bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantized conductance observed during sintering of silver nanoparticles by intense terahertz pulses
Authors: Takano Keisuke , Harada Hirofumi , Yoshimura Masashi , Nakajima Makoto
Published: April 2018

We show that silver nanoparticles, which are deposited on a terahertz-receiving antenna, can be sintered by intense terahertz pulse irradiation. The conductance of the silver nanoparticles between the antenna electrodes is measured under the terahertz pulse irradiation. The dispersant materials surrounding the nanoparticles are peeled off, and conduction paths are created. We reveal that, during sintering, quantum point contacts are formed, leading to quantized conductance between the electrodes with the conductance quantum, which reflects the formation of atomically thin wires. The terahertz electric pulses are sufficiently intense to activate electromigration, i.e., transfer of kinetic energy from the electrons to the silver atoms. The silver atoms move and atomically thin wires form under the intense terahertz pulse irradiation. These findings may inspire nanoscale structural processing by terahertz pulse irradiation.
Interfacial magnetic coupling in hetero-structure of Fe/double-perovskite NdBaMn2O6 single crystal
Authors: Lin W. C. , Tsai C. L. , Ogawa K. , Yamada S. , Gandhi Ashish C. , Lin J. G.
Published: April 2018

The interfacial magnetic coupling between metallic Fe and the double-perovskite NdBaMn2O6 single crystal was investigated in the heterostructure of 4-nm Pd/10-nm Fe/NdBaMn2O6. A considerable magnetic coupling effect was observed in the temperature range coincident with the magnetic phase transition of NdBaMn2O6. When the temperature was elevated above 270 K, NdBaMn2O6 transformed from a state of antiferromagnetic fluctuating domains to a superparamagnetism-like (ferromagnetic fluctuation) state with high magnetic susceptibility. Concurrently, the interfacial magnetic coupling between the Fe layer and the NdBaMn2O6 crystal was observed, as indicated by the considerable squareness reduction and coercivity enhancement in the Fe layer. Moreover, the presence of the Fe layer changed the magnetic structure of NdBaMn2O6 from conventional 4-fold symmetry to 2-fold symmetry. These observations offer applicable insights into the mutual magnetic interaction in the heterostructures of metallic ferromagnetism/perovskite materials.
Anti-parallel polarization switching in a triglycine sulfate organic ferroelectric insulator: The role of surface charges
Authors: Ma He , Wu Zhuangchun , Peng Dongwen , Wang Yaojin , Wang Yiping , Yang Ying , Yuan Guoliang
Published: April 2018

Four consecutive ferroelectric polarization switchings and an abnormal ring-like domain pattern can be introduced by a single tip bias of a piezoresponse force microscope in the (010) triglycine sulfate (TGS) crystal. The external electric field anti-parallel to the original polarization induces the first polarization switching; however, the surface charges of TGS can move toward the tip location and induce the second polarization switching once the tip bias is removed. The two switchings allow a ring-like pattern composed of the central domain with downward polarization and the outer domain with upward polarization. Once the two domains disappear gradually as a result of depolarization, the other two polarization switchings occur one by one at the TGS where the tip contacts. However, the backswitching phenomenon does not occur when the external electric field is parallel to the original polarization. These results can be explained according to the surface charges instead of the charges injected inside.
Temperature-dependent dielectric functions of bcc transition metals Cr, Mo, and W from ultraviolet to infrared regions: A theoretical and experimental study
Authors: Xu Meng , Yang Jia-Yue , Liu Linhua
Published: April 2018

In the bcc transition metals Cr, Mo, and W, the existence of the partially filled d bands makes interband transition occur at low photon frequencies and thus, it is difficult to differentiate it from intraband transition. Here, we present a thorough study on decomposing the intraband and interband contribution to finite temperature dielectric functions of these bcc transition metals by performing electron-phonon and electron-electron interaction calculations, as well as ellipsometry experiments. In this work, the Drude model and interband transition theory are applied to quantitatively describe the intraband and interband transition, respectively. To accurately determine intraband transition, the relevant parameters for the Drude model, such as plasma frequency and electron relaxation time, are calculated from first-principles. The electron-electron interaction within the many-body theory and electron-phonon interaction within the density functional perturbation theory are calculated to obtain the electron relaxation time and intraband dielectric function at finite temperature. As for interband transition, the spin-orbit coupling is included and it shows nontrivial influence on the interband dielectric function of Mo and W, especially at low frequencies. To verify theoretical calculations, ellipsometry experiments are performed to measure dielectric functions of Cr, Mo, and W over the temperature range of 300–700 K and energy range of 0.08–4.8 eV. The experimental results are then fitted by the Drude model, and it shows that the electron-phonon interaction rather than electron-electron interaction dominates the frequency dependence of the relaxation time for transition metals Cr, Mo, and W.
Broadband high sound absorption from labyrinthine metasurfaces
Authors: Chang Huiting , Liu Liu , Zhang Chi , Hu Xinhua
Published: April 2018

