bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intra- and inter-chromosomal chromatin interactions mediate genetic effects on regulatory networks
Authors: Delaneau O. , Zazhytska M. , Borel C. , Howald C. , Kumar S. , Ongen H. , Popadin K. , Marbach D. , Ambrosini G. , Bielser D. , Hacker D. , Romano-Palumbo L. , Ribaux P. , Wiederkehr M. , Falconnet E. , Bucher P. , Bergmann S. , Antonarakis S. E. , Reymond A. , Dermitzakis E. T. 
Published: August 2017

SummaryGenome-wide studies on the genetic basis of gene expression and the structural properties of chromatin have considerably advanced our understanding of the function of the human genome. However, it remains unclear how structure relates to function and, in this work, we aim at bridging both by assembling a dataset that combines the activity of regulatory elements (e.g. enhancers and promoters), expression of genes and genetic variations of 317 individuals and across two cell types. We show that the regulatory activity is structured within 12,583 Cis Regulatory Domains (CRDs) that are cell type specific and highly reflective of the local (i.e. Topologically Associating Domains) and global (i.e. A/B nuclear compartments) nuclear organization of the chromatin. These CRDs essentially delimit the sets of active regulatory elements involved in the transcription of most genes, thereby capturing complex regulatory networks in which the effects of regulatory variants are propagated and combined to finally mediate expression Quantitative Trait Loci. Overall, our analysis reveals the complexity and specificity of cis and trans regulatory networks and their perturbation by genetic variation.
Empirical evidence reveals the phase diagram of patch patterns in Mediterranean drylands
Authors: Meloni Fernando , Granzotti Cristiano R. F. , Martinez Alexandre S. 
Published: August 2017

AbstractDrylands are ecosystems with limited water resources, often subjected to desertification. Conservation and restoration efforts towards these ecosystems depend on the interplay between ecological functioning and spatial patterns formed by local vegetation. Despite recent advances on the subject, an adequate description of phase transitions between the various vegetated phases remains an open issue. Here, we gather vegetation data of drylands from Southern Spain using satellite images. Our findings support three vegetated phases, separated by two distinct phase transitions, including a continuous phase transition, with new relations between scaling exponents of ecological variables. The phase diagram is obtained without a priori assumption about underlying ecological dynamics. We apply our analysis to a different dryland system in the Western United States and verify a compatible critical behavior, in agreement with the universality hypothesis.
New waves: Rhythmic electrical field stimulation systematically alters spontaneous slow dynamics across mouse neocortex
Authors: Greenberg Anastasia , Karimi Abadchi Javad , Dickson Clayton T. , Mohajerani Majid H. 
Published: August 2017

AbstractThe signature rhythm of slow-wave forebrain activity is the large amplitude, slow oscillation (SO: ~1 Hz) made up of alternating synchronous periods of depolarizing and hyperpolarizing states at the single cell and network levels. On each wave, the SO originates at a unique location and propagates across the neocortex. Attempts to manipulate SO activity using electrical fields have been shown to entrain cortical networks and enhance memory performance. However, neural activity during this manipulation has remained elusive due to methodological issues in typical electrical recordings. Here we use voltage-sensitive dye (VSD) imaging in a bilateral cortical preparation of urethane-anesthetized mice to track SO cortical activity and its modulation by sinusoidal electrical field stimulation applied to frontal regions. We show that under spontaneous conditions, the SO propagates in two main opposing directional patterns along an anterior lateral – posterior medial axis. Rhythmic field stimulation alters spontaneous propagation to reflect activity that repeats cycle after cycle with distributed and varied anterior initiation zones and a consistent termination zone in the posterior somatosensory cortex. Our results show that slow electrical field stimulation stereotypes ongoing slow cortical dynamics during sleep-like states.Author ContributionsA.G., J.K.A., M.H.M. and C.T.D. designed the study. A.G. and J.K.A. performed the experiments. A.G. analyzed the data. A.G. wrote the manuscript, which all authors commented on and edited. C.T.D. and M.H.M. supervised the study.
Spot-On: robust model-based analysis of single-particle tracking experiments
Authors: Hansen Anders S , Woringer Maxime , Grimm Jonathan B , Lavis Luke D , Tjian Robert , Darzacq Xavier 
Published: August 2017

