bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary dynamics of selfish DNA explains the abundance distribution of genomic subsequences
Authors: Sheinman Michael , Ramisch Anna , Massip Florian , Arndt Peter F. 
Published: August 2016

AbstractSince the sequencing of large genomes, many statistical features of their sequences have been found. One intriguing feature is that certain subsequences are much more abundant than others. In fact, abundances of subsequences of a given length are distributed with a scale-free power-law tail, resembling properties of human texts, such as Zipf’s law. Despite recent efforts, the understanding of this phenomenon is still lacking. Here we find that selfish DNA elements, such as those belonging to the Alu family of repeats, dominate the power-law tail. Interestingly, for the Alu elements the power-law exponent increases with the length of the considered subsequences. Motivated by these observations, we develop a model of selfish DNA expansion. The predictions of this model qualitatively and quantitatively agree with the empirical observations. This allows us to estimate parameters for the process of selfish DNA spreading in a genome during its evolution. The obtained results shed light on how evolution of selfish DNA elements shapes non-trivial statistical properties of genomes.
Sound tuning of amygdala plasticity in auditory fear conditioning
Authors: Park Sungmo , Lee Junuk , Park Kyungjoon , Kim Jeongyeon , Song Beomjong , Hong Ingie , Kim Jieun , Lee Sukwon , Choi Sukwoo 
Published: August 2016

AbstractVarious auditory tones have been used as conditioned stimuli (CS) for fear conditioning, but researchers have largely neglected the effect that different types of auditory tones may have on fear memory processing. Here, we report that at lateral amygdala (LA) synapses (a storage site for fear memory), conditioning with different types of auditory CSs (2.8 kHz tone, white noise, FM tone) recruits distinct forms of long-term potentiation (LTP) and inserts calcium permeable AMPA receptor (CP-AMPAR) for variable periods. White noise or FM tone conditioning produced brief insertion (<6 hr after conditioning) of CP-AMPARs, whereas 2.8 kHz tone conditioning induced more persistent insertion (≥6 hr). Consistently, conditioned fear to 2.8 kHz tone but not to white noise or FM tones was erased by reconsolidation-update (which depends on the insertion of CP-AMPARs at LA synapses) when it was performed 6 hr after conditioning. Our data suggest that conditioning with different auditory CSs recruits distinct forms of LA synaptic plasticity, resulting in more malleable fear memory to some tones than to others.
Polarization-dependent fluorescence correlation spectroscopy for studying structural properties of proteins in living cell
Authors: Oura Makoto , Yamamoto Johtaro , Ishikawa Hideto , Mikuni Shintaro , Fukushima Ryousuke , Kinjo Masataka 
Published: August 2016

AbstractRotational diffusion measurement is predicted as an important method in cell biology because the rotational properties directly reflect molecular interactions and environment in the cell. To prove this concept, polarization-dependent fluorescence correlation spectroscopy (pol-FCS) measurements of purified fluorescent proteins were conducted in viscous solution. With the comparison between the translational and rotational diffusion coefficients obtained from pol-FCS measurements, the hydrodynamic radius of an enhanced green fluorescent protein (EGFP) was estimated as a control measurement. The orientation of oligomer EGFP in living cells was also estimated by pol-FCS and compared with Monte Carlo simulations. The results of this pol-FCS experiment indicate that this method allows an estimation of the molecular orientation using the characteristics of rotational diffusion. Further, it can be applied to analyze the degree of molecular orientation and multimerization or detection of tiny aggregation of aggregate-prone proteins.
Adaptive busbar differential relaying scheme during saturation period of current transformers based on alienation concept
Authors: Allah Ragab Abd 
Published: August 2016

