bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gastrointestinal stromal tumor enhancers support a transcription factor network predictive of clinical outcome
Authors: Hemming Matthew L. , Lawlor Matthew A. , Zeid Rhamy , Lesluyes Tom , Fletcher Jonathan A. , Raut Chandrajit P. , Sicinska Ewa T. , Chibon Frédéric , Armstrong Scott A. , Demetri George D. , Bradner James E. 
Published: June 2018

Significance
Enhancers are regulatory regions in DNA that govern gene expression and orchestrate cellular phenotype. We describe the enhancer landscape of gastrointestinal stromal tumor (GIST), identifying established and unique GIST-associated genes that characterize this neoplasm. Focusing on transcriptional regulators, we identify a core group of transcription factors underlying GIST biology. Two transcription factors, BARX1 and HAND1, have mutually exclusive enhancers and expression in localized and metastatic GIST, respectively. HAND1 is necessary to sustain GIST proliferation and KIT expression, and binds to enhancers of GIST-associated genes. The relative expression of BARX1 and HAND1 is predictive of clinical behavior in GIST patients. These results expand our understanding of gene regulation in this disease and identify biomarkers that may be helpful in diagnosis and treatment.
Exploitation drives an ontogenetic-like deepening in marine fish
Authors: Frank Kenneth T. , Petrie Brian , Leggett William C. , Boyce Daniel G. 
Published: June 2018

Significance
The occupation of progressively deeper waters with increasing size and age of fish is common among commercially exploited species, a behavior attributed to evolved ontogenies. Recently deepening has been attributed to ocean warming. We evaluated the possibility, ignored in previous analyses, that these patterns result from selective exploitation of larger individuals. We found that size-selective exploitation accounted for >70% of the deepening of cod on the Scotian Shelf (Northwest Atlantic). This deepening declined dramatically when exploitation was banned. Ontogeny contributed to the remaining variance. The claim that deepening can be used as an index of ocean warming should be exercised with caution; the overarching effect of exploitation should be specifically addressed in all such analyses.
A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure
Authors: Steckelberg Anna-Lena , Akiyama Benjamin M. , Costantino David A. , Sit Tim L. , Nix Jay C. , Kieft Jeffrey S. 
Published: June 2018

Significance
Folded RNA elements are essential for diverse biological processes. Recently discovered examples include viral xrRNAs, which co-opt the cellular RNA decay machinery within a novel noncoding RNA production pathway. Here we characterize an xrRNA with no apparent evolutionary link or sequence homology to those described previously. Our results show that xrRNAs are an authentic class of functional RNAs that have arisen independently in different contexts, suggesting that they may be widespread. The detailed 3D structure of one of these xrRNAs reveals that an underlying structural topology may be the key feature that confers exoribonuclease resistance to diverse xrRNAs.
Robust nonequilibrium pathways to microcompartment assembly
Authors: Rotskoff Grant M. , Geissler Phillip L. 
Published: June 2018

Significance
The structure of the carboxysome resembles a viral capsid, but, unlike many viruses, the monomers of its shell do not appear to fit together in a uniquely preferred way. As a result, the size and shape of this bacterial microcompartment must be determined by the dynamics of its self-assembly process. Using theory and simulation of a model system, we show that the mechanism of assembling such a structure can proceed through nonequilibrium dynamics that are both reliable and controllable. We identify experimentally tunable parameters that modulate the shape and size of the assembled structure, advancing strategies to repurpose natural microcompartments and to create synthetic mimics.
TMS-induced neuronal plasticity enables targeted remodeling of visual cortical maps
Authors: Kozyrev Vladislav , Staadt Robert , Eysel Ulf T. , Jancke Dirk 
Published: June 2018

Significance
Transcranial magnetic stimulation (TMS) holds promise as a tool for noninvasively facilitating plastic changes in cortical networks. However, highly resolved visualization of its modulatory effects remains elusive because current neuroimaging techniques applicable in humans are limited in spatiotemporal resolution. Here we used an imaging approach with voltage-sensitive dye and tracked, at submillimeter range, TMS-induced plastic changes across cat primary visual cortex. We show that high-frequency 10-Hz TMS induces a state where visual cortical maps are transiently “destabilized.” In turn, the cortex was sensitized to a bias in input—here imposed by prolonged exposure to a single visual orientation—and primed to relearn connectivity patterns. These findings implicate an early post-TMS time window for promising therapeutic interventions through TMS.
In vitro biomimetic engineering of a human hematopoietic niche with functional properties
Authors: Bourgine Paul E. , Klein Thibaut , Paczulla Anna M. , Shimizu Takafumi , Kunz Leo , Kokkaliaris Konstantinos D. , Coutu Daniel L. , Lengerke Claudia , Skoda Radek , Schroeder Timm , Martin Ivan 
Published: June 2018

