bluuebunny/crossref_metadata_2025 huggingface dataset:
Weak localization behavior observed in graphene grown on germanium substrate
Authors: Sun Yinbo , Zhang Miao , Dong Linxi , Wang Gaofeng , Xie Xiaoming , Wang Xi , Hu Tao , Di Zengfeng
Published: April 2018

Two dimensional electron systems (2DES) usually show the weak localization behavior in consequence of electron interaction in the limited dimension. Distinct from other 2DES, the monolayer graphene, due to the chirality, exhibits unique weak localization behavior sensitive to not only inelastic but also elastic carrier scattering. Grain boundaries, which usually exist in monolayer graphene, are apparently related to the elastic carrier scattering process, thus affecting the weak localization behavior. However, their effect is scarcely studied due to the lack of an ideal platform. Here, a complementary system consisting of both single-crystalline graphene grown on Ge (110) and poly-crystalline graphene grown on Ge (111) is constructed. From the comparison of magnetoresistivity measurements, the weak localization effect is found to be greatly enhanced for the poly-crystalline graphene on Ge(111) compared to the single-crystalline graphene on Ge(110). The degraded transport performance in graphene/Ge(111) is due to the presence of grain boundary in poly-crystalline graphene, which results in the enhanced elastic intervalley scattering. In addition, the inelastic scattering originating from the strong electron-electron interaction at low temperature also contributes to weak localization of poly-crystalline graphene/Ge(111).
Growth patterns of Phragmites karka under saline conditions depend on the bulk elastic modulus
Authors: Shoukat Erum , Aziz Irfan , Ahmed Muhammad Zaheer , Abideen Zainul , Khan Muhammad Ajmal
Published: April 2018

Salt stress is known to hamper steady-state water flow, which may reduce plant growth. This research was aimed to study the roles of leaf turgor, osmotic adjustment and cell wall elasticity under saline conditions which may reduce biomass production in Phragmites karka (Retz.) Trin, ex. Steud. (a marsh grass). Plants were grown in 0, 100 and 300 mM NaCl and harvested on 3, 7, 15 and 30 days to observe periodic changes in growth and water relations. Leaf number, relative growth rate, and relative elongation rates were higher in the non-saline control than in the plants grown under saline conditions. Plants showed a rapid decline in leaf growth rate (7–15 days) in 300 mM NaCl compared with a delayed response (15–30 days) in 100 mM NaCl. Leaf water potential decreased with increases in salinity after the third day of exposure whereas osmotic potential decreased after the fifteenth day. Low leaf turgor (Ψp) on the third day indicated an initial phase of osmotic stress under saline conditions. Plants maintained higher Ψp in 0 and 100 mM than in 300 mM NaCl. Differences between mid-day and pre-dawn water potential and water saturation deficit were higher in 300 mM NaCl than with other treatments. Water potential and hydraulic capacitance at turgor loss point decreased whereas bulk elastic modulus increased in 300 mM NaCl. Maintenance of turgor and growth at 100 mM NaCl could be related to efficient osmotic adjustment (use of K+ and Cl–), higher WUEi, and lower bulk elasticity whereas poor growth at 300 mM NaCl may have been a consequence of low turgor, decreased cell hydraulic capacitance and higher bulk elastic modulus.
Pseudomonas putida inoculation promotes submerged plant Vallisneria natans growth by carbon conversion in a plant–microbe interaction
Authors: Gan Lin , Zhao Hui , Wang Aili , Li Sanshan , Liu Jia , Yang Liuyan
Published: April 2018

Submerged plant growth is limited by the reduction of underwater photosynthesis attributed to low CO2 availability, as well as light limitation associated with underwater conditions. Heterotrophic bacteria and fungi play an important role in local aqueous dissolved inorganic carbon (DIC) content surrounding submerged plants. In order to investigate the effects of carbon conversion in plant–microbe interactions on plant growth, in the present study we inoculated the plant medium of Vallisneria natans with Pseudomonas putida KT2440 and measured carbon conversion in the system, as well as several indices of plant growth. The quantity of P. putida KT2440 increased twofold because of the availability of organic matter produced by V. natans. Similarly, P. putida KT2440 supplied DIC for V. natans, improving its photosynthetic rate. Moreover, the significantly higher leaf area, specific leaf area and fresh biomass of V. natans attributed to the presence of P. putida KT2440 demonstrated that the interaction between V. natans and P. putida enhanced the efficiency of nutrient and CO2 uptake by V. natans, promoting V. natans growth. Therefore, we suggest that the carbon and oxygen microcycle based on the protocooperation of V. natans and P. putida KT2440 may accelerate the transformation of carbon to increase carbon availability to promote the growth of both plant and microbe.
When translation is not about meaning
Authors: Mossop Brian
Published: April 2018

Translation is typically thought of as conveying the meaning of a text written in another language. However translators frequently
engage in operations that do not start from textual meaning but from phonetic form, typographic form or some other formal feature
of a text. In this article, I look at several such operations, and how they are used in handling proper names, numerical
expressions, text in a third language, so-called untranslatable words, passages of uncertain meaning, and poetry, as well as their
use in translation studies and linguistics journals, and in pronunciation guides for tourists and for choirs singing in languages
unknown to their members. I also briefly consider operations that are based on the form of non-linguistic text elements.
On morphological internalization
Authors: García-Castillero Carlos
Published: April 2018

