bluuebunny/crossref_metadata_2025 huggingface dataset:
The evolution of the market for commercial computerized physician order entry and computerized decision support systems for prescribing
Authors: Mozaffar Hajar , Williams Robin , Cresswell Kathrin , Morrison Zoe , Bates David W. , Sheikh Aziz
Published: September 2015

Objective To understand the evolving market of commercial off-the-shelf Computerized Physician Order Entry (CPOE) and Computerized Decision Support (CDS) applications and its effects on their uptake and implementation in English hospitals.

Methods Although CPOE and CDS vendors have been quick to enter the English market, uptake has been slow and uneven. To investigate this, the authors undertook qualitative ethnography of vendors and adopters of hospital CPOE/CDS systems in England. The authors collected data from semi-structured interviews with 11 individuals from 4 vendors, including the 2 most entrenched suppliers, and 6 adopter hospitals, and 21 h of ethnographic observation of 2 user groups, and 1 vendor event. The research and analysis was informed by insights from studies of the evolution of technology fields and the emergence of generic COTS enterprise solutions.

Results Four key themes emerged: (1) adoption of systems that had been developed outside of England, (2) vendors’ configuration and customization strategies, (3) localized adopter practices vs generic systems, and (4) unrealistic adopter demands. Evidence for our over-arching finding concerning the current immaturity of the market was derived from vendors’ strategies, adopters’ reactions to the technology, and policy makers’ incomplete insights.

Conclusions The CPOE/CDS market in England is still in an emergent phase. The rapid entrance of diverse products, triggered by federal policy initiatives, has resulted in premature adoption of systems that do not yet adequately meet the needs of hospitals. Vendors and adopters lacked understanding of how to design and implement generic solutions to meet diverse user needs.
Phobic disorders
Authors: Butler Gillian
Published: September 2015

Chapter 4 discusses phobic disorders. It outlines types of phobia, the frequency of phobias, and explores the theoretical background to treatment, stages of assessment (including phobia treatment suitability, goal determination, phobia measurement), phobia treatment in practice (useful methods of treatment, complicating factors, and alternative treatments), and the effectiveness of exposure-based treatments.
Obsessional disorders
Authors: Salkovskis Paul M. , Kirk Joan
Published: September 2015

Chapter 5 discusses obsessional disorders, such as obsessive-compulsive disorder (OCD). It outlines the nature of obsessional disorders, types of compulsive behaviour, and the psychological model of obsessive-compulsive disorder. Methods of assessment are presented, such as behavioural analysis and interviews, behavioural tests, and physiological factors, as well as treatments of obsessions with overt OCD and overt compulsive behaviour.
Specific Fears and Phobias
Authors: McLean Peter D. , Woody Sheila R.
Published: September 2015

This chapter discusses specific fears and phobias, and provides an informational and theoretical base from which will be expanded into more complex anxiety disorders in later chapters. Specific phobias will be considered within a three-systems perspective, including behavioral, physiological, and cognitive components of the fear response. Unique features of some of the specific phobias will be discussed, and empirically supported treatment procedures will be described.
Panic Disorder and Agoraphobia
Authors: McLean Peter D. , Woody Sheila R.
Published: September 2015

This chapter addresses current understanding of panic disorder, with particular emphasis on assessment and treatment procedures. It first reviews the features of panic attacks and panic disorder, followed by a discussion of various theoretical perspectives on the problem, and assessment and treatment procedures, which focuses on pragmatics of working with clients with panic and agoraphobia.
Obsessive-Compulsive Disorder
Authors: McLean Peter D. , Woody Sheila R.
Published: September 2015

This chapter presents a description of obsessive-compulsive disorder (OCD) and the prevailing theory of OCD. It also reviews assessment issues related to diagnosis and treatment planning, along with the role of triggers, cognitive appraisals, feared consequences, and avoidance in the occurrence of obsessive thoughts. The chapter will concentrate on the detailed application of behavioral and cognitive behavioral models of treatment for OCD, since these approaches have been guided by empirical development.
Generalized Anxiety Disorder
Authors: McLean Peter D. , Woody Sheila R.
Published: September 2015

This chapter discusses generalized anxiety disorder (GAD). This includes the phenomenology of GAD, and its prevalence, as well as theoretical perspectives on GAD (biological approaches, and psychological approaches), assessment, diagnostic criteria, and comorbidity. It discusses treatment models and guidelines (pharmacotherapy, psychological treatment, cognitive behavior therapy (CBT), and worry interventions), as well as treatment evaluation.
Proactive Coping and Quality of Life Management
Authors: Greenglass Esther R.
Published: September 2015

Chapter 3 outlines proactive coping and quality-of-life management. It presents a brief history of coping in psychology, and discusses functions of coping, social support and stress, a theoretical model for proactive coping, the proactive coping inventory (PCI), and an application of the PCI to work stress and burnout.
Alone Together: Comparing Communal Versus Individualistic Resiliency
Authors: Hobfoll Stevan E.
Published: September 2015

