bluuebunny/crossref_metadata_2025_split huggingface dataset:
A common representation of time across visual and auditory modalities
Authors: Barne Louise C. , Sato João R. , de Camargo Raphael Y. , Claessens Peter M. E. , Caetano Marcelo S. , Cravo André M. 
Published: September 2017

AbstractHumans’ and non-human animals’ ability to process time on the scale of milliseconds and seconds is essential for adaptive behaviour. A central question of how brains keep track of time is how specific temporal information across different sensory modalities is. In the present study, we show that encoding of temporal intervals in auditory and visual modalities are qualitatively similar. Human participants were instructed to reproduce intervals in the range from 750 ms to 1500 ms marked by auditory or visual stimuli. Our behavioural results suggest that, although participants were more accurate in reproducing intervals marked by auditory stimuli, there was a strong correlation in performance between modalities. Using multivariate pattern analysis in scalp EEG, we show that activity during late periods of the intervals was similar within and between modalities. Critically, we show that a multivariate pattern classifier was able to accurately predict the elapsed interval, even when trained on an interval marked by a stimulus of a different sensory modality. Taken together, our results suggest that, while there are differences in the processing of intervals marked by auditory and visual stimuli, they also share a common neural representation.
Unbiased Strain-Typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-forward Biosurveillance Protocol
Authors: Russell Joseph A. , Campos Brittany , Stone Jennifer , Blosser Erik M. , Burkett-Cadena Nathan , Jacobs Jonathan 
Published: September 2017

ABSTRACTThe future of infectious disease surveillance and outbreak response is trending towards smaller hand-held solutions for point-of-need pathogen detection.1–4Although recent advances have paved the way for these technologies to include sequencing of pathogens directly from clinical samples, the ability to carry out unbiased sequencing for pathogen discovery and subtyping directly from environmental samples has yet to be demonstrated with hand-held platforms.5Products such as the two3 qPCR system from Biomeme Inc., as well as the MinION from Oxford Nanopore Technologies, have generated renewed prospects for point-of-need diagnostics and near real-time environmental testing and characterization of viral and microbial pathogens. Here, samples ofCulex cedeceimosquitoes collected in Southern Florida, USA were tested for Venezuelan Equine Encephalitis Virus (VEEV), a previously-weaponized arthropod-borne RNA-virus capable of causing acute and fatal encephalitis in animal and human hosts. A single 20-mosquito pool tested positive for VEEV by real-time reverse transcription quantitative PCR (RT-qPCR) on the Biomeme two3. The virus-positive sample was then subjected to unbiased metatranscriptome sequencing on the MinION and determined to contain Everglades Virus (EVEV), a strain of VEEV transmitted exclusively byCulex cedeceiin South Florida. The result was confirmed on “gold standard” thermocyclers and sequencing machines, and comparison to nanopore results is discussed. Our results demonstrate, for the first time, the use of unbiased sequence-based detection and subtyping of a high-consequence biothreat pathogen directly from an environmental sample using field-forward hardware and protocols. The further development and validation of methods designed for field-based diagnostic metagenomics and pathogen discovery, such as those suitable for use in mobile “pocket laboratories”, will address a growing demand for public health teams to carry out their mission where it is most urgent: at the point-of-need.6
Insights into the relation between noise and biological complexity
Authors: Pucci Fabrizio , Rooman Marianne 
Published: September 2017

Understanding under which conditions the increase of systems complexity is evolutionary advantageous, and how this trend is related to the modulation of the intrinsic noise, are fascinating issues of utmost importance for synthetic and systems biology. To get insights into these matters, we analyzed chemical reaction networks with different topologies and degrees of complexity, interacting or not with the environment. We showed that the global level of fluctuations at the steady state, as measured by the sum of the Fano factors of the number of molecules of all species, is directly related to the topology of the network. For systems with zero deficiency, this sum is constant and equal to the rank of the network. For higher deficiencies, we observed an increase or decrease of the fluctuation levels according to the values of the reaction fluxes that link internal species, multiplied by the associated stoichiometry. We showed that the noise is reduced when the fluxes all flow towards the species of higher complexity, whereas it is amplified when the fluxes are directed towards lower complexity species.PACS numbers: 02.50.Ey, 05.10.Gg, 05.40.Ca, 87.18.-h
A predictive model of rats’ calorie intake as a function of diet energy density
Authors: Beheshti Rahmatollah , Treesukosol Yada , Igusa Takeru , Moran Timothy H. 
Published: September 2017

