bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ghrelin affects stopover decisions and food intake in a long-distance migrant
Authors: Goymann Wolfgang , Lupi Sara , Kaiya Hiroyuki , Cardinale Massimiliano , Fusani Leonida 
Published: February 2017

Significance
Twice a year, billions of birds migrate across continents. Along their route, most species spend considerable time at stopover sites to replenish their fuel stores. What physiological signals tell them when they are ready to continue their journey? Ghrelin is a recently discovered hormone involved in appetite regulation. We found that ghrelin concentrations correlated positively with fat stores of wild garden warblers. Further, birds injected with ghrelin decreased their food intake and increased their drive to continue migration. Hence, our study shows that hormones regulating food intake and energy stores control migratory behavior. This is a previously unknown role for a hormonal system shared by birds and mammals, whose disruption causes eating disorders and obesity.
Multifunctional, inexpensive, and reusable nanoparticle-printed biochip for cell manipulation and diagnosis
Authors: Esfandyarpour Rahim , DiDonato Matthew J. , Yang Yuxin , Durmus Naside Gozde , Harris James S. , Davis Ronald W. 
Published: February 2017

Significance
Point-of-care diagnostics in the developing world and resource-limited areas require numerous special design considerations to provide effective early detection of disease. Of particular need for these contexts are diagnostic technologies featuring low costs, ease of use, and broad applicability. Here we present a nanoparticle-inkjet-printable microfluidics-based platform that fulfills these criteria and that we expect to significantly reduce the footprint, complexity, and cost of clinical diagnostics. This reusable $0.01 platform is miniaturized to handle small sample volumes and can perform numerous analyses. It can perform complex, minimally invasive analyses of single cells without specialized equipment and personnel. This inexpensive, accessible platform has broad applications in precision diagnostics and is a step toward the democratization of medical technologies.
Quon 3D language for quantum information
Authors: Liu Zhengwei , Wozniakowski Alex , Jaffe Arthur M. 
Published: February 2017

Significance
We give a 3D picture-language for quantum information. This language is based on an inherently 3D pictorial representation of particle-like excitations (quons) and of transformations acting on them. Mathematical identities and quantum information protocols are expressed through deformations of these pictures. We explore our language, highlighting conceptual insights, 3D visualizations, and suggestive intuition that it motivates for understanding algebra and quantum information.
High-resolution imaging and quantification of plasma membrane cholesterol by NanoSIMS
Authors: He Cuiwen , Hu Xuchen , Jung Rachel S. , Weston Thomas A. , Sandoval Norma P. , Tontonoz Peter , Kilburn Matthew R. , Fong Loren G. , Young Stephen G. , Jiang Haibo 
Published: February 2017

Significance
Biochemical studies have demonstrated that one pool of cholesterol in the plasma membrane is accessible to binding by bacterial cholesterol-binding proteins, whereas another pool is “sequestered” and inaccessible to binding by those proteins. Here, we used nanoscale secondary ion mass spectrometry (NanoSIMS) imaging, along with cholesterol-binding proteins that had been labeled with a stable isotope, to visualize and quantify the distribution of “accessible cholesterol” on the plasma membrane of mammalian cells. Our studies revealed that accessible cholesterol, as judged by cholesterol-binding proteins, is not evenly distributed on the plasma membrane but instead is enriched on the surface of microvilli. The accessible cholesterol on microvilli could be relevant to the movement of cholesterol away from the plasma membrane.
Intestinal NCoR1, a regulator of epithelial cell maturation, controls neonatal hyperbilirubinemia
Authors: Chen Shujuan , Lu Wenqi , Yueh Mei-Fei , Rettenmeier Eva , Liu Miao , Paszek Miles , Auwerx Johan , Yu Ruth T. , Evans Ronald M. , Wang Kepeng , Karin Michael , Tukey Robert H. 
Published: February 2017

