bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patterns and Outcomes of Recurrent Esophageal Cancer After Curative Esophagectomy
Authors: Yamashita Kotaro , Watanabe Masayuki , Mine Shinji , Kurogochi Takanori , Okamura Akihiko , Hayami Masaru , Imamura Yu 
Published: April 2017

AbstractBackgroundThe recurrence patterns and therapeutic outcomes of patients with recurrent esophageal cancer after curative esophagectomy are not fully understood.MethodsData on recurrence patterns and sites of recurrence in patients with recurrent esophageal cancer after curative esophagectomy from 2005 to 2015 were retrospectively analyzed. Time to recurrence after curative esophagectomy and survival after recurrence were compared among groups stratified by recurrence pattern and site. Multivariate analysis was performed to identify clinicopathological parameters influencing survival after recurrence.ResultsOf the 290 patients identified, a single pattern of recurrence occurred in 224 patients (77.2%) and a multiple pattern of recurrence occurred in 66 patients (22.8%). The most frequent recurrence pattern was lymph node in 173 patients (59.7%), followed by distant organ in 133 patients (45.9%). Median time to recurrence and median survival after recurrence of all patients were 228 and 327 days, respectively. Among patients with lymph node or lung recurrence, there were 5‐year survivors after recurrence who underwent multimodal therapy. Multivariate analysis revealed that longer disease‐free interval [hazard ratio (HR) 0.70, 95% confidence interval (95% CI) 0.52–0.93], single pattern of recurrence (HR 0.54, 95% CI 0.39–0.74), and curative treatment for recurrence (HR 0.17, 95% CI 0.10–0.28) were significantly associated with favorable prognosis.ConclusionsAlthough the prognosis of recurrent esophageal cancer remains unfavorable, if multimodal treatment that includes local therapy was curative, prognosis could improve, especially in patients with lymph node or lung recurrence.
Between neo-Ottomanism and Ottomania: navigating state-led and popular cultural representations of the past
Authors: Ergin Murat , Karakaya Yağmur 
Published: April 2017

AbstractIn contemporary Turkey, a growing interest in Ottoman history represents a change in both the official state discourse and popular culture. This nostalgia appropriates, reinterprets, decontextualizes, and juxtaposes formerly distinct symbols, ideas, objects, and histories in unprecedented ways. In this paper, we distinguish between state-led neo-Ottomanism and popular cultural Ottomania, focusing on the ways in which people in Turkey are interpellated by these two different yet interrelated discourses, depending on their social positions. As the boundary between highbrow and popular culture erodes, popular cultural representations come to reinterpret and rehabilitate the Ottoman past while also inventing new insecurities centering on historical “truth.” Utilizing in-depth interviews, we show that individuals juxtapose the popular television seriesMuhteşem Yüzyıl(The Magnificent Century) with what they deem “proper” history, in the process rendering popular culture a “false” version. We also identify four particular interpretive clusters among the consumers of Ottomania: for some, the Ottoman Empire was the epitome of tolerance, where different groups lived peacefully; for others, the imperial past represents Turkish and/or Islamic identities; and finally, critics see the empire as a burden on contemporary Turkey.
How Attachments to the Nation Shape Beliefs About the World: A Theory of Motivated Reasoning
Authors: Herrmann Richard K. 
Published: April 2017

AbstractIf competing beliefs about political events in the world stem largely from information asymmetries, then more information and knowledge should reduce the gap in competing perceptions. Empirical studies of decision making, however, often find just the reverse: as knowledge and the stakes in play go up, the beliefs about what is happening polarize rather than converge. The theory proposed here attributes this to motivated reasoning. Emotions inside the observer shape beliefs along with information coming from the outside world. A series of experiments embedded in a national survey of Americans finds that a primary driver of the beliefs someone forms about globalization, other countries, and the politics in the Middle East is how strongly they attach their social identity to the United States. Attachment produces more intense positive and negative emotions that in turn shape the interpretation of unfolding events and lead norms to be applied in an inconsistent fashion. People, in effect, rewrite reality around their favored course of action, marrying the logic of appropriateness to their own preferences. Beliefs, consequently, are not independent of preferences but related to them. Motivated reasoning, while not consistent with rational models, is predictable and can lead to expensive mistakes and double standards that undermine liberal internationalism.
Why Don't Trade Preferences Reflect Economic Self-Interest?
Authors: Rho Sungmin , Tomz Michael 
Published: April 2017

