bluuebunny/crossref_metadata_2025_split huggingface dataset:
Layered semi-convection and tides in giant planet interiors
Authors: André Q. , Mathis S. , Barker A. J. 
Published: April 2019

Context. Recent Juno observations have suggested that the heavy elements in Jupiter could be diluted throughout a large fraction of its gaseous envelope, providing a stabilising compositional gradient over an extended region of the planet. This could trigger layered semi-convection, which, in the context of giant planets more generally, may explain Saturn’s luminosity excess and play a role in causing the abnormally large radii of some hot Jupiters. In giant planet interiors, it could take the form of density staircases, which are convective layers separated by thin stably stratified interfaces. In addition, the efficiency of tidal dissipation is known to depend strongly on the planetary internal structure.
Aims. We aim to study the resulting tidal dissipation when internal waves are excited in a region of layered semi-convection by tidal gravitational forcing due to other bodies (such as moons in giant planet systems, or stars in hot Jupiter systems).
Methods. We adopt a local Cartesian model with a background layered density profile subjected to an imposed tidal forcing, and we compute the viscous and thermal dissipation rates numerically. We consider two sets of boundary conditions in the vertical direction: periodic boundaries and impenetrable, stress-free boundaries, with periodic conditions in the horizontal directions in each case. These models are appropriate for studying the forcing of short-wavelength tidal waves in part of a region of layered semi-convection, and in an extended envelope containing layered semi-convection, respectively.
Results. We find that the rates of tidal dissipation can be enhanced in a region of layered semi-convection compared to a uniformly convective medium, where the latter corresponds with the usual assumption adopted in giant planet interior models. In particular, a region of layered semi-convection possesses a richer set of resonances, allowing enhanced dissipation for a wider range of tidal frequencies. The details of these results significantly depend on the structural properties of the layered semi-convective regions.
Conclusions. Layered semi-convection could contribute towards explaining the high tidal dissipation rates observed in Jupiter and Saturn, which have not yet been fully explained by theory. Further work is required to explore the efficiency of this mechanism in global models.
High Incidence of Renal Stones in Severely Disabled Children with Epilepsy Treated with Topiramate
Authors: Ishikawa Nobutsune , Tani Hiroo , Kobayashi Yoshiyuki , Kato Akira , Kobayashi Masao 
Published: April 2019

Purpose This study was aimed to assess the accurate incidence of renal stones in severely disabled children treated with topiramate (TPM).
Method We reviewed the medical records of severely disabled children with epilepsy under 15 years old who underwent radiological examinations to investigate urinary stones. The study enrolled 26 patients who were divided into two groups. One group had been treated with TPM for at least 1 year and the other had not been treated with TPM, zonisamide, acetazolamide, or other diuretic drugs. We collected parameters from the medical records and compared the groups.
Results All participants were evaluated radiologically, with computed tomography (CT) in two patients, ultrasonography in 22 patients, and both in two. No patient had any morphological abnormality of the kidneys and history of urinary tract infection. There were no significant differences in sex, age, body weight, or feeding manner between the groups, while the incidence of renal stones or calcifications was significantly higher in the TPM-treated group (60 vs. 0%; p = 0.00241).
Conclusion There is a high incidence of renal stone formation in severely disabled children treated with TPM.
What drives people to believe in Zika conspiracy theories?
Authors: Klofstad Casey A. , Uscinski Joseph E. , Connolly Jennifer M. , West Jonathan P. 
Published: April 2019

AbstractConspiracy theories and other pseudo-scientific claims about the Zika virus have been prominent on social media. To what extent are the public concerned about the virus, and to what extent have the public adopted Zika conspiracy theories? Using data from the 2016 Cooperative Congressional Election Study, we show that a majority of Americans are not concerned about the Zika virus, but approximately one in five Americans believes in at least one Zika-related conspiracy theory. The most widely believed is that the virus is caused by genetically modified mosquitoes. We find that elevated levels of conspiracy thinking are correlated with both concern over Zika and belief in Zika-related conspiracy theories. For example, a person scoring the maximum on the conspiratorial thinking scale is estimated to believe in .61 Zika conspiracy theories while a person scoring the minimum is estimated to believe in only .06 Zika conspiracy theories. This study demonstrates the role of predispositions, specifically underlying conspiracy thinking, in the acceptance of conspiratorial and unscientific beliefs.
O-GlcNAcylation of core components of the translation initiation machinery regulates protein synthesis
Authors: Li Xuexia , Zhu Qiang , Shi Xiaoliu , Cheng Yaxian , Li Xueliu , Xu Huan , Duan Xiaotao , Hsieh-Wilson Linda C. , Chu Jennifer , Pelletier Jerry , Ni Maowei , Zheng Zhiguo , Li Sihui , Yi Wen 
Published: April 2019