SignificanceIn many parts of the world, especially in low- and middle-income countries, severe neonatal hyperbilirubinemia (SNH) is associated with substantial mortality and long-term morbidities. Although the immediate and rapid rise in total serum bilirubin (TSB) originating from lysis of red blood cells has been linked to genetic predisposition, preterm births, and blood type incompatibilities, the inability to efficiently metabolize bilirubin results from delayed expression of UDP-glucuronosyltransferase 1A1 (UGT1A1). In this study, the mechanism associated with delayed expression of the humanUGT1A1gene in neonatal mice that are humanized for theUGT1locus is described. Neonatal humanizedUGT1(hUGT1) mice develop SNH and control TSB levels by nuclear receptor corepressor 1 (NCoR1)-directed repression of intestinal epithelial cell maturation, an event linked to expression of theUGT1A1gene.
Fractal Analysis May Improve the Preoperative Identification of Atypical Meningiomas
Authors: Czyz Marcin , Radwan Hesham , Li Jian Y. , Filippi Christopher G. , Tykocki Tomasz , Schulder Michael 
Published: February 2017

Abstract

BACKGROUND: There is no objective and readily accessible method for the preoperative determination of atypical characteristics of a meningioma grade.

OBJECTIVE: To evaluate the feasibility of using fractal analysis as an adjunctive tool to conventional radiological techniques in visualizing histopathological features of meningiomas.

METHODS: A group of 27 patients diagnosed with atypical (WHO grade II) meningioma and a second group of 27 patients with benign (WHO grade I) meningioma were enrolled in the study. Preoperative brain magnetic resonance (MR) studies (T1-wieghted, post-gadolinium) were processed and analyzed to determine the average fractal dimension (FDa) and maximum fractal dimension (FDm) of the contrast-enhancing region of the tumor using box-count method. FDa and FDm as well as particular radiological features were included in the logistic regression model as possible predictors of malignancy.

RESULTS: The cohort consisted of 34 women and 20 men, mean age of 62 ± 15 yr. Fractal analysis showed good interobserver reproducibility (Kappa >0.70). Both FDa and FDm were significantly higher in the atypical compared to the benign meningioma group (P < .0001). Multivariate logistic regression model reached statistical significance with P = .0001 and AUC = 0.87. The FDm, which was greater than 1.31 (odds ratio [OR], 12.30; P = .039), and nonskull base localization (OR, .052; P = .015) were confirmed to be statistically significant predictors of the atypical phenotype.

CONCLUSION: Fractal analysis of preoperative MR images appears to be a feasible adjunctive diagnostic tool in identifying meningiomas with potentially aggressive clinical behavior.
Search Strategies for Intentionality in the Honeybee Brain
Authors: Menzel Randolf 
Published: February 2017

Abstract
Do insects, like other animals, expect future events, predict the value of potential actions, and decide between behavioral options without having access to the indicating stimuli? These cognitive capacities are captured by the term intentionality. This chapter addresses the question at two levels, behavior and neural correlates. Behavioral studies are performed with freely flying bees in the natural environment and with harnessed bees in the laboratory by applying the proboscis extension response paradigm. Data are presented and discussed on context-dependent learning, selective attention, rule learning, navigation, communication, and sleep-dependent memory consolidation. Although behavioral analyses document the rich repertoire and the cognitive dimensions of honeybee behavior, intentionality is nearly impossible to prove by behavioral analyses only and neural correlates are essential.
The Vertical Lobe of Cephalopods
Authors: Turchetti-Maia Ana , Shomrat Tal , Hochner Binyamin 
Published: February 2017