Metamaterials are artificial structures which exhibit fascinating properties unreachable by traditional materials. Here, we report on the design, fabrication, and characterization of acoustic metasurfaces consisting of dead-end channels coiled in a 2D plane. It is found that when the area of the channel’s cross section is about 1/10 of the area (4.3 cm × 4.3 cm) of the upper surface of the building block, the sound loss in channels approaches to a critical value, resulting in near-perfect absorption (A > 99%) at resonant frequency. When the building block contains ten channels with specially designed lengths, sound waves can be highly absorbed above a cutoff frequency fc (A > 90% for fc < f < 3fc). The wavelength at the cutoff frequency can be 7.1 times of the thickness of the metasurface. Our results could find applications in noise reduction and sound detection.
Photocatalytic activity of silver oxide capped Ag nanoparticles constructed by air plasma irradiation
Authors: Fang Yingcui , Wu Qingmeng , Li Huanhuan , Zhang Bing , Yan Rong , Chen Junling , Sun Mengtao
Published: April 2018

We construct a kind of structure of silver oxide capped silver nanoparticles (AgNPs) by cost-efficient air plasma irradiation, and study its visible-light driven photocatalytic activity (PA). By controlling the oxidization time, the relationship between the intensity of the localized surface plasmon resonance (LSPR) and the PA is well established. The PA reaches the maximum when the LSPR of AgNPs is nearly completely damped (according to absorption spectra); however, under this condition, the LSPR still works, confirmed with the high efficient selective transformation of p-Aminothiophenol (PATP) to p, p′-dimercaptoazobenzene (DMAB) under visible light. The mechanism of the LSPR damping induced PA improvement is discussed. We not only provide a cost-efficient approach to construct a LSPR strong damping structure but also promote the understanding of LSPR strong damping and its relationship with photocatalysis.
Origin and roles of oxygen impurities in hexagonal boron nitride epilayers
Authors: Grenadier S. J. , Maity A. , Li J. , Lin J. Y. , Jiang H. X.
Published: April 2018

Photoluminescence emission spectroscopy and electrical transport measurements have been employed to study the origin and roles of oxygen impurities in hexagonal boron nitride (h-BN) epilayers grown on sapphire substrates. The temperature dependence of the electrical resistivity revealed the presence of a previously unnoticed impurity level of about 0.6 eV in h-BN epilayers grown at high temperatures. The results suggested that in addition to the common nitrogen vacancy (VN) shallow donors in h-BN, oxygen impurities diffused from sapphire substrates during high temperature growth also act as substitutional donors (ON). The presence of ON gives rise to an additional emission peak in the photoluminescence spectrum, corresponding to a donor-acceptor pair recombination involving the ON donor and the CN (carbon occupying nitrogen site) deep level acceptor. Moreover, due to the presence of ON donors, the majority charge carrier type changed to electrons in epilayers grown at high temperatures, in contrast to typical h-BN epilayers which naturally exhibit “p-type” character. The results provided a more coherent picture for common impurities/defects in h-BN as well as a better understanding of the growth mediated impurities in h-BN epilayers, which will be helpful for finding possible ways to further improve the quality and purity of this emerging material.
Spatio-temporal characterisation of changes in the resistance of widely grown soybean cultivars to Soybean mosaic virus across a century of breeding in China
Authors: Gao Le , Sun Shi , Li Kai , Wang Liwei , Hou Wensheng , Wu Cunxiang , Zhi Haijian , Han Tianfu
Published: April 2018

Soybean mosaic virus (SMV) causes significant yield losses and seed-quality deterioration in the soybean (Glycine max (L.) Merr.) growing areas of China, and breeding disease-resistant cultivars is the most common approach for controlling the spread of the disease and the destruction of soybean crop. In this study, 97 widely grown soybean cultivars representing nine decades (1923–2006) of breeding from the four main soybean-producing subregions in China (Northern Heilongjiang (NH), Mid-Southern Heilongjiang (MSH), Jilin-Liaoning (JL) and Yellow–Huai-Hai River Valleys (YHH)) were inoculated with six prevalent SMV strains: SC3, SC7, SC8, SC11, SC15 and SC18. The average disease index (ADI) of the six SMV strains ranged from 26.95 to 48.97, and the numbers of resistant and susceptible cultivars to the six SMV strains ranged from 27 (27.8%) to 64 (66.0%) and 33 (34.0%) to 70 (72.2%), respectively. The ADIs of cultivars from NH, MSH, JL and YHH were 50.82, 47.27, 43.10 and 33.05, respectively. Soybean cultivars released in the 1940s and 1960s had the highest and lowest ADI values, 53.95 and 32.03, respectively. From NH and JL, all individual strain disease index (DI) values exhibited decreasing trend over time, but no decreasing trend in DI values was observed from MSH. From YHH, DI values for SC3 and SC18 displayed apparent increasing trend over time, and DI values for SC15 showed an obvious decreasing trend. In all, 24 soybean cultivars were identified as having broad-spectrum resistance, with ADI values ranging from 0.80 to 35.52 for the six SMV strains, and 13 soybean cultivars were identified as highly resistant to at least one SMV strain. The findings of this study will contribute to monitoring the pattern of spatio-temporal variation in SMV resistance in different soybean-producing areas of China and facilitate conventional and molecular breeding programs for SMV resistance in soybean.
Ideological shifts between bilingual EU texts
Authors: Damaskinidis George
Published: April 2018