This chapter presents a comparison of communal and individualistic resiliency. It discusses the historical context of individualism and collectivism, individual versus communal-mastery, the correlates and impact of communal-versus self-mastery, and case studies of the role of self-and communal-mastery among inner-city women and Native Americans.
Positive Psychology and Health: Situational Dependence and Personal Striving
Authors: Moore Kathleen A.
Published: September 2015

Chapter 6 explores positive psychology and health in the context of situational dependence and personal striving. It includes a history of positive psychology, and relates Maslow’s hierarchy of needs to biopsychosocial health. The chapter discusses categories of coping strategies and strategies that reduce the impact of threats to health (such as unemployment, restructuring changes) as well as mediators (self-efficacy, goals, and optimism).
Positive Emotions in Education
Authors: Pekrun Reinhard , Goetz Thomas , Titz Wolfram , Perry Raymond P.
Published: September 2015

Chapter 8 explores positive emotions (such as hope or pride) in education. It outlines studies into the occurrence of positive academic emotions, measurement of positive academic emotions using the Academic Emotions Questionnaire (AEQ), the impact of positive emotions on students’ learning, self-regulation, and achievement, and cognitive and social origins of students’ positive emotions, including control-value theory.
Sciatic Nerve Intrafascicular Lidocaine Injection-induced Peripheral Neuropathic Pain
Authors: Cheng Kuang-I , Wang Hung-Chen , Wu Yi-Chia , Tseng Kuang-Yi , Chuang Yi-Ta , Chou Chao-Wen , Chen Ping-Luen , Chang Lin-Li , Lai Chung-Sheng
Published: September 2015

Objective:

Peripheral nerve block guidance with a nerve stimulator or echo may not prevent intrafascicular injury. This study investigated whether intrafascicular lidocaine induces peripheral neuropathic pain and whether this pain can be alleviated by minocycline administration.

Methods:

A total of 168 male Sprague-Dawley rats were included. In experiment 1, 2% lidocaine (0.1 mL) was injected into the left sciatic nerve. Hindpaw responses to thermal and mechanical stimuli, and sodium channel and activating transcription factor (ATF-3) expression in dorsal root ganglion (DRG) and glial cells in the spinal dorsal horn (SDH), were measured on days 4, 7, 14, 21, and 28. On the basis of the results in experiment 1, rats in experiment 2 were divided into sham, extraneural, intrafascicular, peri-injury minocycline, and postinjury minocycline groups. Behavioral responses, macrophage recruitment, expression changes of myelin basic protein and Schwann cells in the sciatic nerve, dysregulated expression of ATF-3 in the DRG, and activated glial cells in L5 SDH were assessed on days 7 and 14.

Results:

Intrafascicular lidocaine induced mechanical allodynia, downregulated Nav1.8, increased ATF-3 expression in the DRG, and activated glial cells in the SDH. Increased expression of macrophages, Schwann cells, and myelin basic protein was found in the sciatic nerve. Minocycline attenuated intrafascicular lidocaine-induced neuropathic pain and nerve damage significantly. Peri-injury minocycline was better than postinjury minocycline administration in alleviating mechanical behaviors, mitigating macrophage recruitment into the sciatic nerve, and suppressing activated microglial cells in the spinal cord.

Discussion:

Systemic minocycline administration alleviates intrafascicular lidocaine injection-induced peripheral nerve damage.
Prospective Mediation Models of Sleep, Pain, and Daily Function in Children With Arthritis Using Ecological Momentary Assessment
Authors: Bromberg Maggie H. , Connelly Mark , Anthony Kelly K. , Gil Karen M. , Schanberg Laura E.
Published: September 2015

Objectives:

Sleep is an emerging area of concern in children with juvenile idiopathic arthritis (JIA). Research shows the presence of poor sleep quality and related adverse outcomes in pediatric pain populations, including JIA, but few studies have examined the prospective patterns of association between sleep and associated outcomes. This prospective study evaluated the direction and magnitude of associations between subjective sleep characteristics (sleep quality, difficulty initiating sleep, and sleep duration), pain intensity, and functional limitations in children with JIA. We hypothesized that pain intensity would partially mediate the relationship between sleep and functional limitations.

Methods:

Children and adolescents with JIA (n=59; age range, 8 to 18 y) recruited during clinic visits, completed smartphone-based diaries for 1 month. Subjective sleep characteristics were reported each morning; pain and functioning were assessed 3 times daily.

Results:

As hypothesized, the associations between sleep quality and functional limitations and between difficulty initiating sleep and functional limitations were partially mediated by pain intensity, at any given moment (z=−3.27, P=0.001, z=2.70, P<0.05). Mediation was not detected in a model testing the association between sleep duration, pain intensity, and functional limitations (z=−0.58, P=0.56).