This paper deals with the creation of the Old Irish oblique relative conjunct particle-(s)aN-(e.g.,dianepir“for which he says” =do-(s)aN-epir) as the outcome of the internalization of a demonstrative form used as a light head, which initially stood as a morphologically independent form. The initial step of this change was the grammaticalization of that demonstrative as the oblique element of a paradigm of relative-clause type forms in which the subject and object functions of the antecedent of the relative are also distinguished. Internalization is defined as an abrupt morphological change creating grammatical elements; its specific mechanism is the mirror image of externalization and must be distinguished from other morphological changes such as incorporation.
Introduction
Authors: Jobert Manuel , Sorlin Sandrine
Published: April 2018

This introductory chapter starts with a brief presentation of what triggered our interest in the joint study of irony and banter. We then delve into the theoretical intricacies of these two discursive practices. We review the major theoretical frameworks that have contributed to our understanding of these practices and pinpoint some crucial issues. We conclude with an overview of the different viewpoints expressed and adopted in the following chapters.
Simulating ignorance
Authors: Mandon Natalie
Published: April 2018

This study reflects the importance of interpretation in staged discourse. It shows how in late seventeenth-century Restoration comedy, both verbal irony and banter rely on the simulation of ignorance in order to achieve a common satirical aim. By offering an opportunity to serve up evaluative comments which when taken literally are erroneous, ironic discourse and banter serve to expose a deviation from the norm. However, these discourse practices also serve to ridicule those who, by failing to detect the discrepancy between literal and intended meaning, fail to question those erroneous evaluations. Ultimately it appears that Congreve’s satirical target is above all those who lack judgement, those who have impaired vision, what Currie (2006) has called “a defective view of the world”.
The face-value of place-work in William Makepeace Thackeray’s handling of irony
Authors: Fromonot Jacqueline
Published: April 2018

Irony is admittedly a well-established and well-documented feature in William Makepeace Thackeray’s works, but the present contribution undertakes to study its textual mechanisms in light of pragmatic theories complemented with a specific structural approach, referred to as “place-work.” The purpose is to highlight that from the perspectives of both creation and reception, the mechanisms of Thackerayan irony involve the distribution of one, two or three “places,” alternately or cumulatively occupied by the ironist and his addressee(s), whether narrator, commentator, characters, and readers alike. This ever-changing “topology” of irony results in the constant reshuffling of roles and places typically at work in Thackeray’s writings, and underlines as well the structural instability of irony.
The point of banter in the television show Pointless
Authors: Pillière Linda
Published: April 2018

This paper explores banter within the television quiz show
Pointless
. Building on previous theories of banter, I suggest that the composite nature of the phenomenon can usefully be analysed within an interactional pragmatic model, such as that proposed by Lecercle (1999). Using this model to analyse various episodes of
Pointless
, I seek to demonstrate that banter is created within a dynamic interpersonal process. I focus on the sequential interaction between speaker and the various hearers involved in the exchange, as opposed to isolated utterances. I propose that any analysis of banter needs not only to study the linguistic aspects of a series of utterances, but also the sociocultural context and the encyclopaedic knowledge that each participant brings to the exchange.
Untersuchungen zu den Gründungsdokumenten der färöischen Rechtschreibung
Authors: Lindqvist Christer
Published: April 2018

Die färöische Gegenwartsorthographie ging nicht wie die moderne Rechtschreibung vieler Sprachen aus einer jahrhundertelangen Schrifttradition hervor, sondern wurde im Wesentlichen im 19. Jh. neu erschaffen. Ihre Gründungsdokumente bestehen aus vier färöischen Zaubersprüchen, die in einer bis Mitte des 19. Jh. üblichen, relativ orthophonen Schreibweise gefasst sind. Als die Zaubersprüche 1846 veröffentlicht werden sollten, wurden sie schrittweise in eine stark historisierende Schreibweise überführt, die in der färöischen Gegenwartsorthographie resultiert hat. Diese Orthographie ist bemerkenswert, weil mit ihr synchron gesehen ein sehr großer Abstand zwischen Graphemik und Phonemik sprachplanerisch erfolgreich eingeführt werden konnte, obwohl gerade solche Verhältnisse ansonsten vielfach als reformbedürftig gelten. Das vorliegende Buch enthält eine Edition aller relevanten Handschriften und ordnet diese in ihren kulturhistorischen Kontext ein.

Unlike the modern orthography of many other languages, Modern Faroese spelling did not emerge from centuries of literary tradition, but was re-created mainly in the 19th century. Its founding documents consist of four Faroese spells written in a relatively orthophone spelling that was common up until the middle of the 19th century. Prior to their publication in 1864, the spells were converted step by step into a spelling with orthographic depth along diachronic lines which eventually resulted in Modern Faroese spelling. This spelling is remarkable, since it represents the successful normative implementation of an orthographic system which, seen from a synchronic point of view, maintains a vast gap between graphemes and phonemes, a state of affairs that in most cases would be a reason for, not a result of spelling reforms. The present book contains an edition of all relevant manuscripts, and situates them in their cultural and historical context.
Grammatical fear morphemes in Ese Ejja
Authors: Vuillermet Marine
Published: April 2018

