bluuebunny/crossref_metadata_2025_split huggingface dataset:
A high binary fraction for the most massive close-in giant planets and brown dwarf desert members
Authors: Fontanive C , Rice K , Bonavita M , Lopez E , Mužić K , Biller B 
Published: March 2019

ABSTRACT
Stellar multiplicity is believed to influence planetary formation and evolution, although the precise nature and extent of this role remain ambiguous. We present a study aimed at testing the role of stellar multiplicity in the formation and/or evolution of the most massive, close-in planetary and substellar companions. Using past and new direct imaging observations, as well as the Gaia DR2 catalogue, we searched for wide binary companions to 38 stars hosting massive giant planets or brown dwarfs (M &gt; 7 MJup) on orbits shorter than ∼1 au. We report the discovery of a new component in the WASP-14 system, and present an independent confirmation of a comoving companion to WASP-18. From a robust Bayesian statistical analysis, we derived a binary fraction of $79.0^{+13.2}_{-14.7}$ per cent between 20 and 10 000 au for our sample, twice as high as for field stars with a 3σ significance. This binary frequency was found to be larger than for lower-mass planets on similar orbits, and we observed a marginally higher binary rate for inner companions with periods shorter than 10 d. These results demonstrate that stellar companions greatly influence the formation and/or evolution of these systems, suggesting that the role played by binary companions becomes more important for higher-mass planets, and that this trend may be enhanced for systems with tighter orbits. Our analysis also revealed a peak in binary separation at 250 au, highlighting a shortfall of close binaries among our sample. This indicates that the mechanisms affecting planet and brown dwarf formation or evolution in binaries must operate from wide separations, although we found that the Kozai–Lidov mechanism is unlikely to be the dominant underlying process. We conclude that binarity plays a crucial role in the existence of very massive short-period giant planets and brown dwarf desert inhabitants, which are almost exclusively observed in multiple systems.
Tobacco Cost of Illness Studies: A Systematic Review
Authors: Makate Marshall , Whetton Steve , Tait Robert J , Dey Tania , Scollo Michelle , Banks Emily , Norman Richard , Pidd Ken , Roche Ann M , Allsop Steven 
Published: March 2019

Abstract

Introduction
To identify studies reporting costs arising from tobacco use and detail their (1) economic approaches, (2) health outcomes, and (3) other cost areas included.

Methods
We searched PubMed, Scopus, Cochrane Library, EconLit, and Google Scholar for studies published between 2008 and April 2018 in English. Eligible articles reported tobacco-related costs and included all tobacco-using populations (multinational, national, subpopulations, and involuntary smokers). All economic approaches that resulted in monetary outcomes were included. We reported USD or converted local currencies to USD. Two health economists extracted and two researchers independently reviewed the data.

Results
From 4083 articles, we reviewed 361 abstracts and examined 79 full-texts, with 63 (1.6%) deemed eligible. There were three multinational, thirty-four national, twenty-one subpopulation or condition(s)-specific analyses, and five evaluating involuntary smoking. The diverse approaches and outcomes precluded integrating costs, but these were substantial in all studies. For instance, about USD 1436 billion in global health expenditures and productivity losses in 2012 and USD 9 billion in lost productivity in China, Brazil, and South Africa in 2012. At the national level, costs ranged from USD 4665 in annual per respondent health expenses (Germany 2006–2008) to USD 289–332.5 billion in medical expenses (United States 1964–2014).

Conclusions
Despite wide variations in the methods used, the identified costs of tobacco are substantial. Studies on tobacco cost-of-illness use diverse methods and hence produce data that are not readily comparable across populations, time, and studies, precluding a consistent evidence-base for action and measurement of progress. Recommendations are made to improve comparability.

Implications
In addition to the health and financial costs to individual smokers, smoking imposes costs on the broader community. Production of comparable estimates of the societal cost of tobacco use is impaired by a plethora of economic models and inconsistently included costs and conditions. These inconsistencies also cause difficulties in comparing relative impacts caused by differing factors. The review systematically documents the post-2007 literature on tobacco cost-of-illness estimations and details conditions and costs included. We hope this will encourage replication of models across settings to provide more consistent data, able to be integrated across populations, over time, and across risk factors.
Presenting Seneca in Print: Elizabethan Translations and Thomas Newton’s Seneca His Tenne Tragedies
Authors: Mayne Emily 
Published: March 2019