This article examines the translation of an official English European Council text, namely a Commission Communication, into Greek.
A critical discourse analysis-based methodology is used to probe the manipulation of ideological shifts between the English source
text and its Greek translation. The analysis of both texts aims to shed light on the way culturally-approved patterns reflect and
also influence society’s priorities and preoccupations. The comparative analysis provides an example of how the European Union and
its official working language influenced the translator’s attitudes and motivations in decoding various ideological patterns.
Adopting a social view of political ideologies and their associated readerships, the article discusses how discourse and ideology
mediate in the translation of the English-Greek language pair. It shows how discourse reinforces ideological assumptions and how
it challenges them by emphasizing that the source culture violates the very norms and values the target culture holds dear.
The decade construction rivalry in Russian
Authors: Nesset Tore , Makarova Anastasia
Published: April 2018

This article addresses the diachronic development of so-called rival forms, i.e., words or grammatical constructions that appear to be synonyms, based on a detailed empirical analysis of two seemingly synonymous constructions in Russian. Corresponding to the English ‘decade construction’in the twenties, Russian has two rival constructions, viz.v dvadcatye gody[lit. “in the twentieth years”] (with the numeral and noun in the accusative) andv dvadcatyx godax(with the numeral and noun in the locative case). Three hypotheses about rival forms are considered: leveling (whereby one form ousts its rival), sociolinguistic differentiation (whereby the two rivals survive in different varieties of a language) and semantic differentiation (whereby the two rivals develop different meanings over time). Contrary to what has been suggested in the literature, we find little evidence for semantic and sociolinguistic differentiation. Instead, we demonstrate that leveling is taking place, since the accusative construction is in the process of ousting its rival. While our study shows that corpus data facilitate detailed analysis of the interaction between leveling, sociolinguistic differentiation and semantic differentiation, our analysis also points to limitations, especially when it comes to corpus-based analysis of sociolinguistic and semantic factors.
A Hard Science Spoken Word List
Authors: Dang Thi Ngoc Yen
Published: April 2018

A Hard Science Spoken Word List (HSWL) was developed and validated to help second language learners of hard sciences better comprehend academic speech at English-medium universities. It consists of the 1,595 most frequent and wide ranging word families in a 6.5-million running word hard science spoken corpus which represents 12 subjects across two equally-sized sub-corpora. Its coverage in different discourse types indicates that the HSWL truly reflects the language in hard science academic speech. The comparison between the HSWL withDang, Coxhead, and Webb’s (2017)Academic Spoken Word List shows that the HSWL focuses more on specialized vocabulary in hard science speech. Depending on their vocabulary levels, learners may achieve 93%–96% coverage of hard science academic speech with knowledge of the HSWL words.
Re-examining the effects of word writing on vocabulary learning
Authors: Webb Stuart , Piasecki Anna
Published: April 2018

This study investigated the effects of word writing on vocabulary learning by comparing three conditions in which there was (a) limited time to write words, (b) unlimited time to write words, and (c) a non-writing word-picture pairs comparison. Non-native speakers studying English as a second language encountered 8 word-picture pairs in each condition and were administered a test measuring form recall and another measuring receptive knowledge of written form. The results indicated that there was little difference between scores on both tests when time on task was the same. However, when the participants had as much time as they needed to write and learn words they had higher scores on both dependent measures than when learning in the other two conditions. The findings suggest that an ecologically valid approach to word writing may facilitate vocabulary learning.
The guessing from context test
Authors: Sasao Yosuke , Webb Stuart
Published: April 2018

This study aims to develop two equivalent forms of the Guessing from Context Test (GCT) and provide its preliminary validity evidence. The GCT is a diagnostic test of the guessing skill and measures the following three important steps in guessing: identifying the part of speech of an unknown word, finding its discourse clue, and deriving its meaning. The test was administered to 428 Japanese learners of English. The results indicate that the two forms each with 20 question sets are equivalent in terms of item difficulty distribution and representativeness of the construct being measured. A wide range of validity evidence was provided using Messick’s validation framework, the Rasch model, qualitative investigations into the relationships to actual guessing, and proposals for score interpretation.
Vocabulary knowledge and listening comprehension at an intermediate level in English and French as foreign
languages
Authors: Noreillie Ann-Sophie , Kestemont Britta , Heylen Kris , Desmet Piet , Peters Elke
Published: April 2018

The present study aims to replicate Stæhr’s (2009) study on the relationship between
vocabulary knowledge and listening comprehension. To explore the generalizability of Stæhr’s findings, two experiments were
conducted. However, the study changed the population (Flemish learners) and proficiency level of the materials in the first
experiment (intermediate) and also the language in the second experiment (French). Our results generally confirm Stæhr’s findings.
We also found a positive correlation between vocabulary knowledge and listening comprehension. Although our findings reveal that
learners probably need fewer words for adequate listening comprehension at an intermediate proficiency level, our study also
showed that learners who knew more words had higher listening comprehension scores. Finally, our study seems to suggest that
learners might need less lexical coverage for intermediate listening.
Irony and semantic prosody revisited
Authors: McIntyre Dan
Published: April 2018