Discussion:

Results suggest that sleep is integral to understanding the momentary association between pain intensity and functioning in children with JIA.
Inattentive Attention-Deficit/Hyperactivity Disorder, Stimulant Medication, and Weight Loss in a 15-Year-Old Girl: Are We Enabling the Development of an Eating Disorder?
Authors: Iyer Sai , Kumar Maya , Reiff Michael I. , Stein Martin T.
Published: September 2015

CASE: Nicole is a 15-year-old girl presenting to the Developmental Behavioral Pediatrics Clinic with symptoms of the inattentive type of Attention-Deficit/Hyperactivity Disorder (ADHD) and declining school performance over the last year. She expressed frustration over her inability to concentrate on schoolwork. Assuming that her poor grades were secondary to lack of effort, her parents withdrew privileges. Nicole became increasingly depressed. She stopped participating in activities, she previously enjoyed, and her parents reported that she stopped singing in the shower. After talking to a cousin with ADHD, Nicole concluded that she had ADHD as well. She asked her parents to arrange for an evaluation.

Nicole met DSM-5 criteria for the diagnosis of inattentive ADHD and was started on a stimulant medication (mixed amphetamine salts). She had symptoms of a coexisting depression, although she did not meet criteria for diagnosis of a depressive disorder. At a 3-week follow-up visit, she showed improvement in targeted ADHD symptoms; homework was now easier and her grades improved. At a 2-month follow-up, Nicole's weight dropped from 53 kg (47th percentile) prestimulant treatment to 49 kg (31st percentile). She reported appetite suppression after taking the stimulant but did not feel that her eating habits had changed significantly. Her father reported that she had a preference for junk food and snacks. Nicole did not enjoy exercising and did not participate in extracurricular sports.

She weighed herself several times a day, as she was worried about losing too much weight. Nicole's mood continued to be low, despite the fact that her grades improved, and her parents were more understanding of her challenges. She was otherwise healthy and reported regular menstrual cycles. Nicole requested an increase in the dose of stimulant medication for greater improvement in concentration during homework and in school.

Her pediatric clinician was concerned about the possibility of an eating disorder in addition to depression. She asked herself, “Are we treating inattentive ADHD effectively or are we enabling an eating disorder?”
Follow‐up in Childhood Functional Constipation
Authors: Modin Line , Walsted Anne‐Mette , Rittig Charlotte S. , Hansen Anne V. , Jakobsen Marianne S.
Published: September 2015

Objectives:

Guidelines recommend close follow‐up during the treatment of childhood functional constipation. Only sparse evidence exists on how follow‐up is best implemented. Our aim was to evaluate whether follow‐up by phone or self‐management through Web‐based information improved treatment outcomes.

Methods:

In this randomized controlled trial, conducted in secondary care, 235 children, ages 2 to 16 years, who fulfilled the Rome III criteria of childhood constipation, were assigned to 1 of the 3 follow‐up regimens: control group (no scheduled contact), phone group (2 scheduled phone contacts), and Web group (access to Web‐based information). Primary outcome: number of successfully treated children after 3, 6, and 12 months. Secondary outcomes: phone contacts, relapse, fecal incontinence, and laxative use.

Results:

After 3 and 6 months, significantly more children in the Web group (79.7%/75.9%) were successfully treated compared with the control and phone groups (59.7%/63.6% and 63.3%/64.6%) (P = 0.007/P = 0.03). No difference was found after 12 months (control, 72.7%; phone, 68.4%; Web group, 78.5%; P = 0.40). Extra phone consultations were significantly more frequent in the Web group (44.3%) compared with the control group (28.6%) (P = 0.04). Before 3 months, 45.5% of phone consultations were completed in the Web group versus 28.8% and 25.8% in the control and phone groups (P = 0.05/P = 0.02). Relapses, fecal incontinence, and laxative use were not different between interventions.

Conclusions:

Improved self‐management behavior caused by access to self‐motivated Web‐based information induced faster short‐term recovery during the treatment of functional constipation. Patient empowerment rather than health care–promoted follow‐up may be a step toward more effective treatment for childhood constipation.
Biogeographic calibrations for the molecular clock
Authors: Ho Simon Y. W. , Tong K. Jun , Foster Charles S. P. , Ritchie Andrew M. , Lo Nathan , Crisp Michael D.
Published: September 2015

Molecular estimates of evolutionary timescales have an important role in a range of biological studies. Such estimates can be made using methods based on molecular clocks, including models that are able to account for rate variation across lineages. All clock models share a dependence on calibrations, which enable estimates to be given in absolute time units. There are many available methods for incorporating fossil calibrations, but geological and climatic data can also provide useful calibrations for molecular clocks. However, a number of strong assumptions need to be made when using these biogeographic calibrations, leading to wide variation in their reliability and precision. In this review, we describe the nature of biogeographic calibrations and the assumptions that they involve. We present an overview of the different geological and climatic events that can provide informative calibrations, and explain how such temporal information can be incorporated into dating analyses.
Magnetic particle-mediated magnetoreception
Authors: Shaw Jeremy , Boyd Alastair , House Michael , Woodward Robert , Mathes Falko , Cowin Gary , Saunders Martin , Baer Boris
Published: September 2015