Grammatical morphemes dedicated to emotions have been little described so far, except for surprise, which may be instantiated in a mirative category. It has even been suggested that an equivalent grammatical encoding for other basic emotions does not seem to occur crosslinguistically. This paper examines three grammatical morphemes in the Amazonian language Ese Ejja (Takanan), namely theapprehensive, theavertiveand thetimitive, and argues that all three morphemes express fear or its milder version apprehension, i.e. an emotion triggered by an undesirable, (highly) possible event. The morphemes essentially diverge in their syntactic scope (main verb, subordinated verb, or NP), their perspective (that of the speaker or the subject), and the possible absence vs. obligatory presence of a precautionary situation, i.e. the precautions taken to avoid the (consequences of the) feared event. After describing these features in Ese Ejja, the article outlines a crosslinguistic framework for the study of these categories.
Inhibition of miR-21-5p suppresses high glucose-induced proliferation and angiogenesis of human retinal microvascular endothelial cells by the regulation of AKT and ERK pathways via maspin
Authors: Qiu Feng , Tong Huijuan , Wang Yawen , Tao Jun , Wang Hailin , Chen Lei
Published: April 2018

The aim of the present study is to investigate the role of miR-21-5p in angiogenesis of human retinal microvascular endothelial cells (HRMECs). HRMECs were incubated with 5 mM glucose, 30 mM glucose or 30 mM mannitol for 24 h, 48 h or 72 h. Then, HRMECs exposed to 30 mM glucose were transfected with miR-21-5p inhibitor. We found that high glucose increased the expression of miR-21-5p, VEGF, VEGFR2 and cell proliferation activity. Inhibition of miR-21-5p reduced high glucose-induced proliferation, migration, tube formation of HRMECs, and reversed the decreased expression of maspin as well as the abnormal activation of PI3K/AKT and ERK pathways. Down-regulation of maspin by siRNA significantly increased the activities of PI3K/AKT and ERK pathways. In conclusion, inhibition of miR-21-5p could suppress high glucose-induced proliferation and angiogenesis of HRMECs, and these effects may partly dependent on the regulation of PI3K/AKT and ERK pathways via its target protein maspin.
Room temperature ferromagnetism in Fe-doped semiconductor ZrS2 single crystals
Authors: Muhammad Zahir , Lv Haifeng , Wu Chuanqiang , Habib Muhammad , ur Rehman Zia , Khan Rashid , Chen Shuangming , Wu Xiaojun , Song Li
Published: April 2018

Two dimensional (2D) layered magnetic materials have obtained much attention due to their intriguing properties with a potential application in the field of spintronics. Herein, room-temperature ferromagnetism with 0.2 emu g−1 magnetic moment is realized in Fe-doped ZrS2 single crystals of millimeter size, in comparison with diamagnetic behaviour in ZrS2. The electron paramagnetic resonance spectroscopy reveals that 5.2wt% Fe-doping ZrS2 crystal exhibit high spin value of g-factor about 3.57 at room temperature also confirmed this evidence, due to the unpaired electrons created by doped Fe atoms. First principle static electronic and magnetic calculations further confirm the increased stability of long range ferromagnetic ordering and enhanced magnetic moment in Fe-doped ZrS2, originating from the Fe spin polarized electron near the Fermi level.
Scanner Data‐Based Panel Price Indexes
Authors: Zhen Chen , Finkelstein Eric A. , Karns Shawn A. , Leibtag Ephraim S. , Zhang Chenhua
Published: April 2018

We construct panel price indexes using retail scanner data that allow comparisons of consumption cost across space and time. Two types of panel indexes are examined: the rolling‐window panel extensions of the multilateral Cave‐Christensen‐Diewert index with the Törnqvist index as its elements, and of the multilateral Gini‐Eltetö‐Köves‐Szulc index using the Fisher ideal index as its elements. The rolling window method maintains the nonrevisability of published index numbers while allowing index numbers for new periods and locations to be calculated and the basket of items to be updated. Meanwhile, the multilateral structure of price comparison eliminates significant downward drift in standard chained indexes. Using county‐level bilateral and panel indexes based on retail beverage scanner data, we experimentally adjust for purchasing parity the portion of Supplemental Nutrition Assistance Program (SNAP) benefits that participants spend on beverages. Accounting for temporal and spatial cost differences causes over 2% of SNAP allotment spent on beverages to be reallocated, or approximately a 5% change in allotment on average for a county. About 90% of the relocated SNAP fund is to adjust for spatial differences in food cost. We also compare SNAP allotments implied by the retail scanner data indexes with those implied by indexes based on the USDA Quarterly Food‐at‐Home Price Database (QFAHPD). The treatment of unit values and product quality may have contributed to the significant differences observed between the retail scanner data indexes and the QFAHPD indexes.
Livable Environments and the Quality of Life of Older People: An Ecological Perspective
Authors: Stephens Christine , Szabó Ágnes , Allen Joanne , Alpass Fiona
Published: April 2018

Background and Objectives

The WHO “Framework for Policy for Healthy Ageing’ (2015) focuses on the broader environment and the support it provides for everyday functioning of older people. The concept of “livability” supports this framework by providing a conceptualization of environments that support good quality of life.