AbstractThe dominant approach to the study of international political economy assumes that the policy preferences of individuals and groups reflect economic self-interest. Recent research has called this assumption into question by suggesting that voters do not have economically self-interested preferences about trade policy. We investigate one potential explanation for this puzzling finding: economic ignorance. We show that most voters do not understand the economic consequences of protectionism. We then use experiments to study how voters would respond if they had more information about how trade barriers affect the distribution of income. We find that distributional cues generate two opposing effects: they make people more likely to express self-serving policy preferences, but they also make people more sensitive to the interests of others. In our study both reactions were evident, but selfish responses outweighed altruistic ones. Thus, if people knew more about the distributional effects of trade, the correlation between personal interests and policy preferences would tighten. By showing how the explanatory power of economic self-interest depends on beliefs about causality, this research provides a foundation for more realistic, behaviorally informed theories of international political economy.
Research Bets and Behavioral IR
Authors: Powell Robert 
Published: April 2017

AbstractBehavioral IR faces a fundamental challenge. The actors in most IR models and theories are not individuals—they are aggregates like states, ministries, interest groups, political parties, and rebel factions. There are two broad approaches to attempting to integrate behavioral research about individuals. The first, a quasi-behavioral approach, makes nonstandard assumptions about the preferences, beliefs, or decision-making processes of aggregate actors. The second tries to build theories in which the key actors are individuals. Pursuing the former means that the assumptions about actors will be only weakly linked to the empirical findings propelling behavioral research. The second approach faces formidable obstacles that international relations theory has confronted for a long time and for the most part has not overcome.
Due Deference: Cosmopolitan Social Identity and the Psychology of Legal Obligation in International Politics
Authors: Bayram A. Burcu 
Published: April 2017

AbstractWhy are some politicians guided by a sense of obligation toward international law but others are not? Why do some politicians have a social as opposed to an egoistic preference over compliance with international legal rules? Existing approaches largely assume that the structural features of the compliance environment shape preferences. As a result, they neglect the heterogeneity across decision makers' subjective beliefs in the legitimacy of international law, which is critical for explaining who exhibits a sense of obligation and has a non-egoistic preference for compliance. Drawing upon a large body of psychological research on social identity and influence, I argue that obligation toward international law has a behavioral foundation shaped by cosmopolitan social identity. Using data from an original survey of German politicians that includes two compliance experiments, I show that politicians with a high degree of cosmopolitanism are driven by a sense of legal obligation that results in a social preference for compliance while those low on cosmopolitanism lack the same sense of normative respect. Replicated in a second experimental study conducted with a convenience sample, my results indicate that strategic rationality in compliance applies, but only to a particular set of actors. By illuminating the psychological underpinnings of obligation toward international law, this study contributes to a richer understanding of compliance preferences and builds a bridge between instrumental and normative models.
Warming enhances old organic carbon decomposition through altering functional microbial communities
Authors: Cheng Lei , Zhang Naifang , Yuan Mengting , Xiao Jing , Qin Yujia , Deng Ye , Tu Qichao , Xue Kai , Van Nostrand Joy D , Wu Liyou , He Zhili , Zhou Xuhui , Leigh Mary Beth , Konstantinidis Konstantinos T , Schuur Edward A G , Luo Yiqi , Tiedje James M , Zhou Jizhong 
Published: April 2017