Behavioural studies underpin the weight of experimental evidence for the existence of a magnetic sense in animals. In contrast, studies aimed at understanding the mechanistic basis of magnetoreception by determining the anatomical location, structure and function of sensory cells have been inconclusive. In this review, studies attempting to demonstrate the existence of a magnetoreceptor based on the principles of the magnetite hypothesis are examined. Specific attention is given to the range of techniques, and main animal model systems that have been used in the search for magnetite particulates. Anatomical location/cell rarity and composition are identified as two key obstacles that must be addressed in order to make progress in locating and characterizing a magnetite-based magnetoreceptor cell. Avenues for further study are suggested, including the need for novel experimental, correlative, multimodal and multidisciplinary approaches. The aim of this review is to inspire new efforts towards understanding the cellular basis of magnetoreception in animals, which will in turn inform a new era of behavioural research based on first principles.
Phylogenetic tests reject Emery's rule in the evolution of social parasitism in yellowjackets and hornets (Hymenoptera: Vespidae, Vespinae)
Authors: Lopez-Osorio Federico , Perrard Adrien , Pickett Kurt M. , Carpenter James M. , Agnarsson Ingi
Published: September 2015

Social parasites exploit the brood-care behaviour and social structure of one or more host species. Within the social Hymenoptera there are different types of social parasitism. In its extreme form, species of obligate social parasites, or inquilines, do not have the worker caste and depend entirely on the workers of a host species to raise their reproductive offspring. The strict form of Emery's rule states that social parasites share immediate common ancestry with their hosts. Moreover, this rule has been linked with a sympatric origin of inquilines from their hosts. Here, we conduct phylogenetic analyses of yellowjackets and hornets based on 12 gene fragments and evaluate competing evolutionary scenarios to test Emery's rule. We find that inquilines, as well as facultative social parasites, are not the closest relatives of their hosts. Therefore, Emery's rule in its strict sense is rejected, suggesting that social parasites have not evolved sympatrically from their hosts in yellowjackets and hornets. However, the relaxed version of the rule is supported, as inquilines and their hosts belong to the same
Dolichovespula
clade. Furthermore, inquilinism has evolved only once in
Dolichovespula
.
Unexpected consequences of a drier world: evidence that delay in late summer rains biases the population sex ratio of an insect
Authors: Bonal Raul , Hernández Marisa , Espelta Josep M. , Muñoz Alberto , Aparicio José M.
Published: September 2015

The complexity of animal life histories makes it difficult to predict the consequences of climate change on their populations. In this paper, we show, for the first time, that longer summer drought episodes, such as those predicted for the dry Mediterranean region under climate change, may bias insect population sex ratio. Many Mediterranean organisms, like the weevil
Curculio elephas
, become active again after summer drought. This insect depends on late summer rainfall to soften the soil and allow adult emergence from their underground refuges. We found that, as in many protandric species, more
C. elephas
females emerged later in the season. Male emergence timing was on average earlier and also more dependent on the beginning of late summer rainfall. When these rains were delayed, the observed weevil sex ratio was biased towards females. So far, the effects of global warming on animal sex ratios has been reported for temperature-dependent sex determination in reptiles. Our results show that rainfall timing can also bias the sex ratio in an insect, and highlight the need for keeping a phenological perspective to predict the consequences of climate change. We must consider not just the magnitude of the predicted changes in temperature and rainfall but also the effects of their timing.
Boundary of the set of separable states
Authors: Chen Lin , Ðoković Dragomir Ž
Published: September 2015

Motivated by the separability problem in quantum systems 2⊗4, 3⊗3 and 2⊗2⊗2, we study the maximal (proper) faces of the convex body,

S

1

, of normalized separable states in an arbitrary quantum system with finite-dimensional Hilbert space

H

=

H

1

⊗

H

2

⊗
⋯
⊗

H

n

. To any subspace

V
⊆

H

, we associate a face
F

V

of

S

1

consisting of all states

ρ
∈

S

1

whose range is contained in
V
. We prove that
F

V

is a maximal face if and only if
V
is a hyperplane. If
V
=|
ψ
〉
⊥
, where |
ψ
〉 is a product vector, we prove that

Dim

 

F
V

=

d
2

−
1
−
∏
(
2

d
i

−
1
)

, where

d
i

=

Dim

 

H

i

and

d
=
∏

d
i

. We classify the maximal faces of

S

1

in the cases 2⊗2 and 2⊗3. In particular, we show that the minimum and the maximum dimension of maximal faces is 6 and 8 for 2⊗2, and 20 and 24 for 2⊗3. The boundary,

∂

S

1

, of

S

1

is the union of all maximal faces. When
d
>6, it is easy to show that there exist full states on

∂

S

1

, i.e. states

ρ
∈
∂

S

1

such that all partial transposes of
ρ
(including
ρ
itself) have rank
d
. Ha and Kye have recently constructed explicit such states in 2⊗4 and 3⊗3. In the latter case, they have also constructed a remarkable family of faces, depending on a real parameter
b
>0,
b
≠1. Each face in the family is a nine-dimensional simplex, and any interior point of the face is a full state. We construct suitable optimal entanglement witnesses for these faces and analyse the three limiting cases

b
=
0
,
1
,
∞

.
An ontogenetic perspective on individual differences
Authors: Senner Nathan R. , Conklin Jesse R. , Piersma Theunis
Published: September 2015