This study presents an advanced technique provided with adaptive differential relay characteristics for avoiding current transformer (CT) saturation effects. The proposed technique uses the alienation and differential protection principles to make adaptive logic; if no CT saturation is detected, the differential principle alone is capable of tripping the busbar. If CT saturation is detected, both the alienation and differential principles must pickup in order to trip. The alienation coefficient is useful in CT saturation detection, evaluation of CT saturation degree and adapting the differential relay characteristics during saturation period of CTs to avoid false operation in the event of external faults. The differential current and alienation coefficient are calculated from two terminal currents of the busbar. The proposed protective scheme has several attractive features, including the simplicity of on‐line implementation, not affected by the remanent flux in the CT core, and it is independent of the CT parameters/characteristics and secondary burden. A real 19.57 kV busbar is simulated using Alternate Transients Program/Electro‐Magnetic Transient Program and MATLAB packages to examine the suggested scheme under different types of faults. Under normal operating conditions and external faults, the scheme remains stable and it operates only for the case of internal faults. Moreover, it is unaffected by CT saturation.
Structural basis of HIV inhibition by translocation-defective RT inhibitor 4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA)
Authors: Salie Zhe Li , Kirby Karen A. , Michailidis Eleftherios , Marchand Bruno , Singh Kamalendra , Rohan Lisa C. , Kodama Eiichi N. , Mitsuya Hiroaki , Parniak Michael A. , Sarafianos Stefan G. 
Published: August 2016

Significance
4′-Ethynyl-2-fluoro-2′-deoxyadenosine (EFdA), a potent antiviral with an unusually long half-life, is currently in phase I clinical trials. It inhibits reverse transcriptase (RT) through a mechanism of action different from all approved anti-HIV drugs: After incorporation in the nascent DNA chain, it suppresses the rate of viral replication by diminishing RT translocation on the nucleic acid substrate. Here, we present four crystal structures of various inhibition intermediates. The structures provide insight into the structural basis of the unusual mechanism of inhibition and the exceptional potency of this promising antiviral.
Effect of light exposure on linalool biosynthesis and accumulation in grape berries
Authors: Sasaki Kanako , Takase Hideki , Matsuyama Shuhei , Kobayashi Hironori , Matsuo Hironori , Ikoma Gen , Takata Ryoji 
Published: August 2016

AbstractLinalool is an important compound that contributes to the floral aroma in wines. This study showed the effect of light exposure on linalool accumulation in berries. The grape bunches were covered with films that block the full light spectrum (Shade) and the UV spectrum (UV-block), and a transparent film (Control). The linalool content was significantly higher in juice from Control-covered berries than in juice from Shade- and UV-block-covered berries, and the expression levels of the representative genes in linalool biosynthesis in Shade- and UV-block-covered berries were markedly lower than in Control-covered berries. These findings suggest that exposing berries to light is essential for linalool biosynthesis. To reflect sunlight onto grape clusters, reflective sheets were placed on the ground of a vineyard. The linalool content in berries exposed to sunlight reflected from the reflective sheets was higher than those in the control.
Smoking, physical inactivity and obesity as predictors of healthy and disease-free life expectancy between ages 50 and 75: a multicohort study
Authors: Stenholm Sari , Head Jenny , Kivimäki Mika , Kawachi Ichiro , Aalto Ville , Zins Marie , Goldberg Marcel , Zaninotto Paola , Magnuson Hanson Linda , Westerlund Hugo , Vahtera Jussi 
Published: August 2016