Research Design and Methods

This observational study used an ecological framework of livability to assess cross-sectional relationships between living environments and perceived quality of life among 4,028 respondents, aged 50–89 years who were surveyed in 2016. A 4-step hierarchical model regressed quality of life on individual resources (health, chronic conditions, SES), contextual variables (distance to health care; rural/urban setting), perceptions of housing and neighborhood environments (housing satisfaction, neighborhood quality, neighborhood social cohesion), and interactions between these levels of the ecological model.

Results

As predicted, housing and neighborhood perceptions contributed an additional 5% variance to the model which explained 49% of quality of life. There were significant interactions between the contextual variables and qualities of housing and neighborhood.

Discussion and Implications

These findings support the importance of material and social provisions of housing and neighborhoods to quality of life among older people. The ecological model highlights critical information provided by taking different levels of the environment and personal circumstances into account. The concept of “livability,” focusing on perceptions of the environment, can assist a shift from seeking the universal ideal neighborhood toward understanding the ways in which different communities may achieve quality of housing and neighborhood facilities that meet community members’ needs.
Late toxicity in long-term survivors from a phase 2 study of concurrent radiation therapy, temozolomide and valproic acid for newly diagnosed glioblastoma
Authors: Krauze Andra V , Mackey Megan , Rowe Lindsay , Chang Michal G , Holdford Diane J , Cooley Theresa , Shih Joanna , Tofilon Philip J , Camphausen Kevin
Published: April 2018

Background

Valproic acid (VPA) is an antiepileptic agent with histone deacetylase inhibitor activity shown to enhance overall survival and progression free survival in patients with newly diagnosed glioblastoma (GBM). This reports on the late toxicity of the VPA/radiotherapy (RT)/temozolomide (TMZ) combination in the long-term survivors of a phase 2 study evaluating this regimen.

Methods

37 patients with newly diagnosed GBM were initially enrolled on this trial and received combination therapy. VPA/RT/TMZ related late toxicities were evaluated in the 6 patients that lived greater than 3 years using the Cancer Therapy and Evaluation Program Common Toxicity Criteria (CTC) Version 4.0 for toxicity and adverse event reporting as well as the RTOG/EORTC Radiation Morbidity Scoring Scheme.

Results

The median duration of follow-up for these 6 patients was 69.5m. In this cohort, the median OS was 73.8m (60.8–103.8m) and median PFS was 53.1m (37.3 – 103.8m). The most common late toxicity of VPA in conjunction with RT/TMZ were the CTC classifications of neurological, pain, and blood/ bone marrow toxicity and most were grade 1/2. There were only two grade 3/4 toxicities.

Conclusions

The addition of VPA to concurrent RT/TMZ in patients with newly diagnosed GBM was well tolerated with little late toxicity. Additionally, VPA may result in improved outcomes as compared to historical data and merits further study.
Microelectromechanical system gravimeters as a new tool for gravity imaging
Authors: Middlemiss Richard P. , Bramsiepe Steven G. , Douglas Rebecca , Hild Stefan , Hough James , Paul Douglas J. , Samarelli Antonio , Rowan Sheila , Hammond Giles D.
Published: April 2018

A microelectromechanical system (MEMS) gravimeter has been manufactured with a sensitivity of 40 ppb in an integration time of 1 s. This sensor has been used to measure the Earth tides: the elastic deformation of the globe due to tidal forces. No such measurement has been demonstrated before now with a MEMS gravimeter. Since this measurement, the gravimeter has been miniaturized and tested in the field. Measurements of the free-air and Bouguer effects have been demonstrated by monitoring the change in gravitational acceleration measured while going up and down a lift shaft of 20.7 m, and up and down a local hill of 275 m. These tests demonstrate that the device has the potential to be a useful field-portable instrument. The development of an even smaller device is underway, with a total package size similar to that of a smartphone.

This article is part of a discussion meeting issue ‘The promises of gravitational-wave astronomy’.
The prospects of pulsar timing with new-generation radio telescopes and the Square Kilometre Array
Authors: Stappers B. W. , Keane E. F. , Kramer M. , Possenti A. , Stairs I. H.
Published: April 2018

Pulsars are highly magnetized and rapidly rotating neutron stars. As they spin, the lighthouse-like beam of radio emission from their magnetic poles sweeps across the Earth with a regularity approaching that of the most precise clocks known. This precision combined with the extreme environments in which they are found, often in compact orbits with other neutron stars and white dwarfs, makes them excellent tools for studying gravity. Present and near-future pulsar surveys, especially those using the new generation of telescopes, will find more extreme binary systems and pulsars that are more precise ‘clocks’. These telescopes will also greatly improve the precision to which we can measure the arrival times of the pulses. The Square Kilometre Array will revolutionize pulsar searches and timing precision. The increased number of sources will reveal rare sources, including possibly a pulsar–black hole binary, which can provide the most stringent tests of strong-field gravity. The improved timing precision will reveal new phenomena and also allow us to make a detection of gravitational waves in the nanohertz frequency regime. It is here where we expect to see the signature of the binary black holes that are formed as galaxies merge throughout cosmological history.