ABSTRACTSingle-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding and diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due to biases in both data analysis and experimental design. To address analysis bias, we introduce “Spot-On”, an intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving out-of-focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule trajectories. To minimize inherent experimental biases, we implement and validate stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and tracking errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On outperforms other methods. We then apply Spot-On to spaSPT data from live mammalian cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently and robustly infers subpopulation fractions and diffusion constants.IMPACT STATEMENTSpot-On is an easy-to-use website that makes a rigorous and bias-corrected modeling framework for analysis of single-molecule tracking experiments available to all.
System-level studies of a cell-free transcription-translation platform for metabolic engineering
Authors: Wu Yong Y. , Sato Hirokazu , Huang Hongjun , Culler Stephanie J. , Khandurina Julia , Nagarajan Harish , Yang Tae Hoon , Van Dien Stephen , Murray Richard M. 
Published: August 2017

AbstractCurrent methods for assembling biosynthetic pathways in microorganisms require a process of repeated trial and error and have long design-build-test cycles. We describe the use of a cell-free transcription-translation (TX-TL) system as a biomolecular breadboard for the rapid engineering of the 1,4-butanediol (BDO) pathway. We demonstrate the reliability of TX-TL as a platform for engineering biological systems by undertaking a careful characterization of its transcription and translation capabilities and provide a detailed analysis of its metabolic output. Using TX-TL to survey the design space of the BDO pathway enables rapid tuning of pathway enzyme expression levels for improved product yield. Leveraging TX-TL to screen enzyme variants for improved catalytic activity accelerates design iterations that can be directly applied toin vivostrain development.
The contributions of the actin machinery to endocytic membrane bending and vesicle formation
Authors: Picco Andrea , Kukulski Wanda , Manenschijn Hetty E. , Specht Tanja , Briggs John A. G. , Kaksonen Marko 
Published: August 2017

AbstractBranched and crosslinked actin networks mediate cellular processes that move and shape membranes. To understand how actin contributes during the different stages of endocytic membrane reshaping, we analysed deletion mutants of yeast actin network components using a hybrid imaging approach that combines live imaging with correlative microscopy. We could thereby temporally dissect the effects of different actin network perturbations, revealing distinct stages of actin-based membrane reshaping. Our data show that initiation of membrane bending requires the actin network to be physically linked to the plasma membrane and to be optimally crosslinked. Once initiated, the membrane invagination process is driven by nucleation and polymerization of new actin filaments, independently of the degree of cross-linking and unaffected by a surplus of actin network components. A key transition occurs 2 seconds before scission when the filament nucleation rate drops. From that time point on, invagination growth and vesicle scission are driven by an expansion of the assembled actin network. The expansion is sensitive to the amount of filamentous actin and its crosslinking. Our results suggest that the mechanism by which actin reshapes the membrane adapts to force requirements that vary during the progress of endocytosis.
Midfrontal theta and pupil dilation parametrically track subjective conflict (but also surprise) during intertemporal choice
Authors: Lin Hause , Saunders Blair , Hutcherson Cendri A , Inzlicht Michael 
Published: August 2017

AbstractMany everyday choices are based on personal, subjective preferences. When choosing between two options, we often feel conflicted, especially when trading off costs and benefits occurring at different times (e.g., saving for later versus spending now). Although previous work has investigated the neurophysiological basis of conflict during inhibitory control tasks, less is known about subjective conflict resulting from competing subjective preferences. In this pre-registered study, we investigated subjective conflict during intertemporal choice, whereby participants chose between smaller immediate versus larger delayed rewards (e.g., $15 today vs. $22 in 30 days). We used economic modeling to parametrically vary eleven different levels of conflict, and recorded EEG data and pupil dilation. Midfrontal theta power, derived from EEG, correlated with pupil responses, and our results suggest that these signals track different gradations of subjective conflict. Unexpectedly, both signals were also maximally enhanced when decisions were surprisingly easy. Therefore, these signals may track events requiring increased attention and adaptive shifts in behavioral responses, with subjective conflict being only one type of such event. Our results suggest that the neural systems underlying midfrontal theta and pupil responses interact when weighing costs and benefits during intertemporal choice. Thus, understanding these interactions might elucidate how individuals resolve self-control conflicts.HighlightsModeled conflict during intertemporal choice and measured EEG and pupil responses.Midfrontal theta and pupil responses parametrically tracked subjective conflict.But theta and pupil responses were also large when decisions were surprisingly easy.These signals may implement adaptive control during value-guided choice.
Bots for Software-Assisted Analysis of Image-Based Transcriptomics
Authors: Cicconet Marcelo , Hochbaum Daniel R. , Richmond David , Sabatini Bernardo L. 
Published: August 2017