SignificanceThe development of an in vitro human bone marrow (BM) tissue appears essential to compile information on human hematopoiesis. Conventional systems fail at both capturing the complexity of the bone marrow niche while allowing the maintenance of functional hematopoietic stem cells (HSCs). Here, we report the development of a human 3D (BM) analogue in a perfusion-based bioreactor system, partially recapitulating structural, compositional, and organizational features of the native human osteoblastic niche environment. The engineered tissue supports the maintenance of some hematopoietic stem and progenitor cell (HSPC) properties. This provides an advanced technological platform of broad fundamental and translational relevance, including the study of human HSPC biology and interactions with their niche, the manipulation of functional human HSPCs, or the identification of factors influencing human hematopoiesis.
Memory-related hippocampal activation in the sleeping toddler
Authors: Prabhakar Janani , Johnson Elliott G. , Nordahl Christine Wu , Ghetti Simona 
Published: June 2018

Significance
One of the most fascinating questions in psychology and neuroscience pertains to how young children gain the capacity to remember their past. Early hippocampal processes have been implicated in this ability, but a lack of viable methods has hindered assessments of their contribution in early human development. We employed a functional magnetic resonance imaging paradigm that captures memory-related hippocampal function during natural nocturnal sleep in toddlers. Our results provide direct evidence of a connection between hippocampal function and early memory ability. This experimental approach overcomes previous challenges and promises to pave the way to investigations linking changes in brain function to early development of learning mechanisms, including applications to typical and atypical development.
Historical approaches to AVT reception
Authors: Zanotti Serenella 
Published: June 2018

Abstract
Drawing on insights from historical film audience studies, this chapter aims to explore the role AVT has had in shaping the viewing experience of film audiences in the past, as well as the methods available to researchers for investigating AVT reception in a historical perspective. The chapter is organized into three main sections. Part 1 provides an overview of the range of studies on historical reception and AVT. It is argued that, although there has been wide and growing interest in the lived experiences of film audiences, little attention has been paid to translation and its implication for the reception of films and television products. In Part 2, selected studies conducted by film and AVT scholars are reported to explore how the issue of translation has affected the reception of films as well as the movie-going experience in different cultural contexts and in reference to different translation modes. Part 3 deals with theories, methods and research practices, looking at the vast array of empirical methods that have been employed in historical reception studies. Research methods based on classical sources such as press reviews, interviews, and articles are here illustrated, highlighting their potential and limitations compared to other methodologies. Studies dealing with different research approaches are reported to show how existing methods can be used in historical research and to consider whether new approaches can be devised.
Dubbing, perception and reception
Authors: Di Giovanni Elena 
Published: June 2018

Abstract
Dubbing is one of the oldest, most commonly employed and best known audiovisual translation techniques, yet still relatively underresearched, at least from the point of view of its reception by audiences across the world. This chapter offers an overview of approaches, tools and methods which can be used for reception-centred dubbing research, by drawing from the literature on media and reception studies. Subsequently, it provides an overview of studies on the perception and/or reception of dubbed films and television products as carried out and published by scholars within and outside audiovisual translation studies, in Europe and beyond. In its final sections, the chapter offers a critical reading of the studies previously reviewed, in view of fostering further research along these lines and encouraging audience understanding, involvement and empowerment.
漢語動詞雙音化過程中的形式選擇和功能表現 (Patterns and functions of verbal disyllabification)
Authors: Dong Xiufang 
Published: June 2018

