bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brillouin-scattering-induced transparency and non-reciprocal light storage
Authors: Dong Chun-Hua , Shen Zhen , Zou Chang-Ling , Zhang Yan-Lei , Fu Wei , Guo Guang-Can 
Published: February 2015

AbstractStimulated Brillouin scattering is a fundamental interaction between light and travelling acoustic waves and arises primarily from electrostriction and photoelastic effects, with an interaction strength several orders of magnitude greater than that of other relevant non-linear optical processes. Here we report an experimental demonstration of Brillouin-scattering-induced transparency in a high-quality whispering-gallery-mode optical microresonantor. The triply resonant Stimulated Brillouin scattering process underlying the Brillouin-scattering-induced transparency greatly enhances the light–acoustic interaction, enabling the storage of light as a coherent, circulating acoustic wave with a lifetime up to 10 μs. Furthermore, because of the phase-matching requirement, a circulating acoustic wave can only couple to light with a given propagation direction, leading to non-reciprocal light storage and retrieval. These unique features establish a new avenue towards integrated all-optical switching with low-power consumption, optical isolators and circulators.
KCl ultra-thin films with polar and non-polar surfaces grown on Si(111)7 × 7
Authors: Beinik Igor , Barth Clemens , Hanbücken Margrit , Masson Laurence 
Published: February 2015

AbstractThe growth of ultra-thin KCl films on the Si(111)7 × 7 reconstructed surface has been investigated as a function of KCl coverage and substrate temperature. The structure and morphology of the films were characterized by means of scanning tunneling microscopy (STM) under ultra-high vacuum (UHV) conditions. Detailed analysis of the atomically resolved STM images of islands grown at room and high temperatures (400 K–430 K) revealed the presence of KCl(001) and KCl(111) islands with the ratio between both structures depending on the growth temperature. At room temperature, the growth of the first layer, which covers the initial Si(111)7 × 7 surface, contains double/triple atomic layers of KCl(001) with a small fraction of KCl(111) islands. The high temperature growth promotes the appearance of large KCl(111) areas, which are built up by three atomic layers. At room and high temperatures, flat and atomically well-defined ultra-thin KCl films can be grown on the Si(111)7 × 7 substrate. The formation of the above mentioned (111) polar films is interpreted as a result of the thermally activated dissociative adsorption of KCl molecules on Si(111)7 × 7, which produces an excess of potassium on the Si surface.
Focused-Ion-Beam Induced Rayleigh-Plateau Instability for Diversiform Suspended Nanostructure Fabrication
Authors: Li Can , Zhao Lurui , Mao Yifei , Wu Wengang , Xu Jun 
Published: February 2015

AbstractA novel method for fabricating diversiform suspended nanostructures is reported. The method utilizes focused-ion-beam (FIB) induced material redistribution and Rayleigh-Plateau instability, which determine the resulting shapes of formed nanostructures. By choosing target materials, their predefined patterns as well as FIB settings, we have achieved parallel nanofabrication of various kinds including nanostrings, nanobead chains and nanopore membranes with smooth surfaces due to the self-perfection effect of the material redistribution upon the minimization of system free energy. The diameters of the nanostrings and nanopores reach about 10 nm and 200 nm, respectively. The average period of the nanobead chains is 250 nm.
Inhibition of IAPP aggregation by insulin depends on the insulin oligomeric state regulated by zinc ion concentration
Authors: Nedumpully-Govindan Praveen , Ding Feng 
Published: February 2015