AbstractEasy access to high-energy food has been linked to high rates of obesity in the world. Understanding the way that access to palatable (high fat or high calorie) food can lead to overconsumption is essential for both preventing and treating obesity. Although the body of studies focused on the effects of high energy diets is growing, our understanding of how different factors contribute to food choices is not complete. In this study, we present a mathematical model that is able to predict rats’ calorie intake to a high-energy diet based on their ingestive behavior to a standard chow diet. Specifically, we propose an equation that describes the relation between the body weight (W), energy density (E), time elapsed from the start of diet (T), and daily calorie intake (C). We tested our model on two independent data sets. Our results show that the suggested model is able to predict the calorie intake patterns with high accuracy. Additionally, the only free parameter of our proposed equation (ρ), which is unique to each animal, has a strong correlation with their calorie intake and weight gain. Additionally, we discuss the relevance of our derived parameter in the context of measuring reward sensitivity in reinforcement learning based studies.
Cardiac enriched BAF chromatin remodeling complex subunit Baf60c regulates gene expression programs essential for heart development and function
Authors: Sun Xin , Hota Swetansu K. , Zhou Yu-Qing , Novak Stefanie , Miguel-Perez Dario , Christodoulou Danos , Seidman Christine E. , Seidman J.G. , Gregorio Carol C. , Henkelman R. Mark , Rossant Janet , Bruneau Benoit G. 
Published: September 2017

AbstractHow gene networks controlling organ-specific properties are modulated by chromatin remodeling complexes is not well understood.Baf60c(Smarcd3) encodes a cardiac-enriched subunit of the SWI/SNF-like BAF chromatin complex. Its role throughout heart development is not fully understood. We show that constitutive loss ofBaf60cleads to embryonic cardiac hypoplasia and pronounced cardiac dysfunction. Conditional deletion ofBaf60cin cardiomyocytes results in postnatal dilated cardiomyopathy with impaired contractile function.Baf60cregulates a gene expression program that includes genes encoding contractile proteins, modulators of sarcomere function, and cardiac metabolic genes. Many of the genes deregulated inBaf60cnull embryos are targets of the MEF2/SRF co-factor Myocardin (MYOCD). In a yeast two-hybrid screen we identify MYOCD as a BAF60c interacting factor; we show that BAF60c and MYOCD directly and functionally interact. We conclude that Baf60c is essential for coordinating a program of gene expression that regulates the fundamental functional properties of cardiomyocytes.
IMPROVING MIN HASH VIA THE CONTAINMENT INDEX WITH APPLICATIONS TO METAGENOMIC ANALYSIS
Authors: Koslicki David , Zabeti Hooman 
Published: September 2017

AbstractMin hash is a probabilistic method for estimating the similarity of two sets in terms of their Jaccard index, defined as the ration of the size of their intersection to their union. We demonstrate that this method performs best when the sets under consideration are of similar size and the performance degrades considerably when the sets are of very different size. We introduce a new and efficient approach, called thecontainment min hashapproach, that is more suitable for estimating the Jaccard index of sets of very different size. We accomplish this by leveraging another probabilistic method (in particular, Bloom filters) for fast membership queries. We derive bounds on the probability of estimate errors for the containment min hash approach and show it significantly improves upon the classical min hash approach. We also show significant improvements in terms of time and space complexity. As an application, we use this method to detect the presence/absence of organisms in a metagenomic data set, showing that it can detect the presence of very small, low abundance microorganisms.
An open-source cryo-storage solution
Authors: Ultee Eveline , Schenkel Fred , Yang Wen , Brenzinger Susanne , Depelteau Jamie S. , Briegel Ariane 
Published: September 2017

