bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alfvén waves as a solar-interplanetary driver of the thermospheric disturbances
Authors: Guo Jianpeng , Wei Fengsi , Feng Xueshang , Liu Huixin , Wan Weixing , Yang Zhiliang , Xu Jiyao , Liu Chaoxu 
Published: January 2016

AbstractAlfvén waves have been proposed as an important mechanism for the heating of the Sun’s outer atmosphere and the acceleration of solar wind, but they are generally believed to have no significant impact on the Earth’s upper atmosphere under quiet geomagnetic conditions due to their highly fluctuating nature of interplanetary magnetic field (i.e., intermittent southward magnetic field component). Here we report that a long-duration outward propagating Alfvén wave train carried by a high-speed stream produced continuous (~2 days) and strong (up to ±40%) density disturbances in the Earth’s thermosphere in a way by exciting multiple large-scale gravity waves in auroral regions. The observed ability of Alfvén waves to excite large-scale gravity waves, together with their proved ubiquity in the solar atmosphere and solar wind, suggests that Alfvén waves could be an important solar-interplanetary driver of the global thermospheric disturbances.
Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation
Authors: Jin Minliang , Liu Haijun , He Cheng , Fu Junjie , Xiao Yingjie , Wang Yuebin , Xie Weibo , Wang Guoying , Yan Jianbing 
Published: January 2016

AbstractGene expression variation largely contributes to phenotypic diversity and constructing pan-transcriptome is considered necessary for species with complex genomes. However, the regulation mechanisms and functional consequences of pan-transcriptome is unexplored systematically. By analyzing RNA-seq data from 368 maize diverse inbred lines, we identified almost one-third nuclear genes under expression presence and absence variation, which tend to play regulatory roles and are likely regulated by distant eQTLs. The ePAV was directly used as “genotype” to perform GWAS for 15 agronomic phenotypes and 526 metabolic traits to efficiently explore the associations between transcriptomic and phenomic variations. Through a modified assembly strategy, 2,355 high-confidence novel sequences with total 1.9 Mb lengths were found absent within reference genome. Ten randomly selected novel sequences were fully validated with genomic PCR, including another two NBS_LRR candidates potentially affect flavonoids and disease-resistance. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes and through developing two test-cross populations and surveying several most important yield traits, the dispensable genes were shown to contribute to heterosis. Novel perspectives and resources to discover maize quantitative trait variations were provided to better understand the kernel regulation networks and to enhance maize breeding.
Absence of evidence for increase in risk for autism or attention-deficit hyperactivity disorder following antidepressant exposure during pregnancy: a replication study
Authors: Castro V M , Kong S W , Clements C C , Brady R , Kaimal A J , Doyle A E , Robinson E B , Churchill S E , Kohane I S , Perlis R H 
Published: January 2016

AbstractMultiple studies have examined the risk of prenatal antidepressant exposure and risk for autism spectrum disorder (ASD) or attention-deficit hyperactivity disorder (ADHD), with inconsistent results. Precisely estimating such risk, if any, is of great importance in light of the need to balance such risk with the benefit of depression and anxiety treatment. We developed a method to integrate data from multiple New England health systems, matching offspring and maternal health data in electronic health records to characterize diagnoses and medication exposure. Children with ASD or ADHD were matched 1:3 with children without neurodevelopmental disorders. Association between maternal antidepressant exposure and ASD or ADHD liability was examined using logistic regression, adjusting for potential sociodemographic and psychiatric confounding variables. In new cohorts of 1245 ASD cases and 1701 ADHD cases, along with age-, sex- and socioeconomic status matched controls, neither disorder was significantly associated with prenatal antidepressant exposure in crude or adjusted models (adjusted odds ratio 0.90, 95% confidence interval 0.50−1.54 for ASD; 0.97, 95% confidence interval 0.53−1.69 for ADHD). Pre-pregnancy antidepressant exposure significantly increased risk for both disorders. These results suggest that prior reports of association between prenatal antidepressant exposure and neurodevelopmental disease are likely to represent a false-positive finding, which may arise in part through confounding by indication. They further demonstrate the potential to integrate data across electronic health records studies spanning multiple health systems to enable efficient pharmacovigilance investigation.
Compact ultra‐wideband bandpass filter with good selectivity
Authors: Zhang Ting , Xiao Fei , Bao Jingfu , Tang Xiaohong 
Published: January 2016