Abstract
Soil organic matter (SOM) stocks contain nearly three times as much carbon (C) as the atmosphere and changes in soil C stocks may have a major impact on future atmospheric carbon dioxide concentrations and climate. Over the past two decades, much research has been devoted to examining the influence of warming on SOM decomposition in topsoil. Most SOM, however, is old and stored in subsoil. The fate of subsoil SOM under future warming remains highly uncertain. Here, by combining a long-term field warming experiment and a meta-analysis study, we showed that warming significantly increased SOM decomposition in subsoil. We also showed that a decade of warming promoted decomposition of subsoil SOM with turnover times of decades to millennia in a tall grass prairie and this effect was largely associated with shifts in the functional gene structure of microbial communities. By coupling stable isotope probing with metagenomics, we found that microbial communities in warmed soils possessed a higher relative abundance of key functional genes involved in the degradation of organic materials with varying recalcitrance than those in control soils. These findings suggest warming may considerably alter the stability of the vast pool of old SOM in subsoil, contributing to the long-term positive feedback between the C cycle and climate.
Independence of nutrient limitation and carbon dioxide impacts on the Southern Ocean coccolithophore Emiliania huxleyi
Authors: Müller Marius N , Trull Thomas W , Hallegraeff Gustaaf M 
Published: April 2017

Abstract
Future oceanic conditions induced by anthropogenic greenhouse gas emissions include warming, acidification and reduced nutrient supply due to increased stratification. Some parts of the Southern Ocean are expected to show rapid changes, especially for carbonate mineral saturation. Here we compare the physiological response of the model coccolithophore Emiliania huxleyi (strain EHSO 5.14, originating from 50oS, 149oE) with pH/CO2 gradients (mimicking ocean acidification ranging from 1 to 4 × current pCO2 levels) under nutrient-limited (nitrogen and phosphorus) and -replete conditions. Both nutrient limitations decreased per cell photosynthesis (particulate organic carbon (POC) production) and calcification (particulate inorganic carbon (PIC) production) rates for all pCO2 levels, with more than 50% reductions under nitrogen limitation. These impacts, however, became indistinguishable from nutrient-replete conditions when normalized to cell volume. Calcification decreased three-fold and linearly with increasing pCO2 under all nutrient conditions, and was accompanied by a smaller ~30% nonlinear reduction in POC production, manifested mainly above 3 × current pCO2. Our results suggest that normalization to cell volume allows the major impacts of nutrient limitation (changed cell sizes and reduced PIC and POC production rates) to be treated independently of the major impacts of increasing pCO2 and, additionally, stresses the importance of including cell volume measurements to the toolbox of standard physiological analysis of coccolithophores in field and laboratory studies.
Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds
Authors: Wurzbacher Christian , Nilsson R Henrik , Rautio Milla , Peura Sari 
Published: April 2017

Abstract
In the transition zone of the shifting permafrost border, thaw ponds emerge as hotspots of microbial activity, processing the ancient carbon freed from the permafrost. We analyzed the microbial succession across a gradient of recently emerged to older ponds using three molecular markers: one universal, one bacterial and one fungal. Age was a major modulator of the microbial community of the thaw ponds. Surprisingly, typical freshwater taxa comprised only a small fraction of the community. Instead, thaw ponds of all age classes were dominated by enigmatic bacterial and fungal phyla. Our results on permafrost thaw ponds lead to a revised perception of the thaw pond ecosystem and their microbes, with potential implications for carbon and nutrient cycling in this increasingly important class of freshwaters.
A computational systems approach identifies synergistic specification genes that facilitate lineage conversion to prostate tissue
Authors: Talos Flaminia , Mitrofanova Antonina , Bergren Sarah K. , Califano Andrea , Shen Michael M. 
Published: April 2017

AbstractTo date, reprogramming strategies for generating cell types of interest have been facilitated by detailed understanding of relevant developmental regulatory factors. However, identification of such regulatory drivers often represents a major challenge, as specific gene combinations may be required for reprogramming. Here we show that a computational systems approach can identify cell type specification genes (master regulators) that act synergistically, and demonstrate its application for reprogramming of fibroblasts to prostate tissue. We use three such master regulators (FOXA1, NKX3.1 and androgen receptor, AR) in a primed conversion strategy starting from mouse fibroblasts, resulting in prostate tissue grafts with appropriate histological and molecular properties that respond to androgen-deprivation. Moreover, generation of reprogrammed prostate does not require traversal of a pluripotent state. Thus, we describe a general strategy by which cell types and tissues can be generated even with limited knowledge of the developmental pathways required for their specification in vivo.
Gating of TonB-dependent transporters by substrate-specific forced remodelling
Authors: Hickman Samuel J. , Cooper Rachael E. M. , Bellucci Luca , Paci Emanuele , Brockwell David J. 
Published: April 2017