Abstract
Background: Smoking, physical inactivity and obesity are modifiable risk factors for morbidity and mortality. The aim of this study was to examine the extent to which the co-occurrence of these behaviour-related risk factors predict healthy life expectancy and chronic disease-free life expectancy in four European cohort studies.
Methods: Data were drawn from repeated waves of four cohort studies in England, Finland, France and Sweden. Smoking status, physical inactivity and obesity (body mass index ≥30 kg/m2) were examined separately and in combination. Health expectancy was estimated by using two health indicators: suboptimal self-rated health and having a chronic disease (cardiovascular disease, cancer, respiratory disease and diabetes). Multistate life table models were used to estimate sex-specific healthy life expectancy and chronic disease-free life expectancy from ages 50 to 75 years.
Results: Compared with men and women with at least two behaviour-related risk factors, those with no behaviour-related risk factors could expect to live on average8 years longer in good health and 6 years longer free of chronic diseases between ages 50 and 75. Having any single risk factor was also associated with reduction in healthy years. No consistent differences between cohorts were observed.
Conclusions: Data from four European countries show that persons with individual and co-occurring behaviour-related risk factors have shorter healthy life expectancy and shorter chronic disease-free life expectancy. Population level reductions in smoking, physical inactivity and obesity could increase life-years lived in good health.
Local expectation violations result in global activity gain in primary visual cortex
Authors: Kok Peter , van Lieshout Lieke L.F. , de Lange Floris P. 
Published: August 2016

AbstractDuring natural perception, we often form expectations about upcoming input. These expectations are usually multifaceted – we expect a particular object at a particular location. However, expectations about spatial location and stimulus features have mostly been studied in isolation, and it is unclear whether feature-based expectation can be spatially specific. Interestingly, feature-based attention automatically spreads to unattended locations. It is still an open question whether the neural mechanisms underlying feature-based expectation differ from those underlying feature-based attention. Therefore, establishing whether the effects of feature-based expectation are spatially specific may inform this debate. Here, we investigated this by inducing expectations of a specific stimulus feature at a specific location, and probing the effects on sensory processing across the visual field using fMRI. We found an enhanced sensory response for unexpected stimuli, which was elicited only when there was a violation of expectation at the specific location where participants formed a stimulus expectation. The neural consequences of this expectation violation, however, spread to cortical locations processing the stimulus in the opposite hemifield. This suggests that an expectation violation at one location in the visual world can lead to a spatially non-specific gain increase across the visual field.
Conservation of co-evolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone
Authors: Rodriguez-Rivas Juan , Marsili Simone , Juan David , Valencia Alfonso 
Published: August 2016

AbstractProtein-protein interactions are fundamental for the proper functioning of the cell. As a result, protein interaction surfaces are subject to strong evolutionary constraints. Recent developments have shown that residue co-evolution provides accurate predictions of heterodimeric protein interfaces from sequence information. So far these approaches have been limited to the analysis of families of prokaryotic complexes for which large multiple sequence alignments of homologous sequences can be compiled. We explore the hypothesis that co-evolution points to structurally conserved contacts at protein-protein interfaces, which can be reliably projected to homologous complexes with distantly related sequences. We introduce a novel domain-centred protocol to study the interplay between residue co-evolution and structural conservation of protein-protein interfaces. We show that sequence-based co-evolutionary analysis systematically identifies residue contacts at prokaryotic interfaces that are structurally conserved at the interface of their eukaryotic counterparts. In turn, this allows the prediction of conserved contacts at eukaryotic protein-protein interfaces with high confidence using solely mutational patterns extracted from prokaryotic genomes. Even in the context of high divergence in sequence, where standard homology modelling of protein complexes is unreliable, our approach provides sequence-based accurate information about specific details of protein interactions at the residue level. Selected examples of the application of prokaryotic co-evolutionary analysis to the prediction of eukaryotic interfaces further illustrates the potential of this novel approach.Significance statementInteracting proteins tend to co-evolve through interdependent changes at the interaction interface. This phenomenon leads to patterns of coordinated mutations that can be exploited to systematically predict contacts between interacting proteins in prokaryotes. We explore the hypothesis that co-evolving contacts at protein interfaces are preferentially conserved through long evolutionary periods. We demonstrate that co-evolving residues in prokaryotes identify inter-protein contacts that are particularly well conserved in the corresponding structure of their eukaryotic homologues. Therefore, these contacts have likely been important to maintain protein-protein interactions during evolution. We show that this property can be used to reliably predict interacting residues between eukaryotic proteins with homologues in prokaryotes even if they are very distantly related in sequence.
Habits without Values
Authors: Miller Kevin J. , Shenhav Amitai , Ludvig Elliot A. 
Published: August 2016