This chapter explore Louw’s (1993) claim that deviation from conventionalised semantic prosodies can be indicative of irony. Taking account of criticisms of the concept of semantic prosody, I analyse a short extract from a sketch from the 1960 satirical revue Beyond the Fringe. I argue that the satire in the sketch derives in part from the projected irony and that semantic prosody can be a useful tool in uncovering this. However, I argue that to fully reveal the source of the ironic effects, it is necessary to utilise a more nuanced approach to semantic prosody, as well as to consider how semantic prosodies clash with each other, and how concepts such as semantic preference and Gricean implicature act as further triggers of irony.
Expressiveness and evaluation in Arabic
Authors: Taine-Cheikh Catherine
Published: April 2018

Old Arabic had many expressive derived forms: firstly, the forms with radical repetition, consonant reduplication and/or vowel lengthening; secondly, the forms with prefixes, suffixes or infixes. Most of these formatives survived in the Arabic dialects, but Arabic scholars generally focus on diminutive noun forms (nominal and adjectival forms) namedtaṣġīrin Arabic. This article presents the rules of formation of the diminutive in the Ḥassāniyya Arabic dialect, in which this derivation applies to the whole lexicon, including verbal forms. The derivational morphology of the diminutive constitutes a kind of double derivation, characterized mainly by the infixation of-(a)y- – the position of which varies depending on the patterns and on the nature of the base lexeme. The article then analyzes the use and meaning of diminutives in context, studied within two corpora: a corpus of traditional tales and a corpus of courteous poems. The study of these corpora shows that in Ḥassāniyya, pejorative uses of the diminutive are as prominent as meliorative ones. Finally, the article discusses the “root-and-pattern” mode of formation in Arabic and the diverse derivations attested in Arabic dialects, comparing their values with those reported for other languages in the world. Evaluative morphology is shown to be particularly prevalent in Ḥassāniyya, and it is hypothesized that this correlates with the pragmatic function endorsed by the diminutive in this language. This function allows for both positive or negative interpretations of diminutive forms, depending on the context, so that diminutives can express a broad range of emotions.
Detoxification process of tolaasins, lipodepsipeptides, by Microbacterium sp. K3-5
Authors: Tomita Shun , Sue Masayuki , Kajikawa Akinobu , Igimi Shizunobu , Shinohara Hirosuke , Yokota Kenji
Published: April 2018

Tolaasins are antimicrobial lipodepsipeptides. Here, we report the tolaasins-detoxifying properties of Microbacterium sp. K3-5 (K3-5). The detoxification of tolaasins by K3-5 was performed by hydrolyzation of cyclic structure of tolaasins depending on the tolaasin-K3-5 cell interaction. Our data suggest that the cyclic structure of tolaasins is critical for its interaction to target cells.
Microtubule end tethering of a processive kinesin-8 motor Kif18b is required for spindle positioning
Authors: McHugh Toni , Gluszek Agata A. , Welburn Julie P.I.
Published: April 2018

Mitotic spindle positioning specifies the plane of cell division during anaphase. Spindle orientation and positioning are therefore critical to ensure symmetric division in mitosis and asymmetric division during development. The control of astral microtubule length plays an essential role in positioning the spindle. In this study, using gene knockout, we show that the kinesin-8 Kif18b controls microtubule length to center the mitotic spindle at metaphase. Using in vitro reconstitution, we reveal that Kif18b is a highly processive plus end–directed motor that uses a C-terminal nonmotor microtubule-binding region to accumulate at growing microtubule plus ends. This region is regulated by phosphorylation to spatially control Kif18b accumulation at plus ends and is essential for Kif18b-dependent spindle positioning and regulation of microtubule length. Finally, we demonstrate that Kif18b shortens microtubules by increasing the catastrophe rate of dynamic microtubules. Overall, our work reveals that Kif18b uses its motile properties to reach microtubule ends, where it regulates astral microtubule length to ensure spindle centering.
Free‐riding on Product Quality in Cooperatives: Lessons from an Experiment
Authors: Bonroy Olivier , Garapin Alexis , Hamilton Stephen F. , Souza Monteiro Diogo M.
Published: April 2018

An important issue facing marketing cooperatives is that the overall quality of the product depends on the quality of farm products provided by individual members. We conduct an experiment to empirically investigate producer incentives to free‐ride on quality among the members of a marketing cooperative in a setting where the average quality provided by cooperative members results in a collective rent that is distributed back to members in a patronage dividend levied in proportion to the quantity produced. Hidden actions by cooperative members that impact quality are imperfectly monitored, but free‐riding, when detected, results in exclusion from cooperative returns. The randomized payoff structure of our game results in a novel experimental design that nests public good games and multi‐player assurance games. Our findings indicate that free‐riding on product quality is deterred when (a) cooperatives base patronage dividends on quality outcomes of smaller groups; (b) payoffs from free‐riding are randomized by the possibility of exclusion from cooperative returns; and (c) cooperatives distribute a larger share of returns to members through indirect payments such as capital pooling and cost‐sharing arrangements unrelated to product quality.
Immigration Reform and Farm Labor Markets
Authors: Richards Timothy J
Published: April 2018