Phenotypic differences among individuals can arise during any stage of life. Although several distinct processes underlying individual differences have been defined and studied (e.g. parental effects, senescence), we lack an explicit, unified perspective for understanding how these processes contribute separately and synergistically to observed variation in functional traits. We propose a conceptual framework based on a developmental view of life-history variation, linking each ontogenetic stage with the types of individual differences originating during that period. In our view, the salient differences among these types are encapsulated by three key criteria: timing of onset, when fitness consequences are realized, and potential for reversibility. To fill a critical gap in this framework, we formulate a new term to refer to individual differences generated during adulthood—reversible state effects. We define these as ‘reversible changes in a functional trait resulting from life-history trade-offs during adulthood that affect fitness’, highlighting how the adult phenotype can be repeatedly altered in response to environmental variation. Defining individual differences in terms of trade-offs allows explicit predictions regarding when and where fitness consequences should be expected. Moreover, viewing individual differences in a developmental context highlights how different processes can work in concert to shape phenotype and fitness, and lays a foundation for research linking individual differences to ecological and evolutionary theory.
Transmissible cancer in Tasmanian devils: localized lineage replacement and host population response
Authors: Hamede Rodrigo K. , Pearse Anne-Maree , Swift Kate , Barmuta Leon A. , Murchison Elizabeth P. , Jones Menna E.
Published: September 2015

Tasmanian devil facial tumour disease (DFTD) is a clonally transmissible cancer threatening the Tasmanian devil (Sarcophilus harrisii) with extinction. Live cancer cells are the infectious agent, transmitted to new hosts when individuals bite each other. Over the 18 years since DFTD was first observed, distinct genetic and karyotypic sublineages have evolved. In this longitudinal study, we investigate the associations between tumour karyotype, epidemic patterns and host demographic response to the disease. Reduced host population effects and low DFTD infection rates were associated with high prevalence of tetraploid tumours. Subsequent replacement by a diploid variant of DFTD coincided with a rapid increase in disease prevalence, population decline and reduced mean age of the population. Our results suggest a role for tumour genetics in DFTD transmission dynamics and epidemic outcome. Future research, for this and other highly pathogenic emerging infectious diseases, should focus on understanding the evolution of host and pathogen genotypes, their effects on susceptibility and tolerance to infection, and their implications for designing novel genetic management strategies. This study provides evidence for a rapid localized lineage replacement occurring within a transmissible cancer epidemic and highlights the possibility that distinct DFTD genetic lineages may harbour traits that influence pathogen fitness.
A generalist brood parasite modifies use of a host in response to reproductive success
Authors: Louder Matthew I. M. , Schelsky Wendy M. , Albores Amber N. , Hoover Jeffrey P.
Published: September 2015

Avian obligate brood parasites, which rely solely on hosts to raise their young, should choose the highest quality hosts to maximize reproductive output. Brown-headed cowbirds (Molothrus ater) are extreme host generalists, yet female cowbirds could use information based on past reproductive outcomes to make egg-laying decisions thus minimizing fitness costs associated with parasitizing low-quality hosts. We use a long-term (21 years) nest-box study of a single host, the prothonotary warbler (Protonotaria citrea), to show that local cowbird reproductive success, but not host reproductive success, was positively correlated with the probability of parasitism the following year. Experimental manipulations of cowbird success corroborated that female cowbirds make future decisions about which hosts to use based on information pertaining to past cowbird success, both within and between years. The within-year pattern, in particular, points to local cowbird females selecting hosts based on past reproductive outcomes. This, coupled with high site fidelity of female cowbirds between years, points to information use, rather than cowbird natal returns alone, increasing parasitism rates on highly productive sites between years.
Diversity and origins of anaerobic metabolism in mitochondria and related organelles
Authors: Stairs Courtney W. , Leger Michelle M. , Roger Andrew J.
Published: September 2015

Across the diversity of life, organisms have evolved different strategies to thrive in hypoxic environments, and microbial eukaryotes (protists) are no exception. Protists that experience hypoxia often possess metabolically distinct mitochondria called mitochondrion-related organelles (MROs). While there are some common metabolic features shared between the MROs of distantly related protists, these organelles have evolved independently multiple times across the breadth of eukaryotic diversity. Until recently, much of our knowledge regarding the metabolic potential of different MROs was limited to studies in parasitic lineages. Over the past decade, deep-sequencing studies of free-living anaerobic protists have revealed novel configurations of metabolic pathways that have been co-opted for life in low oxygen environments. Here, we provide recent examples of anaerobic metabolism in the MROs of free-living protists and their parasitic relatives. Additionally, we outline evolutionary scenarios to explain the origins of these anaerobic pathways in eukaryotes.
Evolution of viruses and cells: do we need a fourth domain of life to explain the origin of eukaryotes?
Authors: Moreira David , López-García Purificación
Published: September 2015