AbstractWhile islet amyloid polypeptide (IAPP) aggregation is associated with β-cell death in type-II diabetes (T2D), environmental elements of β-cell granules — e.g. high concentrations of insulin and Zn2+ — inhibit IAPP aggregation in healthy individuals. The inhibition by insulin is experimentally known, but the role of Zn2+ is controversial as both correlations and anti-correlations at the population level are observed between T2D risk and the activity of a β-cell specific zinc ion transporter, ZnT8. Since Zn2+ concentration determines insulin oligomer equilibrium, we computationally investigated interactions of IAPP with different insulin oligomers and compared with IAPP homodimer formation. We found that IAPP binding with insulin oligomers competes with the formation of both higher-molecular-weight insulin oligomers and IAPP homodimers. Therefore, zinc deficiency due to loss-of-function ZnT8 mutations shifts insulin oligomer equilibrium toward zinc-free monomers and dimers, which bind IAPP monomers more efficiently compared to zinc-bound hexamers. The hetero-molecular complex formation prevents IAPP from self-association and subsequent aggregation, reducing T2D risk.
Exploration of diarrhoea seasonality and its drivers in China
Authors: Xu Zhiwei , Hu Wenbiao , Zhang Yewu , Wang Xiaofeng , Zhou Maigeng , Su Hong , Huang Cunrui , Tong Shilu , Guo Qing 
Published: February 2015

AbstractThis study investigated the diarrhoea seasonality and its potential drivers as well as potential opportunities for future diarrhoea control and prevention in China. Data on weekly infectious diarrhoea cases in 31 provinces of China from 2005 to 2012 and data on demographic and geographic characteristics, as well as climatic factors, were complied. A cosinor function combined with a Poisson regression was used to calculate the three seasonal parameters of diarrhoea in different provinces. Regression tree analysis was used to identify the predictors of diarrhoea seasonality. Diarrhoea cases in China showed a bimodal distribution. Diarrhoea in children <5 years was more likely to peak in fall-winter seasons, while diarrhoea in persons > = 5 years peaked in summer. Latitude was significantly associated with spatial pattern of diarrhoea seasonality, with peak and trough times occurring earlier at high latitudes (northern areas) and later at low latitudes (southern areas). The annual amplitudes of diarrhoea in persons > = 5 years increased with latitude (r = 0.62, P<0.001). Latitude 27.8° N and 38.65° N were the latitudinal thresholds for diarrhoea seasonality in China. Regional-specific diarrhoea control and prevention strategies may be optimal for China. More attention should be paid to diarrhoea in children <5 years during fall-winter seasons.
Neuro‐fuzzy controller for battery equalisation in serially connected lithium battery pack
Authors: Ngoc Nguyen Thi Thu , Yoo Hyon‐Gi , Oruganti Sai K. , Bien Franklin 
Published: February 2015

This study presents a non‐linear, dynamic control method for equalising battery cell voltages in a serially connected lithium‐ion battery system based on an adaptive neuro‐fuzzy inference system. By using a combination of neuron networks and fuzzy logic, the optimal control method is obtained by self‐learning capability to equalise the current between battery cells. The duty cycle used to control the metal‐oxide‐semiconductor field‐effect transistors in individual battery cell equalisers are changed based on the dynamic equalising and system status. While energy is transferred from higher voltage cells to lower voltage cells, online measurement is utilised to collect data for tracking. Therefore the duty cycle control has an optimal response in this battery system. The state of the optimal control output is presented in simulation results. To demonstrate the effectiveness of the proposed control scheme and robustness of the acquired neuron‐fuzzy controller, the controller was implemented in a serially connected lithium battery system model using a microprocessor. The proposed system achieved a learning accuracy error of 1.8 × 10−5, and the equalising time was approximately 3000 s for a 0.25‐V voltage gap.
Age-0 Sturgeon Accessibility to Constructed and Modified Chutes in the Lower Missouri River
Authors: Gosch Nathan J. C. , Miller Marcus L. , Gemeinhardt Todd R. , Sampson Schuyler J. , Bonneau Joseph L. 
Published: February 2015