Farmers throughout the United States report a shortage of workers. At the same time, there are proposals to strengthen the enforcement of existing immigration laws. In this paper, we develop an equilibrium approach to examine the impact of removing undocumented workers from the California agricultural labor market, and to infer whether there is evidence of shortages using individual‐worker data. We find evidence that is consistent with a persistent shortage in some sub‐sectors of the California farm labor market. Further, we conduct counter‐factual policy simulations over a range of possible policy alternatives, and find that removing 50% all undocumented farm workers from the state would lead to an increase in wages of over 22%.
SIMPLE: Sparse Interaction Model over Peaks of moLEcules for fast, interpretable metabolite identification from tandem mass spectra
Authors: Nguyen Dai Hai , Nguyen Canh Hao , Mamitsuka Hiroshi
Published: April 2018

Motivation

Recent success in metabolite identification from tandem mass spectra has been led by machine learning, which has two stages: mapping mass spectra to molecular fingerprint vectors and then retrieving candidate molecules from the database. In the first stage, i.e. fingerprint prediction, spectrum peaks are features and considering their interactions would be reasonable for more accurate identification of unknown metabolites. Existing approaches of fingerprint prediction are based on only individual peaks in the spectra, without explicitly considering the peak interactions. Also the current cutting-edge method is based on kernels, which are computationally heavy and difficult to interpret.

Results

We propose two learning models that allow to incorporate peak interactions for fingerprint prediction. First, we extend the state-of-the-art kernel learning method by developing kernels for peak interactions to combine with kernels for peaks through multiple kernel learning (MKL). Second, we formulate a sparse interaction model for metabolite peaks, which we call SIMPLE, which is computationally light and interpretable for fingerprint prediction. The formulation of SIMPLE is convex and guarantees global optimization, for which we develop an alternating direction method of multipliers (ADMM) algorithm. Experiments using the MassBank dataset show that both models achieved comparative prediction accuracy with the current top-performance kernel method. Furthermore SIMPLE clearly revealed individual peaks and peak interactions which contribute to enhancing the performance of fingerprint prediction.

Availability and implementation

The code will be accessed through http://mamitsukalab.org/tools/SIMPLE/.
Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies
Authors: Peng Yisu , Jiang Yuxiang , Radivojac Predrag
Published: April 2018

Motivation

Modern problems of concept annotation associate an object of interest (gene, individual, text document) with a set of interrelated textual descriptors (functions, diseases, topics), often organized in concept hierarchies or ontologies. Most ontology can be seen as directed acyclic graphs (DAGs), where nodes represent concepts and edges represent relational ties between these concepts. Given an ontology graph, each object can only be annotated by a consistent sub-graph; that is, a sub-graph such that if an object is annotated by a particular concept, it must also be annotated by all other concepts that generalize it. Ontologies therefore provide a compact representation of a large space of possible consistent sub-graphs; however, until now we have not been aware of a practical algorithm that can enumerate such annotation spaces for a given ontology.

Results

We propose an algorithm for enumerating consistent sub-graphs of DAGs. The algorithm recursively partitions the graph into strictly smaller graphs until the resulting graph becomes a rooted tree (forest), for which a linear-time solution is computed. It then combines the tallies from graphs created in the recursion to obtain the final count. We prove the correctness of this algorithm, propose several practical accelerations, evaluate it on random graphs and then apply it to characterize four major biomedical ontologies. We believe this work provides valuable insights into the complexity of concept annotation spaces and its potential influence on the predictability of ontological annotation.

Availability and implementation

https://github.com/shawn-peng/counting-consistent-sub-DAG

Supplementary information

Supplementary data are available at Bioinformatics online.
A graph-based approach to diploid genome assembly
Authors: Garg Shilpa , Rautiainen Mikko , Novak Adam M , Garrison Erik , Durbin Richard , Marschall Tobias
Published: April 2018

Motivation

Constructing high-quality haplotype-resolved de novo assemblies of diploid genomes is important for revealing the full extent of structural variation and its role in health and disease. Current assembly approaches often collapse the two sequences into one haploid consensus sequence and, therefore, fail to capture the diploid nature of the organism under study. Thus, building an assembler capable of producing accurate and complete diploid assemblies, while being resource-efficient with respect to sequencing costs, is a key challenge to be addressed by the bioinformatics community.

Results

We present a novel graph-based approach to diploid assembly, which combines accurate Illumina data and long-read Pacific Biosciences (PacBio) data. We demonstrate the effectiveness of our method on a pseudo-diploid yeast genome and show that we require as little as 50× coverage Illumina data and 10× PacBio data to generate accurate and complete assemblies. Additionally, we show that our approach has the ability to detect and phase structural variants.

Availability and implementation

https://github.com/whatshap/whatshap

Supplementary information

Supplementary data are available at Bioinformatics online.
TiSAn: estimating tissue-specific effects of coding and non-coding variants
Authors: Vervier Kévin , Michaelson Jacob J
Published: April 2018

Motivation

Model-based estimates of general deleteriousness, like CADD, DANN or PolyPhen, have become indispensable tools in the interpretation of genetic variants. However, these approaches say little about the tissues in which the effects of deleterious variants will be most meaningful. Tissue-specific annotations have been recently inferred for dozens of tissues/cell types from large collections of cross-tissue epigenomic data, and have demonstrated sensitivity in predicting affected tissues in complex traits. It remains unclear, however, whether including additional genome-scale data specific to the tissue of interest would appreciably improve functional annotations.