Abstract
We show that the cephalopod vertical lobe (VL) is a promising system for assessing the function and organization of the neuronal circuitry mediating complex learning and memory behavior. Studies in octopus and cuttlefish VL networks suggest an independent evolutionary convergence into a matrix organization of a divergence-convergence (“fan-out fan-in”) network with activity-dependent long-term plasticity mechanisms. These studies also show, however, that the properties of the neurons, neurotransmitters, neuromodulators, and mechanisms of induction and maintenance of long-term potentiation are different from those evolved in vertebrates and other invertebrates, and even highly variable among these two cephalopod species. This suggests that complex networks may have evolved independently multiple times and that, even though memory and learning networks share similar organization and cellular processes, there are many molecular ways of constructing them.
Motor Control in Soft-Bodied Animals
Authors: Levy Guy , Nesher Nir , Zullo Letizia , Hochner Binyamin 
Published: February 2017

Abstract
Motor Control is essentially the computations required for producing coordinated sequences of commands from the controlling system (i.e., nervous system) to the actuation system (i.e., muscles) to generate efficient motion. The level of motor control complexity depends on the number of free parameters (degrees of freedom) that have to be coordinated. This number is much smaller in skeletal animals because they have a rather limited number of joints. In soft bodied animals, like the octopus, this number is virtually infinite. Here we show that the efficient motor control system of the octopus uses solutions that are very different from those of articulated animals, and it involves embodied co-evolution of the unique morphology together with the organization of the nervous and muscular systems to enable control strategies that are best suited for a highly active soft-bodied animal like the octopus.
Love and the Law
Authors: Brake Elizabeth 
Published: February 2017

Abstract
Both the free love tradition and philosophers appalled by the “love revolution” in marriage saw an antagonism between love and legal obligation. Marriage abolitionists and queer theorists have more recently argued against state legitimation of love relationships. This chapter briefly outlines the history of the concept of romantic love and its unlawfulness. It describes how law in modern liberal states has treated love, both in marriage law and in legal regulation of sex. It then turns to normative questions: Are love and legal institutions incompatible? What laws should there be regarding love or sex? The chapter considers arguments that legal institutions designed to protect love relationships wrongly burden the choice to remain in relationships, that they threaten spontaneous emotional response, that they are inherently unstable, that they are oppressive, and that love is a political virtue. I conclude that we are still witnessing the love revolution unfold.
Written Media in Antiquity
Authors: Hedrick Charles W. 
Published: February 2017

AbstractThis chapter examines literature from the perspective of written media in the ancient Roman world: material, format, and circulation. More specifically, it proposes a taxonomy of writing based on a consideration of written media that does not correspond precisely to the modern distinction between literary and documentary texts. The discussion is predicated on two oppositions: the unique versus the reproduced and the enduring versus the disposable. In exploring the various forms taken by ancient writing, the article highlights the symbolic or textual value of a written text that is correlated with the text’s uniqueness and reproduction, transience or permanence. It describes four categories of texts: monumental text, literary text, instrumental text, and communicative text. Finally, it considers institutions that enshrine social classifications of writing, namely, libraries and archives: the former contain literature, the latter documents.
The Legacy of Newton for the Pre-Critical Kant
Authors: Massimi Michela 
Published: February 2017

Abstract
This chapter assesses Newton’s legacy for Kant by concentrating on the evolution of Kant’s view of space in the pre-Critical period (1748–1768), with two main goals in mind. The first goal is to draw attention to the role that Newton’s matter theory and chemistry played for the young Kant. The second is to argue against the received view that has portrayed the young Kant as embracing Newton’s absolute space in 1768 via the argument from incongruent counterparts (short-lived as this conversion to Newton’s absolute space proved to be). By contrast to the received view, this chapter shows that in the period 1748–1768, Kant was working with a thoroughgoing relationalism, consonant with Kant’s matter theory, which was, in turn, inspired by speculative Newtonian experimentalism itself. Hence, the case is made for a slightly different interpretive stance on Newton’s legacy for the young Kant.
Newton and the Cartesians
Authors: Schmaltz Tad M. 
Published: February 2017