抽象
以往文獻對於漢語詞彙雙音化中具體是什麼樣的雙音形式替代了什麼樣的單音形式及其中的選擇規律缺乏研究。本文以動詞的雙音化為考察對象，重點討論的是動賓式和動補式這兩種雙音複合模式與單音形式之間的對應規律，發現雙音化時不同的形式選擇與原單音動詞不同的詞彙語義特徵有關。不包含內在終結點的動詞雙音化時，傾向於選擇動賓式。動賓式雙音複合詞和原來的單音動詞形式相比，有的是增加了動詞部分，很多情況下增加的是輕動詞，原單音動詞變為賓語，可以轉類為名詞而成為名詞性賓語，也可以仍然保持動詞性而充當謂詞性賓語；有的是增加了賓語部分，或者是增加一個原單音動詞詞彙語義中本就包含的受事成分作賓語，或者是增加一個環境論元作賓語；還有的是採用了與原來的單音動詞完全沒有相同之處的動賓形式。包含內在終結點的動詞在雙音化時傾向於選擇動補式，詞彙語義中所隱含的結果狀態比較顯著的單音動詞傾向於在前面添加一個動詞來構成動補式雙音詞，而詞彙語義中所隱含的結果狀態不顯著的則傾向於添加一個虛化的補語來構成動補式雙音詞。內部結構不同的雙音形式對應不同的功能特徵。
Establishment of an effective oligotrophic cultivation system for Rhodococcus erythropolis N9T-4
Authors: Matsuoka Tomohiro , Yoshida Nobuyuki 
Published: June 2018

ABSTRACT
Rhodococcus erythropolis N9T-4 grows on an inorganic solid-state medium with no additional carbon and energy sources; however, it is unable to grow well in a liquid culture medium under the oligotrophic conditions. We examined submerged cultivations of N9T-4 using a polyurethane foam sponge to achieve approximately 10 times of the oligotrophic growth of the bacterium in the liquid culture medium.
Ecosystem service of green infrastructure for adaptation to urban growth: function and configuration
Authors: Wang Yun-Cai , Shen Jia-Ke , Xiang Wei-Ning 
Published: June 2018

ABSTRACT

Objectives:
(1) to explore what kind of green infrastructure (GI) meets the demand for urban ecological security of rapid urbanization areas; (2) to figure out how to determine the specific function and configuration of GI from ecosystem service requirements of urban ecological security.

Methods:
(1) Through the literature review, this article summarizes the function and structure evolution of GI in order to adapt to urban growth. (2) Standing on the imperfect ecological functions and unreasonable spatial configurations, this article builds up a conceptual model for the optimization of green infrastructure ecosystem services to meet the demand for the green infrastructure pattern needed by urban growth.

Results:
The optimization framework consists of four central function modules and its regulating and controlling mechanisms, including: (1) Balancing supply and demand of GI’s ecosystem service; (2) Measuring and evaluating GI’s ecosystem services; (3) Elevating and optimizing GI’s ecosystem service; (4) Building urban ecological security pattern with high efficiency of GI’s ecosystem services. Moreover, this framework provides guidance for the planning and design of GI and the urban ecological security pattern building in rapid urbanization areas based on balancing supply and demand of GI’s ecosystem services.

Conclusion:
The conceptual model of GI’s ecosystem service optimization based on balancing supply and demand shows a new path to meet the needs of urban growth and build a city's ecological security pattern through upgrading and optimizing GI.
The effect of addition sucrose concentrations toward weight of Nata DE Lontar (Borassus flabellifer) Linn
Authors: Widiyanti N L P M , Mulyadiharja S , Sukarta I N , Pradnyandari N W I 
Published: June 2018

Abstract
Making nata made from older Borrasus flabellifer wine (namely Nata de Lontar), it needs addition sucrose to produce nata with the optimum weight. The research aimed to know (1) The effect of addition sucrose with different concentrations on older palm wine toward the weight of “nata de lontar” (Borrasus flabellifer) (2) The concentration of sucrose is the most influential part to produce optimum weight of “nata de lontar”. This study belonged to an true experimental research with posttest only control group design. The independent variable in this research was the addition of sucrose with different concentrations of 6%, 9 %, and 12 %. The dependent variable in this study was the weight of nata. The results were analyzed using one-way anova and then followed by a test of Least Significant Difference at the 5 % significance level. The results of the experiment show (1) There have been a weight difference “nata de lontar” from bacterial fermentation in older palm wine Borassus flabellifer Linn medium with the addition of different concentrations of sucrose with p-value less than < 0.05. (2) Addition 12% sucrose concentration to the medium has influenced the formation of nata optimum results with average 46.13 grams.
Altered Cortical and Hippocampal Excitability in TgF344-AD Rats Modeling Alzheimer’s Disease Pathology
Authors: Stoiljkovic Milan , Kelley Craig , Stutz Bernardo , Horvath Tamas L , Hajós Mihály 
Published: June 2018