Results

Herein, we introduce TiSAn, a tool that integrates multiple genome-scale data sources, defined by expert knowledge. TiSAn uses machine learning to discriminate variants relevant to a tissue from those with no bearing on the function of that tissue. Predictions are made genome-wide, and can be used to contextualize and filter variants of interest in whole genome sequencing or genome-wide association studies. We demonstrate the accuracy and flexibility of TiSAn by producing predictive models for human heart and brain, and detecting tissue-relevant variations in large cohorts for autism spectrum disorder (TiSAn-brain) and coronary artery disease (TiSAn-heart). We find the multiomics TiSAn model is better able to prioritize genetic variants according to their tissue-specific action than the current state-of-the-art method, GenoSkyLine.

Availability and implementation

Software and vignettes are available at http://github.com/kevinVervier/TiSAn.

Supplementary information

Supplementary data are available at Bioinformatics online.
Regulation of the heat shock transcription factor Hsf1 in fungi: implications for temperature-dependent virulence traits
Authors: Veri Amanda O , Robbins Nicole , Cowen Leah E
Published: April 2018

The impact of fungal pathogens on human health is devastating. For fungi and other pathogens, a key determinant of virulence is the capacity to thrive at host temperatures, with elevated temperature in the form of fever as a ubiquitous host response to defend against infection. A prominent feature of cells experiencing heat stress is the increased expression of heat shock proteins (Hsps) that play pivotal roles in the refolding of misfolded proteins in order to restore cellular homeostasis. Transcriptional activation of this heat shock response is orchestrated by the essential heat shock transcription factor, Hsf1. Although the influence of Hsf1 on cellular stress responses has been studied for decades, many aspects of its regulation and function remain largely enigmatic. In this review, we highlight our current understanding of how Hsf1 is regulated and activated in the model yeast Saccharomyces cerevisiae, and highlight exciting recent discoveries related to its diverse functions under both basal and stress conditions. Given that thermal adaption is a fundamental requirement for growth and virulence in fungal pathogens, we also compare and contrast Hsf1 activation and function in other fungal species with an emphasis on its role as a critical regulator of virulence traits.
Patterns of SES Health Disparities Among Older Adults in Three Upper Middle- and Two High-Income Countries
Authors: McEniry Mary , Samper-Ternent Rafael , Flórez Carmen Elisa , Pardo Renata , Cano-Gutierrez Carlos
Published: April 2018

Objectives

To examine the socioeconomic status (SES) health gradient for obesity, diabetes, and hypertension within a diverse group of health outcomes and behaviors among older adults (60+) in upper middle-income countries benchmarked with high-income countries.

Method

We used data from three upper middle-income settings (Colombia-SABE-Bogotá, Mexico-SAGE, and South Africa-SAGE) and two high-income countries (England-ELSA and US-HRS) to estimate logistic regression models using age, gender, and education to predict health and health behaviors.

Results

The sharpest gradients appear in middle-income settings but follow expected patterns found in high-income countries for poor self-reported health, functionality, cognitive impairment, and depression. However, weaker gradients appear for obesity, hypertension, diabetes, and other chronic conditions in Colombia and Mexico and the gradient reverses in South Africa. Strong disparities exist in risky health behaviors and in early nutritional status in the middle-income settings.

Discussion

Rapid demographic and nutritional transitions, urbanization, poor early life conditions, social mobility, negative health behavior, and unique country circumstances provide a useful framework for understanding the SES health gradient in middle-income settings. In contrast with high-income countries, the increasing prevalence of obesity, an important risk factor for chronic conditions and other aspects of health, may ultimately change the SES gradient for diseases in the future.
Limits on turbulent propagation of energy in cool-core clusters of galaxies
Authors: Bambic C J , Pinto C , Fabian A C , Sanders J , Reynolds C S
Published: April 2018

We place constraints on the propagation velocity of bulk turbulence within the intracluster medium of three clusters and an elliptical galaxy. Using Reflection Grating Spectrometer measurements of turbulent line broadening, we show that for these clusters, the 90 per cent upper limit on turbulent velocities when accounting for instrumental broadening is too low to propagate energy radially to the cooling radius of the clusters within the required cooling time. In this way, we extend previous Hitomi-based analysis on the Perseus cluster to more clusters, with the intention of applying these results to a future, more extensive catalogue. These results constrain models of turbulent heating in active galactic nucleus feedback by requiring a mechanism which can not only provide sufficient energy to offset radiative cooling but also resupply that energy rapidly enough to balance cooling at each cluster radius.
Gravitational waves from neutron stars and asteroseismology
Authors: Ho Wynn C. G.
Published: April 2018

Neutron stars are born in the supernova explosion of massive stars. Neutron stars rotate as stably as atomic clocks and possess densities exceeding that of atomic nuclei and magnetic fields millions to billions of times stronger than those created in laboratories on the Earth. The physical properties of neutron stars are determined by many areas of fundamental physics, and detection of gravitational waves can provide invaluable insights into our understanding of these areas. Here, we describe some of the physics and astrophysics of neutron stars and how traditional electromagnetic wave observations provide clues to the sorts of gravitational waves we expect from these stars. We pay particular attention to neutron star fluid oscillations, examining their impact on electromagnetic and gravitational wave observations when these stars are in a wide binary or isolated system, then during binary inspiral right before merger, and finally at times soon after merger.