AbstractMembrane proteins play vital roles in inside-out and outside-in signal transduction by responding to inputs that include mechanical stimuli. Mechanical gating may be mediated by the membrane or by protein(s) but evidence for the latter is scarce. Here we use force spectroscopy, protein engineering and bacterial growth assays to investigate the effects of force on complexes formed between TonB and TonB-dependent transporters (TBDT) from Gram-negative bacteria. We confirm the feasibility of protein-only mediated mechanical gating by demonstrating that the interaction between TonB and BtuB (a TBDT) is sufficiently strong under force to create a channel through the TBDT. In addition, by comparing the dimensions of the force-induced channel in BtuB and a second TBDT (FhuA), we show that the mechanical properties of the interaction are perfectly tuned to their function by inducing formation of a channel whose dimensions are tailored to the ligand.
Exploratory adaptation in large random networks
Authors: Schreier Hallel I. , Soen Yoav , Brenner Naama 
Published: April 2017

AbstractThe capacity of cells and organisms to respond to challenging conditions in a repeatable manner is limited by a finite repertoire of pre-evolved adaptive responses. Beyond this capacity, cells can use exploratory dynamics to cope with a much broader array of conditions. However, the process of adaptation by exploratory dynamics within the lifetime of a cell is not well understood. Here we demonstrate the feasibility of exploratory adaptation in a high-dimensional network model of gene regulation. Exploration is initiated by failure to comply with a constraint and is implemented by random sampling of network configurations. It ceases if and when the network reaches a stable state satisfying the constraint. We find that successful convergence (adaptation) in high dimensions requires outgoing network hubs and is enhanced by their auto-regulation. The ability of these empirically validated features of gene regulatory networks to support exploratory adaptation without fine-tuning, makes it plausible for biological implementation.
Phylogenetic analysis of metastatic progression in breast cancer using somatic mutations and copy number aberrations
Authors: Brown David , Smeets Dominiek , Székely Borbála , Larsimont Denis , Szász A. Marcell , Adnet Pierre-Yves , Rothé Françoise , Rouas Ghizlane , Nagy Zsófia I. , Faragó Zsófia , Tőkés Anna-Mária , Dank Magdolna , Szentmártoni Gyöngyvér , Udvarhelyi Nóra , Zoppoli Gabriele , Pusztai Lajos , Piccart Martine , Kulka Janina , Lambrechts Diether , Sotiriou Christos , Desmedt Christine 
Published: April 2017

AbstractSeveral studies using genome-wide molecular techniques have reported various degrees of genetic heterogeneity between primary tumours and their distant metastases. However, it has been difficult to discern patterns of dissemination owing to the limited number of patients and available metastases. Here, we use phylogenetic techniques on data generated using whole-exome sequencing and copy number profiling of primary and multiple-matched metastatic tumours from ten autopsied patients to infer the evolutionary history of breast cancer progression. We observed two modes of disease progression. In some patients, all distant metastases cluster on a branch separate from their primary lesion. Clonal frequency analyses of somatic mutations show that the metastases have a monoclonal origin and descend from a common ‘metastatic precursor’. Alternatively, multiple metastatic lesions are seeded from different clones present within the primary tumour. We further show that a metastasis can be horizontally cross-seeded. These findings provide insights into breast cancer dissemination.
Bi1Te1 is a dual topological insulator
Authors: Eschbach Markus , Lanius Martin , Niu Chengwang , Młyńczak Ewa , Gospodarič Pika , Kellner Jens , Schüffelgen Peter , Gehlmann Mathias , Döring Sven , Neumann Elmar , Luysberg Martina , Mussler Gregor , Plucinski Lukasz , Morgenstern Markus , Grützmacher Detlev , Bihlmayer Gustav , Blügel Stefan , Schneider Claus M. 
Published: April 2017