Abstract
Shallow-water habitat is hypothesized to provide nursery habitat for young fish. The construction of side-channel chutes to restore shallow-water habitat is common in the lower Missouri River; however, a recent adaptive management strategy document (developed by a multiagency, multidiscipline team), as well as previous research, has suggested that the accessibility of chutes to age-0 Scaphirhynchus spp. (sturgeon hereafter) may be limited. Access is a critical prerequisite for young fish utilizing chute habitat; thus, we investigated chute-specific accessibility for age-0 sturgeon at seven chutes (constructed and natural). Age-0 sturgeon were capable of accessing most chutes; however, accessibility appeared limited at sites with highly restrictive inlet structures. Our results suggest that future consideration of chute inlet designs that meet authorized Missouri River purposes while providing improved fish access is warranted. Additionally, capture sites for exogenously feeding age-0 sturgeon were usually deeper (&gt;1.5 m) and faster (&gt;0.5 m/s) than sites without sturgeon in chute and adjacent main-stem habitats. This finding is consistent with previous research that suggests that slow and shallow habitats may not be used by age-0 sturgeon as frequently as other habitat types in the lower Missouri River.
Received June 4, 2014; accepted September 24, 2014
GenoMetric Query Language: a novel approach to large-scale genomic data management
Authors: Masseroli Marco , Pinoli Pietro , Venco Francesco , Kaitoua Abdulrahman , Jalili Vahid , Palluzzi Fernando , Muller Heiko , Ceri Stefano 
Published: February 2015

Abstract
Motivation: Improvement of sequencing technologies and data processing pipelines is rapidly providing sequencing data, with associated high-level features, of many individual genomes in multiple biological and clinical conditions. They allow for data-driven genomic, transcriptomic and epigenomic characterizations, but require state-of-the-art ‘big data’ computing strategies, with abstraction levels beyond available tool capabilities.
Results: We propose a high-level, declarative GenoMetric Query Language (GMQL) and a toolkit for its use. GMQL operates downstream of raw data preprocessing pipelines and supports queries over thousands of heterogeneous datasets and samples; as such it is key to genomic ‘big data’ analysis. GMQL leverages a simple data model that provides both abstractions of genomic region data and associated experimental, biological and clinical metadata and interoperability between many data formats. Based on Hadoop framework and Apache Pig platform, GMQL ensures high scalability, expressivity, flexibility and simplicity of use, as demonstrated by several biological query examples on ENCODE and TCGA datasets.
Availability and implementation: The GMQL toolkit is freely available for non-commercial use at http://www.bioinformatics.deib.polimi.it/GMQL/.
Contact: marco.masseroli@polimi.it
Supplementary information: Supplementary data are available at Bioinformatics online.
Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets
Authors: Wandy Joe , Daly Rónán , Breitling Rainer , Rogers Simon 
Published: February 2015

Abstract
Motivation: The combination of liquid chromatography and mass spectrometry (LC/MS) has been widely used for large-scale comparative studies in systems biology, including proteomics, glycomics and metabolomics. In almost all experimental design, it is necessary to compare chromatograms across biological or technical replicates and across sample groups. Central to this is the peak alignment step, which is one of the most important but challenging preprocessing steps. Existing alignment tools do not take into account the structural dependencies between related peaks that coelute and are derived from the same metabolite or peptide. We propose a direct matching peak alignment method for LC/MS data that incorporates related peaks information (within each LC/MS run) and investigate its effect on alignment performance (across runs). The groupings of related peaks necessary for our method can be obtained from any peak clustering method and are built into a pair-wise peak similarity score function. The similarity score matrix produced is used by an approximation algorithm for the weighted matching problem to produce the actual alignment result.
Results: We demonstrate that related peak information can improve alignment performance. The performance is evaluated on a set of benchmark datasets, where our method performs competitively compared to other popular alignment tools.
Availability: The proposed alignment method has been implemented as a stand-alone application in Python, available for download at http://github.com/joewandy/peak-grouping-alignment.
Contact: Simon.Rogers@glasgow.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Apology for the Abbé Mallet
Authors: McGinnis Reginald 
Published: February 2015

