bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preparation of Low‐Input and Ligation‐Free ChIP‐seq Libraries Using Template‐Switching Technology
Authors: Bolduc Nathalie , Lehman Alisa P. , Farmer Andrew 
Published: October 2016

AbstractChromatin immunoprecipitation (ChIP) followed by high‐throughput sequencing (ChIP‐seq) has become the gold standard for mapping of transcription factors and histone modifications throughout the genome. However, for ChIP experiments involving few cells or targeting low‐abundance transcription factors, the small amount of DNA recovered makes ligation of adapters very challenging. In this unit, we describe a ChIP‐seq workflow that can be applied to small cell numbers, including a robust single‐tube and ligation‐free method for preparation of sequencing libraries from sub‐nanogram amounts of ChIP DNA. An example ChIP protocol is first presented, resulting in selective enrichment of DNA‐binding proteins and cross‐linked DNA fragments immobilized on beads via an antibody bridge. This is followed by a protocol for fast and easy cross‐linking reversal and DNA recovery. Finally, we describe a fast, ligation‐free library preparation protocol, featuring DNA SMART technology, resulting in samples ready for Illumina sequencing. © 2016 by John Wiley & Sons, Inc.
A Novel Approach to Treating CFS and Co‐morbid Health Anxiety: A Case Study
Authors: Daniels Jo , Loades Maria E. 
Published: October 2016

ObjectivesChronic Fatigue Syndrome (CFS) is a debilitating condition that affects 0.2–0.4% of the population. First‐line treatments are Cognitive Behaviour Therapy or graded exercise therapy; however, these treatments yield only moderate effect sizes. Emerging research suggests that anxiety about health may be common in CFS. Health anxiety treatment models demonstrate good therapeutic outcomes; however, these models have yet to be applied to CFS. This paper describes the application of a novel cognitive behavioural approach to the treatment of both physical and anxiety related symptoms in a patient with CFS and, furthermore, presents a conceptual hypothesis regarding the mutually maintaining relationship between these two co‐occurring conditions.DesignA single‐case design was used, with pre‐data, post‐data and follow‐up data. The cognitive behavioural model of health anxiety was adapted and delivered as an eight‐session intervention. The intervention was driven by an individualized formulation developed collaboratively with the patient.ResultsThe application of this approach generated reliable and clinically significant reductions in physical and psychological symptoms, which were maintained at 12‐month follow‐up. The participant no longer fulfilled the criteria for CFS or health anxiety following eight treatment sessions. The treatment approach was found to be agreeable to the patient. All treatment hypotheses were supported.ConclusionsAn adapted cognitive behavioural approach to treating CFS and health anxiety yields positive results and shows promise for application to the broader CFS population. Copyright © 2016 John Wiley & Sons, Ltd.Key Practitioner Messages

Chronic Fatigue Syndrome (CFS) is a debilitating condition that is difficult to treat successfully; first‐line recommended treatments achieve only moderate effect sizes.
Anxiety, particularly about health, is reported to be common in CFS. However, anxiety is not specifically targeted within treatment and may negatively influence outcome due to the potentially mutually maintaining nature of these complex conditions.
The present study demonstrates that an integrated treatment approach designed to encompass physical and psychological symptoms yields reliable and clinically significant outcomes in 50% of time recommend for first line treatments.
Results reflected non‐case level status for both CFS and health anxiety at end of treatment, in addition to reductions across all clinical measures.
This study demonstrates the fundamental importance of an individualized, rather than generic, treatment approach to complex cases; the ‘meaning’ of experience is a central tenet within a cognitive approach that should be reflected in treatment.
Bridging the Gap between Aetiological and Maintaining Factors in Social Anxiety Disorder: The Impact of Socially Traumatic Experiences on Beliefs, Imagery and Symptomatology
Authors: Norton Alice R. , Abbott Maree J. 
Published: October 2016

BackgroundA number of key environmental factors during childhood have been implicated in the aetiology of social anxiety disorder (SAD), including aversive social experiences, traumatic life events and parent–child interaction. However, understanding the nature, interactions and relative contributions of these factors remains unclear. Furthermore, the relation of aversive social experiences to the development of key maintaining factors in SAD requires elucidation.AimsThe current study aimed to extend previous research regarding the aetiology of SAD by investigating the relationship between key environmental factors in childhood, negative beliefs and self‐imagery, and the development of SAD.MethodSocial anxiety disorder individuals (n = 40, 87.5% female, Mage = 20.25 years) completed self‐report measures of social anxiety symptomatology, traumatic experiences and parenting style. In addition, participants were administered interviews assessing various domains of childhood trauma, as well as negative self‐imagery and associated socially traumatic memories.ResultsParticipants reported a high frequency of early traumatic experiences across all domains (physical, emotional, sexual, social and non‐relational), as well as a high degree of parental overcontrol. However, social anxiety symptomatology was most strongly correlated with socially traumatic experiences, and mediation analyses suggest that appraisal of aversive social/peer experiences accounts for the relationship of SAD symptomatology with negative self‐beliefs and imagery.ConclusionsThese outcomes suggest that social trauma may be a key proximal cause of SAD development, leading to the development of negative beliefs and imagery that subsequently maintain the disorder. These findings have implications for understanding SAD aetiology, and improving treatment outcomes for the disorder. Copyright © 2016 John Wiley & Sons, Ltd.Key Practitioner Messages