Abstract
This chapter explores the relation during the early modern period of the views of Isaac Newton and the Newtonians to those of Réne Descartes and the Cartesians. The focus is on the early eighteenth-century conflict within the French Académie des sciences between Newtonian gravitational theory and Cartesian vortical physics. Against a revisionary view in the literature, it is argued that Nicolas Malebranche and Bernard le Bovier de Fontenelle are properly characterized as the main defenders of Cartesianism within the Académie. This is despite the fact that Malebranche and Fontenelle disagreed with each other on fundamental issues, and despite the fact that both deviated substantially from Descartes. There also is a consideration of the distinctive contributions to the development of French Newtonianism in the technical work, within the Académie, of Pierre-Louis Maupertuis, and in the more popular work, outside of that institution, of Voltaire.
Newton and Leibniz on the Relativity of Motion
Authors: Arthur Richard T. W. 
Published: February 2017

Abstract
In some respects, there is more agreement between Newton and Leibniz on the relativity of motion than is generally recognized. Both were convinced Copernicans, and both accepted that motion could not be a merely extrinsic denomination—there would have to be true motions, and not just apparent ones. And both sought to discriminate true from apparent motions by reference to the causes of motion and to force. Where they differed was in their radically divergent understandings of how causes are related to forces, of how forces are to be determined in relation to quantity of motion, and of the ontological status of absolute or mathematical space. This chapter aims to throw light on the two philosophers’ respective views on the relativity of motion by considering them in their historical genesis.
Phase relations in a forced turbulent boundary layer: implications for modelling of high Reynolds number wall turbulence
Authors: Duvvuri Subrahmanyam , McKeon Beverley 
Published: February 2017

Phase relations between specific scales in a turbulent boundary layer are studied here by highlighting the associated nonlinear scale interactions in the flow. This is achieved through an experimental technique that allows for targeted forcing of the flow through the use of a dynamic wall perturbation. Two distinct large-scale modes with well-defined spatial and temporal wavenumbers were simultaneously forced in the boundary layer, and the resulting nonlinear response from their direct interactions was isolated from the turbulence signal for the study. This approach advances the traditional studies of large- and small-scale interactions in wall turbulence by focusing on the direct interactions between scales with triadic wavenumber consistency. The results are discussed in the context of modelling high Reynolds number wall turbulence.This article is part of the themed issue ‘Toward the development of high-fidelity models of wall turbulence at large Reynolds number’.
A statistical state dynamics approach to wall turbulence
Authors: Farrell B. F. , Gayme D. F. , Ioannou P. J. 
Published: February 2017

This paper reviews results obtained using statistical state dynamics (SSD) that demonstrate the benefits of adopting this perspective for understanding turbulence in wall-bounded shear flows. The SSD approach used in this work employs a second-order closure that retains only the interaction between the streamwise mean flow and the streamwise mean perturbation covariance. This closure restricts nonlinearity in the SSD to that explicitly retained in the streamwise constant mean flow together with nonlinear interactions between the mean flow and the perturbation covariance. This dynamical restriction, in which explicit perturbation–perturbation nonlinearity is removed from the perturbation equation, results in a simplified dynamics referred to as the restricted nonlinear (RNL) dynamics. RNL systems, in which a finite ensemble of realizations of the perturbation equation share the same mean flow, provide tractable approximations to the SSD, which is equivalent to an infinite ensemble RNL system. This infinite ensemble system, referred to as the stochastic structural stability theory system, introduces new analysis tools for studying turbulence. RNL systems provide computationally efficient means to approximate the SSD and produce self-sustaining turbulence exhibiting qualitative features similar to those observed in direct numerical simulations despite greatly simplified dynamics. The results presented show that RNL turbulence can be supported by as few as a single streamwise varying component interacting with the streamwise constant mean flow and that judicious selection of this truncated support or ‘band-limiting’ can be used to improve quantitative accuracy of RNL turbulence. These results suggest that the SSD approach provides new analytical and computational tools that allow new insights into wall turbulence.This article is part of the themed issue ‘Toward the development of high-fidelity models of wall turbulence at large Reynolds number’.
Modelling high Reynolds number wall–turbulence interactions in laboratory experiments using large-scale free-stream turbulence
Authors: Dogan Eda , Hearst R. Jason , Ganapathisubramani Bharathram 
Published: February 2017