The recent discovery of diverse very large viruses, such as the mimivirus, has fostered a profusion of hypotheses positing that these viruses define a new domain of life together with the three cellular ones (Archaea, Bacteria and Eucarya). It has also been speculated that they have played a key role in the origin of eukaryotes as donors of important genes or even as the structures at the origin of the nucleus. Thanks to the increasing availability of genome sequences for these giant viruses, those hypotheses are amenable to testing via comparative genomic and phylogenetic analyses. This task is made very difficult by the high evolutionary rate of viruses, which induces phylogenetic artefacts, such as long branch attraction, when inadequate methods are applied. It can be demonstrated that phylogenetic trees supporting viruses as a fourth domain of life are artefactual. In most cases, the presence of homologues of cellular genes in viruses is best explained by recurrent horizontal gene transfer from cellular hosts to their infecting viruses and not the opposite. Today, there is no solid evidence for the existence of a viral domain of life or for a significant implication of viruses in the origin of the cellular domains.
Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes
Authors: Saw Jimmy H. , Spang Anja , Zaremba-Niedzwiedzka Katarzyna , Juzokaite Lina , Dodsworth Jeremy A. , Murugapiran Senthil K. , Colman Dan R. , Takacs-Vesbach Cristina , Hedlund Brian P. , Guy Lionel , Ettema Thijs J. G.
Published: September 2015

The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number of essential pieces. Whereas it is currently accepted that the process of eukaryogenesis involved an interplay between a host cell and an alphaproteobacterial endosymbiont, we currently lack detailed information regarding the identity and nature of these players. A number of studies have provided increasing support for the emergence of the eukaryotic host cell from within the archaeal domain of life, displaying a specific affiliation with the archaeal TACK superphylum. Recent studies have shown that genomic exploration of yet-uncultivated archaea, the so-called archaeal ‘dark matter’, is able to provide unprecedented insights into the process of eukaryogenesis. Here, we provide an overview of state-of-the-art cultivation-independent approaches, and demonstrate how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a
Korarchaeum
-related lineage. The maturation of cultivation-independent genomics approaches, as well as future developments in next-generation sequencing technologies, will revolutionize our current view of microbial evolution and diversity, and provide profound new insights into the early evolution of life, including the enigmatic origin of the eukaryotic cell.
Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?
Authors: Koonin Eugene V.
Published: September 2015

The origin of eukaryotes is a fundamental, forbidding evolutionary puzzle. Comparative genomic analysis clearly shows that the last eukaryotic common ancestor (LECA) possessed most of the signature complex features of modern eukaryotic cells, in particular the mitochondria, the endomembrane system including the nucleus, an advanced cytoskeleton and the ubiquitin network. Numerous duplications of ancestral genes, e.g. DNA polymerases, RNA polymerases and proteasome subunits, also can be traced back to the LECA. Thus, the LECA was not a primitive organism and its emergence must have resulted from extensive evolution towards cellular complexity. However, the scenario of eukaryogenesis, and in particular the relationship between endosymbiosis and the origin of eukaryotes, is far from being clear. Four recent developments provide new clues to the likely routes of eukaryogenesis. First, evolutionary reconstructions suggest complex ancestors for most of the major groups of archaea, with the subsequent evolution dominated by gene loss. Second, homologues of signature eukaryotic proteins, such as actin and tubulin that form the core of the cytoskeleton or the ubiquitin system, have been detected in diverse archaea. The discovery of this ‘dispersed eukaryome’ implies that the archaeal ancestor of eukaryotes was a complex cell that might have been capable of a primitive form of phagocytosis and thus conducive to endosymbiont capture. Third, phylogenomic analyses converge on the origin of most eukaryotic genes of archaeal descent from within the archaeal evolutionary tree, specifically, the TACK superphylum. Fourth, evidence has been presented that the origin of the major archaeal phyla involved massive acquisition of bacterial genes. Taken together, these findings make the symbiogenetic scenario for the origin of eukaryotes considerably more plausible and the origin of the organizational complexity of eukaryotic cells more readily explainable than they appeared until recently.
Genome-scale phylogenetic analysis finds extensive gene transfer among fungi
Authors: Szöllősi Gergely J. , Davín Adrián Arellano , Tannier Eric , Daubin Vincent , Boussau Bastien
Published: September 2015

Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis, we compare the dynamics of genome evolution in two groups of organisms: cyanobacteria and fungi. Ancestral genomes are inferred in both clades using two types of methods: first,Count, a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes present in a genome; second, ALE, a more recent gene tree-aware method that reconciles gene trees with a species tree using a model of gene duplication, loss and transfer. We compare their merits and their ability to quantify the role of transfers, and assess the impact of taxonomic sampling on their inferences. We present what we believe is compelling evidence that gene transfer plays a significant role in the evolution of fungi.
Probabilistic models of eukaryotic evolution: time for integration
Authors: Lartillot Nicolas
Published: September 2015