Negative social experiences have been implicated in the development of social anxiety disorder (SAD), but the role of this predisposing factor remains unclear.
Compared with other risk factors for SAD, social anxiety symptomatology was most strongly correlated with socially traumatic experiences.
Mediation analyses suggested that appraisal of aversive social experiences accounted for the relationship of SAD symptomatology with negative self-beliefs and imagery.
These outcomes suggest that SAD individuals would benefit from interventions targeted at processing socially traumatic memories (e.g., imagery rescripting).
Four Pathways to Anorexia Nervosa: Patients' Perspective on the Emergence of AN
Authors: Gulliksen Kjersti S. , Nordbø Ragnfrid H. S. , Espeset Ester M. S. , Skårderud Finn , Holte Arne 
Published: October 2016

IntroductionStudies show that patients' perception of their illness has a direct influence both on their utilization of health services and their adherence to treatment plans. This may be particularly relevant to the treatment of Anorexia Nervosa (AN). Previous studies on AN have typically explored single psycho‐social factors that patients with AN relate to the emergence of their illness. There is a need for more coherent systematic descriptions of the complexity of the patients' narratives about how their illness emerged. In this study, we sought to identify common components in the participants' narratives. By identifying different combinations of these components in the narratives, we sought to describe differences in patients' perceived pathways to AN.MethodsParticipants were 36 women aged 18–51 years who had been treated for AN within the past 2 years at five clinical institutions in Norway. Semi‐open qualitative interviews were conducted, tape‐recorded, transcribed and analysed using grounded theory techniques.ResultsWe identified the following four distinct perceived pathways into AN: ‘The Avoidant’, ‘The Achiever’, ‘The Transformer’ and ‘The Punisher’. The pathways could be regarded as four different projects for mastering life's challenges.DiscussionOur results suggest that there seem to be at least four pathways into AN. This indicates that a common array of symptoms might cover very different psychological dynamics. These might need to be treated therapeutically in different ways and should probably be taken into account during the refinement of diagnostic tools. Copyright © 2016 John Wiley & Sons, Ltd.Key Practitioner Message

Although patients with AN might present similar symptoms, patients' perspectives on the emergence of their problems indicate that a common array of symptoms cover a variety of subjective psychological dynamics.
From the experienced patient's stance, there are at least four distinct pathways to the emergence of AN.
Attempts to master the challenges of life were found to be a common denominator in the emergence of AN.
Recognition and integration of the patient's understanding of her or his problems should be given high priority in treatment of AN.
PUF‐based solutions for secure communications in Advanced Metering Infrastructure (AMI)
Authors: Delavar Mahshid , Mirzakuchaki Sattar , Ameri Mohammad Hassan , Mohajeri Javad 
Published: October 2016

AbstractAdvanced metering infrastructure (AMI) provides 2‐way communications between the utility and the smart meters. Developing authenticated key exchange (AKE) and broadcast authentication (BA) protocols is essential to provide secure communications in AMI. The security of all existing cryptographic protocols is based on the assumption that secret information is stored in the nonvolatile memories. In the AMI, the attackers can obtain some or all of the stored secret information from memories by a great variety of inexpensive and fast side‐channel attacks. Thus, all existing AKE and BA protocols are no longer secure. In this paper, we investigate how to develop secure AKE and BA protocols in the presence of memory attacks. As a solution, we propose to embed a physical unclonable function (PUF) in each party, which generates the secret values as required without the need to store them. By combining PUFs and 2 well‐known and secure protocols, we propose PUF‐based AKE and BA protocols. We show that our proposed protocols are memory leakage resilient. In addition, we prove their security in the standard model. Performance analysis of both protocols shows their efficiency for AMI applications. The proposed protocols can be easily implemented.
Inheritance genetics of the trait vector competence in Frankliniella occidentalis (Western flower thrips) in the transmission of Tomato spotted wilt virus
Authors: Ogada Pamella Akoth , Debener Thomas , Poehling Hans‐Michael 
Published: October 2016