A turbulent boundary layer subjected to free-stream turbulence is investigated in order to ascertain the scale interactions that dominate the near-wall region. The results are discussed in relation to a canonical high Reynolds number turbulent boundary layer because previous studies have reported considerable similarities between these two flows. Measurements were acquired simultaneously from four hot wires mounted to a rake which was traversed through the boundary layer. Particular focus is given to two main features of both canonical high Reynolds number boundary layers and boundary layers subjected to free-stream turbulence: (i) the footprint of the large scales in the logarithmic region on the near-wall small scales, specifically the modulating interaction between these scales, and (ii) the phase difference in amplitude modulation. The potential for a turbulent boundary layer subjected to free-stream turbulence to ‘simulate’ high Reynolds number wall–turbulence interactions is discussed. The results of this study have encouraging implications for future investigations of the fundamental scale interactions that take place in high Reynolds number flows as it demonstrates that these can be achieved at typical laboratory scales.
This article is part of the themed issue ‘Toward the development of high-fidelity models of wall turbulence at large Reynolds number’.
Daisyfield gene drive systems harness repeated genomic elements as a generational clock to limit spread
Authors: Min John , Noble Charleston , Najjar Devora , Esvelt Kevin M. 
Published: February 2017

AbstractMethods of altering wild populations are most useful when inherently limited to local geographic areas. Here we describe a novel form of gene drive based on the introduction of multiple copies of an engineered ‘daisy’ sequence into repeated elements of the genome. Each introduced copy encodes guide RNAs that target one or more engineered loci carrying the CRISPR nuclease gene and the desired traits. When organisms encoding a drive system are released into the environment, each generation of mating with wild-type organisms will reduce the average number of the guide RNA elements per ‘daisyfield’ organism by half, serving as a generational clock. The loci encoding the nuclease and payload will exhibit drive only as long as a single copy remains, placing an inherent limit on the extent of spread.
The Arabidopsis Framework Model version 2 predicts the organism-level effects of circadian clock gene mis-regulation
Authors: Chew Yin Hoon , Seaton Daniel D. , Mengin Virginie , Flis Anna , Mugford Sam T. , George Gavin M. , Moulin Michael , Hume Alastair , Zeeman Samuel C. , Fitzpatrick Teresa B. , Smith Alison M. , Stitt Mark , Millar Andrew J. 
Published: February 2017

AbstractPredicting a multicellular organism’s phenotype quantitatively from its genotype is challenging, as genetic effects must propagate across scales. Circadian clocks are intracellular regulators that control temporal gene expression patterns and hence metabolism, physiology and behaviour. Here we explain and predict canonical phenotypes of circadian timing in a multicellular, model organism. We used diverse metabolic and physiological data to combine and extend mathematical models of rhythmic gene expression, photoperiod-dependent flowering, elongation growth and starch metabolism within a Framework Model for the vegetative growth ofArabidopsis thaliana, sharing the model and data files in a structured, public resource. The calibrated model predicted the effect of altered circadian timing upon each particular phenotype in clock-mutant plants under standard laboratory conditions. Altered night-time metabolism of stored starch accounted for most of the decrease in whole-plant biomass, as previously proposed. Mobilisation of a secondary store of malate and fumarate was also mis-regulated, accounting for any remaining biomass defect. We test three candidate mechanisms for the accumulation of these organic acids. Our results link genotype through specific processes to higher-level phenotypes, formalising our understanding of a subtle, pleiotropic syndrome at the whole-organism level, and validating the systems approach to understand complex traits starting from intracellular circuits.This work updates the first biorXiv version, February 2017,https://doi.org/10.1101/105437, with an expanded description and additional analysis of the same core data sets and the same FMv2 model, summary tables and supporting, follow-on data from three further studies with further collaborators. This biorXiv revision constitutes the second version of this report.