Abstract

The abbé Edme Mallet was one of the main contributors to the first volumes of Diderot and D'Alembert's
Encyclopédie
, and the work's official theologian. Whereas his reputation, derived largely from D'Alembert's eulogy, was formerly that of a moderate open to dialogue with philosophers, in an article from the 1970s Walter E. Rex argued that Mallet was in fact a rigid defender of orthodoxy recruited for the
Encyclopédie
to offset its anti-religious tendencies. This article offers a refutation of Rex's influential theory, questioning his assumption of a fundamental opposition between Mallet and the other contributors. Beginning with the observation that Rex made his analysis of Mallet's religious articles without realizing that these are, in many instances, either wholly or partly translations from Chambers's
Cyclopaedia
, I move on to consider the censored article ‘Constitution Unigenitus’, where Mallet's opinion of the Jansenists is shown to be similar, rather than opposed, to that of Diderot and D'Alembert. In view of their statements in important sections of the
Encyclopédie
, I suggest that, contrary to common opinion, the editors' association with Mallet may reflect a sincere desire for collaboration with theologians.
Design Characteristics and Tobacco Metal Concentrations in Filtered Cigars
Authors: Caruso Rosalie V. , O’Connor Richard J. , Travers Mark J. , Delnevo Cristine D. , Stephens W. Edryd 
Published: February 2015

AbstractIntroductionWhile U.S. cigarette consumption has declined, cigar use has steadily increased, for reasons including price compared to cigarettes and the availability of filtered varieties resembling cigarettes, and flavors that have been banned in cigarettes (excluding menthol). Little published data exists on the design characteristics of such cigars.MethodsA variety of filtered cigar brands were tested for design characteristics such as whole cigar weight, ventilation, and per-cigar tobacco weight. Cigar sticks were then sent to the University of St. Andrews for metal concentration testing of As, Pb, Cr, Ni, and Cd.ResultsLarge and small cigars were statistically different between cigar weight (p ≤ .001), per-cigar tobacco weight (p = .001), rod diameter (p = .006), and filter diameter (p = .012). The differences in mean ventilation (overall mean = 19.6%, min. = 0.84%, max. = 57.6%) across filtered cigar brands were found to be statistically significant (p = .031), and can be compared to the ventilation of the average of 2013U.S. Marlboro Red, Gold, and Silver packs at 29% ventilation. There were no significant differences for metal concentrations between cigar types (p = .650), with Pb and As levels being similar to U.S. 2009 cigarette concentrations, Cd cigar levels being slightly higher, and Cr and Ni levels much lower than cigarette levels.ConclusionsWith cigar use rising, and filtered cigars displaying substantial similarities to filtered cigarettes, more research on product characteristics is warranted. Future plans include testing tobacco alkaloid and more observation of cigar weight for tax bracket purposes.
Archaeological Theories and Archaeological Sciences
Authors: Martinón-Torres Marcos , Killick David 
Published: February 2015

AbstractArchaeological theory and archaeological science have traditionally been characterized as concerned with different issues and unable to interact productively. In this chapter, we present a brief history of the relationship between these two subdisciplines, and some clarification of the differences between scientific archaeology and archaeological science. We then focus on examples of recent and current projects to argue that we should no longer differentiate between archaeologists on the one hand and archaeological scientists on the other, since many leading practitioners of archaeological sciences are both. We contend that science-based archaeology today plays an important role in the formulation of new theories, and in challenging long-standing assumptions in archaeology and numerous other fields (e.g. ecology). Archaeological science is central to contemporary archaeological theory and practice, and will become increasingly important in the foreseeable future.
Promoting Maths to the General Public
Authors: Budd Chris J. 
Published: February 2015

Abstract
In this chapter I will address the issue that whilst mathematics is vital to all of our lives, playing a vital role in modern technology and even helping us to understand the brain, it is often perceived to be a dry, boring, and useless subject. The chapter will explore various ways that mathematics can be presented to the general public in a way that makes it seem to be exciting and relevant, and captures its essence without dumbing it down. In particular it will look at strategies that have been shown to work well with the public including the use of careful real life examples and relating maths to people, hands on maths at science fairs, and maths in the media and on the Internet. The chapter includes some case studies of what does and does not work in the field of maths communication.
Measuring Spillovers in Markets for Local Public Affairs Coverage
Authors: Hamilton James T. 
Published: February 2015