Abstract
Seneca His Tenne Tragedies (1581) was the first printed collection of Seneca’s tragedies in English. This article re-examines this publication in the context of early modern production of collected unannotated editions of Seneca’s tragedies on the European mainland, and of the editorial and intellectual interests of its compiler, Thomas Newton. It identifies Newton as something of an early modern ‘print professional’, who was involved in the production of a wide variety of texts, translations, and commendatory poetry, and who used a variety of sophisticated strategies in print to draw attention to and to promote his own capacities and achievements; and it shows how the Tenne Tragedies participates in these practices. Attending to Newton’s activities alongside Jasper Heywood’s translation of Hercules furens reveals significant discontinuities in approach between the Tenne Tragedies and one of its constituent texts. Heywood’s translation first appeared in 1561 in a parallel-text format that was not designed for inclusion in a single-language collection such as the Tenne Tragedies, as one early modern reader’s response to the translation in this later printed context may show. Newton’s presentation of the Tenne Tragedies volume, and his particular attitude towards ‘Seneca’, complicates current critical understanding of the reception and uses of Senecan tragedy in Elizabethan England, and of any ‘project’ of Senecan translation in the period, which may be more an effect of Newton’s editorial proclivities, combined with modern understanding of Seneca as a single author, than reflective of attitudes towards Senecan tragedy in early modern England more generally.
Infernovenator steenae, a new serpentine recumbirostran from the ‘Mazon Creek’ Lagerstätte further clarifies lysorophian origins
Authors: Mann Arjan , Pardo Jason D , Maddin Hillary C 
Published: March 2019

Abstract
The Carboniferous (Pennsylvanian; 309–307 Mya) ‘Mazon Creek’ Lagerstätte produces some of the earliest tetrapod fossils of major Palaeozoic lineages. Previously, the Mazon Creek record of lysorophians was known from a single poorly preserved specimen consisting only of a partial vertebral column. Here we describe a new, virtually complete lysorophian genus and species, Infernovenator steenae gen. & sp. nov. on the basis of a unique combination of characters, including a near complete circumorbital series and the retention of a postfrontal. Parsimony-based phylogenetic analysis placed the new taxon in the family Molgophidae, as sister to Brachydectes newberryi. Those results and the more generalized cranial morphology present in Infernovenator further support a recumbirostran origin of Molgophidae. Co-occurrence of two morphologically and functionally distinct molgophids in the Early Moscovian suggests a rapid and underappreciated diversification of this family in the Early Pennsylvanian.
Non-Invasive Assays of Cochlear Synaptopathy -- Candidates and Considerations
Authors: Bharadwaj Hari M. , Mai Alexandra R. , Simpson Jennifer M. , Choi Inyong , Heinz Michael G. , Shinn-Cunningham Barbara G. 
Published: March 2019

AbstractStudies in multiple species, including in post-mortem human tissue, have shown that normal aging and/or acoustic overexposure can lead to a significant loss of afferent synapses innervating the cochlea. Hypothetically, this cochlear synaptopathy can lead to perceptual deficits in challenging environments and can contribute to central neural effects such as tinnitus. However, because cochlear synaptopathy can occur without any measurable changes in audiometric thresholds, synaptopathy can remain hidden from standard clinical diagnostics. To understand the perceptual sequelae of synaptopathy and to evaluate the efficacy of emerging therapies, sensitive and specific non-invasive measures at the individual patient level need to be established. Pioneering experiments in specific mice strains have helped identify many candidate assays. These include auditory brainstem responses, the middle-ear muscle reflex, envelope-following responses, and extended high-frequency audiograms. Unfortunately, because these non-invasive measures can be also affected by extraneous factors other than synaptopathy, their application and interpretation in humans is not straightforward. Here, we systematically examine six extraneous factors through a series of interrelated human experiments aimed at understanding their effects. Using strategies that may help mitigate the effects of such extraneous factors, we then show that these suprathreshold physiological assays exhibit across-individual correlations with each other indicative of contributions from a common physiological source consistent with cochlear synaptopathy. Finally, we discuss the application of these assays to two key outstanding questions, and discuss some barriers that still remain.
A reformulation of the selection ratio shed light on resource selection functions and leads to a unified framework for habitat selection studies
Authors: Chamaillé-Jammes Simon 
Published: March 2019

