAIMT) in subjects with subclinical atherosclerosis. A total of 144 subjects aged 45–68 years were recruited from local communities. All the subjects were randomly assigned to receive 20 mg lutein/d (n 48), 20 mg lutein/d+20 mg lycopene/d (n 48) or placebo (n 48) for 12 months. CAIMT was measured using Doppler ultrasonography at baseline and after 12 months, and serum lutein and lycopene concentrations were determined using HPLC. Serum lutein concentrations increased significantly from 0·34 to 1·96 μmol/l in the lutein group (P< 0·001) and from 0·35 to 1·66 μmol/l in the combination group (P< 0·001). Similarly, serum lycopene concentrations increased significantly from 0·18 to 0·71 μmol/l in the combination group at month 12 (P< 0·001), whereas no significant change was observed in the placebo group. The mean values of CAIMT decreased significantly by 0·035 mm (P= 0·042) and 0·073 mm (P< 0·001) in the lutein and combination groups at month 12, respectively. The change in CAIMT was inversely associated with the increase in serum lutein concentrations (P< 0·05) in both the active treatment groups and with that in serum lycopene concentrations (β = − 0·342, P= 0·031) in the combination group. Lutein and lycopene supplementation significantly increased the serum concentrations of lutein and lycopene with a decrease in CAIMT being associated with both concentrations. In addition, the combination of lutein and lycopene supplementation was more effective than lutein alone for protection against the development of CAIMT in Chinese subjects with subclinical atherosclerosis, and further studies are needed to confirm whether synergistic effects of lutein and lycopene exist.
The Clown Within: Becoming White and Mapuche Ritual Clowns
Authors: Course Magnus
Published: September 2013

This essay takes the antics of ritual clowns,koyong, as an entry point into the ways in which rural Mapuche people in southern Chile come to understand and reflect upon the inevitability of urban migration and the “becoming white” which this migration is said to imply. Utilizing both my own ethnographic data and comparative data from elsewhere in the Americas, I explore the striking continuities in the associations of indigenous ritual clowns: associations with poverty, with uncontrolled bodily desires, with dual ritual performances, and perhaps most significantly, with white people. I suggest that the moral indictment of the “becoming white” instantiated by clowns in their ritual performances emerges from their identities as people who in everyday life are denigrated as “too Mapuche.” Thus, far from being yet another example of indigenous people's “agency” in mimetically co-opting the vitality of white others, I suggest that clowns are one of the means by which rural Mapuche people come to understand precisely their ownlackof agency in the face of Chilean colonialism
Urban Subalterns in the Arab Revolutions: Cairo and Damascus in Comparative Perspective
Authors: Ismail Salwa
Published: September 2013

This paper investigates the role of urban subalterns both as participatory agents in the Arab revolutions and as mediating forces against revolutionary action. It argues that during revolutionary periods the positioning of subalterns as a political force should be understood in relation to their socio-spatial location in the urban political configuration. Looking at the protest movements in Cairo and Damascus, the paper examines the differentiated locations of subaltern actors in each to demonstrate how their positioning in relation to state and government has shaped their engagement in the revolutions. In Cairo, the mobilization of subaltern forces was anchored in spatialized forms of everyday interaction between popular forces and agents of government. These interactions were formative of urban subjectivities that entered into the making of “the people” as the subject of the Revolution. In Damascus, the configuration of the urban space and the Syrian regime's modes of control made it difficult for subaltern forces to mobilize on the same scale as in Cairo or to form a unified opposition. The regime instrumentalized socio-spatial fragmentation among subalterns, in effect turning some segments, as buffers for the regime, against others. In analytical terms, the paper underscores the common conceptual ground between the categories of “urban popular forces” and “urban subalterns.” This ground covers their socio-spatial positionality, their bases of action, and the factors shaping their political subjectivities.
Culture, Nature, and History: The Case of Ancient Sexuality
Authors: Harper Kyle
Published: September 2013

This article analyzes the configuration of biology, anthropology, and history over the last generation by taking the sub-field of the “history of sexuality” as a case study. The history of sexuality developed at a particularly important site of engagement with neighboring disciplines. I argue that the concepts of nature and culture that came to prevail among historians of sexuality were deeply influenced by the debate between a particular strand of evolutionary biology, namely sociobiology, and its critics, who were committed to cultural hermeneutics. This debate encouraged a formulation of nature and culture which is effectively dualist and which remains present within the sub-field. By focusing the analysis on the study ofancient(classical Mediterranean) sexuality, I seek detailed insights into the reception of this debate within a specific domain of historical investigation, one whose stakes have been particularly high because of the intervention of Michel Foucault. The article closes by arguing that biologists and anthropologists in the last two decades have advanced the study of culture as a part of nature, and that historians have much to gain by engaging with more recent models. The institution of monogamy is highlighted as an emerging theme of investigation that can only be approached with the unified insights of history, anthropology, and biology.
“Everyday Politics” in North Korea
Authors: Choi Changyong
Published: September 2013

This article examines daily life in North Korea from the perspectives of recent North Korean defectors from a variety of social backgrounds. The following three questions are explored: how does the individual live from day to day; what tactics does one continuously evolve in order to survive; and, most importantly, what theoretical and methodological frameworks are available to explain the strategies for survival employed by the country's population? Employing the concept of “everyday politics,” this study argues that state-society interactions once constrained by a highly centralized regime, characterized by an emphasis on political and moral motivations, have yielded to more fragmented and autonomous systems strengthened by realization of individual self-interest. In the process, the state and society have reshaped patterns of interaction regarding information flow structures, rules of behavior, and motivations. That is, both the state and society seek coexistence, and the “market” spontaneously developed by the population functions as a shock absorber.