Abstract
This chapter explores the evidence on how media coverage generates spillovers that influence the election and actions of local politicians. If a news story influences a reader’s decisions about turning out to vote, supporting an incumbent, or selecting a particular party’s candidates, these decisions may have spillovers on other people in the community. If politicians anticipate these spillover effects when making their own choices, or if they learn new facts that cause them to change their public actions, this is another way that the media can affect local politics.
Sluggish Cognitive Tempo/Concentration Deficit Disorder
Authors: Barkley Russell A. 
Published: February 2015

Abstract
Sluggish cognitive tempo (SCT), or concentration deficit disorder (CDD), comprises excessive daydreaming, staring, mental fogginess and confusion, drowsiness, lethargy, sluggishness, and hypoactivity, among other symptoms. This article summarizes the findings on CDD/SCT and its relationship to attention deficit hyperactivity disorder (ADHD). The cognitive dysfunction underlying CDD remains to be clarified. But its symptoms comprise a two-dimensional structure that is separate from those in ADHD. CDD is reliably associated with social withdrawal and is more strongly related to internalizing than to externalizing psychopathology, in contrast to ADHD. Both ADHD and CDD are impairing, but ADHD is more so. Little evidence exists on the etiologies of CDD or on response to treatments. More research is needed on all facets of CDD before its status as a new disorder can be confirmed.
Jury Nullification in the United States
Authors: King Nancy J. 
Published: February 2015

Abstract
This essay provides a comprehensive yet compact discussion of jury nullification in the United States. It includes a summary of (a) criminal cases in which juries have deliberately acquitted defendants they believed were guilty under the law as described by the judge, from the nation’s beginning through today; (b) legal rules that prevent nullification from occurring, as well as rules that protect it when it does; (c) constitutional and nonconstitutional arguments for and against recognizing a more robust role for jury nullification; and (d) the findings of empirical research examining how often and under what conditions jurors refuse to convict for reasons other than failure of proof. A list of references includes more than 100 books, articles, cases, and other resources on the topic.
Global Analysis of the Role of Autophagy in Cellular Metabolism and Energy Homeostasis in Arabidopsis Seedlings under Carbon Starvation
Authors: Avin-Wittenberg Tamar , Bajdzienko Krzysztof , Wittenberg Gal , Alseekh Saleh , Tohge Takayuki , Bock Ralph , Giavalisco Patrick , Fernie Alisdair R. 
Published: February 2015

AbstractGermination and early seedling establishment are developmental stages in which plants face limited nutrient supply as their photosynthesis mechanism is not yet active. For this reason, the plant must mobilize the nutrient reserves provided by the mother plant in order to facilitate growth. Autophagy is a catabolic process enabling the bulk degradation of cellular constituents in the vacuole. The autophagy mechanism is conserved among eukaryotes, and homologs of many autophagy-related (ATG) genes have been found in Arabidopsis thaliana. T-DNA insertion mutants (atg mutants) of these genes display higher sensitivity to various stresses, particularly nutrient starvation. However, the direct impact of autophagy on cellular metabolism has not been well studied. In this work, we used etiolated Arabidopsis seedlings as a model system for carbon starvation. atg mutant seedlings display delayed growth in response to carbon starvation compared with wild-type seedlings. High-throughput metabolomic, lipidomic, and proteomic analyses were performed, as well as extensive flux analyses, in order to decipher the underlying causes of the phenotype. Significant differences between atg mutants and wild-type plants have been demonstrated, suggesting global effects of autophagy on central metabolism during carbon starvation as well as severe energy deprivation, resulting in a morphological phenotype.