A compact ultra‐wideband (UWB) bandpass filter based on a novel multi‐mode resonator (MMR) is proposed. The MMR consists of a pair of open‐circuited stubs and three pairs of coupled‐line sections, which can generate four main resonant modes in the desired band, i.e. two odd modes and two even modes. The measured results of a fabricated one show that its bandwidth can cover the UWB frequency range and it has a sharp skirt due to two transmission zeros near its passband. Return loss in the passband is better than −10 dB. Meanwhile, at least −40 dB suppression can be achieved from 11.86 to 15.13 GHz and −30 dB suppression from 12 to 16 GHz.
Dynamic ocean management increases the efficiency and efficacy of fisheries management
Authors: Dunn Daniel C. , Maxwell Sara M. , Boustany Andre M. , Halpin Patrick N. 
Published: January 2016

SignificanceFood security and the economic well-being of millions of people depend on sustainable fisheries, which require innovative approaches to management that can balance ecological, economic, and social objectives. We offer empirical evidence that dynamic ocean management, or real-time ocean management, can increase the efficacy and efficiency of fisheries management over static approaches by better aligning human and ecological scales of use. Furthermore, we show that dynamic management can address critical ecological patterns previously considered to be largely intractable in fisheries management (e.g., competition, niche partitioning, predation, parasitism, or social aggregations) at appropriate scales. The evidence and theory offered supports the use of dynamic ocean management in a range of scenarios to improve the ecological, economic, and social sustainability of fisheries.
Forests synchronize their growth in contrasting Eurasian regions in response to climate warming
Authors: Shestakova Tatiana A. , Gutiérrez Emilia , Kirdyanov Alexander V. , Camarero Jesús Julio , Génova Mar , Knorre Anastasia A. , Linares Juan Carlos , Resco de Dios Víctor , Sánchez-Salguero Raúl , Voltas Jordi 
Published: January 2016

SignificanceForests dominate carbon fluxes in terrestrial ecosystems. We demonstrate how an intensified climatic influence on tree growth during the last 120 y has increased spatial synchrony in annual ring-width patterns within contrasting (boreal and Mediterranean) Eurasian biomes and on broad spatial scales. Current trends in tree growth synchrony are related to regional changes in climate factors controlling productivity, overriding local and taxonomic imprints on forest carbon dynamics. Enhanced synchrony is becoming a widespread, although regionally dependent, phenomenon related to warmer springs and increased temperature variability in high latitudes and to warmer winters and drier growing seasons in mid-latitudes.
PMCA2 regulates HER2 protein kinase localization and signaling and promotes HER2-mediated breast cancer
Authors: Jeong Jaekwang , VanHouten Joshua N. , Dann Pamela , Kim Wonnam , Sullivan Catherine , Yu Herbert , Liotta Lance , Espina Virginia , Stern David F. , Friedman Peter A. , Wysolmerski John J. 
Published: January 2016