AbstractHabits form a crucial component of behavior. In recent years, key computational models have conceptualized habits as arising from model-free reinforcement learning (RL) mechanisms, which typically select between available actions based on the future value expected to result from each. Traditionally, however, habits have been understood as behaviors that can be triggered directly by a stimulus, without requiring the animal to evaluate expected outcomes. Here, we develop a computational model instantiating this traditional view, in which habits develop through the direct strengthening of recently taken actions rather than through the encoding of outcomes. We demonstrate that this model accounts for key behavioral manifestations of habits, including insensitivity to outcome devaluation and contingency degradation, as well as the effects of reinforcement schedule on the rate of habit formation. The model also explains the prevalent observation of perseveration in repeated-choice tasks as an additional behavioral manifestation of the habit system. We suggest that mapping habitual behaviors onto value-free mechanisms provides a parsimonious account of existing behavioral and neural data. This mapping may provide a new foundation for building robust and comprehensive models of the interaction of habits with other, more goal-directed types of behaviors and help to better guide research into the neural mechanisms underlying control of instrumental behavior more generally.
Pollutants and insecticides drive local adaptation in African malaria mosquitoes
Authors: Kamdem Colince , Fouet Caroline , Gamez Stephanie , White Bradley J. 
Published: August 2016

ABSTRACTTheAnopheles gambiaecomplex contains a number of highly anthropophilic mosquito species that have acquired exceptional ability to thrive in complex human habitats. Thus, examining the evolutionary history of this Afrotropical mosquito may yield vital information on the selective processes that occurred during the adaptation to human-dominated environments. We performed reduced representation sequencing on 941 mosquitoes of theAnopheles gambiaecomplex collected across four ecogeographic zones in Cameroon. We find evidence for genetic and geographic subdivision withinAn. coluzziiandAn. gambiaesensu stricto – the two most significant malaria vectors in the region. Importantly, in both species, rural and urban populations are genetically differentiated. Genome scans reveal pervasive signatures of selection centered on genes involved in xenobiotic resistance. Notably, a selective sweep containing detoxification enzymes is prominent in urban mosquitoes that exploit polluted breeding sites. Overall, our study suggests that recent anthropogenic environmental modifications and widespread use of insecticides are driving population differentiation and local adaptation in vectors with potentially significant consequences for malaria epidemiology.
Does social media matter for post typology? Impact of post content on Facebook and Instagram metrics
Authors: Coelho Ricardo Limongi França , Oliveira Denise Santos de , Almeida Marcos Inácio Severo de 
Published: August 2016

Purpose
– The purpose of this paper is to measure the impact of post type (advertising, fan, events, information, and promotion) on two interaction metrics: likes and comments. The measuring involved two popular social media, Facebook and Instagram, and in business profiles of five different segments (food, hairdressing, ladies’ footwear, body design, fashion gym wear).

Design/methodology/approach
– The method used was multiple regression analysis with an estimator of the ordinary least squares for 1,849 posts from five different companies posted on Facebook (680 posts) and Instagram (1,169 Instagram) over an eight-month posting period. Regression analysis was used to identify the relationship between the dependent variables (likes and comments), and the independent variables (post typology, segments, week period, month, characters and hashtag).

Findings
– It was seen that the post types events and promotion led to a greater involvement of followers in Instagram, in particular. In Facebook, the events post type was only significant in the like’s interaction. Another finding of the research is the relevance of the food and body design segment which was significant in both virtual social media. This indicates a user preference involving their day-to-day lives, in this case, having a tattoo done or seeing a photo of a dessert.