Significance
Protein synthesis is essential for cell growth, proliferation, and survival. Deregulation of protein synthesis is an important feature in many diseases. However, how protein synthesis is regulated under physiological and pathological conditions still remains poorly understood. In this study, we report an unknown mechanism for the regulation of protein synthesis in cells. We demonstrate that two important translation initiation factors, namely eIF4A and eIF4G, are modified by a single sugar N-acetylglucosamine. Detailed analyses show that this modification influences the interaction and function of these two proteins, and regulates protein synthesis at the initiation stage. This finding expands the current understanding of protein synthesis and adds a dimension of complexity to translational control of cellular proteins in cells.
Ammonia emission control in China would mitigate haze pollution and nitrogen deposition, but worsen acid rain
Authors: Liu Mingxu , Huang Xin , Song Yu , Tang Jie , Cao Junji , Zhang Xiaoye , Zhang Qiang , Wang Shuxiao , Xu Tingting , Kang Ling , Cai Xuhui , Zhang Hongsheng , Yang Fumo , Wang Huanbo , Yu Jian Zhen , Lau Alexis K. H. , He Lingyan , Huang Xiaofeng , Duan Lei , Ding Aijun , Xue Likun , Gao Jian , Liu Bin , Zhu Tong 
Published: April 2019

Significance
Atmospheric ammonia plays important roles in fine particle pollution, acid rain, and nitrogen deposition. China, known as the world’s top emitter of gaseous ammonia, plans to control ammonia emissions to mitigate the haze pollution that has recently emerged. However, the complex side effects are still unclear. By integrating a chemical transport model, nationwide measurements, and a sophisticated ammonia emission model, we find that ammonia emission control would significantly aggravate acid rain pollution, thereby offsetting the benefit from reduced fine particle pollution and nitrogen deposition. Our work suggests that region-specific ammonia-control strategies provide a more rational and effective way to achieve the dual benefits of protecting human and ecosystem health in China.
A seismically induced onshore surge deposit at the KPg boundary, North Dakota
Authors: DePalma Robert A. , Smit Jan , Burnham David A. , Kuiper Klaudia , Manning Phillip L. , Oleinik Anton , Larson Peter , Maurrasse Florentin J. , Vellekoop Johan , Richards Mark A. , Gurche Loren , Alvarez Walter 
Published: April 2019

SignificanceThe Chicxulub impact played a crucial role in the Cretaceous–Paleogene extinction. However the earliest postimpact effects, critical to fully decode the profound influence on Earth’s biota, are poorly understood due to a lack of high-temporal-resolution contemporaneous deposits. The Tanis site, which preserves a rapidly deposited, ejecta-bearing bed in the Hell Creek Formation, helps to resolve that long-standing deficit. Emplaced immediately (minutes to hours) after impact, Tanis provides a postimpact “snapshot,” including ejecta accretion and faunal mass death, advancing our understanding of the immediate effects of the Chicxulub impact. Moreover, we demonstrate that the depositional event, calculated to have coincided with the arrival of seismic waves from Chicxulub, likely resulted from a seismically coupled local seiche.
Underwater ritual offerings in the Island of the Sun and the formation of the Tiwanaku state
Authors: Delaere Christophe , Capriles José M. , Stanish Charles 
Published: April 2019

SignificanceRitual and religion are significant factors in primary or archaic state formation. These beliefs and practices not only legitimize these new political organizations in their ability to control supernatural forces, but also incentivize intragroup cooperation by punishing freeloading and rewarding cooperative behavior. Recent archaeological excavations from an underwater ceremonial location near the Island of the Sun in Lake Titicaca have revealed the remarkable constituent elements of repetitive rituals practiced by the Tiwanaku state between the 8th and 10th centuries CE. Evidence of animal sacrifice and high-value offerings of vessels, gold, shells, and lapidary stones on a strategically located reef illustrates how power was consolidated in one of the earliest Andean states.
The effect of frequency on learners’ ability to recall the forms of deliberately learned L2 multiword expressions
Authors: Lindstromberg Seth , Eyckmans June 
Published: April 2019