AbstractCurrent findings suggest that accumulation of amyloid-β (Aβ) and hyperphosphorylated tau in the brain disrupt synaptic function in hippocampal–cortical neuronal networks leading to impairment in cognitive and affective functions in Alzheimer’s disease (AD). Development of new disease-modifying AD drugs are challenging due to the lack of predictive animal models and efficacy assays. In the present study we recorded neural activity in TgF344-AD rats, a transgenic model with a full array of AD pathological features, including age-dependent Aβ accumulation, tauopathy, neuronal loss, and cognitive impairments. Under urethane anesthesia, TgF344-AD rats showed significant age-dependent decline in brainstem-elicited hippocampal theta oscillation and decreased theta-phase gamma-amplitude coupling comparing to their age-matched wild-type counterparts. In freely-behaving condition, the power of hippocampal theta oscillation and gamma power during sharp-wave ripples were significantly lower in TgF344-AD rats. Additionally, these rats showed impaired coherence in both intercortical and hippocampal–cortical network dynamics, and increased incidence of paroxysmal high-voltage spindles, which occur during awake, behaviorally quiescent state. TgF344-AD rats demonstrated impairments in sensory processing, having diminished auditory gating and 40-Hz auditory evoked steady-state response. The observed differences in neurophysiological activities in TgF344-AD rats, which mirror several abnormalities described in AD patients, may be used as promising markers to monitor disease-modifying therapies.
Target Interneuron Preference in Thalamocortical Pathways Determines the Temporal Structure of Cortical Responses
Authors: Hay Y Audrey , Naudé Jérémie , Faure Philippe , Lambolez Bertrand 
Published: June 2018

AbstractSensory processing relies on fast detection of changes in environment, as well as integration of contextual cues over time. The mechanisms by which local circuits of the cerebral cortex simultaneously perform these opposite processes remain obscure. Thalamic “specific” nuclei relay sensory information, whereas “nonspecific” nuclei convey information on the environmental and behavioral contexts. We expressed channelrhodopsin in the ventrobasal specific (sensory) or the rhomboid nonspecific (contextual) thalamic nuclei. By selectively activating each thalamic pathway, we found that nonspecific inputs powerfully activate adapting (slow-responding) interneurons but weakly connect fast-spiking interneurons, whereas specific inputs exhibit opposite interneuron preference. Specific inputs thereby induce rapid feedforward inhibition that limits response duration, whereas, in the same cortical area, nonspecific inputs elicit delayed feedforward inhibition that enables lasting recurrent excitation. Using a mean field model, we confirm that cortical response dynamics depends on the type of interneuron targeted by thalamocortical inputs and show that efficient recruitment of adapting interneurons prolongs the cortical response and allows the summation of sensory and contextual inputs. Hence, target choice between slow- and fast-responding inhibitory neurons endows cortical networks with a simple computational solution to perform both sensory detection and integration.
Feeding ecology of early life stages of mesopelagic fishes in the equatorial and tropical Atlantic
Authors: Contreras Tabit , Olivar M Pilar , Hulley P Alexander , Fernández de Puelles M Luz 
Published: June 2018