This article is part of a discussion meeting issue ‘The promises of gravitational-wave astronomy’.
Robust and clinically relevant prediction of response to anti-cancer drugs via network integration of molecular profiles
Authors: Franco Marcela , Jeggari Ashwini , Peuget Sylvain , Böttger Franziska , Selivanova Galina , Alexeyenko Andrey
Published: April 2018

In order to tackle heterogeneity of cancer samples and high data space dimensionality, we propose a method NEAmarker for finding sensitive and robust biomarkers at the pathway level. In this method, scores from network enrichment analysis transform the original space of altered genes into a lower-dimensional space of pathways, which is then correlated with phenotype variables. The analysis was first done onin vitroanti-cancer drug screen datasets and then on clinical data. In parallel, we tested a panel of state-of-the-art enrichment methods. In this comparison, our method proved superior in terms of 1) universal applicability to different data types with a possibility of cross-platform integration, 2) consistency of the discovered correlates between independent drug screens, and 3) ability to explain differential survival of treated patients. Our new in vitro screen validated performance of the discovered multivariate models. Finally, NEAmarker was the only method to discover predictors of bothin vitroresponse and patient survival given administration of the same drug.
Identification of Significant Computational Building Blocks through Comprehensive Investigation of NGS Secondary Analysis Methods
Authors: Vasimuddin Md , Misra Sanchit , Aluru Srinivas
Published: April 2018

Rapid advances in next-generation sequencing technologies are improving the throughput and cost of sequencing at a rate significantly faster than the Moore’s law. This necessitates equivalent rate of acceleration of NGS secondary analysis that assembles reads into full genomes and identifies variants between genomes. Conventional improvement in hardware can at best help accelerate this according to the Moore’s law. Moreover, a majority of the software tools used for secondary analysis do not use the hardware efficiently. Therefore, we need hardware that is designed taking into account the computational requirements of secondary analysis, along with software tools that use it efficiently. Here, we take the first step towards these goals by identifying the computational requirements of secondary analysis. We surveyed dozens of software tools from all the three major problems in secondary analysis – sequence mapping, De novo assembly, and variant calling – to select seven popular tools and a workflow for an in-depth analysis. We performed runtime profiling of the tools using multiple real datasets to find that the majority of the runtime is dominated by just four building blocks – Smith-Waterman alignment, FM-index based sequence search, Debruijn graph construction and traversal, and pairwise hidden markov model algorithm – covering 80.5%-98.2%, 63.9%-99.4% and 72%-93% of the runtime, respectively, for sequence mapping, De novo assembly, and variant calling. The key outcome of this result is that by just targeting software and hardware optimizations to these building blocks, major performance improvements for NGS secondary analysis can be achieved.
Stress relaxation in epithelial monolayers is controlled by actomyosin
Authors: Khalilgharibi Nargess , Fouchard Jonathan , Asadipour Nina , Yonis Amina , Harris Andrew , Mosaffa Payman , Fujita Yasuyuki , Kabla Alexandre , Baum Buzz , Muñoz José J , Miodownik Mark , Charras Guillaume
Published: April 2018

Epithelial monolayers are one-cell thick tissue sheets that separate internal and external environments. As part of their function, they withstand extrinsic mechanical stresses applied at high strain rate. However, little is known about how monolayers respond to mechanical deformations. In stress relaxation tests, monolayers respond in a biphasic manner and stress dissipation is accompanied by an increase in monolayer resting length, pointing to active remodelling of cell architecture during relaxation. Consistent with this, actomyosin remodels at a rate commensurate with mechanical relaxation and governs the rate of monolayer stress relaxation – as in single cells. By contrast, junctional complexes and intermediate filaments form stable connections between cells, enabling monolayers to behave rheologically as single cells. Together, these data show actomyosin cytoskeletal dynamics govern the rheological properties of monolayers by enabling active, ATP-dependent changes in the resting length. These findings have far-reaching consequences for our understanding of developmental morphogenesis and tissue response to mechanical stress.
Cre/lox-controlled spatio-temporal perturbation of FGF signaling in zebrafish
Authors: Kirchgeorg Lucia , Felker Anastasia , Chiavacci Elena , Mosimann Christian
Published: April 2018