In spite of substantial work and recent progress, a global and fully resolved picture of the macroevolutionary history of eukaryotes is still under construction. This concerns not only the phylogenetic relations among major groups, but also the general characteristics of the underlying macroevolutionary processes, including the patterns of gene family evolution associated with endosymbioses, as well as their impact on the sequence evolutionary process. All these questions raise formidable methodological challenges, calling for a more powerful statistical paradigm. In this direction, model-based probabilistic approaches have played an increasingly important role. In particular, improved models of sequence evolution accounting for heterogeneities across sites and across lineages have led to significant, although insufficient, improvement in phylogenetic accuracy. More recently, one main trend has been to move away from simple parametric models and stepwise approaches, towards integrative models explicitly considering the intricate interplay between multiple levels of macroevolutionary processes. Such integrative models are in their infancy, and their application to the phylogeny of eukaryotes still requires substantial improvement of the underlying models, as well as additional computational developments.
Morphological and phylogenetic studies on three members of the genus Pseudochilodonopsis (Ciliophora, Cyrtophoria) isolated from brackish waters in China, including a novel species, Pseudochilodonopsis quadrivacuolata sp. nov.
Authors: Qu Zhishuai , Pan Hongbo , Al-Rasheid Khaled A. S. , Hu Xiaozhong , Gao Shan
Published: September 2015

Three cyrtophorian ciliates isolated from brackish biotopes in China, Pseudochilodonopsis quadrivacuolata sp. nov., Pseudochilodonopsis fluviatilis
Foissner, 1988 and Pseudochilodonopsis mutabilis
Foissner, 1981, were investigated using living observation and protargol-staining methods. P. quadrivacuolata sp. nov. can be characterized as follows: cell size 50–70 × 30–40 μm in vivo; body oval with posterior end rounded; four tetragonally positioned contractile vacuoles; 12–15 nematodesmal rods; five right and six left somatic kineties; terminal fragment positioned apically on dorsal side, consisting of 11–14 basal bodies; four or five fragments in preoral kinety. P. fluviatilis and P. mutabilis were generally consistent with previous descriptions. In addition, a brief revision and a key to Pseudochilodonopsis are presented. The small-subunit (SSU) rRNA gene was also sequenced to support the identification of these species. Phylogenetic analyses based on molecular data indicate that the genera Pseudochilodonopsis and Chilodonella are closely related and both are well outlined; that is, all known congeners for which SSU rRNA gene sequence data are available group together, forming the core part of the family Chilodonellidae.
Taeseokella kangwonensis gen. nov., sp. nov., isolated from a freshwater reservoir
Authors: Joung Yochan , Hong Sunhee , Kim Haneul , Kang Heeyoung , Farrance Christine E. , Joh Kiseong
Published: September 2015

A Gram-stain-negative, non-motile and yellow-pigmented bacterium, designated HME8275T, was isolated from freshwater in Korea. The major fatty acids of strain HME8275T were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and iso-C15 : 0. The only respiratory quinone was MK-7. Polar lipid analysis showed phosphatidylethanolamine, two unidentified aminolipids, two unidentified aminophospholipids and three unidentified polar lipids. The DNA G+C content of strain HME8275T was 37.6 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME8275T formed a lineage within the family Cytophagaceae and was related to Lacihabitans soyangensis HME6675T (92.6 % 16S rRNA gene sequence similarity), Leadbetterella byssophila 4M15T (89.0 %), Fluviimonas pallidilutea TQQ6T (89.7 %) and Emticicia oligotrophica GPTSA100-15T (89.8 %). On the basis of the evidence presented in this study, strain HME8275T represents a novel species of a new genus in the family Cytophagaceae, for which the name Taeseokella kangwonensis, gen. nov., sp. nov. is proposed. The type strain of the type species is HME8275T ( = KACC 16933T = CECT 8198T).
A common polymorphism in the 5′ UTR of ERCC5 creates an upstream ORF that confers resistance to platinum-based chemotherapy
Authors: Somers Joanna , Wilson Lindsay A. , Kilday John-Paul , Horvilleur Emilie , Cannell Ian G. , Pöyry Tuija A.A. , Cobbold Laura C. , Kondrashov Alexander , Knight John R.P. , Puget Stéphanie , Grill Jacques , Grundy Richard G. , Bushell Martin , Willis Anne E.
Published: September 2015

We show that a common polymorphic variant in the ERCC5 5′ untranslated region (UTR) generates an upstream ORF (uORF) that affects both the background expression of this protein and its ability to be synthesized following exposure to agents that cause bulky adduct DNA damage. Individuals that harbor uORF1 have a marked resistance to platinum-based agents, illustrated by the significantly reduced progression-free survival of pediatric ependymoma patients treated with such compounds. Importantly, inhibition of DNA-PKcs restores sensitivity to platinum-based compounds by preventing uORF1-dependent ERCC5 expression. Our data support a model in which a heritable 5′ noncoding mRNA element influences individuals’ responses to platinum-based chemotherapy.
MERIT40 cooperates with BRCA2 to resolve DNA interstrand cross-links
Authors: Jiang Qinqin , Paramasivam Manikandan , Aressy Bernadette , Wu Junmin , Bellani Marina , Tong Wei , Seidman Michael M. , Greenberg Roger A.
Published: September 2015