AbstractThe field of cryo-electron microscopy is a rapidly growing method in structural biology. With this development, access to cryo-EM facilities becomes a bottleneck that results in long wait times between sample preparation and data acquisition. To improve sample storage, we developed a cryo-storage system with a more efficient and larger storage capacity that enables cryo-sample storage in a highly organized manner. This system is simple to use, cost-effective and easily adaptable for any type of grid box and storage dewar and any size cryo-EM laboratory.
ARIGAN: Synthetic Arabidopsis Plants using Generative Adversarial Network
Authors: Giuffrida Mario Valerio , Scharr Hanno , Tsaftaris Sotirios A 
Published: September 2017

AbstractIn recent years, there has been an increasing interest in image-based plant phenotyping, applying state-of-the-art machine learning approaches to tackle challenging problems, such as leaf segmentation (a multi-instance problem) and counting. Most of these algorithms need labelled data to learn a model for the task at hand. Despite the recent release of a few plant phenotyping datasets, large annotated plant image datasets for the purpose of training deep learning algorithms are lacking. One common approach to alleviate the lack of training data is dataset augmentation. Herein, we propose an alternative solution to dataset augmentation for plant phenotyping, creating artificial images of plants using generative neural networks. We propose the Arabidopsis Rosette Image Generator (through) Adversarial Network: a deep convolutional network that is able to generate synthetic rosette-shaped plants, inspired by DC-GAN (a recent adversarial network model using convolutional layers). Specifically, we trained the network using A1, A2, and A4 of the CVPPP 2017 LCC dataset, containing Arabidopsis Thaliana plants. We show that our model is able to generate realistic 128 × 128 colour images of plants. We train our network conditioning on leaf count, such that it is possible to generate plants with a given number of leaves suitable, among others, for training regression based models. We propose a new Ax dataset of artificial plants images, obtained by our ARIGAN. We evaluate this new dataset using a state-of-the-art leaf counting algorithm, showing that the testing error is reduced when Ax is used as part of the training data.
MERIT: a Mutation Error Rate Identification Toolkit for Ultra-deep Sequencing Applications
Authors: Hadigol Mohammad , Khiabanian Hossein 
Published: September 2017

AbstractRapid progress in high-throughput sequencing (HTS) has enabled the molecular characterization of mutational landscapes in heterogeneous populations and has improved our understanding of clonal evolution processes. Analyzing the sensitivity of detecting genomic mutations in HTS requires comprehensive profiling of sequencing artifacts. To this end, we introduce MERIT, designed for in-depth quantification of erroneous substitutions and small insertions and deletions, specifically for ultra-deep applications. MERIT incorporates an all-inclusive variant caller and considers genomic context, including the nucleotides immediately at 5′ and 3′, thereby establishing error rates for 96 possible substitutions as well as four singlebase and 16 double-base indels. We apply MERIT to ultra-deep sequencing data (1,300,000×) and show a significant relationship between error rates and genomic contexts. We devise anin silicoapproach to determine the optimal sequencing depth, where errors occur at rates similar to those of true mutations. Finally, we assess nucleotide-incorporation fidelity of four high-fidelity DNA polymerases in clinically relevant loci, and demonstrate how fixed detection thresholds may result in substantial false positive as well as false negative calls.
Local context influences memory for emotional stimuli but not electrophysiological markers of emotion-dependent attention
Authors: Barnacle Gemma E. , Tsivilis Dimitris , Schaefer Alexandre , Talmi Deborah 
Published: September 2017