AbstractIn incidental learning, open class vocabulary items with high or relatively high objective frequency in input are comparatively likely to be acquired. However, many single words and most multiword expressions (MWEs) occur infrequently in authentic input. It has therefore been argued that learners of school age or older can benefit from episodes of instructed or self-managed deliberate (or intentional) L2 vocabulary learning, especially when L2 is learned in an EFL environment and most especially when productive knowledge is the goal. A relevant question is whether the objective frequency of vocabulary items is an important factor in production-oriented deliberate L2 vocabulary learning. We report three small-scale interim meta-analyses addressing this question with regard to two-word English Adj-Noun and Noun-Noun expressions. The data derive from 8 original studies involving 406 learners and 139 different MWEs. Our results suggest that objective frequency has a weak, possibly negative effect in the deliberate learning of MWE forms.
Statistical knowledge and training in second language acquisition
Authors: Gonulal Talip 
Published: April 2019

AbstractThe present study investigated second language acquisition (SLA) doctoral students’ statistical training and knowledge of statistics. One hundred and twenty SLA doctoral students in North America took a comprehensive statistics survey, and 16 of them participated in follow-up interviews. The results showed that doctoral students were well trained in basic descriptive statistics, while their training in inferential statistics, particularly advanced statistics, was limited. When looking at their statistical knowledge, the results indicated that SLA doctoral students were good at understanding descriptive and inferential statistics, but they found it hard to interpret statistical analyses related to inferential statistics that are commonly encountered in SLA research. Several suggestions directed toward improving statistical literacy in SLA were provided.
Modelling public health improvements as a result of air pollution control policies in the UK over four decades—1970 to 2010
Authors: Carnell E , Vieno M , Vardoulakis S , Beck R , Heaviside C , Tomlinson S , Dragosits U , Heal MR , Reis S 
Published: April 2019

Abstract
In much of the industrialised world, policy interventions to address the challenges of wide-spread air pollution as resulting from development and economic progress in the 2nd half of the 20th century have overall led to reductions in air pollution levels and related health effects since the 1970s. While overall improvements towards reducing health effects from ambient air pollution are recorded, comprehensive and consistent assessments of the long-term impact of policy interventions are still scarce. In this paper, we conduct a model assessment over a 40 year period of air pollution in the UK. In order to correct for the short and longer term variability of meteorological factors contributing to trends in ambient concentrations of priority air pollutants (nitrogen dioxide, sulphur dioxide, fine particulate matter and ozone), we use a fixed meteorological year for all model simulations. Hence, the modelled changes in air pollutant concentrations and related health effects are solely a function of the changes in emissions since 1970. These changes in emissions are primarily driven by policy interventions, ranging from phasing out of specific fuels or substances, to regulating the use of chemicals and driving the development of cleaner, more efficient technologies. Over the 40 year period, UK attributable mortality due to exposure to PM2.5 and NO2 have declined by 56% and 44% respectively, while ozone attributable respiratory mortality increased by 17% over the same period (however, with a slight decrease by 14% between 2000 and 2010).
The effects of climate extremes on global agricultural yields
Authors: Vogel Elisabeth , Donat Markus G , Alexander Lisa V , Meinshausen Malte , Ray Deepak K , Karoly David , Meinshausen Nicolai , Frieler Katja 
Published: April 2019

Abstract
Climate extremes, such as droughts or heat waves, can lead to harvest failures and threaten the livelihoods of agricultural producers and the food security of communities worldwide. Improving our understanding of their impacts on crop yields is crucial to enhance the resilience of the global food system. This study analyses, to our knowledge for the first time, the impacts of climate extremes on yield anomalies of maize, soybeans, rice and spring wheat at the global scale using sub-national yield data and applying a machine-learning algorithm. We find that growing season climate factors—including mean climate as well as climate extremes—explain 20%–49% of the variance of yield anomalies (the range describes the differences between crop types), with 18%–43% of the explained variance attributable to climate extremes, depending on crop type. Temperature-related extremes show a stronger association with yield anomalies than precipitation-related factors, while irrigation partly mitigates negative effects of high temperature extremes. We developed a composite indicator to identify hotspot regions that are critical for global production and particularly susceptible to the effects of climate extremes. These regions include North America for maize, spring wheat and soy production, Asia in the case of maize and rice production as well as Europe for spring wheat production. Our study highlights the importance of considering climate extremes for agricultural predictions and adaptation planning and provides an overview of critical regions that are most susceptible to variations in growing season climate and climate extremes.
Juvenile plumage whiteness is associated with the evolution of clutch size in passerines
Authors: Morales Judith , Cuervo José Javier , Moreno Juan , Soler Juan José 
Published: April 2019