MERIT40 is an essential component of the RAP80 ubiquitin recognition complex that targets BRCA1 to DNA damage sites. Although this complex is required for BRCA1 foci formation, its physiologic role in DNA repair has remained enigmatic, as has its relationship to canonical DNA repair mechanisms. Surprisingly, we found that Merit40−/− mice displayed marked hypersensitivity to DNA interstrand cross-links (ICLs) but not whole-body irradiation. MERIT40 was rapidly recruited to ICL lesions prior to FANCD2, and Merit40-null cells exhibited delayed ICL unhooking coupled with reduced end resection and homologous recombination at ICL damage. Interestingly, Merit40 mutation exacerbated ICL-induced chromosome instability in the context of concomitant Brca2 deficiency but not in conjunction with Fancd2 mutation. These findings implicate MERIT40 in the earliest stages of ICL repair and define specific functional interactions between RAP80 complex-dependent ubiquitin recognition and the Fanconi anemia (FA)–BRCA ICL repair network.
Fgfr1 regulates development through the combinatorial use of signaling proteins
Authors: Brewer J. Richard , Molotkov Andrei , Mazot Pierre , Hoch Renée V. , Soriano Philippe
Published: September 2015

Fibroblast growth factor (Fgf) signaling governs multiple processes important in development and disease. Many lines of evidence have implicated Erk1/2 signaling induced through Frs2 as the predominant effector pathway downstream from Fgf receptors (Fgfrs), but these receptors can also signal through other mechanisms. To explore the functional significance of the full range of signaling downstream from Fgfrs in mice, we engineered an allelic series of knock-in point mutations designed to disrupt Fgfr1 signaling functions individually and in combination. Analysis of each mutant indicates that Frs2 binding to Fgfr1 has the most pleiotropic functions in development but also that the receptor uses multiple proteins additively in vivo. In addition to Frs2, Crk proteins and Plcγ also contribute to Erk1/2 activation, affecting axis elongation and craniofacial and limb development and providing a biochemical mechanism for additive signaling requirements. Disruption of all known signaling functions diminished Erk1/2 and Plcγ activation but did not recapitulate the peri-implantationFgfr1-null phenotype. This suggests that Erk1/2-independent signaling pathways are functionally important for Fgf signaling in vivo.
Leadership and corporate responsibility: a review of the empirical evidence
Authors: Mazutis Daina , Zintel Christopher
Published: September 2015

Purpose

– The purpose of this paper is to consolidate the state of the empirical research to date on the relationship between leadership and corporate responsibility.

Design/methodology/approach

– The authors conduct a comprehensive, systematic and narrative review of all published quantitative studies that have examined the link between leadership and corporate responsibility broadly defined, and the authors put forward an integrative model encapsulating current knowledge in this domain.

Findings

– The authors not only identify validated direct, indirect and moderating effects of leadership on corporate responsibility but also point to gaps in the literature that imply important directions for further research.

Originality/value

– The authors aim to make the following contributions to both the leadership and the corporate responsibility literatures. First, the systematic and narrative review in and of itself provides an important consolidation of existing knowledge in both domains. Second, the authors confirm that the preponderance of empirical evidence supports that leadership matters to corporate responsibility efforts in organizations. Lastly, the review provides a comprehensive model of the relationship between leadership and corporate responsibility that has important implications for future research and theory building in this field.
Institutional shareholder engagement with Japanese firms
Authors: Clark Gordon L. , McGill Sarah , Saito Yukie , Viehs Michael
Published: September 2015

Purpose

– The purpose of this paper is to explore how shareholder engagement on environmental, social, and governance (ESG) issues is informally exercised by a large global institutional investor with locally embedded, geographically remote firms. This field is still a new area of research due to a scarcity of data, and because ordinarily, private engagement activities are conducted confidentially. Therefore, the paper aims to fill this gap in the literature by studying the private corporate engagement activities of a large UK-based institutional investor on ESG issues with Japanese investee firms in order to achieve a greater understanding of the under-researched area of corporate social responsibility.

Design/methodology/approach

– The authors employ a multi-method approach to analyse engagement activities by the institutional investor. The authors have obtained a unique data set of the institutional investor’s engagement activities. The institutional investor is UK-based, has a long history of active engagement, and is considered one of the oldest and largest specialists in responsible investment. Further, the authors have conducted several in-depth interviews with a UK-based ESG service provider as well as one of the largest Japanese trust companies.

Findings

– First, it is found that main target firms of engagement activities are large firms with global operations, and that corporate governance issues are the most important engagement topic in Japan. Second, in trying to effectively exercise voice across societies, engagement activities are conducted with geographically remote target firms on various ESG agendas in a self-enforcing, face-to-face, and sometimes collective manner. Finally, this study argues for the gap between the asset manager’s motivation to engage and local target firms’ readiness to respond due to corporate organisational and language issues.

Originality/value

– The authors contribute to social responsibility literature by focusing on the role of global investors in Japan to diffuse global standards. This area has been largely neglected in this stream of literature, despite the increasing presence of foreign investors in Japan. This is one of the first attempts to analyse a global investor’s engagement strategies with one specific country outside of the USA and Europe. Further, within the literature on shareholder engagement, this is the first paper that focuses on the means of engagement activities and the responses by target firms.