AbstractEmotional Enhancement of free recall can be context dependent. It is readily observed when emotional and neutral scenes are encoded and recalled together, in a ‘mixed’ list, but diminishes when these scenes are encoded separately, in ‘pure’ lists. We examined the hypothesis that this effect is due to differences of allocation of attention to neutral stimuli according to whether they are presented in mixed or pure lists, especially when encoding is intentional. Using picture stimuli that were controlled for semantic relatedness, our results contradicted this hypothesis. The amplitude of well-known electrophysiological markers of emotion-related attention - the Early Posterior Negativity (EPN), the Late Positive Potential (LPP), and the Slow Wave (SW) - was higher for emotional stimuli. Crucially, the emotional modulation of these ERPs was insensitive to list context, observed equally in pure and mixed lists. Although list context did not modulate neural markers of emotion-related attention, list context did modulate the effect of emotion on free recall. The apparent decoupling of the emotional effects on attention and memory challenges existing hypotheses accounting for the emotional enhancement of memory. We close by discussing whether findings are more compatible with an alternative hypothesis, where the magnitude of emotional memory enhancement is, at least in part, a consequence of retrieval dynamics.
The INO80 Chromatin Remodeler Sustains Metabolic Stability by Promoting TOR Signaling and Regulating Histone Acetylation
Authors: Beckwith Sean L. , Schwartz Erin K. , Garcia-Nieto Pablo E. , King Devin A. , Gowans Graeme J. , Wong Ka Man , Yao Wei , Eckley Tessa L. , Paraschuk Alexander P. , Peltan Egan , Lee Laura R. , Morrison Ashby J. 
Published: September 2017

ABSTRACTChromatin remodeling complexes are essential for gene expression programs that coordinate cell function with metabolic status. However, how these remodelers are integrated in metabolic stability pathways is not well known. Here, we report an expansive genetic screen with chromatin remodelers and metabolic regulators inSaccharomyces cerevisiae. We found that, unlike the SWR1 remodeler, the INO80 chromatin remodeling complex is composed of multiple distinct functional subunit modules. We identified a strikingly divergent genetic signature for the Ies6 subunit module that links the INO80 complex to metabolic homeostasis, including mitochondrial maintenance. INO80 is also needed to communicate TORC1-mediated signaling to chromatin and maintains histone acetylation at TORC1-responsive genes. Furthermore, computational analysis reveals subunits of INO80 and mTORC1 have high co-occurrence of alterations in human cancers. Collectively, these results demonstrate that the INO80 complex is a central component of metabolic homeostasis that influences histone acetylation and may contribute to disease when disrupted.
Challenges in use of geographical information systems (GIS) in a research for understanding conservation of cultural heritage in Bursa
Authors: Çakici Alp Sermin , Şahin Güçhan Neriman 
Published: September 2017

Purpose
The purpose of this paper is to present a framework of introducing a proper method to document and to analyze conservation process of cultural heritage in Bursa, known as one of the UNESCO World Heritage Sites in Turkey and to discuss challenges in use of geographical information systems (GIS) for assessment of a complex data collected and analyzed during different phases of the historic researches.

Design/methodology/approach
A systematic approach is used to understand relations between theoretical and practical processes of heritage conservation in Bursa. Due to the complicated structure of input data, GIS was used as the major tool in illustration of cultural heritage in various spatial scales, while providing connection between different timelines of its urban history. Within this concept, at first, conservation history of cultural heritage in Bursa is briefly described. Second, four stages of the method, used to make reliable and convenient assessment, are given. Finally, facilities and challenges in using this system are discussed in relation with the results achieved.

Findings
As a result of this study, both chronological and spatial distribution of all types of conservation practices are described in related with theoretical and legal aspects. There appear both advantages and limitations in use of GIS, during assessment of input data to understand conservation history of Bursa.

Originality/value
Therefore, it would be possible to see if it is adequate to understand the complicated structure of such kind of overlapped sources in a systematic way of information management system.
Impact of value co-creation on logistics customers’ loyalty
Authors: Thiruvattal Eappen 
Published: September 2017

Purpose
This paper aims to examine the influence of value co-creation by external and internal stakeholders of logistics service organizations on both customer loyalty as well as superior service solutions. The mediating role of superior service solutions between the value co-creation strategies of organizations and customer loyalty is also investigated in a marketing channel environment.

Design/methodology/approach
Survey data of small and medium enterprises’ executives (n = 330) are analysed using exploratory factor analysis and structural equation modelling to investigate the impact of six hypothesized relationships through value co-creation.