This article is part of a discussion meeting issue ‘The promises of gravitational-wave astronomy’.
Revolutionising the design and analysis of protein engineering experiments using fractional factorial design
Authors: Harborne Steven P. D. , Wotherspoon Duncan , Michie Jessica , McComb Alasdair , Kotila Tommi , Gilmour Steven G. , Goldman Adrian
Published: April 2018

Protein engineering is one of the foundations of biotechnology, used to increase protein stability, re-assign the catalytic properties of enzymes or increase the interaction affinity between antibody and target. To date, strategies for protein engineering have focussed on systematic, random or computational methods for introducing new mutations. Here, we introduce the statistical approach of fractional factorial design as a convenient and powerful tool for the design and analysis of protein mutations, allowing sampling of a large mutational space whilst minimising the tests to be done. Our test case is the integral membrane protein, Acridine resistance subunit B (AcrB), part of the AcrAB-TolC multi-protein complex, a multi-drug efflux pump of Gram-negative bacteria. E. coli AcrB is naturally histidine-rich, meaning that it is a common contaminant in the purification of recombinantly expressed, histidine-tagged membrane proteins. Coupled with the ability of AcrB to crystallise from picogram quantities causing false positives in 2-D and 3-D crystallisation screening, AcrB contamination represents a significant hindrance to the determination of new membrane protein structures. Here, we demonstrate the use of fractional factorial design for protein engineering, identifying the most important residues involved in the interaction between AcrB and nickel resin. We demonstrate that a combination of spatially close, but sequentially distant histidine residues are important for nickel binding, which were different from those predicted a priori. Fractional factorial methodology has the ability to decrease the time and material costs associated with protein engineering whilst expanding the depth of mutational space explored; a revolutionary concept.

Significance statement

Protein engineering is important for the production of enzymes for bio-manufacturing, stabilised protein for research and production of therapeutic antibodies against human diseases. Here, we introduce a statistical method that can reduce the time and cost required to perform protein engineering. We validate our approach experimentally using the multi-drug efflux pump AcrB, a target for understanding drug-resistance in pathogenic bacteria, but also a persistent contaminant in the purification of membrane proteins from E. coli. This provides a general method for increasing the efficiency of protein engineering.
Rapid Identification of Stable Clusters in Bacterial Populations Using the Adjusted Wallace Coefficient
Authors: Barker Dillon OR , Carriço João A , Kruczkiewicz Peter , Palma Federica , Rossi Mirko , Taboada Eduardo N
Published: April 2018

Whole-genome sequencing (WGS) of microbial pathogens has become an essential part of modern epidemiological investigations. Although WGS data can be analyzed using a number of different approaches, such as traditional phylogenetic methods, a critical requirement for global systems for pathogen surveillance is the development of approaches for transforming sequence data into WGS-based subtypes, which creates a nomenclature that describes their higher-order relationships to one another. To this end, subtype similarity thresholds are needed to define clusters of subtypes representing lineages of interest. WGS-based subtyping presents a challenge since both the addition of novel genome sequences and small adjustments in similarity thresholds can have a dramatic impact on cluster composition and stability. We present the Neighbourhood Adjusted Wallace Coefficient (nAWC), a method for evaluating cluster stability based on computing cluster concordance between neighbouring similarity thresholds. The nAWC can be used to identify areas in in which distance thresholds produce robust clusters. Using datasets fromSalmonella entericaandCampylobacter jejuni, representing strongly and weakly clonal bacterial species respectively, we show that clusters generated using such thresholds are both stable and reflect basic units in their overall population structure. Our results suggest that the nAWC could be useful for defining robust clusters compatible with nomenclatures for global WGS-based surveillance networks, which require stable clusters to be defined that both harness the discriminatory power of WGS data while allowing for long-term tracking of strains of interest.
Improving early epidemiological assessment of emergingAedes-transmitted epidemics using historical data
Authors: Riou Julien , Poletto Chiara , Boëlle Pierre-Yves
Published: April 2018

Model-based epidemiological assessment is useful to support decision-making at the beginning of an emergingAedes-transmitted outbreak. However, early forecasts are generally unreliable as little information is available in the first few incidence data points. Here, we show how pastAedes-transmitted epidemics help improve these predictions. The approach was applied to the 2015-2017 Zika virus epidemics in three islands of the French West Indies, with historical data including otherAedes-transmitted diseases (Chikungunya and Zika) in the same and other locations. Hierarchical models were used to build informativea prioridistributions on the reproduction ratio and the reporting rates. The accuracy and sharpness of forecasts improved substantially when thesea prioridistributions were used in models for prediction. For example, early forecasts of final epidemic size obtained without historical information were 3.3 times too high on average (range: 0.2 to 5.8) with respect to the eventual size, but were far closer (1.1 times the real value on average, range: 0.4 to 1.5) using information on past CHIKV epidemics in the same places. Likewise, the 97.5% upper bound for maximal incidence was 15.3 times (range: 2.0 to 63.1) the actual peak incidence, and became much sharper at 2.4 times (range: 1.3 to 3.9) the actual peak incidence with informativea prioridistributions. Improvements were more limited for the date of peak incidence and the total duration of the epidemic. The framework can adapt to all forecasting models at the early stages of emergingAedes-transmitted outbreaks.
Cross-sectional white matter microstructure differences in aging and trait mindfulness
Authors: Boekel Wouter , Hsieh Shulan
Published: April 2018