AbstractNew three-dimensional (3D) topological phases can emerge in superlattices containing constituents of known two-dimensional topologies. Here we demonstrate that stoichiometric Bi1Te1, which is a natural superlattice of alternating two Bi2Te3 quintuple layers and one Bi bilayer, is a dual 3D topological insulator where a weak topological insulator phase and topological crystalline insulator phase appear simultaneously. By density functional theory, we find "Equation missing" indices (0;001) and a non-zero mirror Chern number. We have synthesized Bi1Te1 by molecular beam epitaxy and found evidence for its topological crystalline and weak topological character by spin- and angle-resolved photoemission spectroscopy. The dual topology opens the possibility to gap the differently protected metallic surface states on different surfaces independently by breaking the respective symmetries, for example, by magnetic field on one surface and by strain on another surface.
Global distribution of particle phase state in atmospheric secondary organic aerosols
Authors: Shiraiwa Manabu , Li Ying , Tsimpidi Alexandra P. , Karydis Vlassis A. , Berkemeier Thomas , Pandis Spyros N. , Lelieveld Jos , Koop Thomas , Pöschl Ulrich 
Published: April 2017

AbstractSecondary organic aerosols (SOA) are a large source of uncertainty in our current understanding of climate change and air pollution. The phase state of SOA is important for quantifying their effects on climate and air quality, but its global distribution is poorly characterized. We developed a method to estimate glass transition temperatures based on the molar mass and molecular O:C ratio of SOA components, and we used the global chemistry climate model EMAC with the organic aerosol module ORACLE to predict the phase state of atmospheric SOA. For the planetary boundary layer, global simulations indicate that SOA are mostly liquid in tropical and polar air with high relative humidity, semi-solid in the mid-latitudes and solid over dry lands. We find that in the middle and upper troposphere SOA should be mostly in a glassy solid phase state. Thus, slow diffusion of water, oxidants and organic molecules could kinetically limit gas–particle interactions of SOA in the free and upper troposphere, promote ice nucleation and facilitate long-range transport of reactive and toxic organic pollutants embedded in SOA.
PIF1 family DNA helicases suppress R-loop mediated genome instability at tRNA genes
Authors: Tran Phong Lan Thao , Pohl Thomas J. , Chen Chi-Fu , Chan Angela , Pott Sebastian , Zakian Virginia A. 
Published: April 2017

AbstractSaccharomyces cerevisiae encodes two Pif1 family DNA helicases, Pif1 and Rrm3. Rrm3 promotes DNA replication past stable protein complexes at tRNA genes (tDNAs). We identify a new role for the Pif1 helicase: promotion of replication and suppression of DNA damage at tDNAs. Pif1 binds multiple tDNAs, and this binding is higher in rrm3Δ cells. Accumulation of replication intermediates and DNA damage at tDNAs is higher in pif1Δ rrm3Δ than in rrm3Δ cells. DNA damage at tDNAs in the absence of these helicases is suppressed by destabilizing R-loops while Pif1 and Rrm3 binding to tDNAs is increased upon R-loop stabilization. We propose that Rrm3 and Pif1 promote genome stability at tDNAs by displacing the stable multi-protein transcription complex and by removing R-loops. Thus, we identify tDNAs as a new source of R-loop-mediated DNA damage. Given their large number and high transcription rate, tDNAs may be a potent source of genome instability.
Single-photon test of hyper-complex quantum theories using a metamaterial
Authors: Procopio Lorenzo M. , Rozema Lee A. , Wong Zi Jing , Hamel Deny R. , O’Brien Kevin , Zhang Xiang , Dakić Borivoje , Walther Philip 
Published: April 2017

AbstractIn standard quantum mechanics, complex numbers are used to describe the wavefunction. Although this has so far proven sufficient to predict experimental results, there is no theoretical reason to choose them over real numbers or generalizations of complex numbers, that is, hyper-complex numbers. Experiments performed to date have proven that real numbers are insufficient, but the need for hyper-complex numbers remains an open question. Here we experimentally probe hyper-complex quantum theories, studying one of their deviations from complex quantum theory: the non-commutativity of phases. We do so by passing single photons through a Sagnac interferometer containing both a metamaterial with a negative refractive index, and a positive phase shifter. To accomplish this we engineered a fishnet metamaterial to have a negative refractive index at 780 nm. We show that the metamaterial phase commutes with other phases with high precision, allowing us to place limits on a particular prediction of hyper-complex quantum theories.