Significance
Unlike other ErbB receptors, human epidermal growth factor receptor 2 (HER2) does not generally become internalized after activation but, instead, remains on the cell surface to signal for prolonged periods. This property is thought to contribute to HER2’s ability to transform cells when overexpressed. The current study demonstrates that HER2’s resistance to endocytosis depends on the presence of the calcium pump, plasma membrane calcium ATPase2 (PMCA2), in specific membrane signaling domains in which intracellular calcium must be kept low to permit continued HER2 biochemical signaling. The dramatic reduction of mammary tumors in mouse mammary tumor virus (MMTV)-Neu mice in the absence of PMCA2 demonstrates its importance in supporting the development of breast tumors. Therefore, targeting interactions between PMCA2 and HER2 may offer therapeutic strategies for breast cancer.
Observed decrease in atmospheric mercury explained by global decline in anthropogenic emissions
Authors: Zhang Yanxu , Jacob Daniel J. , Horowitz Hannah M. , Chen Long , Amos Helen M. , Krabbenhoft David P. , Slemr Franz , St. Louis Vincent L. , Sunderland Elsie M. 
Published: January 2016

SignificanceAnthropogenic mercury poses risks to humans and ecosystems when converted to methylmercury. A longstanding conundrum has been the apparent disconnect between increasing global emissions trends and measured declines in atmospheric mercury in North America and Europe. This work shows that locally deposited mercury close to coal-fired utilities has declined more rapidly than previously anticipated because of shifts in speciation from air pollution control technology targeted at SO2and NOx. Reduced emissions from utilities over the past two decades and the phase-out of mercury in many commercial products has led to lower global anthropogenic emissions and associated deposition to ecosystems. This implies that prior policy assessments underestimated the regional benefits of declines in mercury emissions from coal-fired utilities.
Properties of the shear stress peak radiated ahead of rapidly accelerating rupture fronts that mediate frictional slip
Authors: Svetlizky Ilya , Pino Muñoz Daniel , Radiguet Mathilde , Kammer David S. , Molinari Jean-François , Fineberg Jay 
Published: January 2016

Significance
The transition from stick to slip is governed by rupture fronts propagating along a frictional interface. It has long been suggested that rapid acceleration of these ruptures generates a shear stress peak that propagates ahead of the front. These peaked waves are strong; they can reach amplitudes that are large enough to trigger secondary supershear ruptures. We provide the first extensive quantitative experimental study to our knowledge of these highly directed waves and their relation to the rupture fronts driving them. Combining our experiments with finite-element simulations, we observe how these waves scale. This study provides insight into how rupture fronts accelerate beyond the shear-wave speed and may offer a possibility to obtain illusive information about propagating earthquakes.
Sufficient oxygen for animal respiration 1,400 million years ago
Authors: Zhang Shuichang , Wang Xiaomei , Wang Huajian , Bjerrum Christian J. , Hammarlund Emma U. , Costa M. Mafalda , Connelly James N. , Zhang Baomin , Su Jin , Canfield Donald E. 
Published: January 2016

SignificanceHow have environmental constraints influenced the timing of animal evolution? It is often argued that oxygen first increased to sufficient levels for animal respiration during the Neoproterozoic Eon, 1,000 million to 542 million years ago, thus explaining the timing of animal evolution. We report geochemical evidence for deep-water oxygenation below an ancient oxygen minimum zone 1,400 million years ago. Oceanographic modeling constrains atmospheric oxygen to a minimum of ∼4% of today’s values, sufficient oxygen to have fueled early-evolved animal clades. Therefore, we suggest that there was sufficient atmospheric oxygen for animals long before the evolution of animals themselves, and that rising levels of Neoproterozoic oxygen did not contribute to the relatively late appearance of animal life on Earth.
Cortical cell and neuron density estimates in one chimpanzee hemisphere
Authors: Collins Christine E. , Turner Emily C. , Sawyer Eva Kille , Reed Jamie L. , Young Nicole A. , Flaherty David K. , Kaas Jon H. 
Published: January 2016

Significance
Chimpanzees are our closest relatives, and understanding the organization of their brains can help us understand our own evolution. Here we present a detailed examination of cell and neuron densities across the chimpanzee cortex. We found similarities to other mammals, including primary sensory areas with high neuron densities and a trend of decreasing neuron densities along the posterior to anterior axis of the cortex. However, we also found a prefrontal region with anomalously high neuron density that disrupts the trend of decreased neuron densities in frontal brain regions. The data reported here allow valuable comparisons among the brains of our close relative and those of humans and other primates.
Alcohol Screening Scores and the Risk of Intensive Care Unit Admission and Hospital Readmission
Authors: Clark Brendan J. , Rubinsky Anna D. , Ho P. Michael , Au David H. , Chavez Laura J. , Moss Marc , Bradley Katharine A. 
Published: January 2016