The process of aging can be characterized by a decline in cognitive performance, which may be accompanied by deterioration in specific structural properties of the brain. In this study we sought to investigate to what extent mindfulness changes over the aging process, and which alterations in brain structure can be associated to aging and concomitant changes in mindfulness. We collected Mindful Attention Awareness Scale questionnaire data to assess trait mindfulness and acquired diffusion-weighted imaging data fitted to the diffusion tensor model in a group of 97 middle-aged to elderly participants. Our results showed that trait mindfulness increased with age. In terms of white matter structure our results suggested that there was a general increase of omnidirectional diffusion, which favored radial over axial diffusivity, leading to a decrease in fractional anisotropy (FA) in older participants. We further showed that trait mindfulness mediated the FA-age effect in a localized area consisting of the internal and external capsule, as well as the corona radiata. The implication of this mediation analysis is that trait mindfulness may deter age-associated neurocognitive decline, perhaps by preventing age-associated microlesions specifically in cortico-subcortical white matter tracts. This study can be considered a pioneer of using DTI studies to investigate the relationship between age and trait mindfulness.

Disclosure statement

Conflict of Interest: The authors have no actual or potential conflicts of interest.
Antagonistic Pleiotropy Is Unexpectedly Rare In New Mutations
Authors: Sane Mrudula , Miranda Joshua John , Agashe Deepa
Published: April 2018

Pleiotropic effects of mutations may underlie diverse biological phenomena such as ageing and specialization. In particular, antagonistic pleiotropy (“AP”: when a mutation has opposite fitness effects in different environments) generates tradeoffs, which may constrain adaptation. Models of adaptation typically assume that AP is common – especially among large-effect mutations – and that pleiotropic effect sizes are positively correlated. The rare empirical tests of these assumptions have largely focused on beneficial mutations observed under strong selection, whereas most mutations are actually deleterious or neutral, and are removed by selection. We quantified the incidence, nature and effect size of pleiotropy for carbon utilization across 80 single mutations in Escherichia coli that arose under mutation accumulation (i.e. weak selection). Although ~46% of the mutations were pleiotropic, only 11% showed AP, which is lower than expected given the distributions of fitness effects for each resource. In some environments, AP was more common in large-effect mutations (but not synergistic pleiotropy, SP); whereas pleiotropic effect sizes were positively correlated for SP (but not AP). Thus, AP is generally rare, is not consistently enriched in large-effect mutations, and often involves weakly deleterious antagonistic effects. Our unbiased quantification of mutational effects therefore suggests that antagonistic pleiotropy is unlikely to cause maladaptive tradeoffs.
Inferior parietal lobule and early visual areas support elicitation of individualized meanings during narrative listening
Authors: Saalasti S. , Alho J. , Bar M. , Glerean E. , Honkela T. , Kauppila M. , Sams M. , Jääskeläinen I. P.
Published: April 2018

When listening to a narrative, the verbal expressions translate into meanings and flow of mental imagery, at best vividly immersing the keen listener into the sights, sounds, scents, objects, actions, and events in the story. However, the same narrative can be heard quite differently based on differences in listeners’ previous experiences and knowledge, as the semantics and mental imagery elicited by words and phrases in the story vary extensively between any given two individuals. Here, we capitalized on such inter-individual differences to disclose brain regions that support transformation of narrative into individualized propositional meanings and associated mental imagery by analyzing brain activity associated with behaviorally-assessed individual meanings elicited by a narrative. Sixteen subjects listed words best describing what had come to their minds during each 3–5 sec segment of an eight-minute narrative that they listened during fMRI of brain hemodynamic activity. Similarities in these word listings between subjects, estimated using latent-semantic analysis combined with WordNet knowledge, predicted similarities in brain hemodynamic activity in supramarginal and angular gyri as well as in cuneus. Our results demonstrate how inter-individual differences in semantic representations can be measured and utilized to identify specific brain regions that support the elicitation of individual propositional meanings and the associated mental imagery when one listens to a narrative.
Phylogenomics reveals dynamic evolution of fungal nitric oxide reductases and their relationship to secondary metabolism
Authors: Higgins Steven A. , Schadt Christopher W. , Matheny Patrick B. , Löffler Frank E.
Published: April 2018

Fungi expressing P450nor, an unconventional nitric oxide (NO) reducing cytochrome P450, are thought to be significant contributors to soil nitrous oxide (N2O) emissions. However, fungal contributions to N2O emissions remain uncertain due to inconsistencies in measurements of N2O formation by fungi. Much of the N2O emitted from antibiotic-amended soil microcosms is attributed to fungal activity, yet fungal isolates examined in pure culture are poor N2O producers. To assist in reconciling these conflicting observations and produce a benchmark genomic analysis of fungal denitrifiers, genes underlying fungal denitrification were examined in >700 fungal genomes. Of 167p450nor–containing genomes identified, 0, 30, and 48 also harbored the denitrification genesnarG,napAornirK, respectively. Compared tonapAandnirK,p450norwas twice as abundant and exhibited two to five-fold more gene duplications, losses, and transfers, indicating a disconnect betweenp450norpresence and denitrification potential. Furthermore, co-occurrence ofp450norwith genes encoding NO-detoxifying flavohemoglobins (Spearman r = 0.87,p= 1.6e−10) confounds hypotheses regarding P450nor’s primary role in NO detoxification. Instead, ancestral state reconstruction united P450nor with actinobacterial cytochrome P450s (CYP105) involved in secondary metabolism (SM) and 19 (11 %)p450nor-containing genomic regions were predicted to be SM clusters. Another 40 (24 %) genomes harbored genes nearbyp450norpredicted to encode hallmark SM functions, providing additional contextual evidence linkingp450norto SM. These findings underscore the potential physiological implications of widespreadp450norgene transfer, support the novel affiliation ofp450norwith fungal SM, and challenge the hypothesis ofp450nor’s primary role in denitrification.
Loss of function mutations inepaRconfer resistance to phage NPV1 infection inEnterococcus faecalisOG1RF
Authors: Ho Khang , Huo Wenwen , Pas Savannah , Dao Ryan , Palmer Kelli L.
Published: April 2018