Findings
This study indicates that coordinated efforts to create value by external and internal stakeholders to achieve superior service solutions have a strong impact on creating loyalty among customers.

Research limitations/implications
The effectiveness of this research has been validated in a number of ways including interviewing four of the stakeholders of a case organization that implemented the model. This study offers understanding of the roles of value co-creation, to a key to organizational success in marketing channels.

Originality/value
This paper elucidates the impact of value co-creation on the business performance of logistics service organizations. With empirical evidence, the paper contributes to fill the knowledge gaps on how the process of value co-creation by different stakeholders influences customer loyalty in a service context. The mediating role of superior service solution between value co-creation by different stakeholders and business customer loyalty is also examined, adding to its significance.
You can't always get what you want? Leadership expectations of intrapreneurs
Authors: Deprez Jana , Euwema Martin 
Published: September 2017

PurposeThe purpose of this paper is to examine the leadership expectations of young employees in intrapreneurial jobs.Design/methodology/approachGroup interviews were conducted with 42 young intrapreneurs and 13 leaders of a Dutch ICT consultancy firm. Data were coded and analyzed using qualitative data analysis software.FindingsThe authors find ten different expectations on leadership. Young intrapreneurs expect to have a personal connection, sufficient feedback, ample freedom, and trust, clear directions when asked and a leader who is a role model.Research limitations/implicationsThis qualitative study was conducted in one organization. It however sheds a first light on expectations of employees with intrapreneurial job requirements.Practical implicationsIn order to motivate and guide young intrapreneurs, direct supervisors should aim not to breach expectations. By getting to know their employees on a personal basis, taking the time to coach them in their career goals, showing intrapreneurship themselves, focusing on an open relationship, and providing a challenging and dynamic environment, direct supervisors build a strong and cooperative relationship.Originality/valueThis paper is one of the first to look at the relationship between direct supervisors and intrapreneurial employees. Doing so, it also expands the current knowledge of Implicit Leadership Theory by exploring expectations of young intrapreneurs and adds to the full-range leadership theory by showing the importance of investigating its subdimensions.
The More You Give, the More You Get? The Impact of Corporate Political Activity on the Value of Government Contracts
Authors: Hadani Michael , Munshi Natasha , Clark Kim 
Published: September 2017

AbstractFirms have been relying on corporate political activity (CPA) to achieve access and to affect public policy change for decades. Most research on CPA and public policy outcomes has implicitly assumed that access afforded by CPA results in an either‐ or (dichotomous) policy outcome such as votes or election outcomes. Based on recent research on how CPA can be a strategic signal to government agencies, however, it is possible that CPA may in fact, have a linear association with public policy outcomes as opposed to merely a dichotomous one, and we explore this relationship in the unique public policy context of government contract awards. We specifically analyze how higher levels of CPA impact the financial value of government contracts awarded to firms. Utilizing the S&P 1500 sample for 16 years (1997–2012) we find that CPA has a one to one association with the value of contract awards, indicating that CPA and public policy outcomes can be linked in ways that motivate firms to continuously invest in CPA, to maximize their political rents. We discuss the theoretical and practical implications of this finding in light of extant research on CPA and its direct impact on public policy outcomes.
A Kantian ethics approach to moral bioenhancement
Authors: Carter Sarah 
Published: September 2017

AbstractIt seems, at first glance, that a Kantian ethics approach to moral enhancement would tend towards the position that there could be no place for emotional modulation in any understanding of the endeavour, owing to the typically understood view that Kantian ethics does not allow any role for emotion in morality as a whole. It seems then that any account of moral bioenhancement which places emotion at its centre would therefore be rejected. This article argues, however, that this assumption is incorrect. Given later writings by Kant on the role of sympathy, and taking into account other concerns in Kantian ethics (such as bodily integrity), it may in fact be the case that Kantian ethics would allow for an account of moral bioenhancement through emotional modulation, and that in some (rare) cases such an intervention might even be considered to be a duty.