Originality/value
– With the findings of this study, academics and social media managers can improve the return indicators of interactions in posts and broaden the discussion on the types of post and interaction in different virtual social media.
Understanding the determinants of human computation game acceptance
Authors: Wang Xiaohui , Goh Dion Hoe-Lian , Lim Ee-Peng , Vu Adrian Wei Liang 
Published: August 2016

Purpose
– Human computation games (HCGs) that blend gaming with utilitarian purposes are a potentially effective channel for content creation. The purpose of this paper is to investigate the driving factors behind players’ adoption of HCGs through a music video tagging game. The effects of perceived aesthetic experience (PAE) and perceived output quality (POQ) on HCG acceptance are empirically examined.

Design/methodology/approach
– An integrative structural model is developed to explain how hedonic and utilitarian factors, including PAE and POQ, working with another salient factor – perceived usefulness (PU) – affect the acceptance of HCGs. The structural equation modeling method is used to verify the proposed model with data from 124 participants.

Findings
– Results show that PAE is the strongest predictor of HCGs adoption. PU has a significant impact on individuals’ attitude toward HCGs. POQ is a salient predictor of PU and PAE, and its indirect effect on attitude is significance.

Originality/value
– From an academic point of view, this study provides a good understanding of the driving factors behind player acceptance of HCGs and adds new knowledge to games with utilitarian purposes. It is also one of the first to describe the components of game enjoyment with a taxonomy of aesthetic experiences. From the practical perspective, the investigation of the specific factors behind adoption of HCGs provides specific guidelines for their design and evaluation.
A low frequency persistent reservoir of a genomic island in a pathogen population ensures island survival and improves pathogen fitness in a susceptible host
Authors: Neale Helen C. , Laister Robert , Payne Joseph , Preston Gail , Jackson Robert W. , Arnold Dawn L. 
Published: August 2016

SummaryThe co‐evolution of bacterial plant pathogens and their hosts is a complex and dynamic process. Host resistance imposes stress on invading pathogens that can lead to changes in the bacterial genome enabling the pathogen to escape host resistance. We have observed this phenomenon with the plant pathogen Pseudomonas syringae pv. phaseolicola where isolates that have lost the genomic island PPHGI‐1 carrying the effector gene avrPphB from its chromosome are infective against previously resistant plant hosts. However, we have never observed island extinction from the pathogen population within a host suggesting the island is maintained. Here, we present a mathematical model which predicts different possible fates for the island in the population; one outcome indicated that PPHGI‐1 would be maintained at low frequency in the population long term, if it confers a fitness benefit. We empirically tested this prediction and determined that PPHGI‐1 frequency in the bacterial population drops to a low but consistently detectable level during host resistance. Once PPHGI‐1‐carrying cells encounter a susceptible host, they rapidly increase in the population in a negative frequency‐dependent manner. Importantly, our data show that mobile genetic elements can persist within the bacterial population and increase in frequency under favourable conditions.
The cosmopolitan contradictions of planetary urbanization
Authors: Millington Gareth 
Published: August 2016

AbstractThis paper explores the empirical, conceptual and theoretical gains that can be made using cosmopolitan social theory to think through the urban transformations that scholars have in recent years termed planetary urbanization. Recognizing the global spread of urbanization makes the need for a cosmopolitan urban sociology more pressing than ever. Here, it is suggested that critical urban sociology can be invigorated by focusing upon the disconnect that Henri Lefebvre posits between the planetarization of the urban – which he views as economically and technologically driven – and his dis‐alienated notion of a global urban society. The first aim of this paper is to highlight the benefits of using ‘cosmopolitan’ social theory to understand Lefebvre's urban problematic (and to establish why this is also a cosmopolitan problematic); the second is to identify the core cosmopolitan contradictions of planetary urbanization, tensions that are both actually existing and reproduced in scholarly accounts. The article begins by examining the challenges presented to urban sociology by planetary urbanization, before considering how cosmopolitan sociological theory helps provide an analytical ‘grip’ on the deep lying social realities of contemporary urbanization, especially in relation to questions about difference, culture and history. These insights are used to identify three cosmopolitan contradictions that exist within urbanized (and urbanizing) space; tensions that provide a basis for a thoroughgoing cosmopolitan investigation of planetary urbanization.