AbstractThe selection ratio (SR), i.e. the ratio of proportional use of a habitat over proportional availability of this habitat, has for long been the standard metric of habitat selection analyses. It is easy to compute and directly estimates disproportionate use. Its apparent restriction to habitat selection analyses using categorical predictors led to the development of the resource selection functions (RSF) approach, which has now become the norm.The RSF approach has however led to debates and confusion. For instance, what functional form can be used remains debated, and the concept of relative probability of selection is often misunderstood.I propose a reformulation of the SR demonstrating that it can be estimated in a regression context, and thus even with continuous predictors. This reformulation suggests that RSF can be seen as an intermediate step in the calculation of SR. This reformulation also clarifies some longstanding debates about RSF and data-selection/fitting practices.I further suggest that SR estimates the strength of habitat selection, but that the contribution of selection in determining use, which should be more directly linked to fitness than selection per se, should be estimated by another metric, the selection effect on use (SE). SE could be estimated simply as thedifferencebetween proportional use and proportional availability, and can be computed from SR and a density estimation of availability.I conduct a habitat selection analysis of plains zebras to demonstrate the added-value of going beyond RSF scores and using SR estimated in a regression context, and of combining SR and SE.Overall, I highlight the inter-relation between various metrics used to study habitat selection (i.e., SR, other selection indices, RSF scores, marginality). I conclude by proposing that SR and SE can be the unifying metrics of habitat selection, as together they offer a comprehensive view on the strength of habitat selection and its effect on habitat use.
The Tangent copy-number inference pipeline for cancer genome analyses
Authors: Tabak Barbara , Saksena Gordon , Oh Coyin , Gao Galen F. , Meyers Barbara Hill , Reich Michael , Schumacher Steven E. , Westlake Lindsay C. , Berger Ashton C. , Carter Scott L.b , Cherniack Andrew D. , Meyerson Matthew , Beroukhim Rameen , Getz Gad 
Published: March 2019

AbstractMotivationSomatic copy-number alterations (SCNAs) play an important role in cancer development. Systematic noise in sequencing and array data present a significant challenge to the inference of SCNAs for cancer genome analyses. As part of The Cancer Genome Atlas (TCGA), the Broad Institute Genome Characterization Center developed the Tangent copy-number inference pipeline to generate copy-number profiles using single-nucleotide polymorphism (SNP) array and whole-exome sequencing (WES) data from over 10,000 pairs of tumors and matched normal samples. Here, we describe the Tangent pipeline, which begins with DNA sequencing data in the form of .bam files or raw SNP array probe-level intensity data, and ends with segmented copy-number calls to facilitate the identification of novel genes potentially targeted by SCNAs. We also describe a modification of Tangent, Pseudo-Tangent, which enables denoising through comparisons between tumor profiles when few normal samples are available.ResultsTangent Normalization offers substantial signal-to-noise ratio (SNR) improvements compared to conventional normalization methods in both SNP array and WES analyses. The improvement in SNRs is achieved primarily through noise reduction with minimal effect on signal. Pseudo-Tangent also reduces noise when few normal samples are available. Tangent and Pseudo-Tangent are broadly applicable and enable more accurate inference of SCNAs from DNA sequencing and array data.Availability and ImplementationTangent is available at https://github.com/coyin/tangent and as a Docker image (https://hub.docker.com/r/coyin/tangent). Tangent is also the normalization method for the Copy Number pipeline in Genome Analysis Toolkit 4 (GATK4).Contactmatthew_meyerson@dfci.harvard.edu, rameen@broadinstitute.org, gadgetz@broadinstitute.org
Proteomic profiling of the oncogenic septin 9 reveals isoform-specific interactions in breast cancer cells
Authors: Devlin Louis , Perkins George , Bowen Jonathan R. , Montagna Cristina , Spiliotis Elias T. 
Published: March 2019

AbstractSeptins are a family of multimeric GTP-binding proteins, which are abnormally expressed in cancer. Septin 9(SEPT9)is an essential and ubiquitously expressed septin with multiple isoforms, which have differential expression patterns and effects in breast cancer cells. It is unknown, however, if SEPT9 isoforms associate with different molecular networks and functions. Here, we performed a proteomic screen in MCF-7 breast cancer cells to identify the interactome of GFP-SEPT9 isoforms 1, 4 and 5, which vary significantly in their N-terminal extensions. While all three isoforms associated with SEPT2 and SEPT7, the truncated SEPT9_i4 and SEPT9_i5 interacted with septins of the SEPT6 group more promiscuously than SEPT9_i1, which bound predominately SEPT8. Spatial mapping and functional clustering of non-septin partners showed isoform-specific differences in interactions with proteins of distinct subcellular organelles (e.g., nuclei, centrosomes, cilia) and functions such as cell signaling and ubiquitination. Notably, the interactome of the full length SEPT9_i1 was more enriched in cytoskeletal regulators, while the truncated SEPT9_i4 and SEPT9_i5 exhibited preferential and isoform-specific interactions with nuclear, signaling and ubiquitinating proteins. These data provide evidence for isoform-specific interactions, which arise from truncations in the N-terminal extensions of SEPT9, and point to novel roles in the pathogenesis of breast cancer.
Sex and age don’t matter but breed type does - Factors influencing eye wrinkle expression in horses
Authors: Schanz Lisa , Krueger Konstanze , Hintze Sara 
Published: March 2019