Enterococcus faecalisis a Gram-positive opportunistic pathogen that inhabits the human gastrointestinal tract. Because of the high frequency of antibiotic resistance amongEnterococcusclinical isolates, interest in using phage to treat enterococcal infections and to decolonize high-risk patients for antibiotic-resistantEnterococcusis rising. Bacteria can evolve phage resistance, but there is little published information on these mechanisms inE. faecalis. In this report, we identified genetic determinants ofE. faecalisresistance to ϕNPV1. We found that loss-of-function mutations inepaRconfer ϕNPV1 resistance by blocking phage adsorption. We attribute the inability of the phage to adsorb to the modification or loss of an extracellular polymer in strains with inactivatedepaR. Phage-resistantepaRmutants exhibited increased daptomycin and osmotic stress susceptibilities. Our results demonstrate thatin vitrospontaneous resistance to ϕNPV1 comes at a cost inE. faecalisOG1RF.
Insufficient fumarase contributes to generating reactive oxygen species in Dahl salt sensitive rats
Authors: Hou Entai , Zheng Xuewei , Yang Zhe , Li Xian , Liu Zerong , Chen Meng , Li Xiaoxue , Liang Mingyu , Tian Zhongmin
Published: April 2018

Dahl SS rats exhibit greater levels of renal medullary oxidative stress and lower levels of fumarase activities. Fumarase insufficiencies can increase reactive oxygen species (ROS), the mechanism of which, however, is not clear. A proteomic analysis indicated fumarase knockdown in HK-2 cells resulted in changes in the expression or activity of NADPH oxidase, mitochondrial respiratory chain complex I and III, ATP synthase subunits, and α-oxoglutarate dehydrogenase, all of which are sites of ROS formation. Meantime, the activities of key antioxidant enzymes such as G6PD, 6PGD, GR, GPx and GST increased significantly too. The apparent activation of antioxidant defense appeared insufficient as glutathione precursors, glutathione and GSH/GSSG ratio were decreased. SS rats exhibited changes in redox metabolism similar to HK-2 cells with fumarase knockdown. Supplementation with fumarate and malate, the substrate and product of fumarase, increased and decreased, respectively, blood pressure and the levels of H2O2and MDA in kidney tissues of SS rats. These results indicate fumarase insufficiencies cause a wide range of changes at several sites of ROS production and antioxidant mechanisms.
Sparse reduced-rank regression for exploratory visualization of paired multivariate datasets
Authors: Kobak Dmitry , Bernaerts Yves , Weis Marissa A. , Scala Federico , Tolias Andreas , Berens Philipp
Published: April 2018

In genomics, transcriptomics, and related biological fields (collectively known as omics), it is common to work with n ≪ p datasets with the dimensionality much larger than the sample size. In recent years, combinations of experimental techniques began to yield multiple sets of features for the same set of biological replicates. One example is Patch-seq, a method combining single-cell RNA sequencing with electrophysiological recordings from the same cells. Here we present a framework based on sparse reduced-rank regression for obtaining an interpretable visualization of the relationship between the transcriptomic and the electrophysiological data. We use an elastic net regularization penalty that yields sparse solutions and allows for an efficient computational implementation. Using several publicly available Patch-seq datasets, we show that sparse reduced-rank regression outperforms both sparse full-rank regression and non-sparse reduced-rank regression in terms of predictive performance, and can outperform existing methods for sparse partial least squares and sparse canonical correlation analysis in terms of out-of-sample correlations. We introduce a bibiplot visualization in order to display the dominant factors determining the relationship between transcriptomic and electrophysiological properties of neurons. We believe that sparse reduced-rank regression can provide a valuable tool for the exploration and visualization of paired multivariate datasets, including Patch-seq.
Computational-Observer Analysis of Illumination Discrimination
Authors: Ding Xiaomao , Radonjić Ana , Cottaris Nicolas P. , Jiang Haomiao , Wandell Brian A. , Brainard David H.
Published: April 2018

The spectral properties of the ambient illumination provide useful information about time of day and weather. We study the perceptual representation of illumination by analyzing measurements of how well people discriminate between illuminations across scene configurations. More specifically, we compare human performance to a computational-observer analysis that evaluates the information available in the isomerizations of the cones in a model human photoreceptor mosaic. Some patterns of human performance are predicted by the computational observer, other aspects are not. The analysis clarifies which aspects of performance require additional explanation in terms of the action of visual mechanisms beyond the isomerization of light by the cones.
NO is required for memory formation and expression of memory, and for minor behavioral changes during training with inedible food in Aplysia
Authors: Briskin-Luchinsky Valeria , Tam Shlomit , Shabbat Shlomit , Hurwitz Itay , Susswein Abraham J.
Published: April 2018