Background: The association between alcohol misuse and the need for intensive care unit admission as well as hospital readmission among those discharged from the hospital following a critical illness is unclear. This study sought to determine whether alcohol misuse was associated with (1) admission to an intensive care unit (ICU) among a cohort of patients receiving outpatient care and (2) hospital readmission among those discharged from the hospital following critical illness. Methods: This was a retrospective cohort study conducted with data from 24 Veterans Affairs (VA) health care facilities between 2004 and 2007. Scores on the Alcohol Use Disorders Identification Test—Consumption (AUDIT-C) questionnaire were used to identify patients with past-year abstinence, lower-risk alcohol use, moderate alcohol misuse, or severe alcohol misuse. The primary outcome was admission to a VA intensive care unit within the year following administration of the AUDIT-C. In an analysis focused on patients discharged from the ICU, the 2 main outcomes were hospital readmission within 1 year and within 30 days. Results: Among 486,115 veterans receiving outpatient care, the adjusted probability of ICU admission within 1 year was 2.0% (95% confidence interval [CI]: 1.7%–2.3%) for abstinent patients, 1.6% (95% CI: 1.3%–1.8%) for patients with lower-risk alcohol use, 1.8% (1.4%–2.3%) for patients with moderate alcohol misuse, and 2.5% (2.0%–2.9%) for patients with severe alcohol misuse. Among the 9,030 patients discharged from an ICU, the adjusted probability of hospital readmission within 1 year was 48% (46%–49%) in abstinent patients, 44% (42%–45%) in patients with lower-risk alcohol use, 42% (39%–45%) in patients with moderate alcohol misuse, and 55% (49%–60%) in patients with severe alcohol misuse. Conclusions: Alcohol misuse may represent a modifiable risk factor for a cycle of ICU admission and subsequent hospital readmission.
Network structural features affect stability of Calvin Bassham Benson (CBB) pathway in plants
Authors: Theisen Matthew K 
Published: January 2016

AbstractThe stability of the Calvin Bassham Benson (CBB) cycle remains an area of active computational research. Our understanding of biology and the prospect for bioengineered plants with higher productivity may both be impacted by a greater understanding of this area. Here we use the ensemble modelling robustness analysis (EMRA) framework to show that the action of the phosphate/G3P antiporter is much more significant for maintenance of stability than a recently proposed G6P shunt. Additionally, we interpret recent results suggesting that overexpression of RuBiSCO does not improve growth rate of plants but overexpression of SBPase does. Our simulations reproduce this result, but only in models which do not include the G6P shunt. Taken together, these results may suggest a situational role for the G6P shunt, possibly in dynamic situations under starvation or other stress conditions.
Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations
Authors: Kobert Kassian , Stamatakis Alexandros , Flouri Tomáš 
Published: January 2016

AbstractThe phylogenetic likelihood function is the major computational bottleneck in several applications of evolutionary biology such as phylogenetic inference, species delimitation, model selection and divergence times estimation. Given the alignment, a tree and the evolutionary model parameters, the likelihood function computes the conditional likelihood vectors for every node of the tree. Vector entries for which all input data are identical result in redundant likelihood operations which, in turn, yield identical conditional values. Such operations can be omitted for improving run-time and, using appropriate data structures, reducing memory usage. We present a fast, novel method for identifying and omitting such redundant operations in phylogenetic likelihood calculations, and assess the performance improvement and memory saving attained by our method. Using empirical and simulated data sets, we show that a prototype implementation of our method yields up to 10-fold speedups and uses up to 78% less memory than one of the fastest and most highly tuned implementations of the phylogenetic likelihood function currently available. Our method is generic and can seamlessly be integrated into any phylogenetic likelihood implementation.
Statistical Evidence for Common Ancestry: Testing for Signal in Silent Sites
Authors: Bontrager Martin , Larget Bret , Ané Cécile , Baum David 
Published: January 2016