AbstractIdentifying valid indicators to assess animals’ emotional states is a critical objective of animal welfare science. In horses, eye wrinkles caused by the contraction of the inner eyebrow raiser have been shown to be affected by pain and other emotional states. Whether individual characteristics of a horse systematically affect eye wrinkle expression has not yet been studied. Therefore, the aim of this study was to assess how age, sex, breed type, body condition and coat colour affect the expression and/or the assessment of eye wrinkles in horses. To this end, we adapted the eye wrinkle assessment scale from Hintze et al. (2016) and assessed eye wrinkle expression on pictures taken from the left and the right eye of 181 horses in a presumably neutral situation, using five outcome measures: a qualitative first impression reflecting how worried the horse looks, the extent to which the eyebrow is raised, the number of wrinkles, their markedness and the angle between a line through the eyeball and the topmost wrinkle. All measures could be assessed highly reliable with respect to intra- and inter-observer agreement. Breed type affected the width of the angle (F2, 114= 8.20, p < 0.001), with thoroughbreds having the narrowest angle (M= 23.80,SD= 1.60), followed by warmbloods (M= 28.00,SD= 0.60), and coldbloods (M= 31.00,SD= 0.90). None of the other factors affected any of the outcome measures, and eye wrinkle expression did not differ between the left and the right eye area (all p-values > 0.05). Consequently, horses’ characteristics age, sex and coat colour did not systematically affect eye wrinkle expression, whereas ‘breed type’ explained some variation in ‘angle’; how much eye wrinkle expression is affected by emotion or perhaps mood needs further investigation and validation.
Looking forward does not mean forgetting about the past: ERP evidence for the interplay of predictive coding and interference during language processing
Authors: Schoknecht Pia , Roehm Dietmar , Schlesewsky Matthias , Bornkessel-Schlesewsky Ina 
Published: March 2019

AbstractInterference and prediction have independently been identified as crucial influencing factors during language processing. However, their interaction remains severely underinvestigated. Furthermore, the neurobiological basis of cue-based retrieval and retrieval interference during language processing remains insufficiently understood. Here, we present an ERP experiment that systematically examined the interaction of interference and prediction during language processing. We used the neurobiologically well-established predictive coding framework and insights regarding the neuronal mechanisms of memory for the theoretical framing of our study. German sentence pairs were presented word-by-word, with an article in the second sentence constituting the critical word. We analyzed mean single trial EEG activity in the N400 time window and found an interaction between interference and prediction (measured by cloze probability). Under high predictability, no interference effects were observable. Under the predictive coding account, highly predictable input is totally explained by top-down activity. Therefore the input induces no retrieval operations which could be influenced by interference. In contrast, under low predictability, conditions with high interference or with a close, low-interference distractor showed a broadly distributed negativity compared to conditions with a distant, low-interference distractor. We interpret this result as showing that when unpredicted input induces model updating, this may elicit memory retrieval including the evaluation of distractor items, thus leading to interference effects. We conclude that interference should be included in predictive coding-based accounts of language because prediction errors can trigger retrieval operations and, therefore, induce interference.
Stalk Lodging: A Portable Device for Phenotyping Stalk Bending Strength of Maize and Sorghum
Authors: Cook Douglas D. , de la Chapelle Witold , Lin Ting-Che , Lee Shien Yang , Sun Wenhuan , Robertson Daniel J 
Published: March 2019

ABSTRACTBackgroundStalk lodging (breakage of plant stems prior to harvest) is a major problem for both farmers and plant breeders. A limiting factor in addressing this problem is the lack of a reliable method for phenotyping stalk strength. Previous methods of phenotyping stalk strength induce failure patterns different from those observed in natural lodging events. This paper describes a new device for field-based phenotyping of stalk strength called “DARLING” (Device for Assessing Resistance to Lodging IN Grains). The DARLING apparatus consists of a vertical arm which is connected to a horizontal footplate by a hinge. The operator places the device next to a stalk, aligns the stalk with a force sensor, steps on the footplate, and then pushes the vertical arm forward until the stalk breaks. Force and rotation are continuously recorded during the test and these quantities are used to calculate two quantities: stalk flexural stiffness and stalk bending strength.ResultsField testing of DARLING was performed at multiple sites. Validation was based upon three factors. First, the device induces the characteristic “crease” or Brazier buckling failure patterns observed in naturally lodged stalks. Second, in agreement with prior research, flexural stiffness values attained using the DARLING apparatus are strongly correlated with bending strength measurements. Finally, a paired specimen experimental design was used to determine that the flexural data obtained with DARLING is in agreement with laboratory-based flexural testing results of the same specimens. DARLING was also deployed in the field to assess phenotyping throughput (# of stalks phenotyped per hour). Over approximately 5000 tests, the average testing rate was found to be 210 stalks/hour.ConclusionsThe DARLING apparatus provides a quantitative assessment of stalk strength in a field setting. It induces the same failure patterns observed in natural lodging events. DARLING can also be used to perform non-destructive flexural tests. This new technology has many applications, including breeding, genetic studies on stalk strength, longitudinal studies of stalk flexural stiffness, and risk assessment of lodging propensity.