A learning experience may lead to changes in behavior during the experience, and also to memory expressed at a later time. Are signals causing changes in behavior during the learning experience related to the formation and expression of memory? We examined this question, using learning that food is inedible in Aplysia. Treatment of an isolated buccal ganglia preparation with an NO donor elicited rejection-like motor programs. Rejection initiated by NO production is consistent with aspects of behavioral changes seen while animals learn, and with memory formation. Nonetheless, applying the NO donor during training had only minor effects on behavior during the training, and did not improve memory, indicating that the induction of rejection in the buccal ganglia is unlikely to be the means by which NO during training contributes to memory formation. Block of NO during memory retrieval prevented the expression of memory, as measured by a lack of savings in time to stop responding to food. Applying an NO donor to the cerebral ganglion while eliciting fictive feeding inhibited the expression of feeding activity, indicating that some NO effects on memory consolidation and on expression of memory may be via effects on the cerebral ganglion.
A cryoprotectant induces conformational change in glyceraldehyde-3-phosphate dehydrogenase
Authors: Kim Yong Ju
Published: April 2018

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a glycolytic enzyme, catalyses the conversion of D-glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate. While mammalian and yeast GAPDHs are multifunctional proteins that have additional functions beyond those involved in glycolysis, including reactions related to nuclear RNA transport, DNA replication/repair, membrane fusion and cellular apoptosis,Escherichia coliGAPDH (ecGAPDH) has only been reported to function in glycolysis. The S-loop of GAPDH is required for interaction with its cofactor and with other proteins. In this study, the three-dimensional crystal structure of GAPDH treated with trehalose is reported at 2.0 Å resolution. Trehalose was used as a cryoprotectant for the GAPDH crystals. The structure of trehalose-boundecGAPDH was compared with the structures of both NAD+-free and NAD+-boundecGAPDH. At the S-loop, the bound trehalose in the GAPDH structure induces a 2.4° rotation compared with the NAD+-freeecGAPDH structure and a 3.1° rotation compared with the NAD+-boundecGAPDH structure.
Crystal structure of the mouse innate immunity factor bacterial permeability-increasing family member A1
Authors: Little Michael S. , Redinbo Matthew R.
Published: April 2018

Bacterial permeability-increasing family member A1 (BPIFA1) is an innate immunity factor and one of the most abundantly secreted proteins in the upper airways. BPIFA1 is multifunctional, with antimicrobial, surfactant and lipopolysaccharide-binding activities, as well as established roles in lung hydration. Here, the 2.5 Å resolution crystal structure of BPIFA1 from Mus musculus (mBPIFA1) is presented and compared with those of human BPIFA1 (hBPIFA1) and structural homologs. Structural distinctions between mBPIFA1 and hBPIFA1 suggest potential differences in biological function, including the regulation of a key pulmonary ion channel.
Crystal structures of human CK2α2 in new crystal forms arising from a subtle difference in salt concentration
Authors: Tsuyuguchi Masato , Nakaniwa Tetsuko , Kinoshita Takayoshi
Published: April 2018

The catalytic subunits of protein kinase CK2 are classified into two subtypes: CK2α1 and CK2α2. CK2α1 is an attractive drug-discovery target for various diseases such as cancers and nephritis. CK2α2 is defined as an off-target of CK2α1 and is a potential target in the development of male contraceptive drugs. High-resolution crystal structures of both isozymes are likely to provide crucial clues for the design of selective inhibitors of CK2α1 and/or CK2α2. To date, several crystal structures of CK2α1 have been solved at high resolutions of beyond 1.5 Å. However, crystal structures of CK2α2 have barely achieved a low resolution of around 3 Å because of the formation of needle-shaped crystals. In this study, new crystal forms were exploited and one provided a crystal structure of CK2α2 at 1.89 Å resolution. This result, together with the structure of CK2α1, will assist in the development of highly selective inhibitors for both isozymes.
Experimental and numerical study of ventilation cavitation around a NACA0015 hydrofoil with special emphasis on bubble evolution and air-vapor interactions
Authors: Yu An , Luo Xianwu , Yang Dandan , Zhou Jiajian
Published: April 2018

Purpose

This paper aims to gain a clear understanding of the ventilated cavity evolution around an NACA0015 hydrofoil by using both experimental and numerical investigation.

Design/methodology/approach

The bubble evolution around an NACA0015 hydrofoil with or without air injection was observed in a water tunnel, and the simulation was conducted using a modified turbulence model and homogeneous cavitation model.

Findings

The present simulation method can successfully predict the bubble evolutions around the NACA0015 hydrofoil with or without air injection. Air injection can alleviate the nature cavitation oscillation, and the suppression effect on nature cavitation depends on the air-entrant coefficient. It is confirmed that the air and vapor cavity have the same shedding frequency. It is seen that the air sheet closely attaches to the hydrofoil surface and is surrounded by the vapor sheet. Thus, the injected air promotes vapor growth and results in an increase in the cavity shedding frequency. Further, with a large air-entrant coefficient, the pressure fluctuation is suppressed completely.

Originality/value

The new simulation method is adopted to explore the mechanism of ventilated cavitation. The bubble evolutions with and without air injection have been comprehensively studied by experimental and numerical investigation. The effects of air injection on natural cavity oscillations and pressure fluctuations have been revealed in the present study.