AbstractWe introduce software assistants – bots – for the task of analyzing image-based transcriptomic data. The key steps in this process are detecting nuclei, and counting associated puncta corresponding to labeled RNA. Our main release offers two algorithms for nuclei segmentation, and two for spot detection, to handle data of different complexities. For challenging nuclei segmentation cases, we enable the user to train a stacked Random Forest, which includes novel circularity features that leverage prior knowledge regarding nuclei shape for better instance segmentation. This machine learning model can be trained on a modern CPU-only computer, yet performs comparably with respect to a more hardware-demanding state-of-the-art deep learning approach, as demonstrated through experiments. While the primary motivation for the bots was image-based transcriptomics, we also demonstrate their applicability to the more general problem of scoring “spots” in nuclei.
Ingredients in Victoria’s Secret Bombshell and Ivanka Trump eaux de parfums that repel mosquitoes
Authors: Zeng Fangfang , Xu Pingxi , Tan Kaiming , Zarbin Paulo H. G. , Leal Walter S. 
Published: August 2017

AbstractInsect repellents are widely used to fend off nuisance mosquitoes and, more importantly, to reduce or eliminate mosquito bites in areas where viruses and other vector-borne diseases are circulating. Synthesized more than six decades ago, DEET is the most widely used insect repellent. Plant-derived compounds are used in a plethora of commercial formulations and natural recipes to repel mosquitoes. They are also used as fragrances. We analysed Bombshell®to identify the constituent(s) eliciting a previously reported “off-label” repellence activity. The two major fragrance ingredients in Bombshell, i.e., methyl dihydrojasmonate and lilial, demonstrated strong repellence against the southern house mosquito,Culex quinquefasciatus, in laboratory assays. Both compounds activated a previously identified DEET-sensitive odorant receptor, CquiOR136. These compounds were also major constituents of Ivanka Trump eau de parfum. The methyl dihydrojasmonate content was higher in the Ivanka Trump perfume than in Bombshell, the reverse being true for lilial. Both Bombshell and Ivanka Trump eaux de parfums retained activity for as long as 6 hours in laboratory assays. Although wearing these perfumes may repel nuisance mosquitoes, their use as “off-label” repellents against infected mosquitoes is not recommended. A panel of 104 students (18-23 years old) conducted a blind test to compare the two eaux de parfums and showed a preference for Bombshell over Ivanka Trump’s brand, particularly among women.
Dissociable components of the reward circuit are involved in appraisal versus choice
Authors: Shenhav Amitai , Karmarkar Uma R. 
Published: August 2017

AbstractPeople can evaluate a set of options as a whole, or they can approach those same options with the purpose of making a choice between them. A common network has been implicated across these two types of evaluations, including regions of ventromedial prefrontal cortex and the posterior midline. We test the hypothesis that sub-components of this reward circuit are differentially involved in triggering more automatic appraisal of one’s options (Dorsal Value Network) versus explicitly comparing between those options (Ventral Value Network). Participants undergoing fMRI were instructed to appraise how much they liked a set of products (Like) or to choose the product they most preferred (Choose). Activity in the Dorsal Value Network consistently tracked set liking, across both task-relevant (Like) and task-irrelevant (Choose) trials. In contrast, the Ventral Value Network was sensitive to evaluation condition (more active during Choose than Like trials). Within vmPFC, anatomically distinct regions were dissociated in their sensitivity to choice (ventrally, in medial OFC) versus appraisal (dorsally, in pregenual ACC). Dorsal regions additionally tracked decision certainty across both types of evaluation. These findings suggest that separable mechanisms drive decisions about how good one’s options are versus decisions about which option is best.
A blueprint towards accounting for the management of ecosystems
Authors: Feger Clément , Mermet Laurent 
Published: August 2017

Purpose
The purpose of this paper is to propose a new ecological-issues-centered accounting research agenda, at the crossroads of accounting research and conservation science.

Design/methodology/approach
Based on a case study of the Natural Capital Project, the research examines the efforts and challenges of conservation practitioners regarding the use of evaluative information systems for conservation (EISC) in complex social and ecological contexts. It discusses why and how, to address these challenges, EISC promoters would benefit from theoretical and empirical insights coming from accounting research.

Findings
The paper suggests that the use of new information systems centered on organized collective action for biodiversity conservation should be regarded as a new type of accounting for the management of ecosystems, complementary to organization-centered biodiversity accounting and to ecosystem accounting at the national scale. A research agenda inspired by critical accounting should be developed for EISC design and use by: critically analyzing the organizational models currently underlying the use of new calculative practices for ecosystems; and developing new analytical and practical avenues on the basis of more explicit and powerful theories adapted to collective action for conservation perimeters.