Fibroblast Growth Factor (FGF) signaling guides multiple developmental processes including body axis formation and specific cell fate patterning. In zebrafish, genetic mutants and chemical perturbations affecting FGF signaling have uncovered key developmental processes; however, these approaches cause embryo-wide FGF signaling perturbations, rendering assessment of cell-autonomous versus non-autonomous requirements for FGF signaling in individual processes difficult. Here, we created the novel transgenic linefgfr1-dn-cargo, encoding dominant-negative Fgfr1 with fluorescent tag under combinedCre/loxand heatshock control to provide spatio-temporal perturbation of FGF signaling. Validating efficient perturbation of FGF signaling byfgfr1-dn-cargoprimed with ubiquitous CreERT2, we established that primed, heatshock-inducedfgfr1-dn-cargobehaves akin to pulsed treatment with the FGFR inhibitor SU5402. Primingfgfr1-dn-cargowith CreERT2 in the lateral plate mesoderm, we observed selective cardiac and pectoral fin phenotypes without drastic impact on overall embryo patterning. Harnessing lateral plate mesoderm-specific FGF inhibition, we recapitulated the cell-autonomous and temporal requirement for FGF signaling in pectoral fin outgrow, as previously hypothesized from pan-embryonic FGF inhibition. Altogether, our results establishfgfr1-dn-cargoas a genetic tool to define the spatio-temporal requirements for FGF signaling in zebrafish.
Identification of Key Proteins Involved in Axon Guidance Related Disorders: A Systems Biology Approach
Authors: Ahammad Ishtiaque
Published: April 2018

Axon guidance is a crucial process for growth of the central and peripheral nervous systems. In this study, 3 axon guidance related disorders, namely-Duane Retraction Syndrome (DRS), Horizontal Gaze Palsy with Progressive Scoliosis (HGPPS) and Congenital fibrosis of the extraocular muscles type 3 (CFEOM3) were studied using various Systems Biology tools to identify the genes and proteins involved with them to get a better idea about the underlying molecular mechanisms including the regulatory mechanisms. Based on the analyses carried out, 7 significant modules have been identified from the PPI network. Five pathways/processes have been found to be significantly associated with DRS, HGPPS and CFEOM3 associated genes. From the PPI network, 3 have been identified as hub proteins-DRD2, UBC and CUL3.
Sexual differentiation of contextual fear responses
Authors: Colon Lorianna , Odynocki Natalie , Santarelli Anthony , Poulos Andrew M.
Published: April 2018

Development and sex differentiation impart an organizational influence on the neuroanatomy and behavior of mammalian species. Prior studies suggest that brain regions associated with fear motivated defensive behavior undergo a protracted and sex-dependent development. Outside of adult animals, evidence for developmental sex differences in conditioned fear is sparse. Here, we examined in male and female Long-Evans rats how developmental age and sex affect the long-term retention and generalization of Pavlovian fear responses. Experiments 1 and 2 describe under increasing levels of aversive learning (three and five trials) the long-term retrieval of cued and context fear in preadolescent (P24 and P33), periadolescent (P37), and adult (P60 and P90) rats. Experiments 3 and 4 examined contextual processing under minimal aversive learning (1 trial) procedures in infant (P19, P21), preadolescent (P24), and adult (P60) rats. Here, we found that male and female rats display a divergent developmental trajectory in the expression of context-mediated freezing, such that context fear expression in males tends to increase toward adulthood, while females displayed an opposite pattern of decreasing context fear expression toward adulthood. Longer (14 d) retention intervals produced an overall heightened context fear expression relative to shorter (1 d) retention intervals an observation consistent with fear incubation. Male, but not Female rats showed increasing generalization of context fear across development. Collectively, these findings provide an initial demonstration that sexual differentiation of contextual fear conditioning emerges prior to puberty and follows a distinct developmental trajectory toward adulthood that strikingly parallels sex differences in the etiology and epidemiology of anxiety and trauma- and stressor-related disorders.
miR-132 couples the circadian clock to daily rhythms of neuronal plasticity and cognition
Authors: Aten Sydney , Hansen Katelin F. , Price Kaiden H. , Wheaton Kelin , Kalidindi Anisha , Garcia Ashley , Alzate-Correa Diego , Hoyt Kari R. , Obrietan Karl
Published: April 2018

The microRNA miR-132 serves as a key regulator of a wide range of plasticity-associated processes in the central nervous system. Interestingly, miR-132 expression has also been shown to be under the control of the circadian timing system. This finding, coupled with work showing that miR-132 is expressed in the hippocampus, where it influences neuronal morphology and memory, led us to test the idea that daily rhythms in miR-132 within the forebrain modulate cognition as a function of circadian time. Here, we show that hippocampal miR-132 expression is gated by the time-of-day, with peak levels occurring during the circadian night. Further, in miR-132 knockout mice and in transgenic mice, where miR-132 is constitutively expressed under the control of the tetracycline regulator system, we found that time-of-day dependent memory recall (as assessed via novel object location and contextual fear conditioning paradigms) was suppressed. Given that miRNAs exert their functional effects via the suppression of target gene expression, we examined the effects that transgenic miR-132 manipulations have on MeCP2 and Sirt1—two miR-132 targets that are associated with neuronal plasticity and cognition. In mice where miR-132 was either knocked out, or transgenically expressed, rhythmic expression of MeCP2 and Sirt1 was suppressed. Taken together, these results raise the prospect that miR-132 serves as a key route through which the circadian timing system imparts a daily rhythm on cognitive capacity.