AbstractThe common ancestry of life is supported by an enormous body of evidence and is universally accepted within the scientific community. However, some potential sources of data that can be used to test the thesis of common ancestry have not yet been formally analyzed.We developed a new test of common ancestry based on nucleotide sequences at amino acid invariant sites in aligned homologous protein coding genes. We reasoned that since nucleotide variation at amino acid invariant sites is selectively neutral and, thus, unlikely to be due to convergent evolution, the observation that an amino acid is consistently encoded by the same codon sequence in different species could provide strong evidence of their common ancestry. Our method uses the observed variation in codon sequences at amino acid invariant sites as a test statistic, and compares such variation to that which is expected under three different models of codon frequency under the alternative hypothesis of separate ancestry. We also examine hierarchical structure in the nucleotide sequences at amino acid invariant sites and quantified agreement between trees generated from amino acid sequence and those inferred from the nucleotide sequences at amino acid invariant sites.When these tests are applied to the primate families as a test case, we find that observed nucleotide variation at amino acid invariant sites is considerably lower than nucleotide variation predicted by any model of codon frequency under separate ancestry. Phylogenetic trees generated from amino-acid invariant site nucleotide data agree with those generated from protein-coding data, and there is far more hierarchical structure in amino-acid invariant site data than would be expected under separate ancestry.We definitively reject the separate ancestry of the primate families, and demonstrate that our tests can be applied to any group of interest to test common ancestry.
A qualitative case study of MNE legitimacy
Authors: Pavlovich Kathryn , Sinha Paresha N , Rodrigues Mark 
Published: January 2016

Purpose
– An international joint venture (IJV) helps multinational enterprises (MNEs) overcome the “liability of foreignness.” However, in the presence of institutional voids, MNE’s overreliance on the local partner can result in the MNE unwittingly becoming involved in a corporate scandal. The purpose of this paper is to discuss the causes, impacts and outcomes on the MNE’s legitimacy following a corporate scandal.

Design/methodology/approach
– Using secondary data, this paper presents a qualitative case study of the Fonterra-Sanlu milk-powder scandal in China.

Findings
– The paper identifies the institutional voids that contributed to the scandal. It also examines the effects of the scandal on the MNE’s legitimacies and evaluates the appropriateness of its actions in China during the formation, erosion and repair stages of its legitimacy.

Research limitations/implications
– It contributes to legitimacy literature by discussing the importance of MNE’s active commitment when entering the emerging market. It argues that the building of pragmatic legitimacy is not sufficient, and explains why attendance to moral obligations is part of building moral and cognitive legitimacy.

Originality/value
– This unique case study of a corporate scandal offers deep insights into how, what and why questions regarding how the three forms of legitimacy are necessary for improving IJV performance by MNEs operating in emerging economies. It particularly highlights the importance of moral legitimacy as a mechanism for overcoming institutional voids.
Are you ready? Tasks and roles for academic libraries in supporting Research 2.0
Authors: Koltay Tibor 
Published: January 2016

Purpose
– The purpose of this paper is to identify tasks and roles that academic libraries have to fulfil to react to the developments brought in by the appearance of Research 2.0.

Design/methodology/approach
– A review of current literature about the topic was performed.

Findings
– Literature used reveals that currently, there is a need for providing information literacy (IL) education (mainly in the form of data literacy), providing research data services (RDSs) (addressing data quality and data citation), raising awareness of faculty members on different issues and providing individual support to them.

Originality/value
– The paper intends to be an add-on to the body of knowledge about academic library support to researchers.