Originality/value
The paper shows the importance of combining three domains of research and practice that are usually disconnected: the design and use of innovative information systems in biodiversity conservation research and practice; accounting research; and theories and conceptual models of collective action to resolve ecological challenges.
UK local councils reporting of biodiversity values: a stakeholder perspective
Authors: Gaia Silvia , John Jones Michael 
Published: August 2017

Purpose
The purpose of this paper is to explore the use of narratives in biodiversity reports as a mechanism to raise the awareness of biodiversity’s importance. By classifying biodiversity narratives into 14 categories of biodiversity values this paper investigates whether the explanations for biodiversity conservation used by UK local councils are line with shallow, intermediate or deep philosophies.

Design/methodology/approach
This study used content analysis to examine the disclosures on biodiversity’s importance in the biodiversity action plans published by UK local councils. The narratives were first identified and then allocated into 14 categories of biodiversity value. Then, they were ascribed to either shallow (resource conservation, human welfare ecology and preservationism), intermediate (environmental stewardship and moral extensionism) or deep philosophies.

Findings
UK local councils explained biodiversity’s importance mainly in terms of its instrumental value, in line with shallow philosophies such as human welfare ecology and resource conservation. UK local councils sought to raise awareness of biodiversity’ importance by highlighting values that are important for the stakeholders that are able to contribute towards biodiversity conservation such as landowners, residents, visitors, business and industries. The authors also found that local councils’ biodiversity strategies were strongly influenced by 2010, the International Year of Biodiversity.

Originality/value
This paper is one of the few accounting studies that engages with the literature on environmental ethics to investigate biodiversity. In line with stakeholder theory, it indicates that explanations on biodiversity’s importance based on anthropocentric philosophies are considered more effective in informing those stakeholders whose behaviour needs to be changed to improve biodiversity conservation.
Status and quality of open access journals in Scopus
Authors: Erfanmanesh Mohammadamin 
Published: August 2017

PurposeThis study aims to provide an extensive overview of OA journals’ status and quality in 27 research areas based on all Scopus-indexed journals. It shows the volume of OA journals, proportion of publications in OA journals and the quality of these journals in comparison with subscription-based counterparts.Design/methodology/approachThis research investigated 22,256 active peer-reviewed journals indexed by Scopus in 2015. Data were gathered using the Journal Metrics website. The current research adopted four indicators to compare the quality of OA and non-OA journals indexed in Scopus under each subject area, namely citedness rate, CiteScore, SNIP and SJR.FindingsOA journals comprised approximately 17 per cent out of the total journals indexed by Scopus in 2015. The results revealed an uneven spread of OA journals across disciplines, ranged from 5.5 to 28.7 per cent. Studying the quality of journals as measured by CiteScore, SJR SNIP leads us to the finding that, in all research areas, except for health profession and nursing, non-OA journals attain statistically significant higher average quality than do OA journals.Originality/valueAlthough OA publishing improves the visibility of scholarly journals, this increase is not always coupled with increase in journals’ impact and quality.
Leveraging the corporate brand
Authors: Brexendorf Tim Oliver , Keller Kevin Lane 
Published: August 2017

Purpose
Most research on branding highlights the role of associations for a single brand. Many firms, however, have multiple brands and/or different versions of one brand. The latter is largely the case for many corporate brands. This paper aims to broaden the understanding of corporate brand associations and their transfer within the firm’s brand and product portfolio. In particular, this paper also examines the concept of corporate brand innovativeness and the influence of brand architecture as supportive and restrictive boundary conditions for its transfer.

Design/methodology/approach
This conceptual paper explains the nature, benefits and challenges of corporate brand innovativeness within the context of a firm’s brand architecture. On the basis of a literature review, the authors provide an overview of the domain and derive avenues for future research.

Findings
Research and practice have not fully realised the importance of corporate brand images for supporting a firms’ product portfolio. In particular, (corporate) marketing managers need to consider the potential value of favourable perceptions of corporate brand innovativeness across products and the moderating role of brand architecture.

Research limitations/implications
More empirical research is needed to understand the reciprocal relationship and transfer between corporate and product brand associations and equity.

Practical implications
A corporate marketing perspective allows firms to use corporate brand associations to support products and services for that brand. This paper discusses perceived corporate brand innovativeness as one particularly important corporate brand association.

Originality/value
The authors discuss the use of corporate brand associations under the consideration of brand architectures and boundaries and draw on several research streams in the brand management literature. Much of the branding and innovation literature centres on the product level; research on corporate brand innovativeness has been relatively neglected.