Abstract
We analysed the trophic ecology of the early ontogenetic stages of six mesopelagic fish species (Bathylagoides argyrogaster, Argyropelecus sladeni, Sternoptyx diaphana, Diaphus vanhoeffeni, Hygophum macrochir, and Myctophum affine), which have different morphologies, vertical distributions, and taxonomic affiliations. The larvae and transforming stages of the sternoptychids fed both during the day and at night. However, larvae of the other species fed during the day, as they apparently rely on light for prey capture. The transforming stages of myctophids showed a similar daylight feeding pattern to their larvae, but in D. vanhoeffeni both day and night feeding was evident, thereby indicating the progressive change toward the adult nocturnal feeding pattern. The number of prey and their maximum sizes were linked to predator gut morphology and gape size. Although the maximum prey size increased with predator development, postflexion larvae and transforming stages also preyed on small items, so that the trophic niche breath did not show evidence of specialization. In all the species, copepods dominated the larval diet, but the transforming stages were characterized by increasing diet diversity. Despite the poor development of these early stages, Chesson’s selectivity index calculated for larvae and transforming stages showed positive selection for particular prey.
Stillbirth, newborn and infant mortality: trends and inequalities in four population-based birth cohorts in Pelotas, Brazil, 1982–2015
Authors: Menezes Ana M B , Barros Fernando C , Horta Bernardo L , Matijasevich Alicia , Bertoldi Andréa Dâmaso , Oliveira Paula D , Victora Cesar G ,   Pelotas Cohorts Study Group, Barros Aluisio J D , Bassani Diego G , Wehrmeister Fernando C , Gonçalves Helen , Santos Iná S , Murray Joseph , Tovo-Rodrigues Luciana , Assunção Maria Cecilia F , Silveira Mariangela F , Domingues Marlos Rodrigues , Hallal Pedro R C 
Published: June 2018

Abstract

Background
Infant-mortality rates have been declining in many low- and middle-income countries, including Brazil. Information on causes of death and on socio-economic inequalities is scarce.

Methods
Four birth cohorts were carried out in the city of Pelotas in 1982, 1993, 2004 and 2015, each including all hospital births in the calendar year. Surveillance in hospitals and vital registries, accompanied by interviews with doctors and families, detected fetal and infant deaths and ascertained their causes. Late-fetal (stillbirth)-, neonatal- and post-neonatal-death rates were calculated.

Results
All-cause and cause-specific death rates were reduced. During the study period, stillbirths fell by 47.8% (from 16.1 to 8.4 per 1000), neonatal mortality by 57.0% (from 20.1 to 8.7) and infant mortality by 62.0% (from 36.4 to 13.8). Perinatal causes were the leading causes of death in the four cohorts; deaths due to infectious diseases showed the largest reductions, with diarrhoea causing 25 deaths in 1982 and none in 2015. Late-fetal-, neonatal- and infant-mortality rates were higher for children born to Brown or Black women and to low-income women. Absolute socio-economic inequalities based on income—expressed in deaths per 1000 births—were reduced over time but relative inequalities—expressed as ratios of mortality rates—tended to remain stable.

Conclusion
The observed improvements are likely due to progress in social determinants of health and expansion of health care. In spite of progress, current levels remain substantially greater than those observed in high-income countries, and social and ethnic inequalities persist.
Abstract Bivariant Cuntz Semigroups
Authors: Antoine Ramon , Perera Francesc , Thiel Hannes 
Published: June 2018

Abstract
We show that abstract Cuntz semigroups form a closed symmetric monoidal category. Thus, given Cuntz semigroups $S$ and $T$, there is another Cuntz semigroup $[\![ S,T ]\!] $ playing the role of morphisms from $S$ to $T$. Applied to $C^{\ast }$-algebras $A$ and $B$, the semigroup $[\![ \operatorname{Cu}(A),\operatorname{Cu}(B) ]\!] $ should be considered as the target in analogs of the universal coefficient theorem for bivariant theories of Cuntz semigroups. Abstract bivariant Cuntz semigroups are computable in a number of interesting cases. We also show that order-zero maps between $C^{\ast }$-algebras naturally define elements in the respective bivariant Cuntz semigroup.
Preference Reversals in Willingness to Pay and Choice
Authors: O’Donnell Michael , Evers Ellen R K 
Published: June 2018

Abstract
A fundamental contribution of consumer behavior research is to help marketing scholars develop an understanding of how people think about and express their preferences. In this article we find that two commonly used preference elicitation procedures, willingness to pay (WTP) and choice, are consistently associated with different expressed preferences. Specifically, choices are associated with a relatively greater preference for hedonic goods, while WTP is associated with a relatively greater preference for utilitarian goods. We find that this is caused, in part, by the greater reliance on deliberation in determining WTP values, while preferences in choices are determined by an affect heuristic. Unlike other choice and WTP preference reversals, we find that this effect is not caused by mechanical determinants such as scale compatibility, as the effect persists with continuous scale measures that rely on affect and with choice-based scale measures that rely on determining valuation.