AbstractThe complexity of tospovirus–vector–host plant interaction is linked to a range of factors influencing vector's efficacy in virus transmission, leading to high variability in the transmission efficiency within vector populations. Main shortcomings of most studies are the missing information on the intrinsic potential of individual insects to serve as efficient vectors, both at phenotypic and at genotypic levels. Moreover, detailed analysis of vector competence heredity and monitoring the splitting of both genotypes and phenotypes in filial generations has not been reported. In this study, using the model system Frankliniella occidentalis and Tomato spotted wilt virus, we evaluated the inheritance and stability of the trait vector competence in a population through basic crossings of individually characterized partners, as well as virgin reproduction. We hypothesized that the trait is heritable in F. occidentalis and is controlled by a recessive allele. From the results, 83% and 94% of competent and noncompetent males respectively, inherited their status from their mothers. The trait was only expressed when females were homozygous for the corresponding allele. Furthermore, the allele frequencies were different between males and females, and the competent allele had the highest frequency in the population. These suggest that the trait vector competence is inherited in single recessive gene in F. occidentalis, for which the phenotype is determined by the haplodiploid mechanism. These findings are fundamental for our understanding of the temporal and spatial variability within vector populations with respect to the trait vector competence and at the same time offer an essential basis for further molecular studies.
A loss of heterozygosity, a loss in competition? The effects of inbreeding, pre‐ and postnatal conditions on nestling development
Authors: de Boer Raïssa A. , Eens Marcel , Müller Wendt 
Published: October 2016

AbstractThe early developmental trajectory is affected by genetic and environmental factors that co‐depend and interact often in a complex way. In order to distinguish their respective roles, we used canaries (Serinus canaria) of different genetic backgrounds (inbred and outbred birds). An artificial size hierarchy was created to provoke within‐nest competition, manipulating postnatal conditions. To this end, inbred birds were weight‐matched with outbred birds into duos, and each nest contained one duo of size‐advantaged, and one duo of size‐disadvantaged inbred and outbred nestlings. Prenatal (maternal) effects were taken into account also, enabling us to study the separate as well as the interactive effects of inbreeding, pre‐ and postnatal conditions on nestling development. We find that postnatal conditions were the most important determinant of early growth, with size‐advantaged nestlings growing faster and obtaining larger size/body mass at fledging in comparison with size‐disadvantaged nestlings. Prenatal conditions were important too, with birds that hatched from eggs that were laid late in the laying order obtaining a larger size at fledging than those hatched from early laid eggs. Inbreeding inhibited growth, but surprisingly this did not depend on (dis)advantageous pre‐ or postnatal conditions. Our findings imply that inbred individuals lose when they are in direct competition with same‐sized outbred individuals regardless of the rearing conditions, and we thus propose that reduced competitiveness is one of the driving forces of inbreeding depression.
Environmental selection is a main driver of divergence in house sparrows (Passer domesticus) in Romania and Bulgaria
Authors: Geue Julia C. , Vágási Csongor I. , Schweizer Mona , Pap Péter L. , Thomassen Henri A. 
Published: October 2016

AbstractBoth neutral and adaptive evolutionary processes can cause population divergence, but their relative contributions remain unclear. We investigated the roles of these processes in population divergence in house sparrows (Passer domesticus) from Romania and Bulgaria, regions characterized by high landscape heterogeneity compared to Western Europe. We asked whether morphological divergence, complemented with genetic data in this human commensal species, was best explained by environmental variation, geographic distance, or landscape resistance—the effort it takes for an individual to disperse from one location to the other—caused by either natural or anthropogenic barriers. Using generalized dissimilarity modeling, a matrix regression technique that fits biotic beta diversity to both environmental predictors and geographic distance, we found that a small set of climate and vegetation variables explained up to ~30% of the observed divergence, whereas geographic and resistance distances played much lesser roles. Our results are consistent with signals of selection on morphological traits and of isolation by adaptation in genetic markers, suggesting that selection by natural environmental conditions shapes population divergence in house sparrows. Our study thus contributes to a growing body of evidence that adaptive evolution may be a major driver of diversification.
Divergent immune priming responses across flour beetle life stages and populations
Authors: Khan Imroze , Prakash Arun , Agashe Deepa 
Published: October 2016