AbstractThe offspring of many animals are conspicuous during parental dependence, despite juveniles generally suffering from high predation risk. However, to date, it is unclear whether offspring structural ornaments play a role in intrafamily communication. This is the case of conspicuous plumage in young birds, which is worn unchanged during a long period after fledging, when they still depend on their parents. If plumage color facilitates intrafamily interactions, its role should be more important in large-brooded species, where the strength of intrafamily conflict is potentially stronger. We therefore performed a comparative study in 210 passerine bird species to test whether an offspring structural trait, white plumage, evolves more frequently in lineages with larger clutches. We also explored the number of broods raised per year as another source of intrafamily conflict. First, we found that juvenile whiteness was more frequent in open-nesting species. Moreover, in agreement with our prediction, the presence of juvenile white tail/wing patches was strongly and positively associated with clutch size. This relationship was not due to the strong resemblance between offspring and adult plumage, which was controlled for in the statistical analyses. Moreover, the association remained significant after taking into account predation risk, for which there was information for a subset of species. In contrast, juvenile whiteness was not associated with the number of broods raised per year. These results may suggest that the evolution of juvenile conspicuousness is favored in species with potentially stronger intrabrood sibling conflict.
PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact
Authors: Li Fuyi , Fan Cunshuo , Marquez-Lago Tatiana T , Leier André , Revote Jerico , Jia Cangzhi , Zhu Yan , Smith A Ian , Webb Geoffrey I , Liu Quanzhong , Wei Leyi , Li Jian , Song Jiangning 
Published: April 2019

Abstract
Post-translational modifications (PTMs) play very important roles in various cell signaling pathways and biological process. Due to PTMs’ extremely important roles, many major PTMs have been studied, while the functional and mechanical characterization of major PTMs is well documented in several databases. However, most currently available databases mainly focus on protein sequences, while the real 3D structures of PTMs have been largely ignored. Therefore, studies of PTMs 3D structural signatures have been severely limited by the deficiency of the data. Here, we develop PRISMOID, a novel publicly available and free 3D structure database for a wide range of PTMs. PRISMOID represents an up-to-date and interactive online knowledge base with specific focus on 3D structural contexts of PTMs sites and mutations that occur on PTMs and in the close proximity of PTM sites with functional impact. The first version of PRISMOID encompasses 17 145 non-redundant modification sites on 3919 related protein 3D structure entries pertaining to 37 different types of PTMs. Our entry web page is organized in a comprehensive manner, including detailed PTM annotation on the 3D structure and biological information in terms of mutations affecting PTMs, secondary structure features and per-residue solvent accessibility features of PTM sites, domain context, predicted natively disordered regions and sequence alignments. In addition, high-definition JavaScript packages are employed to enhance information visualization in PRISMOID. PRISMOID equips a variety of interactive and customizable search options and data browsing functions; these capabilities allow users to access data via keyword, ID and advanced options combination search in an efficient and user-friendly way. A download page is also provided to enable users to download the SQL file, computational structural features and PTM sites’ data. We anticipate PRISMOID will swiftly become an invaluable online resource, assisting both biologists and bioinformaticians to conduct experiments and develop applications supporting discovery efforts in the sequence–structural–functional relationship of PTMs and providing important insight into mutations and PTM sites interaction mechanisms. The PRISMOID database is freely accessible at http://prismoid.erc.monash.edu/. The database and web interface are implemented in MySQL, JSP, JavaScript and HTML with all major browsers supported.
IntronDB: a database for eukaryotic intron features
Authors: Wang Dapeng 
Published: April 2019

Abstract

Summary
The rate and extent of unbalanced eukaryotic intron changes exhibit dynamic patterns for different lineages of species or certain functional groups of genes with varied spatio-temporal expression modes affected by selective pressure. To date, only a few key conserved splicing signals or regulatory elements have been identified in introns and little is known about the remaining intronic regions. To trace the evolutionary trajectory of spliceosomal introns from available genomes under a unified framework, we present IntronDB, which catalogs ∼50 000 000 introns from over 1000 genomes spanning the major eukaryotic clades in the tree of life. Based on the position of introns relative to coding regions, it categorizes introns into three groups, such as 5'UTR, CDS and 3'UTR and subsequently divides CDS introns into three categories, such as phase 0, phase 1 and phase 2. It provides the quality evaluation for each sequence entry and characterizes the intronic parameters including number, size, sequence composition and positioning information as well as the features for exons and genes, making possible the comparisons between introns and exons. It reports the dinucleotides around the intron boundary and displays the consensus sequence features for all introns, small introns and large introns for each genome. By incorporating the taxonomic assignment of genomes, it performs high-level or genome-wide statistical analysis for single feature and coupled features both in a single genome and across multiple genomes. It offers functionalities to browse the data from representative protein-coding transcripts and download the data from all transcripts from protein-coding genes.

Availability and implementation
http://www.nextgenbioinformatics.org/IntronDB.

Supplementary information
Supplementary data are available at Bioinformatics online.