AbstractGrowing evidence shows that low doses of pathogens may prime the immune response in many insects, conferring subsequent protection against infection in the same developmental stage (within‐life stage priming), across life stages (ontogenic priming), or to offspring (transgenerational priming). Recent work also suggests that immune priming is a costly response. Thus, depending on host and pathogen ecology and evolutionary history, tradeoffs with other fitness components may constrain the evolution of priming. However, the relative impacts of priming at different life stages and across natural populations remain unknown. We quantified immune priming responses of 10 natural populations of the red flour beetle Tribolium castaneum, primed and infected with the natural insect pathogen Bacillus thuringiensis. We found that priming responses were highly variable both across life stages and populations, ranging from no detectable response to a 13‐fold survival benefit. Comparing across stages, we found that ontogenic immune priming at the larval stage conferred maximum protection against infection. Finally, we found that various forms of priming showed sex‐specific associations that may represent tradeoffs or shared mechanisms. These results indicate the importance of sex‐, life stage‐, and population‐specific selective pressures that can cause substantial divergence in priming responses even within a species. Our work highlights the necessity of further work to understand the mechanistic basis of this variability.
The mating consequences of rewarding vs. deceptive pollination systems: Is there a quantity–quality trade‐off?
Authors: Hobbhahn Nina , Johnson Steven D. , Harder Lawrence D. 
Published: October 2016

AbstractPlant mating commonly involves quality–quantity trade‐offs. Such a trade‐off features explicitly in the cross‐promotion hypothesis for the evolution of pollination by deceit. According to this hypothesis, rewardlessness enhances mating quality by altering pollinator behavior in ways that reduce self‐pollination and increase outcrossing, thus compensating for the reduced pollen dispersal and seed production resulting from lack of reinforcement of pollinator visitation behavior. The high prevalence of rewardlessness in orchids suggests that deceit pollination conveys benefits that outweigh the fecundity advantages of reward production. We test the cross‐promotion hypothesis in Disa, an African orchid genus in which nectar rewards have evolved repeatedly from rewardless ancestors. To address this hypothesis directly, we quantified pollinator behavior and the associated dispersal of stained pollen for four nectar‐producing (N+) and 10 nectarless (N−) species. We also assessed more extensive, if less direct, evidence from a survey of lifetime pollination outcomes for 15 N+ and 32 N− species. Pollinators visited N+ species more frequently and visited 1.5 times more flowers per inflorescence than in N− species. In contrast, pollinators skipped more conspecific plants between visits to donor and recipient plants when visiting N− species than when visiting N+ species. Over floral lifetimes, both N− and N+ species exhibited similar overall pollen‐transfer efficiency (8.2%) and did not differ in the overall fractions of pollen involved in self‐pollination (26% of all pollen deposited), geitonogamy (82% of all self‐pollination), or export to other conspecific plants (74%). N+ species set more fruit per flower (68.8% vs. 48.8%), but equivalent fractions of ovules per fruit were fertilized and subsequently developed into seeds in N− and N+ species. These findings provide only limited evidence that deceit pollination enhances mating quality (nectar production causes more local mating in N+ species than in N− species). Contrary to the hypothesis, deceit does not generally affect pollinator‐mediated self‐pollination. The repeated evolution of nectar production from rewardless ancestors in Disa likely occurred under severe visit limitation, favoring nectar‐producing mutants with higher reproductive output. Given that we did not find any mating quality advantage for rewardlessness in Disa, its persistence in some lineages remains an evolutionary enigma.
Mapping forest vegetation for the western United States using modified random forests imputation ofFIAforest plots
Authors: Riley Karin L. , Grenfell Isaac C. , Finney Mark A. 
Published: October 2016

AbstractMaps of the number, size, and species of trees in forests across the western United States are desirable for many applications such as estimating terrestrial carbon resources, predicting tree mortality following wildfires, and for forest inventory. However, detailed mapping of trees for large areas is not feasible with current technologies, but statistical methods for matching the forest plot data with biophysical characteristics of the landscape offer a practical means to populate landscapes with a limited set of forest plot inventory data. We used a modified random forests approach with Landscape Fire and Resource Management Planning Tools (LANDFIRE) vegetation and biophysical predictors to impute plot data collected by theUSForest Service's Forest Inventory Analysis (FIA) to the landscape at 30‐m grid resolution. This method imputes the plot with the best statistical match, according to a “forest” of decision trees, to each pixel of gridded landscape data. In this work, we used theLANDFIREdata set for gridded input because it is publicly available, offers seamless coverage of variables needed for fire models, and is consistent with other data sets, including burn probabilities and flame length probabilities generated for the continental United States. The main output of this project is a map of imputed plot identifiers at 30 × 30 m spatial resolution for the western United States that can be linked to theFIAdatabases to produce tree‐level maps or to map other plot attributes. In addition, we used the imputed inventory data to generate maps of forest cover, forest height, and vegetation group at 30 × 30 m resolution for all forested pixels in the western United States, as a means of assessing the accuracy of our methodology. The results showed good correspondence between the targetLANDFIREdata and the imputed plot data, with an overall within‐class agreement of 79% for forest cover, 96% for forest height, and 92% for vegetation group.